add autosave

client/src/actions/annotation.js

@@ -387,3 +387,82 @@ export const saveObsAnnotationsAction = () => async (dispatch, getState) => {
     });
   }
 };
+
+export const saveGenesetsAction = () => async (dispatch, getState) => {
+  const state = getState();
+  const { config, genesets, annotations } = state;
+
+  // bail if gene sets not available, or in readonly mode.
+  const genesetsAreAvailable =
+    config?.parameters?.["annotations_genesets"] ?? false;
+  const genesetsReadonly =
+    config?.parameters?.["annotations_genesets_readonly"] ?? true;
+  if (!genesetsAreAvailable || genesetsReadonly) {
+    // our non-save was completed!
+    dispatch({
+      type: "autosave: genesets complete",
+      lastSavedGenesets: genesets,
+    });
+  }
+
+  /*
+   JSON data structure is an array of arrays, where the first
+   element is gene set name, remainder are the genes.  Eg,
+
+    {
+      "genesets": [
+        [ "gs1", ["TNFRSF4","SUMO3","BRWD1"]],
+        [ "gs2", ["DSCR3", "BRWD1", "BACE2", "SIK1", "C21orf33", "ICOSLG", "SUMO3"]]
+      ]
+    }
+
+  Order of gene sets and genes is significant
+  */
+  const gsArr = [];
+  for (const [gsName, gsGenes] of genesets.genesets) {
+    gsArr.push([gsName, Array.from(gsGenes)]);
+  }
+
+  try {
+    const { dataCollectionNameIsReadOnly, dataCollectionName } = 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({
+          genesets: gsArr,
+        }),
+        credentials: "include",
+      }
+    );
+    if (res.ok) {
+      dispatch({
+        type: "autosave: genesets complete",
+        lastSavedGenesets: genesets,
+      });
+    } else {
+      dispatch({
+        type: "autosave: genesets error",
+        message: `HTTP error ${res.status} - ${res.statusText}`,
+        res,
+      });
+    }
+  } catch (error) {
+    dispatch({
+      type: "autosave: genesets error",
+      message: error.toString(),
+      error,
+    });
+  }
+};

client/src/actions/index.js

@@ -52,14 +52,21 @@ async function userInfoFetch(dispatch) {
   });
 }
 
-async function genesetsFetch(dispatch) {
+async function genesetsFetch(dispatch, config) {
-  return fetchJson("genesets").then((response) => {
+  if (config?.parameters?.["annotations_genesets"] ?? false) {
-    const genesets = response?.genesets ?? {};
+    fetchJson("genesets").then((response) => {
+      const genesets = response?.genesets ?? {};
+      dispatch({
+        type: "geneset: initial load",
+        init: genesets,
+      });
+    });
+  } else {
     dispatch({
       type: "geneset: initial load",
-      init: genesets,
+      init: [],
     });
-  })
+  }
 }
 
 function prefetchEmbeddings(annoMatrix) {
@@ -84,9 +91,10 @@ const doInitialDataLoad = () =>
         schemaFetch(dispatch),
         userColorsFetchAndLoad(dispatch),
         userInfoFetch(dispatch),
-        genesetsFetch(dispatch),
       ]);
 
+      genesetsFetch(dispatch, config);
+
       const baseDataUrl = `${globals.API.prefix}${globals.API.version}`;
       const annoMatrix = new AnnoMatrixLoader(baseDataUrl, schema.schema);
       const obsCrossfilter = new AnnoMatrixObsCrossfilter(annoMatrix);
@@ -253,6 +261,7 @@ export default {
   annotationRenameLabelInCategory: annoActions.annotationRenameLabelInCategory,
   annotationLabelCurrentSelection: annoActions.annotationLabelCurrentSelection,
   saveObsAnnotationsAction: annoActions.saveObsAnnotationsAction,
+  saveGenesetsAction: annoActions.saveGenesetsAction,
   needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
   layoutChoiceAction: embActions.layoutChoiceAction,
   setCellSetFromSelection: selnActions.setCellSetFromSelection,

client/src/components/autosave/filenameDialog.js

@@ -17,6 +17,9 @@ import {
   auth: state.config?.authentication,
   userInfo: state.userInfo,
   writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
+  writableGenesetsEnabled: !(
+    state.config?.parameters?.["annotations_genesets_readonly"] ?? true
+  ),
 }))
 class FilenameDialog extends React.Component {
   constructor(props) {
@@ -101,7 +104,7 @@ class FilenameDialog extends React.Component {
     } = this.props;
     const { filenameText } = this.state;
 
-    return writableCategoriesEnabled &&
+    return (writableCategoriesEnabled || writableGenesetsEnabled) &&
       annotations.promptForFilename &&
       !annotations.dataCollectionNameIsReadOnly &&
       !annotations.dataCollectionName &&

client/src/components/autosave/index.js

@@ -5,11 +5,18 @@ import FilenameDialog from "./filenameDialog";
 
 @connect((state) => ({
   annotations: state.annotations,
-  saveInProgress: state.autosave?.saveInProgress ?? false,
+  obsAnnotationSaveInProgress:
+    state.autosave?.obsAnnotationSaveInProgress ?? false,
+  genesetSaveInProgress: state.autosave?.genesetSaveInProgress ?? false,
   error: state.autosave?.error,
   writableCategoriesEnabled: state.config?.parameters?.annotations ?? false,
+  writableGenesetsEnabled: !(
+    state.config?.parameters?.annotations_genesets_readonly ?? true
+  ),
   annoMatrix: state.annoMatrix,
+  genesets: state.genesets,
   lastSavedAnnoMatrix: state.autosave?.lastSavedAnnoMatrix,
+  lastSavedGenesets: state.autosave?.lastSavedGenesets,
 }))
 class Autosave extends React.Component {
   constructor(props) {
@@ -38,18 +45,40 @@ class Autosave extends React.Component {
   }
 
   tick = () => {
-    const { dispatch, saveInProgress } = this.props;
+    const {
-    if (this.needToSave() && !saveInProgress) {
+      dispatch,
+      obsAnnotationSaveInProgress,
+      genesetSaveInProgress,
+    } = this.props;
+    if (!obsAnnotationSaveInProgress && this.needToSaveObsAnnotations()) {
       dispatch(actions.saveObsAnnotationsAction());
     }
+    if (!genesetSaveInProgress && this.needToSaveGenesets()) {
+      dispatch(actions.saveGenesetsAction());
+    }
   };
 
-  needToSave = () => {
+  saveInProgress() {
-    /* return true if we need to save, false if we don't */
+    const { obsAnnotationSaveInProgress, genesetSaveInProgress } = this.props;
+    return obsAnnotationSaveInProgress || genesetSaveInProgress;
+  }
+
+  needToSaveObsAnnotations = () => {
+    /* return true if we need to save obs cell labels, false if we don't */
     const { annoMatrix, lastSavedAnnoMatrix } = this.props;
     return actions.needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix);
   };
 
+  needToSaveGenesets = () => {
+    /* return true if we need to save gene ses, false if we do not */
+    const { genesets, lastSavedGenesets } = this.props;
+    return genesets.initialized && genesets !== lastSavedGenesets;
+  };
+
+  needToSave() {
+    return this.needToSaveGenesets() || this.needToSaveObsAnnotations();
+  }
+
   statusMessage() {
     const { error } = this.props;
     if (error) {
@@ -59,11 +88,7 @@ class Autosave extends React.Component {
   }
 
   render() {
-    const {
+    const { writableCategoriesEnabled, lastSavedAnnoMatrix } = this.props;
-      writableCategoriesEnabled,
-      saveInProgress,
-      lastSavedAnnoMatrix,
-    } = this.props;
     const initialDataLoadComplete = lastSavedAnnoMatrix;
 
     if (!writableCategoriesEnabled) return null;
@@ -74,7 +99,7 @@ class Autosave extends React.Component {
         data-testclass={
           !initialDataLoadComplete
             ? "autosave-init"
-            : this.needToSave() || saveInProgress
+            : this.saveInProgress() || this.needToSave()
             ? "autosave-incomplete"
             : "autosave-complete"
         }