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gene sets summary route (#2099)

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* 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
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local_server/common/rest.py
+33 -3
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@@ -19,6 +19,7 @@ from local_server.common.errors import (
ColorFormatException,
AnnotationsError,
ObsoleteRequest,
UnsupportedSummaryMethod,
)
import json
@@ -336,7 +337,7 @@ def genesets_get(request, data_adaptor):
try:
annotations = data_adaptor.dataset_config.user_annotations
(genesets, tid) = data_adaptor.check_new_gene_sets(annotations.read_gene_sets(data_adaptor))
(genesets, tid) = annotations.read_gene_sets(data_adaptor)
if preferred_mimetype == "text/csv":
return make_response(
@@ -373,10 +374,39 @@ def genesets_put(request, data_adaptor):
if genesets is None:
abort(HTTPStatus.BAD_REQUEST)
(gs, _) = data_adaptor.check_new_gene_sets((genesets, tid))
annotations.write_gene_sets(gs, tid, data_adaptor)
annotations.write_gene_sets(genesets, 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)
except (ObsoleteRequest, TypeError) as e:
return abort(HTTPStatus.NOT_FOUND, description=str(e))
def geneset_summary_get(request, data_adaptor):
preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
if preferred_mimetype != "application/octet-stream":
return abort(HTTPStatus.NOT_ACCEPTABLE)
geneset_name = request.args.get("geneset_name", default=None)
summary_method = request.args.get("method", default="mean")
request_tid = request.args.get("tid", default=None)
try:
annotations = data_adaptor.dataset_config.user_annotations
(genesets, tid) = annotations.read_gene_sets(data_adaptor)
if request_tid is not None and int(request_tid) != tid:
return abort(HTTPStatus.NOT_FOUND, "Obsolete TID")
if geneset_name is None or geneset_name not in genesets:
return abort(HTTPStatus.BAD_REQUEST, "Gene set name not found.")
genes = [g["gene_symbol"] for g in genesets.get(geneset_name)["genes"]]
return make_response(
data_adaptor.get_gene_set_summary(geneset_name, genes, summary_method),
HTTPStatus.OK,
{"Content-Type": "application/octet-stream"},
)
except (ValueError) as e:
return abort(HTTPStatus.NOT_FOUND, description=str(e))
except (UnsupportedSummaryMethod) as e:
return abort(HTTPStatus.BAD_REQUEST, description=str(e))