[Platform]: Credible-set page queries fix (#549)

* variant page query update * credible sets query fix
opentargets · Nov 22, 2024 · bb469ad · bb469ad
1 parent 427ccae
commit bb469ad
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Showing 18 changed files with 124 additions and 123 deletions.
diff --git a/apps/platform/src/pages/CredibleSetPage/CredibleSetPage.gql b/apps/platform/src/pages/CredibleSetPage/CredibleSetPage.gql
@@ -1,5 +1,5 @@
-query CredibleSetPageQuery($studyLocusIds: [String!]!) {
-  credibleSets(studyLocusIds: $studyLocusIds) {
+query CredibleSetPageQuery($studyLocusId: String!) {
+  credibleSet(studyLocusId: $studyLocusId) {
     variant {
       id
       referenceAllele

diff --git a/apps/platform/src/pages/CredibleSetPage/CredibleSetPage.tsx b/apps/platform/src/pages/CredibleSetPage/CredibleSetPage.tsx
@@ -13,14 +13,14 @@ function CredibleSetPage() {
   const { path } = useRouteMatch();
 
   const { loading, data } = useQuery(CREDIBLE_SET_PAGE_QUERY, {
-    variables: { studyLocusIds: [studyLocusId] },
+    variables: { studyLocusId: studyLocusId },
   });
 
-  if (data && !data?.credibleSets.length) {
+  if (data && !data?.credibleSet) {
     return <NotFoundPage />;
   }
 
-  const credibleSet = data?.credibleSets[0];
+  const credibleSet = data?.credibleSet;
   const variantId = credibleSet?.variant?.id;
   const referenceAllele = credibleSet?.variant?.referenceAllele;
   const alternateAllele = credibleSet?.variant?.alternateAllele;

diff --git a/apps/platform/src/pages/CredibleSetPage/Profile.tsx b/apps/platform/src/pages/CredibleSetPage/Profile.tsx
@@ -22,7 +22,7 @@ const GWASColocSection = lazy(() => import("sections/src/credibleSet/GWASColoc/B
 
 const Locus2GeneSection = lazy(() => import("sections/src/credibleSet/Locus2Gene/Body"));
 
-const CREDIBLE_SET = "credibleSets";
+const CREDIBLE_SET = "credibleSet";
 
 const createProfileQuery = (studyType: string) => {
   const summaries = [VariantsSummary, Locus2GeneSummary];
@@ -40,8 +40,8 @@ const createProfileQuery = (studyType: string) => {
   );
 
   const CREDIBLE_SET_PROFILE_QUERY = gql`
-    query CredibleSetProfileQuery($studyLocusIds: [String!]!) {
-      credibleSets(studyLocusIds: $studyLocusIds) {
+    query CredibleSetProfileQuery($studyLocusId: String!, $variantIds: [String!]!) {
+      credibleSet(studyLocusId: $studyLocusId) {
         studyLocusId
         ...CredibleSetProfileHeaderFragment
         ...CredibleSetProfileSummaryFragment
@@ -65,7 +65,7 @@ function Profile({
     <PlatformApiProvider
       entity={CREDIBLE_SET}
       query={CREDIBLE_SET_PROFILE_QUERY}
-      variables={{ studyLocusIds: [studyLocusId] }}
+      variables={{ studyLocusId: studyLocusId, variantIds: [variantId] }}
       client={client}
     >
       <ProfileHeader variantId={variantId} />

diff --git a/apps/platform/src/pages/CredibleSetPage/ProfileHeader.gql b/apps/platform/src/pages/CredibleSetPage/ProfileHeader.gql
@@ -4,14 +4,14 @@ fragment CredibleSetProfileHeaderFragment on credibleSet {
   beta
   standardError
   effectAlleleFrequencyFromSource
-  locus {
-    posteriorProbability
-    pValueMantissa
-    pValueExponent
-    beta
-    standardError
-    variant {
-      id
+  locus(variantIds: $variantIds) {
+    count
+    rows {
+      posteriorProbability
+      pValueMantissa
+      pValueExponent
+      beta
+      standardError
     }
   }
   variant {
@@ -44,4 +44,4 @@ fragment CredibleSetProfileHeaderFragment on credibleSet {
     pubmedId
     nSamples
   }
-}
+}
diff --git a/apps/platform/src/pages/CredibleSetPage/ProfileHeader.tsx b/apps/platform/src/pages/CredibleSetPage/ProfileHeader.tsx
@@ -18,17 +18,16 @@ type ProfileHeaderProps = {
 };
 
 function ProfileHeader({ variantId }: ProfileHeaderProps) {
-
   const { loading, error, data } = usePlatformApi();
 
   // TODO: Errors!
   if (error) return null;
 
-  const credibleSet = data?.credibleSets?.[0];
+  const credibleSet = data?.credibleSet;
   const study = credibleSet?.study;
   const studyCategory = study ? getStudyCategory(study.projectId) : null;
   const target = study?.target;
-  const leadVariant = credibleSet?.locus?.find(loc => loc?.variant.id === variantId);
+  const leadVariant = credibleSet?.locus.rows[0];
   const beta = leadVariant?.beta ?? credibleSet?.beta;
   const standardError = leadVariant?.standardError ?? credibleSet?.standardError;
   const { pValueMantissa, pValueExponent } =
@@ -39,23 +38,22 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
 
   return (
     <BaseProfileHeader>
-
       <Box>
-        <Typography variant="subtitle1" mt={0}>Lead Variant</Typography>
-        {typeof pValueMantissa === "number" && typeof pValueExponent === "number" &&
+        <Typography variant="subtitle1" mt={0}>
+          Lead Variant
+        </Typography>
+        {typeof pValueMantissa === "number" && typeof pValueExponent === "number" && (
           <Field loading={loading} title="P-value">
             <ScientificNotation number={[pValueMantissa, pValueExponent]} />
           </Field>
-        }
-        {typeof beta === 'number' &&
+        )}
+        {typeof beta === "number" && (
           <Field
             loading={loading}
             title={
               <Tooltip
                 title={
-                  <Typography variant="caption">
-                    Beta with respect to the ALT allele
-                  </Typography>
+                  <Typography variant="caption">Beta with respect to the ALT allele</Typography>
                 }
                 showHelpIcon
               >
@@ -65,15 +63,16 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
           >
             {beta.toPrecision(3)}
           </Field>
-        }
-        {typeof standardError === 'number' &&
+        )}
+        {typeof standardError === "number" && (
           <Field
             loading={loading}
             title={
               <Tooltip
                 title={
                   <Typography variant="caption">
-                    Standard error: Estimate of the standard deviation of the sampling distribution of the beta
+                    Standard error: Estimate of the standard deviation of the sampling distribution
+                    of the beta
                   </Typography>
                 }
                 showHelpIcon
@@ -84,13 +83,13 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
           >
             {standardError.toPrecision(3)}
           </Field>
-        }
-        {typeof credibleSet?.effectAlleleFrequencyFromSource === "number" &&
+        )}
+        {typeof credibleSet?.effectAlleleFrequencyFromSource === "number" && (
           <Field loading={loading} title="EAF">
             {credibleSet.effectAlleleFrequencyFromSource.toPrecision(3)}
           </Field>
-        }
-        {typeof leadVariant?.posteriorProbability === "number" &&
+        )}
+        {typeof leadVariant?.posteriorProbability === "number" && (
           <Field
             loading={loading}
             title={
@@ -108,33 +107,31 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
           >
             {leadVariant.posteriorProbability.toPrecision(3)}
           </Field>
-        }
+        )}
         <Field loading={loading} title="GRCh38">
           {credibleSet?.variant &&
-            `${credibleSet.variant.chromosome}:${credibleSet.variant.position}`
-          }
+            `${credibleSet.variant.chromosome}:${credibleSet.variant.position}`}
         </Field>
-        {
-          credibleSet?.variant?.rsIds.length > 0 &&
-            <Field loading={loading} title="Ensembl">
-              {
-                credibleSet.variant.rsIds.map((rsid, index) => (
-                  <Fragment key={rsid}>
-                    {index > 0 && ", "}
-                    <Link
-                      external
-                      to={`https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=${rsid}`}
-                    >
-                      {rsid}
-                    </Link>
-                  </Fragment>
-                ))
-              }
-            </Field>
-        }
+        {credibleSet?.variant?.rsIds.length > 0 && (
+          <Field loading={loading} title="Ensembl">
+            {credibleSet.variant.rsIds.map((rsid, index) => (
+              <Fragment key={rsid}>
+                {index > 0 && ", "}
+                <Link
+                  external
+                  to={`https://www.ensembl.org/Homo_sapiens/Variation/Explore?v=${rsid}`}
+                >
+                  {rsid}
+                </Link>
+              </Fragment>
+            ))}
+          </Field>
+        )}
 
-        <Typography variant="subtitle1" mt={1}>Credible Set</Typography>
-        <Field loading={loading} title="Fine-mapping method">
+        <Typography variant="subtitle1" mt={1}>
+          Credible Set
+        </Typography>
+        <Field loading={loading} title="Finemapping method">
           {credibleSet?.finemappingMethod}
         </Field>
         <Field loading={loading} title="Credible set index within locus">
@@ -152,65 +149,65 @@ function ProfileHeader({ variantId }: ProfileHeaderProps) {
       </Box>
 
       <Box>
-        <Typography variant="subtitle1" mt={0}>Study</Typography>
-        <Field loading={loading} title="First author">
+        <Typography variant="subtitle1" mt={0}>
+          Study
+        </Typography>
+        <Field loading={loading} title="Author">
           {study?.publicationFirstAuthor}
         </Field>
         <Field loading={loading} title="Publication year">
           {study?.publicationDate?.slice(0, 4)}
         </Field>
-        {studyCategory !== "QTL" &&
+        {studyCategory !== "QTL" && (
           <>
             <Field loading={loading} title="Reported trait">
               {study?.traitFromSource}
             </Field>
-            {study?.diseases?.length > 0 &&
-              <Field loading={loading} title="Disease/phenotype">
+            {study?.diseases?.length > 0 && (
+              <Field loading={loading} title="Diseases">
                 {study.diseases.map(({ id, name }, index) => (
                   <Fragment key={id}>
                     {index > 0 ? ", " : null}
                     <Link to={`../disease/${id}`}>{name}</Link>
                   </Fragment>
                 ))}
               </Field>
-            }
+            )}
           </>
-        }
-        {studyCategory === "QTL" &&
+        )}
+        {studyCategory === "QTL" && (
           <>
-            {target?.id &&
+            {target?.id && (
               <Field loading={loading} title="Affected gene">
-                <Link to={`../target/${target.id}`}>
-                  {target.approvedSymbol} 
-                </Link>
+                <Link to={`../target/${target.id}`}>{target.approvedSymbol}</Link>
               </Field>
-            }
-            { study?.biosample?.biosampleId &&
+            )}
+            {study?.biosample?.biosampleId && (
               <Field loading={loading} title="Affected cell/tissue">
-                <Link external to={`https://www.ebi.ac.uk/ols4/search?q=${study.biosample.biosampleId}&ontology=uberon`}>
+                <Link
+                  external
+                  to={`https://www.ebi.ac.uk/ols4/search?q=${study.biosample.biosampleId}&ontology=uberon`}
+                >
                   {study.biosample.biosampleId}
                 </Link>
               </Field>
-            }
+            )}
           </>
-        }
+        )}
         <Field loading={loading} title="Journal">
           {study?.publicationJournal}
         </Field>
-        {study?.pubmedId &&
+        {study?.pubmedId && (
           <Field loading={loading} title="PubMed">
-            <PublicationsDrawer
-              entries={[{ name: study.pubmedId, url: epmcUrl(study.pubmedId)}]}
-            >
+            <PublicationsDrawer entries={[{ name: study.pubmedId, url: epmcUrl(study.pubmedId) }]}>
               {study.pubmedId}
             </PublicationsDrawer>
           </Field>
-        }
+        )}
         <Field loading={loading} title="Sample size">
           {study?.nSamples}
         </Field>
       </Box>
-
     </BaseProfileHeader>
   );
 }
@@ -219,4 +216,4 @@ ProfileHeader.fragments = {
   profileHeader: CREDIBLE_SET_PROFILE_HEADER_FRAGMENT,
 };
 
-export default ProfileHeader;
+export default ProfileHeader;
diff --git a/packages/sections/src/credibleSet/GWASColoc/Body.tsx b/packages/sections/src/credibleSet/GWASColoc/Body.tsx
@@ -157,7 +157,7 @@ type BodyProps = {
 
 function Body({ studyLocusId, entity }: BodyProps) {
   const variables = {
-    studyLocusIds: [studyLocusId],
+    studyLocusId: studyLocusId,
   };
 
   const request = useQuery(GWAS_COLOC_QUERY, {
@@ -180,7 +180,7 @@ function Body({ studyLocusId, entity }: BodyProps) {
             order="asc"
             columns={columns}
             loading={request.loading}
-            rows={request.data?.credibleSets[0].colocalisation}
+            rows={request.data?.credibleSet.colocalisation}
             query={GWAS_COLOC_QUERY.loc.source.body}
             variables={variables}
           />

diff --git a/packages/sections/src/credibleSet/GWASColoc/GWASColocQuery.gql b/packages/sections/src/credibleSet/GWASColoc/GWASColocQuery.gql
@@ -1,5 +1,5 @@
-query GWASColocQuery($studyLocusIds: [String!]!) {
-  credibleSets(studyLocusIds: $studyLocusIds) {
+query GWASColocQuery($studyLocusId: String!) {
+  credibleSet(studyLocusId: $studyLocusId) {
     colocalisation(studyTypes: [gwas], page: { size: 250, index: 0 }) {
       otherStudyLocus {
         studyLocusId
@@ -26,4 +26,4 @@ query GWASColocQuery($studyLocusIds: [String!]!) {
       clpp
     }
   }
-}
+}
diff --git a/packages/sections/src/credibleSet/GWASColoc/index.ts b/packages/sections/src/credibleSet/GWASColoc/index.ts
@@ -3,5 +3,5 @@ export const definition = {
   id,
   name: "GWAS Colocalisation",
   shortName: "GC",
-  hasData: data => data?.[0]?.colocalisation?.length > 0,
-};
+  hasData: data => data?.colocalisation?.length > 0,
+};
diff --git a/packages/sections/src/credibleSet/GWASMolQTL/Body.tsx b/packages/sections/src/credibleSet/GWASMolQTL/Body.tsx
@@ -184,7 +184,7 @@ type BodyProps = {
 
 function Body({ studyLocusId, entity }: BodyProps) {
   const variables = {
-    studyLocusIds: [studyLocusId],
+    studyLocusId: studyLocusId,
   };
 
   const request = useQuery(GWAS_COLOC_QUERY, {
@@ -207,7 +207,7 @@ function Body({ studyLocusId, entity }: BodyProps) {
             order="asc"
             columns={columns}
             loading={request.loading}
-            rows={request.data?.credibleSets[0].colocalisation}
+            rows={request.data?.credibleSet.colocalisation}
             query={GWAS_COLOC_QUERY.loc.source.body}
             variables={variables}
           />

diff --git a/packages/sections/src/credibleSet/GWASMolQTL/GWASMolQTLColocQuery.gql b/packages/sections/src/credibleSet/GWASMolQTL/GWASMolQTLColocQuery.gql
@@ -1,5 +1,5 @@
-query GWASMolQTLColocQuery($studyLocusIds: [String!]!) {
-  credibleSets(studyLocusIds: $studyLocusIds) {
+query GWASMolQTLColocQuery($studyLocusId: String!) {
+  credibleSet(studyLocusId: $studyLocusId) {
     colocalisation(studyTypes: [tuqtl, pqtl, eqtl, sqtl], page: { size: 250, index: 0 }) {
       otherStudyLocus {
         studyLocusId