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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/rest.py
+3 -40
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@@ -196,6 +196,9 @@ def annotations_var_get(request, data_adaptor):
try:
labels = None
annotations = data_adaptor.dataset_config.user_annotations
if annotations is not None:
labels = annotations.read_labels(data_adaptor)
return make_response(
data_adaptor.annotation_to_fbs_matrix(Axis.VAR, fields, labels),
HTTPStatus.OK,
@@ -325,43 +328,3 @@ def layout_obs_put(request, data_adaptor):
return abort_and_log(HTTPStatus.NOT_IMPLEMENTED, str(e))
except (ValueError, DisabledFeatureError, FilterError) as e:
return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)
def genesets_get(request, data_adaptor):
preferred_mimetype = request.accept_mimetypes.best_match(["application/json"])
if preferred_mimetype != "application/json":
return abort(HTTPStatus.NOT_ACCEPTABLE)
annotations = data_adaptor.dataset_config.user_annotations
genesets = annotations.read_genesets(data_adaptor)
return make_response(jsonify({"genesets": genesets}), HTTPStatus.OK)
def genesets_put(request, data_adaptor):
annotations = data_adaptor.dataset_config.user_annotations
if annotations is None:
return abort(HTTPStatus.NOT_IMPLEMENTED)
if data_adaptor.dataset_config.user_annotations__genesets__readonly:
return abort(HTTPStatus.NOT_IMPLEMENTED)
anno_collection = request.args.get("annotation-collection-name", default=None)
if anno_collection is not None:
if not annotations.is_safe_collection_name(anno_collection):
return abort(HTTPStatus.BAD_REQUEST, "Bad annotation collection name")
annotations.set_collection(anno_collection)
args = request.get_json()
try:
genesets = args["genesets"]
if type(genesets) is list:
gs = data_adaptor.check_new_genesets(genesets)
annotations.write_genesets(gs, data_adaptor)
else:
pass
annotations.write_genesets([], data_adaptor)
res = json.dumps({"status": "OK"})
return make_response(res, HTTPStatus.OK, {"Content-Type": "application/json"})
except (ValueError, DisabledFeatureError, KeyError) as e:
return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)