[Platform]: QTL studytype in queries (#602)

opentargets · Dec 9, 2024 · b19b288 · b19b288
1 parent 7e2cebf
commit b19b288
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Showing 7 changed files with 30 additions and 23 deletions.
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/MolQTLColoc/Body.tsx b/packages/sections/src/credibleSet/MolQTLColoc/Body.tsx
@@ -222,17 +222,15 @@ 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/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 {

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/variant/QTLCredibleSets/Body.tsx b/packages/sections/src/variant/QTLCredibleSets/Body.tsx
@@ -14,7 +14,7 @@ import { credsetConfidenceMap, initialResponse, naLabel, table5HChunkSize } from
 import { definition } from ".";
 import Description from "./Description";
 import QTL_CREDIBLE_SETS_QUERY from "./QTLCredibleSetsQuery.gql";
-import { mantissaExponentComparator, nullishComparator, variantComparator } from "../../utils/comparators";
+import { mantissaExponentComparator, variantComparator } from "../../utils/comparators";
 import { ReactNode, useEffect, useState } from "react";
 import { responseType } from "ui/src/types/response";
 
@@ -29,9 +29,7 @@ function getColumns({ id, referenceAllele, alternateAllele }: getColumnsType) {
     {
       id: "studyLocusId",
       label: "Navigate",
-      renderCell: ({ studyLocusId }) => (
-        <Navigate to={`/credible-set/${studyLocusId}`} />
-      ),
+      renderCell: ({ studyLocusId }) => <Navigate to={`/credible-set/${studyLocusId}`} />,
     },
     {
       id: "leadVariant",
@@ -153,8 +151,9 @@ function getColumns({ id, referenceAllele, alternateAllele }: getColumnsType) {
       filterValue: false,
       sortable: true,
       comparator: (a, b) => {
-        return a?.locus?.rows?.[0]?.posteriorProbability -
-          b?.locus?.rows?.[0]?.posteriorProbability;
+        return (
+          a?.locus?.rows?.[0]?.posteriorProbability - b?.locus?.rows?.[0]?.posteriorProbability
+        );
       },
       tooltip: (
         <>
@@ -201,9 +200,7 @@ function getColumns({ id, referenceAllele, alternateAllele }: getColumnsType) {
       sortable: true,
       filterValue: false,
       renderCell: ({ locusSize }) => {
-        return typeof locusSize?.count === "number"
-          ? locusSize.count.toLocaleString()
-          : naLabel;
+        return typeof locusSize?.count === "number" ? locusSize.count.toLocaleString() : naLabel;
       },
       exportValue: ({ locusSize }) => locusSize?.count,
     },
@@ -218,17 +215,15 @@ type BodyProps = {
 function Body({ id, entity }: BodyProps): ReactNode {
   const variables = {
     variantId: id,
+    size: table5HChunkSize,
+    index: 0,
   };
 
   const [request, setRequest] = useState<responseType>(initialResponse);
 
   const getAllQtlData = useBatchQuery({
     query: QTL_CREDIBLE_SETS_QUERY,
-    variables: {
-      variantId: id,
-      size: table5HChunkSize,
-      index: 0,
-    },
+    variables,
     dataPath: "data.variant.qtlCredibleSets",
     size: table5HChunkSize,
   });

diff --git a/packages/sections/src/variant/QTLCredibleSets/QTLCredibleSetsQuery.gql b/packages/sections/src/variant/QTLCredibleSets/QTLCredibleSetsQuery.gql
@@ -4,7 +4,7 @@ query QTLCredibleSetsQuery($variantId: String!, $size: Int!, $index: Int!) {
     referenceAllele
     alternateAllele
     qtlCredibleSets: credibleSets(
-      studyTypes: [sqtl, pqtl, eqtl, tuqtl]
+      studyTypes: [scsqtl, sceqtl, scpqtl, sctuqtl, sqtl, eqtl, pqtl, tuqtl]
       page: { size: $size, index: $index }
     ) {
       count

diff --git a/packages/sections/src/variant/QTLCredibleSets/QTLCredibleSetsSummaryFragment.gql b/packages/sections/src/variant/QTLCredibleSets/QTLCredibleSetsSummaryFragment.gql
@@ -1,6 +1,6 @@
 fragment QTLCredibleSetsSummaryFragment on Variant {
   qtlCredibleSets: credibleSets(
-    studyTypes: [sqtl, pqtl, eqtl, tuqtl]
+    studyTypes: [scsqtl, sceqtl, scpqtl, sctuqtl, sqtl, eqtl, pqtl, tuqtl]
     page: { size: 1, index: 0 }
   ) {
     count