feat: 5673 cell guide tissue specific cell type route

frontend/__snapshots__/tests/features/cellGuide/cellGuide.test.ts-snapshots/tissue-specific-cellType-seoMetaTags-chromium-darwin.txt

@@ -0,0 +1 @@
+["<meta charset=\"utf-8\">","<meta id=\"newsletter-signup-meta\" name=\"viewport\" content=\"width=device-width, initial-scale=1, maximum-scale=1\">","<meta name=\"description\" content=\"Find comprehensive information about brain specific &quot;neuron&quot; cell types (synonyms: nerve cell). Neurons: Essential cells in the nervous system responsible for receiving, processing, and transmitting information, enabling vital body functions.\">","<meta name=\"next-head-count\" content=\"17\">","<meta name=\"theme-color\" content=\"#000000\">","<meta property=\"og:creator\" content=\"@cziscience\">","<meta property=\"og:description\" content=\"Find comprehensive information about brain specific &quot;neuron&quot; cell types (synonyms: nerve cell). Neurons: Essential cells in the nervous system responsible for receiving, processing, and transmitting information, enabling vital body functions.\">","<meta property=\"og:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"og:site\" content=\"@cziscience\">","<meta property=\"og:site_name\" content=\"Cellxgene Data Portal\">","<meta property=\"og:title\" content=\"Brain Specific Neuron Cell Types - CZ CELLxGENE CellGuide\">","<meta property=\"og:type\" content=\"website\">","<meta property=\"og:url\" content=\"https://cellxgene.cziscience.com/\">","<meta property=\"title\" content=\"Brain Specific Neuron Cell Types - CZ CELLxGENE CellGuide\">","<meta property=\"twitter:card\" content=\"summary\">","<meta property=\"twitter:description\" content=\"Find comprehensive information about brain specific &quot;neuron&quot; cell types (synonyms: nerve cell). Neurons: Essential cells in the nervous system responsible for receiving, processing, and transmitting information, enabling vital body functions.\">","<meta property=\"twitter:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"twitter:title\" content=\"Brain Specific Neuron Cell Types - CZ CELLxGENE CellGuide\">"]

frontend/__snapshots__/tests/features/cellGuide/cellGuide.test.ts-snapshots/tissue-specific-cellType-seoMetaTags-chromium-linux.txt

@@ -0,0 +1 @@
+["<meta charset=\"utf-8\">","<meta id=\"newsletter-signup-meta\" name=\"viewport\" content=\"width=device-width, initial-scale=1, maximum-scale=1\">","<meta name=\"description\" content=\"Find comprehensive information about brain specific &quot;neuron&quot; cell types (synonyms: nerve cell). Neurons: Essential cells in the nervous system responsible for receiving, processing, and transmitting information, enabling vital body functions.\">","<meta name=\"next-head-count\" content=\"17\">","<meta name=\"theme-color\" content=\"#000000\">","<meta property=\"og:creator\" content=\"@cziscience\">","<meta property=\"og:description\" content=\"Find comprehensive information about brain specific &quot;neuron&quot; cell types (synonyms: nerve cell). Neurons: Essential cells in the nervous system responsible for receiving, processing, and transmitting information, enabling vital body functions.\">","<meta property=\"og:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"og:site\" content=\"@cziscience\">","<meta property=\"og:site_name\" content=\"Cellxgene Data Portal\">","<meta property=\"og:title\" content=\"Brain Specific Neuron Cell Types - CZ CELLxGENE CellGuide\">","<meta property=\"og:type\" content=\"website\">","<meta property=\"og:url\" content=\"https://cellxgene.cziscience.com/\">","<meta property=\"title\" content=\"Brain Specific Neuron Cell Types - CZ CELLxGENE CellGuide\">","<meta property=\"twitter:card\" content=\"summary\">","<meta property=\"twitter:description\" content=\"Find comprehensive information about brain specific &quot;neuron&quot; cell types (synonyms: nerve cell). Neurons: Essential cells in the nervous system responsible for receiving, processing, and transmitting information, enabling vital body functions.\">","<meta property=\"twitter:image\" content=\"https://cellxgene.cziscience.com/open-graph.jpg\">","<meta property=\"twitter:title\" content=\"Brain Specific Neuron Cell Types - CZ CELLxGENE CellGuide\">"]

frontend/src/common/constants/routes.ts

@@ -16,5 +16,8 @@ export enum ROUTES {
   WMG_DOCS_DATA_PROCESSING = "/docs/04__Analyze%20Public%20Data/4_2__Gene%20Expression%20Documentation/4_2_3__Gene%20Expression%20Data%20Processing",
   SITEMAP = "/sitemap",
   CELL_GUIDE = "/cellguide",
+  CELL_GUIDE_CELL_TYPE = "/cellguide/:cellTypeId",
+  CELL_GUIDE_TISSUE = "/cellguide/tissues/:tissueId",
+  CELL_GUIDE_TISSUE_SPECIFIC_CELL_TYPE = "/cellguide/tissues/:tissueId/cell-types/:cellTypeId",
   DEPLOYED_VERSION = "/api/deployed_version",
 }

frontend/src/common/queries/cellGuide.ts

@@ -472,20 +472,33 @@ export const fetchTissueMetadata =
   };
 
 /* ========== Lookup tables for organs ========== */
-export function useAllOrgansLookupTables(): Map<string, string> {
-  const { data: allOrgansData } = useTissueMetadata();
+export function useAllOrgansLookupTables(): {
+  data: Map<string, string>;
+  isSuccess: boolean;
+} {
+  /**
+   * (thuang): Expose `isSuccess`, so `CellGuide/components/CellGuideCard/connect.ts`
+   * can use it to determine if the data is ready and determine if the user should
+   * be redirected to the tissue agnostic cell type page.
+   */
+  const { data: allOrgansData, isSuccess } = useTissueMetadata();
+
   return useMemo(() => {
     if (!allOrgansData) {
-      return new Map<string, string>();
+      return { data: new Map<string, string>(), isSuccess };
     }
 
     const allOrgansLabelToIdMap = new Map<string, string>();
     for (const organId in allOrgansData) {
       const organData = allOrgansData[organId];
       allOrgansLabelToIdMap.set(organData.name, organData.id);
     }
-    return allOrgansLabelToIdMap;
-  }, [allOrgansData]);
+
+    return {
+      data: allOrgansLabelToIdMap,
+      isSuccess,
+    };
+  }, [allOrgansData, isSuccess]);
 }
 
 /* ========== Lookup tables for tissues ========== */

frontend/src/pages/cellguide/[cellTypeId].tsx

@@ -1,3 +1,11 @@
+/**
+ * IMPORTANT(thuang): `frontend/src/pages/cellguide/tissues/[tissueId]/cell-types/[cellTypeId].tsx`
+ * imports the exports from this file, since both routes use the same components.
+ * If we export more things from this file, we need to export them from the other file as well,
+ * to make sure that /cellguide/tissues/[tissueId]/cell-types/[cellTypeId] route continue
+ * to work.
+ */
+
 import { GetServerSideProps, InferGetServerSidePropsType } from "next";
 import CellGuideCard from "src/views/CellGuide/components/CellGuideCard";
 import {

frontend/src/pages/cellguide/tissues/[tissueId]/cell-types/[cellTypeId].tsx

@@ -0,0 +1,9 @@
+/**
+ * IMPORTANT(thuang): Make sure the exports from this file is in sync with
+ * frontend/src/pages/cellguide/[cellTypeId].tsx
+ */
+
+import Page, { getServerSideProps } from "src/pages/cellguide/[cellTypeId]";
+
+export default Page;
+export { getServerSideProps };

frontend/src/views/CellGuide/common/utils.ts

@@ -28,3 +28,32 @@ export function filterDescendantsOfAncestorTissueId(
 
   return tissueIdList.filter((value) => descendantSet.has(value));
 }
+
+import { ROUTES } from "src/common/constants/routes";
+import { NO_ORGAN_ID } from "src/views/CellGuide/components/CellGuideCard/components/MarkerGeneTables/constants";
+
+export function getCellTypeLink({
+  /**
+   * (thuang): `queryTissueId` can be undefined when a user is on `/cellguide/:cellTypeId` route
+   * instead of `/cellguide/tissues/:tissueId/cell-types/:cellTypeId` route.
+   *
+   * NOTE: `tissue` and `organ` in variable names are interchangeable here.
+   */
+  tissueId = NO_ORGAN_ID,
+  cellTypeId,
+}: {
+  tissueId: string;
+  cellTypeId: string;
+}) {
+  const urlCellTypeId = cellTypeId.replace(":", "_") ?? "";
+  const urlTissueId = tissueId.replace(":", "_") || NO_ORGAN_ID;
+
+  if (tissueId === NO_ORGAN_ID) {
+    return ROUTES.CELL_GUIDE_CELL_TYPE.replace(":cellTypeId", urlCellTypeId);
+  } else {
+    return ROUTES.CELL_GUIDE_TISSUE_SPECIFIC_CELL_TYPE.replace(
+      ":tissueId",
+      urlTissueId
+    ).replace(":cellTypeId", urlCellTypeId);
+  }
+}

frontend/src/views/CellGuide/components/CellGuideCard/components/MarkerGeneTables/hooks/common.ts

@@ -18,10 +18,14 @@ import { ALL_TISSUES, HOMO_SAPIENS, NO_ORGAN_ID } from "../constants";
 export function useOrganAndOrganismFilterListForCellType(cellTypeId: string): {
   organsMap: Map<string, string>;
   organismsList: string[];
+  isSuccess: boolean;
 } {
-  const { data: computationalMarkers } = useComputationalMarkers(cellTypeId);
+  const {
+    data: computationalMarkers,
+    isSuccess: isComputationalMarkersSuccess,
+  } = useComputationalMarkers(cellTypeId);
 
-  const organLabelToIdMap = useAllOrgansLookupTables();
+  const { data: organLabelToIdMap, isSuccess } = useAllOrgansLookupTables();
 
   // eslint-disable-next-line sonarjs/cognitive-complexity
   return useMemo(() => {
@@ -66,6 +70,17 @@ export function useOrganAndOrganismFilterListForCellType(cellTypeId: string): {
     return {
       organsMap: sortedFilteredOrganMap,
       organismsList: sortedOrganismList,
+      /**
+       * (thuang): Expose `isSuccess`, so `CellGuide/components/CellGuideCard/connect.ts`
+       * can use it to determine if the data is ready and determine if the user should
+       * be redirected to the tissue agnostic cell type page.
+       */
+      isSuccess: isComputationalMarkersSuccess && isSuccess,
     };
-  }, [computationalMarkers, organLabelToIdMap]);
+  }, [
+    computationalMarkers,
+    organLabelToIdMap,
+    isSuccess,
+    isComputationalMarkersSuccess,
+  ]);
 }

frontend/src/views/CellGuide/components/CellGuideCard/connect.ts

@@ -0,0 +1,166 @@
+import { DefaultDropdownMenuOption } from "@czi-sds/components";
+import { throttle } from "lodash";
+import { useRouter } from "next/router";
+import { useState, useRef, useCallback, useMemo, useEffect } from "react";
+import { ROUTES } from "src/common/constants/routes";
+import {
+  ALL_TISSUES,
+  NO_ORGAN_ID,
+  TISSUE_AGNOSTIC,
+} from "src/views/CellGuide/components/CellGuideCard/components/MarkerGeneTables/constants";
+import { useOrganAndOrganismFilterListForCellType } from "src/views/CellGuide/components/CellGuideCard/components/MarkerGeneTables/hooks/common";
+import { SKINNY_MODE_BREAKPOINT_WIDTH } from "src/views/CellGuide/components/CellGuideCard/constants";
+import { LEFT_RIGHT_PADDING_PX_XXL } from "src/views/CellGuide/components/CellGuideCard/style";
+import { SDSOrgan } from "src/views/CellGuide/components/CellGuideCard/types";
+import { CellType } from "src/views/CellGuide/components/common/OntologyDagView/common/types";
+import { Gene } from "src/views/WheresMyGeneV2/common/types";
+
+export function useConnect() {
+  const router = useRouter();
+
+  const [pageNavIsOpen, setPageNavIsOpen] = useState(false);
+  const [selectedGene, setSelectedGene] = useState<string | undefined>(
+    undefined
+  );
+
+  const [skinnyMode, setSkinnyMode] = useState<boolean>(false);
+
+  // Navigation
+  const sectionRef0 = useRef<HTMLDivElement>(null);
+  const sectionRef1 = useRef<HTMLDivElement>(null);
+  const sectionRef2 = useRef<HTMLDivElement>(null);
+  const sectionRef3 = useRef<HTMLDivElement>(null);
+
+  const selectGene = useCallback(
+    (gene: string) => {
+      if (gene === selectedGene) {
+        setSelectedGene(undefined);
+      } else {
+        setSelectedGene(gene);
+        if (sectionRef1.current) {
+          window.scrollTo({
+            top:
+              sectionRef1.current.getBoundingClientRect().top +
+              window.scrollY -
+              50,
+            behavior: "smooth",
+          });
+        }
+      }
+    },
+    [selectedGene]
+  );
+
+  // Set the mobile tooltip view content
+  const [tooltipContent, setTooltipContent] = useState<{
+    title: string;
+    element: JSX.Element;
+  } | null>(null);
+
+  const { cellTypeId: queryCellTypeId, tissueId: queryTissueId } = router.query;
+  const cellTypeId = (queryCellTypeId as string)?.replace("_", ":") ?? "";
+
+  /**
+   * (thuang): `queryTissueId` can be undefined when a user is on `/cellguide/:cellTypeId` route
+   * instead of `/cellguide/tissues/:tissueId/cell-types/:cellTypeId` route.
+   *
+   * NOTE: `tissue` and `organ` in variable names are interchangeable here.
+   */
+  const tissueId = (queryTissueId as string)?.replace("_", ":") || NO_ORGAN_ID;
+
+  const handleResize = useCallback(() => {
+    setSkinnyMode(
+      window.innerWidth <
+        SKINNY_MODE_BREAKPOINT_WIDTH + 2 * LEFT_RIGHT_PADDING_PX_XXL
+    );
+  }, [setSkinnyMode]);
+
+  const throttledHandleResize = useMemo(() => {
+    return throttle(handleResize, 100);
+  }, [handleResize]);
+
+  useEffect(() => {
+    throttledHandleResize();
+    window.addEventListener("resize", throttledHandleResize);
+
+    return () => window.removeEventListener("resize", throttledHandleResize);
+  }, [throttledHandleResize]);
+
+  const [geneInfoGene, setGeneInfoGene] = useState<Gene["name"] | null>(null);
+  const [cellInfoCellType, setCellInfoCellType] = useState<CellType | null>(
+    null
+  );
+
+  const { organismsList, organsMap, isSuccess } =
+    useOrganAndOrganismFilterListForCellType(cellTypeId);
+
+  const sdsOrganismsList = useMemo(
+    () =>
+      organismsList.map((organism) => ({
+        name: organism,
+      })),
+    [organismsList]
+  );
+
+  const sdsOrgansList = useMemo<SDSOrgan[]>(
+    () =>
+      Array.from(organsMap).map(([name, id]) => ({
+        name: name === ALL_TISSUES ? TISSUE_AGNOSTIC : name,
+        id,
+      })),
+    [organsMap]
+  );
+
+  const selectedOrgan = sdsOrgansList.find((organ) => organ.id === tissueId);
+
+  /**
+   * (thuang): Push the user to tissue agnostic cell type page if the user is on
+   * a tissue-specific cell type page and the tissue is not in the filter list.
+   */
+  useEffect(() => {
+    if (isSuccess && tissueId !== NO_ORGAN_ID && !selectedOrgan) {
+      router.replace(
+        ROUTES.CELL_GUIDE_CELL_TYPE.replace(
+          ":cellTypeId",
+          queryCellTypeId as string
+        )
+      );
+    }
+  }, [queryCellTypeId, router, selectedOrgan, tissueId, isSuccess]);
+
+  const [selectedOrganism, setSelectedOrganism] =
+    useState<DefaultDropdownMenuOption>(sdsOrganismsList[0]);
+
+  useEffect(() => {
+    setSelectedGene(undefined);
+  }, [selectedOrgan, selectedOrganism, setSelectedGene]);
+
+  return {
+    router,
+    pageNavIsOpen,
+    setPageNavIsOpen,
+    selectedGene,
+    sectionRef0,
+    sectionRef1,
+    sectionRef2,
+    sectionRef3,
+    skinnyMode,
+    selectGene,
+    tooltipContent,
+    setTooltipContent,
+    queryCellTypeId,
+    cellTypeId,
+    geneInfoGene,
+    setGeneInfoGene,
+    cellInfoCellType,
+    setCellInfoCellType,
+    organismsList,
+    organsMap,
+    sdsOrganismsList,
+    sdsOrgansList,
+    selectedOrgan,
+    selectedOrganId: tissueId,
+    selectedOrganism,
+    setSelectedOrganism,
+  };
+}