[UI]: lint on

biome.json

@@ -29,10 +29,10 @@
       "!**/*.d.ts",
       "!**/generated",
       "!**/apps/platform/src",
-      "!**/packages/ui",
       "!**/packages/sections",
       "!**/packages/ot-config",
-      "!**/packages/ot-constants",
+      "**/packages/ot-constants",
+      "!**/packages/ot-constants/src/types",
       "!**/packages/ot-utils"
     ]
   },
@@ -70,7 +70,7 @@
         "useButtonType": "error"
       },
       "correctness": {
-        "useExhaustiveDependencies": "warn",
+        "useExhaustiveDependencies": "off",
         "noUnusedVariables": "warn"
       },
       "suspicious": {

packages/ot-config/src/environment.ts

@@ -1,26 +1,26 @@
 import type { Config, Environment } from "./types";
 
 export const getEnvironmentConfig = (env: Environment): Config => {
-	const configs: Record<Environment, Config> = {
-		development: {
-			urlApi: "http://localhost:8080",
-			urlAiApi: "http://localhost:8081",
-			profile: {},
-			googleTagManagerID: null,
-			geneticsPortalUrl: "https://genetics.opentargets.org",
-			gitVersion: "",
-		},
-		production: {
-			urlApi: "https://api.platform.opentargets.org",
-			urlAiApi: "https://ai.platform.opentargets.org",
-			profile: {},
-			googleTagManagerID: "GTM-XXXXX",
-			geneticsPortalUrl: "https://genetics.opentargets.org",
-			gitVersion: "",
-		},
-	};
+  const configs: Record<Environment, Config> = {
+    development: {
+      urlApi: "http://localhost:8080",
+      urlAiApi: "http://localhost:8081",
+      profile: {},
+      googleTagManagerID: null,
+      geneticsPortalUrl: "https://genetics.opentargets.org",
+      gitVersion: "",
+    },
+    production: {
+      urlApi: "https://api.platform.opentargets.org",
+      urlAiApi: "https://ai.platform.opentargets.org",
+      profile: {},
+      googleTagManagerID: "GTM-XXXXX",
+      geneticsPortalUrl: "https://genetics.opentargets.org",
+      gitVersion: "",
+    },
+  };
 
-	return configs[env];
+  return configs[env];
 };
 
 // Vite environment variables
@@ -29,13 +29,12 @@ const ENV_AI_API_URL: string | undefined = import.meta.env.VITE_AI_API_URL;
 const ENV_GIT_VERSION: string | undefined = import.meta.env.VITE_GIT_VERSION;
 
 export const getConfig = (): Config => {
-	return {
-		urlApi:window.configUrlApi ?? ENV_API_URL ?? "",
-		urlAiApi: window.configOTAiApi ?? ENV_AI_API_URL ?? "",
-		gitVersion: window.gitVersion ?? ENV_GIT_VERSION ?? "",
-		profile: window.configProfile ?? { isPartnerPreview: false },
-		googleTagManagerID: window.configGoogleTagManagerID ?? null,
-		geneticsPortalUrl:
-			window.configGeneticsPortalUrl ?? "https://genetics.opentargets.org",
-	};
+  return {
+    urlApi: window.configUrlApi ?? ENV_API_URL ?? "",
+    urlAiApi: window.configOTAiApi ?? ENV_AI_API_URL ?? "",
+    gitVersion: window.gitVersion ?? ENV_GIT_VERSION ?? "",
+    profile: window.configProfile ?? { isPartnerPreview: false },
+    googleTagManagerID: window.configGoogleTagManagerID ?? null,
+    geneticsPortalUrl: window.configGeneticsPortalUrl ?? "https://genetics.opentargets.org",
+  };
 };

packages/ot-config/src/index.ts

@@ -1,6 +1,6 @@
-export * from "./types";
 export * from "./environment";
 export * from "./theme";
+export * from "./types";
 
 // Add window augmentation
 declare global {

packages/ot-config/src/theme.ts

@@ -1,6 +1,6 @@
-import { lighten, darken } from "polished";
 import { grey } from "@mui/material/colors";
-import { ThemeOptions, createTheme } from "@mui/material/styles";
+import { createTheme, type ThemeOptions } from "@mui/material/styles";
+import { darken, lighten } from "polished";
 import { getConfig } from "./environment";
 
 const config = getConfig();

packages/ot-constants/scripts/generate-graphql-types.js

@@ -1,8 +1,8 @@
 #!/usr/bin/env node
 
-import fs from "fs";
-import path from "path";
-import { fileURLToPath } from "url";
+import fs from "node:fs";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
 
 const __filename = fileURLToPath(import.meta.url);
 const __dirname = path.dirname(__filename);
@@ -148,7 +148,7 @@ function generateTypeScriptInterface(type) {
 
   let interfaceCode = `export interface ${type.name} {\n`;
 
-  fields.forEach(field => {
+  for (const field of fields) {
     const fieldType = graphqlTypeToTypeScript(field.type);
     const isOptional = field.type.kind !== "NON_NULL";
     const optionalMarker = isOptional ? "?" : "";
@@ -157,7 +157,7 @@ function generateTypeScriptInterface(type) {
       interfaceCode += `  /** ${field.description} */\n`;
     }
     interfaceCode += `  ${field.name}${optionalMarker}: ${fieldType};\n`;
-  });
+  }
 
   interfaceCode += "}\n\n";
   return interfaceCode;
@@ -171,12 +171,12 @@ function generateTypeScriptEnum(type) {
 
   let enumCode = `export enum ${type.name} {\n`;
 
-  type.enumValues.forEach(enumValue => {
+  for (const enumValue of type.enumValues) {
     if (enumValue.description) {
       enumCode += `  /** ${enumValue.description} */\n`;
     }
     enumCode += `  ${enumValue.name} = '${enumValue.name}',\n`;
-  });
+  }
 
   enumCode += "}\n\n";
   return enumCode;
@@ -188,7 +188,7 @@ function generateTypeScriptUnion(type) {
     return null;
   }
 
-  const possibleTypes = type.possibleTypes.map(t => t.name).join(" | ");
+  const possibleTypes = type.possibleTypes.map((t) => t.name).join(" | ");
   return `export type ${type.name} = ${possibleTypes};\n\n`;
 }
 
@@ -209,7 +209,7 @@ async function testEndpoint(endpoint) {
 
     if (response.ok) {
       const result = await response.json();
-      if (result.data && result.data.__schema) {
+      if (result.data?.__schema) {
         console.log(`✅ Endpoint working: ${endpoint}`);
         return result;
       }
@@ -246,7 +246,7 @@ async function generateGraphQLTypes() {
 
     const schema = result.data.__schema;
     const types = schema.types.filter(
-      type =>
+      (type) =>
         !type.name.startsWith("__") &&
         type.name !== "Query" &&
         type.name !== "Mutation" &&
@@ -263,32 +263,32 @@ async function generateGraphQLTypes() {
 
     // Generate interfaces and input types
     const objectTypes = types.filter(
-      type => type.kind === "OBJECT" || type.kind === "INPUT_OBJECT"
+      (type) => type.kind === "OBJECT" || type.kind === "INPUT_OBJECT"
     );
-    objectTypes.forEach(type => {
+    for (const type of objectTypes) {
       const interfaceCode = generateTypeScriptInterface(type);
       if (interfaceCode) {
         generatedCode += interfaceCode;
       }
-    });
+    }
 
     // Generate enums
-    const enumTypes = types.filter(type => type.kind === "ENUM");
-    enumTypes.forEach(type => {
+    const enumTypes = types.filter((type) => type.kind === "ENUM");
+    for (const type of enumTypes) {
       const enumCode = generateTypeScriptEnum(type);
       if (enumCode) {
         generatedCode += enumCode;
       }
-    });
+    }
 
     // Generate union types
-    const unionTypes = types.filter(type => type.kind === "UNION");
-    unionTypes.forEach(type => {
+    const unionTypes = types.filter((type) => type.kind === "UNION");
+    for (const type of unionTypes) {
       const unionCode = generateTypeScriptUnion(type);
       if (unionCode) {
         generatedCode += unionCode;
       }
-    });
+    }
 
     // Write the generated types to a file in the types folder
     const outputPath = path.join(__dirname, "..", "src", "types", "graphql-types.ts");

packages/ot-constants/src/alphaFold.ts

@@ -1,4 +1,4 @@
-import { scaleLinear, interpolateLab, rgb, scaleQuantize } from "d3";
+import { interpolateLab, rgb, scaleLinear } from "d3";
 
 export const alphaFoldConfidenceBands = [
   { lowerLimit: 90, label: "Very high", sublabel: "90 > pLDDT", color: "rgb(0, 83, 214)" },
@@ -12,7 +12,10 @@ export const alphaFoldConfidenceBands = [
   { lowerLimit: 0, label: "Very low ", sublabel: "50 > pLDDT", color: "rgb(255, 125, 69)" },
 ];
 
-export function getAlphaFoldConfidence(atom, propertyName = "label") {
+export function getAlphaFoldConfidence(
+  atom: { b: number },
+  propertyName: "label" | "sublabel" | "color" = "label"
+): string {
   for (const obj of alphaFoldConfidenceBands) {
     if (atom.b > obj.lowerLimit) return obj[propertyName];
   }
@@ -35,7 +38,10 @@ export const alphaFoldPathogenicityBands = [
   { lowerLimit: 0, label: "Likely benign", sublabel: "score < 0.34", color: "rgb(61, 84, 147)" },
 ];
 
-export function getAlphaFoldPathogenicity(score, propertyName = "label") {
+export function getAlphaFoldPathogenicity(
+  score: number,
+  propertyName: "label" | "sublabel" | "color" = "label"
+): string {
   for (const obj of alphaFoldPathogenicityBands) {
     if (score > obj.lowerLimit) return obj[propertyName];
   }
@@ -59,7 +65,7 @@ export const alphaFoldPathogenicityColorScale = scaleLinear()
 // only some of the scale breakpoints are meaningful for the legend
 alphaFoldPathogenicityColorScale._primaryDomain = [0, 0.34, 0.564, 1];
 
-export function getAlphaFoldPathogenicityColor(score) {
+export function getAlphaFoldPathogenicityColor(score: number) {
   return alphaFoldPathogenicityColorScale(score);
 }
 
@@ -109,4 +115,4 @@ export const aminoAcidHydrophobicity = {
   GLU: { value: -31, label: "hydrophilic" },
   PRO: { value: -46, label: "hydrophilic" },
   ASP: { value: -55, label: "hydrophilic" },
-};
+};

packages/ot-constants/src/index.ts

@@ -1,12 +1,12 @@
-import { IconDefinition } from "@fortawesome/fontawesome-svg-core";
-import { faBook, faEnvelope } from "@fortawesome/free-solid-svg-icons";
+import type { IconDefinition } from "@fortawesome/fontawesome-svg-core";
 import {
   faDiscourse,
-  faTwitterSquare,
-  faLinkedin,
   faGithubSquare,
+  faLinkedin,
+  faTwitterSquare,
   faYoutubeSquare,
 } from "@fortawesome/free-brands-svg-icons";
+import { faBook, faEnvelope } from "@fortawesome/free-solid-svg-icons";
 import { getConfig } from "@ot/config";
 
 const config = getConfig();
@@ -303,15 +303,17 @@ export const VIEW = {
   table: "Table",
 };
 
-export const getStudyTypeDisplay = (studyType: string | null | undefined): string | null | undefined => {
+export const getStudyTypeDisplay = (
+  studyType: string | null | undefined
+): string | null | undefined => {
   if (studyType) return studyType?.replace(/(qtl|gwas)/gi, (match: string) => match.toUpperCase());
   return studyType;
 };
 
 export const getStudyItemMetaData = ({
   studyType,
   credibleSetsCount,
-  nSamples
+  nSamples,
 }: {
   studyType?: string;
   credibleSetsCount: number;
@@ -326,26 +328,32 @@ export const getStudyItemMetaData = ({
   return metaData;
 };
 
-export const getGenomicLocation = (genomicLocation: {
-  chromosome?: string;
-  start?: number;
-  end?: number;
-  strand?: number;
-} | null | undefined) => {
+export const getGenomicLocation = (
+  genomicLocation:
+    | {
+        chromosome?: string;
+        start?: number;
+        end?: number;
+        strand?: number;
+      }
+    | null
+    | undefined
+) => {
   /****
    * TODO: add GRCh38 to this function
    * check all the locations we are using this
    * option 1:  getGenomicLocation() -> ["GRCh38", "chromosome-string"]
    * option 2:  getGenomicLocation("GRCh38") -> "GRCh38|chromosome-string"
    ****/
-  return `${genomicLocation?.chromosome}:${genomicLocation?.start}-${genomicLocation?.end},${Math.sign(genomicLocation?.strand) === 1 ? "+" : "-"
-    }`;
+  return `${genomicLocation?.chromosome}:${genomicLocation?.start}-${genomicLocation?.end},${
+    Math.sign(genomicLocation?.strand ?? 1) === 1 ? "+" : "-"
+  }`;
 };
-export * from "./dataTypes";
-export * from "./types/response";
-export * from "./types/graphql-types";
-export * from "./searchSuggestions";
-export * from "./partnerPreviewUtils";
 export * from "./alphaFold";
+export * from "./dataTypes";
 export * from "./particlesBackground";
-export * from "./variant";
+export * from "./partnerPreviewUtils";
+export * from "./searchSuggestions";
+export * from "./types/graphql-types";
+export * from "./types/response";
+export * from "./variant";

packages/ot-constants/src/partnerPreviewUtils.ts

@@ -3,11 +3,12 @@ import { getConfig } from "@ot/config";
 const config = getConfig();
 
 // page sections
-export const isPrivateTargetSection = id => config.profile.partnerTargetSectionIds.includes(id);
-export const isPrivateDiseaseSection = id => config.profile.partnerDiseaseSectionIds.includes(id);
-export const isPrivateDrugSection = id => config.profile.partnerDrugSectionIds.includes(id);
-export const isPrivateEvidenceSection = id => config.profile.partnerEvidenceSectionIds.includes(id);
+export const isPrivateTargetSection = (id) => config.profile.partnerTargetSectionIds.includes(id);
+export const isPrivateDiseaseSection = (id) => config.profile.partnerDiseaseSectionIds.includes(id);
+export const isPrivateDrugSection = (id) => config.profile.partnerDrugSectionIds.includes(id);
+export const isPrivateEvidenceSection = (id) =>
+  config.profile.partnerEvidenceSectionIds.includes(id);
 
 // associations
-export const isPrivateDataType = id => config.profile.partnerDataTypes.includes(id);
-export const isPrivateDataSource = id => config.profile.partnerDataSources.includes(id);
+export const isPrivateDataType = (id) => config.profile.partnerDataTypes.includes(id);
+export const isPrivateDataSource = (id) => config.profile.partnerDataSources.includes(id);

packages/ot-constants/src/types/graphql-types.ts

@@ -1438,16 +1438,15 @@ export interface geneticVariation {
 }
 
 export enum StudyTypeEnum {
-  eqtl = 'eqtl',
-  gwas = 'gwas',
-  pqtl = 'pqtl',
-  sceqtl = 'sceqtl',
-  scpqtl = 'scpqtl',
-  scsqtl = 'scsqtl',
-  sctuqtl = 'sctuqtl',
-  sqtl = 'sqtl',
-  tuqtl = 'tuqtl',
+  eqtl = "eqtl",
+  gwas = "gwas",
+  pqtl = "pqtl",
+  sceqtl = "sceqtl",
+  scpqtl = "scpqtl",
+  scsqtl = "scsqtl",
+  sctuqtl = "sctuqtl",
+  sqtl = "sqtl",
+  tuqtl = "tuqtl",
 }
 
 export type EntityUnionType = Target | Drug | Disease | Variant | Study;
-