chore: deploy staging <- main

client/__tests__/e2e/puppeteerUtils.ts

@@ -154,24 +154,11 @@ export async function getElementCoordinates(testId: any) {
   });
 }
 
-async function nameNewAnnotation() {
-  // @ts-expect-error ts-migrate(2554) FIXME: Expected 2 arguments, but got 1.
-  if (await isElementPresent(getTestId("annotation-dialog"))) {
-    await typeInto("new-annotation-name", "ignoreE2E");
-    await clickOn("submit-annotation");
-
-    // wait for the page to load
-    await waitByClass("autosave-complete");
-  }
-}
-
 // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.
 export async function goToPage(url: any) {
   await page.goto(url, {
     waitUntil: "networkidle0",
   });
-
-  await nameNewAnnotation();
 }
 
 // eslint-disable-next-line @typescript-eslint/explicit-module-boundary-types, @typescript-eslint/no-explicit-any --- FIXME: disabled temporarily on migrate to TS.

client/__tests__/reducers/genesetsUI.test.ts

@@ -1,8 +1,8 @@
-import genesetsUIReducer from "../../src/reducers/genesetsUI";
+import genesetsUIReducer, { GeneSetsUIState } from "../../src/reducers/genesetsUI";
 
 // Format: GeneSetsUI(state,action)
 
-const initialState = {
+const initialState: GeneSetsUIState = {
   createGenesetModeActive: false,
   isEditingGenesetName: false,
   isAddingGenesToGeneset: false,
@@ -30,7 +30,7 @@ describe("geneset UI states", () => {
   });
   test("geneset: disable create geneset mode", () => {
     expect(
-      genesetsUIReducer(undefined, { isEditingGenesetName: false })
+      genesetsUIReducer(undefined, { type: "geneset: disable rename geneset mode", isEditingGenesetName: false })
     ).toMatchObject(initialState);
   });
 

client/src/actions/annotation.ts

@@ -2,10 +2,9 @@
  * Action creators for user annotation
  */
 import difference from "lodash.difference";
-import pako from "pako";
 import * as globals from "../globals";
 import { AppDispatch, GetState } from "../reducers";
-import { MatrixFBS, AnnotationsHelpers } from "../util/stateManager";
+import { AnnotationsHelpers } from "../util/stateManager";
 
 const { isUserAnnotation } = AnnotationsHelpers;
 
@@ -313,178 +312,3 @@ export const needToSaveObsAnnotations = (
     (col: any) => annoMatrix.col(col) !== lastSavedAnnoMatrix.col(col)
   );
 };
-
-/**
- * Save the user-created obs annotations IF any have changed.
- */
-export const saveObsAnnotationsAction =
-  () =>
-  async (dispatch: AppDispatch, getState: GetState): Promise<void> => {
-    if (!globals.API) throw new Error("API not set");
-    const state = getState();
-    const { annotations, autosave } = state;
-    const { dataCollectionNameIsReadOnly, dataCollectionName } = annotations;
-    const { lastSavedAnnoMatrix, saveInProgress } = autosave;
-
-    const annoMatrix = state.annoMatrix.base();
-
-    if (saveInProgress || annoMatrix === lastSavedAnnoMatrix) return;
-    if (!needToSaveObsAnnotations(annoMatrix, lastSavedAnnoMatrix)) {
-      dispatch({
-        type: "writable obs annotations - save complete",
-        lastSavedAnnoMatrix: annoMatrix,
-      });
-      return;
-    }
-
-    /**
-     * Else, we really do need to save
-     */
-    dispatch({
-      type: "writable obs annotations - save started",
-    });
-
-    const df = await annoMatrix.fetch("obs", writableAnnotations(annoMatrix));
-    const matrix = MatrixFBS.encodeMatrixFBS(df);
-    const compressedMatrix = pako.deflate(matrix);
-    try {
-      const queryString =
-        !dataCollectionNameIsReadOnly && !!dataCollectionName
-          ? `?annotation-collection-name=${encodeURIComponent(
-              dataCollectionName
-            )}`
-          : "";
-      const res = await fetch(
-        `${globals.API.prefix}${globals.API.version}annotations/obs${queryString}`,
-        {
-          method: "PUT",
-          body: compressedMatrix,
-          headers: new Headers({
-            "Content-Type": "application/octet-stream",
-          }),
-          credentials: "include",
-        }
-      );
-      if (res.ok) {
-        dispatch({
-          type: "writable obs annotations - save complete",
-          lastSavedAnnoMatrix: annoMatrix,
-        });
-      } else {
-        dispatch({
-          type: "writable obs annotations - save error",
-          message: `HTTP error ${res.status} - ${res.statusText}`,
-          res,
-        });
-      }
-    } catch (error) {
-      if (error instanceof Error)
-        dispatch({
-          type: "writable obs annotations - save error",
-          message: error.toString(),
-          error,
-        });
-    }
-  };
-
-export const saveGenesetsAction =
-  () =>
-  async (dispatch: AppDispatch, getState: GetState): Promise<unknown> => {
-    if (!globals.API) throw new Error("API not set");
-    const state = getState();
-
-    // bail if gene sets not available, or in readonly mode.
-    const { config } = state;
-    const { lastTid, genesets } = state.genesets;
-
-    const genesetsAreAvailable =
-      config?.parameters?.annotations_genesets ?? false;
-    const genesetsReadonly =
-      config?.parameters?.annotations_genesets_readonly ?? true;
-    if (!genesetsAreAvailable || genesetsReadonly) {
-      // our non-save was completed!
-      return dispatch({
-        type: "autosave: genesets complete",
-        lastSavedGenesets: genesets,
-      });
-    }
-
-    dispatch({
-      type: "autosave: genesets started",
-    });
-
-    /* Create the JSON OTA data structure */
-    const tid = (lastTid ?? 0) + 1;
-    const genesetsOTA = [];
-    for (const [name, gs] of genesets) {
-      const genes = [];
-      for (const g of gs.genes.values()) {
-        genes.push({
-          gene_symbol: g.geneSymbol,
-          gene_description: g.geneDescription,
-        });
-      }
-      genesetsOTA.push({
-        geneset_name: name,
-        geneset_description: gs.genesetDescription,
-        genes,
-      });
-    }
-    const ota = {
-      tid,
-      genesets: genesetsOTA,
-    };
-
-    /* Save to server */
-    try {
-      const { dataCollectionNameIsReadOnly, dataCollectionName } =
-        state.annotations;
-      const queryString =
-        !dataCollectionNameIsReadOnly && !!dataCollectionName
-          ? `?annotation-collection-name=${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 await Promise.all([
-        dispatch({
-          type: "autosave: genesets complete",
-          lastSavedGenesets: genesets,
-        }),
-        dispatch({
-          type: "geneset: set tid",
-          tid,
-        }),
-      ]);
-    } catch (error) {
-      if (error instanceof Error)
-        return dispatch({
-          type: "autosave: genesets error",
-          message: error.toString(),
-          error,
-        });
-      return dispatch({
-        type: "autosave: genesets error",
-        error,
-      });
-    }
-  };

client/src/actions/index.ts

@@ -504,8 +504,6 @@ export default {
     annoActions.annotationDeleteLabelFromCategory,
   annotationRenameLabelInCategory: annoActions.annotationRenameLabelInCategory,
   annotationLabelCurrentSelection: annoActions.annotationLabelCurrentSelection,
-  saveObsAnnotationsAction: annoActions.saveObsAnnotationsAction,
-  saveGenesetsAction: annoActions.saveGenesetsAction,
   needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
   layoutChoiceAction: embActions.layoutChoiceAction,
   setCellSetFromSelection: selnActions.setCellSetFromSelection,

client/src/common/types/entities.ts

@@ -15,17 +15,13 @@ export const STANDARD_CATEGORY_NAMES = [
   "disease_ontology_term_id",
   "ethnicity",
   "ethnicity_ontology_term_id",
-  "self_reported_ethnicity",
-  "self_reported_ethnicity_ontology_term_id",
   "is_primary_data",
   "organism",
   "organism_ontology_term_id",
   "sex_ontology_term_id",
   "sex",
   "tissue_ontology_term_id",
   "tissue",
-  "suspension_type",
-  "donor_id",
 ];
 
 /**

client/src/components/app.tsx

@@ -16,7 +16,6 @@ import RightSideBar from "./rightSidebar";
 import Legend from "./continuousLegend";
 import Graph from "./graph/graph";
 import MenuBar from "./menubar";
-import Autosave from "./autosave";
 import Embedding from "./embedding";
 
 import actions from "../actions";
@@ -79,7 +78,6 @@ class App extends React.Component<Props> {
                       </Controls>
                       <Embedding />
                       <FloatingButton baseUrl={baseUrl} />
-                      <Autosave />
                       <Legend />
                       <Graph
                         // eslint-disable-next-line @typescript-eslint/ban-ts-comment -- FIXME: added to solve linting error with ts-ignore