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moving server over

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This commit is contained in:
Colin Megill
2021-03-08 11:54:29 -08:00
parent 21d1ca1bc8
commit 9eca912f8c
9 changed files with 33 additions and 222 deletions
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server/common/config/client_config.py
-2
View File
@@ -44,8 +44,6 @@ def get_client_config(app_config, data_adaptor):
"annotations": False,
"annotations_file": None,
"annotations_dir": None,
"annotations_genesets": True, # feature flag
"annotations_genesets_readonly": dataset_config.user_annotations__genesets__readonly,
"annotations_cell_ontology_enabled": False,
"annotations_cell_ontology_obopath": None,
"annotations_cell_ontology_terms": None,
server/common/config/dataset_config.py
+11 -35
View File
@@ -42,10 +42,6 @@ class DatasetConfig(BaseConfig):
self.user_annotations__hosted_tiledb_array__hosted_file_directory = default_config["user_annotations"][
"hosted_tiledb_array"
]["hosted_file_directory"]
self.user_annotations__genesets__readonly = default_config["user_annotations"]["genesets"]["readonly"]
self.user_annotations__local_file_csv__genesets_file = default_config["user_annotations"]["local_file_csv"][
"genesets_file"
]
self.embeddings__names = default_config["embeddings"]["names"]
self.embeddings__enable_reembedding = default_config["embeddings"]["enable_reembedding"]
@@ -102,9 +98,6 @@ 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__local_file_csv__genesets_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)
@@ -115,8 +108,6 @@ class DatasetConfig(BaseConfig):
self.validate_correct_type_of_configuration_attribute(
"user_annotations__hosted_tiledb_array__hosted_file_directory", (type(None), str)
)
self.validate_correct_type_of_configuration_attribute("user_annotations__genesets__readonly", bool)
if self.user_annotations__enable:
server_config = self.app_config.server_config
if not self.app__authentication_enable:
@@ -141,22 +132,14 @@ class DatasetConfig(BaseConfig):
def handle_local_file_csv_annotations(self):
dirname = self.user_annotations__local_file_csv__directory
annotation_filename = self.user_annotations__local_file_csv__file
if annotation_filename is not None and dirname is not None:
filename = self.user_annotations__local_file_csv__file
if filename is not None and dirname is not None:
raise ConfigurationError("'annotations-file' and 'annotations-dir' may not be used together.")
genesets_filename = self.user_annotations__local_file_csv__genesets_file
if genesets_filename is not None and dirname is not None:
raise ConfigurationError("'genesets-file' and 'annotations-dir' may not be used together.")
if annotation_filename is not None:
lf_name, lf_ext = splitext(annotation_filename)
if filename is not None:
lf_name, lf_ext = splitext(filename)
if lf_ext and lf_ext != ".csv":
raise ConfigurationError(f"annotation file type must be .csv: {annotation_filename}")
if genesets_filename is not None:
lf_name, lf_ext = splitext(genesets_filename)
if lf_ext and lf_ext != ".csv":
raise ConfigurationError(f"genesets file type must be .csv: {genesets_filename}")
raise ConfigurationError(f"annotation file type must be .csv: {filename}")
if dirname is not None and not isdir(dirname):
try:
@@ -164,23 +147,16 @@ class DatasetConfig(BaseConfig):
except OSError:
raise ConfigurationError("Unable to create directory specified by --annotations-dir")
self.user_annotations = AnnotationsLocalFile(dirname, annotation_filename, genesets_filename)
self.user_annotations = AnnotationsLocalFile(dirname, filename)
# if the user has specified a fixed label file, go ahead and validate it
# so that we can remove errors early in the process.
server_config = self.app_config.server_config
if server_config.single_dataset__datapath:
if self.user_annotations__local_file_csv__file:
with server_config.matrix_data_cache_manager.data_adaptor(
self.tag, server_config.single_dataset__datapath, self.app_config
) as data_adaptor:
data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor))
if self.user_annotations__local_file_csv__genesets_file:
with server_config.matrix_data_cache_manager.data_adaptor(
self.tag, server_config.single_dataset__datapath, self.app_config
) as data_adaptor:
data_adaptor.check_new_genesets(self.user_annotations.read_genesets(data_adaptor))
if server_config.single_dataset__datapath and self.user_annotations__local_file_csv__file:
with server_config.matrix_data_cache_manager.data_adaptor(
self.tag, server_config.single_dataset__datapath, self.app_config
) as data_adaptor:
data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor))
def handle_hosted_tiledb_annotations(self):
self.validate_correct_type_of_configuration_attribute("user_annotations__hosted_tiledb_array__db_uri", str)