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clean up type inferencing (#2332)

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* unit tests for 64 bit conversion

* clean up type handling

* type inference tests

* more type inference fixes

* use schema to determine user intent for data typing

* stop using deprecated API

* fbs type encoding test

* add missing test

* add more tests

* correctly infer X type for CXG adaptor

* lint

* fix typo

* ts migration

* cleanup from PR review

* lint

* PR review changes
This commit is contained in:
Bruce Martin
2021-07-28 15:10:12 -07:00
committed by GitHub
parent 1140676106
commit 32f60a1547
15 changed files with 730 additions and 346 deletions
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backend/czi_hosted/common/annotations/hosted_tiledb.py
+2 -2
View File
@@ -10,7 +10,7 @@ from flask import current_app
from backend.czi_hosted.common.annotations.annotations import Annotations
from backend.common.errors import AnnotationCategoryNameError
from backend.czi_hosted.common.utils.sanitization_utils import sanitize_values_in_list
from backend.common.utils.type_conversion_utils import get_dtypes_and_schemas_of_dataframe, get_dtype_of_array
from backend.common.utils.type_conversion_utils import get_dtypes_and_schemas_of_dataframe, get_encoding_dtype_of_array
from backend.czi_hosted.db.cellxgene_orm import Annotation
@@ -143,7 +143,7 @@ class AnnotationsHostedTileDB(Annotations):
# convert to tiledb datatypes
for col in df:
df[col] = df[col].astype(get_dtype_of_array(df[col]))
df[col] = df[col].astype(get_encoding_dtype_of_array(df[col]))
tiledb.from_pandas(uri, df, sparse=True)
else:
uri = ""
backend/czi_hosted/common/utils/cxg_generation_utils.py
+2 -2
View File
@@ -3,7 +3,7 @@ import json
import numpy as np
import tiledb
from backend.common.utils.type_conversion_utils import get_dtype_of_array, get_dtype_and_schema_of_array
from backend.common.utils.type_conversion_utils import get_encoding_dtype_of_array, get_dtype_and_schema_of_array
def convert_dictionary_to_cxg_group(cxg_container, metadata_dict, group_metadata_name="cxg_group_metadata"):
@@ -47,7 +47,7 @@ def convert_dataframe_to_cxg_array(cxg_container, dataframe_name, dataframe, ind
]
)
attrs = [
tiledb.Attr(name=column, dtype=get_dtype_of_array(dataframe[column]), filters=tiledb_filter)
tiledb.Attr(name=column, dtype=get_encoding_dtype_of_array(dataframe[column]), filters=tiledb_filter)
for column in dataframe
]
domain = tiledb.Domain(