refacator: format codebase

opentargets · Dec 12, 2024 · 72c5d49 · 72c5d49
1 parent 79db679
commit 72c5d49
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Showing 106 changed files with 933 additions and 1,146 deletions.
diff --git a/apps/platform/src/constants.js b/apps/platform/src/constants.js
@@ -347,4 +347,4 @@ export const populationMap = {
   nfe: "non-Finnish Europeans",
   eas: "East Asian",
   amr: "Admixed American",
-};
+};
diff --git a/apps/platform/src/pages/CredibleSetPage/Header.tsx b/apps/platform/src/pages/CredibleSetPage/Header.tsx
@@ -9,42 +9,33 @@ type HeaderProps = {
   studyId: string;
 };
 
-function Header({
-      loading,
-      variantId,
-      referenceAllele,
-      alternateAllele,
-      studyId 
-    }: HeaderProps) {
-
+function Header({ loading, variantId, referenceAllele, alternateAllele, studyId }: HeaderProps) {
   return (
     <HeaderBase
       loading={loading}
-      title="Credible set" 
+      title="Credible set"
       Icon={faDiagramProject}
       externalLinks={
         <>
           <ExternalLink
             title="Lead variant"
-            id={variantId &&
-              <DisplayVariantId
-                variantId={variantId}
-                referenceAllele={referenceAllele}
-                alternateAllele={alternateAllele}
-                expand={false}
-              />
+            id={
+              variantId && (
+                <DisplayVariantId
+                  variantId={variantId}
+                  referenceAllele={referenceAllele}
+                  alternateAllele={alternateAllele}
+                  expand={false}
+                />
+              )
             }
             url={`../variant/${variantId}`}
           />
-          <ExternalLink
-            title="Study ID"
-            id={studyId}
-            url={`../study/${studyId}`}
-          />
+          <ExternalLink title="Study ID" id={studyId} url={`../study/${studyId}`} />
         </>
       }
     />
   );
 }
 
-export default Header;
+export default Header;
diff --git a/apps/platform/src/pages/DiseasePage/Profile.jsx b/apps/platform/src/pages/DiseasePage/Profile.jsx
@@ -47,7 +47,7 @@ const DISEASE_PROFILE_QUERY = gql`
       ...DiseaseProfileHeaderFragment
       ...DiseaseProfileSummaryFragment
     }
-    studies(diseaseIds: [$efoId], page: { size: 1, index: 0}) {
+    studies(diseaseIds: [$efoId], page: { size: 1, index: 0 }) {
       count
     }
   }

diff --git a/apps/platform/src/pages/SearchPage/SearchContainer.jsx b/apps/platform/src/pages/SearchPage/SearchContainer.jsx
@@ -13,7 +13,7 @@ import {
   faDna,
   faMapPin,
   faPrescriptionBottleAlt,
-  faStethoscope
+  faStethoscope,
 } from "@fortawesome/free-solid-svg-icons";
 import { ErrorBoundary } from "ui";
 
@@ -71,7 +71,9 @@ const SearchFilters = ({ entities, entitiesCount, setEntity }) => {
       />
       <FormControlLabel
         className={classes.label}
-        control={<Checkbox checked={entities.includes("variant")} onChange={setEntity("variant")} />}
+        control={
+          <Checkbox checked={entities.includes("variant")} onChange={setEntity("variant")} />
+        }
         label={
           <>
             <FontAwesomeIcon icon={faMapPin} fixedWidth className={classes.labelIcon} />

diff --git a/apps/platform/src/pages/SearchPage/VariantDetail.jsx b/apps/platform/src/pages/SearchPage/VariantDetail.jsx
@@ -6,11 +6,13 @@ import { Link, DisplayVariantId, LongText } from "ui";
 function VariantDetail({ data }) {
   return (
     <CardContent>
-      <Typography color="primary" variant="h5"
+      <Typography
+        color="primary"
+        variant="h5"
         sx={{
-          whiteSpace: 'nowrap',
-          overflow: 'hidden',
-          textOverflow: 'ellipsis',
+          whiteSpace: "nowrap",
+          overflow: "hidden",
+          textOverflow: "ellipsis",
         }}
       >
         <Link to={`/variant/${data.id}`}>
@@ -26,52 +28,36 @@ function VariantDetail({ data }) {
         <FontAwesomeIcon icon={faMapPin} /> Variant
       </Typography>
       <LongText lineLimit={4}>{data.variantDescription}</LongText>
-      {data.rsIds.length > 0 &&
+      {data.rsIds.length > 0 && (
         <>
-          <Typography variant="subtitle1">
-            Ensembl
-          </Typography>
-          <Typography variant="body2">
-            {data.rsIds.join(", ")}
-          </Typography>
+          <Typography variant="subtitle1">Ensembl</Typography>
+          <Typography variant="body2">{data.rsIds.join(", ")}</Typography>
         </>
-      }
-      <Typography variant="subtitle1">
-        GRCh38
-      </Typography>
+      )}
+      <Typography variant="subtitle1">GRCh38</Typography>
       <Typography variant="body2">
         {data.chromosome}:{data.position}
       </Typography>
-      <Typography variant="subtitle1">
-        Reference Allele
-      </Typography>
+      <Typography variant="subtitle1">Reference Allele</Typography>
       <Typography component="div" variant="body2">
         <LongText lineLimit={2}>
-          <span style={{ textWrap: "wrap", wordWrap: "break-word" }}>
-            {data.referenceAllele}
-          </span>
+          <span style={{ textWrap: "wrap", wordWrap: "break-word" }}>{data.referenceAllele}</span>
         </LongText>
       </Typography>
-      <Typography variant="subtitle1">
-        Alternate Allele
-      </Typography>
+      <Typography variant="subtitle1">Alternate Allele</Typography>
       <Typography component="div" variant="body2">
         <LongText lineLimit={2}>
-          <span style={{ textWrap: "wrap", wordWrap: "break-word" }}>
-            {data.alternateAllele}
-          </span>
+          <span style={{ textWrap: "wrap", wordWrap: "break-word" }}>{data.alternateAllele}</span>
         </LongText>
       </Typography>
-      {data.mostSevereConsequence &&
+      {data.mostSevereConsequence && (
         <>
-          <Typography variant="subtitle1">
-            Most Severe Consequence
-          </Typography>
+          <Typography variant="subtitle1">Most Severe Consequence</Typography>
           <Typography variant="body2">
-            {data.mostSevereConsequence.label.replace(/_/g, ' ')}
+            {data.mostSevereConsequence.label.replace(/_/g, " ")}
           </Typography>
         </>
-      }
+      )}
     </CardContent>
   );
 }

diff --git a/apps/platform/src/pages/SearchPage/VariantResult.jsx b/apps/platform/src/pages/SearchPage/VariantResult.jsx
@@ -36,14 +36,12 @@ function VariantResult({ data, highlights }) {
       <Typography variant="body2" component="div">
         <LongText lineLimit={4}>{data.variantDescription}</LongText>
       </Typography>
-      {data.rsIds.length > 0 &&
-        <Typography variant="body2">
-          Ensembl: {data.rsIds.join(", ")}
-        </Typography>
-      }
+      {data.rsIds.length > 0 && (
+        <Typography variant="body2">Ensembl: {data.rsIds.join(", ")}</Typography>
+      )}
       <Highlights highlights={highlights} />
     </div>
   );
 }
 
-export default VariantResult;
+export default VariantResult;
diff --git a/apps/platform/src/pages/StudyPage/StudyProfileHeader.tsx b/apps/platform/src/pages/StudyPage/StudyProfileHeader.tsx
@@ -18,7 +18,7 @@ import STUDY_PROFILE_HEADER_FRAGMENT from "./StudyProfileHeader.gql";
 function ProfileHeader() {
   const { loading, error, data } = usePlatformApi();
 
-  // TODO: Errors! 
+  // TODO: Errors!
   if (error) return null;
 
   const {
@@ -48,7 +48,6 @@ function ProfileHeader() {
 
   return (
     <BaseProfileHeader>
-
       <Box>
         <Field loading={loading} title="Study type">
           {studyType?.replace(/(qtl|gwas)/gi, match => match.toUpperCase())}
@@ -80,7 +79,7 @@ function ProfileHeader() {
             )}
           </>
         )}
-        {studyType !== "gwas" && (  // QTL
+        {studyType !== "gwas" && ( // QTL
           <>
             {projectId && (
               <Field loading={loading} title="Project">
@@ -94,10 +93,7 @@ function ProfileHeader() {
             )}
             {biosample?.biosampleId && (
               <Field loading={loading} title="Affected cell/tissue">
-                <Link
-                  external
-                  to={`https://www.ebi.ac.uk/ols4/search?q=${biosample.biosampleId}`}
-                >
+                <Link external to={`https://www.ebi.ac.uk/ols4/search?q=${biosample.biosampleId}`}>
                   {biosample.biosampleName}
                 </Link>
               </Field>
@@ -113,53 +109,53 @@ function ProfileHeader() {
             {publicationDate?.slice(0, 4)})
           </Field>
         )}
-        {pubmedId &&
+        {pubmedId && (
           <Field loading={loading} title="PubMed">
-            <PublicationsDrawer
-              name={pubmedId}
-              entries={[{ name: pubmedId }]}
-            />
+            <PublicationsDrawer name={pubmedId} entries={[{ name: pubmedId }]} />
           </Field>
-        }
+        )}
       </Box>
 
       <Box>
         <Field loading={loading} title="Summary statistics">
-          {!hasSumstats
-            ? "Not Available"
-            : sumstatQCValues
-              ? <DetailPopover title="Available">
-                <SummaryStatsTable sumstatQCValues={sumstatQCValues} />
-              </DetailPopover>
-              : "Available"
-          }
+          {!hasSumstats ? (
+            "Not Available"
+          ) : sumstatQCValues ? (
+            <DetailPopover title="Available">
+              <SummaryStatsTable sumstatQCValues={sumstatQCValues} />
+            </DetailPopover>
+          ) : (
+            "Available"
+          )}
         </Field>
-        {qualityControls?.length > 0 &&
+        {qualityControls?.length > 0 && (
           <Box>
             <DetailPopover title="QC warnings">
-              <ul style={{
-                display: "flex",
-                flexDirection: "column",
-                gap: "0.25rem",
-                padding: 0,
-                margin: "0 0 0 1rem"
-              }}>
+              <ul
+                style={{
+                  display: "flex",
+                  flexDirection: "column",
+                  gap: "0.25rem",
+                  padding: 0,
+                  margin: "0 0 0 1rem",
+                }}
+              >
                 {qualityControls.map(warning => (
                   <li key={warning}>{warning}</li>
                 ))}
               </ul>
             </DetailPopover>
           </Box>
-        }
-        {nSamples &&
+        )}
+        {nSamples && (
           <Field loading={loading} title="Sample size">
             <DisplaySampleSize
               nSamples={nSamples}
               cohorts={cohorts}
               initialSampleSize={initialSampleSize}
             />
           </Field>
-        }
+        )}
         <Field loading={loading} title="N cases">
           {/* do not show anything when value 0 */}
           {nCases ? nCases?.toLocaleString() : null}
@@ -171,7 +167,7 @@ function ProfileHeader() {
         <Field loading={loading} title="Analysis">
           {analysisFlags?.join(", ")}
         </Field>
-        {ldPopulationStructure?.length > 0 &&
+        {ldPopulationStructure?.length > 0 && (
           <Box display="flex" sx={{ gap: 1 }}>
             {ldPopulationStructure.map(({ ldPopulation, relativeSampleSize }) => (
               <LabelChip
@@ -182,9 +178,8 @@ function ProfileHeader() {
               />
             ))}
           </Box>
-        }
+        )}
       </Box>
-
     </BaseProfileHeader>
   );
 }