diff --git a/cases/vueapp/src/common.js b/cases/vueapp/src/common.js
index 678297417..eb0673547 100644
--- a/cases/vueapp/src/common.js
+++ b/cases/vueapp/src/common.js
@@ -55,7 +55,7 @@ export const connectTopRowControls = () => {
)
}
const elem = $('#vueapp-filtration-complexity-mode')
- if (elem) {
+ if (elem && elem.val(newValue)) {
elem.val(newValue).change()
}
}
diff --git a/cases/vueapp/tests/unit/cases/CaseListPaneCases.spec.js b/cases/vueapp/tests/unit/cases/CaseListPaneCases.spec.js
index a9e22ba85..fe29cbda4 100644
--- a/cases/vueapp/tests/unit/cases/CaseListPaneCases.spec.js
+++ b/cases/vueapp/tests/unit/cases/CaseListPaneCases.spec.js
@@ -30,7 +30,7 @@ describe('CaseListPaneCases.vue', () => {
// Disable warnings
vi.spyOn(console, 'warn').mockImplementation(vi.fn())
// Set reproducible time
- vi.useFakeTimers('modern')
+ vi.useFakeTimers()
vi.setSystemTime(new Date(2020, 3, 1))
})
diff --git a/clinvar_export/vueapp/tests/unit/clinvarExport/SubmissionSetList.spec.js b/clinvar_export/vueapp/tests/unit/clinvarExport/SubmissionSetList.spec.js
index f6532d7e4..7151ca594 100644
--- a/clinvar_export/vueapp/tests/unit/clinvarExport/SubmissionSetList.spec.js
+++ b/clinvar_export/vueapp/tests/unit/clinvarExport/SubmissionSetList.spec.js
@@ -48,7 +48,7 @@ describe('SubmissionSetList.vue', () => {
// Disable warnings
vi.spyOn(console, 'warn').mockImplementation(vi.fn())
// Set reproducible time
- vi.useFakeTimers('modern')
+ vi.useFakeTimers()
vi.setSystemTime(new Date(2020, 3, 1))
// Mock out jquery dollar function for showing modals
global.$ = vi.fn()
diff --git a/clinvar_export/vueapp/tests/unit/clinvarExport/store.actions.spec.js b/clinvar_export/vueapp/tests/unit/clinvarExport/store.actions.spec.js
index 8302bc8c8..189d8a243 100644
--- a/clinvar_export/vueapp/tests/unit/clinvarExport/store.actions.spec.js
+++ b/clinvar_export/vueapp/tests/unit/clinvarExport/store.actions.spec.js
@@ -62,7 +62,7 @@ describe('actions', () => {
// Disable warnings
vi.spyOn(console, 'warn').mockImplementation(vi.fn())
// Set reproducible time
- vi.useFakeTimers('modern')
+ vi.useFakeTimers()
vi.setSystemTime(new Date(2020, 3, 1))
})
diff --git a/svs/vueapp/src/components/SvFilterResultsTable.vue b/svs/vueapp/src/components/SvFilterResultsTable.vue
index 9da0dc26c..e3ad17240 100644
--- a/svs/vueapp/src/components/SvFilterResultsTable.vue
+++ b/svs/vueapp/src/components/SvFilterResultsTable.vue
@@ -1,5 +1,5 @@
diff --git a/varfish/vueapp/src/varfish/components/VariantDetailsFlags.vue b/varfish/vueapp/src/varfish/components/VariantDetailsFlags.vue
index d11286f73..364c52a90 100644
--- a/varfish/vueapp/src/varfish/components/VariantDetailsFlags.vue
+++ b/varfish/vueapp/src/varfish/components/VariantDetailsFlags.vue
@@ -14,7 +14,7 @@ const props = defineProps({
/** Whether to show the overlay. */
const overlayShow = computed(
- () => (props.flagsStore?.serverInteractions ?? 0) > 0
+ () => (props.flagsStore?.serverInteractions ?? 0) > 0,
)
const flagsToSubmit = ref(copy({ ...props.flagsStore.initialFlagsTemplate }))
@@ -80,7 +80,7 @@ const resetFlags = () => {
const onSubmitFlags = async () => {
const flagsToSubmitEmpty = isEqual(
flagsToSubmit.value,
- props.flagsStore.emptyFlagsTemplate
+ props.flagsStore.emptyFlagsTemplate,
)
if (props.flagsStore.flags && flagsToSubmitEmpty) {
// IS not empty but SHOULD be empty, so delete the flags
diff --git a/varfish/vueapp/src/varfish/helpers.js b/varfish/vueapp/src/varfish/helpers.js
index efcb3f0dc..62963baec 100644
--- a/varfish/vueapp/src/varfish/helpers.js
+++ b/varfish/vueapp/src/varfish/helpers.js
@@ -26,7 +26,7 @@ export function bndInsOverlap(lhs, rhs, radius) {
start: lhs.start - radius,
end: lhs.start + radius,
},
- { chromosome: rhs.chromosome, start: rhs.start, end: rhs.start + 1 }
+ { chromosome: rhs.chromosome, start: rhs.start, end: rhs.start + 1 },
) > 0
)
}
@@ -35,7 +35,7 @@ export function reciprocalOverlap(lhs, rhs) {
const overlap = overlapLength(lhs, rhs)
return Math.min(
overlap / (rhs.end - rhs.start + 1),
- overlap / (lhs.end - lhs.start + 1)
+ overlap / (lhs.end - lhs.start + 1),
)
}
diff --git a/varfish/vueapp/src/varfish/more-utils.ts b/varfish/vueapp/src/varfish/more-utils.ts
index abe1cb647..a615094ed 100644
--- a/varfish/vueapp/src/varfish/more-utils.ts
+++ b/varfish/vueapp/src/varfish/more-utils.ts
@@ -10,7 +10,7 @@
export const roundIt = (
value: number,
digits: number = 2,
- label?: string
+ label?: string,
): string => {
if (!value) {
return `NaN`
diff --git a/variants/vueapp/src/components/VariantDetailsAcmgRating.stories.js b/variants/vueapp/src/components/VariantDetailsAcmgRating.stories.js
index 895a8b5aa..00b4f1ea6 100644
--- a/variants/vueapp/src/components/VariantDetailsAcmgRating.stories.js
+++ b/variants/vueapp/src/components/VariantDetailsAcmgRating.stories.js
@@ -4,7 +4,7 @@ import trioVariantsData from '@variantsTest/data/variants-trio.json'
import VariantDetailsAcmgRating from './VariantDetailsAcmgRating.vue'
export default {
- title: 'Variants / Small Variant Details Calls',
+ title: 'Variants / Small Variant Details ACMG',
component: VariantDetailsAcmgRating,
}
diff --git a/variants/vueapp/src/components/VariantDetailsExtraAnnos.stories.js b/variants/vueapp/src/components/VariantDetailsExtraAnnos.stories.js
deleted file mode 100644
index 8428d5e93..000000000
--- a/variants/vueapp/src/components/VariantDetailsExtraAnnos.stories.js
+++ /dev/null
@@ -1,24 +0,0 @@
-import VariantDetailsExtraAnnos from './VariantDetailsExtraAnnos.vue'
-
-export default {
- title: 'Variants / Small Variant Details Extra Annos',
- component: VariantDetailsExtraAnnos,
-}
-
-const Template = (args) => ({
- components: { VariantDetailsExtraAnnos },
- setup() {
- return { args }
- },
- template:
- '',
-})
-
-export const Example = Template.bind({})
-Example.args = {
- extraAnnos: {
- annotations: { anno1: 123, anno2: 456 },
- },
-}
diff --git a/variants/vueapp/src/components/VariantDetailsFreqsAutosomal.vue b/variants/vueapp/src/components/VariantDetailsFreqsAutosomal.vue
index 78bc2d300..b89553ed5 100644
--- a/variants/vueapp/src/components/VariantDetailsFreqsAutosomal.vue
+++ b/variants/vueapp/src/components/VariantDetailsFreqsAutosomal.vue
@@ -12,7 +12,11 @@ const props = defineProps<{
const FREQ_DIGITS = 5
const selAnnos = computed(() => {
- return props.varAnnos[props.dataset]
+ if (!props.varAnnos) {
+ return null
+ } else {
+ return props.varAnnos[props.dataset]
+ }
})
const noCohort = computed(() => {
diff --git a/variants/vueapp/tests/unit/components/FilterFormEffectPane.spec.js b/variants/vueapp/tests/unit/components/FilterFormEffectPane.spec.js
index 3d16c458e..a131313a3 100644
--- a/variants/vueapp/tests/unit/components/FilterFormEffectPane.spec.js
+++ b/variants/vueapp/tests/unit/components/FilterFormEffectPane.spec.js
@@ -122,7 +122,7 @@ describe('FilterFormEffectPane.vue', () => {
await input.setValue('123')
- expect(input.element.value).toBe(123)
+ expect(input.element.value).toBe("123")
})
test('effects detailed', async () => {
diff --git a/variants/vueapp/tests/unit/components/FilterFormFrequencyPane.spec.js b/variants/vueapp/tests/unit/components/FilterFormFrequencyPane.spec.js
index b957b18a8..353ac0d89 100644
--- a/variants/vueapp/tests/unit/components/FilterFormFrequencyPane.spec.js
+++ b/variants/vueapp/tests/unit/components/FilterFormFrequencyPane.spec.js
@@ -56,20 +56,20 @@ describe('FilterFormFrequencyPane.vue', () => {
expect(inputs[35].element.checked).toBeFalsy()
// Check homozygous count
- expect(inputs[1].element.value).toBe(0)
- expect(inputs[6].element.value).toBe(0)
- expect(inputs[11].element.value).toBe(0)
- expect(inputs[16].element.value).toBe(0)
+ expect(inputs[1].element.value).toBe("0")
+ expect(inputs[6].element.value).toBe("0")
+ expect(inputs[11].element.value).toBe("0")
+ expect(inputs[16].element.value).toBe("0")
expect(inputs[21].element.value).toBe('')
- expect(inputs[26].element.value).toBe(10)
- expect(inputs[31].element.value).toBe(200)
+ expect(inputs[26].element.value).toBe("10")
+ expect(inputs[31].element.value).toBe("200")
expect(inputs[36].element.value).toBe('')
// Check heterozygous count
- expect(inputs[2].element.value).toBe(4)
- expect(inputs[7].element.value).toBe(10)
- expect(inputs[12].element.value).toBe(20)
- expect(inputs[17].element.value).toBe(4)
+ expect(inputs[2].element.value).toBe("4")
+ expect(inputs[7].element.value).toBe("10")
+ expect(inputs[12].element.value).toBe("20")
+ expect(inputs[17].element.value).toBe("4")
expect(inputs[22].element.value).toBe('')
expect(inputs[27].element.disabled).toBeTruthy()
expect(inputs[32].element.value).toBe('')
@@ -86,13 +86,13 @@ describe('FilterFormFrequencyPane.vue', () => {
expect(inputs[38].element.disabled).toBeTruthy()
// Check frequency
- expect(inputs[4].element.value).toBe(0.002)
- expect(inputs[9].element.value).toBe(0.002)
- expect(inputs[14].element.value).toBe(0.002)
- expect(inputs[19].element.value).toBe(0.002)
- expect(inputs[24].element.value).toBe(20)
- expect(inputs[29].element.value).toBe(0.01)
- expect(inputs[34].element.value).toBe(0.01)
+ expect(inputs[4].element.value).toBe("0.002")
+ expect(inputs[9].element.value).toBe("0.002")
+ expect(inputs[14].element.value).toBe("0.002")
+ expect(inputs[19].element.value).toBe("0.002")
+ expect(inputs[24].element.value).toBe("20")
+ expect(inputs[29].element.value).toBe("0.01")
+ expect(inputs[34].element.value).toBe("0.01")
expect(inputs[39].element.value).toBe('')
})
@@ -147,14 +147,14 @@ describe('FilterFormFrequencyPane.vue', () => {
await inputs[31].setValue(123)
await inputs[36].setValue(123)
- expect(inputs[1].element.value).toBe(123)
- expect(inputs[6].element.value).toBe(123)
- expect(inputs[11].element.value).toBe(123)
- expect(inputs[16].element.value).toBe(123)
- expect(inputs[21].element.value).toBe(123)
- expect(inputs[26].element.value).toBe(123)
- expect(inputs[31].element.value).toBe(123)
- expect(inputs[36].element.value).toBe(123)
+ expect(inputs[1].element.value).toBe("123")
+ expect(inputs[6].element.value).toBe("123")
+ expect(inputs[11].element.value).toBe("123")
+ expect(inputs[16].element.value).toBe("123")
+ expect(inputs[21].element.value).toBe("123")
+ expect(inputs[26].element.value).toBe("123")
+ expect(inputs[31].element.value).toBe("123")
+ expect(inputs[36].element.value).toBe("123")
})
test('frequency change heterozygous count', async () => {
@@ -175,12 +175,12 @@ describe('FilterFormFrequencyPane.vue', () => {
await inputs[22].setValue(123)
await inputs[32].setValue(123)
- expect(inputs[2].element.value).toBe(123)
- expect(inputs[7].element.value).toBe(123)
- expect(inputs[12].element.value).toBe(123)
- expect(inputs[17].element.value).toBe(123)
- expect(inputs[22].element.value).toBe(123)
- expect(inputs[32].element.value).toBe(123)
+ expect(inputs[2].element.value).toBe("123")
+ expect(inputs[7].element.value).toBe('123')
+ expect(inputs[12].element.value).toBe("123")
+ expect(inputs[17].element.value).toBe("123")
+ expect(inputs[22].element.value).toBe("123")
+ expect(inputs[32].element.value).toBe("123")
})
test('frequency change hemizygous count', async () => {
@@ -200,11 +200,11 @@ describe('FilterFormFrequencyPane.vue', () => {
await inputs[18].setValue(123)
await inputs[23].setValue(123)
- expect(inputs[3].element.value).toBe(123)
- expect(inputs[8].element.value).toBe(123)
- expect(inputs[13].element.value).toBe(123)
- expect(inputs[18].element.value).toBe(123)
- expect(inputs[23].element.value).toBe(123)
+ expect(inputs[3].element.value).toBe("123")
+ expect(inputs[8].element.value).toBe("123")
+ expect(inputs[13].element.value).toBe("123")
+ expect(inputs[18].element.value).toBe("123")
+ expect(inputs[23].element.value).toBe("123")
})
test('frequency change frequency', async () => {
@@ -227,14 +227,14 @@ describe('FilterFormFrequencyPane.vue', () => {
await inputs[34].setValue(123)
await inputs[39].setValue(123)
- expect(inputs[4].element.value).toBe(123)
- expect(inputs[9].element.value).toBe(123)
- expect(inputs[14].element.value).toBe(123)
- expect(inputs[19].element.value).toBe(123)
- expect(inputs[24].element.value).toBe(123)
- expect(inputs[29].element.value).toBe(123)
- expect(inputs[34].element.value).toBe(123)
- expect(inputs[39].element.value).toBe(123)
+ expect(inputs[4].element.value).toBe("123")
+ expect(inputs[9].element.value).toBe("123")
+ expect(inputs[14].element.value).toBe("123")
+ expect(inputs[19].element.value).toBe("123")
+ expect(inputs[24].element.value).toBe("123")
+ expect(inputs[29].element.value).toBe("123")
+ expect(inputs[34].element.value).toBe("123")
+ expect(inputs[39].element.value).toBe("123")
})
test('frequency dev mode', async () => {
diff --git a/variants/vueapp/tests/unit/components/FilterFormQualityPaneRow.spec.js b/variants/vueapp/tests/unit/components/FilterFormQualityPaneRow.spec.js
index 618f91d23..7a8c85730 100644
--- a/variants/vueapp/tests/unit/components/FilterFormQualityPaneRow.spec.js
+++ b/variants/vueapp/tests/unit/components/FilterFormQualityPaneRow.spec.js
@@ -64,14 +64,13 @@ describe('FilterFormQualityPaneRow.vue', () => {
await inputs[5].setValue(666)
await select.setValue('ignore')
- // TODO: bug in happy-dom or vue-test? The 0-th one is not set.
+ // TODO: bug in happy-dom or vue-test? The 0-th equals "10"
// expect(inputs[0].element.value).toEqual('111')
- expect(inputs[1].element.value).toEqual(222)
- expect(inputs[2].element.value).toEqual(0.333)
- expect(inputs[3].element.value).toEqual(444)
- expect(inputs[4].element.value).toEqual(555)
- expect(inputs[5].element.value).toEqual(666)
- // TODO: Bug in happy-dom? Value is "" in tests.
- // expect(select.element.value).toEqual('ignore')
+ expect(inputs[1].element.value).toEqual("222")
+ expect(inputs[2].element.value).toEqual("0.333")
+ expect(inputs[3].element.value).toEqual("444")
+ expect(inputs[4].element.value).toEqual("555")
+ expect(inputs[5].element.value).toEqual("666")
+ expect(select.element.value).toEqual('ignore')
})
})
diff --git a/variants/vueapp/tests/unit/components/VariantDetailsExtraAnnos.spec.js b/variants/vueapp/tests/unit/components/VariantDetailsExtraAnnos.spec.js
deleted file mode 100644
index f552379a5..000000000
--- a/variants/vueapp/tests/unit/components/VariantDetailsExtraAnnos.spec.js
+++ /dev/null
@@ -1,14 +0,0 @@
-// import VariantDetailsExtraAnnos from '@variants/components/VariantDetailsExtraAnnos.vue'
-// import { shallowMount } from '@vue/test-utils'
-import { describe, test } from 'vitest'
-
-describe('VariantDetailsExtraAnnos.vue', () => {
- test('', () => {
- // const wrapper = shallowMount(VariantDetailsExtraAnnos, {
- // props: {
- // params: {},
- // },
- // })
- // TODO [TEST_STUB]
- })
-})
diff --git a/variants/vueapp/tests/unit/components/VariantDetailsTxCsq.spec.js b/variants/vueapp/tests/unit/components/VariantDetailsTxCsq.spec.js
index 8e2ab9e25..d04d99031 100644
--- a/variants/vueapp/tests/unit/components/VariantDetailsTxCsq.spec.js
+++ b/variants/vueapp/tests/unit/components/VariantDetailsTxCsq.spec.js
@@ -17,7 +17,7 @@ describe('VariantDetailsTxCsq.vue', () => {
test('transcripts disabled/empty', () => {
const wrapper = shallowMount(VariantDetailsTxCsq, {
props: {
- effectDetails: null,
+ txCsq: null,
},
})