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rename "geneset" to "gene set" in CLI (#2088)

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* remove dead code

* rename geneset to gene_set
This commit is contained in:
Bruce Martin
2021-03-02 15:36:01 -08:00
committed by GitHub
parent b00496198d
commit c037f4eaa6
14 changed files with 101 additions and 102 deletions
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local_server/common/config/client_config.py
+1 -1
View File
@@ -45,7 +45,7 @@ def get_client_config(app_config, data_adaptor):
"annotations_file": None,
"annotations_dir": None,
"annotations_genesets": True, # feature flag
"annotations_genesets_readonly": dataset_config.user_annotations__genesets__readonly,
"annotations_genesets_readonly": dataset_config.user_annotations__gene_sets__readonly,
"annotations_genesets_summary_methods": ["mean"],
"annotations_cell_ontology_enabled": False,
"annotations_cell_ontology_obopath": None,
local_server/common/config/dataset_config.py
+10 -10
View File
@@ -32,9 +32,9 @@ class DatasetConfig(BaseConfig):
self.user_annotations__ontology__obo_location = default_config["user_annotations"]["ontology"][
"obo_location"
]
self.user_annotations__genesets__readonly = default_config["user_annotations"]["genesets"]["readonly"]
self.user_annotations__local_file_csv__genesets_file = default_config["user_annotations"]["local_file_csv"][
"genesets_file"
self.user_annotations__gene_sets__readonly = default_config["user_annotations"]["gene_sets"]["readonly"]
self.user_annotations__local_file_csv__gene_sets_file = default_config["user_annotations"]["local_file_csv"][
"gene_sets_file"
]
self.embeddings__names = default_config["embeddings"]["names"]
@@ -99,15 +99,15 @@ class DatasetConfig(BaseConfig):
"user_annotations__local_file_csv__file", (type(None), str)
)
self.validate_correct_type_of_configuration_attribute(
"user_annotations__local_file_csv__genesets_file", (type(None), str)
"user_annotations__local_file_csv__gene_sets_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__genesets__readonly", bool)
self.validate_correct_type_of_configuration_attribute("user_annotations__gene_sets__readonly", bool)
if self.user_annotations__enable or not self.user_annotations__genesets__readonly:
if self.user_annotations__enable or not self.user_annotations__gene_sets__readonly:
server_config = self.app_config.server_config
if not self.app__authentication_enable:
raise ConfigurationError("user annotations requires authentication to be enabled")
@@ -134,7 +134,7 @@ class DatasetConfig(BaseConfig):
def handle_local_file_csv_annotations(self, context):
dirname = self.user_annotations__local_file_csv__directory
filename = self.user_annotations__local_file_csv__file
genesets_filename = self.user_annotations__local_file_csv__genesets_file
genesets_filename = self.user_annotations__local_file_csv__gene_sets_file
if dirname is not None and (filename is not None or genesets_filename is not None):
raise ConfigurationError(
@@ -159,7 +159,7 @@ class DatasetConfig(BaseConfig):
anno_config = {
"user-annotations": self.user_annotations__enable,
"genesets-save": not self.user_annotations__genesets__readonly,
"genesets-save": not self.user_annotations__gene_sets__readonly,
}
self.user_annotations = AnnotationsLocalFile(anno_config, dirname, filename, genesets_filename)
@@ -170,9 +170,9 @@ class DatasetConfig(BaseConfig):
data_adaptor = self.get_data_adaptor()
if self.user_annotations__local_file_csv__file:
data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor))
if self.user_annotations__local_file_csv__genesets_file:
if self.user_annotations__local_file_csv__gene_sets_file:
try:
data_adaptor.check_new_genesets(self.user_annotations.read_genesets(data_adaptor, context), context)
data_adaptor.check_new_gene_sets(self.user_annotations.read_gene_sets(data_adaptor, context), context)
except (ValueError, AnnotationsError, KeyError) as e:
raise ConfigurationError(f"Unable to read genesets CSV file: {str(e)}") from e