TS Revert (1) (#2402)

* revert all commits to before Typescript migration * update compat workflow to match latest deps (#2335) * update compat workflow to match latest deps * attempt to debug * attempt to debug * remove debugging code * typo * update deps to match desktop (#2340) * fix: don't run lint with `--fix` on push tests (#2273) * fix: don't run lint with `--fix` on push tests * npx Co-authored-by: maniarathi <mani.arathi@gmail.com> Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com> * rename X_approx_distribution to X_approximate_distribution (#2337) * Correctly handle non-finite numbers in heuristic determination of X distribution (#2342) * handle non-finites explicitly * improve and test edge case handling for distribution estimation * revert debugging changes * code readability * clean up type inferencing (#2332) * unit tests for 64 bit conversion * clean up type handling * type inference tests * more type inference fixes * use schema to determine user intent for data typing * stop using deprecated API * fbs type encoding test * add missing test * add more tests * correctly infer X type for CXG adaptor * lint * fix typo * ts migration * cleanup from PR review * lint * PR review changes * remove unused packages from client (#2359) * remove unused packages from client * add missing peer dep * fix: disable FE auth testing on compatibility tests (#2377) * update: release process (#2277) Co-authored-by: maniarathi <mani.arathi@gmail.com> * fix: remove spaces in param setup (#2380) * delete deploy workflow (#2396) * undo reformatting which now does not pass lint * fix snapshots which changed due to npm dep changes * add missing quoting to snapshot * another snapshot typo fix * TS Revert (2) - replay PR #2347 and #2354 (#2403) * replay edits from PR 2347 * TS Revert (3) - replay edits in PR #2327 (#2404) * replay edits in PR 2327 * TS Revert (4) - replay PR #2355 (#2405) * replay edits in PR 2355 * add additional babel config * reformat with new prettier config Co-authored-by: Severiano Badajoz <sbadajoz@chanzuckerberg.com> Co-authored-by: maniarathi <mani.arathi@gmail.com> Co-authored-by: Madison Dunitz <madison.dunitz@chanzuckerberg.com>
2026-10-01 14:38:13 +08:00 · 2021-08-23 15:01:36 -07:00
parent 295590a7c6
commit eaae6df5e3
253 changed files with 11175 additions and 22271 deletions
@@ -0,0 +1,287 @@
+import * as globals from "../globals";
+import { AnnoMatrixLoader, AnnoMatrixObsCrossfilter } from "../annoMatrix";
+import {
+  catchErrorsWrap,
+  doJsonRequest,
+  dispatchNetworkErrorMessageToUser,
+} from "../util/actionHelpers";
+import { loadUserColorConfig } from "../util/stateManager/colorHelpers";
+import * as selnActions from "./selection";
+import * as annoActions from "./annotation";
+import * as viewActions from "./viewStack";
+import * as embActions from "./embedding";
+import * as genesetActions from "./geneset";
+
+function setGlobalConfig(config) {
+  /**
+   * Set any global run-time config not _exclusively_ managed by the config reducer.
+   * This should only set fields defined in globals.globalConfig.
+   */
+  globals.globalConfig.maxCategoricalOptionsToDisplay =
+    config?.parameters?.["max-category-items"] ??
+    globals.globalConfig.maxCategoricalOptionsToDisplay;
+}
+
+/*
+return promise fetching user-configured colors
+*/
+async function userColorsFetchAndLoad(dispatch) {
+  return fetchJson("colors").then((response) =>
+    dispatch({
+      type: "universe: user color load success",
+      userColors: loadUserColorConfig(response),
+    })
+  );
+}
+
+async function schemaFetch() {
+  return fetchJson("schema");
+}
+
+async function configFetch(dispatch) {
+  return fetchJson("config").then((response) => {
+    const config = { ...globals.configDefaults, ...response.config };
+
+    setGlobalConfig(config);
+
+    dispatch({
+      type: "configuration load complete",
+      config,
+    });
+    return config;
+  });
+}
+
+async function userInfoFetch(dispatch) {
+  return fetchJson("userinfo").then((response) => {
+    const { userinfo: userInfo } = response || {};
+    dispatch({
+      type: "userInfo load complete",
+      userInfo,
+    });
+    return userInfo;
+  });
+}
+
+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
+  */
+  const { schema } = annoMatrix;
+  const available = schema.layout.obs.map((v) => v.name);
+  available.forEach((embName) => annoMatrix.prefetch("emb", embName));
+}
+
+/*
+Application bootstrap
+*/
+const doInitialDataLoad = () =>
+  catchErrorsWrap(async (dispatch) => {
+    dispatch({ type: "initial data load start" });
+
+    try {
+      const [config, schema] = await Promise.all([
+        configFetch(dispatch),
+        schemaFetch(dispatch),
+        userColorsFetchAndLoad(dispatch),
+        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);
+      prefetchEmbeddings(annoMatrix);
+
+      dispatch({
+        type: "annoMatrix: init complete",
+        annoMatrix,
+        obsCrossfilter,
+      });
+      dispatch({ type: "initial data load complete" });
+
+      const defaultEmbedding = config?.parameters?.default_embedding;
+      const layoutSchema = schema?.schema?.layout?.obs ?? [];
+      if (
+        defaultEmbedding &&
+        layoutSchema.some((s) => s.name === defaultEmbedding)
+      ) {
+        dispatch(embActions.layoutChoiceAction(defaultEmbedding));
+      }
+    } catch (error) {
+      dispatch({ type: "initial data load error", error });
+    }
+  }, true);
+
+function requestSingleGeneExpressionCountsForColoringPOST(gene) {
+  return {
+    type: "color by expression",
+    gene,
+  };
+}
+
+const requestUserDefinedGene = (gene) => ({
+  type: "request user defined gene success",
+  data: {
+    genes: [gene],
+  },
+});
+
+const dispatchDiffExpErrors = (dispatch, response) => {
+  switch (response.status) {
+    case 403:
+      dispatchNetworkErrorMessageToUser(
+        "Too many cells selected for differential experesion calculation - please make a smaller selection."
+      );
+      break;
+    case 501:
+      dispatchNetworkErrorMessageToUser(
+        "Differential expression is not implemented."
+      );
+      break;
+    default: {
+      const msg = `Unexpected differential expression HTTP response ${response.status}, ${response.statusText}`;
+      dispatchNetworkErrorMessageToUser(msg);
+      dispatch({
+        type: "request differential expression error",
+        error: new Error(msg),
+      });
+    }
+  }
+};
+
+const requestDifferentialExpression =
+  (set1, set2, num_genes = 50) =>
+  async (dispatch, getState) => {
+    dispatch({ type: "request differential expression started" });
+    try {
+      /*
+    Steps:
+    1. get the most differentially expressed genes
+    2. get expression data for each
+    */
+      const { annoMatrix } = getState();
+      const varIndexName = annoMatrix.schema.annotations.var.index;
+
+      // Legal values are null, Array or TypedArray.  Null is initial state.
+      if (!set1) set1 = [];
+      if (!set2) set2 = [];
+
+      // These lines ensure that we convert any TypedArray to an Array.
+      // This is necessary because JSON.stringify() does some very strange
+      // things with TypedArrays (they are marshalled to JSON objects, rather
+      // than being marshalled as a JSON array).
+      set1 = Array.isArray(set1) ? set1 : Array.from(set1);
+      set2 = Array.isArray(set2) ? set2 : Array.from(set2);
+
+      const res = await fetch(
+        `${globals.API.prefix}${globals.API.version}diffexp/obs`,
+        {
+          method: "POST",
+          headers: new Headers({
+            Accept: "application/json",
+            "Content-Type": "application/json",
+          }),
+          body: JSON.stringify({
+            mode: "topN",
+            count: num_genes,
+            set1: { filter: { obs: { index: set1 } } },
+            set2: { filter: { obs: { index: set2 } } },
+          }),
+          credentials: "include",
+        }
+      );
+
+      if (!res.ok || res.headers.get("Content-Type") !== "application/json") {
+        return dispatchDiffExpErrors(dispatch, res);
+      }
+
+      const response = await res.json();
+      const varIndex = await annoMatrix.fetch("var", varIndexName);
+      const diffexpLists = { negative: [], positive: [] };
+      for (const polarity of Object.keys(diffexpLists)) {
+        diffexpLists[polarity] = response[polarity].map((v) => [
+          varIndex.at(v[0], varIndexName),
+          ...v.slice(1),
+        ]);
+      }
+
+      /* then send the success case action through */
+      return dispatch({
+        type: "request differential expression success",
+        data: diffexpLists,
+      });
+    } catch (error) {
+      return dispatch({
+        type: "request differential expression error",
+        error,
+      });
+    }
+  };
+
+function fetchJson(pathAndQuery) {
+  return doJsonRequest(
+    `${globals.API.prefix}${globals.API.version}${pathAndQuery}`
+  );
+}
+
+export default {
+  doInitialDataLoad,
+  requestDifferentialExpression,
+  requestSingleGeneExpressionCountsForColoringPOST,
+  requestUserDefinedGene,
+  selectContinuousMetadataAction: selnActions.selectContinuousMetadataAction,
+  selectCategoricalMetadataAction: selnActions.selectCategoricalMetadataAction,
+  selectCategoricalAllMetadataAction:
+    selnActions.selectCategoricalAllMetadataAction,
+  graphBrushStartAction: selnActions.graphBrushStartAction,
+  graphBrushChangeAction: selnActions.graphBrushChangeAction,
+  graphBrushDeselectAction: selnActions.graphBrushDeselectAction,
+  graphBrushCancelAction: selnActions.graphBrushCancelAction,
+  graphBrushEndAction: selnActions.graphBrushEndAction,
+  graphLassoStartAction: selnActions.graphLassoStartAction,
+  graphLassoEndAction: selnActions.graphLassoEndAction,
+  graphLassoCancelAction: selnActions.graphLassoCancelAction,
+  graphLassoDeselectAction: selnActions.graphLassoDeselectAction,
+  clipAction: viewActions.clipAction,
+  subsetAction: viewActions.subsetAction,
+  resetSubsetAction: viewActions.resetSubsetAction,
+  annotationCreateCategoryAction: annoActions.annotationCreateCategoryAction,
+  annotationRenameCategoryAction: annoActions.annotationRenameCategoryAction,
+  annotationDeleteCategoryAction: annoActions.annotationDeleteCategoryAction,
+  annotationCreateLabelInCategory: annoActions.annotationCreateLabelInCategory,
+  annotationDeleteLabelFromCategory:
+    annoActions.annotationDeleteLabelFromCategory,
+  annotationRenameLabelInCategory: annoActions.annotationRenameLabelInCategory,
+  annotationLabelCurrentSelection: annoActions.annotationLabelCurrentSelection,
+  saveObsAnnotationsAction: annoActions.saveObsAnnotationsAction,
+  saveGenesetsAction: annoActions.saveGenesetsAction,
+  needToSaveObsAnnotations: annoActions.needToSaveObsAnnotations,
+  layoutChoiceAction: embActions.layoutChoiceAction,
+  setCellSetFromSelection: selnActions.setCellSetFromSelection,
+  genesetDelete: genesetActions.genesetDelete,
+  genesetAddGenes: genesetActions.genesetAddGenes,
+  genesetDeleteGenes: genesetActions.genesetDeleteGenes,
+};