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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
Download Patch File Download Diff File Expand all files Collapse all files

1
backend/common/errors.py
View File

@@ -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")

18
backend/czi_hosted/cli/launch.py
View File

@@ -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,

34
backend/czi_hosted/common/annotations/annotations.py
View File

@@ -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 """
""" 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 genesets"""
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

6
backend/czi_hosted/common/annotations/hosted_tiledb.py
View File

@@ -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)

8
backend/czi_hosted/common/annotations/local_file_csv.py
View File

@@ -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)

3
backend/czi_hosted/common/config/client_config.py
View File

@@ -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,

24
backend/czi_hosted/common/config/dataset_config.py
View File

@@ -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)

3
backend/czi_hosted/default_config.py
View File

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

1
backend/czi_hosted/requirements.txt
View File

@@ -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

18
backend/server/cli/launch.py
View File

@@ -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,

35
backend/server/common/annotations/annotations.py
View File

@@ -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

10
backend/server/common/annotations/local_file_csv.py
View File

@@ -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)

3
backend/server/common/config/client_config.py
View File

@@ -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,
}

25
backend/server/common/config/dataset_config.py
View File

@@ -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.")

3
backend/server/default_config.py
View File

@@ -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

1
backend/server/requirements.txt
View File

@@ -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

3
backend/test/fixtures/czi_hosted_dataset_config_outline.py vendored
View File

@@ -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}

3
backend/test/fixtures/dataset_config_outline.py vendored
View File

@@ -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}

6
backend/test/test_czi_hosted/unit/common/config/__init__.py
View File

@@ -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",

1
backend/test/test_czi_hosted/unit/common/config/test_base_config.py
View File

@@ -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):

3
backend/test/test_czi_hosted/unit/common/config/test_dataset_config.py
View File

@@ -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"])

6
backend/test/test_server/unit/common/config/__init__.py
View File

@@ -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",

3
backend/test/test_server/unit/common/config/test_app_config.py
View File

@@ -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 = [

1
backend/test/test_server/unit/common/config/test_base_config.py
View File

@@ -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)

3
backend/test/test_server/unit/common/config/test_dataset_config.py
View File

@@ -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"])

3
client/__tests__/e2e/test_config.yaml
View File

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

10
client/src/components/categorical/category/annoDialogAddLabel.js
View File

@@ -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;
return isLabelErroneous(name, metadataField, ontology, schema);
const { metadataField, schema } = this.props;
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 ontologyEnabled = ontology?.enabled ?? false;
const { metadataField, annotations, obsCrossfilter } = this.props;
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={{

6
client/src/components/categorical/category/annoDialogEditCategoryName.js
View File

@@ -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 ontologyEnabled = ontology?.enabled ?? false;
const { metadataField, annotations } = this.props;
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={{

5
client/src/components/categorical/index.js
View File

@@ -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={{

7
client/src/components/categorical/labelUtil.js
View File

@@ -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 */
const termInOntology = ontology?.termSet.has(label) ?? false;
/* check for label syntax errors */
const error = AnnotationsHelpers.annotationNameIsErroneous(label);
if (error && !termInOntology) return error;
if (error) return error;
/* disallow duplicates */
const { obsByName } = schema.annotations;

9
client/src/components/categorical/value/index.js
View File

@@ -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={{

1
client/src/components/geneExpression/menus/createGenesetDialogue.js
View File

@@ -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,

1
client/src/components/geneExpression/menus/editGenesetNameDialogue.js
View File

@@ -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,

2
client/src/reducers/index.js
View File

@@ -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],

31
client/src/reducers/ontology.js
View File

@@ -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;