remove experimental ontology support (#2300)

* remove experimental ontology support

* lint

* remove ontologies from unit tests

* additional test changes

backend/server/common/annotations/annotations.py

@@ -1,22 +1,14 @@
 from abc import ABCMeta, abstractmethod
 
-import fastobo
-import fsspec
-
-from backend.common.errors import OntologyLoadFailure, DisabledFeatureError
+from backend.common.errors import DisabledFeatureError
 from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array
 from backend.common.genesets import write_gene_sets_tidycsv
 
 
 class Annotations(metaclass=ABCMeta):
-    """ baseclass for annotations, including ontologies and gene sets"""
-
-    """ our default ontology is the PURL for the Cell Ontology.
-    See http://www.obofoundry.org/ontology/cl.html """
-    DefaultOnotology = "http://purl.obolibrary.org/obo/cl.obo"
+    """baseclass for annotations and gene sets"""
 
     def __init__(self, config={}):
-        self.ontology_data = None
         self.config = config
 
     def user_annotations_enabled(self):
@@ -33,27 +25,6 @@ class Annotations(metaclass=ABCMeta):
         if not self.gene_sets_save_enabled():
             raise DisabledFeatureError("User gene sets save is disabled.")
 
-    def load_ontology(self, path):
-        """Load and parse ontologies - currently support OBO files only."""
-        if path is None:
-            path = self.DefaultOnotology
-
-        try:
-            with fsspec.open(path) as f:
-                obo = fastobo.iter(f)
-                terms = filter(lambda stanza: type(stanza) is fastobo.term.TermFrame, obo)
-                names = [tag.name for term in terms for tag in term if type(tag) is fastobo.term.NameClause]
-                self.ontology_data = names
-
-        except FileNotFoundError as e:
-            raise OntologyLoadFailure("Unable to find OBO ontology path") from e
-
-        except SyntaxError as e:
-            raise OntologyLoadFailure("Syntax error loading OBO ontology") from e
-
-        except Exception as e:
-            raise OntologyLoadFailure("Error loading OBO file") from e
-
     def get_schema(self, data_adaptor):
         schema = []
         labels = self.read_labels(data_adaptor)
@@ -82,7 +53,7 @@ class Annotations(metaclass=ABCMeta):
 
     @abstractmethod
     def read_gene_sets(self, data_adaptor):
-        """Return the gene sets from persistent storage """
+        """Return the gene sets from persistent storage"""
         pass
 
     @abstractmethod

backend/server/common/annotations/local_file_csv.py

@@ -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)