mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-01 04:28:12 +08:00
remove experimental ontology support (#2300)
* remove experimental ontology support * lint * remove ontologies from unit tests * additional test changes
This commit is contained in:
Bruce Martin
@@ -1,22 +1,14 @@
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from abc import ABCMeta, abstractmethod
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import fastobo
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import fsspec
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from backend.common.errors import OntologyLoadFailure, DisabledFeatureError
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from backend.common.errors import DisabledFeatureError
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from backend.common.utils.type_conversion_utils import get_schema_type_hint_of_array
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from backend.common.genesets import write_gene_sets_tidycsv
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class Annotations(metaclass=ABCMeta):
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""" baseclass for annotations, including ontologies and gene sets"""
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""" our default ontology is the PURL for the Cell Ontology.
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See http://www.obofoundry.org/ontology/cl.html """
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DefaultOnotology = "http://purl.obolibrary.org/obo/cl.obo"
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"""baseclass for annotations and gene sets"""
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def __init__(self, config={}):
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self.ontology_data = None
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self.config = config
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def user_annotations_enabled(self):
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@@ -33,27 +25,6 @@ class Annotations(metaclass=ABCMeta):
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if not self.gene_sets_save_enabled():
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raise DisabledFeatureError("User gene sets save is disabled.")
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def load_ontology(self, path):
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"""Load and parse ontologies - currently support OBO files only."""
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if path is None:
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path = self.DefaultOnotology
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try:
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with fsspec.open(path) as f:
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obo = fastobo.iter(f)
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terms = filter(lambda stanza: type(stanza) is fastobo.term.TermFrame, obo)
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names = [tag.name for term in terms for tag in term if type(tag) is fastobo.term.NameClause]
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self.ontology_data = names
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except FileNotFoundError as e:
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raise OntologyLoadFailure("Unable to find OBO ontology path") from e
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except SyntaxError as e:
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raise OntologyLoadFailure("Syntax error loading OBO ontology") from e
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except Exception as e:
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raise OntologyLoadFailure("Error loading OBO file") from e
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def get_schema(self, data_adaptor):
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schema = []
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labels = self.read_labels(data_adaptor)
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@@ -82,7 +53,7 @@ class Annotations(metaclass=ABCMeta):
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@abstractmethod
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def read_gene_sets(self, data_adaptor):
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"""Return the gene sets from persistent storage """
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"""Return the gene sets from persistent storage"""
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pass
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@abstractmethod
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@@ -193,14 +193,14 @@ class AnnotationsLocalFile(Annotations):
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return os.getcwd()
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def _get_celllabels_filename(self, data_adaptor):
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""" return the current annotation file name """
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"""return the current annotation file name"""
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if self.label_output_file:
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return self.label_output_file
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return self._get_filename(data_adaptor, "cell-labels")
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def _get_genesets_filename(self, data_adaptor):
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""" return the current gene sets file name """
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"""return the current gene sets file name"""
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if self.gene_sets_output_file:
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return self.gene_sets_output_file
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@@ -263,12 +263,6 @@ class AnnotationsLocalFile(Annotations):
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params["annotations_genesets_name_is_read_only"] = self.gene_sets_output_file is not None
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params["user_annotation_collection_name_enabled"] = True
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if self.ontology_data:
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params["annotations_cell_ontology_enabled"] = True
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params["annotations_cell_ontology_terms"] = self.ontology_data
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else:
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params["annotations_cell_ontology_enabled"] = False
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if self.label_output_file is not None:
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# user has hard-wired the name of the annotation cell label data collection
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fname = os.path.basename(self.label_output_file)
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@@ -47,9 +47,6 @@ def get_client_config(app_config, data_adaptor):
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"annotations_genesets": True, # feature flag
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"annotations_genesets_readonly": dataset_config.user_annotations__gene_sets__readonly,
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"annotations_genesets_summary_methods": ["mean"],
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"annotations_cell_ontology_enabled": False,
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"annotations_cell_ontology_obopath": None,
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"annotations_cell_ontology_terms": None,
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"custom_colors": dataset_config.presentation__custom_colors,
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"diffexp-may-be-slow": False,
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}
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@@ -3,7 +3,7 @@ from os.path import splitext, isdir
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from backend.server.common.annotations.local_file_csv import AnnotationsLocalFile
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from backend.server.common.config.base_config import BaseConfig
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from backend.common.errors import ConfigurationError, OntologyLoadFailure, AnnotationsError
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from backend.common.errors import ConfigurationError, AnnotationsError
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from backend.server.compute.scanpy import get_scanpy_module
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from backend.server.data_common.matrix_loader import MatrixDataLoader
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@@ -28,10 +28,6 @@ class DatasetConfig(BaseConfig):
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"directory"
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]
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self.user_annotations__local_file_csv__file = default_config["user_annotations"]["local_file_csv"]["file"]
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self.user_annotations__ontology__enable = default_config["user_annotations"]["ontology"]["enable"]
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self.user_annotations__ontology__obo_location = default_config["user_annotations"]["ontology"][
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"obo_location"
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]
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self.user_annotations__gene_sets__readonly = default_config["user_annotations"]["gene_sets"]["readonly"]
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self.user_annotations__local_file_csv__gene_sets_file = default_config["user_annotations"][
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"local_file_csv"
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@@ -101,10 +97,6 @@ class DatasetConfig(BaseConfig):
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self.validate_correct_type_of_configuration_attribute(
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"user_annotations__local_file_csv__gene_sets_file", (type(None), str)
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)
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self.validate_correct_type_of_configuration_attribute("user_annotations__ontology__enable", bool)
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self.validate_correct_type_of_configuration_attribute(
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"user_annotations__ontology__obo_location", (type(None), str)
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)
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self.validate_correct_type_of_configuration_attribute("user_annotations__gene_sets__readonly", bool)
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if self.user_annotations__enable or not self.user_annotations__gene_sets__readonly:
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@@ -122,13 +114,6 @@ class DatasetConfig(BaseConfig):
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else:
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raise ConfigurationError('The only annotation type support is "local_file_csv"')
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if self.user_annotations__enable:
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if self.user_annotations__ontology__enable or self.user_annotations__ontology__obo_location:
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try:
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self.user_annotations.load_ontology(self.user_annotations__ontology__obo_location)
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except OntologyLoadFailure as e:
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raise ConfigurationError("Unable to load ontology terms\n" + str(e))
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self.check_annotation_config_vars_not_set(context)
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def handle_local_file_csv_annotations(self, context):
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@@ -183,14 +168,6 @@ class DatasetConfig(BaseConfig):
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if not self.user_annotations__enable:
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if filename is not None:
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context["messagefn"]("Warning: --annotations-file ignored as annotations are disabled.")
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if self.user_annotations__ontology__enable:
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context["messagefn"](
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"Warning: --experimental-annotations-ontology ignored as annotations are disabled."
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)
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if self.user_annotations__ontology__obo_location is not None:
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context["messagefn"](
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"Warning: --experimental-annotations-ontology-obo ignored as annotations are disabled."
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)
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if dirname is not None:
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context["messagefn"]("Warning: --user-generated-data-dir ignored as annotations are disabled.")
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