wire e2e gene set loading prototype

server/common/rest.py

@@ -196,9 +196,6 @@ 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,
@@ -328,3 +325,43 @@ 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)