fork/cellxgene
1
0
Fork 0
mirror of https://github.com/chanzuckerberg/cellxgene.git synced 2026-10-05 18:48:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

gene sets summary route (#2099)

Browse Source 
* gene sets summary route

* lint

* clarify return type

* style
This commit is contained in:
Bruce Martin
2021-03-10 16:02:05 -08:00
committed by GitHub
parent 1d3d9237e7
commit 31e0326ded
10 changed files with 228 additions and 38 deletions
Download Patch File Download Diff File Expand all files Collapse all files
local_server/common/config/dataset_config.py
+5 -5
View File
@@ -33,9 +33,9 @@ class DatasetConfig(BaseConfig):
"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"][
"gene_sets_file"
]
self.user_annotations__local_file_csv__gene_sets_file = default_config["user_annotations"][
"local_file_csv"
]["gene_sets_file"]
self.embeddings__names = default_config["embeddings"]["names"]
self.embeddings__enable_reembedding = default_config["embeddings"]["enable_reembedding"]
@@ -169,10 +169,10 @@ class DatasetConfig(BaseConfig):
if server_config.single_dataset__datapath:
data_adaptor = self.get_data_adaptor()
if self.user_annotations__local_file_csv__file:
data_adaptor.check_new_labels(self.user_annotations.read_labels(data_adaptor))
self.user_annotations.read_labels(data_adaptor)
if self.user_annotations__local_file_csv__gene_sets_file:
try:
data_adaptor.check_new_gene_sets(self.user_annotations.read_gene_sets(data_adaptor, context), context)
self.user_annotations.read_gene_sets(data_adaptor, context)
except (ValueError, AnnotationsError, KeyError) as e:
raise ConfigurationError(f"Unable to read genesets CSV file: {str(e)}") from e