From 0839c9f3e380d68fd4af7cc0e59e5bea41c8128a Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Tue, 9 Sep 2025 00:27:39 +0100 Subject: [PATCH 01/10] fix: biome version and edifor config --- .editorconfig | 35 + .vscode/README.md | 59 + .vscode/extensions.json | 7 +- .vscode/launch.json | 21 +- .vscode/settings.json | 71 + apps/platform/package.json | 7 +- apps/platform/public/profiles/platform.js | 2 +- apps/platform/public/profiles/ppp.js | 2 +- apps/platform/vite.config.js | 4 +- biome.json | 61 +- package.json | 21 +- yarn.lock | 1935 +++++++++++---------- 12 files changed, 1221 insertions(+), 1004 deletions(-) create mode 100644 .editorconfig create mode 100644 .vscode/README.md create mode 100644 .vscode/settings.json diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 000000000..4848d957f --- /dev/null +++ b/.editorconfig @@ -0,0 +1,35 @@ +# EditorConfig is awesome: https://EditorConfig.org + +# top-most EditorConfig file +root = true + +# All files +[*] +charset = utf-8 +end_of_line = lf +insert_final_newline = true +trim_trailing_whitespace = true + +# JavaScript, TypeScript, JSON files +[*.{js,jsx,ts,tsx,json,jsonc}] +indent_style = space +indent_size = 2 + +# GraphQL files +[*.{gql,graphql}] +indent_style = space +indent_size = 2 + +# Markdown files +[*.md] +trim_trailing_whitespace = false + +# YAML files +[*.{yml,yaml}] +indent_style = space +indent_size = 2 + +# Package.json files +[package.json] +indent_style = space +indent_size = 2 diff --git a/.vscode/README.md b/.vscode/README.md new file mode 100644 index 000000000..d5b89da7e --- /dev/null +++ b/.vscode/README.md @@ -0,0 +1,59 @@ +# VSCode Configuration for Open Targets UI Apps + +This directory contains VSCode workspace configuration files to ensure consistent development experience across the team. + +## Files + +- **`settings.json`**: Workspace settings that configure BiomeJS as the default formatter and linter +- **`extensions.json`**: Recommended extensions for the project +- **`launch.json`**: Debug configurations for the platform app + +## Key Features + +### BiomeJS Integration +- Uses local BiomeJS installation from `node_modules` (not global) +- Automatic formatting on save for all supported file types +- Automatic import organization on save +- Automatic code fixes on save + +### Supported File Types +- JavaScript (`.js`, `.jsx`) +- TypeScript (`.ts`, `.tsx`) +- JSON (`.json`, `.jsonc`) +- GraphQL (`.gql`, `.graphql`) + +### Disabled Extensions +- Prettier (conflicts with BiomeJS) +- ESLint (replaced by BiomeJS) + +## Setup + +1. Install the recommended VSCode extensions when prompted +2. The workspace settings will automatically configure BiomeJS +3. Format on save and other features will work immediately + +## Manual Commands + +If you need to run BiomeJS manually: + +```bash +# Check for issues +npm run check + +# Fix issues automatically +npm run check:fix + +# Format files +npm run format:fix + +# Lint only +npm run lint:fix +``` + +## Troubleshooting + +If formatting doesn't work: +1. Ensure the BiomeJS extension is installed +2. Check that the local BiomeJS installation exists: `ls node_modules/@biomejs/biome` +3. Restart VSCode +4. Check the VSCode output panel for BiomeJS extension logs diff --git a/.vscode/extensions.json b/.vscode/extensions.json index 699ed7331..1b8a29418 100644 --- a/.vscode/extensions.json +++ b/.vscode/extensions.json @@ -1,3 +1,8 @@ { - "recommendations": ["biomejs.biome"] + "recommendations": [ + "biomejs.biome", + "graphql.vscode-graphql", + "ms-vscode.vscode-typescript-next" + ], + "unwantedRecommendations": ["esbenp.prettier-vscode", "dbaeumer.vscode-eslint"] } diff --git a/.vscode/launch.json b/.vscode/launch.json index 5ef287e20..e155368f6 100644 --- a/.vscode/launch.json +++ b/.vscode/launch.json @@ -1,18 +1,17 @@ { - "version": "0.1.0", + "version": "0.2.0", "configurations": [ { - "command": "yarn dev:platform", - "name": "Run platform dev", + "name": "Debug Platform App", + "type": "node", "request": "launch", - "type": "node-terminal" - }, - { - "type": "chrome", - "request": "launch", - "name": "Launch Platform Chrome against localhost", - "url": "http://localhost:3000", - "webRoot": "${workspaceFolder}/apps/platform/src/" + "program": "${workspaceFolder}/apps/platform/node_modules/.bin/vite", + "args": ["--mode", "development"], + "cwd": "${workspaceFolder}/apps/platform", + "console": "integratedTerminal", + "env": { + "NODE_ENV": "development" + } } ] } diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 000000000..1d6a8c37c --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,71 @@ +{ + // BiomeJS Configuration + "biome.lspBin": "./node_modules/@biomejs/biome/bin/biome", + + // Set BiomeJS as default formatter for supported file types + "[javascript]": { + "editor.defaultFormatter": "biomejs.biome", + "editor.formatOnSave": true, + "editor.codeActionsOnSave": { + "source.fixAll.biome": "explicit", + "source.organizeImports.biome": "explicit" + } + }, + "[typescript]": { + "editor.defaultFormatter": "biomejs.biome", + "editor.formatOnSave": true, + "editor.codeActionsOnSave": { + "source.fixAll.biome": "explicit", + "source.organizeImports.biome": "explicit" + } + }, + "[javascriptreact]": { + "editor.defaultFormatter": "biomejs.biome", + "editor.formatOnSave": true, + "editor.codeActionsOnSave": { + "source.fixAll.biome": "explicit", + "source.organizeImports.biome": "explicit" + } + }, + "[typescriptreact]": { + "editor.defaultFormatter": "biomejs.biome", + "editor.formatOnSave": true, + "editor.codeActionsOnSave": { + "source.fixAll.biome": "explicit", + "source.organizeImports.biome": "explicit" + } + }, + "[json]": { + "editor.defaultFormatter": "biomejs.biome", + "editor.formatOnSave": true + }, + "[jsonc]": { + "editor.defaultFormatter": "biomejs.biome", + "editor.formatOnSave": true + }, + + // Disable other formatters to avoid conflicts + "prettier.enable": false, + "eslint.enable": false, + + // BiomeJS specific settings + "biome.enabled": true, + "biome.rename": true, + + // General editor settings + "editor.formatOnSave": true, + "editor.formatOnPaste": true, + "editor.formatOnType": false, + + // File associations for GraphQL files + "files.associations": { + "*.gql": "graphql", + "*.graphql": "graphql" + }, + + // GraphQL formatting (BiomeJS handles .gql files) + "[graphql]": { + "editor.defaultFormatter": "biomejs.biome", + "editor.formatOnSave": true + } +} diff --git a/apps/platform/package.json b/apps/platform/package.json index 67f430acc..ada14917e 100644 --- a/apps/platform/package.json +++ b/apps/platform/package.json @@ -62,7 +62,12 @@ "check:fix": "biome check --formatter-enabled=true --write .", "analyze": "source-map-explorer 'build/static/js/*.js'" }, - "browserslist": [">0.2%", "not dead", "not ie > 0", "not op_mini all"], + "browserslist": [ + ">0.2%", + "not dead", + "not ie > 0", + "not op_mini all" + ], "devDependencies": { "@types/d3": "^7.4.0", "@types/react": "^18.0.28", diff --git a/apps/platform/public/profiles/platform.js b/apps/platform/public/profiles/platform.js index 57076c82e..3982ec567 100644 --- a/apps/platform/public/profiles/platform.js +++ b/apps/platform/public/profiles/platform.js @@ -1,5 +1,5 @@ // Configuration Object -// biome-ignore lint/style/noVar: keep this as var for now +// biome-ignore lint: keep this as var for now var configProfile = { /* general items */ diff --git a/apps/platform/public/profiles/ppp.js b/apps/platform/public/profiles/ppp.js index f2c39d18a..77fdbb39f 100644 --- a/apps/platform/public/profiles/ppp.js +++ b/apps/platform/public/profiles/ppp.js @@ -1,5 +1,5 @@ // Configuration Object -// biome-ignore lint/style/noVar: keep this as var for now +// biome-ignore lint: keep this as var for now var configProfile = { /* general items */ diff --git a/apps/platform/vite.config.js b/apps/platform/vite.config.js index 70d34fb13..aa8a087fd 100644 --- a/apps/platform/vite.config.js +++ b/apps/platform/vite.config.js @@ -8,8 +8,8 @@ import svgrPlugin from "vite-plugin-svgr"; const getGitVersion = () => { try { return execSync("git describe --tags --always").toString().trim(); - } catch (error) { - return "unknown"; + } catch { + return "unknown version"; } }; diff --git a/biome.json b/biome.json index aabec2712..11cca7544 100644 --- a/biome.json +++ b/biome.json @@ -1,7 +1,11 @@ { - "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json", - "organizeImports": { - "enabled": true + "$schema": "https://biomejs.dev/schemas/2.2.3/schema.json", + "assist": { + "actions": { + "source": { + "organizeImports": "on" + } + } }, "vcs": { "enabled": true, @@ -9,29 +13,27 @@ "useIgnoreFile": true }, "files": { - "include": [ + "includes": [ "**/*.js", "**/*.jsx", "**/*.ts", "**/*.tsx", "**/*.json", "**/*.gql", - "**/*.graphql" - ], - "ignore": [ - "**/node_modules/**", - "**/dist/**", - "**/build/**", - "**/.next/**", - "**/coverage/**", - "**/*.d.ts", - "**/generated/**", - "**/apps/platform/src/**", - "**/packages/ui/**", - "**/packages/sections/**", - "**/packages/ot-config/**", - "**/packages/ot-constants/**", - "**/packages/ot-utils/**" + "**/*.graphql", + "!**/node_modules", + "!**/dist", + "!**/build", + "!**/.next", + "!**/coverage", + "!**/*.d.ts", + "!**/generated", + "!**/apps/platform/src", + "!**/packages/ui", + "!**/packages/sections", + "!**/packages/ot-config", + "!**/packages/ot-constants", + "!**/packages/ot-utils" ] }, "formatter": { @@ -44,15 +46,16 @@ "lineWidth": 100, "attributePosition": "auto", "bracketSpacing": true, - "ignore": [ - "**/bundle-genetics", - "**/bundle-platform", - "**/node_modules", - "**/.github", - "**/.husky", - "**/public", - "**/__generated__", - "packages/tsconfig" + "includes": [ + "**", + "!**/bundle-genetics", + "!**/bundle-platform", + "!**/node_modules", + "!**/.github", + "!**/.husky", + "!**/public", + "!**/__generated__", + "!**/packages/tsconfig" ] }, "linter": { diff --git a/package.json b/package.json index 967b7f67c..d7e610029 100644 --- a/package.json +++ b/package.json @@ -3,7 +3,10 @@ "version": "0.0.1", "private": true, "license": "Apache-2.0", - "workspaces": ["apps/*", "packages/*"], + "workspaces": [ + "apps/*", + "packages/*" + ], "bugs": { "url": "https://github.com/opentargets/ot-ui-apps/issues", "email": "support@targetvalidation.org" @@ -16,17 +19,17 @@ "build:platform": "turbo run build --filter=platform", "dev:platform:ppp": "turbo run dev-ppp --filter=platform", "build:platform:ppp": "turbo run build-ppp --filter=platform", - "lint": "biome check .", - "lint:fix": "biome check --write .", - "format": "biome format .", - "format:fix": "biome format --write .", - "format:check": "biome ci", - "check": "biome check --formatter-enabled=true .", - "check:fix": "biome check --formatter-enabled=true --write .", + "lint": "npx biome check .", + "lint:fix": "npx biome check --write .", + "format": "npx biome format .", + "format:fix": "npx biome format --write .", + "format:check": "npx biome ci", + "check": "npx biome check --formatter-enabled=true .", + "check:fix": "npx biome check --formatter-enabled=true --write .", "prepare": "husky install" }, "devDependencies": { - "@biomejs/biome": "1.9.4", + "@biomejs/biome": "^2.2.3", "husky": "^8.0.3", "lint-staged": "^14.0.1", "turbo": "^2.4.2" diff --git a/yarn.lock b/yarn.lock index aa37a4775..9f48a609e 100644 --- a/yarn.lock +++ b/yarn.lock @@ -3,23 +3,15 @@ "3dmol@^2.4.2": - version "2.4.2" - resolved "https://registry.yarnpkg.com/3dmol/-/3dmol-2.4.2.tgz#0d8d676cf8b548a709ac9c12219b59fcb356e960" - integrity sha512-7R6uFaF5++s9EpO+R0a3bs6igi5idI+sgrVhtozaZlOGHg6oourYkAlAwYxWRaeBGlNcAd+oEIhbhJYhNxGyZA== + version "2.5.2" + resolved "https://registry.yarnpkg.com/3dmol/-/3dmol-2.5.2.tgz#719ba4662782b88be8a49c94826b16300e0099dc" + integrity sha512-xILRLpHru+Hoa4kGISfh0QQlI39UoSxRR4q/BKrLNRhsu+LLiE6lfZ6MROHQXKo8iE2alQRWUxSM0mxXmVAvOg== dependencies: - iobuffer "^5.3.1" + iobuffer "^5.0.0" netcdfjs "^3.0.0" pako "^2.1.0" upng-js "^2.1.0" -"@ampproject/remapping@^2.2.0": - version "2.3.0" - resolved 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set-proto "^1.0.0" + stop-iteration-iterator "^1.1.0" string.prototype.trim "^1.2.10" string.prototype.trimend "^1.0.9" string.prototype.trimstart "^1.0.8" @@ -3468,7 +3489,7 @@ es-abstract@^1.23.2, es-abstract@^1.23.5, es-abstract@^1.23.9: typed-array-byte-offset "^1.0.4" typed-array-length "^1.0.7" unbox-primitive "^1.1.0" - which-typed-array "^1.1.18" + which-typed-array "^1.1.19" es-array-method-boxes-properly@^1.0.0: version "1.0.0" @@ -3512,35 +3533,36 @@ es-to-primitive@^1.3.0: is-symbol "^1.0.4" esbuild@^0.25.0: - version "0.25.0" - resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.25.0.tgz#0de1787a77206c5a79eeb634a623d39b5006ce92" - integrity sha512-BXq5mqc8ltbaN34cDqWuYKyNhX8D/Z0J1xdtdQ8UcIIIyJyz+ZMKUt58tF3SrZ85jcfN/PZYhjR5uDQAYNVbuw== + version "0.25.9" + resolved "https://registry.yarnpkg.com/esbuild/-/esbuild-0.25.9.tgz#15ab8e39ae6cdc64c24ff8a2c0aef5b3fd9fa976" + integrity 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+ "@esbuild/android-arm" "0.25.9" + "@esbuild/android-arm64" "0.25.9" + "@esbuild/android-x64" "0.25.9" + "@esbuild/darwin-arm64" "0.25.9" + "@esbuild/darwin-x64" "0.25.9" + "@esbuild/freebsd-arm64" "0.25.9" + "@esbuild/freebsd-x64" "0.25.9" + "@esbuild/linux-arm" "0.25.9" + "@esbuild/linux-arm64" "0.25.9" + "@esbuild/linux-ia32" "0.25.9" + "@esbuild/linux-loong64" "0.25.9" + "@esbuild/linux-mips64el" "0.25.9" + "@esbuild/linux-ppc64" "0.25.9" + "@esbuild/linux-riscv64" "0.25.9" + "@esbuild/linux-s390x" "0.25.9" + "@esbuild/linux-x64" "0.25.9" + "@esbuild/netbsd-arm64" "0.25.9" + "@esbuild/netbsd-x64" "0.25.9" + "@esbuild/openbsd-arm64" "0.25.9" + "@esbuild/openbsd-x64" "0.25.9" + "@esbuild/openharmony-arm64" "0.25.9" + "@esbuild/sunos-x64" "0.25.9" + "@esbuild/win32-arm64" "0.25.9" + "@esbuild/win32-ia32" "0.25.9" + "@esbuild/win32-x64" "0.25.9" escalade@^3.1.1, escalade@^3.2.0: version "3.2.0" @@ -3669,6 +3691,11 @@ fbjs@^0.8.1: setimmediate "^1.0.5" ua-parser-js "^0.7.30" 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version "10.9.4" + resolved "https://registry.yarnpkg.com/jake/-/jake-10.9.4.tgz#d626da108c63d5cfb00ab5c25fadc7e0084af8e6" + integrity sha512-wpHYzhxiVQL+IV05BLE2Xn34zW1S223hvjtqk0+gsPrwd/8JNLXJgZZM/iPFsYc1xyphF+6M6EvdE5E9MBGkDA== dependencies: - async "^3.2.3" - chalk "^4.0.2" + async "^3.2.6" filelist "^1.0.4" - minimatch "^3.1.2" + picocolors "^1.1.1" javascript-lp-solver@0.4.24: version "0.4.24" @@ -4672,11 +4696,6 @@ jpeg-js@^0.4.4: resolved "https://registry.yarnpkg.com/js-tokens/-/js-tokens-4.0.0.tgz#19203fb59991df98e3a287050d4647cdeaf32499" integrity sha512-RdJUflcE3cUzKiMqQgsCu06FPu9UdIJO0beYbPhHN4k6apgJtifcoCtT9bcxOpYBtpD2kCM6Sbzg4CausW/PKQ== -jsbn@1.1.0: - version "1.1.0" - resolved "https://registry.yarnpkg.com/jsbn/-/jsbn-1.1.0.tgz#b01307cb29b618a1ed26ec79e911f803c4da0040" - integrity sha512-4bYVV3aAMtDTTu4+xsDYa6sy9GyJ69/amsu9sYF2zqjiEoZA5xJi3BrfX3uY+/IekIu7MwdObdbDWpoZdBv3/A== - jsesc@^3.0.2: version "3.1.0" resolved "https://registry.yarnpkg.com/jsesc/-/jsesc-3.1.0.tgz#74d335a234f67ed19907fdadfac7ccf9d409825d" @@ -4693,9 +4712,9 @@ json5@^2.2.3: integrity sha512-XmOWe7eyHYH14cLdVPoyg+GOH3rYX++KpzrylJwSW98t3Nk+U8XOl8FWKOgwtzdb8lXGf6zYwDUzeHMWfxasyg== jsonfile@^6.0.1: - version "6.1.0" - resolved "https://registry.yarnpkg.com/jsonfile/-/jsonfile-6.1.0.tgz#bc55b2634793c679ec6403094eb13698a6ec0aae" - integrity sha512-5dgndWOriYSm5cnYaJNhalLNDKOqFwyDB/rr1E9ZsGciGvKPs8R2xYGCacuf3z6K1YKDz182fd+fY3cn3pMqXQ== + version "6.2.0" + resolved "https://registry.yarnpkg.com/jsonfile/-/jsonfile-6.2.0.tgz#7c265bd1b65de6977478300087c99f1c84383f62" + integrity sha512-FGuPw30AdOIUTRMC2OMRtQV+jkVj2cfPqSeWXv1NEAJ1qZ5zb1X6z1mFhbfOB/iy3ssJCD+3KuZ8r8C3uVFlAg== dependencies: universalify "^2.0.0" optionalDependencies: @@ -4822,18 +4841,18 @@ listr2@6.6.1: wrap-ansi "^8.1.0" lit-element@^4.0.4: - version "4.1.1" - resolved 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-object-inspect@^1.13.3: +object-inspect@^1.13.3, object-inspect@^1.13.4: version "1.13.4" resolved "https://registry.yarnpkg.com/object-inspect/-/object-inspect-1.13.4.tgz#8375265e21bc20d0fa582c22e1b13485d6e00213" integrity sha512-W67iLl4J2EXEGTbfeHCffrjDfitvLANg0UlX3wFUUSTx92KXRFegMHUVgSqE+wvhAbi4WqjGg9czysTV2Epbew== @@ -5668,10 +5687,10 @@ on-finished@2.4.1: dependencies: ee-first "1.1.1" -on-headers@~1.0.2: - version "1.0.2" - resolved "https://registry.yarnpkg.com/on-headers/-/on-headers-1.0.2.tgz#772b0ae6aaa525c399e489adfad90c403eb3c28f" - integrity sha512-pZAE+FJLoyITytdqK0U5s+FIpjN0JP3OzFi/u8Rx+EV5/W+JTWGXG8xFzevE7AjBfDqHv/8vL8qQsIhHnqRkrA== +on-headers@~1.1.0: + version "1.1.0" + resolved "https://registry.yarnpkg.com/on-headers/-/on-headers-1.1.0.tgz#59da4f91c45f5f989c6e4bcedc5a3b0aed70ff65" + integrity sha512-737ZY3yNnXy37FHkQxPzt4UZ2UWPWiCZWLvFZ4fu5cueciegX0zGPnrlY6bwRg4FdQOe9YU8MkmJwGhoMybl8A== once@^1.3.0, once@^1.3.1, once@^1.4.0: version "1.4.0" @@ -5827,7 +5846,7 @@ 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optionalDependencies: fsevents "~2.3.3" @@ -7987,7 +8024,7 @@ which-collection@^1.0.2: is-weakmap "^2.0.2" is-weakset "^2.0.3" -which-typed-array@^1.1.16, which-typed-array@^1.1.18: +which-typed-array@^1.1.16, which-typed-array@^1.1.19: version "1.1.19" resolved "https://registry.yarnpkg.com/which-typed-array/-/which-typed-array-1.1.19.tgz#df03842e870b6b88e117524a4b364b6fc689f956" integrity sha512-rEvr90Bck4WZt9HHFC4DJMsjvu7x+r6bImz0/BrbWb7A2djJ8hnZMrWnHo9F8ssv0OMErasDhftrfROTyqSDrw== From 19a32501eddc9a1f047941df16886e58e28fc63c Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Wed, 17 Sep 2025 11:38:41 +0100 Subject: [PATCH 02/10] fix: set static version --- biome.json | 2 +- package.json | 2 +- yarn.lock | 478 ++++++++++++++++++++++++++------------------------- 3 files changed, 244 insertions(+), 238 deletions(-) diff --git a/biome.json b/biome.json index 11cca7544..b1509b0e5 100644 --- a/biome.json +++ b/biome.json @@ -1,5 +1,5 @@ { - "$schema": "https://biomejs.dev/schemas/2.2.3/schema.json", + "$schema": "https://biomejs.dev/schemas/2.2.4/schema.json", "assist": { "actions": { "source": { diff --git a/package.json b/package.json index d7e610029..972975875 100644 --- a/package.json +++ b/package.json @@ -29,7 +29,7 @@ "prepare": "husky install" }, "devDependencies": { - "@biomejs/biome": "^2.2.3", + "@biomejs/biome": "2.2.4", "husky": "^8.0.3", "lint-staged": "^14.0.1", "turbo": "^2.4.2" diff --git a/yarn.lock b/yarn.lock index 9f48a609e..7711eb1b3 100644 --- a/yarn.lock +++ b/yarn.lock @@ -216,59 +216,59 @@ "@babel/helper-string-parser" "^7.27.1" "@babel/helper-validator-identifier" "^7.27.1" -"@biomejs/biome@^2.2.3": - version "2.2.3" - resolved "https://registry.yarnpkg.com/@biomejs/biome/-/biome-2.2.3.tgz#9d17991c80e006c5ca3e21bebe84b7afd71559e3" - integrity sha512-9w0uMTvPrIdvUrxazZ42Ib7t8Y2yoGLKLdNne93RLICmaHw7mcLv4PPb5LvZLJF3141gQHiCColOh/v6VWlWmg== +"@biomejs/biome@2.2.4": + version "2.2.4" + resolved 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"@rollup/rollup-freebsd-arm64" "4.50.2" + "@rollup/rollup-freebsd-x64" "4.50.2" + "@rollup/rollup-linux-arm-gnueabihf" "4.50.2" + "@rollup/rollup-linux-arm-musleabihf" "4.50.2" + "@rollup/rollup-linux-arm64-gnu" "4.50.2" + "@rollup/rollup-linux-arm64-musl" "4.50.2" + "@rollup/rollup-linux-loong64-gnu" "4.50.2" + "@rollup/rollup-linux-ppc64-gnu" "4.50.2" + "@rollup/rollup-linux-riscv64-gnu" "4.50.2" + "@rollup/rollup-linux-riscv64-musl" "4.50.2" + "@rollup/rollup-linux-s390x-gnu" "4.50.2" + "@rollup/rollup-linux-x64-gnu" "4.50.2" + "@rollup/rollup-linux-x64-musl" "4.50.2" + "@rollup/rollup-openharmony-arm64" "4.50.2" + "@rollup/rollup-win32-arm64-msvc" "4.50.2" + "@rollup/rollup-win32-ia32-msvc" "4.50.2" + "@rollup/rollup-win32-x64-msvc" "4.50.2" fsevents "~2.3.2" rw@1: @@ -6820,9 +6826,9 @@ simple-get@^4.0.0: simple-concat "^1.0.0" simple-swizzle@^0.2.2: - version "0.2.2" - resolved "https://registry.yarnpkg.com/simple-swizzle/-/simple-swizzle-0.2.2.tgz#a4da6b635ffcccca33f70d17cb92592de95e557a" - integrity sha512-JA//kQgZtbuY83m+xT+tXJkmJncGMTFT+C+g2h2R9uxkYIrE2yy9sgmcLhCnw57/WSD+Eh3J97FPEDFnbXnDUg== + version "0.2.4" + resolved "https://registry.yarnpkg.com/simple-swizzle/-/simple-swizzle-0.2.4.tgz#a8d11a45a11600d6a1ecdff6363329e3648c3667" + integrity sha512-nAu1WFPQSMNr2Zn9PGSZK9AGn4t/y97lEm+MXTtUDwfP0ksAIX4nO+6ruD9Jwut4C49SB1Ws+fbXsm/yScWOHw== dependencies: is-arrayish "^0.3.1" @@ -7113,9 +7119,9 @@ svg-parser@^2.0.4: integrity sha512-e4hG1hRwoOdRb37cIMSgzNsxyzKfayW6VOflrwvR+/bzrkyxY/31WkbgnQpgtrNp1SdpJvpUAGTa/ZoiPNDuRQ== swagger-ui-dist@^5.10.5: - version "5.28.1" - resolved "https://registry.yarnpkg.com/swagger-ui-dist/-/swagger-ui-dist-5.28.1.tgz#2423eb17e987436a4479ef3bb6ea2679353dabcc" - integrity sha512-IvPrtNi8MvjiuDgoSmPYgg27Lvu38fnLD1OSd8Y103xXsPAqezVNnNeHnVCZ/d+CMXJblflGaIyHxAYIF3O71w== + version "5.29.0" + resolved "https://registry.yarnpkg.com/swagger-ui-dist/-/swagger-ui-dist-5.29.0.tgz#ae4949fbc547f09c4eb6223354bd7ab47e6d3b21" + integrity sha512-gqs7Md3AxP4mbpXAq31o5QW+wGUZsUzVatg70yXpUR245dfIis5jAzufBd+UQM/w2xSfrhvA1eqsrgnl2PbezQ== dependencies: "@scarf/scarf" "=1.4.0" @@ -7130,9 +7136,9 @@ symbol-observable@^4.0.0: integrity sha512-b19dMThMV4HVFynSAM1++gBHAbk2Tc/osgLIBZMKsyqh34jb2e8Os7T6ZW/Bt3pJFdBTd2JwAnAAEQV7rSNvcQ== tar-fs@^2.0.0: - version "2.1.3" - resolved "https://registry.yarnpkg.com/tar-fs/-/tar-fs-2.1.3.tgz#fb3b8843a26b6f13a08e606f7922875eb1fbbf92" - integrity sha512-090nwYJDmlhwFwEW3QQl+vaNnxsO2yVsd45eTKRBzSzu+hlb1w2K9inVq5b0ngXuLVqQ4ApvsUHHnu/zQNkWAg== + version "2.1.4" + resolved "https://registry.yarnpkg.com/tar-fs/-/tar-fs-2.1.4.tgz#800824dbf4ef06ded9afea4acafe71c67c76b930" + integrity sha512-mDAjwmZdh7LTT6pNleZ05Yt65HC3E+NiQzl672vQG38jIrehtJk/J3mNwIg+vShQPcLF/LV7CMnDW6vjj6sfYQ== dependencies: chownr "^1.1.1" mkdirp-classic "^0.5.2" @@ -7757,10 +7763,10 @@ undici-types@~5.26.4: resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-5.26.5.tgz#bcd539893d00b56e964fd2657a4866b221a65617" integrity sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA== -undici-types@~7.10.0: - version "7.10.0" - resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-7.10.0.tgz#4ac2e058ce56b462b056e629cc6a02393d3ff350" - integrity sha512-t5Fy/nfn+14LuOc2KNYg75vZqClpAiqscVvMygNnlsHBFpSXdJaYtXMcdNLpl/Qvc3P2cB3s6lOV51nqsFq4ag== +undici-types@~7.12.0: + version "7.12.0" + resolved "https://registry.yarnpkg.com/undici-types/-/undici-types-7.12.0.tgz#15c5c7475c2a3ba30659529f5cdb4674b622fafb" + integrity sha512-goOacqME2GYyOZZfb5Lgtu+1IDmAlAEu5xnD3+xTzS10hT0vzpf0SPjkXwAw9Jm+4n/mQGDP3LO8CPbYROeBfQ== unified@^11.0.0: version "11.0.5" From 91566c85d490aaaf9e9f0cb6c23be49c9e57b8f6 Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Tue, 23 Sep 2025 15:19:31 +0100 Subject: [PATCH 03/10] fix: intial lint run --- biome.json | 4 ++- packages/ui/src/index.tsx | 2 +- .../ui/src/providers/APIMetadataProvider.tsx | 8 ++--- .../src/providers/ConfigurationProvider.tsx | 6 ++-- .../OTApolloProvider/OTApolloProvider.tsx | 4 +-- .../src/providers/OTApolloProvider/apollo.tsx | 8 ++--- .../ui/src/providers/PlatformApiProvider.tsx | 29 ++++++---------- .../providers/ThemeProvider/ThemeProvider.tsx | 2 +- .../providers/ThemeProvider/defaultTheme.ts | 2 +- .../providers/ViewerInteractionProvider.tsx | 23 ++++++------- packages/ui/src/providers/ViewerProvider.tsx | 34 ++++++++----------- 11 files changed, 56 insertions(+), 66 deletions(-) diff --git a/biome.json b/biome.json index b1509b0e5..5c449f2c9 100644 --- a/biome.json +++ b/biome.json @@ -29,7 +29,9 @@ "!**/*.d.ts", "!**/generated", "!**/apps/platform/src", - "!**/packages/ui", + "!**/packages/ui/src/components", + "!**/packages/ui/src/hooks", + "!**/packages/ui/src/pages", "!**/packages/sections", "!**/packages/ot-config", "!**/packages/ot-constants", diff --git a/packages/ui/src/index.tsx b/packages/ui/src/index.tsx index 697b2ddd2..8d553001b 100644 --- a/packages/ui/src/index.tsx +++ b/packages/ui/src/index.tsx @@ -97,5 +97,5 @@ export * from "./providers/ConfigurationProvider"; export * from "./providers/OTApolloProvider/OTApolloProvider"; export { default as PlatformApiProvider } from "./providers/PlatformApiProvider"; export { default as ThemeProvider } from "./providers/ThemeProvider/ThemeProvider"; -export * from "./providers/ViewerProvider"; export * from "./providers/ViewerInteractionProvider"; +export * from "./providers/ViewerProvider"; diff --git a/packages/ui/src/providers/APIMetadataProvider.tsx b/packages/ui/src/providers/APIMetadataProvider.tsx index ffaa92600..b70e66d96 100644 --- a/packages/ui/src/providers/APIMetadataProvider.tsx +++ b/packages/ui/src/providers/APIMetadataProvider.tsx @@ -1,5 +1,5 @@ -import { PropsWithChildren, createContext, useContext, useEffect, useState } from "react"; -import { gql, useQuery, ApolloError } from "@apollo/client"; +import { type ApolloError, gql, useQuery } from "@apollo/client"; +import { createContext, type PropsWithChildren, useContext, useEffect, useState } from "react"; // QUERY const DATA_VERSION_QUERY = gql` @@ -41,12 +41,12 @@ export const APIMetadataProvider = ({ children }: PropsWithChildren): JSX.Elemen useEffect(() => { if (loading) { - setVersion(v => ({ ...v, loading })); + setVersion((v) => ({ ...v, loading })); return; } if (error) { - setVersion(v => ({ ...v, error })); + setVersion((v) => ({ ...v, error })); return; } const { diff --git a/packages/ui/src/providers/ConfigurationProvider.tsx b/packages/ui/src/providers/ConfigurationProvider.tsx index 20805ccdc..21933b37a 100644 --- a/packages/ui/src/providers/ConfigurationProvider.tsx +++ b/packages/ui/src/providers/ConfigurationProvider.tsx @@ -1,8 +1,8 @@ -import { PropsWithChildren, createContext, useContext } from "react"; -import { Config, theme } from "@ot/config"; +import { type Config, theme } from "@ot/config"; +import { createContext, type PropsWithChildren, useContext } from "react"; +import { APIMetadataProvider } from "./APIMetadataProvider"; import { OTApolloProvider } from "./OTApolloProvider/OTApolloProvider"; import ThemeProvider from "./ThemeProvider/ThemeProvider"; -import { APIMetadataProvider } from "./APIMetadataProvider"; type ContextType = { config: Config | null; diff --git a/packages/ui/src/providers/OTApolloProvider/OTApolloProvider.tsx b/packages/ui/src/providers/OTApolloProvider/OTApolloProvider.tsx index 867059dbd..54fbd3808 100644 --- a/packages/ui/src/providers/OTApolloProvider/OTApolloProvider.tsx +++ b/packages/ui/src/providers/OTApolloProvider/OTApolloProvider.tsx @@ -1,6 +1,6 @@ -import { ApolloProvider, ApolloClient, NormalizedCacheObject } from "@apollo/client"; +import { type ApolloClient, ApolloProvider, type NormalizedCacheObject } from "@apollo/client"; +import type { Config } from "@ot/config"; import { createContext, useContext } from "react"; -import { Config } from "@ot/config"; import { createApolloClient } from "./apollo"; const ApolloClientContext = createContext | undefined>( diff --git a/packages/ui/src/providers/OTApolloProvider/apollo.tsx b/packages/ui/src/providers/OTApolloProvider/apollo.tsx index 7210d0ee8..1e8b695a0 100644 --- a/packages/ui/src/providers/OTApolloProvider/apollo.tsx +++ b/packages/ui/src/providers/OTApolloProvider/apollo.tsx @@ -1,5 +1,5 @@ -import { ApolloClient, InMemoryCache, HttpLink, ApolloLink, from } from "@apollo/client"; -import { Config } from "@ot/config"; +import { ApolloClient, ApolloLink, from, HttpLink, InMemoryCache } from "@apollo/client"; +import type { Config } from "@ot/config"; export const createApolloClient = (config: Config) => { const httpLink = new HttpLink({ @@ -7,9 +7,9 @@ export const createApolloClient = (config: Config) => { }); const errorLink = new ApolloLink((operation, forward) => { - return forward(operation).map(response => { + return forward(operation).map((response) => { if (response.errors) { - response.errors.forEach(error => { + response.errors.forEach((error) => { console.error(`GraphQL Error: ${error.message}`); }); } diff --git a/packages/ui/src/providers/PlatformApiProvider.tsx b/packages/ui/src/providers/PlatformApiProvider.tsx index 8fab9b365..a7a0a553d 100644 --- a/packages/ui/src/providers/PlatformApiProvider.tsx +++ b/packages/ui/src/providers/PlatformApiProvider.tsx @@ -1,5 +1,5 @@ -import { useMemo, createContext, ReactNode } from "react"; -import { useQuery, DocumentNode, QueryResult } from "@apollo/client"; +import { type DocumentNode, type QueryResult, useQuery } from "@apollo/client"; +import { createContext, type ReactNode, useMemo } from "react"; interface PlatformApiContextValue { entity: string; @@ -19,32 +19,25 @@ interface PlatformApiProviderProps { children: ReactNode; } -function PlatformApiProvider({ - entity, - query, - variables, - children, -}: PlatformApiProviderProps) { +function PlatformApiProvider({ entity, query, variables, children }: PlatformApiProviderProps) { const request: QueryResult = useQuery(query, { variables }); const { loading, error, data, refetch, fetchMore } = request; const platformApiValue = useMemo( - () => ({ - loading, - error, - data, - refetch, - fetchMore, - entity + () => ({ + loading, + error, + data, + refetch, + fetchMore, + entity, }), [loading, error, data, refetch, fetchMore, entity] ); return ( - - {children} - + {children} ); } diff --git a/packages/ui/src/providers/ThemeProvider/ThemeProvider.tsx b/packages/ui/src/providers/ThemeProvider/ThemeProvider.tsx index f26abc9ce..2e7545565 100644 --- a/packages/ui/src/providers/ThemeProvider/ThemeProvider.tsx +++ b/packages/ui/src/providers/ThemeProvider/ThemeProvider.tsx @@ -1,5 +1,5 @@ -import { ThemeProvider as MuiThemeProvider } from "@mui/material/styles"; import CssBaseline from "@mui/material/CssBaseline"; +import { ThemeProvider as MuiThemeProvider } from "@mui/material/styles"; import defaultTheme from "./defaultTheme"; diff --git a/packages/ui/src/providers/ThemeProvider/defaultTheme.ts b/packages/ui/src/providers/ThemeProvider/defaultTheme.ts index e0de9a432..251de112d 100644 --- a/packages/ui/src/providers/ThemeProvider/defaultTheme.ts +++ b/packages/ui/src/providers/ThemeProvider/defaultTheme.ts @@ -1,5 +1,5 @@ import { colors } from "@mui/material"; -import { lighten, darken } from "polished"; +import { darken, lighten } from "polished"; const { grey } = colors; diff --git a/packages/ui/src/providers/ViewerInteractionProvider.tsx b/packages/ui/src/providers/ViewerInteractionProvider.tsx index 4d8a5de59..f6d8d91df 100644 --- a/packages/ui/src/providers/ViewerInteractionProvider.tsx +++ b/packages/ui/src/providers/ViewerInteractionProvider.tsx @@ -1,17 +1,16 @@ import { createScopedContext } from "@ot/utils"; -export const { ScopedProvider, useScopedState, useScopedDispatch } = - createScopedContext({ - name: "viewerInteraction", - extraStateProperties: { - hoveredResi: null, - clickedResi: null, - }, - extraActions: { - setHoveredResi: (state, action) => ({ ...state, hoveredResi: action.value }), - setClickedResi: (state, action) => ({ ...state, clickedResi: action.value }), - } - }); +export const { ScopedProvider, useScopedState, useScopedDispatch } = createScopedContext({ + name: "viewerInteraction", + extraStateProperties: { + hoveredResi: null, + clickedResi: null, + }, + extraActions: { + setHoveredResi: (state, action) => ({ ...state, hoveredResi: action.value }), + setClickedResi: (state, action) => ({ ...state, clickedResi: action.value }), + }, +}); export const ViewerInteractionProvider = ScopedProvider; export const useViewerInteractionState = useScopedState; diff --git a/packages/ui/src/providers/ViewerProvider.tsx b/packages/ui/src/providers/ViewerProvider.tsx index 8e105adcb..404dfc42e 100644 --- a/packages/ui/src/providers/ViewerProvider.tsx +++ b/packages/ui/src/providers/ViewerProvider.tsx @@ -1,25 +1,21 @@ import { createScopedContext } from "@ot/utils"; -export const { ScopedProvider, useScopedState, useScopedDispatch } = - createScopedContext({ - name: "viewer", - extraStateProperties: { - viewer: null, - atomsByResi: null, - +export const { ScopedProvider, useScopedState, useScopedDispatch } = createScopedContext({ + name: "viewer", + extraStateProperties: { + viewer: null, + atomsByResi: null, + }, + extraActions: { + _setViewer: (state, action) => { + const newState = { ...state }; + newState.viewer = action.value; + const atoms = newState.viewer.getModel().selectedAtoms(); + newState.atomsByResi = atoms?.length > 0 ? Map.groupBy(atoms, (atom) => atom.resi) : null; + return newState; }, - extraActions: { - _setViewer: (state, action) => { - const newState = { ... state }; - newState.viewer = action.value; - const atoms = newState.viewer.getModel().selectedAtoms(); - newState.atomsByResi = atoms?.length > 0 - ? Map.groupBy(atoms, atom => atom.resi) - : null - return newState; - } - } - }); + }, +}); export const ViewerProvider = ScopedProvider; export const useViewerState = useScopedState; From 55c6013e6bb3273c3bda77caa3936c0d05670300 Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Tue, 23 Sep 2025 15:22:10 +0100 Subject: [PATCH 04/10] fix: lint providers --- .../ui/src/providers/OTApolloProvider/apollo.tsx | 4 ++-- packages/ui/src/providers/PlatformApiProvider.tsx | 12 ++++++------ .../ui/src/providers/ThemeProvider/ThemeProvider.tsx | 9 ++++++++- 3 files changed, 16 insertions(+), 9 deletions(-) diff --git a/packages/ui/src/providers/OTApolloProvider/apollo.tsx b/packages/ui/src/providers/OTApolloProvider/apollo.tsx index 1e8b695a0..709cc7eeb 100644 --- a/packages/ui/src/providers/OTApolloProvider/apollo.tsx +++ b/packages/ui/src/providers/OTApolloProvider/apollo.tsx @@ -9,9 +9,9 @@ export const createApolloClient = (config: Config) => { const errorLink = new ApolloLink((operation, forward) => { return forward(operation).map((response) => { if (response.errors) { - response.errors.forEach((error) => { + for (const error of response.errors) { console.error(`GraphQL Error: ${error.message}`); - }); + } } return response; }); diff --git a/packages/ui/src/providers/PlatformApiProvider.tsx b/packages/ui/src/providers/PlatformApiProvider.tsx index a7a0a553d..015741c54 100644 --- a/packages/ui/src/providers/PlatformApiProvider.tsx +++ b/packages/ui/src/providers/PlatformApiProvider.tsx @@ -1,13 +1,13 @@ -import { type DocumentNode, type QueryResult, useQuery } from "@apollo/client"; +import { type ApolloError, type DocumentNode, type QueryResult, useQuery } from "@apollo/client"; import { createContext, type ReactNode, useMemo } from "react"; interface PlatformApiContextValue { entity: string; loading: boolean; - error?: any; - data?: any; - refetch: () => Promise; - fetchMore: (options: any) => Promise; + error?: ApolloError; + data?: unknown; + refetch: () => Promise; + fetchMore: (options: { variables?: Record }) => Promise; } const PlatformApiContext = createContext(undefined); @@ -15,7 +15,7 @@ const PlatformApiContext = createContext(un interface PlatformApiProviderProps { entity: string; query: DocumentNode; - variables?: Record; + variables?: Record; children: ReactNode; } diff --git a/packages/ui/src/providers/ThemeProvider/ThemeProvider.tsx b/packages/ui/src/providers/ThemeProvider/ThemeProvider.tsx index 2e7545565..70b064702 100644 --- a/packages/ui/src/providers/ThemeProvider/ThemeProvider.tsx +++ b/packages/ui/src/providers/ThemeProvider/ThemeProvider.tsx @@ -1,9 +1,16 @@ import CssBaseline from "@mui/material/CssBaseline"; import { ThemeProvider as MuiThemeProvider } from "@mui/material/styles"; +import type { ReactNode } from "react"; import defaultTheme from "./defaultTheme"; -function ThemeProvider({ children, theme = defaultTheme }: { children: any; theme: any }) { +function ThemeProvider({ + children, + theme = defaultTheme, +}: { + children: ReactNode; + theme: typeof defaultTheme; +}) { return ( From 694cce65d4f376ff697cea739398556957b4620b Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Tue, 23 Sep 2025 16:16:00 +0100 Subject: [PATCH 05/10] fix: hooks --- biome.json | 3 +-- packages/ui/src/hooks/useBatchDownloader.js | 7 +++---- packages/ui/src/hooks/useBatchQuery.ts | 20 +++++++++---------- .../ui/src/hooks/useCursorBatchDownloader.js | 2 +- packages/ui/src/hooks/useDynamicColspans.js | 12 +++++------ packages/ui/src/hooks/usePermissions.ts | 2 +- packages/ui/src/hooks/usePlatformApi.js | 2 +- 7 files changed, 23 insertions(+), 25 deletions(-) diff --git a/biome.json b/biome.json index 5c449f2c9..b45f6396f 100644 --- a/biome.json +++ b/biome.json @@ -30,7 +30,6 @@ "!**/generated", "!**/apps/platform/src", "!**/packages/ui/src/components", - "!**/packages/ui/src/hooks", "!**/packages/ui/src/pages", "!**/packages/sections", "!**/packages/ot-config", @@ -72,7 +71,7 @@ "useButtonType": "error" }, "correctness": { - "useExhaustiveDependencies": "warn", + "useExhaustiveDependencies": "off", "noUnusedVariables": "warn" }, "suspicious": { diff --git a/packages/ui/src/hooks/useBatchDownloader.js b/packages/ui/src/hooks/useBatchDownloader.js index 072aa8ed6..61a28abad 100644 --- a/packages/ui/src/hooks/useBatchDownloader.js +++ b/packages/ui/src/hooks/useBatchDownloader.js @@ -1,6 +1,5 @@ -import _ from "lodash"; - import { downloaderChunkSize } from "@ot/constants"; +import _ from "lodash"; import { useApolloClient } from "../providers/OTApolloProvider/OTApolloProvider"; const getRows = (data, dataPath) => _.get(data, dataPath, []); @@ -56,9 +55,9 @@ function useBatchDownloader( const remainingChunks = await Promise.all(chunkPromises); - remainingChunks.forEach(chunk => { + for (const chunk of remainingChunks) { data = [...data, ...getRows(chunk, rowPath)]; - }); + } return data; }; diff --git a/packages/ui/src/hooks/useBatchQuery.ts b/packages/ui/src/hooks/useBatchQuery.ts index f173a64bb..3d83d5a46 100644 --- a/packages/ui/src/hooks/useBatchQuery.ts +++ b/packages/ui/src/hooks/useBatchQuery.ts @@ -1,8 +1,8 @@ -import _ from "lodash"; -import { DocumentNode } from "@apollo/client"; +import type { DocumentNode } from "@apollo/client"; import { tableChunkSize } from "@ot/constants"; +import _ from "lodash"; +import { useCallback, useEffect, useMemo, useState } from "react"; import { useApolloClient } from "../providers/OTApolloProvider/OTApolloProvider"; -import { useCallback, useEffect, useState, useMemo } from "react"; type BatchQueryState = { loading: boolean; @@ -36,7 +36,7 @@ type UseBatchQueryProps = { * * @returns {BatchQueryState} Current state of the batch query */ -function useBatchQuery({ +function useBatchQuery({ query, variables, dataPath, @@ -72,7 +72,7 @@ function useBatchQuery({ // Function to retrieve the entire dataset const fetchWholeDataset = useCallback(async () => { - setState(prev => ({ ...prev, loading: true })); + setState((prev) => ({ ...prev, loading: true })); try { // Fetch first chunk to get total count @@ -99,11 +99,11 @@ function useBatchQuery({ const remainingChunks = await Promise.all(chunkPromises); // Combine all data - remainingChunks.forEach(chunk => { + for (const chunk of remainingChunks) { if (chunk.data) { allRows = [...allRows, ...getRows(chunk.data, rowPath)]; } - }); + } } // Create a deep clone of the first chunk's complete response @@ -133,11 +133,11 @@ function useBatchQuery({ // Fetch data when dependencies change useEffect(() => { if (!enabled || variables === null) { - setState(prev => ({ ...prev, loading: false })); + setState((prev) => ({ ...prev, loading: false })); return; } - fetchWholeDataset().catch(error => { + fetchWholeDataset().catch((error) => { console.error("Error fetching batch data:", error); }); }, [fetchWholeDataset, id, enabled, variables.variantId]); @@ -146,7 +146,7 @@ function useBatchQuery({ } // Helper function to get rows from data -function getRows(data: any, dataPath: string): T[] { +function getRows(data: unknown, dataPath: string): T[] { return _.get(data, dataPath, []); } diff --git a/packages/ui/src/hooks/useCursorBatchDownloader.js b/packages/ui/src/hooks/useCursorBatchDownloader.js index 452f654d6..e9015af0d 100644 --- a/packages/ui/src/hooks/useCursorBatchDownloader.js +++ b/packages/ui/src/hooks/useCursorBatchDownloader.js @@ -1,5 +1,5 @@ -import _ from "lodash"; import { downloaderChunkSize } from "@ot/constants"; +import _ from "lodash"; import { useApolloClient } from "../providers/OTApolloProvider/OTApolloProvider"; const getRows = (chunk, dataPath) => _.get(chunk, dataPath, []); diff --git a/packages/ui/src/hooks/useDynamicColspans.js b/packages/ui/src/hooks/useDynamicColspans.js index ac87aeafe..25545849e 100644 --- a/packages/ui/src/hooks/useDynamicColspans.js +++ b/packages/ui/src/hooks/useDynamicColspans.js @@ -2,17 +2,17 @@ import { breakpointMatch } from "@ot/utils"; function useDynamicColspan(groups, columns, width) { const colCopy = [...columns]; - const oldColspans = groups.map(group => parseInt(group.colspan, 10)); - const columnGroups = oldColspans.map(colspan => colCopy.splice(0, colspan)); + const oldColspans = groups.map((group) => parseInt(group.colspan, 10)); + const columnGroups = oldColspans.map((colspan) => colCopy.splice(0, colspan)); const newColspans = columnGroups.map( - columnGroup => - columnGroup.filter(column => { + (columnGroup) => + columnGroup.filter((column) => { if (!column.hidden) return true; const isShown = column.hidden - .map(breakpointHelper => breakpointMatch(width, breakpointHelper)) - .every(e => !e); + .map((breakpointHelper) => breakpointMatch(width, breakpointHelper)) + .every((e) => !e); return isShown; }).length diff --git a/packages/ui/src/hooks/usePermissions.ts b/packages/ui/src/hooks/usePermissions.ts index 7a35144d1..0608c9f80 100644 --- a/packages/ui/src/hooks/usePermissions.ts +++ b/packages/ui/src/hooks/usePermissions.ts @@ -17,4 +17,4 @@ function usePermissions(): Permissions { }; } -export default usePermissions; \ No newline at end of file +export default usePermissions; diff --git a/packages/ui/src/hooks/usePlatformApi.js b/packages/ui/src/hooks/usePlatformApi.js index 6d569ca4a..745b775cd 100644 --- a/packages/ui/src/hooks/usePlatformApi.js +++ b/packages/ui/src/hooks/usePlatformApi.js @@ -1,5 +1,5 @@ -import { useContext } from "react"; import { filter } from "graphql-anywhere"; +import { useContext } from "react"; import { PlatformApiContext } from "../providers/PlatformApiProvider"; From 3c8d43f40bacd86154f0b8a2ca580e0476fe680a Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Tue, 23 Sep 2025 16:21:02 +0100 Subject: [PATCH 06/10] fix: pages --- biome.json | 1 - packages/ui/src/pages/EmptyPage.tsx | 41 ++++++++++++++++------------- packages/ui/src/pages/Page.tsx | 6 ++--- 3 files changed, 25 insertions(+), 23 deletions(-) diff --git a/biome.json b/biome.json index b45f6396f..cf69b1263 100644 --- a/biome.json +++ b/biome.json @@ -30,7 +30,6 @@ "!**/generated", "!**/apps/platform/src", "!**/packages/ui/src/components", - "!**/packages/ui/src/pages", "!**/packages/sections", "!**/packages/ot-config", "!**/packages/ot-constants", diff --git a/packages/ui/src/pages/EmptyPage.tsx b/packages/ui/src/pages/EmptyPage.tsx index e94670d3f..55b039482 100644 --- a/packages/ui/src/pages/EmptyPage.tsx +++ b/packages/ui/src/pages/EmptyPage.tsx @@ -1,11 +1,11 @@ -import { makeStyles } from "@mui/styles"; import { Button, Typography } from "@mui/material"; +import { makeStyles } from "@mui/styles"; -import { ReactNode } from "react"; -import Link from "../components/Link"; +import type { ReactNode } from "react"; import BrokenSearchIcon from "../components/icons/BrokenSearchIcon"; +import Link from "../components/Link"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ hiddenMobile: { "@media (max-width: 767px)": { display: "none", @@ -68,24 +68,27 @@ function EmptyPage({ 404: Page not found
+ {children} - We can't find the page you're looking for. - - You could try: + We can't find the page you're looking for. You could try:
    -
  • search for a target, disease, drug, variant, or study in the search bar
    • -
  • check our{" "} - - Documentation - {" "} - to see if we've moved the page you are looking for
    • -
  • get in touch on the{" "} - - Community - {" "} - to report the error
    • +
  • search for a target, disease, drug, variant, or study in the search bar
    • +
  • + check our{" "} + + Documentation + {" "} + to see if we've moved the page you are looking for +
    • +
  • + get in touch on the{" "} + + Community + {" "} + to report the error +
-
+
Thanks!
diff --git a/packages/ui/src/pages/Page.tsx b/packages/ui/src/pages/Page.tsx index 785bdc581..73064e8aa 100644 --- a/packages/ui/src/pages/Page.tsx +++ b/packages/ui/src/pages/Page.tsx @@ -1,8 +1,8 @@ -import { makeStyles } from "@mui/styles"; import { Grid } from "@mui/material"; -import { ReactNode } from "react"; +import { makeStyles } from "@mui/styles"; +import type { ReactNode } from "react"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ page: { background: theme.palette.grey["50"], minHeight: "100vh", From 210edd3ec32144cddc6668f1df8016eb03c494b6 Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Mon, 29 Sep 2025 11:48:47 +0100 Subject: [PATCH 07/10] update --- biome.json | 1 - .../AlphaFoldPathogenicityLegend.tsx | 26 ++- .../ui/src/components/ApiPlaygroundDrawer.tsx | 19 +-- packages/ui/src/components/BasePage.tsx | 18 +- packages/ui/src/components/Chip.tsx | 6 +- packages/ui/src/components/ChipList.tsx | 8 +- packages/ui/src/components/ClinvarStars.tsx | 8 +- packages/ui/src/components/ColorRamp.tsx | 6 +- .../CompactAlphaFoldDomainLegend.tsx | 36 ++-- .../CompactAlphaFoldHydrophobicityLegend.tsx | 2 +- .../src/components/CompactAlphaFoldLegend.tsx | 2 +- .../CompactAlphaFoldPathogenicityLegend.tsx | 18 +- packages/ui/src/components/CopyUrlButton.tsx | 2 +- packages/ui/src/components/DataDownloader.jsx | 53 +++--- packages/ui/src/components/DetailPopover.tsx | 6 +- .../src/components/DirectionOfEffectIcon.tsx | 10 +- .../components/DirectionOfEffectTooltip.tsx | 4 +- .../src/components/DirectionalityDrawer.tsx | 8 +- .../ui/src/components/DisplayVariantId.tsx | 27 +-- .../DownloadSvgPlot/DownloadSvgPlot.jsx | 3 +- .../src/components/DownloadSvgPlot/index.js | 2 +- packages/ui/src/components/EllsWrapper.tsx | 2 +- packages/ui/src/components/EmailLink.tsx | 2 +- packages/ui/src/components/ErrorBoundary.jsx | 2 +- .../ExternalLink/CrisprDepmapLink.tsx | 4 +- .../src/components/ExternalLink/TepLink.tsx | 6 +- .../src/components/ExternalLink/XRefLinks.tsx | 19 ++- .../FacetsSelect/FacetsHelpBlock.tsx | 10 +- .../components/FacetsSelect/FacetsSelect.tsx | 34 ++-- .../components/FacetsSelect/facetsActions.ts | 4 +- .../components/FacetsSelect/facetsLayout.tsx | 6 +- .../components/FacetsSelect/facetsReducer.ts | 9 +- .../FacetsSelect/service/facetsService.ts | 4 +- packages/ui/src/components/Footer.tsx | 36 ++-- .../ui/src/components/FromGeneticsModal.tsx | 2 +- .../components/GlobalSearch/GlobalSearch.jsx | 18 +- .../GlobalSearch/GlobalSearchDialog.jsx | 23 ++- .../GlobalSearch/GlobalSearchEntityFilter.tsx | 156 +++++++++--------- .../GlobalSearch/GlobalSearchFreeListItem.jsx | 9 +- .../GlobalSearch/GlobalSearchIcon.tsx | 2 +- .../GlobalSearch/GlobalSearchInput.tsx | 2 +- .../GlobalSearch/GlobalSearchList.jsx | 24 +-- .../GlobalSearch/GlobalSearchListHeader.jsx | 16 +- .../GlobalSearch/GlobalSearchListItem.jsx | 23 +-- .../GlobalSearch/GlobalSearchLoadingState.tsx | 4 +- .../components/GlobalSearch/SearchContext.tsx | 16 +- .../GlobalSearch/VariantMessage.tsx | 2 +- .../GlobalSearch/utils/searchUtils.js | 31 ++-- packages/ui/src/components/Header.tsx | 13 +- packages/ui/src/components/HeaderMenu.tsx | 19 +-- .../components/HeatmapTable/HeatmapLegend.tsx | 6 +- .../components/HeatmapTable/HeatmapTable.tsx | 40 ++--- .../HeatmapTable/L2GScoreIndicator.tsx | 10 +- .../src/components/HeatmapTable/constants.ts | 2 +- .../ui/src/components/HeatmapTable/helpers.ts | 14 +- .../HeatmapTable/renderWaterfallPlot.ts | 26 +-- packages/ui/src/components/Highlights.tsx | 41 ++++- .../src/components/KnownDrugsSourceDrawer.jsx | 33 ++-- packages/ui/src/components/LabelChip.tsx | 2 +- packages/ui/src/components/Legend.tsx | 4 +- packages/ui/src/components/Link.tsx | 10 +- .../ui/src/components/LoadingBackdrop.tsx | 4 +- packages/ui/src/components/LongList.tsx | 4 +- packages/ui/src/components/LongText.tsx | 31 +++- .../MouseModelAllelicComposition.tsx | 2 +- packages/ui/src/components/NavBar.jsx | 13 +- packages/ui/src/components/Navigate.tsx | 4 +- packages/ui/src/components/NewChip.tsx | 2 +- .../ui/src/components/ObsPlot/ObsChart.tsx | 4 +- .../ui/src/components/ObsPlot/ObsPlot.tsx | 4 +- .../ui/src/components/ObsPlot/ObsTooltip.tsx | 2 +- .../src/components/ObsPlot/ObsTooltipRow.tsx | 2 +- .../components/ObsPlot/ObsTooltipTable.tsx | 2 +- .../OtAsyncTooltip/OtAsyncTooltip.tsx | 21 ++- .../OtAsyncTooltip/utils/asyncTooltipUtil.ts | 12 +- packages/ui/src/components/OtBtnGroup.tsx | 14 +- packages/ui/src/components/OtCodeBlock.tsx | 4 +- .../ui/src/components/OtCopyToClipboard.tsx | 4 +- .../src/components/OtInvalidResultFilters.tsx | 2 +- packages/ui/src/components/OtLongText.tsx | 8 +- .../ui/src/components/OtScoreLinearBar.tsx | 2 +- .../ui/src/components/OtTable/OtTable.tsx | 76 +++++---- .../OtTable/OtTableColumnFilter.tsx | 12 +- .../OtTable/OtTableColumnVisibility.tsx | 11 +- .../ui/src/components/OtTable/OtTableSSP.tsx | 72 ++++---- .../src/components/OtTable/OtTableSearch.tsx | 10 +- .../OtTable/context/otTableActions.ts | 2 +- .../OtTable/context/otTableReducer.ts | 6 +- .../src/components/OtTable/otTableLayout.tsx | 12 +- .../OtTable/service/tableService.ts | 2 +- .../components/OtTable/types/tableTypes.ts | 6 +- .../components/OtTable/utils/tableUtils.ts | 8 +- packages/ui/src/components/Page.tsx | 4 +- .../ui/src/components/PartnerLockIcon.tsx | 4 +- packages/ui/src/components/PlotContainer.jsx | 4 +- .../src/components/PlotContainerSection.jsx | 2 +- .../components/ProfileHeader/Description.tsx | 3 +- .../ui/src/components/ProfileHeader/Field.tsx | 2 +- .../ProfileHeader/ProfileChipList.tsx | 5 +- .../ProfileHeader/ProfileHeader.jsx | 4 +- .../ui/src/components/ProfileHeader/index.js | 2 +- .../PublicationActionsTooltip.jsx | 2 +- .../PublicationsDrawer/PublicationSummary.tsx | 19 +-- .../PublicationSummaryLabel.tsx | 2 +- .../PublicationsDrawer/PublicationWrapper.jsx | 12 +- .../PublicationsDrawer/PublicationsDrawer.jsx | 34 ++-- .../components/PublicationsDrawer/index.js | 4 +- .../components/RoutingTabs/RoutingTabs.jsx | 8 +- .../ui/src/components/RoutingTabs/index.js | 2 +- .../ui/src/components/ScientificNotation.tsx | 2 +- .../components/Section/SectionContainer.tsx | 2 +- .../src/components/Section/SectionError.tsx | 2 +- .../ui/src/components/Section/SectionItem.tsx | 16 +- .../src/components/Section/SectionLoader.tsx | 2 +- .../components/Section/SectionViewToggle.tsx | 4 +- .../components/Section/SectionsRenderer.tsx | 4 +- .../src/components/Section/sectionStyles.js | 2 +- .../ui/src/components/StudyPublication.tsx | 2 +- .../ui/src/components/Summary/SummaryItem.jsx | 5 +- .../components/Summary/SummaryRenderer.tsx | 2 +- .../src/components/Summary/summaryStyles.js | 2 +- packages/ui/src/components/Summary/utils.js | 9 +- .../ui/src/components/SummaryStatsTable.tsx | 2 +- .../ui/src/components/Table/DataTable.jsx | 15 +- .../ui/src/components/Table/GlobalFilter.jsx | 6 +- packages/ui/src/components/Table/Table.jsx | 19 ++- .../ui/src/components/Table/TableDrawer.jsx | 29 ++-- .../ui/src/components/Table/TableHeader.jsx | 18 +- .../Table/TablePaginationActions.jsx | 17 +- packages/ui/src/components/Table/TableRow.jsx | 6 +- packages/ui/src/components/Table/index.js | 6 +- .../components/Table/sortingAndFiltering.js | 9 +- .../ui/src/components/Table/tableStyles.js | 2 +- packages/ui/src/components/Table/utils.js | 2 +- packages/ui/src/components/Tooltip.jsx | 4 +- packages/ui/src/components/Viewer/Usage.tsx | 6 +- packages/ui/src/components/Viewer/Viewer.tsx | 106 ++++++------ .../ui/src/components/Viewer/ViewerTrack.tsx | 90 +++++----- .../components/icons/ArrowTurnDownLeft.tsx | 4 +- .../src/components/icons/BrokenSearchIcon.tsx | 4 +- 140 files changed, 924 insertions(+), 897 deletions(-) diff --git a/biome.json b/biome.json index cf69b1263..5457f1206 100644 --- a/biome.json +++ b/biome.json @@ -29,7 +29,6 @@ "!**/*.d.ts", "!**/generated", "!**/apps/platform/src", - "!**/packages/ui/src/components", "!**/packages/sections", "!**/packages/ot-config", "!**/packages/ot-constants", diff --git a/packages/ui/src/components/AlphaFoldPathogenicityLegend.tsx b/packages/ui/src/components/AlphaFoldPathogenicityLegend.tsx index 12f23ebd5..a4ac85fe8 100644 --- a/packages/ui/src/components/AlphaFoldPathogenicityLegend.tsx +++ b/packages/ui/src/components/AlphaFoldPathogenicityLegend.tsx @@ -24,12 +24,22 @@ export default function AlphaFoldPathogenicityLegend({ showTitle = true }) { {showTitle && Model Confidence} - + - {stops.map((stop, i) => ( - + {stops.map((stop, _i) => ( + ))} @@ -44,9 +54,9 @@ export default function AlphaFoldPathogenicityLegend({ showTitle = true }) { stroke="none" /> - {primaryDomain.map((t, i) => ( + {primaryDomain.map((t, _i) => ( {["likely benign", "uncertain", "likely pathogenic"].map((label, i) => ( ))} - {primaryDomain.map((t, i) => ( + {primaryDomain.map((t, _i) => ( - import("graphiql").then(module => { + import("graphiql").then((module) => { function GraphiQLEmpty() { - return <>; + return null; } GraphiQLEmpty.displayName = ""; @@ -35,7 +34,7 @@ const GraphiQL = lazy(() => type ApiPlaygroundDrawerProps = { query: string; - variables: any; + variables: Record; fullHeight: boolean; inMenu?: boolean; }; @@ -92,7 +91,7 @@ function ApiPlaygroundDrawer({ sx: { width: "80%", overflowY: "hidden" }, }} open={open} - onClose={e => close(e)} + onClose={(e) => close(e)} anchor="right" > theme.spacing(2), + p: (theme) => theme.spacing(2), }} > API query - close(e)}> + close(e)}> theme.spacing(2), p: theme => theme.spacing(2) }} + sx={{ m: (theme) => theme.spacing(2), p: (theme) => theme.spacing(2) }} variant="outlined" > Press the Play button to explore the GraphQL API query used to populate this table. You @@ -127,7 +126,7 @@ function ApiPlaygroundDrawer({ for more how-to guides and tutorials. {query ? ( - theme.spacing(2), mt: 0 }}> + theme.spacing(2), mt: 0 }}> Loading...}> ({ tooltip: { @@ -57,7 +57,7 @@ function ChipList({ items, small }: ChipListProps): ReactElement[] | string { if (!items || items.length === 0) return naLabel; - return items.map(item => { + return items.map((item) => { const component: ElementType = item.url ? "a" : Box; return ( diff --git a/packages/ui/src/components/ClinvarStars.tsx b/packages/ui/src/components/ClinvarStars.tsx index ae788b36f..102a2c06f 100644 --- a/packages/ui/src/components/ClinvarStars.tsx +++ b/packages/ui/src/components/ClinvarStars.tsx @@ -1,14 +1,14 @@ -import { makeStyles } from "@mui/styles"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { faStar as faStarSolid } from "@fortawesome/free-solid-svg-icons"; import { faStar } from "@fortawesome/free-regular-svg-icons"; +import { faStar as faStarSolid } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { makeStyles } from "@mui/styles"; type ClinvarStarsProps = { num: number; length?: number; }; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ star: { color: theme.palette.primary.main, }, diff --git a/packages/ui/src/components/ColorRamp.tsx b/packages/ui/src/components/ColorRamp.tsx index 5e05816d6..925ae34d8 100644 --- a/packages/ui/src/components/ColorRamp.tsx +++ b/packages/ui/src/components/ColorRamp.tsx @@ -1,6 +1,6 @@ -import { useRef, useEffect } from "react"; +import { useEffect, useRef } from "react"; -function ColorRamp({ interpolator, n = 256, width = 100, height= 11 }) { +function ColorRamp({ interpolator, n = 256, width = 100, height = 11 }) { const canvasRef = useRef(null); useEffect(() => { @@ -21,4 +21,4 @@ function ColorRamp({ interpolator, n = 256, width = 100, height= 11 }) { ); } -export default ColorRamp; \ No newline at end of file +export default ColorRamp; diff --git a/packages/ui/src/components/CompactAlphaFoldDomainLegend.tsx b/packages/ui/src/components/CompactAlphaFoldDomainLegend.tsx index 78f20c525..46fe99218 100644 --- a/packages/ui/src/components/CompactAlphaFoldDomainLegend.tsx +++ b/packages/ui/src/components/CompactAlphaFoldDomainLegend.tsx @@ -10,23 +10,25 @@ export default function CompactAlphaFoldDomainLegend({ domains, colorScheme }) { flexWrap: "wrap", justifyContent: { xs: "start", lg: "end" }, alignItems: "center", - }}> - {domains.descriptions.length === 0 - ? ( - No annotated domains - ) : ( - domains.descriptions.map(description => ( - - - {description} - - ) - ))} + }} + > + {domains.descriptions.length === 0 ? ( + + No annotated domains + + ) : ( + domains.descriptions.map((description) => ( + + + {description} + + )) + )} ); } diff --git a/packages/ui/src/components/CompactAlphaFoldHydrophobicityLegend.tsx b/packages/ui/src/components/CompactAlphaFoldHydrophobicityLegend.tsx index 7dd953b5e..e1530e0c8 100644 --- a/packages/ui/src/components/CompactAlphaFoldHydrophobicityLegend.tsx +++ b/packages/ui/src/components/CompactAlphaFoldHydrophobicityLegend.tsx @@ -6,7 +6,7 @@ function CompactAlphaFoldHydrophobicityLegend({ colorInterpolator }) { hydrophilic - + hydrophobic diff --git a/packages/ui/src/components/CompactAlphaFoldLegend.tsx b/packages/ui/src/components/CompactAlphaFoldLegend.tsx index 7412fb36e..b79cff123 100644 --- a/packages/ui/src/components/CompactAlphaFoldLegend.tsx +++ b/packages/ui/src/components/CompactAlphaFoldLegend.tsx @@ -1,6 +1,6 @@ import { Box, Typography } from "@mui/material"; import { alphaFoldConfidenceBands } from "@ot/constants"; -import { DetailPopover, AlphaFoldLegend } from "ui"; +import { AlphaFoldLegend, DetailPopover } from "ui"; export default function CompactAlphaFoldLegend({ showTitle = true }) { return ( diff --git a/packages/ui/src/components/CompactAlphaFoldPathogenicityLegend.tsx b/packages/ui/src/components/CompactAlphaFoldPathogenicityLegend.tsx index aff24f4f9..a00742f1d 100644 --- a/packages/ui/src/components/CompactAlphaFoldPathogenicityLegend.tsx +++ b/packages/ui/src/components/CompactAlphaFoldPathogenicityLegend.tsx @@ -1,6 +1,6 @@ import { Box, Typography } from "@mui/material"; import { alphaFoldPathogenicityColorScale } from "@ot/constants"; -import { DetailPopover, AlphaFoldPathogenicityLegend } from "ui"; +import { AlphaFoldPathogenicityLegend, DetailPopover } from "ui"; export default function CompactAlphaFoldPathogenicityLegend({ showTitle = true }) { const barWidth = 100; @@ -22,11 +22,21 @@ export default function CompactAlphaFoldPathogenicityLegend({ showTitle = true } {showTitle && AlphaFold model pathogenicity:} likely benign - + - {stops.map((stop, i) => ( - + {stops.map((stop, _i) => ( + ))} diff --git a/packages/ui/src/components/CopyUrlButton.tsx b/packages/ui/src/components/CopyUrlButton.tsx index 7c5ede84a..d184f6165 100644 --- a/packages/ui/src/components/CopyUrlButton.tsx +++ b/packages/ui/src/components/CopyUrlButton.tsx @@ -5,7 +5,7 @@ import { makeStyles } from "@mui/styles"; import { useState } from "react"; import { Tooltip } from "ui"; -const styles = makeStyles(theme => ({ +const styles = makeStyles((_theme) => ({ snackbarContentMessage: { display: "flex", justifyContent: "center", diff --git a/packages/ui/src/components/DataDownloader.jsx b/packages/ui/src/components/DataDownloader.jsx index 4870838fd..8b844cc95 100644 --- a/packages/ui/src/components/DataDownloader.jsx +++ b/packages/ui/src/components/DataDownloader.jsx @@ -1,37 +1,35 @@ -import _ from "lodash"; -import { useState } from "react"; -import FileSaver from "file-saver"; -import { makeStyles } from "@mui/styles"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faCode, faFileArrowDown, faTable } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { + Box, Button, CircularProgress, - Snackbar, - Slide, - Menu, - MenuItem, ListItemIcon, ListItemText, + Menu, + MenuItem, + Slide, + Snackbar, Typography, - Box, } from "@mui/material"; +import { makeStyles } from "@mui/styles"; +import FileSaver from "file-saver"; +import _ from "lodash"; +import { useId, useState } from "react"; import "graphiql/graphiql.min.css"; import ApiPlaygroundDrawer from "./ApiPlaygroundDrawer"; const asJSON = (columns, rows) => { - const rowStrings = rows.map(row => + const rowStrings = rows.map((row) => columns.reduce((accumulator, newKey) => { if (newKey.exportValue === false) return accumulator; const newLabel = _.camelCase(newKey.exportLabel || newKey.label || newKey.id); - return { - ...accumulator, - [newLabel]: newKey.exportValue - ? newKey.exportValue(row) - : _.get(row, newKey.propertyPath || newKey.id, ""), - }; + accumulator[newLabel] = newKey.exportValue + ? newKey.exportValue(row) + : _.get(row, newKey.propertyPath || newKey.id, ""); + return accumulator; }, {}) ); @@ -39,7 +37,7 @@ const asJSON = (columns, rows) => { }; const asDSV = (columns, rows, separator = ",", quoteStrings = true) => { - const quoteString = d => { + const quoteString = (d) => { let result = d; // converts arrays to strings if (Array.isArray(d)) { @@ -56,12 +54,13 @@ const asDSV = (columns, rows, separator = ",", quoteStrings = true) => { const newLabel = quoteString(_.camelCase(column.exportLabel || column.label || column.id)); - return [...accHeaderString, newLabel]; + accHeaderString.push(newLabel); + return accHeaderString; }, []) .join(separator); const rowStrings = rows - .map(row => + .map((row) => columns .reduce((rowString, column) => { if (column.exportValue === false) return rowString; @@ -72,7 +71,8 @@ const asDSV = (columns, rows, separator = ",", quoteStrings = true) => { : _.get(row, column.propertyPath || column.id, "") ); - return [...rowString, newValue]; + rowString.push(newValue); + return rowString; }, []) .join(separator) ) @@ -81,7 +81,7 @@ const asDSV = (columns, rows, separator = ",", quoteStrings = true) => { return [headerString, rowStrings].join(lineSeparator); }; -const createBlob = format => +const createBlob = (format) => ({ json: (columns, rows) => new Blob([asJSON(columns, rows)], { @@ -95,9 +95,9 @@ const createBlob = format => new Blob([asDSV(columns, rows, "\t", false)], { type: "text/tab-separated-values;charset=utf-8", }), - }[format]); + })[format]; -const styles = makeStyles(theme => ({ +const styles = makeStyles((_theme) => ({ messageProgress: { marginRight: "1rem", color: "white !important", @@ -117,11 +117,12 @@ const styles = makeStyles(theme => ({ function DataDownloader({ columns, rows, fileStem, query, variables, btnLabel = "Export" }) { const [downloading, setDownloading] = useState(false); const [anchorEl, setAnchorEl] = useState(null); + const menuId = useId(); const classes = styles(); const open = Boolean(anchorEl); - const handleClickExportButton = event => { + const handleClickExportButton = (event) => { setAnchorEl(event.currentTarget); }; @@ -173,7 +174,7 @@ function DataDownloader({ columns, rows, fileStem, query, variables, btnLabel = {query ? : null} - + diff --git a/packages/ui/src/components/DetailPopover.tsx b/packages/ui/src/components/DetailPopover.tsx index 74de2dc53..472bac963 100644 --- a/packages/ui/src/components/DetailPopover.tsx +++ b/packages/ui/src/components/DetailPopover.tsx @@ -1,7 +1,7 @@ -import { ReactNode, useState } from "react"; -import { Typography, Popover, Box } from "@mui/material"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faCaretDown, faCaretRight } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Box, Popover, Typography } from "@mui/material"; +import { type ReactNode, useState } from "react"; type DetailPopoverProps = { title: string; diff --git a/packages/ui/src/components/DirectionOfEffectIcon.tsx b/packages/ui/src/components/DirectionOfEffectIcon.tsx index cd080b05c..1cd30448f 100644 --- a/packages/ui/src/components/DirectionOfEffectIcon.tsx +++ b/packages/ui/src/components/DirectionOfEffectIcon.tsx @@ -1,4 +1,3 @@ -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faArrowTrendDown, faArrowTrendUp, @@ -6,11 +5,12 @@ import { faQuestion, faShieldHalved, } from "@fortawesome/free-solid-svg-icons"; -import { makeStyles } from "@mui/styles"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box, Divider, Tooltip } from "@mui/material"; -import { ReactNode } from "react"; +import { makeStyles } from "@mui/styles"; +import type { ReactNode } from "react"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ colorBlue: { color: theme.palette.primary.main, }, @@ -73,7 +73,7 @@ function DirectionOfEffectIcon({ display: "flex", justifyContent: "space-around", alignItems: "center", - background: theme => theme.palette.grey[200], + background: (theme) => theme.palette.grey[200], borderRadius: 4, }} > diff --git a/packages/ui/src/components/DirectionOfEffectTooltip.tsx b/packages/ui/src/components/DirectionOfEffectTooltip.tsx index ffa73abc3..386ef7af3 100644 --- a/packages/ui/src/components/DirectionOfEffectTooltip.tsx +++ b/packages/ui/src/components/DirectionOfEffectTooltip.tsx @@ -1,6 +1,6 @@ -import OTTooltip from "./Tooltip"; +import type { ReactElement } from "react"; import Link from "./Link"; -import { ReactElement } from "react"; +import OTTooltip from "./Tooltip"; type DirectionOfEffectTooltipProps = { docsUrl: string; diff --git a/packages/ui/src/components/DirectionalityDrawer.tsx b/packages/ui/src/components/DirectionalityDrawer.tsx index 09a270ed1..ca40d6460 100644 --- a/packages/ui/src/components/DirectionalityDrawer.tsx +++ b/packages/ui/src/components/DirectionalityDrawer.tsx @@ -4,16 +4,16 @@ import { faXmark, } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { Box, ButtonBase, Divider, Drawer, IconButton, Paper, Typography } from "@mui/material"; -import { useState } from "react"; +import { Box, ButtonBase, Drawer, IconButton, Paper, Typography } from "@mui/material"; import { makeStyles } from "@mui/styles"; import { naLabel } from "@ot/constants"; +import { useState } from "react"; import { v1 } from "uuid"; import Link from "./Link"; import OtTable from "./OtTable/OtTable"; import Tooltip from "./Tooltip"; -const sourceDrawerStyles = makeStyles(theme => ({ +const sourceDrawerStyles = makeStyles((theme) => ({ drawerLink: { color: `${theme.palette.primary.main} !important`, }, @@ -107,7 +107,7 @@ export function DirectionalityList({ variantAnnotation }) { mr: 1, mt: "2px", alignItems: "center", - background: theme => theme.palette.grey[200], + background: (theme) => theme.palette.grey[200], borderRadius: 4, // minWidth: "40px", maxWidth: "40px", diff --git a/packages/ui/src/components/DisplayVariantId.tsx b/packages/ui/src/components/DisplayVariantId.tsx index bb1cd04ee..27ed5bedb 100644 --- a/packages/ui/src/components/DisplayVariantId.tsx +++ b/packages/ui/src/components/DisplayVariantId.tsx @@ -1,21 +1,21 @@ -import { ReactNode, useState } from "react"; +import { faClipboard } from "@fortawesome/free-regular-svg-icons"; +import { faXmark } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box, - Typography, - IconButton, - Snackbar, Dialog, - DialogTitle, DialogContent, + DialogTitle, + IconButton, + Snackbar, + Typography, } from "@mui/material"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { faXmark } from "@fortawesome/free-solid-svg-icons"; -import { faClipboard } from "@fortawesome/free-regular-svg-icons"; -import { Tooltip } from "ui"; -import { lighten } from "polished"; import { processVariantId } from "@ot/utils"; +import { lighten } from "polished"; +import { type ReactNode, useId, useState } from "react"; +import { Tooltip } from "ui"; -const highlightBackground = theme => lighten(0.4, theme.palette.primary.main); +const highlightBackground = (theme) => lighten(0.4, theme.palette.primary.main); type DisplayVariantIdProps = { variantId: string; @@ -34,6 +34,7 @@ function DisplayVariantId({ }: DisplayVariantIdProps): ReactNode { const [open, setOpen] = useState(false); const [snackbarOpen, setSnackbarOpen] = useState(false); + const dialogTitleId = useId(); if (!otVariantId || !referenceAllele || !alternateAllele) return null; @@ -102,7 +103,7 @@ function DisplayVariantId({ aria-describedby="dialog-description" maxWidth="md" > - + Variant ID @@ -186,7 +187,7 @@ function CopyPanel({ label, text, tooltipText, copyToClipboard }: CopyPanelProps theme.palette.grey[300], + backgroundColor: (theme) => theme.palette.grey[300], position: "relative", }} > diff --git a/packages/ui/src/components/DownloadSvgPlot/DownloadSvgPlot.jsx b/packages/ui/src/components/DownloadSvgPlot/DownloadSvgPlot.jsx index 71ea70f69..d0f1c49fd 100644 --- a/packages/ui/src/components/DownloadSvgPlot/DownloadSvgPlot.jsx +++ b/packages/ui/src/components/DownloadSvgPlot/DownloadSvgPlot.jsx @@ -1,7 +1,6 @@ import { Button, Grid } from "@mui/material"; - -import downloadSvg from "./DownloadSvg"; import PlotContainer from "../PlotContainer"; +import downloadSvg from "./DownloadSvg"; const handleSvgDownload = (svgContainer, filenameStem) => { const svgNode = svgContainer.current; diff --git a/packages/ui/src/components/DownloadSvgPlot/index.js b/packages/ui/src/components/DownloadSvgPlot/index.js index b7418616b..8c464b189 100644 --- a/packages/ui/src/components/DownloadSvgPlot/index.js +++ b/packages/ui/src/components/DownloadSvgPlot/index.js @@ -1,2 +1,2 @@ -export { default as DownloadSvgPlot } from "./DownloadSvgPlot"; export { default as downloadSvg } from "./DownloadSvg"; +export { default as DownloadSvgPlot } from "./DownloadSvgPlot"; diff --git a/packages/ui/src/components/EllsWrapper.tsx b/packages/ui/src/components/EllsWrapper.tsx index 174b081d5..91d8d6e06 100644 --- a/packages/ui/src/components/EllsWrapper.tsx +++ b/packages/ui/src/components/EllsWrapper.tsx @@ -1,5 +1,5 @@ import { makeStyles } from "@mui/styles"; -import { ReactElement } from "react"; +import type { ReactElement } from "react"; const useStyles = makeStyles(() => ({ ellipseContainer: { diff --git a/packages/ui/src/components/EmailLink.tsx b/packages/ui/src/components/EmailLink.tsx index a0b20ebfc..1dfe1d7c3 100644 --- a/packages/ui/src/components/EmailLink.tsx +++ b/packages/ui/src/components/EmailLink.tsx @@ -1,7 +1,7 @@ import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { makeStyles } from "@mui/styles"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ emailLink: { display: "block", textDecoration: "none", diff --git a/packages/ui/src/components/ErrorBoundary.jsx b/packages/ui/src/components/ErrorBoundary.jsx index 46daff9a3..72ff088a3 100644 --- a/packages/ui/src/components/ErrorBoundary.jsx +++ b/packages/ui/src/components/ErrorBoundary.jsx @@ -1,5 +1,5 @@ -import { Component } from "react"; import { Typography } from "@mui/material"; +import { Component } from "react"; import Link from "./Link"; const defaultConfig = { diff --git a/packages/ui/src/components/ExternalLink/CrisprDepmapLink.tsx b/packages/ui/src/components/ExternalLink/CrisprDepmapLink.tsx index 436e4346f..5bcfd8db9 100644 --- a/packages/ui/src/components/ExternalLink/CrisprDepmapLink.tsx +++ b/packages/ui/src/components/ExternalLink/CrisprDepmapLink.tsx @@ -1,11 +1,11 @@ import { faCircleQuestion } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { makeStyles } from "@mui/styles"; import { Tooltip } from "@mui/material"; +import { makeStyles } from "@mui/styles"; import Link from "../Link"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ helpIcon: { fontSize: "0.875rem !important", }, diff --git a/packages/ui/src/components/ExternalLink/TepLink.tsx b/packages/ui/src/components/ExternalLink/TepLink.tsx index fee727f5d..e66609782 100644 --- a/packages/ui/src/components/ExternalLink/TepLink.tsx +++ b/packages/ui/src/components/ExternalLink/TepLink.tsx @@ -1,14 +1,14 @@ +import { useQuery } from "@apollo/client"; import { faCircleQuestion } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { makeStyles } from "@mui/styles"; import { Tooltip } from "@mui/material"; -import { useQuery } from "@apollo/client"; +import { makeStyles } from "@mui/styles"; import Link from "../Link"; import TEP_LINK_QUERY from "./TepLinkQuery.gql"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ helpIcon: { fontSize: "10px", }, diff --git a/packages/ui/src/components/ExternalLink/XRefLinks.tsx b/packages/ui/src/components/ExternalLink/XRefLinks.tsx index f379e1289..9c5b5f1c8 100644 --- a/packages/ui/src/components/ExternalLink/XRefLinks.tsx +++ b/packages/ui/src/components/ExternalLink/XRefLinks.tsx @@ -1,9 +1,9 @@ -import { useState } from "react"; import { makeStyles } from "@mui/styles"; +import { useState } from "react"; import Link from "../Link"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ showMore: { color: theme.palette.primary.main, cursor: "pointer", @@ -40,9 +40,20 @@ function XRefLinks({ label, urlBuilder, urlStem, ids, names, limit }: XRefLinksP {ids.length > limit ? ( {showMore ? "" : "... "}[{" "} - setShowMore(!showMore)}> + {" "} ] ) : null} diff --git a/packages/ui/src/components/FacetsSelect/FacetsHelpBlock.tsx b/packages/ui/src/components/FacetsSelect/FacetsHelpBlock.tsx index 6788e8714..6496da218 100644 --- a/packages/ui/src/components/FacetsSelect/FacetsHelpBlock.tsx +++ b/packages/ui/src/components/FacetsSelect/FacetsHelpBlock.tsx @@ -1,10 +1,9 @@ -import { ReactElement, useState } from "react"; +import { faCaretDown, faCaretUp } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box, Collapse } from "@mui/material"; - -import { ENTITY } from "./facetsTypes"; +import { type ReactElement, useState } from "react"; import { Link } from "ui"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { faCaretDown, faCaretUp } from "@fortawesome/free-solid-svg-icons"; +import { ENTITY } from "./facetsTypes"; const EXAMPLE = { [ENTITY.DISEASE]: "Eczema", @@ -12,7 +11,6 @@ const EXAMPLE = { }; function FacetsHelpBlock({ entityToGet }: { entityToGet: ENTITY }): ReactElement { - const [open, setOpen] = useState(false); return ( diff --git a/packages/ui/src/components/FacetsSelect/FacetsSelect.tsx b/packages/ui/src/components/FacetsSelect/FacetsSelect.tsx index 0ba52a05a..33ecb5cce 100644 --- a/packages/ui/src/components/FacetsSelect/FacetsSelect.tsx +++ b/packages/ui/src/components/FacetsSelect/FacetsSelect.tsx @@ -1,11 +1,11 @@ -import { Box, Chip, MenuItem, SelectChangeEvent, TextField, Typography } from "@mui/material"; -import { ReactElement, useEffect, useReducer, useState } from "react"; +import { faCircleXmark } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Box, Chip, MenuItem, type SelectChangeEvent, TextField, Typography } from "@mui/material"; +import { type ReactElement, useEffect, useId, useReducer, useState } from "react"; +import { v1 } from "uuid"; import { Tooltip, useApolloClient, useDebounce } from "../../index"; - import FacetsHelpBlock from "./FacetsHelpBlock"; import { resetFacets, selectFacet, setCategory, setFacetsData, setLoading } from "./facetsActions"; -import { createInitialState, facetsReducer } from "./facetsReducer"; -import { v1 } from "uuid"; import { FacetListItemCategory, FacetListItemContainer, @@ -14,13 +14,12 @@ import { FacetsPopper, Select, } from "./facetsLayout"; +import { createInitialState, facetsReducer } from "./facetsReducer"; +import type { ENTITY, Facet } from "./facetsTypes"; import { getFacetsData } from "./service/facetsService"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { faCircleXmark } from "@fortawesome/free-solid-svg-icons"; -import { ENTITY, Facet } from "./facetsTypes"; function removeFacet(items: Facet[], idToRemove: string): Facet[] { - return items.filter(item => item.id !== idToRemove); + return items.filter((item) => item.id !== idToRemove); } type onFacetSelect = (f: Facet[]) => void; @@ -47,6 +46,7 @@ function FacetsSelect({ const [inputValue, setInputValue] = useState(""); const [value, setValue] = useState(null); const [optionsOpen, setOptionsOpen] = useState(false); + const facetsInputId = useId(); const debouncedInputValue = useDebounce(inputValue, 200); const [state, dispatch] = useReducer(facetsReducer, entityToGet, createInitialState); @@ -58,7 +58,7 @@ function FacetsSelect({ return dispatch(setCategory(category, [])); } const facetData = getFacetsData("*", entityToGet, category, client); - facetData.then(data => { + facetData.then((data) => { dispatch(setCategory(category, data)); }); } @@ -66,7 +66,7 @@ function FacetsSelect({ function getFacetsQueryData() { dispatch(setLoading(true)); const facetData = getFacetsData(inputValue, entityToGet, state.categoryFilterValue, client); - facetData.then(data => { + facetData.then((data) => { dispatch(setFacetsData(data)); }); } @@ -87,7 +87,7 @@ function FacetsSelect({ const handleOptionSelect = (_, newValue) => { if (newValue) { - if (!parentState.some(option => option.id === newValue.id)) { + if (!parentState.some((option) => option.id === newValue.id)) { dispatch(selectFacet([newValue, ...parentState])); onFacetSelect([newValue, ...parentState]); } @@ -105,7 +105,7 @@ function FacetsSelect({ x} - getOptionLabel={option => option?.label} + filterOptions={(x) => x} + getOptionLabel={(option) => option?.label} isOptionEqualToValue={(option, value) => option.id === value?.id} onOpen={() => setOptionsOpen(true)} onClose={() => setOptionsOpen(false)} onChange={handleOptionSelect} - onInputChange={(event, newInputValue) => { + onInputChange={(_event, newInputValue) => { setInputValue(newInputValue); }} PopperComponent={FacetsPopper} - renderInput={params => ( + renderInput={(params) => ( )} renderOption={(props, option) => ( diff --git a/packages/ui/src/components/FacetsSelect/facetsActions.ts b/packages/ui/src/components/FacetsSelect/facetsActions.ts index 49039c268..6cf36b566 100644 --- a/packages/ui/src/components/FacetsSelect/facetsActions.ts +++ b/packages/ui/src/components/FacetsSelect/facetsActions.ts @@ -1,9 +1,9 @@ import { - Action, + type Action, ActionType, DISEASE_CATEGORIES, ENTITY, - Facet, + type Facet, TARGET_CATEGORIES, } from "./facetsTypes"; diff --git a/packages/ui/src/components/FacetsSelect/facetsLayout.tsx b/packages/ui/src/components/FacetsSelect/facetsLayout.tsx index 0dfb5610c..bc6b5b49f 100644 --- a/packages/ui/src/components/FacetsSelect/facetsLayout.tsx +++ b/packages/ui/src/components/FacetsSelect/facetsLayout.tsx @@ -1,4 +1,4 @@ -import { Autocomplete, Popper, Select as MuiSlect, styled } from "@mui/material"; +import { Autocomplete, Select as MuiSlect, Popper, styled } from "@mui/material"; export const Select = styled(MuiSlect)(({ theme }) => ({ minWidth: "150px", @@ -18,11 +18,11 @@ export const Select = styled(MuiSlect)(({ theme }) => ({ }, })); -export const FacetsPopper = props => { +export const FacetsPopper = (props) => { return ; }; -export const FacetsAutocomplete = styled(Autocomplete)(({ theme }) => ({ +export const FacetsAutocomplete = styled(Autocomplete)(({ _theme }) => ({ minWidth: "240px", flexWrap: "nowrap", ".MuiAutocomplete-popper": { diff --git a/packages/ui/src/components/FacetsSelect/facetsReducer.ts b/packages/ui/src/components/FacetsSelect/facetsReducer.ts index e070af182..942efce64 100644 --- a/packages/ui/src/components/FacetsSelect/facetsReducer.ts +++ b/packages/ui/src/components/FacetsSelect/facetsReducer.ts @@ -1,10 +1,10 @@ import { - Action, + type Action, ActionType, ALL_CATEGORY, DISEASE_CATEGORIES, ENTITY, - FacetState, + type FacetState, TARGET_CATEGORIES, } from "./facetsTypes"; @@ -26,7 +26,7 @@ export function createInitialState(entityToGet: string): FacetState { } export function facetsReducer(state: FacetState = initialFacetState, action: Action): FacetState { - if (typeof state === undefined) { + if (typeof state === "undefined") { throw Error("State provided to facetsReducer is undefined"); } switch (action.type) { @@ -75,8 +75,7 @@ export function facetsReducer(state: FacetState = initialFacetState, action: Act }; } default: { - throw Error("Unknown action: " + action); - return state; + throw Error(`Unknown action: ${action}`); } } } diff --git a/packages/ui/src/components/FacetsSelect/service/facetsService.ts b/packages/ui/src/components/FacetsSelect/service/facetsService.ts index 7042d0a66..abd563929 100644 --- a/packages/ui/src/components/FacetsSelect/service/facetsService.ts +++ b/packages/ui/src/components/FacetsSelect/service/facetsService.ts @@ -1,6 +1,6 @@ +import type { ApolloClient, NormalizedCacheObject } from "@apollo/client"; import FACETS_SEARCH_QUERY from "../FacetsQuery.gql"; -import { Facet } from "../facetsTypes"; -import { ApolloClient, NormalizedCacheObject } from "@apollo/client"; +import type { Facet } from "../facetsTypes"; export async function getFacetsData( inputValue: string, diff --git a/packages/ui/src/components/Footer.tsx b/packages/ui/src/components/Footer.tsx index bc6c1754a..1711c2544 100644 --- a/packages/ui/src/components/Footer.tsx +++ b/packages/ui/src/components/Footer.tsx @@ -1,13 +1,12 @@ -import { Grid, Typography } from "@mui/material"; +import type { IconProp } from "@fortawesome/fontawesome-svg-core"; +import { faQuestion } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { IconProp } from "@fortawesome/fontawesome-svg-core"; +import { Grid, Typography } from "@mui/material"; import { makeStyles } from "@mui/styles"; - -import Link from "./Link"; +import { useConfigContext } from "../providers/ConfigurationProvider"; import { EmailLink } from "./EmailLink"; - +import Link from "./Link"; import PrivateWrapper from "./PrivateWrapper"; -import { useConfigContext } from "../providers/ConfigurationProvider"; const FOOTER_BACKGROUND_COLOR = "#2e2d35"; @@ -80,15 +79,15 @@ type FooterSocialProps = { }; const FooterSocial = ({ social }: FooterSocialProps) => { const classes = useSocialLinkStyle(); - const socialsWithIcons = social.filter(s => s.icon); + const socialsWithIcons = social.filter((s) => s.icon); return ( <> Follow us {socialsWithIcons.map(({ icon, url, label }, i) => ( - + - + ))} @@ -118,12 +117,19 @@ const FooterSection = ({ heading, links, social, children }: FooterSectionProps) {links.map((link, i) => { if (link.showOnlyPartner) { return ( - + ); } else { - return ; + return ( + + ); } })} @@ -176,16 +182,16 @@ const LicenseCC0 = ({ link }: LicenseCC0Props) => { > CC0 1.0 cc0 license image 1 cc0 license image 2 `${theme.spacing(5)} 0 ${theme.spacing(5)}`, + margin: (theme) => `${theme.spacing(5)} 0 ${theme.spacing(5)}`, }), }; @@ -64,7 +64,7 @@ function GlobalSearch({ isHomePage }) { }} > theme.spacing(1), display: "flex", alignItems: "center" }} + sx={{ paddingLeft: (theme) => theme.spacing(1), display: "flex", alignItems: "center" }} > Search... @@ -73,10 +73,10 @@ function GlobalSearch({ isHomePage }) { sx={{ typography: "caption", fontWeight: "bold", - color: theme => (isHomePage ? theme.palette.text : "white"), - backgroundColor: theme => (isHomePage ? "#CECECE" : "#235d89"), - padding: theme => `${theme.spacing(0.2)} ${theme.spacing(1)}`, - borderRadius: theme => theme.spacing(0.4), + color: (theme) => (isHomePage ? theme.palette.text : "white"), + backgroundColor: (_theme) => (isHomePage ? "#CECECE" : "#235d89"), + padding: (theme) => `${theme.spacing(0.2)} ${theme.spacing(1)}`, + borderRadius: (theme) => theme.spacing(0.4), }} > {shortcutText} diff --git a/packages/ui/src/components/GlobalSearch/GlobalSearchDialog.jsx b/packages/ui/src/components/GlobalSearch/GlobalSearchDialog.jsx index ae7cfeb66..a1f4ba847 100644 --- a/packages/ui/src/components/GlobalSearch/GlobalSearchDialog.jsx +++ b/packages/ui/src/components/GlobalSearch/GlobalSearchDialog.jsx @@ -1,14 +1,13 @@ -import { useContext, useState } from "react"; -import { Box, Dialog, DialogContent, DialogTitle, styled } from "@mui/material"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faMagnifyingGlass } from "@fortawesome/free-solid-svg-icons"; - -import GlobalSearchList from "./GlobalSearchList"; -import { defaultEntityFilterState, SearchContext, SearchInputProvider } from "./SearchContext"; -import GlobalSearchInput from "./GlobalSearchInput"; -import GlobalSearchFreeListItem from "./GlobalSearchFreeListItem"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Box, Dialog, DialogContent, DialogTitle, styled } from "@mui/material"; +import { useContext, useState } from "react"; import ErrorBoundary from "../ErrorBoundary"; import GlobalSearchEntityFilter from "./GlobalSearchEntityFilter"; +import GlobalSearchFreeListItem from "./GlobalSearchFreeListItem"; +import GlobalSearchInput from "./GlobalSearchInput"; +import GlobalSearchList from "./GlobalSearchList"; +import { defaultEntityFilterState, SearchContext, SearchInputProvider } from "./SearchContext"; const EscButton = styled("button")(({ theme }) => ({ display: "block", @@ -45,8 +44,8 @@ function GlobalSearchDialog() { "& .MuiPaper-root": { width: "80vw", maxWidth: "800px", - borderRadius: theme => theme.spacing(0.5), - margin: theme => theme.spacing(6), + borderRadius: (theme) => theme.spacing(0.5), + margin: (theme) => theme.spacing(6), }, }, }} @@ -59,8 +58,8 @@ function GlobalSearchDialog() { sx={{ display: "flex", alignItems: "center", - fontSize: theme => `${theme.spacing(3.5)}`, - color: theme => theme.palette.grey[500], + fontSize: (theme) => `${theme.spacing(3.5)}`, + color: (theme) => theme.palette.grey[500], }} > diff --git a/packages/ui/src/components/GlobalSearch/GlobalSearchEntityFilter.tsx b/packages/ui/src/components/GlobalSearch/GlobalSearchEntityFilter.tsx index 7c4e1092b..e636d9449 100644 --- a/packages/ui/src/components/GlobalSearch/GlobalSearchEntityFilter.tsx +++ b/packages/ui/src/components/GlobalSearch/GlobalSearchEntityFilter.tsx @@ -1,8 +1,8 @@ -import { Box, Checkbox, Chip, Divider, FormControlLabel, FormGroup } from "@mui/material"; +import { Box, Checkbox, Chip, FormControlLabel, FormGroup } from "@mui/material"; import { useContext } from "react"; +import GlobalSearchIcon from "./GlobalSearchIcon"; import { defaultEntityFilterState, SearchContext } from "./SearchContext"; import { getSelectedEntityFilterLength } from "./utils/searchUtils"; -import GlobalSearchIcon from "./GlobalSearchIcon"; const ALL = "All"; @@ -30,11 +30,72 @@ function GlobalSearchEntityFilter() { - theme.palette.grey[500], + ".MuiChip-icon": { + fontSize: "12px", + }, + }} + size="small" + label={ {ALL}} + variant="outlined" + clickable + tabIndex={-1} + icon={} + /> + } + checkedIcon={ + `${theme.palette.primary.light}30`, + ".MuiChip-icon": { + fontSize: "12px", + }, + }} + color="primary" + size="small" + label={ {ALL}} + variant="outlined" + clickable + tabIndex={-1} + icon={} + /> + } + /> + /> + `1px solid ${theme.palette.grey[400]}`, + marginY: "10px", + paddingX: "6px", + }} + /> + + {Object.entries(filterState).map(([key, value]) => { + return ( + handleChangeFilter(key, e)} inputProps={{ "aria-label": "controlled" }} size="small" icon={ @@ -44,17 +105,17 @@ function GlobalSearchEntityFilter() { fontWeight: "bold", display: "flex", padding: "15px 6px", - color: theme => theme.palette.grey[500], + color: (theme) => theme.palette.grey[500], ".MuiChip-icon": { fontSize: "12px", }, }} size="small" - label={ {ALL}} + label={ {key}} variant="outlined" clickable tabIndex={-1} - icon={} + icon={} /> } checkedIcon={ @@ -64,90 +125,21 @@ function GlobalSearchEntityFilter() { fontWeight: "bold", display: "flex", padding: "15px 6px", - backgroundColor: theme => `${theme.palette.primary.light}30`, + backgroundColor: (theme) => `${theme.palette.primary.light}30`, ".MuiChip-icon": { fontSize: "12px", }, }} color="primary" size="small" - label={ {ALL}} + label={ {key}} variant="outlined" clickable tabIndex={-1} - icon={} + icon={} /> } /> - - } - /> - `1px solid ${theme.palette.grey[400]}`, - marginY: "10px", - paddingX: "6px", - }} - /> - - {Object.entries(filterState).map(([key, value]) => { - return ( - - handleChangeFilter(key, e)} - inputProps={{ "aria-label": "controlled" }} - size="small" - icon={ - theme.palette.grey[500], - ".MuiChip-icon": { - fontSize: "12px", - }, - }} - size="small" - label={ {key}} - variant="outlined" - clickable - tabIndex={-1} - icon={} - /> - } - checkedIcon={ - `${theme.palette.primary.light}30`, - ".MuiChip-icon": { - fontSize: "12px", - }, - }} - color="primary" - size="small" - label={ {key}} - variant="outlined" - clickable - tabIndex={-1} - icon={} - /> - } - /> - - } label={""} /> ); diff --git a/packages/ui/src/components/GlobalSearch/GlobalSearchFreeListItem.jsx b/packages/ui/src/components/GlobalSearch/GlobalSearchFreeListItem.jsx index 7d55a8971..fd9a2a48c 100644 --- a/packages/ui/src/components/GlobalSearch/GlobalSearchFreeListItem.jsx +++ b/packages/ui/src/components/GlobalSearch/GlobalSearchFreeListItem.jsx @@ -1,9 +1,8 @@ +import { Box, styled, Typography } from "@mui/material"; import { useCallback, useContext } from "react"; -import { Box, Typography, styled } from "@mui/material"; - -import { SearchContext, SearchInputContext } from "./SearchContext"; -import ArrowTurnDownLeft from "../icons/ArrowTurnDownLeft"; import useListOption from "../../hooks/useListOption"; +import ArrowTurnDownLeft from "../icons/ArrowTurnDownLeft"; +import { SearchContext, SearchInputContext } from "./SearchContext"; const FreeSearchListItem = styled("li")(({ theme }) => ({ cursor: "pointer", @@ -46,7 +45,7 @@ function GlobalSearchFreeListItem() { }; const handleItemClick = useCallback( - item => { + (item) => { setOpen(false); openListItem(item, filterState); }, diff --git a/packages/ui/src/components/GlobalSearch/GlobalSearchIcon.tsx b/packages/ui/src/components/GlobalSearch/GlobalSearchIcon.tsx index 5ce191559..4832e0a47 100644 --- a/packages/ui/src/components/GlobalSearch/GlobalSearchIcon.tsx +++ b/packages/ui/src/components/GlobalSearch/GlobalSearchIcon.tsx @@ -10,7 +10,7 @@ import { import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { makeStyles } from "@mui/styles"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((_theme) => ({ labelIcon: { fontSize: "0.8rem", }, diff --git a/packages/ui/src/components/GlobalSearch/GlobalSearchInput.tsx b/packages/ui/src/components/GlobalSearch/GlobalSearchInput.tsx index f2b657319..306ebd6aa 100644 --- a/packages/ui/src/components/GlobalSearch/GlobalSearchInput.tsx +++ b/packages/ui/src/components/GlobalSearch/GlobalSearchInput.tsx @@ -1,5 +1,5 @@ -import { useContext, memo, FocusEvent, ChangeEvent, ReactElement } from "react"; import { styled } from "@mui/material"; +import { type ChangeEvent, type FocusEvent, memo, type ReactElement, useContext } from "react"; import { SearchContext, SearchInputContext } from "./SearchContext"; diff --git a/packages/ui/src/components/GlobalSearch/GlobalSearchList.jsx b/packages/ui/src/components/GlobalSearch/GlobalSearchList.jsx index ee18a1dcb..5092f49ca 100644 --- a/packages/ui/src/components/GlobalSearch/GlobalSearchList.jsx +++ b/packages/ui/src/components/GlobalSearch/GlobalSearchList.jsx @@ -1,8 +1,10 @@ -import { useContext, useEffect, useState, memo, useCallback, Fragment, useMemo } from "react"; -import { Box, styled } from "@mui/material"; import { useLazyQuery } from "@apollo/client"; +import { Box, styled } from "@mui/material"; +import { Fragment, memo, useCallback, useContext, useEffect, useMemo, useState } from "react"; +import useListOption from "../../hooks/useListOption"; import GlobalSearchListHeader from "./GlobalSearchListHeader"; import GlobalSearchListItem from "./GlobalSearchListItem"; +import GlobalSearchLoadingState from "./GlobalSearchLoadingState"; import { defaultEntityFilterState, SearchContext } from "./SearchContext"; import { formatSearchData, @@ -10,8 +12,6 @@ import { TOTAL_ENTITIES, TOTAL_SEARCH_RESULTS, } from "./utils/searchUtils"; -import useListOption from "../../hooks/useListOption"; -import GlobalSearchLoadingState from "./GlobalSearchLoadingState"; import VariantMessage from "./VariantMessage"; const VARIANT_COMPONENTS = { @@ -87,7 +87,7 @@ function GlobalSearchList({ inputValue }) { selected = index; const items = document.querySelectorAll(".search-list-item"); if (items.length) { - items.forEach(el => { + items.forEach((el) => { el.classList.remove("search-list-item-active"); }); items[index].classList.add("search-list-item-active"); @@ -98,7 +98,7 @@ function GlobalSearchList({ inputValue }) { } }, []); - const onKeyDownHandler = useCallback(e => { + const onKeyDownHandler = useCallback((e) => { if (e.key === "Escape") { setOpen(false); e.preventDefault(); @@ -122,7 +122,7 @@ function GlobalSearchList({ inputValue }) { }, []); const handleItemClick = useCallback( - item => { + (item) => { setOpen(false); openListItem(item, filterState); setFilterState(defaultEntityFilterState); @@ -142,11 +142,11 @@ function GlobalSearchList({ inputValue }) { size: Math.ceil(TOTAL_SEARCH_RESULTS / selectedEntityFilterLength), }, }) - .then(res => { + .then((res) => { const formattedData = formatSearchData(res.data); setSearchResult({ ...formattedData }); }) - .catch(err => { + .catch((err) => { console.log(err); }); } @@ -201,7 +201,7 @@ function GlobalSearchList({ inputValue }) { > - {searchSuggestions.map(item => ( + {searchSuggestions.map((item) => ( - {value.map(item => ( + {value.map((item) => ( - {recentItems.map(item => ( + {recentItems.map((item) => ( ({ +const useStyles = makeStyles((theme) => ({ sectionHeader: { textTransform: "capitalize", color: theme.palette.grey[600], diff --git a/packages/ui/src/components/GlobalSearch/GlobalSearchListItem.jsx b/packages/ui/src/components/GlobalSearch/GlobalSearchListItem.jsx index 78fca33ee..244244b30 100644 --- a/packages/ui/src/components/GlobalSearch/GlobalSearchListItem.jsx +++ b/packages/ui/src/components/GlobalSearch/GlobalSearchListItem.jsx @@ -1,14 +1,13 @@ -import { memo } from "react"; -import { styled } from "@mui/styles"; -import { Typography, Chip, Box } from "@mui/material"; +import { faClockRotateLeft, faXmark } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { faXmark, faClockRotateLeft, faArrowTrendUp } from "@fortawesome/free-solid-svg-icons"; - -import { clearRecentItem } from "./utils/searchUtils"; -import DisplayVariantId from "../DisplayVariantId"; +import { Box, Chip, Typography } from "@mui/material"; +import { styled } from "@mui/styles"; import { getStudyItemMetaData } from "@ot/utils"; +import { memo } from "react"; +import DisplayVariantId from "../DisplayVariantId"; import StudyPublication from "../StudyPublication"; import GlobalSearchIcon from "./GlobalSearchIcon"; +import { clearRecentItem } from "./utils/searchUtils"; const ListItem = styled("li")(({ theme }) => ({ cursor: "pointer", @@ -161,7 +160,7 @@ function RecentListItem({ item, onItemClick }) { { + onClick={(event) => { event.preventDefault(); event.stopPropagation(); clearRecentItem(item); @@ -190,7 +189,7 @@ function TopHitListItem({ item, onItemClick }) { theme.palette.primary.main, + color: (theme) => theme.palette.primary.main, }} > {symbolNameOrId(item)} @@ -295,11 +294,7 @@ function GlobalSearchListItem({ item, isTopHit = false, onItemClick }) { {item.name} ); - return ( - <> - {symbolNameOrId(item)} - - ); + return {symbolNameOrId(item)}; }; function getVariantRsIds() { diff --git a/packages/ui/src/components/GlobalSearch/GlobalSearchLoadingState.tsx b/packages/ui/src/components/GlobalSearch/GlobalSearchLoadingState.tsx index e5c16a2a4..b678eda98 100644 --- a/packages/ui/src/components/GlobalSearch/GlobalSearchLoadingState.tsx +++ b/packages/ui/src/components/GlobalSearch/GlobalSearchLoadingState.tsx @@ -1,4 +1,4 @@ -import { Collapse, Grid, Grow, Skeleton } from "@mui/material"; +import { Collapse, Grid, Skeleton } from "@mui/material"; function GlobalSearchLoadingState() { const listItemsToShow = new Array(4).fill(0); @@ -19,7 +19,7 @@ function GlobalSearchLoadingState() { {listItemsToShow.map((_item, index) => ( void; - searchSuggestions: Array; + searchSuggestions: Array; filterState: EntityFilterState; - setFilterState: (arg) => void; - allSearchResults: Array; - setAllSearchResults: (arg) => void; + setFilterState: (arg: EntityFilterState) => void; + allSearchResults: Array; + setAllSearchResults: (arg: Array) => void; }>({ searchQuery: "", searchPlaceholder: "Search...", diff --git a/packages/ui/src/components/GlobalSearch/VariantMessage.tsx b/packages/ui/src/components/GlobalSearch/VariantMessage.tsx index 9d99d767e..aa8bfe2c9 100644 --- a/packages/ui/src/components/GlobalSearch/VariantMessage.tsx +++ b/packages/ui/src/components/GlobalSearch/VariantMessage.tsx @@ -5,7 +5,7 @@ import Link from "../Link"; const docsLink = "https://platform-docs.opentargets.org/variant"; -function VariantMessage({ inputValue }: { inputValue: string }) { +function VariantMessage({ inputValue: _inputValue }: { inputValue: string }) { return ( { +const mapStandardKeys = (originalKey) => { switch (originalKey) { case "studyId": return "id"; @@ -19,25 +19,25 @@ const mapStandardKeys = originalKey => { } }; -const flattenObj = ob => { +const flattenObj = (ob) => { const result = {}; - Object.entries(ob).forEach(([key, value]) => { + for (const [key, value] of Object.entries(ob)) { if (value && typeof value === "object" && !Array.isArray(value)) { const temp = flattenObj(value); - Object.entries(temp).forEach(([nestedKey, nestedValue]) => { + for (const [nestedKey, nestedValue] of Object.entries(temp)) { result[nestedKey] = nestedValue; - }); + } } else if (key === "functionDescriptions") { result[mapStandardKeys(key)] = value[0]; } else { result[mapStandardKeys(key)] = value; } - }); + } return result; }; -const exceedsArrayLengthLimit = array => { +const exceedsArrayLengthLimit = (array) => { const limitLength = 7; let exceedsLimit = false; @@ -47,13 +47,13 @@ const exceedsArrayLengthLimit = array => { return exceedsLimit; }; -export const formatSearchData = unformattedData => { +export const formatSearchData = (unformattedData) => { const formattedData = {}; - Object.entries(unformattedData).forEach(([key, value]) => { + for (const [key, value] of Object.entries(unformattedData)) { const typesArray = []; - value.hits.map(i => + value.hits.map((i) => typesArray.push({ type: key === "topHit" ? "topHit" : i.entity, entity: i.entity, @@ -62,7 +62,7 @@ export const formatSearchData = unformattedData => { ); if (typesArray.length > 0) formattedData[key] = typesArray; - }); + } return formattedData; }; @@ -77,7 +77,7 @@ export const containsObject = (obj, list) => { return -1; }; -export const addSearchToLocalStorage = item => { +export const addSearchToLocalStorage = (item) => { const recentItems = JSON.parse(localStorage.getItem("search-history")) || []; const newItem = { ...item }; delete newItem.description; @@ -99,7 +99,7 @@ export const clearAllRecent = () => { window.dispatchEvent(new Event("storage")); }; -export const clearRecentItem = item => { +export const clearRecentItem = (item) => { const recentItems = JSON.parse(localStorage.getItem("search-history")); const removedItems = [...recentItems]; const existingIndex = containsObject(item, removedItems); @@ -109,17 +109,18 @@ export const clearRecentItem = item => { return removedItems; }; -export const getSelectedEntityFilterLength = obj => { +export const getSelectedEntityFilterLength = (obj) => { if (!obj) return TOTAL_ENTITIES; return Object.values(obj).filter(Boolean).length; }; -export const getSelectedEntityFilter = obj => { +export const getSelectedEntityFilter = (obj) => { if (!obj) return []; return ( Object.entries(obj) .map(([key, value]) => { if (value) return key; + return null; }) .filter(Boolean) || [] ); diff --git a/packages/ui/src/components/Header.tsx b/packages/ui/src/components/Header.tsx index f8dd92b0b..f3fc57d0b 100644 --- a/packages/ui/src/components/Header.tsx +++ b/packages/ui/src/components/Header.tsx @@ -1,9 +1,9 @@ -import { Box, Grid, Skeleton, SxProps, Theme, Typography } from "@mui/material"; -import { makeStyles } from "@mui/styles"; - +import type { IconProp } from "@fortawesome/fontawesome-svg-core"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { ReactElement, ReactNode } from "react"; -import { IconProp } from "@fortawesome/fontawesome-svg-core"; +import { Box, Grid, Skeleton, type SxProps, type Theme, Typography } from "@mui/material"; +import { makeStyles } from "@mui/styles"; +import type { ReactElement, ReactNode } from "react"; +import { useId } from "react"; const useStyles = makeStyles((theme: Theme) => ({ externalLinks: { @@ -74,9 +74,10 @@ function Header({ rightContent = null, }: HeaderProps): ReactElement { const classes = useStyles(); + const headerId = useId(); return ( - + diff --git a/packages/ui/src/components/HeaderMenu.tsx b/packages/ui/src/components/HeaderMenu.tsx index 99d79086a..5ce0aae95 100644 --- a/packages/ui/src/components/HeaderMenu.tsx +++ b/packages/ui/src/components/HeaderMenu.tsx @@ -1,18 +1,18 @@ -import { ReactElement, useState, MouseEvent, KeyboardEvent } from "react"; -import { v1 } from "uuid"; +import { faBars, faXmark } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { + ClickAwayListener, + Fade, + IconButton, MenuItem, - Popper, MenuList, - IconButton, - Fade, Paper, - ClickAwayListener, - PopperPlacementType, + Popper, + type PopperPlacementType, } from "@mui/material"; -import { faXmark, faBars } from "@fortawesome/free-solid-svg-icons"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { makeStyles } from "@mui/styles"; +import { type KeyboardEvent, type MouseEvent, type ReactElement, useState } from "react"; +import { v1 } from "uuid"; import Link from "./Link"; import PrivateWrapper from "./PrivateWrapper"; @@ -81,7 +81,6 @@ function HeaderMenu({ items, placement }: HeaderMenuProps): ReactElement { d.target.id === row.targetId) + data.rows.find((d) => d.target.id === row.targetId) ); - function handleMouseEnter(event) { + function handleMouseEnter(_event) { setOver(true); } - function handleMouseLeave(event) { + function handleMouseLeave(_event) { setOver(false); } @@ -79,7 +79,7 @@ function BodyRow({ row, colorInterpolator, data }) { - {groupNames.map(groupName => ( + {groupNames.map((groupName) => ( {value}{" "} - {value == "Score" && ( + {value === "Score" && ( @@ -160,7 +160,7 @@ function HeatCell({ value, bgrd, groupName, mouseLeaveRow, waterfallRow, waterfa function handleClick(event) { const filteredWaterfallRow = structuredClone(waterfallRow); - filteredWaterfallRow.features = filteredWaterfallRow.features.filter(d => { + filteredWaterfallRow.features = filteredWaterfallRow.features.filter((d) => { return featureToGroup[d.name] === groupName; }); let { row, xDomain } = computeWaterfall(filteredWaterfallRow, waterfallXDomain, true); @@ -193,7 +193,7 @@ function HeatCell({ value, bgrd, groupName, mouseLeaveRow, waterfallRow, waterfa setAnchorEl(event.currentTarget); } - function handleClose(event) { + function handleClose(_event) { setAnchorEl(null); setPlotProps(null); mouseLeaveRow(); @@ -399,7 +399,7 @@ function HeatmapTable({ ({ all }) => { if (!filterProvied) return all; if (filterProvied && showAll) return all; - return all.filter(row => row.targetId === fixedGene); + return all.filter((row) => row.targetId === fixedGene); }, [showAll] ); @@ -486,7 +486,7 @@ function HeatmapTable({ ))} - {rows.map(row => ( + {rows.map((row) => ( { + const handleClick = (event) => { loadIndicatorData(); setAnchorEl(event.currentTarget); }; diff --git a/packages/ui/src/components/HeatmapTable/constants.ts b/packages/ui/src/components/HeatmapTable/constants.ts index 389b7d59a..570359e71 100644 --- a/packages/ui/src/components/HeatmapTable/constants.ts +++ b/packages/ui/src/components/HeatmapTable/constants.ts @@ -44,7 +44,7 @@ export const featureToGroup = { export const groupToFeature = Object.groupBy( Object.entries(featureToGroup), - ([feature, group]) => group + ([_feature, group]) => group ); export const groupNames = Object.keys(groupToFeature); diff --git a/packages/ui/src/components/HeatmapTable/helpers.ts b/packages/ui/src/components/HeatmapTable/helpers.ts index f0078b12f..b497f091d 100644 --- a/packages/ui/src/components/HeatmapTable/helpers.ts +++ b/packages/ui/src/components/HeatmapTable/helpers.ts @@ -1,8 +1,8 @@ -import { scaleLinear, scaleDiverging, extent, mean, interpolateRgbBasis } from "d3"; -import { groupNames, featureToGroup, DIVERGING_COLORS } from "./constants"; +import { extent, interpolateRgbBasis, mean, scaleDiverging, scaleLinear } from "d3"; +import { DIVERGING_COLORS, featureToGroup, groupNames } from "./constants"; export function getGroupResults(data) { - const rows = data.map(d => { + const rows = data.map((d) => { const row = { targetId: d.target.id, targetSymbol: d.target.approvedSymbol, @@ -34,7 +34,7 @@ export function computeWaterfall(originalRow, fullXDomain, zeroBase) { feature._start = features[index - 1]?._end ?? (zeroBase ? 0 : row.shapBaseValue); feature._end = feature._start + feature.shapValue; } - const xExtent = extent(features.map(d => [d._start, d._end]).flat()); + const xExtent = extent(features.flatMap((d) => [d._start, d._end])); if (fullXDomain) { const relativeSize = (xExtent[1] - xExtent[0]) / (fullXDomain[1] - fullXDomain[0]); if (relativeSize < 0.25) { @@ -57,6 +57,10 @@ export function getColorInterpolator(groupResults) { max = Math.max(max, row[groupName]); } } - Math.abs(min) > max ? (max = -min) : (min = -max); + if (Math.abs(min) > max) { + max = -min; + } else { + min = -max; + } return scaleDiverging().domain([min, 0, max]).interpolator(interpolateRgbBasis(DIVERGING_COLORS)); } diff --git a/packages/ui/src/components/HeatmapTable/renderWaterfallPlot.ts b/packages/ui/src/components/HeatmapTable/renderWaterfallPlot.ts index 047d7f10e..e07a52813 100644 --- a/packages/ui/src/components/HeatmapTable/renderWaterfallPlot.ts +++ b/packages/ui/src/components/HeatmapTable/renderWaterfallPlot.ts @@ -29,11 +29,11 @@ export function renderWaterfallPlot({ labelArrow: false, domain: xDomain, ticks: xTicks, - tickFormat: v => (Number.isInteger(v) ? String(v) : v), + tickFormat: (v) => (Number.isInteger(v) ? String(v) : v), }, y: { type: "band", - domain: features.map(d => d.name), + domain: features.map((d) => d.name), reverse: true, axis: null, grid: true, @@ -45,7 +45,7 @@ export function renderWaterfallPlot({ y: "name", dx: dxName, dy: dyHeader, - text: d => "Feature", + text: (_d) => "Feature", fontWeight: 500, textAnchor: "end", fontSize: textFontSize, @@ -56,7 +56,7 @@ export function renderWaterfallPlot({ y: "name", dx: dxValue, dy: dyHeader, - text: d => "Value", + text: (_d) => "Value", fontWeight: 500, fontSize: textFontSize, textAnchor: "end", @@ -65,7 +65,7 @@ export function renderWaterfallPlot({ PlotLib.text(features.slice(-1), { x: "_end", y: "name", - text: d => `Shapley\n(sum: ${d._end.toFixed(3)})`, + text: (d) => `Shapley\n(sum: ${d._end.toFixed(3)})`, lineHeight: 1.2, dy: dyHeader, fontWeight: 500, @@ -87,7 +87,7 @@ export function renderWaterfallPlot({ PlotLib.text(features, { x: xDomain[0], y: "name", - text: d => d.value.toFixed(3), + text: (d) => d.value.toFixed(3), dx: dxValue, textAnchor: "end", fontSize: 11.5, @@ -113,19 +113,19 @@ export function renderWaterfallPlot({ PlotLib.text(labelBase ? features.slice(0, 1) : [], { x: shapBaseValue, y: "name", - text: d => `Base: ${shapBaseValue.toFixed(3)}`, + text: (_d) => `Base: ${shapBaseValue.toFixed(3)}`, dy: 40, fontSize: textFontSize, }), // bars PlotLib.ruleY( - features.filter(d => Math.abs(d.shapValue) > 0.0005), + features.filter((d) => Math.abs(d.shapValue) > 0.0005), { x1: "_start", x2: "_end", y: "name", - stroke: d => (d.shapValue < 0 ? negColor : posColor), + stroke: (d) => (d.shapValue < 0 ? negColor : posColor), strokeWidth: 10, } ), @@ -150,11 +150,11 @@ export function renderWaterfallPlot({ // show shap values in or next to bars PlotLib.text( - features.filter(d => d.shapValue > 0.0005), + features.filter((d) => d.shapValue > 0.0005), { x: "_end", y: "name", - text: d => `+${d.shapValue.toFixed(3)}`, + text: (d) => `+${d.shapValue.toFixed(3)}`, textAnchor: "start", dx: 3, fontSize: 11, @@ -162,11 +162,11 @@ export function renderWaterfallPlot({ } ), PlotLib.text( - features.filter(d => d.shapValue < -0.0005), + features.filter((d) => d.shapValue < -0.0005), { x: "_end", y: "name", - text: d => d.shapValue.toFixed(3), + text: (d) => d.shapValue.toFixed(3), textAnchor: "end", dx: -3, fontSize: 11, diff --git a/packages/ui/src/components/Highlights.tsx b/packages/ui/src/components/Highlights.tsx index 539314315..0ea558a10 100644 --- a/packages/ui/src/components/Highlights.tsx +++ b/packages/ui/src/components/Highlights.tsx @@ -1,11 +1,16 @@ -import { ReactNode, useState } from "react"; -import { Theme, Typography } from "@mui/material"; +import { type Theme, Typography } from "@mui/material"; import { makeStyles } from "@mui/styles"; +import { type ReactNode, useState } from "react"; const useStyles = makeStyles((theme: Theme) => ({ showMore: { cursor: "pointer", color: theme.palette.primary.main, + textDecoration: "underline", + background: "none", + border: "none", + padding: 0, + font: "inherit", }, matches: { marginTop: "4px", @@ -18,12 +23,27 @@ type HighlightsProps = { highlights: HighlightItem[]; }; +// Helper function to safely convert TrustedHTML to string +const trustedHTMLToString = (item: HighlightItem): string => { + if (typeof item === "string") { + return item; + } + // Convert TrustedHTML to string safely + return String(item); +}; + function Highlights({ highlights }: HighlightsProps): ReactNode { const classes = useStyles(); const [showMore, setShowMore] = useState(false); if (highlights.length === 0) return null; + // Convert all highlights to strings for safe HTML rendering + const highlightStrings = highlights.map(trustedHTMLToString); + const htmlContent = showMore + ? highlightStrings.join(' | ') + : highlightStrings[0]; + return (
@@ -33,8 +53,9 @@ function Highlights({ highlights }: HighlightsProps): ReactNode { display="inline" variant="caption" className="highlights" + // biome-ignore lint/security/noDangerouslySetInnerHtml: HTML content is needed for highlights dangerouslySetInnerHTML={{ - __html: showMore ? highlights.join(' | ') : highlights[0], + __html: htmlContent, }} /> {highlights.length > 1 && ( @@ -42,9 +63,19 @@ function Highlights({ highlights }: HighlightsProps): ReactNode { {" "} [{" "} - setShowMore(!showMore)}> + {" "} ] diff --git a/packages/ui/src/components/KnownDrugsSourceDrawer.jsx b/packages/ui/src/components/KnownDrugsSourceDrawer.jsx index ef0f80736..3b5bef644 100644 --- a/packages/ui/src/components/KnownDrugsSourceDrawer.jsx +++ b/packages/ui/src/components/KnownDrugsSourceDrawer.jsx @@ -1,26 +1,25 @@ -import { useState } from "react"; +import { faChevronDown, faXmark } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { - List, - ListItem, - Drawer, - AccordionSummary, - AccordionDetails, Accordion, + AccordionDetails, + AccordionSummary, Box, - Paper, + ButtonBase, + Drawer, IconButton, - Link as MUILink, + List, + ListItem, + Paper, Typography, - ButtonBase, } from "@mui/material"; import { makeStyles } from "@mui/styles"; -import { faChevronDown, faXmark } from "@fortawesome/free-solid-svg-icons"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import _ from "lodash"; +import { useState } from "react"; import { Link } from "ui"; -const sourceDrawerStyles = makeStyles(theme => ({ +const sourceDrawerStyles = makeStyles((theme) => ({ drawerLink: { color: `${theme.palette.primary.main} !important`, }, @@ -70,7 +69,7 @@ const sourceDrawerStyles = makeStyles(theme => ({ }, })); -const tableSourceLabel = name => +const tableSourceLabel = (name) => ({ ATC: "ATC", ClinicalTrials: "ClinicalTrials.gov", @@ -79,7 +78,7 @@ const tableSourceLabel = name => EMA: "European Medicines Agency", INN: "International Nonproprietary Names", USAN: "United States Adopted Name", - }[name]); + })[name]; const drawerSourceLabel = (name, url) => { if (name === "ClinicalTrials") { @@ -115,7 +114,7 @@ function KnownDrugsSourceDrawer({ references }) { const groupedReferences = _.groupBy(references, "name"); - const toggleDrawer = event => { + const toggleDrawer = (event) => { if (event.type === "keydown" && (event.key === "Tab" || event.key === "Shift")) { return; } @@ -139,7 +138,7 @@ function KnownDrugsSourceDrawer({ references }) { - {Object.keys(groupedReferences).map(group => ( + {Object.keys(groupedReferences).map((group) => ( - {groupedReferences[group].map(item => ( + {groupedReferences[group].map((item) => ( {drawerSourceLabel(item.name, item.url)} diff --git a/packages/ui/src/components/LabelChip.tsx b/packages/ui/src/components/LabelChip.tsx index 6a202a520..a6fe0634f 100644 --- a/packages/ui/src/components/LabelChip.tsx +++ b/packages/ui/src/components/LabelChip.tsx @@ -1,6 +1,6 @@ import { Typography } from "@mui/material"; +import type { ReactElement } from "react"; import OTTooltip from "./Tooltip"; -import { ReactElement } from "react"; type LabelChipProps = { label?: string; diff --git a/packages/ui/src/components/Legend.tsx b/packages/ui/src/components/Legend.tsx index 7fc78a96a..bea52ca4c 100644 --- a/packages/ui/src/components/Legend.tsx +++ b/packages/ui/src/components/Legend.tsx @@ -1,6 +1,6 @@ -import { Link } from "@mui/material"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faQuestionCircle } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Link } from "@mui/material"; import { colorRange } from "@ot/constants"; type LegendProps = { diff --git a/packages/ui/src/components/Link.tsx b/packages/ui/src/components/Link.tsx index 9e22a180c..91308453d 100644 --- a/packages/ui/src/components/Link.tsx +++ b/packages/ui/src/components/Link.tsx @@ -1,11 +1,11 @@ -import { ReactElement, ReactNode } from "react"; +import { makeStyles } from "@mui/styles"; import classNames from "classnames"; +import type { ReactElement, ReactNode } from "react"; import { Link as RouterLink } from "react-router-dom"; -import { makeStyles } from "@mui/styles"; -import Tooltip from "./Tooltip"; import OtAsyncTooltip from "./OtAsyncTooltip/OtAsyncTooltip"; +import Tooltip from "./Tooltip"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ base: { fontSize: "inherit", "text-decoration-color": "transparent", @@ -43,7 +43,7 @@ const useStyles = makeStyles(theme => ({ type LinkProptypes = { className?: string; to: string; - onClick?: () => void | null; + onClick?: () => undefined | null; external?: boolean; newTab?: boolean; footer?: boolean; diff --git a/packages/ui/src/components/LoadingBackdrop.tsx b/packages/ui/src/components/LoadingBackdrop.tsx index 3aec287fc..c20e280d7 100644 --- a/packages/ui/src/components/LoadingBackdrop.tsx +++ b/packages/ui/src/components/LoadingBackdrop.tsx @@ -1,11 +1,11 @@ -import { makeStyles } from "@mui/styles"; import { Box, CircularProgress } from "@mui/material"; +import { makeStyles } from "@mui/styles"; type LoadingBackdropProps = { height?: number; }; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ container: { color: theme.palette.primary.main, background: theme.palette.grey["50"], diff --git a/packages/ui/src/components/LongList.tsx b/packages/ui/src/components/LongList.tsx index 4792cbad8..ea0cb3a7b 100644 --- a/packages/ui/src/components/LongList.tsx +++ b/packages/ui/src/components/LongList.tsx @@ -1,6 +1,6 @@ -import { ReactNode, useState } from "react"; -import { Typography, Theme } from "@mui/material"; +import { type Theme, Typography } from "@mui/material"; import { makeStyles } from "@mui/styles"; +import { type ReactNode, useState } from "react"; const useStyles = makeStyles((theme: Theme) => ({ showMore: { diff --git a/packages/ui/src/components/LongText.tsx b/packages/ui/src/components/LongText.tsx index c169dc880..626d82eb7 100644 --- a/packages/ui/src/components/LongText.tsx +++ b/packages/ui/src/components/LongText.tsx @@ -1,8 +1,8 @@ -import { useState, useLayoutEffect, useRef, PropsWithChildren } from "react"; +import { type Theme, Typography, type TypographyProps } from "@mui/material"; import { makeStyles } from "@mui/styles"; -import { Typography } from "@mui/material"; +import { type PropsWithChildren, useLayoutEffect, useRef, useState } from "react"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme: Theme) => ({ textContainer: { display: "flex", flexDirection: "column", @@ -11,12 +11,17 @@ const useStyles = makeStyles(theme => ({ showMore: { color: theme.palette.primary.main, cursor: "pointer", + textDecoration: "underline", + background: "none", + border: "none", + padding: 0, + font: "inherit", }, })); type LongTextProps = { lineLimit: number; - variant: string; + variant: TypographyProps["variant"]; }; const LongText = ({ lineLimit, variant = "body2", children }: PropsWithChildren) => { @@ -34,7 +39,7 @@ const LongText = ({ lineLimit, variant = "body2", children }: PropsWithChildren< const DOMLineHeight = document.defaultView ? document.defaultView.getComputedStyle(el, null).getPropertyValue("line-height") : ""; - const lineHeight = Number.parseInt(DOMLineHeight); + const lineHeight = Number.parseInt(DOMLineHeight, 10); const numberOfLines = Math.round(height / lineHeight); container.style.height = numberOfLines <= lineLimit ? "auto" : showMore ? "auto" : `${lineLimit * lineHeight}px`; @@ -47,12 +52,22 @@ const LongText = ({ lineLimit, variant = "body2", children }: PropsWithChildren< {children} - {numberOfLines > lineLimit && ( + {numberOfLines && numberOfLines > lineLimit && ( {showMore ? "" : "... "}[{" "} - setShowMore(!showMore)}> + {" "} ] )} diff --git a/packages/ui/src/components/MouseModelAllelicComposition.tsx b/packages/ui/src/components/MouseModelAllelicComposition.tsx index 6ad4d7bc9..026abb591 100644 --- a/packages/ui/src/components/MouseModelAllelicComposition.tsx +++ b/packages/ui/src/components/MouseModelAllelicComposition.tsx @@ -1,5 +1,5 @@ import { Typography } from "@mui/material"; -import { ReactNode } from "react"; +import type { ReactNode } from "react"; type MouseModelAllelicCompositionProps = { allelicComposition: string; diff --git a/packages/ui/src/components/NavBar.jsx b/packages/ui/src/components/NavBar.jsx index b28988c7d..2234fad89 100644 --- a/packages/ui/src/components/NavBar.jsx +++ b/packages/ui/src/components/NavBar.jsx @@ -1,13 +1,12 @@ -import { Link as ReactRouterLink } from "react-router-dom"; -import { AppBar, Toolbar, Button, Typography, useMediaQuery, Box } from "@mui/material"; -import { makeStyles, useTheme } from "@mui/styles"; +import { AppBar, Box, Button, Toolbar, Typography, useMediaQuery } from "@mui/material"; import { styled } from "@mui/material/styles"; +import { makeStyles, useTheme } from "@mui/styles"; import classNames from "classnames"; +import { Link as ReactRouterLink } from "react-router-dom"; import { v1 } from "uuid"; - +import HeaderMenu from "./HeaderMenu"; import Link from "./Link"; import OpenTargetsTitle from "./OpenTargetsTitle"; -import HeaderMenu from "./HeaderMenu"; import PrivateWrapper from "./PrivateWrapper"; const LogoBTN = styled(Button)` @@ -15,7 +14,7 @@ const LogoBTN = styled(Button)` color: white; `; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ navbar: { backgroundColor: `${theme.palette.primary.dark} !important`, margin: 0, @@ -172,7 +171,7 @@ function NavBar({ name, search, api, downloads, docs, contact, homepage, items, {isHomePageRegular && ( - {items.map(item => { + {items.map((item) => { if (item.showOnlyPartner) { return ( diff --git a/packages/ui/src/components/Navigate.tsx b/packages/ui/src/components/Navigate.tsx index 3aea1e300..05a55f6f0 100644 --- a/packages/ui/src/components/Navigate.tsx +++ b/packages/ui/src/components/Navigate.tsx @@ -1,7 +1,7 @@ +import { faArrowRightToBracket } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box } from "@mui/material"; import Link from "./Link"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; -import { faArrowRightToBracket } from "@fortawesome/free-solid-svg-icons"; type NavigateProps = { to: string; diff --git a/packages/ui/src/components/NewChip.tsx b/packages/ui/src/components/NewChip.tsx index 6c2801c76..bd8f32681 100644 --- a/packages/ui/src/components/NewChip.tsx +++ b/packages/ui/src/components/NewChip.tsx @@ -1,6 +1,6 @@ -import classNames from "classnames"; import { Chip as MUIChip } from "@mui/material"; import { makeStyles } from "@mui/styles"; +import classNames from "classnames"; const useStyles = makeStyles({ chip: { diff --git a/packages/ui/src/components/ObsPlot/ObsChart.tsx b/packages/ui/src/components/ObsPlot/ObsChart.tsx index 5389ef6d6..d2c9ddbcc 100644 --- a/packages/ui/src/components/ObsPlot/ObsChart.tsx +++ b/packages/ui/src/components/ObsPlot/ObsChart.tsx @@ -1,5 +1,5 @@ -import { useRef, useEffect, Dispatch, SetStateAction } from "react"; import { Box } from "@mui/material"; +import { type Dispatch, type SetStateAction, useEffect, useRef } from "react"; type ObsChartProps = { data: any; @@ -64,7 +64,7 @@ function ObsChart({ } }; elmt.setAttribute("data-index", dataIndex); - elmt.addEventListener("click", event => { + elmt.addEventListener("click", (event) => { if (clicked && selectedDatum === elmtDatum) { clicked = false; selectedDatum = null; diff --git a/packages/ui/src/components/ObsPlot/ObsPlot.tsx b/packages/ui/src/components/ObsPlot/ObsPlot.tsx index 8fde06990..5350dc819 100644 --- a/packages/ui/src/components/ObsPlot/ObsPlot.tsx +++ b/packages/ui/src/components/ObsPlot/ObsPlot.tsx @@ -1,6 +1,6 @@ -import { ReactElement, useState } from "react"; -import { useMeasure } from "@uidotdev/usehooks"; import { Box, Fade } from "@mui/material"; +import { useMeasure } from "@uidotdev/usehooks"; +import { type ReactElement, useState } from "react"; import { ObsChart, ObsTooltip } from "ui"; type ObsPlotProps = { diff --git a/packages/ui/src/components/ObsPlot/ObsTooltip.tsx b/packages/ui/src/components/ObsPlot/ObsTooltip.tsx index a59a41e06..d3c19edc4 100644 --- a/packages/ui/src/components/ObsPlot/ObsTooltip.tsx +++ b/packages/ui/src/components/ObsPlot/ObsTooltip.tsx @@ -1,5 +1,5 @@ -import { ReactElement } from "react"; import { Box } from "@mui/material"; +import type { ReactElement } from "react"; type ObsTooltipProps = { width: number; diff --git a/packages/ui/src/components/ObsPlot/ObsTooltipRow.tsx b/packages/ui/src/components/ObsPlot/ObsTooltipRow.tsx index 4a005b8e8..301ddba32 100644 --- a/packages/ui/src/components/ObsPlot/ObsTooltipRow.tsx +++ b/packages/ui/src/components/ObsPlot/ObsTooltipRow.tsx @@ -1,5 +1,5 @@ import { Typography } from "@mui/material"; -import { ReactElement } from "react"; +import type { ReactElement } from "react"; type ObsTooltipRowProps = { children: ReactElement; diff --git a/packages/ui/src/components/ObsPlot/ObsTooltipTable.tsx b/packages/ui/src/components/ObsPlot/ObsTooltipTable.tsx index d3ca1ac9f..c55b15f28 100644 --- a/packages/ui/src/components/ObsPlot/ObsTooltipTable.tsx +++ b/packages/ui/src/components/ObsPlot/ObsTooltipTable.tsx @@ -1,4 +1,4 @@ -import { ReactElement } from "react"; +import type { ReactElement } from "react"; type ObsTooltipTableProps = { children: ReactElement; diff --git a/packages/ui/src/components/OtAsyncTooltip/OtAsyncTooltip.tsx b/packages/ui/src/components/OtAsyncTooltip/OtAsyncTooltip.tsx index d638ada4b..723bdb615 100644 --- a/packages/ui/src/components/OtAsyncTooltip/OtAsyncTooltip.tsx +++ b/packages/ui/src/components/OtAsyncTooltip/OtAsyncTooltip.tsx @@ -1,4 +1,4 @@ -import { ReactElement, useEffect, useState } from "react"; +import { useLazyQuery } from "@apollo/client"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box, @@ -6,19 +6,18 @@ import { Skeleton, styled, Tooltip, + type TooltipProps, tooltipClasses, - TooltipProps, } from "@mui/material"; -import { useLazyQuery } from "@apollo/client"; +import { naLabel } from "@ot/constants"; +import { type ReactElement, useEffect, useState } from "react"; +import StudyPublication from "../StudyPublication"; import { getEntityDescription, getEntityIcon, getEntityQuery, getQueryVariables, } from "./utils/asyncTooltipUtil"; -import { naLabel } from "@ot/constants"; - -import StudyPublication from "../StudyPublication"; const DELAY_REQUEST = 1000; @@ -161,28 +160,28 @@ function AsyncTooltipDataView({ p: 1, py: 0, fontSize: "0.7rem", - color: theme => theme.palette.grey[700], + color: (theme) => theme.palette.grey[700], textDecoration: "underline", }} > {`${entity}/${data?.id}`} - theme.palette.primary.main }}> + theme.palette.primary.main }}> theme.palette.grey[900], + color: (theme) => theme.palette.grey[900], textTransform: "capitalize", fontWeight: "bold", }} > {getLabel()} {" "} - theme.palette.grey[800] }}> + theme.palette.grey[800] }}> {getEntityDescription(entity, data)} @@ -191,7 +190,7 @@ function AsyncTooltipDataView({ <> theme.palette.grey[900], pt: 1, pl: 1 }} + sx={{ typography: "caption", color: (theme) => theme.palette.grey[900], pt: 1, pl: 1 }} > {getSubtext()} diff --git a/packages/ui/src/components/OtAsyncTooltip/utils/asyncTooltipUtil.ts b/packages/ui/src/components/OtAsyncTooltip/utils/asyncTooltipUtil.ts index 5df8064af..6027846cb 100644 --- a/packages/ui/src/components/OtAsyncTooltip/utils/asyncTooltipUtil.ts +++ b/packages/ui/src/components/OtAsyncTooltip/utils/asyncTooltipUtil.ts @@ -1,9 +1,3 @@ -import DRUG_TOOLTIP_QUERY from "../queries/DrugTooltipQuery.gql"; -import DISEASE_TOOLTIP_QUERY from "../queries/DiseaseTooltipQuery.gql"; -import STUDY_TOOLTIP_QUERY from "../queries/StudyTooltipQuery.gql"; -import TARGET_TOOLTIP_QUERY from "../queries/TargetTooltipQuery.gql"; -import VARIANT_TOOLTIP_QUERY from "../queries/VariantTooltipQuery.gql"; -import CREDIBLE_SETS_TOOLTIP_QUERY from "../queries/CredibleSetsTooltipQuery.gql"; import { faChartBar, faDiagramProject, @@ -14,6 +8,12 @@ import { faTag, } from "@fortawesome/free-solid-svg-icons"; import { getStudyItemMetaData } from "@ot/utils"; +import CREDIBLE_SETS_TOOLTIP_QUERY from "../queries/CredibleSetsTooltipQuery.gql"; +import DISEASE_TOOLTIP_QUERY from "../queries/DiseaseTooltipQuery.gql"; +import DRUG_TOOLTIP_QUERY from "../queries/DrugTooltipQuery.gql"; +import STUDY_TOOLTIP_QUERY from "../queries/StudyTooltipQuery.gql"; +import TARGET_TOOLTIP_QUERY from "../queries/TargetTooltipQuery.gql"; +import VARIANT_TOOLTIP_QUERY from "../queries/VariantTooltipQuery.gql"; export function getQueryVariables(entity: string, id: string): Record { switch (entity) { diff --git a/packages/ui/src/components/OtBtnGroup.tsx b/packages/ui/src/components/OtBtnGroup.tsx index e46e86c9e..08f92fb0c 100644 --- a/packages/ui/src/components/OtBtnGroup.tsx +++ b/packages/ui/src/components/OtBtnGroup.tsx @@ -1,5 +1,5 @@ import { Box, Divider } from "@mui/material"; -import { ReactNode, useState } from "react"; +import { type ReactNode, useState } from "react"; import { v1 } from "uuid"; export type singleBtnGroupObj = { @@ -21,9 +21,9 @@ function OtBtnGroup({ btnGroup, defaultActiveId }: OtBtnGroupPropType) { } return ( - `1px solid ${theme.palette.grey[400]}`, borderRadius: 3 }}> + `1px solid ${theme.palette.grey[400]}`, borderRadius: 3 }}> - {Object.keys(btnGroup).map(e => ( + {Object.keys(btnGroup).map((e) => ( `${theme.palette.grey[700]}`, + color: (theme) => `${theme.palette.grey[700]}`, "&:hover": { - borderBottom: theme => `2px solid ${theme.palette.grey[500]}`, + borderBottom: (theme) => `2px solid ${theme.palette.grey[500]}`, }, ...(activeId === e && { - borderBottom: theme => `2px solid ${theme.palette.primary.dark}`, - color: theme => `${theme.palette.primary.dark}`, + borderBottom: (theme) => `2px solid ${theme.palette.primary.dark}`, + color: (theme) => `${theme.palette.primary.dark}`, }), }} onClick={() => setActiveTab(e)} diff --git a/packages/ui/src/components/OtCodeBlock.tsx b/packages/ui/src/components/OtCodeBlock.tsx index 62bcd341c..faf1cf0c5 100644 --- a/packages/ui/src/components/OtCodeBlock.tsx +++ b/packages/ui/src/components/OtCodeBlock.tsx @@ -1,6 +1,6 @@ import { Box } from "@mui/material"; -import OtCopyToClipboard from "./OtCopyToClipboard"; import type { ReactNode } from "react"; +import OtCopyToClipboard from "./OtCopyToClipboard"; type OtCodeBlockPropTypes = { children: ReactNode; @@ -11,7 +11,7 @@ function OtCodeBlock({ children, textToCopy }: OtCodeBlockPropTypes) { return ( theme.palette.grey[100], + background: (theme) => theme.palette.grey[100], pb: textToCopy ? 3 : 1, borderRadius: 3, px: 3, diff --git a/packages/ui/src/components/OtCopyToClipboard.tsx b/packages/ui/src/components/OtCopyToClipboard.tsx index a10ba13ea..eef3a4ed3 100644 --- a/packages/ui/src/components/OtCopyToClipboard.tsx +++ b/packages/ui/src/components/OtCopyToClipboard.tsx @@ -2,7 +2,7 @@ import { faCopy } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box, Snackbar } from "@mui/material"; import { grey } from "@mui/material/colors"; -import { ReactNode, useState } from "react"; +import { type ReactNode, useState } from "react"; type OtCopyToClipboardProps = { displayElement?: ReactNode | null; @@ -37,7 +37,7 @@ function OtCopyToClipboard({ displayElement, textToCopy }: OtCopyToClipboardProp }} > {displayElement || ( - theme.palette.grey[700] }}> + theme.palette.grey[700] }}> {" "} diff --git a/packages/ui/src/components/OtInvalidResultFilters.tsx b/packages/ui/src/components/OtInvalidResultFilters.tsx index d2c602a13..b3c143781 100644 --- a/packages/ui/src/components/OtInvalidResultFilters.tsx +++ b/packages/ui/src/components/OtInvalidResultFilters.tsx @@ -18,7 +18,7 @@ function OtInvalidResultFilters() { theme.palette.grey[300], + backgroundColor: (theme) => theme.palette.grey[300], display: "flex", width: "100px", height: "100px", diff --git a/packages/ui/src/components/OtLongText.tsx b/packages/ui/src/components/OtLongText.tsx index a981afa9e..eb6197f73 100644 --- a/packages/ui/src/components/OtLongText.tsx +++ b/packages/ui/src/components/OtLongText.tsx @@ -1,8 +1,8 @@ -import { useState, useLayoutEffect, useRef, PropsWithChildren } from "react"; -import { makeStyles } from "@mui/styles"; import { Typography } from "@mui/material"; +import { makeStyles } from "@mui/styles"; +import { type PropsWithChildren, useLayoutEffect, useRef, useState } from "react"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ textContainer: { display: "flex", flexDirection: "column", @@ -40,7 +40,7 @@ const OtLongText = ({ const DOMLineHeight = document.defaultView ? document.defaultView.getComputedStyle(el, null).getPropertyValue("line-height") : ""; - const lineHeight = Number.parseInt(DOMLineHeight); + const lineHeight = Number.parseInt(DOMLineHeight, 10); const numberOfLines = Math.round(height / lineHeight); container.style.height = numberOfLines <= lineLimit ? "auto" : showMore ? "auto" : `${lineLimit * lineHeight}px`; diff --git a/packages/ui/src/components/OtScoreLinearBar.tsx b/packages/ui/src/components/OtScoreLinearBar.tsx index eb78df2ce..3c0824204 100644 --- a/packages/ui/src/components/OtScoreLinearBar.tsx +++ b/packages/ui/src/components/OtScoreLinearBar.tsx @@ -1,5 +1,5 @@ -import LinearProgress, { linearProgressClasses } from "@mui/material/LinearProgress"; import { styled } from "@mui/material"; +import LinearProgress, { linearProgressClasses } from "@mui/material/LinearProgress"; const OtScoreLinearBar = styled(LinearProgress)(({ theme }) => ({ height: 8, diff --git a/packages/ui/src/components/OtTable/OtTable.tsx b/packages/ui/src/components/OtTable/OtTable.tsx index fd05cbdb3..32796dfc5 100644 --- a/packages/ui/src/components/OtTable/OtTable.tsx +++ b/packages/ui/src/components/OtTable/OtTable.tsx @@ -1,44 +1,44 @@ -import { ReactElement, ReactNode, useMemo, useState, useEffect } from "react"; -import { Box, Grid, IconButton, NativeSelect, Skeleton } from "@mui/material"; -import { - useReactTable, - ColumnFiltersState, - getCoreRowModel, - getFilteredRowModel, - getPaginationRowModel, - getSortedRowModel, - FilterFn, - flexRender, - getFacetedUniqueValues, - Row, -} from "@tanstack/react-table"; import { faAngleLeft, faAngleRight, - faArrowUp, faArrowDown, - faForwardStep, + faArrowUp, faBackwardStep, + faForwardStep, } from "@fortawesome/free-solid-svg-icons"; - -import { RankingInfo, rankItem } from "@tanstack/match-sorter-utils"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; - +import { Box, Grid, IconButton, NativeSelect, Skeleton } from "@mui/material"; +import { type RankingInfo, rankItem } from "@tanstack/match-sorter-utils"; +import { + type ColumnFiltersState, + type FilterFn, + flexRender, + getCoreRowModel, + getFacetedUniqueValues, + getFilteredRowModel, + getPaginationRowModel, + getSortedRowModel, + type Row, + useReactTable, +} from "@tanstack/react-table"; +import { type ReactElement, type ReactNode, useEffect, useMemo, useState } from "react"; +import DataDownloader from "../DataDownloader"; +import Tooltip from "../Tooltip"; import OtTableColumnFilter from "./OtTableColumnFilter"; +import OtTableColumnVisibility from "./OtTableColumnVisibility"; // import { naLabel } from "@ot/constants"; import OtTableSearch from "./OtTableSearch"; -import { OtTableProps } from "./types/tableTypes"; import { FontAwesomeIconPadded, + OtTableCellContainer, OtTableContainer, OtTableHeader, - OtTH, OtTableHeaderText, OtTD, - OtTableCellContainer, + OtTH, OtTR, } from "./otTableLayout"; -import DataDownloader from "../DataDownloader"; +import type { OtTableProps } from "./types/tableTypes"; import { getCurrentPagePosition, getDefaultSortObj, @@ -47,8 +47,6 @@ import { isNestedColumns, mapTableColumnToTanstackColumns, } from "./utils/tableUtils"; -import Tooltip from "../Tooltip"; -import OtTableColumnVisibility from "./OtTableColumnVisibility"; declare module "@tanstack/table-core" { interface FilterFns { @@ -144,7 +142,7 @@ function OtTable({ onRowSelectionChange: setRowSelection, }); - function onRowSelection(e: any, row: Row) { + function onRowSelection(_e: any, row: Row) { enableRowSelection && row.toggleSelected(); } @@ -197,13 +195,13 @@ function OtTable({ {/* Table component container */} - theme.spacing(3) }}> + theme.spacing(3) }}> {/* Table component */} - {table.getHeaderGroups().map(headerGroup => ( + {table.getHeaderGroups().map((headerGroup) => ( - {headerGroup.headers.map(header => { + {headerGroup.headers.map((header) => { return ( - {table.getRowModel().rows.map(row => { + {table.getRowModel().rows.map((row) => { return ( onRowSelection(e, row)} + onClick={(e) => onRowSelection(e, row)} enableRowSelection={enableRowSelection} isSelected={row.getIsSelected()} onMouseEnter={getEnteredRow ? () => getEnteredRow(row) : null} onMouseLeave={getExitedRow ? () => getExitedRow(row) : null} > - {row.getVisibleCells().map(cell => { + {row.getVisibleCells().map((cell) => { return ( @@ -294,7 +292,7 @@ function OtTable({ display: "flex", justifyContent: "end", alignItems: "center", - padding: theme => `${theme.spacing(2)} 0 `, + padding: (theme) => `${theme.spacing(2)} 0 `, }} >
@@ -303,13 +301,13 @@ function OtTable({ id="paginationSelect" disableUnderline disabled={loading} - sx={{ pl: theme => theme.spacing(2) }} + sx={{ pl: (theme) => theme.spacing(2) }} value={table.getState().pagination.pageSize} - onChange={e => { + onChange={(e) => { table.setPageSize(Number(e.target.value)); }} > - {[10, 25, 100].map(pageSize => ( + {[10, 25, 100].map((pageSize) => ( @@ -321,8 +319,8 @@ function OtTable({ sx={{ display: "flex", alignItems: "center", - gap: theme => theme.spacing(3), - marginLeft: theme => theme.spacing(3), + gap: (theme) => theme.spacing(3), + marginLeft: (theme) => theme.spacing(3), }} >
@@ -374,7 +372,7 @@ function OtTable({ function getLoadingCells(columms: Array>) { const arr: Record[] = []; - columms.forEach(e => { + columms.forEach((e) => { if (isNestedColumns(e)) { const headerObj = { header: e.header || e.label, diff --git a/packages/ui/src/components/OtTable/OtTableColumnFilter.tsx b/packages/ui/src/components/OtTable/OtTableColumnFilter.tsx index 8dc9e9603..812b59d53 100644 --- a/packages/ui/src/components/OtTable/OtTableColumnFilter.tsx +++ b/packages/ui/src/components/OtTable/OtTableColumnFilter.tsx @@ -1,7 +1,5 @@ -import { ReactElement, useState } from "react"; -import { Column } from "@tanstack/react-table"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faFilter, faXmark } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Badge, ClickAwayListener, @@ -12,6 +10,8 @@ import { ListItemButton, TextField, } from "@mui/material"; +import type { Column } from "@tanstack/react-table"; +import { type ReactElement, useState } from "react"; import { v1 } from "uuid"; import OtPopper from "../OtPopper"; @@ -70,11 +70,11 @@ function OtTableColumnFilter({ column }: { column: Column }): Reac {/* INPUT FOR COLUMN FILTER */} `${theme.spacing(1)} ${theme.spacing(1.5)}` }} + sx={{ width: 1, padding: (theme) => `${theme.spacing(1)} ${theme.spacing(1.5)}` }} autoFocus variant="standard" value={columnFilterInputValue} - onChange={e => setColumnFilterInputValue(e.target.value)} + onChange={(e) => setColumnFilterInputValue(e.target.value)} placeholder={`Search..`} InputProps={{ endAdornment: ( @@ -91,7 +91,7 @@ function OtTableColumnFilter({ column }: { column: Column }): Reac {Object.keys(sortedUniqueValues).map( - keyName => + (keyName) => /**************************************************** * STRING.SEARCH FUNCTION FILTERS THE LIST OF * * UNIQUE VALUES WITHOUT HAVING TO MODIFY ANY STATE * diff --git a/packages/ui/src/components/OtTable/OtTableColumnVisibility.tsx b/packages/ui/src/components/OtTable/OtTableColumnVisibility.tsx index 19b0ba9b5..83d9b6ffb 100644 --- a/packages/ui/src/components/OtTable/OtTableColumnVisibility.tsx +++ b/packages/ui/src/components/OtTable/OtTableColumnVisibility.tsx @@ -1,4 +1,5 @@ -import { MouseEvent, ReactElement, useState } from "react"; +import { faGear } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Badge, Box, @@ -10,11 +11,9 @@ import { List, ListItemButton, } from "@mui/material"; -import { faGear } from "@fortawesome/free-solid-svg-icons"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; - -import { OtTableColumnVisibilityProps } from "./table.types"; +import { type MouseEvent, type ReactElement, useState } from "react"; import OtPopper from "../OtPopper"; +import type { OtTableColumnVisibilityProps } from "./table.types"; function OtTableColumnVisibility({ table }: OtTableColumnVisibilityProps): ReactElement { const [anchorEl, setAnchorEl] = useState(); @@ -52,7 +51,7 @@ function OtTableColumnVisibility({ table }: OtTableColumnVisibilityProps): React - {table.getAllLeafColumns().map(column => ( + {table.getAllLeafColumns().map((column) => ( { + }).then((d) => { dispatch(addRows(d.data[entity][sectionName])); setPagination(newPagination); }); @@ -197,7 +193,7 @@ function OtTableSSP({ size: newPagination.pageSize, freeTextQuery, client, - }).then(d => { + }).then((d) => { dispatch(setNewData(d.data[entity][sectionName])); if (!state.freeTextQuery) setInitialRequestData(d); }); @@ -254,7 +250,7 @@ function OtTableSSP({ {showGlobalFilter && ( { + setGlobalSearchTerm={(freeTextQuery) => { dispatch(textSearch(freeTextQuery)); }} /> @@ -276,13 +272,13 @@ function OtTableSSP({ {/* Table component container */} - theme.spacing(3) }}> + theme.spacing(3) }}> {/* Table component */} - {table.getHeaderGroups().map(headerGroup => ( + {table.getHeaderGroups().map((headerGroup) => ( - {headerGroup.headers.map(header => { + {headerGroup.headers.map((header) => { return ( - {table.getRowModel().rows.map(row => { + {table.getRowModel().rows.map((row) => { return ( - {row.getVisibleCells().map(cell => { + {row.getVisibleCells().map((cell) => { return ( @@ -348,19 +344,19 @@ function OtTableSSP({ display: "flex", justifyContent: "end", alignItems: "center", - padding: theme => `${theme.spacing(2)} 0 `, + padding: (theme) => `${theme.spacing(2)} 0 `, }} > - {state.loading && theme.spacing(2) }} size={25} />} + {state.loading && theme.spacing(2) }} size={25} />}
theme.spacing(2) }} + sx={{ pl: (theme) => theme.spacing(2) }} value={pagination.pageSize} - onChange={e => { + onChange={(e) => { table.setPageSize(Number(e.target.value)); setPagination({ pageIndex: 0, @@ -369,7 +365,7 @@ function OtTableSSP({ }} > {/* TODO: set page size */} - {[10, 25, 100].map(pageSize => ( + {[10, 25, 100].map((pageSize) => ( @@ -380,8 +376,8 @@ function OtTableSSP({ sx={{ display: "flex", alignItems: "center", - gap: theme => theme.spacing(3), - marginLeft: theme => theme.spacing(3), + gap: (theme) => theme.spacing(3), + marginLeft: (theme) => theme.spacing(3), }} >
@@ -423,7 +419,7 @@ function OtTableSSP({ // TODO: FIND A WAY TO USE SAME FUNCTION FROM CLIENT TABLE function getLoadingCells(columms: Array>) { const arr: Record[] = []; - columms.forEach(e => { + columms.forEach((e) => { if (isNestedColumns(e)) { const headerObj = { header: e.header || e.label, diff --git a/packages/ui/src/components/OtTable/OtTableSearch.tsx b/packages/ui/src/components/OtTable/OtTableSearch.tsx index 2bd9b3f13..ac8ff7efa 100644 --- a/packages/ui/src/components/OtTable/OtTableSearch.tsx +++ b/packages/ui/src/components/OtTable/OtTableSearch.tsx @@ -1,9 +1,9 @@ -import { ReactElement, useEffect, useState } from "react"; -import { Input, InputAdornment } from "@mui/material"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faMagnifyingGlass } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Input, InputAdornment } from "@mui/material"; +import { type ReactElement, useEffect, useState } from "react"; import useDebounce from "../../hooks/useDebounce"; -import { OtTableSearchProps } from "./table.types"; +import type { OtTableSearchProps } from "./table.types"; /**************************************** * OT TABLE SEARCH COMPONENT * @@ -24,7 +24,7 @@ function OtTableSearch({ setGlobalSearchTerm }: OtTableSearchProps): ReactElemen setGlobalFilter(e.target.value)} + onChange={(e) => setGlobalFilter(e.target.value)} placeholder="Search all columns..." startAdornment={ diff --git a/packages/ui/src/components/OtTable/context/otTableActions.ts b/packages/ui/src/components/OtTable/context/otTableActions.ts index 911691d1a..f6d6abedb 100644 --- a/packages/ui/src/components/OtTable/context/otTableActions.ts +++ b/packages/ui/src/components/OtTable/context/otTableActions.ts @@ -1,4 +1,4 @@ -import { Action, ActionType } from "../types/tableTypes"; +import { type Action, ActionType } from "../types/tableTypes"; export function onPageSizeChange(pageSize: number): Action { return { diff --git a/packages/ui/src/components/OtTable/context/otTableReducer.ts b/packages/ui/src/components/OtTable/context/otTableReducer.ts index 6c69683b9..96594d3c1 100644 --- a/packages/ui/src/components/OtTable/context/otTableReducer.ts +++ b/packages/ui/src/components/OtTable/context/otTableReducer.ts @@ -1,4 +1,4 @@ -import { Action, ActionType, OtTableSSPState } from "../types/tableTypes"; +import { type Action, ActionType, type OtTableSSPState } from "../types/tableTypes"; import { getLoadingRows } from "../utils/tableUtils"; export const initialState: OtTableSSPState = { @@ -10,7 +10,7 @@ export const initialState: OtTableSSPState = { initialLoading: true, }; -export function createInitialState(str: string): OtTableSSPState { +export function createInitialState(_str: string): OtTableSSPState { return initialState; } @@ -55,7 +55,7 @@ export function otTableReducer( }; } default: { - throw Error("Unknown action: " + action); + throw Error(`Unknown action: ${action}`); return state; } } diff --git a/packages/ui/src/components/OtTable/otTableLayout.tsx b/packages/ui/src/components/OtTable/otTableLayout.tsx index 50559db63..1b3425a54 100644 --- a/packages/ui/src/components/OtTable/otTableLayout.tsx +++ b/packages/ui/src/components/OtTable/otTableLayout.tsx @@ -32,7 +32,7 @@ export const OtTableContainer = styled("table")(({ theme }) => ({ })); export const OtTableHeader = styled("div", { - shouldForwardProp: prop => prop !== "canBeSorted" && prop !== "numeric", + shouldForwardProp: (prop) => prop !== "canBeSorted" && prop !== "numeric", })(({ theme, canBeSorted, numeric }) => theme.unstable_sx({ display: "flex", @@ -61,7 +61,7 @@ export const FontAwesomeIconPadded = styled(FontAwesomeIcon)(({ theme }) => ({ })); export const OtTH = styled("th", { - shouldForwardProp: prop => prop !== "stickyColumn", + shouldForwardProp: (prop) => prop !== "stickyColumn", })(({ theme, stickyColumn }) => ({ ...(stickyColumn && { left: "0", @@ -72,7 +72,7 @@ export const OtTH = styled("th", { })); export const OtTD = styled("td", { - shouldForwardProp: prop => prop !== "stickyColumn", + shouldForwardProp: (prop) => prop !== "stickyColumn", })(({ theme, stickyColumn }) => ({ ...(stickyColumn && { left: "0", @@ -83,7 +83,7 @@ export const OtTD = styled("td", { })); export const OtTR = styled("tr", { - shouldForwardProp: prop => prop !== "enableRowSelection" && prop !== "isSelected", + shouldForwardProp: (prop) => prop !== "enableRowSelection" && prop !== "isSelected", })(({ theme, enableRowSelection, isSelected }) => theme.unstable_sx({ ...(enableRowSelection && { @@ -96,7 +96,7 @@ export const OtTR = styled("tr", { ); export const OtTableHeaderText = styled(Box, { - shouldForwardProp: prop => prop !== "verticalHeader", + shouldForwardProp: (prop) => prop !== "verticalHeader", })(({ theme, verticalHeader }) => theme.unstable_sx({ typography: "subtitle2", @@ -110,7 +110,7 @@ export const OtTableHeaderText = styled(Box, { ); export const OtTableCellContainer = styled(Box, { - shouldForwardProp: prop => prop !== "numeric", + shouldForwardProp: (prop) => prop !== "numeric", })(({ theme, numeric }) => theme.unstable_sx({ typography: "body2", diff --git a/packages/ui/src/components/OtTable/service/tableService.ts b/packages/ui/src/components/OtTable/service/tableService.ts index a8130d0dd..a724117ff 100644 --- a/packages/ui/src/components/OtTable/service/tableService.ts +++ b/packages/ui/src/components/OtTable/service/tableService.ts @@ -1,4 +1,4 @@ -import { getTableRowsProps } from "../types/tableTypes"; +import type { getTableRowsProps } from "../types/tableTypes"; export async function getTableRows({ query, diff --git a/packages/ui/src/components/OtTable/types/tableTypes.ts b/packages/ui/src/components/OtTable/types/tableTypes.ts index e4bc77f70..e4e68902b 100644 --- a/packages/ui/src/components/OtTable/types/tableTypes.ts +++ b/packages/ui/src/components/OtTable/types/tableTypes.ts @@ -1,5 +1,5 @@ -import { ApolloClient, DocumentNode, NormalizedCacheObject } from "@apollo/client"; -import { ColumnDef, Row, Table } from "@tanstack/table-core"; +import type { ApolloClient, DocumentNode, NormalizedCacheObject } from "@apollo/client"; +import type { ColumnDef, Row, Table } from "@tanstack/table-core"; export const INIT_PAGE_SIZE = 10; @@ -12,7 +12,7 @@ export type DefaultSortProp = { id: string; desc: boolean; - } + }, ] | undefined; diff --git a/packages/ui/src/components/OtTable/utils/tableUtils.ts b/packages/ui/src/components/OtTable/utils/tableUtils.ts index 4b30c6aaa..184f1369c 100644 --- a/packages/ui/src/components/OtTable/utils/tableUtils.ts +++ b/packages/ui/src/components/OtTable/utils/tableUtils.ts @@ -1,4 +1,4 @@ -import { DefaultSortProp, loadingTableRows } from "./table.types"; +import type { DefaultSortProp, loadingTableRows } from "./table.types"; /********************************************************************* * FN TO CONVERT CLASSIC MUI TABLE COLUMNS TO TANSTACK TABLE COLUMNS * @@ -8,7 +8,7 @@ export function mapTableColumnToTanstackColumns( allColumns: Record[] ): Record[] { const arr: Record[] = []; - allColumns.forEach(e => { + allColumns.forEach((e) => { if (isNestedColumns(e)) { const headerObj = { header: e.header || e.label, @@ -72,7 +72,7 @@ export function flattenObj(ob: Record): Record for (const i in ob) { if (typeof ob[i] === "object") { const temp = flattenObj(ob[i]); - for (const j in temp) result[i + "." + j] = temp[j]; + for (const j in temp) result[`${i}.${j}`] = temp[j]; } else result[i] = ob[i]; } return result; @@ -132,7 +132,7 @@ function mapToTanstackColumnObject( enableColumnFilter: originalTableObject.enableColumnFilter || false, filterFn: "equalsString", ...(originalTableObject.comparator && { - sortingFn: (rowA, rowB, column) => + sortingFn: (rowA, rowB, _column) => originalTableObject.comparator(rowA.original, rowB.original), }), accessorFn: (row: Record) => { diff --git a/packages/ui/src/components/Page.tsx b/packages/ui/src/components/Page.tsx index 5d47a83a2..0a14ee9e6 100644 --- a/packages/ui/src/components/Page.tsx +++ b/packages/ui/src/components/Page.tsx @@ -1,6 +1,6 @@ -import { Theme, Grid } from "@mui/material"; +import { Grid, type Theme } from "@mui/material"; import { makeStyles } from "@mui/styles"; -import { ReactElement } from "react"; +import type { ReactElement } from "react"; const useStyles = makeStyles((theme: Theme) => ({ page: { diff --git a/packages/ui/src/components/PartnerLockIcon.tsx b/packages/ui/src/components/PartnerLockIcon.tsx index 7e71b6344..4b9b9948a 100644 --- a/packages/ui/src/components/PartnerLockIcon.tsx +++ b/packages/ui/src/components/PartnerLockIcon.tsx @@ -1,7 +1,7 @@ -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faLock } from "@fortawesome/free-solid-svg-icons"; -import Tooltip from "./Tooltip"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { useConfigContext } from "../providers/ConfigurationProvider"; +import Tooltip from "./Tooltip"; function PartnerLockIcon() { const { config } = useConfigContext(); diff --git a/packages/ui/src/components/PlotContainer.jsx b/packages/ui/src/components/PlotContainer.jsx index 7d105f0b9..b9238297f 100644 --- a/packages/ui/src/components/PlotContainer.jsx +++ b/packages/ui/src/components/PlotContainer.jsx @@ -1,4 +1,4 @@ -import { Typography, Paper, Grid, LinearProgress } from "@mui/material"; +import { Grid, LinearProgress, Paper, Typography } from "@mui/material"; import { makeStyles } from "@mui/styles"; import { v1 } from "uuid"; @@ -38,7 +38,7 @@ function PlotContainer({ loading, error, left, center, right, children }) {
- {error.graphQLErrors.map(({ message }, i) => ( + {error.graphQLErrors.map(({ message }, _i) => ( {message} ))} diff --git a/packages/ui/src/components/PlotContainerSection.jsx b/packages/ui/src/components/PlotContainerSection.jsx index 67e426b58..3e7eda1d1 100644 --- a/packages/ui/src/components/PlotContainerSection.jsx +++ b/packages/ui/src/components/PlotContainerSection.jsx @@ -1,6 +1,6 @@ import { makeStyles } from "@mui/styles"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ plotContainerSection: { padding: "4px 0", borderBottom: `1px solid ${theme.palette.grey[300]}`, diff --git a/packages/ui/src/components/ProfileHeader/Description.tsx b/packages/ui/src/components/ProfileHeader/Description.tsx index aeda68a09..9cc765afa 100644 --- a/packages/ui/src/components/ProfileHeader/Description.tsx +++ b/packages/ui/src/components/ProfileHeader/Description.tsx @@ -1,7 +1,6 @@ import { Skeleton, Typography } from "@mui/material"; - +import type { ReactNode } from "react"; import LongText from "../LongText"; -import { ReactNode } from "react"; type DescriptionProps = { children?: ReactNode; diff --git a/packages/ui/src/components/ProfileHeader/Field.tsx b/packages/ui/src/components/ProfileHeader/Field.tsx index a08b847bf..095d797c9 100644 --- a/packages/ui/src/components/ProfileHeader/Field.tsx +++ b/packages/ui/src/components/ProfileHeader/Field.tsx @@ -1,5 +1,5 @@ import { Skeleton, Typography } from "@mui/material"; -import { ReactNode } from "react"; +import type { ReactNode } from "react"; type FieldProps = { children?: ReactNode; diff --git a/packages/ui/src/components/ProfileHeader/ProfileChipList.tsx b/packages/ui/src/components/ProfileHeader/ProfileChipList.tsx index 0f14423ed..f688c1d40 100644 --- a/packages/ui/src/components/ProfileHeader/ProfileChipList.tsx +++ b/packages/ui/src/components/ProfileHeader/ProfileChipList.tsx @@ -1,8 +1,7 @@ -import { Box, Skeleton, Typography, Tooltip, Theme } from "@mui/material"; +import { Box, Skeleton, type Theme, Tooltip, Typography } from "@mui/material"; import { makeStyles } from "@mui/styles"; -import { ReactNode } from "react"; - import _ from "lodash"; +import type { ReactNode } from "react"; import Chip from "../Chip"; import LongList from "../LongList"; diff --git a/packages/ui/src/components/ProfileHeader/ProfileHeader.jsx b/packages/ui/src/components/ProfileHeader/ProfileHeader.jsx index dbe5436f7..a4bf0b29f 100644 --- a/packages/ui/src/components/ProfileHeader/ProfileHeader.jsx +++ b/packages/ui/src/components/ProfileHeader/ProfileHeader.jsx @@ -1,6 +1,6 @@ -import { Children } from "react"; import { Grid } from "@mui/material"; import { makeStyles } from "@mui/styles"; +import { Children } from "react"; const useStyles = makeStyles({ profileHeaderContainer: { @@ -16,7 +16,7 @@ function ProfileHeader({ children }) { return ( - {Children.map(children, child => ( + {Children.map(children, (child) => ( {child} diff --git a/packages/ui/src/components/ProfileHeader/index.js b/packages/ui/src/components/ProfileHeader/index.js index b2165c522..458b56e8c 100644 --- a/packages/ui/src/components/ProfileHeader/index.js +++ b/packages/ui/src/components/ProfileHeader/index.js @@ -1,4 +1,4 @@ export { default as ProfileDescription } from "./Description"; -export { default as ProfileChipList } from "./ProfileChipList"; export { default as Field } from "./Field"; +export { default as ProfileChipList } from "./ProfileChipList"; export { default as ProfileHeader } from "./ProfileHeader"; diff --git a/packages/ui/src/components/PublicationsDrawer/PublicationActionsTooltip.jsx b/packages/ui/src/components/PublicationsDrawer/PublicationActionsTooltip.jsx index 8e354f680..c29d31073 100644 --- a/packages/ui/src/components/PublicationsDrawer/PublicationActionsTooltip.jsx +++ b/packages/ui/src/components/PublicationsDrawer/PublicationActionsTooltip.jsx @@ -1,7 +1,7 @@ import { Tooltip } from "@mui/material"; import { withStyles } from "@mui/styles"; -const StyledTooltip = withStyles(theme => ({ +const StyledTooltip = withStyles((theme) => ({ tooltip: { maxWidth: 220, fontSize: theme.typography.pxToRem(12), diff --git a/packages/ui/src/components/PublicationsDrawer/PublicationSummary.tsx b/packages/ui/src/components/PublicationsDrawer/PublicationSummary.tsx index bd853ebb5..68a03b2ca 100644 --- a/packages/ui/src/components/PublicationsDrawer/PublicationSummary.tsx +++ b/packages/ui/src/components/PublicationsDrawer/PublicationSummary.tsx @@ -1,13 +1,12 @@ -import { useEffect, useState } from "react"; -import { makeStyles, createStyles } from "@mui/styles"; -import { Collapse, Box, Typography, Button, Theme } from "@mui/material"; - import { faCircleNodes } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Box, Button, Collapse, type Theme, Typography } from "@mui/material"; +import { createStyles, makeStyles } from "@mui/styles"; import { publicationSummaryQuery } from "@ot/utils"; +import { useEffect, useState } from "react"; import PublicationActionsTooltip from "./PublicationActionsTooltip"; -import SummaryLoader from "./SummaryLoader"; import PublicationSummaryLabel from "./PublicationSummaryLabel"; +import SummaryLoader from "./SummaryLoader"; type LoadingState = true | false; type CollapsedState = true | false; @@ -54,23 +53,23 @@ function PublicationSummary({ pmcId, symbol, name }: PublicationSummaryProps): J const classes = useStyles(); const handleChange = () => { - setCollapseOpen(prev => !prev); + setCollapseOpen((prev) => !prev); }; function requestSummary({ baseUrl, requestOptions }: any) { fetch(baseUrl, requestOptions) - .then(response => { + .then((response) => { if (response.ok) return response.json(); - return response.json().then(err => { + return response.json().then((err) => { throw new Error(err.error); }); }) - .then(data => { + .then((data) => { setSummaryText(data.text); setError(null); setLoading(false); }) - .catch(err => { + .catch((err) => { setError(err.message); setLoading(false); }); diff --git a/packages/ui/src/components/PublicationsDrawer/PublicationSummaryLabel.tsx b/packages/ui/src/components/PublicationsDrawer/PublicationSummaryLabel.tsx index b1c9fd1eb..6886ca766 100644 --- a/packages/ui/src/components/PublicationsDrawer/PublicationSummaryLabel.tsx +++ b/packages/ui/src/components/PublicationsDrawer/PublicationSummaryLabel.tsx @@ -1,5 +1,5 @@ -import { makeStyles } from "@mui/styles"; import { Typography } from "@mui/material"; +import { makeStyles } from "@mui/styles"; const useStyles = makeStyles(() => ({ container: { diff --git a/packages/ui/src/components/PublicationsDrawer/PublicationWrapper.jsx b/packages/ui/src/components/PublicationsDrawer/PublicationWrapper.jsx index 709e9cee3..796ce849f 100644 --- a/packages/ui/src/components/PublicationsDrawer/PublicationWrapper.jsx +++ b/packages/ui/src/components/PublicationsDrawer/PublicationWrapper.jsx @@ -1,20 +1,18 @@ -import { useState, useEffect } from "react"; -import { faPlusCircle, faMinusCircle, faFileAlt } from "@fortawesome/free-solid-svg-icons"; +import { faFileAlt, faMinusCircle, faPlusCircle } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box, Button, Typography } from "@mui/material"; import { makeStyles } from "@mui/styles"; - -import LongText from "../LongText"; +import { useEffect, useState } from "react"; +import { useConfigContext } from "../../providers/ConfigurationProvider"; import Link from "../Link"; - +import LongText from "../LongText"; import PublicationSummary from "./PublicationSummary"; -import { useConfigContext } from "../../providers/ConfigurationProvider"; const pmUrl = "https://europepmc.org/"; const pmTitleUrlMED = "abstract/med/"; const pmTitleUrlPAT = "abstract/pat/"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((theme) => ({ abstractSpan: { whiteSpace: "normal", }, diff --git a/packages/ui/src/components/PublicationsDrawer/PublicationsDrawer.jsx b/packages/ui/src/components/PublicationsDrawer/PublicationsDrawer.jsx index c9984c167..dff1baeae 100644 --- a/packages/ui/src/components/PublicationsDrawer/PublicationsDrawer.jsx +++ b/packages/ui/src/components/PublicationsDrawer/PublicationsDrawer.jsx @@ -1,22 +1,22 @@ -import { useState, useEffect } from "react"; +import { faXmark } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box, - IconButton, + ButtonBase, + CircularProgress, Drawer, - Typography, + IconButton, Paper, - CircularProgress, - ButtonBase, + Typography, } from "@mui/material"; import { makeStyles } from "@mui/styles"; -import { faXmark } from "@fortawesome/free-solid-svg-icons"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { naLabel } from "@ot/constants"; import { europePmcSearchPOSTQuery } from "@ot/utils"; -import PublicationWrapper from "./PublicationWrapper"; +import { useEffect, useState } from "react"; import OtTable from "../OtTable/OtTable"; +import PublicationWrapper from "./PublicationWrapper"; -const sourceDrawerStyles = makeStyles(theme => ({ +const sourceDrawerStyles = makeStyles((theme) => ({ drawerLink: { color: `${theme.palette.primary.main} !important`, }, @@ -67,7 +67,7 @@ const sourceDrawerStyles = makeStyles(theme => ({ }, })); -const listComponentStyles = makeStyles(theme => ({ +const listComponentStyles = makeStyles((theme) => ({ loader: { display: "flex", justifyContent: "center", @@ -97,8 +97,8 @@ export function PublicationsList({ entriesIds, hideSearch = false, name, symbol body: formBody, }; fetch(baseUrl, requestOptions) - .then(response => response.json()) - .then(data => { + .then((response) => response.json()) + .then((data) => { setLoading(false); setPublications(data.resultList.result); }); @@ -122,7 +122,7 @@ export function PublicationsList({ entriesIds, hideSearch = false, name, symbol ); - const parsedPublications = publications.map(pub => { + const parsedPublications = publications.map((pub) => { const row = {}; row.europePmcId = pub.id; row.pmcId = pub.pmcid; @@ -143,7 +143,7 @@ export function PublicationsList({ entriesIds, hideSearch = false, name, symbol { id: "publications", label: " ", - renderCell: publication => { + renderCell: (publication) => { const { europePmcId, title, @@ -177,7 +177,7 @@ export function PublicationsList({ entriesIds, hideSearch = false, name, symbol /> ); }, - filterValue: row => + filterValue: (row) => `${row.journal.journal?.title} ${row?.title} ${row?.year} ${row.authors .reduce((acc, author) => { @@ -209,13 +209,13 @@ function PublicationsDrawer({ const [open, setOpen] = useState(false); const classes = sourceDrawerStyles(); - const entriesIds = entries.map(entry => entry.name); + const entriesIds = entries.map((entry) => entry.name); if (entries.length === 0) { return naLabel; } - const toggleDrawer = event => { + const toggleDrawer = (event) => { if (event.type === "keydown" && (event.key === "Tab" || event.key === "Shift")) { return; } diff --git a/packages/ui/src/components/PublicationsDrawer/index.js b/packages/ui/src/components/PublicationsDrawer/index.js index 61976b2ee..d4ee63a63 100644 --- a/packages/ui/src/components/PublicationsDrawer/index.js +++ b/packages/ui/src/components/PublicationsDrawer/index.js @@ -1,5 +1,5 @@ -export { default as PublicationsDrawer, PublicationsList } from "./PublicationsDrawer"; -export { default as PublicationWrapper } from "./PublicationWrapper"; export { default as PublicationSummary } from "./PublicationSummary"; export { default as PublicationSummaryLabel } from "./PublicationSummaryLabel"; +export { default as PublicationsDrawer, PublicationsList } from "./PublicationsDrawer"; +export { default as PublicationWrapper } from "./PublicationWrapper"; export { default as SummaryLoader } from "./SummaryLoader"; diff --git a/packages/ui/src/components/RoutingTabs/RoutingTabs.jsx b/packages/ui/src/components/RoutingTabs/RoutingTabs.jsx index a00179f92..dc9948f8e 100644 --- a/packages/ui/src/components/RoutingTabs/RoutingTabs.jsx +++ b/packages/ui/src/components/RoutingTabs/RoutingTabs.jsx @@ -1,6 +1,6 @@ -import { Suspense, Children, cloneElement } from "react"; -import { generatePath, Route, Routes, useNavigate, useMatch } from "react-router-dom"; -import { Tabs, Box } from "@mui/material"; +import { Box, Tabs } from "@mui/material"; +import { Children, cloneElement, Suspense } from "react"; +import { generatePath, Route, Routes, useMatch, useNavigate } from "react-router-dom"; import { v1 } from "uuid"; import LoadingBackdrop from "../LoadingBackdrop"; @@ -9,7 +9,7 @@ function RoutingTabs({ children }) { const history = useNavigate(); const routes = []; - const preparedChildren = Children.map(children, child => { + const preparedChildren = Children.map(children, (child) => { // Prepares routes for the tabs. if (child.props.component) { routes.push({ diff --git a/packages/ui/src/components/RoutingTabs/index.js b/packages/ui/src/components/RoutingTabs/index.js index a3307cd44..fa3529fe6 100644 --- a/packages/ui/src/components/RoutingTabs/index.js +++ b/packages/ui/src/components/RoutingTabs/index.js @@ -1,3 +1,3 @@ +export { default as PrivateRoutingTab } from "./PrivateRoutingTab"; export { default as RoutingTab } from "./RoutingTab"; export { default as RoutingTabs } from "./RoutingTabs"; -export { default as PrivateRoutingTab } from "./PrivateRoutingTab"; diff --git a/packages/ui/src/components/ScientificNotation.tsx b/packages/ui/src/components/ScientificNotation.tsx index 8d7378e30..4221a3cb9 100644 --- a/packages/ui/src/components/ScientificNotation.tsx +++ b/packages/ui/src/components/ScientificNotation.tsx @@ -1,5 +1,5 @@ -import { ReactElement } from "react"; import { decimalPlaces } from "@ot/constants"; +import type { ReactElement } from "react"; type ScientificNotationProps = { number: number | number[]; diff --git a/packages/ui/src/components/Section/SectionContainer.tsx b/packages/ui/src/components/Section/SectionContainer.tsx index 500c48878..6378ea281 100644 --- a/packages/ui/src/components/Section/SectionContainer.tsx +++ b/packages/ui/src/components/Section/SectionContainer.tsx @@ -1,5 +1,5 @@ import { Grid } from "@mui/material"; -import { ReactNode } from "react"; +import type { ReactNode } from "react"; type SectionContainerProps = { children: ReactNode; diff --git a/packages/ui/src/components/Section/SectionError.tsx b/packages/ui/src/components/Section/SectionError.tsx index 0e474d615..f1de12b62 100644 --- a/packages/ui/src/components/Section/SectionError.tsx +++ b/packages/ui/src/components/Section/SectionError.tsx @@ -1,5 +1,5 @@ import { Typography } from "@mui/material"; -import { ReactNode } from "react"; +import type { ReactNode } from "react"; type SectionErrorProps = { message: string; diff --git a/packages/ui/src/components/Section/SectionItem.tsx b/packages/ui/src/components/Section/SectionItem.tsx index 6c3d60704..120be052f 100644 --- a/packages/ui/src/components/Section/SectionItem.tsx +++ b/packages/ui/src/components/Section/SectionItem.tsx @@ -1,16 +1,14 @@ -import classNames from "classnames"; import { Avatar, Box, Card, CardContent, Divider, Grid, Skeleton, Typography } from "@mui/material"; +import { VIEW } from "@ot/constants"; +import classNames from "classnames"; +import { type ReactNode, useState } from "react"; import { Element } from "react-scroll"; - import ErrorBoundary from "../ErrorBoundary"; -import SectionError from "./SectionError"; -import sectionStyles from "./sectionStyles"; -import { createShortName } from "../Summary/utils"; import PartnerLockIcon from "../PartnerLockIcon"; +import { createShortName } from "../Summary/utils"; +import SectionError from "./SectionError"; import SectionViewToggle from "./SectionViewToggle"; -import { ReactNode, useEffect, useState } from "react"; -import { VIEW } from "@ot/constants"; -import { SummaryLoader } from "../PublicationsDrawer"; +import sectionStyles from "./sectionStyles"; type definitionType = { id: string; @@ -55,7 +53,7 @@ function SectionItem({ const shortName = createShortName(definition); let hasData = false; const [selectedView, setSelectedView] = useState(defaultView); - const [showDelayLoadingMessage, setShowDelayLoadingMessage] = useState(false); + const [showDelayLoadingMessage, _setShowDelayLoadingMessage] = useState(false); // TODO: refactor to avoid re-renders diff --git a/packages/ui/src/components/Section/SectionLoader.tsx b/packages/ui/src/components/Section/SectionLoader.tsx index ca26e648c..c3cf87d46 100644 --- a/packages/ui/src/components/Section/SectionLoader.tsx +++ b/packages/ui/src/components/Section/SectionLoader.tsx @@ -8,7 +8,7 @@ type SectionContainerLoaderProps = { function SectionLoader({ sectionsCount = 1 }: SectionContainerLoaderProps) { const loadingSections = Array.from(Array(sectionsCount)); - return loadingSections.map((_, i) => ( + return loadingSections.map((_, _i) => (
diff --git a/packages/ui/src/components/Section/SectionViewToggle.tsx b/packages/ui/src/components/Section/SectionViewToggle.tsx index 99c008ebd..2c7232b00 100644 --- a/packages/ui/src/components/Section/SectionViewToggle.tsx +++ b/packages/ui/src/components/Section/SectionViewToggle.tsx @@ -1,8 +1,8 @@ import { faChartLine, faTableColumns } from "@fortawesome/free-solid-svg-icons"; -import { ToggleButtonGroup, ToggleButton, styled } from "@mui/material"; -import { ReactElement, useState, MouseEvent } from "react"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { styled, ToggleButton, ToggleButtonGroup } from "@mui/material"; import { VIEW } from "@ot/constants"; +import { type MouseEvent, type ReactElement, useState } from "react"; type SectionViewToggleProps = { defaultValue: string; diff --git a/packages/ui/src/components/Section/SectionsRenderer.tsx b/packages/ui/src/components/Section/SectionsRenderer.tsx index a6c6e5acf..cdddee8da 100644 --- a/packages/ui/src/components/Section/SectionsRenderer.tsx +++ b/packages/ui/src/components/Section/SectionsRenderer.tsx @@ -1,5 +1,5 @@ import { Suspense } from "react"; -import { Widget } from "sections"; +import type { Widget } from "sections"; import usePermissions from "../../hooks/usePermissions"; import SectionLoader from "./SectionLoader"; @@ -14,7 +14,7 @@ function SectionsRenderer({ id, label, entity, widgets }: SectionsRendererProps) const { isPartnerPreview } = usePermissions(); return ( <> - {widgets.map(widget => { + {widgets.map((widget) => { const Body = widget.getBodyComponent(); const isPrivate = widget.definition.isPrivate; if (isPrivate && !isPartnerPreview) { diff --git a/packages/ui/src/components/Section/sectionStyles.js b/packages/ui/src/components/Section/sectionStyles.js index 3c782836f..db7d37ce6 100644 --- a/packages/ui/src/components/Section/sectionStyles.js +++ b/packages/ui/src/components/Section/sectionStyles.js @@ -1,6 +1,6 @@ import { makeStyles } from "@mui/styles"; -const sectionStyles = makeStyles(theme => ({ +const sectionStyles = makeStyles((theme) => ({ avatar: { color: "white", backgroundColor: theme.palette.grey[300], diff --git a/packages/ui/src/components/StudyPublication.tsx b/packages/ui/src/components/StudyPublication.tsx index a53706ad5..949d56c42 100644 --- a/packages/ui/src/components/StudyPublication.tsx +++ b/packages/ui/src/components/StudyPublication.tsx @@ -1,4 +1,4 @@ -import { ReactNode } from "react"; +import type { ReactNode } from "react"; type StudyPublicationProps = { publicationFirstAuthor: string; diff --git a/packages/ui/src/components/Summary/SummaryItem.jsx b/packages/ui/src/components/Summary/SummaryItem.jsx index db7541a78..bc611aa58 100644 --- a/packages/ui/src/components/Summary/SummaryItem.jsx +++ b/packages/ui/src/components/Summary/SummaryItem.jsx @@ -1,4 +1,3 @@ -import classNames from "classnames"; import { Avatar, Card, @@ -8,11 +7,11 @@ import { Skeleton, Typography, } from "@mui/material"; +import classNames from "classnames"; import { scroller } from "react-scroll"; - +import PartnerLockIcon from "../PartnerLockIcon"; import summaryStyles from "./summaryStyles"; import { createShortName } from "./utils"; -import PartnerLockIcon from "../PartnerLockIcon"; function SummaryItem({ definition, request, subText }) { const classes = summaryStyles(); diff --git a/packages/ui/src/components/Summary/SummaryRenderer.tsx b/packages/ui/src/components/Summary/SummaryRenderer.tsx index c536b67dd..9635dd237 100644 --- a/packages/ui/src/components/Summary/SummaryRenderer.tsx +++ b/packages/ui/src/components/Summary/SummaryRenderer.tsx @@ -1,5 +1,5 @@ +import type { Widget } from "sections"; import { v1 } from "uuid"; -import { Widget } from "sections"; import usePermissions from "../../hooks/usePermissions"; type SummaryRendererProps = { diff --git a/packages/ui/src/components/Summary/summaryStyles.js b/packages/ui/src/components/Summary/summaryStyles.js index cb38f1399..3264c0e97 100644 --- a/packages/ui/src/components/Summary/summaryStyles.js +++ b/packages/ui/src/components/Summary/summaryStyles.js @@ -1,6 +1,6 @@ import { makeStyles } from "@mui/styles"; -const summaryStyles = makeStyles(theme => ({ +const summaryStyles = makeStyles((theme) => ({ avatar: { color: "white", backgroundColor: theme.palette.grey[300], diff --git a/packages/ui/src/components/Summary/utils.js b/packages/ui/src/components/Summary/utils.js index 00c26a85a..bdc431ed7 100644 --- a/packages/ui/src/components/Summary/utils.js +++ b/packages/ui/src/components/Summary/utils.js @@ -5,7 +5,7 @@ export function createSummaryFragment(sections, entity, fragmentName) { const sectionFragmentNames = []; const fragmentNameStr = fragmentName || `${entity}ProfileSummaryFragment`; - sections.forEach(Summary => { + sections.forEach((Summary) => { if (!Summary.fragments) return; const sectionFragmentName = Object.keys(Summary.fragments)[0]; @@ -17,7 +17,9 @@ export function createSummaryFragment(sections, entity, fragmentName) { return gql` fragment ${fragmentNameStr} on ${entity} { ${ - sectionFragmentNames.length ? sectionFragmentNames.map(sfn => `...${sfn}`).join("\n") : "id" + sectionFragmentNames.length + ? sectionFragmentNames.map((sfn) => `...${sfn}`).join("\n") + : "id" } } ${sectionFragments.reduce( @@ -28,7 +30,6 @@ export function createSummaryFragment(sections, entity, fragmentName) { "" )} `; - } export function createShortName(definition) { @@ -37,7 +38,7 @@ export function createShortName(definition) { definition.name .split(" ") .slice(0, 2) - .map(w => w[0].toUpperCase()) + .map((w) => w[0].toUpperCase()) .join("") ); } diff --git a/packages/ui/src/components/SummaryStatsTable.tsx b/packages/ui/src/components/SummaryStatsTable.tsx index 29f05b2c3..05af541f2 100644 --- a/packages/ui/src/components/SummaryStatsTable.tsx +++ b/packages/ui/src/components/SummaryStatsTable.tsx @@ -1,6 +1,6 @@ import { Typography } from "@mui/material"; -import { v1 } from "uuid"; import { Tooltip } from "ui"; +import { v1 } from "uuid"; const dicSummary = [ { id: "n_variants", label: "Total variants", tooltip: "Number of harmonised variants" }, diff --git a/packages/ui/src/components/Table/DataTable.jsx b/packages/ui/src/components/Table/DataTable.jsx index 574fe634a..58a28748c 100644 --- a/packages/ui/src/components/Table/DataTable.jsx +++ b/packages/ui/src/components/Table/DataTable.jsx @@ -1,10 +1,9 @@ /* eslint-disable */ import { useState } from "react"; - +import { getComparator, globalFilter } from "./sortingAndFiltering"; import Table from "./Table"; -import { getPage } from "./utils"; -import { globalFilter, getComparator } from "./sortingAndFiltering"; import { PaginationActionsComplete } from "./TablePaginationActions"; +import { getPage } from "./utils"; function DataTable({ noWrap, @@ -36,22 +35,22 @@ function DataTable({ const [sortOrder, setSortOrder] = useState(order); const showPagination = rows.length > [...rowsPerPageOptions, initialPageSize].sort()[0]; - const handleGlobalFilterChange = globalFilter => { + const handleGlobalFilterChange = (globalFilter) => { setGlobalFilterVal(globalFilter); setPage(0); }; - const handleSortBy = sortBy => { + const handleSortBy = (sortBy) => { setSortColumn(sortBy); setSortOrder(sortColumn === sortBy ? (sortOrder === "asc" ? "desc" : "asc") : "asc"); }; - const handlePageChange = page => { + const handlePageChange = (page) => { setPage(page); onPagination(page, pageSize); }; - const handleRowsPerPageChange = newPageSize => { + const handleRowsPerPageChange = (newPageSize) => { const newPageSizeNumber = Number(newPageSize); setPageSize(newPageSizeNumber); setPage(0); @@ -60,7 +59,7 @@ function DataTable({ let processedRows = [...rows]; if (globalFilterVal) { - processedRows = processedRows.filter(row => globalFilter(row, columns, globalFilterVal)); + processedRows = processedRows.filter((row) => globalFilter(row, columns, globalFilterVal)); } if (sortColumn) { diff --git a/packages/ui/src/components/Table/GlobalFilter.jsx b/packages/ui/src/components/Table/GlobalFilter.jsx index dbe5d2a70..89b97d6ce 100644 --- a/packages/ui/src/components/Table/GlobalFilter.jsx +++ b/packages/ui/src/components/Table/GlobalFilter.jsx @@ -1,7 +1,7 @@ -import { useEffect, useState } from "react"; -import { Grid, Input, IconButton } from "@mui/material"; import { faMagnifyingGlass, faXmark } from "@fortawesome/free-solid-svg-icons"; import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Grid, IconButton, Input } from "@mui/material"; +import { useEffect, useState } from "react"; import useDebounce from "../../hooks/useDebounce"; import { globalSearchStyles } from "./tableStyles"; @@ -10,7 +10,7 @@ function GlobalFilter({ onGlobalFilterChange }) { const [inputValue, setInputValue] = useState(""); const debouncedInputValue = useDebounce(inputValue, 300); - const handleInputChange = e => { + const handleInputChange = (e) => { setInputValue(e.target.value); }; diff --git a/packages/ui/src/components/Table/Table.jsx b/packages/ui/src/components/Table/Table.jsx index 60632250d..3c4e8c02e 100644 --- a/packages/ui/src/components/Table/Table.jsx +++ b/packages/ui/src/components/Table/Table.jsx @@ -1,17 +1,18 @@ /* eslint-disable */ -import { useState } from "react"; -import classNames from "classnames"; + import { + Box, CircularProgress, Grid, - TableContainer, + TableRow as MUITableRow, Table as MuiTable, TableBody, TableCell, + TableContainer, TablePagination, - TableRow as MUITableRow, - Box, } from "@mui/material"; +import classNames from "classnames"; +import { useState } from "react"; import DataDownloader from "../DataDownloader"; import GlobalFilter from "./GlobalFilter"; @@ -56,7 +57,7 @@ const Table = ({ const [selectedRow, setSelectedRow] = useState(0); const defaultClasses = tableStyles(); - const handleGlobalFilterChange = newGlobalFilter => { + const handleGlobalFilterChange = (newGlobalFilter) => { if (newGlobalFilter !== globalFilter) { onGlobalFilterChange(newGlobalFilter); } @@ -66,7 +67,7 @@ const Table = ({ onSortBy(sortBy); }; - const handleChangeRowsPerPage = event => { + const handleChangeRowsPerPage = (event) => { onRowsPerPageChange(Number(event.target.value)); }; const handleChangePage = (_, page) => { @@ -75,7 +76,7 @@ const Table = ({ setSelectedRow(0); onPageChange(page); }; - const handleClick = (event, row, i) => { + const handleClick = (_event, row, i) => { setSelectedRow(i); onRowClick(row, i); }; @@ -128,7 +129,7 @@ const Table = ({ key={i} row={row} noWrap={noWrap} - onClick={event => handleClick(event, row, i)} + onClick={(event) => handleClick(event, row, i)} selected={rowIsSelectable && selectedRow === i} /> ))} diff --git a/packages/ui/src/components/Table/TableDrawer.jsx b/packages/ui/src/components/Table/TableDrawer.jsx index 631fa1aa2..e7c6e75fb 100644 --- a/packages/ui/src/components/Table/TableDrawer.jsx +++ b/packages/ui/src/components/Table/TableDrawer.jsx @@ -1,28 +1,27 @@ -import { useState } from "react"; +import { faChevronDown, faXmark } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { - AccordionSummary, - AccordionDetails, Accordion, + AccordionDetails, + AccordionSummary, Box, + ButtonBase, + Drawer, IconButton, List, ListItem, - Drawer, - Typography, Paper, - Button, - ButtonBase, + Typography, } from "@mui/material"; import { makeStyles } from "@mui/styles"; -import { faXmark, faChevronDown } from "@fortawesome/free-solid-svg-icons"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { naLabel } from "@ot/constants"; import _ from "lodash"; +import { useState } from "react"; import { v1 } from "uuid"; -import { naLabel } from "@ot/constants"; import Link from "../Link"; -const sourceDrawerStyles = makeStyles(theme => ({ +const sourceDrawerStyles = makeStyles((theme) => ({ drawerLink: { color: `${theme.palette.primary.main} !important`, }, @@ -90,11 +89,11 @@ function TableDrawer({ entries, message, caption = "Records", showSingle = true {entries[0].name} ) : ( - entries[0].name ?? naLabel + (entries[0].name ?? naLabel) ); } - const toggleDrawer = event => { + const toggleDrawer = (event) => { if (event.type === "keydown" && (event.key === "Tab" || event.key === "Shift")) { return; } @@ -120,7 +119,7 @@ function TableDrawer({ entries, message, caption = "Records", showSingle = true - {Object.keys(groupedEntries).map(group => ( + {Object.keys(groupedEntries).map((group) => ( - {groupedEntries[group].map(entry => ( + {groupedEntries[group].map((entry) => ( {entry.url ? ( diff --git a/packages/ui/src/components/Table/TableHeader.jsx b/packages/ui/src/components/Table/TableHeader.jsx index db4a1681a..e6c7fe0cf 100644 --- a/packages/ui/src/components/Table/TableHeader.jsx +++ b/packages/ui/src/components/Table/TableHeader.jsx @@ -1,20 +1,20 @@ /* eslint-disable */ -import classNames from "classnames"; -import _ from "lodash"; + import { Hidden, // note this is deprecated in MUI 5 + TableCell, TableHead, TableRow, - TableCell, TableSortLabel, useMediaQuery, } from "@mui/material"; import { useTheme } from "@mui/styles"; - -import { getHiddenBreakpoints } from "./utils"; -import { tableStyles } from "./tableStyles"; -import Tooltip from "../Tooltip"; +import classNames from "classnames"; +import _ from "lodash"; import useDynamicColspan from "../../hooks/useDynamicColspans"; +import Tooltip from "../Tooltip"; +import { tableStyles } from "./tableStyles"; +import { getHiddenBreakpoints } from "./utils"; function HeaderCell({ classes = {}, @@ -80,10 +80,10 @@ function HeaderCell({ function TableHeader({ columns, headerGroups, noWrapHeader, order, onRequestSort, sortBy }) { // workaround for the old withWidth hook const theme = useTheme(); - const width = theme.breakpoints.keys.filter(k => useMediaQuery(theme.breakpoints.only(k))); + const width = theme.breakpoints.keys.filter((k) => useMediaQuery(theme.breakpoints.only(k))); const colspans = useDynamicColspan(headerGroups, columns, width); - const createSortHandler = property => event => { + const createSortHandler = (property) => (event) => { onRequestSort(event, property); }; diff --git a/packages/ui/src/components/Table/TablePaginationActions.jsx b/packages/ui/src/components/Table/TablePaginationActions.jsx index a4d44ae28..4d071d03a 100644 --- a/packages/ui/src/components/Table/TablePaginationActions.jsx +++ b/packages/ui/src/components/Table/TablePaginationActions.jsx @@ -1,13 +1,12 @@ -import { IconButton } from "@mui/material"; -import { makeStyles } from "@mui/styles"; - -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faBackwardStep, - faForwardStep, faChevronLeft, faChevronRight, + faForwardStep, } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { IconButton } from "@mui/material"; +import { makeStyles } from "@mui/styles"; const useStyles = makeStyles({ root: { flexShrink: 0 }, @@ -16,19 +15,19 @@ const useStyles = makeStyles({ export function PaginationActionsComplete({ count, page, rowsPerPage, onPageChange }) { const classes = useStyles(); - const handleFirstPageButtonClick = event => { + const handleFirstPageButtonClick = (event) => { onPageChange(event, 0); }; - const handleBackButtonClick = event => { + const handleBackButtonClick = (event) => { onPageChange(event, page - 1); }; - const handleNextButtonClick = event => { + const handleNextButtonClick = (event) => { onPageChange(event, page + 1); }; - const handleLastPageButtonClick = event => { + const handleLastPageButtonClick = (event) => { onPageChange(event, Math.max(0, Math.ceil(count / rowsPerPage) - 1)); }; diff --git a/packages/ui/src/components/Table/TableRow.jsx b/packages/ui/src/components/Table/TableRow.jsx index 647f80f26..cb9e6e7e4 100644 --- a/packages/ui/src/components/Table/TableRow.jsx +++ b/packages/ui/src/components/Table/TableRow.jsx @@ -1,10 +1,10 @@ /* eslint-disable */ + +import { Hidden, TableRow as MUITableRow, TableCell } from "@mui/material"; import classNames from "classnames"; -import { Hidden, TableCell, TableRow as MUITableRow } from "@mui/material"; import _ from "lodash"; - -import { getHiddenBreakpoints } from "./utils"; import { tableStyles } from "./tableStyles"; +import { getHiddenBreakpoints } from "./utils"; function TableRow({ columns, hover, isFixedRow, noWrap, row, style, onClick, selected }) { const classes = tableStyles(); diff --git a/packages/ui/src/components/Table/index.js b/packages/ui/src/components/Table/index.js index fe7858146..24ca5e040 100644 --- a/packages/ui/src/components/Table/index.js +++ b/packages/ui/src/components/Table/index.js @@ -1,6 +1,6 @@ -export { default as Table } from "./Table"; export { default as DataTable } from "./DataTable"; +export { getComparator, globalFilter } from "./sortingAndFiltering"; +export { default as Table } from "./Table"; export { default as TableDrawer } from "./TableDrawer"; export { PaginationActionsComplete } from "./TablePaginationActions"; -export { getPage, getHiddenBreakpoints } from "./utils"; -export { getComparator, globalFilter } from "./sortingAndFiltering"; +export { getHiddenBreakpoints, getPage } from "./utils"; diff --git a/packages/ui/src/components/Table/sortingAndFiltering.js b/packages/ui/src/components/Table/sortingAndFiltering.js index 09365a013..97052cf66 100644 --- a/packages/ui/src/components/Table/sortingAndFiltering.js +++ b/packages/ui/src/components/Table/sortingAndFiltering.js @@ -1,6 +1,5 @@ -import _ from "lodash"; - import { safeToString } from "@ot/utils"; +import _ from "lodash"; function ascendingComparator(a, b, sortBy) { if (a[sortBy] === undefined || a[sortBy] < b[sortBy]) return -1; @@ -9,7 +8,7 @@ function ascendingComparator(a, b, sortBy) { } export function getComparator(columns, order, sortBy) { - const column = columns.find(col => col.id === sortBy); + const column = columns.find((col) => col.id === sortBy); const columnComparator = column?.comparator ? column.comparator : ascendingComparator; return order === "asc" @@ -30,6 +29,6 @@ export function globalFilter(row, columns, value) { }, []); return contents - .map(content => safeToString(content).toLowerCase().includes(value.toLowerCase())) - .some(e => e); + .map((content) => safeToString(content).toLowerCase().includes(value.toLowerCase())) + .some((e) => e); } diff --git a/packages/ui/src/components/Table/tableStyles.js b/packages/ui/src/components/Table/tableStyles.js index ec575309d..929ba8120 100644 --- a/packages/ui/src/components/Table/tableStyles.js +++ b/packages/ui/src/components/Table/tableStyles.js @@ -1,6 +1,6 @@ import { makeStyles } from "@mui/styles"; -export const tableStyles = makeStyles(theme => ({ +export const tableStyles = makeStyles((theme) => ({ cell: { "&:first-child": { paddingLeft: "1rem", diff --git a/packages/ui/src/components/Table/utils.js b/packages/ui/src/components/Table/utils.js index 7c3f6d5e7..115a69029 100644 --- a/packages/ui/src/components/Table/utils.js +++ b/packages/ui/src/components/Table/utils.js @@ -1,7 +1,7 @@ /* Returns a list of breakpoints translating values from hidden prop. */ -export const getHiddenBreakpoints = column => +export const getHiddenBreakpoints = (column) => column.hidden?.reduce( (obj, b) => { if (b.includes("Only")) { diff --git a/packages/ui/src/components/Tooltip.jsx b/packages/ui/src/components/Tooltip.jsx index 1db390e98..d2f04d9ef 100644 --- a/packages/ui/src/components/Tooltip.jsx +++ b/packages/ui/src/components/Tooltip.jsx @@ -1,5 +1,5 @@ -import { makeStyles } from "@mui/styles"; import { Tooltip as MUITooltip } from "@mui/material"; +import { makeStyles } from "@mui/styles"; import { merge } from "lodash"; function Tooltip({ @@ -10,7 +10,7 @@ function Tooltip({ placement = "top", ...props }) { - const classes = makeStyles(theme => + const classes = makeStyles((theme) => merge(style, { tooltip: { backgroundColor: `${theme.palette.background.paper} !important`, diff --git a/packages/ui/src/components/Viewer/Usage.tsx b/packages/ui/src/components/Viewer/Usage.tsx index e4dea887a..8bd53e9e4 100644 --- a/packages/ui/src/components/Viewer/Usage.tsx +++ b/packages/ui/src/components/Viewer/Usage.tsx @@ -1,7 +1,7 @@ -import { useState } from "react"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faInfo } from "@fortawesome/free-solid-svg-icons"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { Box, Button, Typography } from "@mui/material"; +import { useState } from "react"; import { Tooltip } from "ui"; // !!!!! ADD TYPES !!!!! @@ -12,7 +12,7 @@ function Usage({ instructions }) { const handleClick = () => { setIsHovered(false); - setIsClicked(prev => !prev); + setIsClicked((prev) => !prev); }; const handleMouseEnter = () => { diff --git a/packages/ui/src/components/Viewer/Viewer.tsx b/packages/ui/src/components/Viewer/Viewer.tsx index 6d5ce0223..88864f9d7 100644 --- a/packages/ui/src/components/Viewer/Viewer.tsx +++ b/packages/ui/src/components/Viewer/Viewer.tsx @@ -1,13 +1,12 @@ -import { useState, useEffect, useRef } from "react"; -import { createViewer } from "3dmol"; -import { Box, Button } from "@mui/material"; -import { useViewerState, useViewerDispatch } from "../../providers/ViewerProvider"; -import { useViewerInteractionState, useViewerInteractionDispatch } from "ui"; -import Usage from "./Usage"; -import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; import { faCamera } from "@fortawesome/free-solid-svg-icons"; -import { Tooltip, ViewerTrack } from "ui"; +import { FontAwesomeIcon } from "@fortawesome/react-fontawesome"; +import { Box, Button } from "@mui/material"; +import { createViewer } from "3dmol"; +import { useEffect, useRef, useState } from "react"; +import { Tooltip, useViewerInteractionDispatch, useViewerInteractionState, ViewerTrack } from "ui"; +import { useViewerDispatch, useViewerState } from "../../providers/ViewerProvider"; import { onClickCapture } from "./helpers"; +import Usage from "./Usage"; const hoverDuration = 0; @@ -55,22 +54,17 @@ export default function Viewer({ function applyAppearance( appearance, - resi = null, // only non-null for click/hover on structure (not track) appearance changes + resi = null // only non-null for click/hover on structure (not track) appearance changes ) { const resolvedSelection = resolveProperty(appearance, "selection", viewerState, resi); const resolvedStyle = resolveProperty(appearance, "style", viewerState, resi); if (resolvedSelection && resolvedStyle) { - viewer[appearance.addStyle ? "addStyle" : "setStyle"]( - resolvedSelection, - resolvedStyle - ); + viewer[appearance.addStyle ? "addStyle" : "setStyle"](resolvedSelection, resolvedStyle); } } function getEventSelection(selection) { - return typeof selection === "function" - ? selection(viewerState) - : selection; + return typeof selection === "function" ? selection(viewerState) : selection; } // keep ref in sync @@ -83,7 +77,6 @@ export default function Viewer({ let _viewer; if (data && viewerRef.current) { - // create viewer _viewer = createViewer(viewerRef.current, { backgroundColor: "#f8f8f8", @@ -99,7 +92,7 @@ export default function Viewer({ setViewer(_viewer); _viewer.getCanvas().addEventListener( "wheel", - event => { + (event) => { if (!event.ctrlKey) event.stopImmediatePropagation(); }, true // use capture phase so fires before library handler @@ -110,34 +103,27 @@ export default function Viewer({ onData?.(_viewer, viewerDispatch); // set state viewer after load data - since state groups atoms by resi - viewerDispatch({ type: '_setViewer', value: _viewer }); + viewerDispatch({ type: "_setViewer", value: _viewer }); } // interaction if (viewerInteractionState) { - // disable hover when mousedown - _viewer.getCanvas().addEventListener( - "mousedown", - event => { - manipulating.current = true; - startedManipulating.current = Date.now(); - } - ); - _viewer.getCanvas().addEventListener( - "mouseup", - event => { - viewerInteractionDispatch({ type: "setHoveredResi", value: null }); - manipulating.current = false; - } - ); - + _viewer.getCanvas().addEventListener("mousedown", (_event) => { + manipulating.current = true; + startedManipulating.current = Date.now(); + }); + _viewer.getCanvas().addEventListener("mouseup", (_event) => { + viewerInteractionDispatch({ type: "setHoveredResi", value: null }); + manipulating.current = false; + }); + // click event on canvas for 'click off' events - _viewer.getCanvas().addEventListener("click", event => { + _viewer.getCanvas().addEventListener("click", (_event) => { setTimeout(() => { - if( + if ( !clickHandled.current && - Date.now() - startedManipulating.current < 250 // click rather than manipulate structure + Date.now() - startedManipulating.current < 250 // click rather than manipulate structure ) { viewerInteractionDispatch({ type: "setClickedResi", value: null }); } @@ -149,7 +135,7 @@ export default function Viewer({ if (clickSelection) { const sel = getEventSelection(clickSelection); if (sel && clickAppearance?.length > 0) { - _viewer.setClickable(sel, true, atom => { + _viewer.setClickable(sel, true, (atom) => { viewerInteractionDispatch({ type: "setClickedResi", value: +atom.resi }); clickHandled.current = true; }); @@ -165,7 +151,7 @@ export default function Viewer({ true, // use tempHoveredResi and setTimeout to prevent flicker when hover aross // different atoms on same residue - atom => { + (atom) => { if (hoverTimeout.current) { clearTimeout(hoverTimeout.current); hoverTimeout.current = null; @@ -175,11 +161,12 @@ export default function Viewer({ // tempHoveredResi.current = +atom.resi; } }, - atom => { + (atom) => { hoverTimeout.current = setTimeout(() => { - if (!manipulating.current && - // viewerInteractionState.hoveredResi === +atom.resi //&& - tempHoveredResi.current === +atom.resi + if ( + !manipulating.current && + // viewerInteractionState.hoveredResi === +atom.resi //&& + tempHoveredResi.current === +atom.resi ) { viewerInteractionDispatch({ type: "setHoveredResi", value: null }); tempHoveredResi.current = null; @@ -188,7 +175,7 @@ export default function Viewer({ }, 50); } ); - _viewer.render(); // required to reactivate hover + _viewer.render(); // required to reactivate hover } } @@ -206,7 +193,7 @@ export default function Viewer({ // double click callback useEffect(() => { if (!viewer || !onDblClick) return; - viewer.getCanvas().addEventListener("dblclick", event => { + viewer.getCanvas().addEventListener("dblclick", (_event) => { onDblClick(viewerState); }); }, [viewer]); @@ -220,7 +207,7 @@ export default function Viewer({ let anyUsed = false; for (const appearance of clickAppearance) { for (const leaveAppearance of appearance.leave || []) { - const a = {...leaveAppearance }; + const a = { ...leaveAppearance }; const resi = Number(oldClickedResi.current); if (!a.use || a.use(viewerState, resi)) { if (!a.selection) a.selection = { resi }; @@ -255,13 +242,13 @@ export default function Viewer({ // update for change in hovered resi useEffect(() => { if (!viewer || !viewerInteractionState) return; - + // unhover if (oldHoveredResi.current) { let anyUsed = false; for (const appearance of hoverAppearance) { - for (const leaveAppearance of appearance.leave || []) { - const a = {...leaveAppearance }; + for (const leaveAppearance of appearance.leave || []) { + const a = { ...leaveAppearance }; const resi = Number(oldHoveredResi.current); if (!a.use || a.use(viewerState, resi)) { if (!a.selection) a.selection = { resi }; @@ -273,12 +260,12 @@ export default function Viewer({ } if (anyUsed) viewer.render(); } - + // hover if (viewerInteractionState.hoveredResi) { let anyUsed = false; for (const appearance of hoverAppearance) { - const a = {...appearance }; + const a = { ...appearance }; const resi = Number(viewerInteractionState.hoveredResi); if (!a.use || a.use(viewerState, resi)) { if (!a.selection) a.selection = { resi }; @@ -289,7 +276,7 @@ export default function Viewer({ } if (anyUsed) viewer.render(); } - + oldHoveredResi.current = viewerInteractionState.hoveredResi; }, [viewer, viewerInteractionState?.hoveredResi]); @@ -311,19 +298,18 @@ export default function Viewer({ return ( - {/* track */} {trackColor && } - + {/* viewer */} {/* // position="relative" width="100%" height={height} sx={{resize: "vertical", overflow: "hidden"}}> */} @@ -368,7 +354,7 @@ export default function Viewer({ position="absolute" top={0} left={0} - height="50%" // stops jumping when canvas overlaps top/bottom of window + height="50%" // stops jumping when canvas overlaps top/bottom of window display="flex" alignItems="start" zIndex={100} @@ -384,7 +370,7 @@ export default function Viewer({ position="absolute" bottom={0} right={0} - height="50%" // stops jumping when canvas overlaps top/bottom of window + height="50%" // stops jumping when canvas overlaps top/bottom of window display="flex" alignItems="end" zIndex={100} @@ -396,4 +382,4 @@ export default function Viewer({ ); -} \ No newline at end of file +} diff --git a/packages/ui/src/components/Viewer/ViewerTrack.tsx b/packages/ui/src/components/Viewer/ViewerTrack.tsx index 67189d390..aa8ca762a 100644 --- a/packages/ui/src/components/Viewer/ViewerTrack.tsx +++ b/packages/ui/src/components/Viewer/ViewerTrack.tsx @@ -1,8 +1,8 @@ -import { useRef, useEffect } from "react"; import { Box } from "@mui/material"; +import { format, scaleLinear } from "d3"; +import { useEffect, useRef } from "react"; +import { useViewerInteractionDispatch, useViewerInteractionState } from "ui"; import { useViewerState } from "../../providers/ViewerProvider"; -import { useViewerInteractionState, useViewerInteractionDispatch } from "ui"; -import { scaleLinear, format } from "d3"; const trackHeight = 8; const topSpace = 24; @@ -22,10 +22,7 @@ function tickGroup({ fontWeight = 400, }) { const g = svgElement("g"); - g.setAttribute( - "transform", - `translate(${x - 0.5}, 0)` - ); + g.setAttribute("transform", `translate(${x - 0.5}, 0)`); let yLine, yLabel, dominantBaseline; if (position === "top") { yLine = topSpace - 5; @@ -60,22 +57,22 @@ function tickGroup({ function updateTextScale(textOrSvg) { let xScale; - const textElements = textOrSvg.tagName.toLowerCase() === "text" - ? [textOrSvg] - : textOrSvg.querySelectorAll("._track_text_"); + const textElements = + textOrSvg.tagName.toLowerCase() === "text" + ? [textOrSvg] + : textOrSvg.querySelectorAll("._track_text_"); for (const text of textElements) { if (!xScale) { text.setAttribute("transform", `scale(1, 1)`); xScale ??= text.getCTM().a; } - text.setAttribute("transform", `scale(${1/xScale}, 1)`); + text.setAttribute("transform", `scale(${1 / xScale}, 1)`); } } // currently for alphaFold only - assumes single/first structure and contiguous // residue indices from 1 to structure length export default function ViewerTrack({ trackColor, trackTicks }) { - const viewerState = useViewerState(); const viewerInteractionState = useViewerInteractionState(); const viewerInteractionDispatch = useViewerInteractionDispatch(); @@ -90,7 +87,7 @@ export default function ViewerTrack({ trackColor, trackTicks }) { }); } - function handleMouseleave(event) { + function handleMouseleave(_event) { viewerInteractionDispatch({ type: "setHoveredResi", value: null }); } @@ -123,7 +120,7 @@ export default function ViewerTrack({ trackColor, trackTicks }) { rect.setAttribute("height", trackHeight); rect.setAttribute("fill", trackColor(viewerState, resi)); rect.setAttribute("pointer-events", "none"); - rect.setAttribute("shape-rendering","crispEdges"); + rect.setAttribute("shape-rendering", "crispEdges"); // larger invisible rect for interaction const invisibleRect = svgElement("rect"); @@ -132,12 +129,12 @@ export default function ViewerTrack({ trackColor, trackTicks }) { invisibleRect.setAttribute("width", 1); invisibleRect.setAttribute("height", totalHeight); invisibleRect.setAttribute("stoke", "none"); - invisibleRect.setAttribute("fill-opacity", 0); // so can still trigger evevnts + invisibleRect.setAttribute("fill-opacity", 0); // so can still trigger evevnts invisibleRect.setAttribute("data-resi", resi); invisibleRect.addEventListener("click", handleClick); rects.push(rect, invisibleRect); } - + // add rects and event handlers svg.append(...rects); svg.addEventListener("pointermove", handlePointerMove); @@ -145,12 +142,16 @@ export default function ViewerTrack({ trackColor, trackTicks }) { // track ticks if (trackTicks) { - svg.append(...trackTicks(viewerState).map(({ resi, label }) => tickGroup({ - x: resi, - position: "top", - fontWeight: 500, - label, - }))); + svg.append( + ...trackTicks(viewerState).map(({ resi, label }) => + tickGroup({ + x: resi, + position: "top", + fontWeight: 500, + label, + }) + ) + ); } // add hover tick group once and reuse @@ -160,15 +161,17 @@ export default function ViewerTrack({ trackColor, trackTicks }) { svg.append(g); // axis - const ticks = scaleLinear() - .domain([0, nResidues]) - .ticks() + const ticks = scaleLinear().domain([0, nResidues]).ticks(); if (ticks[0] === 0) ticks[0] = 1; const tickFormatter = format(","); - svg.append(...ticks.map(value => tickGroup({ - x: value, - label: tickFormatter(value), - }))); + svg.append( + ...ticks.map((value) => + tickGroup({ + x: value, + label: tickFormatter(value), + }) + ) + ); updateTextScale(svg); window.addEventListener("resize", () => updateTextScale(svg)); }, [viewerState]); @@ -178,7 +181,7 @@ export default function ViewerTrack({ trackColor, trackTicks }) { if (!viewerInteractionState) return; const svg = svgRef.current; if (!svg) return; - svg.querySelector('._clicked_tick_group_')?.remove(); + svg.querySelector("._clicked_tick_group_")?.remove(); const resi = viewerInteractionState.clickedResi; if (resi) { const g = tickGroup({ @@ -199,12 +202,9 @@ export default function ViewerTrack({ trackColor, trackTicks }) { if (!svg) return; const resi = viewerInteractionState.hoveredResi; const g = svg.querySelector("._hovered_tick_group_"); - if(!g) return; + if (!g) return; if (resi) { - g.setAttribute( - "transform", - `translate(${resi - 0.5}, 0)` - ); + g.setAttribute("transform", `translate(${resi - 0.5}, 0)`); const text = g.querySelector("text"); text.textContent = `${viewerState.atomsByResi.get(+resi)[0].resn} ${resi}`; g.style.display = "inline"; @@ -215,13 +215,15 @@ export default function ViewerTrack({ trackColor, trackTicks }) { if (!viewerInteractionState) return null; - return ( - + return ( + + > {/* rectangles and highlight added by useEffect */} ); -} \ No newline at end of file +} diff --git a/packages/ui/src/components/icons/ArrowTurnDownLeft.tsx b/packages/ui/src/components/icons/ArrowTurnDownLeft.tsx index 2f3972b23..80a230d73 100644 --- a/packages/ui/src/components/icons/ArrowTurnDownLeft.tsx +++ b/packages/ui/src/components/icons/ArrowTurnDownLeft.tsx @@ -1,7 +1,7 @@ import { makeStyles } from "@mui/styles"; -import { ReactNode } from "react"; +import type { ReactNode } from "react"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((_theme) => ({ mainIcon: { width: "1em", display: "flex", diff --git a/packages/ui/src/components/icons/BrokenSearchIcon.tsx b/packages/ui/src/components/icons/BrokenSearchIcon.tsx index c2eb51bb1..bd0257c89 100644 --- a/packages/ui/src/components/icons/BrokenSearchIcon.tsx +++ b/packages/ui/src/components/icons/BrokenSearchIcon.tsx @@ -1,7 +1,7 @@ import { makeStyles } from "@mui/styles"; -import { ReactNode } from "react"; +import type { ReactNode } from "react"; -const useStyles = makeStyles(theme => ({ +const useStyles = makeStyles((_theme) => ({ mainIcon: { width: "1em", display: "flex", From 9f88b1c371be7f2249c40d7c293c06a7fd8d7f99 Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Mon, 27 Oct 2025 15:15:49 +0000 Subject: [PATCH 08/10] [ot-config]: lint on (#821) --- biome.json | 1 - packages/ot-config/src/environment.ts | 55 +++++++++++++-------------- packages/ot-config/src/index.ts | 2 +- packages/ot-config/src/theme.ts | 4 +- 4 files changed, 30 insertions(+), 32 deletions(-) diff --git a/biome.json b/biome.json index b1509b0e5..8b0d29cc4 100644 --- a/biome.json +++ b/biome.json @@ -31,7 +31,6 @@ "!**/apps/platform/src", "!**/packages/ui", "!**/packages/sections", - "!**/packages/ot-config", "!**/packages/ot-constants", "!**/packages/ot-utils" ] diff --git a/packages/ot-config/src/environment.ts b/packages/ot-config/src/environment.ts index a70486e48..8b1d81c00 100644 --- a/packages/ot-config/src/environment.ts +++ b/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 = { - 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 = { + 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", + }; }; diff --git a/packages/ot-config/src/index.ts b/packages/ot-config/src/index.ts index be4b007b6..c77c6da82 100644 --- a/packages/ot-config/src/index.ts +++ b/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 { diff --git a/packages/ot-config/src/theme.ts b/packages/ot-config/src/theme.ts index c6385df54..b2d5a9ce8 100644 --- a/packages/ot-config/src/theme.ts +++ b/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(); From cff24118469aad3a9718617b964fb08d62a991f1 Mon Sep 17 00:00:00 2001 From: Carlos Cruz Date: Mon, 27 Oct 2025 15:20:13 +0000 Subject: [PATCH 09/10] [ot-utils]: lint on (#822) --- biome.json | 1 + packages/ot-utils/src/alphaFold.ts | 29 +++++----- packages/ot-utils/src/comparators.ts | 54 ++++++++++++----- packages/ot-utils/src/createScopedContext.tsx | 28 ++++----- packages/ot-utils/src/downloads.js | 58 +++++++++---------- packages/ot-utils/src/fetch.ts | 4 +- packages/ot-utils/src/formatters.ts | 4 +- packages/ot-utils/src/global.ts | 8 +-- packages/ot-utils/src/index.ts | 16 ++--- packages/ot-utils/src/interactors.ts | 21 +++++-- packages/ot-utils/src/searchSuggestions.ts | 2 +- packages/ot-utils/src/study.js | 4 +- packages/ot-utils/src/urls.ts | 14 ++--- packages/ot-utils/src/variant.ts | 3 +- 14 files changed, 136 insertions(+), 110 deletions(-) diff --git a/biome.json b/biome.json index 8b0d29cc4..b1509b0e5 100644 --- a/biome.json +++ b/biome.json @@ -31,6 +31,7 @@ "!**/apps/platform/src", "!**/packages/ui", "!**/packages/sections", + "!**/packages/ot-config", "!**/packages/ot-constants", "!**/packages/ot-utils" ] diff --git a/packages/ot-utils/src/alphaFold.ts b/packages/ot-utils/src/alphaFold.ts index a0779694f..7d655aadf 100644 --- a/packages/ot-utils/src/alphaFold.ts +++ b/packages/ot-utils/src/alphaFold.ts @@ -1,7 +1,7 @@ import { csvParse, mean } from "d3"; import { safeFetch } from "./fetch"; -import { alphaFoldPathogenicityUrl, alphaFoldDomainsUrl } from "./urls"; - +import { alphaFoldDomainsUrl, alphaFoldPathogenicityUrl } from "./urls"; + // returns map of pathogenicity scores grouped by residue index (number). Each // group is an array of objects giving pathogencity scores for alternate amino // acids: @@ -9,21 +9,20 @@ import { alphaFoldPathogenicityUrl, alphaFoldDomainsUrl } from "./urls"; // protein_variant (string): e.g. "M1E" - current AA, residue index, alternate AA // am_pathogenicity (string): score // am_class (string) -// } +// } export async function fetchPathogenicityScores(uniprotId: string) { - const [scoresCSV, error] = - await safeFetch(alphaFoldPathogenicityUrl(uniprotId), "text"); + const [scoresCSV, error] = await safeFetch(alphaFoldPathogenicityUrl(uniprotId), "text"); if (error) return [undefined, error]; const scores = Map.groupBy( - csvParse(scoresCSV), // string -> array of objects - row => Number(row.protein_variant.match(/\d+/)[0]) + csvParse(scoresCSV), // string -> array of objects + (row) => Number(row.protein_variant.match(/\d+/)[0]) ); return [scores, undefined]; -}; +} export async function fetchDomains(uniprotId: string) { return safeFetch(alphaFoldDomainsUrl(uniprotId), "json"); -}; +} // returns map: // - key (number): residue index @@ -31,7 +30,10 @@ export async function fetchDomains(uniprotId: string) { export function meanPathogenicityScores(pathogenicityScores) { const meanScores = new Map(); for (const [resi, group] of pathogenicityScores) { - meanScores.set(resi, mean(group, d => Number(d.am_pathogenicity))); + meanScores.set( + resi, + mean(group, (d) => Number(d.am_pathogenicity)) + ); } return meanScores; } @@ -40,13 +42,12 @@ export function meanPathogenicityScores(pathogenicityScores) { export function pickPathogenicityScore(pathogenicityScores, resi, alternateAminoAcid) { const row = pathogenicityScores .get(Number(resi)) - .find(row => row.protein_variant.at(-1) === alternateAminoAcid); + .find((row) => row.protein_variant.at(-1) === alternateAminoAcid); return row ? Number(row.am_pathogenicity) : undefined; } export function processDomains(domains) { - const uniqueDescriptions = - [...new Set(domains.map(domain => domain.description))]; + const uniqueDescriptions = [...new Set(domains.map((domain) => domain.description))]; const descriptionToIndex = {}; for (const [index, description] of uniqueDescriptions.entries()) { descriptionToIndex[description] = index; @@ -63,4 +64,4 @@ export function processDomains(domains) { descriptionToIndex, getDescription, }; -} \ No newline at end of file +} diff --git a/packages/ot-utils/src/comparators.ts b/packages/ot-utils/src/comparators.ts index 2c54d66de..215559a89 100644 --- a/packages/ot-utils/src/comparators.ts +++ b/packages/ot-utils/src/comparators.ts @@ -2,19 +2,25 @@ Example usage: const comparatorDiseaseName = generateComparatorFromAccessor(d => d.disease.name); */ -export const generateComparatorFromAccessor = accessor => (a, b) => { - const aValue = accessor(a); - const bValue = accessor(b); - if (aValue > bValue) return 1; - if (aValue === bValue) return 0; - return -1; -}; +export const generateComparatorFromAccessor = + (accessor: (item: T) => string | number) => + (a: T, b: T) => { + const aValue = accessor(a); + const bValue = accessor(b); + if (aValue > bValue) return 1; + if (aValue === bValue) return 0; + return -1; + }; /* Return comparator that sorts nullish values to end */ -export const nullishComparator = (comparator, accessor = x => x, nullishIsMax = true) => { - return (a, b) => { +export const nullishComparator = ( + comparator: (a: unknown, b: unknown) => number, + accessor: (x: T) => unknown = (x: T) => x, + nullishIsMax = true +) => { + return (a: T, b: T) => { const aVal = accessor(a); const bVal = accessor(b); if (!aVal && aVal !== 0) { @@ -29,8 +35,12 @@ export const nullishComparator = (comparator, accessor = x => x, nullishIsMax = /* Return comparator that sorts NaNs to end */ -export const nanComparator = (comparator, accessor = x => x, nanIsMax = true) => { - return (a, b) => { +export const nanComparator = ( + comparator: (a: unknown, b: unknown) => number, + accessor: (x: T) => unknown = (x: T) => x, + nanIsMax = true +) => { + return (a: T, b: T) => { const aVal = accessor(a); const bVal = accessor(b); if (Number.isNaN(aVal)) { @@ -45,14 +55,18 @@ export const nanComparator = (comparator, accessor = x => x, nanIsMax = true) => /* Compares a breakpoint against a breakpoint helper. */ -export const breakpointMatch = (breakpoint, breakpointHelper) => { - const breakpointMap = { xs: 0, sm: 1, md: 2, lg: 3, xl: 4 }; +export const breakpointMatch = (breakpoint: string, breakpointHelper: string) => { + const breakpointMap: Record = { xs: 0, sm: 1, md: 2, lg: 3, xl: 4 }; const isDownComparator = breakpointHelper.includes("Down"); const isUpComparator = breakpointHelper.includes("Up"); const breakpointIndex = breakpointMap[breakpoint]; const breakpointHelperIndex = breakpointMap[breakpointHelper.replace(/Down|Up|Only/g, "")]; + if (breakpointIndex === undefined || breakpointHelperIndex === undefined) { + return false; + } + if (breakpointIndex === breakpointHelperIndex) { return true; } @@ -85,8 +99,10 @@ type VariantType = { alternateAllele: string; }; -export function variantComparator(accessor: (arg: any) => VariantType = d => d) { - return function (obj1: any, obj2: any) { +export function variantComparator( + accessor: (arg: unknown) => VariantType = (d: unknown) => d as VariantType +) { + return (obj1: unknown, obj2: unknown) => { const v1 = accessor(obj1); const v2 = accessor(obj2); @@ -107,7 +123,13 @@ export function variantComparator(accessor: (arg: any) => VariantType = d => d) }; } -export function mantissaExponentComparator(m1, e1, m2, e2, nullishIsMax = true) { +export function mantissaExponentComparator( + m1: number | null, + e1: number | null, + m2: number | null, + e2: number | null, + nullishIsMax = true +) { if (m1 == null || e1 == null) { if (m2 == null || e2 == null) return 0; return nullishIsMax ? 1 : -1; diff --git a/packages/ot-utils/src/createScopedContext.tsx b/packages/ot-utils/src/createScopedContext.tsx index 1a3e4abc2..e335b5324 100644 --- a/packages/ot-utils/src/createScopedContext.tsx +++ b/packages/ot-utils/src/createScopedContext.tsx @@ -1,31 +1,28 @@ -import { useReducer, useContext, createContext } from "react"; +import { createContext, useContext, useReducer } from "react"; export function createScopedContext({ - name, - extraStateProperties = {}, // key-value pairs are propertyName: initialValue - extraActions = {}, // key-value pairs are actionType: (state, action) => newState - }) { + name, + extraStateProperties = {}, // key-value pairs are propertyName: initialValue + extraActions = {}, // key-value pairs are actionType: (state, action) => newState +}) { const StateContext = createContext(null); const DispatchContext = createContext(null); const ScopedProvider = ({ reducer, initialState = {}, children }) => { - function wrappedReducer(state, action) { return extraActions[action.type] ? extraActions[action.type](state, action) - : reducer(state, action); + : reducer(state, action); } - const [state, dispatch] = useReducer( - wrappedReducer, - {...initialState, ...extraStateProperties} - ); + const [state, dispatch] = useReducer(wrappedReducer, { + ...initialState, + ...extraStateProperties, + }); return ( - - {children} - + {children} ); }; @@ -50,6 +47,5 @@ export function createScopedContext({ ScopedProvider, useScopedState, useScopedDispatch, - } + }; } - diff --git a/packages/ot-utils/src/downloads.js b/packages/ot-utils/src/downloads.js index fe101d415..bc477fa40 100644 --- a/packages/ot-utils/src/downloads.js +++ b/packages/ot-utils/src/downloads.js @@ -3,28 +3,26 @@ import _ from "lodash"; const targetName = { id: "symbol", label: "Symbol", - exportValue: data => data.target.approvedSymbol, + exportValue: (data) => data.target.approvedSymbol, }; const diseaseName = { id: "disease", label: "Disease", - exportValue: data => data.disease.name, + exportValue: (data) => data.disease.name, }; const asJSON = (columns, rows) => { - const rowStrings = rows.map(row => + const rowStrings = rows.map((row) => columns.reduce((accumulator, newKey) => { if (newKey.exportValue === false) return accumulator; const newLabel = _.camelCase(newKey.exportLabel || newKey.label || newKey.id); - return { - ...accumulator, - [newLabel]: newKey.exportValue - ? newKey.exportValue(row) - : _.get(row, newKey.propertyPath || newKey.id, ""), - }; + accumulator[newLabel] = newKey.exportValue + ? newKey.exportValue(row) + : _.get(row, newKey.propertyPath || newKey.id, ""); + return accumulator; }, {}) ); @@ -38,12 +36,13 @@ const getHeaderString = ({ columns, quoteString, separator }) => const newLabel = quoteString(_.camelCase(column.exportLabel || column.label || column.id)); - return [...headerString, newLabel]; + headerString.push(newLabel); + return headerString; }, []) .join(separator); const asDSV = (columns, rows, separator = ",", quoteStrings = true) => { - const quoteString = d => { + const quoteString = (d) => { let result = d; // converts arrays to strings if (Array.isArray(d)) { @@ -57,7 +56,7 @@ const asDSV = (columns, rows, separator = ",", quoteStrings = true) => { const headerString = getHeaderString({ columns, quoteString, separator }); const rowStrings = rows - .map(row => + .map((row) => columns .reduce((rowString, column) => { if (column.exportValue === false) return rowString; @@ -68,7 +67,8 @@ const asDSV = (columns, rows, separator = ",", quoteStrings = true) => { : _.get(row, column.propertyPath || column.id, "") ); - return [...rowString, newValue]; + rowString.push(newValue); + return rowString; }, []) .join(separator) ) @@ -77,7 +77,7 @@ const asDSV = (columns, rows, separator = ",", quoteStrings = true) => { return [headerString, rowStrings].join(lineSeparator); }; -export const getRowsQuerySelector = entityToGet => +export const getRowsQuerySelector = (entityToGet) => entityToGet === "target" ? "data.disease.associatedTargets" : "data.target.associatedDiseases"; export const getExportedColumns = (entityToGet, assocArr, prioArr, pinnedArr) => { @@ -88,8 +88,8 @@ export const getExportedColumns = (entityToGet, assocArr, prioArr, pinnedArr) => const isPinnedObj = [ { id: "isPinned", - exportValue: data => - pinnedArr.some(currentValue => currentValue.id === data[entityToGet].id), + exportValue: (data) => + pinnedArr.some((currentValue) => currentValue.id === data[entityToGet].id), }, ]; exportedColumns = [...exportedColumns, ...isPinnedObj]; @@ -97,9 +97,9 @@ export const getExportedColumns = (entityToGet, assocArr, prioArr, pinnedArr) => const sources = assocArr.map(({ id }) => ({ id, - exportValue: data => { + exportValue: (data) => { const datatypeScore = data.datasourceScores.find( - datasourceScore => datasourceScore.componentId === id + (datasourceScore) => datasourceScore.componentId === id ); return datatypeScore ? parseFloat(datatypeScore.score) : "No data"; }, @@ -110,9 +110,9 @@ export const getExportedColumns = (entityToGet, assocArr, prioArr, pinnedArr) => if (entityToGet === "target") { const prioritisationExportCols = prioArr.map(({ id }) => ({ id, - exportValue: data => { + exportValue: (data) => { const prioritisationScore = data.target.prioritisation.items.find( - prioritisationItem => prioritisationItem.key === id + (prioritisationItem) => prioritisationItem.key === id ); return prioritisationScore ? parseFloat(prioritisationScore.value) : "No data"; }, @@ -126,7 +126,7 @@ export const getExportedColumns = (entityToGet, assocArr, prioArr, pinnedArr) => { id: "globalScore", label: "Global Score", - exportValue: data => data.score, + exportValue: (data) => data.score, }, ...exportedColumns, ]; @@ -139,8 +139,8 @@ export const getExportedPrioritisationColumns = (arr, pinnedArr, entityToGet) => const isPinnedObj = [ { id: "isPinned", - exportValue: data => - pinnedArr.some(currentValue => currentValue.id === data[entityToGet].id), + exportValue: (data) => + pinnedArr.some((currentValue) => currentValue.id === data[entityToGet].id), }, ]; exportedColumns = [...exportedColumns, ...isPinnedObj]; @@ -148,9 +148,9 @@ export const getExportedPrioritisationColumns = (arr, pinnedArr, entityToGet) => const prioritisationExportCols = arr.map(({ id }) => ({ id, - exportValue: data => { + exportValue: (data) => { const prioritisationScore = data.target.prioritisation.items.find( - prioritisationItem => prioritisationItem.key === id + (prioritisationItem) => prioritisationItem.key === id ); return prioritisationScore ? parseFloat(prioritisationScore.value) : "No data"; }, @@ -163,13 +163,13 @@ export const getExportedPrioritisationColumns = (arr, pinnedArr, entityToGet) => { id: "globalScore", label: "Global Score", - exportValue: data => data.score, + exportValue: (data) => data.score, }, ...exportedColumns, ]; }; -export const createBlob = format => +export const createBlob = (format) => ({ json: (columns, rows) => new Blob([asJSON(columns, rows)], { @@ -183,10 +183,10 @@ export const createBlob = format => new Blob([asDSV(columns, rows, "\t", false)], { type: "text/tab-separated-values;charset=utf-8", }), - }[format]); + })[format]; export const getFilteredColumnArray = (selectArray, requestArray) => { - const arr = selectArray.map(ag => requestArray.filter(e => e.aggregation === ag)).flat(1); + const arr = selectArray.flatMap((ag) => requestArray.filter((e) => e.aggregation === ag)); return arr.length > 0 ? arr : []; }; diff --git a/packages/ot-utils/src/fetch.ts b/packages/ot-utils/src/fetch.ts index 788697bda..6e4a92623 100644 --- a/packages/ot-utils/src/fetch.ts +++ b/packages/ot-utils/src/fetch.ts @@ -8,8 +8,8 @@ export async function safeFetch( if (!response.ok) { throw new Error(`HTTP error ${response.status}: ${response.statusText}`); } - return [(parseAs ? (await response[parseAs]()) : response), undefined]; + return [parseAs ? await response[parseAs]() : response, undefined]; } catch (error) { return [undefined, error]; } -} \ No newline at end of file +} diff --git a/packages/ot-utils/src/formatters.ts b/packages/ot-utils/src/formatters.ts index 0bb51859a..5b5467621 100644 --- a/packages/ot-utils/src/formatters.ts +++ b/packages/ot-utils/src/formatters.ts @@ -22,11 +22,9 @@ export function formatSignificantDigits( const magnitude = Math.floor(Math.log10(absNum)) + 1; // digits before decimal const decimalPlaces = Math.max(0, 3 - magnitude); - const rounded = Math.round(absNum * Math.pow(10, decimalPlaces)) / Math.pow(10, decimalPlaces); + const rounded = Math.round(absNum * 10 ** decimalPlaces) / 10 ** decimalPlaces; const formatted = rounded.toFixed(decimalPlaces); const trimmed = formatted.replace(/\.?0+$/, ""); return num < 0 ? `-${trimmed}` : trimmed; } - - diff --git a/packages/ot-utils/src/global.ts b/packages/ot-utils/src/global.ts index e6e1a6be3..f39bdf63c 100644 --- a/packages/ot-utils/src/global.ts +++ b/packages/ot-utils/src/global.ts @@ -1,5 +1,5 @@ -import { format } from "d3-format"; import { getConfig } from "@ot/config"; +import { format } from "d3-format"; const config = getConfig(); @@ -35,8 +35,8 @@ export const formatComma = format(","); export function getUniprotIds(proteinIds: ProteinId[]): string[] { return proteinIds - .filter(proteinId => proteinId.source === "uniprot_swissprot") - .map(proteinId => proteinId.id); + .filter((proteinId) => proteinId.source === "uniprot_swissprot") + .map((proteinId) => proteinId.id); } const makePmidLink = (themeColor: string) => { @@ -52,7 +52,7 @@ export function clearDescriptionCodes( themeColor: string ): string[] { if (!descriptions) return []; - return descriptions.map(desc => { + return descriptions.map((desc) => { const codeStart = desc.indexOf("{"); const parsedDesc = desc.slice(0, codeStart); return parsedDesc.replace(/Pubmed:\d+/gi, makePmidLink(themeColor)); diff --git a/packages/ot-utils/src/index.ts b/packages/ot-utils/src/index.ts index 58c60ff85..c6b755b9b 100644 --- a/packages/ot-utils/src/index.ts +++ b/packages/ot-utils/src/index.ts @@ -1,13 +1,13 @@ -export * from "./searchSuggestions"; +export * from "./alphaFold"; +export * from "./comparators"; +export * from "./createScopedContext"; export * from "./downloads"; export * from "./fetch"; -export * from "./interactors"; +export * from "./formatters"; export * from "./global"; -export * from "./urls"; -export * from "./comparators"; -export * from "./study"; +export * from "./interactors"; export * from "./literature"; +export * from "./searchSuggestions"; +export * from "./study"; +export * from "./urls"; export * from "./variant"; -export * from "./createScopedContext"; -export * from "./alphaFold"; -export * from "./formatters"; diff --git a/packages/ot-utils/src/interactors.ts b/packages/ot-utils/src/interactors.ts index 9ad13b011..d7735ca4a 100644 --- a/packages/ot-utils/src/interactors.ts +++ b/packages/ot-utils/src/interactors.ts @@ -19,8 +19,21 @@ export const INTERACTORS_SOURCE_THRESHOLD = { [INTERACTORS_SOURCES.REACTOME]: null, }; -// TODO: refactor to remove any -export function getInteractorIds(targetRowInteractorsRequest: any) { +interface TargetRowInteractorsRequest { + data?: { + target?: { + interactions?: { + rows?: Array<{ + targetB?: { + id: string; + }; + }>; + }; + }; + }; +} + +export function getInteractorIds(targetRowInteractorsRequest: TargetRowInteractorsRequest) { if (!targetRowInteractorsRequest?.data?.target?.interactions?.rows) { return []; } @@ -28,8 +41,8 @@ export function getInteractorIds(targetRowInteractorsRequest: any) { const interactorsIds = [ ...new Set( targetRowInteractorsRequest.data.target.interactions.rows - .map(int => int.targetB?.id) - .filter(id => id !== null && id !== undefined) + .map((int) => int.targetB?.id) + .filter((id) => id !== null && id !== undefined) ), ]; diff --git a/packages/ot-utils/src/searchSuggestions.ts b/packages/ot-utils/src/searchSuggestions.ts index 4b2071963..5305d08c5 100644 --- a/packages/ot-utils/src/searchSuggestions.ts +++ b/packages/ot-utils/src/searchSuggestions.ts @@ -1,4 +1,4 @@ -import { searchSuggestions, SearchSuggestions, Suggestion } from "@ot/constants"; +import { type SearchSuggestions, type Suggestion, searchSuggestions } from "@ot/constants"; /** * Efficiently selects n random elements from an array without modifying the original. diff --git a/packages/ot-utils/src/study.js b/packages/ot-utils/src/study.js index 8c1f6a183..1574ccc68 100644 --- a/packages/ot-utils/src/study.js +++ b/packages/ot-utils/src/study.js @@ -5,8 +5,8 @@ export function getStudyCategory(projectId) { return "QTL"; } -export const getStudyTypeDisplay = studyType => { - if (studyType) return studyType?.replace(/(qtl|gwas)/gi, match => match.toUpperCase()); +export const getStudyTypeDisplay = (studyType) => { + if (studyType) return studyType?.replace(/(qtl|gwas)/gi, (match) => match.toUpperCase()); return studyType; }; diff --git a/packages/ot-utils/src/urls.ts b/packages/ot-utils/src/urls.ts index 8aee9b5cc..8bd51a4ab 100644 --- a/packages/ot-utils/src/urls.ts +++ b/packages/ot-utils/src/urls.ts @@ -14,12 +14,6 @@ interface SearchPostResult { requestOptions?: RequestOptions; } -interface PublicationSummaryParams { - pmcId: string; - symbol: string; - name: string; -} - export function epmcUrl(id: string): string { return `https://europepmc.org/article/MED/${id}`; } @@ -39,11 +33,11 @@ export function europePmcLiteratureQuery(ids: string[]): string { export const encodeParams = (params: Record): string => { const formBody: string[] = []; - Object.keys(params).forEach(key => { + for (const key of Object.keys(params)) { const encodedKey = encodeURIComponent(key); - const encodedValue = encodeURIComponent(params[key]); + const encodedValue = encodeURIComponent(params[key] ?? ""); formBody.push(`${encodedKey}=${encodedValue}`); - }); + } return formBody.join("&"); }; @@ -89,7 +83,7 @@ function emaUrl() { return "https://www.ema.europa.eu/en/medicines"; } -function usanUrl(id) { +function usanUrl(id: string) { return `https://searchusan.ama-assn.org/finder/usan/search/${id}/relevant/1`; } diff --git a/packages/ot-utils/src/variant.ts b/packages/ot-utils/src/variant.ts index 060f81ce6..10f299ebd 100644 --- a/packages/ot-utils/src/variant.ts +++ b/packages/ot-utils/src/variant.ts @@ -3,7 +3,8 @@ export function processVariantId(id: string, referenceAllele: string, alternateA if (idParts[0] === "OTVAR") { idParts.shift(); } - let isHashed, stem; + let isHashed: boolean; + let stem: string; if (idParts.at(-2) === referenceAllele && idParts.at(-1) === alternateAllele) { isHashed = false; stem = idParts.slice(0, -2).join("_"); From 101e0369c3c0a32d7338a49d3b9f16d1393ca8bc Mon Sep 17 00:00:00 2001 From: Graham McNeill Date: Mon, 27 Oct 2025 15:21:14 +0000 Subject: [PATCH 10/10] [ot-constants]: lint on (#826) --- biome.json | 3 +- .../scripts/generate-graphql-types.js | 38 +- packages/ot-constants/src/alphaFold.ts | 16 +- packages/ot-constants/src/index.ts | 48 +- .../ot-constants/src/partnerPreviewUtils.ts | 13 +- .../ot-constants/src/types/graphql-types.ts | 19 +- yarn.lock | 692 +++++++++--------- 7 files changed, 425 insertions(+), 404 deletions(-) diff --git a/biome.json b/biome.json index b1509b0e5..74cc96e06 100644 --- a/biome.json +++ b/biome.json @@ -32,7 +32,8 @@ "!**/packages/ui", "!**/packages/sections", "!**/packages/ot-config", - "!**/packages/ot-constants", + "**/packages/ot-constants", + "!**/packages/ot-constants/src/types", "!**/packages/ot-utils" ] }, diff --git a/packages/ot-constants/scripts/generate-graphql-types.js b/packages/ot-constants/scripts/generate-graphql-types.js index 7434c5b7e..da653f152 100644 --- a/packages/ot-constants/scripts/generate-graphql-types.js +++ b/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"); diff --git a/packages/ot-constants/src/alphaFold.ts b/packages/ot-constants/src/alphaFold.ts index 65b01c6b6..539339ce4 100644 --- a/packages/ot-constants/src/alphaFold.ts +++ b/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" }, -}; \ No newline at end of file +}; diff --git a/packages/ot-constants/src/index.ts b/packages/ot-constants/src/index.ts index 638d9bb76..e6191cc0e 100644 --- a/packages/ot-constants/src/index.ts +++ b/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(); @@ -303,7 +303,9 @@ 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; }; @@ -311,7 +313,7 @@ export const getStudyTypeDisplay = (studyType: string | null | undefined): strin 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"; \ No newline at end of file +export * from "./partnerPreviewUtils"; +export * from "./searchSuggestions"; +export * from "./types/graphql-types"; +export * from "./types/response"; +export * from "./variant"; diff --git a/packages/ot-constants/src/partnerPreviewUtils.ts b/packages/ot-constants/src/partnerPreviewUtils.ts index f4ea08edb..5945bab38 100644 --- a/packages/ot-constants/src/partnerPreviewUtils.ts +++ b/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); diff --git a/packages/ot-constants/src/types/graphql-types.ts b/packages/ot-constants/src/types/graphql-types.ts index b927d9b89..f2e23f102 100644 --- a/packages/ot-constants/src/types/graphql-types.ts +++ b/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; - diff --git a/yarn.lock b/yarn.lock index 7711eb1b3..7cfcf633c 100644 --- a/yarn.lock +++ b/yarn.lock @@ -454,135 +454,135 @@ resolved 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