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Code Issues Packages Projects Releases Wiki Activity

remove experimental ontology support (#2300)

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* remove experimental ontology support

* lint

* remove ontologies from unit tests

* additional test changes
This commit is contained in:
Bruce Martin
2021-07-14 07:23:38 -07:00
committed by GitHub
parent 45a8984223
commit e334fbe96e
35 changed files with 28 additions and 269 deletions
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backend/czi_hosted/common/config/client_config.py
-3
View File
@@ -47,9 +47,6 @@ def get_client_config(app_config, data_adaptor):
"annotations_genesets": True, # feature flag
"annotations_genesets_readonly": True,
"annotations_genesets_summary_methods": ["mean"],
"annotations_cell_ontology_enabled": False,
"annotations_cell_ontology_obopath": None,
"annotations_cell_ontology_terms": None,
"custom_colors": dataset_config.presentation__custom_colors,
"diffexp-may-be-slow": False,
"about_legal_tos": dataset_config.app__about_legal_tos,
backend/czi_hosted/common/config/dataset_config.py
+2 -22
View File
@@ -5,7 +5,7 @@ from backend.czi_hosted.common.annotations.annotations import Annotations
from backend.czi_hosted.common.annotations.hosted_tiledb import AnnotationsHostedTileDB
from backend.czi_hosted.common.annotations.local_file_csv import AnnotationsLocalFile
from backend.czi_hosted.common.config.base_config import BaseConfig
from backend.common.errors import ConfigurationError, OntologyLoadFailure
from backend.common.errors import ConfigurationError
from backend.czi_hosted.compute.scanpy import get_scanpy_module
from backend.czi_hosted.data_common.matrix_loader import MatrixDataLoader, MatrixDataType
from backend.czi_hosted.db.db_utils import DbUtils
@@ -33,10 +33,6 @@ class DatasetConfig(BaseConfig):
"directory"
]
self.user_annotations__local_file_csv__file = default_config["user_annotations"]["local_file_csv"]["file"]
self.user_annotations__ontology__enable = default_config["user_annotations"]["ontology"]["enable"]
self.user_annotations__ontology__obo_location = default_config["user_annotations"]["ontology"][
"obo_location"
]
self.user_annotations__hosted_tiledb_array__db_uri = default_config["user_annotations"][
"hosted_tiledb_array"
]["db_uri"]
@@ -55,7 +51,7 @@ class DatasetConfig(BaseConfig):
raise ConfigurationError(f"Unexpected config: {str(e)}")
# Create the default annotation, which supports gene set reading without
# further configuration. Depending on configuration options, `complete_config`
# further configuration. Depending on configuration options, `complete_config`
# may create a more specialized annotation object and replace this default.
self.user_annotations = Annotations()
@@ -101,10 +97,6 @@ class DatasetConfig(BaseConfig):
self.validate_correct_type_of_configuration_attribute(
"user_annotations__local_file_csv__file", (type(None), str)
)
self.validate_correct_type_of_configuration_attribute("user_annotations__ontology__enable", bool)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__ontology__obo_location", (type(None), str)
)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__hosted_tiledb_array__db_uri", (type(None), str)
)
@@ -125,11 +117,6 @@ class DatasetConfig(BaseConfig):
self.handle_hosted_tiledb_annotations()
else:
raise ConfigurationError('The only annotation type support is "local_file_csv" or "hosted_tiledb_array')
if self.user_annotations__ontology__enable or self.user_annotations__ontology__obo_location:
try:
self.user_annotations.load_ontology(self.user_annotations__ontology__obo_location)
except OntologyLoadFailure as e:
raise ConfigurationError("Unable to load ontology terms\n" + str(e))
else:
self.check_annotation_config_vars_not_set(context)
@@ -197,13 +184,6 @@ class DatasetConfig(BaseConfig):
"Warning: hosted_file_directory for hosted_tiledb_array ignored as annotations are disabled."
)
if self.user_annotations__ontology__enable:
context["messagefn"]("Warning: --experimental-annotations-ontology ignored as annotations are disabled.")
if self.user_annotations__ontology__obo_location is not None:
context["messagefn"](
"Warning: --experimental-annotations-ontology-obo ignored as annotations are disabled."
)
def handle_embeddings(self):
self.validate_correct_type_of_configuration_attribute("embeddings__names", list)
self.validate_correct_type_of_configuration_attribute("embeddings__enable_reembedding", bool)