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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/server/common/annotations/local_file_csv.py
+2 -8
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@@ -193,14 +193,14 @@ class AnnotationsLocalFile(Annotations):
return os.getcwd()
def _get_celllabels_filename(self, data_adaptor):
""" return the current annotation file name """
"""return the current annotation file name"""
if self.label_output_file:
return self.label_output_file
return self._get_filename(data_adaptor, "cell-labels")
def _get_genesets_filename(self, data_adaptor):
""" return the current gene sets file name """
"""return the current gene sets file name"""
if self.gene_sets_output_file:
return self.gene_sets_output_file
@@ -263,12 +263,6 @@ class AnnotationsLocalFile(Annotations):
params["annotations_genesets_name_is_read_only"] = self.gene_sets_output_file is not None
params["user_annotation_collection_name_enabled"] = True
if self.ontology_data:
params["annotations_cell_ontology_enabled"] = True
params["annotations_cell_ontology_terms"] = self.ontology_data
else:
params["annotations_cell_ontology_enabled"] = False
if self.label_output_file is not None:
# user has hard-wired the name of the annotation cell label data collection
fname = os.path.basename(self.label_output_file)