diff --git a/.github/workflows/compatibility_tests.yml b/.github/workflows/compatibility_tests.yml index 8ec9309e..190dbd29 100644 --- a/.github/workflows/compatibility_tests.yml +++ b/.github/workflows/compatibility_tests.yml @@ -28,8 +28,8 @@ jobs: continue-on-error: true strategy: matrix: - python-version: [3.6, 3.7] # As of Oct 2020 Anndata is not compatible with 3.8 - anndata-version: [0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.7.4, 0.7.5] + python-version: [3.6, 3.7, 3.8] + anndata-version: [0.7.6] test-suite: [smoke-test, smoke-test-annotations] steps: - uses: actions/checkout@v2 @@ -47,8 +47,6 @@ jobs: make pydist install-dist # 3. install anndata pip install anndata==${{ matrix.anndata-version }} - # workaround for anndata 0.6.22.post1 bug - [[ "0.6.22.post1" = "${{ matrix.anndata-version }}" ]] && pip install h5py==2.9.0 || true - name: Tests run: make unit-test ${{ matrix.test-suite }} diff --git a/.github/workflows/push_tests.yml b/.github/workflows/push_tests.yml index a14227f4..a0ab94b7 100644 --- a/.github/workflows/push_tests.yml +++ b/.github/workflows/push_tests.yml @@ -40,7 +40,7 @@ jobs: - name: Lint src with eslint working-directory: ./client run: | - make lint + npx eslint src __tests__ unit-test: runs-on: ubuntu-latest diff --git a/.github/workflows/sastisfaction.yml b/.github/workflows/sastisfaction.yml new file mode 100644 index 00000000..d48d3eeb --- /dev/null +++ b/.github/workflows/sastisfaction.yml @@ -0,0 +1,27 @@ +name: Run SASTisfaction +on: + - pull_request + +jobs: + sastisfaction: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - uses: actions/checkout@v2 + with: + repository: chanzuckerberg/sastisfaction + ref: main + path: .github/actions/sastisfaction + ssh-key: ${{ secrets.SASTISFACTION_READ_KEY }} + - name: Login to GitHub Container Registry + uses: docker/login-action@v1 + with: + registry: ghcr.io + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + - name: Docker pull + run: docker pull ghcr.io/chanzuckerberg/sastisfaction:main + - name: Run SASTisfaction + uses: ./.github/actions/sastisfaction + with: + snowflake_private_key: ${{ secrets.SASTISFACTION_RSA_KEY }} diff --git a/backend/common/compute/diffexp_generic.py b/backend/common/compute/diffexp_generic.py index 3b2be195..92d532ef 100644 --- a/backend/common/compute/diffexp_generic.py +++ b/backend/common/compute/diffexp_generic.py @@ -1,6 +1,6 @@ import numpy as np from scipy import sparse, stats -from backend.common.constants import XApproxDistribution +from backend.common.constants import XApproximateDistribution def diffexp_ttest(adaptor, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01): @@ -30,13 +30,13 @@ def diffexp_ttest(adaptor, maskA, maskB, top_n=8, diffexp_lfc_cutoff=0.01): :return: for top N genes, {"positive": for top N genes, [ varindex, foldchange, pval, pval_adj ], "negative": for top N genes, [ varindex, foldchange, pval, pval_adj ]} """ - X_approx_distribution = adaptor.get_X_approx_distribution() + X_approximate_distribution = adaptor.get_X_approximate_distribution() dataA = adaptor.get_X_array(maskA, None) dataB = adaptor.get_X_array(maskB, None) # mean, variance, N - calculate for both selections - meanA, vA, nA = mean_var_n(dataA, X_approx_distribution) - meanB, vB, nB = mean_var_n(dataB, X_approx_distribution) + meanA, vA, nA = mean_var_n(dataA, X_approximate_distribution) + meanB, vB, nB = mean_var_n(dataB, X_approximate_distribution) res = diffexp_ttest_from_mean_var(meanA, vA, nA, meanB, vB, nB, top_n, diffexp_lfc_cutoff) return res @@ -113,7 +113,7 @@ def diffexp_ttest_from_mean_var(meanA, varA, nA, meanB, varB, nB, top_n, diffexp # Convenience function which handles sparse data -def mean_var_n(X, X_approx_distribution=XApproxDistribution.NORMAL): +def mean_var_n(X, X_approximate_distribution=XApproximateDistribution.NORMAL): """ Two-pass variance calculation. Numerically (more) stable than naive methods (and same method used by numpy.var()) @@ -131,14 +131,14 @@ def mean_var_n(X, X_approx_distribution=XApproxDistribution.NORMAL): with np.errstate(divide="call", invalid="call", call=fp_err_set): n = X.shape[0] if sparse.issparse(X): - if X_approx_distribution == XApproxDistribution.COUNT: + if X_approximate_distribution == XApproximateDistribution.COUNT: X = X.log1p() mean = X.mean(axis=0).A1 dfm = X - mean sumsq = np.sum(np.multiply(dfm, dfm), axis=0).A1 v = sumsq / (n - 1) else: - if X_approx_distribution == XApproxDistribution.COUNT: + if X_approximate_distribution == XApproximateDistribution.COUNT: X = np.log1p(X) mean = X.mean(axis=0) dfm = X - mean diff --git a/backend/common/compute/estimate_distribution.py b/backend/common/compute/estimate_distribution.py index 69fea708..85a66a76 100644 --- a/backend/common/compute/estimate_distribution.py +++ b/backend/common/compute/estimate_distribution.py @@ -2,34 +2,52 @@ import numba import concurrent.futures import numpy as np from scipy import sparse -from backend.common.constants import XApproxDistribution +from backend.common.constants import XApproximateDistribution -@numba.njit(fastmath=True, error_model="numpy", nogil=True) -def min_max(arr): +@numba.njit(error_model="numpy", nogil=True) +def min_max(arr: np.ndarray): """Return (min, max) values for the ndarray.""" - n = arr.size - odd = n % 2 - if not odd: - n -= 1 - max_val = min_val = arr[0] - i = 1 - while i < n: + + # initialize to first finite value in array. Normally, + # this will exit on the first value. + for i in range(arr.size): + min_val = max_val = arr[i] + if np.isfinite(min_val): + break + + # now find min/max, unrolled by two + odd = arr.size % 2 + unrolled_loop_limit = arr.size - 1 if odd else arr.size + i = 0 + while i < unrolled_loop_limit: x = arr[i] y = arr[i + 1] + + # ignore non-finites + x = x if np.isfinite(x) else min_val + y = y if np.isfinite(y) else min_val + if x > y: x, y = y, x min_val = min(x, min_val) max_val = max(y, max_val) i += 2 - if not odd: - x = arr[n] + + # handle the tail if any + if odd: + x = arr[arr.size - 1] + + # ignore non-finites + x = x if np.isfinite(x) else min_val + min_val = min(x, min_val) max_val = max(x, max_val) + return min_val, max_val -def estimate_approximate_distribution(X) -> XApproxDistribution: +def estimate_approximate_distribution(X) -> XApproximateDistribution: """ Estimate the distribution (normal, count) of the X matrix. @@ -38,6 +56,13 @@ def estimate_approximate_distribution(X) -> XApproxDistribution: any (max-min) range in excess of 24 is implies tens of millions of observations of a single feature and so is extremely unlikely. """ + if X.dtype.kind not in ["i", "u", "f"]: + raise TypeError(f"Unsupported matrix dtype: {X.dtype.name}") + + if X.size == 0: + # default for empty array + return XApproximateDistribution.NORMAL + if sparse.isspmatrix_csc(X) or sparse.isspmatrix_csr(X): Xdata = X.data elif type(X) is np.ndarray: @@ -45,7 +70,7 @@ def estimate_approximate_distribution(X) -> XApproxDistribution: X.size, ) else: - raise TypeError(f"Unsupported matrix type: {str(type(X))}") + raise TypeError(f"Unsupported matrix format: {str(type(X))}") CHUNKSIZE = 1 << 24 if Xdata.size > CHUNKSIZE: @@ -59,4 +84,4 @@ def estimate_approximate_distribution(X) -> XApproxDistribution: min_val, max_val = min_max(Xdata) excess_range = (max_val - min_val) > 24 - return XApproxDistribution.COUNT if excess_range else XApproxDistribution.NORMAL + return XApproximateDistribution.COUNT if excess_range else XApproximateDistribution.NORMAL diff --git a/backend/common/constants.py b/backend/common/constants.py index 4d80a5a0..972b574c 100644 --- a/backend/common/constants.py +++ b/backend/common/constants.py @@ -24,7 +24,7 @@ class DiffExpMode(AugmentedEnum): VAR_FILTER = "varFilter" -class XApproxDistribution(AugmentedEnum): +class XApproximateDistribution(AugmentedEnum): NORMAL = "normal" COUNT = "count" diff --git a/backend/common/fbs/matrix.py b/backend/common/fbs/matrix.py index 0cb696d7..fd8f1cf6 100644 --- a/backend/common/fbs/matrix.py +++ b/backend/common/fbs/matrix.py @@ -5,6 +5,8 @@ import pandas as pd from flatbuffers import Builder from scipy import sparse +from backend.common.utils.type_conversion_utils import get_encoding_dtype_of_array + import backend.common.fbs.NetEncoding.Column as Column import backend.common.fbs.NetEncoding.Float32Array as Float32Array import backend.common.fbs.NetEncoding.Float64Array as Float64Array @@ -14,6 +16,7 @@ import backend.common.fbs.NetEncoding.Matrix as Matrix import backend.common.fbs.NetEncoding.TypedArray as TypedArray import backend.common.fbs.NetEncoding.Uint32Array as Uint32Array + # Serialization helper def serialize_column(builder, typed_arr): """ Serialize NetEncoding.Column """ @@ -84,7 +87,7 @@ def serialize_typed_array(builder, source_array, encoding_info): def column_encoding(arr): column_encoding_type_map = { # array protocol string: ( array_type, as_type ) - np.dtype(np.float64).str: (TypedArray.TypedArray.Float64Array, np.float64), + np.dtype(np.float64).str: (TypedArray.TypedArray.Float32Array, np.float32), np.dtype(np.float32).str: (TypedArray.TypedArray.Float32Array, np.float32), np.dtype(np.float16).str: (TypedArray.TypedArray.Float32Array, np.float32), np.dtype(np.int8).str: (TypedArray.TypedArray.Int32Array, np.int32), @@ -98,7 +101,8 @@ def column_encoding(arr): } column_encoding_default = (TypedArray.TypedArray.JSONEncodedArray, "json") - return column_encoding_type_map.get(arr.dtype.str, column_encoding_default) + encoding_dtype = np.dtype(get_encoding_dtype_of_array(arr)) + return column_encoding_type_map.get(encoding_dtype.str, column_encoding_default) def index_encoding(arr): @@ -198,7 +202,7 @@ def deserialize_typed_array(tarr): arr.Init(u.Bytes, u.Pos) narr = arr.DataAsNumpy() if u_type == TypedArray.TypedArray.JSONEncodedArray: - narr = json.loads(narr.tostring().decode("utf-8")) + narr = json.loads(narr.tobytes().decode("utf-8")) return narr diff --git a/backend/common/utils/type_conversion_utils.py b/backend/common/utils/type_conversion_utils.py index 971bf641..f054cfdb 100644 --- a/backend/common/utils/type_conversion_utils.py +++ b/backend/common/utils/type_conversion_utils.py @@ -1,8 +1,42 @@ +from typing import Union, Tuple import logging import numpy as np import pandas as pd +""" +These routines drive all type inference for the schema generation and the +FBS (REST OTA) encoding. They are also used for CXG generation. + + +H5AD Type REST REST +(ndarray, Series, Index) FBS encoding schema type ERROR/exceptions +---------------------------- -------------- --------------- ---------------------- +bool_/bool uint8 boolean +(u)int8, (u)int16, int32 int32 int32 +uint32, (u)int64 int32 int32 CHECKS value bounds +float16, float32, float64 float32 float32[0] + +categorical[T is numeric[4]]: + hasna = False T categorical[1] + hasna = True float32 categorical[1] CHECKS value bounds + +categorical[T not numeric] JSON/str categorical[1,2] + +(other object) JSON/str string + +(all other) Always an ERROR[3] + + +Notes: +[0] IEEE format, includes non-finite numbers (NaN, Inf, ...) +[1] with NO categories enumerated (client side does it to handle rounding) +[2] NA (undefined) categories are assigned a JSON null value +[3] Includes all other numpy types: datetime, complex, etc. +[4] means float, int, uint (dtype.kind in ['i','u','f']) + +""" + def get_dtypes_and_schemas_of_dataframe(dataframe: pd.DataFrame): dtypes_by_column_name = {} @@ -17,133 +51,132 @@ def get_dtypes_and_schemas_of_dataframe(dataframe: pd.DataFrame): return dtypes_by_column_name, schema_type_hints_by_column_name -def get_dtype_of_array(array: pd.Series): - return get_dtype_and_schema_of_array(array)[0] +def get_encoding_dtype_of_array(array: Union[np.ndarray, pd.Series, pd.Index]) -> np.dtype: + return _get_type_info(array)[0] -def get_schema_type_hint_of_array(array: pd.Series): - return get_dtype_and_schema_of_array(array)[1] +def get_schema_type_hint_of_array(array: Union[np.ndarray, pd.Series, pd.Index]) -> dict: + return _get_type_info(array)[1] -def get_dtype_and_schema_of_array(array: pd.Series): - return ( - get_dtype_from_dtype(array.dtype, array_values=array), - get_schema_type_hint_from_dtype(array.dtype, array_values=array), - ) +def get_dtype_and_schema_of_array(array: Union[np.ndarray, pd.Series, pd.Index]) -> Tuple[np.dtype, dict]: + """Return tuple (encoding_dtype, schema_type_hint)""" + return _get_type_info(array) -def get_dtype_from_dtype(dtype, array_values=None): +def get_schema_type_hint_from_dtype(dtype) -> dict: + res = _get_type_info_from_dtype(dtype) + if res is None: + raise TypeError(f"Annotations of type {dtype} are unsupported.") + else: + return res[1] + + +def _get_type_info_from_dtype(dtype) -> Union[Tuple[np.dtype, dict], None]: """ - Given a data type, finds the equivalent data type that the array should be encoded as. Notably, this is relevant - for 64 bit values which will get downcast to 32 bit. + Best-effort to determine encoding type and schema hint from a dtype. + If this is not possible, or the type is unsupported, return None. + + This should be a subset of the cases which are supported by + _get_type_info(). The latter should be preferred if the array (values) + are available for typing. """ + if dtype.kind == "b": + return (np.uint8, {"type": "boolean"}) - dtype_name = dtype.name - dtype_kind = dtype.kind - - if dtype_name == "bool": - return np.uint8 - if dtype_name == "object" and dtype_kind == "O": - return str - if dtype_name == "category": - return get_dtype_from_dtype(dtype.categories.dtype, array_values) - - if can_cast_to_int32(dtype, array_values): - return np.int32 - if can_cast_to_float32(dtype, array_values): - return np.float32 - if not can_cast_to_float32(dtype, array_values): - return np.float64 - - raise TypeError(f"Annotations of type {dtype} are unsupported.") - - -def get_schema_type_hint_from_dtype(dtype, array_values=None): - """ - Returns a dictionary that contains type hints about the data type given, especially if the data type is 64 bit - and will be downcast to 32 bit. - """ - - dtype_name = dtype.name - dtype_kind = dtype.kind - - if dtype == np.float32 or dtype == np.int32: - return {"type": dtype_name} - if dtype_name == "bool": - return {"type": "boolean"} - if dtype_name == "object" and dtype_kind == "O": - return {"type": "string"} - if dtype_name == "category": - return {"type": "categorical", "categories": dtype.categories.tolist()} - - if can_cast_to_int32(dtype, array_values): - return {"type": "int32"} - if can_cast_to_float32(dtype, array_values): - return {"type": "float32"} - if dtype_kind == "f" and not can_cast_to_float32(dtype, array_values): - return {"type": "float64"} - - raise TypeError(f"Annotations of type {dtype} are unsupported.") - - -def can_cast_to_float32(dtype, array_values): - """ - Optimistically returns True signifying that a type downcast to float32 is possible whenever the incoming type is - a float. - - We also handle a special case here where the array is a Series object with integer categorical values AND NaNs. - Since NaNs are floating points in numpy, we upcast the integer array to float32 and return True. - """ - - if dtype.kind == "f": - if not np.can_cast(dtype, np.float32): - logging.warning(f"Type {dtype.name} will be converted to 32 bit float and may lose precision.") - - return True - - if dtype.kind == "O" and array_values.hasnans: - return True - - return False - - -def can_cast_to_int32(dtype, array_values=None): - """ - A type can be cast to 32 bit, overriding the numpy `cast_cast` function if the values in the array that are of - the higher precision type has values that are entirely within the range of the downcast type. - """ - - # Since a NaN is technically a float, any array that contains NaNs cannot be cast to an integer so immediately - # return False. - if array_values.hasnans: - return False - - # If the array is categorical, then we need to order the array values so that functions min and max that occur - # later, can function. They do not function on unordered categories. - ordered_array_values = array_values - if array_values.dtype.name == "category" and not array_values.cat.ordered: - ordered_array_values = array_values.cat.as_ordered() + if dtype.kind == "U": + return (np.dtype(str), {"type": "string"}) if dtype.kind in ["i", "u"]: if np.can_cast(dtype, np.int32): - return True - ii32 = np.iinfo(np.int32) - if ( - not ordered_array_values.empty - and (ordered_array_values.min() >= ii32.min and ordered_array_values.max() <= ii32.max) - or ordered_array_values.empty - ): - return True + return (np.int32, {"type": "int32"}) + + if dtype.kind == "f": + _float64_warning(dtype) + return (np.float32, {"type": "float32"}) + + if dtype.kind == "O" and not dtype.name == "category": + return (np.dtype(str), {"type": "string"}) + + return None + + +def _get_type_info(array: Union[np.ndarray, pd.Series, pd.Index]) -> Tuple[np.dtype, dict]: + """ + Determine encoding type and schema hint from an array. This allows more + flexible casting than may be possible by using just the dtype, as it can + account for category types and array values. + """ + if ( + not isinstance(array, np.ndarray) + and not isinstance(array, pd.Series) + and not isinstance(array, pd.Index) + and not hasattr(array, "dtype") + ): + raise TypeError("Unsupported data type.") + + dtype = array.dtype + + res = _get_type_info_from_dtype(dtype) + if res is not None: + return res + + if dtype.kind == "O": + if dtype.name == "category": + # Sometimes CategoricalDType can be encoded as int or float without further fuss. + # Do not specify the categories in the schema - let the client-side figure it out + # on its own. Utilize Series.to_numpy() to do casting that handles categorical + # NA/NaN (missing or undefined) categories. + if dtype.categories.dtype.kind in ["f", "i", "u"]: + return ( + _get_type_info(array.to_numpy())[0], + {"type": "categorical"}, + ) + else: + return (np.dtype(str), {"type": "categorical", "categories": dtype.categories.to_list()}) + + # all other extension types are str-encoded + return (np.dtype(str), {"type": "string"}) + + if dtype.kind in ["i", "u"] and _can_cast_array_values_to_int32(array): + return (np.int32, {"type": "int32"}) + + if dtype.kind == "f": + _float64_warning(array.dtype) + return (np.float32, {"type": "float32"}) + + raise TypeError(f"Annotations of type {dtype} are unsupported.") + + +def _float64_warning(dtype): + """ + Warn the user if we are down-casting a float64 to float32, and may potentially lose information. + """ + if dtype.kind == "f" and not np.can_cast(dtype, np.float32): + logging.warning(f"Type {dtype.name} will be converted to 32 bit float and may lose precision.") + + +def _can_cast_array_values_to_int32(array: Union[np.ndarray, pd.Series, pd.Index]) -> bool: + """ + Return true if the (U)INT array values can be safely cast to int32. We allow size reducing + casts (ie, int64 to int32) if no actual values require the larger size (ie, actual values + can be represented by the smaller type). + """ + assert array.dtype.kind in ["u", "i"] + + if np.can_cast(array.dtype, np.int32): + return True + + if array.size == 0: + return True + + int32_machine_limits = np.iinfo(np.int32) + if array.min() >= int32_machine_limits.min and array.max() <= int32_machine_limits.max: + return True + return False -def convert_pandas_series_to_numpy(series_to_convert: pd.Series, dtype): - if series_to_convert.hasnans and dtype == np.int32: - logging.error("Cannot convert a pandas Series object to an integer dtype if it contains NaNs.") - - return series_to_convert.to_numpy(dtype) - - def convert_string_to_value(value: str): """convert a string to value with the most appropriate type""" if value.lower() == "true": diff --git a/backend/czi_hosted/common/annotations/hosted_tiledb.py b/backend/czi_hosted/common/annotations/hosted_tiledb.py index f86fec5a..733185a3 100644 --- a/backend/czi_hosted/common/annotations/hosted_tiledb.py +++ b/backend/czi_hosted/common/annotations/hosted_tiledb.py @@ -10,7 +10,7 @@ from flask import current_app from backend.czi_hosted.common.annotations.annotations import Annotations from backend.common.errors import AnnotationCategoryNameError from backend.czi_hosted.common.utils.sanitization_utils import sanitize_values_in_list -from backend.common.utils.type_conversion_utils import get_dtypes_and_schemas_of_dataframe, get_dtype_of_array +from backend.common.utils.type_conversion_utils import get_dtypes_and_schemas_of_dataframe, get_encoding_dtype_of_array from backend.czi_hosted.db.cellxgene_orm import Annotation @@ -143,7 +143,7 @@ class AnnotationsHostedTileDB(Annotations): # convert to tiledb datatypes for col in df: - df[col] = df[col].astype(get_dtype_of_array(df[col])) + df[col] = df[col].astype(get_encoding_dtype_of_array(df[col])) tiledb.from_pandas(uri, df, sparse=True) else: uri = "" diff --git a/backend/czi_hosted/common/config/dataset_config.py b/backend/czi_hosted/common/config/dataset_config.py index 8432c278..50d96787 100644 --- a/backend/czi_hosted/common/config/dataset_config.py +++ b/backend/czi_hosted/common/config/dataset_config.py @@ -44,7 +44,7 @@ class DatasetConfig(BaseConfig): self.diffexp__lfc_cutoff = default_config["diffexp"]["lfc_cutoff"] self.diffexp__top_n = default_config["diffexp"]["top_n"] - self.X_approx_distribution = default_config["X_approx_distribution"] + self.X_approximate_distribution = default_config["X_approximate_distribution"] except KeyError as e: raise ConfigurationError(f"Unexpected config: {str(e)}") @@ -60,7 +60,7 @@ class DatasetConfig(BaseConfig): self.handle_user_annotations(context) self.handle_embeddings() self.handle_diffexp(context) - self.handle_X_approx_distribution() + self.handle_X_approximate_distribution() def handle_app(self): self.validate_correct_type_of_configuration_attribute("app__scripts", list) @@ -203,9 +203,9 @@ class DatasetConfig(BaseConfig): "running differential expression may take longer or fail." ) - def handle_X_approx_distribution(self): - self.validate_correct_type_of_configuration_attribute("X_approx_distribution", str) - if self.X_approx_distribution not in ["normal", "count"]: + def handle_X_approximate_distribution(self): + self.validate_correct_type_of_configuration_attribute("X_approximate_distribution", str) + if self.X_approximate_distribution not in ["normal", "count"]: raise ConfigurationError( - "X_approx_distribution has unknown value -- must be 'normal' or 'count'." + "X_approximate_distribution has unknown value -- must be 'normal' or 'count'." ) diff --git a/backend/czi_hosted/common/utils/cxg_generation_utils.py b/backend/czi_hosted/common/utils/cxg_generation_utils.py index 3f3ee48e..c3c1c867 100644 --- a/backend/czi_hosted/common/utils/cxg_generation_utils.py +++ b/backend/czi_hosted/common/utils/cxg_generation_utils.py @@ -3,7 +3,7 @@ import json import numpy as np import tiledb -from backend.common.utils.type_conversion_utils import get_dtype_of_array, get_dtype_and_schema_of_array +from backend.common.utils.type_conversion_utils import get_encoding_dtype_of_array, get_dtype_and_schema_of_array def convert_dictionary_to_cxg_group(cxg_container, metadata_dict, group_metadata_name="cxg_group_metadata"): @@ -47,7 +47,7 @@ def convert_dataframe_to_cxg_array(cxg_container, dataframe_name, dataframe, ind ] ) attrs = [ - tiledb.Attr(name=column, dtype=get_dtype_of_array(dataframe[column]), filters=tiledb_filter) + tiledb.Attr(name=column, dtype=get_encoding_dtype_of_array(dataframe[column]), filters=tiledb_filter) for column in dataframe ] domain = tiledb.Domain( diff --git a/backend/czi_hosted/data_anndata/anndata_adaptor.py b/backend/czi_hosted/data_anndata/anndata_adaptor.py index f6d3447a..8badd8de 100644 --- a/backend/czi_hosted/data_anndata/anndata_adaptor.py +++ b/backend/czi_hosted/data_anndata/anndata_adaptor.py @@ -8,7 +8,7 @@ from scipy import sparse import backend.common.compute.diffexp_generic as diffexp_generic from backend.common.colors import convert_anndata_category_colors_to_cxg_category_colors -from backend.common.constants import Axis, MAX_LAYOUTS, XApproxDistribution +from backend.common.constants import Axis, MAX_LAYOUTS, XApproximateDistribution from backend.czi_hosted.common.corpora import corpora_get_props_from_anndata from backend.common.errors import PrepareError, DatasetAccessError, ConfigurationError from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array @@ -28,7 +28,7 @@ class AnndataAdaptor(DataAdaptor): def __init__(self, data_locator, app_config=None, dataset_config=None): super().__init__(data_locator, app_config, dataset_config) self.data = None - self.X_approx_distribution = None + self.X_approximate_distribution = None self._load_data(data_locator) self._validate_and_initialize() @@ -66,11 +66,11 @@ class AnndataAdaptor(DataAdaptor): @staticmethod def _create_unique_column_name(df, col_name_prefix): - """ given the columns of a dataframe, and a name prefix, return a column name which - does not exist in the dataframe, AND which is prefixed by `prefix` + """given the columns of a dataframe, and a name prefix, return a column name which + does not exist in the dataframe, AND which is prefixed by `prefix` - The approach is to append a numeric suffix, starting at zero and increasing by - one, until an unused name is found (eg, prefix_0, prefix_1, ...). + The approach is to append a numeric suffix, starting at zero and increasing by + one, until an unused name is found (eg, prefix_0, prefix_1, ...). """ suffix = 0 while f"{col_name_prefix}{suffix}" in df: @@ -124,7 +124,11 @@ class AnndataAdaptor(DataAdaptor): def _create_schema(self): self.schema = { - "dataframe": {"nObs": self.cell_count, "nVar": self.gene_count, "type": str(self.data.X.dtype)}, + "dataframe": { + "nObs": self.cell_count, + "nVar": self.gene_count, + **get_schema_type_hint_of_array(self.data.X), + }, "annotations": { "obs": {"index": self.parameters.get("obs_names"), "columns": []}, "var": {"index": self.parameters.get("var_names"), "columns": []}, @@ -191,9 +195,9 @@ class AnndataAdaptor(DataAdaptor): self.gene_count = self.data.shape[1] self._create_schema() - if self.dataset_config.X_approx_distribution == "auto": - raise ConfigurationError("X-approx-distribution 'auto' mode unsupported.") - self.X_approx_distribution = self.dataset_config.X_approx_distribution + if self.dataset_config.X_approximate_distribution == "auto": + raise ConfigurationError("X-approximate-distribution 'auto' mode unsupported.") + self.X_approximate_distribution = self.dataset_config.X_approximate_distribution # heuristic n_values = self.data.shape[0] * self.data.shape[1] @@ -201,10 +205,10 @@ class AnndataAdaptor(DataAdaptor): self.parameters.update({"diffexp_may_be_slow": True}) def _is_valid_layout(self, arr): - """ return True if this layout data is a valid array for front-end presentation: - * ndarray, dtype float/int/uint - * with shape (n_obs, >= 2) - * with all values finite or NaN (no +Inf or -Inf) + """return True if this layout data is a valid array for front-end presentation: + * ndarray, dtype float/int/uint + * with shape (n_obs, >= 2) + * with all values finite or NaN (no +Inf or -Inf) """ is_valid = type(arr) == np.ndarray and arr.dtype.kind in "fiu" is_valid = is_valid and arr.shape[0] == self.data.n_obs and arr.shape[1] >= 2 @@ -327,8 +331,8 @@ class AnndataAdaptor(DataAdaptor): X = self.data.X[obs_mask, var_mask] return X - def get_X_approx_distribution(self) -> XApproxDistribution: - return self.X_approx_distribution + def get_X_approximate_distribution(self) -> XApproximateDistribution: + return self.X_approximate_distribution def get_shape(self): return self.data.shape diff --git a/backend/czi_hosted/data_common/data_adaptor.py b/backend/czi_hosted/data_common/data_adaptor.py index 8c3aadc1..c287fbaa 100644 --- a/backend/czi_hosted/data_common/data_adaptor.py +++ b/backend/czi_hosted/data_common/data_adaptor.py @@ -7,7 +7,7 @@ from scipy import sparse from server_timing import Timing as ServerTiming from backend.czi_hosted.common.config.app_config import AppConfig -from backend.common.constants import Axis, XApproxDistribution +from backend.common.constants import Axis, XApproximateDistribution from backend.common.errors import ( FilterError, JSONEncodingValueError, @@ -84,7 +84,7 @@ class DataAdaptor(metaclass=ABCMeta): pass @abstractmethod - def get_X_approx_distribution(self) -> XApproxDistribution: + def get_X_approximate_distribution(self) -> XApproximateDistribution: """return the approximate distribution of the X matrix.""" pass diff --git a/backend/czi_hosted/data_cxg/cxg_adaptor.py b/backend/czi_hosted/data_cxg/cxg_adaptor.py index 4afeafcd..a0643935 100644 --- a/backend/czi_hosted/data_cxg/cxg_adaptor.py +++ b/backend/czi_hosted/data_cxg/cxg_adaptor.py @@ -8,7 +8,7 @@ import pandas as pd import tiledb from server_timing import Timing as ServerTiming -from backend.common.constants import Axis, XApproxDistribution +from backend.common.constants import Axis, XApproximateDistribution from backend.common.errors import DatasetAccessError, ConfigurationError from backend.czi_hosted.common.immutable_kvcache import ImmutableKVCache from backend.common.utils.type_conversion_utils import get_schema_type_hint_from_dtype @@ -37,7 +37,7 @@ class CxgAdaptor(DataAdaptor): self.lsuri_results = ImmutableKVCache(lambda key: self._lsuri(uri=key, tiledb_ctx=self.tiledb_ctx)) self.arrays = ImmutableKVCache(lambda key: self._open_array(uri=key, tiledb_ctx=self.tiledb_ctx)) self.schema = None - self.X_approx_distribution = None + self.X_approximate_distribution = None self._validate_and_initialize() @@ -176,9 +176,9 @@ class CxgAdaptor(DataAdaptor): if cxg_version not in ["0.0", "0.1", "0.2.0"]: raise DatasetAccessError(f"cxg matrix is not valid: {self.url}") - if self.dataset_config.X_approx_distribution == "auto": - raise ConfigurationError("X-approx-distribution 'auto' mode unsupported.") - self.X_approx_distribution = self.dataset_config.X_approx_distribution + if self.dataset_config.X_approximate_distribution == "auto": + raise ConfigurationError("X-approximate-distribution 'auto' mode unsupported.") + self.X_approximate_distribution = self.dataset_config.X_approximate_distribution self.title = title self.about = about @@ -210,7 +210,8 @@ class CxgAdaptor(DataAdaptor): if lfc_cutoff is None: lfc_cutoff = self.dataset_config.diffexp__lfc_cutoff return diffexp_cxg.diffexp_ttest( - adaptor=self, maskA=maskA, maskB=maskB, top_n=top_n, diffexp_lfc_cutoff=lfc_cutoff) + adaptor=self, maskA=maskA, maskB=maskB, top_n=top_n, diffexp_lfc_cutoff=lfc_cutoff + ) def get_colors(self): if self.cxg_version == "0.0": @@ -286,8 +287,8 @@ class CxgAdaptor(DataAdaptor): data = X.multi_index[obs_items, var_items][""] return data - def get_X_approx_distribution(self) -> XApproxDistribution: - return self.X_approx_distribution + def get_X_approximate_distribution(self) -> XApproximateDistribution: + return self.X_approximate_distribution def get_shape(self): X = self.open_array("X") @@ -357,7 +358,7 @@ class CxgAdaptor(DataAdaptor): shape = self.get_shape() dtype = self.get_X_array_dtype() - dataframe = {"nObs": shape[0], "nVar": shape[1], "type": dtype.name} + dataframe = {"nObs": shape[0], "nVar": shape[1], **get_schema_type_hint_from_dtype(dtype)} annotations = {} for ax in ("obs", "var"): diff --git a/backend/czi_hosted/default_config.py b/backend/czi_hosted/default_config.py index 436aa739..214eeb31 100644 --- a/backend/czi_hosted/default_config.py +++ b/backend/czi_hosted/default_config.py @@ -203,7 +203,7 @@ dataset: lfc_cutoff: 0.01 top_n: 10 - X_approx_distribution: normal # currently fixed config + X_approximate_distribution: normal # currently fixed config external: # You can retrieve configuration parameters from this config file, the environment, diff --git a/backend/czi_hosted/requirements.txt b/backend/czi_hosted/requirements.txt index 08136006..504ad432 100644 --- a/backend/czi_hosted/requirements.txt +++ b/backend/czi_hosted/requirements.txt @@ -1,9 +1,9 @@ -anndata>=0.7.6 # we use to_memory(), added in 0.7.6 +anndata>=0.7.6 # we need to_memory(), added in 0.7.6 boto3>=1.12.18 click>=7.1.2 Flask>=1.0.2,<2.0.0 # Flask 2.0 is not compatible with the latest version of Flask-RESTful (0.3.8) Flask-Compress>=1.4.0 -Flask-Cors>=3.0.6 +Flask-Cors>=3.0.9 # CVE-2020-25032 Flask-RESTful>=0.3.6 flask-server-timing>=0.1.2 flask-talisman>=0.7.0 @@ -12,12 +12,12 @@ flatten-dict>=0.2.0 fsspec>=0.4.4,<0.8.0 gunicorn>=20.0.4 h5py>=3.0.0 -numba>=0.49.1,<0.53.0 -numpy>=1.15.0 +numba>=0.51.2 +numpy>=1.17.5 packaging>=20.0 pandas>=1.0,!=1.1 # pandas 1.1 breaks tests, https://github.com/pandas-dev/pandas/issues/35446 -PyYAML>=5.3 -scipy>=1.0 +PyYAML>=5.4 # CVE-2020-14343 +scipy>=1.4 requests>=2.22.0 tiledb>=0.5.9,>=0.6.2,!=0.7.2, !=0.8.6 s3fs==0.4.2 diff --git a/backend/server/cli/launch.py b/backend/server/cli/launch.py index 9a4fad7f..7fb49b0b 100644 --- a/backend/server/cli/launch.py +++ b/backend/server/cli/launch.py @@ -151,8 +151,8 @@ def dataset_args(func): help="URL providing more information about the dataset (hint: must be a fully specified absolute URL).", ) @click.option( - "--X-approx-distribution", - default=DEFAULT_CONFIG.dataset_config.X_approx_distribution, + "--X-approximate-distribution", + default=DEFAULT_CONFIG.dataset_config.X_approximate_distribution, show_default=True, type=click.Choice(["auto", "normal", "count"], case_sensitive=False), help="Specify the approximate distribution of X matrix values. 'auto' will use a heuristic " @@ -326,7 +326,7 @@ def launch( disable_diffexp, config_file, dump_default_config, - x_approx_distribution, + x_approximate_distribution, ): """Launch the cellxgene data viewer. This web app lets you explore single-cell expression data. @@ -385,7 +385,7 @@ def launch( embeddings__names=embedding, diffexp__enable=not disable_diffexp, diffexp__lfc_cutoff=diffexp_lfc_cutoff, - X_approx_distribution=x_approx_distribution, + X_approximate_distribution=x_approximate_distribution, ) diff = cli_config.server_config.changes_from_default() diff --git a/backend/server/common/config/dataset_config.py b/backend/server/common/config/dataset_config.py index 14115af7..0f5cebe2 100644 --- a/backend/server/common/config/dataset_config.py +++ b/backend/server/common/config/dataset_config.py @@ -38,7 +38,7 @@ class DatasetConfig(BaseConfig): self.diffexp__lfc_cutoff = default_config["diffexp"]["lfc_cutoff"] self.diffexp__top_n = default_config["diffexp"]["top_n"] - self.X_approx_distribution = default_config["X_approx_distribution"] + self.X_approximate_distribution = default_config["X_approximate_distribution"] except KeyError as e: raise ConfigurationError(f"Unexpected config: {str(e)}") @@ -52,7 +52,7 @@ class DatasetConfig(BaseConfig): self.handle_user_annotations(context) self.handle_embeddings() self.handle_diffexp(context) - self.handle_X_approx_distribution() + self.handle_X_approximate_distribution() def get_data_adaptor(self): server_config = self.app_config.server_config @@ -186,9 +186,9 @@ class DatasetConfig(BaseConfig): "CAUTION: due to the size of your dataset, " "running differential expression may take longer or fail." ) - def handle_X_approx_distribution(self): - self.validate_correct_type_of_configuration_attribute("X_approx_distribution", str) - if self.X_approx_distribution not in ["auto", "normal", "count"]: + def handle_X_approximate_distribution(self): + self.validate_correct_type_of_configuration_attribute("X_approximate_distribution", str) + if self.X_approximate_distribution not in ["auto", "normal", "count"]: raise ConfigurationError( - "X_approx_distribution has unknown value -- must be 'auto', 'normal' or 'count'." + "X_approximate_distribution has unknown value -- must be 'auto', 'normal' or 'count'." ) diff --git a/backend/server/data_anndata/anndata_adaptor.py b/backend/server/data_anndata/anndata_adaptor.py index 69d58fcc..d0f108ac 100644 --- a/backend/server/data_anndata/anndata_adaptor.py +++ b/backend/server/data_anndata/anndata_adaptor.py @@ -9,7 +9,7 @@ from scipy import sparse import backend.common.compute.diffexp_generic as diffexp_generic import backend.common.compute.estimate_distribution as estimate_distribution from backend.common.colors import convert_anndata_category_colors_to_cxg_category_colors -from backend.common.constants import Axis, MAX_LAYOUTS, XApproxDistribution +from backend.common.constants import Axis, MAX_LAYOUTS, XApproximateDistribution from backend.server.common.corpora import corpora_get_props_from_anndata from backend.common.errors import PrepareError, DatasetAccessError from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array @@ -29,7 +29,7 @@ class AnndataAdaptor(DataAdaptor): def __init__(self, data_locator, app_config=None, dataset_config=None): super().__init__(data_locator, app_config, dataset_config) self.data = None - self.X_approx_distribution = None + self.X_approximate_distribution = None self._load_data(data_locator) self._validate_and_initialize() @@ -125,7 +125,11 @@ class AnndataAdaptor(DataAdaptor): def _create_schema(self): self.schema = { - "dataframe": {"nObs": self.cell_count, "nVar": self.gene_count, "type": str(self.data.X.dtype)}, + "dataframe": { + "nObs": self.cell_count, + "nVar": self.gene_count, + **get_schema_type_hint_of_array(self.data.X), + }, "annotations": { "obs": {"index": self.parameters.get("obs_names"), "columns": []}, "var": {"index": self.parameters.get("var_names"), "columns": []}, @@ -192,12 +196,12 @@ class AnndataAdaptor(DataAdaptor): self.gene_count = self.data.shape[1] self._create_schema() - if self.dataset_config.X_approx_distribution == "auto": + if self.dataset_config.X_approximate_distribution == "auto": """Lazy evaluate the heuristic if we are backed.""" if not self.data.isbacked: - self.X_approx_distribution = estimate_distribution.estimate_approximate_distribution(self.data.X) + self.X_approximate_distribution = estimate_distribution.estimate_approximate_distribution(self.data.X) else: - self.X_approx_distribution = self.dataset_config.X_approx_distribution + self.X_approximate_distribution = self.dataset_config.X_approximate_distribution # heuristic n_values = self.data.shape[0] * self.data.shape[1] @@ -331,15 +335,15 @@ class AnndataAdaptor(DataAdaptor): X = self.data.X[obs_mask, var_mask] return X - def get_X_approx_distribution(self) -> XApproxDistribution: + def get_X_approximate_distribution(self) -> XApproximateDistribution: """return the approximate distribution of the X matrix.""" - if self.X_approx_distribution is None: + if self.X_approximate_distribution is None: """Not yet evaluated.""" - assert(self.dataset_config.X_approx_distribution == "auto") + assert self.dataset_config.X_approximate_distribution == "auto" self.data = self.data.to_memory() # loads data - self.X_approx_distribution = estimate_distribution.estimate_approximate_distribution(self.data.X) + self.X_approximate_distribution = estimate_distribution.estimate_approximate_distribution(self.data.X) - return self.X_approx_distribution + return self.X_approximate_distribution def get_shape(self): return self.data.shape diff --git a/backend/server/data_common/data_adaptor.py b/backend/server/data_common/data_adaptor.py index f0a60592..26f59665 100644 --- a/backend/server/data_common/data_adaptor.py +++ b/backend/server/data_common/data_adaptor.py @@ -6,7 +6,7 @@ from scipy import sparse from server_timing import Timing as ServerTiming from backend.server.common.config.app_config import AppConfig -from backend.common.constants import Axis, XApproxDistribution +from backend.common.constants import Axis, XApproximateDistribution from backend.common.errors import FilterError, JSONEncodingValueError, ExceedsLimitError, UnsupportedSummaryMethod from backend.common.utils.utils import jsonify_numpy from backend.common.fbs.matrix import encode_matrix_fbs @@ -72,9 +72,9 @@ class DataAdaptor(metaclass=ABCMeta): the return type is either ndarray or scipy.sparse.spmatrix.""" pass - def get_X_approx_distribution(self) -> XApproxDistribution: + def get_X_approximate_distribution(self) -> XApproximateDistribution: """return the approximate distribution of the X matrix.""" - return XApproxDistribution.NORMAL + return XApproximateDistribution.NORMAL @abstractmethod def get_shape(self): diff --git a/backend/server/default_config.py b/backend/server/default_config.py index 886de6a9..9dc15f16 100644 --- a/backend/server/default_config.py +++ b/backend/server/default_config.py @@ -77,7 +77,7 @@ dataset: lfc_cutoff: 0.01 top_n: 10 - X_approx_distribution: auto + X_approximate_distribution: auto external: # You can retrieve configuration parameters from this config file, the environment, diff --git a/backend/test/fixtures/czi_hosted_dataset_config_outline.py b/backend/test/fixtures/czi_hosted_dataset_config_outline.py index 44c06341..81ca0df7 100644 --- a/backend/test/fixtures/czi_hosted_dataset_config_outline.py +++ b/backend/test/fixtures/czi_hosted_dataset_config_outline.py @@ -31,5 +31,5 @@ dataset: lfc_cutoff: {lfc_cutoff} top_n: {top_n} - X_approx_distribution: {X_approx_distribution} + X_approximate_distribution: {X_approximate_distribution} """ diff --git a/backend/test/fixtures/dataset_config_outline.py b/backend/test/fixtures/dataset_config_outline.py index 27aeda9f..ff8a6e03 100644 --- a/backend/test/fixtures/dataset_config_outline.py +++ b/backend/test/fixtures/dataset_config_outline.py @@ -28,5 +28,5 @@ dataset: lfc_cutoff: {lfc_cutoff} top_n: {top_n} - X_approx_distribution: {X_approx_distribution} + X_approximate_distribution: {X_approximate_distribution} """ diff --git a/backend/test/fixtures/pbmc3k-genesets.csv b/backend/test/fixtures/pbmc3k-genesets.csv index 83340d4c..ebd079de 100644 --- a/backend/test/fixtures/pbmc3k-genesets.csv +++ b/backend/test/fixtures/pbmc3k-genesets.csv @@ -16,6 +16,6 @@ summary test,,F5, summary test,,PIGU, geneset_to_delete,,, geneset_to_edit,,, -fill_this_geneset,,RER1, +fill_this_geneset,,, empty_this_geneset,,SIK1, brush_this_gene,,SIK1, \ No newline at end of file diff --git a/backend/test/fixtures/pbmc3k_64.h5ad b/backend/test/fixtures/pbmc3k_64.h5ad new file mode 100644 index 00000000..3a6a4e52 Binary files /dev/null and b/backend/test/fixtures/pbmc3k_64.h5ad differ diff --git a/backend/test/test_common/unit/fbs/test_matrix.py b/backend/test/test_common/unit/fbs/test_matrix.py index ece1c918..a8e854f9 100644 --- a/backend/test/test_common/unit/fbs/test_matrix.py +++ b/backend/test/test_common/unit/fbs/test_matrix.py @@ -2,16 +2,20 @@ import unittest import pandas as pd import numpy as np from scipy import sparse +from parameterized import parameterized_class +import json -import backend.test.decode_fbs as decode_fbs +from backend.test import decode_fbs from backend.common.fbs.matrix import encode_matrix_fbs, decode_matrix_fbs +from backend.common.utils.type_conversion_utils import get_dtypes_and_schemas_of_dataframe +import backend.common.fbs as fbs class FbsTests(unittest.TestCase): - """Test Case for Matrix FBS data encode/decode """ + """Test Case for Matrix FBS data encode/decode""" def test_encode_boundary(self): - """ test various boundary checks """ + """test various boundary checks""" # row indexing is unsupported with self.assertRaises(ValueError): @@ -46,7 +50,7 @@ class FbsTests(unittest.TestCase): "d": pd.Series(["x", "y", "z", "x", "y", "z", "a", "x", "y", "z"], dtype="category"), } ) - expected_types = ((np.ndarray, np.float32), (np.ndarray, np.int32), (np.ndarray, np.uint32), (list, None)) + expected_types = ((np.ndarray, np.float32), (np.ndarray, np.int32), (np.ndarray, np.int32), (list, None)) fbs = encode_matrix_fbs(matrix=df, row_idx=None, col_idx=df.columns) self.fbs_checks(fbs, (10, 4), expected_types, ["a", "b", "c", "d"]) @@ -80,3 +84,133 @@ class FbsTests(unittest.TestCase): self.assertTrue(np.all(dfSrc[c] == dfDst[c])) else: self.assertEqual(dfSrc[c], dfDst[c]) + + +""" +Test type consistency between FBS encoding and the underlying schema hint. + +Basic assertion: the FBS type returned by encode_matrix_fbs() will be consistent +with the schema hint returned by type_conversion_utils (which is in turn used +to create the client schema). + +The following test cases are all dicts which contain the following keys: + - dataframe - the dataframe used as input for encode_matrix_fbs + - expected_fbs_types - upon success, dict of FBS column types expected (eg, Float32Array) + - expected_schema_hints - upon success, dict of schema hint +All are keyed by column name. +""" + +# simple tests that we convert all ints to int32 +int_dtypes = [np.dtype(d) for d in [np.int8, np.uint8, np.int16, np.uint16, np.int32, np.uint32, np.int64, np.uint64]] +int_test_cases = [ + { + "dataframe": pd.DataFrame({dtype.name: np.zeros((10,), dtype=dtype) for dtype in int_dtypes}), + "expected_fbs_types": dict( + [(dtype.name, fbs.NetEncoding.TypedArray.TypedArray.Int32Array) for dtype in int_dtypes] + ), + "expected_schema_hints": dict([(dtype.name, {"type": "int32"}) for dtype in int_dtypes]), + } +] + +# simple tests that we convert all floats to float32 +float_dtypes = [np.dtype(d) for d in [np.float16, np.float32, np.float64]] +float_test_cases = [ + { + "dataframe": pd.DataFrame({dtype.name: np.zeros((10,), dtype=dtype) for dtype in float_dtypes}), + "expected_fbs_types": dict( + [(dtype.name, fbs.NetEncoding.TypedArray.TypedArray.Float32Array) for dtype in float_dtypes] + ), + "expected_schema_hints": dict([(dtype.name, {"type": "float32"}) for dtype in float_dtypes]), + } +] + +# boolean - should be encoded as an uint32 +bool_dtypes = [np.dtype(d) for d in [np.bool_, bool]] +bool_test_cases = [ + { + "dataframe": pd.DataFrame({dtype.name: np.ones((10,), dtype=dtype) for dtype in bool_dtypes}), + "expected_fbs_types": dict( + [(dtype.name, fbs.NetEncoding.TypedArray.TypedArray.Uint32Array) for dtype in bool_dtypes] + ), + "expected_schema_hints": dict([(dtype.name, {"type": "boolean"}) for dtype in bool_dtypes]), + } +] + +cat_test_cases = [ + { + "dataframe": pd.DataFrame({"a": pd.Series(["a", "b", "c", "a", "b", "c"], dtype="category")}), + "expected_fbs_types": {"a": fbs.NetEncoding.TypedArray.TypedArray.JSONEncodedArray}, + "expected_schema_hints": {"a": {"type": "categorical", "categories": ["a", "b", "c"]}}, + }, + { + "dataframe": pd.DataFrame( + {"a": pd.Series(["a", "b", "c", "a", "b", "c"], dtype="category").cat.remove_categories("b")} + ), + "expected_fbs_types": {"a": fbs.NetEncoding.TypedArray.TypedArray.JSONEncodedArray}, + "expected_schema_hints": {"a": {"type": "categorical", "categories": ["a", "c"]}}, + }, + { + "dataframe": pd.DataFrame({"a": pd.Series(np.arange(0, 10, dtype=np.int64), dtype="category")}), + "expected_fbs_types": {"a": fbs.NetEncoding.TypedArray.TypedArray.Int32Array}, + "expected_schema_hints": {"a": {"type": "categorical"}}, + }, + { + "dataframe": pd.DataFrame( + {"a": pd.Series(np.arange(0, 10, dtype=np.int64), dtype="category").cat.remove_categories(2)} + ), + "expected_fbs_types": {"a": fbs.NetEncoding.TypedArray.TypedArray.Float32Array}, + "expected_schema_hints": {"a": {"type": "categorical"}}, + }, + { + "dataframe": pd.DataFrame({"a": pd.Series(np.arange(0, 10, dtype=np.float64), dtype="category")}), + "expected_fbs_types": {"a": fbs.NetEncoding.TypedArray.TypedArray.Float32Array}, + "expected_schema_hints": {"a": {"type": "categorical"}}, + }, + { + "dataframe": pd.DataFrame( + {"a": pd.Series(np.arange(0, 10, dtype=np.float64), dtype="category").cat.remove_categories(2)} + ), + "expected_fbs_types": {"a": fbs.NetEncoding.TypedArray.TypedArray.Float32Array}, + "expected_schema_hints": {"a": {"type": "categorical"}}, + }, +] + + +test_cases = [ + *int_test_cases, + *float_test_cases, + *bool_test_cases, + *cat_test_cases, +] + + +@parameterized_class(test_cases) +class TestTypeConversionConsistency(unittest.TestCase): + def test_type_conversion_consistency(self): + self.assertEqual(self.dataframe.shape[1], len(self.expected_fbs_types)) + self.assertEqual(self.dataframe.shape[1], len(self.expected_schema_hints)) + + buf = encode_matrix_fbs(matrix=self.dataframe, col_idx=self.dataframe.columns) + encoding_dtypes, schema_hints = get_dtypes_and_schemas_of_dataframe(self.dataframe) + + # check schema hints + # print(schema_hints) + # print(self.expected_schema_hints) + self.assertEqual(schema_hints, self.expected_schema_hints) + + # inspect the FBS types + matrix = fbs.NetEncoding.Matrix.Matrix.GetRootAsMatrix(buf, 0) + columns_length = matrix.ColumnsLength() + self.assertEqual(columns_length, self.dataframe.shape[1]) + + self.assertEqual(matrix.ColIndexType(), fbs.NetEncoding.TypedArray.TypedArray.JSONEncodedArray) + col_labels_arr = fbs.NetEncoding.JSONEncodedArray.JSONEncodedArray() + col_labels_arr.Init(matrix.ColIndex().Bytes, matrix.ColIndex().Pos) + col_index_labels = json.loads(col_labels_arr.DataAsNumpy().tobytes().decode("utf-8")) + self.assertEqual(len(col_index_labels), self.dataframe.shape[1]) + + for col_idx in range(0, columns_length): + col_label = col_index_labels[col_idx] + col = matrix.Columns(col_idx) + col_type = col.UType() + self.assertEqual(self.expected_fbs_types[col_label], col_type) diff --git a/backend/test/test_common/unit/utils/test_type_conversion_utils.py b/backend/test/test_common/unit/utils/test_type_conversion_utils.py index 70fba125..deacaa29 100644 --- a/backend/test/test_common/unit/utils/test_type_conversion_utils.py +++ b/backend/test/test_common/unit/utils/test_type_conversion_utils.py @@ -1,179 +1,22 @@ import unittest -from time import time -from unittest.mock import patch +import logging +from parameterized import parameterized_class import numpy as np +import pandas as pd from pandas import Series, DataFrame +from scipy import sparse from backend.common.utils.type_conversion_utils import ( - can_cast_to_float32, - can_cast_to_int32, - get_dtype_of_array, + get_encoding_dtype_of_array, get_schema_type_hint_of_array, get_dtypes_and_schemas_of_dataframe, - convert_pandas_series_to_numpy, + get_dtype_and_schema_of_array, + get_schema_type_hint_from_dtype, ) class TestTypeConversionUtils(unittest.TestCase): - def test__can_cast_to_float32__string_is_false(self): - array_to_convert = Series(data=["1", "2", "3"], dtype=str) - - can_cast = can_cast_to_float32(array_to_convert.dtype, array_to_convert) - - self.assertFalse(can_cast) - - def test__can_cast_to_float32__float64_is_true_warning_outputted(self): - array_to_convert = Series(data=[1, 2, 3], dtype=np.dtype(np.float64)) - - with self.assertLogs(level="WARN") as logger: - can_cast = can_cast_to_float32(array_to_convert.dtype, array_to_convert) - self.assertIn("may lose precision", logger.output[0]) - - self.assertTrue(can_cast) - - @patch("logging.warning") - def test__can_cast_to_float32__float32_is_false(self, mock_log_warning): - array_to_convert = Series(data=[1, 2, 3], dtype=np.dtype(np.float32)) - - can_cast = can_cast_to_float32(array_to_convert.dtype, array_to_convert) - - self.assertTrue(can_cast) - assert not mock_log_warning.called - - def test__can_cast_to_float32__categorical_float64_is_false(self): - array_to_convert = Series(data=[1.1, 2.2, 3.3], dtype="category") - - can_cast = can_cast_to_float32(array_to_convert.dtype, array_to_convert) - - self.assertFalse(can_cast) - - def test__can_cast_to_float32__categorical_int64_with_nans_is_true(self): - array_to_convert = Series(data=[1, 2, np.NaN], dtype="category") - - can_cast = can_cast_to_float32(array_to_convert.dtype, array_to_convert) - - self.assertTrue(can_cast) - - def test__can_cast_to_float_32__float_32_with_nans_is_true(self): - array_to_convert = Series(data=[1, 2, np.NaN], dtype=np.dtype(np.float32)) - - can_cast = can_cast_to_float32(array_to_convert.dtype, array_to_convert) - - self.assertTrue(can_cast) - - def test__can_cast_to_int32__string_is_false(self): - array_to_convert = Series(data=["1", "2", "3"], dtype=str) - - can_cast = can_cast_to_int32(array_to_convert.dtype, array_to_convert) - - self.assertFalse(can_cast) - - def test__can_cast_to_int32__int64_is_true(self): - array_to_convert = Series(data=[1, 2, 3], dtype=np.dtype(np.int64)) - - can_cast = can_cast_to_int32(array_to_convert.dtype, array_to_convert) - - self.assertTrue(can_cast) - - def test__can_cast_to_int32__int16_is_true(self): - array_to_convert = Series(data=[1, 2, 3], dtype=np.dtype(np.int16)) - - can_cast = can_cast_to_int32(array_to_convert.dtype, array_to_convert) - - self.assertTrue(can_cast) - - def test__can_cast_to_int32__int64_with_large_value_is_false(self): - array_to_convert = Series(data=[3000000000, 2, 3], dtype=np.dtype(np.int64)) - - can_cast = can_cast_to_int32(array_to_convert.dtype, array_to_convert) - - self.assertFalse(can_cast) - - def test__can_cast_to_int32__int64_with_nans_is_false(self): - array_to_convert = Series(data=[np.NaN, "2", "3"], dtype="category") - - can_cast = can_cast_to_int32(array_to_convert.dtype, array_to_convert) - - self.assertFalse(can_cast) - - def test__get_dtype_of_array__supported_dtypes_return_as_expected(self): - types = [np.float32, np.int32, np.bool_, str] - expected_dtypes = [np.float32, np.int32, np.uint8, str] - - for test_type_index in range(len(types)): - with self.subTest( - f"Testing get_dtype_of_array with type {types[test_type_index].__name__}", i=test_type_index - ): - array = Series(data=[], dtype=types[test_type_index]) - self.assertEqual(get_dtype_of_array(array), expected_dtypes[test_type_index]) - - def test__get_dtype_of_array__categories_return_as_expected(self): - array = Series(data=["a", "b", "c"], dtype="category") - expected_dtype = str - - actual_dtype = get_dtype_of_array(array) - - self.assertEqual(expected_dtype, actual_dtype) - - def test__get_dtype_of_array__unordered_integer_categories_return_as_expected(self): - array = Series(data=[2, 3, 1, 3, 1, 2], dtype="category") - expected_dtype = np.int32 - - actual_dtype = get_dtype_of_array(array) - - self.assertEqual(expected_dtype, actual_dtype) - - def test__get_dtype_of_array__castable_dtypes_return_as_expected(self): - types = [np.float64, np.int64] - expected_dtypes = [np.float32, np.int32] - - for test_type_index in range(len(types)): - with self.subTest( - f"Testing get_dtype_of_array with castable type {types[test_type_index].__name__}", i=test_type_index - ): - array = Series(data=[], dtype=types[test_type_index]) - self.assertEqual(get_dtype_of_array(array), expected_dtypes[test_type_index]) - - def test__get_dtype_of_array__unsupported_type_raises_exception(self): - unsupported_array = Series(list([time() for _ in range(2)]), dtype="datetime64[ns]") - - with self.assertRaises(TypeError) as exception_context: - get_dtype_of_array(unsupported_array) - - self.assertIn("unsupported", str(exception_context.exception)) - - def test__get_schema_type_hint_of_array__supported_dtypes_return_as_expected(self): - types = [np.float32, np.int32, np.bool_, str] - expected_schema_hints = [{"type": "float32"}, {"type": "int32"}, {"type": "boolean"}, {"type": "string"}] - - for test_type_index in range(len(types)): - with self.subTest( - f"Testing get_schema_type_hint_of_array with type {types[test_type_index].__name__}", i=test_type_index - ): - array = Series(data=[], dtype=types[test_type_index]) - self.assertEqual(get_schema_type_hint_of_array(array), expected_schema_hints[test_type_index]) - - def test__get_schema_type_hint_of_array__categories_return_as_expected(self): - array = Series(data=["a", "b", "b"], dtype="category") - expected_schema_hint = {"type": "categorical", "categories": ["a", "b"]} - - actual_schema_hint = get_schema_type_hint_of_array(array) - - self.assertEqual(expected_schema_hint, actual_schema_hint) - - def test__get_schema_type_hint_of_array__castable_dtypes_return_as_expected(self): - types = [np.float64, np.int64] - expected_schema_hints = [{"type": "float32"}, {"type": "int32"}] - - for test_type_index in range(len(types)): - with self.subTest( - f"Testing get_schema_type_hint_of_array with castable type {types[test_type_index].__name__}", - i=test_type_index, - ): - array = Series(data=[], dtype=types[test_type_index]) - self.assertEqual(get_schema_type_hint_of_array(array), expected_schema_hints[test_type_index]) - def test__get_dtypes_and_schemas_of_dataframe__dtype_and_schema_returns_as_expected(self): float_array = Series(data=[1, 2, 3], dtype=np.dtype(np.float64)) category_array = Series(data=["a", "b", "b"], dtype="category") @@ -190,28 +33,292 @@ class TestTypeConversionUtils(unittest.TestCase): self.assertEqual(expected_data_types_dict, actual_dataframe_data_types) self.assertEqual(expected_schema_type_hints_dict, actual_dataframe_schema_type_hints) - def test__convert_pandas_series_to_numpy__categorical_float64_to_float64_with_nans(self): - expected_float_array = np.array([1.1, 2.2, np.NaN], dtype=np.float64) - float_series = Series(data=[1.1, 2.2, np.NaN], dtype="category") + def test__get_schema_type_hint_from_dtype(self): + self.assertEqual(get_schema_type_hint_from_dtype(np.dtype(np.bool_)), {"type": "boolean"}) - actual_float_array = convert_pandas_series_to_numpy(float_series, np.float64) + for dtype in [np.int8, np.int8, np.int16, np.uint16, np.int32]: + self.assertEqual(get_schema_type_hint_from_dtype(np.dtype(dtype)), {"type": "int32"}) + for dtype in [np.uint32, np.int64, np.uint64]: + with self.assertRaises(TypeError): + get_schema_type_hint_from_dtype(np.dtype(dtype)) - np.testing.assert_equal(expected_float_array, actual_float_array) + for dtype in [np.float16, np.float32, np.float64]: + self.assertEqual(get_schema_type_hint_from_dtype(np.dtype(dtype)), {"type": "float32"}) - def test__convert_pandas_series_to_numpy__float64_to_float64(self): - expected_float_array = np.array([1.1, 2.2], dtype=np.float64) - float_series = Series(data=[1.1, 2.2], dtype=np.dtype(np.float64)) + for dtype in [np.dtype(object), np.dtype(str)]: + self.assertEqual(get_schema_type_hint_from_dtype(dtype), {"type": "string"}) - actual_float_array = convert_pandas_series_to_numpy(float_series, np.float64) - np.testing.assert_equal(expected_float_array, actual_float_array) +# Credit: https://stackoverflow.com/questions/35871815/python-3-unit-testing-assert-logger-not-called/64774103#64774103 +class AssertNoLog: + def assertNoLogs(self, logger, level): + """functions as a context manager. To be introduced in python 3.10""" - def test__convert_pandas_series_to_numpy__int64_to_int32_with_nans_throws_error(self): - int_series = Series(data=[1, 2, np.NaN], dtype="category") + class AssertNoLogsContext(unittest.TestCase): + def __init__(self, logger, level): + self.logger = logger + self.level = level + self.context = self.assertLogs(logger, level) - with self.assertLogs(level="ERROR") as logger: - convert_pandas_series_to_numpy(int_series, np.int32) + def __enter__(self): + """enter self.assertLogs as context manager, and log something""" + self.initial_logmsg = "sole message" + self.cm = self.context.__enter__() + self.logger.log(self.level, self.initial_logmsg) + return self.cm - self.assertIn( - "Cannot convert a pandas Series object to an integer dtype if it contains NaNs", logger.output[0] - ) + def __exit__(self, exc_type, exc_val, exc_tb): + """cleanup logs, and then check nothing extra was logged""" + # assertLogs.__exit__ should never fail because of initial msg + self.context.__exit__(exc_type, exc_val, exc_tb) + if len(self.cm.output) > 1: + """override any exception passed to __exit__""" + self.context._raiseFailure( + "logs of level {} or higher triggered on {} : {}".format( + logging.getLevelName(self.level), self.logger.name, self.cm.output[1:] + ) + ) + + return AssertNoLogsContext(logger, level) + + +""" +See table of expected cases in type_conversion_utils.py. + +This probes all edge cases. Each case is a dict containing keys: + - data - the array to be introspected + - throws - if not None, the expected Error (eg, TypeError) + - expected_encoding_dtype - upon success + - expected_schema_hint - upon success + - logs - if not None, specify expected log output +""" + +bool_OK_cases = [ + { + "data": data, + "expected_encoding_dtype": np.uint8, + "expected_schema_hint": {"type": "boolean"}, + } + for data in [ + np.array([0, 1, 0, 1], dtype=np.bool_), + pd.Series(np.array([0, 1, 0, 1], dtype=np.bool_)), + # pd.Index with bools doesn't really make any sense...and becomes dtype=object + ] +] + +int_OK_cases = [ + { + "data": data, + "expected_encoding_dtype": np.int32, + "expected_schema_hint": {"type": "int32"}, + } + for dtype in [np.int8, np.uint8, np.int16, np.uint16, np.int32, np.uint32, np.int64, np.uint64] + for data in [ + np.arange(0, 1000, dtype=dtype), + pd.Series(np.arange(0, 1000, dtype=dtype)), + pd.Index(np.arange(0, 1000, dtype=dtype)), + sparse.csr_matrix((10, 100), dtype=dtype), + ] +] + +float_OK_cases = [ + { + "data": data, + "expected_encoding_dtype": np.float32, + "expected_schema_hint": {"type": "float32"}, + "logs": None if data.dtype != np.float64 else {"level": logging.WARNING, "output": "may lose precision"}, + } + for dtype in [np.float16, np.float32, np.float64] + for data in [ + np.arange(-128, 1000, dtype=dtype), + pd.Series(np.arange(-128, 1000, dtype=dtype)), + pd.Index(np.arange(-129, 1000, dtype=dtype)), + np.array([-np.nan, np.NINF, -1, np.NZERO, 0, np.PZERO, 1, np.PINF, np.nan], dtype=dtype), + np.array([np.finfo(dtype).min, 0, np.finfo(dtype).max], dtype=dtype), + sparse.csr_matrix((10, 100), dtype=dtype), + ] +] + + +numeric_ERR_cases = [ + { + "data": data, + "throws": TypeError, + } + for data in [ + np.array([np.iinfo(np.int64).min, np.iinfo(np.int64).max], dtype=np.int64), + np.array([np.iinfo(np.uint64).min, np.iinfo(np.uint64).max], dtype=np.uint64), + np.array([np.iinfo(np.uint32).min, np.iinfo(np.uint32).max], dtype=np.uint32), + ] +] + + +string_OK_cases = [ + { + "data": data, + "expected_encoding_dtype": np.dtype(str), + "expected_schema_hint": {"type": "string"}, + } + for data in [ + np.array(["a", "b", "c"]), + np.array(["a", "b", "c"], dtype="object"), + pd.Series(["a", "b", "c"]), + pd.Index(["a", "b", "c"]), + np.array(["a", [], {}, None, True, False, 383.2], dtype="object"), + ] +] + +category_nonnumeric_OK_cases = [ + { + "data": data, + "expected_encoding_dtype": np.dtype(str), + "expected_schema_hint": {"type": "categorical", "categories": data.dtype.categories.to_list()}, + } + for data in [ + pd.Series(["a", "b", "c"], dtype="category"), + pd.Series(["a", "b", "c", 0, 1, 2], dtype="category"), + pd.Series(["a", "b", "c"], dtype="category").cat.remove_categories(["b"]), + pd.Series(["a", "b", "c", 0, 1, 2], dtype="category").cat.remove_categories(["b", 0]), + ] +] + +category_numeric_OK_cases = [ + # numeric, no NA/NaN, int + *[ + { + "data": data, + "expected_encoding_dtype": np.int32, + "expected_schema_hint": {"type": "categorical"}, + } + for dtype in [np.int8, np.uint8, np.int16, np.uint16, np.int32, np.uint32, np.int64, np.uint64] + for data in [ + pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category"), + ] + ], + # numeric, no NA/NaN, float + *[ + { + "data": data, + "expected_encoding_dtype": np.float32, + "expected_schema_hint": {"type": "categorical"}, + "logs": {"level": logging.WARNING, "output": "may lose precision"}, + } + for dtype in [np.float16, np.float32, np.float64] + for data in [ + pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category"), + pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category").cat.remove_categories([1]), + pd.Categorical(np.array([0, 1, 2], dtype=dtype)), + ] + ], + # numeric, has NA-induced cast to float32 + *[ + { + "data": data, + "expected_encoding_dtype": np.float32, + "expected_schema_hint": {"type": "categorical"}, + "logs": {"level": logging.WARNING, "output": "may lose precision"}, + } + for dtype in [ + np.int8, + np.uint8, + np.int16, + np.uint16, + np.int32, + np.uint32, + np.int64, + np.uint64, + np.float16, + np.float32, + np.float64, + ] + for data in [ + pd.Series(np.array([0, 1, 2], dtype=dtype), dtype="category").cat.remove_categories([1]), + pd.Categorical(np.array([0, 1, 2], dtype=dtype), categories=np.array([0, 1], dtype=dtype)), + ] + ], +] + +category_ERR_cases = [ + # catch expected categorical exceptions for Int64(etc) that have large values + { + "data": data, + "throws": TypeError, + } + for data in [ + pd.Categorical(np.array([np.iinfo(np.int64).min, np.iinfo(np.int64).max], dtype=np.int64)), + pd.Categorical(np.array([np.iinfo(np.uint64).min, np.iinfo(np.uint64).max], dtype=np.uint64)), + pd.Categorical(np.array([np.iinfo(np.uint32).min, np.iinfo(np.uint32).max], dtype=np.uint32)), + ] +] + +object_OK_cases = [ + { + "data": data, + "expected_encoding_dtype": np.dtype(str), + "expected_schema_hint": {"type": "string"}, + } + for data in [ + np.array(["a", True, 1, [], {}], dtype="object"), + pd.Series(["a", True, 1, [], {}], dtype="object"), + pd.Index(["a", True, 1, [], {}], dtype="object"), + ] +] + +err_cases = [ + {"data": np.array, "throws": TypeError} + for data in [ + np.ones((10,), dtype=np.complex64), + np.ones((10,), dtype=np.complex128), + np.array([b"foobar"], dtype=np.bytes_), + np.ones((10,), dtype=np.void), + np.arange("2005-02", "2005-03", dtype="datetime64[D]"), + np.arange("2005-02", "2005-03", dtype="datetime64[D]") - np.datetime64("2008-01-01"), + [], + {}, + ] +] + +test_cases = [ + *bool_OK_cases, + *int_OK_cases, + *float_OK_cases, + *numeric_ERR_cases, + *string_OK_cases, + *category_nonnumeric_OK_cases, + *category_numeric_OK_cases, + *category_ERR_cases, + *object_OK_cases, + *err_cases, +] + + +@parameterized_class(test_cases) +class TestTypeInference(unittest.TestCase, AssertNoLog): + def test_type_inference(self): + throws = getattr(self, "throws", None) + if throws: + with self.assertRaises(throws): + get_dtype_and_schema_of_array(self.data) + with self.assertRaises(throws): + get_encoding_dtype_of_array(self.data) + with self.assertRaises(throws): + get_schema_type_hint_of_array(self.data) + + else: + logs = getattr(self, "logs", None) + if logs is not None: + with self.assertLogs(level=logs["level"]) as logger: + encoding_dtype, schema_hint = get_dtype_and_schema_of_array(self.data) + self.assertEqual(encoding_dtype, self.expected_encoding_dtype) + self.assertEqual(schema_hint, self.expected_schema_hint) + self.assertIn(logs["output"], logger.output[0]) + + else: + with self.assertNoLogs(logging.getLogger(), logging.WARNING): + encoding_dtype, schema_hint = get_dtype_and_schema_of_array(self.data) + self.assertEqual(encoding_dtype, self.expected_encoding_dtype) + self.assertEqual(schema_hint, self.expected_schema_hint) + + # also test the other public API + self.assertEqual(get_encoding_dtype_of_array(self.data), self.expected_encoding_dtype) + self.assertEqual(get_schema_type_hint_of_array(self.data), self.expected_schema_hint) diff --git a/backend/test/test_czi_hosted/unit/common/config/__init__.py b/backend/test/test_czi_hosted/unit/common/config/__init__.py index 77a9a6d3..1cfebb17 100644 --- a/backend/test/test_czi_hosted/unit/common/config/__init__.py +++ b/backend/test/test_czi_hosted/unit/common/config/__init__.py @@ -131,7 +131,7 @@ class ConfigTests(BaseTest): environment=None, aws_secrets_manager_region=None, aws_secrets_manager_secrets=[], - X_approx_distribution="normal", + X_approximate_distribution="normal", config_file_name="app_config.yml", ): random_num = random.randrange(999999) @@ -195,7 +195,7 @@ class ConfigTests(BaseTest): enable_difexp=enable_difexp, lfc_cutoff=lfc_cutoff, top_n=top_n, - X_approx_distribution=X_approx_distribution, + X_approximate_distribution=X_approximate_distribution, config_file_name=f"temp_dataset_config_{random_num}.yml", ) external_config = self.custom_external_config( @@ -231,7 +231,7 @@ class ConfigTests(BaseTest): enable_difexp="true", lfc_cutoff=0.01, top_n=10, - X_approx_distribution="normal", + X_approximate_distribution="normal", config_file_name="dataset_config.yml", ): configfile = os.path.join(self.tmp_fixtures_directory, config_file_name) diff --git a/backend/test/test_czi_hosted/unit/common/test_api.py b/backend/test/test_czi_hosted/unit/common/test_api.py index 59af031d..6072ee53 100644 --- a/backend/test/test_czi_hosted/unit/common/test_api.py +++ b/backend/test/test_czi_hosted/unit/common/test_api.py @@ -444,7 +444,7 @@ class EndPointsCxg(EndPoints): {'genes': [], 'geneset_description': '', 'geneset_name': 'geneset_to_delete'}, {'genes': [], 'geneset_description': '', 'geneset_name': 'geneset_to_edit'}, { - 'genes': [{'gene_description': '', 'gene_symbol': 'RER1'}], + 'genes': [], 'geneset_description': '', 'geneset_name': 'fill_this_geneset' }, @@ -485,7 +485,7 @@ summary test,,F5,\r summary test,,PIGU,\r geneset_to_delete,,,\r geneset_to_edit,,,\r -fill_this_geneset,,RER1,\r +fill_this_geneset,,,\r empty_this_geneset,,SIK1,\r brush_this_gene,,SIK1,\r """ diff --git a/backend/test/test_czi_hosted/unit/compute/test_diffexp_cxg.py b/backend/test/test_czi_hosted/unit/compute/test_diffexp_cxg.py index 9134a163..14ddf400 100644 --- a/backend/test/test_czi_hosted/unit/compute/test_diffexp_cxg.py +++ b/backend/test/test_czi_hosted/unit/compute/test_diffexp_cxg.py @@ -20,7 +20,7 @@ class DiffExpTest(unittest.TestCase): adaptor types and different algorithms.""" def load_dataset(self, path, extra_server_config={}, extra_dataset_config={}): - extra_dataset_config["X_approx_distribution"] = "normal" # hardwired for now + extra_dataset_config["X_approximate_distribution"] = "normal" # hardwired for now config = app_config(path, extra_server_config=extra_server_config, extra_dataset_config=extra_dataset_config) loader = MatrixDataLoader(path) adaptor = loader.open(config) diff --git a/backend/test/test_czi_hosted/unit/data_common/fbs/test_matrix.py b/backend/test/test_czi_hosted/unit/data_common/fbs/test_matrix.py index 9b80d042..21389fe0 100644 --- a/backend/test/test_czi_hosted/unit/data_common/fbs/test_matrix.py +++ b/backend/test/test_czi_hosted/unit/data_common/fbs/test_matrix.py @@ -46,7 +46,7 @@ class FbsTests(unittest.TestCase): "d": pd.Series(["x", "y", "z", "x", "y", "z", "a", "x", "y", "z"], dtype="category"), } ) - expected_types = ((np.ndarray, np.float32), (np.ndarray, np.int32), (np.ndarray, np.uint32), (list, None)) + expected_types = ((np.ndarray, np.float32), (np.ndarray, np.int32), (np.ndarray, np.int32), (list, None)) fbs = encode_matrix_fbs(matrix=df, row_idx=None, col_idx=df.columns) self.fbs_checks(fbs, (10, 4), expected_types, ["a", "b", "c", "d"]) diff --git a/backend/test/test_server/unit/common/config/__init__.py b/backend/test/test_server/unit/common/config/__init__.py index 6f0c48eb..371038a2 100644 --- a/backend/test/test_server/unit/common/config/__init__.py +++ b/backend/test/test_server/unit/common/config/__init__.py @@ -103,7 +103,7 @@ class ConfigTests(unittest.TestCase): environment=None, aws_secrets_manager_region=None, aws_secrets_manager_secrets=[], - X_approx_distribution="auto", + X_approximate_distribution="auto", config_file_name="app_config.yml", ): random_num = random.randrange(999999) @@ -151,7 +151,7 @@ class ConfigTests(unittest.TestCase): enable_difexp=enable_difexp, lfc_cutoff=lfc_cutoff, top_n=top_n, - X_approx_distribution=X_approx_distribution, + X_approximate_distribution=X_approximate_distribution, config_file_name=f"temp_dataset_config_{random_num}.yml", ) external_config = self.custom_external_config( @@ -187,7 +187,7 @@ class ConfigTests(unittest.TestCase): enable_difexp="true", lfc_cutoff=0.01, top_n=10, - X_approx_distribution="auto", + X_approximate_distribution="auto", config_file_name="dataset_config.yml", ): configfile = os.path.join(self.tmp_fixtures_directory, config_file_name) diff --git a/backend/test/test_server/unit/common/test_api.py b/backend/test/test_server/unit/common/test_api.py index 84f79413..bb02b037 100644 --- a/backend/test/test_server/unit/common/test_api.py +++ b/backend/test/test_server/unit/common/test_api.py @@ -6,9 +6,13 @@ from http import HTTPStatus import tempfile from os import path import hashlib +from os.path import basename, splitext import pandas as pd import requests +import numpy as np + +from parameterized import parameterized_class import backend.test.decode_fbs as decode_fbs from backend.server.data_common.matrix_loader import MatrixDataType @@ -44,6 +48,14 @@ class EndPoints(object): len(result_data["schema"]["annotations"]["obs"]["columns"]), 6 if self.ANNOTATIONS_ENABLED else 5 ) + # Check that all schema types are legal + legal_types = ["boolean", "string", "categorical", "float32", "int32"] + self.assertEqual(result_data["schema"]["dataframe"]["type"], "float32") + for column in result_data["schema"]["annotations"]["obs"]["columns"]: + self.assertIn(column["type"], legal_types) + for column in result_data["schema"]["annotations"]["var"]["columns"]: + self.assertIn(column["type"], legal_types) + def test_config(self): endpoint = "config" url = f"{self.URL_BASE}{endpoint}" @@ -52,7 +64,12 @@ class EndPoints(object): self.assertEqual(result.headers["Content-Type"], "application/json") result_data = result.json() self.assertIn("library_versions", result_data["config"]) - self.assertEqual(result_data["config"]["displayNames"]["dataset"], "pbmc3k") + + if hasattr(self, "data_locator"): + title = splitext(basename(self.data_locator))[0] + else: + title = "pbmc3k" + self.assertEqual(result_data["config"]["displayNames"]["dataset"], title) self.assertIsNotNone(result_data["config"]["parameters"]) def test_get_layout_fbs(self): @@ -72,6 +89,8 @@ class EndPoints(object): ) self.assertIsNone(df["row_idx"]) self.assertEqual(len(df["columns"]), df["n_cols"]) + for column in df["columns"]: + self.assertEqual(column.dtype, np.float32) def test_bad_filter(self): endpoint = "data/var" @@ -98,6 +117,9 @@ class EndPoints(object): [obs_index_col_name, "n_genes", "percent_mito", "n_counts", "louvain"] + (["cluster-test"] if self.ANNOTATIONS_ENABLED else []), ) + for column in df["columns"]: + if type(column) is np.ndarray: + self.assertIn(column.dtype, [np.float32, np.int32]) def test_get_annotations_obs_keys_fbs(self): endpoint = "annotations/obs" @@ -137,6 +159,9 @@ class EndPoints(object): self.assertEqual(len(df["columns"]), df["n_cols"]) var_index_col_name = self.schema["schema"]["annotations"]["var"]["index"] self.assertCountEqual(df["col_idx"], [var_index_col_name, "n_cells"]) + for column in df["columns"]: + if type(column) is np.ndarray: + self.assertIn(column.dtype, [np.float32, np.int32]) def test_get_annotations_var_keys_fbs(self): endpoint = "annotations/var" @@ -207,6 +232,9 @@ class EndPoints(object): self.assertIsNone(df["row_idx"]) self.assertEqual(len(df["columns"]), df["n_cols"]) self.assertListEqual(df["col_idx"].tolist(), [0, 1, 4]) + for column in df["columns"]: + if type(column) is np.ndarray: + self.assertIn(column.dtype, [np.float32, np.int32]) def test_data_get_filter_fbs(self): index_col_name = self.schema["schema"]["annotations"]["var"]["index"] @@ -220,6 +248,9 @@ class EndPoints(object): df = decode_fbs.decode_matrix_FBS(result.content) self.assertEqual(df["n_rows"], 2638) self.assertEqual(df["n_cols"], 1) + for column in df["columns"]: + if type(column) is np.ndarray: + self.assertIn(column.dtype, [np.float32, np.int32]) def test_data_get_unknown_filter_fbs(self): index_col_name = self.schema["schema"]["annotations"]["var"]["index"] @@ -246,6 +277,9 @@ class EndPoints(object): df = decode_fbs.decode_matrix_FBS(result.content) self.assertEqual(df["n_rows"], 2638) self.assertEqual(df["n_cols"], 1) + for column in df["columns"]: + if type(column) is np.ndarray: + self.assertIn(column.dtype, [np.float32, np.int32]) def test_colors(self): endpoint = "colors" @@ -347,6 +381,14 @@ class EndPointsAnnotations(EndPoints): self.assertTrue(matching_columns[0]["writable"]) +@parameterized_class( + [ + {"data_locator": f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad"}, + {"data_locator": f"{FIXTURES_ROOT}/pbmc3k_64.h5ad"}, + {"data_locator": f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad"}, + {"data_locator": f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad"}, + ] +) class EndPointsAnndata(unittest.TestCase, EndPoints): """Test Case for endpoints""" @@ -355,10 +397,13 @@ class EndPointsAnndata(unittest.TestCase, EndPoints): @classmethod def setUpClass(cls): + if cls == EndPointsAnndata: + raise unittest.SkipTest("`parameterized_class` bug") + cls._setupClass( cls, [ - f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad", + cls.data_locator, "--disable-annotations", "--disable-gene-sets-save", ], @@ -385,8 +430,8 @@ class EndPointsAnndata(unittest.TestCase, EndPoints): self.assertEqual(result.status_code, HTTPStatus.OK) self.assertEqual(result.headers["Content-Type"], "application/json") result_data = result.json() - self.assertEqual(len(result_data['positive']), 7) - self.assertEqual(len(result_data['negative']), 7) + self.assertEqual(len(result_data["positive"]), 7) + self.assertEqual(len(result_data["negative"]), 7) def test_diff_exp_indices(self): endpoint = "diffexp/obs" @@ -401,8 +446,8 @@ class EndPointsAnndata(unittest.TestCase, EndPoints): self.assertEqual(result.status_code, HTTPStatus.OK) self.assertEqual(result.headers["Content-Type"], "application/json") result_data = result.json() - self.assertEqual(len(result_data['positive']), 10) - self.assertEqual(len(result_data['negative']), 10) + self.assertEqual(len(result_data["positive"]), 10) + self.assertEqual(len(result_data["negative"]), 10) def test_get_summaryvar(self): index_col_name = self.schema["schema"]["annotations"]["var"]["index"] @@ -561,23 +606,23 @@ class EndPointsAnnDataGenesets(unittest.TestCase, EndPoints): "geneset_description": "", "geneset_name": "summary test", }, - {'genes': [], 'geneset_description': '', 'geneset_name': 'geneset_to_delete'}, - {'genes': [], 'geneset_description': '', 'geneset_name': 'geneset_to_edit'}, + {"genes": [], "geneset_description": "", "geneset_name": "geneset_to_delete"}, + {"genes": [], "geneset_description": "", "geneset_name": "geneset_to_edit"}, { - 'genes': [{'gene_description': '', 'gene_symbol': 'RER1'}], - 'geneset_description': '', - 'geneset_name': 'fill_this_geneset' + "genes": [], + "geneset_description": "", + "geneset_name": "fill_this_geneset", }, { - 'genes': [{'gene_description': '', 'gene_symbol': 'SIK1'}], - 'geneset_description': '', - 'geneset_name': 'empty_this_geneset' + "genes": [{"gene_description": "", "gene_symbol": "SIK1"}], + "geneset_description": "", + "geneset_name": "empty_this_geneset", }, { - 'genes': [{'gene_description': '', 'gene_symbol': 'SIK1'}], - 'geneset_description': '', - 'geneset_name': 'brush_this_gene' - } + "genes": [{"gene_description": "", "gene_symbol": "SIK1"}], + "geneset_description": "", + "geneset_name": "brush_this_gene", + }, ], "tid": 0, }, @@ -606,7 +651,7 @@ summary test,,F5,\r summary test,,PIGU,\r geneset_to_delete,,,\r geneset_to_edit,,,\r -fill_this_geneset,,RER1,\r +fill_this_geneset,,,\r empty_this_geneset,,SIK1,\r brush_this_gene,,SIK1,\r """, @@ -680,7 +725,7 @@ brush_this_gene,,SIK1,\r self.assertEqual(result.json(), test3) def test_put_genesets_malformed(self): - """ test malformed submissions that we expect the backend to catch/tolerate """ + """test malformed submissions that we expect the backend to catch/tolerate""" endpoint = "genesets" url = f"{self.URL_BASE}{endpoint}" @@ -690,7 +735,7 @@ brush_this_gene,,SIK1,\r tid = original_data["tid"] def test_case(test, expected_code, original_data): - """ check for expected error AND that no change was made to the original state """ + """check for expected error AND that no change was made to the original state""" result = self.session.put(url, json=test) self.assertEqual(result.status_code, expected_code) result = self.session.get(url, headers={"Accept": "application/json"}) diff --git a/backend/test/test_server/unit/compute/test_est_dist.py b/backend/test/test_server/unit/compute/test_est_dist.py index 85cb88de..2fb7bace 100644 --- a/backend/test/test_server/unit/compute/test_est_dist.py +++ b/backend/test/test_server/unit/compute/test_est_dist.py @@ -2,7 +2,7 @@ import unittest import numpy as np from scipy import sparse from backend.common.compute.estimate_distribution import estimate_approximate_distribution -from backend.common.constants import XApproxDistribution +from backend.common.constants import XApproximateDistribution from backend.server.data_common.matrix_loader import MatrixDataLoader from backend.test.test_server.unit import app_config from backend.test import PROJECT_ROOT @@ -20,22 +20,101 @@ class EstDistTest(unittest.TestCase): def test_adaptestimate_approximate_distribution(self): adaptor = self.load_dataset(f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad") - self.assertEqual(adaptor.get_X_approx_distribution(), XApproxDistribution.NORMAL) + self.assertEqual(adaptor.get_X_approximate_distribution(), XApproximateDistribution.NORMAL) def test_estimate_approximate_distribution(self): raw = np.random.exponential(scale=1000, size=(100, 40)) + # empty + self.assertEqual(estimate_approximate_distribution(np.zeros((0,))), XApproximateDistribution.NORMAL) + # ndarray - self.assertEqual(estimate_approximate_distribution(raw), XApproxDistribution.COUNT) - self.assertEqual(estimate_approximate_distribution(np.log1p(raw)), XApproxDistribution.NORMAL) + self.assertEqual(estimate_approximate_distribution(raw), XApproximateDistribution.COUNT) + self.assertEqual(estimate_approximate_distribution(np.log1p(raw)), XApproximateDistribution.NORMAL) # csr_matrix - self.assertEqual(estimate_approximate_distribution(sparse.csr_matrix(raw)), XApproxDistribution.COUNT) + self.assertEqual(estimate_approximate_distribution(sparse.csr_matrix(raw)), XApproximateDistribution.COUNT) self.assertEqual( - estimate_approximate_distribution(sparse.csr_matrix(np.log1p(raw))), XApproxDistribution.NORMAL + estimate_approximate_distribution(sparse.csr_matrix(np.log1p(raw))), XApproximateDistribution.NORMAL + ) + + # csc_matrix + self.assertEqual(estimate_approximate_distribution(sparse.csc_matrix(raw)), XApproximateDistribution.COUNT) + self.assertEqual( + estimate_approximate_distribution(sparse.csc_matrix(np.log1p(raw))), XApproximateDistribution.NORMAL ) # BIG (ie, trigger MT) big = np.random.exponential(scale=100, size=(1_000_000, 100)) - self.assertEqual(estimate_approximate_distribution(big), XApproxDistribution.COUNT) - self.assertEqual(estimate_approximate_distribution(np.log1p(big)), XApproxDistribution.NORMAL) + self.assertEqual(estimate_approximate_distribution(big), XApproximateDistribution.COUNT) + self.assertEqual(estimate_approximate_distribution(np.log1p(big)), XApproximateDistribution.NORMAL) + + def test_unsupported_throws(self): + # dtypes and matrix formats we do not support + with self.assertRaises(TypeError): + estimate_approximate_distribution(np.array(["a", "b"])) + with self.assertRaises(TypeError): + estimate_approximate_distribution(sparse.coo_matrix(np.array([[0, 1, 2], [3, 0, 2]]))) + + def test_nonfinites(self): + def put(arr, ind, vals): + # like np.put, but creates and returns a modified copy of original array + a = arr.copy() + np.put(a, ind, vals) + return a + + # non-finites + self.assertEqual(estimate_approximate_distribution(np.array([np.nan])), XApproximateDistribution.NORMAL) + self.assertEqual(estimate_approximate_distribution(np.array([np.PINF])), XApproximateDistribution.NORMAL) + self.assertEqual(estimate_approximate_distribution(np.array([np.NINF])), XApproximateDistribution.NORMAL) + self.assertEqual( + estimate_approximate_distribution(np.array([np.PINF, np.NINF, 0])), XApproximateDistribution.NORMAL + ) + self.assertEqual( + estimate_approximate_distribution(np.array([np.nan, np.PINF, np.NINF])), XApproximateDistribution.NORMAL + ) + + raw = np.random.exponential(scale=1000, size=(50, 3)) + logged = np.log1p(raw) + + self.assertEqual( + estimate_approximate_distribution(put(raw, [1], [np.nan])), + XApproximateDistribution.COUNT, + ) + self.assertEqual( + estimate_approximate_distribution(put(raw, [1], [np.PINF])), + XApproximateDistribution.COUNT, + ) + self.assertEqual( + estimate_approximate_distribution(put(raw, [1], [np.NINF])), + XApproximateDistribution.COUNT, + ) + self.assertEqual( + estimate_approximate_distribution(put(raw, [1, 3, 88], [np.nan, np.PINF, np.NINF])), + XApproximateDistribution.COUNT, + ) + self.assertEqual( + estimate_approximate_distribution(put(raw, [0, 1], [np.nan, np.nan])), + XApproximateDistribution.COUNT, + ) + + self.assertEqual( + estimate_approximate_distribution(put(logged, [1], [np.nan])), + XApproximateDistribution.NORMAL, + ) + self.assertEqual( + estimate_approximate_distribution(put(logged, [1], [np.PINF])), + XApproximateDistribution.NORMAL, + ) + self.assertEqual( + estimate_approximate_distribution(put(logged, [1], [np.NINF])), + XApproximateDistribution.NORMAL, + ) + self.assertEqual( + estimate_approximate_distribution(put(logged, [1, 3, 88], [np.nan, np.PINF, np.NINF])), + XApproximateDistribution.NORMAL, + ) + self.assertEqual( + estimate_approximate_distribution(put(logged, [0, 1], [np.nan, np.nan])), + XApproximateDistribution.NORMAL, + ) diff --git a/backend/test/test_server/unit/data_anndata/test_anndata_adaptor.py b/backend/test/test_server/unit/data_anndata/test_anndata_adaptor.py index 2d046bde..19ba07aa 100644 --- a/backend/test/test_server/unit/data_anndata/test_anndata_adaptor.py +++ b/backend/test/test_server/unit/data_anndata/test_anndata_adaptor.py @@ -22,7 +22,7 @@ Test the anndata adaptor using the pbmc3k data set. @parameterized_class( - ("data_locator", "backed", "X_approx_distribution"), + ("data_locator", "backed", "X_approximate_distribution"), [ (f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad", False, "auto"), (f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", False, "auto"), @@ -36,12 +36,15 @@ Test the anndata adaptor using the pbmc3k data set. (f"{PROJECT_ROOT}/example-dataset/pbmc3k.h5ad", True, "normal"), (f"{FIXTURES_ROOT}/pbmc3k-CSC-gz.h5ad", True, "normal"), (f"{FIXTURES_ROOT}/pbmc3k-CSR-gz.h5ad", True, "normal"), + (f"{FIXTURES_ROOT}/pbmc3k_64.h5ad", False, "auto"), # 64 bit conversion tests ], ) class AdaptorTest(unittest.TestCase): def setUp(self): config = app_config( - self.data_locator, self.backed, extra_dataset_config=dict(X_approx_distribution=self.X_approx_distribution) + self.data_locator, + self.backed, + extra_dataset_config=dict(X_approximate_distribution=self.X_approximate_distribution), ) self.data = AnndataAdaptor(DataLocator(self.data_locator), config) diff --git a/client/__tests__/e2e/__snapshots__/e2e.test.js.snap b/client/__tests__/e2e/__snapshots__/e2e.test.ts.snap similarity index 79% rename from client/__tests__/e2e/__snapshots__/e2e.test.js.snap rename to client/__tests__/e2e/__snapshots__/e2e.test.ts.snap index bcbca82f..211c5106 100644 --- a/client/__tests__/e2e/__snapshots__/e2e.test.js.snap +++ b/client/__tests__/e2e/__snapshots__/e2e.test.ts.snap @@ -2,4 +2,4 @@ exports[`did launch page launched 1`] = `"pbmc3kc3k"`; -exports[`metadata loads categories and values from dataset appear 1`] = `"
louvainvain
tint
"`; +exports[`metadata loads categories and values from dataset appear 1`] = `"
louvainvain
tint
"`; diff --git a/client/__tests__/e2e/__snapshots__/e2eAnnotations.test.js.snap b/client/__tests__/e2e/__snapshots__/e2eAnnotations.test.ts.snap similarity index 99% rename from client/__tests__/e2e/__snapshots__/e2eAnnotations.test.js.snap rename to client/__tests__/e2e/__snapshots__/e2eAnnotations.test.ts.snap index ca759215..de1517ef 100644 --- a/client/__tests__/e2e/__snapshots__/e2eAnnotations.test.js.snap +++ b/client/__tests__/e2e/__snapshots__/e2eAnnotations.test.ts.snap @@ -2,15 +2,15 @@ exports[`annotations stacked bar graph renders 1`] = ` Array [ - "
TEST-LABELLABEL
0
", - "
unassignedigned
2133
", + "
TEST-LABELLABEL
0
", + "
unassignedigned
2133
", ] `; exports[`annotations stacked bar graph renders 2`] = ` Array [ - "
TEST-LABELLABEL
0
", - "
unassignedigned
2638
", + "
TEST-LABELLABEL
0
", + "
unassignedigned
2638
", ] `; diff --git a/client/__tests__/e2e/cellxgeneActions.js b/client/__tests__/e2e/cellxgeneActions.js deleted file mode 100644 index 0f5bf77c..00000000 --- a/client/__tests__/e2e/cellxgeneActions.js +++ /dev/null @@ -1,516 +0,0 @@ -/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions */ -import { strict as assert } from "assert"; -import { - clearInputAndTypeInto, - clickOn, - getAllByClass, - getOneElementInnerText, - typeInto, - waitByID, - waitByClass, - waitForAllByIds, - clickOnUntil, - getTestClass, - getTestId, - isElementPresent, - goToPage, -} from "./puppeteerUtils"; - -import { appUrlBase, TEST_EMAIL, TEST_PASSWORD } from "./config"; - -export async function drag(testId, start, end, lasso = false) { - const layout = await waitByID(testId); - const elBox = await layout.boxModel(); - const x1 = elBox.content[0].x + start.x; - const x2 = elBox.content[0].x + end.x; - const y1 = elBox.content[0].y + start.y; - const y2 = elBox.content[0].y + end.y; - await page.mouse.move(x1, y1); - await page.mouse.down(); - if (lasso) { - await page.mouse.move(x2, y1); - await page.mouse.move(x2, y2); - await page.mouse.move(x1, y2); - await page.mouse.move(x1, y1); - } else { - await page.mouse.move(x2, y2); - } - await page.mouse.up(); -} - -export async function clickOnCoordinate(testId, coord) { - const layout = await expect(page).toMatchElement(getTestId(testId)); - const elBox = await layout.boxModel(); - - if (!elBox) { - throw Error("Layout's boxModel is not available!"); - } - - const x = elBox.content[0].x + coord.x; - const y = elBox.content[0].y + coord.y; - await page.mouse.click(x, y); -} - -export async function getAllHistograms(testclass, testIds) { - const histTestIds = testIds.map((tid) => `histogram-${tid}`); - - // these load asynchronously, so we need to wait for each histogram individually, - // and they may be quite slow in some cases. - await waitForAllByIds(histTestIds, { timeout: 4 * 60 * 1000 }); - - const allHistograms = await getAllByClass(testclass); - - const testIDs = await Promise.all( - allHistograms.map((hist) => { - return page.evaluate((elem) => { - return elem.dataset.testid; - }, hist); - }) - ); - - return testIDs.map((id) => id.replace(/^histogram-/, "")); -} - -export async function getAllCategoriesAndCounts(category) { - // these load asynchronously, so we have to wait for the specific category. - await waitByID(`category-${category}`); - - return page.$$eval( - `[data-testid="category-${category}"] [data-testclass='categorical-row']`, - (rows) => - Object.fromEntries( - rows.map((row) => { - const cat = row - .querySelector("[data-testclass='categorical-value']") - .getAttribute("aria-label"); - - const count = row.querySelector( - "[data-testclass='categorical-value-count']" - ).innerText; - - return [cat, count]; - }) - ) - ); -} - -export async function getCellSetCount(num) { - await clickOn(`cellset-button-${num}`); - return getOneElementInnerText(`[data-testid='cellset-count-${num}']`); -} - -export async function resetCategory(category) { - const checkboxId = `${category}:category-select`; - await waitByID(checkboxId); - const checkedPseudoclass = await page.$eval( - `[data-testid='${checkboxId}']`, - (el) => el.matches(":checked") - ); - if (!checkedPseudoclass) await clickOn(checkboxId); - - const categoryRow = await waitByID(`${category}:category-expand`); - - const isExpanded = await categoryRow.$( - "[data-testclass='category-expand-is-expanded']" - ); - - if (isExpanded) await clickOn(`${category}:category-expand`); -} - -export async function calcCoordinate(testId, xAsPercent, yAsPercent) { - const el = await waitByID(testId); - const size = await el.boxModel(); - return { - x: Math.floor(size.width * xAsPercent), - y: Math.floor(size.height * yAsPercent), - }; -} - -export async function calcDragCoordinates(testId, coordinateAsPercent) { - return { - start: await calcCoordinate( - testId, - coordinateAsPercent.x1, - coordinateAsPercent.y1 - ), - end: await calcCoordinate( - testId, - coordinateAsPercent.x2, - coordinateAsPercent.y2 - ), - }; -} - -export async function selectCategory(category, values, reset = true) { - if (reset) await resetCategory(category); - - await clickOn(`${category}:category-expand`); - await clickOn(`${category}:category-select`); - - for (const value of values) { - await clickOn(`categorical-value-select-${category}-${value}`); - } -} - -export async function expandCategory(category) { - const expand = await waitByID(`${category}:category-expand`); - const notExpanded = await expand.$( - "[data-testclass='category-expand-is-not-expanded']" - ); - if (notExpanded) await clickOn(`${category}:category-expand`); -} - -export async function clip(min = 0, max = 100) { - await clickOn("visualization-settings"); - await clearInputAndTypeInto("clip-min-input", min); - await clearInputAndTypeInto("clip-max-input", max); - await clickOn("clip-commit"); -} - -export async function createCategory(categoryName) { - await clickOnUntil("open-annotation-dialog", async () => { - await expect(page).toMatchElement(getTestId("new-category-name")); - }); - - await typeInto("new-category-name", categoryName); - await clickOn("submit-category"); -} - -/* - - GENESET - -*/ - -export async function colorByGeneset(genesetName) { - await clickOn(`${genesetName}:colorby-entire-geneset`); -} - -export async function colorByGene(gene) { - await clickOn(`colorby-${gene}`); -} - -export async function assertColorLegendLabel(label) { - const handle = await waitByID("continuous_legend_color_by_label"); - - const result = await handle.evaluate((node) => { - return node.getAttribute("aria-label"); - }); - - return expect(result).toBe(label); -} - -export async function expandGeneset(genesetName) { - const expand = await waitByID(`${genesetName}:geneset-expand`); - const notExpanded = await expand.$( - "[data-testclass='geneset-expand-is-not-expanded']" - ); - if (notExpanded) await clickOn(`${genesetName}:geneset-expand`); -} - -export async function createGeneset(genesetName) { - await clickOnUntil("open-create-geneset-dialog", async () => { - await expect(page).toMatchElement(getTestId("create-geneset-input")); - }); - - await typeInto("create-geneset-input", genesetName); - await clickOn("submit-geneset"); - await waitByClass("autosave-complete"); -} - -export async function editGenesetName(genesetName, editText) { - const editButton = `${genesetName}:edit-genesetName-mode`; - const submitButton = `${genesetName}:submit-geneset`; - await clickOnUntil(`${genesetName}:see-actions`, async () => { - await expect(page).toMatchElement(getTestId(editButton)); - }); - await clickOn(editButton); - await typeInto("rename-geneset-modal", editText); - await clickOn(submitButton); -} - -export async function deleteGeneset(genesetName) { - const targetId = `${genesetName}:delete-geneset`; - - await clickOnUntil(`${genesetName}:see-actions`, async () => { - await expect(page).toMatchElement(getTestId(targetId)); - }); - - await clickOn(targetId); - - await assertGenesetDoesNotExist(genesetName); - await waitByClass("autosave-complete"); -} - -export async function assertGenesetDoesNotExist(genesetName) { - const result = await isElementPresent( - getTestId(`${genesetName}:geneset-name`) - ); - await expect(result).toBe(false); -} - -export async function assertGenesetExists(genesetName) { - const handle = await waitByID(`${genesetName}:geneset-name`); - - const result = await handle.evaluate((node) => { - return node.getAttribute("aria-label"); - }); - - return expect(result).toBe(genesetName); -} - -/* - - GENE - -*/ - -export async function addGeneToSet(genesetName, geneToAddToSet) { - const submitButton = `${genesetName}:submit-gene`; - - await clickOn(`${genesetName}:add-new-gene-to-geneset`); - await typeInto("add-genes", geneToAddToSet); - await clickOn(submitButton); -} - -export async function removeGene(geneSymbol) { - const targetId = `delete-from-geneset:${geneSymbol}`; - - await clickOn(targetId); - - await waitByClass("autosave-complete"); -} - -export async function assertGeneExistsInGeneset(geneSymbol) { - const handle = await waitByID(`${geneSymbol}:gene-label`); - - const result = await handle.evaluate((node) => { - return node.getAttribute("aria-label"); - }); - - return expect(result).toBe(geneSymbol); -} - -export async function assertGeneDoesNotExist(geneSymbol) { - const result = await isElementPresent(getTestId(`${geneSymbol}:gene-label`)); - - await expect(result).toBe(false); -} - -export async function expandGene(geneSymbol) { - await clickOn(`maximize-${geneSymbol}`); -} - -/* - - CATEGORY - -*/ - -export async function duplicateCategory(categoryName) { - await clickOn("open-annotation-dialog"); - - await typeInto("new-category-name", categoryName); - - const dropdownOptionClass = "duplicate-category-dropdown-option"; - - await clickOnUntil("duplicate-category-dropdown", async () => { - await expect(page).toMatchElement(getTestClass(dropdownOptionClass)); - }); - - const option = await expect(page).toMatchElement( - getTestClass(dropdownOptionClass) - ); - - await option.click(); - - await clickOnUntil("submit-category", async () => { - await expect(page).toMatchElement( - getTestId(`${categoryName}:category-expand`) - ); - }); - - await waitByClass("autosave-complete"); -} - -export async function renameCategory(oldCategoryName, newCategoryName) { - await clickOn(`${oldCategoryName}:see-actions`); - await clickOn(`${oldCategoryName}:edit-category-mode`); - await clearInputAndTypeInto( - `${oldCategoryName}:edit-category-name-text`, - newCategoryName - ); - await clickOn(`${oldCategoryName}:submit-category-edit`); -} - -export async function deleteCategory(categoryName) { - const targetId = `${categoryName}:delete-category`; - - await clickOnUntil(`${categoryName}:see-actions`, async () => { - await expect(page).toMatchElement(getTestId(targetId)); - }); - - await clickOn(targetId); - - await assertCategoryDoesNotExist(); -} - -export async function createLabel(categoryName, labelName) { - /** - * (thuang): This explicit wait is needed, since currently showing - * the modal again quickly after the previous action dismissing the - * modal will persist the input value from the previous action. - * - * To reproduce: - * 1. Click on the plus sign to show the modal to add a new label to the category - * 2. Type `123` in the input box - * 3. Hover over your mouse over the plus sign and double click to quickly dismiss and - * invoke the modal again - * 4. You will see `123` is persisted in the input box - * 5. Expected behavior is to get an empty input box - */ - await page.waitForTimeout(500); - - await clickOn(`${categoryName}:see-actions`); - - await clickOn(`${categoryName}:add-new-label-to-category`); - - await typeInto(`${categoryName}:new-label-name`, labelName); - - await clickOn(`${categoryName}:submit-label`); -} - -export async function deleteLabel(categoryName, labelName) { - await expandCategory(categoryName); - await clickOn(`${categoryName}:${labelName}:see-actions`); - await clickOn(`${categoryName}:${labelName}:delete-label`); -} - -export async function renameLabel(categoryName, oldLabelName, newLabelName) { - await expandCategory(categoryName); - await clickOn(`${categoryName}:${oldLabelName}:see-actions`); - await clickOn(`${categoryName}:${oldLabelName}:edit-label`); - await clearInputAndTypeInto( - `${categoryName}:${oldLabelName}:edit-label-name`, - newLabelName - ); - await clickOn(`${categoryName}:${oldLabelName}:submit-label-edit`); -} - -export async function addGeneToSearch(geneName) { - await typeInto("gene-search", geneName); - await page.keyboard.press("Enter"); - await page.waitForSelector(`[data-testid='histogram-${geneName}']`); -} - -export async function subset(coordinatesAsPercent) { - // In order to deselect the selection after the subset, make sure we have some clear part - // of the scatterplot we can click on - assert(coordinatesAsPercent.x2 < 0.99 || coordinatesAsPercent.y2 < 0.99); - const lassoSelection = await calcDragCoordinates( - "layout-graph", - coordinatesAsPercent - ); - await drag("layout-graph", lassoSelection.start, lassoSelection.end, true); - await clickOn("subset-button"); - const clearCoordinate = await calcCoordinate("layout-graph", 0.5, 0.99); - await clickOnCoordinate("layout-graph", clearCoordinate); -} - -export async function setSellSet(cellSet, cellSetNum) { - const selections = cellSet.filter((sel) => sel.kind === "categorical"); - - for (const selection of selections) { - await selectCategory(selection.metadata, selection.values, true); - } - - await getCellSetCount(cellSetNum); -} - -export async function runDiffExp(cellSet1, cellSet2) { - await setSellSet(cellSet1, 1); - await setSellSet(cellSet2, 2); - await clickOn("diffexp-button"); -} - -export async function bulkAddGenes(geneNames) { - await clickOn("section-bulk-add"); - await typeInto("input-bulk-add", geneNames.join(",")); - await page.keyboard.press("Enter"); -} - -export async function assertCategoryDoesNotExist(categoryName) { - const result = await isElementPresent( - getTestId(`${categoryName}:category-label`) - ); - - await expect(result).toBe(false); -} - -export async function login() { - await goToPage(appUrlBase); - - await clickOn("log-in"); - - // (thuang): Auth0 form is unstable and unsafe for input until verified - await waitUntilFormFieldStable('[name="email"]'); - - await expect(page).toFillForm("form", { - email: TEST_EMAIL, - password: TEST_PASSWORD, - }); - - await Promise.all([ - page.waitForNavigation({ waitUntil: "networkidle0" }), - expect(page).toClick('[name="submit"]'), - ]); - - expect(page.url()).toContain(appUrlBase); -} - -export async function logout() { - await clickOnUntil("user-info", async () => { - await waitByID("log-out"); - await Promise.all([ - page.waitForNavigation({ waitUntil: "networkidle0" }), - clickOn("log-out"), - ]); - }); - - await waitByID("log-in"); -} - -async function waitUntilFormFieldStable(selector) { - const MAX_RETRY = 10; - const WAIT_FOR_MS = 200; - - const EXPECTED_VALUE = "aaa"; - - let retry = 0; - - while (retry < MAX_RETRY) { - try { - await expect(page).toFill(selector, EXPECTED_VALUE); - - const fieldHandle = await expect(page).toMatchElement(selector); - - const fieldValue = await page.evaluate( - (input) => input.value, - fieldHandle - ); - - expect(fieldValue).toBe(EXPECTED_VALUE); - - break; - } catch (error) { - retry += 1; - - await page.waitForTimeout(WAIT_FOR_MS); - } - } - - if (retry === MAX_RETRY) { - throw Error("clickOnUntil() assertion failed!"); - } -} -/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */ diff --git a/client/__tests__/e2e/cellxgeneActions.ts b/client/__tests__/e2e/cellxgeneActions.ts new file mode 100644 index 00000000..d54e884f --- /dev/null +++ b/client/__tests__/e2e/cellxgeneActions.ts @@ -0,0 +1,596 @@ +/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions */ +import { strict as assert } from "assert"; +import { + clearInputAndTypeInto, + clickOn, + getAllByClass, + getOneElementInnerText, + typeInto, + waitByID, + waitByClass, + waitForAllByIds, + clickOnUntil, + getTestClass, + getTestId, + isElementPresent, + goToPage, +} from "./puppeteerUtils"; + +import { appUrlBase, TEST_EMAIL, TEST_PASSWORD } from "./config"; + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function drag(testId: any, start: any, end: any, lasso = false) { + const layout = await waitByID(testId); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const elBox = await layout.boxModel(); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const x1 = elBox.content[0].x + start.x; + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const x2 = elBox.content[0].x + end.x; + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const y1 = elBox.content[0].y + start.y; + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const y2 = elBox.content[0].y + end.y; + await page.mouse.move(x1, y1); + await page.mouse.down(); + if (lasso) { + await page.mouse.move(x2, y1); + await page.mouse.move(x2, y2); + await page.mouse.move(x1, y2); + await page.mouse.move(x1, y1); + } else { + await page.mouse.move(x2, y2); + } + await page.mouse.up(); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function clickOnCoordinate(testId: any, coord: any) { + const layout = await expect(page).toMatchElement(getTestId(testId)); + const elBox = await layout.boxModel(); + + if (!elBox) { + throw Error("Layout's boxModel is not available!"); + } + + const x = elBox.content[0].x + coord.x; + const y = elBox.content[0].y + coord.y; + await page.mouse.click(x, y); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function getAllHistograms(testclass: any, testIds: any) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const histTestIds = testIds.map((tid: any) => `histogram-${tid}`); + + // these load asynchronously, so we need to wait for each histogram individually, + // and they may be quite slow in some cases. + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 2. + await waitForAllByIds(histTestIds, { timeout: 4 * 60 * 1000 }); + + const allHistograms = await getAllByClass(testclass); + + const testIDs = await Promise.all( + allHistograms.map((hist) => + page.evaluate((elem) => elem.dataset.testid, hist) + ) + ); + + return testIDs.map((id) => id.replace(/^histogram-/, "")); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function getAllCategoriesAndCounts(category: any) { + // these load asynchronously, so we have to wait for the specific category. + await waitByID(`category-${category}`); + + return page.$$eval( + `[data-testid="category-${category}"] [data-testclass='categorical-row']`, + (rows) => + Object.fromEntries( + rows.map((row) => { + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const cat = row + .querySelector("[data-testclass='categorical-value']") + .getAttribute("aria-label"); + + const count = (row.querySelector( + "[data-testclass='categorical-value-count']" + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + ) as any).innerText; + + return [cat, count]; + }) + ) + ); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function getCellSetCount(num: any) { + await clickOn(`cellset-button-${num}`); + return getOneElementInnerText(`[data-testid='cellset-count-${num}']`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function resetCategory(category: any) { + const checkboxId = `${category}:category-select`; + await waitByID(checkboxId); + const checkedPseudoclass = await page.$eval( + `[data-testid='${checkboxId}']`, + (el) => el.matches(":checked") + ); + if (!checkedPseudoclass) await clickOn(checkboxId); + + const categoryRow = await waitByID(`${category}:category-expand`); + + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const isExpanded = await categoryRow.$( + "[data-testclass='category-expand-is-expanded']" + ); + + if (isExpanded) await clickOn(`${category}:category-expand`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export async function calcCoordinate( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + testId: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + xAsPercent: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + yAsPercent: any +) { + const el = await waitByID(testId); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const size = await el.boxModel(); + return { + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + x: Math.floor(size.width * xAsPercent), + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + y: Math.floor(size.height * yAsPercent), + }; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export async function calcDragCoordinates( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + testId: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + coordinateAsPercent: any +) { + return { + start: await calcCoordinate( + testId, + coordinateAsPercent.x1, + coordinateAsPercent.y1 + ), + end: await calcCoordinate( + testId, + coordinateAsPercent.x2, + coordinateAsPercent.y2 + ), + }; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function selectCategory(category: any, values: any, reset = true) { + if (reset) await resetCategory(category); + + await clickOn(`${category}:category-expand`); + await clickOn(`${category}:category-select`); + + for (const value of values) { + await clickOn(`categorical-value-select-${category}-${value}`); + } +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function expandCategory(category: any) { + const expand = await waitByID(`${category}:category-expand`); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const notExpanded = await expand.$( + "[data-testclass='category-expand-is-not-expanded']" + ); + if (notExpanded) await clickOn(`${category}:category-expand`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export async function clip(min = 0, max = 100) { + await clickOn("visualization-settings"); + await clearInputAndTypeInto("clip-min-input", min); + await clearInputAndTypeInto("clip-max-input", max); + await clickOn("clip-commit"); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function createCategory(categoryName: any) { + await clickOnUntil("open-annotation-dialog", async () => { + await expect(page).toMatchElement(getTestId("new-category-name")); + }); + + await typeInto("new-category-name", categoryName); + await clickOn("submit-category"); +} + +/** + * GENESET + */ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function colorByGeneset(genesetName: any) { + await clickOn(`${genesetName}:colorby-entire-geneset`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function colorByGene(gene: any) { + await clickOn(`colorby-${gene}`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function assertColorLegendLabel(label: any) { + const handle = await waitByID("continuous_legend_color_by_label"); + + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const result = await handle.evaluate((node) => + node.getAttribute("aria-label") + ); + + return expect(result).toBe(label); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function expandGeneset(genesetName: any) { + const expand = await waitByID(`${genesetName}:geneset-expand`); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const notExpanded = await expand.$( + "[data-testclass='geneset-expand-is-not-expanded']" + ); + if (notExpanded) await clickOn(`${genesetName}:geneset-expand`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function createGeneset(genesetName: any) { + await clickOnUntil("open-create-geneset-dialog", async () => { + await expect(page).toMatchElement(getTestId("create-geneset-input")); + }); + + await typeInto("create-geneset-input", genesetName); + await clickOn("submit-geneset"); + await waitByClass("autosave-complete"); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function editGenesetName(genesetName: any, editText: any) { + const editButton = `${genesetName}:edit-genesetName-mode`; + const submitButton = `${genesetName}:submit-geneset`; + await clickOnUntil(`${genesetName}:see-actions`, async () => { + await expect(page).toMatchElement(getTestId(editButton)); + }); + await clickOn(editButton); + await typeInto("rename-geneset-modal", editText); + await clickOn(submitButton); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function deleteGeneset(genesetName: any) { + const targetId = `${genesetName}:delete-geneset`; + + await clickOnUntil(`${genesetName}:see-actions`, async () => { + await expect(page).toMatchElement(getTestId(targetId)); + }); + + await clickOn(targetId); + + await assertGenesetDoesNotExist(genesetName); + await waitByClass("autosave-complete"); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function assertGenesetDoesNotExist(genesetName: any) { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. + const result = await isElementPresent( + getTestId(`${genesetName}:geneset-name`) + ); + await expect(result).toBe(false); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function assertGenesetExists(genesetName: any) { + const handle = await waitByID(`${genesetName}:geneset-name`); + + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const result = await handle.evaluate((node) => + node.getAttribute("aria-label") + ); + + return expect(result).toBe(genesetName); +} + +/** + * GENE + */ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function addGeneToSet(genesetName: any, geneToAddToSet: any) { + const submitButton = `${genesetName}:submit-gene`; + + await clickOn(`${genesetName}:add-new-gene-to-geneset`); + await typeInto("add-genes", geneToAddToSet); + await clickOn(submitButton); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function removeGene(geneSymbol: any) { + const targetId = `delete-from-geneset:${geneSymbol}`; + + await clickOn(targetId); + + await waitByClass("autosave-complete"); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function assertGeneExistsInGeneset(geneSymbol: any) { + const handle = await waitByID(`${geneSymbol}:gene-label`); + + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + const result = await handle.evaluate((node) => + node.getAttribute("aria-label") + ); + + return expect(result).toBe(geneSymbol); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function assertGeneDoesNotExist(geneSymbol: any) { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. + const result = await isElementPresent(getTestId(`${geneSymbol}:gene-label`)); + + await expect(result).toBe(false); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function expandGene(geneSymbol: any) { + await clickOn(`maximize-${geneSymbol}`); +} + +/** + * CATEGORY + */ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function duplicateCategory(categoryName: any) { + await clickOn("open-annotation-dialog"); + + await typeInto("new-category-name", categoryName); + + const dropdownOptionClass = "duplicate-category-dropdown-option"; + + await clickOnUntil("duplicate-category-dropdown", async () => { + await expect(page).toMatchElement(getTestClass(dropdownOptionClass)); + }); + + const option = await expect(page).toMatchElement( + getTestClass(dropdownOptionClass) + ); + + await option.click(); + + await clickOnUntil("submit-category", async () => { + await expect(page).toMatchElement( + getTestId(`${categoryName}:category-expand`) + ); + }); + + await waitByClass("autosave-complete"); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export async function renameCategory( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + oldCategoryName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + newCategoryName: any +) { + await clickOn(`${oldCategoryName}:see-actions`); + await clickOn(`${oldCategoryName}:edit-category-mode`); + await clearInputAndTypeInto( + `${oldCategoryName}:edit-category-name-text`, + newCategoryName + ); + await clickOn(`${oldCategoryName}:submit-category-edit`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function deleteCategory(categoryName: any) { + const targetId = `${categoryName}:delete-category`; + + await clickOnUntil(`${categoryName}:see-actions`, async () => { + await expect(page).toMatchElement(getTestId(targetId)); + }); + + await clickOn(targetId); + + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. + await assertCategoryDoesNotExist(); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function createLabel(categoryName: any, labelName: any) { + /** + * (thuang): This explicit wait is needed, since currently showing + * the modal again quickly after the previous action dismissing the + * modal will persist the input value from the previous action. + * + * To reproduce: + * 1. Click on the plus sign to show the modal to add a new label to the category + * 2. Type `123` in the input box + * 3. Hover over your mouse over the plus sign and double click to quickly dismiss and + * invoke the modal again + * 4. You will see `123` is persisted in the input box + * 5. Expected behavior is to get an empty input box + */ + await page.waitForTimeout(500); + + await clickOn(`${categoryName}:see-actions`); + + await clickOn(`${categoryName}:add-new-label-to-category`); + + await typeInto(`${categoryName}:new-label-name`, labelName); + + await clickOn(`${categoryName}:submit-label`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function deleteLabel(categoryName: any, labelName: any) { + await expandCategory(categoryName); + await clickOn(`${categoryName}:${labelName}:see-actions`); + await clickOn(`${categoryName}:${labelName}:delete-label`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export async function renameLabel( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoryName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + oldLabelName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + newLabelName: any +) { + await expandCategory(categoryName); + await clickOn(`${categoryName}:${oldLabelName}:see-actions`); + await clickOn(`${categoryName}:${oldLabelName}:edit-label`); + await clearInputAndTypeInto( + `${categoryName}:${oldLabelName}:edit-label-name`, + newLabelName + ); + await clickOn(`${categoryName}:${oldLabelName}:submit-label-edit`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function addGeneToSearch(geneName: any) { + await typeInto("gene-search", geneName); + await page.keyboard.press("Enter"); + await page.waitForSelector(`[data-testid='histogram-${geneName}']`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function subset(coordinatesAsPercent: any) { + // In order to deselect the selection after the subset, make sure we have some clear part + // of the scatterplot we can click on + assert(coordinatesAsPercent.x2 < 0.99 || coordinatesAsPercent.y2 < 0.99); + const lassoSelection = await calcDragCoordinates( + "layout-graph", + coordinatesAsPercent + ); + await drag("layout-graph", lassoSelection.start, lassoSelection.end, true); + await clickOn("subset-button"); + const clearCoordinate = await calcCoordinate("layout-graph", 0.5, 0.99); + await clickOnCoordinate("layout-graph", clearCoordinate); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function setSellSet(cellSet: any, cellSetNum: any) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const selections = cellSet.filter((sel: any) => sel.kind === "categorical"); + + for (const selection of selections) { + await selectCategory(selection.metadata, selection.values, true); + } + + await getCellSetCount(cellSetNum); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function runDiffExp(cellSet1: any, cellSet2: any) { + await setSellSet(cellSet1, 1); + await setSellSet(cellSet2, 2); + await clickOn("diffexp-button"); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function bulkAddGenes(geneNames: any) { + await clickOn("section-bulk-add"); + await typeInto("input-bulk-add", geneNames.join(",")); + await page.keyboard.press("Enter"); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function assertCategoryDoesNotExist(categoryName: any) { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. + const result = await isElementPresent( + getTestId(`${categoryName}:category-label`) + ); + + await expect(result).toBe(false); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export async function login() { + await goToPage(appUrlBase); + + await clickOn("log-in"); + + // (thuang): Auth0 form is unstable and unsafe for input until verified + await waitUntilFormFieldStable('[name="email"]'); + + await expect(page).toFillForm("form", { + email: TEST_EMAIL, + password: TEST_PASSWORD, + }); + + await Promise.all([ + page.waitForNavigation({ waitUntil: "networkidle0" }), + expect(page).toClick('[name="submit"]'), + ]); + + expect(page.url()).toContain(appUrlBase); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export async function logout() { + await clickOnUntil("user-info", async () => { + await waitByID("log-out"); + await Promise.all([ + page.waitForNavigation({ waitUntil: "networkidle0" }), + clickOn("log-out"), + ]); + }); + + await waitByID("log-in"); +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +async function waitUntilFormFieldStable(selector: any) { + const MAX_RETRY = 10; + const WAIT_FOR_MS = 200; + + const EXPECTED_VALUE = "aaa"; + + let retry = 0; + + while (retry < MAX_RETRY) { + try { + await expect(page).toFill(selector, EXPECTED_VALUE); + + const fieldHandle = await expect(page).toMatchElement(selector); + + const fieldValue = await page.evaluate( + (input) => input.value, + fieldHandle + ); + + expect(fieldValue).toBe(EXPECTED_VALUE); + + break; + } catch (error) { + retry += 1; + + await page.waitForTimeout(WAIT_FOR_MS); + } + } + + if (retry === MAX_RETRY) { + throw Error("clickOnUntil() assertion failed!"); + } +} +/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */ diff --git a/client/__tests__/e2e/config.js b/client/__tests__/e2e/config.ts similarity index 100% rename from client/__tests__/e2e/config.js rename to client/__tests__/e2e/config.ts diff --git a/client/__tests__/e2e/data.js b/client/__tests__/e2e/data.ts similarity index 100% rename from client/__tests__/e2e/data.js rename to client/__tests__/e2e/data.ts diff --git a/client/__tests__/e2e/diffexpGeneSets.js b/client/__tests__/e2e/diffexpGeneSets.ts similarity index 100% rename from client/__tests__/e2e/diffexpGeneSets.js rename to client/__tests__/e2e/diffexpGeneSets.ts diff --git a/client/__tests__/e2e/e2e.test.js b/client/__tests__/e2e/e2e.test.ts similarity index 90% rename from client/__tests__/e2e/e2e.test.js rename to client/__tests__/e2e/e2e.test.ts index bd3e852a..f8f34ca7 100644 --- a/client/__tests__/e2e/e2e.test.js +++ b/client/__tests__/e2e/e2e.test.ts @@ -58,10 +58,12 @@ describe("metadata loads", () => { const categories = await getAllCategoriesAndCounts(label); expect(Object.keys(categories)).toMatchObject( + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message Object.keys(data.categorical[label]) ); expect(Object.values(categories)).toMatchObject( + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message Object.values(data.categorical[label]) ); } @@ -159,10 +161,12 @@ describe("subset", () => { const categories = await getAllCategoriesAndCounts(label); expect(Object.keys(categories)).toMatchObject( + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message Object.keys(data.subset.categorical[label]) ); expect(Object.values(categories)).toMatchObject( + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message Object.values(data.subset.categorical[label]) ); } @@ -195,6 +199,7 @@ describe("clipping", () => { test("clip continuous", async () => { await goToPage(appUrlBase); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string' is not assignable to par... Remove this comment to see the full error message await clip(data.clip.min, data.clip.max); const histBrushableAreaId = `histogram-${data.clip.metadata}-plot-brushable-area`; const coords = await calcDragCoordinates( @@ -254,6 +259,7 @@ describe("centroid labels", () => { const generatedLabels = await getAllByClass("centroid-label"); // Number of labels generated should be equal to size of the object expect(generatedLabels).toHaveLength( + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message Object.keys(data.categorical[label]).length ); } @@ -275,6 +281,7 @@ describe("graph overlay", () => { data.pan["coordinates-as-percent"] ); + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message const categoryValue = Object.keys(data.categorical[category])[0]; const initialCoordinates = await getElementCoordinates( `${categoryValue}-centroid-label` diff --git a/client/__tests__/e2e/e2eAnnotations.test.js b/client/__tests__/e2e/e2eAnnotations.test.ts similarity index 80% rename from client/__tests__/e2e/e2eAnnotations.test.js rename to client/__tests__/e2e/e2eAnnotations.test.ts index 1430600c..470a36ba 100644 --- a/client/__tests__/e2e/e2eAnnotations.test.js +++ b/client/__tests__/e2e/e2eAnnotations.test.ts @@ -12,6 +12,7 @@ import { getTestId, getTestClass, getAllByClass, + clickOnUntil, getOneElementInnerHTML, } from "./puppeteerUtils"; @@ -76,7 +77,13 @@ const brushThisGeneGeneset = "brush_this_gene"; const geneBrushedCellCount = "109"; const subsetGeneBrushedCellCount = "96"; -async function setup(config) { +const genesetDescriptionID = + "geneset-description-tooltip-fourth_gene_set: fourth description"; +const genesetDescriptionString = "fourth_gene_set: fourth description"; +const genesetToCheckForDescription = "fourth_gene_set"; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +async function setup(config: any) { await goToPage(appUrlBase); if (config.categoricalAnno) { @@ -150,7 +157,8 @@ describe.each([ await expect(page).toClick(getTestClass("pop-1-geneset-expand")); await page.waitForFunction( - (selector) => !document.querySelector(selector), + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (selector: any) => !document.querySelector(selector), {}, getTestClass("gene-loading-spinner") ); @@ -165,7 +173,8 @@ describe.each([ await expect(page).toClick(getTestClass("pop-2-geneset-expand")); await page.waitForFunction( - (selector) => !document.querySelector(selector), + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (selector: any) => !document.querySelector(selector), {}, getTestClass("gene-loading-spinner") ); @@ -174,7 +183,7 @@ describe.each([ expect(genesHTML).toMatchSnapshot(); }); - test("create a new geneset", async () => { + test("create a new geneset and undo/redo", async () => { if (config.withSubset) return; await setup(config); @@ -184,19 +193,45 @@ describe.each([ await createGeneset(genesetName); /* note: as of June 2021, the aria label is in the truncate component which clones the element */ await assertGenesetExists(genesetName); + await clickOn("undo"); + await assertGenesetDoesNotExist(genesetName); + await clickOn("redo"); + await assertGenesetExists(genesetName); }); - test("edit geneset name", async () => { + test("edit geneset name and undo/redo", async () => { await setup(config); await editGenesetName(editableGenesetName, editText); await assertGenesetExists(newGenesetName); + await clickOn("undo"); + await assertGenesetExists(editableGenesetName); + await clickOn("redo"); + await assertGenesetExists(newGenesetName); }); - test("delete a geneset", async () => { + test("delete a geneset and undo/redo", async () => { if (config.withSubset) return; await setup(config); await deleteGeneset(genesetToDeleteName); + await clickOn("undo"); + await assertGenesetExists(genesetToDeleteName); + await clickOn("redo"); + await assertGenesetDoesNotExist(genesetToDeleteName); + }); + test("geneset description", async () => { + if (config.withSubset) return; + + await setup(config); + + await clickOnUntil( + `${genesetToCheckForDescription}:geneset-expand`, + async () => { + expect(page).toMatchElement(getTestId(genesetDescriptionID), { + text: genesetDescriptionString, + }); + } + ); }); }); @@ -204,12 +239,16 @@ describe.each([ { withSubset: true, tag: "subset" }, { withSubset: false, tag: "whole" }, ])("GENE crud operations and interactions", (config) => { - test("add a gene to geneset", async () => { + test("add a gene to geneset and undo/redo", async () => { await setup(config); await addGeneToSet(setToAddGeneTo, geneToAddToSet); await expandGeneset(setToAddGeneTo); await assertGeneExistsInGeneset(geneToAddToSet); + await clickOn("undo"); + await assertGeneDoesNotExist(geneToAddToSet); + await clickOn("redo"); + await assertGeneExistsInGeneset(geneToAddToSet); }); test("expand gene and brush", async () => { await setup(config); @@ -240,7 +279,7 @@ describe.each([ await colorByGene(geneToBrushAndColorBy); await assertColorLegendLabel(geneToBrushAndColorBy); }); - test("delete gene from geneset", async () => { + test("delete gene from geneset and undo/redo", async () => { // We've already deleted the gene if (config.withSubset) return; @@ -249,6 +288,10 @@ describe.each([ await expandGeneset(setToRemoveFrom); await removeGene(geneToRemove); await assertGeneDoesNotExist(geneToRemove); + await clickOn("undo"); + await assertGeneExistsInGeneset(geneToRemove); + await clickOn("redo"); + await assertGeneDoesNotExist(geneToRemove); }); }); @@ -362,8 +405,13 @@ describe.each([ expect(actualLabelName).toBe(expectedLabelName); expect(actualLabelCount).toBe(expectedLabelCount); - async function getInnerText(element, className) { - return element.$eval(getTestClass(className), (node) => node?.innerText); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + async function getInnerText(element: any, className: any) { + return element.$eval( + getTestClass(className), + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (node: any) => node?.innerText + ); } }); @@ -388,7 +436,9 @@ describe.each([ `categorical-value-count-${perTestCategoryName}-${perTestLabelName}` ); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. expect(await result.evaluate((node) => node.innerText)).toBe( + // @ts-expect-error ts-migrate(2538) FIXME: Type 'boolean' cannot be used as an index type. data.categoryLabel.newCount.bySubsetConfig[config.withSubset] ); }); @@ -448,6 +498,7 @@ describe.each([ await createLabel(perTestCategoryName, labelName); await assertLabelExists(perTestCategoryName, labelName); await clickOn("undo"); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. await assertLabelDoesNotExist(perTestCategoryName); await clickOn("redo"); await assertLabelExists(perTestCategoryName, labelName); @@ -457,10 +508,12 @@ describe.each([ await setup(config); await deleteLabel(perTestCategoryName, perTestLabelName); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. await assertLabelDoesNotExist(perTestCategoryName); await clickOn("undo"); await assertLabelExists(perTestCategoryName, perTestLabelName); await clickOn("redo"); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. await assertLabelDoesNotExist(perTestCategoryName); }); @@ -491,11 +544,9 @@ describe.each([ const labels = await getAllByClass("categorical-row"); const result = await Promise.all( - labels.map((label) => { - return page.evaluate((element) => { - return element.outerHTML; - }, label); - }) + labels.map((label) => + page.evaluate((element) => element.outerHTML, label) + ) ); expect(result).toMatchSnapshot(); @@ -523,9 +574,11 @@ describe.each([ expect(result).toMatchSnapshot(); }); - async function assertCategoryExists(categoryName) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + async function assertCategoryExists(categoryName: any) { const handle = await waitByID(`${categoryName}:category-label`); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. const result = await handle.evaluate((node) => node.getAttribute("aria-label") ); @@ -533,7 +586,8 @@ describe.each([ return expect(result).toBe(categoryName); } - async function assertLabelExists(categoryName, labelName) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + async function assertLabelExists(categoryName: any, labelName: any) { await expect(page).toMatchElement( getTestId(`${categoryName}:category-expand`) ); @@ -545,11 +599,13 @@ describe.each([ ); expect( + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. await previous.evaluate((node) => node.getAttribute("aria-label")) ).toBe(labelName); } - async function assertLabelDoesNotExist(categoryName, labelName) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + async function assertLabelDoesNotExist(categoryName: any, labelName: any) { await expandCategory(categoryName); const result = await page.$( `[data-testid='categorical-value-${categoryName}-${labelName}']` diff --git a/client/__tests__/e2e/e2eJestConfig.json b/client/__tests__/e2e/e2eJestConfig.json index cc00d0db..d3db4295 100644 --- a/client/__tests__/e2e/e2eJestConfig.json +++ b/client/__tests__/e2e/e2eJestConfig.json @@ -1,10 +1,10 @@ { "testRunner": "jest-circus/runner", "preset": "jest-puppeteer", - "testMatch": ["**/__tests__/**/?(*.)(spec|test).js?(x)"], - "setupFiles": ["../setupMissingGlobals.js"], - "setupFilesAfterEnv": ["expect-puppeteer", "./puppeteer.setup.js"], - "globalSetup": "../globalSetup.js", + "testMatch": ["**/__tests__/**/?(*.)(spec|test).ts?(x)"], + "setupFiles": ["../setupMissingGlobals.ts"], + "setupFilesAfterEnv": ["expect-puppeteer", "./puppeteer.setup.ts"], + "globalSetup": "../globalSetup.ts", "globalTeardown": "jest-environment-puppeteer/teardown", "testEnvironment": "./screenshot_env.js" } diff --git a/client/__tests__/e2e/puppeteer.setup.js b/client/__tests__/e2e/puppeteer.setup.ts similarity index 85% rename from client/__tests__/e2e/puppeteer.setup.js rename to client/__tests__/e2e/puppeteer.setup.ts index 6c593b93..a910f023 100644 --- a/client/__tests__/e2e/puppeteer.setup.js +++ b/client/__tests__/e2e/puppeteer.setup.ts @@ -23,6 +23,7 @@ beforeEach(async () => { const userAgent = await browser.userAgent(); await page.setUserAgent(`${userAgent}bot`); + // @ts-expect-error ts-migrate(2341) FIXME: Property '_client' is private and only accessible ... Remove this comment to see the full error message await page._client.send("Animation.setPlaybackRate", { playbackRate: 12 }); page.on("pageerror", (err) => { @@ -49,7 +50,8 @@ beforeEach(async () => { } const errorMsgText = await Promise.all( // TODO can we do this without internal properties? - msg.args().map((arg) => arg._remoteObject.description) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + msg.args().map((arg: any) => arg._remoteObject.description) ); throw new Error(`Console error: ${errorMsgText}`); } diff --git a/client/__tests__/e2e/puppeteerUtils.js b/client/__tests__/e2e/puppeteerUtils.js deleted file mode 100644 index 8d3a497f..00000000 --- a/client/__tests__/e2e/puppeteerUtils.js +++ /dev/null @@ -1,131 +0,0 @@ -/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions */ -export function getTestId(id) { - return `[data-testid='${id}']`; -} - -export function getTestClass(className) { - return `[data-testclass='${className}']`; -} - -export async function waitByID(testId, props = {}) { - return page.waitForSelector(getTestId(testId), props); -} - -export async function waitByClass(testClass, props = {}) { - return page.waitForSelector(`[data-testclass='${testClass}']`, props); -} - -export async function waitForAllByIds(testIds) { - await Promise.all( - testIds.map((testId) => page.waitForSelector(getTestId(testId))) - ); -} - -export async function getAllByClass(testClass) { - return page.$$(`[data-testclass=${testClass}]`); -} - -export async function typeInto(testId, text) { - // blueprint's typeahead is treating typing weird, clicking & waiting first solves this - // only works for text without special characters - await waitByID(testId); - const selector = getTestId(testId); - // type ahead can be annoying if you don't pause before you type - await page.click(selector); - await page.waitForTimeout(200); - await page.type(selector, text); -} - -export async function clearInputAndTypeInto(testId, text) { - await waitByID(testId); - const selector = getTestId(testId); - // only works for text without special characters - // type ahead can be annoying if you don't pause before you type - await page.click(selector); - await page.waitForTimeout(200); - // select all - await page.click(selector, { clickCount: 3 }); - await page.keyboard.press("Backspace"); - await page.type(selector, text); -} - -export async function clickOn(testId, options = {}) { - await expect(page).toClick(getTestId(testId), options); -} - -/** - * (thuang): There are times when Puppeteer clicks on a button and the page doesn't respond. - * So I added clickOnUntil() to retry clicking until a given condition is met. - */ -export async function clickOnUntil(testId, assert) { - const MAX_RETRY = 10; - const WAIT_FOR_MS = 200; - - let retry = 0; - - while (retry < MAX_RETRY) { - try { - await clickOn(testId); - await assert(); - - break; - } catch (error) { - retry += 1; - - await page.waitForTimeout(WAIT_FOR_MS); - } - } - - if (retry === MAX_RETRY) { - throw Error("clickOnUntil() assertion failed!"); - } -} - -export async function getOneElementInnerHTML(selector, options = {}) { - await page.waitForSelector(selector, options); - - return page.$eval(selector, (el) => el.innerHTML); -} - -export async function getOneElementInnerText(selector) { - expect(page).toMatchElement(selector); - - return page.$eval(selector, (el) => el.innerText); -} - -export async function getElementCoordinates(testId) { - return page.$eval(getTestId(testId), (elem) => { - const { left, top } = elem.getBoundingClientRect(); - return [left, top]; - }); -} - -async function clickTermsOfService() { - if (!(await isElementPresent(getTestId("tos-cookies-accept")))) return; - - await clickOn("tos-cookies-accept"); -} - -async function nameNewAnnotation() { - if (await isElementPresent(getTestId("annotation-dialog"))) { - await typeInto("new-annotation-name", "ignoreE2E"); - await clickOn("submit-annotation"); - - // wait for the page to load - await waitByClass("autosave-complete"); - } -} - -export async function goToPage(url) { - await page.goto(url, { - waitUntil: "networkidle0", - }); - - await nameNewAnnotation(); - await clickTermsOfService(); -} - -export async function isElementPresent(selector, options) { - return Boolean(await page.$(selector, options)); -} -/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */ diff --git a/client/__tests__/e2e/puppeteerUtils.ts b/client/__tests__/e2e/puppeteerUtils.ts new file mode 100644 index 00000000..6438adf6 --- /dev/null +++ b/client/__tests__/e2e/puppeteerUtils.ts @@ -0,0 +1,151 @@ +/* eslint-disable no-await-in-loop -- await in loop is needed to emulate sequential user actions */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export function getTestId(id: any) { + return `[data-testid='${id}']`; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export function getTestClass(className: any) { + return `[data-testclass='${className}']`; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function waitByID(testId: any, props = {}) { + return page.waitForSelector(getTestId(testId), props); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function waitByClass(testClass: any, props = {}) { + return page.waitForSelector(`[data-testclass='${testClass}']`, props); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function waitForAllByIds(testIds: any) { + await Promise.all( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + testIds.map((testId: any) => page.waitForSelector(getTestId(testId))) + ); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function getAllByClass(testClass: any) { + return page.$$(`[data-testclass=${testClass}]`); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function typeInto(testId: any, text: any) { + // blueprint's typeahead is treating typing weird, clicking & waiting first solves this + // only works for text without special characters + await waitByID(testId); + const selector = getTestId(testId); + // type ahead can be annoying if you don't pause before you type + await page.click(selector); + await page.waitForTimeout(200); + await page.type(selector, text); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function clearInputAndTypeInto(testId: any, text: any) { + await waitByID(testId); + const selector = getTestId(testId); + // only works for text without special characters + // type ahead can be annoying if you don't pause before you type + await page.click(selector); + await page.waitForTimeout(200); + // select all + await page.click(selector, { clickCount: 3 }); + await page.keyboard.press("Backspace"); + await page.type(selector, text); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function clickOn(testId: any, options = {}) { + await expect(page).toClick(getTestId(testId), options); +} + +/** + * (thuang): There are times when Puppeteer clicks on a button and the page doesn't respond. + * So I added clickOnUntil() to retry clicking until a given condition is met. + */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function clickOnUntil(testId: any, assert: any) { + const MAX_RETRY = 10; + const WAIT_FOR_MS = 200; + + let retry = 0; + + while (retry < MAX_RETRY) { + try { + await clickOn(testId); + await assert(); + + break; + } catch (error) { + retry += 1; + + await page.waitForTimeout(WAIT_FOR_MS); + } + } + + if (retry === MAX_RETRY) { + throw Error("clickOnUntil() assertion failed!"); + } +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function getOneElementInnerHTML(selector: any, options = {}) { + await page.waitForSelector(selector, options); + + return page.$eval(selector, (el) => el.innerHTML); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function getOneElementInnerText(selector: any) { + expect(page).toMatchElement(selector); + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return page.$eval(selector, (el) => (el as any).innerText); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function getElementCoordinates(testId: any) { + return page.$eval(getTestId(testId), (elem) => { + const { left, top } = elem.getBoundingClientRect(); + return [left, top]; + }); +} + +async function clickTermsOfService() { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. + if (!(await isElementPresent(getTestId("tos-cookies-accept")))) return; + + await clickOn("tos-cookies-accept"); +} + +async function nameNewAnnotation() { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. + if (await isElementPresent(getTestId("annotation-dialog"))) { + await typeInto("new-annotation-name", "ignoreE2E"); + await clickOn("submit-annotation"); + + // wait for the page to load + await waitByClass("autosave-complete"); + } +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function goToPage(url: any) { + await page.goto(url, { + waitUntil: "networkidle0", + }); + + await nameNewAnnotation(); + await clickTermsOfService(); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export async function isElementPresent(selector: any, options: any) { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 2. + return Boolean(await page.$(selector, options)); +} +/* eslint-enable no-await-in-loop -- await in loop is needed to emulate sequential user actions */ diff --git a/client/__tests__/e2e/screenshot_env.js b/client/__tests__/e2e/screenshot_env.js index 4701d8ca..742579d1 100644 --- a/client/__tests__/e2e/screenshot_env.js +++ b/client/__tests__/e2e/screenshot_env.js @@ -1,7 +1,11 @@ +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const PuppeteerEnvironment = require("jest-environment-puppeteer"); require("jest-circus"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const ENV_DEFAULT = require("../../../environment.default.json"); +// @ts-expect-error ts-migrate(2451) FIXME: Cannot redeclare block-scoped variable 'takeScreen... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const takeScreenshot = require("./takeScreenshot"); class ScreenshotEnvironment extends PuppeteerEnvironment { diff --git a/client/__tests__/globalSetup.js b/client/__tests__/globalSetup.ts similarity index 60% rename from client/__tests__/globalSetup.js rename to client/__tests__/globalSetup.ts index e5163056..6fdfed94 100644 --- a/client/__tests__/globalSetup.js +++ b/client/__tests__/globalSetup.ts @@ -1,8 +1,12 @@ +// eslint-disable-next-line @typescript-eslint/ban-ts-comment --- FIXME: disabled temporarily on migrate to TS. +// @ts-ignore FIXME: 'globalSetup.ts' cannot be compiled under '--isola... Remove this comment to see the full error message const { SecretsManagerClient, GetSecretValueCommand, + // eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. } = require("@aws-sdk/client-secrets-manager"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const { setup } = require("jest-environment-puppeteer"); const client = new SecretsManagerClient({ region: "us-west-2" }); diff --git a/client/__tests__/reducers/cascade.test.js b/client/__tests__/reducers/cascade.test.ts similarity index 51% rename from client/__tests__/reducers/cascade.test.js rename to client/__tests__/reducers/cascade.test.ts index a61e579e..4b086881 100644 --- a/client/__tests__/reducers/cascade.test.js +++ b/client/__tests__/reducers/cascade.test.ts @@ -20,7 +20,16 @@ describe("cascade", () => { const reducer = cascadeReducers([ [ "foo", - (currentState, action, nextSharedState, prevSharedState) => { + ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + currentState: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + action: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + nextSharedState: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + prevSharedState: any + ) => { expect(currentState).toBeUndefined(); expect(action).toEqual(topLevelAction); expect(nextSharedState).toStrictEqual({}); @@ -30,7 +39,16 @@ describe("cascade", () => { ], [ "bar", - (currentState, action, nextSharedState, prevSharedState) => { + ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + currentState: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + action: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + nextSharedState: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + prevSharedState: any + ) => { expect(currentState).toBeUndefined(); expect(action).toEqual(topLevelAction); expect(nextSharedState).toStrictEqual({ foo: 0 }); diff --git a/client/__tests__/reducers/genesets.test.js b/client/__tests__/reducers/genesets.test.ts similarity index 97% rename from client/__tests__/reducers/genesets.test.js rename to client/__tests__/reducers/genesets.test.ts index ad377f6c..ede5a758 100644 --- a/client/__tests__/reducers/genesets.test.js +++ b/client/__tests__/reducers/genesets.test.ts @@ -501,6 +501,7 @@ describe("geneset: set tid", () => { test("not a number error", () => { expect(() => { genesetsReducer( + // @ts-expect-error ts-migrate(2322) FIXME: Type 'number' is not assignable to type 'undefined... Remove this comment to see the full error message { lastTid: 1 }, { type: "geneset: set tid", @@ -513,6 +514,7 @@ describe("geneset: set tid", () => { test("decrement error", () => { expect(() => { genesetsReducer( + // @ts-expect-error ts-migrate(2322) FIXME: Type 'number' is not assignable to type 'undefined... Remove this comment to see the full error message { lastTid: 1 }, { type: "geneset: set tid", diff --git a/client/__tests__/reducers/genesetsUI.test.js b/client/__tests__/reducers/genesetsUI.test.ts similarity index 100% rename from client/__tests__/reducers/genesetsUI.test.js rename to client/__tests__/reducers/genesetsUI.test.ts diff --git a/client/__tests__/reducers/undoable.test.js b/client/__tests__/reducers/undoable.test.ts similarity index 80% rename from client/__tests__/reducers/undoable.test.js rename to client/__tests__/reducers/undoable.test.ts index 5e27b5af..86e787e5 100644 --- a/client/__tests__/reducers/undoable.test.js +++ b/client/__tests__/reducers/undoable.test.ts @@ -2,6 +2,7 @@ import undoable from "../../src/reducers/undoable"; describe("create", () => { test("no keys", () => { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2-3 arguments, but got 1. expect(() => undoable(() => {})).toThrow(); expect(() => undoable(() => {}, null)).toThrow(); expect(() => undoable(() => {}, [])).toThrow(); @@ -23,9 +24,8 @@ describe("create", () => { describe("undo", () => { test("expected state modifications", () => { const initialState = { a: 0, b: 1000 }; - const reducer = (state) => { - return { a: state.a + 1, b: state.b + 1 }; - }; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const reducer = (state: any) => ({ a: state.a + 1, b: state.b + 1 }); const undoableReducer = undoable(reducer, ["a"]); const s1 = undoableReducer(initialState, { type: "test" }); @@ -43,10 +43,10 @@ describe("undo", () => { describe("redo", () => { const initialState = { a: 0, b: 1000 }; - const reducer = (state) => { - return { a: state.a + 1, b: state.b + 1 }; - }; - let UR; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const reducer = (state: any) => ({ a: state.a + 1, b: state.b + 1 }); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let UR: any; beforeEach(() => { UR = undoable(reducer, ["a"]); diff --git a/client/__tests__/setupMissingGlobals.js b/client/__tests__/setupMissingGlobals.ts similarity index 61% rename from client/__tests__/setupMissingGlobals.js rename to client/__tests__/setupMissingGlobals.ts index 679cc21f..72d14319 100644 --- a/client/__tests__/setupMissingGlobals.js +++ b/client/__tests__/setupMissingGlobals.ts @@ -5,5 +5,6 @@ the jest test environment). import { TextDecoder, TextEncoder } from "util"; +// @ts-expect-error ts-migrate(2322) FIXME: Type 'typeof TextDecoder' is not assignable to typ... Remove this comment to see the full error message global.TextDecoder = TextDecoder; global.TextEncoder = TextEncoder; diff --git a/client/__tests__/util/actionHelpers.test.js b/client/__tests__/util/actionHelpers.test.ts similarity index 100% rename from client/__tests__/util/actionHelpers.test.js rename to client/__tests__/util/actionHelpers.test.ts diff --git a/client/__tests__/util/annoMatrix/annoMatrix.test.js b/client/__tests__/util/annoMatrix/annoMatrix.test.ts similarity index 74% rename from client/__tests__/util/annoMatrix/annoMatrix.test.js rename to client/__tests__/util/annoMatrix/annoMatrix.test.ts index c178a5f7..3567cf1c 100644 --- a/client/__tests__/util/annoMatrix/annoMatrix.test.js +++ b/client/__tests__/util/annoMatrix/annoMatrix.test.ts @@ -14,10 +14,13 @@ import { Dataframe } from "../../../src/util/dataframe"; enableFetchMocks(); describe("AnnoMatrix", () => { - let annoMatrix; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let annoMatrix: any; beforeEach(async () => { - fetch.resetMocks(); // reset all fetch mocking state + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).resetMocks(); // reset all fetch mocking state + // reset all fetch mocking state annoMatrix = new AnnoMatrixLoader( serverMocks.baseDataURL, serverMocks.schema.schema @@ -36,7 +39,8 @@ describe("AnnoMatrix", () => { }); test("simple single column fetch", async () => { - fetch.once(serverMocks.annotationsObs(["name_0"])); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once(serverMocks.annotationsObs(["name_0"])); const df = await annoMatrix.fetch("obs", "name_0"); expect(df).toBeInstanceOf(Dataframe); @@ -45,7 +49,8 @@ describe("AnnoMatrix", () => { }); test("simple multi column fetch", async () => { - fetch + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any) .once(serverMocks.annotationsObs(["name_0"])) .once(serverMocks.annotationsObs(["n_genes"])); @@ -55,9 +60,13 @@ describe("AnnoMatrix", () => { }); describe("fetch from field", () => { - const getLastTwo = async (field) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const getLastTwo = async (field: any) => { const columnNames = annoMatrix.getMatrixColumns(field).slice(-2); - fetch.mockResponses(...columnNames.map(() => serverMocks.responder)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockResponses( + ...columnNames.map(() => serverMocks.responder) + ); await expect( annoMatrix.fetch(field, columnNames) ).resolves.toBeInstanceOf(Dataframe); @@ -70,19 +79,22 @@ describe("AnnoMatrix", () => { test("fetch - test all query forms", async () => { // single string is a column name - fetch.once(serverMocks.annotationsObs(["n_genes"])); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once(serverMocks.annotationsObs(["n_genes"])); await expect(annoMatrix.fetch("obs", "n_genes")).resolves.toBeInstanceOf( Dataframe ); // array of column names, expecting n_genes to be cached. - fetch.once(serverMocks.annotationsObs(["percent_mito"])); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once(serverMocks.annotationsObs(["percent_mito"])); await expect( annoMatrix.fetch("obs", ["n_genes", "percent_mito"]) ).resolves.toBeInstanceOf(Dataframe); // more complex value filter query, enumerated - fetch.once(serverMocks.responder); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once(serverMocks.responder); await expect( annoMatrix.fetch("X", { where: { @@ -95,7 +107,8 @@ describe("AnnoMatrix", () => { // more complex value filter query, range const varIndex = annoMatrix.schema.annotations.var.index; - fetch + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any) .once( serverMocks.withExpected("/data/var", [[`var:${varIndex}`, "SUMO3"]]) ) @@ -171,7 +184,8 @@ describe("AnnoMatrix", () => { expect(am1.nObs).toEqual(am2.nObs); expect(am1.nVar).toEqual(am2.nVar); - fetch + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any) .once(serverMocks.annotationsObs(["n_genes"])) .once(serverMocks.annotationsObs(["n_genes"])); const ng1 = await am1.fetch("obs", "n_genes"); @@ -185,9 +199,11 @@ describe("AnnoMatrix", () => { }); describe("add/drop column", () => { + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'base' implicitly has an 'any' type. async function addDrop(base) { expect(base.getMatrixColumns("obs")).not.toContain("foo"); - fetch.mockRejectOnce(new Error("unknown column name")); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockRejectOnce(new Error("unknown column name")); await expect(base.fetch("obs", "foo")).rejects.toThrow( "unknown column name" ); @@ -212,7 +228,8 @@ describe("AnnoMatrix", () => { const am2 = am1.dropObsColumn("foo"); expect(base.getMatrixColumns("obs")).not.toContain("foo"); expect(am2.getMatrixColumns("obs")).not.toContain("foo"); - fetch.mockRejectOnce(new Error("unknown column name")); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockRejectOnce(new Error("unknown column name")); await expect(am2.fetch("obs", "foo")).rejects.toThrow( "unknown column name" ); @@ -235,14 +252,16 @@ describe("AnnoMatrix", () => { const am4 = clip(am3, 0, 1); await addDrop(am4); - fetch.mockResponse(serverMocks.responder); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockResponse(serverMocks.responder); await am1.fetch("obs", am1.getMatrixColumns("obs")); await am2.fetch("obs", am2.getMatrixColumns("obs")); await am3.fetch("obs", am3.getMatrixColumns("obs")); await am4.fetch("obs", am4.getMatrixColumns("obs")); - fetch.resetMocks(); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).resetMocks(); await addDrop(am1); await addDrop(am2); @@ -252,6 +271,7 @@ describe("AnnoMatrix", () => { }); describe("setObsColumnValues", () => { + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'base' implicitly has an 'any' type. async function addSetDrop(base) { /* add column */ let am = base.addObsColumn( @@ -287,7 +307,8 @@ describe("AnnoMatrix", () => { ); /* drop column */ - fetch.mockRejectOnce(new Error("unknown column name")); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockRejectOnce(new Error("unknown column name")); am = am1.dropObsColumn("test"); await expect(am.fetch("obs", "test")).rejects.toThrow( "unknown column name" @@ -308,7 +329,8 @@ describe("AnnoMatrix", () => { const am3 = isubset(annoMatrix, [10, 1, 0, 30, 2]); await addSetDrop(am3); - fetch.mockResponse(serverMocks.responder); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockResponse(serverMocks.responder); await am1.fetch("obs", am1.getMatrixColumns("obs")); await am2.fetch("obs", am2.getMatrixColumns("obs")); diff --git a/client/__tests__/util/annoMatrix/crossfilter.test.js b/client/__tests__/util/annoMatrix/crossfilter.test.ts similarity index 71% rename from client/__tests__/util/annoMatrix/crossfilter.test.js rename to client/__tests__/util/annoMatrix/crossfilter.test.ts index 873334ca..a87eae08 100644 --- a/client/__tests__/util/annoMatrix/crossfilter.test.js +++ b/client/__tests__/util/annoMatrix/crossfilter.test.ts @@ -17,11 +17,15 @@ import { rangeFill } from "../../../src/util/range"; enableFetchMocks(); describe("AnnoMatrixCrossfilter", () => { - let annoMatrix; - let crossfilter; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let annoMatrix: any; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let crossfilter: any; beforeEach(async () => { - fetch.resetMocks(); // reset all fetch mocking state + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).resetMocks(); // reset all fetch mocking state + // reset all fetch mocking state annoMatrix = new AnnoMatrixLoader( serverMocks.baseDataURL, serverMocks.schema.schema @@ -67,7 +71,10 @@ describe("AnnoMatrixCrossfilter", () => { crossfilter.obsCrossfilter.hasDimension("obs/louvain") ).toBeFalsy(); - fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain])); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once( + serverMocks.dataframeResponse(["louvain"], [obsLouvain]) + ); let newCrossfilter = await crossfilter.select("obs", "louvain", { mode: "none", }); @@ -76,7 +83,8 @@ describe("AnnoMatrixCrossfilter", () => { expect( newCrossfilter.obsCrossfilter.hasDimension("obs/louvain") ).toBeTruthy(); - expect(fetch.mock.calls).toHaveLength(1); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + expect((fetch as any).mock.calls).toHaveLength(1); newCrossfilter = await crossfilter.select("obs", "louvain", { mode: "all", @@ -87,7 +95,10 @@ describe("AnnoMatrixCrossfilter", () => { test("simple column select", async () => { let xfltr; - fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain])); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once( + serverMocks.dataframeResponse(["louvain"], [obsLouvain]) + ); xfltr = await crossfilter.select("obs", "louvain", { mode: "exact", values: ["NK cells", "B cells"], @@ -105,6 +116,7 @@ describe("AnnoMatrixCrossfilter", () => { expect(xfltr.allSelectedLabels()).toEqual( Int32Array.from( obsLouvain.reduce((acc, val, idx) => { + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number' is not assignable to par... Remove this comment to see the full error message if (val === "NK cells" || val === "B cells") acc.push(idx); return acc; }, []) @@ -124,10 +136,13 @@ describe("AnnoMatrixCrossfilter", () => { const values = df.col("louvain").asArray(); const selected = xfltr.allSelectedMask(); values.every( - (val, idx) => !["NK cells", "B cells"].includes(val) !== !selected[idx] + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (val: any, idx: any) => + !["NK cells", "B cells"].includes(val) !== !selected[idx] ); - fetch.once( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once( serverMocks.dataframeResponse(["n_genes"], [new Int32Array(obsNGenes)]) ); xfltr = await xfltr.select("obs", "n_genes", { @@ -146,6 +161,7 @@ describe("AnnoMatrixCrossfilter", () => { val < 500 && (louvain === "NK cells" || louvain === "B cells") ) + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number' is not assignable to par... Remove this comment to see the full error message acc.push(idx); return acc; }, []) @@ -160,7 +176,8 @@ describe("AnnoMatrixCrossfilter", () => { const varIndex = annoMatrix.schema.annotations.var.index; const { nObs } = annoMatrix.schema.dataframe; - fetch.once( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once( serverMocks.dataframeResponse( ["TEST"], [rangeFill(new Float32Array(nObs), 0, 0.1)] @@ -196,14 +213,19 @@ describe("AnnoMatrixCrossfilter", () => { }); const values = df.icol(0).asArray(); const selected = xfltr.allSelectedMask(); - values.every((val, idx) => !(val >= 0 && val <= 50) !== !selected[idx]); - expect(selected.reduce((acc, val) => (val ? acc + 1 : acc), 0)).toEqual( - xfltr.countSelected() + values.every( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (val: any, idx: any) => !(val >= 0 && val <= 50) !== !selected[idx] ); + expect( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + selected.reduce((acc: any, val: any) => (val ? acc + 1 : acc), 0) + ).toEqual(xfltr.countSelected()); }); test("spatial column select", async () => { - fetch.once( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once( serverMocks.dataframeResponse( ["umap_0", "umap_1"], [Float32Array.from(embUmap[0]), Float32Array.from(embUmap[1])] @@ -222,6 +244,7 @@ describe("AnnoMatrixCrossfilter", () => { test("select on subset", async () => { const mask = new Uint8Array(annoMatrix.nObs).fill(0); for (let i = 0; i < mask.length; i += 2) { + // @ts-expect-error ts-migrate(2322) FIXME: Type 'boolean' is not assignable to type 'number'. mask[i] = true; } const annoMatrixSubset = isubsetMask(annoMatrix, mask); @@ -230,7 +253,10 @@ describe("AnnoMatrixCrossfilter", () => { let xfltr = new AnnoMatrixObsCrossfilter(annoMatrixSubset); expect(xfltr.countSelected()).toEqual(annoMatrixSubset.nObs); - fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain])); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once( + serverMocks.dataframeResponse(["louvain"], [obsLouvain]) + ); xfltr = await xfltr.select("obs", "louvain", { mode: "exact", values: ["NK cells", "B cells"], @@ -243,7 +269,9 @@ describe("AnnoMatrixCrossfilter", () => { const values = df.col("louvain").asArray(); const selected = xfltr.allSelectedMask(); values.every( - (val, idx) => !["NK cells", "B cells"].includes(val) !== !selected[idx] + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (val: any, idx: any) => + !["NK cells", "B cells"].includes(val) !== !selected[idx] ); }); @@ -256,7 +284,8 @@ describe("AnnoMatrixCrossfilter", () => { "unable to obsSelect upon the var dimension" ); - fetch.mockRejectOnce(new Error("unknown column name")); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockRejectOnce(new Error("unknown column name")); await expect(crossfilter.select("obs", "foo")).rejects.toThrow( "unknown column name" ); @@ -267,24 +296,29 @@ describe("AnnoMatrixCrossfilter", () => { /* test the matrix mutators via crossfilter proxy */ - async function helperAddTestCol(cf, colName, colSchema = null) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + async function helperAddTestCol(cf: any, colName: any, colSchema = null) { expect( cf.annoMatrix.getMatrixColumns("obs").includes(colName) ).toBeFalsy(); if (colSchema === null) { + // @ts-expect-error ts-migrate(2322) FIXME: Type '{ name: any; type: string; categories: strin... Remove this comment to see the full error message colSchema = { name: colName, type: "categorical", categories: ["toasty"], }; } + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. colSchema.name = colName; + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. const initValue = colSchema.categories[0]; const xfltr = cf.addObsColumn(colSchema, Array, initValue); expect( xfltr.annoMatrix.schema.annotations.obs.columns.filter( - (v) => v.name === colName + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (v: any) => v.name === colName ) ).toHaveLength(1); const df = await xfltr.annoMatrix.fetch("obs", colName); @@ -314,7 +348,8 @@ describe("AnnoMatrixCrossfilter", () => { }); expect( xfltr.annoMatrix.schema.annotations.obs.columns.filter( - (v) => v.name === "foo" + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (v: any) => v.name === "foo" ) ).toHaveLength(1); @@ -323,8 +358,8 @@ describe("AnnoMatrixCrossfilter", () => { expect( df .col("foo") - .asArray() - .every((v) => v === "A") + .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .every((v: any) => v === "A") ).toBeTruthy(); // check that we catch dups @@ -361,11 +396,13 @@ describe("AnnoMatrixCrossfilter", () => { xfltr = xfltr.dropObsColumn("foo"); expect( xfltr.annoMatrix.schema.annotations.obs.columns.filter( - (v) => v.name === "foo" + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (v: any) => v.name === "foo" ) ).toHaveLength(0); expect(xfltr.annoMatrix.schema.annotations.obsByName.foo).toBeUndefined(); - fetch.mockRejectOnce(new Error("unknown column name")); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockRejectOnce(new Error("unknown column name")); await expect(xfltr.annoMatrix.fetch("obs", "foo")).rejects.toThrow( "unknown column name" ); @@ -378,7 +415,8 @@ describe("AnnoMatrixCrossfilter", () => { }); xfltr = xfltr.dropObsColumn("bar"); - fetch.mockRejectOnce(new Error("unknown column name")); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockRejectOnce(new Error("unknown column name")); await expect(xfltr.select("obs", "bar", { mode: "all" })).rejects.toThrow( "unknown column name" ); @@ -404,7 +442,8 @@ describe("AnnoMatrixCrossfilter", () => { type: "categorical", }); - fetch.mockRejectOnce(new Error("unknown column name")); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockRejectOnce(new Error("unknown column name")); await expect(xfltr.annoMatrix.fetch("obs", "foo")).rejects.toThrow( "unknown column name" ); @@ -419,7 +458,8 @@ describe("AnnoMatrixCrossfilter", () => { }); xfltr = xfltr.renameObsColumn("bar", "xyz"); - fetch.mockRejectOnce(new Error("unknown column name")); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).mockRejectOnce(new Error("unknown column name")); await expect(xfltr.select("obs", "bar", { mode: "all" })).rejects.toThrow( "unknown column name" ); @@ -429,7 +469,8 @@ describe("AnnoMatrixCrossfilter", () => { }); test("addObsAnnoCategory", async () => { - let xfltr; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let xfltr: any; // catch unknown or readonly columns expect(() => crossfilter.addObsAnnoCategory("louvain", "mumble")).toThrow( @@ -440,6 +481,7 @@ describe("AnnoMatrixCrossfilter", () => { ).toThrow("Unknown or readonly obs column"); // add a column and then add category to it + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message xfltr = await helperAddTestCol(crossfilter, "foo", { name: "foo", type: "categorical", @@ -458,6 +500,7 @@ describe("AnnoMatrixCrossfilter", () => { ); // now same, but ensure we have built an index before doing the operation + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message xfltr = await helperAddTestCol(crossfilter, "bar", { name: "bar", type: "categorical", @@ -486,6 +529,7 @@ describe("AnnoMatrixCrossfilter", () => { crossfilter.removeObsAnnoCategory("undefined-name", "mumble") ).rejects.toThrow("Unknown or readonly obs column"); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message xfltr = await helperAddTestCol(crossfilter, "foo", { name: "foo", type: "categorical", @@ -495,8 +539,8 @@ describe("AnnoMatrixCrossfilter", () => { expect( (await xfltr.annoMatrix.fetch("obs", "foo")) .col("foo") - .asArray() - .every((v) => v === "unassigned") + .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .every((v: any) => v === "unassigned") ).toBeTruthy(); expect(xfltr.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({ name: "foo", @@ -514,8 +558,8 @@ describe("AnnoMatrixCrossfilter", () => { expect( (await xfltr1.annoMatrix.fetch("obs", "foo")) .col("foo") - .asArray() - .every((v) => v === "unassigned") + .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .every((v: any) => v === "unassigned") ).toBeTruthy(); expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({ name: "foo", @@ -537,8 +581,8 @@ describe("AnnoMatrixCrossfilter", () => { expect( (await xfltr2.annoMatrix.fetch("obs", "foo")) .col("foo") - .asArray() - .every((v) => v === "red") + .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .every((v: any) => v === "red") ).toBeTruthy(); expect(xfltr2.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({ name: "foo", @@ -556,6 +600,7 @@ describe("AnnoMatrixCrossfilter", () => { crossfilter.setObsColumnValues("undefined-name", [0], "mumble") ).rejects.toThrow("Unknown or readonly obs column"); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message let xfltr = await helperAddTestCol(crossfilter, "foo", { name: "foo", type: "categorical", @@ -572,8 +617,8 @@ describe("AnnoMatrixCrossfilter", () => { expect( (await xfltr.annoMatrix.fetch("obs", "foo")) .col("foo") - .asArray() - .every((v) => v === "unassigned") + .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .every((v: any) => v === "unassigned") ).toBeTruthy(); const xfltr1 = await xfltr.setObsColumnValues("foo", [0, 10], "purple"); expect( @@ -581,7 +626,8 @@ describe("AnnoMatrixCrossfilter", () => { .col("foo") .asArray() .every( - (v, i) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (v: any, i: any) => v === "unassigned" || (v === "purple" && (i === 0 || i === 10)) ) ).toBeTruthy(); @@ -615,6 +661,7 @@ describe("AnnoMatrixCrossfilter", () => { crossfilter.resetObsColumnValues("undefined-name", "red", "blue") ).rejects.toThrow("Unknown or readonly obs column"); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{ name: string; type: string; ca... Remove this comment to see the full error message let xfltr = await helperAddTestCol(crossfilter, "foo", { name: "foo", type: "categorical", @@ -638,22 +685,22 @@ describe("AnnoMatrixCrossfilter", () => { expect( (await xfltr1.annoMatrix.fetch("obs", "foo")) .col("foo") - .asArray() - .filter((v) => v === "purple") + .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .filter((v: any) => v === "purple") ).toHaveLength(2); xfltr1 = await xfltr1.resetObsColumnValues("foo", "purple", "magenta"); expect( (await xfltr1.annoMatrix.fetch("obs", "foo")) .col("foo") - .asArray() - .filter((v) => v === "magenta") + .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .filter((v: any) => v === "magenta") ).toHaveLength(2); expect( (await xfltr1.annoMatrix.fetch("obs", "foo")) .col("foo") - .asArray() - .filter((v) => v === "purple") + .asArray() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .filter((v: any) => v === "purple") ).toHaveLength(0); expect(xfltr1.annoMatrix.getColumnSchema("obs", "foo")).toMatchObject({ name: "foo", @@ -673,12 +720,16 @@ describe("AnnoMatrixCrossfilter", () => { describe("edge cases", () => { test("transition from empty annoMatrix", async () => { // select before fetch needs to work - fetch.once(serverMocks.dataframeResponse(["louvain"], [obsLouvain])); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (fetch as any).once( + serverMocks.dataframeResponse(["louvain"], [obsLouvain]) + ); const xfltr = await crossfilter.select("obs", "louvain", { mode: "exact", values: "B cells", }); - expect(fetch.mock.calls).toHaveLength(1); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + expect((fetch as any).mock.calls).toHaveLength(1); expect(xfltr.obsCrossfilter.hasDimension("obs/louvain")).toBeTruthy(); expect(xfltr.obsCrossfilter.all()).toBe(xfltr.annoMatrix._cache.obs); expect(xfltr.countSelected()).toEqual( diff --git a/client/__tests__/util/annoMatrix/serverMocks/index.js b/client/__tests__/util/annoMatrix/serverMocks/index.ts similarity index 56% rename from client/__tests__/util/annoMatrix/serverMocks/index.js rename to client/__tests__/util/annoMatrix/serverMocks/index.ts index a8ef1285..525c4ea5 100644 --- a/client/__tests__/util/annoMatrix/serverMocks/index.js +++ b/client/__tests__/util/annoMatrix/serverMocks/index.ts @@ -1,6 +1,7 @@ export const baseDataURL = "https://a.fake.url/api/v0.2"; -window.CELLXGENE = { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +(window as any).CELLXGENE = { API: { prefix: baseDataURL, version: "v0.2/", diff --git a/client/__tests__/util/annoMatrix/serverMocks/routes.js b/client/__tests__/util/annoMatrix/serverMocks/routes.js deleted file mode 100644 index 94fbe3f6..00000000 --- a/client/__tests__/util/annoMatrix/serverMocks/routes.js +++ /dev/null @@ -1,211 +0,0 @@ -import { schema } from "./schema"; -import { Dataframe, KeyIndex } from "../../../../src/util/dataframe"; -import { encodeMatrixFBS } from "../../../../src/util/stateManager/matrix"; - -const indexedSchema = { - obsByName: Object.fromEntries( - schema.schema.annotations.obs.columns.map((v) => [v.name, v]) ?? [] - ), - varByName: Object.fromEntries( - schema.schema.annotations.var.columns.map((v) => [v.name, v]) ?? [] - ), - embByName: Object.fromEntries( - schema.schema.layout.obs.map((v) => [v.name, v]) ?? [] - ), -}; - -function makeMockColumn(s, length) { - const { type } = s; - switch (type) { - case "int32": - return new Int32Array(length).fill(Math.floor(99 * Math.random())); - - case "string": - return new Array(length).fill("test"); - - case "float32": - return new Float32Array(length).fill(99 * Math.random()); - - case "boolean": - return new Array(length).fill(false); - - case "categorical": - return new Array(length).fill(s.categories[0]); - - default: - throw new Error("unkonwn type"); - } -} - -function getEncodedDataframe(colNames, length, colSchemas) { - const colIndex = new KeyIndex(colNames); - const columns = colSchemas.map((s) => makeMockColumn(s, length)); - const df = new Dataframe([length, colNames.length], columns, null, colIndex); - const body = encodeMatrixFBS(df); - return body; -} - -export function dataframeResponse(colNames, columns) { - const colIndex = new KeyIndex(colNames); - const df = new Dataframe( - [columns[0].length, colNames.length], - columns, - null, - colIndex - ); - const body = encodeMatrixFBS(df); - const headers = new Headers({ - "Content-Type": "application/octet-stream", - }); - return () => Promise.resolve({ body, init: { status: 200, headers } }); -} - -function annotationObsResponse(request) { - const url = new URL(request.url); - const params = Array.from(url.searchParams.entries()); - const names = params - .filter(([k]) => k === "annotation-name") - .map(([, v]) => v); - if (!names.every((n) => indexedSchema.obsByName[n])) { - return Promise.reject(new Error("bad obs annotation name in URL")); - } - const colSchemas = names.map((n) => indexedSchema.obsByName[n]); - const body = getEncodedDataframe( - names, - schema.schema.dataframe.nObs, - colSchemas - ); - - const headers = new Headers({ - "Content-Type": "application/octet-stream", - }); - return Promise.resolve({ - body, - init: { status: 200, headers }, - }); -} - -function annotationVarResponse(request) { - const url = new URL(request.url); - const params = Array.from(url.searchParams.entries()); - const names = params - .filter(([k]) => k === "annotation-name") - .map(([, v]) => v); - if (!names.every((n) => indexedSchema.varByName[n])) { - return Promise.reject(new Error("bad var annotation name in URL")); - } - const colSchemas = names.map((n) => indexedSchema.varByName[n]); - const body = getEncodedDataframe( - names, - schema.schema.dataframe.nVar, - colSchemas - ); - - const headers = new Headers({ - "Content-Type": "application/octet-stream", - }); - return Promise.resolve({ - body, - init: { status: 200, headers }, - }); -} - -function layoutObsResponse(request) { - const url = new URL(request.url); - const params = Array.from(url.searchParams.entries()); - const names = params.filter(([k]) => k === "layout-name").map(([, v]) => v); - if (!names.every((n) => indexedSchema.embByName[n])) { - return Promise.reject(new Error("bad layout name in URL")); - } - const dims = names.map((n) => indexedSchema.embByName[n].dims).flat(); - const colSchemas = names - .map((n) => [indexedSchema.embByName[n], indexedSchema.embByName[n]]) - .flat(); - const body = getEncodedDataframe( - dims, - schema.schema.dataframe.nObs, - colSchemas - ); - - const headers = new Headers({ - "Content-Type": "application/octet-stream", - }); - return Promise.resolve({ - body, - init: { status: 200, headers }, - }); -} - -function dataVarResponse(request) { - const url = new URL(request.url); - const params = Array.from(url.searchParams.entries()); - - const colNames = params.map((v) => `${v[0]}/${v[1]}`); - const colSchemas = colNames.map(() => schema.schema.dataframe); - const body = getEncodedDataframe( - colNames, - schema.schema.dataframe.nObs, - colSchemas - ); - - const headers = new Headers({ - "Content-Type": "application/octet-stream", - }); - return Promise.resolve({ - body, - init: { status: 200, headers }, - }); -} - -export function responder(request) { - const url = new URL(request.url); - const { pathname } = url; - if (pathname.endsWith("/annotations/obs")) { - return annotationObsResponse(request); - } - if (pathname.endsWith("/annotations/var")) { - return annotationVarResponse(request); - } - if (pathname.endsWith("/layout/obs")) { - return layoutObsResponse(request); - } - if (pathname.endsWith("/data/var")) { - return dataVarResponse(request); - } - return Promise.reject(new Error("bad URL")); -} - -export function withExpected(expectedURL, expectedParams) { - /* - Do some additional error checking - */ - return (request) => { - // if URL is bogus, reject the promise - const url = new URL(request.url); - if (!url.pathname.endsWith(expectedURL)) { - return Promise.reject(new Error("Unexpected URL!")); - } - const params = Array.from(url.searchParams.entries()).sort( - (a, b) => a[0] < b[0] - ); - expectedParams = expectedParams.slice().sort((a, b) => a[0] < b[0]); - - if ( - params.length !== expectedParams.length || - !params.every( - (p, i) => p[0] === expectedParams[i][0] && p[1] === expectedParams[i][1] - ) - ) { - return Promise.reject(new Error("unexpected name requested in URL")); - } - - return responder(request); - }; -} - -export function annotationsObs(names) { - return withExpected( - "/annotations/obs", - names.map((name) => ["annotation-name", name]) - ); -} diff --git a/client/__tests__/util/annoMatrix/serverMocks/routes.ts b/client/__tests__/util/annoMatrix/serverMocks/routes.ts new file mode 100644 index 00000000..f195026a --- /dev/null +++ b/client/__tests__/util/annoMatrix/serverMocks/routes.ts @@ -0,0 +1,251 @@ +import { schema } from "./schema"; +import { Dataframe, KeyIndex } from "../../../../src/util/dataframe"; +import { encodeMatrixFBS } from "../../../../src/util/stateManager/matrix"; + +const indexedSchema = { + obsByName: Object.fromEntries( + schema.schema.annotations.obs.columns.map((v) => [v.name, v]) ?? [] + ), + varByName: Object.fromEntries( + schema.schema.annotations.var.columns.map((v) => [v.name, v]) ?? [] + ), + embByName: Object.fromEntries( + schema.schema.layout.obs.map((v) => [v.name, v]) ?? [] + ), +}; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function makeMockColumn(s: any, length: any) { + const { type } = s; + switch (type) { + case "int32": + return new Int32Array(length).fill(Math.floor(99 * Math.random())); + + case "string": + return new Array(length).fill("test"); + + case "float32": + return new Float32Array(length).fill(99 * Math.random()); + + case "boolean": + return new Array(length).fill(false); + + case "categorical": + return new Array(length).fill(s.categories[0]); + + default: + throw new Error("unkonwn type"); + } +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function getEncodedDataframe(colNames: any, length: any, colSchemas: any) { + const colIndex = new KeyIndex(colNames); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const columns = colSchemas.map((s: any) => makeMockColumn(s, length)); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message + const df = new Dataframe([length, colNames.length], columns, null, colIndex); + const body = encodeMatrixFBS(df); + return body; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function dataframeResponse(colNames: any, columns: any) { + const colIndex = new KeyIndex(colNames); + const df = new Dataframe( + [columns[0].length, colNames.length], + columns, + null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message + colIndex + ); + const body = encodeMatrixFBS(df); + const headers = new Headers({ + "Content-Type": "application/octet-stream", + }); + return () => Promise.resolve({ body, init: { status: 200, headers } }); +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function annotationObsResponse(request: any) { + const url = new URL(request.url); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const params = Array.from((url.searchParams as any).entries()); + const names = params + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. + .filter(([k]) => k === "annotation-name") + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '([, v]: [any, any]) => any' is n... Remove this comment to see the full error message + .map(([, v]) => v); + // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type. + if (!names.every((n) => indexedSchema.obsByName[n])) { + return Promise.reject(new Error("bad obs annotation name in URL")); + } + // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type. + const colSchemas = names.map((n) => indexedSchema.obsByName[n]); + const body = getEncodedDataframe( + names, + schema.schema.dataframe.nObs, + colSchemas + ); + + const headers = new Headers({ + "Content-Type": "application/octet-stream", + }); + return Promise.resolve({ + body, + init: { status: 200, headers }, + }); +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function annotationVarResponse(request: any) { + const url = new URL(request.url); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const params = Array.from((url.searchParams as any).entries()); + const names = params + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. + .filter(([k]) => k === "annotation-name") + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '([, v]: [any, any]) => any' is n... Remove this comment to see the full error message + .map(([, v]) => v); + // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type. + if (!names.every((n) => indexedSchema.varByName[n])) { + return Promise.reject(new Error("bad var annotation name in URL")); + } + // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type. + const colSchemas = names.map((n) => indexedSchema.varByName[n]); + const body = getEncodedDataframe( + names, + schema.schema.dataframe.nVar, + colSchemas + ); + + const headers = new Headers({ + "Content-Type": "application/octet-stream", + }); + return Promise.resolve({ + body, + init: { status: 200, headers }, + }); +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function layoutObsResponse(request: any) { + const url = new URL(request.url); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const params = Array.from((url.searchParams as any).entries()); + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. + const names = params.filter(([k]) => k === "layout-name").map(([, v]) => v); + // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type. + if (!names.every((n) => indexedSchema.embByName[n])) { + return Promise.reject(new Error("bad layout name in URL")); + } + // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type. + const dims = names.map((n) => indexedSchema.embByName[n].dims).flat(); + const colSchemas = names + // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type. + .map((n) => [indexedSchema.embByName[n], indexedSchema.embByName[n]]) + .flat(); + const body = getEncodedDataframe( + dims, + schema.schema.dataframe.nObs, + colSchemas + ); + + const headers = new Headers({ + "Content-Type": "application/octet-stream", + }); + return Promise.resolve({ + body, + init: { status: 200, headers }, + }); +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function dataVarResponse(request: any) { + const url = new URL(request.url); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const params = Array.from((url.searchParams as any).entries()); + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const colNames = params.map((v) => `${(v as any)[0]}/${(v as any)[1]}`); + const colSchemas = colNames.map(() => schema.schema.dataframe); + const body = getEncodedDataframe( + colNames, + schema.schema.dataframe.nObs, + colSchemas + ); + + const headers = new Headers({ + "Content-Type": "application/octet-stream", + }); + return Promise.resolve({ + body, + init: { status: 200, headers }, + }); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function responder(request: any) { + const url = new URL(request.url); + const { pathname } = url; + if (pathname.endsWith("/annotations/obs")) { + return annotationObsResponse(request); + } + if (pathname.endsWith("/annotations/var")) { + return annotationVarResponse(request); + } + if (pathname.endsWith("/layout/obs")) { + return layoutObsResponse(request); + } + if (pathname.endsWith("/data/var")) { + return dataVarResponse(request); + } + return Promise.reject(new Error("bad URL")); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function withExpected(expectedURL: any, expectedParams: any) { + /* + Do some additional error checking + */ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + return (request: any) => { + // if URL is bogus, reject the promise + const url = new URL(request.url); + if (!url.pathname.endsWith(expectedURL)) { + return Promise.reject(new Error("Unexpected URL!")); + } + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const params = Array.from((url.searchParams as any).entries()).sort( + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '(a: unknown, b: unknown) => bool... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (a, b) => (a as any)[0] < (b as any)[0] + ); + expectedParams = expectedParams + .slice() // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .sort((a: any, b: any) => a[0] < b[0]); + + if ( + params.length !== expectedParams.length || + !params.every( + (p, i) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (p as any)[0] === expectedParams[i][0] && // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (p as any)[1] === expectedParams[i][1] + ) + ) { + return Promise.reject(new Error("unexpected name requested in URL")); + } + + return responder(request); + }; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function annotationsObs(names: any) { + return withExpected( + "/annotations/obs", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + names.map((name: any) => ["annotation-name", name]) + ); +} diff --git a/client/__tests__/util/annoMatrix/serverMocks/schema.js b/client/__tests__/util/annoMatrix/serverMocks/schema.ts similarity index 100% rename from client/__tests__/util/annoMatrix/serverMocks/schema.js rename to client/__tests__/util/annoMatrix/serverMocks/schema.ts diff --git a/client/__tests__/util/annoMatrix/whereCache.test.js b/client/__tests__/util/annoMatrix/whereCache.test.ts similarity index 91% rename from client/__tests__/util/annoMatrix/whereCache.test.js rename to client/__tests__/util/annoMatrix/whereCache.test.ts index e087399e..640ac523 100644 --- a/client/__tests__/util/annoMatrix/whereCache.test.js +++ b/client/__tests__/util/annoMatrix/whereCache.test.ts @@ -218,10 +218,18 @@ describe("whereCache", () => { }, }) ); - expect(wc.where.field.queryField.has("queryColumn")).toEqual(true); - expect(wc.where.field.queryField.get("queryColumn")).toBeInstanceOf(Map); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + expect((wc.where as any).field.queryField.has("queryColumn")).toEqual(true); expect( - wc.where.field.queryField.get("queryColumn").has("queryValue") + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (wc.where as any).field.queryField.get("queryColumn") + ).toBeInstanceOf(Map); + expect( + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (wc.where as any).field.queryField.get("queryColumn").has("queryValue") ).toEqual(true); expect(_whereCacheGet(wc, schema, "field", query)).toEqual([0, 1, 2]); }); diff --git a/client/__tests__/util/centroid.test.js b/client/__tests__/util/centroid.test.ts similarity index 72% rename from client/__tests__/util/centroid.test.js rename to client/__tests__/util/centroid.test.ts index b8bee126..3766375e 100644 --- a/client/__tests__/util/centroid.test.js +++ b/client/__tests__/util/centroid.test.ts @@ -5,19 +5,22 @@ import quantile from "../../src/util/quantile"; import { matrixFBSToDataframe } from "../../src/util/stateManager/matrix"; import * as REST from "./stateManager/sampleResponses"; import { indexEntireSchema } from "../../src/util/stateManager/schemaHelpers"; -import { _normalizeCategoricalSchema } from "../../src/annoMatrix/schema"; +import { normalizeWritableCategoricalSchema } from "../../src/annoMatrix/normalize"; describe("centroid", () => { - let schema; - let obsAnnotations; - let obsLayout; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let schema: any; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let obsAnnotations: any; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let obsLayout: any; beforeAll(() => { schema = indexEntireSchema(cloneDeep(REST.schema.schema)); obsAnnotations = matrixFBSToDataframe(REST.annotationsObs); obsLayout = matrixFBSToDataframe(REST.layoutObs); - _normalizeCategoricalSchema( + normalizeWritableCategoricalSchema( schema.annotations.obsByName.field3, obsAnnotations.col("field3") ); @@ -44,7 +47,8 @@ describe("centroid", () => { quantile([0.5], obsLayout.col("umap_1").asArray())[0], ]; - centroidResult.forEach((coordinate) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + centroidResult.forEach((coordinate: any) => { expect(coordinate).toEqual(expectedResult); }); }); @@ -68,7 +72,8 @@ describe("centroid", () => { quantile([0.5], obsLayout.col("umap_1").asArray())[0], ]; - centroidResult.forEach((coordinate) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + centroidResult.forEach((coordinate: any) => { expect(coordinate).toEqual(expectedResult); }); }); diff --git a/client/__tests__/util/dataframe/dataframe.test.js b/client/__tests__/util/dataframe/dataframe.test.ts similarity index 89% rename from client/__tests__/util/dataframe/dataframe.test.js rename to client/__tests__/util/dataframe/dataframe.test.ts index 727f0a7f..e6aa9eb5 100644 --- a/client/__tests__/util/dataframe/dataframe.test.js +++ b/client/__tests__/util/dataframe/dataframe.test.ts @@ -29,6 +29,7 @@ describe("dataframe constructor", () => { const df = new Dataframe.Dataframe( [3, 2], [new Int32Array([0, 1, 2]), new Int32Array([3, 4, 5])], + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message new Dataframe.DenseInt32Index([2, 1, 0]), new Dataframe.KeyIndex(["A", "B"]) ); @@ -55,6 +56,7 @@ describe("simple data access", () => { new Float64Array([0.0, Number.NaN, Number.POSITIVE_INFINITY, 3.14159]), ["red", "blue", "green", "nan"], ], + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message new Dataframe.DenseInt32Index([3, 2, 1, 0]), new Dataframe.KeyIndex(["numbers", "colors"]) ); @@ -139,10 +141,12 @@ describe("dataframe subsetting", () => { ["red", "green", "blue"], ], null, // identity index + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["int32", "string", "float32", "colors"]) ); test("all rows, one column", () => { + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message const dfA = sourceDf.subset(null, ["colors"]); expect(dfA).toBeDefined(); expect(dfA.dims).toEqual([3, 1]); @@ -158,6 +162,7 @@ describe("dataframe subsetting", () => { }); test("all rows, two columns", () => { + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message const dfB = sourceDf.subset(null, ["float32", "colors"]); expect(dfB).toBeDefined(); expect(dfB.dims).toEqual([3, 2]); @@ -227,6 +232,7 @@ describe("dataframe subsetting", () => { }); test("two rows, two colums", () => { + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message const dfF = sourceDf.subset([0, 2], ["int32", "float32"]); expect(dfF).toBeDefined(); expect(dfF.dims).toEqual([2, 2]); @@ -236,6 +242,7 @@ describe("dataframe subsetting", () => { expect(dfF.colIndex.labels()).toEqual(["int32", "float32"]); // reverse the row and column order + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message const dfFr = sourceDf.subset([2, 0], ["float32", "int32"]); expect(dfFr).toBeDefined(); expect(dfFr.dims).toEqual([2, 2]); @@ -248,6 +255,7 @@ describe("dataframe subsetting", () => { test("withRowIndex", () => { const df = sourceDf.subset( null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message ["int32", "float32"], new Dataframe.DenseInt32Index([3, 2, 1]) ); @@ -258,12 +266,15 @@ describe("dataframe subsetting", () => { test("withRowIndex error checks", () => { expect(() => + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message sourceDf.subset(null, ["red"], new Dataframe.IdentityInt32Index(1)) ).toThrow(RangeError); expect(() => + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message sourceDf.subset(null, ["red"], new Dataframe.DenseInt32Index([0, 1])) ).toThrow(RangeError); expect(() => + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message sourceDf.subset(null, ["red"], new Dataframe.KeyIndex([0, 1, 2, 3])) ).toThrow(RangeError); }); @@ -278,12 +289,14 @@ describe("dataframe subsetting", () => { new Float32Array([4.4, 5.5, 6.6]), ["red", "green", "blue"], ], + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message new Dataframe.DenseInt32Index([2, 4, 6]), new Dataframe.KeyIndex(["int32", "string", "float32", "colors"]) ); const dfA = sourceDf.isubsetMask( new Uint8Array([0, 1, 1]), + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'Uint8Array' is not assignable to... Remove this comment to see the full error message new Uint8Array([1, 0, 0, 1]) ); expect(dfA.dims).toEqual([2, 2]); @@ -303,6 +316,7 @@ describe("dataframe subsetting", () => { ["red", "green", "blue"], ], null, // identity index + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["int32", "string", "float32", "colors"]) ); @@ -316,6 +330,7 @@ describe("dataframe subsetting", () => { }); test("all rows, two cols", () => { + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number[]' is not assignable to p... Remove this comment to see the full error message const dfA = sourceDf.isubset(null, [1, 2]); expect(dfA.dims).toEqual([3, 2]); expect(dfA.icol(0).asArray()).toEqual(["A", "B", "C"]); @@ -361,6 +376,7 @@ describe("dataframe factories", () => { const dfA = new Dataframe.Dataframe( [3, 2], [new Int32Array([0, 1, 2]), new Int32Array([3, 4, 5])], + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message new Dataframe.DenseInt32Index([2, 1, 0]), new Dataframe.KeyIndex(["A", "B"]) ); @@ -385,6 +401,7 @@ describe("dataframe factories", () => { [true, false], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colors", "bools"]) ); const dfA = df.withCol("numbers", [1, 0]); @@ -408,6 +425,7 @@ describe("dataframe factories", () => { [true, false], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message new Dataframe.DenseInt32Index([74, 75]) ); const dfA = df.withCol(72, [1, 0]); @@ -433,6 +451,7 @@ describe("dataframe factories", () => { [true, false], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message new Dataframe.DenseInt32Index([74, 75]) ); const dfA = df.withCol(999, [1, 0]); @@ -541,6 +560,7 @@ describe("dataframe factories", () => { [1, 0], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colors", "bools", "numbers"]) ); @@ -549,11 +569,14 @@ describe("dataframe factories", () => { [3, 1], [["red", "blue", "green"]], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colorsA"]) ); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. expect(() => dfA.withColsFrom(dfB)).toThrow(RangeError); /* duplicate labels should throw an error */ + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. expect(() => dfA.withColsFrom(dfA)).toThrow(Error); }); @@ -564,15 +587,18 @@ describe("dataframe factories", () => { [2, 1], [["red", "blue"]], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colors"]) ); const dfB = new Dataframe.Dataframe( [2, 1], [[true, false]], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["bools"]) ); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. const dfLikeA = dfEmpty.withColsFrom(dfA); expect(dfLikeA).toBeDefined(); expect(dfLikeA.dims).toEqual(dfA.dims); @@ -581,6 +607,7 @@ describe("dataframe factories", () => { expect(dfLikeA.rowIndex.labels()).toEqual(dfA.rowIndex.labels()); expect(dfLikeA.icol(0).asArray()).toEqual(dfA.icol(0).asArray()); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. const dfAlsoLikeA = dfA.withColsFrom(dfEmpty); expect(dfAlsoLikeA).toBeDefined(); expect(dfAlsoLikeA.dims).toEqual(dfA.dims); @@ -589,6 +616,7 @@ describe("dataframe factories", () => { expect(dfAlsoLikeA.rowIndex.labels()).toEqual(dfA.rowIndex.labels()); expect(dfAlsoLikeA.icol(0).asArray()).toEqual(dfA.icol(0).asArray()); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. const dfC = dfA.withColsFrom(dfB); expect(dfC).toBeDefined(); expect(dfC.dims).toEqual([2, 2]); @@ -605,6 +633,7 @@ describe("dataframe factories", () => { [2, 1], [["red", "blue"]], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colors"]) ); const dfB = new Dataframe.Dataframe( @@ -615,6 +644,7 @@ describe("dataframe factories", () => { [1, 0], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colors", "bools", "numbers"]) ); @@ -647,6 +677,7 @@ describe("dataframe factories", () => { [2, 1], [["red", "blue"]], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colors"]) ); const dfB = new Dataframe.Dataframe( @@ -657,6 +688,7 @@ describe("dataframe factories", () => { [1, 0], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colors", "bools", "numbers"]) ); @@ -680,6 +712,7 @@ describe("dataframe factories", () => { [1, 0], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["colors", "bools", "numbers"]) ); const dfA = df.dropCol("colors"); @@ -751,6 +784,7 @@ describe("dataframe factories", () => { [1, 0], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'DenseInt32Index' is not assignab... Remove this comment to see the full error message new Dataframe.DenseInt32Index([102, 101, 100]) ); const dfA = df.dropCol(101); @@ -777,7 +811,8 @@ describe("dataframe factories", () => { new Float64Array(3).fill(1.1), ] ); - const dfB = dfA.mapColumns((col, idx) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const dfB = dfA.mapColumns((col: any, idx: any) => { expect(dfA.icol(idx).asArray()).toBe(col); return col; }); @@ -793,9 +828,7 @@ describe("dataframe factories", () => { [3, 3], [new Array(3).fill(0), new Array(3).fill(0), new Array(3).fill(0)] ); - const dfB = dfA.mapColumns(() => { - return new Array(3).fill(1); - }); + const dfB = dfA.mapColumns(() => new Array(3).fill(1)); expect(dfA).not.toBe(dfB); expect(dfB.iat(0, 0)).toEqual(1); expect(dfB.iat(0, 1)).toEqual(1); @@ -822,6 +855,7 @@ describe("dataframe factories", () => { [1, 0], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["A", "B"]) ); const dfB = dfA.renameCol("B", "C"); @@ -834,7 +868,8 @@ describe("dataframe factories", () => { }); describe("dataframe col", () => { - let df = null; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let df: any = null; beforeEach(() => { df = new Dataframe.Dataframe( [2, 2], @@ -843,6 +878,7 @@ describe("dataframe col", () => { [1, 0], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["A", "B"]) ); }); @@ -1195,6 +1231,7 @@ describe("label indexing", () => { test("create", () => { expect(Dataframe.isLabelIndex(idx)).toBeTruthy(); expect(() => new Dataframe.KeyIndex(["dup", "dup"])).toThrow(Error); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. expect(new Dataframe.KeyIndex().size()).toEqual(0); }); @@ -1367,6 +1404,7 @@ describe("corner cases", () => { [1, 0], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["A", "B"]) ); diff --git a/client/__tests__/util/dataframe/histogram.test.js b/client/__tests__/util/dataframe/histogram.test.ts similarity index 81% rename from client/__tests__/util/dataframe/histogram.test.js rename to client/__tests__/util/dataframe/histogram.test.ts index ce4c4943..2de3edfc 100644 --- a/client/__tests__/util/dataframe/histogram.test.js +++ b/client/__tests__/util/dataframe/histogram.test.ts @@ -6,6 +6,7 @@ describe("Dataframe column histogram", () => { [3, 3], [["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["name", "cat", "value"]) ); @@ -26,6 +27,7 @@ describe("Dataframe column histogram", () => { [3, 3], [["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["name", "cat", "value"]) ); @@ -48,6 +50,7 @@ describe("Dataframe column histogram", () => { [3, 3], [["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["name", "cat", "value"]) ); @@ -68,6 +71,7 @@ describe("Dataframe column histogram", () => { [3, 3], [["n1", "n2", "n3"], ["c1", "c2", "c3"], new Int32Array([0, 1, 2])], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["name", "cat", "value"]) ); diff --git a/client/__tests__/util/dataframe/summarize.test.js b/client/__tests__/util/dataframe/summarize.test.ts similarity index 89% rename from client/__tests__/util/dataframe/summarize.test.js rename to client/__tests__/util/dataframe/summarize.test.ts index ec98d7be..4a3dfed0 100644 --- a/client/__tests__/util/dataframe/summarize.test.js +++ b/client/__tests__/util/dataframe/summarize.test.ts @@ -1,6 +1,7 @@ import * as Dataframe from "../../../src/util/dataframe"; -function float32Conversion(f) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function float32Conversion(f: any) { return new Float32Array([f])[0]; } @@ -30,6 +31,7 @@ describe("Dataframe column summary", () => { [1], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex([ "name", "nameString", @@ -106,6 +108,7 @@ describe("Dataframe column summary", () => { [1, false, "0"], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex([ "name", "nameString", @@ -174,6 +177,7 @@ describe("Dataframe column summary", () => { expect.objectContaining({ categorical: true, categories: expect.arrayContaining([1, false, "0"]), + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. categoryCounts: new Map([ [1, 1], [false, 1], @@ -201,6 +205,7 @@ describe("Dataframe column summary", () => { [1, false, "0", "0"], ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex([ "name", "nameString", @@ -269,6 +274,7 @@ describe("Dataframe column summary", () => { expect.objectContaining({ categorical: true, categories: expect.arrayContaining([1, false, "0"]), + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. categoryCounts: new Map([ [1, 1], [false, 1], diff --git a/client/__tests__/util/nameCreators.test.js b/client/__tests__/util/nameCreators.test.ts similarity index 100% rename from client/__tests__/util/nameCreators.test.js rename to client/__tests__/util/nameCreators.test.ts diff --git a/client/__tests__/util/promiseLimit.test.js b/client/__tests__/util/promiseLimit.test.ts similarity index 85% rename from client/__tests__/util/promiseLimit.test.js rename to client/__tests__/util/promiseLimit.test.ts index b22ff5b1..897e1366 100644 --- a/client/__tests__/util/promiseLimit.test.js +++ b/client/__tests__/util/promiseLimit.test.ts @@ -1,7 +1,8 @@ import PromiseLimit from "../../src/util/promiseLimit"; import { range } from "../../src/util/range"; -const delay = (t) => new Promise((resolve) => setTimeout(resolve, t)); +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const delay = (t: any) => new Promise((resolve) => setTimeout(resolve, t)); describe("PromiseLimit", () => { test("simple evaluation, concurrency 1", async () => { @@ -51,7 +52,9 @@ describe("PromiseLimit", () => { running -= 1; }; - await Promise.all(range(10).map((i) => plimit.add(() => callback(i)))); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1. + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + await Promise.all(range(10).map((i: any) => plimit.add(() => callback(i)))); expect(maxRunning).toEqual(2); }); diff --git a/client/__tests__/util/quantile.test.js b/client/__tests__/util/quantile.test.ts similarity index 100% rename from client/__tests__/util/quantile.test.js rename to client/__tests__/util/quantile.test.ts diff --git a/client/__tests__/util/range.test.js b/client/__tests__/util/range.test.ts similarity index 73% rename from client/__tests__/util/range.test.js rename to client/__tests__/util/range.test.ts index 5da8821d..b7aa0a66 100644 --- a/client/__tests__/util/range.test.js +++ b/client/__tests__/util/range.test.ts @@ -6,14 +6,20 @@ describe("range", () => { }); test("range(stop)", () => { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1. expect(range(3)).toMatchObject([0, 1, 2]); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1. expect(range(0)).toMatchObject([]); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 1. expect(range(1)).toMatchObject([0]); }); test("range(start,stop)", () => { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2. expect(range(0, 0)).toMatchObject([]); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2. expect(range(0, 2)).toMatchObject([0, 1]); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2. expect(range(4, 8)).toMatchObject([4, 5, 6, 7]); }); diff --git a/client/__tests__/util/stateManager/colorHelpers.test.js b/client/__tests__/util/stateManager/colorHelpers.test.ts similarity index 70% rename from client/__tests__/util/stateManager/colorHelpers.test.js rename to client/__tests__/util/stateManager/colorHelpers.test.ts index 5ac9973c..ec8285fa 100644 --- a/client/__tests__/util/stateManager/colorHelpers.test.js +++ b/client/__tests__/util/stateManager/colorHelpers.test.ts @@ -81,6 +81,7 @@ describe("categorical color helpers", () => { ), ], null, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message new Dataframe.KeyIndex(["continuousColumn", "categoricalColumn"]) ); @@ -95,6 +96,7 @@ describe("categorical color helpers", () => { const data = obsDataframe.col("categoricalColumn").asArray(); const cats = schema.annotations.obsByName.categoricalColumn.categories; for (let i = 0; i < schema.dataframe.nObs; i += 1) { + // @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message expect(makeScale(ct.rgb[i])).toEqual(ct.scale(cats.indexOf(data[i]))); } }); @@ -112,6 +114,7 @@ describe("categorical color helpers", () => { const data = obsDataframe.col("categoricalColumn").asArray(); const cats = schemaClone.annotations.obsByName.categoricalColumn.categories; for (let i = 0; i < schemaClone.dataframe.nObs; i += 1) { + // @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message expect(makeScale(ct.rgb[i])).toEqual(ct.scale(cats.indexOf(data[i]))); } }); @@ -122,7 +125,8 @@ describe("categorical color helpers", () => { Array.from(schema.annotations.obsByName.categoricalColumn.categories) ); const userDefinedColorTable = { - categoricalColumn: shuffleCats.reduce((acc, label) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoricalColumn: shuffleCats.reduce((acc: any, label: any) => { acc[label] = randRGBColor(); return acc; }, {}), @@ -136,12 +140,14 @@ describe("categorical color helpers", () => { "categoricalColumn", obsDataframe, schema, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '{}' is not assignable to paramet... Remove this comment to see the full error message userColors ); expect(ct).toBeDefined(); const data = obsDataframe.col("categoricalColumn").asArray(); for (let i = 0; i < schema.dataframe.nObs; i += 1) { expect(makeScale(ct.rgb[i])).toEqual( + // @ts-expect-error ts-migrate(2722) FIXME: Cannot invoke an object which is possibly 'undefin... Remove this comment to see the full error message ct.scale(cats.indexOf(data[i])).toString() ); } @@ -154,31 +160,38 @@ TODO: 2. user defined colors */ -function indexSchema(schema) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function indexSchema(schema: any) { schema.annotations.obsByName = Object.fromEntries( - schema.annotations?.obs?.columns?.map((v) => [v.name, v]) ?? [] + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.annotations?.obs?.columns?.map((v: any) => [v.name, v]) ?? [] ); schema.annotations.varByName = Object.fromEntries( - schema.annotations?.var?.columns?.map((v) => [v.name, v]) ?? [] + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.annotations?.var?.columns?.map((v: any) => [v.name, v]) ?? [] ); schema.layout.obsByName = Object.fromEntries( - schema.layout?.obs?.map((v) => [v.name, v]) ?? [] + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.layout?.obs?.map((v: any) => [v.name, v]) ?? [] ); schema.layout.varByName = Object.fromEntries( - schema.layout?.var?.map((v) => [v.name, v]) ?? [] + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.layout?.var?.map((v: any) => [v.name, v]) ?? [] ); return schema; } -function makeScale(rgb) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function makeScale(rgb: any) { // make a scale string from a rgb float triple return `rgb(${(rgb[0] * 255) >>> 0}, ${(rgb[1] * 255) >>> 0}, ${ (rgb[2] * 256) >>> 0 })`; } -function shuffle(array) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function shuffle(array: any) { for (let i = array.length - 1; i > 0; i -= 1) { const j = (Math.random() * (i + 1)) >>> 0; [array[i], array[j]] = [array[j], array[i]]; diff --git a/client/__tests__/util/stateManager/controlsHelpers.test.js b/client/__tests__/util/stateManager/controlsHelpers.test.ts similarity index 53% rename from client/__tests__/util/stateManager/controlsHelpers.test.js rename to client/__tests__/util/stateManager/controlsHelpers.test.ts index d4e856ba..1ccb3c0c 100644 --- a/client/__tests__/util/stateManager/controlsHelpers.test.js +++ b/client/__tests__/util/stateManager/controlsHelpers.test.ts @@ -2,7 +2,7 @@ test controls helpers */ // TODO #2227 test: improve test coverage on control helper functions -// (`topNCategories()`, `isSelectableCategoryName()`, `selectableCategoryNames()`, `createCategorySummaryFromDfCol()`, `createCategoricalSelection()`, ) +// (`isSelectableCategoryName()`, `selectableCategoryNames()`, `createCategorySummaryFromDfCol()`, `createCategoricalSelection()`, ) describe("controls helpers", () => { test("placeholder", () => {}); diff --git a/client/__tests__/util/stateManager/fbs.test.js b/client/__tests__/util/stateManager/fbs.test.ts similarity index 87% rename from client/__tests__/util/stateManager/fbs.test.js rename to client/__tests__/util/stateManager/fbs.test.ts index b8bd3742..156dc53f 100644 --- a/client/__tests__/util/stateManager/fbs.test.js +++ b/client/__tests__/util/stateManager/fbs.test.ts @@ -24,6 +24,7 @@ describe("encode/decode", () => { expect(dfA.columns).toEqual(columns); const colIndex = new KeyIndex(["a", "b", "c", "d"]); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message const dfWithColIdx = new Dataframe([3, 4], columns, null, colIndex); const dfB = decodeMatrixFBS(encodeMatrixFBS(dfWithColIdx)); expect([dfB.nRows, dfB.nCols]).toEqual(dfWithColIdx.dims); diff --git a/client/__tests__/util/stateManager/sampleResponses.js b/client/__tests__/util/stateManager/sampleResponses.ts similarity index 82% rename from client/__tests__/util/stateManager/sampleResponses.js rename to client/__tests__/util/stateManager/sampleResponses.ts index 7c54635a..2efd786e 100644 --- a/client/__tests__/util/stateManager/sampleResponses.js +++ b/client/__tests__/util/stateManager/sampleResponses.ts @@ -75,6 +75,7 @@ const aSchemaResponse = { const anAnnotationsObsJSONResponse = { names: ["name", "field1", "field2", "field3", "field4"], + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. data: _() .range(nObs) .map((idx) => [ @@ -91,6 +92,7 @@ const anAnnotationsObsJSONResponse = { const anAnnotationsVarJSONResponse = { names: ["fieldA", "fieldB", "fieldC", "fieldD", "name"], + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. data: _() .range(nVar) .map((idx) => [ @@ -105,8 +107,11 @@ const anAnnotationsVarJSONResponse = { .value(), }; -function encodeTypedArray(builder, uType, uData) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function encodeTypedArray(builder: any, uType: any, uData: any) { + // @ts-expect-error --- FIXME: Element implicitly has an 'any' type. const uTypeName = NetEncoding.TypedArray[uType]; + // @ts-expect-error --- FIXME: Element implicitly has an 'any' type. const ArrayType = NetEncoding[uTypeName]; const dv = ArrayType.createDataVector(builder, uData); builder.startObject(1); @@ -114,7 +119,8 @@ function encodeTypedArray(builder, uType, uData) { return builder.endObject(); } -function encodeMatrix(columns, colIndex = undefined) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function encodeMatrix(columns: any, colIndex = undefined) { /* IMPORTANT: this is not a general purpose encoder. in particular, it doesn't correctly handle all column index types, nor does it @@ -123,6 +129,7 @@ function encodeMatrix(columns, colIndex = undefined) { encodeMatrixFBS in matrix.py is more general. This is used only as a testing santity check (alt implementation). */ + // @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1. const utf8Encoder = new TextEncoder("utf-8"); const builder = new flatbuffers.Builder(1024); const cols = map(columns, (carr) => { @@ -172,11 +179,13 @@ function encodeMatrix(columns, colIndex = undefined) { const anAnnotationsObsFBSResponse = (() => { const columns = zip(...anAnnotationsObsJSONResponse.data).slice(1); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message return encodeMatrix(columns, anAnnotationsObsJSONResponse.names); })(); const anAnnotationsVarFBSResponse = (() => { const columns = zip(...anAnnotationsVarJSONResponse.data).slice(1); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message return encodeMatrix(columns, anAnnotationsVarJSONResponse.names); })(); @@ -185,11 +194,13 @@ const aLayoutFBSResponse = (() => { new Float32Array(nObs).fill(Math.random()), new Float32Array(nObs).fill(Math.random()), ]; + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'string[]' is not assignable to p... Remove this comment to see the full error message return encodeMatrix(coords, ["umap_0", "umap_1"]); })(); const aDataObsResponse = { var: [2, 4, 29], + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. obs: _() .range(nObs) .map((idx) => [idx, Math.random(), Math.random(), Math.random()]) diff --git a/client/__tests__/util/typedCrossfilter/bitArray.test.js b/client/__tests__/util/typedCrossfilter/bitArray.test.ts similarity index 100% rename from client/__tests__/util/typedCrossfilter/bitArray.test.js rename to client/__tests__/util/typedCrossfilter/bitArray.test.ts diff --git a/client/__tests__/util/typedCrossfilter/crossfilter.test.js b/client/__tests__/util/typedCrossfilter/crossfilter.test.ts similarity index 79% rename from client/__tests__/util/typedCrossfilter/crossfilter.test.js rename to client/__tests__/util/typedCrossfilter/crossfilter.test.ts index 58fa60bb..fc6e18bf 100644 --- a/client/__tests__/util/typedCrossfilter/crossfilter.test.js +++ b/client/__tests__/util/typedCrossfilter/crossfilter.test.ts @@ -126,7 +126,8 @@ const someData = [ }, ]; -let payments = null; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +let payments: any = null; beforeEach(() => { payments = new Crossfilter(someData); }); @@ -138,7 +139,13 @@ describe("ImmutableTypedCrossfilter", () => { expect(payments.all()).toEqual(someData); const p = payments - .addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array) + .addDimension( + "quantity", + "scalar", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any, d: any) => d[i].quantity, + Int32Array + ) .select("quantity", { mode: "all" }); expect(p).toBeDefined(); expect(p.all()).toEqual(someData); @@ -158,7 +165,8 @@ describe("ImmutableTypedCrossfilter", () => { const p2 = payments.addDimension( "quantity", "scalar", - (i, data) => data[i].quantity, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any, data: any) => data[i].quantity, Int32Array ); @@ -175,10 +183,22 @@ describe("ImmutableTypedCrossfilter", () => { test("select all and none", () => { let p = payments - .addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array) - .addDimension("tip", "scalar", (i, d) => d[i].tip, Float32Array) - .addDimension("total", "scalar", (i, d) => d[i].total, Float32Array) - .addDimension("type", "enum", (i, d) => d[i].type); + .addDimension( + "quantity", + "scalar", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any, d: any) => d[i].quantity, + Int32Array + ) // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .addDimension("tip", "scalar", (i: any, d: any) => d[i].tip, Float32Array) + .addDimension( + "total", + "scalar", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any, d: any) => d[i].total, + Float32Array + ) // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .addDimension("type", "enum", (i: any, d: any) => d[i].type); expect(p).toBeDefined(); /* expect all records to be selected - default init state */ @@ -230,11 +250,24 @@ describe("ImmutableTypedCrossfilter", () => { }); describe("scalar dimension", () => { - let p; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let p: any; beforeEach(() => { p = payments - .addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array) - .addDimension("tip", "scalar", (i, d) => d[i].tip, Float32Array) + .addDimension( + "quantity", + "scalar", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any, d: any) => d[i].quantity, + Int32Array + ) + .addDimension( + "tip", + "scalar", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any, d: any) => d[i].tip, + Float32Array + ) .select("tip", { mode: "all" }); }); @@ -277,9 +310,11 @@ describe("ImmutableTypedCrossfilter", () => { }); describe("enum dimension", () => { - let p; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let p: any; beforeEach(() => { - p = payments.addDimension("type", "enum", (i, d) => d[i].type); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + p = payments.addDimension("type", "enum", (i: any, d: any) => d[i].type); }); test("all", () => { @@ -317,7 +352,8 @@ describe("ImmutableTypedCrossfilter", () => { }); describe("spatial dimension", () => { - let p; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let p: any; beforeEach(() => { const X = someData.map((r) => r.coords[0]); const Y = someData.map((r) => r.coords[1]); @@ -406,14 +442,22 @@ describe("ImmutableTypedCrossfilter", () => { }); describe("non-finite scalars", () => { - let p; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let p: any; beforeEach(() => { p = payments - .addDimension("quantity", "scalar", (i, d) => d[i].quantity, Int32Array) + .addDimension( + "quantity", + "scalar", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any, d: any) => d[i].quantity, + Int32Array + ) .addDimension( "nonFinite", "scalar", - (i, d) => d[i].nonFinite, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any, d: any) => d[i].nonFinite, Float32Array ) .select("quantity", { mode: "all" }); diff --git a/client/__tests__/util/typedCrossfilter/positiveInterval.test.js b/client/__tests__/util/typedCrossfilter/positiveInterval.test.ts similarity index 100% rename from client/__tests__/util/typedCrossfilter/positiveInterval.test.js rename to client/__tests__/util/typedCrossfilter/positiveInterval.test.ts diff --git a/client/__tests__/util/typedCrossfilter/sort.test.js b/client/__tests__/util/typedCrossfilter/sort.test.ts similarity index 84% rename from client/__tests__/util/typedCrossfilter/sort.test.js rename to client/__tests__/util/typedCrossfilter/sort.test.ts index f7650f4f..21d1affd 100644 --- a/client/__tests__/util/typedCrossfilter/sort.test.js +++ b/client/__tests__/util/typedCrossfilter/sort.test.ts @@ -15,7 +15,8 @@ paths for: const pInf = Number.POSITIVE_INFINITY; const nInf = Number.NEGATIVE_INFINITY; -function fillRange(arr, start = 0) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function fillRange(arr: any, start = 0) { const larr = arr; for (let i = 0, len = larr.length; i < len; i += 1) { larr[i] = i + start; @@ -23,7 +24,8 @@ function fillRange(arr, start = 0) { return larr; } -function fillRand(arr) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function fillRand(arr: any) { for (let i = 0, len = arr.length; i < len; i += 1) { arr[i] = Math.random(); } @@ -48,16 +50,22 @@ describe("sortArray", () => { describe("finite numbers", () => { [Array, Float32Array, Uint32Array, Int32Array, Float64Array].map((Type) => test(Type.name, () => { + // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable. expect(sortArray(Type.from([6, 5, 4, 3, 2, 1, 0]))).toMatchObject( + // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable. Type.from([0, 1, 2, 3, 4, 5, 6]) ); + // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable. expect(sortArray(Type.from([6, 5, 4, 3, 2, 1]))).toMatchObject( + // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable. Type.from([1, 2, 3, 4, 5, 6]) ); const source = fillRand(new Type(1000)); + // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable. expect(sortArray(Type.from(source))).toMatchObject( + // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable. Type.from(source).sort() ); }) @@ -130,22 +138,27 @@ describe("sortIndex", () => { describe("finite numbers", () => { [Array, Float32Array, Uint32Array, Int32Array, Float64Array].map((Type) => test(Type.name, () => { + // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable. const source1 = Type.from([6, 5, 4, 3, 2, 1, 0]); const index1 = fillRange(new Uint32Array(source1.length)); expect(sortIndex(index1, source1)).toMatchObject( - index1.sort((a, b) => source1[a] - source1[b]) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + index1.sort((a: any, b: any) => source1[a] - source1[b]) ); + // @ts-expect-error ts-migrate(2349) FIXME: This expression is not callable. const source2 = Type.from([6, 5, 4, 3, 2, 1]); const index2 = fillRange(new Uint32Array(source2.length)); expect(sortIndex(index2, source2)).toMatchObject( - index2.sort((a, b) => source1[a] - source1[b]) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + index2.sort((a: any, b: any) => source1[a] - source1[b]) ); const source3 = fillRand(new Type(1000)); const index3 = fillRange(new Uint32Array(source3.length)); expect(sortIndex(index3, source3)).toMatchObject( - index3.sort((a, b) => source1[a] - source1[b]) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + index3.sort((a: any, b: any) => source1[a] - source1[b]) ); }) ); diff --git a/client/__tests__/util/typedCrossfilter/util.test.js b/client/__tests__/util/typedCrossfilter/util.test.ts similarity index 100% rename from client/__tests__/util/typedCrossfilter/util.test.js rename to client/__tests__/util/typedCrossfilter/util.test.ts diff --git a/client/configuration/babel/babel.dev.js b/client/configuration/babel/babel.dev.js index 117f6da5..e86290c5 100644 --- a/client/configuration/babel/babel.dev.js +++ b/client/configuration/babel/babel.dev.js @@ -11,11 +11,13 @@ module.exports = { }, ], "@babel/preset-react", + "@babel/preset-typescript", ], plugins: [ "@babel/plugin-proposal-function-bind", ["@babel/plugin-proposal-decorators", { legacy: true }], ["@babel/plugin-proposal-class-properties", { loose: true }], + ["@babel/plugin-proposal-private-methods", { loose: true }], "@babel/plugin-proposal-export-namespace-from", "@babel/plugin-proposal-optional-chaining", "@babel/plugin-proposal-nullish-coalescing-operator", diff --git a/client/configuration/babel/babel.prod.js b/client/configuration/babel/babel.prod.js index 620cd563..d113bc96 100644 --- a/client/configuration/babel/babel.prod.js +++ b/client/configuration/babel/babel.prod.js @@ -10,11 +10,13 @@ module.exports = { }, ], "@babel/preset-react", + "@babel/preset-typescript", ], plugins: [ "@babel/plugin-proposal-function-bind", ["@babel/plugin-proposal-decorators", { legacy: true }], ["@babel/plugin-proposal-class-properties", { loose: true }], + ["@babel/plugin-proposal-private-methods", { loose: true }], "@babel/plugin-proposal-export-namespace-from", "@babel/plugin-transform-react-constant-elements", "@babel/plugin-transform-runtime", diff --git a/client/configuration/eslint/eslint.js b/client/configuration/eslint/eslint.js index 43d98059..a0767384 100644 --- a/client/configuration/eslint/eslint.js +++ b/client/configuration/eslint/eslint.js @@ -1,12 +1,17 @@ +/* eslint-disable @blueprintjs/classes-constants -- we don't import blueprint here */ module.exports = { root: true, - parser: "babel-eslint", + parser: "@typescript-eslint/parser", extends: [ - "airbnb", + "airbnb-typescript", + "plugin:@typescript-eslint/recommended", "plugin:eslint-comments/recommended", "plugin:@blueprintjs/recommended", "plugin:compat/recommended", - "plugin:prettier/recommended", + "plugin:jsx-a11y/recommended", + // (thuang) disable eslint formatting rules, so prettier can do its job + // Do not use `plugin:prettier/recommended` per doc below: + // https://prettier.io/docs/en/integrating-with-linters.html "prettier", ], settings: { @@ -32,18 +37,47 @@ module.exports = { jsx: true, generators: true, }, + project: "./tsconfig.json", }, rules: { "react/jsx-no-target-blank": "off", "eslint-comments/require-description": ["error"], "no-magic-numbers": "off", + "@typescript-eslint/no-magic-numbers": "off", "no-nested-ternary": "off", "func-style": "off", "arrow-parens": "off", "no-use-before-define": "off", + "@typescript-eslint/no-use-before-define": "off", "react/jsx-filename-extension": "off", "comma-dangle": "off", + "@typescript-eslint/comma-dangle": "off", "no-underscore-dangle": "off", + // Override airbnb config to allow leading underscore + // https://github.com/iamturns/eslint-config-airbnb-typescript/blob/master/lib/shared.js#L35 + "@typescript-eslint/naming-convention": [ + "error", + { + selector: "class", + format: ["PascalCase"], + leadingUnderscore: "allow", + }, + { + selector: "function", + format: ["camelCase", "PascalCase"], + leadingUnderscore: "allowSingleOrDouble", + }, + { + selector: "typeLike", + format: ["PascalCase"], + }, + { + selector: "variable", + format: ["camelCase", "PascalCase", "UPPER_CASE"], + leadingUnderscore: "allowSingleOrDouble", + trailingUnderscore: "allowDouble", + }, + ], "implicit-arrow-linebreak": "off", "no-console": "off", "spaced-comment": ["error", "always", { exceptions: ["*"] }], @@ -51,6 +85,7 @@ module.exports = { "object-curly-newline": ["error", { consistent: true }], "react/prop-types": [0], "space-before-function-paren": "off", + "@typescript-eslint/space-before-function-paren": "off", "function-paren-newline": "off", "prefer-destructuring": ["error", { object: true, array: false }], "import/prefer-default-export": "off", @@ -69,9 +104,9 @@ module.exports = { }, overrides: [ { - files: ["**/*.test.js"], + files: ["**/*.test.ts"], env: { - jest: true, // now **/*.test.js files' env has both es6 *and* jest + jest: true, // now **/*.test.ts files' env has both es6 *and* jest }, // Can't extend in overrides: https://github.com/eslint/eslint/issues/8813 // "extends": ["plugin:jest/recommended"] @@ -86,3 +121,4 @@ module.exports = { }, ], }; +/* eslint-enable @blueprintjs/classes-constants -- we don't import blueprint here */ diff --git a/client/configuration/lint-staged/lint-staged.config.js b/client/configuration/lint-staged/lint-staged.config.js index e8a2415d..74d52576 100644 --- a/client/configuration/lint-staged/lint-staged.config.js +++ b/client/configuration/lint-staged/lint-staged.config.js @@ -1,3 +1,4 @@ module.exports = { - "*.js": "eslint --fix", + "*.{js,ts,jsx,tsx}": "eslint --fix", + "**/*": "prettier --write --ignore-unknown", }; diff --git a/client/configuration/webpack/cspHashPlugin.js b/client/configuration/webpack/cspHashPlugin.js index 3b32efc0..99d533b1 100644 --- a/client/configuration/webpack/cspHashPlugin.js +++ b/client/configuration/webpack/cspHashPlugin.js @@ -1,6 +1,10 @@ /* eslint-disable import/no-extraneous-dependencies -- this file is a devDependency*/ +/* eslint-disable @blueprintjs/classes-constants -- we don't import blueprint here */ +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const cheerio = require("cheerio"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const crypto = require("crypto"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const HtmlWebpackPlugin = require("html-webpack-plugin"); const digest = (str) => { @@ -50,4 +54,5 @@ class CspHashPlugin { } module.exports = CspHashPlugin; +/* eslint-enable @blueprintjs/classes-constants -- we don't import blueprint here */ /* eslint-enable import/no-extraneous-dependencies -- enable*/ diff --git a/client/configuration/webpack/obsoleteHTMLTemplate.html b/client/configuration/webpack/obsoleteHTMLTemplate.html index d5ca7df4..2283ad3c 100644 --- a/client/configuration/webpack/obsoleteHTMLTemplate.html +++ b/client/configuration/webpack/obsoleteHTMLTemplate.html @@ -22,7 +22,7 @@ >
-
+
Unsupported Browser
-
+
cellxgene is currently supported on the following browsers
-
+
Chrome > 60
Firefox ≥ 60
Edge ≥ 79
 diff --git a/client/configuration/webpack/webpack.config.dev.js b/client/configuration/webpack/webpack.config.dev.js index 408cb1e0..d4a69b71 100644 --- a/client/configuration/webpack/webpack.config.dev.js +++ b/client/configuration/webpack/webpack.config.dev.js @@ -1,13 +1,23 @@ +/* eslint-disable @blueprintjs/classes-constants -- we don't import blueprint here */ +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const path = require("path"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const webpack = require("webpack"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const HtmlWebpackPlugin = require("html-webpack-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const FaviconsWebpackPlugin = require("favicons-webpack-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const ScriptExtHtmlWebpackPlugin = require("script-ext-html-webpack-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const MiniCssExtractPlugin = require("mini-css-extract-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const { merge } = require("webpack-merge"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const sharedConfig = require("./webpack.config.shared"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const babelOptions = require("../babel/babel.dev"); const fonts = path.resolve("src/fonts"); @@ -23,7 +33,7 @@ const devConfig = { module: { rules: [ { - test: /\.jsx?$/, + test: /\.(ts|js)x?$/, loader: "babel-loader", options: babelOptions, }, @@ -83,3 +93,4 @@ const devConfig = { }; module.exports = merge(sharedConfig, devConfig); +/* eslint-enable @blueprintjs/classes-constants -- we don't import blueprint here */ diff --git a/client/configuration/webpack/webpack.config.prod.js b/client/configuration/webpack/webpack.config.prod.js index f9a63403..9d9192ec 100644 --- a/client/configuration/webpack/webpack.config.prod.js +++ b/client/configuration/webpack/webpack.config.prod.js @@ -1,18 +1,31 @@ +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const path = require("path"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const webpack = require("webpack"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const HtmlWebpackPlugin = require("html-webpack-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const { CleanWebpackPlugin } = require("clean-webpack-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const TerserJSPlugin = require("terser-webpack-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const CleanCss = require("clean-css"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const OptimizeCSSAssetsPlugin = require("optimize-css-assets-webpack-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const FaviconsWebpackPlugin = require("favicons-webpack-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const MiniCssExtractPlugin = require("mini-css-extract-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const { merge } = require("webpack-merge"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const babelOptions = require("../babel/babel.prod"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const CspHashPlugin = require("./cspHashPlugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const sharedConfig = require("./webpack.config.shared"); const fonts = path.resolve("src/fonts"); @@ -38,7 +51,7 @@ const prodConfig = { module: { rules: [ { - test: /\.jsx?$/, + test: /\.(ts|js)x?$/, loader: "babel-loader", options: babelOptions, }, diff --git a/client/configuration/webpack/webpack.config.shared.js b/client/configuration/webpack/webpack.config.shared.js index 0f98b59d..282d1220 100644 --- a/client/configuration/webpack/webpack.config.shared.js +++ b/client/configuration/webpack/webpack.config.shared.js @@ -1,8 +1,13 @@ +/* eslint-disable @blueprintjs/classes-constants -- we don't import blueprint here */ +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const path = require("path"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const fs = require("fs"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const MiniCssExtractPlugin = require("mini-css-extract-plugin"); +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const ObsoleteWebpackPlugin = require("obsolete-webpack-plugin"); -// eslint-disable-next-line @blueprintjs/classes-constants -- incorrect match +// eslint-disable-next-line @typescript-eslint/no-var-requires --- FIXME: disabled temporarily on migrate to TS. const ScriptExtHtmlWebpackPlugin = require("script-ext-html-webpack-plugin"); const src = path.resolve("src"); @@ -29,6 +34,9 @@ module.exports = { path: path.resolve("build"), publicPath, }, + resolve: { + extensions: [".ts", ".tsx", "..."], + }, module: { rules: [ { @@ -72,3 +80,4 @@ module.exports = { }), ], }; +/* eslint-enable @blueprintjs/classes-constants -- we don't import blueprint here */ diff --git a/client/package-lock.json b/client/package-lock.json index c61504e8..de350e24 100644 --- a/client/package-lock.json +++ b/client/package-lock.json @@ -35,11 +35,9 @@ "react": "^17.0.2", "react-async": "^10.0.1", "react-dom": "^17.0.2", - "react-easy-emoji": "^1.4.0", "react-flip-toolkit": "^7.0.12", "react-helmet": "^6.1.0", "react-icons": "^4.2.0", - "react-popper": "^2.2.4", "react-redux": "^7.2.0", "redux": "^4.0.5", "redux-thunk": "^2.3.0", @@ -61,10 +59,38 @@ "@babel/plugin-transform-runtime": "^7.13.15", "@babel/preset-env": "^7.13.15", "@babel/preset-react": "^7.13.13", + "@babel/preset-typescript": "^7.14.5", "@babel/register": "^7.13.16", "@babel/runtime": "^7.13.16", "@blueprintjs/eslint-plugin": "^0.3.0", "@sentry/webpack-plugin": "^1.15.0", + "@types/d3": "^7.0.0", + "@types/d3-scale-chromatic": "^3.0.0", + "@types/expect-puppeteer": "^4.4.6", + "@types/flatbuffers": "^1.10.0", + "@types/is-number": "^7.0.1", + "@types/jest": "^26.0.24", + "@types/jest-environment-puppeteer": "^4.4.1", + "@types/lodash.clonedeep": "^4.5.6", + "@types/lodash.difference": "^4.5.6", + "@types/lodash.every": "^4.6.6", + "@types/lodash.filter": "^4.6.6", + "@types/lodash.foreach": "^4.5.6", + "@types/lodash.isnumber": "^3.0.6", + "@types/lodash.map": "^4.6.13", + "@types/lodash.pull": "^4.1.6", + "@types/lodash.sortby": "^4.7.6", + "@types/lodash.uniq": "^4.5.6", + "@types/lodash.zip": "^4.2.6", + "@types/pako": "^1.0.2", + "@types/puppeteer": "^5.4.4", + "@types/react": "^17.0.14", + "@types/react-dom": "^17.0.9", + "@types/react-helmet": "^6.1.2", + "@types/react-redux": "^7.1.18", + "@types/sha1": "^1.1.3", + "@typescript-eslint/eslint-plugin": "^4.28.4", + "@typescript-eslint/parser": "^4.28.4", "babel-eslint": "^10.1.0", "babel-jest": "^26.1.0", "babel-loader": "^8.1.0", @@ -74,10 +100,9 @@ "clean-css": "^5.1.2", "clean-webpack-plugin": "^4.0.0-alpha.0", "codecov": "^3.7.1", - "connect-history-api-fallback": "^1.6.0", "css-loader": "^5.2.4", "eslint": "^7.24.0", - "eslint-config-airbnb": "^18.2.0", + "eslint-config-airbnb-typescript": "^12.3.1", "eslint-config-prettier": "^8.2.0", "eslint-loader": "^4.0.2", "eslint-plugin-compat": "^3.8.0", @@ -86,12 +111,11 @@ "eslint-plugin-import": "^2.22.0", "eslint-plugin-jest": "^24.3.5", "eslint-plugin-jsx-a11y": "^6.3.1", - "eslint-plugin-prettier": "^3.4.0", "eslint-plugin-react": "^7.23.2", "eslint-plugin-react-hooks": "^4.0.8", "expect-puppeteer": "^5.0.0", "express": "^4.17.1", - "favicons": "^6.2.1", + "favicons": "^6.2.2", "favicons-webpack-plugin": "^5.0.2", "file-loader": "^6.0.0", "html-webpack-plugin": "^5.3.1", @@ -117,10 +141,8 @@ "rimraf": "^3.0.2", "script-ext-html-webpack-plugin": "^2.1.4", "serve-favicon": "^2.5.0", - "style-loader": "^2.0.0", - "sw-precache-webpack-plugin": "^1.0.0", "terser-webpack-plugin": "^5.1.1", - "url-loader": "^4.1.0", + "typescript": "^4.3.5", "webpack": "^5.34.0", "webpack-cli": "^4.6.0", "webpack-dev-middleware": "^4.1.0", @@ -144,9 +166,9 @@ "integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==" }, "node_modules/@aws-crypto/sha256-browser": { - "version": "1.1.0", - "resolved": "https://registry.npmjs.org/@aws-crypto/sha256-browser/-/sha256-browser-1.1.0.tgz", - "integrity": "sha512-VIpuLRDonMAHgomrsm/zKbeXTnxpr4aHDQmS4pF+NcpvBp64l675yjGA9hyUYs/QJwBjUl8WqMjh9tIRgi85Sg==", + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/@aws-crypto/sha256-browser/-/sha256-browser-1.1.1.tgz", + "integrity": "sha512-nS4vdan97It6HcweV58WXtjPbPSc0JXd3sAwlw3Ou5Mc3WllSycAS32Tv2LRn8butNQoU9AE3jEQAOgiMdNC1Q==", "dependencies": { "@aws-crypto/ie11-detection": "^1.0.0", "@aws-crypto/sha256-js": "^1.1.0", @@ -191,58 +213,53 @@ "integrity": "sha512-Xni35NKzjgMrwevysHTCArtLDpPvye8zV/0E4EyYn43P7/7qvQwPh9BGkHewbMulVntbigmcT7rdX3BNo9wRJg==" }, "node_modules/@aws-sdk/abort-controller": { - "version": "3.12.0", - "resolved": "https://registry.npmjs.org/@aws-sdk/abort-controller/-/abort-controller-3.12.0.tgz", - "integrity": "sha512-oJcxAgtXWueed9j9UF59ytc/5zbq+pMEN85bJGUI8a0abZe/4Li54CsU2AQph1oijyHk9FQ3VtBkjripXBEaag==", + "version": "3.23.0", + "resolved": "https://registry.npmjs.org/@aws-sdk/abort-controller/-/abort-controller-3.23.0.tgz", + "integrity": "sha512-M69Sdoi6TH2UrnXKKNJNDaW6iCqpras7w274CZq4NjFOGwrb23KO2Aexgxr3g3hsUidfjuA38oFbHgC8odFrIQ==", "dependencies": { - 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"sha512-kQ/dHIzuLrS6Je9+uv81ueZomEwH0qVYstcAQ4/Z93K8zeko9gtAbttJWzoC5ukqXY1PpoouV3+VSOqEAFt5wg==", + "dev": true, + "requires": {} }, "xhr": { "version": "2.6.0", @@ -40163,42 +42231,6 @@ "which-module": "^2.0.0", "y18n": "^4.0.0", "yargs-parser": "^18.1.2" - }, - "dependencies": { - "find-up": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/find-up/-/find-up-4.1.0.tgz", - "integrity": "sha512-PpOwAdQ/YlXQ2vj8a3h8IipDuYRi3wceVQQGYWxNINccq40Anw7BlsEXCMbt1Zt+OLA6Fq9suIpIWD0OsnISlw==", - "dev": true, - "requires": { - "locate-path": "^5.0.0", - "path-exists": "^4.0.0" - } - }, - "locate-path": { - "version": "5.0.0", - "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-5.0.0.tgz", - "integrity": "sha512-t7hw9pI+WvuwNJXwk5zVHpyhIqzg2qTlklJOf0mVxGSbe3Fp2VieZcduNYjaLDoy6p9uGpQEGWG87WpMKlNq8g==", - "dev": true, - "requires": { - "p-locate": "^4.1.0" - } - }, - "p-locate": { - "version": "4.1.0", - "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-4.1.0.tgz", - "integrity": "sha512-R79ZZ/0wAxKGu3oYMlz8jy/kbhsNrS7SKZ7PxEHBgJ5+F2mtFW2fK2cOtBh1cHYkQsbzFV7I+EoRKe6Yt0oK7A==", - "dev": true, - "requires": { - "p-limit": "^2.2.0" - } - }, - "path-exists": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz", - "integrity": "sha512-ak9Qy5Q7jYb2Wwcey5Fpvg2KoAc/ZIhLSLOSBmRmygPsGwkVVt0fZa0qrtMz+m6tJTAHfZQ8FnmB4MG4LWy7/w==", - "dev": true - } } }, "yargs-parser": { diff --git a/client/package.json b/client/package.json index 11b7d5fe..073e5a97 100644 --- a/client/package.json +++ b/client/package.json @@ -8,9 +8,9 @@ "build": "npm run clean && webpack --config", "clean": "rimraf build", "dev": "npm run build -- configuration/webpack/webpack.config.dev.js", - "e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js", - "e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.js", - "e2e-prod": "CXG_URL_BASE='https://cellxgene.cziscience.com/d/pbmc3k.cxg/' jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js", + "e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.ts", + "e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.ts", + "e2e-prod": "CXG_URL_BASE='https://cellxgene.cziscience.com/d/pbmc3k.cxg/' jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.ts", "fmt": "eslint --fix src __tests__", "lint": "eslint --fix src __tests__", "prod": "npm run build -- configuration/webpack/webpack.config.prod.js", @@ -64,11 +64,9 @@ "react": "^17.0.2", "react-async": "^10.0.1", "react-dom": "^17.0.2", - "react-easy-emoji": "^1.4.0", "react-flip-toolkit": "^7.0.12", "react-helmet": "^6.1.0", "react-icons": "^4.2.0", - "react-popper": "^2.2.4", "react-redux": "^7.2.0", "redux": "^4.0.5", "redux-thunk": "^2.3.0", @@ -90,10 +88,38 @@ "@babel/plugin-transform-runtime": "^7.13.15", "@babel/preset-env": "^7.13.15", "@babel/preset-react": "^7.13.13", + "@babel/preset-typescript": "^7.14.5", "@babel/register": "^7.13.16", "@babel/runtime": "^7.13.16", "@blueprintjs/eslint-plugin": "^0.3.0", "@sentry/webpack-plugin": "^1.15.0", + "@types/d3": "^7.0.0", + "@types/d3-scale-chromatic": "^3.0.0", + "@types/expect-puppeteer": "^4.4.6", + "@types/flatbuffers": "^1.10.0", + "@types/is-number": "^7.0.1", + "@types/jest": "^26.0.24", + "@types/jest-environment-puppeteer": "^4.4.1", + "@types/lodash.clonedeep": "^4.5.6", + "@types/lodash.difference": "^4.5.6", + "@types/lodash.every": "^4.6.6", + "@types/lodash.filter": "^4.6.6", + "@types/lodash.foreach": "^4.5.6", + "@types/lodash.isnumber": "^3.0.6", + "@types/lodash.map": "^4.6.13", + "@types/lodash.pull": "^4.1.6", + "@types/lodash.sortby": "^4.7.6", + "@types/lodash.uniq": "^4.5.6", + "@types/lodash.zip": "^4.2.6", + "@types/pako": "^1.0.2", + "@types/puppeteer": "^5.4.4", + "@types/react": "^17.0.14", + "@types/react-dom": "^17.0.9", + "@types/react-helmet": "^6.1.2", + "@types/react-redux": "^7.1.18", + "@types/sha1": "^1.1.3", + "@typescript-eslint/eslint-plugin": "^4.28.4", + "@typescript-eslint/parser": "^4.28.4", "babel-eslint": "^10.1.0", "babel-jest": "^26.1.0", "babel-loader": "^8.1.0", @@ -103,10 +129,9 @@ "clean-css": "^5.1.2", "clean-webpack-plugin": "^4.0.0-alpha.0", "codecov": "^3.7.1", - "connect-history-api-fallback": "^1.6.0", "css-loader": "^5.2.4", "eslint": "^7.24.0", - "eslint-config-airbnb": "^18.2.0", + "eslint-config-airbnb-typescript": "^12.3.1", "eslint-config-prettier": "^8.2.0", "eslint-loader": "^4.0.2", "eslint-plugin-compat": "^3.8.0", @@ -115,12 +140,11 @@ "eslint-plugin-import": "^2.22.0", "eslint-plugin-jest": "^24.3.5", "eslint-plugin-jsx-a11y": "^6.3.1", - "eslint-plugin-prettier": "^3.4.0", "eslint-plugin-react": "^7.23.2", "eslint-plugin-react-hooks": "^4.0.8", "expect-puppeteer": "^5.0.0", "express": "^4.17.1", - "favicons": "^6.2.1", + "favicons": "^6.2.2", "favicons-webpack-plugin": "^5.0.2", "file-loader": "^6.0.0", "html-webpack-plugin": "^5.3.1", @@ -146,10 +170,8 @@ "rimraf": "^3.0.2", "script-ext-html-webpack-plugin": "^2.1.4", "serve-favicon": "^2.5.0", - "style-loader": "^2.0.0", - "sw-precache-webpack-plugin": "^1.0.0", "terser-webpack-plugin": "^5.1.1", - "url-loader": "^4.1.0", + "typescript": "^4.3.5", "webpack": "^5.34.0", "webpack-cli": "^4.6.0", "webpack-dev-middleware": "^4.1.0", @@ -157,10 +179,10 @@ }, "jest": { "testMatch": [ - "**/__tests__/**/?(*.)(spec|test).js?(x)" + "**/__tests__/**/?(*.)(spec|test).ts?(x)" ], "setupFiles": [ - "./__tests__/setupMissingGlobals.js" + "./__tests__/setupMissingGlobals.ts" ], "coverageDirectory": "./coverage/", "collectCoverage": true @@ -170,7 +192,8 @@ "test": { "presets": [ "@babel/preset-env", - "@babel/preset-react" + "@babel/preset-react", + "@babel/preset-typescript" ], "plugins": [ "@babel/plugin-proposal-function-bind", @@ -186,6 +209,12 @@ "loose": true } ], + [ + "@babel/plugin-proposal-private-methods", + { + "loose": true + } + ], "@babel/plugin-proposal-export-namespace-from", "@babel/plugin-transform-react-constant-elements", "@babel/plugin-transform-runtime", diff --git a/client/src/actions/annotation.js b/client/src/actions/annotation.ts similarity index 64% rename from client/src/actions/annotation.js rename to client/src/actions/annotation.ts index 4b7ca9bf..df1406d1 100644 --- a/client/src/actions/annotation.js +++ b/client/src/actions/annotation.ts @@ -9,9 +9,12 @@ import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager"; const { isUserAnnotation } = AnnotationsHelpers; export const annotationCreateCategoryAction = ( - newCategoryName, - categoryToDuplicate -) => async (dispatch, getState) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + newCategoryName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryToDuplicate: any + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { /* Add a new user-created category to the obs annotations. @@ -89,9 +92,12 @@ export const annotationCreateCategoryAction = ( }; export const annotationRenameCategoryAction = ( - oldCategoryName, - newCategoryName -) => (dispatch, getState) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + oldCategoryName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + newCategoryName: any + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => (dispatch: any, getState: any) => { /* Rename a user-created annotation category */ @@ -124,9 +130,12 @@ export const annotationRenameCategoryAction = ( }); }; -export const annotationDeleteCategoryAction = (categoryName) => ( - dispatch, - getState +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const annotationDeleteCategoryAction = (categoryName: any) => ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any ) => { /* Delete a user-created category @@ -149,10 +158,13 @@ export const annotationDeleteCategoryAction = (categoryName) => ( }; export const annotationCreateLabelInCategory = ( - categoryName, - labelName, - assignSelected -) => async (dispatch, getState) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + labelName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + assignSelected: any // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { /* Add a new label to a user-defined category. If assignSelected is true, assign the label to all currently selected cells. @@ -188,9 +200,11 @@ export const annotationCreateLabelInCategory = ( }; export const annotationDeleteLabelFromCategory = ( - categoryName, - labelName -) => async (dispatch, getState) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + labelName: any // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { /* delete a label from a user-defined category */ @@ -218,10 +232,14 @@ export const annotationDeleteLabelFromCategory = ( }; export const annotationRenameLabelInCategory = ( - categoryName, - oldLabelName, - newLabelName -) => async (dispatch, getState) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + oldLabelName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + newLabelName: any + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { /* label name change */ @@ -255,9 +273,12 @@ export const annotationRenameLabelInCategory = ( }; export const annotationLabelCurrentSelection = ( - categoryName, - labelName -) => async (dispatch, getState) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryName: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + labelName: any + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { /* set the label on all currently selected */ @@ -284,13 +305,24 @@ export const annotationLabelCurrentSelection = ( }); }; -function writableAnnotations(annoMatrix) { - return annoMatrix.schema.annotations.obs.columns - .filter((s) => s.writable) - .map((s) => s.name); +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function writableAnnotations(annoMatrix: any) { + return ( + annoMatrix.schema.annotations.obs.columns + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .filter((s: any) => s.writable) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .map((s: any) => s.name) + ); } -export const needToSaveObsAnnotations = (annoMatrix, lastSavedAnnoMatrix) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export const needToSaveObsAnnotations = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + annoMatrix: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + lastSavedAnnoMatrix: any +) => { /* Return true if there are LIKELY user-defined annotation modifications between the two annoMatrices. Technically not an action creator, but intimately intertwined @@ -314,11 +346,18 @@ export const needToSaveObsAnnotations = (annoMatrix, lastSavedAnnoMatrix) => { // no schema changes; check for change in contents return currentWritable.some( - (col) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (col: any) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col) ); }; -export const saveObsAnnotationsAction = () => async (dispatch, getState) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export const saveObsAnnotationsAction = () => async ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any +) => { /* Save the user-created obs annotations IF any have changed. */ @@ -388,7 +427,13 @@ export const saveObsAnnotationsAction = () => async (dispatch, getState) => { } }; -export const saveGenesetsAction = () => async (dispatch, getState) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export const saveGenesetsAction = () => async ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any +) => { const state = getState(); // bail if gene sets not available, or in readonly mode. @@ -465,7 +510,7 @@ export const saveGenesetsAction = () => async (dispatch, getState) => { res, }); } - return Promise.all([ + return await Promise.all([ dispatch({ type: "autosave: genesets complete", lastSavedGenesets: genesets, diff --git a/client/src/actions/embedding.js b/client/src/actions/embedding.js deleted file mode 100644 index a4494dbd..00000000 --- a/client/src/actions/embedding.js +++ /dev/null @@ -1,51 +0,0 @@ -/* -action creators related to embeddings choice -*/ - -import { AnnoMatrixObsCrossfilter } from "../annoMatrix"; -import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers"; - -export async function _switchEmbedding( - prevAnnoMatrix, - prevCrossfilter, - newEmbeddingName -) { - /* - DRY helper used by embedding action creators - */ - const base = prevAnnoMatrix.base(); - const embeddingDf = await base.fetch("emb", newEmbeddingName); - const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf); - const obsCrossfilter = await new AnnoMatrixObsCrossfilter( - annoMatrix, - prevCrossfilter.obsCrossfilter - ).select("emb", newEmbeddingName, { - mode: "all", - }); - return [annoMatrix, obsCrossfilter]; -} - -export const layoutChoiceAction = (newLayoutChoice) => async ( - dispatch, - getState -) => { - /* - On layout choice, make sure we have selected all on the previous layout, AND the new - layout. - */ - const { - annoMatrix: prevAnnoMatrix, - obsCrossfilter: prevCrossfilter, - } = getState(); - const [annoMatrix, obsCrossfilter] = await _switchEmbedding( - prevAnnoMatrix, - prevCrossfilter, - newLayoutChoice - ); - dispatch({ - type: "set layout choice", - layoutChoice: newLayoutChoice, - obsCrossfilter, - annoMatrix, - }); -}; diff --git a/client/src/actions/embedding.ts b/client/src/actions/embedding.ts new file mode 100644 index 00000000..fa4835e6 --- /dev/null +++ b/client/src/actions/embedding.ts @@ -0,0 +1,58 @@ +/* +action creators related to embeddings choice +*/ + +import { AnnoMatrixObsCrossfilter } from "../annoMatrix"; +import { _setEmbeddingSubset } from "../util/stateManager/viewStackHelpers"; + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export async function _switchEmbedding( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + prevAnnoMatrix: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + prevCrossfilter: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + newEmbeddingName: any +) { + /* + DRY helper used by embedding action creators + */ + const base = prevAnnoMatrix.base(); + const embeddingDf = await base.fetch("emb", newEmbeddingName); + const annoMatrix = _setEmbeddingSubset(prevAnnoMatrix, embeddingDf); + const obsCrossfilter = await new AnnoMatrixObsCrossfilter( + annoMatrix, + prevCrossfilter.obsCrossfilter + ).select("emb", newEmbeddingName, { + mode: "all", + }); + return [annoMatrix, obsCrossfilter]; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const layoutChoiceAction = (newLayoutChoice: any) => async ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any +) => { + /* + On layout choice, make sure we have selected all on the previous layout, AND the new + layout. + */ + const { + annoMatrix: prevAnnoMatrix, + obsCrossfilter: prevCrossfilter, + } = getState(); + const [annoMatrix, obsCrossfilter] = await _switchEmbedding( + prevAnnoMatrix, + prevCrossfilter, + newLayoutChoice + ); + dispatch({ + type: "set layout choice", + layoutChoice: newLayoutChoice, + obsCrossfilter, + annoMatrix, + }); +}; diff --git a/client/src/actions/geneset.js b/client/src/actions/geneset.ts similarity index 50% rename from client/src/actions/geneset.js rename to client/src/actions/geneset.ts index 49b2cf56..7e8f8ff8 100644 --- a/client/src/actions/geneset.js +++ b/client/src/actions/geneset.ts @@ -21,7 +21,13 @@ The behavior manifest in these action creators: Note that crossfilter indices are lazy created, as needed. */ -export const genesetDelete = (genesetName) => (dispatch, getState) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const genesetDelete = (genesetName: any) => ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any +) => { const state = getState(); const { genesets } = state; const gs = genesets?.genesets?.get(genesetName) ?? {}; @@ -40,9 +46,12 @@ export const genesetDelete = (genesetName) => (dispatch, getState) => { }); }; -export const genesetAddGenes = (genesetName, genes) => async ( - dispatch, - getState +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const genesetAddGenes = (genesetName: any, genes: any) => async ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any ) => { const state = getState(); const { obsCrossfilter: prevObsCrossfilter, annoMatrix } = state; @@ -50,7 +59,8 @@ export const genesetAddGenes = (genesetName, genes) => async ( const varIndex = schema.annotations.var.index; const df = await annoMatrix.fetch("var", varIndex); const geneNames = df.col(varIndex).asArray(); - genes = genes.reduce((acc, gene) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genes = genes.reduce((acc: any, gene: any) => { if (geneNames.indexOf(gene.geneSymbol) === -1) { postUserErrorToast( `${gene.geneSymbol} doesn't appear to be a valid gene name.` @@ -78,9 +88,12 @@ export const genesetAddGenes = (genesetName, genes) => async ( }); }; -export const genesetDeleteGenes = (genesetName, geneSymbols) => ( - dispatch, - getState +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const genesetDeleteGenes = (genesetName: any, geneSymbols: any) => ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any ) => { const state = getState(); const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols); @@ -97,7 +110,14 @@ export const genesetDeleteGenes = (genesetName, geneSymbols) => ( Private */ -function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) { +function dropGenesetSummaryDimension( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + obsCrossfilter: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + state: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesetName: any +) { const { annoMatrix, genesets } = state; const varIndex = annoMatrix.schema.annotations?.var?.index; const gs = genesets?.genesets?.get(genesetName) ?? {}; @@ -113,7 +133,8 @@ function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) { return obsCrossfilter.dropDimension("X", query); } -function dropGeneDimension(obsCrossfilter, state, gene) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function dropGeneDimension(obsCrossfilter: any, state: any, gene: any) { const { annoMatrix } = state; const varIndex = annoMatrix.schema.annotations?.var?.index; const query = { @@ -126,10 +147,21 @@ function dropGeneDimension(obsCrossfilter, state, gene) { return obsCrossfilter.dropDimension("X", query); } -function dropGeneset(dispatch, state, genesetName, geneSymbols) { +function dropGeneset( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + state: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesetName: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + geneSymbols: any +) { const { obsCrossfilter: prevObsCrossfilter } = state; const obsCrossfilter = geneSymbols.reduce( - (crossfilter, gene) => dropGeneDimension(crossfilter, state, gene), + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (crossfilter: any, gene: any) => + dropGeneDimension(crossfilter, state, gene), dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName) ); dispatch({ @@ -137,7 +169,8 @@ function dropGeneset(dispatch, state, genesetName, geneSymbols) { continuousNamespace: { isGeneSetSummary: true }, selection: genesetName, }); - geneSymbols.forEach((g) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + geneSymbols.forEach((g: any) => dispatch({ type: "continuous metadata histogram cancel", continuousNamespace: { isUserDefined: true }, diff --git a/client/src/actions/index.js b/client/src/actions/index.ts similarity index 66% rename from client/src/actions/index.js rename to client/src/actions/index.ts index 6626c6cd..5f68f0d3 100644 --- a/client/src/actions/index.js +++ b/client/src/actions/index.ts @@ -12,10 +12,22 @@ import * as viewActions from "./viewStack"; import * as embActions from "./embedding"; import * as genesetActions from "./geneset"; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function setGlobalConfig(config: any) { + /** + * Set any global run-time config not _exclusively_ managed by the config reducer. + * This should only set fields defined in globals.globalConfig. + */ + globals.globalConfig.maxCategoricalOptionsToDisplay = + config?.parameters?.["max-category-items"] ?? + globals.globalConfig.maxCategoricalOptionsToDisplay; +} + /* return promise fetching user-configured colors */ -async function userColorsFetchAndLoad(dispatch) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +async function userColorsFetchAndLoad(dispatch: any) { return fetchJson("colors").then((response) => dispatch({ type: "universe: user color load success", @@ -28,9 +40,13 @@ async function schemaFetch() { return fetchJson("schema"); } -async function configFetch(dispatch) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +async function configFetch(dispatch: any) { return fetchJson("config").then((response) => { const config = { ...globals.configDefaults, ...response.config }; + + setGlobalConfig(config); + dispatch({ type: "configuration load complete", config, @@ -39,7 +55,8 @@ async function configFetch(dispatch) { }); } -async function userInfoFetch(dispatch) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +async function userInfoFetch(dispatch: any) { return fetchJson("userinfo").then((response) => { const { userinfo: userInfo } = response || {}; dispatch({ @@ -50,7 +67,8 @@ async function userInfoFetch(dispatch) { }); } -async function genesetsFetch(dispatch, config) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +async function genesetsFetch(dispatch: any, config: any) { /* request genesets ONLY if the backend supports the feature */ const defaultResponse = { genesets: [], @@ -71,25 +89,31 @@ async function genesetsFetch(dispatch, config) { } } -function prefetchEmbeddings(annoMatrix) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function prefetchEmbeddings(annoMatrix: any) { /* prefetch requests for all embeddings */ const { schema } = annoMatrix; - const available = schema.layout.obs.map((v) => v.name); - available.forEach((embName) => annoMatrix.prefetch("emb", embName)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const available = schema.layout.obs.map((v: any) => v.name); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + available.forEach((embName: any) => annoMatrix.prefetch("emb", embName)); } /* Application bootstrap */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const doInitialDataLoad = () => - catchErrorsWrap(async (dispatch) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + catchErrorsWrap(async (dispatch: any) => { dispatch({ type: "initial data load start" }); try { const [config, schema] = await Promise.all([ configFetch(dispatch), + // @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1. schemaFetch(dispatch), userColorsFetchAndLoad(dispatch), userInfoFetch(dispatch), @@ -113,7 +137,8 @@ const doInitialDataLoad = () => const layoutSchema = schema?.schema?.layout?.obs ?? []; if ( defaultEmbedding && - layoutSchema.some((s) => s.name === defaultEmbedding) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutSchema.some((s: any) => s.name === defaultEmbedding) ) { dispatch(embActions.layoutChoiceAction(defaultEmbedding)); } @@ -122,21 +147,25 @@ const doInitialDataLoad = () => } }, true); -function requestSingleGeneExpressionCountsForColoringPOST(gene) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +function requestSingleGeneExpressionCountsForColoringPOST(gene: any) { return { type: "color by expression", gene, }; } -const requestUserDefinedGene = (gene) => ({ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const requestUserDefinedGene = (gene: any) => ({ type: "request user defined gene success", + data: { genes: [gene], }, }); -const dispatchDiffExpErrors = (dispatch, response) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const dispatchDiffExpErrors = (dispatch: any, response: any) => { switch (response.status) { case 403: dispatchNetworkErrorMessageToUser( @@ -159,10 +188,14 @@ const dispatchDiffExpErrors = (dispatch, response) => { } }; -const requestDifferentialExpression = (set1, set2, num_genes = 50) => async ( - dispatch, - getState -) => { +const requestDifferentialExpression = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + set1: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + set2: any, + num_genes = 50 + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { dispatch({ type: "request differential expression started" }); try { /* @@ -210,7 +243,9 @@ const requestDifferentialExpression = (set1, set2, num_genes = 50) => async ( const varIndex = await annoMatrix.fetch("var", varIndexName); const diffexpLists = { negative: [], positive: [] }; for (const polarity of Object.keys(diffexpLists)) { - diffexpLists[polarity] = response[polarity].map((v) => [ + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + diffexpLists[polarity] = response[polarity].map((v: any) => [ varIndex.at(v[0], varIndexName), ...v.slice(1), ]); @@ -229,7 +264,8 @@ const requestDifferentialExpression = (set1, set2, num_genes = 50) => async ( } }; -function fetchJson(pathAndQuery) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function fetchJson(pathAndQuery: any) { return doJsonRequest( `${globals.API.prefix}${globals.API.version}${pathAndQuery}` ); diff --git a/client/src/actions/selection.js b/client/src/actions/selection.js deleted file mode 100644 index 4657bcdd..00000000 --- a/client/src/actions/selection.js +++ /dev/null @@ -1,199 +0,0 @@ -/* -Action creators for selection -*/ -export const selectContinuousMetadataAction = ( - type, - query, - range, - oldProps = {} -) => async (dispatch, getState) => { - const { obsCrossfilter: prevObsCrossfilter } = getState(); - - const selection = range - ? { - mode: "range", - lo: range[0], - hi: range[1], - inclusive: true, // [lo, hi] incluisve selection - } - : { mode: "all" }; - - const obsCrossfilter = await prevObsCrossfilter.select(...query, selection); - - dispatch({ - type, - obsCrossfilter, - range, - ...oldProps, - }); -}; - -export const selectCategoricalMetadataAction = ( - type, // action type - metadataField, // annotation category name - labels, - label, // the label being selected/deselected - isSelected, // bool - oldProps = {} -) => async (dispatch, getState) => { - const { - obsCrossfilter: prevObsCrossfilter, - categoricalSelection, - } = getState(); - - const labelSelectionState = new Map(categoricalSelection[metadataField]); - labels.forEach( - (l) => labelSelectionState.has(l) || labelSelectionState.set(l, true) - ); - labelSelectionState.set(label, isSelected); - - const values = Array.from(labelSelectionState.keys()).filter((k) => - labelSelectionState.get(k) - ); - const selection = { - mode: "exact", - values, - }; - const obsCrossfilter = await prevObsCrossfilter.select( - "obs", - metadataField, - selection - ); - - dispatch({ - type, - obsCrossfilter, - metadataField, - labelSelectionState, - ...oldProps, - }); -}; - -export const selectCategoricalAllMetadataAction = ( - type, // action type - metadataField, // annotation category name - labels, - isSelected, // bool, select all or none - oldProps = {} -) => async (dispatch, getState) => { - const { - obsCrossfilter: prevObsCrossfilter, - categoricalSelection, - } = getState(); - - const labelSelectionState = new Map(categoricalSelection[metadataField]); - labels.forEach((label) => labelSelectionState.set(label, isSelected)); - - const selection = { mode: isSelected ? "all" : "none" }; - const obsCrossfilter = await prevObsCrossfilter.select( - "obs", - metadataField, - selection - ); - - dispatch({ - type, - obsCrossfilter, - metadataField, - labelSelectionState, - ...oldProps, - }); -}; - -/** - ** Graph selection-related actions - **/ - -export const graphBrushStartAction = () => - /* no change to crossfilter until a change fires */ - ({ type: "graph brush start" }); - -const _graphBrushWithinRectAction = (type, embName, brushCoords) => async ( - dispatch, - getState -) => { - const { obsCrossfilter: prevObsCrossfilter } = getState(); - - const selection = { mode: "within-rect", ...brushCoords }; - const obsCrossfilter = await prevObsCrossfilter.select( - "emb", - embName, - selection - ); - - dispatch({ - type, - obsCrossfilter, - brushCoords, - }); -}; - -const _graphAllAction = (type, embName) => async (dispatch, getState) => { - const { obsCrossfilter: prevObsCrossfilter } = getState(); - - const obsCrossfilter = await prevObsCrossfilter.select("emb", embName, { - mode: "all", - }); - - dispatch({ - type, - obsCrossfilter, - }); -}; - -export const graphBrushChangeAction = (embName, brushCoords) => - _graphBrushWithinRectAction("graph brush change", embName, brushCoords); - -export const graphBrushEndAction = (embName, brushCoords) => - _graphBrushWithinRectAction("graph brush end", embName, brushCoords); - -export const graphBrushCancelAction = (embName) => - _graphAllAction("graph brush cancel", embName); -export const graphBrushDeselectAction = (embName) => - _graphAllAction("graph brush deselect", embName); - -export const graphLassoStartAction = () => - /* no change to crossfilter until a change fires */ - ({ type: "graph lasso start" }); - -export const graphLassoCancelAction = (embName) => - _graphAllAction("graph lasso cancel", embName); - -export const graphLassoDeselectAction = (embName) => - _graphAllAction("graph lasso cancel", embName); - -export const graphLassoEndAction = (embName, polygon) => async ( - dispatch, - getState -) => { - const { obsCrossfilter: prevObsCrossfilter } = getState(); - - const selection = { - mode: "within-polygon", - polygon, - }; - const obsCrossfilter = await prevObsCrossfilter.select( - "emb", - embName, - selection - ); - - dispatch({ - type: "graph lasso end", - obsCrossfilter, - polygon, - }); -}; - -/* -Differential expression set selection -*/ -export const setCellSetFromSelection = (cellSetId) => (dispatch, getState) => { - const { obsCrossfilter } = getState(); - const selected = obsCrossfilter.allSelectedLabels(); - - dispatch({ - type: `store current cell selection as differential set ${cellSetId}`, - data: selected.length > 0 ? selected : null, - }); -}; diff --git a/client/src/actions/selection.ts b/client/src/actions/selection.ts new file mode 100644 index 00000000..0c4eace4 --- /dev/null +++ b/client/src/actions/selection.ts @@ -0,0 +1,248 @@ +/* +Action creators for selection +*/ +export const selectContinuousMetadataAction = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + type: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + query: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + range: any, + oldProps = {} // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { + const { obsCrossfilter: prevObsCrossfilter } = getState(); + + const selection = range + ? { + mode: "range", + lo: range[0], + hi: range[1], + inclusive: true, // [lo, hi] incluisve selection + } + : { mode: "all" }; + + const obsCrossfilter = await prevObsCrossfilter.select(...query, selection); + + dispatch({ + type, + obsCrossfilter, + range, + ...oldProps, + }); +}; + +export const selectCategoricalMetadataAction = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + type: any, // action type + // annotation category name + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + metadataField: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + labels: any, + // the label being selected/deselected + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + label: any, + // bool + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isSelected: any, + oldProps = {} + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { + const { + obsCrossfilter: prevObsCrossfilter, + categoricalSelection, + } = getState(); + + const labelSelectionState = new Map(categoricalSelection[metadataField]); + labels.forEach( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (l: any) => labelSelectionState.has(l) || labelSelectionState.set(l, true) + ); + labelSelectionState.set(label, isSelected); + + const values = Array.from(labelSelectionState.keys()).filter((k) => + labelSelectionState.get(k) + ); + const selection = { + mode: "exact", + values, + }; + const obsCrossfilter = await prevObsCrossfilter.select( + "obs", + metadataField, + selection + ); + + dispatch({ + type, + obsCrossfilter, + metadataField, + labelSelectionState, + ...oldProps, + }); +}; + +export const selectCategoricalAllMetadataAction = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + type: any, // action type + // annotation category name + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + metadataField: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + labels: any, + // bool, select all or none + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isSelected: any, + oldProps = {} + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { + const { + obsCrossfilter: prevObsCrossfilter, + categoricalSelection, + } = getState(); + + const labelSelectionState = new Map(categoricalSelection[metadataField]); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + labels.forEach((label: any) => labelSelectionState.set(label, isSelected)); + + const selection = { mode: isSelected ? "all" : "none" }; + const obsCrossfilter = await prevObsCrossfilter.select( + "obs", + metadataField, + selection + ); + + dispatch({ + type, + obsCrossfilter, + metadataField, + labelSelectionState, + ...oldProps, + }); +}; + +/** + ** Graph selection-related actions + **/ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export const graphBrushStartAction = () => + /* no change to crossfilter until a change fires */ + ({ type: "graph brush start" }); + +const _graphBrushWithinRectAction = ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + type: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + embName: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + brushCoords: any + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +) => async (dispatch: any, getState: any) => { + const { obsCrossfilter: prevObsCrossfilter } = getState(); + + const selection = { mode: "within-rect", ...brushCoords }; + const obsCrossfilter = await prevObsCrossfilter.select( + "emb", + embName, + selection + ); + + dispatch({ + type, + obsCrossfilter, + brushCoords, + }); +}; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const _graphAllAction = (type: any, embName: any) => async ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getState: any +) => { + const { obsCrossfilter: prevObsCrossfilter } = getState(); + + const obsCrossfilter = await prevObsCrossfilter.select("emb", embName, { + mode: "all", + }); + + dispatch({ + type, + obsCrossfilter, + }); +}; + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const graphBrushChangeAction = (embName: any, brushCoords: any) => + _graphBrushWithinRectAction("graph brush change", embName, brushCoords); + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const graphBrushEndAction = (embName: any, brushCoords: any) => + _graphBrushWithinRectAction("graph brush end", embName, brushCoords); + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const graphBrushCancelAction = (embName: any) => + _graphAllAction("graph brush cancel", embName); +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const graphBrushDeselectAction = (embName: any) => + _graphAllAction("graph brush deselect", embName); + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export const graphLassoStartAction = () => + /* no change to crossfilter until a change fires */ + ({ type: "graph lasso start" }); + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const graphLassoCancelAction = (embName: any) => + _graphAllAction("graph lasso cancel", embName); + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const graphLassoDeselectAction = (embName: any) => + _graphAllAction("graph lasso cancel", embName); + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const graphLassoEndAction = (embName: any, polygon: any) => async ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any +) => { + const { obsCrossfilter: prevObsCrossfilter } = getState(); + + const selection = { + mode: "within-polygon", + polygon, + }; + const obsCrossfilter = await prevObsCrossfilter.select( + "emb", + embName, + selection + ); + + dispatch({ + type: "graph lasso end", + obsCrossfilter, + polygon, + }); +}; + +/* +Differential expression set selection +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const setCellSetFromSelection = (cellSetId: any) => ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any +) => { + const { obsCrossfilter } = getState(); + const selected = obsCrossfilter.allSelectedLabels(); + + dispatch({ + type: `store current cell selection as differential set ${cellSetId}`, + data: selected.length > 0 ? selected : null, + }); +}; diff --git a/client/src/actions/viewStack.js b/client/src/actions/viewStack.ts similarity index 66% rename from client/src/actions/viewStack.js rename to client/src/actions/viewStack.ts index 9d402cbd..81f69335 100644 --- a/client/src/actions/viewStack.js +++ b/client/src/actions/viewStack.ts @@ -18,7 +18,13 @@ import { _userResetSubsetAnnoMatrix, } from "../util/stateManager/viewStackHelpers"; -export const clipAction = (min, max) => (dispatch, getState) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const clipAction = (min: any, max: any) => ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dispatch: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getState: any +) => { /* apply a clip to the current annoMatrix. By convention, the clip view is ALWAYS the top view. @@ -34,7 +40,8 @@ export const clipAction = (min, max) => (dispatch, getState) => { }); }; -export const subsetAction = () => (dispatch, getState) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const subsetAction = () => (dispatch: any, getState: any) => { /* Subset the annoMatrix to the current crossfilter selection by pushing a subset view. @@ -58,7 +65,8 @@ export const subsetAction = () => (dispatch, getState) => { }); }; -export const resetSubsetAction = () => (dispatch, getState) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const resetSubsetAction = () => (dispatch: any, getState: any) => { /* Reset the annoMatrix to all data. Because we may have multiple views stacked, we pop them all. By convention, any clip transformation will diff --git a/client/src/annoMatrix/annoMatrix.js b/client/src/annoMatrix/annoMatrix.ts similarity index 66% rename from client/src/annoMatrix/annoMatrix.js rename to client/src/annoMatrix/annoMatrix.ts index 1ed90995..3619a8b5 100644 --- a/client/src/annoMatrix/annoMatrix.js +++ b/client/src/annoMatrix/annoMatrix.ts @@ -17,6 +17,39 @@ import { _queryValidate, _queryCacheKey } from "./query"; const _dataframeCache = dataframeMemo(128); export default class AnnoMatrix { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + public isView: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + public nObs: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + public nVar: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + public rowIndex: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + public schema: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + public userFlags: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + public viewOf: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + protected _cache: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + private _pendingLoad: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + private _whereCache: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + private _gcInfo: any; + /* Abstract base class for all AnnoMatrix objects. This class provides a proxy to the annotated matrix data authoritatively served by the server/back-end. @@ -47,6 +80,7 @@ export default class AnnoMatrix { subset(annoMatrix, rowLabels) -> annoMatrix etc. */ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. static fields() { /* return the fields present in the AnnoMatrix instance. @@ -54,7 +88,8 @@ export default class AnnoMatrix { return ["obs", "var", "emb", "X"]; } - constructor(schema, nObs, nVar, rowIndex = null) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(schema: any, nObs: any, nVar: any, rowIndex = null) { /* Private constructor - this is an abstract base class. Do not use. */ @@ -83,13 +118,13 @@ export default class AnnoMatrix { this.userFlags = {}; /* - Private instance variables. + Private instance variables. - These are caches - lazily loaded. The only guarantee is that if they - are loaded, they will conform to the schema & dimensionality constraints. + These are caches - lazily loaded. The only guarantee is that if they + are loaded, they will conform to the schema & dimensionality constraints. - Do NOT use directly - instead, use the fetch() and preload() API. - */ + Do NOT use directly - instead, use the fetch() and preload() API. + */ this._cache = { obs: Dataframe.empty(this.rowIndex), var: Dataframe.empty(this.rowIndex), @@ -109,6 +144,8 @@ export default class AnnoMatrix { /** ** Schema helper/accessors **/ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. getMatrixColumns(field) { /* Return array of column names in the field. ONLY supported on the @@ -121,7 +158,7 @@ export default class AnnoMatrix { return _schemaColumns(this.schema, field); } - // eslint-disable-next-line class-methods-use-this -- need to be able to call this on instances + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/explicit-module-boundary-types -- need to be able to call this on instances getMatrixFields() { /* Return array of fields in this annoMatrix. Currently hard-wired to @@ -132,6 +169,8 @@ export default class AnnoMatrix { return AnnoMatrix.fields(); } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. getColumnSchema(field, col) { /* Return the schema for the field & column ,eg, @@ -144,6 +183,8 @@ export default class AnnoMatrix { return _getColumnSchema(this.schema, field, col); } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. getColumnDimensions(field, col) { /* Return the dimensions on this field / column. For most fields, which are 1D, @@ -162,10 +203,12 @@ export default class AnnoMatrix { /** ** General utility methods **/ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. base() { /* return the base of view, or `this` if not a view. */ + // eslint-disable-next-line @typescript-eslint/no-this-alias --- FIXME: disabled temporarily on migrate to TS. let annoMatrix = this; while (annoMatrix.isView) annoMatrix = annoMatrix.viewOf; return annoMatrix; @@ -174,6 +217,8 @@ export default class AnnoMatrix { /** ** Load / read interfaces **/ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. fetch(field, q) { /* Return the given query on a single matrix field as a single dataframe. @@ -231,6 +276,8 @@ export default class AnnoMatrix { return this._fetch(field, q); } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. prefetch(field, q) { /* Start a data fetch & cache fill. Identical to fetch() except it does @@ -261,7 +308,8 @@ export default class AnnoMatrix { ** The actual implementation is in the sub-classes, which MUST override these. **/ - // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements + // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read. + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements addObsAnnoCategory(col, category) { /* Add a new category value (aka "label") to a writable obs column, and return the new AnnoMatrix. @@ -278,7 +326,8 @@ export default class AnnoMatrix { _subclassResponsibility(); } - // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements + // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read. + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements async removeObsAnnoCategory(col, category, unassignedCategory) { /* Remove a category value from an obs column, reassign any obs having that value @@ -299,7 +348,8 @@ export default class AnnoMatrix { _subclassResponsibility(); } - // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements + // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read. + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements dropObsColumn(col) { /* Drop an entire writable column, eg a user-created obs annotation. Typical use @@ -315,7 +365,8 @@ export default class AnnoMatrix { _subclassResponsibility(); } - // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements + // @ts-expect-error ts-migrate(6133) FIXME: 'colSchema' is declared but its value is never rea... Remove this comment to see the full error message + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements addObsColumn(colSchema, Ctor, value) { /* Add a new writable OBS annotation column, with the caller-specified schema, initial value @@ -344,7 +395,8 @@ export default class AnnoMatrix { _subclassResponsibility(); } - // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements + // @ts-expect-error ts-migrate(6133) FIXME: 'oldCol' is declared but its value is never read. + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements renameObsColumn(oldCol, newCol) { /* Rename the obs column 'oldCol' to have name 'newCol' and returns new AnnoMatrix. @@ -359,7 +411,8 @@ export default class AnnoMatrix { _subclassResponsibility(); } - // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements + // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read. + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements async setObsColumnValues(col, obsLabels, value) { /* Set all obs with label in array 'obsLabels' to have 'value'. Typical use would be @@ -377,7 +430,8 @@ export default class AnnoMatrix { _subclassResponsibility(); } - // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements + // @ts-expect-error ts-migrate(6133) FIXME: 'col' is declared but its value is never read. + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements async resetObsColumnValues(col, oldValue, newValue) { /* Set by value - all elements in the column with value 'oldValue' are set to 'newValue'. @@ -394,7 +448,8 @@ export default class AnnoMatrix { _subclassResponsibility(); } - // eslint-disable-next-line class-methods-use-this, no-unused-vars -- make sure subclass implements + // @ts-expect-error ts-migrate(6133) FIXME: 'colSchema' is declared but its value is never rea... Remove this comment to see the full error message + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/no-unused-vars, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements addEmbedding(colSchema) { /* Add a new obs embedding to the AnnoMatrix, with provided schema. @@ -407,28 +462,38 @@ export default class AnnoMatrix { _subclassResponsibility(); } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. getCacheKeys(field, query) { /* - Return cache keys for columns associated with this query. May return - [unknown] if no keys are known (ie, nothing is or was cached). - */ +Return cache keys for columns associated with this query. May return +[unknown] if no keys are known (ie, nothing is or was cached). +*/ return _whereCacheGet(this._whereCache, this.schema, field, query); } /** ** Private interfaces below. **/ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _resolveCachedQueries(field, queries) { - return queries - .map((query) => - _whereCacheGet(this._whereCache, this.schema, field, query).filter( - (cacheKey) => - cacheKey !== undefined && this._cache[field].hasCol(cacheKey) + return ( + queries + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'query' implicitly has an 'any' type. + .map((query) => + _whereCacheGet(this._whereCache, this.schema, field, query).filter( + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'cacheKey' implicitly has an 'any' type. + (cacheKey) => + cacheKey !== undefined && this._cache[field].hasCol(cacheKey) + ) ) - ) - .flat(); + .flat() + ); } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. async _fetch(field, q) { if (!AnnoMatrix.fields().includes(field)) return undefined; const queries = Array.isArray(q) ? q : [q]; @@ -441,6 +506,7 @@ export default class AnnoMatrix { /* find any query not already cached */ const uncachedQueries = queries.filter((query) => _whereCacheGet(this._whereCache, this.schema, field, query).some( + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'cacheKey' implicitly has an 'any' type. (cacheKey) => cacheKey === undefined || !this._cache[field].hasCol(cacheKey) ) @@ -450,8 +516,10 @@ export default class AnnoMatrix { if (uncachedQueries.length > 0) { await Promise.all( uncachedQueries.map((query) => + // @ts-expect-error ts-migrate(7006) FIXME: Parameter '_field' implicitly has an 'any' type. this._getPendingLoad(field, query, async (_field, _query) => { /* fetch, then index. _doLoad is subclass interface */ + // @ts-expect-error ts-migrate(2488) FIXME: Type 'void' must have a '[Symbol.iterator]()' meth... Remove this comment to see the full error message const [whereCacheUpdate, df] = await this._doLoad(_field, _query); this._cache[_field] = this._cache[_field].withColsFrom(df); this._whereCache = _whereCacheMerge( @@ -472,6 +540,8 @@ export default class AnnoMatrix { return response; } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. async _getPendingLoad(field, query, fetchFn) { /* Given a query on a field, ensure that we only have a single outstanding @@ -493,7 +563,7 @@ export default class AnnoMatrix { return this._pendingLoad[field][key]; } - // eslint-disable-next-line class-methods-use-this -- make sure subclass implements + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/explicit-module-boundary-types -- make sure subclass implements async _doLoad() { _subclassResponsibility(); } @@ -527,19 +597,22 @@ export default class AnnoMatrix { To be effective, the GC callback needs to be invoked from the undo/redo code, as much of the cache is pinned by that data structure. */ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _gcField(field, isHot, pinnedColumns) { - const maxColumns = isHot ? 256 : 10; // maybe to aggressive? - + const maxColumns = isHot ? 256 : 10; const cache = this._cache[field]; if (cache.colIndex.size() < maxColumns) return; // trivial rejection const candidates = cache.colIndex .labels() + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. .filter((col) => !pinnedColumns.includes(col)); const excessCount = candidates.length + pinnedColumns.length - maxColumns; if (excessCount > 0) { const { _gcInfo } = this; + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'a' implicitly has an 'any' type. candidates.sort((a, b) => { let atime = _gcInfo.get(_columnCacheKey(field, a)); if (atime === undefined) atime = 0; @@ -558,13 +631,17 @@ export default class AnnoMatrix { // )}]` // ); this._cache[field] = toDrop.reduce( + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type. (df, col) => df.dropCol(col), this._cache[field] ); + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. toDrop.forEach((col) => _gcInfo.delete(_columnCacheKey(field, col))); } } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _gcFetchCleanup(field, pinnedColumns) { /* Called during data load/fetch. By definition, this is 'hot', so we @@ -579,6 +656,8 @@ export default class AnnoMatrix { } } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'hints' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _gc(hints) { /* Called from middleware, or elsewhere. isHot is true if we are in the active store, @@ -591,6 +670,8 @@ export default class AnnoMatrix { ); } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _gcUpdateStats(field, dataframe) { /* called each time a query is performed, allowing the gc to update any bookkeeping @@ -600,6 +681,7 @@ export default class AnnoMatrix { const cols = dataframe.colIndex.labels(); const { _gcInfo } = this; const now = Date.now(); + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'c' implicitly has an 'any' type. cols.forEach((c) => { _gcInfo.set(_columnCacheKey(field, c), now); }); @@ -617,6 +699,8 @@ export default class AnnoMatrix { Do not override _clone(); **/ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'clone' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _cloneDeeper(clone) { clone._cache = _shallowClone(this._cache); clone._gcInfo = new Map(); @@ -629,6 +713,7 @@ export default class AnnoMatrix { return clone; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _clone() { const clone = _shallowClone(this); this._cloneDeeper(clone); @@ -640,6 +725,7 @@ export default class AnnoMatrix { /* private utility functions below */ +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. function _columnCacheKey(field, column) { return `${field}/${column}`; } diff --git a/client/src/annoMatrix/clone.js b/client/src/annoMatrix/clone.js deleted file mode 100644 index 97cad4b5..00000000 --- a/client/src/annoMatrix/clone.js +++ /dev/null @@ -1,6 +0,0 @@ -/* -Shallow clone an object, correctly handling prototype -*/ -export default function _shallowClone(orig) { - return Object.assign(Object.create(Object.getPrototypeOf(orig)), orig); -} diff --git a/client/src/annoMatrix/clone.ts b/client/src/annoMatrix/clone.ts new file mode 100644 index 00000000..dabe3d8e --- /dev/null +++ b/client/src/annoMatrix/clone.ts @@ -0,0 +1,7 @@ +/* +Shallow clone an object, correctly handling prototype +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function _shallowClone(orig: any) { + return Object.assign(Object.create(Object.getPrototypeOf(orig)), orig); +} diff --git a/client/src/annoMatrix/crossfilter.js b/client/src/annoMatrix/crossfilter.js deleted file mode 100644 index e2310731..00000000 --- a/client/src/annoMatrix/crossfilter.js +++ /dev/null @@ -1,286 +0,0 @@ -/* -Row crossfilter proxy for an AnnoMatrix. This wraps Crossfilter, -providing a number of services, and ensuring that the crossfilter and -AnnoMatrix stay in sync: - - on-demand index creation as data is loaded - - transparently mapping between queries and crossfilter index names. - - for mutation of the matrix by user annotations, maintain synchronization - between Crossfilter and AnnoMatrix. -*/ -import Crossfilter from "../util/typedCrossfilter"; -import { _getColumnSchema } from "./schema"; - -function _dimensionNameFromDf(field, df) { - const colNames = df.colIndex.labels(); - return _dimensionName(field, colNames); -} - -function _dimensionName(field, colNames) { - if (!Array.isArray(colNames)) return `${field}/${colNames}`; - return `${field}/${colNames.join(":")}`; -} - -export default class AnnoMatrixObsCrossfilter { - constructor(annoMatrix, _obsCrossfilter = null) { - this.annoMatrix = annoMatrix; - this.obsCrossfilter = - _obsCrossfilter || new Crossfilter(annoMatrix._cache.obs); - this.obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs); - } - - size() { - return this.obsCrossfilter.size(); - } - - /** - Managing the associated annoMatrix. These wrappers are necessary to - make coordinated changes to BOTH the crossfilter and annoMatrix, and - ensure that all state stays synchronized. - - See API documentation in annoMatrix.js. - **/ - addObsColumn(colSchema, Ctor, value) { - const annoMatrix = this.annoMatrix.addObsColumn(colSchema, Ctor, value); - const obsCrossfilter = this.obsCrossfilter.setData(annoMatrix._cache.obs); - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - dropObsColumn(col) { - const annoMatrix = this.annoMatrix.dropObsColumn(col); - let { obsCrossfilter } = this; - const dimName = _dimensionName("obs", col); - if (obsCrossfilter.hasDimension(dimName)) { - obsCrossfilter = obsCrossfilter.delDimension(dimName); - } - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - renameObsColumn(oldCol, newCol) { - const annoMatrix = this.annoMatrix.renameObsColumn(oldCol, newCol); - const oldDimName = _dimensionName("obs", oldCol); - const newDimName = _dimensionName("obs", newCol); - let { obsCrossfilter } = this; - if (obsCrossfilter.hasDimension(oldDimName)) { - obsCrossfilter = obsCrossfilter.renameDimension(oldDimName, newDimName); - } - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - addObsAnnoCategory(col, category) { - const annoMatrix = this.annoMatrix.addObsAnnoCategory(col, category); - const dimName = _dimensionName("obs", col); - let { obsCrossfilter } = this; - if (obsCrossfilter.hasDimension(dimName)) { - obsCrossfilter = obsCrossfilter.delDimension(dimName); - } - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - async removeObsAnnoCategory(col, category, unassignedCategory) { - const annoMatrix = await this.annoMatrix.removeObsAnnoCategory( - col, - category, - unassignedCategory - ); - const dimName = _dimensionName("obs", col); - let { obsCrossfilter } = this; - if (obsCrossfilter.hasDimension(dimName)) { - obsCrossfilter = obsCrossfilter.delDimension(dimName); - } - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - async setObsColumnValues(col, rowLabels, value) { - const annoMatrix = await this.annoMatrix.setObsColumnValues( - col, - rowLabels, - value - ); - const dimName = _dimensionName("obs", col); - let { obsCrossfilter } = this; - if (obsCrossfilter.hasDimension(dimName)) { - obsCrossfilter = obsCrossfilter.delDimension(dimName); - } - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - async resetObsColumnValues(col, oldValue, newValue) { - const annoMatrix = await this.annoMatrix.resetObsColumnValues( - col, - oldValue, - newValue - ); - const dimName = _dimensionName("obs", col); - let { obsCrossfilter } = this; - if (obsCrossfilter.hasDimension(dimName)) { - obsCrossfilter = obsCrossfilter.delDimension(dimName); - } - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - addEmbedding(colSchema) { - const annoMatrix = this.annoMatrix.addEmbedding(colSchema); - return new AnnoMatrixObsCrossfilter(annoMatrix, this.obsCrossfilter); - } - - /** - * Drop the crossfilter dimension. Do not change the annoMatrix. Useful when we - * want to stop trackin the selection state, but aren't sure we want to blow the - * annomatrix cache. - */ - dropDimension(field, query) { - const { annoMatrix } = this; - let { obsCrossfilter } = this; - const keys = annoMatrix - .getCacheKeys(field, query) - .filter((k) => k !== undefined); - const dimName = _dimensionName(field, keys); - if (obsCrossfilter.hasDimension(dimName)) { - obsCrossfilter = obsCrossfilter.delDimension(dimName); - } - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - /** - Selection state - API is identical to ImmutableTypedCrossfilter, as these - are just wrappers to lazy create indices. - **/ - - async select(field, query, spec) { - const { annoMatrix } = this; - let { obsCrossfilter } = this; - - if (!annoMatrix?._cache?.[field]) { - throw new Error("Unknown field name"); - } - if (field === "var") { - throw new Error("unable to obsSelect upon the var dimension"); - } - - // grab the data, so we can grab the index. - const df = await annoMatrix.fetch(field, query); - - const dimName = _dimensionNameFromDf(field, df); - if (!obsCrossfilter.hasDimension(dimName)) { - // lazy index generation - add dimension when first used - obsCrossfilter = this._addObsCrossfilterDimension( - annoMatrix, - obsCrossfilter, - field, - df - ); - } - - // select - obsCrossfilter = obsCrossfilter.select(dimName, spec); - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - selectAll() { - /* - Select all on any dimension in this field. - */ - const { annoMatrix } = this; - const currentDims = this.obsCrossfilter.dimensionNames(); - const obsCrossfilter = currentDims.reduce((xfltr, dim) => { - return xfltr.select(dim, { mode: "all" }); - }, this.obsCrossfilter); - return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); - } - - countSelected() { - /* if no data yet indexed in the crossfilter, just say everything is selected */ - if (this.obsCrossfilter.size() === 0) return this.annoMatrix.nObs; - return this.obsCrossfilter.countSelected(); - } - - allSelectedMask() { - /* if no data yet indexed in the crossfilter, just say everything is selected */ - if ( - this.obsCrossfilter.size() === 0 || - this.obsCrossfilter.dimensionNames().length === 0 - ) { - /* fake the mask */ - return new Uint8Array(this.annoMatrix.nObs).fill(1); - } - return this.obsCrossfilter.allSelectedMask(); - } - - allSelectedLabels() { - /* if no data yet indexed in the crossfilter, just say everything is selected */ - if ( - this.obsCrossfilter.size() === 0 || - this.obsCrossfilter.dimensionNames().length === 0 - ) { - return this.annoMatrix.rowIndex.labels(); - } - - const mask = this.obsCrossfilter.allSelectedMask(); - const index = this.annoMatrix.rowIndex.isubsetMask(mask); - return index.labels(); - } - - fillByIsSelected(array, selectedValue, deselectedValue) { - /* if no data yet indexed in the crossfilter, just say everything is selected */ - if ( - this.obsCrossfilter.size() === 0 || - this.obsCrossfilter.dimensionNames().length === 0 - ) { - return array.fill(selectedValue); - } - return this.obsCrossfilter.fillByIsSelected( - array, - selectedValue, - deselectedValue - ); - } - - /** - ** Private below - **/ - - _addObsCrossfilterDimension(annoMatrix, obsCrossfilter, field, df) { - if (field === "var") return obsCrossfilter; - const dimName = _dimensionNameFromDf(field, df); - const dimParams = this._getObsDimensionParams(field, df); - obsCrossfilter = obsCrossfilter.setData(annoMatrix._cache.obs); - obsCrossfilter = obsCrossfilter.addDimension(dimName, ...dimParams); - return obsCrossfilter; - } - - _getColumnBaseType(field, col) { - /* Look up the primitive type for this field/col */ - const colSchema = _getColumnSchema(this.annoMatrix.schema, field, col); - return colSchema.type; - } - - _getObsDimensionParams(field, df) { - /* return the crossfilter dimensiontype type and params for this field/dataframe */ - - if (field === "emb") { - /* assumed to be 2D */ - return ["spatial", df.icol(0).asArray(), df.icol(1).asArray()]; - } - - /* assumed to be 1D */ - const col = df.icol(0); - const colName = df.colIndex.getLabel(0); - const type = this._getColumnBaseType(field, colName); - if (type === "string" || type === "categorical" || type === "boolean") { - return ["enum", col.asArray()]; - } - if (type === "int32") { - return ["scalar", col.asArray(), Int32Array]; - } - if (type === "float32") { - return ["scalar", col.asArray(), Float32Array]; - } - // Currently not supporting boolean and categorical types. - console.error( - `Warning - unknown metadata schema (${type}) for field ${field} ${colName}.` - ); - // skip it - we don't know what to do with this type - - return undefined; - } -} diff --git a/client/src/annoMatrix/crossfilter.ts b/client/src/annoMatrix/crossfilter.ts new file mode 100644 index 00000000..f45dfa8e --- /dev/null +++ b/client/src/annoMatrix/crossfilter.ts @@ -0,0 +1,389 @@ +/* +Row crossfilter proxy for an AnnoMatrix. This wraps Crossfilter, +providing a number of services, and ensuring that the crossfilter and +AnnoMatrix stay in sync: + - on-demand index creation as data is loaded + - transparently mapping between queries and crossfilter index names. + - for mutation of the matrix by user annotations, maintain synchronization + between Crossfilter and AnnoMatrix. +*/ +import Crossfilter from "../util/typedCrossfilter"; +import { _getColumnSchema } from "./schema"; + +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. +function _dimensionNameFromDf(field, df) { + const colNames = df.colIndex.labels(); + return _dimensionName(field, colNames); +} + +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. +function _dimensionName(field, colNames) { + if (!Array.isArray(colNames)) return `${field}/${colNames}`; + return `${field}/${colNames.join(":")}`; +} + +export default class AnnoMatrixObsCrossfilter { + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + constructor(annoMatrix, _obsCrossfilter = null) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).annoMatrix = annoMatrix; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter = + _obsCrossfilter || new Crossfilter(annoMatrix._cache.obs); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter = (this as any).obsCrossfilter.setData( + annoMatrix._cache.obs + ); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + size() { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (this as any).obsCrossfilter.size(); + } + + /** + Managing the associated annoMatrix. These wrappers are necessary to + make coordinated changes to BOTH the crossfilter and annoMatrix, and + ensure that all state stays synchronized. + + See API documentation in annoMatrix.js. + **/ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + addObsColumn(colSchema, Ctor, value) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const annoMatrix = (this as any).annoMatrix.addObsColumn( + colSchema, + Ctor, + value + ); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const obsCrossfilter = (this as any).obsCrossfilter.setData( + annoMatrix._cache.obs + ); + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + dropObsColumn(col) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const annoMatrix = (this as any).annoMatrix.dropObsColumn(col); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message + let { obsCrossfilter } = this; + const dimName = _dimensionName("obs", col); + if (obsCrossfilter.hasDimension(dimName)) { + obsCrossfilter = obsCrossfilter.delDimension(dimName); + } + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + renameObsColumn(oldCol, newCol) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const annoMatrix = (this as any).annoMatrix.renameObsColumn(oldCol, newCol); + const oldDimName = _dimensionName("obs", oldCol); + const newDimName = _dimensionName("obs", newCol); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message + let { obsCrossfilter } = this; + if (obsCrossfilter.hasDimension(oldDimName)) { + obsCrossfilter = obsCrossfilter.renameDimension(oldDimName, newDimName); + } + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + addObsAnnoCategory(col, category) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const annoMatrix = (this as any).annoMatrix.addObsAnnoCategory( + col, + category + ); + const dimName = _dimensionName("obs", col); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message + let { obsCrossfilter } = this; + if (obsCrossfilter.hasDimension(dimName)) { + obsCrossfilter = obsCrossfilter.delDimension(dimName); + } + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + async removeObsAnnoCategory(col, category, unassignedCategory) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const annoMatrix = await (this as any).annoMatrix.removeObsAnnoCategory( + col, + category, + unassignedCategory + ); + const dimName = _dimensionName("obs", col); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message + let { obsCrossfilter } = this; + if (obsCrossfilter.hasDimension(dimName)) { + obsCrossfilter = obsCrossfilter.delDimension(dimName); + } + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + async setObsColumnValues(col, rowLabels, value) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const annoMatrix = await (this as any).annoMatrix.setObsColumnValues( + col, + rowLabels, + value + ); + const dimName = _dimensionName("obs", col); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message + let { obsCrossfilter } = this; + if (obsCrossfilter.hasDimension(dimName)) { + obsCrossfilter = obsCrossfilter.delDimension(dimName); + } + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + async resetObsColumnValues(col, oldValue, newValue) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const annoMatrix = await (this as any).annoMatrix.resetObsColumnValues( + col, + oldValue, + newValue + ); + const dimName = _dimensionName("obs", col); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message + let { obsCrossfilter } = this; + if (obsCrossfilter.hasDimension(dimName)) { + obsCrossfilter = obsCrossfilter.delDimension(dimName); + } + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + addEmbedding(colSchema) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const annoMatrix = (this as any).annoMatrix.addEmbedding(colSchema); + return new AnnoMatrixObsCrossfilter( + annoMatrix, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter + ); + } + + /** + * Drop the crossfilter dimension. Do not change the annoMatrix. Useful when we + * want to stop trackin the selection state, but aren't sure we want to blow the + * annomatrix cache. + */ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + dropDimension(field, query) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message + const { annoMatrix } = this; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message + let { obsCrossfilter } = this; + const keys = annoMatrix + .getCacheKeys(field, query) + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'k' implicitly has an 'any' type. + .filter((k) => k !== undefined); + const dimName = _dimensionName(field, keys); + if (obsCrossfilter.hasDimension(dimName)) { + obsCrossfilter = obsCrossfilter.delDimension(dimName); + } + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + /** + Selection state - API is identical to ImmutableTypedCrossfilter, as these + are just wrappers to lazy create indices. + **/ + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + async select(field, query, spec) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message + const { annoMatrix } = this; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message + let { obsCrossfilter } = this; + + if (!annoMatrix?._cache?.[field]) { + throw new Error("Unknown field name"); + } + if (field === "var") { + throw new Error("unable to obsSelect upon the var dimension"); + } + + // grab the data, so we can grab the index. + const df = await annoMatrix.fetch(field, query); + + const dimName = _dimensionNameFromDf(field, df); + if (!obsCrossfilter.hasDimension(dimName)) { + // lazy index generation - add dimension when first used + obsCrossfilter = this._addObsCrossfilterDimension( + annoMatrix, + obsCrossfilter, + field, + df + ); + } + + // select + obsCrossfilter = obsCrossfilter.select(dimName, spec); + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + selectAll() { + /* + Select all on any dimension in this field. + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Anno... Remove this comment to see the full error message + const { annoMatrix } = this; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const currentDims = (this as any).obsCrossfilter.dimensionNames(); + const obsCrossfilter = currentDims.reduce( + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'xfltr' implicitly has an 'any' type. + (xfltr, dim) => xfltr.select(dim, { mode: "all" }), + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter + ); // eslint-disable-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return new AnnoMatrixObsCrossfilter(annoMatrix, obsCrossfilter); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + countSelected() { + /* if no data yet indexed in the crossfilter, just say everything is selected */ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + if ((this as any).obsCrossfilter.size() === 0) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (this as any).annoMatrix.nObs; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (this as any).obsCrossfilter.countSelected(); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + allSelectedMask() { + /* if no data yet indexed in the crossfilter, just say everything is selected */ + if ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter.size() === 0 || + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter.dimensionNames().length === 0 + ) { + /* fake the mask */ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return new Uint8Array((this as any).annoMatrix.nObs).fill(1); + } + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (this as any).obsCrossfilter.allSelectedMask(); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + allSelectedLabels() { + /* if no data yet indexed in the crossfilter, just say everything is selected */ + if ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter.size() === 0 || + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter.dimensionNames().length === 0 + ) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (this as any).annoMatrix.rowIndex.labels(); + } + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const mask = (this as any).obsCrossfilter.allSelectedMask(); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const index = (this as any).annoMatrix.rowIndex.isubsetMask(mask); + return index.labels(); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'array' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + fillByIsSelected(array, selectedValue, deselectedValue) { + /* if no data yet indexed in the crossfilter, just say everything is selected */ + if ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter.size() === 0 || + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).obsCrossfilter.dimensionNames().length === 0 + ) { + return array.fill(selectedValue); + } + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (this as any).obsCrossfilter.fillByIsSelected( + array, + selectedValue, + deselectedValue + ); + } + + /** + ** Private below + **/ + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + _addObsCrossfilterDimension(annoMatrix, obsCrossfilter, field, df) { + if (field === "var") return obsCrossfilter; + const dimName = _dimensionNameFromDf(field, df); + const dimParams = this._getObsDimensionParams(field, df); + obsCrossfilter = obsCrossfilter.setData(annoMatrix._cache.obs); + // @ts-expect-error ts-migrate(2488) FIXME: Type 'any[] | undefined' must have a '[Symbol.iter... Remove this comment to see the full error message + obsCrossfilter = obsCrossfilter.addDimension(dimName, ...dimParams); + return obsCrossfilter; + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + _getColumnBaseType(field, col) { + /* Look up the primitive type for this field/col */ + const colSchema = _getColumnSchema( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).annoMatrix.schema, + field, + col + ); + return colSchema.type; + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + _getObsDimensionParams(field, df) { + /* return the crossfilter dimensiontype type and params for this field/dataframe */ + + if (field === "emb") { + /* assumed to be 2D */ + return ["spatial", df.icol(0).asArray(), df.icol(1).asArray()]; + } + + /* assumed to be 1D */ + const col = df.icol(0); + const colName = df.colIndex.getLabel(0); + const type = this._getColumnBaseType(field, colName); + if (type === "string" || type === "categorical" || type === "boolean") { + return ["enum", col.asArray()]; + } + if (type === "int32") { + return ["scalar", col.asArray(), Int32Array]; + } + if (type === "float32") { + return ["scalar", col.asArray(), Float32Array]; + } + // Currently not supporting boolean and categorical types. + console.error( + `Warning - unknown metadata schema (${type}) for field ${field} ${colName}.` + ); + // skip it - we don't know what to do with this type + + return undefined; + } +} diff --git a/client/src/annoMatrix/fetchHelpers.js b/client/src/annoMatrix/fetchHelpers.js deleted file mode 100644 index 43f99705..00000000 --- a/client/src/annoMatrix/fetchHelpers.js +++ /dev/null @@ -1,27 +0,0 @@ -export { doBinaryRequest, doFetch } from "../util/actionHelpers"; - -/* double URI encode - needed for query-param filters */ -export function _dubEncURIComp(s) { - return encodeURIComponent(encodeURIComponent(s)); -} - -/* currently unused, consider deleting */ -export function _fetchResult(promise) { - let _status = "pending"; - const res = promise.then( - (r) => { - _status = "success"; - return r; - }, - (e) => { - _status = "error"; - throw e; - } - ); - - res.status = () => { - return _status; - }; - - return res; -} diff --git a/client/src/annoMatrix/fetchHelpers.ts b/client/src/annoMatrix/fetchHelpers.ts new file mode 100644 index 00000000..994979f9 --- /dev/null +++ b/client/src/annoMatrix/fetchHelpers.ts @@ -0,0 +1,29 @@ +export { doBinaryRequest, doFetch } from "../util/actionHelpers"; + +/* double URI encode - needed for query-param filters */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _dubEncURIComp(s: any) { + return encodeURIComponent(encodeURIComponent(s)); +} + +/* currently unused, consider deleting */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _fetchResult(promise: any) { + let _status = "pending"; + const res = promise.then( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (r: any) => { + _status = "success"; + return r; + }, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (e: any) => { + _status = "error"; + throw e; + } + ); + + res.status = () => _status; + + return res; +} diff --git a/client/src/annoMatrix/index.js b/client/src/annoMatrix/index.ts similarity index 100% rename from client/src/annoMatrix/index.js rename to client/src/annoMatrix/index.ts diff --git a/client/src/annoMatrix/loader.js b/client/src/annoMatrix/loader.ts similarity index 60% rename from client/src/annoMatrix/loader.js rename to client/src/annoMatrix/loader.ts index c33e8be7..25b263c9 100644 --- a/client/src/annoMatrix/loader.js +++ b/client/src/annoMatrix/loader.ts @@ -1,6 +1,6 @@ import { doBinaryRequest, doFetch } from "./fetchHelpers"; import { matrixFBSToDataframe } from "../util/stateManager/matrix"; -import { _getColumnSchema, _normalizeCategoricalSchema } from "./schema"; +import { _getColumnSchema } from "./schema"; import { addObsAnnoColumn, removeObsAnnoColumn, @@ -19,10 +19,17 @@ import { _urlEncodeComplexQuery, _hashStringValues, } from "./query"; +import { + normalizeResponse, + normalizeWritableCategoricalSchema, +} from "./normalize"; const promiseThrottle = new PromiseLimit(5); export default class AnnoMatrixLoader extends AnnoMatrix { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + baseURL: any; + /* AnnoMatrix implementation which proxies to HTTP server using the CXG REST API. Used as the base (non-view) instance. @@ -33,7 +40,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix { new AnnoMatrixLoader(serverBaseURL, schema) -> instance */ - constructor(baseURL, schema) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(baseURL: any, schema: any) { const { nObs, nVar } = schema.dataframe; super(schema, nObs, nVar); @@ -48,7 +56,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix { /** ** Public. API described in base class. **/ - addObsAnnoCategory(col, category) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + addObsAnnoCategory(col: any, category: any) { /* Add a new category (aka label) to the schema for an obs column. */ @@ -60,7 +69,15 @@ export default class AnnoMatrixLoader extends AnnoMatrix { return newAnnoMatrix; } - async removeObsAnnoCategory(col, category, unassignedCategory) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + async removeObsAnnoCategory( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + col: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + category: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + unassignedCategory: any + ) { /* Remove a single "category" (aka "label") from the data & schema of an obs column. */ @@ -80,7 +97,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix { return newAnnoMatrix; } - dropObsColumn(col) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dropObsColumn(col: any) { /* drop column from field */ @@ -88,11 +106,14 @@ export default class AnnoMatrixLoader extends AnnoMatrix { _writableCheck(colSchema); // throws on error const newAnnoMatrix = this._clone(); - newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + newAnnoMatrix._cache.obs = (this as any)._cache.obs.dropCol(col); newAnnoMatrix.schema = removeObsAnnoColumn(this.schema, col); return newAnnoMatrix; } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. addObsColumn(colSchema, Ctor, value) { /* add a column to field, initializing with value. Value may @@ -105,7 +126,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix { const colName = colSchema.name; if ( _getColumnSchema(this.schema, "obs", colName) || - this._cache.obs.hasCol(colName) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any)._cache.obs.hasCol(colName) ) { throw new Error("column already exists"); } @@ -121,8 +143,9 @@ export default class AnnoMatrixLoader extends AnnoMatrix { } else { data = new Ctor(this.nObs).fill(value); } - newAnnoMatrix._cache.obs = this._cache.obs.withCol(colName, data); - _normalizeCategoricalSchema( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + newAnnoMatrix._cache.obs = (this as any)._cache.obs.withCol(colName, data); + normalizeWritableCategoricalSchema( colSchema, newAnnoMatrix._cache.obs.col(colName) ); @@ -130,15 +153,18 @@ export default class AnnoMatrixLoader extends AnnoMatrix { return newAnnoMatrix; } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'oldCol' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renameObsColumn(oldCol, newCol) { /* Rename the obs oldColName to newColName. oldCol must be writable. */ const oldColSchema = _getColumnSchema(this.schema, "obs", oldCol); - _writableCheck(oldColSchema); // throws on error - - const value = this._cache.obs.hasCol(oldCol) - ? this._cache.obs.col(oldCol).asArray() + _writableCheck(oldColSchema); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const value = (this as any)._cache.obs.hasCol(oldCol) + ? // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any)._cache.obs.col(oldCol).asArray() : undefined; return this.dropObsColumn(oldCol).addObsColumn( { @@ -150,6 +176,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix { ); } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. async setObsColumnValues(col, rowLabels, value) { /* Set all rows identified by rowLabels to value. @@ -159,11 +187,13 @@ export default class AnnoMatrixLoader extends AnnoMatrix { // ensure that we have the data in cache before we manipulate it await this.fetch("obs", col); - if (!this._cache.obs.hasCol(col)) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + if (!(this as any)._cache.obs.hasCol(col)) throw new Error("Internal error - user annotation data missing"); const rowIndices = this.rowIndex.getOffsets(rowLabels); - const data = this._cache.obs.col(col).asArray().slice(); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const data = (this as any)._cache.obs.col(col).asArray().slice(); for (let i = 0, len = rowIndices.length; i < len; i += 1) { const idx = rowIndices[i]; if (idx === undefined) throw new Error("Unknown row label"); @@ -171,7 +201,11 @@ export default class AnnoMatrixLoader extends AnnoMatrix { } const newAnnoMatrix = this._clone(); - newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData( + col, + data + ); const { categories } = colSchema; if (!categories?.includes(value)) { newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, value); @@ -179,6 +213,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix { return newAnnoMatrix; } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'col' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. async resetObsColumnValues(col, oldValue, newValue) { /* Set all rows with value 'oldValue' to 'newValue'. @@ -192,16 +228,22 @@ export default class AnnoMatrixLoader extends AnnoMatrix { // ensure that we have the data in cache before we manipulate it await this.fetch("obs", col); - if (!this._cache.obs.hasCol(col)) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + if (!(this as any)._cache.obs.hasCol(col)) throw new Error("Internal error - user annotation data missing"); - const data = this._cache.obs.col(col).asArray().slice(); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const data = (this as any)._cache.obs.col(col).asArray().slice(); for (let i = 0, l = data.length; i < l; i += 1) { if (data[i] === oldValue) data[i] = newValue; } const newAnnoMatrix = this._clone(); - newAnnoMatrix._cache.obs = this._cache.obs.replaceColData(col, data); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + newAnnoMatrix._cache.obs = (this as any)._cache.obs.replaceColData( + col, + data + ); const { categories } = colSchema; if (!categories?.includes(newValue)) { newAnnoMatrix.schema = addObsAnnoCategory(this.schema, col, newValue); @@ -209,6 +251,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix { return newAnnoMatrix; } + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. addEmbedding(colSchema) { /* add new layout to the obs embeddings @@ -226,6 +270,8 @@ export default class AnnoMatrixLoader extends AnnoMatrix { /** ** Private below **/ + // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixLoader' is n... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. async _doLoad(field, query) { /* _doLoad - evaluates the query against the field. Returns: @@ -255,7 +301,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix { } const buffer = await promiseThrottle.priorityAdd(priority, doRequest); - const result = matrixFBSToDataframe(buffer); + let result = matrixFBSToDataframe(buffer); if (!result || result.isEmpty()) throw Error("Unknown field/col"); const whereCacheUpdate = _whereCacheCreate( @@ -264,13 +310,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix { result.colIndex.labels() ); - if (field === "obs") { - /* cough, cough - see comment on the function called */ - _normalizeCategoricalSchema( - this.schema.annotations.obsByName[query], - result.col(query) - ); - } + result = normalizeResponse(field, this.schema, result); return [whereCacheUpdate, result]; } @@ -280,12 +320,14 @@ export default class AnnoMatrixLoader extends AnnoMatrix { Utility functions below */ +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message function _writableCheck(colSchema) { if (!colSchema?.writable) { throw new Error("Unknown or readonly obs column"); } } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colSchema' implicitly has an 'any' type... Remove this comment to see the full error message function _writableCategoryTypeCheck(colSchema) { _writableCheck(colSchema); if (colSchema.type !== "categorical") { @@ -293,6 +335,7 @@ function _writableCategoryTypeCheck(colSchema) { } } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type. function _embLoader(baseURL, _field, query) { _expectSimpleQuery(query); @@ -302,6 +345,7 @@ function _embLoader(baseURL, _field, query) { return () => doBinaryRequest(url); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type. function _obsOrVarLoader(baseURL, field, query) { _expectSimpleQuery(query); @@ -311,6 +355,7 @@ function _obsOrVarLoader(baseURL, field, query) { return () => doBinaryRequest(url); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'baseURL' implicitly has an 'any' type. function _XLoader(baseURL, field, query) { _expectComplexQuery(query); diff --git a/client/src/annoMatrix/middleware.js b/client/src/annoMatrix/middleware.ts similarity index 58% rename from client/src/annoMatrix/middleware.js rename to client/src/annoMatrix/middleware.ts index d332b79a..581dc24b 100644 --- a/client/src/annoMatrix/middleware.js +++ b/client/src/annoMatrix/middleware.ts @@ -11,7 +11,8 @@ Undoable metareducer and the AnnoMatrix private API. It would be helpful to make the Undoable interface better factored. */ -const annoMatrixGC = (store) => (next) => (action) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const annoMatrixGC = (store: any) => (next: any) => (action: any) => { if (_itIsTimeForGC()) { _doGC(store); } @@ -34,7 +35,8 @@ function _itIsTimeForGC() { return false; } -function _doGC(store) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _doGC(store: any) { const state = store.getState(); // these should probably be a function imported from undoable.js, etc, as @@ -43,8 +45,10 @@ function _doGC(store) { const undoableFuture = state["@@undoable/future"]; const undoableStack = undoablePast .concat(undoableFuture) - .flatMap((snapshot) => - snapshot.filter((v) => v[0] === "annoMatrix").map((v) => v[1]) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .flatMap((snapshot: any) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + snapshot.filter((v: any) => v[0] === "annoMatrix").map((v: any) => v[1]) ); const currentAnnoMatrix = state.annoMatrix; @@ -53,14 +57,18 @@ function _doGC(store) { as our current gc algo is more aggressive with those not hot. */ const allAnnoMatrices = new Map( - undoableStack.map((m) => [m, { isHot: false }]) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + undoableStack.map((m: any) => [m, { isHot: false }]) ); let am = currentAnnoMatrix; while (am) { allAnnoMatrices.set(am, { isHot: true }); am = am.viewOf; } - allAnnoMatrices.forEach((hints, annoMatrix) => annoMatrix._gc(hints)); + allAnnoMatrices.forEach((hints, annoMatrix) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (annoMatrix as any)._gc(hints) + ); } export default annoMatrixGC; diff --git a/client/src/annoMatrix/normalize.ts b/client/src/annoMatrix/normalize.ts new file mode 100644 index 00000000..f71cc799 --- /dev/null +++ b/client/src/annoMatrix/normalize.ts @@ -0,0 +1,164 @@ +import { _getColumnSchema, _isIndex } from "./schema"; +import catLabelSort from "../util/catLabelSort"; +import { + unassignedCategoryLabel, + overflowCategoryLabel, + globalConfig, +} from "../globals"; +import { Dataframe } from "../util/dataframe"; + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function normalizeResponse( + field: string, + schema: any, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + response: Dataframe +): Dataframe { + /** + * There are a number of assumptions in the front-end about data typing and data + * characteristics. This routine will normalize a server response dataframe + * to match front-end expectations and UI conventions. This includes cast/transform + * of the data and schema updates. + * + * This consolidates all assumptions into one location, for ease of update. + * + * Currently, this includes normalization for obs/var columns only: + * + * - Dataframe columns in var/obs that are declared type: boolean may be sent by + * the server in a variety of formats (eg uint8, etc). Cast to JS Array[boolean] + * + * - "Categorical" columns may not have all categories represented in the server-provided + * schema (for valid reasons, eg, floating point rounding differences). For all + * types we treat as categorical in the UI (string, boolean, categorical), update + * the schema to contain all categories as a convenience. + * + * - "Categorical" columns (ie, string, boolean, categorical) may contain an excess + * of category values (aka labels). Consolidate any excess into an "all other" + * category. + */ + + // currently no data or schema normalization necessary for X or emb + if (field !== "obs" && field !== "var") return response; + + const colLabels = response.colIndex.labels(); + for (const colLabel of colLabels) { + const colSchema = _getColumnSchema(schema, field, colLabel); + const isIndex = _isIndex(schema, field, colLabel); + const { type, writable } = colSchema; + + // Boolean data -- cast entire array to Array[bool] + if (type === "boolean") { + response = castColumnToBoolean(response, colLabel); + } + + // Types that are categorical in UI (string, boolean, categorical) OR are writable + // are introspected to ensure the schema `categories` field and data values match, + // and that we do not have an excess of category values (for non-writable columns) + const isEnumType = + type === "boolean" || + type === "string" || + type === "categorical" || + writable; + if (!isIndex && isEnumType) { + response = normalizeCategorical(response, colLabel, colSchema); + } + } + return response; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +function castColumnToBoolean(df: Dataframe, label: any): Dataframe { + const colData = df.col(label).asArray(); + const newColData = new Array(colData.length); + for (let i = 0; i < colData.length; i += 1) newColData[i] = !!colData[i]; + df = df.replaceColData(label, newColData); + return df; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function normalizeWritableCategoricalSchema(colSchema: any, col: any) { + /* + Ensure all enum writable / categorical schema have a categories array, that + the categories array contains all unique values in the data array, AND that + the array is UI sorted. + */ + const categorySet = new Set( + col.summarizeCategorical().categories.concat(colSchema.categories ?? []) + ); + if (!categorySet.has(unassignedCategoryLabel)) { + categorySet.add(unassignedCategoryLabel); + } + colSchema.categories = catLabelSort(true, Array.from(categorySet)); + return colSchema; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function normalizeCategorical( + df: Dataframe, + colLabel: any, // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colSchema: any // eslint-disable-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +) { + /* + If writable, ensure schema matches data and we have an unassigned label + + If not writable, ensure schema matches data and that we consolidate labels in excess + of "top N" into an overflow labels. + */ + const { writable } = colSchema; + const col = df.col(colLabel); + + if (writable) { + // writable (aka user) annotations + normalizeWritableCategoricalSchema(colSchema, col); + return df; + } + + // else read-only, categorical columns + const TopN = globalConfig.maxCategoricalOptionsToDisplay; + + // consolidate all categories from data and schema into a single list + const colDataSummary = col.summarizeCategorical(); + const allCategories = new Set( + colDataSummary.categories.concat(colSchema.categories ?? []) + ); + + // if no overflow, just UI sort schema categories and return + if (allCategories.size <= TopN) { + colSchema.categories = catLabelSort(writable, [...allCategories.keys()]); + return df; + } + + // Otherwise, pick top N categories by count and rewrite data + + // choose unique overflow category label + let overflowCatName = `${colLabel}${overflowCategoryLabel}`; + while (allCategories.has(overflowCatName)) { + overflowCatName += "_"; + } + + // pick top N category labels and add overflow label + const topNCategories = new Set( + [...colDataSummary.categoryCounts.keys()].slice(0, TopN) + ); + topNCategories.add(overflowCatName); + + // rewrite data - consolidate all excess labels into overflow label + const newColData = Array.from(col.asArray()); + for (let i = 0; i < newColData.length; i += 1) { + if (!topNCategories.has(newColData[i])) { + newColData[i] = overflowCatName; + } + } + + // replace data in dataframe + df = df.replaceColData(colLabel, newColData); + + // Update schema with categories, in UI sort order. Ensure overflow label is at end + // of list for display purposes. + const revisedCategories = df.col(colLabel).summarizeCategorical().categories; + revisedCategories.push( + revisedCategories.splice(revisedCategories.indexOf(overflowCatName), 1)[0] + ); + colSchema.categories = catLabelSort(writable, revisedCategories); + + return df; +} diff --git a/client/src/annoMatrix/query.js b/client/src/annoMatrix/query.ts similarity index 59% rename from client/src/annoMatrix/query.js rename to client/src/annoMatrix/query.ts index 55017858..a01a58c0 100644 --- a/client/src/annoMatrix/query.js +++ b/client/src/annoMatrix/query.ts @@ -10,7 +10,8 @@ import { _dubEncURIComp } from "./fetchHelpers"; * @param {object | string} query - the query * @returns {object | string} - the normalized query */ -export function _queryValidate(query) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _queryValidate(query: any) { if (typeof query !== "object") return query; if (query.where && query.summarize) @@ -40,11 +41,13 @@ export function _queryValidate(query) { throw new Error("query must specify one of where or summarize"); } -export function _expectSimpleQuery(query) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _expectSimpleQuery(query: any) { if (typeof query === "object") throw new Error("expected simple query"); } -export function _expectComplexQuery(query) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _expectComplexQuery(query: any) { if (typeof query !== "object") throw new Error("expected complex query"); } @@ -55,7 +58,8 @@ export function _expectComplexQuery(query) { * @param {string|object} query * @returns the key */ -export function _queryCacheKey(field, query) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _queryCacheKey(field: any, query: any) { if (typeof query === "object") { // complex query if (query.where) { @@ -84,22 +88,25 @@ export function _queryCacheKey(field, query) { return `${field}/${query}`; } -function _urlEncodeWhereQuery(q) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _urlEncodeWhereQuery(q: any) { const { field: queryField, column: queryColumn, value: queryValue } = q; return `${_dubEncURIComp(queryField)}:${_dubEncURIComp( queryColumn )}=${_dubEncURIComp(queryValue)}`; } -function _urlEncodeSummarizeQuery(q) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _urlEncodeSummarizeQuery(q: any) { const { method, field, column, values } = q; - const filter = values - .map((value) => _urlEncodeWhereQuery({ field, column, value })) + const filter = values // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .map((value: any) => _urlEncodeWhereQuery({ field, column, value })) .join("&"); return `method=${method}&${filter}`; } -export function _urlEncodeComplexQuery(q) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _urlEncodeComplexQuery(q: any) { if (typeof q === "object") { if (q.where) { return _urlEncodeWhereQuery(q.where); @@ -111,7 +118,8 @@ export function _urlEncodeComplexQuery(q) { throw new Error("Unrecognized complex query type"); } -export function _urlEncodeLabelQuery(colKey, q) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _urlEncodeLabelQuery(colKey: any, q: any) { if (!colKey) throw new Error("Unsupported query by name"); if (typeof q !== "string") throw new Error("Query must be a simple label."); return `${colKey}=${encodeURIComponent(q)}`; @@ -120,7 +128,8 @@ export function _urlEncodeLabelQuery(colKey, q) { /** * Generate the column key the server will send us for this query. */ -export function _hashStringValues(arrayOfString) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _hashStringValues(arrayOfString: any) { const hash = sha1(arrayOfString.join("")); return hash; } diff --git a/client/src/annoMatrix/schema.js b/client/src/annoMatrix/schema.js deleted file mode 100644 index aade2c20..00000000 --- a/client/src/annoMatrix/schema.js +++ /dev/null @@ -1,88 +0,0 @@ -/* -Private helper functions related to schema -*/ -import catLabelSort from "../util/catLabelSort"; -import { unassignedCategoryLabel } from "../globals"; - -export function _getColumnSchema(schema, field, col) { - /* look up the column definition */ - switch (field) { - case "obs": - if (typeof col === "object") - throw new Error("unable to get column schema by query"); - return schema.annotations.obsByName[col]; - case "var": - if (typeof col === "object") - throw new Error("unable to get column schema by query"); - return schema.annotations.varByName[col]; - case "emb": - if (typeof col === "object") - throw new Error("unable to get column schema by query"); - return schema.layout.obsByName[col]; - case "X": - return schema.dataframe; - default: - throw new Error(`unknown field name: ${field}`); - } -} - -export function _getColumnDimensionNames(schema, field, col) { - /* - field/col may be an alias for multiple columns. Currently used to map ND - values to 1D dataframe columns for embeddings/layout. Signified by the presence - of the "dims" value in the schema. - */ - const colSchema = _getColumnSchema(schema, field, col); - if (!colSchema) { - return undefined; - } - return colSchema.dims || [col]; -} - -export function _schemaColumns(schema, field) { - switch (field) { - case "obs": - return Object.keys(schema.annotations.obsByName); - case "var": - return Object.keys(schema.annotations.varByName); - case "emb": - return Object.keys(schema.layout.obsByName); - default: - throw new Error(`unknown field name: ${field}`); - } -} - -export function _getWritableColumns(schema, field) { - if (field !== "obs") return []; - return schema.annotations.obs.columns - .filter((v) => v.writable) - .map((v) => v.name); -} - -export function _isContinuousType(schema) { - const { type } = schema; - return !(type === "string" || type === "boolean" || type === "categorical"); -} - -export function _normalizeCategoricalSchema(colSchema, col) { - const { type, writable } = colSchema; - if ( - type === "string" || - type === "boolean" || - type === "categorical" || - writable - ) { - const categorySet = new Set( - col.summarizeCategorical().categories.concat(colSchema.categories ?? []) - ); - if (writable && !categorySet.has(unassignedCategoryLabel)) { - categorySet.add(unassignedCategoryLabel); - } - colSchema.categories = Array.from(categorySet); - } - - if (colSchema.categories) { - colSchema.categories = catLabelSort(writable, colSchema.categories); - } - return colSchema; -} diff --git a/client/src/annoMatrix/schema.ts b/client/src/annoMatrix/schema.ts new file mode 100644 index 00000000..28e88ab5 --- /dev/null +++ b/client/src/annoMatrix/schema.ts @@ -0,0 +1,80 @@ +/* +Private helper functions related to schema +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _getColumnSchema(schema: any, field: any, col: any) { + /* look up the column definition */ + switch (field) { + case "obs": + if (typeof col === "object") + throw new Error("unable to get column schema by query"); + return schema.annotations.obsByName[col]; + case "var": + if (typeof col === "object") + throw new Error("unable to get column schema by query"); + return schema.annotations.varByName[col]; + case "emb": + if (typeof col === "object") + throw new Error("unable to get column schema by query"); + return schema.layout.obsByName[col]; + case "X": + return schema.dataframe; + default: + throw new Error(`unknown field name: ${field}`); + } +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function _isIndex(schema: any, field: any, col: any): boolean { + const index = schema.annotations?.[field].index; + return index && index === col; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +export function _getColumnDimensionNames(schema: any, field: any, col: any) { + /* + field/col may be an alias for multiple columns. Currently used to map ND + values to 1D dataframe columns for embeddings/layout. Signified by the presence + of the "dims" value in the schema. + */ + const colSchema = _getColumnSchema(schema, field, col); + if (!colSchema) { + return undefined; + } + return colSchema.dims || [col]; +} + +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function _schemaColumns(schema, field) { + switch (field) { + case "obs": + return Object.keys(schema.annotations.obsByName); + case "var": + return Object.keys(schema.annotations.varByName); + case "emb": + return Object.keys(schema.layout.obsByName); + default: + throw new Error(`unknown field name: ${field}`); + } +} + +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function _getWritableColumns(schema, field) { + if (field !== "obs") return []; + return ( + schema.annotations.obs.columns + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'v' implicitly has an 'any' type. + .filter((v) => v.writable) + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'v' implicitly has an 'any' type. + .map((v) => v.name) + ); +} + +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function _isContinuousType(schema) { + const { type } = schema; + return !(type === "string" || type === "boolean" || type === "categorical"); +} diff --git a/client/src/annoMatrix/viewCreators.js b/client/src/annoMatrix/viewCreators.ts similarity index 56% rename from client/src/annoMatrix/viewCreators.js rename to client/src/annoMatrix/viewCreators.ts index 28991b44..bc5a6eab 100644 --- a/client/src/annoMatrix/viewCreators.js +++ b/client/src/annoMatrix/viewCreators.ts @@ -5,7 +5,8 @@ instances of AnnoMatrix, implementing common UI functions. import { AnnoMatrixRowSubsetView, AnnoMatrixClipView } from "./views"; -export function isubsetMask(annoMatrix, obsMask) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function isubsetMask(annoMatrix: any, obsMask: any) { /* Subset annomatrix to contain the rows which have truish value in the mask. Maks length must equal annoMatrix.nObs (row count). @@ -13,6 +14,8 @@ export function isubsetMask(annoMatrix, obsMask) { return isubset(annoMatrix, _maskToList(obsMask)); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function isubset(annoMatrix, obsOffsets) { /* Subset annomatrix to contain the positions contained in the obsOffsets array @@ -25,6 +28,8 @@ export function isubset(annoMatrix, obsOffsets) { return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function subset(annoMatrix, obsLabels) { /* subset based on labels @@ -33,6 +38,8 @@ export function subset(annoMatrix, obsLabels) { return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function subsetByIndex(annoMatrix, obsIndex) { /* subset based upon the new obs index. @@ -40,6 +47,8 @@ export function subsetByIndex(annoMatrix, obsIndex) { return new AnnoMatrixRowSubsetView(annoMatrix, obsIndex); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function clip(annoMatrix, qmin, qmax) { /* Create a view that clips all continuous data to the [min, max] range. @@ -53,6 +62,7 @@ export function clip(annoMatrix, qmin, qmax) { Private utility functions below */ +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'mask' implicitly has an 'any' type. function _maskToList(mask) { /* convert masks to lists - method wastes space, but is fast */ if (!mask) { diff --git a/client/src/annoMatrix/views.js b/client/src/annoMatrix/views.ts similarity index 55% rename from client/src/annoMatrix/views.js rename to client/src/annoMatrix/views.ts index 5b9b9c26..2b533577 100644 --- a/client/src/annoMatrix/views.js +++ b/client/src/annoMatrix/views.ts @@ -9,21 +9,31 @@ import { _whereCacheCreate } from "./whereCache"; import { _isContinuousType, _getColumnSchema } from "./schema"; class AnnoMatrixView extends AnnoMatrix { - constructor(viewOf, rowIndex = null) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + constructor(viewOf: any, rowIndex = null) { + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. const nObs = rowIndex ? rowIndex.size() : viewOf.nObs; super(viewOf.schema, nObs, viewOf.nVar, rowIndex || viewOf.rowIndex); this.viewOf = viewOf; this.isView = true; } - addObsAnnoCategory(col, category) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + addObsAnnoCategory(col: any, category: any) { const newAnnoMatrix = this._clone(); newAnnoMatrix.viewOf = this.viewOf.addObsAnnoCategory(col, category); newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema; return newAnnoMatrix; } - async removeObsAnnoCategory(col, category, unassignedCategory) { + async removeObsAnnoCategory( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + col: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + category: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + unassignedCategory: any + ) { const newAnnoMatrix = this._clone(); newAnnoMatrix.viewOf = await this.viewOf.removeObsAnnoCategory( col, @@ -34,7 +44,8 @@ class AnnoMatrixView extends AnnoMatrix { return newAnnoMatrix; } - dropObsColumn(col) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dropObsColumn(col: any) { const newAnnoMatrix = this._clone(); newAnnoMatrix.viewOf = this.viewOf.dropObsColumn(col); newAnnoMatrix._cache.obs = this._cache.obs.dropCol(col); @@ -42,21 +53,24 @@ class AnnoMatrixView extends AnnoMatrix { return newAnnoMatrix; } - addObsColumn(colSchema, Ctor, value) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + addObsColumn(colSchema: any, Ctor: any, value: any) { const newAnnoMatrix = this._clone(); newAnnoMatrix.viewOf = this.viewOf.addObsColumn(colSchema, Ctor, value); newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema; return newAnnoMatrix; } - renameObsColumn(oldCol, newCol) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + renameObsColumn(oldCol: any, newCol: any) { const newAnnoMatrix = this._clone(); newAnnoMatrix.viewOf = this.viewOf.renameObsColumn(oldCol, newCol); newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema; return newAnnoMatrix; } - async setObsColumnValues(col, rowLabels, value) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + async setObsColumnValues(col: any, rowLabels: any, value: any) { const newAnnoMatrix = this._clone(); newAnnoMatrix.viewOf = await this.viewOf.setObsColumnValues( col, @@ -68,7 +82,8 @@ class AnnoMatrixView extends AnnoMatrix { return newAnnoMatrix; } - async resetObsColumnValues(col, oldValue, newValue) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + async resetObsColumnValues(col: any, oldValue: any, newValue: any) { const newAnnoMatrix = this._clone(); newAnnoMatrix.viewOf = await this.viewOf.resetObsColumnValues( col, @@ -80,7 +95,8 @@ class AnnoMatrixView extends AnnoMatrix { return newAnnoMatrix; } - addEmbedding(colSchema) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + addEmbedding(colSchema: any) { const newAnnoMatrix = this._clone(); newAnnoMatrix.viewOf = this.viewOf.addEmbedding(colSchema); newAnnoMatrix.schema = newAnnoMatrix.viewOf.schema; @@ -92,17 +108,22 @@ class AnnoMatrixMapView extends AnnoMatrixView { /* A view which knows how to transform its data. */ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type. constructor(viewOf, mapFn) { super(viewOf); - this.mapFn = mapFn; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).mapFn = mapFn; } + // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixMapView' is ... Remove this comment to see the full error message async _doLoad(field, query) { const df = await this.viewOf._fetch(field, query); + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'colData' implicitly has an 'any' type. const dfMapped = df.mapColumns((colData, colIdx) => { const colLabel = df.colIndex.getLabel(colIdx); const colSchema = _getColumnSchema(this.schema, field, colLabel); - return this.mapFn(field, colLabel, colSchema, colData, df); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (this as any).mapFn(field, colLabel, colSchema, colData, df); }); const whereCacheUpdate = _whereCacheCreate( field, @@ -117,12 +138,17 @@ export class AnnoMatrixClipView extends AnnoMatrixMapView { /* A view which is a clipped transformation of its parent */ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. constructor(viewOf, qmin, qmax) { + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. super(viewOf, (field, colLabel, colSchema, colData, df) => _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax) ); - this.isClipped = true; - this.clipRange = [qmin, qmax]; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).isClipped = true; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).clipRange = [qmin, qmax]; Object.seal(this); } } @@ -131,11 +157,15 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView { /* A view which is a subset of total rows. */ + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'viewOf' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. constructor(viewOf, rowIndex) { super(viewOf, rowIndex); Object.seal(this); } + // @ts-expect-error ts-migrate(2416) FIXME: Property '_doLoad' in type 'AnnoMatrixRowSubsetVie... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. async _doLoad(field, query) { const df = await this.viewOf._fetch(field, query); @@ -158,6 +188,7 @@ export class AnnoMatrixRowSubsetView extends AnnoMatrixView { Utility functions below */ +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. function _clipAnnoMatrix(field, colLabel, colSchema, colData, df, qmin, qmax) { /* only clip obs and var scalar columns */ if (field !== "obs" && field !== "X") return colData; diff --git a/client/src/annoMatrix/whereCache.js b/client/src/annoMatrix/whereCache.ts similarity index 72% rename from client/src/annoMatrix/whereCache.js rename to client/src/annoMatrix/whereCache.ts index e67c5d49..79fb0d95 100644 --- a/client/src/annoMatrix/whereCache.js +++ b/client/src/annoMatrix/whereCache.ts @@ -51,7 +51,17 @@ creates a cache entry of: import { _getColumnDimensionNames } from "./schema"; import { _hashStringValues } from "./query"; -export function _whereCacheGet(whereCache, schema, field, query) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function _whereCacheGet( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + whereCache: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + schema: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + field: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + query: any +) { /* query will either be an where query (object) or a column name (string). @@ -85,6 +95,8 @@ export function _whereCacheGet(whereCache, schema, field, query) { return _getColumnDimensionNames(schema, field, query) ?? [undefined]; } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'field' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function _whereCacheCreate(field, query, columnLabels) { /* Create a new whereCache @@ -131,10 +143,12 @@ export function _whereCacheCreate(field, query, columnLabels) { return {}; } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'dst' implicitly has an 'any' type. function __mergeQueries(dst, src) { for (const [queryField, columnMap] of Object.entries(src)) { dst[queryField] = dst[queryField] || new Map(); - for (const [queryColumn, valueMap] of columnMap) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + for (const [queryColumn, valueMap] of columnMap as any) { if (!dst[queryField].has(queryColumn)) dst[queryField].set(queryColumn, new Map()); for (const [queryValue, columnLabels] of valueMap) { @@ -144,6 +158,7 @@ function __mergeQueries(dst, src) { } } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'dst' implicitly has an 'any' type. function __whereCacheMerge(dst, src) { /* merge src into dst (modifies dst) @@ -161,6 +176,7 @@ function __whereCacheMerge(dst, src) { dst.summarize = dst.summarize || {}; for (const [field, method] of Object.entries(src.summarize)) { dst.summarize[field] = dst.summarize[field] || {}; + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. for (const [methodName, query] of Object.entries(method)) { dst.summarize[field][methodName] = dst.summarize[field][methodName] || {}; @@ -171,6 +187,8 @@ function __whereCacheMerge(dst, src) { return dst; } +// @ts-expect-error ts-migrate(7019) FIXME: Rest parameter 'caches' implicitly has an 'any[]' ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function _whereCacheMerge(...caches) { return caches.reduce(__whereCacheMerge, {}); } diff --git a/client/src/common/types/entities.ts b/client/src/common/types/entities.ts new file mode 100644 index 00000000..bdeea455 --- /dev/null +++ b/client/src/common/types/entities.ts @@ -0,0 +1 @@ +// If a globally shared type or interface doesn't have a clear owner, put it here diff --git a/client/src/components/annoDialog.js b/client/src/components/annoDialog.js deleted file mode 100644 index 8064b146..00000000 --- a/client/src/components/annoDialog.js +++ /dev/null @@ -1,94 +0,0 @@ -import React from "react"; -import { Button, Tooltip, Dialog, Classes, Colors } from "@blueprintjs/core"; - -class AnnoDialog extends React.PureComponent { - constructor(props) { - super(props); - this.state = {}; - } - - render() { - const { - isActive, - text, - title, - instruction, - cancelTooltipContent, - errorMessage, - validationError, - annoSelect, - annoInput, - secondaryInstructions, - secondaryInput, - handleCancel, - handleSubmit, - primaryButtonText, - secondaryButtonText, - handleSecondaryButtonSubmit, - primaryButtonProps, - } = this.props; - - return ( - -
{ - e.preventDefault(); - }} - > -
-
-

{instruction}

- {annoInput || null} -

- {errorMessage} -

- {/* we might rename, secondary button and secondary input are not related */} - {secondaryInstructions && ( -

- {secondaryInstructions} -

- )} - {secondaryInput || null} -
- {annoSelect || null} -
-
-
- - - - {/* we might rename, secondary button and secondary input are not related */} - {handleSecondaryButtonSubmit && secondaryButtonText ? ( - - ) : null} - -
-
-
- - ); - } -} - -export default AnnoDialog; diff --git a/client/src/components/annoDialog.tsx b/client/src/components/annoDialog.tsx new file mode 100644 index 00000000..04042378 --- /dev/null +++ b/client/src/components/annoDialog.tsx @@ -0,0 +1,117 @@ +import React from "react"; +import { Button, Tooltip, Dialog, Classes, Colors } from "@blueprintjs/core"; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class AnnoDialog extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { + super(props); + this.state = {}; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isActive' does not exist on type 'Readon... Remove this comment to see the full error message + isActive, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'text' does not exist on type 'Readonly<{... Remove this comment to see the full error message + text, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'title' does not exist on type 'Readonly<... Remove this comment to see the full error message + title, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'instruction' does not exist on type 'Rea... Remove this comment to see the full error message + instruction, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'cancelTooltipContent' does not exist on ... Remove this comment to see the full error message + cancelTooltipContent, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'errorMessage' does not exist on type 'Re... Remove this comment to see the full error message + errorMessage, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'validationError' does not exist on type ... Remove this comment to see the full error message + validationError, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoSelect' does not exist on type 'Read... Remove this comment to see the full error message + annoSelect, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoInput' does not exist on type 'Reado... Remove this comment to see the full error message + annoInput, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'secondaryInstructions' does not exist on... Remove this comment to see the full error message + secondaryInstructions, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'secondaryInput' does not exist on type '... Remove this comment to see the full error message + secondaryInput, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleCancel' does not exist on type 'Re... Remove this comment to see the full error message + handleCancel, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleSubmit' does not exist on type 'Re... Remove this comment to see the full error message + handleSubmit, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'primaryButtonText' does not exist on typ... Remove this comment to see the full error message + primaryButtonText, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'secondaryButtonText' does not exist on t... Remove this comment to see the full error message + secondaryButtonText, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleSecondaryButtonSubmit' does not ex... Remove this comment to see the full error message + handleSecondaryButtonSubmit, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'primaryButtonProps' does not exist on ty... Remove this comment to see the full error message + primaryButtonProps, + } = this.props; + + return ( + +
{ + e.preventDefault(); + }} + > +
+
+

{instruction}

+ {annoInput || null} +

+ {errorMessage} +

+ {/* we might rename, secondary button and secondary input are not related */} + {secondaryInstructions && ( +

+ {secondaryInstructions} +

+ )} + {secondaryInput || null} +
+ {annoSelect || null} +
+
+
+ + + + {/* we might rename, secondary button and secondary input are not related */} + {handleSecondaryButtonSubmit && secondaryButtonText ? ( + + ) : null} + +
+
+
+ + ); + } +} + +export default AnnoDialog; diff --git a/client/src/components/app.js b/client/src/components/app.tsx similarity index 55% rename from client/src/components/app.js rename to client/src/components/app.tsx index f2dfa489..560053bf 100644 --- a/client/src/components/app.js +++ b/client/src/components/app.tsx @@ -16,31 +16,39 @@ import TermsOfServicePrompt from "./termsPrompt"; import actions from "../actions"; +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - loading: state.controls.loading, - error: state.controls.error, - graphRenderCounter: state.controls.graphRenderCounter, - layoutChoice: state.layoutChoice, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + loading: (state as any).controls.loading, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + error: (state as any).controls.error, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + graphRenderCounter: (state as any).controls.graphRenderCounter, + layoutChoice: (state as any).layoutChoice, })) class App extends React.Component { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. componentDidMount() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; - /* listen for url changes, fire one when we start the app up */ window.addEventListener("popstate", this._onURLChanged); this._onURLChanged(); - + // @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1. dispatch(actions.doInitialDataLoad(window.location.search)); this.forceUpdate(); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _onURLChanged() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; - dispatch({ type: "url changed", url: document.location.href }); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'loading' does not exist on type 'Readonl... Remove this comment to see the full error message const { loading, error, graphRenderCounter, layoutChoice } = this.props; return ( @@ -72,14 +80,18 @@ class App extends React.Component { {loading || error ? null : ( - {(viewportRef) => ( + {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. */} + {(viewportRef: any) => ( <> + {/* @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. */} {layoutChoice.dotplot && } + + {/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ key: any; viewportRef: any; }' is not assi... Remove this comment to see the full error message */} ({ - idhash: state.config?.parameters?.["annotations-user-data-idhash"] ?? null, - annotations: state.annotations, - auth: state.config?.authentication, - userInfo: state.userInfo, - writableCategoriesEnabled: state.config?.parameters?.annotations ?? false, + idhash: + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (state as any).config?.parameters?.["annotations-user-data-idhash"] ?? null, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annotations: (state as any).annotations, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + auth: (state as any).config?.authentication, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userInfo: (state as any).userInfo, + writableCategoriesEnabled: + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (state as any).config?.parameters?.annotations ?? false, writableGenesetsEnabled: !( - state.config?.parameters?.annotations_genesets_readonly ?? true + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + ((state as any).config?.parameters?.annotations_genesets_readonly ?? true) ), })) -class FilenameDialog extends React.Component { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class FilenameDialog extends React.Component<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { filenameText: "", }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. dismissFilenameDialog = () => {}; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleCreateFilename = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; const { filenameText } = this.state; - dispatch({ type: "set annotations collection name", data: filenameText, }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. filenameError = () => { const legalNames = /^\w+$/; const { filenameText } = this.state; let err = false; - if (filenameText === "") { + // @ts-expect-error ts-migrate(2322) FIXME: Type 'string' is not assignable to type 'boolean'. err = "empty_string"; } else if (!legalNames.test(filenameText)) { /* - IMPORTANT: this test must ultimately match the test applied by the - backend, which is designed to ensure a safe file name can be created - from the data collection name. If you change this, you will also need - to change the validation code in the backend, or it will have no effect. - */ + IMPORTANT: this test must ultimately match the test applied by the + backend, which is designed to ensure a safe file name can be created + from the data collection name. If you change this, you will also need + to change the validation code in the backend, or it will have no effect. + */ + // @ts-expect-error ts-migrate(2322) FIXME: Type 'string' is not assignable to type 'boolean'. err = "characters"; } - return err; }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. filenameErrorMessage = () => { const err = this.filenameError(); let markup = null; - + // @ts-expect-error ts-migrate(2367) FIXME: This condition will always return 'false' since th... Remove this comment to see the full error message if (err === "empty_string") { markup = ( ); + // @ts-expect-error ts-migrate(2367) FIXME: This condition will always return 'false' since th... Remove this comment to see the full error message } else if (err === "characters") { markup = ( this.setState({ filenameText: e.target.value }) @@ -138,12 +163,14 @@ class FilenameDialog extends React.Component {

+ {/* @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1. */} {this.filenameErrorMessage(filenameText)}

@@ -171,6 +198,7 @@ class FilenameDialog extends React.Component {
-
-
- ); -}; - -export default StillLoading; diff --git a/client/src/components/brushableHistogram/loading.tsx b/client/src/components/brushableHistogram/loading.tsx new file mode 100644 index 00000000..65b73e16 --- /dev/null +++ b/client/src/components/brushableHistogram/loading.tsx @@ -0,0 +1,41 @@ +import React from "react"; +import { Button } from "@blueprintjs/core"; + +import * as globals from "../../globals"; + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const StillLoading = ({ zebra, displayName }: any) => ( + /* + Render a loading indicator for the field. + */ +
+
+
+
+ {displayName} +
+
+
+
+
+); +export default StillLoading; diff --git a/client/src/components/categorical/annoSelect.js b/client/src/components/categorical/annoSelect.js deleted file mode 100644 index f2d3cd84..00000000 --- a/client/src/components/categorical/annoSelect.js +++ /dev/null @@ -1,56 +0,0 @@ -import React from "react"; -import { Button, MenuItem } from "@blueprintjs/core"; -import { Select } from "@blueprintjs/select"; - -class DuplicateCategorySelect extends React.PureComponent { - constructor(props) { - super(props); - this.state = {}; - } - - render() { - const { - allCategoryNames, - categoryToDuplicate, - handleModalDuplicateCategorySelection, - } = this.props; - return ( -
-

- Optionally duplicate all labels & cell assignments from existing - category into new category: -

- -
- ); - } -} - -export default DuplicateCategorySelect; diff --git a/client/src/components/categorical/annoSelect.tsx b/client/src/components/categorical/annoSelect.tsx new file mode 100644 index 00000000..a803156b --- /dev/null +++ b/client/src/components/categorical/annoSelect.tsx @@ -0,0 +1,65 @@ +import React from "react"; +import { Button, MenuItem } from "@blueprintjs/core"; +import { Select } from "@blueprintjs/select"; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class DuplicateCategorySelect extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { + super(props); + this.state = {}; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'allCategoryNames' does not exist on type... Remove this comment to see the full error message + allCategoryNames, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryToDuplicate' does not exist on t... Remove this comment to see the full error message + categoryToDuplicate, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleModalDuplicateCategorySelection' d... Remove this comment to see the full error message + handleModalDuplicateCategorySelection, + } = this.props; + return ( +
+

+ Optionally duplicate all labels & cell assignments from existing + category into new category: +

+ +
+ ); + } +} + +export default DuplicateCategorySelect; diff --git a/client/src/components/categorical/category/annoDialogAddLabel.js b/client/src/components/categorical/category/annoDialogAddLabel.js deleted file mode 100644 index 0347653f..00000000 --- a/client/src/components/categorical/category/annoDialogAddLabel.js +++ /dev/null @@ -1,115 +0,0 @@ -import React from "react"; -import { connect } from "react-redux"; -import AnnoDialog from "../../annoDialog"; -import LabelInput from "../../labelInput"; -import { labelPrompt, isLabelErroneous } from "../labelUtil"; -import actions from "../../../actions"; - -@connect((state) => ({ - annotations: state.annotations, - schema: state.annoMatrix?.schema, - obsCrossfilter: state.obsCrossfilter, -})) -class Category extends React.PureComponent { - constructor(props) { - super(props); - this.state = { - newLabelText: "", - }; - } - - disableAddNewLabelMode = (e) => { - const { dispatch } = this.props; - this.setState({ - newLabelText: "", - }); - dispatch({ - type: "annotation: disable add new label mode", - }); - if (e) e.preventDefault(); - }; - - handleAddNewLabelToCategory = (e) => { - const { dispatch, metadataField } = this.props; - const { newLabelText } = this.state; - - this.disableAddNewLabelMode(); - dispatch( - actions.annotationCreateLabelInCategory( - metadataField, - newLabelText, - false - ) - ); - e.preventDefault(); - }; - - addLabelAndAssignCells = (e) => { - const { dispatch, metadataField } = this.props; - const { newLabelText } = this.state; - - this.disableAddNewLabelMode(); - dispatch( - actions.annotationCreateLabelInCategory(metadataField, newLabelText, true) - ); - e.preventDefault(); - }; - - labelNameError = (name) => { - const { metadataField, schema } = this.props; - return isLabelErroneous(name, metadataField, schema); - }; - - instruction = (label) => { - return labelPrompt(this.labelNameError(label), "New, unique label", ":"); - }; - - handleChangeOrSelect = (label) => { - this.setState({ newLabelText: label }); - }; - - render() { - const { newLabelText } = this.state; - const { metadataField, annotations, obsCrossfilter } = this.props; - - return ( - <> - - } - /> - - ); - } -} - -export default Category; diff --git a/client/src/components/categorical/category/annoDialogAddLabel.tsx b/client/src/components/categorical/category/annoDialogAddLabel.tsx new file mode 100644 index 00000000..29235feb --- /dev/null +++ b/client/src/components/categorical/category/annoDialogAddLabel.tsx @@ -0,0 +1,136 @@ +import React from "react"; +import { connect } from "react-redux"; +import AnnoDialog from "../../annoDialog"; +import LabelInput from "../../labelInput"; +import { labelPrompt, isLabelErroneous } from "../labelUtil"; +import actions from "../../../actions"; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annotations: (state as any).annotations, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + obsCrossfilter: (state as any).obsCrossfilter, +})) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class Category extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { + super(props); + this.state = { + newLabelText: "", + }; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + disableAddNewLabelMode = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + this.setState({ + newLabelText: "", + }); + dispatch({ + type: "annotation: disable add new label mode", + }); + if (e) e.preventDefault(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleAddNewLabelToCategory = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, metadataField } = this.props; + const { newLabelText } = this.state; + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. + this.disableAddNewLabelMode(); + dispatch( + actions.annotationCreateLabelInCategory( + metadataField, + newLabelText, + false + ) + ); + e.preventDefault(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + addLabelAndAssignCells = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, metadataField } = this.props; + const { newLabelText } = this.state; + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. + this.disableAddNewLabelMode(); + dispatch( + actions.annotationCreateLabelInCategory(metadataField, newLabelText, true) + ); + e.preventDefault(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + labelNameError = (name: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message + const { metadataField, schema } = this.props; + return isLabelErroneous(name, metadataField, schema); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + instruction = (label: any) => + labelPrompt(this.labelNameError(label), "New, unique label", ":"); + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChangeOrSelect = (label: any) => { + this.setState({ newLabelText: label }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { newLabelText } = this.state; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message + const { metadataField, annotations, obsCrossfilter } = this.props; + return ( + <> + + } + /> + + ); + } +} + +export default Category; diff --git a/client/src/components/categorical/category/annoDialogEditCategoryName.js b/client/src/components/categorical/category/annoDialogEditCategoryName.js deleted file mode 100644 index 24a8c41b..00000000 --- a/client/src/components/categorical/category/annoDialogEditCategoryName.js +++ /dev/null @@ -1,151 +0,0 @@ -import React from "react"; -import { connect } from "react-redux"; -import AnnoDialog from "../../annoDialog"; -import LabelInput from "../../labelInput"; -import { labelPrompt } from "../labelUtil"; - -import { AnnotationsHelpers } from "../../../util/stateManager"; -import actions from "../../../actions"; - -@connect((state) => ({ - annotations: state.annotations, - schema: state.annoMatrix?.schema, -})) -class AnnoDialogEditCategoryName extends React.PureComponent { - constructor(props) { - super(props); - this.state = { - newCategoryText: props.metadataField, - }; - } - - handleChangeOrSelect = (name) => { - this.setState({ - newCategoryText: name, - }); - }; - - disableEditCategoryMode = () => { - const { dispatch, metadataField } = this.props; - dispatch({ - type: "annotation: disable category edit mode", - }); - this.setState({ newCategoryText: metadataField }); - }; - - handleEditCategory = (e) => { - const { dispatch, metadataField } = this.props; - const { newCategoryText } = this.state; - - /* - test for uniqueness against *all* annotation names, not just the subset - we render as categorical. - */ - const { schema } = this.props; - const allCategoryNames = schema.annotations.obs.columns.map((c) => c.name); - - if ( - (allCategoryNames.indexOf(newCategoryText) > -1 && - newCategoryText !== metadataField) || - newCategoryText === "" - ) { - return; - } - - this.disableEditCategoryMode(); - - if (metadataField !== newCategoryText) - dispatch( - actions.annotationRenameCategoryAction(metadataField, newCategoryText) - ); - e.preventDefault(); - }; - - editedCategoryNameError = (name) => { - const { metadataField } = this.props; - - /* check for syntax errors in category name */ - const error = AnnotationsHelpers.annotationNameIsErroneous(name); - if (error) { - return error; - } - - /* check for duplicative categories */ - - /* - test for uniqueness against *all* annotation names, not just the subset - we render as categorical. - */ - const { schema } = this.props; - const allCategoryNames = schema.annotations.obs.columns.map((c) => c.name); - - const categoryNameAlreadyExists = allCategoryNames.indexOf(name) > -1; - const sameName = name === metadataField; - if (categoryNameAlreadyExists && !sameName) { - return "duplicate"; - } - - /* otherwise, no error */ - return false; - }; - - instruction = (name) => { - return labelPrompt( - this.editedCategoryNameError(name), - "New, unique category name", - ":" - ); - }; - - allCategoryNames() { - const { schema } = this.props; - return schema.annotations.obs.columns.map((c) => c.name); - } - - render() { - const { newCategoryText } = this.state; - const { metadataField, annotations } = this.props; - - return ( - <> - - } - /> - - ); - } -} - -export default AnnoDialogEditCategoryName; diff --git a/client/src/components/categorical/category/annoDialogEditCategoryName.tsx b/client/src/components/categorical/category/annoDialogEditCategoryName.tsx new file mode 100644 index 00000000..8ae27444 --- /dev/null +++ b/client/src/components/categorical/category/annoDialogEditCategoryName.tsx @@ -0,0 +1,172 @@ +import React from "react"; +import { connect } from "react-redux"; +import AnnoDialog from "../../annoDialog"; +import LabelInput from "../../labelInput"; +import { labelPrompt } from "../labelUtil"; + +import { AnnotationsHelpers } from "../../../util/stateManager"; +import actions from "../../../actions"; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annotations: (state as any).annotations, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, +})) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class AnnoDialogEditCategoryName extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { + super(props); + this.state = { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message + newCategoryText: props.metadataField, + }; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChangeOrSelect = (name: any) => { + this.setState({ + newCategoryText: name, + }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + disableEditCategoryMode = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, metadataField } = this.props; + dispatch({ + type: "annotation: disable category edit mode", + }); + this.setState({ newCategoryText: metadataField }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleEditCategory = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, metadataField } = this.props; + const { newCategoryText } = this.state; + /* + test for uniqueness against *all* annotation names, not just the subset + we render as categorical. + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message + const { schema } = this.props; + const allCategoryNames = schema.annotations.obs.columns.map( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (c: any) => c.name + ); + if ( + (allCategoryNames.indexOf(newCategoryText) > -1 && + newCategoryText !== metadataField) || + newCategoryText === "" + ) { + return; + } + this.disableEditCategoryMode(); + if (metadataField !== newCategoryText) + dispatch( + actions.annotationRenameCategoryAction(metadataField, newCategoryText) + ); + e.preventDefault(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + editedCategoryNameError = (name: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message + const { metadataField } = this.props; + /* check for syntax errors in category name */ + const error = AnnotationsHelpers.annotationNameIsErroneous(name); + if (error) { + return error; + } + /* check for duplicative categories */ + /* + test for uniqueness against *all* annotation names, not just the subset + we render as categorical. + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message + const { schema } = this.props; + const allCategoryNames = schema.annotations.obs.columns.map( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (c: any) => c.name + ); + const categoryNameAlreadyExists = allCategoryNames.indexOf(name) > -1; + const sameName = name === metadataField; + if (categoryNameAlreadyExists && !sameName) { + return "duplicate"; + } + /* otherwise, no error */ + return false; + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + instruction = (name: any) => + labelPrompt( + this.editedCategoryNameError(name), + "New, unique category name", + ":" + ); + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + allCategoryNames() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message + const { schema } = this.props; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return schema.annotations.obs.columns.map((c: any) => c.name); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { newCategoryText } = this.state; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message + const { metadataField, annotations } = this.props; + return ( + <> + + } + /> + + ); + } +} + +export default AnnoDialogEditCategoryName; diff --git a/client/src/components/categorical/category/annoMenuCategory.js b/client/src/components/categorical/category/annoMenuCategory.tsx similarity index 54% rename from client/src/components/categorical/category/annoMenuCategory.js rename to client/src/components/categorical/category/annoMenuCategory.tsx index 706ff63a..d8c132c4 100644 --- a/client/src/components/categorical/category/annoMenuCategory.js +++ b/client/src/components/categorical/category/annoMenuCategory.tsx @@ -16,16 +16,25 @@ import { IconNames } from "@blueprintjs/icons"; import * as globals from "../../../globals"; import actions from "../../../actions"; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - annotations: state.annotations, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annotations: (state as any).annotations, })) -class AnnoMenuCategory extends React.PureComponent { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class AnnoMenuCategory extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = {}; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. activateAddNewLabelMode = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField } = this.props; dispatch({ type: "annotation: activate add new label mode", @@ -33,30 +42,39 @@ class AnnoMenuCategory extends React.PureComponent { }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. activateEditCategoryMode = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField } = this.props; - dispatch({ type: "annotation: activate category edit mode", data: metadataField, }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleDeleteCategory = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField } = this.props; dispatch(actions.annotationDeleteCategoryAction(metadataField)); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annotations' does not exist on type 'Rea... Remove this comment to see the full error message annotations, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type 'Read... Remove this comment to see the full error message isUserAnno, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'createText' does not exist on type 'Read... Remove this comment to see the full error message createText, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'editText' does not exist on type 'Readon... Remove this comment to see the full error message editText, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'deleteText' does not exist on type 'Read... Remove this comment to see the full error message deleteText, } = this.props; - return ( <> {isUserAnno ? ( diff --git a/client/src/components/categorical/category/index.js b/client/src/components/categorical/category/index.js deleted file mode 100644 index 1facf4c5..00000000 --- a/client/src/components/categorical/category/index.js +++ /dev/null @@ -1,653 +0,0 @@ -import React, { useRef, useEffect } from "react"; -import { connect, shallowEqual } from "react-redux"; -import { FaChevronRight, FaChevronDown } from "react-icons/fa"; -import { - AnchorButton, - Button, - Classes, - Position, - Tooltip, -} from "@blueprintjs/core"; -import { Flipper, Flipped } from "react-flip-toolkit"; -import Async from "react-async"; -import memoize from "memoize-one"; - -import Value from "../value"; -import AnnoMenu from "./annoMenuCategory"; -import AnnoDialogEditCategoryName from "./annoDialogEditCategoryName"; -import AnnoDialogAddLabel from "./annoDialogAddLabel"; -import Truncate from "../../util/truncate"; -import { CategoryCrossfilterContext } from "../categoryContext"; - -import * as globals from "../../../globals"; -import { createCategorySummaryFromDfCol } from "../../../util/stateManager/controlsHelpers"; -import { - createColorTable, - createColorQuery, -} from "../../../util/stateManager/colorHelpers"; -import actions from "../../../actions"; - -const LABEL_WIDTH = globals.leftSidebarWidth - 100; -const ANNO_BUTTON_WIDTH = 50; -const LABEL_WIDTH_ANNO = LABEL_WIDTH - ANNO_BUTTON_WIDTH; - -@connect((state, ownProps) => { - const schema = state.annoMatrix?.schema; - const { metadataField } = ownProps; - const isUserAnno = schema?.annotations?.obsByName[metadataField]?.writable; - const categoricalSelection = state.categoricalSelection?.[metadataField]; - const isDotplotRows = metadataField === state.dotplot.row; - return { - colors: state.colors, - categoricalSelection, - annotations: state.annotations, - annoMatrix: state.annoMatrix, - schema, - crossfilter: state.obsCrossfilter, - isUserAnno, - genesets: state.genesets.genesets, - layoutChoiceIsDotplot: state.layoutChoice.dotplot, - isDotplotRows, - }; -}) -class Category extends React.PureComponent { - static getSelectionState( - categoricalSelection, - metadataField, - categorySummary - ) { - // total number of categories in this dimension - const totalCatCount = categorySummary.numCategoryValues; - // number of selected options in this category - const selectedCatCount = categorySummary.categoryValues.reduce( - (res, label) => (categoricalSelection.get(label) ?? true ? res + 1 : res), - 0 - ); - return selectedCatCount === totalCatCount - ? "all" - : selectedCatCount === 0 - ? "none" - : "some"; - } - - static watchAsync(props, prevProps) { - return !shallowEqual(props.watchProps, prevProps.watchProps); - } - - createCategorySummaryFromDfCol = memoize(createCategorySummaryFromDfCol); - - getSelectionState(categorySummary) { - const { categoricalSelection, metadataField } = this.props; - return Category.getSelectionState( - categoricalSelection, - metadataField, - categorySummary - ); - } - - handleColorChange = () => { - const { dispatch, metadataField, layoutChoiceIsDotplot } = this.props; - - if (layoutChoiceIsDotplot) { - dispatch({ - type: "set dotplot row", - data: metadataField, - }); - } else { - dispatch({ - type: "color by categorical metadata", - colorAccessor: metadataField, - }); - } - }; - - handleCategoryClick = () => { - const { annotations, metadataField, onExpansionChange } = this.props; - const editingCategory = - annotations.isEditingCategoryName && - annotations.categoryBeingEdited === metadataField; - if (!editingCategory) { - onExpansionChange(metadataField); - } - }; - - handleCategoryKeyPress = (e) => { - if (e.key === "Enter") { - this.handleCategoryClick(); - } - }; - - handleToggleAllClick = (categorySummary) => { - const isChecked = this.getSelectionState(categorySummary); - if (isChecked === "all") { - this.toggleNone(categorySummary); - } else { - this.toggleAll(categorySummary); - } - }; - - fetchAsyncProps = async (props) => { - const { annoMatrix, metadataField, colors } = props.watchProps; - const { crossfilter } = this.props; - - const [categoryData, categorySummary, colorData] = await this.fetchData( - annoMatrix, - metadataField, - colors - ); - - return { - categoryData, - categorySummary, - colorData, - crossfilter, - ...this.updateColorTable(colorData), - handleCategoryToggleAllClick: () => - this.handleToggleAllClick(categorySummary), - }; - }; - - async fetchData(annoMatrix, metadataField, colors) { - /* - fetch our data and the color-by data if appropriate, and then build a summary - of our category and a color table for the color-by annotation. - */ - const { schema } = annoMatrix; - const { colorAccessor, colorMode } = colors; - const { genesets } = this.props; - let colorDataPromise = Promise.resolve(null); - if (colorAccessor) { - const query = createColorQuery( - colorMode, - colorAccessor, - schema, - genesets - ); - if (query) colorDataPromise = annoMatrix.fetch(...query); - } - const [categoryData, colorData] = await Promise.all([ - annoMatrix.fetch("obs", metadataField), - colorDataPromise, - ]); - - // our data - const column = categoryData.icol(0); - const colSchema = schema.annotations.obsByName[metadataField]; - const categorySummary = this.createCategorySummaryFromDfCol( - column, - colSchema - ); - return [categoryData, categorySummary, colorData]; - } - - updateColorTable(colorData) { - // color table, which may be null - const { schema, colors, metadataField } = this.props; - const { colorAccessor, userColors, colorMode } = colors; - return { - isColorAccessor: colorAccessor === metadataField, - colorAccessor, - colorMode, - colorTable: createColorTable( - colorMode, - colorAccessor, - colorData, - schema, - userColors - ), - }; - } - - toggleNone(categorySummary) { - const { dispatch, metadataField } = this.props; - dispatch( - actions.selectCategoricalAllMetadataAction( - "categorical metadata filter none of these", - metadataField, - categorySummary.allCategoryValues, - false - ) - ); - } - - toggleAll(categorySummary) { - const { dispatch, metadataField } = this.props; - dispatch( - actions.selectCategoricalAllMetadataAction( - "categorical metadata filter all of these", - metadataField, - categorySummary.allCategoryValues, - true - ) - ); - } - - render() { - const { - metadataField, - isExpanded, - categoricalSelection, - crossfilter, - colors, - annoMatrix, - isUserAnno, - layoutChoiceIsDotplot, - isDotplotRows, - } = this.props; - - const checkboxID = `category-select-${metadataField}`; - - return ( - - - - - - - {(error) => ( - - )} - - - {(asyncProps) => { - const { - colorAccessor, - colorTable, - colorData, - categoryData, - categorySummary, - isColorAccessor, - handleCategoryToggleAllClick, - } = asyncProps; - const isTruncated = !!categorySummary?.isTruncated; - const selectionState = this.getSelectionState(categorySummary); - return ( - - ); - }} - - - - ); - } -} - -export default Category; - -const StillLoading = ({ metadataField, checkboxID }) => { - /* - We are still loading this category, so render a "busy" signal. - */ - return ( -
-
-
- - - - {metadataField} - - -
-
-
-
-
- ); -}; - -const ErrorLoading = ({ metadataField, error }) => { - console.error(error); // log error to console as it is unexpected. - return ( -
- - {`Failure loading ${metadataField}`} - -
- ); -}; - -const CategoryHeader = React.memo( - ({ - metadataField, - checkboxID, - isUserAnno, - isTruncated, - isColorAccessor, - isExpanded, - selectionState, - onColorChangeClick, - onCategoryMenuClick, - onCategoryMenuKeyPress, - onCategoryToggleAllClick, - layoutChoiceIsDotplot, - isDotplotRows, - }) => { - /* - Render category name and controls (eg, color-by button). - */ - const checkboxRef = useRef(null); - - useEffect(() => { - checkboxRef.current.indeterminate = selectionState === "some"; - }, [checkboxRef.current, selectionState]); - - return ( - <> -
- - - - - {metadataField} - - - {isExpanded ? ( - - ) : ( - - )} - -
- {} - {} -
- - - - - -
- - ); - } -); - -const CategoryRender = React.memo( - ({ - metadataField, - checkboxID, - isUserAnno, - isTruncated, - isColorAccessor, - isExpanded, - selectionState, - categoryData, - categorySummary, - colorAccessor, - colorData, - colorTable, - onColorChangeClick, - onCategoryMenuClick, - onCategoryMenuKeyPress, - onCategoryToggleAllClick, - layoutChoiceIsDotplot, - isDotplotRows, - }) => { - /* - Render the core of the category, including checkboxes, controls, etc. - */ - const { numCategoryValues } = categorySummary; - const isSingularValue = !isUserAnno && numCategoryValues === 1; - - if (isSingularValue) { - /* - Entire category has a single value, special case. - */ - return null; - } - - /* - Otherwise, our normal multi-layout layout - */ - return ( -
-
- -
-
- { - /* values*/ - isExpanded ? ( - - ) : null - } -
-
- {isExpanded && isTruncated ? ( -

... truncated list ...

- ) : null} -
-
- ); - } -); - -const CategoryValueList = React.memo( - ({ - isUserAnno, - metadataField, - categoryData, - categorySummary, - colorAccessor, - colorData, - colorTable, - }) => { - const tuples = [...categorySummary.categoryValueIndices]; - - /* - Render the value list. If this is a user annotation, we use a flipper - animation, if read-only, we don't bother and save a few bits of perf. - */ - if (!isUserAnno) { - return ( - <> - {tuples.map(([value, index]) => ( - - ))} - - ); - } - - /* User annotation */ - const flipKey = tuples.map((t) => t[0]).join(""); - return ( - - {tuples.map(([value, index]) => ( - - - - ))} - - ); - } -); diff --git a/client/src/components/categorical/category/index.tsx b/client/src/components/categorical/category/index.tsx new file mode 100644 index 00000000..b6b55f5f --- /dev/null +++ b/client/src/components/categorical/category/index.tsx @@ -0,0 +1,711 @@ +import React, { useRef, useEffect } from "react"; +import { connect, shallowEqual } from "react-redux"; +import { FaChevronRight, FaChevronDown } from "react-icons/fa"; +import { + AnchorButton, + Button, + Classes, + Position, + Tooltip, +} from "@blueprintjs/core"; +import { Flipper, Flipped } from "react-flip-toolkit"; +import Async from "react-async"; +import memoize from "memoize-one"; + +import Value from "../value"; +import AnnoMenu from "./annoMenuCategory"; +import AnnoDialogEditCategoryName from "./annoDialogEditCategoryName"; +import AnnoDialogAddLabel from "./annoDialogAddLabel"; +import Truncate from "../../util/truncate"; +import { CategoryCrossfilterContext } from "../categoryContext"; + +import * as globals from "../../../globals"; +import { createCategorySummaryFromDfCol } from "../../../util/stateManager/controlsHelpers"; +import { + createColorTable, + createColorQuery, +} from "../../../util/stateManager/colorHelpers"; +import actions from "../../../actions"; + +const LABEL_WIDTH = globals.leftSidebarWidth - 100; +const ANNO_BUTTON_WIDTH = 50; +const LABEL_WIDTH_ANNO = LABEL_WIDTH - ANNO_BUTTON_WIDTH; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state, ownProps) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const schema = (state as any).annoMatrix?.schema; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message + const { metadataField } = ownProps; + const isUserAnno = schema?.annotations?.obsByName[metadataField]?.writable; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const categoricalSelection = (state as any).categoricalSelection?.[ + metadataField + ]; + return { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colors: (state as any).colors, + categoricalSelection, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annotations: (state as any).annotations, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annoMatrix: (state as any).annoMatrix, + schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + crossfilter: (state as any).obsCrossfilter, + isUserAnno, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesets: (state as any).genesets.genesets, + }; +}) +class Category extends React.PureComponent { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + static getSelectionState( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoricalSelection: any, + // @ts-expect-error ts-migrate(6133) FIXME: 'metadataField' is declared but its value is never... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + metadataField: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categorySummary: any + ) { + // total number of categories in this dimension + const totalCatCount = categorySummary.numCategoryValues; + // number of selected options in this category + const selectedCatCount = categorySummary.categoryValues.reduce( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (res: any, label: any) => + categoricalSelection.get(label) ?? true ? res + 1 : res, + 0 + ); + return selectedCatCount === totalCatCount + ? "all" + : selectedCatCount === 0 + ? "none" + : "some"; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static watchAsync(props: any, prevProps: any) { + return !shallowEqual(props.watchProps, prevProps.watchProps); + } + + createCategorySummaryFromDfCol = memoize(createCategorySummaryFromDfCol); + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getSelectionState(categorySummary: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoricalSelection' does not exist on ... Remove this comment to see the full error message + const { categoricalSelection, metadataField } = this.props; + return Category.getSelectionState( + categoricalSelection, + metadataField, + categorySummary + ); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleColorChange = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, metadataField } = this.props; + dispatch({ + type: "color by categorical metadata", + colorAccessor: metadataField, + }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleCategoryClick = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annotations' does not exist on type 'Rea... Remove this comment to see the full error message + const { annotations, metadataField, onExpansionChange } = this.props; + const editingCategory = + annotations.isEditingCategoryName && + annotations.categoryBeingEdited === metadataField; + if (!editingCategory) { + onExpansionChange(metadataField); + } + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleCategoryKeyPress = (e: any) => { + if (e.key === "Enter") { + this.handleCategoryClick(); + } + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleToggleAllClick = (categorySummary: any) => { + const isChecked = this.getSelectionState(categorySummary); + if (isChecked === "all") { + this.toggleNone(categorySummary); + } else { + this.toggleAll(categorySummary); + } + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + fetchAsyncProps = async (props: any) => { + const { annoMatrix, metadataField, colors } = props.watchProps; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'crossfilter' does not exist on type 'Rea... Remove this comment to see the full error message + const { crossfilter } = this.props; + + const [categoryData, categorySummary, colorData] = await this.fetchData( + annoMatrix, + metadataField, + colors + ); + + return { + categoryData, + categorySummary, + colorData, + crossfilter, + ...this.updateColorTable(colorData), + handleCategoryToggleAllClick: () => + this.handleToggleAllClick(categorySummary), + }; + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + async fetchData(annoMatrix: any, metadataField: any, colors: any) { + /* + fetch our data and the color-by data if appropriate, and then build a summary + of our category and a color table for the color-by annotation. + */ + const { schema } = annoMatrix; + const { colorAccessor, colorMode } = colors; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'genesets' does not exist on type 'Readon... Remove this comment to see the full error message + const { genesets } = this.props; + let colorDataPromise = Promise.resolve(null); + if (colorAccessor) { + const query = createColorQuery( + colorMode, + colorAccessor, + schema, + genesets + ); + if (query) colorDataPromise = annoMatrix.fetch(...query); + } + const [categoryData, colorData] = await Promise.all([ + annoMatrix.fetch("obs", metadataField), + colorDataPromise, + ]); + + // our data + const column = categoryData.icol(0); + const colSchema = schema.annotations.obsByName[metadataField]; + const categorySummary = this.createCategorySummaryFromDfCol( + column, + colSchema + ); + return [categoryData, categorySummary, colorData]; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + updateColorTable(colorData: any) { + // color table, which may be null + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message + const { schema, colors, metadataField } = this.props; + const { colorAccessor, userColors, colorMode } = colors; + return { + isColorAccessor: colorAccessor === metadataField, + colorAccessor, + colorMode, + colorTable: createColorTable( + colorMode, + colorAccessor, + colorData, + schema, + userColors + ), + }; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + toggleNone(categorySummary: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, metadataField } = this.props; + dispatch( + actions.selectCategoricalAllMetadataAction( + "categorical metadata filter none of these", + metadataField, + categorySummary.allCategoryValues, + false + ) + ); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + toggleAll(categorySummary: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, metadataField } = this.props; + dispatch( + actions.selectCategoricalAllMetadataAction( + "categorical metadata filter all of these", + metadataField, + categorySummary.allCategoryValues, + true + ) + ); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message + metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isExpanded' does not exist on type 'Read... Remove this comment to see the full error message + isExpanded, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoricalSelection' does not exist on ... Remove this comment to see the full error message + categoricalSelection, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'crossfilter' does not exist on type 'Rea... Remove this comment to see the full error message + crossfilter, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colors' does not exist on type 'Readonly... Remove this comment to see the full error message + colors, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message + annoMatrix, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type 'Read... Remove this comment to see the full error message + isUserAnno, + } = this.props; + + const checkboxID = `category-select-${metadataField}`; + + return ( + + + + + + + {(error) => ( + + )} + + + {(asyncProps) => { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'u... Remove this comment to see the full error message + colorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'unkn... Remove this comment to see the full error message + colorTable, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'unkno... Remove this comment to see the full error message + colorData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'un... Remove this comment to see the full error message + categoryData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message + categorySummary, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message + isColorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleCategoryToggleAllClick' does not e... Remove this comment to see the full error message + handleCategoryToggleAllClick, + } = asyncProps; + const selectionState = this.getSelectionState(categorySummary); + return ( + + ); + }} + + + + ); + } +} + +export default Category; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const StillLoading = ({ metadataField, checkboxID }: any) => ( + /* + We are still loading this category, so render a "busy" signal. + */ +
+
+
+ + + + {metadataField} + + +
+
+
+
+
+); +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const ErrorLoading = ({ metadataField, error }: any) => { + console.error(error); // log error to console as it is unexpected. + return ( +
+ + {`Failure loading ${metadataField}`} + +
+ ); +}; + +const CategoryHeader = React.memo( + ({ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message + metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'checkboxID' does not exist on type '{ ch... Remove this comment to see the full error message + checkboxID, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type '{ ch... Remove this comment to see the full error message + isUserAnno, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message + isColorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isExpanded' does not exist on type '{ ch... Remove this comment to see the full error message + isExpanded, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionState' does not exist on type '... Remove this comment to see the full error message + selectionState, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onColorChangeClick' does not exist on ty... Remove this comment to see the full error message + onColorChangeClick, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryMenuClick' does not exist on t... Remove this comment to see the full error message + onCategoryMenuClick, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryMenuKeyPress' does not exist o... Remove this comment to see the full error message + onCategoryMenuKeyPress, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryToggleAllClick' does not exist... Remove this comment to see the full error message + onCategoryToggleAllClick, + }) => { + /* + Render category name and controls (eg, color-by button). + */ + const checkboxRef = useRef(null); + + useEffect(() => { + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + checkboxRef.current.indeterminate = selectionState === "some"; + }, [checkboxRef.current, selectionState]); + + return ( + <> +
+ + + + + {metadataField} + + + {isExpanded ? ( + + ) : ( + + )} + +
+ {/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ metadataField: any; }' is not assignable t... Remove this comment to see the full error message */} + + {/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ metadataField: any; }' is not assignable t... Remove this comment to see the full error message */} + +
+ + + + + +
+ + ); + } +); + +const CategoryRender = React.memo( + ({ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message + metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'checkboxID' does not exist on type '{ ch... Remove this comment to see the full error message + checkboxID, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type '{ ch... Remove this comment to see the full error message + isUserAnno, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message + isColorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isExpanded' does not exist on type '{ ch... Remove this comment to see the full error message + isExpanded, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionState' does not exist on type '... Remove this comment to see the full error message + selectionState, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type '{ ... Remove this comment to see the full error message + categoryData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message + categorySummary, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type '{... Remove this comment to see the full error message + colorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type '{ chi... Remove this comment to see the full error message + colorData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type '{ ch... Remove this comment to see the full error message + colorTable, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onColorChangeClick' does not exist on ty... Remove this comment to see the full error message + onColorChangeClick, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryMenuClick' does not exist on t... Remove this comment to see the full error message + onCategoryMenuClick, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryMenuKeyPress' does not exist o... Remove this comment to see the full error message + onCategoryMenuKeyPress, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onCategoryToggleAllClick' does not exist... Remove this comment to see the full error message + onCategoryToggleAllClick, + }) => { + /* + Render the core of the category, including checkboxes, controls, etc. + */ + const { numCategoryValues } = categorySummary; + const isSingularValue = !isUserAnno && numCategoryValues === 1; + + if (isSingularValue) { + /* + Entire category has a single value, special case. + */ + return null; + } + + /* + Otherwise, our normal multi-layout layout + */ + return ( +
+
+ +
+
+ { + /* values*/ + isExpanded ? ( + + ) : null + } +
+
+ ); + } +); + +const CategoryValueList = React.memo( + ({ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type '{ ch... Remove this comment to see the full error message + isUserAnno, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message + metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type '{ ... Remove this comment to see the full error message + categoryData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message + categorySummary, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type '{... Remove this comment to see the full error message + colorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type '{ chi... Remove this comment to see the full error message + colorData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type '{ ch... Remove this comment to see the full error message + colorTable, + }) => { + const tuples = [...categorySummary.categoryValueIndices]; + + /* + Render the value list. If this is a user annotation, we use a flipper + animation, if read-only, we don't bother and save a few bits of perf. + */ + if (!isUserAnno) { + return ( + <> + {tuples.map(([value, index]) => ( + + ))} + + ); + } + + /* User annotation */ + const flipKey = tuples.map((t) => t[0]).join(""); + return ( + + {tuples.map(([value, index]) => ( + + + + ))} + + ); + } +); diff --git a/client/src/components/categorical/categoryContext.js b/client/src/components/categorical/categoryContext.ts similarity index 100% rename from client/src/components/categorical/categoryContext.js rename to client/src/components/categorical/categoryContext.ts diff --git a/client/src/components/categorical/index.js b/client/src/components/categorical/index.tsx similarity index 55% rename from client/src/components/categorical/index.js rename to client/src/components/categorical/index.tsx index 376dc48c..195675b2 100644 --- a/client/src/components/categorical/index.js +++ b/client/src/components/categorical/index.tsx @@ -10,13 +10,23 @@ import LabelInput from "../labelInput"; import { labelPrompt } from "./labelUtil"; import actions from "../../actions"; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - writableCategoriesEnabled: state.config?.parameters?.annotations ?? false, - schema: state.annoMatrix?.schema, - userInfo: state.userInfo, + writableCategoriesEnabled: + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (state as any).config?.parameters?.annotations ?? false, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userInfo: (state as any).userInfo, })) -class Categories extends React.Component { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class Categories extends React.Component<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { createAnnoModeActive: false, @@ -26,7 +36,9 @@ class Categories extends React.Component { }; } - handleCreateUserAnno = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleCreateUserAnno = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; const { newCategoryText, categoryToDuplicate } = this.state; dispatch( @@ -43,10 +55,12 @@ class Categories extends React.Component { e.preventDefault(); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleEnableAnnoMode = () => { this.setState({ createAnnoModeActive: true }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleDisableAnnoMode = () => { this.setState({ createAnnoModeActive: false, @@ -55,58 +69,58 @@ class Categories extends React.Component { }); }; - handleModalDuplicateCategorySelection = (d) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleModalDuplicateCategorySelection = (d: any) => { this.setState({ categoryToDuplicate: d }); }; - categoryNameError = (name) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryNameError = (name: any) => { /* - return false if this is a LEGAL/acceptable category name or NULL/empty string, - or return an error type. - */ - + return false if this is a LEGAL/acceptable category name or NULL/empty string, + or return an error type. + */ /* allow empty string */ if (name === "") return false; - /* - test for uniqueness against *all* annotation names, not just the subset - we render as categorical. - */ + test for uniqueness against *all* annotation names, not just the subset + we render as categorical. + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message const { schema } = this.props; - const allCategoryNames = schema.annotations.obs.columns.map((c) => c.name); - + const allCategoryNames = schema.annotations.obs.columns.map( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (c: any) => c.name + ); /* check category name syntax */ const error = AnnotationsHelpers.annotationNameIsErroneous(name); if (error) { return error; } - /* disallow duplicates */ if (allCategoryNames.indexOf(name) !== -1) { return "duplicate"; } - /* otherwise, no error */ return false; }; - handleChange = (name) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChange = (name: any) => { this.setState({ newCategoryText: name }); }; - handleSelect = (name) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleSelect = (name: any) => { this.setState({ newCategoryText: name }); }; - instruction = (name) => { - return labelPrompt( - this.categoryNameError(name), - "New, unique category name", - ":" - ); - }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + instruction = (name: any) => + labelPrompt(this.categoryNameError(name), "New, unique category name", ":"); - onExpansionChange = (catName) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + onExpansionChange = (catName: any) => { const { expandedCats } = this.state; if (expandedCats.has(catName)) { const _expandedCats = new Set(expandedCats); @@ -119,6 +133,7 @@ class Categories extends React.Component { } }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { createAnnoModeActive, @@ -126,16 +141,13 @@ class Categories extends React.Component { newCategoryText, expandedCats, } = this.state; - const { - writableCategoriesEnabled, - schema, - userInfo, - } = this.props; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'writableCategoriesEnabled' does not exis... Remove this comment to see the full error message + const { writableCategoriesEnabled, schema, userInfo } = this.props; /* all names, sorted in display order. Will be rendered in this order */ + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. const allCategoryNames = ControlsHelpers.selectableCategoryNames( schema ).sort(); - return (
} /> - {writableCategoriesEnabled ? (
) : null} - {/* READ ONLY CATEGORICAL FIELDS */} {/* this is duplicative but flat, could be abstracted */} - {allCategoryNames.map((catName) => + {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS */} + {allCategoryNames.map((catName: any) => !schema.annotations.obsByName[catName].writable && (schema.annotations.obsByName[catName].categories?.length > 1 || !schema.annotations.obsByName[catName].categories) ? ( + {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS */} + {allCategoryNames.map((catName: any) => schema.annotations.obsByName[catName].writable ? ( { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'pointDilation' does not exist on type 'D... Remove this comment to see the full error message const { pointDilation, categoricalSelection } = state; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type '{... Remove this comment to see the full error message const { metadataField, categorySummary, categoryIndex } = ownProps; const isDilated = pointDilation.metadataField === metadataField && @@ -48,27 +56,35 @@ function _currentLabelAsString(ownProps) { const isSelected = category.get(label) ?? true; return { - annotations: state.annotations, - schema: state.annoMatrix?.schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annotations: (state as any).annotations, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, isDilated, isSelected, label, }; }) -class CategoryValue extends React.Component { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class CategoryValue extends React.Component<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { editedLabelText: this.currentLabelAsString(), }; } - componentDidUpdate(prevProps) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + componentDidUpdate(prevProps: {}) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message const { metadataField, categoryIndex, categorySummary } = this.props; if ( - prevProps.metadataField !== metadataField || - prevProps.categoryIndex !== categoryIndex || - prevProps.categorySummary !== categorySummary + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (prevProps as any).metadataField !== metadataField || + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (prevProps as any).categoryIndex !== categoryIndex || // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (prevProps as any).categorySummary !== categorySummary ) { // eslint-disable-next-line react/no-did-update-set-state --- adequately checked to prevent looping this.setState({ @@ -78,23 +94,31 @@ class CategoryValue extends React.Component { } // If coloring by and this isn't the colorAccessor and it isn't being edited + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. get shouldRenderStackedBarOrHistogram() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message const { colorAccessor, isColorBy, annotations } = this.props; return !!colorAccessor && !isColorBy && !annotations.isEditingLabelName; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleDeleteValue = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField, label } = this.props; dispatch(actions.annotationDeleteLabelFromCategory(metadataField, label)); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleAddCurrentSelectionToThisLabel = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField, label } = this.props; dispatch(actions.annotationLabelCurrentSelection(metadataField, label)); }; - handleEditValue = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleEditValue = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField, label } = this.props; const { editedLabelText } = this.state; this.cancelEditMode(); @@ -108,7 +132,9 @@ class CategoryValue extends React.Component { e.preventDefault(); }; - handleCreateArbitraryLabel = (txt) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleCreateArbitraryLabel = (txt: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField, label } = this.props; this.cancelEditMode(); dispatch( @@ -116,17 +142,21 @@ class CategoryValue extends React.Component { ); }; - labelNameError = (name) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + labelNameError = (name: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message const { metadataField, schema } = this.props; if (name === this.currentLabelAsString()) return false; return isLabelErroneous(name, metadataField, schema); }; - instruction = (label) => { - return labelPrompt(this.labelNameError(label), "New, unique label", ":"); - }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + instruction = (label: any) => + labelPrompt(this.labelNameError(label), "New, unique label", ":"); + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. activateEditLabelMode = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField, categoryIndex, label } = this.props; dispatch({ type: "annotation: activate edit label mode", @@ -136,7 +166,9 @@ class CategoryValue extends React.Component { }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. cancelEditMode = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField, categoryIndex, label } = this.props; this.setState({ editedLabelText: this.currentLabelAsString(), @@ -149,11 +181,16 @@ class CategoryValue extends React.Component { }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. toggleOff = () => { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message dispatch, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryIndex' does not exist on type 'R... Remove this comment to see the full error message categoryIndex, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message categorySummary, } = this.props; const label = categorySummary.categoryValues[categoryIndex]; @@ -168,7 +205,8 @@ class CategoryValue extends React.Component { ); }; - shouldComponentUpdate = (nextProps, nextState) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + shouldComponentUpdate = (nextProps: any, nextState: any) => { /* Checks to see if at least one of the following changed: * world state @@ -179,6 +217,7 @@ class CategoryValue extends React.Component { If and only if true, update the component */ const { props, state } = this; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryIndex' does not exist on type 'R... Remove this comment to see the full error message const { categoryIndex, categorySummary, isSelected } = props; const { categoryIndex: newCategoryIndex, @@ -191,10 +230,15 @@ class CategoryValue extends React.Component { const labelChanged = label !== newLabel; const valueSelectionChange = isSelected !== newIsSelected; - const colorAccessorChange = props.colorAccessor !== nextProps.colorAccessor; - const annotationsChange = props.annotations !== nextProps.annotations; + const colorAccessorChange = + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (props as any).colorAccessor !== nextProps.colorAccessor; + const annotationsChange = + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (props as any).annotations !== nextProps.annotations; const editingLabel = state.editedLabelText !== nextState.editedLabelText; - const dilationChange = props.isDilated !== nextProps.isDilated; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const dilationChange = (props as any).isDilated !== nextProps.isDilated; const count = categorySummary.categoryValueCounts[categoryIndex]; const newCount = newCategorySummary.categoryValueCounts[newCategoryIndex]; @@ -205,7 +249,8 @@ class CategoryValue extends React.Component { // if any one changes, but only for the currently colored-by category. const colorMightHaveChanged = nextProps.colorAccessor === nextProps.metadataField && - props.categorySummary !== nextProps.categorySummary; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (props as any).categorySummary !== nextProps.categorySummary; return ( labelChanged || @@ -219,11 +264,16 @@ class CategoryValue extends React.Component { ); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. toggleOn = () => { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message dispatch, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryIndex' does not exist on type 'R... Remove this comment to see the full error message categoryIndex, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message categorySummary, } = this.props; const label = categorySummary.categoryValues[categoryIndex]; @@ -238,7 +288,9 @@ class CategoryValue extends React.Component { ); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleMouseEnter = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField, categoryIndex, label } = this.props; dispatch({ type: "category value mouse hover start", @@ -248,7 +300,9 @@ class CategoryValue extends React.Component { }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleMouseExit = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, metadataField, categoryIndex, label } = this.props; dispatch({ type: "category value mouse hover end", @@ -258,23 +312,34 @@ class CategoryValue extends React.Component { }); }; - handleTextChange = (text) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleTextChange = (text: any) => { this.setState({ editedLabelText: text }); }; - handleChoice = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChoice = (e: any) => { /* Blueprint Suggest format */ this.setState({ editedLabelText: e.target }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. createHistogramBins = ( - metadataField, - categoryData, - colorAccessor, - colorData, - categoryValue, - width, - height + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + metadataField: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryData: any, + // @ts-expect-error ts-migrate(6133) FIXME: 'colorAccessor' is declared but its value is never... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorAccessor: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorData: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryValue: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + width: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + height: any ) => { /* Knowing that colorScale is based off continuous data, @@ -308,15 +373,25 @@ class CategoryValue extends React.Component { }; }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. createStackedGraphBins = ( - metadataField, - categoryData, - colorAccessor, - colorData, - categoryValue, - colorTable, - schema, - width + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + metadataField: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryData: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorAccessor: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorData: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + categoryValue: any, + // @ts-expect-error ts-migrate(6133) FIXME: 'colorTable' is declared but its value is never re... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorTable: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + schema: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + width: any ) => { /* Knowing that the color scale is based off of categorical data, @@ -353,16 +428,19 @@ class CategoryValue extends React.Component { return null; }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. currentLabelAsString() { return _currentLabelAsString(this.props); } - isAddCurrentSelectionDisabled(crossfilter, category, value) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isAddCurrentSelectionDisabled(crossfilter: any, category: any, value: any) { /* disable "add current selection to label", if one of the following is true: 1. no cells are selected 2. all currently selected cells already have this label, on this category */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message const { categoryData } = this.props; // 1. no cells selected? @@ -380,14 +458,22 @@ class CategoryValue extends React.Component { return false; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renderMiniStackedBar = () => { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message colorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message categoryData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'Reado... Remove this comment to see the full error message colorData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message colorTable, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message schema, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'label' does not exist on type 'Readonly<... Remove this comment to see the full error message label, } = this.props; const isColorBy = metadataField === colorAccessor; @@ -425,20 +511,29 @@ class CategoryValue extends React.Component { domain, occupancy, }} + // @ts-expect-error ts-migrate(2322) FIXME: Type '{ height: number; width: number; colorTable:... Remove this comment to see the full error message height={STACKED_BAR_HEIGHT} width={STACKED_BAR_WIDTH} /> ); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renderMiniHistogram = () => { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message colorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'Reado... Remove this comment to see the full error message colorData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message categoryData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message colorTable, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message schema, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'label' does not exist on type 'Readonly<... Remove this comment to see the full error message label, } = this.props; const colorScale = colorTable?.scale; @@ -473,6 +568,7 @@ class CategoryValue extends React.Component { yScale, bins, }} + // @ts-expect-error ts-migrate(2322) FIXME: Type '{ obsOrVarContinuousFieldDisplayName: any; d... Remove this comment to see the full error message obsOrVarContinuousFieldDisplayName={colorAccessor} domainLabel={label} height={STACKED_BAR_HEIGHT} @@ -481,17 +577,28 @@ class CategoryValue extends React.Component { ); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryIndex' does not exist on type 'R... Remove this comment to see the full error message categoryIndex, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message colorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message colorTable, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isUserAnno' does not exist on type 'Read... Remove this comment to see the full error message isUserAnno, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annotations' does not exist on type 'Rea... Remove this comment to see the full error message annotations, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isDilated' does not exist on type 'Reado... Remove this comment to see the full error message isDilated, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isSelected' does not exist on type 'Read... Remove this comment to see the full error message isSelected, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categorySummary' does not exist on type ... Remove this comment to see the full error message categorySummary, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'label' does not exist on type 'Readonly<... Remove this comment to see the full error message label, } = this.props; const colorScale = colorTable?.scale; @@ -587,6 +694,7 @@ class CategoryValue extends React.Component { ({ - schema: state.annoMatrix?.schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, })) class Occupancy extends React.PureComponent { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + canvas: any; + _WIDTH = 100; _HEIGHT = 11; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. createHistogram = () => { /* - Knowing that colorScale is based off continous data, - createHistogram fetches the continous data in relation to the cells releveant to the catagory value. - It then seperates that data into 50 bins for drawing the mini-histogram - */ + Knowing that colorScale is based off continous data, + createHistogram fetches the continous data in relation to the cells releveant to the catagory value. + It then seperates that data into 50 bins for drawing the mini-histogram + */ const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message categoryData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'Reado... Remove this comment to see the full error message colorData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryValue' does not exist on type 'R... Remove this comment to see the full error message categoryValue, } = this.props; - if (!this.canvas) return; - const groupBy = categoryData.col(metadataField); const col = colorData.icol(0); const range = col.summarize(); - const histogramMap = col.histogram( 50, [range.min, range.max], groupBy ); /* Because the signature changes we really need different names for histogram to differentiate signatures */ - const bins = histogramMap.has(categoryValue) ? histogramMap.get(categoryValue) : new Array(50).fill(0); - const xScale = d3 .scaleLinear() .domain([0, bins.length]) .range([0, this._WIDTH]); - const largestBin = Math.max(...bins); - const yScale = d3 .scaleLinear() .domain([0, largestBin]) .range([0, this._HEIGHT]); - const ctx = this.canvas.getContext("2d"); - ctx.fillStyle = "#000"; - let x; let y; - const rectWidth = this._WIDTH / bins.length; - for (let i = 0, { length } = bins; i < length; i += 1) { x = xScale(i); y = yScale(bins[i]); @@ -73,34 +71,37 @@ class Occupancy extends React.PureComponent { } }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. createOccupancyStack = () => { /* - Knowing that the color scale is based off of catagorical data, - createOccupancyStack obtains a map showing the number if cells per colored value - Using the colorScale a stack of colored bars is drawn representing the map - */ + Knowing that the color scale is based off of catagorical data, + createOccupancyStack obtains a map showing the number if cells per colored value + Using the colorScale a stack of colored bars is drawn representing the map + */ const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'metadataField' does not exist on type 'R... Remove this comment to see the full error message metadataField, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryData' does not exist on type 'Re... Remove this comment to see the full error message categoryData, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message colorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoryValue' does not exist on type 'R... Remove this comment to see the full error message categoryValue, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message colorTable, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message schema, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorData' does not exist on type 'Reado... Remove this comment to see the full error message colorData, } = this.props; const { scale: colorScale } = colorTable; - const ctx = this.canvas?.getContext("2d"); - if (!ctx) return; - const groupBy = categoryData.col(metadataField); const occupancyMap = colorData .col(colorAccessor) .histogramCategorical(groupBy); - const occupancy = occupancyMap.get(categoryValue); - if (occupancy && occupancy.size > 0) { // not all categories have occupancy, so occupancy may be undefined. const x = d3 @@ -110,15 +111,12 @@ class Occupancy extends React.PureComponent { .range([0, this._WIDTH]); const categories = schema.annotations.obsByName[colorAccessor]?.categories; - let currentOffset = 0; const dfColumn = colorData.col(colorAccessor); const categoryValues = dfColumn.summarizeCategorical().categories; - let o; let scaledValue; let value; - for (let i = 0, { length } = categoryValues; i < length; i += 1) { value = categoryValues[i]; o = occupancy.get(value); @@ -132,12 +130,13 @@ class Occupancy extends React.PureComponent { } }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message const { colorAccessor, categoryValue, colorByIsCategorical } = this.props; const { canvas } = this; if (canvas) canvas.getContext("2d").clearRect(0, 0, this._WIDTH, this._HEIGHT); - return ( ({ - schema: state.annoMatrix?.schema, -})) -class Continuous extends React.PureComponent { - render() { - /* initial value for iterator to simulate index, ranges is an object */ - const { schema } = this.props; - if (!schema) return null; - const obsIndex = schema.annotations.obs.index; - const allContinuousNames = schema.annotations.obs.columns - .filter((col) => col.type === "int32" || col.type === "float32") - .filter((col) => col.name !== obsIndex) - .filter((col) => !col.writable) // skip user annotations - they will be treated as categorical - .map((col) => col.name); - - return ( -
- {allContinuousNames.map((key, zebra) => ( - - ))} -
- ); - } -} - -export default Continuous; diff --git a/client/src/components/continuous/continuous.tsx b/client/src/components/continuous/continuous.tsx new file mode 100644 index 00000000..1ca9066c --- /dev/null +++ b/client/src/components/continuous/continuous.tsx @@ -0,0 +1,41 @@ +/* rc slider https://www.npmjs.com/package/rc-slider */ + +import React from "react"; +import { connect } from "react-redux"; +import HistogramBrush from "../brushableHistogram"; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, +})) +class Continuous extends React.PureComponent { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + /* initial value for iterator to simulate index, ranges is an object */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message + const { schema } = this.props; + if (!schema) return null; + const obsIndex = schema.annotations.obs.index; + const allContinuousNames = schema.annotations.obs.columns + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .filter((col: any) => col.type === "int32" || col.type === "float32") + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .filter((col: any) => col.name !== obsIndex) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .filter((col: any) => !col.writable) // skip user annotations - they will be treated as categorical + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .map((col: any) => col.name); + return ( +
+ {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. */} + {allContinuousNames.map((key: any, zebra: any) => ( + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. + + ))} +
+ ); + } +} + +export default Continuous; diff --git a/client/src/components/continuous/setupParallelCoordinates.js b/client/src/components/continuous/setupParallelCoordinates.ts similarity index 64% rename from client/src/components/continuous/setupParallelCoordinates.js rename to client/src/components/continuous/setupParallelCoordinates.ts index 56e5c5fb..c09d6646 100644 --- a/client/src/components/continuous/setupParallelCoordinates.js +++ b/client/src/components/continuous/setupParallelCoordinates.ts @@ -5,7 +5,8 @@ ******************************************/ import * as d3 from "d3"; -const setupParallelCoordinates = (width, height, margin) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const setupParallelCoordinates = (width: any, height: any, margin: any) => { const container = d3.select("#parcoords"); const svg = container @@ -24,10 +25,15 @@ const setupParallelCoordinates = (width, height, margin) => { .style("margin-top", `${margin.top}px`) .style("margin-left", `${margin.left}px`); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. const ctx = canvas.node().getContext("2d"); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. ctx.globalCompositeOperation = "darken"; + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. ctx.globalAlpha = 0.15; + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. ctx.lineWidth = 1.5; + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. ctx.scale(devicePixelRatio, devicePixelRatio); return { diff --git a/client/src/components/continuous/util.js b/client/src/components/continuous/util.js deleted file mode 100644 index 8b05d940..00000000 --- a/client/src/components/continuous/util.js +++ /dev/null @@ -1,49 +0,0 @@ -import each from "lodash.foreach"; -import * as d3 from "d3"; - -const paddingRight = 120; -const continuousChartWidth = 1200; - -export const margin = { top: 66, right: 110, bottom: 20, left: 60 }; -export const width = - continuousChartWidth - margin.left - margin.right - paddingRight; -export const height = 340 - margin.top - margin.bottom; -export const innerHeight = height - 2; - -export const devicePixelRatio = window.devicePixelRatio || 1; - -export const createDimensions = (data) => { - const newArr = []; - each(data, (value, key) => { - if (value.range) { - newArr.push({ - key /* room for confusion: lodash calls this key, it's also the name of the property parallel coords code is looking for */, - type: { - within: (d, extent, dim) => - extent[0] <= dim.scale(d) && dim.scale(d) <= extent[1], - }, - scale: d3 - .scaleSqrt() - .range([innerHeight, 0]) - .domain([0, value.range.max]), - }); - } - }); - return newArr; -}; - -export const yAxis = d3.axisLeft(); - -export const brushstart = () => { - d3.event.sourceEvent.stopPropagation(); -}; - -// Unused. -// export const d3_functor = v => (typeof v === "function" ? v : () => v); -export const project = (d, dimensions, xscale) => - dimensions.map((p, i) => { - // check if data element has property and contains a value - if (!(p.key in d) || d[p.key] === null) return null; - - return [xscale(i), p.scale(d[p.key])]; - }); diff --git a/client/src/components/continuous/util.ts b/client/src/components/continuous/util.ts new file mode 100644 index 00000000..8bda22d6 --- /dev/null +++ b/client/src/components/continuous/util.ts @@ -0,0 +1,57 @@ +import each from "lodash.foreach"; +import * as d3 from "d3"; + +const paddingRight = 120; +const continuousChartWidth = 1200; + +export const margin = { top: 66, right: 110, bottom: 20, left: 60 }; +export const width = + continuousChartWidth - margin.left - margin.right - paddingRight; +export const height = 340 - margin.top - margin.bottom; +export const innerHeight = height - 2; + +export const devicePixelRatio = window.devicePixelRatio || 1; + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const createDimensions = (data: any) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const newArr: any = []; + each(data, (value, key) => { + if (value.range) { + newArr.push({ + key /* room for confusion: lodash calls this key, it's also the name of the property parallel coords code is looking for */, + type: { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + within: (d: any, extent: any, dim: any) => + extent[0] <= dim.scale(d) && dim.scale(d) <= extent[1], + }, + scale: d3 + .scaleSqrt() + .range([innerHeight, 0]) + .domain([0, value.range.max]), + }); + } + }); + return newArr; +}; + +// @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. +export const yAxis = d3.axisLeft(); + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export const brushstart = () => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (d3 as any).event.sourceEvent.stopPropagation(); +}; + +// Unused. +// export const d3_functor = v => (typeof v === "function" ? v : () => v); +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const project = (d: any, dimensions: any, xscale: any) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dimensions.map((p: any, i: any) => { + // check if data element has property and contains a value + if (!(p.key in d) || d[p.key] === null) return null; + + return [xscale(i), p.scale(d[p.key])]; + }); diff --git a/client/src/components/continuousLegend/index.js b/client/src/components/continuousLegend/index.tsx similarity index 70% rename from client/src/components/continuousLegend/index.js rename to client/src/components/continuousLegend/index.tsx index a4d1f1d3..bf8c365f 100644 --- a/client/src/components/continuousLegend/index.js +++ b/client/src/components/continuousLegend/index.tsx @@ -9,7 +9,8 @@ import { } from "../../util/stateManager/colorHelpers"; // create continuous color legend -const continuous = (selectorId, colorScale, colorAccessor) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const continuous = (selectorId: any, colorScale: any, colorAccessor: any) => { const legendHeight = 200; const legendWidth = 80; const margin = { top: 10, right: 60, bottom: 10, left: 2 }; @@ -33,6 +34,7 @@ const continuous = (selectorId, colorScale, colorAccessor) => { we flip the color scale as well [1, 0] instead of [0, 1] */ .node(); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. const ctx = canvas.getContext("2d"); const legendScale = d3 @@ -44,6 +46,7 @@ const continuous = (selectorId, colorScale, colorAccessor) => { ]); /* we flip this to make viridis colors dark if high in the color scale */ // image data hackery based on http://bl.ocks.org/mbostock/048d21cf747371b11884f75ad896e5a5 + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. const image = ctx.createImageData(1, legendHeight); d3.range(legendHeight).forEach((i) => { const c = d3.rgb(colorScale(legendScale.invert(i))); @@ -52,6 +55,7 @@ const continuous = (selectorId, colorScale, colorAccessor) => { image.data[4 * i + 2] = c.b; image.data[4 * i + 3] = 255; }); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. ctx.putImageData(image, 0, 0); // A simpler way to do the above, but possibly slower. keep in mind the legend @@ -105,27 +109,30 @@ const continuous = (selectorId, colorScale, colorAccessor) => { .text(colorAccessor); }; +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - annoMatrix: state.annoMatrix, - colors: state.colors, - genesets: state.genesets.genesets, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annoMatrix: (state as any).annoMatrix, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colors: (state as any).colors, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesets: (state as any).genesets.genesets, })) class ContinuousLegend extends React.Component { - async componentDidUpdate(prevProps) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + async componentDidUpdate(prevProps: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix, colors, genesets } = this.props; if (!colors || !annoMatrix) return; - if (colors !== prevProps?.colors || annoMatrix !== prevProps?.annoMatrix) { const { schema } = annoMatrix; const { colorMode, colorAccessor, userColors } = colors; - const colorQuery = createColorQuery( colorMode, colorAccessor, schema, genesets ); - const colorDf = colorQuery ? await annoMatrix.fetch(...colorQuery) : null; const colorTable = createColorTable( colorMode, @@ -134,19 +141,19 @@ class ContinuousLegend extends React.Component { schema, userColors ); - const colorScale = colorTable.scale; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'range' does not exist on type '((idx: an... Remove this comment to see the full error message const range = colorScale?.range; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'domain' does not exist on type '((idx: a... Remove this comment to see the full error message const [domainMin, domainMax] = colorScale?.domain?.() ?? [0, 0]; - /* always remove it, if it's not continuous we don't put it back. */ d3.select("#continuous_legend").selectAll("*").remove(); - if (colorAccessor && colorScale && range && domainMin < domainMax) { /* fragile! continuous range is 0 to 1, not [#fa4b2c, ...], make this a flag? */ if (range()[0][0] !== "#") { continuous( "#continuous_legend", + // @ts-expect-error ts-migrate(2339) FIXME: Property 'domain' does not exist on type '((idx: a... Remove this comment to see the full error message d3.scaleSequential(interpolateCool).domain(colorScale.domain()), colorAccessor ); @@ -155,6 +162,7 @@ class ContinuousLegend extends React.Component { } } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { return (
({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutChoice: (state as any).layoutChoice, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + crossfilter: (state as any).obsCrossfilter, +})) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class Embedding extends React.PureComponent<{}, EmbeddingState> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { + super(props); + this.state = {}; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleLayoutChoiceChange = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + dispatch(actions.layoutChoiceAction(e.currentTarget.value)); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'layoutChoice' does not exist on type 'Re... Remove this comment to see the full error message + const { layoutChoice, schema, crossfilter } = this.props; + const { annoMatrix } = crossfilter; + return ( + + + + + } + // minimal /* removes arrow */ + position={Position.TOP_LEFT} + content={ +
+

Embedding Choice

+

+ There are {schema?.dataframe?.nObs} cells in the entire dataset. +

+ +
+ } + /> + + ); + } +} + +export default Embedding; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const loadAllEmbeddingCounts = async ({ annoMatrix, available }: any) => { + const embeddings = await Promise.all( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + available.map((name: any) => annoMatrix.base().fetch("emb", name)) + ); + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'name' implicitly has an 'any' type. + return available.map((name, idx) => ({ + embeddingName: name, + embedding: embeddings[idx], + discreteCellIndex: getDiscreteCellEmbeddingRowIndex(embeddings[idx]), + })); +}; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const EmbeddingChoices = ({ onChange, annoMatrix, layoutChoice }: any) => { + const { available } = layoutChoice; + const { data, error, isPending } = useAsync({ + promiseFn: loadAllEmbeddingCounts, + annoMatrix, + available, + }); + + if (error) { + /* log, as this is unexpected */ + console.error(error); + } + if (error || isPending) { + /* still loading, or errored out - just omit counts (TODO: spinner?) */ + return ( + + {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. */} + {layoutChoice.available.map((name: any) => ( + + ))} + + ); + } + if (data) { + return ( + + {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. */} + {data.map((summary: any) => { + const { discreteCellIndex, embeddingName } = summary; + const sizeHint = `${discreteCellIndex.size()} cells`; + return ( + + ); + })} + + ); + } + return null; +}; diff --git a/client/src/components/framework/container.js b/client/src/components/framework/container.tsx similarity index 64% rename from client/src/components/framework/container.js rename to client/src/components/framework/container.tsx index db9e2e19..a50e25e6 100644 --- a/client/src/components/framework/container.js +++ b/client/src/components/framework/container.tsx @@ -1,6 +1,7 @@ import React from "react"; -function Container(props) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +function Container(props: any) { const { children } = props; return (
{ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const Logo = (props: any) => { const { size } = props; return ( diff --git a/client/src/components/framework/toasters.js b/client/src/components/framework/toasters.js deleted file mode 100644 index 29e15cdf..00000000 --- a/client/src/components/framework/toasters.js +++ /dev/null @@ -1,52 +0,0 @@ -import { Position, Toaster, Intent } from "@blueprintjs/core"; - -/** Singleton toaster instance. Create separate instances for different options. */ - -const ToastTopCenter = Toaster.create({ - className: "recipe-toaster", - position: Position.TOP, - maxToasts: 4, -}); - -/* -A "user" error - eg, bad input -*/ -export const postUserErrorToast = (message) => - ToastTopCenter.show({ message, intent: Intent.WARNING }); - -/* -A toast the user must dismiss manually, because they need to act on its information, -ie., 8 bulk add genes out of 40 were bad. Manually see which ones and fix. -*/ -export const keepAroundErrorToast = (message) => - ToastTopCenter.show({ message, timeout: 0, intent: Intent.WARNING }); - -/* -a hard network error -*/ -export const postNetworkErrorToast = (message, key = undefined) => - ToastTopCenter.show( - { - message, - timeout: 30000, - intent: Intent.DANGER, - }, - key - ); - -/* -Async message to user -*/ -export const postAsyncSuccessToast = (message) => - ToastTopCenter.show({ - message, - timeout: 10000, - intent: Intent.SUCCESS, - }); - -export const postAsyncFailureToast = (message) => - ToastTopCenter.show({ - message, - timeout: 10000, - intent: Intent.WARNING, - }); diff --git a/client/src/components/framework/toasters.ts b/client/src/components/framework/toasters.ts new file mode 100644 index 00000000..bffbd885 --- /dev/null +++ b/client/src/components/framework/toasters.ts @@ -0,0 +1,57 @@ +import { Position, Toaster, Intent } from "@blueprintjs/core"; + +/** Singleton toaster instance. Create separate instances for different options. */ + +const ToastTopCenter = Toaster.create({ + className: "recipe-toaster", + position: Position.TOP, + maxToasts: 4, +}); + +/* +A "user" error - eg, bad input +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const postUserErrorToast = (message: any) => + ToastTopCenter.show({ message, intent: Intent.WARNING }); + +/* +A toast the user must dismiss manually, because they need to act on its information, +ie., 8 bulk add genes out of 40 were bad. Manually see which ones and fix. +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const keepAroundErrorToast = (message: any) => + ToastTopCenter.show({ message, timeout: 0, intent: Intent.WARNING }); + +/* +a hard network error +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const postNetworkErrorToast = (message: any, key = undefined) => + ToastTopCenter.show( + { + message, + timeout: 30000, + intent: Intent.DANGER, + }, + key + ); + +/* +Async message to user +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const postAsyncSuccessToast = (message: any) => + ToastTopCenter.show({ + message, + timeout: 10000, + intent: Intent.SUCCESS, + }); + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const postAsyncFailureToast = (message: any) => + ToastTopCenter.show({ + message, + timeout: 10000, + intent: Intent.WARNING, + }); diff --git a/client/src/components/geneExpression/gene.js b/client/src/components/geneExpression/gene.tsx similarity index 56% rename from client/src/components/geneExpression/gene.js rename to client/src/components/geneExpression/gene.tsx index 47efc6cd..912aace6 100644 --- a/client/src/components/geneExpression/gene.js +++ b/client/src/components/geneExpression/gene.tsx @@ -9,34 +9,51 @@ import actions from "../../actions"; const MINI_HISTOGRAM_WIDTH = 110; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state, ownProps) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'gene' does not exist on type '{}'. const { gene } = ownProps; return { - isColorAccessor: state.colors.colorAccessor === gene, - isScatterplotXXaccessor: state.controls.scatterplotXXaccessor === gene, - isScatterplotYYaccessor: state.controls.scatterplotYYaccessor === gene, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + isColorAccessor: (state as any).colors.colorAccessor === gene, + isScatterplotXXaccessor: + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (state as any).controls.scatterplotXXaccessor === gene, + isScatterplotYYaccessor: + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (state as any).controls.scatterplotYYaccessor === gene, }; }) -class Gene extends React.Component { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class Gene extends React.Component<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { geneIsExpanded: false, }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. onColorChangeClick = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, gene } = this.props; dispatch(actions.requestSingleGeneExpressionCountsForColoringPOST(gene)); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleGeneExpandClick = () => { const { geneIsExpanded } = this.state; this.setState({ geneIsExpanded: !geneIsExpanded }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleSetGeneAsScatterplotX = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, gene } = this.props; dispatch({ type: "set scatterplot x", @@ -44,7 +61,9 @@ class Gene extends React.Component { }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleSetGeneAsScatterplotY = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, gene } = this.props; dispatch({ type: "set scatterplot y", @@ -52,19 +71,29 @@ class Gene extends React.Component { }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleDeleteGeneFromSet = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, gene, geneset } = this.props; dispatch(actions.genesetDeleteGenes(geneset, [gene])); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'gene' does not exist on type 'Readonly<{... Remove this comment to see the full error message gene, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'geneDescription' does not exist on type ... Remove this comment to see the full error message geneDescription, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isColorAccessor' does not exist on type ... Remove this comment to see the full error message isColorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterplotXXaccessor' does not exist ... Remove this comment to see the full error message isScatterplotXXaccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isScatterplotYYaccessor' does not exist ... Remove this comment to see the full error message isScatterplotYYaccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'quickGene' does not exist on type 'Reado... Remove this comment to see the full error message quickGene, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'removeGene' does not exist on type 'Read... Remove this comment to see the full error message removeGene, } = this.props; const { geneIsExpanded } = this.state; @@ -84,6 +113,7 @@ class Gene extends React.Component { >
{!geneIsExpanded ? (
+ {/* @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. */} {geneIsExpanded && }
); diff --git a/client/src/components/geneExpression/geneSet.js b/client/src/components/geneExpression/geneSet.tsx similarity index 67% rename from client/src/components/geneExpression/geneSet.js rename to client/src/components/geneExpression/geneSet.tsx index b6ac08db..bc26382e 100644 --- a/client/src/components/geneExpression/geneSet.js +++ b/client/src/components/geneExpression/geneSet.tsx @@ -9,20 +9,28 @@ import HistogramBrush from "../brushableHistogram"; import { diffexpPopNamePrefix1, diffexpPopNamePrefix2 } from "../../globals"; -class GeneSet extends React.Component { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class GeneSet extends React.Component<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { isOpen: false, }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. onGenesetMenuClick = () => { const { isOpen } = this.state; this.setState({ isOpen: !isOpen }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renderGenes() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'setName' does not exist on type 'Readonl... Remove this comment to see the full error message const { setName, setGenes } = this.props; const setGenesNames = [...setGenes.keys()]; return ( @@ -32,6 +40,7 @@ class GeneSet extends React.Component { return (
+ {/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ isOpen: any; genesetsEditable: true; genes... Remove this comment to see the full error message */}
@@ -117,6 +131,7 @@ class GeneSet extends React.Component {
{isOpen && !genesetIsEmpty && ( diff --git a/client/src/components/geneExpression/index.js b/client/src/components/geneExpression/index.tsx similarity index 50% rename from client/src/components/geneExpression/index.js rename to client/src/components/geneExpression/index.tsx index e3f807d6..6f711a32 100644 --- a/client/src/components/geneExpression/index.js +++ b/client/src/components/geneExpression/index.tsx @@ -7,25 +7,33 @@ import GeneSet from "./geneSet"; import QuickGene from "./quickGene"; import CreateGenesetDialogue from "./menus/createGenesetDialogue"; -@connect((state) => { - return { - genesets: state.genesets.genesets, - }; -}) -class GeneExpression extends React.Component { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesets: (state as any).genesets.genesets, +})) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class GeneExpression extends React.Component<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { geneSetsExpanded: true }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renderGeneSets = () => { const sets = []; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'genesets' does not exist on type 'Readon... Remove this comment to see the full error message const { genesets } = this.props; for (const [name, geneset] of genesets) { sets.push( { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; const { geneSetsExpanded } = this.state; dispatch({ type: "geneset: activate add new geneset mode" }); if (!geneSetsExpanded) { - this.setState((state) => { - return { ...state, geneSetsExpanded: true }; - }); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.setState((state: any) => ({ ...state, geneSetsExpanded: true })); } }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleExpandGeneSets = () => { - this.setState((state) => { - return { ...state, geneSetsExpanded: !state.geneSetsExpanded }; - }); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.setState((state: any) => ({ + ...state, + geneSetsExpanded: !state.geneSetsExpanded, + })); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { geneSetsExpanded } = this.state; return ( @@ -67,6 +80,7 @@ class GeneExpression extends React.Component { >

({ - genesetsUI: state.genesetsUI, -})) -class AddGeneToGenesetDialogue extends React.PureComponent { - constructor(props) { - super(props); - this.state = { - genesToAdd: "", - }; - } - - disableAddGeneMode = () => { - const { dispatch } = this.props; - dispatch({ - type: "geneset: disable add new genes mode", - }); - }; - - handleAddGeneToGeneSet = (e) => { - const { geneset, dispatch } = this.props; - const { genesToAdd } = this.state; - - const genesTmpHardcodedFormat = []; - - const genesArrayFromString = parseBulkGeneString(genesToAdd); - - genesArrayFromString.forEach((_gene) => { - genesTmpHardcodedFormat.push({ - geneSymbol: _gene, - }); - }); - - dispatch(actions.genesetAddGenes(geneset, genesTmpHardcodedFormat)); - dispatch({ - type: "geneset: disable add new genes mode", - }); - if (e) e.preventDefault(); - }; - - handleChange = (e) => { - this.setState({ genesToAdd: e }); - }; - - render() { - const { geneset, genesetsUI } = this.props; - const { genesToAdd } = this.state; - - return ( - <> - - } - handleSubmit={this.handleAddGeneToGeneSet} - handleCancel={this.disableAddGeneMode} - /> - - ); - } -} - -export default AddGeneToGenesetDialogue; diff --git a/client/src/components/geneExpression/menus/addGeneToGenesetDialogue.tsx b/client/src/components/geneExpression/menus/addGeneToGenesetDialogue.tsx new file mode 100644 index 00000000..204df743 --- /dev/null +++ b/client/src/components/geneExpression/menus/addGeneToGenesetDialogue.tsx @@ -0,0 +1,101 @@ +import React from "react"; +import { connect } from "react-redux"; +import AnnoDialog from "../../annoDialog"; +import LabelInput from "../../labelInput"; +import parseBulkGeneString from "../../../util/parseBulkGeneString"; +import actions from "../../../actions"; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesetsUI: (state as any).genesetsUI, +})) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class AddGeneToGenesetDialogue extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { + super(props); + this.state = { + genesToAdd: "", + }; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + disableAddGeneMode = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + dispatch({ + type: "geneset: disable add new genes mode", + }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleAddGeneToGeneSet = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'geneset' does not exist on type 'Readonl... Remove this comment to see the full error message + const { geneset, dispatch } = this.props; + const { genesToAdd } = this.state; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const genesTmpHardcodedFormat: any = []; + const genesArrayFromString = parseBulkGeneString(genesToAdd); + genesArrayFromString.forEach((_gene) => { + genesTmpHardcodedFormat.push({ + geneSymbol: _gene, + }); + }); + dispatch(actions.genesetAddGenes(geneset, genesTmpHardcodedFormat)); + dispatch({ + type: "geneset: disable add new genes mode", + }); + if (e) e.preventDefault(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChange = (e: any) => { + this.setState({ genesToAdd: e }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'geneset' does not exist on type 'Readonl... Remove this comment to see the full error message + const { geneset, genesetsUI } = this.props; + const { genesToAdd } = this.state; + return ( + <> + void; inputProps: { ... Remove this comment to see the full error message + onChange={this.handleChange} + inputProps={{ + "data-testid": "add-genes", + leftIcon: "manually-entered-data", + intent: "none", + autoFocus: true, + }} + newLabelMessage="New category" + /> + } + handleSubmit={this.handleAddGeneToGeneSet} + handleCancel={this.disableAddGeneMode} + /> + + ); + } +} + +export default AddGeneToGenesetDialogue; diff --git a/client/src/components/geneExpression/menus/addGenes.js b/client/src/components/geneExpression/menus/addGenes.tsx similarity index 68% rename from client/src/components/geneExpression/menus/addGenes.js rename to client/src/components/geneExpression/menus/addGenes.tsx index fb4db8d6..ab3ec5fb 100644 --- a/client/src/components/geneExpression/menus/addGenes.js +++ b/client/src/components/geneExpression/menus/addGenes.tsx @@ -20,7 +20,8 @@ import { import { memoize } from "../../../util/dataframe/util"; import parseBulkGeneString from "../../../util/parseBulkGeneString"; -const renderGene = (fuzzySortResult, { handleClick, modifiers }) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const renderGene = (fuzzySortResult: any, { handleClick, modifiers }: any) => { if (!modifiers.matchesPredicate) { return null; } @@ -33,8 +34,8 @@ const renderGene = (fuzzySortResult, { handleClick, modifiers }) => { disabled={modifiers.disabled} data-testid={`suggest-menu-item-${geneName}`} key={geneName} - onClick={(g) => - /* this fires when user clicks a menu item */ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + onClick={(g: any /* this fires when user clicks a menu item */) => handleClick(g) } text={geneName} @@ -42,22 +43,30 @@ const renderGene = (fuzzySortResult, { handleClick, modifiers }) => { ); }; -const filterGenes = (query, genes) => +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const filterGenes = (query: any, genes: any) => /* fires on load, once, and then for each character typed into the input */ fuzzysort.go(query, genes, { limit: 5, threshold: -10000, // don't return bad results }); -@connect((state) => { - return { - annoMatrix: state.annoMatrix, - userDefinedGenes: state.controls.userDefinedGenes, - userDefinedGenesLoading: state.controls.userDefinedGenesLoading, - }; -}) -class AddGenes extends React.Component { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type AddGenesState = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annoMatrix: (state as any).annoMatrix, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userDefinedGenes: (state as any).controls.userDefinedGenes, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userDefinedGenesLoading: (state as any).controls.userDefinedGenesLoading, +})) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class AddGenes extends React.Component<{}, AddGenesState> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { bulkAdd: "", @@ -68,15 +77,20 @@ class AddGenes extends React.Component { }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. componentDidMount() { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. this.updateState(); } - componentDidUpdate(prevProps) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + componentDidUpdate(prevProps: {}) { this.updateState(prevProps); } - handleClick(g) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleClick(g: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, userDefinedGenes } = this.props; const { geneNames } = this.state; if (!g) return; @@ -96,7 +110,8 @@ class AddGenes extends React.Component { } } - _genesToUpper = (listGenes) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + _genesToUpper = (listGenes: any) => { // Has to be a Map to preserve index const upperGenes = new Map(); for (let i = 0, { length } = listGenes; i < length; i += 1) { @@ -106,10 +121,12 @@ class AddGenes extends React.Component { return upperGenes; }; - // eslint-disable-next-line react/sort-comp -- memo requires a defined _genesToUpper - _memoGenesToUpper = memoize(this._genesToUpper, (arr) => arr); + // eslint-disable-next-line react/sort-comp, @typescript-eslint/no-explicit-any -- memo requires a defined _genesToUpper + _memoGenesToUpper = memoize(this._genesToUpper, (arr: any) => arr); + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleBulkAddClick = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, userDefinedGenes } = this.props; const { bulkAdd, geneNames } = this.state; @@ -159,7 +176,9 @@ class AddGenes extends React.Component { return undefined; }; - async updateState(prevProps) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + async updateState(prevProps: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix } = this.props; if (!annoMatrix) return; if (annoMatrix !== prevProps?.annoMatrix) { @@ -180,6 +199,7 @@ class AddGenes extends React.Component { } } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. placeholderGeneNames() { /* return a string containing gene name suggestions for use as a user hint. @@ -209,7 +229,9 @@ class AddGenes extends React.Component { return "Apod, Cd74, ..."; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'userDefinedGenesLoading' does not exist ... Remove this comment to see the full error message const { userDefinedGenesLoading } = this.props; const { tab, bulkAdd, activeItem, status, geneNames } = this.state; @@ -265,10 +287,10 @@ class AddGenes extends React.Component { this.handleClick(g); }} initialContent={} + // @ts-expect-error ts-migrate(2322) FIXME: Type '{ "data-testid": string; }' is not assignabl... Remove this comment to see the full error message inputProps={{ "data-testid": "gene-search" }} - inputValueRenderer={() => { - return ""; - }} + inputValueRenderer={() => ""} + // @ts-expect-error ts-migrate(2322) FIXME: Type '(query: any, genes: any) => Fuzzysort.Result... Remove this comment to see the full error message itemListPredicate={filterGenes} onActiveItemChange={(item) => this.setState({ activeItem: item })} itemRenderer={renderGene} diff --git a/client/src/components/geneExpression/menus/createGenesetDialogue.js b/client/src/components/geneExpression/menus/createGenesetDialogue.tsx similarity index 56% rename from client/src/components/geneExpression/menus/createGenesetDialogue.js rename to client/src/components/geneExpression/menus/createGenesetDialogue.tsx index 2f90b80a..28e35815 100644 --- a/client/src/components/geneExpression/menus/createGenesetDialogue.js +++ b/client/src/components/geneExpression/menus/createGenesetDialogue.tsx @@ -7,15 +7,26 @@ import { Tooltip2 } from "@blueprintjs/popover2"; import LabelInput from "../../labelInput"; import actions from "../../../actions"; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - annotations: state.annotations, - schema: state.annoMatrix?.schema, - obsCrossfilter: state.obsCrossfilter, - genesets: state.genesets.genesets, - genesetsUI: state.genesetsUI, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annotations: (state as any).annotations, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + obsCrossfilter: (state as any).obsCrossfilter, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesets: (state as any).genesets.genesets, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesetsUI: (state as any).genesetsUI, })) -class CreateGenesetDialogue extends React.PureComponent { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class CreateGenesetDialogue extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { genesetName: "", @@ -24,7 +35,9 @@ class CreateGenesetDialogue extends React.PureComponent { }; } - disableCreateGenesetMode = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + disableCreateGenesetMode = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; this.setState({ genesetName: "", @@ -38,33 +51,32 @@ class CreateGenesetDialogue extends React.PureComponent { if (e) e.preventDefault(); }; - createGeneset = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + createGeneset = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; const { genesetName, genesToPopulateGeneset, genesetDescription, } = this.state; - dispatch({ type: "geneset: create", genesetName: genesetName.trim(), genesetDescription, }); if (genesToPopulateGeneset) { - const genesTmpHardcodedFormat = []; - + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const genesTmpHardcodedFormat: any = []; const genesArrayFromString = pull( uniq(genesToPopulateGeneset.split(/[ ,]+/)), "" ); - genesArrayFromString.forEach((_gene) => { genesTmpHardcodedFormat.push({ geneSymbol: _gene, }); }); - dispatch(actions.genesetAddGenes(genesetName, genesTmpHardcodedFormat)); } dispatch({ @@ -77,38 +89,41 @@ class CreateGenesetDialogue extends React.PureComponent { e.preventDefault(); }; - genesetNameError = () => { - return false; - }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + genesetNameError = () => false; - handleChange = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChange = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'genesets' does not exist on type 'Readon... Remove this comment to see the full error message const { genesets } = this.props; this.setState({ genesetName: e }); this.validate(e, genesets); }; - handleGenesetInputChange = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleGenesetInputChange = (e: any) => { this.setState({ genesToPopulateGeneset: e }); }; - handleDescriptionInputChange = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleDescriptionInputChange = (e: any) => { this.setState({ genesetDescription: e }); }; - instruction = (genesetName, genesets) => { - return genesets.has(genesetName) + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + instruction = (genesetName: any, genesets: any) => + genesets.has(genesetName) ? "Gene set name must be unique." : "New, unique gene set name"; - }; - validate = (genesetName, genesets) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + validate = (genesetName: any, genesets: any) => { if (genesets.has(genesetName)) { this.setState({ nameErrorMessage: "There is already a geneset with that name", }); return false; } - if ( genesetName.length > 1 && // eslint-disable-next-line no-control-regex -- unicode 0-31 127-65535 @@ -126,10 +141,11 @@ class CreateGenesetDialogue extends React.PureComponent { return true; }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { genesetName, nameErrorMessage } = this.state; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'genesetsUI' does not exist on type 'Read... Remove this comment to see the full error message const { genesetsUI, genesets } = this.props; - return ( <>

{this.instruction(genesetName, genesets)}

void; inputProps: { ... Remove this comment to see the full error message onChange={this.handleChange} inputProps={{ "data-testid": "create-geneset-input", @@ -171,6 +188,7 @@ class CreateGenesetDialogue extends React.PureComponent { gene set

void; inputProps: { ... Remove this comment to see the full error message onChange={this.handleDescriptionInputChange} inputProps={{ "data-testid": "add-geneset-description", @@ -186,6 +204,7 @@ class CreateGenesetDialogue extends React.PureComponent { gene set

void; inputProps: { ... Remove this comment to see the full error message onChange={this.handleGenesetInputChange} inputProps={{ "data-testid": "add-genes", diff --git a/client/src/components/geneExpression/menus/editGenesetNameDialogue.js b/client/src/components/geneExpression/menus/editGenesetNameDialogue.js deleted file mode 100644 index fc2204eb..00000000 --- a/client/src/components/geneExpression/menus/editGenesetNameDialogue.js +++ /dev/null @@ -1,132 +0,0 @@ -import React from "react"; -import { connect } from "react-redux"; -import AnnoDialog from "../../annoDialog"; -import LabelInput from "../../labelInput"; - -@connect((state) => ({ - annotations: state.annotations, - schema: state.annoMatrix?.schema, - obsCrossfilter: state.obsCrossfilter, - genesetsUI: state.genesetsUI, - genesets: state.genesets.genesets, -})) -class RenameGeneset extends React.PureComponent { - constructor(props) { - super(props); - this.state = { - newGenesetName: props.parentGeneset, - newGenesetDescription: props.parentGenesetDescription, - }; - } - - disableEditGenesetNameMode = (e) => { - const { dispatch } = this.props; - this.setState({ - newGenesetName: "", - newGenesetDescription: "", - }); - dispatch({ - type: "geneset: disable rename geneset mode", - }); - if (e) e.preventDefault(); - }; - - renameGeneset = (e) => { - const { dispatch, genesetsUI } = this.props; - const { newGenesetName, newGenesetDescription } = this.state; - - dispatch({ - type: "geneset: update", - genesetName: genesetsUI.isEditingGenesetName, - update: { - genesetName: newGenesetName, - genesetDescription: newGenesetDescription, - }, - }); - dispatch({ - type: "geneset: disable rename geneset mode", - }); - e.preventDefault(); - }; - - genesetNameError = () => { - return false; - }; - - handleChange = (e) => { - this.setState({ newGenesetName: e }); - }; - - handleChangeDescription = (e) => { - this.setState({ newGenesetDescription: e }); - }; - - validate = (genesetName, genesets) => { - return ( - !genesets.has(genesetName) && - // eslint-disable-next-line no-control-regex -- unicode 0-31 127-65535 - genesetName.match(/^\s|[\u0000-\u001F\u007F-\uFFFF]|[ ]{2,}|^$|\s$/g) - ?.length - ); - }; - - render() { - const { newGenesetName, newGenesetDescription } = this.state; - const { - genesetsUI, - parentGeneset, - parentGenesetDescription, - genesets, - } = this.props; - - return ( - <> - - } - secondaryInstructions="Edit description" - secondaryInput={ - - } - handleSubmit={this.renameGeneset} - handleCancel={this.disableEditGenesetNameMode} - /> - - ); - } -} - -export default RenameGeneset; diff --git a/client/src/components/geneExpression/menus/editGenesetNameDialogue.tsx b/client/src/components/geneExpression/menus/editGenesetNameDialogue.tsx new file mode 100644 index 00000000..cc183057 --- /dev/null +++ b/client/src/components/geneExpression/menus/editGenesetNameDialogue.tsx @@ -0,0 +1,154 @@ +import React from "react"; +import { connect } from "react-redux"; +import AnnoDialog from "../../annoDialog"; +import LabelInput from "../../labelInput"; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annotations: (state as any).annotations, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix?.schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + obsCrossfilter: (state as any).obsCrossfilter, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesetsUI: (state as any).genesetsUI, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesets: (state as any).genesets.genesets, +})) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class RenameGeneset extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { + super(props); + this.state = { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'parentGeneset' does not exist on type '{... Remove this comment to see the full error message + newGenesetName: props.parentGeneset, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'parentGenesetDescription' does not exist... Remove this comment to see the full error message + newGenesetDescription: props.parentGenesetDescription, + }; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + disableEditGenesetNameMode = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + this.setState({ + newGenesetName: "", + newGenesetDescription: "", + }); + dispatch({ + type: "geneset: disable rename geneset mode", + }); + if (e) e.preventDefault(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + renameGeneset = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, genesetsUI } = this.props; + const { newGenesetName, newGenesetDescription } = this.state; + dispatch({ + type: "geneset: update", + genesetName: genesetsUI.isEditingGenesetName, + update: { + genesetName: newGenesetName, + genesetDescription: newGenesetDescription, + }, + }); + dispatch({ + type: "geneset: disable rename geneset mode", + }); + e.preventDefault(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + genesetNameError = () => false; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChange = (e: any) => { + this.setState({ newGenesetName: e }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChangeDescription = (e: any) => { + this.setState({ newGenesetDescription: e }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + validate = (genesetName: any, genesets: any) => + !genesets.has(genesetName) && + // eslint-disable-next-line no-control-regex -- unicode 0-31 127-65535 + genesetName.match(/^\s|[\u0000-\u001F\u007F-\uFFFF]|[ ]{2,}|^$|\s$/g) + ?.length; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { newGenesetName, newGenesetDescription } = this.state; + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'genesetsUI' does not exist on type 'Read... Remove this comment to see the full error message + genesetsUI, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'parentGeneset' does not exist on type 'Read... Remove this comment to see the full error message + parentGeneset, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'parentGenesetDescription' does not exist on type 'Read... Remove this comment to see the full error message + parentGenesetDescription, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'genesets' does not exist on type 'Read... Remove this comment to see the full error message + genesets, + } = this.props; + return ( + <> + void; in... Remove this comment to see the full error message + label={newGenesetName} + onChange={this.handleChange} + inputProps={{ + "data-testid": "rename-geneset-modal", + leftIcon: "manually-entered-data", + intent: "none", + autoFocus: true, + }} + /> + } + secondaryInstructions="Edit description" + secondaryInput={ + void; in... Remove this comment to see the full error message + label={newGenesetDescription} + onChange={this.handleChangeDescription} + inputProps={{ "data-testid": "change geneset description" }} + intent="none" + autoFocus={false} + /> + } + handleSubmit={this.renameGeneset} + handleCancel={this.disableEditGenesetNameMode} + /> + + ); + } +} + +export default RenameGeneset; diff --git a/client/src/components/geneExpression/menus/genesetMenus.js b/client/src/components/geneExpression/menus/genesetMenus.tsx similarity index 56% rename from client/src/components/geneExpression/menus/genesetMenus.js rename to client/src/components/geneExpression/menus/genesetMenus.tsx index 8c030611..251ea859 100644 --- a/client/src/components/geneExpression/menus/genesetMenus.js +++ b/client/src/components/geneExpression/menus/genesetMenus.tsx @@ -17,21 +17,27 @@ import * as globals from "../../../globals"; import actions from "../../../actions"; import AddGeneToGenesetDialogue from "./addGeneToGenesetDialogue"; -@connect((state) => { - return { - genesetsUI: state.genesetsUI, - colorAccessor: state.colors.colorAccessor, - dotplot: state.layoutChoice.dotplot, - dotplotColumns: state.dotplot.column, - }; -}) -class GenesetMenus extends React.PureComponent { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesetsUI: (state as any).genesetsUI, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colorAccessor: (state as any).colors.colorAccessor, +})) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class GenesetMenus extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = {}; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. activateAddGeneToGenesetMode = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, geneset } = this.props; dispatch({ type: "geneset: activate add new genes mode", @@ -39,7 +45,9 @@ class GenesetMenus extends React.PureComponent { }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. activateEditGenesetNameMode = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, geneset } = this.props; dispatch({ @@ -48,39 +56,30 @@ class GenesetMenus extends React.PureComponent { }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleColorByEntireGeneset = () => { - const { dispatch, geneset, dotplot } = this.props; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, geneset } = this.props; - if (dotplot) { - dispatch({ - type: "set dotplot column", - data: geneset, - }); - } else { - dispatch({ - type: "color by geneset mean expression", - geneset, - }); - } + dispatch({ + type: "color by geneset mean expression", + geneset, + }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleDeleteGeneset = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, geneset } = this.props; dispatch(actions.genesetDelete(geneset)); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { - const { - geneset, - genesetsEditable, - createText, - colorAccessor, - dotplot, - dotplotColumns, - } = this.props; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'geneset' does not exist on type 'Readonl... Remove this comment to see the full error message + const { geneset, genesetsEditable, createText, colorAccessor } = this.props; const isColorBy = geneset === colorAccessor; - const isDotplotColumns = geneset === dotplotColumns; return ( <> @@ -101,6 +100,7 @@ class GenesetMenus extends React.PureComponent { minimal /> + {/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ geneset: any; }' is not assignable to type... Remove this comment to see the full error message */} - } + icon={} /> diff --git a/client/src/components/geneExpression/quickGene.js b/client/src/components/geneExpression/quickGene.tsx similarity index 56% rename from client/src/components/geneExpression/quickGene.js rename to client/src/components/geneExpression/quickGene.tsx index aa414a98..1f89d24c 100644 --- a/client/src/components/geneExpression/quickGene.js +++ b/client/src/components/geneExpression/quickGene.tsx @@ -10,7 +10,8 @@ import Gene from "./gene"; import { postUserErrorToast } from "../framework/toasters"; import actions from "../../actions"; -const usePrevious = (value) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const usePrevious = (value: any) => { const ref = useRef(); useEffect(() => { ref.current = value; @@ -18,6 +19,7 @@ const usePrevious = (value) => { return ref.current; }; +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. function QuickGene() { const dispatch = useDispatch(); @@ -26,20 +28,23 @@ function QuickGene() { const [, setStatus] = useState("pending"); const { annoMatrix, userDefinedGenes, userDefinedGenesLoading } = useSelector( - (state) => { - return { - annoMatrix: state.annoMatrix, - userDefinedGenes: state.controls.userDefinedGenes, - userDefinedGenesLoading: state.controls.userDefinedGenesLoading, - }; - } + (state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annoMatrix: (state as any).annoMatrix, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userDefinedGenes: (state as any).controls.userDefinedGenes, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userDefinedGenesLoading: (state as any).controls.userDefinedGenesLoading, + }) ); const prevProps = usePrevious({ annoMatrix }); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '() => Promise' is not assi... Remove this comment to see the full error message useEffect(async () => { if (!annoMatrix) return; - if (annoMatrix !== prevProps?.annoMatrix) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + if (annoMatrix !== (prevProps as any)?.annoMatrix) { const { schema } = annoMatrix; const varIndex = schema.annotations.var.index; @@ -57,7 +62,12 @@ function QuickGene() { const handleExpand = () => setIsExpanded(!isExpanded); - const renderGene = (fuzzySortResult, { handleClick, modifiers }) => { + const renderGene = ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + fuzzySortResult: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + { handleClick, modifiers }: any + ) => { if (!modifiers.matchesPredicate) { return null; } @@ -70,8 +80,8 @@ function QuickGene() { disabled={modifiers.disabled} data-testid={`suggest-menu-item-${geneName}`} key={geneName} - onClick={(g) => - /* this fires when user clicks a menu item */ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + onClick={(g: any /* this fires when user clicks a menu item */) => handleClick(g) } text={geneName} @@ -79,11 +89,13 @@ function QuickGene() { ); }; - const handleClick = (g) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const handleClick = (g: any) => { if (!g) return; const gene = g.target; if (userDefinedGenes.indexOf(gene) !== -1) { postUserErrorToast("That gene already exists"); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'any' is not assignable to parame... Remove this comment to see the full error message } else if (geneNames.indexOf(gene) === undefined) { postUserErrorToast("That doesn't appear to be a valid gene name."); } else { @@ -93,34 +105,39 @@ function QuickGene() { } }; - const filterGenes = (query, genes) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const filterGenes = (query: any, genes: any) => /* fires on load, once, and then for each character typed into the input */ fuzzysort.go(query, genes, { limit: 5, threshold: -10000, // don't return bad results }); - const removeGene = (gene) => () => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const removeGene = (gene: any) => () => { dispatch({ type: "clear user defined gene", data: gene }); }; - const QuickGenes = useMemo(() => { - return userDefinedGenes.map((gene) => { - return ( + const QuickGenes = useMemo( + () => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userDefinedGenes.map((gene: any) => ( - ); - }); - }, [userDefinedGenes]); + )), + [userDefinedGenes] + ); return (

} inputProps={{ + // @ts-expect-error ts-migrate(2322) FIXME: Type '{ "data-testid": string; placeholder: string... Remove this comment to see the full error message "data-testid": "gene-search", placeholder: "Quick Gene Search", leftIcon: IconNames.SEARCH, fill: true, }} - inputValueRenderer={() => { - return ""; - }} + inputValueRenderer={() => ""} + // @ts-expect-error ts-migrate(2322) FIXME: Type '(query: any, genes: any) => Fuzzysort.Result... Remove this comment to see the full error message itemListPredicate={filterGenes} itemRenderer={renderGene} items={geneNames || ["No genes"]} diff --git a/client/src/components/graph/drawPointsRegl.js b/client/src/components/graph/drawPointsRegl.ts similarity index 89% rename from client/src/components/graph/drawPointsRegl.js rename to client/src/components/graph/drawPointsRegl.ts index 01ecc99f..ad75e211 100644 --- a/client/src/components/graph/drawPointsRegl.js +++ b/client/src/components/graph/drawPointsRegl.ts @@ -1,6 +1,7 @@ import { glPointFlags, glPointSize } from "../../util/glHelpers"; -export default function drawPointsRegl(regl) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function drawPointsRegl(regl: any) { return regl({ vert: ` precision mediump float; diff --git a/client/src/components/graph/graph.js b/client/src/components/graph/graph.tsx similarity index 52% rename from client/src/components/graph/graph.js rename to client/src/components/graph/graph.tsx index 3f3c2097..af5fdf83 100644 --- a/client/src/components/graph/graph.js +++ b/client/src/components/graph/graph.tsx @@ -34,7 +34,8 @@ Simple 2D transforms control all point painting. There are three: * camera - apply a 2D camera transformation (pan, zoom) * projection - apply any transformation required for screen size and layout */ -function createProjectionTF(viewportWidth, viewportHeight) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function createProjectionTF(viewportWidth: any, viewportHeight: any) { /* the projection transform accounts for the screen size & other layout */ @@ -53,6 +54,7 @@ function createProjectionTF(viewportWidth, viewportHeight) { 0, (bottomGutterSizePx - topGutterSizePx) / viewportHeight / aspectScale[1], ]); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number[]' is not assignable to p... Remove this comment to see the full error message mat3.scale(m, m, aspectScale); return m; } @@ -67,32 +69,48 @@ function createModelTF() { return m; } +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type GraphState = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - annoMatrix: state.annoMatrix, - crossfilter: state.obsCrossfilter, - selectionTool: state.graphSelection.tool, - currentSelection: state.graphSelection.selection, - layoutChoice: state.layoutChoice, - graphInteractionMode: state.controls.graphInteractionMode, - colors: state.colors, - pointDilation: state.pointDilation, - genesets: state.genesets.genesets, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annoMatrix: (state as any).annoMatrix, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + crossfilter: (state as any).obsCrossfilter, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + selectionTool: (state as any).graphSelection.tool, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + currentSelection: (state as any).graphSelection.selection, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutChoice: (state as any).layoutChoice, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + graphInteractionMode: (state as any).controls.graphInteractionMode, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colors: (state as any).colors, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + pointDilation: (state as any).pointDilation, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesets: (state as any).genesets.genesets, })) -class Graph extends React.Component { - static createReglState(canvas) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class Graph extends React.Component<{}, GraphState> { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static createReglState(canvas: any) { /* - Must be created for each canvas - */ + Must be created for each canvas + */ // setup canvas, webgl draw function and camera const camera = _camera(canvas); const regl = _regl(canvas); const drawPoints = _drawPoints(regl); - // preallocate webgl buffers + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. const pointBuffer = regl.buffer(); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. const colorBuffer = regl.buffer(); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. const flagBuffer = regl.buffer(); - return { camera, regl, @@ -103,14 +121,21 @@ class Graph extends React.Component { }; } - static watchAsync(props, prevProps) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static watchAsync(props: any, prevProps: any) { return !shallowEqual(props.watchProps, prevProps.watchProps); } + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + cachedAsyncProps: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + reglCanvas: any; + computePointPositions = memoize((X, Y, modelTF) => { /* - compute the model coordinate for each point - */ + compute the model coordinate for each point + */ const positions = new Float32Array(2 * X.length); for (let i = 0, len = X.length; i < len; i += 1) { const p = vec2.fromValues(X[i], Y[i]); @@ -123,8 +148,8 @@ class Graph extends React.Component { computePointColors = memoize((rgb) => { /* - compute webgl colors for each point - */ + compute webgl colors for each point + */ const colors = new Float32Array(3 * rgb.length); for (let i = 0, len = rgb.length; i < len; i += 1) { colors.set(rgb[i], 3 * i); @@ -173,21 +198,20 @@ class Graph extends React.Component { computePointFlags = memoize( (crossfilter, colorByData, pointDilationData, pointDilationLabel) => { /* - We communicate with the shader using three flags: - - isNaN -- the value is a NaN. Only makes sense when we have a colorAccessor - - isSelected -- the value is selected - - isHightlighted -- the value is highlighted in the UI (orthogonal from selection highlighting) - - Due to constraints in webgl vertex shader attributes, these are encoded in a float, "kinda" - like bitmasks. - - We also have separate code paths for generating flags for categorical and - continuous metadata, as they rely on different tests, and some of the flags - (eg, isNaN) are meaningless in the face of categorical metadata. - */ + We communicate with the shader using three flags: + - isNaN -- the value is a NaN. Only makes sense when we have a colorAccessor + - isSelected -- the value is selected + - isHightlighted -- the value is highlighted in the UI (orthogonal from selection highlighting) + + Due to constraints in webgl vertex shader attributes, these are encoded in a float, "kinda" + like bitmasks. + + We also have separate code paths for generating flags for categorical and + continuous metadata, as they rely on different tests, and some of the flags + (eg, isNaN) are meaningless in the face of categorical metadata. + */ const nObs = crossfilter.size(); const flags = new Float32Array(nObs); - const selectedFlags = this.computeSelectedFlags( crossfilter, flagSelected, @@ -199,16 +223,15 @@ class Graph extends React.Component { pointDilationLabel ); const colorByFlags = this.computeColorByFlags(nObs, colorByData); - for (let i = 0; i < nObs; i += 1) { flags[i] = selectedFlags[i] + highlightFlags[i] + colorByFlags[i]; } - return flags; } ); - constructor(props) { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); const viewport = this.getViewportDimensions(); this.reglCanvas = null; @@ -219,20 +242,18 @@ class Graph extends React.Component { tool: null, container: null, viewport, - // projection camera: null, modelTF, + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type '[]' is not assignable to paramet... Remove this comment to see the full error message modelInvTF: mat3.invert([], modelTF), projectionTF: createProjectionTF(viewport.width, viewport.height), - // regl state regl: null, drawPoints: null, pointBuffer: null, colorBuffer: null, flagBuffer: null, - // component rendering derived state - these must stay synchronized // with the reducer state they were generated from. layoutState: { @@ -251,14 +272,19 @@ class Graph extends React.Component { }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. componentDidMount() { window.addEventListener("resize", this.handleResize); } - componentDidUpdate(prevProps, prevState) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + componentDidUpdate(prevProps: {}, prevState: GraphState) { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionTool' does not exist on type 'R... Remove this comment to see the full error message selectionTool, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'currentSelection' does not exist on type 'R... Remove this comment to see the full error message currentSelection, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'graphInteractionMode' does not exist on type 'R... Remove this comment to see the full error message graphInteractionMode, } = this.props; const { toolSVG, viewport } = this.state; @@ -266,11 +292,12 @@ class Graph extends React.Component { prevState.viewport.height !== viewport.height || prevState.viewport.width !== viewport.width; let stateChanges = {}; - if ( (viewport.height && viewport.width && !toolSVG) || // first time init hasResized || // window size has changed we want to recreate all SVGs + // @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionTool' does not exist on type '{... Remove this comment to see the full error message selectionTool !== prevProps.selectionTool || // change of selection tool + // @ts-expect-error ts-migrate(2339) FIXME: Property 'graphInteractionMode' does not exist on ... Remove this comment to see the full error message prevProps.graphInteractionMode !== graphInteractionMode // lasso/zoom mode is switched ) { stateChanges = { @@ -278,19 +305,23 @@ class Graph extends React.Component { ...this.createToolSVG(), }; } - /* - if the selection tool or state has changed, ensure that the selection - tool correctly reflects the underlying selection. - */ + if the selection tool or state has changed, ensure that the selection + tool correctly reflects the underlying selection. + */ if ( + // @ts-expect-error ts-migrate(2339) FIXME: Property 'currentSelection' does not exist on type... Remove this comment to see the full error message currentSelection !== prevProps.currentSelection || + // @ts-expect-error ts-migrate(2339) FIXME: Property 'graphInteractionMode' does not exist on ... Remove this comment to see the full error message graphInteractionMode !== prevProps.graphInteractionMode || + // @ts-expect-error ts-migrate(2339) FIXME: Property 'toolSVG' does not exist on type '{}'. stateChanges.toolSVG ) { const { tool, container } = this.state; this.selectionToolUpdate( + // @ts-expect-error ts-migrate(2339) FIXME: Property 'tool' does not exist on type '{}'. stateChanges.tool ? stateChanges.tool : tool, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'container' does not exist on type '{}'. stateChanges.container ? stateChanges.container : container ); } @@ -300,10 +331,12 @@ class Graph extends React.Component { } } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. componentWillUnmount() { window.removeEventListener("resize", this.handleResize); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleResize = () => { const { state } = this.state; const viewport = this.getViewportDimensions(); @@ -315,29 +348,35 @@ class Graph extends React.Component { }); }; - handleCanvasEvent = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleCanvasEvent = (e: any) => { const { camera, projectionTF } = this.state; if (e.type !== "wheel") e.preventDefault(); if (camera.handleEvent(e, projectionTF)) { this.renderCanvas(); - this.setState((state) => { - return { ...state, updateOverlay: !state.updateOverlay }; - }); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.setState((state: any) => ({ + ...state, + updateOverlay: !state.updateOverlay, + })); } }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleBrushDragAction() { /* - event describing brush position: - @-------| - | | - | | - |-------@ - */ + event describing brush position: + @-------| + | | + | | + |-------@ + */ // ignore programatically generated events + // @ts-expect-error ts-migrate(2339) FIXME: Property 'event' does not exist on type 'typeof im... Remove this comment to see the full error message if (d3.event.sourceEvent === null || !d3.event.selection) return; - + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, layoutChoice } = this.props; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'event' does not exist on type 'typeof im... Remove this comment to see the full error message const s = d3.event.selection; const northwest = this.mapScreenToPoint(s[0]); const southeast = this.mapScreenToPoint(s[1]); @@ -355,23 +394,28 @@ class Graph extends React.Component { ); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleBrushStartAction() { // Ignore programatically generated events. + // @ts-expect-error ts-migrate(2339) FIXME: Property 'event' does not exist on type 'typeof im... Remove this comment to see the full error message if (!d3.event.sourceEvent) return; - + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; dispatch(actions.graphBrushStartAction()); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleBrushEndAction() { // Ignore programatically generated events. + // @ts-expect-error ts-migrate(2339) FIXME: Property 'event' does not exist on type 'typeof im... Remove this comment to see the full error message if (!d3.event.sourceEvent) return; - /* - coordinates will be included if selection made, null - if selection cleared. - */ + coordinates will be included if selection made, null + if selection cleared. + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, layoutChoice } = this.props; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'event' does not exist on type 'typeof im... Remove this comment to see the full error message const s = d3.event.selection; if (s) { const northwest = this.mapScreenToPoint(s[0]); @@ -393,21 +437,27 @@ class Graph extends React.Component { } } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleBrushDeselectAction() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, layoutChoice } = this.props; dispatch(actions.graphBrushDeselectAction(layoutChoice.current)); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleLassoStart() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, layoutChoice } = this.props; + // @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1. dispatch(actions.graphLassoStartAction(layoutChoice.current)); } // when a lasso is completed, filter to the points within the lasso polygon - handleLassoEnd(polygon) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleLassoEnd(polygon: any) { const minimumPolygonArea = 10; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, layoutChoice } = this.props; - if ( polygon.length < 3 || Math.abs(d3.polygonArea(polygon)) < minimumPolygonArea @@ -418,29 +468,38 @@ class Graph extends React.Component { dispatch( actions.graphLassoEndAction( layoutChoice.current, - polygon.map((xy) => this.mapScreenToPoint(xy)) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + polygon.map((xy: any) => this.mapScreenToPoint(xy)) ) ); } } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleLassoCancel() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, layoutChoice } = this.props; dispatch(actions.graphLassoCancelAction(layoutChoice.current)); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleLassoDeselectAction() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, layoutChoice } = this.props; dispatch(actions.graphLassoDeselectAction(layoutChoice.current)); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleDeselectAction() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionTool' does not exist on type 'R... Remove this comment to see the full error message const { selectionTool } = this.props; if (selectionTool === "brush") this.handleBrushDeselectAction(); if (selectionTool === "lasso") this.handleLassoDeselectAction(); } - handleOpacityRangeChange(e) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleOpacityRangeChange(e: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch } = this.props; dispatch({ type: "change opacity deselected cells in 2d graph background", @@ -448,14 +507,17 @@ class Graph extends React.Component { }); } - setReglCanvas = (canvas) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + setReglCanvas = (canvas: any) => { this.reglCanvas = canvas; this.setState({ ...Graph.createReglState(canvas), }); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. getViewportDimensions = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'viewportRef' does not exist on type 'Rea... Remove this comment to see the full error message const { viewportRef } = this.props; return { height: viewportRef.clientHeight, @@ -463,19 +525,19 @@ class Graph extends React.Component { }; }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. createToolSVG = () => { /* - Called from componentDidUpdate. Create the tool SVG, and return any - state changes that should be passed to setState(). - */ + Called from componentDidUpdate. Create the tool SVG, and return any + state changes that should be passed to setState(). + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionTool' does not exist on type 'R... Remove this comment to see the full error message const { selectionTool, graphInteractionMode } = this.props; const { viewport } = this.state; - /* clear out whatever was on the div, even if nothing, but usually the brushes etc */ const lasso = d3.select("#lasso-layer"); if (lasso.empty()) return {}; // still initializing lasso.selectAll(".lasso-group").remove(); - // Don't render or recreate toolSVG if currently in zoom mode if (graphInteractionMode !== "select") { // don't return "change" of state unless we are really changing it! @@ -483,7 +545,6 @@ class Graph extends React.Component { if (toolSVG === undefined) return {}; return { toolSVG: undefined }; } - let handleStart; let handleDrag; let handleEnd; @@ -497,7 +558,6 @@ class Graph extends React.Component { handleEnd = this.handleLassoEnd.bind(this); handleCancel = this.handleLassoCancel.bind(this); } - const { svg: newToolSVG, tool, container } = setupSVGandBrushElements( selectionTool, handleStart, @@ -506,11 +566,11 @@ class Graph extends React.Component { handleCancel, viewport ); - return { toolSVG: newToolSVG, tool, container }; }; - fetchAsyncProps = async (props) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + fetchAsyncProps = async (props: any) => { const { annoMatrix, colors: colorsProp, @@ -520,22 +580,18 @@ class Graph extends React.Component { viewport, } = props.watchProps; const { modelTF } = this.state; - const [layoutDf, colorDf, pointDilationDf] = await this.fetchData( annoMatrix, layoutChoice, colorsProp, pointDilation ); - const { currentDimNames } = layoutChoice; const X = layoutDf.col(currentDimNames[0]).asArray(); const Y = layoutDf.col(currentDimNames[1]).asArray(); const positions = this.computePointPositions(X, Y, modelTF); - const colorTable = this.updateColorTable(colorsProp, colorDf); const colors = this.computePointColors(colorTable.rgb); - const { colorAccessor } = colorsProp; const colorByData = colorDf?.col(colorAccessor)?.asArray(); const { @@ -551,7 +607,6 @@ class Graph extends React.Component { pointDilationData, pointDilationLabel ); - const { width, height } = viewport; return { positions, @@ -562,19 +617,27 @@ class Graph extends React.Component { }; }; - async fetchData(annoMatrix, layoutChoice, colors, pointDilation) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + async fetchData( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + annoMatrix: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + layoutChoice: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colors: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + pointDilation: any + ) { /* - fetch all data needed. Includes: - - the color by dataframe - - the layout dataframe - - the point dilation dataframe - */ + fetch all data needed. Includes: + - the color by dataframe + - the layout dataframe + - the point dilation dataframe + */ const { metadataField: pointDilationAccessor } = pointDilation; - const promises = []; // layout promises.push(annoMatrix.fetch("emb", layoutChoice.current)); - // color const query = this.createColorByQuery(colors); if (query) { @@ -582,30 +645,29 @@ class Graph extends React.Component { } else { promises.push(Promise.resolve(null)); } - // point highlighting if (pointDilationAccessor) { promises.push(annoMatrix.fetch("obs", pointDilationAccessor)); } else { promises.push(Promise.resolve(null)); } - return Promise.all(promises); } - brushToolUpdate(tool, container) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + brushToolUpdate(tool: any, container: any) { /* - this is called from componentDidUpdate(), so be very careful using - anything from this.state, which may be updated asynchronously. - */ + this is called from componentDidUpdate(), so be very careful using + anything from this.state, which may be updated asynchronously. + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'currentSelection' does not exist on type... Remove this comment to see the full error message const { currentSelection } = this.props; if (container) { const toolCurrentSelection = d3.brushSelection(container.node()); - if (currentSelection.mode === "within-rect") { /* - if there is a selection, make sure the brush tool matches - */ + if there is a selection, make sure the brush tool matches + */ const screenCoords = [ this.mapPointToScreen(currentSelection.brushCoords.northwest), this.mapPointToScreen(currentSelection.brushCoords.southeast), @@ -620,6 +682,7 @@ class Graph extends React.Component { for (let x = 0; x < 2; x += 1) { for (let y = 0; y < 2; y += 1) { delta += Math.abs( + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message screenCoords[x][y] - toolCurrentSelection[x][y] ); } @@ -635,17 +698,20 @@ class Graph extends React.Component { } } - lassoToolUpdate(tool) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + lassoToolUpdate(tool: any) { /* - this is called from componentDidUpdate(), so be very careful using - anything from this.state, which may be updated asynchronously. - */ + this is called from componentDidUpdate(), so be very careful using + anything from this.state, which may be updated asynchronously. + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'currentSelection' does not exist on type... Remove this comment to see the full error message const { currentSelection } = this.props; if (currentSelection.mode === "within-polygon") { /* - if there is a current selection, make sure the lasso tool matches - */ - const polygon = currentSelection.polygon.map((p) => + if there is a current selection, make sure the lasso tool matches + */ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const polygon = currentSelection.polygon.map((p: any) => this.mapPointToScreen(p) ); tool.move(polygon); @@ -654,17 +720,20 @@ class Graph extends React.Component { } } - selectionToolUpdate(tool, container) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectionToolUpdate(tool: any, container: any) { /* - this is called from componentDidUpdate(), so be very careful using - anything from this.state, which may be updated asynchronously. - */ + this is called from componentDidUpdate(), so be very careful using + anything from this.state, which may be updated asynchronously. + */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionTool' does not exist on type 'R... Remove this comment to see the full error message const { selectionTool } = this.props; switch (selectionTool) { case "brush": this.brushToolUpdate(tool, container); break; case "lasso": + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 2. this.lassoToolUpdate(tool, container); break; default: @@ -673,19 +742,17 @@ class Graph extends React.Component { } } - mapScreenToPoint(pin) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + mapScreenToPoint(pin: any) { /* - Map an XY coordinates from screen domain to cell/point range, - accounting for current pan/zoom camera. - */ - + Map an XY coordinates from screen domain to cell/point range, + accounting for current pan/zoom camera. + */ const { camera, projectionTF, modelInvTF, viewport } = this.state; const cameraInvTF = camera.invView(); - /* screen -> gl */ const x = (2 * pin[0]) / viewport.width - 1; const y = 2 * (1 - pin[1] / viewport.height) - 1; - const xy = vec2.fromValues(x, y); const projectionInvTF = mat3.invert(mat3.create(), projectionTF); vec2.transformMat3(xy, xy, projectionInvTF); @@ -694,19 +761,17 @@ class Graph extends React.Component { return xy; } - mapPointToScreen(xyCell) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + mapPointToScreen(xyCell: any) { /* - Map an XY coordinate from cell/point domain to screen range. Inverse - of mapScreenToPoint() - */ - + Map an XY coordinate from cell/point domain to screen range. Inverse + of mapScreenToPoint() + */ const { camera, projectionTF, modelTF, viewport } = this.state; const cameraTF = camera.view(); - const xy = vec2.transformMat3(vec2.create(), xyCell, modelTF); vec2.transformMat3(xy, xy, cameraTF); vec2.transformMat3(xy, xy, projectionTF); - return [ Math.round(((xy[0] + 1) * viewport.width) / 2), Math.round(-((xy[1] + 1) / 2 - 1) * viewport.height), @@ -734,12 +799,12 @@ class Graph extends React.Component { ); }); - updateReglAndRender(asyncProps, prevAsyncProps) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + updateReglAndRender(asyncProps: any, prevAsyncProps: any) { const { positions, colors, flags, height, width } = asyncProps; this.cachedAsyncProps = asyncProps; const { pointBuffer, colorBuffer, flagBuffer } = this.state; let needToRenderCanvas = false; - if (height !== prevAsyncProps?.height || width !== prevAsyncProps?.width) { needToRenderCanvas = true; } @@ -758,10 +823,11 @@ class Graph extends React.Component { if (needToRenderCanvas) this.renderCanvas(); } - updateColorTable(colors, colorDf) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + updateColorTable(colors: any, colorDf: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix } = this.props; const { schema } = annoMatrix; - /* update color table state */ if (!colors || !colorDf) { return createColorTable( @@ -772,7 +838,6 @@ class Graph extends React.Component { null ); } - const { colorAccessor, userColors, colorMode } = colors; return createColorTable( colorMode, @@ -783,26 +848,35 @@ class Graph extends React.Component { ); } - createColorByQuery(colors) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + createColorByQuery(colors: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix, genesets } = this.props; const { schema } = annoMatrix; const { colorMode, colorAccessor } = colors; - return createColorQuery(colorMode, colorAccessor, schema, genesets); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renderPoints( - regl, - drawPoints, - colorBuffer, - pointBuffer, - flagBuffer, - camera, - projectionTF + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + regl: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + drawPoints: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorBuffer: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + pointBuffer: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + flagBuffer: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + camera: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + projectionTF: any ) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix } = this.props; if (!this.reglCanvas || !annoMatrix) return; - const { schema } = annoMatrix; const cameraTF = camera.view(); const projView = mat3.multiply(mat3.create(), projectionTF, cameraTF); @@ -825,19 +899,25 @@ class Graph extends React.Component { regl._gl.flush(); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'graphInteractionMode' does not exist on ... Remove this comment to see the full error message graphInteractionMode, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on ... Remove this comment to see the full error message annoMatrix, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colors' does not exist on ... Remove this comment to see the full error message colors, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'layoutChoice' does not exist on ... Remove this comment to see the full error message layoutChoice, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'pointDilation' does not exist on ... Remove this comment to see the full error message pointDilation, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'crossfilter' does not exist on ... Remove this comment to see the full error message crossfilter, dotplotMode, } = this.props; const { modelTF, projectionTF, camera, viewport, regl } = this.state; const cameraTF = camera?.view()?.slice(); - return (
+ {/* eslint-disable-next-line @typescript-eslint/no-use-before-define --- StillLoading used before defined */} {(error) => ( + // eslint-disable-next-line @typescript-eslint/no-use-before-define --- ErrorLoading used before defined { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const ErrorLoading = ({ displayName, error, width, height }: any) => { console.log(error); // log to console as this is an unepected error return (
{ ); }; -const StillLoading = ({ displayName, width, height }) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const StillLoading = ({ displayName, width, height }: any) => ( /* Render a busy/loading indicator */ - return ( +
-
-
+
- ); -}; - +
+); export default Graph; diff --git a/client/src/components/graph/overlays/centroidLabels.js b/client/src/components/graph/overlays/centroidLabels.js deleted file mode 100644 index 3f4d19aa..00000000 --- a/client/src/components/graph/overlays/centroidLabels.js +++ /dev/null @@ -1,218 +0,0 @@ -import React, { PureComponent } from "react"; -import { connect, shallowEqual } from "react-redux"; -import Async from "react-async"; - -import { categoryLabelDisplayStringLongLength } from "../../../globals"; -import calcCentroid from "../../../util/centroid"; -import { createColorQuery } from "../../../util/stateManager/colorHelpers"; - -export default -@connect((state) => ({ - annoMatrix: state.annoMatrix, - colors: state.colors, - layoutChoice: state.layoutChoice, - dilatedValue: state.pointDilation.categoryField, - categoricalSelection: state.categoricalSelection, - showLabels: state.centroidLabels?.showLabels, - genesets: state.genesets.genesets, -})) -class CentroidLabels extends PureComponent { - static watchAsync(props, prevProps) { - return !shallowEqual(props.watchProps, prevProps.watchProps); - } - - fetchAsyncProps = async (props) => { - const { - annoMatrix, - colors, - layoutChoice, - categoricalSelection, - showLabels, - } = props.watchProps; - const { schema } = annoMatrix; - const { colorAccessor } = colors; - - const [layoutDf, colorDf] = await this.fetchData(); - let labels; - if (colorDf) { - labels = calcCentroid( - schema, - colorAccessor, - colorDf, - layoutChoice, - layoutDf - ); - } else { - labels = new Map(); - } - - const { overlaySetShowing } = this.props; - overlaySetShowing("centroidLabels", showLabels && labels.size > 0); - - return { - labels, - colorAccessor, - category: categoricalSelection[colorAccessor], - }; - }; - - handleMouseEnter = (e, colorAccessor, label) => { - const { dispatch } = this.props; - dispatch({ - type: "category value mouse hover start", - metadataField: colorAccessor, - categoryField: label, - }); - }; - - handleMouseOut = (e, colorAccessor, label) => { - const { dispatch } = this.props; - dispatch({ - type: "category value mouse hover end", - metadataField: colorAccessor, - categoryField: label, - }); - }; - - colorByQuery() { - const { annoMatrix, colors, genesets } = this.props; - const { schema } = annoMatrix; - const { colorMode, colorAccessor } = colors; - return createColorQuery(colorMode, colorAccessor, schema, genesets); - } - - async fetchData() { - const { annoMatrix, layoutChoice } = this.props; - // fetch all data we need: layout, category - const promises = []; - // layout - promises.push(annoMatrix.fetch("emb", layoutChoice.current)); - // category to label - we ONLY label on obs, never on X, etc. - const query = this.colorByQuery(); - if (query && query[0] === "obs") { - promises.push(annoMatrix.fetch(...query)); - } else { - promises.push(Promise.resolve(null)); - } - - return Promise.all(promises); - } - - render() { - const { - inverseTransform, - dilatedValue, - categoricalSelection, - showLabels, - colors, - annoMatrix, - layoutChoice, - } = this.props; - - return ( - - - {(asyncProps) => { - if (!showLabels) return null; - - const labelSVGS = []; - const deselectOpacity = 0.375; - const { category, colorAccessor, labels } = asyncProps; - - labels.forEach((coords, label) => { - const selected = category.get(label) ?? true; - - // Mirror LSB middle truncation - let displayLabel = label; - if (displayLabel.length > categoryLabelDisplayStringLongLength) { - displayLabel = `${label.slice( - 0, - categoryLabelDisplayStringLongLength / 2 - )}…${label.slice(-categoryLabelDisplayStringLongLength / 2)}`; - } - - labelSVGS.push( - // eslint-disable-next-line jsx-a11y/mouse-events-have-key-events -- the mouse actions for centroid labels do not have a screen reader alternative - - - ); - } -} - -const Label = ({ - label, - dilatedValue, - coords, - inverseTransform, - opacity, - colorAccessor, - displayLabel, - onMouseEnter, - onMouseOut, -}) => { - /* - Render a label at a given coordinate. - */ - let fontSize = "15px"; - let fontWeight = null; - if (label === dilatedValue) { - fontSize = "18px"; - fontWeight = "800"; - } - - return ( - - {/* eslint-disable-next-line jsx-a11y/mouse-events-have-key-events --- the mouse actions for centroid labels do not have a screen reader alternative*/} - onMouseEnter(e, colorAccessor, label)} - onMouseOut={(e) => onMouseOut(e, colorAccessor, label)} - pointerEvents="visiblePainted" - > - {displayLabel} - - - ); -}; diff --git a/client/src/components/graph/overlays/centroidLabels.tsx b/client/src/components/graph/overlays/centroidLabels.tsx new file mode 100644 index 00000000..0f0da386 --- /dev/null +++ b/client/src/components/graph/overlays/centroidLabels.tsx @@ -0,0 +1,241 @@ +import React, { PureComponent } from "react"; +import { connect, shallowEqual } from "react-redux"; +import Async from "react-async"; + +import { categoryLabelDisplayStringLongLength } from "../../../globals"; +import calcCentroid from "../../../util/centroid"; +import { createColorQuery } from "../../../util/stateManager/colorHelpers"; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annoMatrix: (state as any).annoMatrix, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colors: (state as any).colors, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutChoice: (state as any).layoutChoice, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dilatedValue: (state as any).pointDilation.categoryField, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoricalSelection: (state as any).categoricalSelection, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + showLabels: (state as any).centroidLabels?.showLabels, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesets: (state as any).genesets.genesets, +})) +export default class CentroidLabels extends PureComponent { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static watchAsync(props: any, prevProps: any) { + return !shallowEqual(props.watchProps, prevProps.watchProps); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + fetchAsyncProps = async (props: any) => { + const { + annoMatrix, + colors, + layoutChoice, + categoricalSelection, + showLabels, + } = props.watchProps; + const { schema } = annoMatrix; + const { colorAccessor } = colors; + const [layoutDf, colorDf] = await this.fetchData(); + let labels; + if (colorDf) { + labels = calcCentroid( + schema, + colorAccessor, + colorDf, + layoutChoice, + layoutDf + ); + } else { + labels = new Map(); + } + // @ts-expect-error ts-migrate(2339) FIXME: Property 'overlaySetShowing' does not exist on typ... Remove this comment to see the full error message + const { overlaySetShowing } = this.props; + overlaySetShowing("centroidLabels", showLabels && labels.size > 0); + return { + labels, + colorAccessor, + category: categoricalSelection[colorAccessor], + }; + }; + + // @ts-expect-error ts-migrate(6133) FIXME: 'e' is declared but its value is never read. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleMouseEnter = (e: any, colorAccessor: any, label: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + dispatch({ + type: "category value mouse hover start", + metadataField: colorAccessor, + categoryField: label, + }); + }; + + // @ts-expect-error ts-migrate(6133) FIXME: 'e' is declared but its value is never read. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleMouseOut = (e: any, colorAccessor: any, label: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + dispatch({ + type: "category value mouse hover end", + metadataField: colorAccessor, + categoryField: label, + }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + colorByQuery() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message + const { annoMatrix, colors, genesets } = this.props; + const { schema } = annoMatrix; + const { colorMode, colorAccessor } = colors; + return createColorQuery(colorMode, colorAccessor, schema, genesets); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + async fetchData() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message + const { annoMatrix, layoutChoice } = this.props; + // fetch all data we need: layout, category + const promises = []; + // layout + promises.push(annoMatrix.fetch("emb", layoutChoice.current)); + // category to label - we ONLY label on obs, never on X, etc. + const query = this.colorByQuery(); + if (query && query[0] === "obs") { + promises.push(annoMatrix.fetch(...query)); + } else { + promises.push(Promise.resolve(null)); + } + return Promise.all(promises); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'inverseTransform' does not exist on type... Remove this comment to see the full error message + inverseTransform, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dilatedValue' does not exist on type 'Re... Remove this comment to see the full error message + dilatedValue, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoricalSelection' does not exist on ... Remove this comment to see the full error message + categoricalSelection, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'showLabels' does not exist on type 'Read... Remove this comment to see the full error message + showLabels, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colors' does not exist on type 'Readonly... Remove this comment to see the full error message + colors, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message + annoMatrix, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'layoutChoice' does not exist on type 'Re... Remove this comment to see the full error message + layoutChoice, + } = this.props; + return ( + + + {(asyncProps) => { + if (!showLabels) return null; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const labelSVGS: any = []; + const deselectOpacity = 0.375; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'category' does not exist on type 'unknow... Remove this comment to see the full error message + const { category, colorAccessor, labels } = asyncProps; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + labels.forEach((coords: any, label: any) => { + const selected = category.get(label) ?? true; + // Mirror LSB middle truncation + let displayLabel = label; + if (displayLabel.length > categoryLabelDisplayStringLongLength) { + displayLabel = `${label.slice( + 0, + categoryLabelDisplayStringLongLength / 2 + )}…${label.slice(-categoryLabelDisplayStringLongLength / 2)}`; + } + labelSVGS.push( + // eslint-disable-next-line jsx-a11y/mouse-events-have-key-events -- the mouse actions for centroid labels do not have a screen reader alternative + + + ); + } +} + +const Label = ({ + label, + dilatedValue, + coords, + inverseTransform, + opacity, + colorAccessor, + displayLabel, + onMouseEnter, + onMouseOut, // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +}: any) => { + /* + Render a label at a given coordinate. + */ + let fontSize = "15px"; + let fontWeight = null; + if (label === dilatedValue) { + fontSize = "18px"; + fontWeight = "800"; + } + + return ( + + {/* eslint-disable-next-line jsx-a11y/mouse-events-have-key-events --- the mouse actions for centroid labels do not have a screen reader alternative*/} + onMouseEnter(e, colorAccessor, label)} + onMouseOut={(e) => onMouseOut(e, colorAccessor, label)} + pointerEvents="visiblePainted" + > + {displayLabel} + + + ); +}; diff --git a/client/src/components/graph/overlays/graphOverlayLayer.js b/client/src/components/graph/overlays/graphOverlayLayer.tsx similarity index 54% rename from client/src/components/graph/overlays/graphOverlayLayer.js rename to client/src/components/graph/overlays/graphOverlayLayer.tsx index eb8d43bb..feab192e 100644 --- a/client/src/components/graph/overlays/graphOverlayLayer.js +++ b/client/src/components/graph/overlays/graphOverlayLayer.tsx @@ -1,22 +1,29 @@ import React, { PureComponent, cloneElement } from "react"; +// @ts-expect-error ts-migrate(2307) FIXME: Cannot find module '../graph.css' or its correspon... Remove this comment to see the full error message import styles from "../graph.css"; -export default class GraphOverlayLayer extends PureComponent { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +export default class GraphOverlayLayer extends PureComponent<{}, State> { /* This component takes its children (assumed in the data coordinate space ([0, 1] range, origin in bottom left corner)) and transforms itself multiple times resulting in screen space ([0, screenWidth/Height] range, origin in top left corner) Children are assigned in the graph component and must implement onDisplayChange() */ - constructor(props) { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); this.state = { display: {}, }; } - matrixToTransformString = (m) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + matrixToTransformString = (m: any) => /* Translates the gl-matrix mat3 to SVG matrix transform style @@ -25,28 +32,37 @@ export default class GraphOverlayLayer extends PureComponent { b d f / [a, b, 0, c, d, 0, e, f, 1] => matrix(a, b, c, d, e, f) / matrix(sx, 0, 0, sy, tx, ty) / matrix(m[0] m[3] m[1] m[4] m[6] m[7]) 0 0 1 */ - return `matrix(${m[0]} ${m[1]} ${m[3]} ${m[4]} ${m[6]} ${m[7]})`; - }; + `matrix(${m[0]} ${m[1]} ${m[3]} ${m[4]} ${m[6]} ${m[7]})`; - reverseMatrixScaleTransformString = (m) => { - return `matrix(${1 / m[0]} 0 0 ${1 / m[4]} 0 0)`; - }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + reverseMatrixScaleTransformString = (m: any) => + `matrix(${1 / m[0]} 0 0 ${1 / m[4]} 0 0)`; // This is passed to all children, should be called when an overlay's display state is toggled along with the overlay name and its new display state in boolean form - overlaySetShowing = (overlay, displaying) => { - this.setState((state) => { - return { ...state, display: { ...state.display, [overlay]: displaying } }; - }); + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + overlaySetShowing = (overlay: any, displaying: any) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.setState((state: any) => ({ + ...state, + display: { ...state.display, [overlay]: displaying }, + })); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'cameraTF' does not exist on type 'Readon... Remove this comment to see the full error message cameraTF, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'modelTF' does not exist on type 'Readonl... Remove this comment to see the full error message modelTF, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'projectionTF' does not exist on type 'Re... Remove this comment to see the full error message projectionTF, children, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleCanvasEvent' does not exist on typ... Remove this comment to see the full error message handleCanvasEvent, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'width' does not exist on type 'Readonly<... Remove this comment to see the full error message width, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'height' does not exist on type 'Readonly... Remove this comment to see the full error message height, } = this.props; const { display } = this.state; @@ -65,6 +81,7 @@ export default class GraphOverlayLayer extends PureComponent { // Copy the children passed with the overlay and add the inverse transform and onDisplayChange props const newChildren = React.Children.map(children, (child) => + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. cloneElement(child, { inverseTransform, overlaySetShowing: this.overlaySetShowing, diff --git a/client/src/components/graph/setupLasso.js b/client/src/components/graph/setupLasso.ts similarity index 59% rename from client/src/components/graph/setupLasso.js rename to client/src/components/graph/setupLasso.ts index 095b4ec6..afbe3678 100644 --- a/client/src/components/graph/setupLasso.js +++ b/client/src/components/graph/setupLasso.ts @@ -1,19 +1,28 @@ import * as d3 from "d3"; import { Colors } from "@blueprintjs/core"; +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const Lasso = () => { const dispatch = d3.dispatch("start", "end", "cancel"); - const lasso = (svg) => { - let lassoPolygon; - let lassoPath; - let closePath; - let lassoInProgress; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const lasso = (svg: any) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let lassoPolygon: any; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let lassoPath: any; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let closePath: any; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let lassoInProgress: any; - const polygonToPath = (polygon) => - `M${polygon.map((d) => d.join(",")).join("L")}`; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const polygonToPath = (polygon: any) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + `M${polygon.map((d: any) => d.join(",")).join("L")}`; - const distance = (pt1, pt2) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const distance = (pt1: any, pt2: any) => Math.sqrt((pt2[0] - pt1[0]) ** 2 + (pt2[1] - pt1[1]) ** 2); // distance last point has to be to first point before it auto closes when mouse is released @@ -21,12 +30,14 @@ const Lasso = () => { const lassoPathColor = Colors.BLUE5; const handleDragStart = () => { - lassoPolygon = [d3.mouse(svg.node())]; // current x y of mouse within element + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + lassoPolygon = [(d3 as any).mouse(svg.node())]; // current x y of mouse within element if (lassoPath) { // If the existing path is in progress if (lassoInProgress) { // cancel the existing lasso + // eslint-disable-next-line @typescript-eslint/no-use-before-define --- handleCancel used before defined handleCancel(); // Don't continue with current drag start return; @@ -37,12 +48,14 @@ const Lasso = () => { // We're starting a new drag lassoInProgress = true; + // eslint-disable-next-line @typescript-eslint/no-use-before-define --- g used before defined lassoPath = g .append("path") .attr("data-testid", "lasso-element") .attr("fill-opacity", 0.1) .attr("stroke-dasharray", "3, 3"); + // eslint-disable-next-line @typescript-eslint/no-use-before-define --- g used before defined closePath = g .append("line") .attr("x2", lassoPolygon[0][0]) @@ -53,7 +66,8 @@ const Lasso = () => { }; const handleDrag = () => { - const point = d3.mouse(svg.node()); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const point = (d3 as any).mouse(svg.node()); lassoPolygon.push(point); lassoPath.attr("d", polygonToPath(lassoPolygon)); @@ -123,12 +137,12 @@ const Lasso = () => { area.call(drag); - lasso.reset = () => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (lasso as any).reset = () => { if (lassoPath) { lassoPath.remove(); lassoPath = null; } - lassoPolygon = null; if (closePath) { closePath.remove(); @@ -136,10 +150,11 @@ const Lasso = () => { } }; - lasso.move = (polygon) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (lasso as any).move = (polygon: any) => { if (polygon !== lassoPolygon || polygon.length !== lassoPolygon.length) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'reset' does not exist on type '(svg: any... Remove this comment to see the full error message lasso.reset(); - lassoPolygon = polygon; lassoPath = g .append("path") @@ -148,13 +163,13 @@ const Lasso = () => { .attr("fill-opacity", 0.1) .attr("stroke", lassoPathColor) .attr("stroke-dasharray", "3, 3"); - lassoPath.attr("d", `${polygonToPath(lassoPolygon)}Z`); } }; }; - lasso.on = (type, callback) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + lasso.on = (type: any, callback: any) => { dispatch.on(type, callback); return lasso; }; diff --git a/client/src/components/graph/setupSVGandBrush.js b/client/src/components/graph/setupSVGandBrush.js deleted file mode 100644 index bedf96a9..00000000 --- a/client/src/components/graph/setupSVGandBrush.js +++ /dev/null @@ -1,54 +0,0 @@ -import * as d3 from "d3"; -import Lasso from "./setupLasso"; - -/****************************************** -******************************************* - put svg & brush in DOM -******************************************* -******************************************/ - -export default ( - selectionToolType, - handleStartAction, - handleDragAction, - handleEndAction, - handleCancelAction, - viewport -) => { - const svg = d3.select("#graph-wrapper").select("#lasso-layer"); - if (svg.empty()) return {}; - - if (selectionToolType === "brush") { - const brush = d3 - .brush() - .extent([ - [0, 0], - [viewport.width, viewport.height], - ]) - .on("start", handleStartAction) - .on("brush", handleDragAction) - // FYI, brush doesn't generate cancel - .on("end", handleEndAction); - - const brushContainer = svg - .append("g") - .attr("class", "graph_brush") - .call(brush); - - return { svg, container: brushContainer, tool: brush }; - } - - if (selectionToolType === "lasso") { - const lasso = Lasso() - .on("end", handleEndAction) - // FYI, Lasso doesn't generate drag - .on("start", handleStartAction) - .on("cancel", handleCancelAction); - - const lassoContainer = svg.call(lasso); - - return { svg, container: lassoContainer, tool: lasso }; - } - - throw new Error("unknown graph selection tool"); -}; diff --git a/client/src/components/graph/setupSVGandBrush.ts b/client/src/components/graph/setupSVGandBrush.ts new file mode 100644 index 00000000..e8071b1e --- /dev/null +++ b/client/src/components/graph/setupSVGandBrush.ts @@ -0,0 +1,62 @@ +import * as d3 from "d3"; +import Lasso from "./setupLasso"; + +/****************************************** +******************************************* + put svg & brush in DOM +******************************************* +******************************************/ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export default ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectionToolType: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleStartAction: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleDragAction: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleEndAction: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleCancelAction: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + viewport: any +) => { + const svg = d3.select("#graph-wrapper").select("#lasso-layer"); + if (svg.empty()) return {}; + + if (selectionToolType === "brush") { + const brush = d3 + .brush() + .extent([ + [0, 0], + [viewport.width, viewport.height], + ]) + .on("start", handleStartAction) + .on("brush", handleDragAction) + // FYI, brush doesn't generate cancel + .on("end", handleEndAction); + + const brushContainer = svg + .append("g") + .attr("class", "graph_brush") + .call(brush); + + return { svg, container: brushContainer, tool: brush }; + } + + if (selectionToolType === "lasso") { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const lasso = (Lasso() as any) + .on("end", handleEndAction) + // FYI, Lasso doesn't generate drag + .on("start", handleStartAction) + .on("cancel", handleCancelAction); + + const lassoContainer = svg.call(lasso); + + return { svg, container: lassoContainer, tool: lasso }; + } + + throw new Error("unknown graph selection tool"); +}; diff --git a/client/src/components/infoDrawer/infoDrawer.js b/client/src/components/infoDrawer/infoDrawer.js deleted file mode 100644 index 86e5c6df..00000000 --- a/client/src/components/infoDrawer/infoDrawer.js +++ /dev/null @@ -1,63 +0,0 @@ -import React, { PureComponent } from "react"; -import { connect } from "react-redux"; -import { Drawer } from "@blueprintjs/core"; - -import InfoFormat from "./infoFormat"; -import { selectableCategoryNames } from "../../util/stateManager/controlsHelpers"; - -@connect((state) => { - return { - schema: state.annoMatrix.schema, - datasetTitle: state.config?.displayNames?.dataset ?? "", - aboutURL: state.config?.links?.["about-dataset"], - isOpen: state.controls.datasetDrawer, - dataPortalProps: state.config?.corpora_props, - }; -}) -class InfoDrawer extends PureComponent { - handleClose = () => { - const { dispatch } = this.props; - - dispatch({ type: "toggle dataset drawer" }); - }; - - render() { - const { - position, - aboutURL, - datasetTitle, - schema, - isOpen, - dataPortalProps, - } = this.props; - - const allCategoryNames = selectableCategoryNames(schema).sort(); - const singleValueCategories = new Map(); - - allCategoryNames.forEach((catName) => { - const isUserAnno = schema?.annotations?.obsByName[catName]?.writable; - const colSchema = schema.annotations.obsByName[catName]; - if (!isUserAnno && colSchema.categories?.length === 1) { - singleValueCategories.set(catName, colSchema.categories[0]); - } - }); - - return ( - - - - ); - } -} -export default InfoDrawer; diff --git a/client/src/components/infoDrawer/infoDrawer.tsx b/client/src/components/infoDrawer/infoDrawer.tsx new file mode 100644 index 00000000..806f7225 --- /dev/null +++ b/client/src/components/infoDrawer/infoDrawer.tsx @@ -0,0 +1,78 @@ +import React, { PureComponent } from "react"; +import { connect } from "react-redux"; +import { Drawer } from "@blueprintjs/core"; + +import InfoFormat from "./infoFormat"; +import { selectableCategoryNames } from "../../util/stateManager/controlsHelpers"; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => ({ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: (state as any).annoMatrix.schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + datasetTitle: (state as any).config?.displayNames?.dataset ?? "", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + aboutURL: (state as any).config?.links?.["about-dataset"], + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + isOpen: (state as any).controls.datasetDrawer, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dataPortalProps: (state as any).config?.corpora_props, +})) +class InfoDrawer extends PureComponent { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleClose = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + + dispatch({ type: "toggle dataset drawer" }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'position' does not exist on type 'Readon... Remove this comment to see the full error message + position, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'aboutURL' does not exist on type 'Readon... Remove this comment to see the full error message + aboutURL, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'datasetTitle' does not exist on type 'Re... Remove this comment to see the full error message + datasetTitle, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'schema' does not exist on type 'Readonly... Remove this comment to see the full error message + schema, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isOpen' does not exist on type 'Readonly... Remove this comment to see the full error message + isOpen, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dataPortalProps' does not exist on type ... Remove this comment to see the full error message + dataPortalProps, + } = this.props; + + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. + const allCategoryNames = selectableCategoryNames(schema).sort(); + const singleValueCategories = new Map(); + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + allCategoryNames.forEach((catName: any) => { + const isUserAnno = schema?.annotations?.obsByName[catName]?.writable; + const colSchema = schema.annotations.obsByName[catName]; + if (!isUserAnno && colSchema.categories?.length === 1) { + singleValueCategories.set(catName, colSchema.categories[0]); + } + }); + + return ( + + + + ); + } +} +export default InfoDrawer; diff --git a/client/src/components/infoDrawer/infoFormat.js b/client/src/components/infoDrawer/infoFormat.tsx similarity index 63% rename from client/src/components/infoDrawer/infoFormat.js rename to client/src/components/infoDrawer/infoFormat.tsx index b9059fb4..b1a1d956 100644 --- a/client/src/components/infoDrawer/infoFormat.js +++ b/client/src/components/infoDrawer/infoFormat.tsx @@ -1,14 +1,16 @@ import { H3, H1, UL, HTMLTable, Classes } from "@blueprintjs/core"; import React from "react"; -const renderContributors = (contributors, affiliations) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const renderContributors = (contributors: any, affiliations: any) => { // eslint-disable-next-line no-constant-condition -- Temp removed contributor section to avoid publishing PII if (!contributors || contributors.length === 0 || true) return null; return ( <>

Contributors

- {contributors.map((contributor) => { + {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. */} + {contributors.map((contributor: any) => { const { email, name, institution } = contributor; return ( @@ -27,7 +29,8 @@ const renderContributors = (contributors, affiliations) => { // generates a list of unique institutions by order of appearance in contributors const buildAffiliations = (contributors = []) => { - const affiliations = []; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const affiliations: any = []; contributors.forEach((contributor) => { const { institution } = contributor; if (affiliations.indexOf(institution) === -1) { @@ -37,13 +40,15 @@ const buildAffiliations = (contributors = []) => { return affiliations; }; -const renderAffiliations = (affiliations) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const renderAffiliations = (affiliations: any) => { if (affiliations.length === 0) return null; return ( <>

Affiliations

    - {affiliations.map((item, index) => ( + {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. */} + {affiliations.map((item: any, index: any) => (
    {index + 1} {" "} @@ -55,7 +60,8 @@ const renderAffiliations = (affiliations) => { ); }; -const renderDOILink = (type, doi) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const renderDOILink = (type: any, doi: any) => { if (!doi) return null; return ( <> @@ -71,7 +77,12 @@ const renderDOILink = (type, doi) => { const ONTOLOGY_KEY = "ontology_term_id"; // Render list of metadata attributes found in categorical field -const renderDatasetMetadata = (singleValueCategories, corporaMetadata) => { +const renderDatasetMetadata = ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + singleValueCategories: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + corporaMetadata: any +) => { if (singleValueCategories.size === 0) return null; return ( <> @@ -89,32 +100,35 @@ const renderDatasetMetadata = (singleValueCategories, corporaMetadata) => { - {Object.entries(corporaMetadata).map(([key, value]) => { - return ( - - {`${key}:`} - {value} - - - ); - })} + {Object.entries(corporaMetadata).map(([key, value]) => ( + + {`${key}:`} + {/* @ts-expect-error ts-migrate(2322) FIXME: Type 'unknown' is not assignable to type 'ReactNod... Remove this comment to see the full error message */} + {value} + + + ))} {Array.from(singleValueCategories).reduce((elems, pair) => { + // @ts-expect-error ts-migrate(2488) FIXME: Type 'unknown' must have a '[Symbol.iterator]()' m... Remove this comment to see the full error message const [category, value] = pair; // If the value is empty skip it if (!value) return elems; // If this category is a ontology term, let's add its value to the previous node if (String(category).includes(ONTOLOGY_KEY)) { - const prevElem = elems.pop(); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const prevElem = (elems as any).pop(); const newChildren = [...prevElem.props.children]; newChildren.splice(2, 1, [{value}]); // Props aren't extensible so we must clone and alter the component to append the new child - elems.push( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (elems as any).push( React.cloneElement(prevElem, prevElem.props, newChildren) ); } else { // Create the list item - elems.push( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (elems as any).push( {`${category}:`} {value} @@ -132,14 +146,16 @@ const renderDatasetMetadata = (singleValueCategories, corporaMetadata) => { // Renders any links found in the config where link_type is not "SUMMARY" // If there are no links in the config, render the aboutURL -const renderLinks = (projectLinks, aboutURL) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const renderLinks = (projectLinks: any, aboutURL: any) => { if (!projectLinks && !aboutURL) return null; if (projectLinks) return ( <>

    Project Links

      - {projectLinks.map((link) => { + {/* eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. */} + {projectLinks.map((link: any) => { if (link.link_type === "SUMMARY") return null; return (
    • @@ -166,6 +182,7 @@ const renderLinks = (projectLinks, aboutURL) => { }; const InfoFormat = React.memo( + // @ts-expect-error ts-migrate(2339) FIXME: Property 'datasetTitle' does not exist on type '{ ... Remove this comment to see the full error message ({ datasetTitle, singleValueCategories, aboutURL, dataPortalProps = {} }) => { if ( ["1.0.0", "1.1.0"].indexOf( diff --git a/client/src/components/labelInput.js b/client/src/components/labelInput.tsx similarity index 50% rename from client/src/components/labelInput.js rename to client/src/components/labelInput.tsx index be460a6d..d6b5e766 100644 --- a/client/src/components/labelInput.js +++ b/client/src/components/labelInput.tsx @@ -3,7 +3,11 @@ import { InputGroup, MenuItem, Keys } from "@blueprintjs/core"; import { Suggest } from "@blueprintjs/select"; import fuzzysort from "fuzzysort"; -export default class LabelInput extends React.PureComponent { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +export default class LabelInput extends React.PureComponent<{}, State> { /* Input widget for text labels, which acts like an InputGroup, but will also accept a suggestion list (of labels), with sublime-like suggest search. @@ -26,9 +30,11 @@ export default class LabelInput extends React.PureComponent { /* maxinum number of suggestions */ static QueryResultLimit = 100; - constructor(props) { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'label' does not exist on type '{}'. const { label } = props; const query = label || ""; const queryResults = this.filterLabels(query); @@ -38,7 +44,8 @@ export default class LabelInput extends React.PureComponent { }; } - handleQueryChange = (query, event) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleQueryChange = (query: any, event: any) => { // https://github.com/palantir/blueprint/issues/2983 if (!event) return; @@ -48,19 +55,23 @@ export default class LabelInput extends React.PureComponent { queryResults, }); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onChange' does not exist on type 'Readon... Remove this comment to see the full error message const { onChange } = this.props; if (onChange) onChange(query, event); }; - handleItemSelect = (item, event) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleItemSelect = (item: any, event: any) => { /* only report the select if not already reported via onChange() */ const { target } = item; const { query } = this.state; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onSelect' does not exist on type 'Readon... Remove this comment to see the full error message const { onSelect } = this.props; if (target !== query && onSelect) onSelect(target, event); }; - handleKeyDown = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleKeyDown = (e: any) => { /* prevent these events from propagating to containing form/dialog and causing further side effects (eg, closing dialog, submitting @@ -75,13 +86,22 @@ export default class LabelInput extends React.PureComponent { } }; - handleChange = (e) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleChange = (e: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'onChange' does not exist on type 'Readon... Remove this comment to see the full error message const { onChange } = this.props; if (onChange) onChange(e.target.value); }; - renderLabelSuggestion = (queryResult, { handleClick, modifiers }) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + renderLabelSuggestion = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + queryResult: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + { handleClick, modifiers }: any + ) => { if (queryResult.newLabel) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'newLabelMessage' does not exist on type ... Remove this comment to see the full error message const { newLabelMessage } = this.props; return ( ({ - target: l, - score: -10000, - })); + return ( + labelSuggestions + .slice(0, LabelInput.QueryResultLimit) + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .map((l: any) => ({ + target: l, + score: -10000, + })) + ); } /* else, do a fuzzy query */ @@ -128,13 +153,16 @@ export default class LabelInput extends React.PureComponent { let queryResults = fuzzysort.go(query, labelSuggestions, options); /* exact match will always be first in list */ if (query !== "" && queryResults[0]?.target !== query) + // @ts-expect-error ts-migrate(2322) FIXME: Type '{ target: any; newLabel: true; }' is not ass... Remove this comment to see the full error message queryResults = [{ target: query, newLabel: true }, ...queryResults]; return queryResults; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { props } = this; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'labelSuggestions' does not exist on type... Remove this comment to see the full error message const { labelSuggestions, label, autoFocus = true } = props; const suggestEnabled = !!labelSuggestions && labelSuggestions.length > 0; @@ -142,7 +170,8 @@ export default class LabelInput extends React.PureComponent { return ( @@ -151,10 +180,12 @@ export default class LabelInput extends React.PureComponent { const popoverProps = { minimal: true, - ...props.popoverProps, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + ...(props as any).popoverProps, }; const inputProps = { - ...props.inputProps, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + ...(props as any).inputProps, autoFocus: false, }; const { queryResults } = this.state; @@ -170,6 +201,7 @@ export default class LabelInput extends React.PureComponent { onQueryChange={this.handleQueryChange} popoverProps={popoverProps} inputProps={inputProps} + // @ts-expect-error ts-migrate(2322) FIXME: Type '{ fill: true; inputValueRenderer: (i: any) =... Remove this comment to see the full error message onKeyDown={this.handleKeyDown} /> diff --git a/client/src/components/leftSidebar/index.js b/client/src/components/leftSidebar/index.tsx similarity index 58% rename from client/src/components/leftSidebar/index.js rename to client/src/components/leftSidebar/index.tsx index 6d72b424..19d71d4a 100644 --- a/client/src/components/leftSidebar/index.js +++ b/client/src/components/leftSidebar/index.tsx @@ -6,12 +6,17 @@ import DynamicScatterplot from "../scatterplot/scatterplot"; import TopLeftLogoAndTitle from "./topLeftLogoAndTitle"; import Continuous from "../continuous/continuous"; +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - scatterplotXXaccessor: state.controls.scatterplotXXaccessor, - scatterplotYYaccessor: state.controls.scatterplotYYaccessor, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + scatterplotXXaccessor: (state as any).controls.scatterplotXXaccessor, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + scatterplotYYaccessor: (state as any).controls.scatterplotYYaccessor, })) class LeftSideBar extends React.Component { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'scatterplotXXaccessor' does not exist on... Remove this comment to see the full error message const { scatterplotXXaccessor, scatterplotYYaccessor } = this.props; return (
      { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'libraryVersions' does not exist on type ... Remove this comment to see the full error message const { libraryVersions, tosURL, privacyURL } = props; return ( { - const { corpora_props: corporaProps } = state.config; - const correctVersion = - ["1.0.0", "1.1.0"].indexOf(corporaProps?.version?.corpora_schema_version) > - -1; - return { - datasetTitle: state.config?.displayNames?.dataset ?? "", - libraryVersions: state.config?.library_versions, - aboutLink: state.config?.links?.["about-dataset"], - tosURL: state.config?.parameters?.about_legal_tos, - privacyURL: state.config?.parameters?.about_legal_privacy, - title: correctVersion ? corporaProps?.title : undefined, - }; -}) -class LeftSideBar extends React.Component { - handleClick = () => { - const { dispatch } = this.props; - dispatch({ type: "toggle dataset drawer" }); - }; - - render() { - const { - datasetTitle, - libraryVersions, - aboutLink, - privacyURL, - tosURL, - dispatch, - title, - } = this.props; - - return ( -
      -
      - - - cell - - × - - gene - -
      -
      - - - -
      -
      - ); - } -} - -export default LeftSideBar; diff --git a/client/src/components/leftSidebar/topLeftLogoAndTitle.tsx b/client/src/components/leftSidebar/topLeftLogoAndTitle.tsx new file mode 100644 index 00000000..8eb407d2 --- /dev/null +++ b/client/src/components/leftSidebar/topLeftLogoAndTitle.tsx @@ -0,0 +1,133 @@ +import React from "react"; +import { connect } from "react-redux"; +import { Button } from "@blueprintjs/core"; + +import * as globals from "../../globals"; +import Logo from "../framework/logo"; +import Truncate from "../util/truncate"; +import InfoDrawer from "../infoDrawer/infoDrawer"; +import InformationMenu from "./infoMenu"; + +const DATASET_TITLE_FONT_SIZE = 14; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message +@connect((state) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const { corpora_props: corporaProps } = (state as any).config; + const correctVersion = + ["1.0.0", "1.1.0"].indexOf(corporaProps?.version?.corpora_schema_version) > + -1; + return { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + datasetTitle: (state as any).config?.displayNames?.dataset ?? "", + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + libraryVersions: (state as any).config?.library_versions, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + aboutLink: (state as any).config?.links?.["about-dataset"], + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + tosURL: (state as any).config?.parameters?.about_legal_tos, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + privacyURL: (state as any).config?.parameters?.about_legal_privacy, + title: correctVersion ? corporaProps?.title : undefined, + }; +}) +class LeftSideBar extends React.Component { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleClick = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + dispatch({ type: "toggle dataset drawer" }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'datasetTitle' does not exist on type 'Re... Remove this comment to see the full error message + datasetTitle, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'libraryVersions' does not exist on type ... Remove this comment to see the full error message + libraryVersions, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'aboutLink' does not exist on type 'Reado... Remove this comment to see the full error message + aboutLink, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'privacyURL' does not exist on type 'Read... Remove this comment to see the full error message + privacyURL, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'tosURL' does not exist on type 'Readonly... Remove this comment to see the full error message + tosURL, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + dispatch, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'title' does not exist on type 'Readonly<... Remove this comment to see the full error message + title, + } = this.props; + + return ( +
      +
      + + + cell + + × + + gene + +
      +
      + + + +
      +
      + ); + } +} + +export default LeftSideBar; diff --git a/client/src/components/menubar/authButtons.js b/client/src/components/menubar/authButtons.tsx similarity index 81% rename from client/src/components/menubar/authButtons.js rename to client/src/components/menubar/authButtons.tsx index 91af0b42..28f3d616 100644 --- a/client/src/components/menubar/authButtons.js +++ b/client/src/components/menubar/authButtons.tsx @@ -17,6 +17,7 @@ import { IconNames } from "@blueprintjs/icons"; import * as globals from "../../globals"; +// @ts-expect-error ts-migrate(2307) FIXME: Cannot find module './menubar.css' or its correspo... Remove this comment to see the full error message import styles from "./menubar.css"; import { storageGet, storageSet, KEYS } from "../util/localStorage"; @@ -31,11 +32,13 @@ const LOGIN_PROMPT_OFF = "off"; const Auth = React.memo((props) => { const [isPromptOpen, setIsPromptOpen] = useState(shouldShowPrompt()); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'auth' does not exist on type '{ children... Remove this comment to see the full error message const { auth, userInfo } = props; const isAuthenticated = userInfo && userInfo.is_authenticated; - window.userInfo = userInfo; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (window as any).userInfo = userInfo; const randomInt = Math.random() * 15; const sexIndex = Math.floor(randomInt / 5); @@ -75,6 +78,7 @@ const Auth = React.memo((props) => { > {/* eslint-disable-next-line no-constant-condition -- disable profile picture until CSP is tweaked */} {userInfo?.picture && false ? ( + // @ts-expect-error ts-migrate(2322) FIXME: Type '{ alt: string; size: string; src: any; }' is... Remove this comment to see the full error message profile ) : ( {scientist} @@ -123,11 +127,13 @@ const Auth = React.memo((props) => { function shouldShowPrompt() { if (storageGet(KEYS.LOGIN_PROMPT) === LOGIN_PROMPT_OFF) return false; + // @ts-expect-error ts-migrate(2774) FIXME: This condition will always return true since the f... Remove this comment to see the full error message return shouldShowAuth && !isAuthenticated; } }); -function PromptContent({ setIsPromptOpen }) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function PromptContent({ setIsPromptOpen }: any) { const [isChecked, setIsChecked] = useState(false); function handleOKClick() { diff --git a/client/src/components/menubar/cellSetButtons.js b/client/src/components/menubar/cellSetButtons.tsx similarity index 60% rename from client/src/components/menubar/cellSetButtons.js rename to client/src/components/menubar/cellSetButtons.tsx index f1d915a4..3f4b645f 100644 --- a/client/src/components/menubar/cellSetButtons.js +++ b/client/src/components/menubar/cellSetButtons.tsx @@ -4,17 +4,22 @@ import { connect } from "react-redux"; import { tooltipHoverOpenDelay } from "../../globals"; import actions from "../../actions"; +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - differential: state.differential, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + differential: (state as any).differential, })) class CellSetButton extends React.PureComponent { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. set() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, eitherCellSetOneOrTwo } = this.props; - dispatch(actions.setCellSetFromSelection(eitherCellSetOneOrTwo)); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'differential' does not exist on type 'Re... Remove this comment to see the full error message const { differential, eitherCellSetOneOrTwo } = this.props; const cellListName = `celllist${eitherCellSetOneOrTwo}`; const cellsSelected = differential[cellListName] diff --git a/client/src/components/menubar/clip.js b/client/src/components/menubar/clip.tsx similarity index 68% rename from client/src/components/menubar/clip.js rename to client/src/components/menubar/clip.tsx index 5bc1d18d..cf1558c6 100644 --- a/client/src/components/menubar/clip.js +++ b/client/src/components/menubar/clip.tsx @@ -12,19 +12,30 @@ import { import { IconNames } from "@blueprintjs/icons"; import { tooltipHoverOpenDelay } from "../../globals"; +// @ts-expect-error ts-migrate(2307) FIXME: Cannot find module './menubar.css' or its correspo... Remove this comment to see the full error message import styles from "./menubar.css"; const Clip = React.memo((props) => { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'pendingClipPercentiles' does not exist o... Remove this comment to see the full error message pendingClipPercentiles, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'clipPercentileMin' does not exist on typ... Remove this comment to see the full error message clipPercentileMin, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'clipPercentileMax' does not exist on typ... Remove this comment to see the full error message clipPercentileMax, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleClipOpening' does not exist on typ... Remove this comment to see the full error message handleClipOpening, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleClipClosing' does not exist on typ... Remove this comment to see the full error message handleClipClosing, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleClipCommit' does not exist on type... Remove this comment to see the full error message handleClipCommit, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'isClipDisabled' does not exist on type '... Remove this comment to see the full error message isClipDisabled, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleClipOnKeyPress' does not exist on ... Remove this comment to see the full error message handleClipOnKeyPress, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleClipPercentileMaxValueChange' does... Remove this comment to see the full error message handleClipPercentileMaxValueChange, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleClipPercentileMinValueChange' does... Remove this comment to see the full error message handleClipPercentileMinValueChange, } = props; @@ -34,7 +45,8 @@ const Clip = React.memo((props) => { pendingClipPercentiles?.clipPercentileMax ?? clipPercentileMax; const intent = clipPercentileMin > 0 || clipPercentileMax < 100 - ? Intent.INTENT_WARNING + ? // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (Intent as any).INTENT_WARNING : Intent.NONE; return ( diff --git a/client/src/components/menubar/diffexpButtons.js b/client/src/components/menubar/diffexpButtons.tsx similarity index 60% rename from client/src/components/menubar/diffexpButtons.js rename to client/src/components/menubar/diffexpButtons.tsx index a94890ac..823639ab 100644 --- a/client/src/components/menubar/diffexpButtons.js +++ b/client/src/components/menubar/diffexpButtons.tsx @@ -2,17 +2,25 @@ import React from "react"; import { connect } from "react-redux"; import { ButtonGroup, AnchorButton, Tooltip } from "@blueprintjs/core"; import * as globals from "../../globals"; +// @ts-expect-error ts-migrate(2307) FIXME: Cannot find module './menubar.css' or its correspo... Remove this comment to see the full error message import styles from "./menubar.css"; import actions from "../../actions"; import CellSetButton from "./cellSetButtons"; +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - differential: state.differential, - diffexpMayBeSlow: state.config?.parameters?.["diffexp-may-be-slow"] ?? false, - diffexpCellcountMax: state.config?.limits?.diffexp_cellcount_max, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + differential: (state as any).differential, + diffexpMayBeSlow: + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (state as any).config?.parameters?.["diffexp-may-be-slow"] ?? false, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + diffexpCellcountMax: (state as any).config?.limits?.diffexp_cellcount_max, })) class DiffexpButtons extends React.PureComponent { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. computeDiffExp = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message const { dispatch, differential } = this.props; if (differential.celllist1 && differential.celllist2) { dispatch( @@ -24,33 +32,32 @@ class DiffexpButtons extends React.PureComponent { } }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { /* diffexp-related buttons may be disabled */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'differential' does not exist on type 'Re... Remove this comment to see the full error message const { differential, diffexpMayBeSlow, diffexpCellcountMax } = this.props; - const haveBothCellSets = !!differential.celllist1 && !!differential.celllist2; - const haveEitherCellSet = !!differential.celllist1 || !!differential.celllist2; - const slowMsg = diffexpMayBeSlow ? " (CAUTION: large dataset - may take longer or fail)" : ""; const tipMessage = `See top 10 differentially expressed genes${slowMsg}`; const tipMessageWarn = `The total number of cells for differential expression computation may not exceed ${diffexpCellcountMax}. Try reselecting new cell sets.`; - const warnMaxSizeExceeded = haveEitherCellSet && !!diffexpCellcountMax && (differential.celllist1?.length ?? 0) + (differential.celllist2?.length ?? 0) > diffexpCellcountMax; - return ( + {/* @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. */} + {/* @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. */} { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Defa... Remove this comment to see the full error message + const { annoMatrix } = state; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const crossfilter = (state as any).obsCrossfilter; + const selectedCount = crossfilter.countSelected(); + + const subsetPossible = + selectedCount !== 0 && selectedCount !== crossfilter.size(); // ie, not all and not none are selected + const embSubsetView = getEmbSubsetView(annoMatrix); + const subsetResetPossible = !embSubsetView + ? annoMatrix.nObs !== annoMatrix.schema.dataframe.nObs + : annoMatrix.nObs !== embSubsetView.nObs; + + return { + subsetPossible, + subsetResetPossible, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + graphInteractionMode: (state as any).controls.graphInteractionMode, + clipPercentileMin: Math.round(100 * (annoMatrix?.clipRange?.[0] ?? 0)), + clipPercentileMax: Math.round(100 * (annoMatrix?.clipRange?.[1] ?? 1)), + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userDefinedGenes: (state as any).controls.userDefinedGenes, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colorAccessor: (state as any).colors.colorAccessor, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + scatterplotXXaccessor: (state as any).controls.scatterplotXXaccessor, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + scatterplotYYaccessor: (state as any).controls.scatterplotYYaccessor, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + libraryVersions: (state as any).config?.library_versions, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + auth: (state as any).config?.authentication, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userInfo: (state as any).userInfo, + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message + undoDisabled: state["@@undoable/past"].length === 0, + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message + redoDisabled: state["@@undoable/future"].length === 0, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + aboutLink: (state as any).config?.links?.["about-dataset"], + disableDiffexp: + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (state as any).config?.parameters?.["disable-diffexp"] ?? false, + diffexpMayBeSlow: + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (state as any).config?.parameters?.["diffexp-may-be-slow"] ?? false, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + showCentroidLabels: (state as any).centroidLabels.showLabels, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + tosURL: (state as any).config?.parameters?.about_legal_tos, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + privacyURL: (state as any).config?.parameters?.about_legal_privacy, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoricalSelection: (state as any).categoricalSelection, + }; +}) +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class MenuBar extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static isValidDigitKeyEvent(e: any) { + /* + Return true if this event is necessary to enter a percent number input. + Return false if not. + + Returns true for events with keys: backspace, control, alt, meta, [0-9], + or events that don't have a key. + */ + if (e.key === null) return true; + if (e.ctrlKey || e.altKey || e.metaKey) return true; + + // concept borrowed from blueprint's numericInputUtils: + // keys that print a single character when pressed have a `key` name of + // length 1. every other key has a longer `key` name (e.g. "Backspace", + // "ArrowUp", "Shift"). since none of those keys can print a character + // to the field--and since they may have important native behaviors + // beyond printing a character--we don't want to disable their effects. + const isSingleCharKey = e.key.length === 1; + if (!isSingleCharKey) return true; + + const key = e.key.charCodeAt(0) - 48; /* "0" */ + return key >= 0 && key <= 9; + } + + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { + super(props); + this.state = { + pendingClipPercentiles: null, + }; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + isClipDisabled = () => { + /* + return true if clip button should be disabled. + */ + const { pendingClipPercentiles } = this.state; + const clipPercentileMin = pendingClipPercentiles?.clipPercentileMin; + const clipPercentileMax = pendingClipPercentiles?.clipPercentileMax; + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'clipPercentileMin' does not exist on typ... Remove this comment to see the full error message + clipPercentileMin: currentClipMin, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'clipPercentileMax' does not exist on typ... Remove this comment to see the full error message + clipPercentileMax: currentClipMax, + } = this.props; + + // if you change this test, be careful with logic around + // comparisons between undefined / NaN handling. + const isDisabled = + !(clipPercentileMin < clipPercentileMax) || + (clipPercentileMin === currentClipMin && + clipPercentileMax === currentClipMax); + + return isDisabled; + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleClipOnKeyPress = (e: any) => { + /* + allow only numbers, plus other critical keys which + may be required to make a number + */ + if (!MenuBar.isValidDigitKeyEvent(e)) { + e.preventDefault(); + } + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleClipPercentileMinValueChange = (v: any) => { + /* + Ignore anything that isn't a legit number + */ + if (!Number.isFinite(v)) return; + + const { pendingClipPercentiles } = this.state; + const clipPercentileMax = pendingClipPercentiles?.clipPercentileMax; + + /* + clamp to [0, currentClipPercentileMax] + */ + if (v <= 0) v = 0; + if (v > 100) v = 100; + const clipPercentileMin = Math.round(v); // paranoia + this.setState({ + pendingClipPercentiles: { clipPercentileMin, clipPercentileMax }, + }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + handleClipPercentileMaxValueChange = (v: any) => { + /* + Ignore anything that isn't a legit number + */ + if (!Number.isFinite(v)) return; + + const { pendingClipPercentiles } = this.state; + const clipPercentileMin = pendingClipPercentiles?.clipPercentileMin; + + /* + clamp to [0, 100] + */ + if (v < 0) v = 0; + if (v > 100) v = 100; + const clipPercentileMax = Math.round(v); // paranoia + + this.setState({ + pendingClipPercentiles: { clipPercentileMin, clipPercentileMax }, + }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleClipCommit = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + const { pendingClipPercentiles } = this.state; + const { clipPercentileMin, clipPercentileMax } = pendingClipPercentiles; + const min = clipPercentileMin / 100; + const max = clipPercentileMax / 100; + dispatch(actions.clipAction(min, max)); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleClipOpening = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'clipPercentileMin' does not exist on typ... Remove this comment to see the full error message + const { clipPercentileMin, clipPercentileMax } = this.props; + this.setState({ + pendingClipPercentiles: { clipPercentileMin, clipPercentileMax }, + }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleClipClosing = () => { + this.setState({ pendingClipPercentiles: null }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleCentroidChange = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch, showCentroidLabels } = this.props; + + dispatch({ + type: "show centroid labels for category", + showLabels: !showCentroidLabels, + }); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleSubset = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + dispatch(actions.subsetAction()); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + handleSubsetReset = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + const { dispatch } = this.props; + dispatch(actions.resetSubsetAction()); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message + dispatch, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'disableDiffexp' does not exist on type '... Remove this comment to see the full error message + disableDiffexp, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'undoDisabled' does not exist on type 'Re... Remove this comment to see the full error message + undoDisabled, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'redoDisabled' does not exist on type 'Re... Remove this comment to see the full error message + redoDisabled, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'selectionTool' does not exist on type 'R... Remove this comment to see the full error message + selectionTool, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'clipPercentileMin' does not exist on typ... Remove this comment to see the full error message + clipPercentileMin, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'clipPercentileMax' does not exist on typ... Remove this comment to see the full error message + clipPercentileMax, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'graphInteractionMode' does not exist on ... Remove this comment to see the full error message + graphInteractionMode, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'showCentroidLabels' does not exist on ty... Remove this comment to see the full error message + showCentroidLabels, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'categoricalSelection' does not exist on ... Remove this comment to see the full error message + categoricalSelection, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorAccessor' does not exist on type 'R... Remove this comment to see the full error message + colorAccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'subsetPossible' does not exist on type '... Remove this comment to see the full error message + subsetPossible, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'subsetResetPossible' does not exist on t... Remove this comment to see the full error message + subsetResetPossible, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'userInfo' does not exist on type 'Readon... Remove this comment to see the full error message + userInfo, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'auth' does not exist on type 'Readonly<{... Remove this comment to see the full error message + auth, + } = this.props; + const { pendingClipPercentiles } = this.state; + + const isColoredByCategorical = !!categoricalSelection?.[colorAccessor]; + + // constants used to create selection tool button + const [selectionTooltip, selectionButtonIcon] = + selectionTool === "brush" + ? ["Brush selection", "Lasso selection"] + : ["select", "polygon-filter"]; + + return ( +
      + + + + + + + + + { + dispatch({ + type: "change graph interaction mode", + data: "select", + }); + }} + /> + + + { + dispatch({ + type: "change graph interaction mode", + data: "zoom", + }); + }} + /> + + + + {disableDiffexp ? null : } +
      + ); + } +} + +export default MenuBar; diff --git a/client/src/components/menubar/subset.js b/client/src/components/menubar/subset.tsx similarity index 62% rename from client/src/components/menubar/subset.js rename to client/src/components/menubar/subset.tsx index 03025cb3..ca96329e 100644 --- a/client/src/components/menubar/subset.js +++ b/client/src/components/menubar/subset.tsx @@ -1,13 +1,18 @@ import React from "react"; import { AnchorButton, ButtonGroup, Tooltip } from "@blueprintjs/core"; +// @ts-expect-error ts-migrate(2307) FIXME: Cannot find module './menubar.css' or its correspo... Remove this comment to see the full error message import styles from "./menubar.css"; import * as globals from "../../globals"; const Subset = React.memo((props) => { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'subsetPossible' does not exist on type '... Remove this comment to see the full error message subsetPossible, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'subsetResetPossible' does not exist on t... Remove this comment to see the full error message subsetResetPossible, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleSubset' does not exist on type '{ ... Remove this comment to see the full error message handleSubset, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'handleSubsetReset' does not exist on typ... Remove this comment to see the full error message handleSubsetReset, } = props; diff --git a/client/src/components/menubar/undoRedo.js b/client/src/components/menubar/undoRedo.tsx similarity index 81% rename from client/src/components/menubar/undoRedo.js rename to client/src/components/menubar/undoRedo.tsx index 8591505c..39c8ea5d 100644 --- a/client/src/components/menubar/undoRedo.js +++ b/client/src/components/menubar/undoRedo.tsx @@ -2,9 +2,11 @@ import React from "react"; import { AnchorButton, ButtonGroup, Tooltip } from "@blueprintjs/core"; import { IconNames } from "@blueprintjs/icons"; import { tooltipHoverOpenDelay } from "../../globals"; +// @ts-expect-error ts-migrate(2307) FIXME: Cannot find module './menubar.css' or its correspo... Remove this comment to see the full error message import styles from "./menubar.css"; const UndoRedo = React.memo((props) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'undoDisabled' does not exist on type '{ ... Remove this comment to see the full error message const { undoDisabled, redoDisabled, dispatch } = props; return ( diff --git a/client/src/components/miniHistogram/index.js b/client/src/components/miniHistogram/index.tsx similarity index 56% rename from client/src/components/miniHistogram/index.js rename to client/src/components/miniHistogram/index.tsx index c74fb1dd..3d0d9f99 100644 --- a/client/src/components/miniHistogram/index.js +++ b/client/src/components/miniHistogram/index.tsx @@ -7,12 +7,18 @@ import { } from "@blueprintjs/core"; export default class MiniHistogram extends React.PureComponent { - constructor(props) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + canvasRef: any; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(props: any) { super(props); this.canvasRef = React.createRef(); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. drawHistogram = () => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'xScale' does not exist on type 'Readonly... Remove this comment to see the full error message const { xScale, yScale, bins, width, height } = this.props; if (!bins) return; @@ -35,11 +41,14 @@ export default class MiniHistogram extends React.PureComponent { } }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. componentDidMount = () => { this.drawHistogram(); }; - componentDidUpdate = (prevProps) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + componentDidUpdate = (prevProps: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsOrVarContinuousFieldDisplayName' does... Remove this comment to see the full error message const { obsOrVarContinuousFieldDisplayName, bins } = this.props; if ( prevProps.obsOrVarContinuousFieldDisplayName !== @@ -49,11 +58,16 @@ export default class MiniHistogram extends React.PureComponent { this.drawHistogram(); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'domainLabel' does not exist on type 'Rea... Remove this comment to see the full error message domainLabel, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsOrVarContinuousFieldDisplayName' does... Remove this comment to see the full error message obsOrVarContinuousFieldDisplayName, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'width' does not exist on type 'Readonly<... Remove this comment to see the full error message width, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'height' does not exist on type 'Readonly... Remove this comment to see the full error message height, } = this.props; diff --git a/client/src/components/miniStackedBar/index.js b/client/src/components/miniStackedBar/index.js deleted file mode 100644 index 15a05002..00000000 --- a/client/src/components/miniStackedBar/index.js +++ /dev/null @@ -1,73 +0,0 @@ -import React from "react"; - -export default class MiniStackedBar extends React.PureComponent { - constructor(props) { - super(props); - this.canvasRef = React.createRef(); - } - - drawStacks = () => { - const { - domainValues, - scale, - domain, - colorTable, - occupancy, - width, - height, - } = this.props; - - if (!colorTable || !domainValues) return; - - const { scale: colorScale } = colorTable; - - const ctx = this.canvasRef?.current.getContext("2d"); - - ctx.clearRect(0, 0, width, height); - let currentOffset = 0; - - let occupancyValue; - let scaledValue; - let value; - - for (let i = 0, { length } = domainValues; i < length; i += 1) { - value = domainValues[i]; - occupancyValue = occupancy.get(value); - scaledValue = scale(occupancyValue); - ctx.fillStyle = occupancyValue - ? colorScale(domain.indexOf(value)) - : "rgb(255,255,255)"; - ctx.fillRect(currentOffset, 0, occupancyValue ? scaledValue : 0, height); - currentOffset += occupancyValue ? scaledValue : 0; - } - }; - - componentDidUpdate = (prevProps) => { - const { occupancy } = this.props; - if (occupancy !== prevProps.occupancy) this.drawStacks(); - }; - - componentDidMount = () => { - this.drawStacks(); - }; - - render() { - const { width, height } = this.props; - const { canvas } = this; - if (canvas) canvas.getContext("2d").clearRect(0, 0, width, height); - - return ( - - ); - } -} diff --git a/client/src/components/miniStackedBar/index.tsx b/client/src/components/miniStackedBar/index.tsx new file mode 100644 index 00000000..519d0194 --- /dev/null +++ b/client/src/components/miniStackedBar/index.tsx @@ -0,0 +1,91 @@ +import React from "react"; + +export default class MiniStackedBar extends React.PureComponent { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + canvasRef: any; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(props: any) { + super(props); + this.canvasRef = React.createRef(); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + drawStacks = () => { + const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'domainValues' does not exist on type 'Re... Remove this comment to see the full error message + domainValues, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'scale' does not exist on type 'Readonly<... Remove this comment to see the full error message + scale, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'domain' does not exist on type 'Readonly... Remove this comment to see the full error message + domain, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colorTable' does not exist on type 'Read... Remove this comment to see the full error message + colorTable, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'occupancy' does not exist on type 'Reado... Remove this comment to see the full error message + occupancy, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'width' does not exist on type 'Readonly<... Remove this comment to see the full error message + width, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'height' does not exist on type 'Readonly... Remove this comment to see the full error message + height, + } = this.props; + + if (!colorTable || !domainValues) return; + + const { scale: colorScale } = colorTable; + + const ctx = this.canvasRef?.current.getContext("2d"); + + ctx.clearRect(0, 0, width, height); + let currentOffset = 0; + + let occupancyValue; + let scaledValue; + let value; + + for (let i = 0, { length } = domainValues; i < length; i += 1) { + value = domainValues[i]; + occupancyValue = occupancy.get(value); + scaledValue = scale(occupancyValue); + ctx.fillStyle = occupancyValue + ? colorScale(domain.indexOf(value)) + : "rgb(255,255,255)"; + ctx.fillRect(currentOffset, 0, occupancyValue ? scaledValue : 0, height); + currentOffset += occupancyValue ? scaledValue : 0; + } + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + componentDidUpdate = (prevProps: any) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'occupancy' does not exist on type 'Reado... Remove this comment to see the full error message + const { occupancy } = this.props; + if (occupancy !== prevProps.occupancy) this.drawStacks(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + componentDidMount = () => { + this.drawStacks(); + }; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + render() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'width' does not exist on type 'Readonly<... Remove this comment to see the full error message + const { width, height } = this.props; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'canvas' does not exist on type 'MiniStac... Remove this comment to see the full error message + const { canvas } = this; + if (canvas) canvas.getContext("2d").clearRect(0, 0, width, height); + + return ( + + ); + } +} diff --git a/client/src/components/rightSidebar/index.js b/client/src/components/rightSidebar/index.tsx similarity index 52% rename from client/src/components/rightSidebar/index.js rename to client/src/components/rightSidebar/index.tsx index 43802b99..baaf23a0 100644 --- a/client/src/components/rightSidebar/index.js +++ b/client/src/components/rightSidebar/index.tsx @@ -3,11 +3,15 @@ import { connect } from "react-redux"; import GeneExpression from "../geneExpression"; import * as globals from "../../globals"; +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - scatterplotXXaccessor: state.controls.scatterplotXXaccessor, - scatterplotYYaccessor: state.controls.scatterplotYYaccessor, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + scatterplotXXaccessor: (state as any).controls.scatterplotXXaccessor, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + scatterplotYYaccessor: (state as any).controls.scatterplotYYaccessor, })) class RightSidebar extends React.Component { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { return (
      { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'obsCrossfilter' does not exist on type '... Remove this comment to see the full error message const { obsCrossfilter: crossfilter } = state; - const { scatterplotXXaccessor, scatterplotYYaccessor } = state.controls; + const { + scatterplotXXaccessor, + scatterplotYYaccessor, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + } = (state as any).controls; return { - annoMatrix: state.annoMatrix, - colors: state.colors, - pointDilation: state.pointDilation, - + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + annoMatrix: (state as any).annoMatrix, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colors: (state as any).colors, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + pointDilation: (state as any).pointDilation, // Accessors are var/gene names (strings) scatterplotXXaccessor, scatterplotYYaccessor, - crossfilter, - genesets: state.genesets.genesets, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + genesets: (state as any).genesets.genesets, }; }) -class Scatterplot extends React.PureComponent { - static createReglState(canvas) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class Scatterplot extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static createReglState(canvas: any) { /* Must be created for each canvas */ @@ -70,8 +86,11 @@ class Scatterplot extends React.PureComponent { const drawPoints = _drawPoints(regl); // preallocate webgl buffers + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. const pointBuffer = regl.buffer(); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. const colorBuffer = regl.buffer(); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. const flagBuffer = regl.buffer(); return { @@ -83,10 +102,20 @@ class Scatterplot extends React.PureComponent { }; } - static watchAsync(props, prevProps) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static watchAsync(props: any, prevProps: any) { return !shallowEqual(props.watchProps, prevProps.watchProps); } + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + axes: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + reglCanvas: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + renderCache: any; + computePointPositions = memoize((X, Y, xScale, yScale) => { const positions = new Float32Array(2 * X.length); for (let i = 0, len = X.length; i < len; i += 1) { @@ -183,7 +212,8 @@ class Scatterplot extends React.PureComponent { } ); - constructor(props) { + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); const viewport = this.getViewportDimensions(); this.axes = false; @@ -198,16 +228,19 @@ class Scatterplot extends React.PureComponent { }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. componentDidMount() { // this affect point render size for the scatterplot window.addEventListener("resize", this.handleResize); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. componentWillUnmount() { window.removeEventListener("resize", this.handleResize); } - setReglCanvas = (canvas) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + setReglCanvas = (canvas: any) => { this.reglCanvas = canvas; if (canvas) { // no need to update this state if we are detaching. @@ -217,13 +250,13 @@ class Scatterplot extends React.PureComponent { } }; - getViewportDimensions = () => { - return { - height: window.innerHeight, - width: window.innerWidth, - }; - }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + getViewportDimensions = () => ({ + height: window.innerHeight, + width: window.innerWidth, + }); + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleResize = () => { const { state } = this.state; const viewport = this.getViewportDimensions(); @@ -233,7 +266,8 @@ class Scatterplot extends React.PureComponent { }); }; - fetchAsyncProps = async (props) => { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + fetchAsyncProps = async (props: any) => { const { scatterplotXXaccessor, scatterplotYYaccessor, @@ -295,7 +329,9 @@ class Scatterplot extends React.PureComponent { }; }; - createXQuery(geneName) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + createXQuery(geneName: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix } = this.props; const { schema } = annoMatrix; const varIndex = schema?.annotations?.var?.index; @@ -312,15 +348,19 @@ class Scatterplot extends React.PureComponent { ]; } - createColorByQuery(colors) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + createColorByQuery(colors: any) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix, genesets } = this.props; const { schema } = annoMatrix; const { colorMode, colorAccessor } = colors; return createColorQuery(colorMode, colorAccessor, schema, genesets); } - updateColorTable(colors, colorDf) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + updateColorTable(colors: any, colorDf: any) { /* update color table state */ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix } = this.props; const { schema } = annoMatrix; const { colorAccessor, userColors, colorMode } = colors; @@ -333,18 +373,25 @@ class Scatterplot extends React.PureComponent { ); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. async fetchData( - scatterplotXXaccessor, - scatterplotYYaccessor, - colors, - pointDilation + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + scatterplotXXaccessor: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + scatterplotYYaccessor: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colors: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + pointDilation: any ) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix } = this.props; const { metadataField: pointDilationAccessor } = pointDilation; const promises = []; // X and Y dimensions promises.push( + // @ts-expect-error ts-migrate(2488) FIXME: Type '(string | { where: { field: string; column: ... Remove this comment to see the full error message annoMatrix.fetch(...this.createXQuery(scatterplotXXaccessor)) ); promises.push( @@ -388,7 +435,8 @@ class Scatterplot extends React.PureComponent { ); }); - updateReglAndRender(newRenderCache) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + updateReglAndRender(newRenderCache: any) { const { positions, colors, flags } = newRenderCache; this.renderCache = newRenderCache; const { pointBuffer, colorBuffer, flagBuffer } = this.state; @@ -398,14 +446,22 @@ class Scatterplot extends React.PureComponent { this.renderCanvas(); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renderPoints( - regl, - drawPoints, - flagBuffer, - colorBuffer, - pointBuffer, - projectionTF + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + regl: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + drawPoints: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + flagBuffer: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorBuffer: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + pointBuffer: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + projectionTF: any ) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message const { annoMatrix } = this.props; if (!this.reglCanvas || !annoMatrix) return; @@ -431,14 +487,22 @@ class Scatterplot extends React.PureComponent { regl._gl.flush(); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'dispatch' does not exist on type 'Readon... Remove this comment to see the full error message dispatch, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'annoMatrix' does not exist on type 'Read... Remove this comment to see the full error message annoMatrix, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'scatterplotXXaccessor' does not exist on... Remove this comment to see the full error message scatterplotXXaccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'scatterplotYYaccessor' does not exist on... Remove this comment to see the full error message scatterplotYYaccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'colors' does not exist on type 'Readonly... Remove this comment to see the full error message colors, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'crossfilter' does not exist on type 'Rea... Remove this comment to see the full error message crossfilter, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'pointDilation' does not exist on type 'R... Remove this comment to see the full error message pointDilation, } = this.props; const { minimized, regl, viewport } = this.state; @@ -506,6 +570,7 @@ class Scatterplot extends React.PureComponent { style={{ marginLeft: margin.left, marginTop: margin.top, + // @ts-expect-error ts-migrate(2322) FIXME: Type '"none" | null' is not assignable to type 'Di... Remove this comment to see the full error message display: minimized ? "none" : null, }} ref={this.setReglCanvas} @@ -532,11 +597,14 @@ class Scatterplot extends React.PureComponent { } return ( ); }} @@ -552,10 +620,15 @@ export default Scatterplot; const ScatterplotAxis = React.memo( ({ + // @ts-expect-error ts-migrate(2339) FIXME: Property 'minimized' does not exist on type '{ chi... Remove this comment to see the full error message minimized, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'scatterplotYYaccessor' does not exist on... Remove this comment to see the full error message scatterplotYYaccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'scatterplotXXaccessor' does not exist on... Remove this comment to see the full error message scatterplotXXaccessor, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'xScale' does not exist on type '{ childr... Remove this comment to see the full error message xScale, + // @ts-expect-error ts-migrate(2339) FIXME: Property 'yScale' does not exist on type '{ childr... Remove this comment to see the full error message yScale, }) => { /* @@ -579,7 +652,9 @@ const ScatterplotAxis = React.memo( // the axes are much cleaner and easier now. No need to rotate and orient // the axis, just call axisBottom, axisLeft etc. + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. const xAxis = d3.axisBottom().ticks(7).scale(xScale); + // @ts-expect-error ts-migrate(2554) FIXME: Expected 1 arguments, but got 0. const yAxis = d3.axisLeft().ticks(7).scale(yScale); // adding axes is also simpler now, just translate x-axis to (0,height) @@ -622,6 +697,7 @@ const ScatterplotAxis = React.memo( height={height + margin.top + margin.bottom} data-testid="scatterplot-svg" style={{ + // @ts-expect-error ts-migrate(2322) FIXME: Type '"none" | null' is not assignable to type 'Di... Remove this comment to see the full error message display: minimized ? "none" : null, }} > diff --git a/client/src/components/scatterplot/util.js b/client/src/components/scatterplot/util.ts similarity index 100% rename from client/src/components/scatterplot/util.js rename to client/src/components/scatterplot/util.ts diff --git a/client/src/components/termsPrompt/index.js b/client/src/components/termsPrompt/index.tsx similarity index 53% rename from client/src/components/termsPrompt/index.js rename to client/src/components/termsPrompt/index.tsx index 11f1313d..9ad491d2 100644 --- a/client/src/components/termsPrompt/index.js +++ b/client/src/components/termsPrompt/index.tsx @@ -10,13 +10,25 @@ import { } from "@blueprintjs/core"; import { storageGet, storageSet, KEYS } from "../util/localStorage"; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +type State = any; + +// @ts-expect-error ts-migrate(1238) FIXME: Unable to resolve signature of class decorator whe... Remove this comment to see the full error message @connect((state) => ({ - tosURL: state.config?.parameters?.about_legal_tos, - privacyURL: state.config?.parameters?.about_legal_privacy, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + tosURL: (state as any).config?.parameters?.about_legal_tos, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + privacyURL: (state as any).config?.parameters?.about_legal_privacy, })) -class TermsPrompt extends React.PureComponent { - constructor(props) { +// eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. +class TermsPrompt extends React.PureComponent<{}, State> { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + drawerClose: any; + + // eslint-disable-next-line @typescript-eslint/ban-types --- FIXME: disabled temporarily on migrate to TS. + constructor(props: {}) { super(props); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'tosURL' does not exist on type 'Readonly... Remove this comment to see the full error message const { tosURL, privacyURL } = this.props; const cookieDecision = storageGet(KEYS.COOKIE_DECISION, null); const hasDecided = cookieDecision !== null; @@ -27,6 +39,7 @@ class TermsPrompt extends React.PureComponent { }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. componentDidMount() { const { hasDecided, isEnabled } = this.state; if (isEnabled && !hasDecided) { @@ -34,11 +47,14 @@ class TermsPrompt extends React.PureComponent { } } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleOK = () => { this.setState({ isOpen: false }); storageSet(KEYS.COOKIE_DECISION, "yes"); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'cookieDecisionCallback' does not exist o... Remove this comment to see the full error message if (window.cookieDecisionCallback instanceof Function) { try { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'cookieDecisionCallback' does not exist o... Remove this comment to see the full error message window.cookieDecisionCallback(); } catch (e) { // continue @@ -46,12 +62,15 @@ class TermsPrompt extends React.PureComponent { } }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. handleNo = () => { this.setState({ isOpen: false }); storageSet(KEYS.COOKIE_DECISION, "no"); }; + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renderTos() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'tosURL' does not exist on type 'Readonly... Remove this comment to see the full error message const { tosURL } = this.props; if (!tosURL) return null; return ( @@ -74,7 +93,9 @@ class TermsPrompt extends React.PureComponent { ); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. renderPrivacy() { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'privacyURL' does not exist on type 'Read... Remove this comment to see the full error message const { privacyURL } = this.props; if (!privacyURL) return null; return ( @@ -96,18 +117,22 @@ class TermsPrompt extends React.PureComponent { ); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. render() { const { isOpen, isEnabled } = this.state; if (!isEnabled || !isOpen) return null; return ( @@ -143,5 +168,4 @@ class TermsPrompt extends React.PureComponent { ); } } - export default TermsPrompt; diff --git a/client/src/components/util/localStorage.js b/client/src/components/util/localStorage.js deleted file mode 100644 index 5766d9f9..00000000 --- a/client/src/components/util/localStorage.js +++ /dev/null @@ -1,22 +0,0 @@ -export const KEYS = { - COOKIE_DECISION: "cxg.cookieDecision", - LOGIN_PROMPT: "cxg.LOGIN_PROMPT", -}; - -export function storageGet(key, defaultValue = null) { - try { - const val = window.localStorage.getItem(key); - if (val === null) return defaultValue; - return val; - } catch (e) { - return defaultValue; - } -} - -export function storageSet(key, value) { - try { - window.localStorage.setItem(key, value); - } catch { - // continue - } -} diff --git a/client/src/components/util/localStorage.ts b/client/src/components/util/localStorage.ts new file mode 100644 index 00000000..8f411fc0 --- /dev/null +++ b/client/src/components/util/localStorage.ts @@ -0,0 +1,24 @@ +export const KEYS = { + COOKIE_DECISION: "cxg.cookieDecision", + LOGIN_PROMPT: "cxg.LOGIN_PROMPT", +}; + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function storageGet(key: any, defaultValue = null) { + try { + const val = window.localStorage.getItem(key); + if (val === null) return defaultValue; + return val; + } catch (e) { + return defaultValue; + } +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function storageSet(key: any, value: any) { + try { + window.localStorage.setItem(key, value); + } catch { + // continue + } +} diff --git a/client/src/components/util/truncate.js b/client/src/components/util/truncate.tsx similarity index 66% rename from client/src/components/util/truncate.js rename to client/src/components/util/truncate.tsx index 85aaf26e..09b80952 100644 --- a/client/src/components/util/truncate.js +++ b/client/src/components/util/truncate.tsx @@ -32,8 +32,9 @@ const SECOND_HALF_INNER_STYLE = { right: 0, }; -export default (props) => { - const { children, tooltipAddendum = "" } = props; +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default (props: any) => { + const { children, isGenesetDescription, tooltipAddendum = "" } = props; // Truncate only support a single child with a text child if ( @@ -70,9 +71,12 @@ export default (props) => { const truncatedJSX = ( + {/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ overflow: string; textOverflow: string; wh... Remove this comment to see the full error message */} {firstString} + {/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ position: string; overflow: string; whiteS... Remove this comment to see the full error message */} {secondString} + {/* @ts-expect-error ts-migrate(2322) FIXME: Type '{ color: any; position: string; right: numbe... Remove this comment to see the full error message */} {secondString} @@ -85,10 +89,24 @@ export default (props) => { "aria-label": originalString, }) ); + // we need an ID to check for this content, since this is the only place the geneset description appears + const descriptionContent = ( + + {originalString} + {tooltipAddendum} + + ); return ( {newChildren} diff --git a/client/src/globals.js b/client/src/globals.ts similarity index 77% rename from client/src/globals.js rename to client/src/globals.ts index ea9dd77d..d23867f6 100644 --- a/client/src/globals.js +++ b/client/src/globals.ts @@ -2,14 +2,14 @@ import { Colors } from "@blueprintjs/core"; import { dispatchNetworkErrorMessageToUser } from "./util/actionHelpers"; import ENV_DEFAULT from "../../environment.default.json"; -/* if a categorical metadata field has more options than this, truncate */ -export const maxCategoricalOptionsToDisplay = 200; +/* overflow category values are created using this string */ +export const overflowCategoryLabel = ": all other labels"; /* default "unassigned" value for user-created categorical metadata */ export const unassignedCategoryLabel = "unassigned"; /* -these are default values for configuration the CLI may supply. +these are default values for configuration the CLI may supply. See the REST API and CLI specs for more info. */ export const configDefaults = { @@ -22,6 +22,18 @@ export const configDefaults = { links: {}, }; +/* +Most configuration is stored in the reducer. A handful of values +are global and stored here. They are typically set by the config +action handler, which pull the information from the backend/CLI. + +All should be set here to their default value. +*/ +export const globalConfig = { + /* if a categorical metadata field has more options than this, truncate */ + maxCategoricalOptionsToDisplay: 200, +}; + /* colors */ export const blue = Colors.BLUE3; export const linkBlue = Colors.BLUE5; @@ -91,8 +103,10 @@ const CXG_SERVER_PORT = let _API; -if (window.CELLXGENE && window.CELLXGENE.API) { - _API = window.CELLXGENE.API; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +if ((window as any).CELLXGENE && (window as any).CELLXGENE.API) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + _API = (window as any).CELLXGENE.API; } else { if (CXG_SERVER_PORT === undefined) { const errorMessage = "Please set the CXG_SERVER_PORT environment variable."; diff --git a/client/src/index.js b/client/src/index.tsx similarity index 100% rename from client/src/index.js rename to client/src/index.tsx diff --git a/client/src/reducers/annoMatrix.js b/client/src/reducers/annoMatrix.js deleted file mode 100644 index 830e1834..00000000 --- a/client/src/reducers/annoMatrix.js +++ /dev/null @@ -1,12 +0,0 @@ -/* -Reducer for the annoMatrix -*/ - -const AnnoMatrix = (state = null, action) => { - if (action.annoMatrix) { - return action.annoMatrix; - } - return state; -}; - -export default AnnoMatrix; diff --git a/client/src/reducers/annoMatrix.ts b/client/src/reducers/annoMatrix.ts new file mode 100644 index 00000000..82e30228 --- /dev/null +++ b/client/src/reducers/annoMatrix.ts @@ -0,0 +1,13 @@ +/* +Reducer for the annoMatrix +*/ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const AnnoMatrix = (state = null, action: any) => { + if (action.annoMatrix) { + return action.annoMatrix; + } + return state; +}; + +export default AnnoMatrix; diff --git a/client/src/reducers/annotations.js b/client/src/reducers/annotations.ts similarity index 91% rename from client/src/reducers/annotations.js rename to client/src/reducers/annotations.ts index 5178d0cf..b2282c91 100644 --- a/client/src/reducers/annotations.js +++ b/client/src/reducers/annotations.ts @@ -1,6 +1,7 @@ /* Reducers for annotation UI-state. */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const Annotations = ( state = { /* @@ -28,7 +29,8 @@ const Annotations = ( labelEditable: { category: null, label: null }, promptForFilename: true, }, - action + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any ) => { switch (action.type) { case "configuration load complete": { diff --git a/client/src/reducers/autosave.js b/client/src/reducers/autosave.ts similarity index 78% rename from client/src/reducers/autosave.js rename to client/src/reducers/autosave.ts index 26d67387..6b4611a2 100644 --- a/client/src/reducers/autosave.js +++ b/client/src/reducers/autosave.ts @@ -1,3 +1,4 @@ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const Autosave = ( state = { // cell labels @@ -11,8 +12,10 @@ const Autosave = ( // error state error: false, }, - action, - nextSharedState + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + nextSharedState: any ) => { switch (action.type) { case "annoMatrix: init complete": { diff --git a/client/src/reducers/cascade.js b/client/src/reducers/cascade.ts similarity index 74% rename from client/src/reducers/cascade.js rename to client/src/reducers/cascade.ts index 3c023f67..046c6520 100644 --- a/client/src/reducers/cascade.js +++ b/client/src/reducers/cascade.ts @@ -1,4 +1,5 @@ -export default function cascadeReducers(arg) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function cascadeReducers(arg: any) { /* Combine a set of cascading reducers into a single reducer. Cascading reducers are reducers which may rely on state computed by another reducer. @@ -23,7 +24,8 @@ export default function cascadeReducers(arg) { */ const reducers = arg instanceof Map ? arg : new Map(arg); const reducerKeys = [...reducers.keys()]; - return (prevState, action) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (prevState: any, action: any) => { const nextState = {}; let stateChange = false; for (let i = 0, l = reducerKeys.length; i < l; i += 1) { @@ -36,6 +38,7 @@ export default function cascadeReducers(arg) { nextState, prevState ); + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message nextState[key] = nextStateForKey; stateChange = stateChange || nextStateForKey !== prevStateForKey; } diff --git a/client/src/reducers/categoricalSelection.js b/client/src/reducers/categoricalSelection.ts similarity index 72% rename from client/src/reducers/categoricalSelection.js rename to client/src/reducers/categoricalSelection.ts index d1080699..791a126a 100644 --- a/client/src/reducers/categoricalSelection.js +++ b/client/src/reducers/categoricalSelection.ts @@ -11,7 +11,15 @@ Label state default (if missing) is up to the component, but typically true. ... } */ -const CategoricalSelection = (state, action, nextSharedState) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +const CategoricalSelection = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + state: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + nextSharedState: any +) => { switch (action.type) { case "initial data load complete": case "subset to selection": @@ -19,6 +27,7 @@ const CategoricalSelection = (state, action, nextSharedState) => { case "set clip quantiles": { const { annoMatrix } = nextSharedState; const newState = CH.createCategoricalSelection( + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. CH.selectableCategoryNames(annoMatrix.schema) ); return newState; diff --git a/client/src/reducers/centroidLabels.js b/client/src/reducers/centroidLabels.ts similarity index 53% rename from client/src/reducers/centroidLabels.js rename to client/src/reducers/centroidLabels.ts index 6481ec1d..af2703b9 100644 --- a/client/src/reducers/centroidLabels.js +++ b/client/src/reducers/centroidLabels.ts @@ -2,7 +2,14 @@ const initialState = { showLabels: false, }; -const centroidLabels = (state = initialState, action, sharedNextState) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +const centroidLabels = ( + state = initialState, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + sharedNextState: any +) => { const { colors: { colorAccessor }, } = sharedNextState; diff --git a/client/src/reducers/colors.js b/client/src/reducers/colors.ts similarity index 89% rename from client/src/reducers/colors.js rename to client/src/reducers/colors.ts index 0235117f..e9111283 100644 --- a/client/src/reducers/colors.js +++ b/client/src/reducers/colors.ts @@ -2,13 +2,15 @@ Color By UI state */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const ColorsReducer = ( state = { /* TODO(colinmegill) #632 remove hardcode for dev */ colorMode: null /* by continuous, by expression */, colorAccessor: null /* tissue, Apod */, }, - action + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any ) => { switch (action.type) { case "universe: user color load success": { diff --git a/client/src/reducers/config.js b/client/src/reducers/config.ts similarity index 65% rename from client/src/reducers/config.js rename to client/src/reducers/config.ts index 22858c8f..a5a57e26 100644 --- a/client/src/reducers/config.js +++ b/client/src/reducers/config.ts @@ -1,10 +1,12 @@ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const Config = ( state = { displayNames: null, features: null, parameters: null, }, - action + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any ) => { switch (action.type) { case "initial data load start": diff --git a/client/src/reducers/continuousSelection.js b/client/src/reducers/continuousSelection.ts similarity index 70% rename from client/src/reducers/continuousSelection.js rename to client/src/reducers/continuousSelection.ts index 2060d3bf..d80cffe6 100644 --- a/client/src/reducers/continuousSelection.js +++ b/client/src/reducers/continuousSelection.ts @@ -1,6 +1,7 @@ import { makeContinuousDimensionName } from "../util/nameCreators"; -const ContinuousSelection = (state = {}, action) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const ContinuousSelection = (state = {}, action: any) => { switch (action.type) { case "reset subset": case "subset to selection": @@ -24,6 +25,7 @@ const ContinuousSelection = (state = {}, action) => { action.continuousNamespace, action.selection ); + // @ts-expect-error ts-migrate(2537) FIXME: Type '{}' has no matching index signature for type... Remove this comment to see the full error message const { [name]: deletedField, ...newState } = state; return newState; } diff --git a/client/src/reducers/controls.js b/client/src/reducers/controls.ts similarity index 92% rename from client/src/reducers/controls.js rename to client/src/reducers/controls.ts index e9232030..f94f5d56 100644 --- a/client/src/reducers/controls.js +++ b/client/src/reducers/controls.ts @@ -1,6 +1,7 @@ import uniq from "lodash.uniq"; import filter from "lodash.filter"; +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const Controls = ( state = { // data loading flag @@ -20,7 +21,8 @@ const Controls = ( datasetDrawer: false, }, - action + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any ) => { /* For now, log anything looking like an error to the console. diff --git a/client/src/reducers/differential.js b/client/src/reducers/differential.ts similarity index 77% rename from client/src/reducers/differential.js rename to client/src/reducers/differential.ts index 6401cce7..6cab67ba 100644 --- a/client/src/reducers/differential.js +++ b/client/src/reducers/differential.ts @@ -1,3 +1,4 @@ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const Differential = ( state = { loading: null, @@ -5,7 +6,8 @@ const Differential = ( celllist1: null, celllist2: null, }, - action + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any ) => { switch (action.type) { case "request differential expression started": diff --git a/client/src/reducers/genesets.js b/client/src/reducers/genesets.ts similarity index 92% rename from client/src/reducers/genesets.js rename to client/src/reducers/genesets.ts index 94356ce9..d91f5c8c 100644 --- a/client/src/reducers/genesets.js +++ b/client/src/reducers/genesets.ts @@ -24,13 +24,15 @@ */ import { diffexpPopNamePrefix1, diffexpPopNamePrefix2 } from "../globals"; +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const GeneSets = ( state = { initialized: false, lastTid: undefined, genesets: new Map(), }, - action + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any ) => { switch (action.type) { /** @@ -353,6 +355,7 @@ const GeneSets = ( const { tid } = action; if (!Number.isInteger(tid) || tid < 0) throw new Error("TID must be a positive integer number"); + // @ts-expect-error ts-migrate(2532) FIXME: Object is possibly 'undefined'. if (state.lastTid !== undefined && tid < state.lastTid) throw new Error("TID may not be decremented."); return { @@ -374,7 +377,8 @@ const GeneSets = ( const diffExpGeneSets = []; for (const polarity of Object.keys(genesetNames)) { const genes = new Map( - data[polarity].map((diffExpGene) => [ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + data[polarity].map((diffExpGene: any) => [ diffExpGene[0], { geneSymbol: diffExpGene[0], @@ -382,8 +386,10 @@ const GeneSets = ( ]) ); diffExpGeneSets.push([ + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message genesetNames[polarity], { + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message genesetName: genesetNames[polarity], genesetDescription: "", genes, @@ -391,6 +397,7 @@ const GeneSets = ( ]); } + // @ts-expect-error ts-migrate(2769) FIXME: No overload matches this call. const genesets = new Map([...diffExpGeneSets, ...state.genesets]); // clone return { diff --git a/client/src/reducers/genesetsUI.js b/client/src/reducers/genesetsUI.ts similarity index 87% rename from client/src/reducers/genesetsUI.js rename to client/src/reducers/genesetsUI.ts index a49aa9b9..6a11a7c1 100644 --- a/client/src/reducers/genesetsUI.js +++ b/client/src/reducers/genesetsUI.ts @@ -1,13 +1,15 @@ /* Reducers for geneset UI-state. */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const GeneSetsUI = ( state = { createGenesetModeActive: false, isEditingGenesetName: false, isAddingGenesToGeneset: false, }, - action + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any ) => { switch (action.type) { /** diff --git a/client/src/reducers/graphSelection.js b/client/src/reducers/graphSelection.ts similarity index 79% rename from client/src/reducers/graphSelection.js rename to client/src/reducers/graphSelection.ts index 15589462..8145aae4 100644 --- a/client/src/reducers/graphSelection.js +++ b/client/src/reducers/graphSelection.ts @@ -1,9 +1,11 @@ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const GraphSelection = ( state = { tool: "lasso", // what selection tool mode (lasso, brush, ...) selection: { mode: "all" }, // current selection, which is tool specific }, - action + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any ) => { switch (action.type) { case "set clip quantiles": diff --git a/client/src/reducers/index.js b/client/src/reducers/index.ts similarity index 100% rename from client/src/reducers/index.js rename to client/src/reducers/index.ts diff --git a/client/src/reducers/layoutChoice.js b/client/src/reducers/layoutChoice.ts similarity index 60% rename from client/src/reducers/layoutChoice.js rename to client/src/reducers/layoutChoice.ts index a8820885..4d324c3a 100644 --- a/client/src/reducers/layoutChoice.js +++ b/client/src/reducers/layoutChoice.ts @@ -7,20 +7,24 @@ about commonly used names. Preferentially, pick in the following order: 3. "pca" 4. give up, use the first available */ -function bestDefaultLayout(layouts) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function bestDefaultLayout(layouts: any) { const preferredNames = ["umap", "tsne", "pca"]; const idx = preferredNames.findIndex((name) => layouts.indexOf(name) !== -1); if (idx !== -1) return preferredNames[idx]; return layouts[0]; } -function setToDefaultLayout(schema) { - const available = schema.layout.obs.map((v) => v.name).sort(); +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function setToDefaultLayout(schema: any) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const available = schema.layout.obs.map((v: any) => v.name).sort(); const current = bestDefaultLayout(available); const currentDimNames = schema.layout.obsByName[current].dims; return { available, current, currentDimNames }; } +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. const LayoutChoice = ( state = { available: [], // all available choices @@ -28,8 +32,10 @@ const LayoutChoice = ( current: undefined, // name of the current layout, eg, 'umap' currentDimNames: [], // dimension name }, - action, - nextSharedState + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + action: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + nextSharedState: any ) => { switch (action.type) { case "initial data load complete": { diff --git a/client/src/reducers/obsCrossfilter.js b/client/src/reducers/obsCrossfilter.js deleted file mode 100644 index 5fc2199a..00000000 --- a/client/src/reducers/obsCrossfilter.js +++ /dev/null @@ -1,12 +0,0 @@ -/* -Reducer for the obsCrossfilter -*/ - -const ObsCrossfilter = (state = null, action) => { - if (action.obsCrossfilter) { - return action.obsCrossfilter; - } - return state; -}; - -export default ObsCrossfilter; diff --git a/client/src/reducers/obsCrossfilter.ts b/client/src/reducers/obsCrossfilter.ts new file mode 100644 index 00000000..7c38652d --- /dev/null +++ b/client/src/reducers/obsCrossfilter.ts @@ -0,0 +1,13 @@ +/* +Reducer for the obsCrossfilter +*/ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const ObsCrossfilter = (state = null, action: any) => { + if (action.obsCrossfilter) { + return action.obsCrossfilter; + } + return state; +}; + +export default ObsCrossfilter; diff --git a/client/src/reducers/pointDilation.js b/client/src/reducers/pointDilation.ts similarity index 71% rename from client/src/reducers/pointDilation.js rename to client/src/reducers/pointDilation.ts index f8155545..8c0ed83f 100644 --- a/client/src/reducers/pointDilation.js +++ b/client/src/reducers/pointDilation.ts @@ -3,7 +3,8 @@ const initialState = { categoryField: "", }; -const pointDialation = (state = initialState, action) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const pointDialation = (state = initialState, action: any) => { const { metadataField, label: categoryField } = action; switch (action.type) { diff --git a/client/src/reducers/undoable.js b/client/src/reducers/undoable.ts similarity index 79% rename from client/src/reducers/undoable.js rename to client/src/reducers/undoable.ts index d18d0f4b..f9269989 100644 --- a/client/src/reducers/undoable.js +++ b/client/src/reducers/undoable.ts @@ -61,13 +61,17 @@ const filterActionKey = `${historyKeyPrefix}filterAction`; const pendingKey = `${historyKeyPrefix}pending`; const defaultHistoryLimit = -100; -const Undoable = (reducer, undoableKeys, options = {}) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const Undoable = (reducer: any, undoableKeys: any, options = {}) => { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'debug' does not exist on type '{}'. const { debug } = options; + // @ts-expect-error ts-migrate(2339) FIXME: Property 'historyLimit' does not exist on type '{}... Remove this comment to see the full error message let { historyLimit } = options; if (!historyLimit) historyLimit = defaultHistoryLimit; if (historyLimit > 0) historyLimit = -historyLimit; const actionFilter = - options.actionFilter || (() => ({ [filterActionKey]: "save" })); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (options as any).actionFilter || (() => ({ [filterActionKey]: "save" })); if (!Array.isArray(undoableKeys) || undoableKeys.length === 0) throw new Error("undoable keys array must be specified"); @@ -76,7 +80,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { /* Undo the current to previous history */ - function undo(currentState) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + function undo(currentState: any) { const past = currentState[pastKey]; const future = currentState[futureKey]; if (past.length === 0) return currentState; @@ -99,7 +104,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { /* Replay future, previously undone. */ - function redo(currentState) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + function redo(currentState: any) { const past = currentState[pastKey] || []; const future = currentState[futureKey] || []; if (future.length === 0) return currentState; @@ -122,7 +128,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { /* Clear the history state. No side-effects on current state. */ - function clear(currentState) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + function clear(currentState: any) { return { ...currentState, [pastKey]: [], @@ -135,7 +142,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { /* Reduce current action, with no history side-effects */ - function skip(currentState, action, filterState) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + function skip(currentState: any, action: any, filterState: any) { const past = currentState[pastKey] || []; const future = currentState[futureKey] || []; const pending = currentState[pendingKey]; @@ -152,7 +160,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { /* Save current state in the history, then reduce action. */ - function save(currentState, action, filterState) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + function save(currentState: any, action: any, filterState: any) { const past = currentState[pastKey] || []; const currentUndoableState = Object.entries(currentState).filter((kv) => undoableKeysSet.has(kv[0]) @@ -172,7 +181,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { /* Save current state as pending history change. No other side effects. */ - function stashPending(currentState) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + function stashPending(currentState: any) { const currentUndoableState = Object.entries(currentState).filter((kv) => undoableKeysSet.has(kv[0]) ); @@ -185,7 +195,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { /* Cancel pending history state change. No other side effects. */ - function cancelPending(currentState) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + function cancelPending(currentState: any) { return { ...currentState, [pendingKey]: null, @@ -195,7 +206,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { /* Push pending state onto the history stack */ - function applyPending(currentState) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + function applyPending(currentState: any) { const past = currentState[pastKey] || []; const pendingState = currentState[pendingKey]; const newPast = push(past, pendingState, historyLimit); @@ -215,7 +227,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { [filterStateKey]: {}, [pendingKey]: null, }, - action + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + action: any ) => { if (debug > 1) console.log("---- ACTION", action.type); const aType = action.type; @@ -275,7 +288,8 @@ const Undoable = (reducer, undoableKeys, options = {}) => { }; }; -function push(arr, val, limit = undefined) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function push(arr: any, val: any, limit = undefined) { /* functional array push, with a max length limit to the new array. Like Array.push, except it returns new array and discards as needed diff --git a/client/src/reducers/undoableConfig.js b/client/src/reducers/undoableConfig.ts similarity index 84% rename from client/src/reducers/undoableConfig.js rename to client/src/reducers/undoableConfig.ts index 2d8fc60b..b97b620e 100644 --- a/client/src/reducers/undoableConfig.js +++ b/client/src/reducers/undoableConfig.ts @@ -129,7 +129,8 @@ See graph definition for the transitions that use each. Signature: (fsm, transition, reducerState, reducerAction) => undoableAction */ -const stashPending = (fsm) => ({ +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const stashPending = (fsm: any) => ({ [actionKey]: "stashPending", [stateKey]: { fsm }, }); @@ -141,11 +142,13 @@ const applyPending = () => ({ [actionKey]: "applyPending", [stateKey]: { fsm: null }, }); +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'fsm' implicitly has an 'any' type. const skip = (fsm, transition) => ({ [actionKey]: "skip", [stateKey]: { fsm: transition.to !== "done" ? fsm : null }, }); const clear = () => ({ [actionKey]: "clear", [stateKey]: { fsm: null } }); +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'fsm' implicitly has an 'any' type. const save = (fsm, transition) => ({ [actionKey]: "save", [stateKey]: { fsm: transition.to !== "done" ? fsm : null }, @@ -157,7 +160,8 @@ StateMachine when it doesn't know what to do. Signature: (fsm, event, from) => undoableAction */ -const onFsmError = (fsm, event, from) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const onFsmError = (fsm: any, event: any, from: any) => { console.error(`FSM error [event: "${event}", state: "${from}"]`, fsm); // In production, try to recover gracefully if we have unexpected state return clear(); @@ -185,7 +189,15 @@ Basic approach: * only implement complex state machines where absolutely required (eg, multi-event selection and the like) */ -const actionFilter = (debug) => (state, action, prevFilterState) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const actionFilter = (debug: any) => ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + state: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + action: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + prevFilterState: any +) => { const actionType = action.type; const filterState = { ...prevFilterState, @@ -195,6 +207,7 @@ const actionFilter = (debug) => (state, action, prevFilterState) => { return { [actionKey]: "skip", [stateKey]: filterState }; } if ( + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'any' is not assignable to parame... Remove this comment to see the full error message debounceOnActions.has(actionType) && shallowObjectEq(action, prevFilterState.prevAction) ) { @@ -230,7 +243,8 @@ return true if objA and objB are ===, OR if: - have same own properties - all values are strict equal (===) */ -function shallowObjectEq(objA, objB) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function shallowObjectEq(objA: any, objB: any) { if (objA === objB) return true; if (!objA || !objB) return false; if (!shallowArrayEq(Object.keys(objA), Object.keys(objB))) return false; @@ -242,7 +256,8 @@ function shallowObjectEq(objA, objB) { return true if arrA and arrB contain the same strict-equal values, in the same order. */ -function shallowArrayEq(arrA, arrB) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function shallowArrayEq(arrA: any, arrB: any) { if (arrA.length !== arrB.length) return false; for (let i = 0, l = arrA.length; i < l; i += 1) { if (arrA[i] !== arrB[i]) return false; diff --git a/client/src/reducers/undoableFsm.js b/client/src/reducers/undoableFsm.js deleted file mode 100644 index 674f3204..00000000 --- a/client/src/reducers/undoableFsm.js +++ /dev/null @@ -1,198 +0,0 @@ -/* -State transition graph for complex action/history interactions. - -Assumed configuration from undoableConfig: - * By convention, "init" is used as the start state for all, and "done" - as the final state. - * Unexpected states will result in an error, plus a clear and cancelPending - side-effect. - -TODO: is is possible there is a more concise format for this, as it is -a fairly repetitive pattern. - -These events are largely one of two types: -a) async operations or multi-event options that should only be committed -upon some success criteria, otherwise cancelled. - -b) compound actions that should be collapsed into a single history change. - -*/ - -const createFsmTransitions = ( - stashPending, - cancelPending, - applyPending, - skip, - clear, - save -) => { - return [ - /* graph selection brushing */ - { - event: "graph brush start", - from: "init", - to: "graph brush in progress", - action: stashPending, - }, - { - event: "graph brush cancel", - from: "graph brush in progress", - to: "done", - action: applyPending, - }, - { - event: "graph brush deselect", - from: "graph brush in progress", - to: "done", - /* if current selection is all, cancelPending. Else, applyPending */ - action: (fsm, transition, data) => - data.state.graphSelection.selection.mode === "all" - ? cancelPending() - : applyPending(), - }, - { - event: "graph brush end", - from: "graph brush in progress", - to: "done", - action: applyPending, - }, - - /* graph selection lasso */ - { - event: "graph lasso start", - from: "init", - to: "graph lasso in progress", - action: stashPending, - }, - { - event: "graph lasso cancel", - from: "graph lasso in progress", - to: "done", - action: applyPending, - }, - { - event: "graph lasso deselect", - from: "graph lasso in progress", - to: "done", - /* if current selection is all, cancelPending. Else, applyPending */ - action: (fsm, transition, data) => - data.state.graphSelection.selection.mode === "all" - ? cancelPending() - : applyPending(), - }, - { - event: "graph lasso end", - from: "graph lasso in progress", - to: "done", - action: applyPending, - }, - - /* Continuous metadata histogram brush selection */ - { - event: "continuous metadata histogram start", - from: "init", - to: "continuous histo select in progress", - action: stashPending, - }, - { - event: "continuous metadata histogram cancel", - from: "continuous histo select in progress", - to: "done", - action: cancelPending, - }, - { - event: "continuous metadata histogram cancel", - from: "init", - to: "done", - action: save, - }, - { - event: "continuous metadata histogram end", - from: "continuous histo select in progress", - to: "done", - action: applyPending, - }, - - /* Single gene request by user */ - { - event: "single user defined gene start", - from: "init", - to: "single user gene request in progress", - action: stashPending, - }, - { - event: "request user defined gene error", - from: "single user gene request in progress", - to: "single user gene error in progress", - action: skip, - }, - { - event: "single user defined gene error", - from: "single user gene error in progress", - to: "done", - action: cancelPending, - }, - { - event: "single user defined gene complete", - from: "single user gene request in progress", - to: "done", - action: applyPending, - }, - - /* Bulk gene request by user */ - { - event: "bulk user defined gene start", - from: "init", - to: "bulk user gene request in progress", - action: stashPending, - }, - { - event: "request user defined gene error", - from: "bulk user gene request in progress", - to: "bulk user gene request error in progress", - action: skip, - }, - { - event: "bulk user defined gene error", - from: "bulk user gene request error in progress", - to: "done", - action: cancelPending, - }, - { - event: "bulk user defined gene complete", - from: "bulk user gene request in progress", - to: "done", - action: applyPending, - }, - - /* Compute Differential Expression button user action */ - { - event: "request differential expression started", - from: "init", - to: "diffexp in progress", - action: stashPending, - }, - { - event: "request user defined gene error", - from: "diffexp in progress", - to: "done", - action: cancelPending, - }, - { - event: "request differential expression success", - from: "diffexp in progress", - to: "done", - action: applyPending, - }, - - /* clear scatter plot button (eg, on scatterplot view) */ - { - event: "clear scatterplot", - from: "init", - to: "done", - action: save, - }, - ]; -}; - -export default createFsmTransitions; diff --git a/client/src/reducers/undoableFsm.ts b/client/src/reducers/undoableFsm.ts new file mode 100644 index 00000000..642145fa --- /dev/null +++ b/client/src/reducers/undoableFsm.ts @@ -0,0 +1,208 @@ +/* +State transition graph for complex action/history interactions. + +Assumed configuration from undoableConfig: + * By convention, "init" is used as the start state for all, and "done" + as the final state. + * Unexpected states will result in an error, plus a clear and cancelPending + side-effect. + +TODO: is is possible there is a more concise format for this, as it is +a fairly repetitive pattern. + +These events are largely one of two types: +a) async operations or multi-event options that should only be committed +upon some success criteria, otherwise cancelled. + +b) compound actions that should be collapsed into a single history change. + +*/ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +const createFsmTransitions = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + stashPending: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + cancelPending: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + applyPending: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + skip: any, + // @ts-expect-error ts-migrate(6133) FIXME: 'clear' is declared but its value is never read. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + clear: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + save: any +) => [ + /* graph selection brushing */ + { + event: "graph brush start", + from: "init", + to: "graph brush in progress", + action: stashPending, + }, + { + event: "graph brush cancel", + from: "graph brush in progress", + to: "done", + action: applyPending, + }, + { + event: "graph brush deselect", + from: "graph brush in progress", + to: "done", + /* if current selection is all, cancelPending. Else, applyPending */ + // @ts-expect-error ts-migrate(6133) FIXME: 'fsm' is declared but its value is never read. + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + action: (fsm: any, transition: any, data: any) => + data.state.graphSelection.selection.mode === "all" + ? cancelPending() + : applyPending(), + }, + { + event: "graph brush end", + from: "graph brush in progress", + to: "done", + action: applyPending, + }, + + /* graph selection lasso */ + { + event: "graph lasso start", + from: "init", + to: "graph lasso in progress", + action: stashPending, + }, + { + event: "graph lasso cancel", + from: "graph lasso in progress", + to: "done", + action: applyPending, + }, + { + event: "graph lasso deselect", + from: "graph lasso in progress", + to: "done", + /* if current selection is all, cancelPending. Else, applyPending */ + // @ts-expect-error ts-migrate(6133) FIXME: 'fsm' is declared but its value is never read. + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + action: (fsm: any, transition: any, data: any) => + data.state.graphSelection.selection.mode === "all" + ? cancelPending() + : applyPending(), + }, + { + event: "graph lasso end", + from: "graph lasso in progress", + to: "done", + action: applyPending, + }, + + /* Continuous metadata histogram brush selection */ + { + event: "continuous metadata histogram start", + from: "init", + to: "continuous histo select in progress", + action: stashPending, + }, + { + event: "continuous metadata histogram cancel", + from: "continuous histo select in progress", + to: "done", + action: cancelPending, + }, + { + event: "continuous metadata histogram cancel", + from: "init", + to: "done", + action: save, + }, + { + event: "continuous metadata histogram end", + from: "continuous histo select in progress", + to: "done", + action: applyPending, + }, + + /* Single gene request by user */ + { + event: "single user defined gene start", + from: "init", + to: "single user gene request in progress", + action: stashPending, + }, + { + event: "request user defined gene error", + from: "single user gene request in progress", + to: "single user gene error in progress", + action: skip, + }, + { + event: "single user defined gene error", + from: "single user gene error in progress", + to: "done", + action: cancelPending, + }, + { + event: "single user defined gene complete", + from: "single user gene request in progress", + to: "done", + action: applyPending, + }, + + /* Bulk gene request by user */ + { + event: "bulk user defined gene start", + from: "init", + to: "bulk user gene request in progress", + action: stashPending, + }, + { + event: "request user defined gene error", + from: "bulk user gene request in progress", + to: "bulk user gene request error in progress", + action: skip, + }, + { + event: "bulk user defined gene error", + from: "bulk user gene request error in progress", + to: "done", + action: cancelPending, + }, + { + event: "bulk user defined gene complete", + from: "bulk user gene request in progress", + to: "done", + action: applyPending, + }, + + /* Compute Differential Expression button user action */ + { + event: "request differential expression started", + from: "init", + to: "diffexp in progress", + action: stashPending, + }, + { + event: "request user defined gene error", + from: "diffexp in progress", + to: "done", + action: cancelPending, + }, + { + event: "request differential expression success", + from: "diffexp in progress", + to: "done", + action: applyPending, + }, + + /* clear scatter plot button (eg, on scatterplot view) */ + { + event: "clear scatterplot", + from: "init", + to: "done", + action: save, + }, +]; + +export default createFsmTransitions; diff --git a/client/src/reducers/userInfo.js b/client/src/reducers/userInfo.ts similarity index 68% rename from client/src/reducers/userInfo.js rename to client/src/reducers/userInfo.ts index 6939e949..59b04d4a 100644 --- a/client/src/reducers/userInfo.js +++ b/client/src/reducers/userInfo.ts @@ -1,4 +1,5 @@ -const UserInfo = (state = {}, action) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +const UserInfo = (state = {}, action: any) => { switch (action.type) { case "initial data load start": return { diff --git a/client/src/util/actionHelpers.js b/client/src/util/actionHelpers.ts similarity index 58% rename from client/src/util/actionHelpers.js rename to client/src/util/actionHelpers.ts index ccae04af..82b874e8 100644 --- a/client/src/util/actionHelpers.js +++ b/client/src/util/actionHelpers.ts @@ -6,8 +6,10 @@ import { postNetworkErrorToast } from "../components/framework/toasters"; dispatch an action error to the user. Currently we use async toasts. */ -let networkErrorToastKey = null; -export const dispatchNetworkErrorMessageToUser = (message) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +let networkErrorToastKey: any = null; +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const dispatchNetworkErrorMessageToUser = (message: any) => { if (!networkErrorToastKey) { networkErrorToastKey = postNetworkErrorToast(message); } else { @@ -18,9 +20,12 @@ export const dispatchNetworkErrorMessageToUser = (message) => { /* Catch unexpected errors and make sure we don't lose them! */ -export function catchErrorsWrap(fn, dispatchToUser = false) { - return (dispatch, getState) => { - fn(dispatch, getState).catch((error) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function catchErrorsWrap(fn: any, dispatchToUser = false) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + return (dispatch: any, getState: any) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + fn(dispatch, getState).catch((error: any) => { console.error(error); if (dispatchToUser) { dispatchNetworkErrorMessageToUser(error.message); @@ -34,7 +39,8 @@ export function catchErrorsWrap(fn, dispatchToUser = false) { * Wrapper to perform async fetch with some modest error handling * and decoding. Arguments are identical to standard fetch. */ -export const doFetch = async (url, init = {}) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const doFetch = async (url: any, init = {}) => { try { // add defaults to the fetch init param. init = { @@ -42,10 +48,12 @@ export const doFetch = async (url, init = {}) => { credentials: "include", ...init, }; - const acceptType = init.headers?.get("Accept"); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const acceptType = (init as any).headers?.get("Accept"); const res = await fetch(url, init); if ( res.ok && + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. (!acceptType || res.headers.get("Content-Type").includes(acceptType)) ) { return res; @@ -66,7 +74,8 @@ export const doFetch = async (url, init = {}) => { /* Wrapper to perform an async fetch and JSON decode response. */ -export const doJsonRequest = async (url, init = {}) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const doJsonRequest = async (url: any, init = {}) => { const res = await doFetch(url, { ...init, headers: new Headers({ Accept: "application/json" }), @@ -77,7 +86,8 @@ export const doJsonRequest = async (url, init = {}) => { /* Wrapper to perform an async fetch for binary data. */ -export const doBinaryRequest = async (url, init = {}) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const doBinaryRequest = async (url: any, init = {}) => { const res = await doFetch(url, { ...init, headers: new Headers({ Accept: "application/octet-stream" }), @@ -100,8 +110,10 @@ Parameters: So [1, 2, 3, 4, 10, 11, 14] -> [ [1, 4], [10, 11], 14] */ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export const rangeEncodeIndices = ( - indices, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + indices: any, minRangeLength = 3, sorted = false ) => { diff --git a/client/src/util/camera.js b/client/src/util/camera.ts similarity index 64% rename from client/src/util/camera.js rename to client/src/util/camera.ts index 659ea121..6df7d644 100644 --- a/client/src/util/camera.js +++ b/client/src/util/camera.ts @@ -11,12 +11,26 @@ const panBound = 0.8; const scratch0 = new Float32Array(16); const scratch1 = new Float32Array(16); -function clamp(val, rng) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function clamp(val: any, rng: any) { return Math.max(Math.min(val, rng[1]), rng[0]); } class Camera { - constructor(canvas) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + canvas: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + prevEvent: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + viewMatrix: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + viewMatrixInv: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + constructor(canvas: any) { this.prevEvent = { clientX: 0, clientY: 0, @@ -39,7 +53,8 @@ class Camera { return this.viewMatrix[0]; } - pan(dx, dy) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + pan(dx: any, dy: any) { const m = this.viewMatrix; const dyRange = [ -panBound - (m[7] + 1) / m[4], @@ -59,7 +74,8 @@ class Camera { mat3.invert(this.viewMatrixInv, m); } - zoomAt(d, x = 0, y = 0) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + zoomAt(d: any, x = 0, y = 0) { /* Camera zoom at [x,y] */ @@ -82,13 +98,15 @@ class Camera { Event handling */ - flush(e) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + flush(e: any) { this.prevEvent.type = e.type; this.prevEvent.clientX = e.clientX; this.prevEvent.clientY = e.clientY; } - localPosition(target, canvasX, canvasY, projectionInvTF) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + localPosition(target: any, canvasX: any, canvasY: any, projectionInvTF: any) { /* Convert mouse position to local */ @@ -108,7 +126,8 @@ class Camera { return pos; } - mousePan(e, projectionTF) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + mousePan(e: any, projectionTF: any) { const projectionInvTF = mat3.invert(scratch0, projectionTF); const pos = this.localPosition( this.canvas, @@ -128,7 +147,8 @@ class Camera { return true; } - wheelZoom(e, projectionTF) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + wheelZoom(e: any, projectionTF: any) { const { height } = this.canvas; const { deltaY, deltaMode, clientX, clientY } = e; const scale = scaleSpeed * (deltaMode === 1 ? 12 : 1) * (deltaY || 0); @@ -144,7 +164,8 @@ class Camera { return true; } - handleEvent(e, projectionTF) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + handleEvent(e: any, projectionTF: any) { /* process the event, and return true if camera view changed */ @@ -173,7 +194,8 @@ class Camera { } } -function attachCamera(canvas) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +function attachCamera(canvas: any) { return new Camera(canvas); } diff --git a/client/src/util/catLabelSort.js b/client/src/util/catLabelSort.ts similarity index 53% rename from client/src/util/catLabelSort.js rename to client/src/util/catLabelSort.ts index 030749b7..e1a25de6 100644 --- a/client/src/util/catLabelSort.js +++ b/client/src/util/catLabelSort.ts @@ -11,20 +11,24 @@ TL;DR: sort order is: import isNumber from "is-number"; import * as globals from "../globals"; -function caseInsensitiveCompare(a, b) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function caseInsensitiveCompare(a: any, b: any) { const textA = String(a).toUpperCase(); const textB = String(b).toUpperCase(); return textA < textB ? -1 : textA > textB ? 1 : 0; } -const catLabelSort = (isUserAnno, values) => { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const catLabelSort = (isUserAnno: boolean, values: any[]): any[] => { /* this sort could be memoized for perf */ - const strings = []; - const ints = []; - const unassignedOrNaN = []; + const strings: string[] = []; + const ints: number[] = []; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const unassignedOrNaN: any = []; - values.forEach((v) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + values.forEach((v: any) => { if (isUserAnno && v === globals.unassignedCategoryLabel) { unassignedOrNaN.push(v); } else if (String(v).toLowerCase() === "nan") { @@ -40,7 +44,8 @@ const catLabelSort = (isUserAnno, values) => { ints.sort((a, b) => +a - +b); unassignedOrNaN.sort(caseInsensitiveCompare); - return ints.concat(strings, unassignedOrNaN); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (ints).concat(strings, unassignedOrNaN); }; export default catLabelSort; diff --git a/client/src/util/centroid.js b/client/src/util/centroid.ts similarity index 66% rename from client/src/util/centroid.js rename to client/src/util/centroid.ts index ea515eb4..8af12d29 100644 --- a/client/src/util/centroid.js +++ b/client/src/util/centroid.ts @@ -23,11 +23,16 @@ label -> { } */ const getCoordinatesByLabel = ( - schema, - categoryName, - categoryDf, - layoutChoice, - layoutDf + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoryName: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoryDf: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutChoice: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutDf: any ) => { const coordsByCategoryLabel = new Map(); // If the coloredBy is not a categorical col @@ -72,6 +77,7 @@ const getCoordinatesByLabel = ( let coords = coordsByCategoryLabel.get(label); if (coords === undefined) { // Get the number of cells which are in the label + // @ts-expect-error ts-migrate(2538) FIXME: Type 'unknown' cannot be used as an index type. const numInLabel = categoryValueCounts[labelIndex]; coords = { hasFinite: false, @@ -104,11 +110,16 @@ const getCoordinatesByLabel = ( */ const calcMedianCentroid = ( - schema, - categoryName, - categoryDf, - layoutChoice, - layoutDf + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoryName: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoryDf: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutChoice: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutDf: any ) => { // generate a map describing the coordinates for each label within the given category const dataMap = getCoordinatesByLabel( @@ -143,11 +154,17 @@ const calcMedianCentroid = ( // A simple function to hash the parameters const hashMedianCentroid = ( - schema, - categoryName, - categoryDf, - layoutChoice, - layoutDf + // @ts-expect-error ts-migrate(6133) FIXME: 'schema' is declared but its value is never read. + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoryName: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoryDf: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutChoice: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + layoutDf: any ) => { const category = categoryDf.col(categoryName); const layoutDimNames = layoutChoice.currentDimNames; diff --git a/client/src/util/clamp.js b/client/src/util/clamp.ts similarity index 64% rename from client/src/util/clamp.js rename to client/src/util/clamp.ts index b1ae5f1d..715ac18f 100644 --- a/client/src/util/clamp.js +++ b/client/src/util/clamp.ts @@ -8,6 +8,7 @@ * @returns a number */ -export default function clamp(val, rng) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function clamp(val: any, rng: any) { return Math.max(Math.min(val, rng[1]), rng[0]); } diff --git a/client/src/util/clip.js b/client/src/util/clip.ts similarity index 73% rename from client/src/util/clip.js rename to client/src/util/clip.ts index 16514bcd..735c8ab9 100644 --- a/client/src/util/clip.js +++ b/client/src/util/clip.ts @@ -10,7 +10,8 @@ If `setTo` is not undefined, values outside the [lower, upper] range will be set `setTo`. */ -export default function clip(arr, lower, upper, setTo) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function clip(arr: any, lower: any, upper: any, setTo: any) { const lowerSet = setTo === undefined ? lower : setTo; const upperSet = setTo === undefined ? upper : setTo; for (let i = 0, l = arr.length; i < l; i += 1) { diff --git a/client/src/util/dataframe/cache.js b/client/src/util/dataframe/cache.js deleted file mode 100644 index bfffeef3..00000000 --- a/client/src/util/dataframe/cache.js +++ /dev/null @@ -1,26 +0,0 @@ -/* - -DataframeCache - to improve memoization, we often want to have the same -Dataframe object returned when the contents of the dataframe are identical. -The core dataframe class does not support this, but it does attempt to maintain -strict eq and immutability of columns indices. - -This is a function that will maintain a least-recently created cache of Dataframe -objects. -*/ - -import { memoize } from "./util"; - -function hashDataframe(df) { - if (df.isEmpty()) return ""; - return df.__columnsAccessor.map((c) => c.__id).join(","); -} - -function noop(df) { - return df; -} - -const dataframeMemo = (capacity = 100) => - memoize(noop, hashDataframe, capacity); - -export default dataframeMemo; diff --git a/client/src/util/dataframe/cache.ts b/client/src/util/dataframe/cache.ts new file mode 100644 index 00000000..3737bb74 --- /dev/null +++ b/client/src/util/dataframe/cache.ts @@ -0,0 +1,30 @@ +/* + +DataframeCache - to improve memoization, we often want to have the same +Dataframe object returned when the contents of the dataframe are identical. +The core dataframe class does not support this, but it does attempt to maintain +strict eq and immutability of columns indices. + +This is a function that will maintain a least-recently created cache of Dataframe +objects. +*/ + +import { memoize } from "./util"; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function hashDataframe(df: any) { + if (df.isEmpty()) return ""; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return df.__columnsAccessor.map((c: any) => c.__id).join(","); +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function noop(df: any) { + return df; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +const dataframeMemo = (capacity = 100) => + memoize(noop, hashDataframe, capacity); + +export default dataframeMemo; diff --git a/client/src/util/dataframe/dataframe.js b/client/src/util/dataframe/dataframe.ts similarity index 67% rename from client/src/util/dataframe/dataframe.js rename to client/src/util/dataframe/dataframe.ts index 98693bd0..2fb2e873 100644 --- a/client/src/util/dataframe/dataframe.js +++ b/client/src/util/dataframe/dataframe.ts @@ -73,13 +73,35 @@ Dataframe **/ class Dataframe { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + __columns: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + __columnsAccessor: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + __id: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colIndex: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dims: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + length: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + rowIndex: any; /** Constructors & factories **/ constructor( - dims, - columnarData, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dims: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + columnarData: any, rowIndex = null, colIndex = null, __columnsAccessor = [] // private interface @@ -104,9 +126,11 @@ class Dataframe { throw new RangeError("Dataframe dimensions must be positive"); } if (!rowIndex) { + // @ts-expect-error ts-migrate(2322) FIXME: Type 'IdentityInt32Index' is not assignable to typ... Remove this comment to see the full error message rowIndex = new IdentityInt32Index(nRows); } if (!colIndex) { + // @ts-expect-error ts-migrate(2322) FIXME: Type 'IdentityInt32Index' is not assignable to typ... Remove this comment to see the full error message colIndex = new IdentityInt32Index(nCols); } Dataframe.__errorChecks(dims, columnarData, rowIndex, colIndex); @@ -122,7 +146,17 @@ class Dataframe { Object.freeze(this); } - static __errorChecks(dims, columnarData, rowIndex, colIndex) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + static __errorChecks( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dims: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + columnarData: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + rowIndex: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colIndex: any + ) { const [nRows, nCols] = dims; /* check for expected types */ @@ -160,7 +194,8 @@ class Dataframe { } } - static __compileColumn(column, getRowByOffset, getRowByLabel) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static __compileColumn(column: any, getRowByOffset: any, getRowByLabel: any) { /* Each column accessor is a function which will lookup data by index (ie, is equivalent to dataframe.get(row, col), where 'col' @@ -195,12 +230,14 @@ class Dataframe { const __id = __getMemoId(); /* get value by row label */ - const get = function get(rlabel) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const get = function get(rlabel: any) { return column[getRowByOffset(rlabel)]; }; /* get value by row offset */ - const iget = function iget(roffset) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const iget = function iget(roffset: any) { return column[roffset]; }; @@ -210,12 +247,14 @@ class Dataframe { }; /* test for row label inclusion in column */ - const has = function has(rlabel) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const has = function has(rlabel: any) { const offset = getRowByOffset(rlabel); return offset >= 0 && offset < length; }; - const ihas = function ihas(offset) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const ihas = function ihas(offset: any) { return offset >= 0 && offset < length; }; @@ -226,7 +265,8 @@ class Dataframe { NOTE: not found return is DIFFERENT than the default Array.indexOf as -1 is a plausible Dataframe row/col label. */ - const indexOf = function indexOf(value) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const indexOf = function indexOf(value: any) { const offset = column.indexOf(value); if (offset === -1) { return undefined; @@ -250,11 +290,14 @@ class Dataframe { Create histogram bins for this column. Memoized. */ const _memoHistoCat = memoize(_histogramCategorical, hashCategorical); - const histogramCategorical = (by) => _memoHistoCat(get, by); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const histogramCategorical = (by: any) => _memoHistoCat(get, by); let histogram = null; if (isTypedArray(column)) { const mFn = memoize(histogramContinuous, hashContinuous); - histogram = (bins, domain, by) => mFn(get, bins, domain, by); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + histogram = (bins: any, domain: any, by: any) => + mFn(get, bins, domain, by); } else { histogram = histogramCategorical; } @@ -274,7 +317,8 @@ class Dataframe { return get; } - __compile(accessors) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + __compile(accessors: any) { /* Compile data accessors for each column. @@ -282,7 +326,8 @@ class Dataframe { */ const getRowByOffset = this.rowIndex.getOffset.bind(this.rowIndex); const getRowByLabel = this.rowIndex.getLabel.bind(this.rowIndex); - this.__columnsAccessor = this.__columns.map((column, idx) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.__columnsAccessor = this.__columns.map((column: any, idx: any) => { if (accessors[idx]) { return accessors[idx]; } @@ -291,10 +336,12 @@ class Dataframe { Object.freeze(this.__columnsAccessor); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. clone() { /* Clone this dataframe */ + // @ts-expect-error ts-migrate(2351) FIXME: This expression is not constructable. return new this.constructor( this.dims, [...this.__columns], @@ -304,7 +351,8 @@ class Dataframe { ); } - withCol(label, colData, withRowIndex = null) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + withCol(label: any, colData: any, withRowIndex = null) { /* Create a new DF, which is `this` plus the new column. Example: const newDf = df.withCol("foo", [1,2,3]); @@ -337,6 +385,7 @@ class Dataframe { columns.push(colData); const colIndex = this.colIndex.withLabel(label); const columnsAccessor = [...this.__columnsAccessor]; + // @ts-expect-error ts-migrate(2351) FIXME: This expression is not constructable. return new this.constructor( dims, columns, @@ -346,7 +395,8 @@ class Dataframe { ); } - withColsFrom(dataframe, labels) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + withColsFrom(dataframe: any, labels: any) { /* return a new dataframe containing all columns from both `this` and the provided dataframe argument. @@ -410,7 +460,10 @@ class Dataframe { // otherwise, bulid a new dataframe combining columns from both - const srcOffsets = srcLabels.map((l) => dataframe.colIndex.getOffset(l)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const srcOffsets = srcLabels.map((l: any) => + dataframe.colIndex.getOffset(l) + ); // check for label collisions if (dstLabels.some(this.hasCol, this)) { @@ -422,14 +475,17 @@ class Dataframe { const { rowIndex } = this; const columns = [ ...this.__columns, - ...srcOffsets.map((i) => dataframe.__columns[i]), + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + ...srcOffsets.map((i: any) => dataframe.__columns[i]), ]; const colIndex = this.colIndex.withLabels(dstLabels); const columnsAccessor = [ ...this.__columnsAccessor, - ...srcOffsets.map((i) => dataframe.__columnsAccessor[i]), + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + ...srcOffsets.map((i: any) => dataframe.__columnsAccessor[i]), ]; + // @ts-expect-error ts-migrate(2351) FIXME: This expression is not constructable. return new this.constructor( dims, columns, @@ -439,12 +495,15 @@ class Dataframe { ); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. withColsFromAll(dataframes = []) { dataframes = Array.isArray(dataframes) ? dataframes : [dataframes]; + // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1. return dataframes.reduce((acc, df) => acc.withColsFrom(df), this); } - dropCol(label) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dropCol(label: any) { /* Create a new dataframe, omitting one columns. @@ -470,6 +529,7 @@ class Dataframe { const colIndex = this.colIndex.dropLabel(label); const columnsAccessor = [...this.__columnsAccessor]; columnsAccessor.splice(coffset, 1); + // @ts-expect-error ts-migrate(2351) FIXME: This expression is not constructable. return new this.constructor( dims, columns, @@ -479,7 +539,8 @@ class Dataframe { ); } - renameCol(oldLabel, newLabel) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + renameCol(oldLabel: any, newLabel: any) { /* Accelerator for dropping a column and then adding it again with a new label */ @@ -494,6 +555,7 @@ class Dataframe { columnsAccessor.push(columnsAccessor[coffset]); columnsAccessor.splice(coffset, 1); + // @ts-expect-error ts-migrate(2351) FIXME: This expression is not constructable. return new this.constructor( this.dims, columns, @@ -503,7 +565,8 @@ class Dataframe { ); } - replaceColData(label, newColData) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + replaceColData(label: any, newColData: any) { /* Accelerator for dropping a column then adding it again with same label and different values. @@ -514,6 +577,7 @@ class Dataframe { const columnsAccessor = [...this.__columnsAccessor]; columnsAccessor[coffset] = null; + // @ts-expect-error ts-migrate(2351) FIXME: This expression is not constructable. return new this.constructor( this.dims, columns, @@ -523,16 +587,20 @@ class Dataframe { ); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. static empty(rowIndex = null, colIndex = null) { const dims = [ + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. rowIndex ? rowIndex.size() : 0, + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. colIndex ? colIndex.size() : 0, ]; if (dims[0] && dims[1]) throw new Error("not an empty dataframe"); return new Dataframe(dims, new Array(dims[1]), rowIndex, colIndex); } - static create(dims, columnarData) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static create(dims: any, columnarData: any) { /* Create a dataframe from raw columnar data. All column arrays must have the same length. Identity indexing will be used. @@ -543,7 +611,8 @@ class Dataframe { return new Dataframe(dims, columnarData, null, null); } - __subset(newRowIndex, newColIndex) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + __subset(newRowIndex: any, newColIndex: any) { const dims = [...this.dims]; /* subset columns */ @@ -563,7 +632,8 @@ class Dataframe { let { rowIndex } = this; if (newRowIndex) { const rowOffsets = this.rowIndex.getOffsets(newRowIndex.labels()); - __columns = __columns.map((col) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + __columns = __columns.map((col: any) => { const newCol = new col.constructor(rowOffsets.length); for (let i = 0, l = rowOffsets.length; i < l; i += 1) { newCol[i] = col[rowOffsets[i]]; @@ -585,7 +655,8 @@ class Dataframe { ); } - subset(rowLabels, colLabels = null, withRowIndex = null) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + subset(rowLabels: any, colLabels = null, withRowIndex = null) { /* Subset by row/col labels. @@ -607,7 +678,8 @@ class Dataframe { return this.__subset(rowIndex, colIndex); } - isubset(rowOffsets, colOffsets = null, withRowIndex = null) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isubset(rowOffsets: any, colOffsets = null, withRowIndex = null) { /* Subset by row/col offset. @@ -631,7 +703,8 @@ class Dataframe { return this.__subset(rowIndex, colIndex); } - isubsetMask(rowMask, colMask = null, withRowIndex = null) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isubsetMask(rowMask: any, colMask = null, withRowIndex = null) { /* Subset on row/column based upon a truthy/falsey array (a mask). @@ -643,13 +716,15 @@ class Dataframe { const [nRows, nCols] = this.dims; if ( (rowMask && rowMask.length !== nRows) || + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. (colMask && colMask.length !== nCols) ) { throw new RangeError("boolean arrays must match row/col dimensions"); } /* convert masks to lists - method wastes space, but is fast */ - const toList = (mask, maxSize) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const toList = (mask: any, maxSize: any) => { if (!mask) { return null; } @@ -665,6 +740,7 @@ class Dataframe { }; const rowOffsets = toList(rowMask, nRows); const colOffsets = toList(colMask, nCols); + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'Int32Array | null' is not assign... Remove this comment to see the full error message return this.isubset(rowOffsets, colOffsets, withRowIndex); } @@ -672,12 +748,14 @@ class Dataframe { Data access with row/col. **/ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. columns() { /* return all column accessors as an array, in offset order */ return [...this.__columnsAccessor]; } - col(columnLabel) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + col(columnLabel: any) { /* Return accessor bound to a column. Allows random row access based upon the row indexing. Returns undefined if the @@ -697,7 +775,8 @@ class Dataframe { return this.__columnsAccessor[coff]; } - icol(columnOffset) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + icol(columnOffset: any) { /* Return column accessor by offset. */ @@ -706,7 +785,8 @@ class Dataframe { : undefined; } - at(r, c) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + at(r: any, c: any) { /* Access a single value, for a row/col label pair. @@ -723,7 +803,8 @@ class Dataframe { return this.__columns[coff][roff]; } - iat(r, c) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + iat(r: any, c: any) { /* Access a single value, for a row/col offset (integer) position. @@ -736,7 +817,8 @@ class Dataframe { return this.__columns[c][r]; } - has(r, c) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + has(r: any, c: any) { /* Test if row/col labels exist in the dataframe - returns true/false */ @@ -746,7 +828,8 @@ class Dataframe { return coff >= 0 && coff < nCols && roff >= 0 && roff < nRows; } - ihas(r, c) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + ihas(r: any, c: any) { /* Test if row/col offset (integer) position exists in the dataframe - returns true/false @@ -762,13 +845,15 @@ class Dataframe { ); } - hasCol(c) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + hasCol(c: any) { /* Test if col label exists - return true/false */ return !!this.col(c); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. isEmpty() { /* Return true if this is an empty dataframe, ie, has dimensions [0,0] @@ -784,19 +869,23 @@ class Dataframe { add these as useful. ****/ - mapColumns(callback) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + mapColumns(callback: any) { /* map all columns in the dataframe, returning a new dataframe comprised of the return values, with the same index as the original dataframe. callback MUST not modify the column, but instead return a mutated copy. */ - const columns = this.__columns.map((colData, colIdx) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const columns = this.__columns.map((colData: any, colIdx: any) => callback(colData, colIdx, this) ); - const columnsAccessor = columns.map((c, idx) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const columnsAccessor = columns.map((c: any, idx: any) => this.__columns[idx] === c ? this.__columnsAccessor[idx] : undefined ); + // @ts-expect-error ts-migrate(2351) FIXME: This expression is not constructable. return new this.constructor( this.dims, columns, diff --git a/client/src/util/dataframe/histogram.js b/client/src/util/dataframe/histogram.ts similarity index 52% rename from client/src/util/dataframe/histogram.js rename to client/src/util/dataframe/histogram.ts index 48d6a19e..4949955a 100644 --- a/client/src/util/dataframe/histogram.js +++ b/client/src/util/dataframe/histogram.ts @@ -3,7 +3,8 @@ Dataframe histogram */ import { isTypedArray } from "./util"; -function _histogramContinuous(column, bins, min, max) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _histogramContinuous(column: any, bins: any, min: any, max: any) { const valBins = new Array(bins).fill(0); if (!column) { return valBins; @@ -21,7 +22,18 @@ function _histogramContinuous(column, bins, min, max) { return valBins; } -function _histogramContinuousBy(column, bins, min, max, by) { +function _histogramContinuousBy( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + column: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + bins: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + min: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + max: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + by: any +) { const byMap = new Map(); if (!column || !by) { return byMap; @@ -46,7 +58,8 @@ function _histogramContinuousBy(column, bins, min, max, by) { return byMap; } -function _histogramCategorical(column) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _histogramCategorical(column: any) { const valMap = new Map(); if (!column) { return valMap; @@ -63,7 +76,8 @@ function _histogramCategorical(column) { return valMap; } -function _histogramCategoricalBy(column, by) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _histogramCategoricalBy(column: any, by: any) { const byMap = new Map(); if (!column || !by) { return byMap; @@ -90,7 +104,8 @@ function _histogramCategoricalBy(column, by) { /* Count category occupancy. Optional group-by category. */ -export function histogramCategorical(column, by) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function histogramCategorical(column: any, by: any) { if (by && isTypedArray(by)) { throw new Error("Group by column must be categorical"); } @@ -102,7 +117,8 @@ export function histogramCategorical(column, by) { /* Memoization hash for histogramCategorical() */ -export function hashCategorical(column, by) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function hashCategorical(column: any, by: any) { if (by) { return `${column.__id}:${by.__id}`; } @@ -113,7 +129,15 @@ export function hashCategorical(column, by) { Bin counts for continuous/scalar values, with optional group-by category. Values outside domain are ignored. */ -export function histogramContinuous(column, bins = 40, domain = [0, 1], by) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function histogramContinuous( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + column: any, + bins = 40, + domain = [0, 1], + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + by: any +) { if (by && isTypedArray(by)) { throw new Error("Group by column must be categorical"); } @@ -126,7 +150,15 @@ export function histogramContinuous(column, bins = 40, domain = [0, 1], by) { /* Memoization hash for histogramContinuous */ -export function hashContinuous(column, bins = "", domain = [0, 0], by) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function hashContinuous( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + column: any, + bins = "", + domain = [0, 0], + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + by: any +) { const [min, max] = domain; if (by) { return `${column.__id}:${bins}:${min}:${max}:${by.__id}`; diff --git a/client/src/util/dataframe/index.js b/client/src/util/dataframe/index.ts similarity index 100% rename from client/src/util/dataframe/index.js rename to client/src/util/dataframe/index.ts diff --git a/client/src/util/dataframe/labelIndex.js b/client/src/util/dataframe/labelIndex.js deleted file mode 100644 index fe8a48fe..00000000 --- a/client/src/util/dataframe/labelIndex.js +++ /dev/null @@ -1,396 +0,0 @@ -/* eslint-disable max-classes-per-file -- Classes are interrelated*/ -/** -Label indexing - map a label to & from an integer offset. See Dataframe -for how this is used. -**/ - -import { rangeFill as fillRange } from "../range"; -import { __getMemoId } from "./util"; - -/* -Private utility functions -*/ -function extent(tarr) { - let min = 0x7fffffff; - let max = ~min; // eslint-disable-line no-bitwise -- Establishes 0 of same size - for (let i = 0, l = tarr.length; i < l; i += 1) { - const v = tarr[i]; - if (v < min) { - min = v; - } - if (v > max) { - max = v; - } - } - return [min, max]; -} - -class IdentityInt32Index { - /* - identity/noop index, with small assumptions that labels are int32 - */ - constructor(maxOffset) { - this.maxOffset = maxOffset; - } - - get __id() { - return `IdentityInt32Index_${this.maxOffset}`; - } - - labels() { - // memoize - const k = fillRange(new Int32Array(this.maxOffset)); - this.labels = function labels() { - return k; - }; - return k; - } - - getOffset(i) { - // label to offset - return Number.isInteger(i) && i >= 0 && i < this.maxOffset ? i : undefined; - } - - getOffsets(arr) { - // labels to offsets - return arr.map((i) => this.getOffset(i)); - } - - getLabel(i) { - // offset to label - return Number.isInteger(i) && i >= 0 && i < this.maxOffset ? i : undefined; - } - - getLabels(arr) { - // offsets to labels - return arr.map((i) => this.getLabel(i)); - } - - size() { - return this.maxOffset; - } - - __promote(labelArray) { - /* - time/space decision - based on the resulting density - */ - const [minLabel, maxLabel] = extent(labelArray); - if (minLabel === 0 && maxLabel === labelArray.length - 1) - return new IdentityInt32Index(labelArray.length); - - const labelSpaceSize = maxLabel - minLabel + 1; - const density = labelSpaceSize / this.maxOffset; - /* 0.1 is a magic number, that needs testing to optimize */ - if (density < 0.1) { - return new KeyIndex(labelArray); - } - return new DenseInt32Index(labelArray, [minLabel, maxLabel]); - } - - subset(labels) { - /* validate subset */ - const { maxOffset } = this; - for (let i = 0, l = labels.length; i < l; i += 1) { - const label = labels[i]; - if (!Number.isInteger(label) || label < 0 || label >= maxOffset) - throw new RangeError(`offset or label: ${label}`); - } - return this.__promote(labels); - } - - /* identity index - labels are offsets */ - isubset(offsets) { - return this.subset(offsets); - } - - /* identity index - labels are offsets */ - isubsetMask(mask) { - let count = 0; - if (mask.length !== this.maxOffset) { - throw new RangeError("mask has invalid length for index"); - } - let labels = new Int32Array(mask.length); - for (let i = 0, l = mask.length; i < l; i += 1) { - if (mask[i]) { - labels[count] = i; - count += 1; - } - } - labels = labels.slice(0, count); - return this.subset(labels); - } - - withLabel(label) { - if (label === this.maxOffset) { - return new IdentityInt32Index(label + 1); - } - return this.__promote([...this.labels(), label]); - } - - withLabels(labels) { - return this.__promote([...this.labels(), ...labels]); - } - - dropLabel(label) { - if (label === this.maxOffset - 1) { - return new IdentityInt32Index(label); - } - const labelArray = [...this.labels()]; - labelArray.splice(labelArray.indexOf(label), 1); - return this.__promote(labelArray); - } -} - -class DenseInt32Index { - /* - DenseInt32Index indexes integer labels, and uses Int32Array typed arrays - for both forward and reverse indexing. This means that the min/max range - of the forward index labels must be known a priori (so that the index - array can be pre-allocated). - */ - constructor(labels, labelRange = null) { - if (labels.constructor !== Int32Array) { - labels = new Int32Array(labels); - } - - if (!labelRange) { - labelRange = extent(labels); - } - const [minLabel, maxLabel] = labelRange; - const labelSpaceSize = maxLabel - minLabel + 1; - const index = new Int32Array(labelSpaceSize).fill(-1); - for (let i = 0, l = labels.length; i < l; i += 1) { - const label = labels[i]; - index[label - minLabel] = i; - } - - this.minLabel = minLabel; - this.rindex = labels; - this.index = index; - this.__id = __getMemoId(); - this.__compile(); - } - - __compile() { - const { minLabel, index, rindex } = this; - this.getOffset = function getOffset(l) { - if (!Number.isInteger(l)) return undefined; - const offset = index[l - minLabel]; - return offset === -1 ? undefined : offset; - }; - - this.getOffsets = function getOffsets(arr) { - return arr.map((i) => this.getOffset(i)); - }; - - this.getLabel = function getLabel(i) { - return Number.isInteger(i) ? rindex[i] : undefined; - }; - - this.getLabels = function getLabels(arr) { - return arr.map((i) => this.getLabel(i)); - }; - } - - labels() { - return this.rindex; - } - - size() { - return this.rindex.length; - } - - __promote(labelArray) { - /* - time/space decision - if we are going to use less than 10% of the - dense index space, switch to a KeyIndex (which is slower, but uses - less memory for sparse label spaces). - */ - const [minLabel, maxLabel] = extent(labelArray); - const labelSpaceSize = maxLabel - minLabel + 1; - const density = labelSpaceSize / this.rindex.length; - /* 0.1 is a magic number, that needs testing to optimize */ - if (density < 0.1) { - return new KeyIndex(labelArray); - } - return new DenseInt32Index(labelArray, [minLabel, maxLabel]); - } - - subset(labels) { - /* validate subset */ - for (let i = 0, l = labels.length; i < l; i += 1) { - const label = labels[i]; - const offset = this.getOffset(label); - if (offset === undefined || offset === -1) - throw new RangeError(`unknown label: ${label}`); - } - return this.__promote(labels); - } - - isubset(offsets) { - /* validate subset */ - const { rindex } = this; - const maxOffset = rindex.length; - const labels = new Int32Array(offsets.length); - for (let i = 0, l = offsets.length; i < l; i += 1) { - const offset = offsets[i]; - if (offset < 0 || offset >= maxOffset) - throw new RangeError(`out of bounds offset: ${offset}`); - labels[i] = rindex[offset]; - } - return this.__promote(labels); - } - - isubsetMask(mask) { - const { rindex } = this; - if (mask.length !== rindex.length) - throw new RangeError("mask has invalid length for index"); - let count = 0; - let labels = new Int32Array(mask.length); - for (let i = 0, l = mask.length; i < l; i += 1) { - if (mask[i]) { - labels[count] = rindex[i]; - count += 1; - } - } - labels = labels.slice(0, count); - return this.__promote(labels); - } - - withLabel(label) { - return this.__promote([...this.labels(), label]); - } - - withLabels(labels) { - return this.__promote([...this.labels(), ...labels]); - } - - dropLabel(label) { - const labelArray = [...this.labels()]; - labelArray.splice(labelArray.indexOf(label), 1); - return this.__promote(labelArray); - } -} - -class KeyIndex { - /* - KeyIndex indexes arbitrary JS primitive types, and uses a Map() - as its core data structure. - */ - constructor(labels) { - const index = new Map(); - if (labels === undefined) { - labels = []; - } - const rindex = labels; - labels.forEach((v, i) => { - index.set(v, i); - }); - - if (index.size !== rindex.length) { - /* if true, there was a duplicate in the keys */ - throw new Error("duplicate label provided to KeyIndex"); - } - - this.index = index; - this.rindex = rindex; - this.__id = __getMemoId(); - this.__compile(); - } - - __compile() { - const { index, rindex } = this; - this.getOffset = function getOffset(k) { - return index.get(k); - }; - - this.getOffsets = function getOffsets(arr) { - return arr.map((l) => this.getOffset(l)); - }; - - this.getLabel = function getLabel(i) { - return Number.isInteger(i) ? rindex[i] : undefined; - }; - - this.getLabels = function getLabels(arr) { - return arr.map((i) => this.getLabel(i)); - }; - } - - labels() { - return this.rindex; - } - - size() { - return this.rindex.length; - } - - subset(labels) { - /* validate subset */ - for (let i = 0, l = labels.length; i < l; i += 1) { - const label = labels[i]; - const offset = this.getOffset(label); - if (offset === undefined || offset === -1) { - throw new RangeError(`unknown label: ${label}`); - } - } - - return new KeyIndex(labels); - } - - isubset(offsets) { - const { rindex } = this; - const maxOffset = rindex.length; - const labels = new Array(offsets.length); - for (let i = 0, l = offsets.length; i < l; i += 1) { - const offset = offsets[i]; - if (offset < 0 || offset >= maxOffset) - throw new RangeError(`out of bounds offset: ${offset}`); - labels[i] = rindex[offset]; - } - - return new KeyIndex(labels); - } - - isubsetMask(mask) { - const { rindex } = this; - if (mask.length !== rindex.length) - throw new RangeError("mask has invalid length for index"); - let labels = new Array(mask.length); - let count = 0; - for (let i = 0, l = mask.length; i < l; i += 1) { - if (mask[i]) { - labels[count] = rindex[i]; - count += 1; - } - } - labels = labels.slice(0, count); - return new KeyIndex(labels); - } - - withLabel(label) { - return new KeyIndex([...this.rindex, label]); - } - - withLabels(labels) { - return new KeyIndex([...this.rindex, ...labels]); - } - - dropLabel(label) { - const idx = this.rindex.indexOf(label); - const labelArray = [...this.rindex]; - labelArray.splice(idx, 1); - return new KeyIndex(labelArray); - } -} - -function isLabelIndex(i) { - return ( - i instanceof IdentityInt32Index || - i instanceof DenseInt32Index || - i instanceof KeyIndex - ); -} - -export { DenseInt32Index, IdentityInt32Index, KeyIndex, isLabelIndex }; -/* eslint-enable max-classes-per-file -- enable*/ diff --git a/client/src/util/dataframe/labelIndex.ts b/client/src/util/dataframe/labelIndex.ts new file mode 100644 index 00000000..1c07f47c --- /dev/null +++ b/client/src/util/dataframe/labelIndex.ts @@ -0,0 +1,501 @@ +/* eslint-disable max-classes-per-file -- Classes are interrelated*/ +/** +Label indexing - map a label to & from an integer offset. See Dataframe +for how this is used. +**/ + +import { rangeFill as fillRange } from "../range"; +import { __getMemoId } from "./util"; + +/* +Private utility functions +*/ +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function extent(tarr: any) { + let min = 0x7fffffff; + let max = ~min; // eslint-disable-line no-bitwise -- Establishes 0 of same size + for (let i = 0, l = tarr.length; i < l; i += 1) { + const v = tarr[i]; + if (v < min) { + min = v; + } + if (v > max) { + max = v; + } + } + return [min, max]; +} + +class IdentityInt32Index { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + maxOffset: any; + + /* + identity/noop index, with small assumptions that labels are int32 + */ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(maxOffset: any) { + this.maxOffset = maxOffset; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + get __id() { + return `IdentityInt32Index_${this.maxOffset}`; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + labels() { + // memoize + const k = fillRange(new Int32Array(this.maxOffset)); + this.labels = function labels() { + return k; + }; + return k; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getOffset(i: any) { + // label to offset + return Number.isInteger(i) && i >= 0 && i < this.maxOffset ? i : undefined; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getOffsets(arr: any) { + // labels to offsets + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return arr.map((i: any) => this.getOffset(i)); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getLabel(i: any) { + // offset to label + return Number.isInteger(i) && i >= 0 && i < this.maxOffset ? i : undefined; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + getLabels(arr: any) { + // offsets to labels + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return arr.map((i: any) => this.getLabel(i)); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + size() { + return this.maxOffset; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + __promote(labelArray: any) { + /* + time/space decision - based on the resulting density + */ + const [minLabel, maxLabel] = extent(labelArray); + if (minLabel === 0 && maxLabel === labelArray.length - 1) + return new IdentityInt32Index(labelArray.length); + + const labelSpaceSize = maxLabel - minLabel + 1; + const density = labelSpaceSize / this.maxOffset; + /* 0.1 is a magic number, that needs testing to optimize */ + if (density < 0.1) { + return new KeyIndex(labelArray); + } + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number[]' is not assignable to p... Remove this comment to see the full error message + return new DenseInt32Index(labelArray, [minLabel, maxLabel]); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + subset(labels: any) { + /* validate subset */ + const { maxOffset } = this; + for (let i = 0, l = labels.length; i < l; i += 1) { + const label = labels[i]; + if (!Number.isInteger(label) || label < 0 || label >= maxOffset) + throw new RangeError(`offset or label: ${label}`); + } + return this.__promote(labels); + } + + /* identity index - labels are offsets */ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isubset(offsets: any) { + return this.subset(offsets); + } + + /* identity index - labels are offsets */ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isubsetMask(mask: any) { + let count = 0; + if (mask.length !== this.maxOffset) { + throw new RangeError("mask has invalid length for index"); + } + let labels = new Int32Array(mask.length); + for (let i = 0, l = mask.length; i < l; i += 1) { + if (mask[i]) { + labels[count] = i; + count += 1; + } + } + labels = labels.slice(0, count); + return this.subset(labels); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + withLabel(label: any) { + if (label === this.maxOffset) { + return new IdentityInt32Index(label + 1); + } + return this.__promote([...this.labels(), label]); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + withLabels(labels: any) { + return this.__promote([...this.labels(), ...labels]); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dropLabel(label: any) { + if (label === this.maxOffset - 1) { + return new IdentityInt32Index(label); + } + const labelArray = [...this.labels()]; + labelArray.splice(labelArray.indexOf(label), 1); + return this.__promote(labelArray); + } +} + +class DenseInt32Index { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + __id: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getLabel: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getLabels: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getOffset: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getOffsets: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + index: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + minLabel: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + rindex: any; + + /* + DenseInt32Index indexes integer labels, and uses Int32Array typed arrays + for both forward and reverse indexing. This means that the min/max range + of the forward index labels must be known a priori (so that the index + array can be pre-allocated). + */ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(labels: any, labelRange = null) { + if (labels.constructor !== Int32Array) { + labels = new Int32Array(labels); + } + + if (!labelRange) { + // @ts-expect-error ts-migrate(2322) FIXME: Type 'number[]' is not assignable to type 'null'. + labelRange = extent(labels); + } + // @ts-expect-error ts-migrate(2488) FIXME: Type 'null' must have a '[Symbol.iterator]()' meth... Remove this comment to see the full error message + const [minLabel, maxLabel] = labelRange; + const labelSpaceSize = maxLabel - minLabel + 1; + const index = new Int32Array(labelSpaceSize).fill(-1); + for (let i = 0, l = labels.length; i < l; i += 1) { + const label = labels[i]; + index[label - minLabel] = i; + } + + this.minLabel = minLabel; + this.rindex = labels; + this.index = index; + this.__id = __getMemoId(); + this.__compile(); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + __compile() { + const { minLabel, index, rindex } = this; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.getOffset = function getOffset(l: any) { + if (!Number.isInteger(l)) return undefined; + const offset = index[l - minLabel]; + return offset === -1 ? undefined : offset; + }; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.getOffsets = function getOffsets(arr: any) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return arr.map((i: any) => this.getOffset(i)); + }; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.getLabel = function getLabel(i: any) { + return Number.isInteger(i) ? rindex[i] : undefined; + }; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.getLabels = function getLabels(arr: any) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return arr.map((i: any) => this.getLabel(i)); + }; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + labels() { + return this.rindex; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + size() { + return this.rindex.length; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + __promote(labelArray: any) { + /* + time/space decision - if we are going to use less than 10% of the + dense index space, switch to a KeyIndex (which is slower, but uses + less memory for sparse label spaces). + */ + const [minLabel, maxLabel] = extent(labelArray); + const labelSpaceSize = maxLabel - minLabel + 1; + const density = labelSpaceSize / this.rindex.length; + /* 0.1 is a magic number, that needs testing to optimize */ + if (density < 0.1) { + return new KeyIndex(labelArray); + } + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'number[]' is not assignable to p... Remove this comment to see the full error message + return new DenseInt32Index(labelArray, [minLabel, maxLabel]); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + subset(labels: any) { + /* validate subset */ + for (let i = 0, l = labels.length; i < l; i += 1) { + const label = labels[i]; + const offset = this.getOffset(label); + if (offset === undefined || offset === -1) + throw new RangeError(`unknown label: ${label}`); + } + return this.__promote(labels); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isubset(offsets: any) { + /* validate subset */ + const { rindex } = this; + const maxOffset = rindex.length; + const labels = new Int32Array(offsets.length); + for (let i = 0, l = offsets.length; i < l; i += 1) { + const offset = offsets[i]; + if (offset < 0 || offset >= maxOffset) + throw new RangeError(`out of bounds offset: ${offset}`); + labels[i] = rindex[offset]; + } + return this.__promote(labels); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isubsetMask(mask: any) { + const { rindex } = this; + if (mask.length !== rindex.length) + throw new RangeError("mask has invalid length for index"); + let count = 0; + let labels = new Int32Array(mask.length); + for (let i = 0, l = mask.length; i < l; i += 1) { + if (mask[i]) { + labels[count] = rindex[i]; + count += 1; + } + } + labels = labels.slice(0, count); + return this.__promote(labels); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + withLabel(label: any) { + return this.__promote([...this.labels(), label]); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + withLabels(labels: any) { + return this.__promote([...this.labels(), ...labels]); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dropLabel(label: any) { + const labelArray = [...this.labels()]; + labelArray.splice(labelArray.indexOf(label), 1); + return this.__promote(labelArray); + } +} + +class KeyIndex { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + __id: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getLabel: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getLabels: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getOffset: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + getOffsets: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + index: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + rindex: any; + + /* + KeyIndex indexes arbitrary JS primitive types, and uses a Map() + as its core data structure. + */ + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(labels: any) { + const index = new Map(); + if (labels === undefined) { + labels = []; + } + const rindex = labels; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + labels.forEach((v: any, i: any) => { + index.set(v, i); + }); + + if (index.size !== rindex.length) { + /* if true, there was a duplicate in the keys */ + throw new Error("duplicate label provided to KeyIndex"); + } + + this.index = index; + this.rindex = rindex; + this.__id = __getMemoId(); + this.__compile(); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + __compile() { + const { index, rindex } = this; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.getOffset = function getOffset(k: any) { + return index.get(k); + }; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.getOffsets = function getOffsets(arr: any) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return arr.map((l: any) => this.getOffset(l)); + }; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.getLabel = function getLabel(i: any) { + return Number.isInteger(i) ? rindex[i] : undefined; + }; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.getLabels = function getLabels(arr: any) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return arr.map((i: any) => this.getLabel(i)); + }; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + labels() { + return this.rindex; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + size() { + return this.rindex.length; + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + subset(labels: any) { + /* validate subset */ + for (let i = 0, l = labels.length; i < l; i += 1) { + const label = labels[i]; + const offset = this.getOffset(label); + if (offset === undefined || offset === -1) { + throw new RangeError(`unknown label: ${label}`); + } + } + + return new KeyIndex(labels); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isubset(offsets: any) { + const { rindex } = this; + const maxOffset = rindex.length; + const labels = new Array(offsets.length); + for (let i = 0, l = offsets.length; i < l; i += 1) { + const offset = offsets[i]; + if (offset < 0 || offset >= maxOffset) + throw new RangeError(`out of bounds offset: ${offset}`); + labels[i] = rindex[offset]; + } + + return new KeyIndex(labels); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isubsetMask(mask: any) { + const { rindex } = this; + if (mask.length !== rindex.length) + throw new RangeError("mask has invalid length for index"); + let labels = new Array(mask.length); + let count = 0; + for (let i = 0, l = mask.length; i < l; i += 1) { + if (mask[i]) { + labels[count] = rindex[i]; + count += 1; + } + } + labels = labels.slice(0, count); + return new KeyIndex(labels); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + withLabel(label: any) { + return new KeyIndex([...this.rindex, label]); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + withLabels(labels: any) { + return new KeyIndex([...this.rindex, ...labels]); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + dropLabel(label: any) { + const idx = this.rindex.indexOf(label); + const labelArray = [...this.rindex]; + labelArray.splice(idx, 1); + return new KeyIndex(labelArray); + } +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +function isLabelIndex(i: any) { + return ( + i instanceof IdentityInt32Index || + i instanceof DenseInt32Index || + i instanceof KeyIndex + ); +} + +export { DenseInt32Index, IdentityInt32Index, KeyIndex, isLabelIndex }; +/* eslint-enable max-classes-per-file -- enable*/ diff --git a/client/src/util/dataframe/summarize.js b/client/src/util/dataframe/summarize.ts similarity index 70% rename from client/src/util/dataframe/summarize.js rename to client/src/util/dataframe/summarize.ts index b7dc90d6..f275522a 100644 --- a/client/src/util/dataframe/summarize.js +++ b/client/src/util/dataframe/summarize.ts @@ -10,9 +10,11 @@ import quantile from "../quantile"; import { sortArray } from "../typedCrossfilter/sort"; // [ 0, 0.01, 0.02, ..., 1.0] +// @ts-expect-error ts-migrate(6133) FIXME: 'v' is declared but its value is never read. const centileNames = new Array(101).fill(0).map((v, idx) => idx / 100); -export function summarizeContinuous(col) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function summarizeContinuous(col: any) { let min; let max; let nan = 0; @@ -63,7 +65,8 @@ export function summarizeContinuous(col) { }; } -export function summarizeCategorical(col) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function summarizeCategorical(col: any) { const categoryCounts = new Map(); if (col) { for (let r = 0, l = col.length; r < l; r += 1) { @@ -73,10 +76,13 @@ export function summarizeCategorical(col) { categoryCounts.set(val, curCount + 1); } } + const sortedCategoryByCounts = new Map( + [...categoryCounts.entries()].sort((a, b) => b[1] - a[1]) + ); return { categorical: true, - categories: [...categoryCounts.keys()], - categoryCounts, - numCategories: categoryCounts.size, + categories: [...sortedCategoryByCounts.keys()], + categoryCounts: sortedCategoryByCounts, + numCategories: sortedCategoryByCounts.size, }; } diff --git a/client/src/util/dataframe/util.js b/client/src/util/dataframe/util.ts similarity index 57% rename from client/src/util/dataframe/util.js rename to client/src/util/dataframe/util.ts index aa00e0c8..ed27258f 100644 --- a/client/src/util/dataframe/util.js +++ b/client/src/util/dataframe/util.ts @@ -4,14 +4,17 @@ Private utility code for dataframe export { isTypedArray, isArrayOrTypedArray } from "../typeHelpers"; -export function callOnceLazy(f) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function callOnceLazy(f: any) { /* call function once, and save the result, regardless of arguments (this is not the same as typical memoization). */ - let value; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let value: any; let calledOnce = false; - const result = function result(...args) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const result = function result(...args: any[]) { if (!calledOnce) { value = f(...args); calledOnce = true; @@ -21,7 +24,8 @@ export function callOnceLazy(f) { return result; } -export function memoize(fn, hashFn, maxResultsCached = -1) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function memoize(fn: any, hashFn: any, maxResultsCached = -1) { /* function memoization, with user-provided hash. hashFn must return a key which will be unique as a Map key (ie, obeys "sameValueZero" algorithm @@ -29,7 +33,8 @@ export function memoize(fn, hashFn, maxResultsCached = -1) { https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/Map#Key_equality */ const cache = new Map(); - const wrap = function wrap(...args) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const wrap = function wrap(...args: any[]) { const key = hashFn(...args); if (cache.has(key)) { return cache.get(key); @@ -57,6 +62,7 @@ export function memoize(fn, hashFn, maxResultsCached = -1) { memoization helpers - just a global counter. **/ let __DataframeMemoId__ = 0; +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function __getMemoId() { const id = __DataframeMemoId__; __DataframeMemoId__ += 1; diff --git a/client/src/util/finiteExtent.js b/client/src/util/finiteExtent.ts similarity index 76% rename from client/src/util/finiteExtent.js rename to client/src/util/finiteExtent.ts index 24239113..e3352ce2 100644 --- a/client/src/util/finiteExtent.js +++ b/client/src/util/finiteExtent.ts @@ -6,7 +6,8 @@ If undefined or empty array, or array contains only non-finite numbers, will return [undefined, undefined] */ -function finiteExtent(tarr) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +function finiteExtent(tarr: any) { let min; let max; let i; diff --git a/client/src/util/fromEntries.js b/client/src/util/fromEntries.js deleted file mode 100644 index 747c8e2f..00000000 --- a/client/src/util/fromEntries.js +++ /dev/null @@ -1,13 +0,0 @@ -export default function fromEntries(arr) { - /* - Similar to Object.fromEntries, but only handles array. - This could be replaced with the standard fucnction once it - is widely available. As of 3/20/2019, it has not yet - been released in the Chrome stable channel. - */ - const obj = {}; - for (let i = 0, l = arr.length; i < l; i += 1) { - obj[arr[i][0]] = arr[i][1]; - } - return obj; -} diff --git a/client/src/util/fromEntries.ts b/client/src/util/fromEntries.ts new file mode 100644 index 00000000..22ae60b9 --- /dev/null +++ b/client/src/util/fromEntries.ts @@ -0,0 +1,15 @@ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function fromEntries(arr: any) { + /* + Similar to Object.fromEntries, but only handles array. + This could be replaced with the standard fucnction once it + is widely available. As of 3/20/2019, it has not yet + been released in the Chrome stable channel. + */ + const obj = {}; + for (let i = 0, l = arr.length; i < l; i += 1) { + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message + obj[arr[i][0]] = arr[i][1]; + } + return obj; +} diff --git a/client/src/util/glHelpers.js b/client/src/util/glHelpers.ts similarity index 100% rename from client/src/util/glHelpers.js rename to client/src/util/glHelpers.ts diff --git a/client/src/util/maybeScientific.js b/client/src/util/maybeScientific.ts similarity index 64% rename from client/src/util/maybeScientific.js rename to client/src/util/maybeScientific.ts index 234f49e1..a3e25151 100644 --- a/client/src/util/maybeScientific.js +++ b/client/src/util/maybeScientific.ts @@ -10,11 +10,13 @@ import significantDigits from "./significantDigits"; * @returns - the number formatted as scientific, if it's big enough */ -export default function maybeScientific(x) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function maybeScientific(x: any) { let format = ","; const _ticks = x.ticks(4); - if (x.domain().some((n) => Math.abs(n) >= 10000)) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + if (x.domain().some((n: any) => Math.abs(n) >= 10000)) { /* heuristic: if the last tick d3 wants to render has one significant digit ie., 2000, render 2e+3, but if it's anything else ie., 42000000 render diff --git a/client/src/util/nameCreators.js b/client/src/util/nameCreators.js deleted file mode 100644 index 415e30ac..00000000 --- a/client/src/util/nameCreators.js +++ /dev/null @@ -1,53 +0,0 @@ -/* - -The original motivation for this file is name collision. It's possible -to have two of the same gene, user defined and diffexpressed, on the client -simultaneously, looking at the same data in the cache but with two -dimensions and two crossfilters. It's also possible that someone could -have a obsAnnotation named X, but we are using that for layout. So -we namespace, and abstract to avoid proliferating strings throughout the -codebase. - -It is _no longer_ used to remove collisions in the crossfilter or -anno matrix namespaces. It is still used by the component tier. - -*/ - -const makeDimensionName = (namespace, key) => `${namespace}_${key}`; - -export const layoutDimensionName = (key) => makeDimensionName("layout", key); -export const obsAnnoDimensionName = (key) => makeDimensionName("obsAnno", key); -export const diffexpDimensionName = (key) => - makeDimensionName("varData_diffexp", key); -export const userDefinedDimensionName = (key) => - makeDimensionName("varData_userDefined", key); -export const geneSetSummaryDimensionName = (key) => - makeDimensionName("geneSetSummary", key); - -/* - continuousNamespace = { - isObs: true, - isDiffExp: false, - isUserDefined: false, - isGeneSet: false, - } - - ie., makeContinuousDimensionName(continuousNamespace = {isObs: true}, "total_reads") - see: histogram brush, as it doesn't know what type of continuous it was with only field -*/ -export const makeContinuousDimensionName = (continuousNamespace, key) => { - let name; - if (continuousNamespace.isObs) { - name = obsAnnoDimensionName(key); - } else if (continuousNamespace.isDiffExp) { - name = diffexpDimensionName(key); - } else if (continuousNamespace.isUserDefined) { - name = userDefinedDimensionName(key); - } else if (continuousNamespace.isGeneSetSummary) { - name = geneSetSummaryDimensionName(key); - } else { - throw new Error("unknown continuous dimension"); - } - - return name; -}; diff --git a/client/src/util/nameCreators.ts b/client/src/util/nameCreators.ts new file mode 100644 index 00000000..015884c6 --- /dev/null +++ b/client/src/util/nameCreators.ts @@ -0,0 +1,67 @@ +/* + +The original motivation for this file is name collision. It's possible +to have two of the same gene, user defined and diffexpressed, on the client +simultaneously, looking at the same data in the cache but with two +dimensions and two crossfilters. It's also possible that someone could +have a obsAnnotation named X, but we are using that for layout. So +we namespace, and abstract to avoid proliferating strings throughout the +codebase. + +It is _no longer_ used to remove collisions in the crossfilter or +anno matrix namespaces. It is still used by the component tier. + +*/ + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +const makeDimensionName = (namespace: any, key: any) => `${namespace}_${key}`; + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const layoutDimensionName = (key: any) => + makeDimensionName("layout", key); +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const obsAnnoDimensionName = (key: any) => + makeDimensionName("obsAnno", key); +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const diffexpDimensionName = (key: any) => + makeDimensionName("varData_diffexp", key); +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const userDefinedDimensionName = (key: any) => + makeDimensionName("varData_userDefined", key); +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export const geneSetSummaryDimensionName = (key: any) => + makeDimensionName("geneSetSummary", key); + +/* + continuousNamespace = { + isObs: true, + isDiffExp: false, + isUserDefined: false, + isGeneSet: false, + } + + ie., makeContinuousDimensionName(continuousNamespace = {isObs: true}, "total_reads") + see: histogram brush, as it doesn't know what type of continuous it was with only field +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export const makeContinuousDimensionName = ( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + continuousNamespace: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + key: any +) => { + let name; + if (continuousNamespace.isObs) { + name = obsAnnoDimensionName(key); + } else if (continuousNamespace.isDiffExp) { + name = diffexpDimensionName(key); + } else if (continuousNamespace.isUserDefined) { + name = userDefinedDimensionName(key); + } else if (continuousNamespace.isGeneSetSummary) { + name = geneSetSummaryDimensionName(key); + } else { + throw new Error("unknown continuous dimension"); + } + + return name; +}; diff --git a/client/src/util/parseBulkGeneString.js b/client/src/util/parseBulkGeneString.ts similarity index 55% rename from client/src/util/parseBulkGeneString.js rename to client/src/util/parseBulkGeneString.ts index 015c4e88..6dbe58e5 100644 --- a/client/src/util/parseBulkGeneString.js +++ b/client/src/util/parseBulkGeneString.ts @@ -6,6 +6,7 @@ import pull from "lodash.pull"; import uniq from "lodash.uniq"; -export default function parseBulkGeneString(geneString) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function parseBulkGeneString(geneString: any) { return pull(uniq(geneString.split(/[ ,]+/)), ""); } diff --git a/client/src/util/parseRGB.js b/client/src/util/parseRGB.js deleted file mode 100644 index d8546d87..00000000 --- a/client/src/util/parseRGB.js +++ /dev/null @@ -1,29 +0,0 @@ -import scaleRGB from "./scaleRGB"; - -// maintain a cache of already parsed RGB names, as it is reasonably expensive -// to do this operation. This lets us have speed, but keep the pleasant ability -// to talk about colors by their text description eg, 'rgb(0,0,1)' -// -const colorCache = {}; - -function parseColorName(c) { - if (c[0] !== "#") { - const _c = c.replace(/[^\d,.]/g, "").split(","); - return [scaleRGB(+_c[0]), scaleRGB(+_c[1]), scaleRGB(+_c[2])]; - } - const parsedHex = /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(c); - return [ - scaleRGB(parseInt(parsedHex[1], 16)), - scaleRGB(parseInt(parsedHex[2], 16)), - scaleRGB(parseInt(parsedHex[3], 16)), - ]; -} - -export default (c) => { - let cv = colorCache[c]; - if (!cv) { - cv = parseColorName(c); - colorCache[c] = cv; - } - return cv; -}; diff --git a/client/src/util/parseRGB.ts b/client/src/util/parseRGB.ts new file mode 100644 index 00000000..98a2083e --- /dev/null +++ b/client/src/util/parseRGB.ts @@ -0,0 +1,36 @@ +import scaleRGB from "./scaleRGB"; + +// maintain a cache of already parsed RGB names, as it is reasonably expensive +// to do this operation. This lets us have speed, but keep the pleasant ability +// to talk about colors by their text description eg, 'rgb(0,0,1)' +// +const colorCache = {}; + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function parseColorName(c: any) { + if (c[0] !== "#") { + const _c = c.replace(/[^\d,.]/g, "").split(","); + return [scaleRGB(+_c[0]), scaleRGB(+_c[1]), scaleRGB(+_c[2])]; + } + const parsedHex = /^#?([a-f\d]{2})([a-f\d]{2})([a-f\d]{2})$/i.exec(c); + return [ + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + scaleRGB(parseInt(parsedHex[1], 16)), + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + scaleRGB(parseInt(parsedHex[2], 16)), + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. + scaleRGB(parseInt(parsedHex[3], 16)), + ]; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default (c: any) => { + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message + let cv = colorCache[c]; + if (!cv) { + cv = parseColorName(c); + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message + colorCache[c] = cv; + } + return cv; +}; diff --git a/client/src/util/promiseLimit.js b/client/src/util/promiseLimit.js deleted file mode 100644 index dde85bd8..00000000 --- a/client/src/util/promiseLimit.js +++ /dev/null @@ -1,91 +0,0 @@ -/* -This class provides a means to resolve Promises asynchronously, -and limit the number concurrently executed. For example, if -you want to involve a large number of API endpoints using fetch(), -but want to limit the number simultaneously outstanding. - -Example usage: - -const plimit = new PromiseLimit(2); -return Promise.all([ - plimit.add(() => fetch('/foo')), - plimit.add(() => fetch('/bar')), - plimit.add(() => fetch('/baz')) -]) - -if you want a priority queue based implementation, just -use priorityAdd() instead of add(): - -const plimit = new PromiseLimit(2); -return Promise.all([ - plimit.priorityAdd(0, () => fetch('/foo')), - plimit.priorityAdd(10, () => fetch('/bar')), - plimit.priorityAdd(-1, () => fetch('/baz')) -]) - -Priority is a numeric value. Lower first. Stable ordering. -*/ - -import TinyQueue from "tinyqueue"; - -function compare(a, b) { - const diff = a.priority - b.priority; - if (diff) return diff; - return a.order - b.order; -} - -export default class PromiseLimit { - constructor(maxConcurrency = 5) { - this.queue = new TinyQueue([], compare); - this.maxConcurrency = maxConcurrency; - this.pending = 0; - this.insertCounter = 0; - } - - priorityAdd(p, fn, ...args) { - // p - numermic priority (lower first) - // fn - must return a promise - // args - will be passed to fn - return this._push(p, fn, args); - } - - add(fn, ...args) { - // fn - must return a promise - // args - will be passed to fn - return this._push(0, fn, args); - } - - /** - Private below - **/ - - _push(priority, fn, args) { - const order = this.insertCount; - this.insertCount += 1; - return new Promise((resolve, reject) => { - this.queue.push({ priority, order, fn, args, resolve, reject }); - this._resolveNext(false); - }); - } - - _resolveNext = (completed = true) => { - if (completed) this.pending -= 1; - - while (this.queue.length > 0 && this.pending < this.maxConcurrency) { - const task = this.queue.pop(); // order of insertion - this.pending += 1; - const { resolve, reject, fn, args } = task; - - try { - const result = fn(...args); - result.then( - () => this._resolveNext(true), - () => this._resolveNext(true) - ); - result.then(resolve, reject); - } catch (err) { - reject(err); - } - } - }; -} diff --git a/client/src/util/promiseLimit.ts b/client/src/util/promiseLimit.ts new file mode 100644 index 00000000..aea61444 --- /dev/null +++ b/client/src/util/promiseLimit.ts @@ -0,0 +1,114 @@ +/* +This class provides a means to resolve Promises asynchronously, +and limit the number concurrently executed. For example, if +you want to involve a large number of API endpoints using fetch(), +but want to limit the number simultaneously outstanding. + +Example usage: + +const plimit = new PromiseLimit(2); +return Promise.all([ + plimit.add(() => fetch('/foo')), + plimit.add(() => fetch('/bar')), + plimit.add(() => fetch('/baz')) +]) + +if you want a priority queue based implementation, just +use priorityAdd() instead of add(): + +const plimit = new PromiseLimit(2); +return Promise.all([ + plimit.priorityAdd(0, () => fetch('/foo')), + plimit.priorityAdd(10, () => fetch('/bar')), + plimit.priorityAdd(-1, () => fetch('/baz')) +]) + +Priority is a numeric value. Lower first. Stable ordering. +*/ + +import TinyQueue from "tinyqueue"; + +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'a' implicitly has an 'any' type. +function compare(a, b) { + const diff = a.priority - b.priority; + if (diff) return diff; + return a.order - b.order; +} + +export default class PromiseLimit { + constructor(maxConcurrency = 5) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).queue = new TinyQueue([], compare); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).maxConcurrency = maxConcurrency; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).pending = 0; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).insertCounter = 0; + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'p' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + priorityAdd(p, fn, ...args) { + // p - numermic priority (lower first) + // fn - must return a promise + // args - will be passed to fn + return this._push(p, fn, args); + } + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'fn' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + add(fn, ...args) { + // fn - must return a promise + // args - will be passed to fn + return this._push(0, fn, args); + } + + /** + Private below + **/ + + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'priority' implicitly has an 'any' type. + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + _push(priority, fn, args) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const order = (this as any).insertCount; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).insertCount += 1; + return new Promise((resolve, reject) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).queue.push({ priority, order, fn, args, resolve, reject }); + this._resolveNext(false); + }); + } + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + _resolveNext = (completed = true) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + if (completed) (this as any).pending -= 1; + + while ( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).queue.length > 0 && + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).pending < (this as any).maxConcurrency + ) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const task = (this as any).queue.pop(); // order of insertion + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (this as any).pending += 1; + const { resolve, reject, fn, args } = task; + + try { + const result = fn(...args); + result.then( + () => this._resolveNext(true), + () => this._resolveNext(true) + ); + result.then(resolve, reject); + } catch (err) { + reject(err); + } + } + }; +} diff --git a/client/src/util/quantile.js b/client/src/util/quantile.ts similarity index 71% rename from client/src/util/quantile.js rename to client/src/util/quantile.ts index 0dc528da..53a0fbf0 100644 --- a/client/src/util/quantile.js +++ b/client/src/util/quantile.ts @@ -14,12 +14,15 @@ Arguments: import { sortArray } from "./typedCrossfilter/sort"; +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'quantArr' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export default function quantile(quantArr, tarr, sorted = false) { /* start with the naive (sort) implementation. Later, use a faster partition */ const arr = sorted ? tarr : sortArray(new tarr.constructor(tarr)); // copy const len = arr.length; + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'q' implicitly has an 'any' type. return quantArr.map((q) => { if (q === 1) { return arr[len - 1]; diff --git a/client/src/util/range.js b/client/src/util/range.ts similarity index 56% rename from client/src/util/range.js rename to client/src/util/range.ts index 3d43c8b3..c05f0869 100644 --- a/client/src/util/range.js +++ b/client/src/util/range.ts @@ -22,6 +22,7 @@ rangeFill(array, start, step) -> array */ +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'arr' implicitly has an 'any' type. function _doFill(arr, start, step, count) { for (let idx = 0, val = start; idx < count; idx += 1, val += step) { arr[idx] = val; @@ -29,10 +30,14 @@ function _doFill(arr, start, step, count) { return arr; } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'arr' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function rangeFill(arr, start = 0, step = 1) { return _doFill(arr, start, step, arr.length); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'start' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function range(start, stop, step) { if (start === undefined) return []; if (stop === undefined) { @@ -44,7 +49,11 @@ export function range(start, stop, step) { return _doFill(new Array(len), start, step, len); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'start' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function linspace(start, stop, nsteps) { + // @ts-expect-error ts-migrate(2363) FIXME: The right-hand side of an arithmetic operation mus... Remove this comment to see the full error message const delta = (stop - start) / (nsteps - 1).toFixed(); + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'i' implicitly has an 'any' type. return range(0, nsteps, 1).map((i) => start + i * delta); } diff --git a/client/src/util/renderThrottle.js b/client/src/util/renderThrottle.js deleted file mode 100644 index 36c813c1..00000000 --- a/client/src/util/renderThrottle.js +++ /dev/null @@ -1,17 +0,0 @@ -export default function renderThrottle(callback) { - /* - This wraps a call to requestAnimationFrame(), enforcing a single - render callback at any given time (ie, you can call this any number - of times, and it will coallesce multiple inter-frame calls into a - single render). - */ - let rafCurrentlyInProgress = null; - return function f() { - if (rafCurrentlyInProgress) return; - const context = this; - rafCurrentlyInProgress = window.requestAnimationFrame(() => { - callback.apply(context); - rafCurrentlyInProgress = null; - }); - }; -} diff --git a/client/src/util/renderThrottle.ts b/client/src/util/renderThrottle.ts new file mode 100644 index 00000000..6f0c8439 --- /dev/null +++ b/client/src/util/renderThrottle.ts @@ -0,0 +1,21 @@ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default function renderThrottle(callback: any) { + /* + This wraps a call to requestAnimationFrame(), enforcing a single + render callback at any given time (ie, you can call this any number + of times, and it will coallesce multiple inter-frame calls into a + single render). + */ + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + let rafCurrentlyInProgress: any = null; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return function f(this: any) { + if (rafCurrentlyInProgress) return; + // eslint-disable-next-line @typescript-eslint/no-this-alias --- FIXME: disabled temporarily on migrate to TS. + const context = this; + rafCurrentlyInProgress = window.requestAnimationFrame(() => { + callback.apply(context); + rafCurrentlyInProgress = null; + }); + }; +} diff --git a/client/src/util/scaleLinear.js b/client/src/util/scaleLinear.js deleted file mode 100644 index 239a5dc0..00000000 --- a/client/src/util/scaleLinear.js +++ /dev/null @@ -1,20 +0,0 @@ -// Substitute for a d3 linear scale - less flexible, more performant. -// Returns a function which will scale a value. -// -// Example will scale [0,1] to [-1,1] -// var myScale = scaleLinear([0, 1], [-1, 1]); -// myScale(0) === -1 -// this is is equivalent to d3.scaleLinear().domain([0,1]).range([-1,1]) - -export default (domain, range) => { - const domainStart = domain[0]; - const scale = (range[1] - range[0]) / (domain[1] - domain[0]); - const invScale = 1 / scale; - const rangeStart = range[0]; - const f = (value) => (value - domainStart) * scale + rangeStart; - - // inverter - f.invert = (value) => (value - rangeStart) * invScale + domainStart; - - return f; -}; diff --git a/client/src/util/scaleLinear.ts b/client/src/util/scaleLinear.ts new file mode 100644 index 00000000..0701ab68 --- /dev/null +++ b/client/src/util/scaleLinear.ts @@ -0,0 +1,23 @@ +// Substitute for a d3 linear scale - less flexible, more performant. +// Returns a function which will scale a value. +// +// Example will scale [0,1] to [-1,1] +// var myScale = scaleLinear([0, 1], [-1, 1]); +// myScale(0) === -1 +// this is is equivalent to d3.scaleLinear().domain([0,1]).range([-1,1]) + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default (domain: any, range: any) => { + const domainStart = domain[0]; + const scale = (range[1] - range[0]) / (domain[1] - domain[0]); + const invScale = 1 / scale; + const rangeStart = range[0]; + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const f = (value: any) => (value - domainStart) * scale + rangeStart; + + // inverter + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + f.invert = (value: any) => (value - rangeStart) * invScale + domainStart; + + return f; +}; diff --git a/client/src/util/scaleRGB.js b/client/src/util/scaleRGB.ts similarity index 52% rename from client/src/util/scaleRGB.js rename to client/src/util/scaleRGB.ts index 10b42d35..c86ced8b 100644 --- a/client/src/util/scaleRGB.js +++ b/client/src/util/scaleRGB.ts @@ -1,4 +1,5 @@ -export default (input) => { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default (input: any) => { const outputMax = 1; const outputMin = 0; diff --git a/client/src/util/significantDigits.js b/client/src/util/significantDigits.js deleted file mode 100644 index 21fbf83f..00000000 --- a/client/src/util/significantDigits.js +++ /dev/null @@ -1,10 +0,0 @@ -/* - via https://github.com/nodef/extra-number/blob/master/scripts/significantDigits.js -*/ - -export default (n) => { - return n - .toExponential() - .replace(/e[+\-0-9]*$/, "") - .replace(/^0\.?0*|\./, "").length; -}; diff --git a/client/src/util/significantDigits.ts b/client/src/util/significantDigits.ts new file mode 100644 index 00000000..4d3107db --- /dev/null +++ b/client/src/util/significantDigits.ts @@ -0,0 +1,10 @@ +/* + via https://github.com/nodef/extra-number/blob/master/scripts/significantDigits.js +*/ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export default (n: any) => + n + .toExponential() + .replace(/e[+\-0-9]*$/, "") + .replace(/^0\.?0*|\./, "").length; diff --git a/client/src/util/stateManager/annotationsHelpers.js b/client/src/util/stateManager/annotationsHelpers.ts similarity index 68% rename from client/src/util/stateManager/annotationsHelpers.js rename to client/src/util/stateManager/annotationsHelpers.ts index 999ee961..e8ad554e 100644 --- a/client/src/util/stateManager/annotationsHelpers.js +++ b/client/src/util/stateManager/annotationsHelpers.ts @@ -17,6 +17,8 @@ In addition, the current state management only allows for categorical annotations to be writable. */ +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function isCategoricalAnnotation(schema, name) { /* we treat any string, categorical or boolean as a categorical. @@ -28,6 +30,8 @@ export function isCategoricalAnnotation(schema, name) { return type === "string" || type === "boolean" || type === "categorical"; } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function isContinuousAnnotation(schema, name) { /* Return true/false/undefined @@ -38,14 +42,19 @@ export function isContinuousAnnotation(schema, name) { return !(type === "string" || type === "boolean" || type === "categorical"); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'schema' implicitly has an 'any' type. function _isUserAnnotation(schema, name) { return schema.annotations.obsByName[name]?.writable || false; } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function isUserAnnotation(annoMatrix, name) { return _isUserAnnotation(annoMatrix.schema, name); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function allHaveLabelByMask(df, colName, label, mask) { // return true if all rows as indicated by mask have the colname set to label. // False if not. @@ -63,6 +72,8 @@ export function allHaveLabelByMask(df, colName, label, mask) { } const legalCharacters = /^(\w|[ .()-])+$/; +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'name' implicitly has an 'any' type. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function annotationNameIsErroneous(name) { /* Validate the name - return: diff --git a/client/src/util/stateManager/colorHelpers.js b/client/src/util/stateManager/colorHelpers.ts similarity index 58% rename from client/src/util/stateManager/colorHelpers.js rename to client/src/util/stateManager/colorHelpers.ts index 024c1daf..fb30e6a5 100644 --- a/client/src/util/stateManager/colorHelpers.js +++ b/client/src/util/stateManager/colorHelpers.ts @@ -12,7 +12,17 @@ import { range } from "../range"; given a color mode & accessor, generate an annoMatrix query that will fulfill it */ -export function createColorQuery(colorMode, colorByAccessor, schema, genesets) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function createColorQuery( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorMode: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + colorByAccessor: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + schema: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + genesets: any +) { if (!colorMode || !colorByAccessor || !schema || !genesets) return null; switch (colorMode) { @@ -83,7 +93,8 @@ export function createColorQuery(colorMode, colorByAccessor, schema, genesets) { } } -function _defaultColors(nObs) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _defaultColors(nObs: any) { const defaultCellColor = parseRGB(globals.defaultCellColor); return { rgb: new Array(nObs).fill(defaultCellColor), @@ -106,15 +117,20 @@ Returns: } */ function _createColorTable( - colorMode, - colorByAccessor, - colorByData, - schema, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colorMode: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colorByAccessor: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colorByData: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: any, userColors = null ) { switch (colorMode) { case "color by categorical metadata": { const data = colorByData.col(colorByAccessor).asArray(); + // @ts-expect-error ts-migrate(2531) FIXME: Object is possibly 'null'. if (userColors && colorByAccessor in userColors) { return createUserColors(data, colorByAccessor, schema, userColors); } @@ -148,25 +164,40 @@ export const createColorTable = memoize(_createColorTable); * - scale: function which given label returns d3 color scale for label * Order doesn't matter - everything is keyed by label value. */ -export function loadUserColorConfig(userColors) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function loadUserColorConfig(userColors: any) { const convertedUserColors = {}; Object.keys(userColors).forEach((category) => { const [colors, scaleMap] = Object.keys(userColors[category]).reduce( (acc, label) => { const color = parseRGB(userColors[category][label]); + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message acc[0][label] = color; + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message acc[1][label] = d3.rgb(255 * color[0], 255 * color[1], 255 * color[2]); return acc; }, [{}, {}] ); - const scale = (label) => scaleMap[label]; + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const scale = (label: any) => scaleMap[label]; + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message convertedUserColors[category] = { colors, scale }; }); return convertedUserColors; } -function _createUserColors(data, colorAccessor, schema, userColors) { +function _createUserColors( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + data: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colorAccessor: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + userColors: any +) { const { colors, scale: scaleByLabel } = userColors[colorAccessor]; const rgb = createRgbArray(data, colors); @@ -174,14 +205,23 @@ function _createUserColors(data, colorAccessor, schema, userColors) { // See createColorsByCategoricalMetadata() for another example. const { categories } = schema.annotations.obsByName[colorAccessor]; const categoryMap = new Map(); - categories.forEach((label, idx) => categoryMap.set(idx, label)); - const scale = (idx) => scaleByLabel(categoryMap.get(idx)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categories.forEach((label: any, idx: any) => categoryMap.set(idx, label)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const scale = (idx: any) => scaleByLabel(categoryMap.get(idx)); return { rgb, scale }; } const createUserColors = memoize(_createUserColors); -function _createColorsByCategoricalMetadata(data, colorAccessor, schema) { +function _createColorsByCategoricalMetadata( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + data: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + colorAccessor: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema: any +) { const { categories } = schema.annotations.obsByName[colorAccessor]; const scale = d3 @@ -189,7 +229,8 @@ function _createColorsByCategoricalMetadata(data, colorAccessor, schema) { .domain([0, categories.length]); /* pre-create colors - much faster than doing it for each obs */ - const colors = categories.reduce((acc, cat, idx) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const colors = categories.reduce((acc: any, cat: any, idx: any) => { acc[cat] = parseRGB(scale(idx)); return acc; }, {}); @@ -201,7 +242,8 @@ const createColorsByCategoricalMetadata = memoize( _createColorsByCategoricalMetadata ); -function createRgbArray(data, colors) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function createRgbArray(data: any, colors: any) { const rgb = new Array(data.length); for (let i = 0, len = data.length; i < len; i += 1) { const label = data[i]; @@ -210,7 +252,8 @@ function createRgbArray(data, colors) { return rgb; } -function _createColorsByContinuousMetadata(data, min, max) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _createColorsByContinuousMetadata(data: any, min: any, max: any) { const colorBins = 100; const scale = d3 .scaleQuantile() diff --git a/client/src/util/stateManager/controlsHelpers.js b/client/src/util/stateManager/controlsHelpers.ts similarity index 61% rename from client/src/util/stateManager/controlsHelpers.js rename to client/src/util/stateManager/controlsHelpers.ts index 59a3e433..d4ce919e 100644 --- a/client/src/util/stateManager/controlsHelpers.js +++ b/client/src/util/stateManager/controlsHelpers.ts @@ -4,8 +4,6 @@ Helper functions for the controls reducer import difference from "lodash.difference"; -import * as globals from "../../globals"; -import { rangeFill as fillRange } from "../range"; import fromEntries from "../fromEntries"; import { isCategoricalAnnotation } from "./annotationsHelpers"; @@ -29,40 +27,12 @@ Remember that option values can be ANY js type, except undefined/null. // number of options numCategoryValues: number, - - // isTruncated - true if the options for selection has - // been truncated (ie, was too large to implement) } } */ -function topNCategories(colSchema, summary, N) { - /* return top N categories by occurrences in the data */ - const { categories: allCategories } = colSchema; - const counts = allCategories.map( - (cat) => summary.categoryCounts.get(cat) ?? 0 - ); - if (allCategories.length <= N) { - return [allCategories, allCategories, counts]; - } - - const sortIndex = fillRange(new Array(allCategories.length)).sort( - (a, b) => counts[b] - counts[a] - ); - const topNindices = new Set(sortIndex.slice(0, N)); - - const _topNCategories = []; - const topNCounts = []; - for (let i = 0; i < allCategories.length; i += 1) { - if (topNindices.has(i)) { - _topNCategories.push(allCategories[i]); - topNCounts.push(counts[i]); - } - } - return [allCategories, _topNCategories, topNCounts]; -} - -export function isSelectableCategoryName(schema, name) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function isSelectableCategoryName(schema: any, name: any) { const { index } = schema.annotations.obs; const colSchema = schema.annotations.obsByName[name]; return ( @@ -72,7 +42,8 @@ export function isSelectableCategoryName(schema, name) { ); } -export function selectableCategoryNames(schema, names) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function selectableCategoryNames(schema: any, names: any) { /* return all obs annotation names that are categorical AND have a "reasonably" small number of categories AND are not the index column. @@ -80,12 +51,14 @@ export function selectableCategoryNames(schema, names) { If the initial name list not provided, use everything in the schema. */ if (!schema) return []; - if (!names) names = schema.annotations.obs.columns.map((c) => c.name); - return names.filter((name) => isSelectableCategoryName(schema, name)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + if (!names) names = schema.annotations.obs.columns.map((c: any) => c.name); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return names.filter((name: any) => isSelectableCategoryName(schema, name)); } -export function createCategorySummaryFromDfCol(dfCol, colSchema) { - const N = globals.maxCategoricalOptionsToDisplay; +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function createCategorySummaryFromDfCol(dfCol: any, colSchema: any) { const { writable: isUserAnno } = colSchema; /* @@ -94,31 +67,36 @@ export function createCategorySummaryFromDfCol(dfCol, colSchema) { if they are not actively used in the current annoMatrix view. */ const summary = dfCol.summarizeCategorical(); - const [ - allCategoryValues, - categoryValues, - categoryValueCounts, - ] = topNCategories(colSchema, summary, N); - const categoryValueIndices = new Map(categoryValues.map((v, i) => [v, i])); + const { categories: allCategoryValues } = colSchema; + const categoryValues = allCategoryValues; + const categoryValueCounts = allCategoryValues.map( + // eslint-disable-next-line @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + (cat: any) => summary.categoryCounts.get(cat) ?? 0 + ); + const categoryValueIndices = new Map( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + categoryValues.map((v: any, i: any) => [v, i]) + ); const numCategoryValues = categoryValueIndices.size; - const isTruncated = categoryValues.length < summary.numCategories; return { allCategoryValues, // array: of natively typed category values (all of them) categoryValues, // array: of natively typed category values (top N only) categoryValueIndices, // map: category value (native type) -> category index (top N only) numCategoryValues, // number: of values in the category (top N) - isTruncated, // bool: true if list was truncated (ie, if topN != all) categoryValueCounts, // array: cardinality of each category, (top N) isUserAnno, // bool }; } -export function createCategoricalSelection(names) { - return fromEntries(names.map((name) => [name, new Map()])); +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function createCategoricalSelection(names: any) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return fromEntries(names.map((name: any) => [name, new Map()])); } -export function pruneVarDataCache(varData, needed) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function pruneVarDataCache(varData: any, needed: any) { /* Remove any unneeded columns from the varData dataframe. Will only prune / remove if the total column count exceeds VarDataCacheLowWatermark diff --git a/client/src/util/stateManager/index.js b/client/src/util/stateManager/index.ts similarity index 100% rename from client/src/util/stateManager/index.js rename to client/src/util/stateManager/index.ts diff --git a/client/src/util/stateManager/matrix.js b/client/src/util/stateManager/matrix.ts similarity index 67% rename from client/src/util/stateManager/matrix.js rename to client/src/util/stateManager/matrix.ts index 52717157..7e76f129 100644 --- a/client/src/util/stateManager/matrix.js +++ b/client/src/util/stateManager/matrix.ts @@ -17,12 +17,14 @@ Matrix flatbuffer decoding support. See fbs/matrix.fbs /* Decode NetEncoding.TypedArray */ -function decodeTypedArray(uType, uValF, inplace = false) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function decodeTypedArray(uType: any, uValF: any, inplace = false) { if (uType === NetEncoding.TypedArray.NONE) { return null; } // Convert to a JS class that supports this type + // @ts-expect-error --- FIXME: Element implicitly has an 'any' type. const TypeClass = NetEncoding[NetEncoding.TypedArray[uType]]; // Create a TypedArray that references the underlying buffer let arr = uValF(new TypeClass()).dataArray(); @@ -48,7 +50,8 @@ Returns: object containing decoded Matrix: colIdx: []|null } */ -export function decodeMatrixFBS(arrayBuffer, inplace = false) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function decodeMatrixFBS(arrayBuffer: any, inplace = false) { const bb = new flatbuffers.ByteBuffer(new Uint8Array(arrayBuffer)); const matrix = NetEncoding.Matrix.getRootAsMatrix(bb); @@ -79,8 +82,11 @@ export function decodeMatrixFBS(arrayBuffer, inplace = false) { }; } -function encodeTypedArray(builder, uType, uData) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function encodeTypedArray(builder: any, uType: any, uData: any) { + // @ts-expect-error --- FIXME: Element implicitly has an 'any' type. const uTypeName = NetEncoding.TypedArray[uType]; + // @ts-expect-error --- FIXME: Element implicitly has an 'any' type. const ArrayType = NetEncoding[uTypeName]; const dv = ArrayType.createDataVector(builder, uData); builder.startObject(1); @@ -88,7 +94,8 @@ function encodeTypedArray(builder, uType, uData) { return builder.endObject(); } -export function encodeMatrixFBS(df) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function encodeMatrixFBS(df: any) { /* encode the dataframe as an FBS Matrix */ @@ -99,6 +106,7 @@ export function encodeMatrixFBS(df) { } const shape = df.dims; + // @ts-expect-error ts-migrate(2554) FIXME: Expected 0 arguments, but got 1. const utf8Encoder = new TextEncoder("utf-8"); const builder = new flatbuffers.Builder(1024); @@ -107,12 +115,15 @@ export function encodeMatrixFBS(df) { let encColumns; if (shape[0] > 0 && shape[1] > 0) { - const columns = df.columns().map((col) => col.asArray()); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const columns = df.columns().map((col: any) => col.asArray()); - const cols = columns.map((carr) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const cols = columns.map((carr: any) => { let uType; let tarr; if (isTypedArray(carr)) { + // @ts-expect-error --- FIXME: Element implicitly has an 'any' type. uType = NetEncoding.TypedArray[carr.constructor.name]; tarr = encodeTypedArray(builder, uType, carr); } else { @@ -168,7 +179,8 @@ export function encodeMatrixFBS(df) { return builder.asUint8Array(); } -function promoteTypedArray(o) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function promoteTypedArray(o: any) { /* Decide what internal data type to use for the data returned from the server. @@ -200,7 +212,8 @@ function promoteTypedArray(o) { return new TypedArrayCtor(o); } -export function matrixFBSToDataframe(arrayBuffers) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function matrixFBSToDataframe(arrayBuffers: any) { /* Convert array of Matrix FBS to a Dataframe. @@ -216,30 +229,37 @@ export function matrixFBSToDataframe(arrayBuffers) { arrayBuffers = [arrayBuffers]; } if (arrayBuffers.length === 0) { - return Dataframe.Dataframe.empty(); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + return (Dataframe as any).Dataframe.empty(); } - const fbs = arrayBuffers.map((ab) => decodeMatrixFBS(ab, true)); // leave in place + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + const fbs = arrayBuffers.map((ab: any) => decodeMatrixFBS(ab, true)); // leave in place /* check that all FBS have same row dimensionality */ const { nRows } = fbs[0]; - fbs.forEach((b) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + fbs.forEach((b: any) => { if (b.nRows !== nRows) throw new Error("FBS with inconsistent dimensionality"); }); - const columns = fbs - .map((fb) => - fb.columns.map((c) => { + const columns = fbs // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .map((fb: any) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + fb.columns.map((c: any) => { if (isFpTypedArray(c) || Array.isArray(c)) return c; return promoteTypedArray(c); }) ) .flat(); // colIdx may be TypedArray or Array - const colIdx = fbs - .map((b) => (Array.isArray(b.colIdx) ? b.colIdx : Array.from(b.colIdx))) + const colIdx = fbs // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + .map((b: any) => + Array.isArray(b.colIdx) ? b.colIdx : Array.from(b.colIdx) + ) .flat(); const nCols = columns.length; + // @ts-expect-error ts-migrate(2345) FIXME: Argument of type 'KeyIndex' is not assignable to p... Remove this comment to see the full error message const df = new Dataframe([nRows, nCols], columns, null, new KeyIndex(colIdx)); return df; } diff --git a/client/src/util/stateManager/schemaHelpers.js b/client/src/util/stateManager/schemaHelpers.js deleted file mode 100644 index 6a49b5ff..00000000 --- a/client/src/util/stateManager/schemaHelpers.js +++ /dev/null @@ -1,134 +0,0 @@ -/* -Helpers for schema management - -TODO: all this would be much more natural if done with a framework -like immutable.js -*/ -import cloneDeep from "lodash.clonedeep"; - -import fromEntries from "../fromEntries"; -import catLabelSort from "../catLabelSort"; - -/* -System wide schema assumptions: - - schema and data wil be consistent (eg, for user-created annotations) - - schema will be internally self-consistent (eg, index matches columns) -*/ - -export function indexEntireSchema(schema) { - /* Index schema for ease of use */ - schema.annotations.obsByName = fromEntries( - schema.annotations?.obs?.columns?.map((v) => [v.name, v]) ?? [] - ); - schema.annotations.varByName = fromEntries( - schema.annotations?.var?.columns?.map((v) => [v.name, v]) ?? [] - ); - schema.layout.obsByName = fromEntries( - schema.layout?.obs?.map((v) => [v.name, v]) ?? [] - ); - schema.layout.varByName = fromEntries( - schema.layout?.var?.map((v) => [v.name, v]) ?? [] - ); - - return schema; -} - -function _copyObsAnno(schema) { - /* redux copy conventions - WARNING, only for modifying obs annotations */ - return { - ...schema, - annotations: { - ...schema.annotations, - obs: cloneDeep(schema.annotations.obs), - }, - }; -} - -function _copyObsLayout(schema) { - return { - ...schema, - layout: { - ...schema.layout, - obs: cloneDeep(schema.layout.obs), - }, - }; -} - -function _reindexObsAnno(schema) { - /* reindex obs annotations ONLY */ - schema.annotations.obsByName = fromEntries( - schema.annotations.obs.columns.map((v) => [v.name, v]) - ); - return schema; -} - -function _reindexObsLayout(schema) { - schema.layout.obsByName = fromEntries( - schema.layout.obs.map((v) => [v.name, v]) - ); - return schema; -} - -export function removeObsAnnoColumn(schema, name) { - const newSchema = _copyObsAnno(schema); - newSchema.annotations.obs.columns = schema.annotations.obs.columns.filter( - (v) => v.name !== name - ); - return _reindexObsAnno(newSchema); -} - -export function addObsAnnoColumn(schema, name, defn) { - const newSchema = _copyObsAnno(schema); - newSchema.annotations.obs.columns.push(defn); - return _reindexObsAnno(newSchema); -} - -export function removeObsAnnoCategory(schema, name, category) { - /* remove a category from a categorical annotation */ - const categories = schema.annotations.obsByName[name]?.categories; - if (!categories) - throw new Error("column does not exist or is not categorical"); - - const idx = categories.indexOf(category); - if (idx === -1) throw new Error("category does not exist"); - - const newSchema = _reindexObsAnno(_copyObsAnno(schema)); - - /* remove category. Do not need to resort as this can't change presentation order */ - newSchema.annotations.obsByName[name].categories.splice(idx, 1); - return newSchema; -} - -export function addObsAnnoCategory(schema, name, category) { - /* add a category to a categorical annotation */ - const categories = schema.annotations.obsByName[name]?.categories; - if (!categories) - throw new Error("column does not exist or is not categorical"); - - const idx = categories.indexOf(category); - if (idx !== -1) throw new Error("category already exists"); - - const newSchema = _reindexObsAnno(_copyObsAnno(schema)); - - /* add category, retaining presentation sort order */ - const catAnno = newSchema.annotations.obsByName[name]; - catAnno.categories = catLabelSort(catAnno.writable, [ - ...catAnno.categories, - category, - ]); - return newSchema; -} - -export function addObsLayout(schema, layout) { - /* add or replace a layout */ - const newSchema = _copyObsLayout(schema); - newSchema.layout.obs.push(layout); - return _reindexObsLayout(newSchema); -} - -export function removeObsLayout(schema, name) { - /* remove a layout */ - const newSchema = _copyObsLayout(schema); - newSchema.layout.obs = schema.layout.obs.filter((v) => v.name !== name); - return _reindexObsLayout(newSchema); -} diff --git a/client/src/util/stateManager/schemaHelpers.ts b/client/src/util/stateManager/schemaHelpers.ts new file mode 100644 index 00000000..090e18cf --- /dev/null +++ b/client/src/util/stateManager/schemaHelpers.ts @@ -0,0 +1,154 @@ +/* +Helpers for schema management + +TODO: all this would be much more natural if done with a framework +like immutable.js +*/ +import cloneDeep from "lodash.clonedeep"; + +import fromEntries from "../fromEntries"; +import catLabelSort from "../catLabelSort"; + +/* +System wide schema assumptions: + - schema and data wil be consistent (eg, for user-created annotations) + - schema will be internally self-consistent (eg, index matches columns) +*/ + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function indexEntireSchema(schema: any) { + /* Index schema for ease of use */ + schema.annotations.obsByName = fromEntries( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.annotations?.obs?.columns?.map((v: any) => [v.name, v]) ?? [] + ); + schema.annotations.varByName = fromEntries( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.annotations?.var?.columns?.map((v: any) => [v.name, v]) ?? [] + ); + schema.layout.obsByName = fromEntries( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.layout?.obs?.map((v: any) => [v.name, v]) ?? [] + ); + schema.layout.varByName = fromEntries( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.layout?.var?.map((v: any) => [v.name, v]) ?? [] + ); + + return schema; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _copyObsAnno(schema: any) { + /* redux copy conventions - WARNING, only for modifying obs annotations */ + return { + ...schema, + annotations: { + ...schema.annotations, + obs: cloneDeep(schema.annotations.obs), + }, + }; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _copyObsLayout(schema: any) { + return { + ...schema, + layout: { + ...schema.layout, + obs: cloneDeep(schema.layout.obs), + }, + }; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _reindexObsAnno(schema: any) { + /* reindex obs annotations ONLY */ + schema.annotations.obsByName = fromEntries( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.annotations.obs.columns.map((v: any) => [v.name, v]) + ); + return schema; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function _reindexObsLayout(schema: any) { + schema.layout.obsByName = fromEntries( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + schema.layout.obs.map((v: any) => [v.name, v]) + ); + return schema; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function removeObsAnnoColumn(schema: any, name: any) { + const newSchema = _copyObsAnno(schema); + newSchema.annotations.obs.columns = schema.annotations.obs.columns.filter( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (v: any) => v.name !== name + ); + return _reindexObsAnno(newSchema); +} + +// @ts-expect-error ts-migrate(6133) FIXME: 'name' is declared but its value is never read. +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function addObsAnnoColumn(schema: any, name: any, defn: any) { + const newSchema = _copyObsAnno(schema); + newSchema.annotations.obs.columns.push(defn); + return _reindexObsAnno(newSchema); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function removeObsAnnoCategory(schema: any, name: any, category: any) { + /* remove a category from a categorical annotation */ + const categories = schema.annotations.obsByName[name]?.categories; + if (!categories) + throw new Error("column does not exist or is not categorical"); + + const idx = categories.indexOf(category); + if (idx === -1) throw new Error("category does not exist"); + + const newSchema = _reindexObsAnno(_copyObsAnno(schema)); + + /* remove category. Do not need to resort as this can't change presentation order */ + newSchema.annotations.obsByName[name].categories.splice(idx, 1); + return newSchema; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function addObsAnnoCategory(schema: any, name: any, category: any) { + /* add a category to a categorical annotation */ + const categories = schema.annotations.obsByName[name]?.categories; + if (!categories) + throw new Error("column does not exist or is not categorical"); + + const idx = categories.indexOf(category); + if (idx !== -1) throw new Error("category already exists"); + + const newSchema = _reindexObsAnno(_copyObsAnno(schema)); + + /* add category, retaining presentation sort order */ + const catAnno = newSchema.annotations.obsByName[name]; + catAnno.categories = catLabelSort(catAnno.writable, [ + ...catAnno.categories, + category, + ]); + return newSchema; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function addObsLayout(schema: any, layout: any) { + /* add or replace a layout */ + const newSchema = _copyObsLayout(schema); + newSchema.layout.obs.push(layout); + return _reindexObsLayout(newSchema); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function removeObsLayout(schema: any, name: any) { + /* remove a layout */ + const newSchema = _copyObsLayout(schema); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + newSchema.layout.obs = schema.layout.obs.filter((v: any) => v.name !== name); + return _reindexObsLayout(newSchema); +} diff --git a/client/src/util/stateManager/viewStackHelpers.js b/client/src/util/stateManager/viewStackHelpers.ts similarity index 71% rename from client/src/util/stateManager/viewStackHelpers.js rename to client/src/util/stateManager/viewStackHelpers.ts index c1f3bac8..d2e22583 100644 --- a/client/src/util/stateManager/viewStackHelpers.js +++ b/client/src/util/stateManager/viewStackHelpers.ts @@ -38,6 +38,8 @@ Views can be interogated for their type with the following: import { clip, isubsetMask, isubset } from "../../annoMatrix"; import { memoize } from "../dataframe/util"; +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function _clipAnnoMatrix(annoMatrix, min, max) { /* clip the annoMatrix. @@ -47,6 +49,8 @@ export function _clipAnnoMatrix(annoMatrix, min, max) { : clip(annoMatrix, min, max); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function _userSubsetAnnoMatrix(annoMatrix, mask) { /* user-requested row subset of annoMatrix, to be added on top of any @@ -61,12 +65,15 @@ export function _userSubsetAnnoMatrix(annoMatrix, mask) { annoMatrix.userFlags.isUserSubsetView = true; if (clipRange) { + // @ts-expect-error ts-migrate(2556) FIXME: Expected 3 arguments, but got 1 or more. annoMatrix = clip(annoMatrix, ...clipRange); } return annoMatrix; } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function _userResetSubsetAnnoMatrix(annoMatrix) { /* Reset/remove all user-requested subsets. Do not remove clip or embedding subset. @@ -85,12 +92,15 @@ export function _userResetSubsetAnnoMatrix(annoMatrix) { /* re-apply the clip, if any */ if (clipRange) { + // @ts-expect-error ts-migrate(2556) FIXME: Expected 3 arguments, but got 1 or more. annoMatrix = clip(annoMatrix, ...clipRange); } return annoMatrix; } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function _setEmbeddingSubset(annoMatrix, embeddingDf) { /* Set the embedding subset view. Only create a subset view for the embedding @@ -124,12 +134,14 @@ export function _setEmbeddingSubset(annoMatrix, embeddingDf) { /* re-apply clip, if needed */ if (clipRange) { + // @ts-expect-error ts-migrate(2556) FIXME: Expected 3 arguments, but got 1 or more. annoMatrix = clip(annoMatrix, ...clipRange); } return annoMatrix; } +// @ts-expect-error ts-migrate(6133) FIXME: 'baseRowIndex' is declared but its value is never ... Remove this comment to see the full error message function _getEmbeddingRowOffsets(baseRowIndex, embeddingDf) { /* given a dataframe containing an embedding: @@ -155,6 +167,8 @@ function _getEmbeddingRowOffsets(baseRowIndex, embeddingDf) { return offsets.subarray(0, numOffsets); } +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'embeddingDf' implicitly has an 'any' ty... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function _getDiscreteCellEmbeddingRowIndex(embeddingDf) { const idx = _getEmbeddingRowOffsets(embeddingDf.rowIndex, embeddingDf); if (idx === null) return embeddingDf.rowIndex; @@ -162,9 +176,12 @@ export function _getDiscreteCellEmbeddingRowIndex(embeddingDf) { } export const getDiscreteCellEmbeddingRowIndex = memoize( _getDiscreteCellEmbeddingRowIndex, + // @ts-expect-error ts-migrate(7006) FIXME: Parameter 'df' implicitly has an 'any' type. (df) => df.__id ); +// @ts-expect-error ts-migrate(7006) FIXME: Parameter 'annoMatrix' implicitly has an 'any' typ... Remove this comment to see the full error message +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. export function getEmbSubsetView(annoMatrix) { /* if there is an embedding subset in the view stack, return it. Falsish if not. */ while (annoMatrix.isView) { diff --git a/client/src/util/statemachine/index.js b/client/src/util/statemachine/index.ts similarity index 59% rename from client/src/util/statemachine/index.js rename to client/src/util/statemachine/index.ts index 3c3f11e0..05e7edd7 100644 --- a/client/src/util/statemachine/index.js +++ b/client/src/util/statemachine/index.ts @@ -43,13 +43,30 @@ Example: */ export default class StateMachine { - constructor(initState, transitions, onError) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + events: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + graph: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + onError: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + state: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + states: any; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(initState: any, transitions: any, onError: any) { this.onError = onError || (() => undefined); this.state = initState; // all states this.states = new Set( - transitions.reduce((names, tsn) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + transitions.reduce((names: any, tsn: any) => { names.push(tsn.from); names.push(tsn.to); return names; @@ -57,11 +74,13 @@ export default class StateMachine { ); // all transition names (aka events) - this.events = new Set(transitions.map((tsn) => tsn.event)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.events = new Set(transitions.map((tsn: any) => tsn.event)); // the transition graph. // graph[event][from] -> transition - this.graph = transitions.reduce((graph, tsn) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + this.graph = transitions.reduce((graph: any, tsn: any) => { const { event, from } = tsn; if (!graph.has(event)) graph.set(event, new Map()); const tsnMap = graph.get(event); @@ -70,7 +89,9 @@ export default class StateMachine { }, new Map()); } - clone(initState) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + clone(initState: any) { + // @ts-expect-error ts-migrate(2554) FIXME: Expected 3 arguments, but got 2. const fsm = new StateMachine(initState, []); fsm.onError = this.onError; fsm.states = this.states; @@ -79,7 +100,8 @@ export default class StateMachine { return fsm; } - next(event, data) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + next(event: any, data: any) { const { graph, state } = this; const tsnMap = graph.get(event); if (!tsnMap) return this.onError(this, event, state, undefined); diff --git a/client/src/util/typeHelpers.js b/client/src/util/typeHelpers.js deleted file mode 100644 index 67858c4f..00000000 --- a/client/src/util/typeHelpers.js +++ /dev/null @@ -1,29 +0,0 @@ -/* -Various type and schema related helper functions. -*/ - -/* -Utility function to test for a typed array -*/ -export function isTypedArray(x) { - return ( - ArrayBuffer.isView(x) && - Object.prototype.toString.call(x) !== "[object DataView]" - ); -} - -/* -Test for float typed array, ie, Float32TypedArray or Float64TypedArray -*/ -export function isFpTypedArray(x) { - let constructor; - const isFloatArray = - x && - ({ constructor } = x) && - (constructor === Float32Array || constructor === Float64Array); - return isFloatArray; -} - -export function isArrayOrTypedArray(x) { - return Array.isArray(x) || isTypedArray(x); -} diff --git a/client/src/util/typeHelpers.ts b/client/src/util/typeHelpers.ts new file mode 100644 index 00000000..179be5c9 --- /dev/null +++ b/client/src/util/typeHelpers.ts @@ -0,0 +1,32 @@ +/* +Various type and schema related helper functions. +*/ + +/* +Utility function to test for a typed array +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function isTypedArray(x: any) { + return ( + ArrayBuffer.isView(x) && + Object.prototype.toString.call(x) !== "[object DataView]" + ); +} + +/* +Test for float typed array, ie, Float32TypedArray or Float64TypedArray +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function isFpTypedArray(x: any) { + let constructor; + const isFloatArray = + x && + ({ constructor } = x) && + (constructor === Float32Array || constructor === Float64Array); + return isFloatArray; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function isArrayOrTypedArray(x: any) { + return Array.isArray(x) || isTypedArray(x); +} diff --git a/client/src/util/typedCrossfilter/bitArray.js b/client/src/util/typedCrossfilter/bitArray.ts similarity index 66% rename from client/src/util/typedCrossfilter/bitArray.js rename to client/src/util/typedCrossfilter/bitArray.ts index 73f7aa78..5ee893db 100644 --- a/client/src/util/typedCrossfilter/bitArray.js +++ b/client/src/util/typedCrossfilter/bitArray.ts @@ -17,7 +17,23 @@ // The underlying data structure uses TypedArrays for performance. // class BitArray { - constructor(length) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + bitarray: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + bitmask: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dimensionCount: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + length: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + width: any; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(length: any) { // Initially allocate a 32 bit wide array. allocDimension() will expand // as necessary. // @@ -40,12 +56,14 @@ class BitArray { // Return the number of records that are selected, ie, have a one bit in // all allocated dimensions. // + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. selectionCount() { return this.countAllOnes(); } // Count all records that have a 'one' bit in allocated dimensions. // + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. countAllOnes() { let count = 0; const { bitarray, length, width } = this; @@ -76,7 +94,8 @@ class BitArray { // count trailing zeros - hard to do fast in JS! // https://en.wikipedia.org/wiki/Find_first_set#CTZ - static ctz(av) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static ctz(av: any) { let c = 32; let v = av; v &= -v; // isolate lowest non-zero bit @@ -90,6 +109,7 @@ class BitArray { } // find a free dimension. Return undefined if none + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _findFreeDimension() { let dim; for (let col = 0; col < this.width; col += 1) { @@ -105,6 +125,7 @@ class BitArray { // allocate and return the dimension ID (bit position) // + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. allocDimension() { let dim = this._findFreeDimension(); @@ -130,7 +151,8 @@ class BitArray { // free a dimension for later use. MUST deselect the dimension, as other // code assume the column will be zero valued. // - freeDimension(dim) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + freeDimension(dim: any) { // all selection tests assume unallocated dimensions are zero valued. this.deselectAll(dim); const col = dim >>> 5; @@ -140,7 +162,8 @@ class BitArray { // return true if this index is selected in ALL dimensions. // - isSelected(index) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isSelected(index: any) { const { width, length, bitarray } = this; for (let w = 0; w < width; w += 1) { @@ -152,7 +175,8 @@ class BitArray { // return true if this index is selected in ALL dimensions IGNORING dim // - isSelectedIgnoringDim(index, dim) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isSelectedIgnoringDim(index: any, dim: any) { const ignoreOffset = dim >>> 5; const ignoreMask = ~(1 << dim % 32); @@ -176,7 +200,8 @@ class BitArray { // select index on dimension // - selectOne(dim, index) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectOne(dim: any, index: any) { const col = dim >>> 5; const before = this.bitarray[col * this.length + index]; const after = before | (1 << dim % 32); @@ -185,7 +210,8 @@ class BitArray { // deselect index on dimension // - deselectOne(dim, index) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + deselectOne(dim: any, index: any) { const col = dim >>> 5; const before = this.bitarray[col * this.length + index]; const after = before & ~(1 << dim % 32); @@ -194,7 +220,8 @@ class BitArray { // select all indices on dimension. // - selectAll(dim) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectAll(dim: any) { const col = dim >> 5; const one = 1 << dim % 32; for (let i = col * this.length, len = i + this.length; i < len; i += 1) { @@ -204,7 +231,8 @@ class BitArray { // deselect all indices on dimension // - deselectAll(dim) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + deselectAll(dim: any) { const col = dim >> 5; const zero = ~(1 << dim % 32); for (let i = col * this.length, len = i + this.length; i < len; i += 1) { @@ -214,7 +242,8 @@ class BitArray { // select range of indices on a dimension // - selectFromRange(dim, range) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectFromRange(dim: any, range: any) { const col = dim >>> 5; const first = range[0]; const last = range[1]; @@ -228,7 +257,8 @@ class BitArray { // select range of indices on a dimension, indirect through a sort map. // Indirect functions are used to map between sort and natural order. // - selectIndirectFromRange(dim, indirect, range) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectIndirectFromRange(dim: any, indirect: any, range: any) { const col = dim >>> 5; const first = range[0]; const last = range[1]; @@ -241,7 +271,8 @@ class BitArray { // deselect range of indices on a dimension // - deselectFromRange(dim, range) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + deselectFromRange(dim: any, range: any) { const col = dim >>> 5; const first = range[0]; const last = range[1]; @@ -254,7 +285,8 @@ class BitArray { // deselect range of indices on a dimension, indirect through a sort map. // - deselectIndirectFromRange(dim, indirect, range) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + deselectIndirectFromRange(dim: any, indirect: any, range: any) { const col = dim >>> 5; const first = range[0]; const last = range[1]; @@ -268,7 +300,8 @@ class BitArray { // Fill the array with selected|deselected value based upon the // current selection state. // - fillBySelection(result, selectedValue, deselectedValue) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + fillBySelection(result: any, selectedValue: any, deselectedValue: any) { // special case (width === 1) for performance if (this.width === 1) { const { bitmask, bitarray } = this; diff --git a/client/src/util/typedCrossfilter/crossfilter.js b/client/src/util/typedCrossfilter/crossfilter.ts similarity index 63% rename from client/src/util/typedCrossfilter/crossfilter.js rename to client/src/util/typedCrossfilter/crossfilter.ts index 6e51d331..7b4ec264 100644 --- a/client/src/util/typedCrossfilter/crossfilter.js +++ b/client/src/util/typedCrossfilter/crossfilter.ts @@ -11,7 +11,8 @@ import { import { makeSortIndex } from "./util"; class NotImplementedError extends Error { - constructor(...params) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + constructor(...params: any[]) { super(...params); // Maintains proper stack trace for where our error was thrown (only available on V8) @@ -22,7 +23,17 @@ class NotImplementedError extends Error { } export default class ImmutableTypedCrossfilter { - constructor(data, dimensions = {}, selectionCache = {}) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + data: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dimensions: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + selectionCache: any; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(data: any, dimensions = {}, selectionCache = {}) { /* Typically, parameter 'data' is one of: - Array of objects/records @@ -51,31 +62,37 @@ export default class ImmutableTypedCrossfilter { Object.preventExtensions(this); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. size() { return this.data.length; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. all() { return this.data; } - setData(data) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + setData(data: any) { if (this.data === data) return this; // please leave, WIP // console.log("...crossfilter set data, will drop cache"); return new ImmutableTypedCrossfilter(data, this.dimensions); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. dimensionNames() { /* return array of all dimensions (by name) */ return Object.keys(this.dimensions); } - hasDimension(name) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + hasDimension(name: any) { return !!this.dimensions[name]; } - addDimension(name, type, ...rest) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + addDimension(name: any, type: any, ...rest: any[]) { /* Add a new dimension to this crossfilter, of type DimensionType. Remainder of parameters are dimension-type-specific. @@ -94,6 +111,7 @@ export default class ImmutableTypedCrossfilter { id = bitArray.allocDimension(); bitArray.selectAll(id); } + // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message const DimensionType = DimTypes[type]; const dim = new DimensionType(name, data, ...rest); Object.freeze(dim); @@ -112,7 +130,8 @@ export default class ImmutableTypedCrossfilter { }); } - delDimension(name) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + delDimension(name: any) { const { data } = this; const { bitArray } = this.selectionCache; const dimensions = { ...this.dimensions }; @@ -132,7 +151,8 @@ export default class ImmutableTypedCrossfilter { }); } - renameDimension(oldName, newName) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + renameDimension(oldName: any, newName: any) { const { [oldName]: dim, ...dimensions } = this.dimensions; const { data, selectionCache } = this; const newDimensions = { @@ -146,7 +166,8 @@ export default class ImmutableTypedCrossfilter { return new ImmutableTypedCrossfilter(data, newDimensions, selectionCache); } - select(name, spec) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + select(name: any, spec: any) { /* select on named dimension, as indicated by `spec`. Spec is an object specifying the selection, and must contain at least a `mode` field. @@ -174,7 +195,17 @@ export default class ImmutableTypedCrossfilter { return new ImmutableTypedCrossfilter(data, dimensions, newSelectionCache); } - static _dimSelnHasUpdated(selectionCache, id, newSeln, oldSeln) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. + static _dimSelnHasUpdated( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectionCache: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + id: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + newSeln: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + oldSeln: any + ) { /* Selection has updated from oldSeln to newSeln. Update the bit array if it exists. If not, we will lazy create it when @@ -208,24 +239,29 @@ export default class ImmutableTypedCrossfilter { If sort index exists in the dimension, assume sort ordered ranges. */ if (oldSeln.index) { - dels.forEach((interval) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dels.forEach((interval: any) => bitArray.deselectIndirectFromRange(id, oldSeln.index, interval) ); } else { - dels.forEach((interval) => bitArray.deselectFromRange(id, interval)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + dels.forEach((interval: any) => bitArray.deselectFromRange(id, interval)); } if (newSeln.index) { - adds.forEach((interval) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + adds.forEach((interval: any) => bitArray.selectIndirectFromRange(id, newSeln.index, interval) ); } else { - adds.forEach((interval) => bitArray.selectFromRange(id, interval)); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + adds.forEach((interval: any) => bitArray.selectFromRange(id, interval)); } return { bitArray }; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _getSelectionCache() { if (!this.selectionCache) this.selectionCache = {}; @@ -237,7 +273,8 @@ export default class ImmutableTypedCrossfilter { const id = bitArray.allocDimension(); this.dimensions[name].id = id; const { ranges, index } = selection; - ranges.forEach((range) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + ranges.forEach((range: any) => { if (index) { bitArray.selectIndirectFromRange(id, index, range); } else { @@ -250,16 +287,19 @@ export default class ImmutableTypedCrossfilter { return this.selectionCache; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _clearSelectionCache() { this.selectionCache = {}; return this.selectionCache; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. _setSelectionCache(vals = {}) { Object.assign(this.selectionCache, vals); return this.selectionCache; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. allSelected() { /* return array of all records currently selected by all dimensions @@ -280,6 +320,7 @@ export default class ImmutableTypedCrossfilter { return data.isubsetMask(this.allSelectedMask()); } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. allSelectedMask() { /* return Uint8Array containing selection state (truthy/falsey) for each record. @@ -298,6 +339,7 @@ export default class ImmutableTypedCrossfilter { return allSelectedMask; } + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. countSelected() { /* return number of records selected on all dimensions @@ -312,7 +354,8 @@ export default class ImmutableTypedCrossfilter { return countSelected; } - isElementSelected(i) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + isElementSelected(i: any) { /* return truthy/falsey if this record is selected on all dimensions */ @@ -320,7 +363,8 @@ export default class ImmutableTypedCrossfilter { return selectionCache.bitArray.isSelected(i); } - fillByIsSelected(array, selectedValue, deselectedValue) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + fillByIsSelected(array: any, selectedValue: any, deselectedValue: any) { /* fill array with one of two values, based upon selection state. */ @@ -345,7 +389,11 @@ for a dimension: - name - the dimension name/label. */ class _ImmutableBaseDimension { - constructor(name) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + name: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + constructor(name: any) { this.name = name; } @@ -353,13 +401,15 @@ class _ImmutableBaseDimension { return Object.assign(Object.create(Object.getPrototypeOf(this)), this); } - rename(name) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + rename(name: any) { const d = this.clone(); d.name = name; return d; } - select(spec) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + select(spec: any) { const { mode } = spec; if (mode === undefined) { throw new Error("select spec does not contain 'mode'"); @@ -371,7 +421,14 @@ class _ImmutableBaseDimension { } class ImmutableScalarDimension extends _ImmutableBaseDimension { - constructor(name, data, value, ValueArrayType) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + index: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + value: any; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(name: any, data: any, value: any, ValueArrayType: any) { super(name); // Three modes - caller can provide a pre-created value array, @@ -398,7 +455,8 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension { // only by enumerated dimensions array = this._createValueArray( data, - (i) => value[i], + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + (i: any) => value[i], new ValueArrayType(data.length) ); } else { @@ -412,8 +470,8 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension { this.index = makeSortIndex(array); } - // eslint-disable-next-line class-methods-use-this -- needed for polymorphism - _createValueArray(data, mapf, array) { + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- needed for polymorphism + _createValueArray(data: any, mapf: any, array: any) { // create dimension value array const len = data.length; const larray = array; @@ -423,7 +481,8 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension { return larray; } - select(spec) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + select(spec: any) { const { mode } = spec; const { index } = this; switch (mode) { @@ -440,7 +499,8 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension { } } - selectExact(spec) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectExact(spec: any) { const { value, index } = this; let { values } = spec; if (!Array.isArray(values)) { @@ -459,7 +519,8 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension { return { ranges, index }; } - selectRange(spec) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectRange(spec: any) { const { value, index } = this; /* if !inclusive: [lo, hi) else [lo, hi] @@ -478,11 +539,13 @@ class ImmutableScalarDimension extends _ImmutableBaseDimension { } class ImmutableEnumDimension extends ImmutableScalarDimension { - constructor(name, data, value) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(name: any, data: any, value: any) { super(name, data, value, Uint32Array); } - _createValueArray(data, mapf, array) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + _createValueArray(data: any, mapf: any, array: any) { const len = data.length; const larray = array; @@ -493,6 +556,7 @@ class ImmutableEnumDimension extends ImmutableScalarDimension { s.add(mapf(i, data)); } const enumIndex = sortArray(Array.from(s)); + // @ts-expect-error FIXME Adding enumIndex as member variable results in "undefined" enumIndex value this.enumIndex = enumIndex; // create dimension value array @@ -505,7 +569,9 @@ class ImmutableEnumDimension extends ImmutableScalarDimension { return larray; } - selectExact(spec) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectExact(spec: any) { + // @ts-expect-error FIXME Adding enumIndex as member variable results in "undefined" enumIndex value const { enumIndex } = this; let { values } = spec; if (!Array.isArray(values)) { @@ -513,20 +579,35 @@ class ImmutableEnumDimension extends ImmutableScalarDimension { } return super.selectExact({ mode: spec.mode, - values: values.map((v) => + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + values: values.map((v: any) => binarySearch(enumIndex, v, 0, enumIndex.length) ), }); } - // eslint-disable-next-line class-methods-use-this -- enables polymorphism + // @ts-expect-error ts-migrate(2416) FIXME: Property 'selectRange' in type 'ImmutableEnumDimen... Remove this comment to see the full error message + // eslint-disable-next-line class-methods-use-this, @typescript-eslint/explicit-module-boundary-types -- enables polymorphism selectRange() { throw new Error("range selection unsupported on Enumerated dimension"); } } class ImmutableSpatialDimension extends _ImmutableBaseDimension { - constructor(name, data, X, Y) { + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + X: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + Xindex: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + Y: any; + + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + Yindex: any; + + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + constructor(name: any, data: any, X: any, Y: any) { super(name); if (X.length !== Y.length && X.length !== data.length) { @@ -541,7 +622,8 @@ class ImmutableSpatialDimension extends _ImmutableBaseDimension { this.Yindex = makeSortIndex(Y); } - select(spec) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + select(spec: any) { const { mode } = spec; switch (mode) { case "all": @@ -557,7 +639,8 @@ class ImmutableSpatialDimension extends _ImmutableBaseDimension { } } - selectWithinRect(spec) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectWithinRect(spec: any) { /* { mode: "within-rect", minX: 1, minY: 0, maxX: 3, maxY: 9 } */ @@ -590,7 +673,8 @@ class ImmutableSpatialDimension extends _ImmutableBaseDimension { * then the polygon test is applied */ - selectWithinPolygon(spec) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + selectWithinPolygon(spec: any) { /* { mode: "within-polygon", polygon: [ [x0, y0], ... ] } */ @@ -645,7 +729,8 @@ export const DimTypes = { spatial: ImmutableSpatialDimension, }; -function isArrayOrTypedArray(x) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function isArrayOrTypedArray(x: any) { return ( Array.isArray(x) || (ArrayBuffer.isView(x) && @@ -654,7 +739,8 @@ function isArrayOrTypedArray(x) { } /* return bounding box of the polygon */ -function polygonBoundingBox(polygon) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function polygonBoundingBox(polygon: any) { let minX = Number.MAX_VALUE; let minY = Number.MAX_VALUE; let maxX = Number.MIN_VALUE; @@ -678,7 +764,8 @@ function polygonBoundingBox(polygon) { * @param {float} y - point y coordinate * @type {boolean} */ -function withinPolygon(polygon, x, y) { +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function withinPolygon(polygon: any, x: any, y: any) { const n = polygon.length; let p = polygon[n - 1]; let x0 = p[0]; diff --git a/client/src/util/typedCrossfilter/index.js b/client/src/util/typedCrossfilter/index.ts similarity index 100% rename from client/src/util/typedCrossfilter/index.js rename to client/src/util/typedCrossfilter/index.ts diff --git a/client/src/util/typedCrossfilter/positiveIntervals.js b/client/src/util/typedCrossfilter/positiveIntervals.ts similarity index 75% rename from client/src/util/typedCrossfilter/positiveIntervals.js rename to client/src/util/typedCrossfilter/positiveIntervals.ts index 8fe7e54f..2545fd4c 100644 --- a/client/src/util/typedCrossfilter/positiveIntervals.js +++ b/client/src/util/typedCrossfilter/positiveIntervals.ts @@ -16,10 +16,12 @@ class PositiveIntervals { // 1. no overlapping intervals // 2. sorted in order of interval min. // - static canonicalize(A) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static canonicalize(A: any) { if (A.length <= 1) return A; const copy = A.slice(); - copy.sort((a, b) => a[0] - b[0]); + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + copy.sort((a: any, b: any) => a[0] - b[0]); const res = []; res.push(copy[0]); for (let i = 1, len = copy.length; i < len; i += 1) { @@ -38,11 +40,13 @@ class PositiveIntervals { // Return interval with values belonging to both A and B. Essentially // a set union operation. // - static union(A, B) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static union(A: any, B: any) { return PositiveIntervals.canonicalize([...A, ...B]); } - static _flatten(A, B) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static _flatten(A: any, B: any) { const points = []; /* point, A, start */ for (let a = 0; a < A.length; a += 1) { points.push([A[a][0], true, true]); @@ -60,7 +64,8 @@ class PositiveIntervals { // A - B, ie, the interval with all values in A that are not in B. Essentially // a set difference operation. // - static difference(A, B) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static difference(A: any, B: any) { // Corner cases if (A.length === 0 || B.length === 0) { return PositiveIntervals.canonicalize(A); @@ -96,7 +101,8 @@ class PositiveIntervals { // Return interval with values belonging to A or B. Essentially a set // intersection. // - static intersection(A, B) { + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + static intersection(A: any, B: any) { if (A.length === 0 || B.length === 0) { return []; } diff --git a/client/src/util/typedCrossfilter/sort.js b/client/src/util/typedCrossfilter/sort.js deleted file mode 100644 index 700d1de4..00000000 --- a/client/src/util/typedCrossfilter/sort.js +++ /dev/null @@ -1,429 +0,0 @@ -import { isTypedArray, isFpTypedArray } from "../typeHelpers"; - -/* eslint-disable no-bitwise -- code relies on bitwise ops */ - -/* - ** fast sort and search, with separate code paths for floats (NaN ordering), - ** indirect and direct search/sort. - */ - -/* -Comparators for float sort. -Infinity < finite < Infinity < NaN -*/ -function lt(a, b) { - if (Number.isNaN(b)) return !Number.isNaN(a); - return a < b; -} - -function gt(a, b) { - if (Number.isNaN(a)) return !Number.isNaN(b); - return a > b; -} - -/* -insertion sort, used for small arrays (controlled by SMALL_ARRAY constant) -*/ -const SMALL_ARRAY = 32; -function insertionsort(a, lo, hi) { - for (let i = lo + 1; i < hi + 1; i += 1) { - const x = a[i]; - let j; - for (j = i; j > lo && a[j - 1] > x; j -= 1) { - a[j] = a[j - 1]; - } - a[j] = x; - } - return a; -} - -function insertionsortFloats(a, lo, hi) { - for (let i = lo + 1; i < hi + 1; i += 1) { - const x = a[i]; - let j; - for (j = i; j > lo && gt(a[j - 1], x); j -= 1) { - a[j] = a[j - 1]; - } - a[j] = x; - } - return a; -} - -function insertionsortIndirect(a, s, lo, hi) { - for (let i = lo + 1; i < hi + 1; i += 1) { - const x = a[i]; - const t = s[x]; - let j; - for (j = i; j > lo && s[a[j - 1]] > t; j -= 1) { - a[j] = a[j - 1]; - } - a[j] = x; - } - return a; -} - -function insertionsortFloatsIndirect(a, s, lo, hi) { - for (let i = lo + 1; i < hi + 1; i += 1) { - const x = a[i]; - const t = s[x]; - let j; - for (j = i; j > lo && gt(s[a[j - 1]], t); j -= 1) { - a[j] = a[j - 1]; - } - a[j] = x; - } - return a; -} - -/* -Quicksort - used for larger arrays -*/ -function quicksort(a, lo, hi) { - if (hi - lo < SMALL_ARRAY) { - return insertionsort(a, lo, hi); - } - if (lo < hi) { - // partition - const mid = Math.floor((lo + hi) / 2); - const p = a[mid]; - let i = lo - 1; - let j = hi + 1; - while (i < j) { - do { - i += 1; - } while (a[i] < p); - do { - j -= 1; - } while (a[j] > p); - if (i < j) { - const tmp = a[i]; - a[i] = a[j]; - a[j] = tmp; - } - } - // sort - quicksort(a, lo, j); - quicksort(a, j + 1, hi); - } - return a; -} - -function quicksortFloats(a, lo, hi) { - if (hi - lo < SMALL_ARRAY) { - return insertionsortFloats(a, lo, hi); - } - if (lo < hi) { - // partition - const mid = Math.floor((lo + hi) / 2); - const p = a[mid]; - let i = lo - 1; - let j = hi + 1; - while (i < j) { - do { - i += 1; - } while (lt(a[i], p)); - do { - j -= 1; - } while (gt(a[j], p)); - if (i < j) { - const tmp = a[i]; - a[i] = a[j]; - a[j] = tmp; - } - } - // sort - quicksortFloats(a, lo, j); - quicksortFloats(a, j + 1, hi); - } - return a; -} - -function quicksortIndirect(a, s, lo, hi) { - if (hi - lo < SMALL_ARRAY) { - return insertionsortIndirect(a, s, lo, hi); - } - if (lo < hi) { - // partition - const mid = Math.floor((lo + hi) / 2); - const p = a[mid]; - const t = s[p]; - let i = lo - 1; - let j = hi + 1; - while (i < j) { - do { - i += 1; - } while (s[a[i]] < t); - do { - j -= 1; - } while (s[a[j]] > t); - if (i < j) { - const tmp = a[i]; - a[i] = a[j]; - a[j] = tmp; - } - } - // sort - quicksortIndirect(a, s, lo, j); - quicksortIndirect(a, s, j + 1, hi); - } - return a; -} - -function quicksortFloatsIndirect(a, s, lo, hi) { - if (hi - lo < SMALL_ARRAY) { - return insertionsortFloatsIndirect(a, s, lo, hi); - } - if (lo < hi) { - // partition - const mid = Math.floor((lo + hi) / 2); - const p = a[mid]; - const t = s[p]; - let i = lo - 1; - let j = hi + 1; - while (i < j) { - do { - i += 1; - } while (lt(s[a[i]], t)); - do { - j -= 1; - } while (gt(s[a[j]], t)); - if (i < j) { - const tmp = a[i]; - a[i] = a[j]; - a[j] = tmp; - } - } - // sort - quicksortFloatsIndirect(a, s, lo, j); - quicksortFloatsIndirect(a, s, j + 1, hi); - } - return a; -} - -/* -Convenience wrappers, handling optimization paths and default -handlers for NaN comparisons. Sorts in place. -*/ -export function sortArray(arr) { - if (Array.isArray(arr)) { - return quicksort(arr, 0, arr.length - 1); - } - if (isTypedArray(arr)) { - if (isFpTypedArray(arr)) { - return quicksortFloats(arr, 0, arr.length - 1); - } - return quicksort(arr, 0, arr.length - 1); - } - /* else unsupported */ - throw new Error("sortArray received unsupported object type"); -} - -export function sortIndex(index, source) { - if (isFpTypedArray(source)) - return quicksortFloatsIndirect(index, source, 0, index.length - 1); - return quicksortIndirect(index, source, 0, index.length - 1); -} - -// Search for `value` in the sorted array `arr`, in the range [first, last). -// Return the first (left most) index where arr[index] >= value. -// -// In other words, return array index I where: -// arr[i] < value for all tarr[lo:I] -// arr[i] >= value for all tarr[I:last] -// -// The same semantics/behavior as: -// C++: lower_bound() -// Python: bisect.bisect_left() -// -function lowerBoundNonFloat(valueArray, value, first, last) { - let lfirst = first; - let llast = last; - // this is just a binary search - while (lfirst < llast) { - const middle = (lfirst + llast) >>> 1; - if (valueArray[middle] < value) { - lfirst = middle + 1; - } else { - llast = middle; - } - } - return lfirst; -} - -// lowerBound, but with NaN handling -// -// If the underlying array is a Float32Array or Float64Array, will enforce -// the ordering -Infinity < finite < Infinity < NaN. -// -function lowerBoundFloat(valueArray, value, first, last) { - let lfirst = first; - let llast = last; - // this is just a binary search - while (lfirst < llast) { - const middle = (lfirst + llast) >>> 1; - if (lt(valueArray[middle], value)) { - lfirst = middle + 1; - } else { - llast = middle; - } - } - return lfirst; -} - -export function lowerBound(valueArray, value, first, last) { - if (isFpTypedArray(valueArray)) { - return lowerBoundFloat(valueArray, value, first, last); - } - return lowerBoundNonFloat(valueArray, value, first, last); -} - -// Inlined performance optimization - used to indirect through a sort map. -// -function lowerBoundNonFloatIndirect( - valueArray, - indexArray, - value, - first, - last -) { - let lfirst = first; - let llast = last; - // this is just a binary search - while (lfirst < llast) { - const middle = (lfirst + llast) >>> 1; - if (valueArray[indexArray[middle]] < value) { - lfirst = middle + 1; - } else { - llast = middle; - } - } - return lfirst; -} - -function lowerBoundFloatIndirect(valueArray, indexArray, value, first, last) { - let lfirst = first; - let llast = last; - // this is just a binary search - while (lfirst < llast) { - const middle = (lfirst + llast) >>> 1; - if (lt(valueArray[indexArray[middle]], value)) { - lfirst = middle + 1; - } else { - llast = middle; - } - } - return lfirst; -} - -export function lowerBoundIndirect(valueArray, indexArray, value, first, last) { - if (isFpTypedArray(valueArray)) { - return lowerBoundFloatIndirect(valueArray, indexArray, value, first, last); - } - return lowerBoundNonFloatIndirect(valueArray, indexArray, value, first, last); -} - -// Search for `value in the sorted array `arr`, in the range [first, last). -// Return the first value where arr[index] > value. -// -// In other words, return array index I, where: -// arr[i] <= value for all tarr[lo:I] -// arr[i] > value for all tarr[I:last] -// -// The same semantics/behavior as: -// C++: upper_bound() -// Python: bisect.bisect_right() -// -function upperBoundNonFloat(valueArray, value, first, last) { - let lfirst = first; - let llast = last; - // this is just a binary search - while (lfirst < llast) { - const middle = (lfirst + llast) >>> 1; - if (valueArray[middle] > value) { - llast = middle; - } else { - lfirst = middle + 1; - } - } - return lfirst; -} - -function upperBoundFloat(valueArray, value, first, last) { - let lfirst = first; - let llast = last; - // this is just a binary search - while (lfirst < llast) { - const middle = (lfirst + llast) >>> 1; - if (gt(valueArray[middle], value)) { - llast = middle; - } else { - lfirst = middle + 1; - } - } - return lfirst; -} - -export function upperBound(valueArray, value, first, last) { - if (isFpTypedArray(valueArray)) { - return upperBoundFloat(valueArray, value, first, last); - } - return upperBoundNonFloat(valueArray, value, first, last); -} - -// Inline performance optimization -// -function upperBoundNonFloatIndirect( - valueArray, - indexArray, - value, - first, - last -) { - let lfirst = first; - let llast = last; - // this is just a binary search - while (lfirst < llast) { - const middle = (lfirst + llast) >>> 1; - if (valueArray[indexArray[middle]] > value) { - llast = middle; - } else { - lfirst = middle + 1; - } - } - return lfirst; -} - -function upperBoundFloatIndirect(valueArray, indexArray, value, first, last) { - let lfirst = first; - let llast = last; - // this is just a binary search - while (lfirst < llast) { - const middle = (lfirst + llast) >>> 1; - if (gt(valueArray[indexArray[middle]], value)) { - llast = middle; - } else { - lfirst = middle + 1; - } - } - return lfirst; -} - -export function upperBoundIndirect(valueArray, indexArray, value, first, last) { - if (isFpTypedArray(valueArray)) { - return upperBoundFloatIndirect(valueArray, indexArray, value, first, last); - } - return upperBoundNonFloatIndirect(valueArray, indexArray, value, first, last); -} - -// Search for `value` in the sorted array `arr`, in the range [first, last). -// Return the first index where arr[index] == value, OR if value not present, -// return `last` -// -// The same semantics/behavior as: -// C++: binary_search() -// -export function binarySearch(valueArray, value, first, last) { - const index = lowerBound(valueArray, value, first, last); - if (index !== last && value === valueArray[index]) return index; - return last; -} -/* eslint-enable no-bitwise -- enable */ diff --git a/client/src/util/typedCrossfilter/sort.ts b/client/src/util/typedCrossfilter/sort.ts new file mode 100644 index 00000000..f23eea49 --- /dev/null +++ b/client/src/util/typedCrossfilter/sort.ts @@ -0,0 +1,529 @@ +import { isTypedArray, isFpTypedArray } from "../typeHelpers"; + +/* eslint-disable no-bitwise -- code relies on bitwise ops */ + +/* + ** fast sort and search, with separate code paths for floats (NaN ordering), + ** indirect and direct search/sort. + */ + +/* +Comparators for float sort. -Infinity < finite < Infinity < NaN +*/ +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function lt(a: any, b: any) { + if (Number.isNaN(b)) return !Number.isNaN(a); + return a < b; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function gt(a: any, b: any) { + if (Number.isNaN(a)) return !Number.isNaN(b); + return a > b; +} + +/* +insertion sort, used for small arrays (controlled by SMALL_ARRAY constant) +*/ +const SMALL_ARRAY = 32; +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function insertionsort(a: any, lo: any, hi: any) { + for (let i = lo + 1; i < hi + 1; i += 1) { + const x = a[i]; + let j; + for (j = i; j > lo && a[j - 1] > x; j -= 1) { + a[j] = a[j - 1]; + } + a[j] = x; + } + return a; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function insertionsortFloats(a: any, lo: any, hi: any) { + for (let i = lo + 1; i < hi + 1; i += 1) { + const x = a[i]; + let j; + for (j = i; j > lo && gt(a[j - 1], x); j -= 1) { + a[j] = a[j - 1]; + } + a[j] = x; + } + return a; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function insertionsortIndirect(a: any, s: any, lo: any, hi: any) { + for (let i = lo + 1; i < hi + 1; i += 1) { + const x = a[i]; + const t = s[x]; + let j; + for (j = i; j > lo && s[a[j - 1]] > t; j -= 1) { + a[j] = a[j - 1]; + } + a[j] = x; + } + return a; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function insertionsortFloatsIndirect(a: any, s: any, lo: any, hi: any) { + for (let i = lo + 1; i < hi + 1; i += 1) { + const x = a[i]; + const t = s[x]; + let j; + for (j = i; j > lo && gt(s[a[j - 1]], t); j -= 1) { + a[j] = a[j - 1]; + } + a[j] = x; + } + return a; +} + +/* +Quicksort - used for larger arrays +*/ +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function quicksort(a: any, lo: any, hi: any) { + if (hi - lo < SMALL_ARRAY) { + return insertionsort(a, lo, hi); + } + if (lo < hi) { + // partition + const mid = Math.floor((lo + hi) / 2); + const p = a[mid]; + let i = lo - 1; + let j = hi + 1; + while (i < j) { + do { + i += 1; + } while (a[i] < p); + do { + j -= 1; + } while (a[j] > p); + if (i < j) { + const tmp = a[i]; + a[i] = a[j]; + a[j] = tmp; + } + } + // sort + quicksort(a, lo, j); + quicksort(a, j + 1, hi); + } + return a; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function quicksortFloats(a: any, lo: any, hi: any) { + if (hi - lo < SMALL_ARRAY) { + return insertionsortFloats(a, lo, hi); + } + if (lo < hi) { + // partition + const mid = Math.floor((lo + hi) / 2); + const p = a[mid]; + let i = lo - 1; + let j = hi + 1; + while (i < j) { + do { + i += 1; + } while (lt(a[i], p)); + do { + j -= 1; + } while (gt(a[j], p)); + if (i < j) { + const tmp = a[i]; + a[i] = a[j]; + a[j] = tmp; + } + } + // sort + quicksortFloats(a, lo, j); + quicksortFloats(a, j + 1, hi); + } + return a; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function quicksortIndirect(a: any, s: any, lo: any, hi: any) { + if (hi - lo < SMALL_ARRAY) { + return insertionsortIndirect(a, s, lo, hi); + } + if (lo < hi) { + // partition + const mid = Math.floor((lo + hi) / 2); + const p = a[mid]; + const t = s[p]; + let i = lo - 1; + let j = hi + 1; + while (i < j) { + do { + i += 1; + } while (s[a[i]] < t); + do { + j -= 1; + } while (s[a[j]] > t); + if (i < j) { + const tmp = a[i]; + a[i] = a[j]; + a[j] = tmp; + } + } + // sort + quicksortIndirect(a, s, lo, j); + quicksortIndirect(a, s, j + 1, hi); + } + return a; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function quicksortFloatsIndirect(a: any, s: any, lo: any, hi: any) { + if (hi - lo < SMALL_ARRAY) { + return insertionsortFloatsIndirect(a, s, lo, hi); + } + if (lo < hi) { + // partition + const mid = Math.floor((lo + hi) / 2); + const p = a[mid]; + const t = s[p]; + let i = lo - 1; + let j = hi + 1; + while (i < j) { + do { + i += 1; + } while (lt(s[a[i]], t)); + do { + j -= 1; + } while (gt(s[a[j]], t)); + if (i < j) { + const tmp = a[i]; + a[i] = a[j]; + a[j] = tmp; + } + } + // sort + quicksortFloatsIndirect(a, s, lo, j); + quicksortFloatsIndirect(a, s, j + 1, hi); + } + return a; +} + +/* +Convenience wrappers, handling optimization paths and default +handlers for NaN comparisons. Sorts in place. +*/ +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function sortArray(arr: any) { + if (Array.isArray(arr)) { + return quicksort(arr, 0, arr.length - 1); + } + if (isTypedArray(arr)) { + if (isFpTypedArray(arr)) { + return quicksortFloats(arr, 0, arr.length - 1); + } + return quicksort(arr, 0, arr.length - 1); + } + /* else unsupported */ + throw new Error("sortArray received unsupported object type"); +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function sortIndex(index: any, source: any) { + if (isFpTypedArray(source)) + return quicksortFloatsIndirect(index, source, 0, index.length - 1); + return quicksortIndirect(index, source, 0, index.length - 1); +} + +// Search for `value` in the sorted array `arr`, in the range [first, last). +// Return the first (left most) index where arr[index] >= value. +// +// In other words, return array index I where: +// arr[i] < value for all tarr[lo:I] +// arr[i] >= value for all tarr[I:last] +// +// The same semantics/behavior as: +// C++: lower_bound() +// Python: bisect.bisect_left() +// +function lowerBoundNonFloat( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + last: any +) { + let lfirst = first; + let llast = last; + // this is just a binary search + while (lfirst < llast) { + const middle = (lfirst + llast) >>> 1; + if (valueArray[middle] < value) { + lfirst = middle + 1; + } else { + llast = middle; + } + } + return lfirst; +} + +// lowerBound, but with NaN handling +// +// If the underlying array is a Float32Array or Float64Array, will enforce +// the ordering -Infinity < finite < Infinity < NaN. +// +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function lowerBoundFloat(valueArray: any, value: any, first: any, last: any) { + let lfirst = first; + let llast = last; + // this is just a binary search + while (lfirst < llast) { + const middle = (lfirst + llast) >>> 1; + if (lt(valueArray[middle], value)) { + lfirst = middle + 1; + } else { + llast = middle; + } + } + return lfirst; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function lowerBound(valueArray: any, value: any, first: any, last: any) { + if (isFpTypedArray(valueArray)) { + return lowerBoundFloat(valueArray, value, first, last); + } + return lowerBoundNonFloat(valueArray, value, first, last); +} + +// Inlined performance optimization - used to indirect through a sort map. +// +function lowerBoundNonFloatIndirect( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + indexArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + last: any +) { + let lfirst = first; + let llast = last; + // this is just a binary search + while (lfirst < llast) { + const middle = (lfirst + llast) >>> 1; + if (valueArray[indexArray[middle]] < value) { + lfirst = middle + 1; + } else { + llast = middle; + } + } + return lfirst; +} + +function lowerBoundFloatIndirect( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + indexArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + last: any +) { + let lfirst = first; + let llast = last; + // this is just a binary search + while (lfirst < llast) { + const middle = (lfirst + llast) >>> 1; + if (lt(valueArray[indexArray[middle]], value)) { + lfirst = middle + 1; + } else { + llast = middle; + } + } + return lfirst; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function lowerBoundIndirect( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + indexArray: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + last: any +) { + if (isFpTypedArray(valueArray)) { + return lowerBoundFloatIndirect(valueArray, indexArray, value, first, last); + } + return lowerBoundNonFloatIndirect(valueArray, indexArray, value, first, last); +} + +// Search for `value in the sorted array `arr`, in the range [first, last). +// Return the first value where arr[index] > value. +// +// In other words, return array index I, where: +// arr[i] <= value for all tarr[lo:I] +// arr[i] > value for all tarr[I:last] +// +// The same semantics/behavior as: +// C++: upper_bound() +// Python: bisect.bisect_right() +// +function upperBoundNonFloat( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + last: any +) { + let lfirst = first; + let llast = last; + // this is just a binary search + while (lfirst < llast) { + const middle = (lfirst + llast) >>> 1; + if (valueArray[middle] > value) { + llast = middle; + } else { + lfirst = middle + 1; + } + } + return lfirst; +} + +// eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. +function upperBoundFloat(valueArray: any, value: any, first: any, last: any) { + let lfirst = first; + let llast = last; + // this is just a binary search + while (lfirst < llast) { + const middle = (lfirst + llast) >>> 1; + if (gt(valueArray[middle], value)) { + llast = middle; + } else { + lfirst = middle + 1; + } + } + return lfirst; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function upperBound(valueArray: any, value: any, first: any, last: any) { + if (isFpTypedArray(valueArray)) { + return upperBoundFloat(valueArray, value, first, last); + } + return upperBoundNonFloat(valueArray, value, first, last); +} + +// Inline performance optimization +// +function upperBoundNonFloatIndirect( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + indexArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + last: any +) { + let lfirst = first; + let llast = last; + // this is just a binary search + while (lfirst < llast) { + const middle = (lfirst + llast) >>> 1; + if (valueArray[indexArray[middle]] > value) { + llast = middle; + } else { + lfirst = middle + 1; + } + } + return lfirst; +} + +function upperBoundFloatIndirect( + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + indexArray: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS. + last: any +) { + let lfirst = first; + let llast = last; + // this is just a binary search + while (lfirst < llast) { + const middle = (lfirst + llast) >>> 1; + if (gt(valueArray[indexArray[middle]], value)) { + llast = middle; + } else { + lfirst = middle + 1; + } + } + return lfirst; +} + +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function upperBoundIndirect( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + indexArray: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + last: any +) { + if (isFpTypedArray(valueArray)) { + return upperBoundFloatIndirect(valueArray, indexArray, value, first, last); + } + return upperBoundNonFloatIndirect(valueArray, indexArray, value, first, last); +} + +// Search for `value` in the sorted array `arr`, in the range [first, last). +// Return the first index where arr[index] == value, OR if value not present, +// return `last` +// +// The same semantics/behavior as: +// C++: binary_search() +// +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types --- FIXME: disabled temporarily on migrate to TS. +export function binarySearch( + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + valueArray: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + value: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + first: any, + // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. + last: any +) { + const index = lowerBound(valueArray, value, first, last); + if (index !== last && value === valueArray[index]) return index; + return last; +} +/* eslint-enable no-bitwise -- enable */ diff --git a/client/src/util/typedCrossfilter/util.js b/client/src/util/typedCrossfilter/util.ts similarity index 54% rename from client/src/util/typedCrossfilter/util.js rename to client/src/util/typedCrossfilter/util.ts index 8d28d65a..a56f954f 100644 --- a/client/src/util/typedCrossfilter/util.js +++ b/client/src/util/typedCrossfilter/util.ts @@ -7,7 +7,8 @@ import { rangeFill as fillRange } from "../range"; // slice out of one array into another, using an index array // -export function sliceByIndex(src, index) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function sliceByIndex(src: any, index: any) { if (index === undefined || index === null) { return src; } @@ -18,7 +19,8 @@ export function sliceByIndex(src, index) { return dst; } -export function makeSortIndex(src) { +// eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any -- - FIXME: disabled temporarily on migrate to TS. +export function makeSortIndex(src: any) { const index = fillRange(new Uint32Array(src.length)); sortIndex(index, src); return index; diff --git a/client/tsconfig.json b/client/tsconfig.json new file mode 100644 index 00000000..502c05a8 --- /dev/null +++ b/client/tsconfig.json @@ -0,0 +1,35 @@ +{ + "compilerOptions": { + "allowJs": true, + "esModuleInterop": true, + // Allow @connect + "experimentalDecorators": true, + // Ensure Babel can safely transpile files + "isolatedModules": true, + "jsx": "preserve", + "lib": ["dom", "es2020"], + "module": "esnext", + "moduleResolution": "node", + "noEmit": true, + "noUnusedLocals": true, + "noUnusedParameters": true, + "skipLibCheck": true, + "strict": true, + "target": "esnext", + "types": [ + "jest", + "puppeteer", + "jest-environment-puppeteer", + "expect-puppeteer" + ], + "forceConsistentCasingInFileNames": true, + "resolveJsonModule": true + }, + "include": [ + "src/**/*", + "configuration/**/*", + "__tests__/**/*", + "jest-puppeteer.config.js" + ], + "exclude": ["__tests__/e2e/__snapshots__/**/*"] +} diff --git a/dev_docs/e2e_tests.md b/dev_docs/e2e_tests.md index c2730fed..4c1bd101 100644 --- a/dev_docs/e2e_tests.md +++ b/dev_docs/e2e_tests.md @@ -79,10 +79,10 @@ See [developer guidelines](developer_guidelines.md) ```ts { - "e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js", + "e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.ts", } ``` - which tells `jest` to use `e2eJestConfig.json` as the config file to run e2e test file `e2e.test.js` + which tells `jest` to use `e2eJestConfig.json` as the config file to run e2e test file `e2e.test.ts` 1. [puppeteer.setup.js](../client/__tests__/e2e/puppeteer.setup.js) is for configuring `jest`, `browser`, and `page` objects at runtime