diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml new file mode 100644 index 00000000..dc931e81 --- /dev/null +++ b/.github/workflows/run-tests.yml @@ -0,0 +1,28 @@ +name: Run Tests + +on: + push: + branches: + - main + - 'release-*' + pull_request: + +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - uses: actions/setup-node@v4 + with: + node-version: 20 + cache: npm + + - run: npm ci + + - run: npm run test:unit:coverage + + - name: Upload coverage to Coveralls + uses: coverallsapp/github-action@v2 + with: + path-to-lcov: coverage/lcov.info diff --git a/package-lock.json b/package-lock.json index 1523cd68..bbc0b683 100644 --- a/package-lock.json +++ b/package-lock.json @@ -77,6 +77,7 @@ "@types/uuid": "^9.0.8", "@vitejs/plugin-basic-ssl": "^1.0.2", "@vitejs/plugin-vue": "^6.0.1", + "@vitest/coverage-v8": "2.1.9", "@vue/eslint-config-prettier": "^10.2.0", "@vue/eslint-config-typescript": "^14.6.0", "@vue/tsconfig": "^0.8.1", @@ -88,6 +89,9 @@ "vite": "^5.4.21", "vitest": "^2.1.9", "vue-tsc": "^3.0.7" + }, + "optionalDependencies": { + "@rollup/rollup-linux-x64-gnu": "4.46.3" } }, "node_modules/@aashutoshrathi/word-wrap": { @@ -98,6 +102,20 @@ "node": ">=0.10.0" } }, + "node_modules/@ampproject/remapping": { + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", + "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==", + "dev": true, + "license": "Apache-2.0", + "dependencies": { + "@jridgewell/gen-mapping": "^0.3.5", + "@jridgewell/trace-mapping": "^0.3.24" + }, + "engines": { + "node": ">=6.0.0" + } + }, "node_modules/@babel/helper-string-parser": { "version": "7.27.1", "license": "MIT", @@ -136,6 +154,13 @@ "node": ">=6.9.0" } }, + "node_modules/@bcoe/v8-coverage": { + "version": "0.2.3", + "resolved": "https://registry.npmjs.org/@bcoe/v8-coverage/-/v8-coverage-0.2.3.tgz", + 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Please update. Support for old versions may be purchased (at exorbitant rates) by contacting i@izs.me", + "dev": true, + "license": "ISC", + "dependencies": { + "foreground-child": "^3.1.0", + "jackspeak": "^3.1.2", + "minimatch": "^9.0.4", + "minipass": "^7.1.2", + "package-json-from-dist": "^1.0.0", + "path-scurry": "^1.11.1" + }, + "bin": { + "glob": "dist/esm/bin.mjs" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, "node_modules/glob-parent": { "version": "6.0.2", "dev": true, @@ -4378,6 +4554,32 @@ "node": ">=10.13.0" } }, + "node_modules/glob/node_modules/brace-expansion": { + "version": "2.1.1", + "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.1.1.tgz", + "integrity": "sha512-WR1cURNjuvBLMZBMbqM0UoE+WAfdUcEV1ccD8PVBVOI+Z3ND4+SZbN8RsfT2bMuG1qwz5RFvPukSZm5fF2D5eA==", + "dev": true, + "license": "MIT", + "dependencies": { + "balanced-match": "^1.0.0" + } + }, + "node_modules/glob/node_modules/minimatch": { + "version": "9.0.9", + "resolved": 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"license": "MIT", diff --git a/package.json b/package.json index efea3258..1cc6f90d 100644 --- a/package.json +++ b/package.json @@ -8,7 +8,8 @@ "dev": "./scripts/build-docs.sh && vite --mode=${MODE=dev}", "docs": "mkdocs serve -f docs/mkdocs.yml", "preview": "./scripts/build-docs.sh && vite build --mode=${MODE=live} --watch & vite preview --mode=${MODE=live}", - "test:unit": "vitest run" + "test:unit": "vitest run", + "test:unit:coverage": "vitest run --coverage" }, "dependencies": { "@fontsource/exo-2": "^5.2.8", @@ -80,6 +81,7 @@ "@types/uuid": "^9.0.8", "@vitejs/plugin-basic-ssl": "^1.0.2", "@vitejs/plugin-vue": "^6.0.1", + "@vitest/coverage-v8": "2.1.9", "@vue/eslint-config-prettier": "^10.2.0", "@vue/eslint-config-typescript": "^14.6.0", "@vue/tsconfig": "^0.8.1", @@ -92,9 +94,12 @@ "vitest": "^2.1.9", "vue-tsc": "^3.0.7" }, + "optionalDependencies": { + "@rollup/rollup-linux-x64-gnu": "4.46.3" + }, "browserslist": [ "> 1%", "last 2 versions", "not dead" ] -} \ No newline at end of file +} diff --git a/src/assets/app.css b/src/assets/app.css index 2c646737..49b1e8b6 100644 --- a/src/assets/app.css +++ b/src/assets/app.css @@ -121,12 +121,15 @@ --color-ga4gh-light: #e3f0f9; /* ── Measurement Types (variant screen) ────────────────────── */ - --color-nucleotide: var(--color-published); - --color-nucleotide-light: var(--color-published-light); - --color-nucleotide-border: var(--color-light-green); - --color-protein: var(--color-help); - --color-protein-light: var(--color-help-light); - --color-protein-border: var(--color-help-border); + --color-nucleotide: #2e7d32; + --color-nucleotide-light: #e8f5e9; + --color-nucleotide-border: #c8e4c6; + --color-protein: #7e5daf; + --color-protein-light: #f1ecf8; + --color-protein-border: #b5a0d0; + --color-synonymous-nucleotide: #8a5700; + --color-synonymous-nucleotide-light: #fef8e1; + --color-synonymous-nucleotide-border: #f5c97a; /* ── Role Badges ───────────────────────────────────────────── */ --color-role-admin: #1a56a0; diff --git a/src/assets/mave-registry-logo.png b/src/assets/mave-registry-logo.png new file mode 100644 index 00000000..b4c33b8a Binary files /dev/null and b/src/assets/mave-registry-logo.png differ diff --git a/src/components/screens/AboutView.vue b/src/components/screens/AboutView.vue index 2d8c7a01..0612ca29 100644 --- a/src/components/screens/AboutView.vue +++ b/src/components/screens/AboutView.vue @@ -60,9 +60,18 @@ class="h-7 object-contain object-left" :src="partner.logoSrc" /> -
{{ partner.name }}
-
{{ partner.name }}
+
{{ partner.name }}
{{ partner.description }}
+ + Visit site → + @@ -83,7 +92,7 @@
+ +
+

Clinical application

+

+ The Alliance for Variant Effects (AVE) maintains a + Clinical Application of Variant Effect Data + page covering how MAVE functional scores can be used in clinical genomics and for variant interpretation. +

+
+

Contact us

@@ -89,7 +106,7 @@ import AccordionContent from 'primevue/accordioncontent' import MvLayout from '@/components/layout/MvLayout.vue' import MvPageHeader from '@/components/layout/MvPageHeader.vue' -import {ZULIP_CHAT, GITHUB_UI_ISSUES} from '@/lib/links' +import {ZULIP_CHAT, GITHUB_UI_ISSUES, AVE_CLINICAL_APPLICATION} from '@/lib/links' const CHANNELS = [ { @@ -174,7 +191,8 @@ export default defineComponent({ channels: CHANNELS, faqs: FAQS, ZULIP_CHAT, - GITHUB_UI_ISSUES + GITHUB_UI_ISSUES, + AVE_CLINICAL_APPLICATION } } }) diff --git a/src/components/screens/HomeScreen.vue b/src/components/screens/HomeScreen.vue index 3620f7dc..535dac8c 100644 --- a/src/components/screens/HomeScreen.vue +++ b/src/components/screens/HomeScreen.vue @@ -81,10 +81,12 @@

Find a variant with functional data via HGVS, - ClinGen CAId, - ClinVar ID, - dbSNP rsid, or - VRS digest. + VRS digest, and more. +
+ No variant identifier? + Try guided search →

diff --git a/src/components/screens/SearchVariantsScreen.vue b/src/components/screens/SearchVariantsScreen.vue index 84882b07..07b2eaa7 100644 --- a/src/components/screens/SearchVariantsScreen.vue +++ b/src/components/screens/SearchVariantsScreen.vue @@ -12,6 +12,17 @@ calibrations, provide intuitive visualizations, and export structured evidence compatible with ACMG/AMP variant classification guidelines.

+

+ Learn more about + evaluating MAVE functional assays and integrating them into clinical practice. +

@@ -132,6 +143,7 @@ v-model="inputGene" class="w-full !rounded-none !border-none !bg-transparent !pt-4 !pb-2 !shadow-none" placeholder="e.g. BRCA1" + style="text-transform: uppercase" />
@@ -675,6 +687,7 @@ import {components} from '@/schema/openapi' import {getScoreSetShortName} from '@/lib/score-sets' import {clinVarHgvsSearchStringRegex, hgvsSearchStringRegex} from '@/lib/mave-hgvs' import {SEARCH_COLORS} from '@/data/search' +import {AVE_CLINICAL_APPLICATION} from '@/lib/links' import { HOW_IT_WORKS_STEPS, MAVEMD_COLLECTION_URN, @@ -714,7 +727,7 @@ export default defineComponent({ const router = useRouter() const toast = useToast() const {getEntity} = useEntityCache() - return {route, router, toast, getEntity, getScoreSetShortName, scoreSetUrnFromVariantUrn} + return {route, router, toast, getEntity, getScoreSetShortName, scoreSetUrnFromVariantUrn, AVE_CLINICAL_APPLICATION} }, data: function () { @@ -849,7 +862,14 @@ export default defineComponent({ this.inputVariantType = typeof newVal === 'string' ? newVal : '' } }, - inputGene() { + inputGene(newVal) { + const normalized = newVal?.toUpperCase() ?? null + if (newVal && newVal !== normalized) { + // Setting inputGene re-triggers this watcher with the normalized value, return + // early to avoid syncing query params twice. + this.inputGene = normalized + return + } this.syncGuidedQueryParams() }, inputVariantType(newVal, oldVal) { @@ -992,6 +1012,7 @@ export default defineComponent({ delete query.search delete query.searchType query.mode = 'guided' + this.searchType = 'hgvs' } else { delete query.gene delete query.variantType @@ -1027,8 +1048,8 @@ export default defineComponent({ this.loading = false await this.searchVariants() }, - fetchDefaultSearchResults: async function (searchString: string, maneStatus: string | null = null) { - const searchType = this.searchType + fetchDefaultSearchResults: async function (searchString: string, maneStatus: string | null = null, forcedSearchType?: string) { + const searchType = forcedSearchType ?? this.searchType let searchStr = searchString.trim() try { @@ -1288,7 +1309,7 @@ export default defineComponent({ } for (const hgvsString of hgvsStrings) { - await this.fetchDefaultSearchResults(hgvsString.hgvsString, hgvsString.maneStatus) + await this.fetchDefaultSearchResults(hgvsString.hgvsString, hgvsString.maneStatus, 'hgvs') } } catch (error: unknown) { this.alleles = [] diff --git a/src/components/screens/VariantScreen.vue b/src/components/screens/VariantScreen.vue index 7960af29..14239880 100644 --- a/src/components/screens/VariantScreen.vue +++ b/src/components/screens/VariantScreen.vue @@ -75,6 +75,15 @@ :count="lookup.proteinCount.value" label="Protein level" /> +
diff --git a/src/composables/use-variant-lookup.ts b/src/composables/use-variant-lookup.ts index 6d8ece67..f7b6bd57 100644 --- a/src/composables/use-variant-lookup.ts +++ b/src/composables/use-variant-lookup.ts @@ -45,8 +45,10 @@ export interface UseVariantLookupReturn { // Filters showNucleotide: Ref showProtein: Ref + showAssociatedNucleotide: Ref nucleotideCount: ComputedRef proteinCount: ComputedRef + associatedNucleotideCount: ComputedRef filteredVariants: ComputedRef // Selection @@ -115,19 +117,22 @@ export function useVariantLookup( const selectedVariantUrn = ref(null) const showNucleotide = ref(true) const showProtein = ref(true) + const showAssociatedNucleotide = ref(true) const variantDetailCache = ref>({}) const scoresCache = shallowRef>({}) const selectedCalibration = ref(null) // ── Filters ─────────────────────────────────────────────── - const nucleotideCount = computed( - () => variants.value.filter((v) => v.type === 'nucleotide' || v.type === 'associatedNucleotide').length - ) + const nucleotideCount = computed(() => variants.value.filter((v) => v.type === 'nucleotide').length) const proteinCount = computed(() => variants.value.filter((v) => v.type === 'protein').length) + const associatedNucleotideCount = computed( + () => variants.value.filter((v) => v.type === 'associatedNucleotide').length + ) const filteredVariants = computed(() => variants.value.filter((v) => { - if (v.type === 'nucleotide' || v.type === 'associatedNucleotide') return showNucleotide.value + if (v.type === 'nucleotide') return showNucleotide.value if (v.type === 'protein') return showProtein.value + if (v.type === 'associatedNucleotide') return showAssociatedNucleotide.value return true }) ) @@ -383,8 +388,10 @@ export function useVariantLookup( fetchVariants, showNucleotide, showProtein, + showAssociatedNucleotide, nucleotideCount, proteinCount, + associatedNucleotideCount, filteredVariants, selectedVariantUrn, selectVariant, diff --git a/src/lib/links.ts b/src/lib/links.ts index 84d433cc..26a79c09 100644 --- a/src/lib/links.ts +++ b/src/lib/links.ts @@ -12,6 +12,14 @@ export const GITHUB_API_ISSUES = `${GITHUB_API_URL}/issues` export const MAVEDB_PRODUCTION = 'https://mavedb.org' +export const AVE_CLINICAL_APPLICATION = 'https://www.varianteffect.org/clinical-application/' +export const MAVE_REGISTRY = 'https://registry.varianteffect.org/' + +export const IGVF_URL = 'https://www.igvf.org/' +export const CLINGEN_URL = 'https://clinicalgenome.org/' +export const GA4GH_URL = 'https://www.ga4gh.org/' +export const CLINVAR_URL = 'https://www.ncbi.nlm.nih.gov/clinvar/' + /** * Build a Zulip link to report a dataset issue for a specific URN. */ diff --git a/src/lib/measurement-types.ts b/src/lib/measurement-types.ts index 4e532d16..2d41bf07 100644 --- a/src/lib/measurement-types.ts +++ b/src/lib/measurement-types.ts @@ -3,11 +3,11 @@ export type MeasurementType = 'nucleotide' | 'protein' | 'associatedNucleotide' export const MEASUREMENT_TYPE_LABELS: Record = { nucleotide: {full: 'Nucleotide level', short: 'Nucleotide'}, protein: {full: 'Protein level', short: 'Protein'}, - associatedNucleotide: {full: 'Associated nucleotide', short: 'Assoc. nucleotide'} + associatedNucleotide: {full: 'Synonymous nucleotide', short: 'Synonymous'} } export const MEASUREMENT_TYPE_CLASSES: Record = { nucleotide: 'bg-nucleotide-light text-nucleotide', protein: 'bg-protein-light text-protein', - associatedNucleotide: 'bg-nucleotide-light text-nucleotide' + associatedNucleotide: 'bg-synonymous-nucleotide-light text-synonymous-nucleotide' } diff --git a/src/main.js b/src/main.js index 3635d84f..d22af0d1 100644 --- a/src/main.js +++ b/src/main.js @@ -32,16 +32,28 @@ initializeOrcidAuthentication() // Provide a smooth migration path from vue-router's hash navigation mode to its history navigation mode. If the user // arrived via an old bookmark that uses the URL fragment (hash) for routing, redirect to the corresponding current URL. router.beforeEach((to) => { - const redirectPathAndQuery = to.hash.split('#')[1] - if (redirectPathAndQuery) { - const [redirectPath, redirectQueryStr] = redirectPathAndQuery.split('?', 2) - const redirectQuery = redirectQueryStr ? Object.fromEntries(new URLSearchParams(redirectQueryStr)) : undefined - - // Attempt to resolve the path using vue-router. If the router finds a matching named route, then the path - // represents a valid screen, and we should redirect the user to that screen's current URL. + const regex = /^\/score-sets\/([^#]+)#(\d+)$/ + const match = to.fullPath.match(regex) + if (match) { + const urnBeforeHash = match[1] + const fullUrn = `${urnBeforeHash}#${match[2]}` + const redirectPath = `/score-sets/${urnBeforeHash}` + const redirectQuery = {variant: fullUrn} if (router.resolve({path: redirectPath})?.name) { return {path: redirectPath, query: redirectQuery} } + } else if (to.fullPath.startsWith('/#/')) { + const redirectPathAndQuery = to.fullPath.replace('/#/', '/') + if (redirectPathAndQuery) { + const [redirectPath, redirectQueryStr] = redirectPathAndQuery.split('?', 2) + const redirectQuery = redirectQueryStr ? Object.fromEntries(new URLSearchParams(redirectQueryStr)) : undefined + + // Attempt to resolve the path using vue-router. If the router finds a matching named route, then the path + // represents a valid screen, and we should redirect the user to that screen's current URL. + if (router.resolve({path: redirectPath})?.name) { + return {path: redirectPath, query: redirectQuery} + } + } } }) diff --git a/vitest.config.ts b/vitest.config.ts index a09b0880..8fb3128f 100644 --- a/vitest.config.ts +++ b/vitest.config.ts @@ -9,6 +9,13 @@ export default defineConfig({ } }, test: { - environment: 'node' + environment: 'node', + coverage: { + all: true, + provider: 'v8', + reporter: ['text', 'lcov'], + include: ['src/**/*.{js,ts}'], + exclude: ['src/**/*.d.ts', 'src/**/*.test.{js,ts}'] + } } })