remove Get genesets call (#498)

* remove genesets
* removing initial fetch genesets call

Co-authored-by: ashin-czi <ashin@contractor.chanzuckerberg.com>

client/src/actions/index.ts

@@ -110,34 +110,6 @@ async function datasetMetadataFetchAndLoad(
     portalUrl: links["collections-home-page"],
   });
 }
-/**
- *
- * @param dispatch Function facilitating update of store.
- * @param config Config object returned from config endpoint, notifies if genesets is enabled.
- */
-async function genesetsFetchAndLoad(
-  dispatch: AppDispatch,
-  config: Config
-): Promise<void> {
-  /* request genesets ONLY if the backend supports the feature */
-  const defaultResponse = {
-    genesets: [],
-    tid: 0,
-  };
-  if (config?.parameters?.annotations_genesets ?? false) {
-    fetchJson("genesets").then((response) => {
-      dispatch({
-        type: "geneset: initial load",
-        data: response ?? defaultResponse,
-      });
-    });
-  } else {
-    dispatch({
-      type: "geneset: initial load",
-      data: defaultResponse,
-    });
-  }
-}
 
 interface GeneInfoAPI {
   ncbi_url: string;
@@ -194,8 +166,6 @@ const doInitialDataLoad = (): ((
 
       datasetMetadataFetchAndLoad(dispatch, oldPrefix, config);
 
-      genesetsFetchAndLoad(dispatch, config);
-
       const baseDataUrl = `${globals.API.prefix}${globals.API.version}`;
       const annoMatrix = new AnnoMatrixLoader(baseDataUrl, schema.schema);
       const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);

client/src/reducers/genesets.ts

@@ -53,51 +53,6 @@ const GeneSets = (
   action: AnyAction
 ): State => {
   switch (action.type) {
-    /**
-     * Initial, load-time bootstrap.
-     * {
-     *    type: "geneset: initial load"
-     *    data: JSON response
-     * }
-     */
-    case "geneset: initial load": {
-      const { data } = action;
-
-      if (
-        !data ||
-        typeof data.tid !== "number" ||
-        !Array.isArray(data.genesets)
-      )
-        throw new Error("missing or malformed JSON response");
-
-      const lastTid = data.tid;
-      const genesetsData = data.genesets;
-      const genesets = new Map();
-
-      for (const gsData of genesetsData) {
-        const genes = new Map();
-        for (const gene of gsData.genes) {
-          genes.set(gene.gene_symbol, {
-            geneSymbol: gene.gene_symbol,
-            geneDescription: gene?.gene_description ?? "",
-          });
-        }
-        const gs = {
-          genesetName: gsData.geneset_name,
-          genesetDescription: gsData?.geneset_description ?? "",
-          genes,
-        };
-        genesets.set(gsData.geneset_name, gs);
-      }
-
-      return {
-        ...state,
-        initialized: true,
-        lastTid,
-        genesets,
-      };
-    }
-
     /**
      * Creates a new & empty geneset with the given name and description.
      * {

server/app/api/v3.py

@@ -129,13 +129,6 @@ def get(self, data_adaptor):
         return common_rest.layout_obs_get(request, data_adaptor)
 
 
-class GenesetsAPI(S3URIResource):
-    @cache_control(immutable=True, max_age=ONE_YEAR)
-    @rest_get_s3uri_data_adaptor
-    def get(self, data_adaptor):
-        return common_rest.genesets_get(request, data_adaptor)
-
-
 class SummarizeVarAPI(S3URIResource):
     @rest_get_s3uri_data_adaptor
     @cache_control(immutable=True, max_age=ONE_YEAR)
@@ -214,7 +207,6 @@ def add_resource(resource, url):
     add_resource(AnnotationsVarAPI, "/annotations/var")
     add_resource(DataVarAPI, "/data/var")
     add_resource(GeneInfoAPI, "/geneinfo")
-    add_resource(GenesetsAPI, "/genesets")
     add_resource(SummarizeVarAPI, "/summarize/var")
     # Display routes
     add_resource(ColorsAPI, "/colors")

server/common/rest.py

@@ -357,18 +357,6 @@ def layout_obs_get(request, data_adaptor):
         )
 
 
-# TODO: I think this is no longer useful, but it is called. So just returning an effectively empty response for now
-def genesets_get(request, data_adaptor):
-    preferred_mimetype = request.accept_mimetypes.best_match(["application/json", "text/csv"])
-    if preferred_mimetype not in ("application/json"):
-        return abort(HTTPStatus.NOT_ACCEPTABLE)
-
-    try:
-        return make_response(jsonify({"genesets": [], "tid": 0}), HTTPStatus.OK)
-    except (ValueError, KeyError) as e:
-        return abort_and_log(HTTPStatus.BAD_REQUEST, str(e))
-
-
 def summarize_var_helper(request, data_adaptor, key, raw_query):
     preferred_mimetype = request.accept_mimetypes.best_match(["application/octet-stream"])
     if preferred_mimetype != "application/octet-stream":

server/tests/e2e/test_api_cache.py

@@ -72,7 +72,7 @@ def test_cached_endpoints(self):
         url_base = "/".join(
             [self.api_url_base, "cellxgene", "s3_uri", quote(quote(body, safe=""), safe=""), "api/v0.3"]
         )
-        endpoints = ["config", "schema", "colors", "genesets", "layout/obs", "annotations/obs", "annotations/var"]
+        endpoints = ["config", "schema", "colors", "layout/obs", "annotations/obs", "annotations/var"]
 
         for endpoint in endpoints:
             with self.subTest(endpoint):

server/tests/unit/common/apis/test_api_v3.py

@@ -556,17 +556,6 @@ def test_genesets_config(self):
                 self.assertTrue(annotations_genesets_readonly)
                 self.assertEqual(annotations_genesets_summary_methods, ["mean"])
 
-    def test_get_genesets(self):
-        endpoint = "genesets"
-        for url_base in [self.TEST_URL_BASE, self.TEST_URL_BASE_SPARSE]:
-            with self.subTest(url_base=url_base):
-                url = f"{url_base}{endpoint}"
-                result = self.client.get(url, headers={"Accept": "application/json"})
-                self.assertEqual(result.status_code, HTTPStatus.OK)
-                self.assertEqual(result.headers["Content-Type"], "application/json")
-                result_data = json.loads(result.data)
-                self.assertIsNotNone(result_data["genesets"])
-
     def test_get_summaryvar(self):
         index_col_name = self.schema["schema"]["annotations"]["var"]["index"]
         endpoint = "summarize/var"