Merge branch 'main' of github.com:opentargets/ot-ui-apps into cc-upgr…

…ade-react-router
opentargets · Dec 10, 2024 · 23c717f · 23c717f
2 parents eb2dc64 + 2058ade
commit 23c717f
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diff --git a/apps/platform/src/components/AssociationsToolkit/static_datasets/dataSourcesAssoc.js b/apps/platform/src/components/AssociationsToolkit/static_datasets/dataSourcesAssoc.js
@@ -2,7 +2,7 @@ const dataSources = [
   {
     id: "gwas_credible_sets",
     sectionId: "gwasCredibleSets",
-    label: "GWAS credible sets",
+    label: "GWAS associations",
     aggregation: "Genetic association",
     aggregationId: "genetic_association",
     weight: 1,

diff --git a/apps/platform/src/pages/CredibleSetPage/ProfileHeader.tsx b/apps/platform/src/pages/CredibleSetPage/ProfileHeader.tsx
@@ -221,6 +221,11 @@ function ProfileHeader() {
         )}
         {study?.studyType !== "gwas" && (
           <>
+            {study?.projectId && (
+              <Field loading={loading} title="Project">
+                {study?.projectId?.replace(/_/gi, " ")}
+              </Field>
+            )}
             {target?.id && (
               <Field loading={loading} title="Affected gene">
                 <Link to={`../target/${target.id}`}>{target.approvedSymbol}</Link>

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/apps/platform/src/pages/StudyPage/StudyProfileHeader.gql b/apps/platform/src/pages/StudyPage/StudyProfileHeader.gql
@@ -5,6 +5,7 @@ fragment StudyProfileHeaderFragment on Gwas {
   publicationJournal
   pubmedId
   traitFromSource
+  projectId
   backgroundTraits {
     id
     name

diff --git a/apps/platform/src/pages/StudyPage/StudyProfileHeader.tsx b/apps/platform/src/pages/StudyPage/StudyProfileHeader.tsx
@@ -8,6 +8,7 @@ import {
   SummaryStatsTable,
   LabelChip,
   DisplaySampleSize,
+  PublicationsDrawer,
 } from "ui";
 import { Box } from "@mui/material";
 import { populationMap } from "../../constants";
@@ -33,6 +34,7 @@ function ProfileHeader() {
     traitFromSource,
     backgroundTraits,
     diseases,
+    projectId,
     target,
     nCases,
     nControls,
@@ -80,6 +82,11 @@ function ProfileHeader() {
         )}
         {studyType !== "gwas" && (  // QTL
           <>
+            {projectId && (
+              <Field loading={loading} title="Project">
+                {projectId?.replace(/_/gi, " ")}
+              </Field>
+            )}
             {target?.id && (
               <Field loading={loading} title="Affected gene">
                 <Link to={`../target/${target.id}`}>{target.approvedSymbol}</Link>
@@ -108,9 +115,10 @@ function ProfileHeader() {
         )}
         {pubmedId &&
           <Field loading={loading} title="PubMed">
-            <Link external to={`https://europepmc.org/article/med/${pubmedId}`}>
-              {pubmedId}
-            </Link>
+            <PublicationsDrawer
+              name={pubmedId}
+              entries={[{ name: pubmedId }]}
+            />
           </Field>
         }
       </Box>

diff --git a/packages/sections/src/constants.js b/packages/sections/src/constants.js
@@ -119,3 +119,14 @@ export const initialResponse = {
   error: null,
   loading: true,
 };
+
+export const QTLStudyType = [
+  "scsqtl",
+  "sceqtl",
+  "scpqtl",
+  "sctuqtl",
+  "sqtl",
+  "eqtl",
+  "pqtl",
+  "tuqtl",
+];
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/GWASColoc/Description.tsx b/packages/sections/src/credibleSet/GWASColoc/Description.tsx
@@ -4,7 +4,7 @@ function Description() {
   return (
     <>
       Colocalisation metrics for overlapping credible sets from GWAS studies. Source:{" "}
-      <Link to="../" >
+      <Link to="https://home.opentargets.org/merged-product-documentation" external>
         Open Targets
       </Link>
     </>

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/credibleSet/Locus2Gene/Description.tsx b/packages/sections/src/credibleSet/Locus2Gene/Description.tsx
@@ -5,7 +5,9 @@ function Description(): ReactElement {
   return (
     <>
       Gene assignment based on machine-learning prioritisation of credible set features. Source:{" "}
-      <Link to="../">Open Targets</Link>
+      <Link to="https://home.opentargets.org/merged-product-documentation" external>
+        Open Targets
+      </Link>
     </>
   );
 }

diff --git a/packages/sections/src/credibleSet/MolQTLColoc/Body.tsx b/packages/sections/src/credibleSet/MolQTLColoc/Body.tsx
@@ -13,7 +13,6 @@ import { definition } from ".";
 import Description from "./Description";
 import MOLQTL_COLOC_QUERY from "./MolQTLColocQuery.gql";
 import { mantissaExponentComparator, variantComparator } from "../../utils/comparators";
-import { getStudyCategory } from "../../utils/getStudyCategory";
 import { useEffect, useState } from "react";
 
 const columns = [
@@ -35,45 +34,41 @@ const columns = [
     },
   },
   {
-    id: "otherStudyLocus.study.traitFromSource",
-    label: "Reported trait",
+    id: "otherStudyLocus.study.studyType",
+    label: "Type",
     renderCell: ({ otherStudyLocus }) => {
-      const trait = otherStudyLocus?.study?.traitFromSource;
-      if (!trait) return naLabel;
-      return trait;
+      const studyType = otherStudyLocus?.study?.studyType;
+      if (!studyType) return naLabel;
+      return studyType;
     },
   },
   {
-    id: "otherStudyLocus.study.publicationFirstAuthor",
-    label: "First author",
+    id: "otherStudyLocus.study.target.approvedSymbol",
+    label: "Affected gene",
     renderCell: ({ otherStudyLocus }) => {
-      const { projectId, publicationFirstAuthor } = otherStudyLocus?.study || {};
-      return getStudyCategory(projectId) === "FINNGEN"
-        ? "FinnGen"
-        : publicationFirstAuthor || naLabel;
-    },
-    exportValue: ({ otherStudyLocus }) => {
-      const { projectId, publicationFirstAuthor } = otherStudyLocus.study || {};
-      getStudyCategory(projectId) === "FINNGEN" ? "FinnGen" : publicationFirstAuthor;
+      const target = otherStudyLocus?.study?.target;
+      if (!target) return naLabel;
+      return <Link to={`/target/${target.id}`}>{target.approvedSymbol}</Link>;
     },
   },
+
   {
-    id: "otherStudyLocus.study.studyType",
+    id: "otherStudyLocus.study.biosample.biosampleName",
     label: "Affected tissue/cell",
     renderCell: ({ otherStudyLocus }) => {
       const biosample = otherStudyLocus?.study?.biosample;
       if (!biosample) return naLabel;
-      return <Link to={`../study/${biosample.biosampleId}`}>{biosample.name}</Link>;
+      return (
+        <Link external to={`https://www.ebi.ac.uk/ols4/search?q=${biosample.biosampleId}&ontology=uberon`}>
+          {biosample.biosampleName}
+        </Link>
+      );
     },
   },
   {
-    id: "otherStudyLocus.study.studyType",
-    label: "QTL type",
-    renderCell: ({ otherStudyLocus }) => {
-      const studyType = otherStudyLocus?.study?.studyType;
-      if (!studyType) return naLabel;
-      return studyType;
-    },
+    id: "otherStudyLocus.study.condition",
+    label: "Condition",
+    renderCell: ({ otherStudyLocus }) => otherStudyLocus?.study?.condition || naLabel,
   },
   {
     id: "otherStudyLocus.variant.id",
@@ -222,17 +217,15 @@ type BodyProps = {
 function Body({ studyLocusId, entity }: BodyProps) {
   const variables = {
     studyLocusId: studyLocusId,
+    size: table5HChunkSize,
+    index: 0,
   };
 
   const [request, setRequest] = useState<responseType>(initialResponse);
 
   const getData = useBatchQuery({
     query: MOLQTL_COLOC_QUERY,
-    variables: {
-      studyLocusId,
-      size: table5HChunkSize,
-      index: 0,
-    },
+    variables,
     dataPath: "data.credibleSet.colocalisation",
     size: table5HChunkSize,
   });

diff --git a/packages/sections/src/credibleSet/MolQTLColoc/Description.tsx b/packages/sections/src/credibleSet/MolQTLColoc/Description.tsx
@@ -4,7 +4,7 @@ function Description() {
   return (
     <>
       Colocalisation metrics for overlapping credible sets from molecular QTL studies. Source:{" "}
-      <Link to="../" >
+      <Link to="https://home.opentargets.org/merged-product-documentation" external>
         Open Targets
       </Link>
     </>

diff --git a/packages/sections/src/credibleSet/MolQTLColoc/MolQTLColocQuery.gql b/packages/sections/src/credibleSet/MolQTLColoc/MolQTLColocQuery.gql
@@ -1,6 +1,9 @@
 query MolQTLColocQuery($studyLocusId: String!, $size: Int!, $index: Int!) {
   credibleSet(studyLocusId: $studyLocusId) {
-    colocalisation(studyTypes: [tuqtl, pqtl, eqtl, sqtl], page: { size: $size, index: $index }) {
+    colocalisation(
+      studyTypes: [scsqtl, sceqtl, scpqtl, sctuqtl, sqtl, eqtl, pqtl, tuqtl]
+      page: { size: $size, index: $index }
+    ) {
       count
       rows {
         otherStudyLocus {
@@ -11,6 +14,7 @@ query MolQTLColocQuery($studyLocusId: String!, $size: Int!, $index: Int!) {
             projectId
             traitFromSource
             publicationFirstAuthor
+            condition
             target {
               approvedSymbol
               id

diff --git a/packages/sections/src/credibleSet/MolQTLColoc/MolQTLColocSummaryFragment.gql b/packages/sections/src/credibleSet/MolQTLColoc/MolQTLColocSummaryFragment.gql
@@ -1,6 +1,6 @@
 fragment MolQTLColocSummaryFragment on credibleSet {
   molqtlcolocalisation: colocalisation(
-    studyTypes: [tuqtl, pqtl, eqtl, sqtl]
+    studyTypes: [scsqtl, sceqtl, scpqtl, sctuqtl, sqtl, eqtl, pqtl, tuqtl]
     page: { size: 1, index: 0 }
   ) {
     count

diff --git a/packages/sections/src/credibleSet/Variants/Body.tsx b/packages/sections/src/credibleSet/Variants/Body.tsx
@@ -91,7 +91,7 @@ function getColumns({ leadVariantId, leadReferenceAllele, leadAlternateAllele }:
       tooltip: "Beta with respect to the ALT allele",
       renderCell: ({ beta }) => {
         if (typeof beta !== "number") return naLabel;
-        return beta.toFixed(3);
+        return beta.toPrecision(3);
       },
     },
     {
@@ -138,7 +138,7 @@ function getColumns({ leadVariantId, leadReferenceAllele, leadAlternateAllele }:
       sortable: true,
       renderCell: ({ posteriorProbability }) => {
         if (typeof posteriorProbability !== "number") return naLabel;
-        return posteriorProbability.toFixed(3);
+        return posteriorProbability.toPrecision(3);
       },
     },
     {

diff --git a/packages/sections/src/credibleSet/Variants/Description.tsx b/packages/sections/src/credibleSet/Variants/Description.tsx
@@ -4,7 +4,7 @@ function Description() {
   return (
     <>
       Set of variants with 95% probability of containing the causal variant. Source:{" "}
-      <Link to="../" >
+      <Link to="https://home.opentargets.org/merged-product-documentation" external>
         Open Targets
       </Link>
     </>

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/evidence/GWASCredibleSets/Description.jsx b/packages/sections/src/evidence/GWASCredibleSets/Description.jsx
@@ -6,8 +6,8 @@ function Description({ symbol, name }) {
     <>
       95% GWAS credible sets prioritisating <strong>{symbol}</strong> as likely causal gene for{" "}
       <strong>{name}</strong>. Source:{" "}
-      <Link to={config.geneticsPortalUrl} external>
-        Open Targets Genetics
+      <Link to="https://home.opentargets.org/merged-product-documentation" external>
+        Open Targets
       </Link>
     </>
   );

diff --git a/packages/sections/src/evidence/GWASCredibleSets/index.js b/packages/sections/src/evidence/GWASCredibleSets/index.js
@@ -3,8 +3,8 @@ import { isPrivateEvidenceSection } from "../../utils/partnerPreviewUtils";
 const id = "gwas_credible_sets";
 export const definition = {
   id,
-  name: "GWAS credible sets",
-  shortName: "GC",
+  name: "GWAS associations",
+  shortName: "GW",
   hasData: data => data.gwasCredibleSets.count > 0,
   isPrivate: isPrivateEvidenceSection(id),
 };
diff --git a/packages/sections/src/study/GWASCredibleSets/Body.tsx b/packages/sections/src/study/GWASCredibleSets/Body.tsx
@@ -79,7 +79,7 @@ const columns = [
     tooltip: "Beta with respect to the ALT allele",
     renderCell: ({ beta }) => {
       if (typeof beta !== "number") return naLabel;
-      return beta.toFixed(3);
+      return beta.toPrecision(3);
     },
   },
   {
@@ -134,6 +134,7 @@ const columns = [
         </Tooltip>
       );
     },
+    exportValue: ({ l2GPredictions }) => l2GPredictions?.rows[0]?.score,
   },
   {
     id: "credibleSetSize",