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Refactoring cxg utility classes in preparation for CXG conversion tooling (#1739)

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This commit is contained in:
maniarathi
2020-08-14 16:51:13 -07:00
committed by GitHub
parent b034055c35
commit 508889f74b
23 changed files with 607 additions and 177 deletions
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server/common/app_config.py
+19 -19
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@@ -1,23 +1,23 @@
from server import display_version as cellxgene_display_version
from flatten_dict import flatten, unflatten
import os
from os.path import splitext, basename, isdir
import sys
from urllib.parse import urlparse, quote_plus
import yaml
import copy
from server.common.default_config import get_default_config
from server.common.errors import ConfigurationError, DatasetAccessError, OntologyLoadFailure
from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataCacheManager, MatrixDataType
from server.common.utils import find_available_port, is_port_available
import os
import sys
import warnings
from os.path import splitext, basename, isdir
from urllib.parse import urlparse, quote_plus
import yaml
from flatten_dict import flatten, unflatten
import server.compute.diffexp_cxg as diffexp_tiledb
from server import display_version as cellxgene_display_version
from server.auth.auth import AuthTypeFactory
from server.common.annotations.hosted_tiledb import AnnotationsHostedTileDB
from server.common.annotations.local_file_csv import AnnotationsLocalFile
from server.common.utils import custom_format_warning
import server.compute.diffexp_cxg as diffexp_tiledb
from server.common.data_locator import discover_s3_region_name
from server.auth.auth import AuthTypeFactory
from server.common.default_config import get_default_config
from server.common.errors import ConfigurationError, DatasetAccessError, OntologyLoadFailure
from server.common.utils.utils import custom_format_warning, find_available_port, is_port_available
from server.data_common.matrix_loader import MatrixDataLoader, MatrixDataCacheManager, MatrixDataType
from server.db.db_utils import DbUtils
DEFAULT_SERVER_PORT = 5005
@@ -150,7 +150,6 @@ class AppConfig(object):
parameters is done"""
if messagefn is None:
def noop(message):
pass
@@ -284,7 +283,7 @@ class AppConfig(object):
if auth.requires_client_login():
config["authentication"].update({
"login": auth.get_login_url(data_adaptor),
"logout" : auth.get_logout_url(data_adaptor),
"logout": auth.get_logout_url(data_adaptor),
})
return c
@@ -748,7 +747,8 @@ class DatasetConfig(BaseConfig):
self.user_annotations__ontology__enable = dc["user_annotations"]["ontology"]["enable"]
self.user_annotations__ontology__obo_location = dc["user_annotations"]["ontology"]["obo_location"]
self.user_annotations__hosted_tiledb_array__db_uri = dc["user_annotations"]["hosted_tiledb_array"]["db_uri"]
self.user_annotations__hosted_tiledb_array__hosted_file_directory = dc["user_annotations"]["hosted_tiledb_array"]["hosted_file_directory"] # noqa E501
self.user_annotations__hosted_tiledb_array__hosted_file_directory = \
dc["user_annotations"]["hosted_tiledb_array"]["hosted_file_directory"] # noqa E501
self.embeddings__names = dc["embeddings"]["names"]
self.embeddings__enable_reembedding = dc["embeddings"]["enable_reembedding"]
@@ -896,7 +896,7 @@ class DatasetConfig(BaseConfig):
server_config = self.app_config.server_config
if server_config.single_dataset__datapath:
with server_config.matrix_data_cache_manager.data_adaptor(
self.tag, server_config.single_dataset__datapath, self.app_config
self.tag, server_config.single_dataset__datapath, self.app_config
) as data_adaptor:
if self.diffexp__enable and data_adaptor.parameters.get("diffexp_may_be_slow", False):
context["messagefn"](