remove experimental ontology support (#2300)

* remove experimental ontology support

* lint

* remove ontologies from unit tests

* additional test changes

backend/server/cli/launch.py

@@ -44,20 +44,6 @@ def annotation_args(func):
         help="Directory of where to save output annotations; filename will be specified in the application. "
         "Incompatible with --annotations-file and --gene-sets-file.",
     )
-    @click.option(
-        "--experimental-annotations-ontology",
-        is_flag=True,
-        default=DEFAULT_CONFIG.dataset_config.user_annotations__ontology__enable,
-        show_default=True,
-        help="When creating annotations, optionally autocomplete names from ontology terms.",
-    )
-    @click.option(
-        "--experimental-annotations-ontology-obo",
-        default=DEFAULT_CONFIG.dataset_config.user_annotations__ontology__obo_location,
-        show_default=True,
-        metavar="<path or url>",
-        help="Location of OBO file defining cell annotation autosuggest terms.",
-    )
     @click.option(
         "--disable-gene-sets-save",
         is_flag=True,
@@ -338,8 +324,6 @@ def launch(
     disable_gene_sets_save,
     backed,
     disable_diffexp,
-    experimental_annotations_ontology,
-    experimental_annotations_ontology_obo,
     experimental_enable_reembedding,
     config_file,
     dump_default_config,
@@ -396,8 +380,6 @@ def launch(
             user_annotations__local_file_csv__directory=user_generated_data_dir,
             user_annotations__local_file_csv__gene_sets_file=gene_sets_file,
             user_annotations__gene_sets__readonly=disable_gene_sets_save,
-            user_annotations__ontology__enable=experimental_annotations_ontology,
-            user_annotations__ontology__obo_location=experimental_annotations_ontology_obo,
             presentation__max_categories=max_category_items,
             presentation__custom_colors=not disable_custom_colors,
             embeddings__names=embedding,

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)

backend/server/common/config/client_config.py

@@ -47,9 +47,6 @@ def get_client_config(app_config, data_adaptor):
         "annotations_genesets": True,  # feature flag
         "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,
-        "annotations_cell_ontology_terms": None,
         "custom_colors": dataset_config.presentation__custom_colors,
         "diffexp-may-be-slow": False,
     }

backend/server/common/config/dataset_config.py

@@ -3,7 +3,7 @@ from os.path import splitext, isdir
 
 from backend.server.common.annotations.local_file_csv import AnnotationsLocalFile
 from backend.server.common.config.base_config import BaseConfig
-from backend.common.errors import ConfigurationError, OntologyLoadFailure, AnnotationsError
+from backend.common.errors import ConfigurationError, AnnotationsError
 from backend.server.compute.scanpy import get_scanpy_module
 from backend.server.data_common.matrix_loader import MatrixDataLoader
 
@@ -28,10 +28,6 @@ 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__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"
@@ -101,10 +97,6 @@ class DatasetConfig(BaseConfig):
         self.validate_correct_type_of_configuration_attribute(
             "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__gene_sets__readonly", bool)
 
         if self.user_annotations__enable or not self.user_annotations__gene_sets__readonly:
@@ -122,13 +114,6 @@ class DatasetConfig(BaseConfig):
         else:
             raise ConfigurationError('The only annotation type support is "local_file_csv"')
 
-        if self.user_annotations__enable:
-            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))
-
         self.check_annotation_config_vars_not_set(context)
 
     def handle_local_file_csv_annotations(self, context):
@@ -183,14 +168,6 @@ class DatasetConfig(BaseConfig):
             if not self.user_annotations__enable:
                 if filename is not None:
                     context["messagefn"]("Warning: --annotations-file 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."
-                    )
                 if dirname is not None:
                     context["messagefn"]("Warning: --user-generated-data-dir ignored as annotations are disabled.")
 

backend/server/default_config.py

@@ -66,9 +66,6 @@ dataset:
       directory: null
       file: null            # annotations file name
       gene_sets_file: null  # gene sets file name
-    ontology:
-      enable: false
-      obo_location: null
     gene_sets:
       readonly: false       # gene sets CRUD enabled/disabled
 

backend/server/requirements.txt

@@ -1,7 +1,6 @@
 anndata>=0.7.0
 boto3>=1.12.18
 click>=7.1.2
-fastobo>=0.6.1
 Flask>=1.0.2,<2.0.0 # Flask 2.0 is not compatible with the latest version of Flask-RESTful (0.3.8)
 Flask-Compress>=1.4.0
 Flask-Cors>=3.0.9  # CVE-2020-25032