diff --git a/frontend/.eslintrc.cjs b/frontend/.eslintrc.cjs index 6f40582d..e426be59 100644 --- a/frontend/.eslintrc.cjs +++ b/frontend/.eslintrc.cjs @@ -4,11 +4,14 @@ require('@rushstack/eslint-patch/modern-module-resolution') module.exports = { root: true, 'extends': [ - 'plugin:vue/vue3-essential', - 'eslint:recommended', + '@vue/typescript/recommended', + 'plugin:vue/vue3-recommended', '@vue/eslint-config-typescript', '@vue/eslint-config-prettier/skip-formatting' ], + rules: { + "@typescript-eslint/no-explicit-any": "off", + }, parserOptions: { ecmaVersion: 'latest' } diff --git a/frontend/Makefile b/frontend/Makefile index b967d9c3..b0720b1a 100644 --- a/frontend/Makefile +++ b/frontend/Makefile @@ -44,3 +44,7 @@ ci: \ .PHONY: serve serve: MODE=development npm run dev + +.PHONY: serve-public +serve-public: + MODE=development npm run dev-public diff --git a/frontend/package-lock.json b/frontend/package-lock.json index f60ecf8e..eb364dcd 100644 --- a/frontend/package-lock.json +++ b/frontend/package-lock.json @@ -10,16 +10,18 @@ "dependencies": { "@mdi/font": "^7.2.96", "@reactgular/chunks": "^1.0.1", + "@vue/eslint-config-standard": "^8.0.1", "igv": "^2.15.11", "lodash": "^4.17.21", "pinia": "^2.1.6", + "title-case": "^4.1.2", "vega": "^5.25.0", "vega-embed": "^6.22.2", "vue": "^3.3.4", "vue-matomo": "^4.2.0", "vue-router": "^4.2.5", "vue3-easy-data-table": "^1.5.47", - "vuetify": "^3.3.19" + "vuetify": "^3.4.0" }, "devDependencies": { "@pinia/testing": "^0.1.3", @@ -58,7 +60,6 @@ "version": "1.2.6", "resolved": "https://registry.npmjs.org/@aashutoshrathi/word-wrap/-/word-wrap-1.2.6.tgz", "integrity": "sha512-1Yjs2SvM8TflER/OD3cOjhWWOZb58A2t7wpE2S9XfBYTiIl+XFhQG2bjy4Pu1I+EAlCNUzRDYDdFwFYUKvXcIA==", - "dev": true, "engines": { "node": ">=0.10.0" } @@ -77,12 +78,12 @@ } }, "node_modules/@babel/code-frame": { - "version": "7.22.13", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.22.13.tgz", - "integrity": 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"node_modules/@babel/core/node_modules/@babel/traverse": { + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/traverse/-/traverse-7.23.4.tgz", + "integrity": "sha512-IYM8wSUwunWTB6tFC2dkKZhxbIjHoWemdK+3f8/wq8aKhbUscxD5MX72ubd90fxvFknaLPeGw5ycU84V1obHJg==", + "dev": true, + "dependencies": { + "@babel/code-frame": "^7.23.4", + "@babel/generator": "^7.23.4", + "@babel/helper-environment-visitor": "^7.22.20", + "@babel/helper-function-name": "^7.23.0", + "@babel/helper-hoist-variables": "^7.22.5", + "@babel/helper-split-export-declaration": "^7.22.6", + "@babel/parser": "^7.23.4", + "@babel/types": "^7.23.4", + "debug": "^4.1.0", + "globals": "^11.1.0" + }, + "engines": { + "node": ">=6.9.0" + } + }, + "node_modules/@babel/core/node_modules/@babel/types": { + "version": "7.23.4", + "resolved": "https://registry.npmjs.org/@babel/types/-/types-7.23.4.tgz", + "integrity": "sha512-7uIFwVYpoplT5jp/kVv6EF93VaJ8H+Yn5IczYiaAi98ajzjfoZfslet/e0sLh+wVBjb2qqIut1b0S26VSafsSQ==", + "dev": true, + "dependencies": { + "@babel/helper-string-parser": "^7.23.4", + "@babel/helper-validator-identifier": "^7.22.20", + "to-fast-properties": "^2.0.0" + }, + "engines": { + "node": ">=6.9.0" + } + }, + "node_modules/@babel/generator": { + "version": "7.17.7", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.17.7.tgz", + "integrity": "sha512-oLcVCTeIFadUoArDTwpluncplrYBmTCCZZgXCbgNGvOBBiSDDK3eWO4b/+eOTli5tKv1lg+a5/NAXg+nTcei1w==", + "dev": true, + "dependencies": { + "@babel/types": "^7.17.0", + "jsesc": "^2.5.1", + "source-map": "^0.5.0" + }, + "engines": { + "node": ">=6.9.0" + } + }, "node_modules/@babel/helper-annotate-as-pure": { "version": "7.22.5", "resolved": "https://registry.npmjs.org/@babel/helper-annotate-as-pure/-/helper-annotate-as-pure-7.22.5.tgz", @@ -155,6 +205,20 @@ "node": ">=6.9.0" } }, + "node_modules/@babel/helper-annotate-as-pure/node_modules/@babel/types": { + "version": "7.23.4", + "resolved": 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"node_modules/wrap-ansi/node_modules/ansi-regex": { "version": "6.0.1", "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-6.0.1.tgz", @@ -12212,29 +12941,6 @@ "url": "https://github.com/chalk/ansi-styles?sponsor=1" } }, - "node_modules/wrap-ansi/node_modules/emoji-regex": { - "version": "9.2.2", - "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-9.2.2.tgz", - "integrity": "sha512-L18DaJsXSUk2+42pv8mLs5jJT2hqFkFE4j21wOmgbUqsZ2hL72NsUU785g9RXgo3s0ZNgVl42TiHp3ZtOv/Vyg==", - "dev": true - }, - "node_modules/wrap-ansi/node_modules/string-width": { - "version": "5.1.2", - "resolved": "https://registry.npmjs.org/string-width/-/string-width-5.1.2.tgz", - "integrity": "sha512-HnLOCR3vjcY8beoNLtcjZ5/nxn2afmME6lhrDrebokqMap+XbeW8n9TXpPDOqdGK5qcI3oT0GKTW6wC7EMiVqA==", - "dev": true, - "dependencies": { - "eastasianwidth": "^0.2.0", - "emoji-regex": "^9.2.2", - "strip-ansi": "^7.0.1" - }, - "engines": { - "node": ">=12" - }, - "funding": { - "url": "https://github.com/sponsors/sindresorhus" - } - }, "node_modules/wrap-ansi/node_modules/strip-ansi": { "version": "7.1.0", "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz", @@ -12253,8 +12959,7 @@ "node_modules/wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", - "dev": true + "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==" }, "node_modules/write-file-atomic": { "version": "3.0.3", @@ -12268,6 +12973,12 @@ "typedarray-to-buffer": "^3.1.5" } }, + "node_modules/write-file-atomic/node_modules/signal-exit": { + "version": "3.0.7", + "resolved": "https://registry.npmjs.org/signal-exit/-/signal-exit-3.0.7.tgz", + "integrity": "sha512-wnD2ZE+l+SPC/uoS0vXeE9L1+0wuaMqKlfz9AMUo38JsyLSBWSFcHR1Rri62LZc12vLr1gb3jl7iwQhgwpAbGQ==", + "dev": true + }, "node_modules/ws": { "version": "8.14.2", "resolved": "https://registry.npmjs.org/ws/-/ws-8.14.2.tgz", @@ -12305,7 +13016,6 @@ "version": "4.0.0", "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz", "integrity": "sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==", - "dev": true, "engines": { "node": ">=12" } @@ -12358,11 +13068,30 @@ "node": ">=12" } }, + "node_modules/yargs/node_modules/emoji-regex": { + "version": "8.0.0", + "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", + "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==", + "peer": true + }, + "node_modules/yargs/node_modules/string-width": { + "version": "4.2.3", + "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz", + "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==", + "peer": true, + "dependencies": { + "emoji-regex": "^8.0.0", + "is-fullwidth-code-point": "^3.0.0", + "strip-ansi": "^6.0.1" + }, + "engines": { + "node": ">=8" + } + }, "node_modules/yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", - "dev": true, "engines": { "node": ">=10" }, diff --git a/frontend/package.json b/frontend/package.json index 3081fb6a..4dfe70fa 100644 --- a/frontend/package.json +++ b/frontend/package.json @@ -4,6 +4,7 @@ "private": true, "scripts": { "dev": "vite --port 8081", + "dev-public": "vite --host 0.0.0.0 --port 8081", "build": "run-p type-check build-only", "preview": "vite preview", "test:unit": "vitest --coverage", @@ -16,16 +17,18 @@ "dependencies": { "@mdi/font": "^7.2.96", "@reactgular/chunks": "^1.0.1", + "@vue/eslint-config-standard": "^8.0.1", "igv": "^2.15.11", "lodash": "^4.17.21", "pinia": "^2.1.6", + "title-case": "^4.1.2", "vega": "^5.25.0", "vega-embed": "^6.22.2", "vue": "^3.3.4", "vue-matomo": "^4.2.0", "vue-router": "^4.2.5", "vue3-easy-data-table": "^1.5.47", - "vuetify": "^3.3.19" + "vuetify": "^3.4.0" }, "devDependencies": { "@pinia/testing": "^0.1.3", diff --git a/frontend/src/api/dotty.ts b/frontend/src/api/dotty.ts index b822030f..7ce504db 100644 --- a/frontend/src/api/dotty.ts +++ b/frontend/src/api/dotty.ts @@ -33,7 +33,7 @@ export class DottyClient { this.csrfToken = csrfToken ?? null } - async toSpdi(q: String, assembly: 'GRCh37' | 'GRCh38' = 'GRCh38'): Promise { + async toSpdi(q: string, assembly: 'GRCh37' | 'GRCh38' = 'GRCh38'): Promise { const url = `${API_INTERNAL_BASE_PREFIX_DOTTY}/api/v1/to-spdi?q=${q}&assembly=${assembly}` const response = await fetch(url, { method: 'GET' diff --git a/frontend/src/api/viguno.ts b/frontend/src/api/viguno.ts index 2fc64fdb..b23c1b82 100644 --- a/frontend/src/api/viguno.ts +++ b/frontend/src/api/viguno.ts @@ -2,6 +2,22 @@ import { API_INTERNAL_BASE_PREFIX_VIGUNO } from '@/api/common' const API_BASE_URL = `${API_INTERNAL_BASE_PREFIX_VIGUNO}/` +/** HPO term as returned by the API */ +export interface HpoTerm { + /** Term ID with `HP:` prefix. */ + term_id: string + /** Human-readable term name. */ + name: string +} + +/** Gene as returned by the API. */ +export interface Gene { + gene_ncbi_id: number + gene_symbol: string + hgnc_id: string + hpo_terms?: HpoTerm[] +} + export class VigunoClient { private apiBaseUrl: string private csrfToken: string | null @@ -66,4 +82,31 @@ export class VigunoClient { return await response.json() } + + /** + * Retrieves HPO terms associated with a gene. + * + * @param hgncId + * @returns List of HPO terms associated with the gene. + */ + async fetchHpoTermsForHgncId(hgncId: string): Promise { + const url = `${this.apiBaseUrl}hpo/genes?gene_id=${hgncId}&hpo_terms=true` + const response = await fetch(url, { + method: 'GET' + }) + + if (!response.ok) { + const errorBody = await response.json() + throw new Error(errorBody.msg || response.statusText) + } + + const res = await response.json() + if (!res.result?.length || res.result.length === 0) { + return [] + } + return (res.result[0].hpo_terms ?? []).map((term: HpoTerm) => ({ + term_id: term.term_id, + name: term.name + })) + } } diff --git a/frontend/src/components/AcmgCriteriaCard.vue b/frontend/src/components/AcmgCriteriaCard.vue index cdeca892..42daff07 100644 --- a/frontend/src/components/AcmgCriteriaCard.vue +++ b/frontend/src/components/AcmgCriteriaCard.vue @@ -63,20 +63,19 @@ const switchCriteria = (criteria: AcmgCriteria, presence: Presence) => { :color="findSwitchColor()" :label="props.criteria" :model-value="props.criteriaState.presence === Presence.Present" - @update:model-value="switchCriteria(props.criteria, props.criteriaState.presence)" hide-details="auto" density="compact" class="switch" + @update:model-value="switchCriteria(props.criteria, props.criteriaState.presence)" /> - diff --git a/frontend/src/components/BookmarkButton.vue b/frontend/src/components/BookmarkButton.vue index 8898711f..d5c2238c 100644 --- a/frontend/src/components/BookmarkButton.vue +++ b/frontend/src/components/BookmarkButton.vue @@ -60,9 +60,9 @@ const toggleBookmark = async () => {