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rename "geneset" to "gene set" in CLI (#2088)

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* remove dead code

* rename geneset to gene_set
This commit is contained in:
Bruce Martin
2021-03-02 15:36:01 -08:00
committed by GitHub
parent b00496198d
commit c037f4eaa6
14 changed files with 101 additions and 102 deletions
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local_server/common/rest.py
+6 -6
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@@ -336,11 +336,11 @@ def genesets_get(request, data_adaptor):
try:
annotations = data_adaptor.dataset_config.user_annotations
(genesets, tid) = data_adaptor.check_new_genesets(annotations.read_genesets(data_adaptor))
(genesets, tid) = data_adaptor.check_new_gene_sets(annotations.read_gene_sets(data_adaptor))
if preferred_mimetype == "text/csv":
return make_response(
annotations.genesets_to_csv(genesets),
annotations.gene_sets_to_csv(genesets),
HTTPStatus.OK,
{
"Content-Type": "text/csv",
@@ -349,7 +349,7 @@ def genesets_get(request, data_adaptor):
)
else:
return make_response(
jsonify({"genesets": annotations.genesets_to_response(genesets), "tid": tid}), HTTPStatus.OK
jsonify({"genesets": annotations.gene_sets_to_response(genesets), "tid": tid}), HTTPStatus.OK
)
except (ValueError, KeyError, AnnotationsError) as e:
return abort_and_log(HTTPStatus.BAD_REQUEST, str(e))
@@ -357,7 +357,7 @@ def genesets_get(request, data_adaptor):
def genesets_put(request, data_adaptor):
annotations = data_adaptor.dataset_config.user_annotations
if not annotations.genesets_save_enabled():
if not annotations.gene_sets_save_enabled():
return abort(HTTPStatus.NOT_IMPLEMENTED)
anno_collection = request.args.get("annotation-collection-name", default=None)
@@ -373,8 +373,8 @@ def genesets_put(request, data_adaptor):
if genesets is None:
abort(HTTPStatus.BAD_REQUEST)
(gs, _) = data_adaptor.check_new_genesets((genesets, tid))
annotations.write_genesets(gs, tid, data_adaptor)
(gs, _) = data_adaptor.check_new_gene_sets((genesets, tid))
annotations.write_gene_sets(gs, tid, data_adaptor)
return make_response(jsonify({"status": "OK"}), HTTPStatus.OK)
except (ValueError, DisabledFeatureError, KeyError) as e:
return abort_and_log(HTTPStatus.BAD_REQUEST, str(e), include_exc_info=True)