[Platform]: study profile feedback (#565)

opentargets · Nov 29, 2024 · ab1df24 · ab1df24
1 parent d0875d7
commit ab1df24
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Showing 19 changed files with 278 additions and 314 deletions.
diff --git a/apps/platform/src/pages/StudyPage/Header.tsx b/apps/platform/src/pages/StudyPage/Header.tsx
@@ -17,54 +17,71 @@ type HeaderProps = {
 };
 
 function Header({
-      loading,
-      studyId,
-      backgroundTraits,
-      targetId,
-      diseases,
-      studyCategory
-    }: HeaderProps) {
-
+  loading,
+  studyId,
+  backgroundTraits,
+  targetId,
+  diseases,
+  projectId,
+}: HeaderProps) {
   let traitLinks, sourceLink;
-  if (studyCategory === 'GWAS') {
+  if (projectId === "GCST") {
     if (diseases?.length) {
-      traitLinks = <XRefLinks
-        label="Trait"
-        urlStem="../disease/"
-        ids={diseases.map(d => d.id)}
-        names={diseases.map(d => d.name)}
-      />
+      traitLinks = (
+        <XRefLinks
+          label="Trait"
+          urlStem="../disease/"
+          ids={diseases.map(d => d.id)}
+          names={diseases.map(d => d.name)}
+        />
+      );
     }
     sourceLink = {
       id: "GWAS Catalog",
       url: `https://www.ebi.ac.uk/gwas/studies/${studyId}`,
     };
-  } else if (studyCategory === 'FINNGEN') {
+  } else if (projectId === "FINNGEN_R11") {
     if (diseases?.length) {
-      traitLinks = <XRefLinks
-        label="Trait"
-        urlStem="../disease/"
-        ids={diseases.map(d => d.id)}
-        names={diseases.map(d => d.name)}
-      />
+      traitLinks = (
+        <XRefLinks
+          label="Trait"
+          urlStem="../disease/"
+          ids={diseases.map(d => d.id)}
+          names={diseases.map(d => d.name)}
+        />
+      );
     }
     sourceLink = {
       id: "FinnGen",
       url: `https://r10.finngen.fi/pheno/${studyId}`,
     };
-  } else {  // QTL
+  } else if (projectId === "UKB_PPP_EUR") {
+    if (diseases?.length) {
+      traitLinks = (
+        <XRefLinks
+          label="Trait"
+          urlStem="../disease/"
+          ids={diseases.map(d => d.id)}
+          names={diseases.map(d => d.name)}
+        />
+      );
+    }
+    sourceLink = {
+      id: "UKB",
+      url: "https://www.synapse.org/Synapse:syn51364943/wiki/622119",
+    };
+  } else {
+    // QTL
     if (targetId) {
-      traitLinks = <ExternalLink
-        title="Affected gene"
-        id={targetId}
-        url={`../target/${targetId}`}
-      />
+      traitLinks = (
+        <ExternalLink title="Affected gene" id={targetId} url={`../target/${targetId}`} />
+      );
     }
     sourceLink = {
       id: "eQTL Catalog",
       url: "https://www.ebi.ac.uk/eqtl/Studies/",
     };
-  };
+  }
 
   return (
     <HeaderBase
@@ -73,27 +90,21 @@ function Header({
       subtitle={null}
       Icon={faChartBar}
       externalLinks={
-        <> 
+        <>
           {traitLinks}
-          { 
-            studyCategory === "GWAS" && backgroundTraits?.length > 0 &&
-              <XRefLinks
-                label="Background traits"
-                urlStem="../disease/"
-                ids={backgroundTraits.map(t => t.id)}
-                names={backgroundTraits.map(t => t.name)}
-              />
-          }
-          <ExternalLink
-            title="Source"
-            id={sourceLink.id}
-            url={sourceLink.url}
-          />
+          {projectId === "GWAS" && backgroundTraits?.length > 0 && (
+            <XRefLinks
+              label="Background traits"
+              urlStem="../disease/"
+              ids={backgroundTraits.map(t => t.id)}
+              names={backgroundTraits.map(t => t.name)}
+            />
+          )}
+          <ExternalLink title="Source" id={sourceLink.id} url={sourceLink.url} />
         </>
       }
     />
   );
-
 }
 
-export default Header;
+export default Header;
diff --git a/apps/platform/src/pages/StudyPage/Profile.tsx b/apps/platform/src/pages/StudyPage/Profile.tsx
@@ -13,7 +13,7 @@ import GWASCredidbleSetsSummary from "sections/src/study/GWASCredibleSets/Summar
 import QTLCredibleSetsSummary from "sections/src/study/QTLCredibleSets/Summary";
 
 import client from "../../client";
-import ProfileHeader from "./ProfileHeader";
+import ProfileHeader from "./StudyProfileHeader";
 
 const SharedTraitStudiesSection = lazy(() => import("sections/src/study/SharedTraitStudies/Body"));
 const GWASCredibleSetsSection = lazy(() => import("sections/src/study/GWASCredibleSets/Body"));
@@ -23,21 +23,23 @@ const QTLCredibleSetsSection = lazy(() => import("sections/src/study/QTLCredible
 // (the summary cannot be written as a fragment as it gets further studies)
 const summaries = [GWASCredidbleSetsSummary, QTLCredibleSetsSummary];
 
-const STUDY = "gwasStudy";
+const STUDY = "study";
 const STUDY_PROFILE_SUMMARY_FRAGMENT = summaryUtils.createSummaryFragment(
   summaries,
   "Gwas",
   "StudyProfileSummaryFragment"
 );
 const STUDY_PROFILE_QUERY = gql`
   query StudyProfileQuery($studyId: String!, $diseaseIds: [String!]!) {
-    gwasStudy(studyId: $studyId) {
-      studyId
+    study(studyId: $studyId) {
+      id
       ...StudyProfileHeaderFragment
       ...StudyProfileSummaryFragment
     }
-    sharedTraitStudies: gwasStudy(diseaseIds: $diseaseIds, page: { size: 2, index: 0 }) {
-      studyId
+    sharedTraitStudies: studies(diseaseIds: $diseaseIds, page: { size: 2, index: 0 }) {
+      rows {
+        id
+      }
     }
   }
   ${ProfileHeader.fragments.profileHeader}
@@ -53,11 +55,9 @@ type ProfileProps = {
   }[];
 };
 
-function Profile({ studyId, studyType, diseases }: ProfileProps) {
+function Profile({ studyId, studyType, projectId, diseases }: ProfileProps) {
   const diseaseIds = diseases?.map(d => d.id) || [];
 
-  console.log({ studyType });
-
   return (
     <PlatformApiProvider
       entity={STUDY}
@@ -68,7 +68,7 @@ function Profile({ studyId, studyType, diseases }: ProfileProps) {
       }}
       client={client}
     >
-      <ProfileHeader studyCategory={studyType} />
+      <ProfileHeader projectId={projectId} />
 
       <SummaryContainer>
         {studyType === "gwas" && (

diff --git a/apps/platform/src/pages/StudyPage/ProfileHeader.tsx b/apps/platform/src/pages/StudyPage/ProfileHeader.tsx
diff --git a/apps/platform/src/pages/StudyPage/StudyPage.gql b/apps/platform/src/pages/StudyPage/StudyPage.gql
@@ -1,6 +1,6 @@
 query StudyPageQuery($studyId: String!) {
-  gwasStudy(studyId: $studyId) {
-    studyId
+  study(studyId: $studyId) {
+    id
     studyType
     projectId
     backgroundTraits {