[AppConfig]: format codebase to match prettier rules (#318)

* feat: add format script on packages * fix: format platform codebase * fix: format genetics codebase * fix: format platform/sections codebase * fix: format ui package codebase * feat: update turbo config
opentargets · Jan 30, 2024 · b6f640c · b6f640c
1 parent 970f0d3
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diff --git a/apps/genetics/src/client.js b/apps/genetics/src/client.js
@@ -1,5 +1,5 @@
-import config from './config';
-import { ApolloClient, InMemoryCache } from '@apollo/client';
+import config from "./config";
+import { ApolloClient, InMemoryCache } from "@apollo/client";
 
 const client = new ApolloClient({
   uri: config.apiUrl,

diff --git a/apps/genetics/src/components/ColocForGeneTable/index.js b/apps/genetics/src/components/ColocForGeneTable/index.js
@@ -1 +1 @@
-export { default } from './ColocForGeneTable';
+export { default } from "./ColocForGeneTable";
diff --git a/apps/genetics/src/components/ColocQTLGeneTissueTable/index.js b/apps/genetics/src/components/ColocQTLGeneTissueTable/index.js
@@ -1,7 +1,7 @@
-import ColocQTLGeneTissueTableCmp from './ColocQTLGeneTissueTable';
+import ColocQTLGeneTissueTableCmp from "./ColocQTLGeneTissueTable";
 
-export { getTableColumns } from './ColumnRenderers';
+export { getTableColumns } from "./ColumnRenderers";
 
-export { useColocTable } from './useColocTable';
+export { useColocTable } from "./useColocTable";
 
 export default ColocQTLGeneTissueTableCmp;
diff --git a/apps/genetics/src/components/ColocQTLGeneTissueTable/useColocTable.js b/apps/genetics/src/components/ColocQTLGeneTissueTable/useColocTable.js
@@ -1,5 +1,5 @@
-import { descending } from 'd3';
-import { getPhenotypeId, getSpliceId } from '../../utils';
+import { descending } from "d3";
+import { getPhenotypeId, getSpliceId } from "../../utils";
 
 export const useColocTable = data => {
   const uniqueStudyGenePhenotypes = data.reduce((acc, d) => {
@@ -21,42 +21,37 @@ export const useColocTable = data => {
     }, {})
   );
 
-  const dataByPhenotypeId = uniquePhenotypeIds.map(
-    ({ phenotypeId, gene, qtlStudyName }) => ({
-      phenotypeId,
-      gene,
-      qtlStudyName,
-      ...uniqueTissues.reduce((acc, t) => {
-        const items = data
-          .filter(
-            d =>
-              d.gene.id === gene.id &&
-              d.qtlStudyName === qtlStudyName &&
-              d.tissue.id === t.id
-          )
-          .map(d => ({
-            h3: d.h3,
-            h4: d.h4,
-            log2h4h3: d.log2h4h3,
-            beta: d.beta,
-            splice: getSpliceId(d.phenotypeId),
-          }))
-          .sort((a, b) => descending(a.log2h4h3, b.log2h4h3));
+  const dataByPhenotypeId = uniquePhenotypeIds.map(({ phenotypeId, gene, qtlStudyName }) => ({
+    phenotypeId,
+    gene,
+    qtlStudyName,
+    ...uniqueTissues.reduce((acc, t) => {
+      const items = data
+        .filter(
+          d => d.gene.id === gene.id && d.qtlStudyName === qtlStudyName && d.tissue.id === t.id
+        )
+        .map(d => ({
+          h3: d.h3,
+          h4: d.h4,
+          log2h4h3: d.log2h4h3,
+          beta: d.beta,
+          splice: getSpliceId(d.phenotypeId),
+        }))
+        .sort((a, b) => descending(a.log2h4h3, b.log2h4h3));
 
-        // there could be multiple loci for gene-tissue, so pick
-        // by highest log2h4h3 value (this should not happen due
-        // to deduplication on index variants)
-        if (items.length > 1) {
-          console.info(
-            `Multiple entries found: ${gene.symbol}, ${qtlStudyName}, ${phenotypeId}`,
-            items
-          );
-        }
-        acc[t.id] = items.length > 0 ? items[0] : null;
-        return acc;
-      }, {}),
-    })
-  );
+      // there could be multiple loci for gene-tissue, so pick
+      // by highest log2h4h3 value (this should not happen due
+      // to deduplication on index variants)
+      if (items.length > 1) {
+        console.info(
+          `Multiple entries found: ${gene.symbol}, ${qtlStudyName}, ${phenotypeId}`,
+          items
+        );
+      }
+      acc[t.id] = items.length > 0 ? items[0] : null;
+      return acc;
+    }, {}),
+  }));
 
   return {
     uniqueTissues,

diff --git a/apps/genetics/src/components/ColocQTLGeneTissueTable/utils.js b/apps/genetics/src/components/ColocQTLGeneTissueTable/utils.js
@@ -1,10 +1,6 @@
 export const tissueComparator = t => (a, b) => {
   if (a[t] && b[t]) {
-    return a[t].log2h4h3 > b[t].log2h4h3
-      ? 1
-      : a[t].log2h4h3 === b[t].log2h4h3
-      ? 0
-      : -1;
+    return a[t].log2h4h3 > b[t].log2h4h3 ? 1 : a[t].log2h4h3 === b[t].log2h4h3 ? 0 : -1;
   } else if (a[t] && !b[t]) {
     return 1;
   } else if (!a[t] && b[t]) {

diff --git a/apps/genetics/src/components/ExternalLink/index.js b/apps/genetics/src/components/ExternalLink/index.js
@@ -1,2 +1,2 @@
-export { default as ExternalLink } from './ExternalLink';
-export { default as XRefLinks } from './XRefLinks';
+export { default as ExternalLink } from "./ExternalLink";
+export { default as XRefLinks } from "./XRefLinks";
diff --git a/apps/genetics/src/components/Search/index.js b/apps/genetics/src/components/Search/index.js
@@ -1 +1 @@
-export { default } from './Search';
+export { default } from "./Search";
diff --git a/apps/genetics/src/components/theme.js b/apps/genetics/src/components/theme.js
@@ -1,23 +1,23 @@
-import { lighten, darken } from 'polished';
+import { lighten, darken } from "polished";
 
-const PRIMARY = '#0091eb';
-const SECONDARY = '#ff6350';
+const PRIMARY = "#0091eb";
+const SECONDARY = "#ff6350";
 // const TERTIARY = '#00a252';
 const GREY = {
-  50: '#fafafa',
-  100: '#f5f5f5',
-  200: '#eeeeee',
-  300: '#e0e0e0',
-  400: '#bdbdbd',
-  500: '#9e9e9e',
-  600: '#757575',
-  700: '#616161',
-  800: '#424242',
-  900: '#212121',
-  A100: '#d5d5d5',
-  A200: '#aaaaaa',
-  A400: '#303030',
-  A700: '#616161',
+  50: "#fafafa",
+  100: "#f5f5f5",
+  200: "#eeeeee",
+  300: "#e0e0e0",
+  400: "#bdbdbd",
+  500: "#9e9e9e",
+  600: "#757575",
+  700: "#616161",
+  800: "#424242",
+  900: "#212121",
+  A100: "#d5d5d5",
+  A200: "#aaaaaa",
+  A400: "#303030",
+  A700: "#616161",
 };
 
 const theme = {
@@ -48,13 +48,13 @@ const theme = {
   },
   gecko: {
     color: GREY[500],
-    backgroundColor: 'white',
+    backgroundColor: "white",
     finemappingColor: GREY[600],
     colorSelected: PRIMARY,
-    backgroundColorSelected: 'white',
+    backgroundColorSelected: "white",
     finemappingColorSelected: darken(0.3, PRIMARY),
     colorChained: SECONDARY,
-    backgroundColorChained: 'white',
+    backgroundColorChained: "white",
     finemappingColorChained: darken(0.3, SECONDARY),
     connectorColor: GREY[300],
     connectorColorSelected: lighten(0.2, PRIMARY),

diff --git a/apps/genetics/src/config.js b/apps/genetics/src/config.js
@@ -1,13 +1,12 @@
 const config = {
-  apiUrl:
-  window.configApiUrl ?? 'https://api.genetics.opentargets.org/graphql',
-    // window.configApiUrl ?? 'https://api.genetics.dev.opentargets.xyz/graphql',
+  apiUrl: window.configApiUrl ?? "https://api.genetics.opentargets.org/graphql",
+  // window.configApiUrl ?? 'https://api.genetics.dev.opentargets.xyz/graphql',
   googleTagManagerID: window.configGoogleTagManagerID ?? null,
-  helpdeskEmail: window.configHelpdeskEmail ?? '[email protected]',
+  helpdeskEmail: window.configHelpdeskEmail ?? "[email protected]",
   profile: window.configProfile ?? {},
   platformUrl: window.configPlatformUrl
-    ? window.configPlatformUrl.replace(/\/$/, '')
-    : 'https://platform.opentargets.org',
+    ? window.configPlatformUrl.replace(/\/$/, "")
+    : "https://platform.opentargets.org",
 };
 
 export default config;
diff --git a/apps/genetics/src/configuration.js b/apps/genetics/src/configuration.js
@@ -1,17 +1,17 @@
-import pkg from '../package.json';
+import pkg from "../package.json";
 
 const defaults = {
-  REACT_APP_GRAPHQL_API_URL: 'https://genetics-api.opentargets.io',
-  REACT_APP_PLATFORM_URL: 'https://platform.opentargets.org/',
-  REACT_APP_GIT_REVISION: '2222ccc',
-  REACT_APP_CONTACT_URL: 'mailto:[email protected]',
+  REACT_APP_GRAPHQL_API_URL: "https://genetics-api.opentargets.io",
+  REACT_APP_PLATFORM_URL: "https://platform.opentargets.org/",
+  REACT_APP_GIT_REVISION: "2222ccc",
+  REACT_APP_CONTACT_URL: "mailto:[email protected]",
 };
 
 const envVarOrDefault = envVarName =>
   process.env[envVarName] ? process.env[envVarName] : defaults[envVarName];
 
 export const packageVersion = pkg.version;
-export const graphqlApiUrl = envVarOrDefault('REACT_APP_GRAPHQL_API_URL');
-export const platformUrl = envVarOrDefault('REACT_APP_PLATFORM_URL');
-export const gitRevision = envVarOrDefault('REACT_APP_GIT_REVISION');
-export const contactUrl = envVarOrDefault('REACT_APP_CONTACT_URL');
+export const graphqlApiUrl = envVarOrDefault("REACT_APP_GRAPHQL_API_URL");
+export const platformUrl = envVarOrDefault("REACT_APP_PLATFORM_URL");
+export const gitRevision = envVarOrDefault("REACT_APP_GIT_REVISION");
+export const contactUrl = envVarOrDefault("REACT_APP_CONTACT_URL");
diff --git a/apps/genetics/src/constants.js b/apps/genetics/src/constants.js
@@ -1,102 +1,102 @@
-import { faBook, faEnvelope } from '@fortawesome/free-solid-svg-icons';
+import { faBook, faEnvelope } from "@fortawesome/free-solid-svg-icons";
 import {
   faDiscourse,
   faTwitterSquare,
   faLinkedin,
   faGithubSquare,
   faYoutubeSquare,
-} from '@fortawesome/free-brands-svg-icons';
+} from "@fortawesome/free-brands-svg-icons";
 
-import { contactUrl as contactUrlConfig } from './configuration';
-import config from './config';
+import { contactUrl as contactUrlConfig } from "./configuration";
+import config from "./config";
 
 export const pvalThreshold = 4.94e-322;
 
 export const contactUrl = contactUrlConfig;
 
-export const naLabel = 'N/A';
+export const naLabel = "N/A";
 
 export const mainMenuItems = [
   // Documentation
   {
-    name: 'Documentation',
-    url: 'https://genetics-docs.opentargets.org',
+    name: "Documentation",
+    url: "https://genetics-docs.opentargets.org",
     external: true,
   },
   // Data downloads
   {
-    name: 'Data downloads',
-    url: 'https://genetics-docs.opentargets.org/data-access/data-download',
+    name: "Data downloads",
+    url: "https://genetics-docs.opentargets.org/data-access/data-download",
     external: true,
   },
   // API
   // TODO: update config
   {
-    name: 'API',
-    url: '/api',
+    name: "API",
+    url: "/api",
     // url: config.apiUrl.split('/graphql')[0],
     external: false,
   },
   // Community
   {
-    name: 'Community',
-    url: 'https://community.opentargets.org/',
+    name: "Community",
+    url: "https://community.opentargets.org/",
     external: true,
   },
 ];
 
 export const externalLinks = {
   about: [
     {
-      label: 'Community forum',
-      url: 'https://community.opentargets.org/',
+      label: "Community forum",
+      url: "https://community.opentargets.org/",
     },
     {
-      label: 'Privacy notice',
-      url: 'https://www.ebi.ac.uk/data-protection/privacy-notice/open-targets',
+      label: "Privacy notice",
+      url: "https://www.ebi.ac.uk/data-protection/privacy-notice/open-targets",
     },
     {
-      label: 'Terms of use',
+      label: "Terms of use",
       url: `https://genetics-docs.opentargets.org/terms-of-use`,
     },
   ],
   license: {
-    label: 'Open Targets Genetics',
-    url: 'https://genetics.opentargets.org/',
+    label: "Open Targets Genetics",
+    url: "https://genetics.opentargets.org/",
   },
   network: [
-    { label: 'Science', url: 'https://www.opentargets.org/science' },
-    { label: 'Publications', url: 'https://www.opentargets.org/publications' },
-    { label: 'Platform', url: 'https://platform.opentargets.org/' },
-    { label: 'Jobs', url: 'https://www.opentargets.org/jobs' },
-    { label: 'Blog', url: 'https://blog.opentargets.org' },
+    { label: "Science", url: "https://www.opentargets.org/science" },
+    { label: "Publications", url: "https://www.opentargets.org/publications" },
+    { label: "Platform", url: "https://platform.opentargets.org/" },
+    { label: "Jobs", url: "https://www.opentargets.org/jobs" },
+    { label: "Blog", url: "https://blog.opentargets.org" },
   ],
   partners: [
-    { label: 'Bristol Myers Squibb', url: 'https://www.bms.com' },
-    { label: 'EMBL-EBI', url: 'http://www.ebi.ac.uk' },
-    { label: 'Genentech', url: 'https://www.gene.com' },
-    { label: 'GSK', url: 'http://www.gsk.com' },
-    { label: 'Pfizer', url: 'https://pfizer.com/' },
-    { label: 'Sanofi', url: 'https://www.sanofi.com' },
-    { label: 'Wellcome Sanger Institute', url: 'http://www.sanger.ac.uk' },
+    { label: "Bristol Myers Squibb", url: "https://www.bms.com" },
+    { label: "EMBL-EBI", url: "http://www.ebi.ac.uk" },
+    { label: "Genentech", url: "https://www.gene.com" },
+    { label: "GSK", url: "http://www.gsk.com" },
+    { label: "Pfizer", url: "https://pfizer.com/" },
+    { label: "Sanofi", url: "https://www.sanofi.com" },
+    { label: "Wellcome Sanger Institute", url: "http://www.sanger.ac.uk" },
   ],
   help: [
     {
-      label: 'Documentation',
+      label: "Documentation",
       icon: faBook,
-      url: 'https://genetics-docs.opentargets.org',
+      url: "https://genetics-docs.opentargets.org",
     },
     {
-      label: 'Community',
+      label: "Community",
       icon: faDiscourse,
-      url: 'https://community.opentargets.org',
+      url: "https://community.opentargets.org",
       external: true,
-    }
+    },
   ],
   social: [
-    { icon: faTwitterSquare, url: 'https://twitter.com/opentargets' },
-    { icon: faLinkedin, url: 'https://www.linkedin.com/company/open-targets' },
-    { icon: faYoutubeSquare, url: 'https://www.youtube.com/opentargets' },
-    { icon: faGithubSquare, url: 'https://github.com/opentargets' },
+    { icon: faTwitterSquare, url: "https://twitter.com/opentargets" },
+    { icon: faLinkedin, url: "https://www.linkedin.com/company/open-targets" },
+    { icon: faYoutubeSquare, url: "https://www.youtube.com/opentargets" },
+    { icon: faGithubSquare, url: "https://github.com/opentargets" },
   ],
 };
diff --git a/apps/genetics/src/hooks/useDebounce.js b/apps/genetics/src/hooks/useDebounce.js
@@ -1,19 +1,16 @@
-import { useEffect, useState } from 'react';
+import { useEffect, useState } from "react";
 
 function useDebounce(value, delay) {
   const [debouncedValue, setDebouncedValue] = useState(value);
 
-  useEffect(
-    () => {
-      const handler = setTimeout(() => {
-        if (debouncedValue !== value) setDebouncedValue(value);
-      }, delay);
-      return () => {
-        clearTimeout(handler);
-      };
-    },
-    [value, delay, debouncedValue]
-  );
+  useEffect(() => {
+    const handler = setTimeout(() => {
+      if (debouncedValue !== value) setDebouncedValue(value);
+    }, delay);
+    return () => {
+      clearTimeout(handler);
+    };
+  }, [value, delay, debouncedValue]);
 
   return debouncedValue;
 }