remove experimental ontology support (#2300)

* remove experimental ontology support

* lint

* remove ontologies from unit tests

* additional test changes

backend/common/errors.py

@@ -51,7 +51,6 @@ define_request_exception(
     default_status_code=HTTPStatus.UNPROCESSABLE_ENTITY,
 )
 
-define_exception("OntologyLoadFailure", "Raised when reading the ontology file fails")
 define_exception("ConfigurationError", "Raised when checking configuration errors")
 define_exception("PrepareError", "Raised when data is misprepared")
 define_exception("SecretKeyRetrievalError", "Raised when get_secret_key from AWS fails")

backend/czi_hosted/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.",
     )
-    @click.option(
-        "--experimental-annotations-ontology",
-        is_flag=True,
-        default=DEFAULT_CONFIG.default_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.default_dataset_config.user_annotations__ontology__obo_location,
-        show_default=True,
-        metavar="<path or url>",
-        help="Location of OBO file defining cell annotation autosuggest terms.",
-    )
     @functools.wraps(func)
     def wrapper(*args, **kwargs):
         return func(*args, **kwargs)
@@ -328,8 +314,6 @@ def launch(
     annotations_dir,
     backed,
     disable_diffexp,
-    experimental_annotations_ontology,
-    experimental_annotations_ontology_obo,
     experimental_enable_reembedding,
     config_file,
     dump_default_config,
@@ -389,8 +373,6 @@ def launch(
             user_annotations__enable=not disable_annotations,
             user_annotations__local_file_csv__file=annotations_file,
             user_annotations__local_file_csv__directory=annotations_dir,
-            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/czi_hosted/common/annotations/annotations.py

@@ -1,10 +1,8 @@
-import fastobo
-import fsspec
 import os
 
 from flask import current_app, has_request_context
 
-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, read_gene_sets_tidycsv, validate_gene_sets
 from backend.common.utils.data_locator import DataLocator
@@ -12,14 +10,9 @@ from backend.common.utils.utils import path_join
 
 
 class Annotations:
-    """ baseclass for annotations, including ontologies and genesets """
+    """baseclass for annotations and genesets"""
-
-    """ 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"
 
     def __init__(self, config={}):
-        self.ontology_data = None
         self.config = config
 
     def user_annotations_enabled(self):
@@ -29,27 +22,6 @@ class Annotations:
         if not self.user_annotations_enabled():
             raise DisabledFeatureError("User annotations are 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(f"{path}:{e.lineno}:{e.offset} OBO syntax error, unable to read ontology") from e
-
-        except Exception as e:
-            raise OntologyLoadFailure(f"{path}:Error loading OBO file") from e
-
     def get_schema(self, data_adaptor):
         schema = []
         labels = self.read_labels(data_adaptor)
@@ -126,7 +98,7 @@ class Annotations:
 
 
 def dataset_uri_to_geneset_uri(data_uri_or_path):
-    """ given a dataset URI, return the associated gene set URI """
+    """given a dataset URI, return the associated gene set URI"""
     data_basename = os.path.basename(data_uri_or_path)
     base, ext = os.path.splitext(data_basename)
     if ext is not None:  # strip extension, if any

backend/czi_hosted/common/annotations/hosted_tiledb.py

@@ -164,10 +164,4 @@ class AnnotationsHostedTileDB(Annotations):
         params["annotations"] = True
         params["user_annotation_collection_name_enabled"] = False
 
-        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
-
         parameters.update(params)

backend/czi_hosted/common/annotations/local_file_csv.py

@@ -115,7 +115,7 @@ class AnnotationsLocalFile(Annotations):
         return os.getcwd()
 
     def _get_filename(self, data_adaptor):
-        """ return the current annotation file name """
+        """return the current annotation file name"""
         if self.output_file:
             return self.output_file
 
@@ -175,12 +175,6 @@ class AnnotationsLocalFile(Annotations):
         params["annotations"] = True
         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.output_file is not None:
             # user has hard-wired the name of the annotation data collection
             fname = os.path.basename(self.output_file)

backend/czi_hosted/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": 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

@@ -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)

backend/czi_hosted/default_config.py

@@ -194,9 +194,6 @@ dataset:
     local_file_csv:
       directory: null
       file: null
-    ontology:
-      enable: false
-      obo_location: null
 
   embeddings:
     names : []

backend/czi_hosted/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>=3.0.6

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
+from backend.common.errors import DisabledFeatureError
-import fsspec
-
-from backend.common.errors import OntologyLoadFailure, 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"""
+    """baseclass for annotations 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"
 
     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

backend/test/fixtures/czi_hosted_dataset_config_outline.py

@@ -22,9 +22,6 @@ dataset:
     local_file_csv:
       directory: {local_file_csv_directory}
       file: {local_file_csv_file}
-    ontology:
-      enable: {ontology_enabled}
-      obo_location: {obo_location}
 
   embeddings:
     names: {embedding_names}

backend/test/fixtures/dataset_config_outline.py

@@ -17,9 +17,6 @@ dataset:
       directory: {local_file_csv_directory}
       file: {local_file_csv_file}
       gene_sets_file: {local_file_csv_gene_sets_file}
-    ontology:
-      enable: {ontology_enabled}
-      obo_location: {obo_location}
     gene_sets:
       readonly: {gene_sets_readonly}
 

backend/test/test_czi_hosted/unit/common/config/__init__.py

@@ -124,8 +124,6 @@ class ConfigTests(BaseTest):
         hosted_file_directory="null",
         local_file_csv_directory="null",
         local_file_csv_file="null",
-        ontology_enabled="false",
-        obo_location="null",
         embedding_names=[],
         enable_reembedding="false",
         enable_difexp="true",
@@ -193,8 +191,6 @@ class ConfigTests(BaseTest):
             hosted_file_directory=hosted_file_directory,
             local_file_csv_directory=local_file_csv_directory,
             local_file_csv_file=local_file_csv_file,
-            ontology_enabled=ontology_enabled,
-            obo_location=obo_location,
             embedding_names=embedding_names,
             enable_reembedding=enable_reembedding,
             enable_difexp=enable_difexp,
@@ -231,8 +227,6 @@ class ConfigTests(BaseTest):
         hosted_file_directory="null",
         local_file_csv_directory="null",
         local_file_csv_file="null",
-        ontology_enabled="false",
-        obo_location="null",
         embedding_names=[],
         enable_reembedding="false",
         enable_difexp="true",

backend/test/test_czi_hosted/unit/common/config/test_base_config.py

@@ -36,7 +36,6 @@ class BaseConfigTest(ConfigTests):
         mapping = config.default_dataset_config.create_mapping(config.default_config)
         self.assertIsNotNone(mapping["server__app__verbose"])
         self.assertIsNotNone(mapping["dataset__presentation__max_categories"])
-        self.assertIsNotNone(mapping["dataset__user_annotations__ontology__obo_location"])
         self.assertIsNotNone(mapping["server__multi_dataset__allowed_matrix_types"])
 
     def test_changes_from_default_returns_list_of_nondefault_config_values(self):

backend/test/test_czi_hosted/unit/common/config/test_dataset_config.py

@@ -44,13 +44,12 @@ class TestDatasetConfig(ConfigTests):
         self.assertEqual(config.default_dataset_config.presentation__max_categories, 1000)
         self.assertEqual(config.default_dataset_config.user_annotations__type, "local_file_csv")
         self.assertEqual(config.default_dataset_config.diffexp__lfc_cutoff, 0.01)
-        self.assertIsNone(config.default_dataset_config.user_annotations__ontology__obo_location)
 
     @patch("backend.czi_hosted.common.config.dataset_config.BaseConfig.validate_correct_type_of_configuration_attribute")
     def test_complete_config_checks_all_attr(self, mock_check_attrs):
         mock_check_attrs.side_effect = BaseConfig.validate_correct_type_of_configuration_attribute()
         self.dataset_config.complete_config(self.context)
-        self.assertEqual(mock_check_attrs.call_count, 21)
+        self.assertEqual(mock_check_attrs.call_count, 19)
 
     def test_app_sets_script_vars(self):
         config = self.get_config(scripts=["path/to/script"])

backend/test/test_server/unit/common/config/__init__.py

@@ -95,8 +95,6 @@ class ConfigTests(unittest.TestCase):
         local_file_csv_directory="null",
         local_file_csv_file="null",
         local_file_csv_gene_sets_file="null",
-        ontology_enabled="false",
-        obo_location="null",
         gene_sets_readonly="false",
         embedding_names=[],
         enable_reembedding="false",
@@ -148,8 +146,6 @@ class ConfigTests(unittest.TestCase):
             local_file_csv_directory=local_file_csv_directory,
             local_file_csv_file=local_file_csv_file,
             local_file_csv_gene_sets_file=local_file_csv_gene_sets_file,
-            ontology_enabled=ontology_enabled,
-            obo_location=obo_location,
             gene_sets_readonly=gene_sets_readonly,
             embedding_names=embedding_names,
             enable_reembedding=enable_reembedding,
@@ -186,8 +182,6 @@ class ConfigTests(unittest.TestCase):
         local_file_csv_directory="null",
         local_file_csv_file="null",
         local_file_csv_gene_sets_file="null",
-        ontology_enabled="false",
-        obo_location="null",
         gene_sets_readonly="false",
         embedding_names=[],
         enable_reembedding="false",

backend/test/test_server/unit/common/config/test_app_config.py

@@ -131,9 +131,8 @@ class AppConfigTest(ConfigTests):
 
         # test simple value in default dataset
         config.update_single_config_from_path_and_value(
-            ["dataset", "user_annotations", "ontology", "obo_location"], "dummy_location",
+            ["dataset", "user_annotations"], "dummy_location",
         )
-        self.assertEqual(config.dataset_config.user_annotations__ontology__obo_location, "dummy_location")
 
         # error checking
         bad_paths = [

backend/test/test_server/unit/common/config/test_base_config.py

@@ -36,7 +36,6 @@ class BaseConfigTest(ConfigTests):
         mapping = config.dataset_config.create_mapping(config.default_config)
         self.assertIsNotNone(mapping["server__app__verbose"])
         self.assertIsNotNone(mapping["dataset__presentation__max_categories"])
-        self.assertIsNotNone(mapping["dataset__user_annotations__ontology__obo_location"])
 
     def test_changes_from_default_returns_list_of_nondefault_config_values(self):
         config = self.get_config(verbose="true", lfc_cutoff=0.05)

backend/test/test_server/unit/common/config/test_dataset_config.py

@@ -40,14 +40,13 @@ class TestDatasetConfig(ConfigTests):
         self.assertEqual(config.dataset_config.presentation__max_categories, 1000)
         self.assertEqual(config.dataset_config.user_annotations__type, "local_file_csv")
         self.assertEqual(config.dataset_config.diffexp__lfc_cutoff, 0.01)
-        self.assertIsNone(config.dataset_config.user_annotations__ontology__obo_location)
 
     @patch("backend.server.common.config.dataset_config.BaseConfig.validate_correct_type_of_configuration_attribute")
     def test_complete_config_checks_all_attr(self, mock_check_attrs):
         mock_check_attrs.side_effect = BaseConfig.validate_correct_type_of_configuration_attribute()
         self.dataset_config.complete_config(self.context)
         self.assertIsNotNone(self.config.server_config.data_adaptor)
-        self.assertEqual(mock_check_attrs.call_count, 19)
+        self.assertEqual(mock_check_attrs.call_count, 17)
 
     def test_app_sets_script_vars(self):
         config = self.get_config(scripts=["path/to/script"])

client/__tests__/e2e/test_config.yaml

@@ -22,9 +22,6 @@ dataset:
     local_file_csv:
       directory: null
       file: null
-    ontology:
-      enable: false
-      obo_location: null
 
   embeddings:
     names: []

client/src/components/categorical/category/annoDialogAddLabel.js

@@ -8,7 +8,6 @@ import actions from "../../../actions";
 @connect((state) => ({
   annotations: state.annotations,
   schema: state.annoMatrix?.schema,
-  ontology: state.ontology,
   obsCrossfilter: state.obsCrossfilter,
 }))
 class Category extends React.PureComponent {
@@ -57,8 +56,8 @@ class Category extends React.PureComponent {
   };
 
   labelNameError = (name) => {
-    const { metadataField, ontology, schema } = this.props;
+    const { metadataField, schema } = this.props;
-    return isLabelErroneous(name, metadataField, ontology, schema);
+    return isLabelErroneous(name, metadataField, schema);
   };
 
   instruction = (label) => {
@@ -71,8 +70,7 @@ class Category extends React.PureComponent {
 
   render() {
     const { newLabelText } = this.state;
-    const { metadataField, annotations, ontology, obsCrossfilter } = this.props;
+    const { metadataField, annotations, obsCrossfilter } = this.props;
-    const ontologyEnabled = ontology?.enabled ?? false;
 
     return (
       <>
@@ -97,7 +95,7 @@ class Category extends React.PureComponent {
           handleCancel={this.disableAddNewLabelMode}
           annoInput={
             <LabelInput
-              labelSuggestions={ontologyEnabled ? ontology.terms : null}
+              labelSuggestions={null}
               onChange={this.handleChangeOrSelect}
               onSelect={this.handleChangeOrSelect}
               inputProps={{

client/src/components/categorical/category/annoDialogEditCategoryName.js

@@ -10,7 +10,6 @@ import actions from "../../../actions";
 @connect((state) => ({
   annotations: state.annotations,
   schema: state.annoMatrix?.schema,
-  ontology: state.ontology,
 }))
 class AnnoDialogEditCategoryName extends React.PureComponent {
   constructor(props) {
@@ -105,8 +104,7 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
 
   render() {
     const { newCategoryText } = this.state;
-    const { metadataField, annotations, ontology } = this.props;
+    const { metadataField, annotations } = this.props;
-    const ontologyEnabled = ontology?.enabled ?? false;
 
     return (
       <>
@@ -132,7 +130,7 @@ class AnnoDialogEditCategoryName extends React.PureComponent {
           annoInput={
             <LabelInput
               label={newCategoryText}
-              labelSuggestions={ontologyEnabled ? ontology.terms : null}
+              labelSuggestions={null}
               onChange={this.handleChangeOrSelect}
               onSelect={this.handleChangeOrSelect}
               inputProps={{

client/src/components/categorical/index.js

@@ -13,7 +13,6 @@ import actions from "../../actions";
 @connect((state) => ({
   writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
   schema: state.annoMatrix?.schema,
-  ontology: state.ontology,
   userInfo: state.userInfo,
 }))
 class Categories extends React.Component {
@@ -130,10 +129,8 @@ class Categories extends React.Component {
     const {
       writableCategoriesEnabled,
       schema,
-      ontology,
       userInfo,
     } = this.props;
-    const ontologyEnabled = ontology?.enabled ?? false;
     /* all names, sorted in display order.  Will be rendered in this order */
     const allCategoryNames = ControlsHelpers.selectableCategoryNames(
       schema
@@ -158,7 +155,7 @@ class Categories extends React.Component {
           handleCancel={this.handleDisableAnnoMode}
           annoInput={
             <LabelInput
-              labelSuggestions={ontologyEnabled ? ontology.terms : null}
+              labelSuggestions={null}
               onChange={this.handleChange}
               onSelect={this.handleSelect}
               inputProps={{

client/src/components/categorical/labelUtil.js

@@ -3,7 +3,7 @@ import { Colors } from "@blueprintjs/core";
 
 import { AnnotationsHelpers } from "../../util/stateManager";
 
-export function isLabelErroneous(label, metadataField, ontology, schema) {
+export function isLabelErroneous(label, metadataField, schema) {
   /*
     return false if this is a LEGAL/acceptable category name or NULL/empty string,
     or return an error type.
@@ -12,10 +12,9 @@ export function isLabelErroneous(label, metadataField, ontology, schema) {
   /* allow empty string */
   if (label === "") return false;
 
-  /* check for label syntax errors, but allow terms in ontology */
+  /* check for label syntax errors */
-  const termInOntology = ontology?.termSet.has(label) ?? false;
   const error = AnnotationsHelpers.annotationNameIsErroneous(label);
-  if (error && !termInOntology) return error;
+  if (error) return error;
 
   /* disallow duplicates */
   const { obsByName } = schema.annotations;

client/src/components/categorical/value/index.js

@@ -50,7 +50,6 @@ function _currentLabelAsString(ownProps) {
   return {
     annotations: state.annotations,
     schema: state.annoMatrix?.schema,
-    ontology: state.ontology,
     isDilated,
     isSelected,
     label,
@@ -118,9 +117,9 @@ class CategoryValue extends React.Component {
   };
 
   labelNameError = (name) => {
-    const { metadataField, ontology, schema } = this.props;
+    const { metadataField, schema } = this.props;
     if (name === this.currentLabelAsString()) return false;
-    return isLabelErroneous(name, metadataField, ontology, schema);
+    return isLabelErroneous(name, metadataField, schema);
   };
 
   instruction = (label) => {
@@ -490,14 +489,12 @@ class CategoryValue extends React.Component {
       colorTable,
       isUserAnno,
       annotations,
-      ontology,
       isDilated,
       isSelected,
       categorySummary,
       label,
     } = this.props;
     const colorScale = colorTable?.scale;
-    const ontologyEnabled = ontology?.enabled ?? false;
 
     const { editedLabelText } = this.state;
 
@@ -634,7 +631,7 @@ class CategoryValue extends React.Component {
                   annoInput={
                     <LabelInput
                       label={editedLabelText}
-                      labelSuggestions={ontologyEnabled ? ontology.terms : null}
+                      labelSuggestions={null}
                       onChange={this.handleTextChange}
                       onSelect={this.handleTextChange}
                       inputProps={{

client/src/components/geneExpression/menus/createGenesetDialogue.js

@@ -10,7 +10,6 @@ import actions from "../../../actions";
 @connect((state) => ({
   annotations: state.annotations,
   schema: state.annoMatrix?.schema,
-  ontology: state.ontology,
   obsCrossfilter: state.obsCrossfilter,
   genesets: state.genesets.genesets,
   genesetsUI: state.genesetsUI,

client/src/components/geneExpression/menus/editGenesetNameDialogue.js

@@ -6,7 +6,6 @@ import LabelInput from "../../labelInput";
 @connect((state) => ({
   annotations: state.annotations,
   schema: state.annoMatrix?.schema,
-  ontology: state.ontology,
   obsCrossfilter: state.obsCrossfilter,
   genesetsUI: state.genesetsUI,
   genesets: state.genesets.genesets,

client/src/reducers/index.js

@@ -18,7 +18,6 @@ import annotations from "./annotations";
 import genesets from "./genesets";
 import genesetsUI from "./genesetsUI";
 import autosave from "./autosave";
-import ontology from "./ontology";
 import centroidLabels from "./centroidLabels";
 import pointDialation from "./pointDilation";
 import { reembedController } from "./reembed";
@@ -31,7 +30,6 @@ const Reducer = undoable(
     ["config", config],
     ["annoMatrix", annoMatrix],
     ["obsCrossfilter", obsCrossfilter],
-    ["ontology", ontology],
     ["annotations", annotations],
     ["genesets", genesets],
     ["genesetsUI", genesetsUI],

client/src/reducers/ontology.js

@@ -1,31 +0,0 @@
-const Ontology = (
-  state = {
-    enabled: false, // are ontology terms enabled?
-    terms: null, // an array of term names, eg, ['cell', 'lung cell', ...]
-    termSet: null, // a Set object containing all terms, for fast lookup
-    loading: true,
-  },
-  action
-) => {
-  switch (action.type) {
-    case "configuration load complete": {
-      const enabled =
-        action.config?.parameters?.annotations_cell_ontology_enabled ?? false;
-      const terms = action.config?.parameters?.annotations_cell_ontology_terms;
-
-      const termSet = new Set(terms);
-      return {
-        ...state,
-        loading: false,
-        enabled,
-        terms,
-        termSet,
-      };
-    }
-    default: {
-      return state;
-    }
-  }
-};
-
-export default Ontology;