Merge branch 'main' into thuang-5397-next-upgrade

chanzuckerberg · Jan 18, 2024 · 0ca8504 · 0ca8504
2 parents b439453 + 0f05229
commit 0ca8504
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Showing 11 changed files with 53 additions and 123 deletions.
diff --git a/.github/workflows/rdev-tests.yml b/.github/workflows/rdev-tests.yml
@@ -16,8 +16,6 @@ jobs:
   functional-test:
     runs-on: ubuntu-22.04
     timeout-minutes: 30
-    needs:
-      - seed-wmg-cellguide-rdev
     steps:
       - name: Configure AWS Credentials
         uses: aws-actions/configure-aws-credentials@v4
@@ -37,29 +35,6 @@ jobs:
           pip3 install -r tests/functional/requirements.txt
           DEPLOYMENT_STAGE=rdev STACK_NAME=${{ env.STACK_NAME }} make functional-test
 
-  seed-wmg-cellguide-rdev:
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Configure AWS Credentials
-        uses: aws-actions/configure-aws-credentials@v4
-        with:
-          aws-region: us-west-2
-          role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }}
-          role-duration-seconds: 1800
-      - name: Checkout Repository
-        uses: actions/checkout@v2
-
-      - name: Grant Execute Permission to Bash Script
-        run: |
-          chmod +x ./scripts/populate_rdev_with_cellguide_data.sh ./scripts/populate_rdev_with_wmg_data.sh
-
-      - name: Seed cell guide data
-        run: |
-          ./scripts/populate_rdev_with_cellguide_data.sh ${{ env.STACK_NAME }}
-      - name: Seed WMG data
-        run: |
-          ./scripts/populate_rdev_with_wmg_data.sh ${{ env.STACK_NAME }}
-
   seed-database-e2e-tests:
     runs-on: ubuntu-22.04
     steps:
@@ -80,7 +55,6 @@ jobs:
 
   run-e2e-tests:
     needs:
-      - seed-wmg-cellguide-rdev
       - seed-database-e2e-tests
     timeout-minutes: 30
     name: e2e-tests ${{ matrix.project }} ${{ matrix.shardCurrent }} of ${{ matrix.shardTotal }}
@@ -224,7 +198,6 @@ jobs:
       run:
         working-directory: frontend
     needs:
-      - seed-wmg-cellguide-rdev
       - seed-database-e2e-tests
     steps:
       - uses: actions/setup-node@v2

diff --git a/.github/workflows/rdev-update-for-pr.yml b/.github/workflows/rdev-update-for-pr.yml
@@ -60,6 +60,29 @@ jobs:
       group: pr-${{ github.event.number }}-build
       cancel-in-progress: true
 
+  seed-wmg-cellguide-rdev:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Configure AWS Credentials
+        uses: aws-actions/configure-aws-credentials@v4
+        with:
+          aws-region: us-west-2
+          role-to-assume: ${{ secrets.AWS_ROLE_TO_ASSUME }}
+          role-duration-seconds: 1800
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - name: Grant Execute Permission to Bash Script
+        run: |
+          chmod +x ./scripts/populate_rdev_with_cellguide_data.sh ./scripts/populate_rdev_with_wmg_data.sh
+
+      - name: Seed cell guide data
+        run: |
+          ./scripts/populate_rdev_with_cellguide_data.sh ${{ env.STACK_NAME }}
+      - name: Seed WMG data
+        run: |
+          ./scripts/populate_rdev_with_wmg_data.sh ${{ env.STACK_NAME }}
+
   deploy-rdev:
     runs-on: ubuntu-22.04
     concurrency:
@@ -68,6 +91,7 @@ jobs:
     needs:
       - build_images
       - get_previous_image_digests
+      - seed-wmg-cellguide-rdev
     steps:
       - name: Configure AWS Credentials
         uses: aws-actions/configure-aws-credentials@v4

diff --git a/backend/wmg/data/ontology_labels.py b/backend/wmg/data/ontology_labels.py
@@ -17,8 +17,6 @@
     "genes_mus_musculus.csv.gz",
 ]
 
-SUFFIXES_TO_STRIP = ["organoid", "cell culture"]
-
 
 def ontology_term_label(ontology_term_id: str) -> Optional[str]:
     """
@@ -27,21 +25,7 @@ def ontology_term_label(ontology_term_id: str) -> Optional[str]:
     """
     global ontology_term_id_labels
 
-    # this catches the organoid tissue edge case (e.g. UBERON:0000995 (organoid)) or the cell culture edge case
-    # (e.g. CL:0000082 (cell culture))
-    suffix_to_strip = None
-    for suffix in SUFFIXES_TO_STRIP:
-        if suffix in ontology_term_id:
-            suffix_to_strip = suffix
-            break
-
-    if suffix_to_strip:
-        ontology_term_id = ontology_term_id.split(f"({suffix_to_strip})")[0].strip()
-    ontology_term_id_label = ontology_term_id_labels.get(ontology_term_id)
-    if suffix_to_strip:
-        ontology_term_id_label = ontology_term_id_label + f" ({suffix_to_strip})"
-
-    return ontology_term_id_label
+    return ontology_term_id_labels.get(ontology_term_id)
 
 
 def gene_term_label(gene_ontology_term_id: str) -> Optional[str]:

diff --git a/frontend/next.config.js b/frontend/next.config.js
@@ -20,8 +20,6 @@ const HUBSPOT_FORMS_URL = "https://forms.hsforms.com";
 
 const CROSS_REF_URL = "https://api.crossref.org";
 
-const DATADOG_URL = "browser-intake-datadoghq.com";
-
 const GOOGLE_FONTS_URL = "https://fonts.gstatic.com";
 
 const SCRIPT_SRC = [
@@ -47,7 +45,6 @@ const defaultSecureHeaders = {
         configs.CELLGUIDE_DATA_URL,
         configs.CENSUS_MODELS_DATA_URL,
         CROSS_REF_URL,
-        DATADOG_URL,
         GOOGLE_FONTS_URL,
       ],
       defaultSrc: ["'self'", HUBSPOT_FORMS_URL],

diff --git a/frontend/package-lock.json b/frontend/package-lock.json
diff --git a/frontend/package.json b/frontend/package.json
@@ -10,7 +10,6 @@
     "@blueprintjs/select": "^5.0.23",
     "@czi-sds/components": "^18.1.2",
     "@czi-sds/data-viz": "^0.3.0",
-    "@datadog/browser-rum": "^5.1.0",
     "@emotion/css": "^11.11.2",
     "@emotion/react": "^11.11.1",
     "@emotion/styled": "^11.11.0",

diff --git a/frontend/src/pages/_app.tsx b/frontend/src/pages/_app.tsx
@@ -1,6 +1,5 @@
 import { ThemeProvider as EmotionThemeProvider } from "@emotion/react";
 import { StyledEngineProvider, ThemeProvider } from "@mui/material/styles";
-import { datadogRum } from "@datadog/browser-rum";
 import { NextPage } from "next";
 import { AppProps } from "next/app";
 import Head from "next/head";
@@ -42,20 +41,6 @@ type AppPropsWithLayout = AppProps & {
   Component: NextPageWithLayout;
 };
 
-datadogRum.init({
-  applicationId: "44f77ca2-1482-404a-ad38-23499bb925e5",
-  clientToken: "pub55d4baaac2091f9656a83da732732a89",
-  site: "datadoghq.com",
-  service: "single-cell-data-portal",
-  env: process.env.NODE_ENV,
-  sessionSampleRate: 100,
-  sessionReplaySampleRate: 20,
-  trackUserInteractions: true,
-  trackResources: true,
-  trackLongTasks: true,
-  defaultPrivacyLevel: "mask-user-input",
-});
-
 function App({ Component, pageProps }: AppPropsWithLayout): JSX.Element {
   const Layout = Component.Layout || DefaultLayout;
 

diff --git a/frontend/src/views/CellGuide/components/CellGuideCard/components/Description/index.tsx b/frontend/src/views/CellGuide/components/CellGuideCard/components/Description/index.tsx
@@ -58,7 +58,7 @@ interface DescriptionProps {
   cellTypeName: string;
   cellTypeId: string;
   skinnyMode: boolean;
-  setTooltipContent: Dispatch<
+  setTooltipContent?: Dispatch<
     SetStateAction<{
       title: string;
       element: JSX.Element;
@@ -209,17 +209,19 @@ export default function Description({
           }}
           onClick={() => {
             skinnyMode &&
+              setTooltipContent &&
               setTooltipContent({
                 title: "ChatGPT Descriptions",
                 element: tooltipContent,
               });
           }}
           // only setting mobile Tooltip View on touch and not click
           onTouchEnd={() => {
-            setTooltipContent({
-              title: "ChatGPT Descriptions",
-              element: tooltipContent,
-            });
+            setTooltipContent &&
+              setTooltipContent({
+                title: "ChatGPT Descriptions",
+                element: tooltipContent,
+              });
           }}
         >
           <StyledIconImage alt="question mark" src={questionMarkIcon} />

diff --git a/frontend/src/views/WheresMyGeneV2/components/CellInfoSideBar/index.tsx b/frontend/src/views/WheresMyGeneV2/components/CellInfoSideBar/index.tsx
@@ -59,6 +59,7 @@ import {
   DivTableHead,
   DivTableRow,
 } from "../../common/styles";
+import Description from "src/views/CellGuide/components/CellGuideCard/components/Description";
 
 function CellInfoSideBar({
   cellInfoCellType,
@@ -91,6 +92,12 @@ function CellInfoSideBar({
   return (
     <>
       <TissueName>{tissueInfo.name}</TissueName>
+      <Description
+        cellTypeId={cellInfoCellType.cellType.id}
+        cellTypeName={cellInfoCellType.cellType.name}
+        skinnyMode={true}
+        inSideBar
+      />
       <Link
         href={`${ROUTES.CELL_GUIDE}/${cellInfoCellType.cellType.id}`}
         onClick={() =>
@@ -103,6 +110,7 @@ function CellInfoSideBar({
       >
         {MARKER_SCORE_CELLGUIDE_LINK_TEXT}
       </Link>
+
       <ButtonContainer>
         <ButtonWrapper>
           <StyledMarkerGeneHeader>{MARKER_GENE_LABEL}</StyledMarkerGeneHeader>

diff --git a/frontend/tests/features/wheresMyGene/wheresMyGene.test.ts b/frontend/tests/features/wheresMyGene/wheresMyGene.test.ts
@@ -53,6 +53,7 @@ import {
   SPECIFICITY_TOOLTIP_CONTENT_SECOND_HALF,
   SPECIFICITY_TOOLTIP_TEST_ID,
 } from "src/common/constants/markerGenes";
+import { CELL_GUIDE_CARD_GPT_DESCRIPTION } from "src/views/CellGuide/components/CellGuideCard/components/Description/constants";
 
 const HOMO_SAPIENS_TERM_ID = "NCBITaxon:9606";
 
@@ -335,6 +336,18 @@ describe("Where's My Gene", () => {
       expect(numGenes).toBeGreaterThan(0);
     });
 
+    test("Marker gene panel displays cell type description", async ({
+      page,
+    }) => {
+      await goToWMG(page);
+
+      await expandTissue(page, "lung");
+
+      await getCellTypeFmgButtonAndClick(page, "memory B cell");
+
+      await waitForElement(page, CELL_GUIDE_CARD_GPT_DESCRIPTION);
+    });
+
     // need to find a tissue, cell type with no marker genes
     test.skip("Cell types with no marker genes display warning", async ({
       page,

diff --git a/tests/unit/wmg_processing/test_ontology_labels.py b/tests/unit/wmg_processing/test_ontology_labels.py
@@ -18,8 +18,6 @@ def test__ontology_term_label(self):
             "MmusDv:0000000": "mouse life cycle stage",
             "MONDO:0000001": "disease",
             "UBERON:0002539": "pharyngeal arch",
-            "UBERON:0000995 (organoid)": "uterus (organoid)",
-            "CL:0000082 (cell culture)": "epithelial cell of lung (cell culture)",
         }
         for ontology_term_id, expected_ontology_term_label in test_cases.items():
             with self.subTest(ontology_term_id):