[Platform]: fix several issues in exports (#608)

* feat: gwas credible set exports * fix: molQTL cred sets add affectetd tissue cell * fix: l2g score in gwas cred set in study page * fix: shared trait studies export in study page * fix: l2g widget in credible set page to export gene * fix: first author in gwas colocalisation * fix: transcript consequences export * fix: minor tweak to a header * fix: wrong query returning no top L2G in credible set widget * fix: credible set exports and bugs
opentargets · Dec 9, 2024 · a558eff · a558eff
1 parent cb58479
commit a558eff
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Showing 10 changed files with 30 additions and 6 deletions.
diff --git a/apps/platform/src/pages/StudyPage/Header.tsx b/apps/platform/src/pages/StudyPage/Header.tsx
@@ -67,7 +67,7 @@ function Header({
       );
     }
     sourceLink = {
-      id: "UKB",
+      id: "UKB-PPP",
       url: "https://www.synapse.org/Synapse:syn51364943/wiki/622119",
     };
   } else {

diff --git a/packages/sections/src/credibleSet/GWASColoc/Body.tsx b/packages/sections/src/credibleSet/GWASColoc/Body.tsx
@@ -53,8 +53,7 @@ const columns = [
         : publicationFirstAuthor || naLabel;
     },
     exportValue: ({ otherStudyLocus }) => {
-      const { projectId, publicationFirstAuthor } = otherStudyLocus.study || {};
-      getStudyCategory(projectId) === "FINNGEN" ? "FinnGen" : publicationFirstAuthor;
+      return otherStudyLocus?.study?.publicationFirstAuthor;
     },
   },
   {

diff --git a/packages/sections/src/credibleSet/Locus2Gene/Body.tsx b/packages/sections/src/credibleSet/Locus2Gene/Body.tsx
@@ -21,6 +21,7 @@ const columns = [
       if (!target) return naLabel;
       return <Link to={`../target/${target?.id}`}>{target?.approvedSymbol}</Link>;
     },
+    exportValue: ({ target }) => target?.id,
   },
   {
     id: "score",

diff --git a/packages/sections/src/evidence/GWASCredibleSets/Body.jsx b/packages/sections/src/evidence/GWASCredibleSets/Body.jsx
@@ -27,6 +27,7 @@ function getColumns(targetSymbol) {
       renderCell: ({ credibleSet }) => {
         return <Navigate to={`/credible-set/${credibleSet?.studyLocusId}`} />;
       },
+      exportValue: ({ credibleSet }) => credibleSet?.studyLocusId,
     },
     {
       id: "variantId",
@@ -45,26 +46,30 @@ function getColumns(targetSymbol) {
           />
         </Link>
       },
-      filterValue: ({ variant: v }) =>
+      filterValue: ({ credibleSet: { variant: v } }) =>
         `${v?.chromosome}_${v?.position}_${v?.referenceAllele}_${v?.alternateAllele}`,
+      exportValue: ({ credibleSet: { variant: v } }) => `${v?.chromosome}_${v?.position}_${v?.referenceAllele}_${v?.alternateAllele}`,
     },
     {
       id: "trait",
       label: "Reported trait",
       renderCell: ({ credibleSet }) => credibleSet?.study.traitFromSource,
+      exportValue: ({ credibleSet }) => credibleSet?.study.traitFromSource,
     },
     {
       id: "disease",
       label: "Disease/phenotype",
       renderCell: ({ disease }) => <Link to={`/disease/${disease.id}`}>{disease.name}</Link>,
       filterValue: ({ disease }) => disease.name,
+      exportValue: ({ disease }) => `${disease.name} (${disease.id})`,
     },
     {
       id: "study",
       label: "Study",
       renderCell: ({ credibleSet }) => {
         return <Link to={`/study/${credibleSet?.study.id}`}>{credibleSet?.study.id}</Link>;
       },
+      exportValue: ({ credibleSet }) => credibleSet?.study.id,
     },
     {
       id: "nSamples",
@@ -76,6 +81,7 @@ function getColumns(targetSymbol) {
           ? parseInt(credibleSet?.study.nSamples, 10).toLocaleString()
           : naLabel,
       filterValue: ({ credibleSet }) => parseInt(credibleSet?.study.nSamples, 10).toLocaleString(),
+      exportValue: ({ credibleSet }) => credibleSet?.study.nSamples,
     },
     {
       id: "pValue",
@@ -126,11 +132,13 @@ function getColumns(targetSymbol) {
         );
       },
       filterValue: ({ credibleSet }) => credsetConfidenceMap[credibleSet?.confidence],
+      exportValue: ({ credibleSet }) => credibleSet?.confidence,
     },
     {
       id: "finemappingMethod",
       label: "Fine-mapping method",
       renderCell: ({ credibleSet }) => credibleSet?.finemappingMethod || naLabel,
+      exportValue: ({ credibleSet }) => credibleSet?.finemappingMethod,
     },
     {
       id: "score",
@@ -176,6 +184,7 @@ function getColumns(targetSymbol) {
       },
       filterValue: ({ literature, publicationYear, publicationFirstAuthor }) =>
         `${literature} ${publicationYear} ${publicationFirstAuthor}`,
+      exportValue: ({ credibleSet }) => credibleSet?.study.pubmedId,
     },
   ];
 }

diff --git a/packages/sections/src/study/GWASCredibleSets/Body.tsx b/packages/sections/src/study/GWASCredibleSets/Body.tsx
@@ -134,6 +134,7 @@ const columns = [
         </Tooltip>
       );
     },
+    exportValue: ({ l2GPredictions }) => l2GPredictions?.rows[0]?.score,
   },
   {
     id: "credibleSetSize",

diff --git a/packages/sections/src/study/SharedTraitStudies/Body.tsx b/packages/sections/src/study/SharedTraitStudies/Body.tsx
@@ -23,6 +23,7 @@ function getColumns(diseaseIds: string[]) {
       id: "studyId",
       label: "Study",
       renderCell: ({ id }) => <Link to={`./${id}`}>{id}</Link>,
+      exportValue: ({ id }) => id,
     },
     {
       id: "sharedDiseases",
@@ -111,6 +112,8 @@ function getColumns(diseaseIds: string[]) {
       },
       filterValue: ({ publicationYear, publicationFirstAuthor }) =>
         `${publicationYear} ${publicationFirstAuthor}`,
+      exportValue: ({ pubmedId }) =>
+        `${pubmedId}`,
     },
   ];
 }

diff --git a/packages/sections/src/variant/GWASCredibleSets/Body.tsx b/packages/sections/src/variant/GWASCredibleSets/Body.tsx
@@ -100,6 +100,7 @@ function getColumns({ id, referenceAllele, alternateAllele }: getColumnsType) {
         if (!study) return naLabel;
         return <Link to={`../study/${study.id}`}>{study.id}</Link>;
       },
+      exportValue: ({ study }) => study?.id,
     },
     {
       id: "pValue",
@@ -193,7 +194,7 @@ function getColumns({ id, referenceAllele, alternateAllele }: getColumnsType) {
         const { target } = l2GPredictions?.rows[0];
         return <Link to={`/target/${target.id}`}>{target.approvedSymbol}</Link>;
       },
-      exportValue: ({ l2GPredictions }) => l2GPredictions?.target.approvedSymbol,
+      exportValue: ({ l2GPredictions }) => l2GPredictions?.rows[0]?.target.approvedSymbol,
     },
     {
       id: "l2gScore",
@@ -214,6 +215,7 @@ function getColumns({ id, referenceAllele, alternateAllele }: getColumnsType) {
           </Tooltip>
         );
       },
+      exportValue: ({ l2GPredictions }) => l2GPredictions?.rows[0]?.score,
     },
     {
       id: "credibleSetSize",

diff --git a/packages/sections/src/variant/GWASCredibleSets/GWASCredibleSetsQuery.gql b/packages/sections/src/variant/GWASCredibleSets/GWASCredibleSetsQuery.gql
@@ -39,7 +39,7 @@ query GWASCredibleSetsQuery($variantId: String!, $size: Int!, $index: Int!) {
         locusSize: locus {
           count
         }
-        l2GPredictions(page: { size: 1, index: 1 }) {
+        l2GPredictions(page: { size: 1, index: 0 }) {
           rows {
             target {
               id

diff --git a/packages/sections/src/variant/QTLCredibleSets/Body.tsx b/packages/sections/src/variant/QTLCredibleSets/Body.tsx
@@ -103,6 +103,7 @@ function getColumns({ id, referenceAllele, alternateAllele }: getColumnsType) {
           </Link>
         );
       },
+      exportValue: ({ study }) => { return `[${study?.biosample?.biosampleId}]:${study?.biosample?.biosampleName}`},
     },
     {
       id: "study.condition",

diff --git a/packages/sections/src/variant/VariantEffectPredictor/Body.tsx b/packages/sections/src/variant/VariantEffectPredictor/Body.tsx
@@ -78,6 +78,14 @@ const columns = [
       }
       return displayElement;
     },
+    exportValue: ({ target, transcriptId, uniprotAccessions, aminoAcidChange }) => {
+      const geneInfo = `Gene: ${target?.id};`;
+      const canonicalTranscript = transcriptId ? `Canonical transcript: ${transcriptId};` : "";
+      const biotype = `Biotype: ${target?.biotype};`;
+      const protein = uniprotAccessions?.length ? `Protein(s): ${uniprotAccessions.join(", ")}` : "";
+      const aaChange = aminoAcidChange ? `AA: ${aminoAcidChange};` : "";
+      return [geneInfo, canonicalTranscript, biotype, protein, aaChange].join("");
+    }      
   },
   {
     id: "variantConsequences.label",
-Original file line number
+Diff line change
@@ Expand Up / @@ -134,6 +134,7 @@ const columns = [ @@
             </Tooltip>
           );
         },
+        exportValue: ({ l2GPredictions }) => l2GPredictions?.rows[0]?.score,
       },
       {
         id: "credibleSetSize",
@@ Expand Down @@