[Platform] Add metadata to variant page

README.md

@@ -26,7 +26,7 @@ As same as development, you can run `yarn build:platform` or `yarn build:genetic
 
 ## Copyright
 
-Copyright 2014-2018 Biogen, Celgene Corporation, EMBL - European Bioinformatics Institute, GlaxoSmithKline, Takeda Pharmaceutical Company and Wellcome Sanger Institute
+Copyright 2014-2024 EMBL - European Bioinformatics Institute, Genentech, GSK, MSD, Pfizer, Sanofi and Wellcome Sanger Institute
 
 This software was developed as part of the Open Targets project. For more information please see: http://www.opentargets.org
 

apps/platform/src/pages/VariantPage/Header.tsx

@@ -5,7 +5,7 @@ import { MetadataType } from "./types";
 type HeaderProps = {
   loading: boolean;
   metadata: MetadataType;
-}
+};
 
 function Header({ loading, metadata }: HeaderProps) {
   const {

apps/platform/src/pages/VariantPage/Profile.tsx

@@ -0,0 +1,13 @@
+import ProfileHeader from "./ProfileHeader";
+
+type ProfileProps = {
+  varId: string;
+};
+
+function Profile({ varId }: ProfileProps) {
+
+  return <ProfileHeader varId={varId} />
+
+}
+
+export default Profile;

apps/platform/src/pages/VariantPage/ProfileHeader.tsx

@@ -0,0 +1,111 @@
+import { useState, useEffect } from "react";
+import { Field, ProfileHeader as BaseProfileHeader } from "ui";
+import { Box, Typography } from "@mui/material";
+import { InSilicoPredictorsType, MetadataType } from "./types";
+
+type ProfileHeaderProps = {
+  varId: string;
+};
+
+function ProfileHeader({ varId }: ProfileHeaderProps) {
+
+  // temp: data will come from gql, fetch local json file for now
+  const [metadata, setMetadata] =
+    useState<MetadataType | "waiting" | undefined>("waiting");
+  useEffect(() => {
+    fetch("../data/variant-data-2.json")
+      .then(response => response.json())
+      .then((allData: MetadataType[]) =>
+        setMetadata(allData.find(v => v.variantId === varId)));
+  }, []);
+
+  // temp: always set loading to false for now
+  const loading = false;
+
+  // temp: revisit this (use same as other pages) once using gql to get data
+  if (!metadata) {
+    return <b>Metadata not found!</b>
+  } else if (metadata === "waiting") {
+    return <b>Waiting</b>;
+  }
+
+  return (
+    <BaseProfileHeader>
+
+      <Box>
+        <Typography variant="subtitle1" mt={0}>Location</Typography>
+        <Field loading={loading} title="GRCh38">
+          {metadata.chromosome}:{metadata.position}
+        </Field>
+        <Field loading={loading} title="Reference Allele">
+          {metadata.referenceAllele}
+        </Field>
+        <Field loading={loading} title="Alternative Allele (effect allele)">
+          {metadata.alternateAllele}
+        </Field>
+        <Typography variant="subtitle1" mt={1}>Variant Effect Predictor (VEP)</Typography>
+        <Field loading={loading} title="most severe consequence">
+          {metadata.vep.mostSevereConsequence.replace(/_/g, ' ')}
+        </Field>
+        <Typography variant="subtitle1" mt={1}>Insilico predictors</Typography>
+        {
+          Object.keys(metadata.inSilicoPredictors).map(key => (key === 'cadd'
+            ? <>
+                <Field key={key} loading={loading} title={key}>&nbsp;</Field>
+                <Box ml={2}>
+                <Field loading={loading} title="phred">
+                  {metadata.inSilicoPredictors.cadd!.phred}
+                </Field>
+                <Field loading={loading} title="raw">
+                  {metadata.inSilicoPredictors.cadd!.raw}
+                </Field>
+                </Box>
+              </>
+            : <Field key={key} loading={loading} title={key}>
+                {String(metadata.inSilicoPredictors[key as keyof InSilicoPredictorsType])}
+              </Field>
+          ))
+        }
+      </Box>
+
+      <Box>
+        <Typography variant="subtitle2">Population Allele Frequencies</Typography>
+        <table>
+          {metadata.alleleFrequencies
+            .map(({populationName, alleleFrequency }) => (
+              <tr key={populationName}>
+                <td style={{padding: '0 2em 0 0'}}>
+                  <Typography variant="body2" lineHeight={1.35}>
+                    {populationLabels[populationName as keyof typeof populationLabels]}
+                  </Typography>
+                </td>
+                <td style={{padding: 0}}>
+                  <Typography variant="body2" align="right" lineHeight={1}>
+                    {alleleFrequency.toFixed(3)}
+                  </Typography>
+                </td>
+              </tr>
+            ))
+          }
+        </table>
+      </Box>
+
+    </BaseProfileHeader>
+  )
+}
+
+export default ProfileHeader;
+
+// !! NEEDS CHECKED SINCE DIFFERENT KEYS TO THOSE USED ON CURRENT VARIANT PAGE
+const populationLabels = {
+  afr_adj: 'African/African-American',
+  amr_adj: 'Latino/Admixed American',
+  asj_adj: 'Ashkenazi Jewish',
+  eas_adj: 'East Asian',
+  fin_adj: 'Finnish',
+  nfe_adj: 'Non-Finnish European',
+  ami_adj: 'Non-Finnish European Estonian',
+  mid_adj: 'Non-Finnish European North-Western European',
+  sas_adj: 'Non-Finnish European Southern European',
+  remaining_adj: 'Other (population not assigned)',
+};

apps/platform/src/pages/VariantPage/VariantPage.tsx

@@ -1,34 +1,40 @@
-
-import { useState, useEffect } from "react";
-import { useLocation, useParams } from "react-router-dom";
-import { BasePage } from "ui";
+import { useState, useEffect, lazy, Suspense } from "react";
+import {
+  useLocation,
+  useParams,
+  Switch,
+  Route,
+  useRouteMatch,
+  Link,
+} from "react-router-dom";
+import { Box, Tabs, Tab } from "@mui/material";
+import { BasePage, ScrollToTop, LoadingBackdrop } from "ui";
 import Header from "./Header";
 import NotFoundPage from "../NotFoundPage";
 import { MetadataType } from "./types";
 
-// const Profile = lazy(() => import("./Profile"));
+const Profile = lazy(() => import("./Profile"));
 
 function VariantPage() {
   const location = useLocation();
   const { varId } = useParams() as { varId: string };
-  const [metadata, setMetadata] =
-    useState<MetadataType | 'waiting' | undefined>('waiting');
-
-  // temp: loading is set by useQuery, set to false for now
-  const loading = false;
+  const { path } = useRouteMatch();
 
   // temp: data will come from gql, fetch local json file for now
-  useEffect(() => {
-    fetch('../data/variant-data-2.json')
-      .then(response => response.json())
-      .then((allData: MetadataType[]) =>
-        setMetadata(allData.find(v => v.variantId === varId)));
-  }, []);
+  const [metadata, setMetadata] = useState<MetadataType | "waiting" | undefined>("waiting");
+   useEffect(() => {
+      fetch("../data/variant-data-2.json")
+        .then(response => response.json())
+        .then((allData: MetadataType[]) => setMetadata(allData.find(v => v.variantId === varId)));
+    }, []);
+
+    // temp: loading is set by useQuery, set to false for now
+  const loading = false;
 
   // temp: revisit this (use same as other pages) once using gql to get data
   if (!metadata) {
     return <NotFoundPage />;
-  } else if (metadata === 'waiting') {
+  } else if (metadata === "waiting") {
     return <b>Waiting</b>;
   }
 
@@ -39,8 +45,31 @@ function VariantPage() {
       location={location}
     >
       <Header loading={loading} metadata={metadata} />
+      <ScrollToTop />
+      <Route
+        path="/"
+        render={history => (
+          <Box sx={{ borderBottom: 1, borderColor: "divider" }}>
+            <Tabs value={history.location.pathname !== "/" ? history.location.pathname : false}>
+              <Tab
+                label={<Box sx={{ textTransform: "capitalize" }}>Profile</Box>}
+                value={`/variant/${varId}`}
+                component={Link}
+                to={`/variant/${varId}`}
+              />
+            </Tabs>
+          </Box>
+        )}
+      />
+      <Suspense fallback={<LoadingBackdrop height={11500} />}>
+        <Switch>
+          <Route exact path={path}>
+            <Profile varId={varId} />
+          </Route>
+        </Switch>
+      </Suspense>
     </BasePage>
   );
 }
 
-export default VariantPage;
+export default VariantPage;

apps/platform/src/pages/VariantPage/index.ts

@@ -0,0 +1 @@
+export { default } from "./VariantPage";

apps/platform/src/pages/VariantPage/types.ts

@@ -1,4 +1,4 @@
-type AlleleFrequencyType = {
+export type AlleleFrequencyType = {
   populationName: string;
   alleleFrequency: number;
 };
@@ -12,6 +12,19 @@ type VepType = {
   }[];
 };
 
+export type InSilicoPredictorsType = {
+  cadd?: {
+    phred: number;
+    raw: number;
+  };
+  revelMax?: number;
+  spliceaiDsMax?: number;
+  pangolinLargestDs?: number;
+  phylop?: number;
+  siftMax?: number;
+  polyphenMax?: number;
+};
+
 export type MetadataType = {
   variantId: string,
   chromosome: string,
@@ -24,16 +37,5 @@ export type MetadataType = {
   alleleType: string;
   alleleFrequencies: AlleleFrequencyType[];
   vep: VepType;
-  inSilicoPredictors: {
-    cadd?: {
-      phred: number;
-      raw: number;
-    };
-    revelMax?: number;
-    spliceaiDsMax?: number;
-    pangolinLargestDs?: number;
-    phylop?: number;
-    siftMax?: number;
-    polyphenMax?: number;
-  };
+  inSilicoPredictors: InSilicoPredictorsType;
 };