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feat: integration of strucvars from REEV (#1300) #1379

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merged 1 commit into from
Feb 23, 2024
Merged

feat: integration of strucvars from REEV (#1300) #1379

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25 changes: 0 additions & 25 deletions cases/vueapp/src/components/CaseDetail/Content.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@ import PaneAnnotations from '@cases/components/CaseDetail/PaneAnnotations.vue'
import { useRouter } from 'vue-router'
import { useCaseDetailsStore } from '@cases/stores/caseDetails'
import { useCaseQcStore } from '@cases_qc/stores/caseQc'
import GenomeBrowser from '@svs/components/GenomeBrowser.vue'

const router = useRouter()

Expand Down Expand Up @@ -38,7 +37,6 @@ const Tabs = Object.freeze({
overview: 'overview',
qc: 'qc',
annotation: 'annotation',
browser: 'browser',
})

const caseDetailsStore = useCaseDetailsStore()
Expand Down Expand Up @@ -113,18 +111,6 @@ const updateCurrentTab = (newValue) => {
</span>
</a>
</li>
<li class="nav-item">
<a
class="nav-link"
:class="{ active: props.currentTab === Tabs.browser }"
role="button"
@click="updateCurrentTab(Tabs.browser)"
>
<i-mdi-safety-goggles />

Browser
</a>
</li>
</ul>
<div id="cases-content" class="tab-content flex-grow-1 d-flex flex-column">
<div
Expand Down Expand Up @@ -166,17 +152,6 @@ const updateCurrentTab = (newValue) => {
<template #fallback> Loading ... </template>
</Suspense>
</div>
<div
v-if="props.currentTab === Tabs.browser"
id="case-list"
class="border border-top-0 tab-pane fade show active flex-grow-1 d-flex flex-column"
role="tabpanel"
>
<GenomeBrowser
:case-uuid="caseDetailsStore.caseObj?.sodar_uuid"
:genome="caseDetailsStore.caseObj?.release"
/>
</div>
</div>
</div>
</template>
Expand Down
2 changes: 1 addition & 1 deletion cases/vueapp/src/components/CaseDetail/PaneAnnotations.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@ const showSmallVariantDetails = async (event) => {

const showStructuralVariantDetails = async (event) => {
router.push({
name: 'sv-details',
name: 'strucvar-details',
params: {
row: event.svresultrow,
selectedSection: event.selectedSection ?? null,
Expand Down
2 changes: 1 addition & 1 deletion cases/vueapp/src/plugins/reevFrontend.ts
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Expand Up @@ -4,7 +4,7 @@ export function setupBackendUrls() {
urlConfig.baseUrlAnnonars = '/proxy/varfish/annonars'
urlConfig.baseUrlMehari = '/proxy/varfish/mehari'
urlConfig.baseUrlViguno = '/proxy/varfish/viguno'
urlConfig.baseUrlNginx = '/proxy/varfish/nginx'
urlConfig.baseUrlNginx = '/proxy/varfish/nginx/'
urlConfig.baseUrlPubtator = '/proxy/remote/pubtator3-api'
urlConfig.baseUrlVariantValidator = '/proxy/variantvalidator'

Expand Down
12 changes: 6 additions & 6 deletions cases/vueapp/src/router/index.ts
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
import CaseDetailApp from '@cases/components/CaseDetailApp.vue'
import CaseListApp from '@cases/components/CaseListApp.vue'
import SvDetails from '@svs/components/SvDetails.vue'
import StrucvarDetails from '@svs/views/StrucvarDetails/StrucvarDetails.vue'
import SvFilterApp from '@svs/components/SvFilterApp.vue'
import { useHistoryStore } from '@varfish/stores/history'
import FilterApp from '@variants/components/FilterApp.vue'
Expand Down Expand Up @@ -110,12 +110,12 @@ const routes: RouteRecordRaw[] = [
}),
},
{
name: 'sv-details',
path: '/svs/details/:row/:selectedSection?',
component: SvDetails,
name: 'strucvar-details',
path: '/strucvar/details/:row/:selectedSection?',
component: StrucvarDetails,
props: (route: RouteLocationNormalized) => ({
resultRowUuid: route.params.row,
selectedSection: route.params.selectedSection || 'genes',
selectedSection: route.params.selectedSection || 'top',
}),
},
]
Expand All @@ -135,7 +135,7 @@ export const router = createRouter({
savedPosition: null | _ScrollPositionNormalized,
) {
if (
['seqvar-details', 'sv-details'].includes(String(to.name)) &&
['seqvar-details', 'strucvar-details'].includes(String(to.name)) &&
to.params.selectedSection
) {
const res = { el: `#${to.params.selectedSection}` }
Expand Down
44 changes: 5 additions & 39 deletions cases/vueapp/tests/unit/cases/CaseDetail/Content.spec.js
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,7 @@ describe('CaseDetailContent.vue', () => {
expect(wrapper.html()).matches(/<pane-case-stub/)
expect(wrapper.html()).not.matches(/<pane-qc-stub/)
expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
expect(wrapper.html()).not.matches(/<genome-browser-stub/)
expect(wrapper.findAll('a.nav-link').length).toBe(4)
expect(wrapper.findAll('a.nav-link').length).toBe(3)
})

test('test with some data', async () => {
Expand All @@ -45,8 +44,7 @@ describe('CaseDetailContent.vue', () => {
expect(wrapper.html()).matches(/<pane-case-stub/)
expect(wrapper.html()).not.matches(/<pane-qc-stub/)
expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
expect(wrapper.html()).not.matches(/<genome-browser-stub/)
expect(wrapper.findAll('a.nav-link').length).toBe(4)
expect(wrapper.findAll('a.nav-link').length).toBe(3)
})

test('test click quality control', async () => {
Expand All @@ -57,9 +55,8 @@ describe('CaseDetailContent.vue', () => {
expect(wrapper.html()).matches(/<pane-case-stub/)
expect(wrapper.html()).not.matches(/<pane-qc-stub/)
expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
expect(wrapper.html()).not.matches(/<genome-browser-stub/)

expect(wrapper.findAll('a.nav-link').length).toBe(4)
expect(wrapper.findAll('a.nav-link').length).toBe(3)
await wrapper.findAll('a.nav-link')[1].trigger('click')

expect(router.push).toHaveBeenCalledTimes(1)
Expand All @@ -73,7 +70,6 @@ describe('CaseDetailContent.vue', () => {
// expect(wrapper.html()).not.matches(/<pane-case-stub/)
// expect(wrapper.html()).matches(/<pane-qc-stub/)
// expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
// expect(wrapper.html()).not.matches(/<genome-browser-stub/)
})

test('test click quality control, then overview', async () => {
Expand All @@ -84,9 +80,8 @@ describe('CaseDetailContent.vue', () => {
expect(wrapper.html()).matches(/<pane-case-stub/)
expect(wrapper.html()).not.matches(/<pane-qc-stub/)
expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
expect(wrapper.html()).not.matches(/<genome-browser-stub/)

expect(wrapper.findAll('a.nav-link').length).toBe(4)
expect(wrapper.findAll('a.nav-link').length).toBe(3)
await wrapper.findAll('a.nav-link')[1].trigger('click')
await wrapper.findAll('a.nav-link')[0].trigger('click')

Expand All @@ -107,7 +102,6 @@ describe('CaseDetailContent.vue', () => {
expect(wrapper.html()).matches(/<pane-case-stub/)
expect(wrapper.html()).not.matches(/<pane-qc-stub/)
expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
expect(wrapper.html()).not.matches(/<genome-browser-stub/)
})

test('test click variant annotation', async () => {
Expand All @@ -120,7 +114,7 @@ describe('CaseDetailContent.vue', () => {
expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
expect(wrapper.html()).not.matches(/<genome-browser-stub/)

expect(wrapper.findAll('a.nav-link').length).toBe(4)
expect(wrapper.findAll('a.nav-link').length).toBe(3)
await wrapper.findAll('a.nav-link')[2].trigger('click')

expect(router.push).toHaveBeenCalledTimes(1)
Expand All @@ -134,33 +128,5 @@ describe('CaseDetailContent.vue', () => {
// expect(wrapper.html()).not.matches(/<pane-case-stub/)
// expect(wrapper.html()).not.matches(/<pane-qc-stub/)
// expect(wrapper.html()).matches(/<pane-annotations-stub/)
// expect(wrapper.html()).not.matches(/<genome-browser-stub/)
})

test('test click genome browser', async () => {
const wrapper = makeWrapper(CaseDetailContent, {
caseDetails: caseDetailsStoreData,
})

expect(wrapper.html()).matches(/<pane-case-stub/)
expect(wrapper.html()).not.matches(/<pane-qc-stub/)
expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
expect(wrapper.html()).not.matches(/<genome-browser-stub/)

expect(wrapper.findAll('a.nav-link').length).toBe(4)
await wrapper.findAll('a.nav-link')[3].trigger('click')

expect(router.push).toHaveBeenCalledTimes(1)
expect(router.push).toHaveBeenCalledWith({
name: 'case-detail-browser',
params: {
case: caseDetailsStoreData.caseObj.sodar_uuid,
},
})

// expect(wrapper.html()).not.matches(/<pane-case-stub/)
// expect(wrapper.html()).not.matches(/<pane-qc-stub/)
// expect(wrapper.html()).not.matches(/<pane-annotations-stub/)
// expect(wrapper.html()).matches(/<genome-browser-stub/)
})
})
154 changes: 0 additions & 154 deletions svs/vueapp/src/components/GenomeBrowser.tracks.js
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