mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-26 02:18:11 +08:00
gene set summary progress (#2127)
* revert removal of cache control headers * checkpoint work on revising summary route * add summary query support to annoMatrix * summarize route cleanup * add mising file * clean up summarize route * add summary histogram * update deps * lint * more lint * lint * manage crossfiler during gene set state changes * remove obsolete debugging code * correctly perform async watch in histogram * better error handling
This commit is contained in:
Bruce Martin
@@ -206,11 +206,16 @@ class GenesetsAPI(Resource):
|
||||
return common_rest.genesets_put(request, data_adaptor)
|
||||
|
||||
|
||||
class GenesetSummaryAPI(Resource):
|
||||
class SummarizeVarAPI(Resource):
|
||||
@rest_get_data_adaptor
|
||||
@cache_control(public=True, max_age=ONE_WEEK)
|
||||
def get(self, data_adaptor):
|
||||
return common_rest.summarize_var_get(request, data_adaptor)
|
||||
|
||||
@rest_get_data_adaptor
|
||||
@cache_control(no_store=True)
|
||||
def get(self, data_adaptor):
|
||||
return common_rest.geneset_summary_get(request, data_adaptor)
|
||||
def post(self, data_adaptor):
|
||||
return common_rest.summarize_var_post(request, data_adaptor)
|
||||
|
||||
|
||||
def get_api_base_resources(bp_base):
|
||||
@@ -239,7 +244,7 @@ def get_api_dataroot_resources(bp_dataroot):
|
||||
add_resource(AnnotationsVarAPI, "/annotations/var")
|
||||
add_resource(DataVarAPI, "/data/var")
|
||||
add_resource(GenesetsAPI, "/genesets")
|
||||
add_resource(GenesetSummaryAPI, "/geneset_summary")
|
||||
add_resource(SummarizeVarAPI, "/summarize/var")
|
||||
# Display routes
|
||||
add_resource(ColorsAPI, "/colors")
|
||||
# Computation routes
|
||||
|
||||
@@ -3,6 +3,7 @@ import logging
|
||||
import sys
|
||||
from http import HTTPStatus
|
||||
import zlib
|
||||
import hashlib
|
||||
|
||||
from flask import make_response, jsonify, current_app, abort
|
||||
from werkzeug.urls import url_unquote
|
||||
@@ -383,31 +384,42 @@ def genesets_put(request, data_adaptor):
|
||||
return abort(HTTPStatus.NOT_FOUND, description=str(e))
|
||||
|
||||
|
||||
def geneset_summary_get(request, data_adaptor):
|
||||
def summarize_var_helper(request, data_adaptor, key, raw_query):
|
||||
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
|
||||
if preferred_mimetype != "application/octet-stream":
|
||||
return abort(HTTPStatus.NOT_ACCEPTABLE)
|
||||
|
||||
geneset_name = request.args.get("geneset_name", default=None)
|
||||
summary_method = request.args.get("method", default="mean")
|
||||
request_tid = request.args.get("tid", default=None)
|
||||
summary_method = request.values.get("method", default="mean")
|
||||
query_hash = hashlib.sha1(raw_query).hexdigest() # cache helper
|
||||
if key and query_hash != key:
|
||||
return abort(HTTPStatus.BAD_REQUEST, description="query key did not match")
|
||||
|
||||
try:
|
||||
annotations = data_adaptor.dataset_config.user_annotations
|
||||
(genesets, tid) = annotations.read_gene_sets(data_adaptor)
|
||||
|
||||
if request_tid is not None and int(request_tid) != tid:
|
||||
return abort(HTTPStatus.NOT_FOUND, "Obsolete TID")
|
||||
if geneset_name is None or geneset_name not in genesets:
|
||||
return abort(HTTPStatus.BAD_REQUEST, "Gene set name not found.")
|
||||
genes = [g["gene_symbol"] for g in genesets.get(geneset_name)["genes"]]
|
||||
args_filter_only = request.values.copy()
|
||||
args_filter_only.poplist("method")
|
||||
args_filter_only.poplist("key")
|
||||
|
||||
try:
|
||||
filter = _query_parameter_to_filter(args_filter_only)
|
||||
return make_response(
|
||||
data_adaptor.get_gene_set_summary(geneset_name, genes, summary_method),
|
||||
data_adaptor.summarize_var(summary_method, filter, query_hash),
|
||||
HTTPStatus.OK,
|
||||
{"Content-Type": "application/octet-stream"},
|
||||
)
|
||||
except (ValueError) as e:
|
||||
return abort(HTTPStatus.NOT_FOUND, description=str(e))
|
||||
except (UnsupportedSummaryMethod) as e:
|
||||
except (UnsupportedSummaryMethod, FilterError) as e:
|
||||
return abort(HTTPStatus.BAD_REQUEST, description=str(e))
|
||||
|
||||
|
||||
def summarize_var_get(request, data_adaptor):
|
||||
return summarize_var_helper(request, data_adaptor, None, request.query_string)
|
||||
|
||||
|
||||
def summarize_var_post(request, data_adaptor):
|
||||
if not request.content_type or "application/x-www-form-urlencoded" not in request.content_type:
|
||||
return abort(HTTPStatus.UNSUPPORTED_MEDIA_TYPE)
|
||||
if request.content_length > 1_000_000: # just a sanity check to avoid memory exhaustion
|
||||
return abort(HTTPStatus.BAD_REQUEST)
|
||||
|
||||
key = request.args.get("key", default=None)
|
||||
return summarize_var_helper(request, data_adaptor, key, request.get_data())
|
||||
|
||||
@@ -5,7 +5,6 @@ import anndata
|
||||
import numpy as np
|
||||
from packaging import version
|
||||
from pandas.core.dtypes.dtypes import CategoricalDtype
|
||||
import pandas as pd
|
||||
from scipy import sparse
|
||||
from server_timing import Timing as ServerTiming
|
||||
|
||||
@@ -13,7 +12,7 @@ import backend.server.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
|
||||
from backend.server.common.corpora import corpora_get_props_from_anndata
|
||||
from backend.common.errors import PrepareError, DatasetAccessError, FilterError, UnsupportedSummaryMethod
|
||||
from backend.common.errors import PrepareError, DatasetAccessError, FilterError
|
||||
from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array
|
||||
from backend.server.compute.scanpy import scanpy_umap
|
||||
from backend.server.data_common.data_adaptor import DataAdaptor
|
||||
@@ -69,11 +68,11 @@ 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:
|
||||
@@ -200,10 +199,10 @@ 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
|
||||
@@ -368,29 +367,3 @@ class AnndataAdaptor(DataAdaptor):
|
||||
def get_var_keys(self):
|
||||
# return list of keys
|
||||
return self.data.var.keys().to_list()
|
||||
|
||||
def get_gene_set_summary(self, geneset_name, genes, method):
|
||||
if method != "mean":
|
||||
raise UnsupportedSummaryMethod("Unknown gene set summary method.")
|
||||
|
||||
var_index = self.parameters.get("var_names")
|
||||
obs_selector, var_selector = self._filter_to_mask(
|
||||
{
|
||||
"var": {
|
||||
"annotation_value": [
|
||||
{
|
||||
"name": var_index,
|
||||
"values": genes,
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
)
|
||||
|
||||
X = self.get_X_array(obs_selector, var_selector)
|
||||
if sparse.issparse(X):
|
||||
mean = X.mean(axis=1)
|
||||
else:
|
||||
mean = X.mean(axis=1, keepdims=True)
|
||||
col_idx = pd.Index([geneset_name])
|
||||
return encode_matrix_fbs(mean, col_idx=col_idx, row_idx=None)
|
||||
|
||||
@@ -1,14 +1,14 @@
|
||||
from abc import ABCMeta, abstractmethod
|
||||
from os.path import basename, splitext
|
||||
import re
|
||||
|
||||
import numpy as np
|
||||
import pandas as pd
|
||||
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
|
||||
from backend.common.errors import FilterError, JSONEncodingValueError, ExceedsLimitError
|
||||
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
|
||||
|
||||
@@ -482,6 +482,25 @@ class DataAdaptor(metaclass=ABCMeta):
|
||||
lastmod = None
|
||||
return lastmod
|
||||
|
||||
@abstractmethod
|
||||
def get_gene_set_summary(self, geneset_name, genes, method):
|
||||
pass
|
||||
def summarize_var(self, method, filter, query_hash):
|
||||
if method != "mean":
|
||||
raise UnsupportedSummaryMethod("Unknown gene set summary method.")
|
||||
|
||||
obs_selector, var_selector = self._filter_to_mask(filter)
|
||||
if obs_selector is not None:
|
||||
raise FilterError("filtering on obs unsupported")
|
||||
|
||||
# if no filter, just return zeros. We don't have a use case
|
||||
# for summarizing the entire X without a filter, and it would
|
||||
# potentially be quite compute / memory intensive.
|
||||
if var_selector is None or np.count_nonzero(var_selector) == 0:
|
||||
mean = np.zeros((self.get_shape()[0], 1), dtype=np.float32)
|
||||
else:
|
||||
X = self.get_X_array(obs_selector, var_selector)
|
||||
if sparse.issparse(X):
|
||||
mean = X.mean(axis=1)
|
||||
else:
|
||||
mean = X.mean(axis=1, keepdims=True)
|
||||
|
||||
col_idx = pd.Index([query_hash])
|
||||
return encode_matrix_fbs(mean, col_idx=col_idx, row_idx=None)
|
||||
|
||||
@@ -5,6 +5,7 @@ import zlib
|
||||
from http import HTTPStatus
|
||||
import tempfile
|
||||
from os import path
|
||||
import hashlib
|
||||
|
||||
import pandas as pd
|
||||
import requests
|
||||
@@ -430,6 +431,75 @@ class EndPointsAnndata(unittest.TestCase, EndPoints):
|
||||
result_data = result.json()
|
||||
self.assertEqual(len(result_data), 10)
|
||||
|
||||
def test_get_summaryvar(self):
|
||||
index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
|
||||
endpoint = "summarize/var"
|
||||
|
||||
# single column
|
||||
filter = f"var:{index_col_name}=F5"
|
||||
query = f"method=mean&{filter}"
|
||||
query_hash = hashlib.sha1(query.encode()).hexdigest()
|
||||
url = f"{self.URL_BASE}{endpoint}?{query}"
|
||||
header = {"Accept": "application/octet-stream"}
|
||||
result = self.session.get(url, headers=header)
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
|
||||
df = decode_fbs.decode_matrix_FBS(result.content)
|
||||
self.assertEqual(df["n_rows"], 2638)
|
||||
self.assertEqual(df["n_cols"], 1)
|
||||
self.assertEqual(df["col_idx"], [query_hash])
|
||||
self.assertAlmostEqual(df["columns"][0][0], -0.110451095)
|
||||
|
||||
# multi-column
|
||||
col_names = ["F5", "BEB3", "SIK1"]
|
||||
filter = "&".join([f"var:{index_col_name}={name}" for name in col_names])
|
||||
query = f"method=mean&{filter}"
|
||||
query_hash = hashlib.sha1(query.encode()).hexdigest()
|
||||
url = f"{self.URL_BASE}{endpoint}?{query}"
|
||||
header = {"Accept": "application/octet-stream"}
|
||||
result = self.session.get(url, headers=header)
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
|
||||
df = decode_fbs.decode_matrix_FBS(result.content)
|
||||
self.assertEqual(df["n_rows"], 2638)
|
||||
self.assertEqual(df["n_cols"], 1)
|
||||
self.assertEqual(df["col_idx"], [query_hash])
|
||||
self.assertAlmostEqual(df["columns"][0][0], -0.16628358)
|
||||
|
||||
def test_post_summaryvar(self):
|
||||
index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
|
||||
endpoint = "summarize/var"
|
||||
headers = {"Content-Type": "application/x-www-form-urlencoded", "Accept": "application/octet-stream"}
|
||||
|
||||
# single column
|
||||
filter = f"var:{index_col_name}=F5"
|
||||
query = f"method=mean&{filter}"
|
||||
query_hash = hashlib.sha1(query.encode()).hexdigest()
|
||||
url = f"{self.URL_BASE}{endpoint}?key={query_hash}"
|
||||
result = self.session.post(url, headers=headers, data=query)
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
|
||||
df = decode_fbs.decode_matrix_FBS(result.content)
|
||||
self.assertEqual(df["n_rows"], 2638)
|
||||
self.assertEqual(df["n_cols"], 1)
|
||||
self.assertEqual(df["col_idx"], [query_hash])
|
||||
self.assertAlmostEqual(df["columns"][0][0], -0.110451095)
|
||||
|
||||
# multi-column
|
||||
col_names = ["F5", "BEB3", "SIK1"]
|
||||
filter = "&".join([f"var:{index_col_name}={name}" for name in col_names])
|
||||
query = f"method=mean&{filter}"
|
||||
query_hash = hashlib.sha1(query.encode()).hexdigest()
|
||||
url = f"{self.URL_BASE}{endpoint}?key={query_hash}"
|
||||
result = self.session.post(url, headers=headers, data=query)
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
|
||||
df = decode_fbs.decode_matrix_FBS(result.content)
|
||||
self.assertEqual(df["n_rows"], 2638)
|
||||
self.assertEqual(df["n_cols"], 1)
|
||||
self.assertEqual(df["col_idx"], [query_hash])
|
||||
self.assertAlmostEqual(df["columns"][0][0], -0.16628358)
|
||||
|
||||
|
||||
class EndPointsAnndataAnnotations(unittest.TestCase, EndPointsAnnotations):
|
||||
"""Test Case for endpoints"""
|
||||
@@ -738,86 +808,25 @@ summary test,,PIGU,\r
|
||||
original_data,
|
||||
)
|
||||
|
||||
def test_get_geneset_summary(self):
|
||||
endpoint = "geneset_summary?geneset_name=summary%20test&method=mean"
|
||||
url = f"{self.URL_BASE}{endpoint}"
|
||||
header = {"Accept": "application/octet-stream"}
|
||||
result = self.session.get(url, headers=header)
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
|
||||
df = decode_fbs.decode_matrix_FBS(result.content)
|
||||
self.assertEqual(df["n_rows"], 2638)
|
||||
self.assertEqual(df["n_cols"], 1)
|
||||
self.assertEqual(df["col_idx"], ["summary test"])
|
||||
self.assertAlmostEqual(df["columns"][0][0], -0.19863907)
|
||||
|
||||
def test_get_geneset_summary_default_method(self):
|
||||
endpoint = "geneset_summary?geneset_name=summary%20test"
|
||||
url = f"{self.URL_BASE}{endpoint}"
|
||||
header = {"Accept": "application/octet-stream"}
|
||||
result = self.session.get(url, headers=header)
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
|
||||
df = decode_fbs.decode_matrix_FBS(result.content)
|
||||
self.assertEqual(df["n_rows"], 2638)
|
||||
self.assertEqual(df["n_cols"], 1)
|
||||
self.assertEqual(df["col_idx"], ["summary test"])
|
||||
self.assertAlmostEqual(df["columns"][0][0], -0.19863907)
|
||||
|
||||
def test_get_geneset_summary_check_tid(self):
|
||||
# get the TID
|
||||
result = self.session.get(f"{self.URL_BASE}genesets", headers={"Accept": "application/json"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
tid = result.json()["tid"]
|
||||
|
||||
# current tid
|
||||
endpoint = f"geneset_summary?geneset_name=summary%20test&tid={tid}"
|
||||
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
|
||||
# future tid
|
||||
endpoint = f"geneset_summary?geneset_name=summary%20test&tid={tid+1}"
|
||||
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.NOT_FOUND)
|
||||
|
||||
# past tid
|
||||
endpoint = f"geneset_summary?geneset_name=summary%20test&tid={tid-1}"
|
||||
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.NOT_FOUND)
|
||||
|
||||
# No tid - ie, skip check
|
||||
endpoint = "geneset_summary?geneset_name=summary%20test"
|
||||
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
|
||||
def test_get_geneset_summary_edge_cases(self):
|
||||
# attempt to summarize _all_ genesets, including edge cases with zero or one gene
|
||||
result = self.session.get(f"{self.URL_BASE}genesets", headers={"Accept": "application/json"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
geneset_names = [gs["geneset_name"] for gs in result.json()["genesets"]]
|
||||
genesets = result.json()["genesets"]
|
||||
|
||||
for gs in geneset_names:
|
||||
endpoint = f"geneset_summary?geneset_name={gs}"
|
||||
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
|
||||
endpoint = "summarize/var"
|
||||
index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
|
||||
for gs in genesets:
|
||||
genes = [g["gene_symbol"] for g in gs["genes"]]
|
||||
filter = "&".join([f"var:{index_col_name}={gene}" for gene in genes])
|
||||
query = f"method=mean&{filter}"
|
||||
query_hash = hashlib.sha1(query.encode()).hexdigest()
|
||||
url = f"{self.URL_BASE}{endpoint}?{query}"
|
||||
|
||||
result = self.session.get(url, headers={"Accept": "application/octet-stream"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.OK)
|
||||
self.assertEqual(result.headers["Content-Type"], "application/octet-stream")
|
||||
df = decode_fbs.decode_matrix_FBS(result.content)
|
||||
self.assertEqual(df["n_rows"], 2638)
|
||||
self.assertEqual(df["n_cols"], 1)
|
||||
self.assertEqual(df["col_idx"], [gs])
|
||||
|
||||
def test_get_geneset_error_handling(self):
|
||||
# no geneset
|
||||
endpoint = "geneset_summary"
|
||||
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
|
||||
|
||||
# unknown geneset
|
||||
endpoint = "geneset_summary?geneset_name=NO_SUCH_GENE_SET"
|
||||
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
|
||||
|
||||
# unknown method
|
||||
endpoint = "geneset_summary?geneset_name=summary%20test&method=NO_SUCH_METHOD"
|
||||
result = self.session.get(f"{self.URL_BASE}{endpoint}", headers={"Accept": "application/octet-stream"})
|
||||
self.assertEqual(result.status_code, HTTPStatus.BAD_REQUEST)
|
||||
self.assertEqual(df["col_idx"], [query_hash])
|
||||
|
||||
@@ -85,9 +85,11 @@ describe("AnnoMatrix", () => {
|
||||
fetch.once(serverMocks.responder);
|
||||
await expect(
|
||||
annoMatrix.fetch("X", {
|
||||
field: "var",
|
||||
column: annoMatrix.schema.annotations.var.index,
|
||||
value: "TYMP",
|
||||
where: {
|
||||
field: "var",
|
||||
column: annoMatrix.schema.annotations.var.index,
|
||||
value: "TYMP",
|
||||
},
|
||||
})
|
||||
).resolves.toBeInstanceOf(Dataframe);
|
||||
|
||||
@@ -103,14 +105,18 @@ describe("AnnoMatrix", () => {
|
||||
await expect(
|
||||
annoMatrix.fetch("X", [
|
||||
{
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: "SUMO3",
|
||||
where: {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: "SUMO3",
|
||||
},
|
||||
},
|
||||
{
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: "TYMP",
|
||||
where: {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: "TYMP",
|
||||
},
|
||||
},
|
||||
])
|
||||
).resolves.toBeInstanceOf(Dataframe);
|
||||
|
||||
@@ -170,9 +170,11 @@ describe("AnnoMatrixCrossfilter", () => {
|
||||
const xfltr = await crossfilter.select(
|
||||
"X",
|
||||
{
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: "TYMP",
|
||||
where: {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: "TYMP",
|
||||
},
|
||||
},
|
||||
{
|
||||
mode: "range",
|
||||
@@ -186,9 +188,11 @@ describe("AnnoMatrixCrossfilter", () => {
|
||||
expect(xfltr.countSelected()).toEqual(501);
|
||||
|
||||
const df = await annoMatrix.fetch("X", {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: "TYMP",
|
||||
where: {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: "TYMP",
|
||||
},
|
||||
});
|
||||
const values = df.icol(0).asArray();
|
||||
const selected = xfltr.allSelectedMask();
|
||||
|
||||
@@ -1,3 +1,4 @@
|
||||
import sha1 from "sha1";
|
||||
import {
|
||||
_whereCacheGet,
|
||||
_whereCacheCreate,
|
||||
@@ -7,37 +8,82 @@ import {
|
||||
const schema = {};
|
||||
|
||||
describe("whereCache", () => {
|
||||
test("whereCacheGet - missing cache values", () => {
|
||||
test("whereCacheGet - where query, missing cache values", () => {
|
||||
expect(
|
||||
_whereCacheGet({}, schema, "X", {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
where: {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
expect(
|
||||
_whereCacheGet({ X: {} }, schema, "X", {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
_whereCacheGet({}, schema, "X", {
|
||||
summarize: {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
values: ["bar"],
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
expect(
|
||||
_whereCacheGet({ X: { var: new Map() } }, schema, "X", {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
_whereCacheGet({ where: { X: {} } }, schema, "X", {
|
||||
where: {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
expect(
|
||||
_whereCacheGet({ where: { X: { var: new Map() } } }, schema, "X", {
|
||||
where: {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
expect(
|
||||
_whereCacheGet(
|
||||
{ X: { var: new Map([["foo", new Map()]]) } },
|
||||
{ where: { X: { var: new Map([["foo", new Map()]]) } } },
|
||||
schema,
|
||||
"X",
|
||||
{
|
||||
where: {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
},
|
||||
}
|
||||
)
|
||||
).toEqual([undefined]);
|
||||
});
|
||||
|
||||
test("whereCacheGet - summarize query, missing cache values", () => {
|
||||
expect(
|
||||
_whereCacheGet({}, schema, "X", {
|
||||
summarize: {
|
||||
method: "mean",
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
values: ["bar"],
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
expect(
|
||||
_whereCacheGet(
|
||||
{ summarize: { X: { mean: { var: new Map() } } } },
|
||||
schema,
|
||||
"X",
|
||||
{
|
||||
summarize: {
|
||||
method: "mean",
|
||||
field: "var",
|
||||
column: "foo",
|
||||
values: ["bar"],
|
||||
},
|
||||
}
|
||||
)
|
||||
).toEqual([undefined]);
|
||||
@@ -45,140 +91,292 @@ describe("whereCache", () => {
|
||||
|
||||
test("whereCacheGet - varied lookups", () => {
|
||||
const whereCache = {
|
||||
X: {
|
||||
var: new Map([
|
||||
[
|
||||
"foo",
|
||||
new Map([
|
||||
["bar", [0]],
|
||||
["baz", [1, 2]],
|
||||
where: {
|
||||
X: {
|
||||
var: new Map([
|
||||
[
|
||||
"foo",
|
||||
new Map([
|
||||
["bar", [0]],
|
||||
["baz", [1, 2]],
|
||||
]),
|
||||
],
|
||||
]),
|
||||
},
|
||||
},
|
||||
summarize: {
|
||||
X: {
|
||||
mean: {
|
||||
var: new Map([
|
||||
[
|
||||
"foo",
|
||||
new Map([
|
||||
[sha1("bar"), [0]],
|
||||
[sha1("baz"), [1, 2]],
|
||||
]),
|
||||
],
|
||||
]),
|
||||
],
|
||||
]),
|
||||
},
|
||||
},
|
||||
},
|
||||
};
|
||||
|
||||
expect(
|
||||
_whereCacheGet(whereCache, schema, "X", {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
where: {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "bar",
|
||||
},
|
||||
})
|
||||
).toEqual([0]);
|
||||
expect(
|
||||
_whereCacheGet(whereCache, schema, "X", {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "baz",
|
||||
summarize: {
|
||||
method: "mean",
|
||||
field: "var",
|
||||
column: "foo",
|
||||
values: ["bar"],
|
||||
},
|
||||
})
|
||||
).toEqual([0]);
|
||||
expect(
|
||||
_whereCacheGet(whereCache, schema, "X", {
|
||||
where: {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "baz",
|
||||
},
|
||||
})
|
||||
).toEqual([1, 2]);
|
||||
expect(
|
||||
_whereCacheGet(whereCache, schema, "X", {
|
||||
summarize: {
|
||||
method: "mean",
|
||||
field: "var",
|
||||
column: "foo",
|
||||
values: ["baz"],
|
||||
},
|
||||
})
|
||||
).toEqual([1, 2]);
|
||||
expect(_whereCacheGet(whereCache, schema, "Y", {})).toEqual([undefined]);
|
||||
expect(
|
||||
_whereCacheGet(whereCache, schema, "X", {
|
||||
field: "whoknows",
|
||||
column: "whatever",
|
||||
value: "snork",
|
||||
where: {
|
||||
field: "whoknows",
|
||||
column: "whatever",
|
||||
value: "snork",
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
expect(
|
||||
_whereCacheGet(whereCache, schema, "X", {
|
||||
field: "var",
|
||||
column: "whatever",
|
||||
value: "snork",
|
||||
where: {
|
||||
field: "var",
|
||||
column: "whatever",
|
||||
value: "snork",
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
expect(
|
||||
_whereCacheGet(whereCache, schema, "X", {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "snork",
|
||||
where: {
|
||||
field: "var",
|
||||
column: "foo",
|
||||
value: "snork",
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
});
|
||||
|
||||
test("whereCacheCreate", () => {
|
||||
test("whereCacheCreate, where query", () => {
|
||||
const query = {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "queryValue",
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "queryValue",
|
||||
},
|
||||
};
|
||||
const wc = _whereCacheCreate(
|
||||
"field",
|
||||
{ field: "queryField", column: "queryColumn", value: "queryValue" },
|
||||
{
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "queryValue",
|
||||
},
|
||||
},
|
||||
[0, 1, 2]
|
||||
);
|
||||
expect(wc).toBeDefined();
|
||||
expect(wc).toEqual(
|
||||
expect.objectContaining({
|
||||
field: {
|
||||
queryField: expect.any(Map),
|
||||
where: {
|
||||
field: {
|
||||
queryField: expect.any(Map),
|
||||
},
|
||||
},
|
||||
})
|
||||
);
|
||||
expect(wc.field.queryField.has("queryColumn")).toEqual(true);
|
||||
expect(wc.field.queryField.get("queryColumn")).toBeInstanceOf(Map);
|
||||
expect(wc.field.queryField.get("queryColumn").has("queryValue")).toEqual(
|
||||
true
|
||||
);
|
||||
expect(wc.where.field.queryField.has("queryColumn")).toEqual(true);
|
||||
expect(wc.where.field.queryField.get("queryColumn")).toBeInstanceOf(Map);
|
||||
expect(
|
||||
wc.where.field.queryField.get("queryColumn").has("queryValue")
|
||||
).toEqual(true);
|
||||
expect(_whereCacheGet(wc, schema, "field", query)).toEqual([0, 1, 2]);
|
||||
});
|
||||
|
||||
test("whereCacheMerge", () => {
|
||||
test("whereCacheCreate, summarize query", () => {
|
||||
const query = {
|
||||
summarize: {
|
||||
method: "method",
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
values: ["queryValue"],
|
||||
},
|
||||
};
|
||||
const wc = _whereCacheCreate("field", query, [0, 1, 2]);
|
||||
expect(_whereCacheGet(wc, schema, "field", query)).toEqual([0, 1, 2]);
|
||||
});
|
||||
|
||||
test("whereCacheCreate, unknown query type", () => {
|
||||
expect(_whereCacheCreate("field", { foobar: true }, [1])).toEqual({});
|
||||
});
|
||||
|
||||
test("whereCacheMerge, where queries", () => {
|
||||
let wc;
|
||||
|
||||
// remember, will mutate dst
|
||||
const src = _whereCacheCreate(
|
||||
"field",
|
||||
{ field: "queryField", column: "queryColumn", value: "foo" },
|
||||
{ where: { field: "queryField", column: "queryColumn", value: "foo" } },
|
||||
["foo"]
|
||||
);
|
||||
|
||||
const dst1 = _whereCacheCreate(
|
||||
"field",
|
||||
{ field: "queryField", column: "queryColumn", value: "bar" },
|
||||
{ where: { field: "queryField", column: "queryColumn", value: "bar" } },
|
||||
["dst1"]
|
||||
);
|
||||
wc = _whereCacheMerge(dst1, src);
|
||||
expect(
|
||||
_whereCacheGet(wc, schema, "field", {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "foo",
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "foo",
|
||||
},
|
||||
})
|
||||
).toEqual(["foo"]);
|
||||
expect(
|
||||
_whereCacheGet(wc, schema, "field", {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "bar",
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "bar",
|
||||
},
|
||||
})
|
||||
).toEqual(["dst1"]);
|
||||
|
||||
const dst2 = _whereCacheCreate(
|
||||
"field",
|
||||
{ field: "queryField", column: "queryColumn", value: "bar" },
|
||||
{ where: { field: "queryField", column: "queryColumn", value: "bar" } },
|
||||
["dst2"]
|
||||
);
|
||||
wc = _whereCacheMerge(dst2, dst1, src);
|
||||
expect(
|
||||
_whereCacheGet(wc, schema, "field", {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "foo",
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "foo",
|
||||
},
|
||||
})
|
||||
).toEqual(["foo"]);
|
||||
expect(
|
||||
_whereCacheGet(wc, schema, "field", {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "bar",
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "bar",
|
||||
},
|
||||
})
|
||||
).toEqual(["dst1"]);
|
||||
|
||||
wc = _whereCacheMerge({}, src);
|
||||
expect(wc).toEqual(src);
|
||||
|
||||
wc = _whereCacheMerge({ field: { queryField: new Map() } }, src);
|
||||
wc = _whereCacheMerge({ where: { field: { queryField: new Map() } } }, src);
|
||||
expect(wc).toEqual(src);
|
||||
});
|
||||
|
||||
test("whereCacheMerge, mixed queries", () => {
|
||||
const wc = _whereCacheMerge(
|
||||
_whereCacheCreate(
|
||||
"field",
|
||||
{
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "foo",
|
||||
},
|
||||
},
|
||||
["a"]
|
||||
),
|
||||
_whereCacheCreate(
|
||||
"field",
|
||||
{
|
||||
summarize: {
|
||||
method: "mean",
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
values: ["foo", "bar", "baz"],
|
||||
},
|
||||
},
|
||||
["b"]
|
||||
)
|
||||
);
|
||||
|
||||
expect(
|
||||
_whereCacheGet(wc, schema, "field", {
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "foo",
|
||||
},
|
||||
})
|
||||
).toEqual(["a"]);
|
||||
|
||||
expect(
|
||||
_whereCacheGet(wc, schema, "field", {
|
||||
summarize: {
|
||||
method: "mean",
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
values: ["foo", "bar", "baz"],
|
||||
},
|
||||
})
|
||||
).toEqual(["b"]);
|
||||
|
||||
expect(
|
||||
_whereCacheGet(wc, schema, "field", {
|
||||
where: {
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
value: "does-not-exist",
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
|
||||
expect(
|
||||
_whereCacheGet(wc, schema, "field", {
|
||||
summarize: {
|
||||
method: "no-such-method",
|
||||
field: "queryField",
|
||||
column: "queryColumn",
|
||||
values: ["does-not-exist"],
|
||||
},
|
||||
})
|
||||
).toEqual([undefined]);
|
||||
});
|
||||
});
|
||||
|
||||
Generated
+27362
-8536
File diff suppressed because it is too large
Load Diff
@@ -70,6 +70,7 @@
|
||||
"regenerator-runtime": "^0.13.7",
|
||||
"regl": "^1.6.1",
|
||||
"script-ext-html-webpack-plugin": "^2.1.4",
|
||||
"sha1": "^1.1.1",
|
||||
"tinyqueue": "^2.0.3",
|
||||
"webpack-merge": "^5.0.9",
|
||||
"whatwg-fetch": "^3.2.0"
|
||||
|
||||
@@ -396,9 +396,9 @@ export const saveGenesetsAction = () => async (dispatch, getState) => {
|
||||
const { lastTid, genesets } = state.genesets;
|
||||
|
||||
const genesetsAreAvailable =
|
||||
config?.parameters?.["annotations_genesets"] ?? false;
|
||||
config?.parameters?.annotations_genesets ?? false;
|
||||
const genesetsReadonly =
|
||||
config?.parameters?.["annotations_genesets_readonly"] ?? true;
|
||||
config?.parameters?.annotations_genesets_readonly ?? true;
|
||||
if (!genesetsAreAvailable || genesetsReadonly) {
|
||||
// our non-save was completed!
|
||||
return dispatch({
|
||||
|
||||
@@ -0,0 +1,126 @@
|
||||
/*
|
||||
Action creators for gene sets
|
||||
|
||||
Primarily used to keep the crossfilter and underlying data in sync with the UI.
|
||||
|
||||
The behavior manifest in these action creators:
|
||||
|
||||
Delete a gene set, will
|
||||
* drop index & clear selection state on the gene set summary
|
||||
* drop index & clear selection state of each gene in the geneset
|
||||
|
||||
Delete a gene from a gene set, will:
|
||||
* drop index & clear selection state on the gene set summary
|
||||
* drop index & clear selection state on the gene
|
||||
|
||||
Add a gene to a gene set, will:
|
||||
* drop index & clear selection state on the gene set summary
|
||||
* will NOT touch the selection state for the gene
|
||||
|
||||
Note that crossfilter indices are lazy created, as needed.
|
||||
*/
|
||||
|
||||
export const genesetDelete = (genesetName) => (dispatch, getState) => {
|
||||
const state = getState();
|
||||
const { genesets } = state;
|
||||
const gs = genesets?.genesets?.get(genesetName) ?? {};
|
||||
const geneSymbols = Array.from(gs.genes.keys());
|
||||
const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
|
||||
dispatch({
|
||||
type: "geneset: delete",
|
||||
genesetName,
|
||||
obsCrossfilter,
|
||||
annoMatrix: obsCrossfilter.annoMatrix,
|
||||
});
|
||||
};
|
||||
|
||||
export const genesetAddGenes = (genesetName, genes) => (dispatch, getState) => {
|
||||
const state = getState();
|
||||
const { obsCrossfilter: prevObsCrossfilter } = state;
|
||||
const obsCrossfilter = dropGenesetSummaryDimension(
|
||||
prevObsCrossfilter,
|
||||
state,
|
||||
genesetName
|
||||
);
|
||||
dispatch({
|
||||
type: "continuous metadata histogram cancel",
|
||||
continuousNamespace: { isGeneSetSummary: true },
|
||||
selection: genesetName,
|
||||
});
|
||||
return dispatch({
|
||||
type: "geneset: add genes",
|
||||
genesetName,
|
||||
genes,
|
||||
obsCrossfilter,
|
||||
annoMatrix: obsCrossfilter.annoMatrix,
|
||||
});
|
||||
};
|
||||
|
||||
export const genesetDeleteGenes = (genesetName, geneSymbols) => (
|
||||
dispatch,
|
||||
getState
|
||||
) => {
|
||||
const state = getState();
|
||||
const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
|
||||
return dispatch({
|
||||
type: "geneset: delete genes",
|
||||
genesetName,
|
||||
geneSymbols,
|
||||
obsCrossfilter,
|
||||
annoMatrix: obsCrossfilter.annoMatrix,
|
||||
});
|
||||
};
|
||||
|
||||
/*
|
||||
Private
|
||||
*/
|
||||
|
||||
function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) {
|
||||
const { annoMatrix, genesets } = state;
|
||||
const varIndex = annoMatrix.schema.annotations?.var?.index;
|
||||
const gs = genesets?.genesets?.get(genesetName) ?? {};
|
||||
const genes = Array.from(gs.genes.keys());
|
||||
const query = {
|
||||
summarize: {
|
||||
method: "mean",
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
values: genes,
|
||||
},
|
||||
};
|
||||
return obsCrossfilter.dropDimension("X", query);
|
||||
}
|
||||
|
||||
function dropGeneDimension(obsCrossfilter, state, gene) {
|
||||
const { annoMatrix } = state;
|
||||
const varIndex = annoMatrix.schema.annotations?.var?.index;
|
||||
const query = {
|
||||
where: {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: gene,
|
||||
},
|
||||
};
|
||||
return obsCrossfilter.dropDimension("X", query);
|
||||
}
|
||||
|
||||
function dropGeneset(dispatch, state, genesetName, geneSymbols) {
|
||||
const { obsCrossfilter: prevObsCrossfilter } = state;
|
||||
const obsCrossfilter = geneSymbols.reduce(
|
||||
(crossfilter, gene) => dropGeneDimension(crossfilter, state, gene),
|
||||
dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName)
|
||||
);
|
||||
dispatch({
|
||||
type: "continuous metadata histogram cancel",
|
||||
continuousNamespace: { isGeneSetSummary: true },
|
||||
selection: genesetName,
|
||||
});
|
||||
geneSymbols.forEach((g) =>
|
||||
dispatch({
|
||||
type: "continuous metadata histogram cancel",
|
||||
continuousNamespace: { isUserDefined: true },
|
||||
selection: g,
|
||||
})
|
||||
);
|
||||
return obsCrossfilter;
|
||||
}
|
||||
@@ -13,6 +13,7 @@ import * as selnActions from "./selection";
|
||||
import * as annoActions from "./annotation";
|
||||
import * as viewActions from "./viewStack";
|
||||
import * as embActions from "./embedding";
|
||||
import * as genesetActions from "./geneset";
|
||||
|
||||
/*
|
||||
return promise fetching user-configured colors
|
||||
@@ -58,7 +59,7 @@ async function genesetsFetch(dispatch, config) {
|
||||
genesets: [],
|
||||
tid: 0,
|
||||
};
|
||||
if (config?.parameters?.["annotations_genesets"] ?? false) {
|
||||
if (config?.parameters?.annotations_genesets ?? false) {
|
||||
fetchJson("genesets").then((response) => {
|
||||
dispatch({
|
||||
type: "geneset: initial load",
|
||||
@@ -111,7 +112,7 @@ const doInitialDataLoad = () =>
|
||||
});
|
||||
dispatch({ type: "initial data load complete" });
|
||||
|
||||
const defaultEmbedding = config?.parameters?.["default_embedding"];
|
||||
const defaultEmbedding = config?.parameters?.default_embedding;
|
||||
const layoutSchema = schema?.schema?.layout?.obs ?? [];
|
||||
if (
|
||||
defaultEmbedding &&
|
||||
@@ -269,4 +270,7 @@ export default {
|
||||
needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
|
||||
layoutChoiceAction: embActions.layoutChoiceAction,
|
||||
setCellSetFromSelection: selnActions.setCellSetFromSelection,
|
||||
genesetDelete: genesetActions.genesetDelete,
|
||||
genesetAddGenes: genesetActions.genesetAddGenes,
|
||||
genesetDeleteGenes: genesetActions.genesetDeleteGenes,
|
||||
};
|
||||
|
||||
@@ -12,6 +12,7 @@ import {
|
||||
import { indexEntireSchema } from "../util/stateManager/schemaHelpers";
|
||||
import { _whereCacheGet, _whereCacheMerge } from "./whereCache";
|
||||
import _shallowClone from "./clone";
|
||||
import { _queryValidate, _queryCacheKey } from "./query";
|
||||
|
||||
const _dataframeCache = dataframeMemo(128);
|
||||
|
||||
@@ -181,7 +182,7 @@ export default class AnnoMatrix {
|
||||
Returns a Promise for the query result, which will resolve to a dataframe.
|
||||
|
||||
Field must be one of the matrix fields: 'obs', 'var', 'X', 'emb'. Value
|
||||
represents the underlying object upon which the query is occuring.
|
||||
represents the underlying object upon which the query is occurring.
|
||||
|
||||
Query is one of:
|
||||
* a string, representing a single column name from the field, eg,
|
||||
@@ -197,12 +198,6 @@ export default class AnnoMatrix {
|
||||
field/column, similar to a join. Currently only supported on the var
|
||||
dimension, allowing query of X columns by var value (eg, gene name)
|
||||
|
||||
The query filter is a single value filter:
|
||||
{ "field name": [
|
||||
{name: "column name", values: [ list of values ]}
|
||||
]}
|
||||
One and only one value filter is allowed in a value query.
|
||||
|
||||
Examples:
|
||||
|
||||
1. Fetch the "n_genes" column the "obs":
|
||||
@@ -220,7 +215,9 @@ export default class AnnoMatrix {
|
||||
value "TYMP" in the var index.
|
||||
|
||||
fetch("X", {
|
||||
where: {field: "var", column: this.schema.annotations.var.index, value: "TYMP"}
|
||||
where: {
|
||||
field: "var", column: this.schema.annotations.var.index, value: "TYMP"
|
||||
}
|
||||
})
|
||||
|
||||
In AnnData & Pandas DataFrame API, this is equivalent to:
|
||||
@@ -410,6 +407,14 @@ export default class AnnoMatrix {
|
||||
_subclassResponsibility();
|
||||
}
|
||||
|
||||
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 _whereCacheGet(this._whereCache, this.schema, field, query);
|
||||
}
|
||||
|
||||
/**
|
||||
** Private interfaces below.
|
||||
**/
|
||||
@@ -427,6 +432,7 @@ export default class AnnoMatrix {
|
||||
async _fetch(field, q) {
|
||||
if (!AnnoMatrix.fields().includes(field)) return undefined;
|
||||
const queries = Array.isArray(q) ? q : [q];
|
||||
queries.forEach(_queryValidate);
|
||||
|
||||
/* find cached columns we need, and GC the rest */
|
||||
const cachedColumns = this._resolveCachedQueries(field, queries);
|
||||
@@ -507,7 +513,7 @@ export default class AnnoMatrix {
|
||||
* obs, var and emb do not grow without bounds, and are needed constantly
|
||||
for rendering.
|
||||
a) There is no upside to GC'ing these in the base (loader)
|
||||
b) The undo/redo cache can hold a large number in views, which is worht GC'ing
|
||||
b) The undo/redo cache can hold a large number in views, which is worth GC'ing
|
||||
* X is often much larger than memory, and the UI allows add/del from
|
||||
this. Most of the GC potential is here in both the base and views.
|
||||
|
||||
@@ -522,7 +528,7 @@ export default class AnnoMatrix {
|
||||
as much of the cache is pinned by that data structure.
|
||||
*/
|
||||
_gcField(field, isHot, pinnedColumns) {
|
||||
const maxColumns = isHot ? 256 : 10; // maybe to aggessive?
|
||||
const maxColumns = isHot ? 256 : 10; // maybe to aggressive?
|
||||
|
||||
const cache = this._cache[field];
|
||||
if (cache.colIndex.size() < maxColumns) return; // trivial rejection
|
||||
@@ -590,23 +596,18 @@ export default class AnnoMatrix {
|
||||
called each time a query is performed, allowing the gc to update any bookkeeping
|
||||
information. Currently, this is just a simple last-fetched timestamp, stored
|
||||
in a Map.
|
||||
|
||||
Map objects preserve order of insertion. This is leveraged as a cheap way to
|
||||
do LRU, by removing and re-inserting keys. IMPORTANT: the cleanup code assumes
|
||||
the map insertion order is least-recently-used first.
|
||||
*/
|
||||
const cols = dataframe.colIndex.labels();
|
||||
const { _gcInfo } = this;
|
||||
const now = Date.now();
|
||||
cols.forEach((c) => {
|
||||
// gcInfo.delete(c);
|
||||
_gcInfo.set(_columnCacheKey(field, c), now);
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
Cloning sublcass protocol - we rely in cloning to preserve immutable
|
||||
symantics while not causing races or other side effects in internal
|
||||
Cloning subclass protocol - we rely in cloning to preserve immutable
|
||||
semantics while not causing races or other side effects in internal
|
||||
cache management.
|
||||
|
||||
Subclasses must override _cloneDeeper() if they have state which requires
|
||||
@@ -639,15 +640,6 @@ export default class AnnoMatrix {
|
||||
/*
|
||||
private utility functions below
|
||||
*/
|
||||
|
||||
function _queryCacheKey(field, query) {
|
||||
if (typeof query === "object") {
|
||||
const { field: queryField, column: queryColumn, value: queryValue } = query;
|
||||
return `${field}/${queryField}/${queryColumn}/${queryValue}`;
|
||||
}
|
||||
return `${field}/${query}`;
|
||||
}
|
||||
|
||||
function _columnCacheKey(field, column) {
|
||||
return `${field}/${column}`;
|
||||
}
|
||||
|
||||
@@ -123,6 +123,24 @@ export default class AnnoMatrixObsCrossfilter {
|
||||
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.
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
export { doBinaryRequest } from "../util/actionHelpers";
|
||||
export { doBinaryRequest, doFetch } from "../util/actionHelpers";
|
||||
|
||||
/* double URI encode - needed for query-param filters */
|
||||
export function _dubEncURIComp(s) {
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
import { doBinaryRequest, _dubEncURIComp } from "./fetchHelpers";
|
||||
import { doBinaryRequest, doFetch } from "./fetchHelpers";
|
||||
import { matrixFBSToDataframe } from "../util/stateManager/matrix";
|
||||
import { _getColumnSchema, _normalizeCategoricalSchema } from "./schema";
|
||||
import {
|
||||
@@ -12,6 +12,13 @@ import { isArrayOrTypedArray } from "../util/typeHelpers";
|
||||
import { _whereCacheCreate } from "./whereCache";
|
||||
import AnnoMatrix from "./annoMatrix";
|
||||
import PromiseLimit from "../util/promiseLimit";
|
||||
import {
|
||||
_expectSimpleQuery,
|
||||
_expectComplexQuery,
|
||||
_urlEncodeLabelQuery,
|
||||
_urlEncodeComplexQuery,
|
||||
_hashStringValues,
|
||||
} from "./query";
|
||||
|
||||
const promiseThrottle = new PromiseLimit(5);
|
||||
|
||||
@@ -223,27 +230,23 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
|
||||
/*
|
||||
_doLoad - evaluates the query against the field. Returns:
|
||||
* whereCache update: column query map mapping the query to the column labels
|
||||
* Dataframe containing the new colums (one per dimension)
|
||||
* Dataframe containing the new columns (one per dimension)
|
||||
*/
|
||||
let urlQuery;
|
||||
let urlBase;
|
||||
let doRequest;
|
||||
let priority = 10; // default fetch priority
|
||||
|
||||
switch (field) {
|
||||
case "obs":
|
||||
case "var": {
|
||||
urlBase = `${this.baseURL}annotations/${field}`;
|
||||
urlQuery = _encodeQuery("annotation-name", query);
|
||||
doRequest = _obsOrVarLoader(this.baseURL, field, query);
|
||||
break;
|
||||
}
|
||||
case "X": {
|
||||
urlBase = `${this.baseURL}data/var`;
|
||||
urlQuery = _encodeQuery(undefined, query);
|
||||
doRequest = _XLoader(this.baseURL, field, query);
|
||||
break;
|
||||
}
|
||||
case "emb": {
|
||||
urlBase = `${this.baseURL}layout/obs`;
|
||||
urlQuery = _encodeQuery("layout-name", query);
|
||||
doRequest = _embLoader(this.baseURL, field, query);
|
||||
priority = 0; // high prio load for embeddings
|
||||
break;
|
||||
}
|
||||
@@ -251,12 +254,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
|
||||
throw new Error("Unknown field name");
|
||||
}
|
||||
|
||||
const url = `${urlBase}?${urlQuery}`;
|
||||
const buffer = await promiseThrottle.priorityAdd(
|
||||
priority,
|
||||
doBinaryRequest,
|
||||
url
|
||||
);
|
||||
const buffer = await promiseThrottle.priorityAdd(priority, doRequest);
|
||||
const result = matrixFBSToDataframe(buffer);
|
||||
if (!result || result.isEmpty()) throw Error("Unknown field/col");
|
||||
|
||||
@@ -267,7 +265,7 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
|
||||
);
|
||||
|
||||
if (field === "obs") {
|
||||
/* cough, cough - see comment on method */
|
||||
/* cough, cough - see comment on the function called */
|
||||
_normalizeCategoricalSchema(
|
||||
this.schema.annotations.obsByName[query],
|
||||
result.col(query)
|
||||
@@ -282,17 +280,6 @@ export default class AnnoMatrixLoader extends AnnoMatrix {
|
||||
Utility functions below
|
||||
*/
|
||||
|
||||
function _encodeQuery(colKey, q) {
|
||||
if (typeof q === "object") {
|
||||
const { field: queryField, column: queryColumn, value: queryValue } = q;
|
||||
return `${_dubEncURIComp(queryField)}:${_dubEncURIComp(
|
||||
queryColumn
|
||||
)}=${_dubEncURIComp(queryValue)}`;
|
||||
}
|
||||
if (!colKey) throw new Error("Unsupported query by name");
|
||||
return `${colKey}=${encodeURIComponent(q)}`;
|
||||
}
|
||||
|
||||
function _writableCheck(colSchema) {
|
||||
if (!colSchema?.writable) {
|
||||
throw new Error("Unknown or readonly obs column");
|
||||
@@ -305,3 +292,57 @@ function _writableCategoryTypeCheck(colSchema) {
|
||||
throw new Error("column must be categorical");
|
||||
}
|
||||
}
|
||||
|
||||
function _embLoader(baseURL, _field, query) {
|
||||
_expectSimpleQuery(query);
|
||||
|
||||
const urlBase = `${baseURL}layout/obs`;
|
||||
const urlQuery = _urlEncodeLabelQuery("layout-name", query);
|
||||
const url = `${urlBase}?${urlQuery}`;
|
||||
return () => doBinaryRequest(url);
|
||||
}
|
||||
|
||||
function _obsOrVarLoader(baseURL, field, query) {
|
||||
_expectSimpleQuery(query);
|
||||
|
||||
const urlBase = `${baseURL}annotations/${field}`;
|
||||
const urlQuery = _urlEncodeLabelQuery("annotation-name", query);
|
||||
const url = `${urlBase}?${urlQuery}`;
|
||||
return () => doBinaryRequest(url);
|
||||
}
|
||||
|
||||
function _XLoader(baseURL, field, query) {
|
||||
_expectComplexQuery(query);
|
||||
|
||||
if (query.where) {
|
||||
const urlBase = `${baseURL}data/var`;
|
||||
const urlQuery = _urlEncodeComplexQuery(query);
|
||||
const url = `${urlBase}?${urlQuery}`;
|
||||
return () => doBinaryRequest(url);
|
||||
}
|
||||
|
||||
if (query.summarize) {
|
||||
const urlBase = `${baseURL}summarize/var`;
|
||||
const urlQuery = _urlEncodeComplexQuery(query);
|
||||
|
||||
if (urlBase.length + urlQuery.length < 2000) {
|
||||
const url = `${urlBase}?${urlQuery}`;
|
||||
return () => doBinaryRequest(url);
|
||||
}
|
||||
|
||||
const url = `${urlBase}?key=${_hashStringValues([urlQuery])}`;
|
||||
return async () => {
|
||||
const res = await doFetch(url, {
|
||||
method: "POST",
|
||||
body: urlQuery,
|
||||
headers: new Headers({
|
||||
Accept: "application/octet-stream",
|
||||
"Content-Type": "application/x-www-form-urlencoded",
|
||||
}),
|
||||
});
|
||||
return res.arrayBuffer();
|
||||
};
|
||||
}
|
||||
|
||||
throw new Error("Unknown query structure");
|
||||
}
|
||||
|
||||
@@ -0,0 +1,126 @@
|
||||
import sha1 from "sha1";
|
||||
import { _dubEncURIComp } from "./fetchHelpers";
|
||||
|
||||
/**
|
||||
* Query utilities, mostly for debugging support and validation.
|
||||
*/
|
||||
|
||||
/**
|
||||
* Normalize & error check the query.
|
||||
* @param {object | string} query - the query
|
||||
* @returns {object | string} - the normalized query
|
||||
*/
|
||||
export function _queryValidate(query) {
|
||||
if (typeof query !== "object") return query;
|
||||
|
||||
if (query.where && query.summarize)
|
||||
throw new Error("query may not specify both where and summarize");
|
||||
if (query.where) {
|
||||
const {
|
||||
field: queryField,
|
||||
column: queryColumn,
|
||||
value: queryValue,
|
||||
} = query.where;
|
||||
if (!queryField || !queryColumn || !queryValue)
|
||||
throw new Error("Incomplete where query");
|
||||
return query;
|
||||
}
|
||||
if (query.summarize) {
|
||||
const {
|
||||
field: queryField,
|
||||
column: queryColumn,
|
||||
values: queryValues,
|
||||
} = query.summarize;
|
||||
if (!queryField || !queryColumn || !queryValues)
|
||||
throw new Error("Incomplete where query");
|
||||
if (!Array.isArray(queryValues))
|
||||
throw new Error("Summarize query values must be an array");
|
||||
return query;
|
||||
}
|
||||
throw new Error("query must specify one of where or summarize");
|
||||
}
|
||||
|
||||
export function _expectSimpleQuery(query) {
|
||||
if (typeof query === "object") throw new Error("expected simple query");
|
||||
}
|
||||
|
||||
export function _expectComplexQuery(query) {
|
||||
if (typeof query !== "object") throw new Error("expected complex query");
|
||||
}
|
||||
|
||||
/**
|
||||
* Generate a unique key which can be used to reference this query.
|
||||
*
|
||||
* @param {string} field
|
||||
* @param {string|object} query
|
||||
* @returns the key
|
||||
*/
|
||||
export function _queryCacheKey(field, query) {
|
||||
if (typeof query === "object") {
|
||||
// complex query
|
||||
if (query.where) {
|
||||
const {
|
||||
field: queryField,
|
||||
column: queryColumn,
|
||||
value: queryValue,
|
||||
} = query.where;
|
||||
return `${field}/${queryField}/${queryColumn}/${queryValue}`;
|
||||
}
|
||||
if (query.summarize) {
|
||||
const {
|
||||
method,
|
||||
field: queryField,
|
||||
column: queryColumn,
|
||||
values: queryValues,
|
||||
} = query.summarize;
|
||||
return `${field}/${method}/${queryField}/${queryColumn}/${queryValues.join(
|
||||
","
|
||||
)}`;
|
||||
}
|
||||
throw new Error("Unrecognized complex query type");
|
||||
}
|
||||
|
||||
// simple query
|
||||
return `${field}/${query}`;
|
||||
}
|
||||
|
||||
function _urlEncodeWhereQuery(q) {
|
||||
const { field: queryField, column: queryColumn, value: queryValue } = q;
|
||||
return `${_dubEncURIComp(queryField)}:${_dubEncURIComp(
|
||||
queryColumn
|
||||
)}=${_dubEncURIComp(queryValue)}`;
|
||||
}
|
||||
|
||||
function _urlEncodeSummarizeQuery(q) {
|
||||
const { method, field, column, values } = q;
|
||||
const filter = values
|
||||
.map((value) => _urlEncodeWhereQuery({ field, column, value }))
|
||||
.join("&");
|
||||
return `method=${method}&${filter}`;
|
||||
}
|
||||
|
||||
export function _urlEncodeComplexQuery(q) {
|
||||
if (typeof q === "object") {
|
||||
if (q.where) {
|
||||
return _urlEncodeWhereQuery(q.where);
|
||||
}
|
||||
if (q.summarize) {
|
||||
return _urlEncodeSummarizeQuery(q.summarize);
|
||||
}
|
||||
}
|
||||
throw new Error("Unrecognized complex query type");
|
||||
}
|
||||
|
||||
export function _urlEncodeLabelQuery(colKey, q) {
|
||||
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)}`;
|
||||
}
|
||||
|
||||
/**
|
||||
* Generate the column key the server will send us for this query.
|
||||
*/
|
||||
export function _hashStringValues(arrayOfString) {
|
||||
const hash = sha1(arrayOfString.join(""));
|
||||
return hash;
|
||||
}
|
||||
@@ -29,7 +29,7 @@ export function _getColumnSchema(schema, field, col) {
|
||||
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. Signfied by the presence
|
||||
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);
|
||||
|
||||
@@ -1,27 +1,55 @@
|
||||
/*
|
||||
Private support functions.
|
||||
|
||||
Support for a "where" query, eg,
|
||||
This implements a query resolver cache, mapping a query onto the column labels
|
||||
resolved by that query. These labels are then used to manage the acutal data cache,
|
||||
which stores data by the resolved label.
|
||||
|
||||
{ where: { field: "var", column: "gene", value: "FOXP2" }}
|
||||
There are three query forms:
|
||||
* primitive (string, number) - which is just reference the column label of same value
|
||||
* where query (object) - eg, { where: { field: "var", column: "gene", value: "FOXP2" }}
|
||||
* summary query (object) - eg, { summarize: { method: "mean", field: "var", column: "gene", values: ["FOXP2", "GNE", "F5"]}}
|
||||
|
||||
These evaluate to a given column label.
|
||||
These queries all resolve to one or more column labels on a field. This
|
||||
cache maintains a record of this, allowing direct access to the data caches
|
||||
without a server round-trip.
|
||||
|
||||
The "where cache" is a map that saves evaluated queries and points
|
||||
to the column label they resolve to.
|
||||
The data structure for where queries, the following query against X as an example:
|
||||
{ where: { field: "var", column: "column_label_in_var", value: "value_in_var_column" } }
|
||||
results in the following cached entry:
|
||||
{
|
||||
where: {
|
||||
X: {
|
||||
var: Map(
|
||||
column_label_in_var => Map(
|
||||
value_in_var_column => [column_label_in_X, ...]
|
||||
)
|
||||
)
|
||||
}
|
||||
},
|
||||
summarize: {},
|
||||
}
|
||||
|
||||
Data structure, using X as the example field being queried, and var as
|
||||
the index.
|
||||
|
||||
{
|
||||
X: {
|
||||
var: Map(
|
||||
column_label_in_var => Map(value_in_var_column => [column_label_in_X, ...])
|
||||
)
|
||||
}
|
||||
And for summarize queries, for the following summary on X:
|
||||
{ summarize: { method: "mean", field: "var", column: "gene", values: ["G1", "G2"]}}
|
||||
creates a cache entry of:
|
||||
{
|
||||
where: {},
|
||||
summarize: {
|
||||
X: {
|
||||
mean: {
|
||||
var: Map(
|
||||
"gene" => Map(
|
||||
"G1,G2" => [summary_column_label, ...]
|
||||
)
|
||||
)
|
||||
}
|
||||
},
|
||||
},
|
||||
}
|
||||
*/
|
||||
import { _getColumnDimensionNames } from "./schema";
|
||||
import { _hashStringValues } from "./query";
|
||||
|
||||
export function _whereCacheGet(whereCache, schema, field, query) {
|
||||
/*
|
||||
@@ -31,20 +59,30 @@ export function _whereCacheGet(whereCache, schema, field, query) {
|
||||
*/
|
||||
|
||||
if (typeof query === "object") {
|
||||
const { field: queryField, column: queryColumn, value: queryValue } = query;
|
||||
|
||||
const columnMap = whereCache?.[field]?.[queryField];
|
||||
if (columnMap === undefined) return [undefined];
|
||||
|
||||
const valueMap = columnMap.get(queryColumn);
|
||||
if (valueMap === undefined) return [undefined];
|
||||
|
||||
const columnLabels = valueMap.get(queryValue);
|
||||
return columnLabels === undefined ? [undefined] : columnLabels;
|
||||
if (query.where) {
|
||||
const {
|
||||
field: queryField,
|
||||
column: queryColumn,
|
||||
value: queryValue,
|
||||
} = query.where;
|
||||
const columnMap = whereCache?.where?.[field]?.[queryField];
|
||||
return columnMap?.get(queryColumn)?.get(queryValue) ?? [undefined];
|
||||
}
|
||||
if (query.summarize) {
|
||||
const {
|
||||
method,
|
||||
field: queryField,
|
||||
column: queryColumn,
|
||||
values: queryValues,
|
||||
} = query.summarize;
|
||||
const columnMap = whereCache?.summarize?.[field]?.[method]?.[queryField];
|
||||
const queryValueHash = _hashStringValues(queryValues);
|
||||
return columnMap?.get(queryColumn)?.get(queryValueHash) ?? [undefined];
|
||||
}
|
||||
return [undefined];
|
||||
}
|
||||
|
||||
const colDims = _getColumnDimensionNames(schema, field, query);
|
||||
return colDims === undefined ? [undefined] : colDims;
|
||||
return _getColumnDimensionNames(schema, field, query) ?? [undefined];
|
||||
}
|
||||
|
||||
export function _whereCacheCreate(field, query, columnLabels) {
|
||||
@@ -53,40 +91,86 @@ export function _whereCacheCreate(field, query, columnLabels) {
|
||||
*/
|
||||
if (typeof query !== "object") return null;
|
||||
|
||||
const { field: queryField, column: queryColumn, value: queryValue } = query;
|
||||
const whereCache = {
|
||||
[field]: {
|
||||
[queryField]: new Map([
|
||||
[queryColumn, new Map([[queryValue, columnLabels]])],
|
||||
]),
|
||||
},
|
||||
};
|
||||
return whereCache;
|
||||
if (query.where) {
|
||||
const {
|
||||
field: queryField,
|
||||
column: queryColumn,
|
||||
value: queryValue,
|
||||
} = query.where;
|
||||
return {
|
||||
where: {
|
||||
[field]: {
|
||||
[queryField]: new Map([
|
||||
[queryColumn, new Map([[queryValue, columnLabels]])],
|
||||
]),
|
||||
},
|
||||
},
|
||||
};
|
||||
}
|
||||
if (query.summarize) {
|
||||
const {
|
||||
method,
|
||||
field: queryField,
|
||||
column: queryColumn,
|
||||
values: queryValues,
|
||||
} = query.summarize;
|
||||
const queryValueHash = _hashStringValues(queryValues);
|
||||
return {
|
||||
summarize: {
|
||||
[field]: {
|
||||
[method]: {
|
||||
[queryField]: new Map([
|
||||
[queryColumn, new Map([[queryValueHash, columnLabels]])],
|
||||
]),
|
||||
},
|
||||
},
|
||||
},
|
||||
};
|
||||
}
|
||||
// oops, not sure what that query is!
|
||||
return {};
|
||||
}
|
||||
|
||||
function __mergeQueries(dst, src) {
|
||||
for (const [queryField, columnMap] of Object.entries(src)) {
|
||||
dst[queryField] = dst[queryField] || new Map();
|
||||
for (const [queryColumn, valueMap] of columnMap) {
|
||||
if (!dst[queryField].has(queryColumn))
|
||||
dst[queryField].set(queryColumn, new Map());
|
||||
for (const [queryValue, columnLabels] of valueMap) {
|
||||
dst[queryField].get(queryColumn).set(queryValue, columnLabels);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
function __whereCacheMerge(dst, src) {
|
||||
/*
|
||||
merge src into dst (modifies dst)
|
||||
*/
|
||||
if (!dst) dst = {};
|
||||
if (!src || typeof src !== "object") return dst;
|
||||
Object.entries(src).forEach(([field, query]) => {
|
||||
if (!Object.prototype.hasOwnProperty.call(dst, field)) dst[field] = {};
|
||||
Object.entries(query).forEach(([queryField, columnMap]) => {
|
||||
if (!Object.prototype.hasOwnProperty.call(dst[field], queryField))
|
||||
dst[field][queryField] = new Map();
|
||||
columnMap.forEach((valueMap, queryColumn) => {
|
||||
if (!dst[field][queryField].has(queryColumn))
|
||||
dst[field][queryField].set(queryColumn, new Map());
|
||||
valueMap.forEach((columnLabels, queryValue) => {
|
||||
dst[field][queryField].get(queryColumn).set(queryValue, columnLabels);
|
||||
});
|
||||
});
|
||||
});
|
||||
});
|
||||
|
||||
if (src.where) {
|
||||
dst.where = dst.where || {};
|
||||
for (const [field, query] of Object.entries(src.where)) {
|
||||
dst.where[field] = dst.where[field] || {};
|
||||
__mergeQueries(dst.where[field], query);
|
||||
}
|
||||
}
|
||||
if (src.summarize) {
|
||||
dst.summarize = dst.summarize || {};
|
||||
for (const [field, method] of Object.entries(src.summarize)) {
|
||||
dst.summarize[field] = dst.summarize[field] || {};
|
||||
for (const [methodName, query] of Object.entries(method)) {
|
||||
dst.summarize[field][methodName] =
|
||||
dst.summarize[field][methodName] || {};
|
||||
__mergeQueries(dst.summarize[field][methodName], query);
|
||||
}
|
||||
}
|
||||
}
|
||||
return dst;
|
||||
}
|
||||
|
||||
export function _whereCacheMerge(...caches) {
|
||||
return caches.reduce((dst, src) => __whereCacheMerge(dst, src), {});
|
||||
return caches.reduce(__whereCacheMerge, {});
|
||||
}
|
||||
|
||||
@@ -18,7 +18,7 @@ import {
|
||||
userInfo: state.userInfo,
|
||||
writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
|
||||
writableGenesetsEnabled: !(
|
||||
state.config?.parameters?.["annotations_genesets_readonly"] ?? true
|
||||
state.config?.parameters?.annotations_genesets_readonly ?? true
|
||||
),
|
||||
}))
|
||||
class FilenameDialog extends React.Component {
|
||||
|
||||
@@ -11,7 +11,7 @@ import FilenameDialog from "./filenameDialog";
|
||||
error: state.autosave?.error,
|
||||
writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
|
||||
writableGenesetsEnabled: !(
|
||||
state.config?.parameters?.["annotations_genesets_readonly"] ?? true
|
||||
state.config?.parameters?.annotations_genesets_readonly ?? true
|
||||
),
|
||||
annoMatrix: state.annoMatrix,
|
||||
genesets: state.genesets,
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
import React from "react";
|
||||
import { connect } from "react-redux";
|
||||
import { connect, shallowEqual } from "react-redux";
|
||||
import * as d3 from "d3";
|
||||
import Async from "react-async";
|
||||
import memoize from "memoize-one";
|
||||
@@ -14,9 +14,9 @@ import StillLoading from "./loading";
|
||||
import ErrorLoading from "./error";
|
||||
|
||||
@connect((state, ownProps) => {
|
||||
const { isObs, isUserDefined, isDiffExp, field } = ownProps;
|
||||
const { isObs, isUserDefined, isDiffExp, isGeneSetSummary, field } = ownProps;
|
||||
const myName = makeContinuousDimensionName(
|
||||
{ isObs, isUserDefined, isDiffExp },
|
||||
{ isObs, isUserDefined, isDiffExp, isGeneSetSummary },
|
||||
field
|
||||
);
|
||||
return {
|
||||
@@ -28,6 +28,10 @@ import ErrorLoading from "./error";
|
||||
};
|
||||
})
|
||||
class HistogramBrush extends React.PureComponent {
|
||||
static watchAsync(props, prevProps) {
|
||||
return !shallowEqual(props.watchProps, prevProps.watchProps);
|
||||
}
|
||||
|
||||
/* memoized closure to prevent HistogramHeader unecessary repaint */
|
||||
handleColorAction = memoize((dispatch) => (field, isObs) => {
|
||||
if (isObs) {
|
||||
@@ -71,7 +75,14 @@ class HistogramBrush extends React.PureComponent {
|
||||
onBrush = (selection, x, eventType) => {
|
||||
const type = `continuous metadata histogram ${eventType}`;
|
||||
return () => {
|
||||
const { dispatch, field, isObs, isUserDefined, isDiffExp } = this.props;
|
||||
const {
|
||||
dispatch,
|
||||
field,
|
||||
isObs,
|
||||
isUserDefined,
|
||||
isDiffExp,
|
||||
isGeneSetSummary,
|
||||
} = this.props;
|
||||
|
||||
// ignore programmatically generated events
|
||||
if (!d3.event.sourceEvent) return;
|
||||
@@ -88,6 +99,7 @@ class HistogramBrush extends React.PureComponent {
|
||||
isObs,
|
||||
isUserDefined,
|
||||
isDiffExp,
|
||||
isGeneSetSummary,
|
||||
},
|
||||
};
|
||||
dispatch(
|
||||
@@ -98,7 +110,14 @@ class HistogramBrush extends React.PureComponent {
|
||||
|
||||
onBrushEnd = (selection, x) => {
|
||||
return () => {
|
||||
const { dispatch, field, isObs, isUserDefined, isDiffExp } = this.props;
|
||||
const {
|
||||
dispatch,
|
||||
field,
|
||||
isObs,
|
||||
isUserDefined,
|
||||
isDiffExp,
|
||||
isGeneSetSummary,
|
||||
} = this.props;
|
||||
const minAllowedBrushSize = 10;
|
||||
const smallAmountToAvoidInfiniteLoop = 0.1;
|
||||
|
||||
@@ -138,6 +157,7 @@ class HistogramBrush extends React.PureComponent {
|
||||
isObs,
|
||||
isUserDefined,
|
||||
isDiffExp,
|
||||
isGeneSetSummary,
|
||||
},
|
||||
};
|
||||
dispatch(
|
||||
@@ -300,19 +320,37 @@ class HistogramBrush extends React.PureComponent {
|
||||
}
|
||||
|
||||
createQuery() {
|
||||
const { isObs, field, annoMatrix } = this.props;
|
||||
const { isObs, isGeneSetSummary, field, setGenes, annoMatrix } = this.props;
|
||||
const { schema } = annoMatrix;
|
||||
if (isObs) {
|
||||
return ["obs", field];
|
||||
}
|
||||
const varIndex = schema?.annotations?.var?.index;
|
||||
if (!varIndex) return null;
|
||||
|
||||
if (isGeneSetSummary) {
|
||||
return [
|
||||
"X",
|
||||
{
|
||||
summarize: {
|
||||
method: "mean",
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
values: setGenes,
|
||||
},
|
||||
},
|
||||
];
|
||||
}
|
||||
|
||||
// else, we assume it is a gene expression
|
||||
return [
|
||||
"X",
|
||||
{
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: field,
|
||||
where: {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: field,
|
||||
},
|
||||
},
|
||||
];
|
||||
}
|
||||
@@ -333,6 +371,7 @@ class HistogramBrush extends React.PureComponent {
|
||||
continuousSelectionRange,
|
||||
isObs,
|
||||
mini,
|
||||
setGenes,
|
||||
} = this.props;
|
||||
const {
|
||||
margin,
|
||||
@@ -346,7 +385,11 @@ class HistogramBrush extends React.PureComponent {
|
||||
const showScatterPlot = isDiffExp || isUserDefined;
|
||||
|
||||
return (
|
||||
<Async watch={annoMatrix} promiseFn={this.fetchAsyncProps}>
|
||||
<Async
|
||||
watchFn={HistogramBrush.watchAsync}
|
||||
promiseFn={this.fetchAsyncProps}
|
||||
watchProps={{ annoMatrix, setGenes }}
|
||||
>
|
||||
<Async.Pending initial>
|
||||
<StillLoading displayName={field} zebra={zebra} />
|
||||
</Async.Pending>
|
||||
|
||||
@@ -53,12 +53,7 @@ class Gene extends React.Component {
|
||||
|
||||
handleDeleteGeneFromSet = () => {
|
||||
const { dispatch, gene, geneset } = this.props;
|
||||
|
||||
dispatch({
|
||||
type: "geneset: delete genes",
|
||||
genesetName: geneset,
|
||||
geneSymbols: [gene],
|
||||
});
|
||||
dispatch(actions.genesetDeleteGenes(geneset, [gene]));
|
||||
};
|
||||
|
||||
render() {
|
||||
|
||||
@@ -9,6 +9,7 @@ import { memoize } from "../../util/dataframe/util";
|
||||
import Truncate from "../util/truncate";
|
||||
import * as globals from "../../globals";
|
||||
import GenesetMenus from "./menus/genesetMenus";
|
||||
import HistogramBrush from "../brushableHistogram";
|
||||
|
||||
@connect((state, ownProps) => {
|
||||
return {
|
||||
@@ -163,18 +164,25 @@ class GeneSet extends React.Component {
|
||||
) : null}
|
||||
</div>
|
||||
|
||||
{isOpen && !toggleSummaryHisto
|
||||
? _.map(setGenes, (gene) => {
|
||||
return (
|
||||
<Gene
|
||||
key={gene}
|
||||
gene={gene}
|
||||
geneset={setName}
|
||||
isDiffexp={isDiffexp}
|
||||
{isOpen &&
|
||||
(!toggleSummaryHisto
|
||||
? _.map(setGenes, (gene) => {
|
||||
return (
|
||||
<Gene
|
||||
key={gene}
|
||||
gene={gene}
|
||||
geneset={setName}
|
||||
isDiffexp={isDiffexp}
|
||||
/>
|
||||
);
|
||||
})
|
||||
: setGenes.length > 0 && (
|
||||
<HistogramBrush
|
||||
isGeneSetSummary
|
||||
field={setName}
|
||||
setGenes={setGenes}
|
||||
/>
|
||||
);
|
||||
})
|
||||
: null}
|
||||
))}
|
||||
</div>
|
||||
);
|
||||
}
|
||||
|
||||
@@ -3,6 +3,7 @@ import { connect } from "react-redux";
|
||||
import AnnoDialog from "../../annoDialog";
|
||||
import LabelInput from "../../labelInput";
|
||||
import parseBulkGeneString from "../../../util/parseBulkGeneString";
|
||||
import actions from "../../../actions";
|
||||
|
||||
@connect((state) => ({
|
||||
genesetsUI: state.genesetsUI,
|
||||
@@ -36,11 +37,7 @@ class AddGeneToGenesetDialogue extends React.PureComponent {
|
||||
});
|
||||
});
|
||||
|
||||
dispatch({
|
||||
type: "geneset: add genes",
|
||||
genesetName: geneset,
|
||||
genes: genesTmpHardcodedFormat,
|
||||
});
|
||||
dispatch(actions.genesetAddGenes(geneset, genesTmpHardcodedFormat));
|
||||
dispatch({
|
||||
type: "geneset: disable add new genes mode",
|
||||
});
|
||||
|
||||
@@ -77,6 +77,26 @@ class AddGenes extends React.Component {
|
||||
this.updateState(prevProps);
|
||||
}
|
||||
|
||||
handleClick(g) {
|
||||
const { dispatch, userDefinedGenes } = this.props;
|
||||
const { geneNames } = this.state;
|
||||
if (!g) return;
|
||||
const gene = g.target;
|
||||
if (userDefinedGenes.indexOf(gene) !== -1) {
|
||||
postUserErrorToast("That gene already exists");
|
||||
} else if (userDefinedGenes.length > globals.maxUserDefinedGenes) {
|
||||
postUserErrorToast(
|
||||
`That's too many genes, you can have at most ${globals.maxUserDefinedGenes} user defined genes`
|
||||
);
|
||||
} else if (geneNames.indexOf(gene) === undefined) {
|
||||
postUserErrorToast("That doesn't appear to be a valid gene name.");
|
||||
} else {
|
||||
dispatch({ type: "single user defined gene start" });
|
||||
dispatch(actions.requestUserDefinedGene(gene));
|
||||
dispatch({ type: "single user defined gene complete" });
|
||||
}
|
||||
}
|
||||
|
||||
_genesToUpper = (listGenes) => {
|
||||
// Has to be a Map to preserve index
|
||||
const upperGenes = new Map();
|
||||
@@ -190,26 +210,6 @@ class AddGenes extends React.Component {
|
||||
return "Apod, Cd74, ...";
|
||||
}
|
||||
|
||||
handleClick(g) {
|
||||
const { dispatch, userDefinedGenes } = this.props;
|
||||
const { geneNames } = this.state;
|
||||
if (!g) return;
|
||||
const gene = g.target;
|
||||
if (userDefinedGenes.indexOf(gene) !== -1) {
|
||||
postUserErrorToast("That gene already exists");
|
||||
} else if (userDefinedGenes.length > globals.maxUserDefinedGenes) {
|
||||
postUserErrorToast(
|
||||
`That's too many genes, you can have at most ${globals.maxUserDefinedGenes} user defined genes`
|
||||
);
|
||||
} else if (geneNames.indexOf(gene) === undefined) {
|
||||
postUserErrorToast("That doesn't appear to be a valid gene name.");
|
||||
} else {
|
||||
dispatch({ type: "single user defined gene start" });
|
||||
dispatch(actions.requestUserDefinedGene(gene));
|
||||
dispatch({ type: "single user defined gene complete" });
|
||||
}
|
||||
}
|
||||
|
||||
render() {
|
||||
const { userDefinedGenesLoading } = this.props;
|
||||
const { tab, bulkAdd, activeItem, status, geneNames } = this.state;
|
||||
|
||||
@@ -3,6 +3,7 @@ import React from "react";
|
||||
import { connect } from "react-redux";
|
||||
import AnnoDialog from "../../annoDialog";
|
||||
import LabelInput from "../../labelInput";
|
||||
import actions from "../../../actions";
|
||||
|
||||
@connect((state) => ({
|
||||
annotations: state.annotations,
|
||||
@@ -56,11 +57,7 @@ class CreateGenesetDialogue extends React.PureComponent {
|
||||
});
|
||||
});
|
||||
|
||||
dispatch({
|
||||
type: "geneset: add genes",
|
||||
genesetName,
|
||||
genes: genesTmpHardcodedFormat,
|
||||
});
|
||||
dispatch(actions.genesetAddGenes(genesetName, genesTmpHardcodedFormat));
|
||||
}
|
||||
dispatch({
|
||||
type: "geneset: disable create geneset mode",
|
||||
|
||||
@@ -12,6 +12,7 @@ import {
|
||||
} from "@blueprintjs/core";
|
||||
|
||||
import * as globals from "../../../globals";
|
||||
import actions from "../../../actions";
|
||||
import AddGeneToGenesetDialogue from "./addGeneToGenesetDialogue";
|
||||
|
||||
@connect((state) => {
|
||||
@@ -44,7 +45,7 @@ class GenesetMenus extends React.PureComponent {
|
||||
|
||||
handleDeleteCategory = () => {
|
||||
const { dispatch, geneset } = this.props;
|
||||
dispatch({ type: "geneset: delete", genesetName: geneset });
|
||||
dispatch(actions.genesetDelete(geneset));
|
||||
};
|
||||
|
||||
render() {
|
||||
|
||||
@@ -303,13 +303,6 @@ class Graph extends React.Component {
|
||||
window.removeEventListener("resize", this.handleResize);
|
||||
}
|
||||
|
||||
setReglCanvas = (canvas) => {
|
||||
this.reglCanvas = canvas;
|
||||
this.setState({
|
||||
...Graph.createReglState(canvas),
|
||||
});
|
||||
};
|
||||
|
||||
handleResize = () => {
|
||||
const { state } = this.state;
|
||||
const viewport = this.getViewportDimensions();
|
||||
@@ -321,14 +314,6 @@ class Graph extends React.Component {
|
||||
});
|
||||
};
|
||||
|
||||
getViewportDimensions = () => {
|
||||
const { viewportRef } = this.props;
|
||||
return {
|
||||
height: viewportRef.clientHeight,
|
||||
width: viewportRef.clientWidth,
|
||||
};
|
||||
};
|
||||
|
||||
handleCanvasEvent = (e) => {
|
||||
const { camera, projectionTF } = this.state;
|
||||
if (e.type !== "wheel") e.preventDefault();
|
||||
@@ -340,6 +325,143 @@ class Graph extends React.Component {
|
||||
}
|
||||
};
|
||||
|
||||
handleBrushDragAction() {
|
||||
/*
|
||||
event describing brush position:
|
||||
@-------|
|
||||
| |
|
||||
| |
|
||||
|-------@
|
||||
*/
|
||||
// ignore programatically generated events
|
||||
if (d3.event.sourceEvent === null || !d3.event.selection) return;
|
||||
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
const s = d3.event.selection;
|
||||
const northwest = this.mapScreenToPoint(s[0]);
|
||||
const southeast = this.mapScreenToPoint(s[1]);
|
||||
const [minX, maxY] = northwest;
|
||||
const [maxX, minY] = southeast;
|
||||
dispatch(
|
||||
actions.graphBrushChangeAction(layoutChoice.current, {
|
||||
minX,
|
||||
minY,
|
||||
maxX,
|
||||
maxY,
|
||||
northwest,
|
||||
southeast,
|
||||
})
|
||||
);
|
||||
}
|
||||
|
||||
handleBrushStartAction() {
|
||||
// Ignore programatically generated events.
|
||||
if (!d3.event.sourceEvent) return;
|
||||
|
||||
const { dispatch } = this.props;
|
||||
dispatch(actions.graphBrushStartAction());
|
||||
}
|
||||
|
||||
handleBrushEndAction() {
|
||||
// Ignore programatically generated events.
|
||||
if (!d3.event.sourceEvent) return;
|
||||
|
||||
/*
|
||||
coordinates will be included if selection made, null
|
||||
if selection cleared.
|
||||
*/
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
const s = d3.event.selection;
|
||||
if (s) {
|
||||
const northwest = this.mapScreenToPoint(s[0]);
|
||||
const southeast = this.mapScreenToPoint(s[1]);
|
||||
const [minX, maxY] = northwest;
|
||||
const [maxX, minY] = southeast;
|
||||
dispatch(
|
||||
actions.graphBrushEndAction(layoutChoice.current, {
|
||||
minX,
|
||||
minY,
|
||||
maxX,
|
||||
maxY,
|
||||
northwest,
|
||||
southeast,
|
||||
})
|
||||
);
|
||||
} else {
|
||||
dispatch(actions.graphBrushDeselectAction(layoutChoice.current));
|
||||
}
|
||||
}
|
||||
|
||||
handleBrushDeselectAction() {
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
dispatch(actions.graphBrushDeselectAction(layoutChoice.current));
|
||||
}
|
||||
|
||||
handleLassoStart() {
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
dispatch(actions.graphLassoStartAction(layoutChoice.current));
|
||||
}
|
||||
|
||||
// when a lasso is completed, filter to the points within the lasso polygon
|
||||
handleLassoEnd(polygon) {
|
||||
const minimumPolygonArea = 10;
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
|
||||
if (
|
||||
polygon.length < 3 ||
|
||||
Math.abs(d3.polygonArea(polygon)) < minimumPolygonArea
|
||||
) {
|
||||
// if less than three points, or super small area, treat as a clear selection.
|
||||
dispatch(actions.graphLassoDeselectAction(layoutChoice.current));
|
||||
} else {
|
||||
dispatch(
|
||||
actions.graphLassoEndAction(
|
||||
layoutChoice.current,
|
||||
polygon.map((xy) => this.mapScreenToPoint(xy))
|
||||
)
|
||||
);
|
||||
}
|
||||
}
|
||||
|
||||
handleLassoCancel() {
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
dispatch(actions.graphLassoCancelAction(layoutChoice.current));
|
||||
}
|
||||
|
||||
handleLassoDeselectAction() {
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
dispatch(actions.graphLassoDeselectAction(layoutChoice.current));
|
||||
}
|
||||
|
||||
handleDeselectAction() {
|
||||
const { selectionTool } = this.props;
|
||||
if (selectionTool === "brush") this.handleBrushDeselectAction();
|
||||
if (selectionTool === "lasso") this.handleLassoDeselectAction();
|
||||
}
|
||||
|
||||
handleOpacityRangeChange(e) {
|
||||
const { dispatch } = this.props;
|
||||
dispatch({
|
||||
type: "change opacity deselected cells in 2d graph background",
|
||||
data: e.target.value,
|
||||
});
|
||||
}
|
||||
|
||||
setReglCanvas = (canvas) => {
|
||||
this.reglCanvas = canvas;
|
||||
this.setState({
|
||||
...Graph.createReglState(canvas),
|
||||
});
|
||||
};
|
||||
|
||||
getViewportDimensions = () => {
|
||||
const { viewportRef } = this.props;
|
||||
return {
|
||||
height: viewportRef.clientHeight,
|
||||
width: viewportRef.clientWidth,
|
||||
};
|
||||
};
|
||||
|
||||
createToolSVG = () => {
|
||||
/*
|
||||
Called from componentDidUpdate. Create the tool SVG, and return any
|
||||
@@ -589,128 +711,6 @@ class Graph extends React.Component {
|
||||
];
|
||||
}
|
||||
|
||||
handleBrushDragAction() {
|
||||
/*
|
||||
event describing brush position:
|
||||
@-------|
|
||||
| |
|
||||
| |
|
||||
|-------@
|
||||
*/
|
||||
// ignore programatically generated events
|
||||
if (d3.event.sourceEvent === null || !d3.event.selection) return;
|
||||
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
const s = d3.event.selection;
|
||||
const northwest = this.mapScreenToPoint(s[0]);
|
||||
const southeast = this.mapScreenToPoint(s[1]);
|
||||
const [minX, maxY] = northwest;
|
||||
const [maxX, minY] = southeast;
|
||||
dispatch(
|
||||
actions.graphBrushChangeAction(layoutChoice.current, {
|
||||
minX,
|
||||
minY,
|
||||
maxX,
|
||||
maxY,
|
||||
northwest,
|
||||
southeast,
|
||||
})
|
||||
);
|
||||
}
|
||||
|
||||
handleBrushStartAction() {
|
||||
// Ignore programatically generated events.
|
||||
if (!d3.event.sourceEvent) return;
|
||||
|
||||
const { dispatch } = this.props;
|
||||
dispatch(actions.graphBrushStartAction());
|
||||
}
|
||||
|
||||
handleBrushEndAction() {
|
||||
// Ignore programatically generated events.
|
||||
if (!d3.event.sourceEvent) return;
|
||||
|
||||
/*
|
||||
coordinates will be included if selection made, null
|
||||
if selection cleared.
|
||||
*/
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
const s = d3.event.selection;
|
||||
if (s) {
|
||||
const northwest = this.mapScreenToPoint(s[0]);
|
||||
const southeast = this.mapScreenToPoint(s[1]);
|
||||
const [minX, maxY] = northwest;
|
||||
const [maxX, minY] = southeast;
|
||||
dispatch(
|
||||
actions.graphBrushEndAction(layoutChoice.current, {
|
||||
minX,
|
||||
minY,
|
||||
maxX,
|
||||
maxY,
|
||||
northwest,
|
||||
southeast,
|
||||
})
|
||||
);
|
||||
} else {
|
||||
dispatch(actions.graphBrushDeselectAction(layoutChoice.current));
|
||||
}
|
||||
}
|
||||
|
||||
handleBrushDeselectAction() {
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
dispatch(actions.graphBrushDeselectAction(layoutChoice.current));
|
||||
}
|
||||
|
||||
handleLassoStart() {
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
dispatch(actions.graphLassoStartAction(layoutChoice.current));
|
||||
}
|
||||
|
||||
// when a lasso is completed, filter to the points within the lasso polygon
|
||||
handleLassoEnd(polygon) {
|
||||
const minimumPolygonArea = 10;
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
|
||||
if (
|
||||
polygon.length < 3 ||
|
||||
Math.abs(d3.polygonArea(polygon)) < minimumPolygonArea
|
||||
) {
|
||||
// if less than three points, or super small area, treat as a clear selection.
|
||||
dispatch(actions.graphLassoDeselectAction(layoutChoice.current));
|
||||
} else {
|
||||
dispatch(
|
||||
actions.graphLassoEndAction(
|
||||
layoutChoice.current,
|
||||
polygon.map((xy) => this.mapScreenToPoint(xy))
|
||||
)
|
||||
);
|
||||
}
|
||||
}
|
||||
|
||||
handleLassoCancel() {
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
dispatch(actions.graphLassoCancelAction(layoutChoice.current));
|
||||
}
|
||||
|
||||
handleLassoDeselectAction() {
|
||||
const { dispatch, layoutChoice } = this.props;
|
||||
dispatch(actions.graphLassoDeselectAction(layoutChoice.current));
|
||||
}
|
||||
|
||||
handleDeselectAction() {
|
||||
const { selectionTool } = this.props;
|
||||
if (selectionTool === "brush") this.handleBrushDeselectAction();
|
||||
if (selectionTool === "lasso") this.handleLassoDeselectAction();
|
||||
}
|
||||
|
||||
handleOpacityRangeChange(e) {
|
||||
const { dispatch } = this.props;
|
||||
dispatch({
|
||||
type: "change opacity deselected cells in 2d graph background",
|
||||
data: e.target.value,
|
||||
});
|
||||
}
|
||||
|
||||
renderCanvas = renderThrottle(() => {
|
||||
const {
|
||||
regl,
|
||||
|
||||
@@ -11,7 +11,7 @@ import { selectableCategoryNames } from "../../util/stateManager/controlsHelpers
|
||||
datasetTitle: state.config?.displayNames?.dataset ?? "",
|
||||
aboutURL: state.config?.links?.["about-dataset"],
|
||||
isOpen: state.controls.datasetDrawer,
|
||||
dataPortalProps: state.config?.["corpora_props"],
|
||||
dataPortalProps: state.config?.corpora_props,
|
||||
};
|
||||
})
|
||||
class InfoDrawer extends PureComponent {
|
||||
|
||||
@@ -169,7 +169,7 @@ const InfoFormat = React.memo(
|
||||
({ datasetTitle, singleValueCategories, aboutURL, dataPortalProps = {} }) => {
|
||||
if (
|
||||
["1.0.0", "1.1.0"].indexOf(
|
||||
dataPortalProps.version?.["corpora_schema_version"]
|
||||
dataPortalProps.version?.corpora_schema_version
|
||||
) === -1
|
||||
) {
|
||||
dataPortalProps = {};
|
||||
|
||||
@@ -13,15 +13,14 @@ const DATASET_TITLE_FONT_SIZE = 14;
|
||||
@connect((state) => {
|
||||
const { corpora_props: corporaProps } = state.config;
|
||||
const correctVersion =
|
||||
["1.0.0", "1.1.0"].indexOf(
|
||||
corporaProps?.version?.["corpora_schema_version"]
|
||||
) > -1;
|
||||
["1.0.0", "1.1.0"].indexOf(corporaProps?.version?.corpora_schema_version) >
|
||||
-1;
|
||||
return {
|
||||
datasetTitle: state.config?.displayNames?.dataset ?? "",
|
||||
libraryVersions: state.config?.["library_versions"],
|
||||
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"],
|
||||
tosURL: state.config?.parameters?.about_legal_tos,
|
||||
privacyURL: state.config?.parameters?.about_legal_privacy,
|
||||
title: correctVersion ? corporaProps?.title : undefined,
|
||||
};
|
||||
})
|
||||
|
||||
@@ -11,7 +11,7 @@ import CellSetButton from "./cellSetButtons";
|
||||
celllist1: state.differential?.celllist1,
|
||||
celllist2: state.differential?.celllist2,
|
||||
diffexpMayBeSlow: state.config?.parameters?.["diffexp-may-be-slow"] ?? false,
|
||||
diffexpCellcountMax: state.config?.limits?.["diffexp_cellcount_max"],
|
||||
diffexpCellcountMax: state.config?.limits?.diffexp_cellcount_max,
|
||||
}))
|
||||
class DiffexpButtons extends React.PureComponent {
|
||||
computeDiffExp = () => {
|
||||
|
||||
@@ -40,7 +40,7 @@ import { getEmbSubsetView } from "../../util/stateManager/viewStackHelpers";
|
||||
scatterplotYYaccessor: state.controls.scatterplotYYaccessor,
|
||||
celllist1: state.differential.celllist1,
|
||||
celllist2: state.differential.celllist2,
|
||||
libraryVersions: state.config?.["library_versions"],
|
||||
libraryVersions: state.config?.library_versions,
|
||||
auth: state.config?.authentication,
|
||||
userInfo: state.userInfo,
|
||||
undoDisabled: state["@@undoable/past"].length === 0,
|
||||
@@ -50,8 +50,8 @@ import { getEmbSubsetView } from "../../util/stateManager/viewStackHelpers";
|
||||
diffexpMayBeSlow:
|
||||
state.config?.parameters?.["diffexp-may-be-slow"] ?? false,
|
||||
showCentroidLabels: state.centroidLabels.showLabels,
|
||||
tosURL: state.config?.parameters?.["about_legal_tos"],
|
||||
privacyURL: state.config?.parameters?.["about_legal_privacy"],
|
||||
tosURL: state.config?.parameters?.about_legal_tos,
|
||||
privacyURL: state.config?.parameters?.about_legal_privacy,
|
||||
categoricalSelection: state.categoricalSelection,
|
||||
enableReembedding:
|
||||
state.config?.parameters?.["enable-reembedding"] ?? false,
|
||||
|
||||
@@ -303,9 +303,11 @@ class Scatterplot extends React.PureComponent {
|
||||
return [
|
||||
"X",
|
||||
{
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: geneName,
|
||||
where: {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: geneName,
|
||||
},
|
||||
},
|
||||
];
|
||||
}
|
||||
|
||||
@@ -11,8 +11,8 @@ import {
|
||||
import { storageGet, storageSet, KEYS } from "../util/localStorage";
|
||||
|
||||
@connect((state) => ({
|
||||
tosURL: state.config?.parameters?.["about_legal_tos"],
|
||||
privacyURL: state.config?.parameters?.["about_legal_privacy"],
|
||||
tosURL: state.config?.parameters?.about_legal_tos,
|
||||
privacyURL: state.config?.parameters?.about_legal_privacy,
|
||||
}))
|
||||
class TermsPrompt extends React.PureComponent {
|
||||
constructor(props) {
|
||||
|
||||
@@ -39,7 +39,7 @@ const Annotations = (
|
||||
"annotations-data-collection-name-is-read-only"
|
||||
] ?? false;
|
||||
const promptForFilename =
|
||||
action.config.parameters?.["user_annotation_collection_name_enabled"];
|
||||
action.config.parameters?.user_annotation_collection_name_enabled;
|
||||
return {
|
||||
...state,
|
||||
dataCollectionNameIsReadOnly,
|
||||
|
||||
@@ -76,7 +76,7 @@ const Autosave = (
|
||||
const { lastSavedGenesets } = action;
|
||||
return {
|
||||
...state,
|
||||
genesetSaveInProgess: false,
|
||||
genesetSaveInProgress: false,
|
||||
error: false,
|
||||
lastSavedGenesets,
|
||||
};
|
||||
|
||||
@@ -57,12 +57,12 @@ const GeneSets = (
|
||||
for (const gene of gsData.genes) {
|
||||
genes.set(gene.gene_symbol, {
|
||||
geneSymbol: gene.gene_symbol,
|
||||
geneDescription: gene?.["gene_description"] ?? "",
|
||||
geneDescription: gene?.gene_description ?? "",
|
||||
});
|
||||
}
|
||||
const gs = {
|
||||
genesetName: gsData.geneset_name,
|
||||
genesetDescription: gsData?.["geneset_description"] ?? "",
|
||||
genesetDescription: gsData?.geneset_description ?? "",
|
||||
genes,
|
||||
};
|
||||
genesets.set(gsData.geneset_name, gs);
|
||||
|
||||
@@ -10,10 +10,8 @@ const Ontology = (
|
||||
switch (action.type) {
|
||||
case "configuration load complete": {
|
||||
const enabled =
|
||||
action.config?.parameters?.["annotations_cell_ontology_enabled"] ??
|
||||
false;
|
||||
const terms =
|
||||
action.config?.parameters?.["annotations_cell_ontology_terms"];
|
||||
action.config?.parameters?.annotations_cell_ontology_enabled ?? false;
|
||||
const terms = action.config?.parameters?.annotations_cell_ontology_terms;
|
||||
|
||||
const termSet = new Set(terms);
|
||||
return {
|
||||
|
||||
@@ -178,7 +178,7 @@ See undoable.js for description action filter interface description.
|
||||
Basic approach:
|
||||
* trivial handlers for skip, clear & save cases to keep config simple.
|
||||
* only implement complex state machines where absolutely required (eg,
|
||||
multi-event seleciton and the like)
|
||||
multi-event selection and the like)
|
||||
*/
|
||||
const actionFilter = (debug) => (state, action, prevFilterState) => {
|
||||
const actionType = action.type;
|
||||
|
||||
@@ -100,6 +100,12 @@ const createFsmTransitions = (
|
||||
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",
|
||||
|
||||
@@ -30,22 +30,27 @@ export function catchErrorsWrap(fn, dispatchToUser = false) {
|
||||
};
|
||||
}
|
||||
|
||||
/*
|
||||
Wrapper to perform async fetch with some modest error handling
|
||||
and decoding.
|
||||
*/
|
||||
const doFetch = async (url, acceptType) => {
|
||||
/**
|
||||
* Wrapper to perform async fetch with some modest error handling
|
||||
* and decoding. Arguments are identical to standard fetch.
|
||||
*/
|
||||
export const doFetch = async (url, init = {}) => {
|
||||
try {
|
||||
const res = await fetch(url, {
|
||||
// add defaults to the fetch init param.
|
||||
init = {
|
||||
method: "get",
|
||||
headers: new Headers({
|
||||
Accept: acceptType,
|
||||
}),
|
||||
credentials: "include",
|
||||
});
|
||||
if (res.ok && res.headers.get("Content-Type").includes(acceptType)) {
|
||||
...init,
|
||||
};
|
||||
const acceptType = init.headers?.get("Accept");
|
||||
const res = await fetch(url, init);
|
||||
if (
|
||||
res.ok &&
|
||||
(!acceptType || res.headers.get("Content-Type").includes(acceptType))
|
||||
) {
|
||||
return res;
|
||||
}
|
||||
|
||||
// else an error
|
||||
const msg = `Unexpected HTTP response ${res.status}, ${res.statusText}`;
|
||||
dispatchNetworkErrorMessageToUser(msg);
|
||||
@@ -61,16 +66,22 @@ const doFetch = async (url, acceptType) => {
|
||||
/*
|
||||
Wrapper to perform an async fetch and JSON decode response.
|
||||
*/
|
||||
export const doJsonRequest = async (url) => {
|
||||
const res = await doFetch(url, "application/json");
|
||||
export const doJsonRequest = async (url, init = {}) => {
|
||||
const res = await doFetch(url, {
|
||||
...init,
|
||||
headers: new Headers({ Accept: "application/json" }),
|
||||
});
|
||||
return res.json();
|
||||
};
|
||||
|
||||
/*
|
||||
Wrapper to perform an async fetch for binary data.
|
||||
*/
|
||||
export const doBinaryRequest = async (url) => {
|
||||
const res = await doFetch(url, "application/octet-stream");
|
||||
export const doBinaryRequest = async (url, init = {}) => {
|
||||
const res = await doFetch(url, {
|
||||
...init,
|
||||
headers: new Headers({ Accept: "application/octet-stream" }),
|
||||
});
|
||||
return res.arrayBuffer();
|
||||
};
|
||||
|
||||
|
||||
@@ -8,6 +8,9 @@ have a obsAnnotation named X, but we are using that for layout. So
|
||||
we namespace, and abstract to avoid proliferating strings throughout the
|
||||
codebase.
|
||||
|
||||
It is _no longer_ used to remove collisions in the crossfilter or
|
||||
anno matrix namespaces. It is still used by the component tier.
|
||||
|
||||
*/
|
||||
|
||||
const makeDimensionName = (namespace, key) => `${namespace}_${key}`;
|
||||
@@ -18,12 +21,15 @@ 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
|
||||
isUserDefined: false,
|
||||
isGeneSet: false,
|
||||
}
|
||||
|
||||
ie., makeContinuousDimensionName(continuousNamespace = {isObs: true}, "total_reads")
|
||||
@@ -37,6 +43,8 @@ export const makeContinuousDimensionName = (continuousNamespace, key) => {
|
||||
name = diffexpDimensionName(key);
|
||||
} else if (continuousNamespace.isUserDefined) {
|
||||
name = userDefinedDimensionName(key);
|
||||
} else if (continuousNamespace.isGeneSetSummary) {
|
||||
name = geneSetSummaryDimensionName(key);
|
||||
} else {
|
||||
throw new Error("unknown continuous dimension");
|
||||
}
|
||||
|
||||
@@ -25,9 +25,11 @@ export function createColorQuery(colorMode, colorByAccessor, schema) {
|
||||
return [
|
||||
"X",
|
||||
{
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: colorByAccessor,
|
||||
where: {
|
||||
field: "var",
|
||||
column: varIndex,
|
||||
value: colorByAccessor,
|
||||
},
|
||||
},
|
||||
];
|
||||
}
|
||||
|
||||
@@ -4,8 +4,16 @@ This is all VERY tightly integrated with reducers and actions, and
|
||||
exists to support those concepts.
|
||||
*/
|
||||
|
||||
export * as ColorHelpers from "./colorHelpers";
|
||||
export * as ControlsHelpers from "./controlsHelpers";
|
||||
export * as AnnotationsHelpers from "./annotationsHelpers";
|
||||
export * as SchemaHelpers from "./schemaHelpers";
|
||||
export * as MatrixFBS from "./matrix";
|
||||
import * as ColorHelpers from "./colorHelpers";
|
||||
import * as ControlsHelpers from "./controlsHelpers";
|
||||
import * as AnnotationsHelpers from "./annotationsHelpers";
|
||||
import * as SchemaHelpers from "./schemaHelpers";
|
||||
import * as MatrixFBS from "./matrix";
|
||||
|
||||
export {
|
||||
ColorHelpers,
|
||||
ControlsHelpers,
|
||||
AnnotationsHelpers,
|
||||
SchemaHelpers,
|
||||
MatrixFBS,
|
||||
};
|
||||
|
||||
Reference in New Issue
Block a user