hosted gene sets routes, plus a few bug fixes (#2155)

* first cut at hosted gs routes

* lint

* update tests to match csv parser changes

* update tests to new API

* update gene set name validation rules to match requirements

* add path mapping from dataset to geneset

* add test cases for geneset GET route

* fix test assertion

* remove debugging code

* update gene set uri mapping function

* fix error message

* allow extra user-specified headers in gene set csv file

* clarify comment
This commit is contained in:
Bruce Martin
2021-04-27 13:58:58 -07:00
committed by GitHub
parent ebeb1c8818
commit f2e9aecebe
19 changed files with 702 additions and 267 deletions
@@ -17,8 +17,8 @@ from backend.czi_hosted.db.cellxgene_orm import Annotation
class AnnotationsHostedTileDB(Annotations):
CXG_ANNO_COLLECTION = "cxg_anno_collection"
def __init__(self, directory_path, db):
super().__init__()
def __init__(self, config, directory_path, db):
super().__init__(config)
self.db = db
if directory_path[-1] == "/":
self.directory_path = directory_path
@@ -158,6 +158,8 @@ class AnnotationsHostedTileDB(Annotations):
self.db.session.commit()
def update_parameters(self, parameters, data_adaptor):
super().update_parameters(parameters, data_adaptor)
params = {}
params["annotations"] = True
params["user_annotation_collection_name_enabled"] = False