wire up geneset reducer (#2082)

* first cut at GET /genesets route

* update existing tests to match code changes

* more GET /genesets and initial tests

* add missing test fixture

* geneset validation accepts OTA format

* genesets route: better error handling, more tests

* lint

* genesets reducer and initial load

* fix lint

* add autosave support for genesets

* remove debug logging

* fix typo

* fix another typo

* update smoke test config for genesets

* smoke test fixes

* more fiddling with smoke tests

client/src/actions/annotation.js

@@ -387,3 +387,96 @@ export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
     });
   }
 };
+
+export const saveGenesetsAction = () => async (dispatch, getState) => {
+  const state = getState();
+
+  // bail if gene sets not available, or in readonly mode.
+  const { config } = state;
+  const genesetsAreAvailable =
+    config?.parameters?.["annotations_genesets"] ?? false;
+  const genesetsReadonly =
+    config?.parameters?.["annotations_genesets_readonly"] ?? true;
+  if (!genesetsAreAvailable || genesetsReadonly) {
+    // our non-save was completed!
+    return dispatch({
+      type: "autosave: genesets complete",
+      lastSavedGenesets: state.genesets,
+    });
+  }
+
+  const { lastTid, genesets: lastGenesets } = state.genesets;
+
+  /* Create the JSON OTA data structure */
+  const tid = (lastTid ?? 0) + 1;
+  const genesets = [];
+  for (const [name, gs] of lastGenesets) {
+    // const genes = Array.from(gs.genes.values());
+    const genes = [];
+    for (const g of gs.genes.values()) {
+      genes.push({
+        gene_symbol: g.geneSymbol,
+        gene_description: g.geneDescription,
+      });
+    }
+    genesets.push({
+      geneset_name: name,
+      geneset_description: gs.genesetDescription,
+      genes,
+    });
+  }
+  const ota = {
+    tid,
+    genesets,
+  };
+
+  /* Save to server */
+  try {
+    const {
+      dataCollectionNameIsReadOnly,
+      dataCollectionName,
+    } = state.annotations;
+    const queryString =
+      !dataCollectionNameIsReadOnly && !!dataCollectionName
+        ? `?annotation-collection-name=${encodeURIComponent(
+            dataCollectionName
+          )}`
+        : "";
+
+    const res = await fetch(
+      `${globals.API.prefix}${globals.API.version}genesets${queryString}`,
+      {
+        method: "PUT",
+        headers: new Headers({
+          Accept: "application/json",
+          "Content-Type": "application/json",
+        }),
+        body: JSON.stringify(ota),
+        credentials: "include",
+      }
+    );
+    if (!res.ok) {
+      return dispatch({
+        type: "autosave: genesets error",
+        message: `HTTP error ${res.status} - ${res.statusText}`,
+        res,
+      });
+    }
+    return Promise.all([
+      dispatch({
+        type: "autosave: genesets complete",
+        lastSavedGenesets: genesets,
+      }),
+      dispatch({
+        type: "geneset: set tid",
+        tid,
+      }),
+    ]);
+  } catch (error) {
+    return dispatch({
+      type: "autosave: genesets error",
+      message: error.toString(),
+      error,
+    });
+  }
+};

client/src/actions/index.js

@@ -52,6 +52,27 @@ async function userInfoFetch(dispatch) {
   });
 }
 
+async function genesetsFetch(dispatch, config) {
+  /* 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,
+    });
+  }
+}
+
 function prefetchEmbeddings(annoMatrix) {
   /*
   prefetch requests for all embeddings
@@ -76,6 +97,8 @@ const doInitialDataLoad = () =>
         userInfoFetch(dispatch),
       ]);
 
+      genesetsFetch(dispatch, config);
+
       const baseDataUrl = `${globals.API.prefix}${globals.API.version}`;
       const annoMatrix = new AnnoMatrixLoader(baseDataUrl, schema.schema);
       const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
@@ -242,6 +265,7 @@ export default {
   annotationRenameLabelInCategory: annoActions.annotationRenameLabelInCategory,
   annotationLabelCurrentSelection: annoActions.annotationLabelCurrentSelection,
   saveObsAnnotationsAction: annoActions.saveObsAnnotationsAction,
+  saveGenesetsAction: annoActions.saveGenesetsAction,
   needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
   layoutChoiceAction: embActions.layoutChoiceAction,
   setCellSetFromSelection: selnActions.setCellSetFromSelection,