(\\d+(,\\d+)*)))?' + // optional range
- '$' // end
+ '$', // end
)
/** Load Genome England PanelApp presets. */
@@ -77,19 +77,19 @@ const loadPanelPage = async (page) => {
label: `${panel.name} (v${panel.version})`,
value: panel,
}
- })
+ }),
)
if (responseJson.next) {
await loadPanelPage(page + 1)
}
- }
+ },
)
}
/** Insert genomics england panel. */
const insertGenomicsEnglandPanel = async (panel) => {
await fetch(
- `/proxy/panelapp/v1/panels/${panel.id}/?version=${panel.version}`
+ `/proxy/panelapp/v1/panels/${panel.id}/?version=${panel.version}`,
).then(async (response) => {
const responseJson = await response.json()
let symbols = []
@@ -211,7 +211,7 @@ const loadGenePanelCategories = async () => {
await fetch('/geneinfo/api/genepanel-category/list/').then(
async (response) => {
genePanelCategories.value = await response.json()
- }
+ },
)
}
diff --git a/variants/vueapp/src/components/FilterFormGenotypePane.vue b/variants/vueapp/src/components/FilterFormGenotypePane.vue
index 4981a9572..282918d95 100644
--- a/variants/vueapp/src/components/FilterFormGenotypePane.vue
+++ b/variants/vueapp/src/components/FilterFormGenotypePane.vue
@@ -60,12 +60,12 @@ const getRole = (name) => {
/** Precomputed mapping of father for each pedigree member. */
const memberToFather = Object.fromEntries(
- props.case.pedigree.map((member) => [member.name, member.father])
+ props.case.pedigree.map((member) => [member.name, member.father]),
)
/** Precomputed mapping of mother for each pedigree member. */
const memberToMother = Object.fromEntries(
- props.case.pedigree.map((member) => [member.name, member.mother])
+ props.case.pedigree.map((member) => [member.name, member.mother]),
)
/** Build a wrapper to go into `genotypeWrappers` below. */
@@ -91,7 +91,7 @@ const makeWrapper = (name) =>
key !== memberToFather[name] &&
key !== memberToMother[name] &&
['comphet-index', 'recessive-index', 'recessive-parent'].includes(
- value
+ value,
)
) {
props.querySettings[key] = 'any'
@@ -133,8 +133,11 @@ const makeWrapper = (name) =>
/** Access wrapper for the form elements' models. */
const genotypeWrappers = reactive(
Object.fromEntries(
- props.case.pedigree.map((member) => [member.name, makeWrapper(member.name)])
- )
+ props.case.pedigree.map((member) => [
+ member.name,
+ makeWrapper(member.name),
+ ]),
+ ),
)
/** Initialize vuelidate. */
diff --git a/variants/vueapp/src/components/FilterFormQualityPane.vue b/variants/vueapp/src/components/FilterFormQualityPane.vue
index 73b9b785e..b103cd847 100644
--- a/variants/vueapp/src/components/FilterFormQualityPane.vue
+++ b/variants/vueapp/src/components/FilterFormQualityPane.vue
@@ -33,7 +33,7 @@ const keyMap = {
const v$ = useVuelidate(rules, tplValues)
const membersWithGtEntries = props.caseObj.pedigree.filter(
- (member) => member.has_gt_entries
+ (member) => member.has_gt_entries,
)
const childRefs = ref([])
diff --git a/variants/vueapp/src/components/FilterFormQualityPaneRow.vue b/variants/vueapp/src/components/FilterFormQualityPaneRow.vue
index c6553a43e..0b452f45f 100644
--- a/variants/vueapp/src/components/FilterFormQualityPaneRow.vue
+++ b/variants/vueapp/src/components/FilterFormQualityPaneRow.vue
@@ -43,7 +43,7 @@ const mappers = {
}
const formModel = Object.fromEntries(
- allKeys.map((key) => [key, declareWrapper(props, key, emit)])
+ allKeys.map((key) => [key, declareWrapper(props, key, emit)]),
)
const v$ = useVuelidate(rules, formModel)
diff --git a/variants/vueapp/src/components/FilterFormQuickPresets.vue b/variants/vueapp/src/components/FilterFormQuickPresets.vue
index 26e85adb0..c2d61c007 100644
--- a/variants/vueapp/src/components/FilterFormQuickPresets.vue
+++ b/variants/vueapp/src/components/FilterFormQuickPresets.vue
@@ -26,7 +26,7 @@ const inheritanceRef = ref(null)
/** Refresh qualityRef from actual form values. Check each for compatibility and pick first matching. */
const refreshInheritanceRef = () => {
for (const [presetName, presetValues] of Object.entries(
- props.categoryPresets.inheritance
+ props.categoryPresets.inheritance,
)) {
let isCompatible = true
for (const member of Object.values(props.case.pedigree)) {
@@ -45,7 +45,7 @@ const refreshInheritanceRef = () => {
) &&
!isEqual(
props.querySettings.genotype[member.name],
- presetValues.genotype[member.name]
+ presetValues.genotype[member.name],
)
) {
isCompatible = false
@@ -55,7 +55,7 @@ const refreshInheritanceRef = () => {
if (
!isEqual(
props.querySettings.recessive_index,
- presetValues.recessive_index
+ presetValues.recessive_index,
) ||
!isEqual(props.querySettings.recessive_mode, presetValues.recessive_mode)
) {
@@ -78,7 +78,7 @@ const inheritanceWrapper = computed({
set(newValue) {
if (newValue !== 'custom') {
props.querySettings.genotype = copy(
- props.categoryPresets.inheritance[newValue].genotype
+ props.categoryPresets.inheritance[newValue].genotype,
)
const recessiveIndex =
props.categoryPresets.inheritance[newValue].recessive_index
@@ -117,14 +117,14 @@ const _keysToStrip = [
/** Return copy of obj without keys. */
const _objectWithoutKeys = (obj, keys) => {
return Object.fromEntries(
- Object.entries(obj).filter(([key, _value]) => !keys.includes(key))
+ Object.entries(obj).filter(([key, _value]) => !keys.includes(key)),
)
}
/** Refresh qualityRef from actual form values. Check each for compatibility and pick first matching. */
const refreshQualityRef = () => {
for (const [presetName, presetValues] of Object.entries(
- props.categoryPresets.quality
+ props.categoryPresets.quality,
)) {
const strippedPresetValues = _objectWithoutKeys(presetValues, _keysToStrip)
let isCompatible = true
@@ -154,7 +154,7 @@ const qualityWrapper = computed({
for (const member of Object.values(props.case.pedigree)) {
props.querySettings.quality[member.name] = _objectWithoutKeys(
props.categoryPresets.quality[newValue],
- _keysToStrip
+ _keysToStrip,
)
}
refreshQualityRef()
@@ -179,7 +179,7 @@ const refreshValueRefs = () => {
continue // not fully loaded yet
}
for (const [presetName, presetValues] of Object.entries(
- props.categoryPresets[category]
+ props.categoryPresets[category],
)) {
isCompatible = true
for (const [key, value] of Object.entries(presetValues)) {
@@ -216,7 +216,7 @@ const makeWrapper = (name) =>
const oldBlockRefresh = blockRefresh.value
blockRefresh.value = true
for (const [key, value] of Object.entries(
- props.categoryPresets[name][newValue]
+ props.categoryPresets[name][newValue],
)) {
if (!_keysToStrip.includes(key)) {
props.querySettings[key] = value
diff --git a/variants/vueapp/src/components/FilterResultsTable.columnDefs.js b/variants/vueapp/src/components/FilterResultsTable.columnDefs.js
index 259287198..7e957a035 100644
--- a/variants/vueapp/src/components/FilterResultsTable.columnDefs.js
+++ b/variants/vueapp/src/components/FilterResultsTable.columnDefs.js
@@ -314,7 +314,7 @@ export function defineColumnDefs({
field: 'hgvs_p',
headerName: 'hgvs_p',
hide: !(displayColumns || []).includes(
- DisplayColumns.EffectProtein.value
+ DisplayColumns.EffectProtein.value,
),
},
{
@@ -326,7 +326,7 @@ export function defineColumnDefs({
field: 'exon_dist',
headerName: 'exon dist',
hide: !(displayColumns || []).includes(
- DisplayColumns.DistanceSplicesite.value
+ DisplayColumns.DistanceSplicesite.value,
),
},
...extraAnnoColumnDefs,
diff --git a/variants/vueapp/src/components/FilterResultsTable.vue b/variants/vueapp/src/components/FilterResultsTable.vue
index c5e57b20e..99b375dff 100644
--- a/variants/vueapp/src/components/FilterResultsTable.vue
+++ b/variants/vueapp/src/components/FilterResultsTable.vue
@@ -72,7 +72,7 @@ const displayFrequencyWrapper = declareWrapper(props, 'displayFrequency', emit)
const displayConstraintWrapper = declareWrapper(
props,
'displayConstraint',
- emit
+ emit,
)
/** Wrapper around {@code displayColumns} prop. */
const displayColumnsWrapper = declareWrapper(props, 'displayColumns', emit)
@@ -355,7 +355,7 @@ const goToLocus = async (item) => {
? item.chromosome
: `chr${item.chromosome}`
await fetch(
- `http://127.0.0.1:60151/goto?locus=${chrPrefixed}:${item.start}-${item.end}`
+ `http://127.0.0.1:60151/goto?locus=${chrPrefixed}:${item.start}-${item.end}`,
).catch((e) => {
const msg =
"Couldn't connect to IGV. Please make sure IGV is running and try again."
@@ -461,7 +461,7 @@ const loadFromServer = async () => {
? 'genotype_' + genotypeMapping[tableServerOptions.value.sortBy]
: tableServerOptions.value.sortBy,
orderDir: tableServerOptions.value.sortType,
- }
+ },
)
tableRows.value = response.results.map((row) => transmogrify(row))
tableLoading.value = false
@@ -478,7 +478,7 @@ watch(
(_newValue, _oldValue) => {
loadFromServer()
},
- { deep: true }
+ { deep: true },
)
watch(
@@ -486,7 +486,7 @@ watch(
(_newValue, _oldValue) => {
loadFromServer()
},
- { deep: true }
+ { deep: true },
)
watch(
@@ -494,7 +494,7 @@ watch(
(_newValue, _oldValue) => {
loadFromServer()
},
- { deep: true }
+ { deep: true },
)
diff --git a/variants/vueapp/src/components/FilterResultsTableCellRendererIgv.vue b/variants/vueapp/src/components/FilterResultsTableCellRendererIgv.vue
index aff6b7f6d..2a2f513a2 100644
--- a/variants/vueapp/src/components/FilterResultsTableCellRendererIgv.vue
+++ b/variants/vueapp/src/components/FilterResultsTableCellRendererIgv.vue
@@ -8,7 +8,7 @@ const goToLocus = async () => {
? props.params.data.chromosome
: `chr${props.params.data.chromosome}`
await fetch(
- `http://127.0.0.1:60151/goto?locus=${chrPrefixed}:${props.params.data.start}-${props.params.data.end}`
+ `http://127.0.0.1:60151/goto?locus=${chrPrefixed}:${props.params.data.start}-${props.params.data.end}`,
).catch((e) => {
console.error('IGV not available')
})
diff --git a/variants/vueapp/src/components/HpoTermInput.vue b/variants/vueapp/src/components/HpoTermInput.vue
index af70732d5..65267247f 100644
--- a/variants/vueapp/src/components/HpoTermInput.vue
+++ b/variants/vueapp/src/components/HpoTermInput.vue
@@ -69,7 +69,7 @@ const refreshTextValue = async (termsArray) => {
} else {
return null
}
- })
+ }),
)
const withLabel = withLabelUnfiltered.filter((elem) => elem !== null)
textValue.value = withLabel.join('; ')
@@ -133,7 +133,7 @@ watch(
() => props.modelValue,
(newValue, _oldValue) => {
refreshTextValue(newValue)
- }
+ },
)
onMounted(() => {
diff --git a/variants/vueapp/src/components/QueryPresets.vue b/variants/vueapp/src/components/QueryPresets.vue
index 0409f8bdf..3325e12dc 100644
--- a/variants/vueapp/src/components/QueryPresets.vue
+++ b/variants/vueapp/src/components/QueryPresets.vue
@@ -118,7 +118,7 @@ const handleCloneClicked = async () => {
} else {
clonedPresetSet = await queryPresetsStore.cloneOtherPresetSet(
presetSetModel.value,
- label
+ label,
)
}
presetSetModel.value = clonedPresetSet.sodar_uuid
@@ -181,7 +181,7 @@ const handleEditClicked = async () => {
const showOverlay = computed(
() =>
queryPresetsStore.storeState !== StoreState.active ||
- queryPresetsStore.serverInteractions > 0
+ queryPresetsStore.serverInteractions > 0,
)
/** Initialize store on first mount. */
@@ -189,7 +189,7 @@ onBeforeMount(() => {
casesStore.initializeRes.then(() => {
queryPresetsStore.initialize(
casesStore.appContext.csrf_token,
- casesStore.appContext.project.sodar_uuid
+ casesStore.appContext.project.sodar_uuid,
)
})
})
diff --git a/variants/vueapp/src/components/QueryPresetsSetEditor.vue b/variants/vueapp/src/components/QueryPresetsSetEditor.vue
index 941d93cc4..3ad48bd82 100644
--- a/variants/vueapp/src/components/QueryPresetsSetEditor.vue
+++ b/variants/vueapp/src/components/QueryPresetsSetEditor.vue
@@ -161,7 +161,7 @@ const handleRevertClicked = async (category, presetsUuid) => {
await queryPresetsStore.revertPresets(
category,
props.presetSetUuid,
- presetsUuid
+ presetsUuid,
)
}
toastRef.value.show({
@@ -189,14 +189,14 @@ const handleSaveClicked = async (category, presetsUuid) => {
if (category === 'presetset') {
await queryPresetsStore.updatePresetSet(
props.presetSetUuid,
- presetSet.value.label
+ presetSet.value.label,
)
} else {
await queryPresetsStore.updatePresets(
category,
props.presetSetUuid,
presetsUuid,
- selectedPresets.value
+ selectedPresets.value,
)
}
toastRef.value.show({
@@ -251,7 +251,7 @@ const handleAddClicked = async (category) => {
await queryPresetsStore.createPresets(
category,
props.presetSetUuid,
- payload
+ payload,
)
toastRef.value.show({
level: 'success',
@@ -288,7 +288,7 @@ const handleRenameClicked = async (category, presetsUuid) => {
category,
props.presetSetUuid,
presetsUuid,
- { label }
+ { label },
)
toastRef.value.show({
level: 'success',
@@ -348,7 +348,7 @@ const handleCloneClicked = async (category, presetsUuid) => {
category,
props.presetSetUuid,
presetsUuid,
- label
+ label,
)
toastRef.value.show({
level: 'success',
@@ -380,7 +380,7 @@ const handleDeleteClicked = async (category, presetsUuid) => {
await queryPresetsStore.destroyPresets(
category,
props.presetSetUuid,
- presetsUuid
+ presetsUuid,
)
toastRef.value.show({
level: 'success',
@@ -403,7 +403,7 @@ onBeforeMount(() => {
queryPresetsStore
.initialize(
casesStore.appContext.csrf_token,
- casesStore.appContext.project.sodar_uuid
+ casesStore.appContext.project.sodar_uuid,
)
.then(() => {
handleCategoryClicked('presetset')
@@ -416,7 +416,7 @@ watch(
() => props.presetSetUuid,
(newValue) => {
handleCategoryClicked('presetset')
- }
+ },
)
diff --git a/variants/vueapp/src/components/TokenizingTextarea.vue b/variants/vueapp/src/components/TokenizingTextarea.vue
index 66910c8c3..04440e0e3 100644
--- a/variants/vueapp/src/components/TokenizingTextarea.vue
+++ b/variants/vueapp/src/components/TokenizingTextarea.vue
@@ -148,7 +148,7 @@ const highlightToken = (token) => {
validationResults[token].state = 'rejected'
updateIsValidationRunning()
runValidationAndUpdateBackdrop()
- }
+ },
)
}).then(),
}
@@ -157,7 +157,7 @@ const highlightToken = (token) => {
validationResults[token].result = cbResult
} else {
throw new Error(
- 'Invalid result, not boolean, or has valid, or is Promise! ' + cbResult
+ 'Invalid result, not boolean, or has valid, or is Promise! ' + cbResult,
)
}
}
@@ -249,7 +249,7 @@ const runValidationAndUpdateBackdrop = debounce(
leading: true,
maxWait: 2,
trailing: true,
- }
+ },
)
/** Event handler that keeps the textarea's and backdrop's scrolling in sync. */
@@ -288,7 +288,7 @@ watch(
() => props.modelValue,
(newValue, _oldValue) => {
modelValueWrapper.value = newValue
- }
+ },
)
/** Define the exposed functions. */
diff --git a/variants/vueapp/src/components/VariantDetails.vue b/variants/vueapp/src/components/VariantDetails.vue
index fe954f067..e4b473e56 100644
--- a/variants/vueapp/src/components/VariantDetails.vue
+++ b/variants/vueapp/src/components/VariantDetails.vue
@@ -38,7 +38,7 @@ const flagsStore = useVariantFlagsStore()
const commentsStore = useVariantCommentsStore()
commentsStore.initialize(
{ csrf_token: queryStore.csrfToken },
- queryStore.caseUuid
+ queryStore.caseUuid,
)
const navItems = allNavItems.filter((navItem) => {
diff --git a/variants/vueapp/src/components/VariantDetailsAcmgRating.vue b/variants/vueapp/src/components/VariantDetailsAcmgRating.vue
index 649e5c19e..f88665782 100644
--- a/variants/vueapp/src/components/VariantDetailsAcmgRating.vue
+++ b/variants/vueapp/src/components/VariantDetailsAcmgRating.vue
@@ -204,7 +204,7 @@ const onSubmitAcmgRating = async () => {
delete acmgRatingToSubmitNoAuto['class_auto']
const acmgRatingToSubmitEmpty = isEqual(
acmgRatingToSubmitNoAuto,
- emptyAcmgRatingTemplate
+ emptyAcmgRatingTemplate,
)
if (acmgRatingStore.acmgRating && acmgRatingToSubmitEmpty) {
// IS not empty but SHOULD be empty, so delete the ACMG rating
@@ -219,7 +219,7 @@ const onSubmitAcmgRating = async () => {
// IS empty but SHOULD not be empty, so create the ACMG rating
await acmgRatingStore.createAcmgRating(
detailsStore.smallVariant,
- acmgRatingToSubmit.value
+ acmgRatingToSubmit.value,
)
}
}
diff --git a/variants/vueapp/src/components/VariantDetailsCallDetails.vue b/variants/vueapp/src/components/VariantDetailsCallDetails.vue
index 9d3c6cbac..cebb7dda8 100644
--- a/variants/vueapp/src/components/VariantDetailsCallDetails.vue
+++ b/variants/vueapp/src/components/VariantDetailsCallDetails.vue
@@ -89,7 +89,7 @@ const allelicBalance = (value) => {
|
{{
allelicBalance(
- props.smallVariant.genotype[member.name]
+ props.smallVariant.genotype[member.name],
).toFixed(2)
}}
|
diff --git a/variants/vueapp/src/components/VariantDetailsFreqsAutosomal.vue b/variants/vueapp/src/components/VariantDetailsFreqsAutosomal.vue
index b89553ed5..ea1e38f44 100644
--- a/variants/vueapp/src/components/VariantDetailsFreqsAutosomal.vue
+++ b/variants/vueapp/src/components/VariantDetailsFreqsAutosomal.vue
@@ -72,7 +72,7 @@ const sexExpanded = ref({})
{
v-html="
roundIt(
(gnomadMtDna?.ac_het + gnomadMtDna?.ac_hom) / gnomadMtDna?.an,
- 4
+ 4,
)
"
/>
@@ -78,7 +78,7 @@ const gnomadMtDna = computed(() => {
roundIt(
(helixMtDb?.num_het + helixMtDb?.num_hom) /
helixMtDb?.num_total,
- 4
+ 4,
)
"
/>
diff --git a/variants/vueapp/src/components/VariantDetailsGene.vue b/variants/vueapp/src/components/VariantDetailsGene.vue
index 5f10704e0..e13563cd7 100644
--- a/variants/vueapp/src/components/VariantDetailsGene.vue
+++ b/variants/vueapp/src/components/VariantDetailsGene.vue
@@ -155,7 +155,7 @@ const props = withDefaults(defineProps(), {
roundIt(
gene?.gnomad_constraints?.oe_lof_upper,
2,
- 'LOEUF'
+ 'LOEUF',
)
"
/>)
diff --git a/variants/vueapp/src/components/VariantDetailsModalWrapper.vue b/variants/vueapp/src/components/VariantDetailsModalWrapper.vue
index b7bd8cddd..16446ddf3 100644
--- a/variants/vueapp/src/components/VariantDetailsModalWrapper.vue
+++ b/variants/vueapp/src/components/VariantDetailsModalWrapper.vue
@@ -42,12 +42,12 @@ const showModal = async () => {
const resultRow = await variantsApi.retrieveQueryResultRow(
filterQueryStore.csrfToken,
- props.resultRowUuid
+ props.resultRowUuid,
)
smallVariant.value = resultRow.payload
variantDetailsStore.fetchVariantDetails(
resultRow,
- filterQueryStore.previousQueryDetails.query_settings.database_select
+ filterQueryStore.previousQueryDetails.query_settings.database_select,
)
}
@@ -64,7 +64,7 @@ watch(
} else {
$(modalRef.value).modal('hide')
}
- }
+ },
)
/** Event handler called when the modal is hidden.
diff --git a/variants/vueapp/src/components/VariantDetailsVariantTools.vue b/variants/vueapp/src/components/VariantDetailsVariantTools.vue
index b1f0fd6ac..880f6b10b 100644
--- a/variants/vueapp/src/components/VariantDetailsVariantTools.vue
+++ b/variants/vueapp/src/components/VariantDetailsVariantTools.vue
@@ -58,13 +58,13 @@ const decodeMultiDbnsfp = (s: string): number | null => {
...s
.split(';')
.filter((s) => s != '.')
- .map(parseFloat)
+ .map(parseFloat),
)
}
}
const siftScore = computed((): number | null =>
- decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.SIFT_score)
+ decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.SIFT_score),
)
const translatedSiftScore = computed((): number | null => {
@@ -77,7 +77,7 @@ const translatedSiftScore = computed((): number | null => {
})
const fathmmScore = computed((): number | null =>
- decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.FATHMM_score)
+ decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.FATHMM_score),
)
const translatedFathmmScore = computed((): number | null => {
@@ -98,15 +98,15 @@ const gerpScore = computed((): number | null => {
})
const mpcScore = computed((): number | null =>
- decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.MPC_score)
+ decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.MPC_score),
)
const revelScore = computed((): number | null =>
- decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.REVEL_score)
+ decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.REVEL_score),
)
const polyphenScore = computed((): number | null =>
- decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.Polyphen2_HVAR_score)
+ decodeMultiDbnsfp(props.varAnnos?.dbnsfp?.Polyphen2_HVAR_score),
)
const ucscLinkout = computed((): str => {
diff --git a/variants/vueapp/src/components/VariantDetailsVariantValidator.vue b/variants/vueapp/src/components/VariantDetailsVariantValidator.vue
index 4a0d2ad4c..27b8d6b68 100644
--- a/variants/vueapp/src/components/VariantDetailsVariantValidator.vue
+++ b/variants/vueapp/src/components/VariantDetailsVariantValidator.vue
@@ -17,20 +17,20 @@ const emit = defineEmits([
const variantValidatorStateWrapper = declareWrapper(
props,
'variantValidatorState',
- emit
+ emit,
)
/** Wrapper around {@code variantValidatorResults} prop. */
const variantValidatorResultsWrapper = declareWrapper(
props,
'variantValidatorResults',
- emit
+ emit,
)
const queryVariantValidatorApi = async () => {
variantValidatorResultsWrapper.value = null
variantValidatorStateWrapper.value = VariantValidatorStates.Running
const res = await fetch(
- `/proxy/variantvalidator/${props.smallVariant.release}/${props.smallVariant.chromosome}-${props.smallVariant.start}-${props.smallVariant.reference}-${props.smallVariant.alternative}/all?content-type=application%2Fjson`
+ `/proxy/variantvalidator/${props.smallVariant.release}/${props.smallVariant.chromosome}-${props.smallVariant.start}-${props.smallVariant.reference}-${props.smallVariant.alternative}/all?content-type=application%2Fjson`,
)
if (res.ok) {
variantValidatorResultsWrapper.value = await res.json()
diff --git a/variants/vueapp/src/stores/filterQuery.funcs.js b/variants/vueapp/src/stores/filterQuery.funcs.js
index e6ec49965..82c5940e8 100644
--- a/variants/vueapp/src/stores/filterQuery.funcs.js
+++ b/variants/vueapp/src/stores/filterQuery.funcs.js
@@ -5,7 +5,7 @@ import { copy } from '@variants/helpers'
// This function can be removed once support for the fold forms is removed.
export function previousQueryDetailsToQuerySettings(
caseObj,
- previousQueryDetails
+ previousQueryDetails,
) {
const freqKeys = [
'exac_enabled',
@@ -80,7 +80,7 @@ export function previousQueryDetailsToQuerySettings(
`${name}_dp_hom`,
`${name}_gq`,
`${name}_fail`,
- `${name}_gt`
+ `${name}_gt`,
)
}
diff --git a/variants/vueapp/src/stores/filterQuery.js b/variants/vueapp/src/stores/filterQuery.js
index fd2492229..a4a834ff9 100644
--- a/variants/vueapp/src/stores/filterQuery.js
+++ b/variants/vueapp/src/stores/filterQuery.js
@@ -20,7 +20,7 @@ const fetchPresets = async (
csrfToken,
caseObj,
quickPresets,
- categoryPresets
+ categoryPresets,
) => {
// TODO: move fetch calls into queryPresetsApi
const fetchFactoryPresets = async () => {
@@ -40,7 +40,7 @@ const fetchPresets = async (
.then((presets) => {
categoryPresets.value[category] = presets
})
- }
+ },
),
])
}
@@ -64,7 +64,7 @@ const fetchPresets = async (
flagsetc: qp.flagsetc,
database: apiPresetSet.database,
},
- ])
+ ]),
)
const categories = [
@@ -82,7 +82,7 @@ const fetchPresets = async (
apiPresetSet[`${category2}presets_set`].map((ps) => [
ps.sodar_uuid,
ps,
- ])
+ ]),
)
}
}),
@@ -108,7 +108,7 @@ const fetchDefaultSettings = async (
csrfToken,
caseUuid,
querySettingsPresets,
- querySettings
+ querySettings,
) => {
const resJson = await variantsApi.fetchQueryShortcuts(csrfToken, caseUuid)
querySettingsPresets.value = resJson.presets
@@ -160,7 +160,7 @@ const fetchHpoTerms = async (csrfToken, hpoTerms) => {
console.warn(
"Multiple terms for HPO ID '" +
hpoTerm +
- "' found. Taking first one."
+ "' found. Taking first one.",
)
}
_hpoNames.push(res[0].name)
@@ -276,7 +276,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
try {
const queryStatus = await variantsApi.retrieveQuery(
csrfToken.value,
- queryUuid
+ queryUuid,
)
queryLogs.value = queryStatus.logs
queryState.value = apiQueryStateToQueryState(queryStatus.query_state)
@@ -289,7 +289,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
failuresSeen += 1
console.warn(
`There was a problem retrieving the query status (${failuresSeen} / ${FETCH_LOOP_ALLOW_FAILURES}`,
- err
+ err,
)
if (failuresSeen > FETCH_LOOP_ALLOW_FAILURES) {
queryState.value = QueryStates.Error.value
@@ -304,7 +304,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
// List the results
const responseResultSetList = await variantsApi.listQueryResultSet(
csrfToken.value,
- queryUuid
+ queryUuid,
)
if (!responseResultSetList.length) {
console.error('ERROR: no results in response')
@@ -330,7 +330,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
previousQueryDetails.value = await variantsApi.createQuery(
csrfToken.value,
caseUuid.value,
- { query_settings: copy(querySettings.value) }
+ { query_settings: copy(querySettings.value) },
)
queryState.value = QueryStates.Running.value
downloadStatusTsv.value = null
@@ -341,7 +341,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
exportJobUuidXlsx.value = null
hpoNames.value = await fetchHpoTerms(
csrfToken.value,
- querySettings.value.prio_hpo_terms
+ querySettings.value.prio_hpo_terms,
)
await nextTick()
await runFetchLoop(previousQueryDetails.value.sodar_uuid)
@@ -406,13 +406,13 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
const runFetchDownloadLoop = async (
exportJobUuid,
fileType,
- failuresSeen = 0
+ failuresSeen = 0,
) => {
// Fetch query status, allowing up to FETCH_LOOP_ALLOW_FAILURES errors.
try {
const response = await variantsApi.statusDownloadResults(
csrfToken.value,
- exportJobUuid
+ exportJobUuid,
)
if (fileType === 'tsv') {
downloadStatusTsv.value = response.status
@@ -432,7 +432,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
failuresSeen += 1
console.warn(
`There was a problem retrieving the download status (${failuresSeen} / ${FETCH_LOOP_ALLOW_FAILURES}`,
- err
+ err,
)
if (failuresSeen > FETCH_LOOP_ALLOW_FAILURES) {
if (fileType === 'tsv') {
@@ -460,7 +460,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
FETCH_LOOP_DELAY,
exportJobUuid,
fileType,
- failuresSeen
+ failuresSeen,
)
}
@@ -506,7 +506,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
csrfToken.value,
caseUuid.value,
querySettingsPresets,
- querySettings
+ querySettings,
),
// 2. fetch previous query UUID
fetchPreviousQueryUuid(csrfToken.value, caseUuid.value)
@@ -518,7 +518,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
if (queryUuid.value) {
return variantsApi.retrieveQuery(
csrfToken.value,
- queryUuid.value
+ queryUuid.value,
)
}
})
@@ -528,7 +528,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
previousQueryDetails.value = result
querySettings.value = previousQueryDetailsToQuerySettings(
caseObj.value,
- previousQueryDetails.value
+ previousQueryDetails.value,
)
}
})
@@ -545,7 +545,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
if (querySettings.value?.prio_hpo_terms.length > 0) {
hpoNames.value = fetchHpoTerms(
csrfToken.value,
- querySettings.value.prio_hpo_terms
+ querySettings.value.prio_hpo_terms,
)
}
}),
@@ -554,7 +554,7 @@ export const useFilterQueryStore = defineStore('filterQuery', () => {
csrfToken.value,
caseObj.value,
quickPresets,
- categoryPresets
+ categoryPresets,
),
// 4. fetch extra anno fields
fetchExtraAnnoFields(csrfToken.value).then((result) => {
diff --git a/variants/vueapp/src/stores/queryPresets.js b/variants/vueapp/src/stores/queryPresets.js
index 2e47103c5..d8161cf55 100644
--- a/variants/vueapp/src/stores/queryPresets.js
+++ b/variants/vueapp/src/stores/queryPresets.js
@@ -72,7 +72,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
.then((result) => {
serverInteractions.value -= 1
presetSets.value = Object.fromEntries(
- result.map((presetSet) => [presetSet.sodar_uuid, presetSet])
+ result.map((presetSet) => [presetSet.sodar_uuid, presetSet]),
)
storeState.value = StoreState.active
resolve()
@@ -95,7 +95,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
try {
resultPresetSet = await queryPresetsApi.cloneFactoryPresetSet(
csrfToken.value,
- { project: projectUuid.value, label }
+ { project: projectUuid.value, label },
)
presetSets.value[resultPresetSet.sodar_uuid] = resultPresetSet
} finally {
@@ -113,7 +113,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
resultPresetSet = await queryPresetsApi.cloneOtherPresetSet(
csrfToken.value,
presetSetUuid,
- { project: projectUuid.value, label }
+ { project: projectUuid.value, label },
)
presetSets.value[resultPresetSet.sodar_uuid] = resultPresetSet
} finally {
@@ -130,7 +130,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
try {
revertedPresetSet = await queryPresetsApi.retrievePresetSet(
csrfToken.value,
- presetSetUuid
+ presetSetUuid,
)
presetSets.value[presetSetUuid] = revertedPresetSet
} finally {
@@ -148,7 +148,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
updatedPresetSet = await queryPresetsApi.updatePresetSet(
csrfToken.value,
presetSetUuid,
- { label }
+ { label },
)
presetSets.value[presetSetUuid] = updatedPresetSet
} finally {
@@ -179,7 +179,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
createdPresets = await queryPresetsApi[`create${cat.name}`](
csrfToken.value,
presetSetUuid,
- payload
+ payload,
)
presetSets.value[presetSetUuid][`${category}_set`] = presetSets.value[
presetSetUuid
@@ -199,7 +199,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
resultPresets = await queryPresetsApi[`cloneOther${cat.name}`](
csrfToken.value,
presetsUuid,
- { label, presetset: presetSetUuid }
+ { label, presetset: presetSetUuid },
)
presetSets.value[presetSetUuid][`${category}_set`] = presetSets.value[
presetSetUuid
@@ -218,7 +218,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
try {
revertedPresets = await queryPresetsApi[`retrieve${cat.name}`](
csrfToken.value,
- presetUuid
+ presetUuid,
)
const presetsSet = presetSets.value[presetSetUuid][`${category}_set`]
for (let i = 0; i < presetsSet.length; i++) {
@@ -238,7 +238,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
category,
presetSetUuid,
presetsUuid,
- presetsObj
+ presetsObj,
) => {
const cat = Category[category]
storeStateMessage.value = `Updating ${cat.title}...`
@@ -248,7 +248,7 @@ export const useQueryPresetsStore = defineStore('queryPresets', () => {
updatedPresets = await queryPresetsApi[`update${cat.name}`](
csrfToken.value,
presetsUuid,
- presetsObj
+ presetsObj,
)
const presetsSet = presetSets.value[presetSetUuid][`${category}_set`]
for (let i = 0; i < presetsSet.length; i++) {
diff --git a/variants/vueapp/src/stores/variantAcmgRating.js b/variants/vueapp/src/stores/variantAcmgRating.js
index 5d22305ae..328692c68 100644
--- a/variants/vueapp/src/stores/variantAcmgRating.js
+++ b/variants/vueapp/src/stores/variantAcmgRating.js
@@ -51,10 +51,10 @@ export const useVariantAcmgRatingStore = defineStore(
try {
const res = await variantsApi.listAcmgRating(
csrfToken.value,
- caseUuid.value
+ caseUuid.value,
)
caseAcmgRatings.value = Object.fromEntries(
- res.map((acmgRating) => [acmgRating.sodar_uuid, acmgRating])
+ res.map((acmgRating) => [acmgRating.sodar_uuid, acmgRating]),
)
} catch (err) {
storeState.value = StoreState.error
@@ -75,7 +75,7 @@ export const useVariantAcmgRatingStore = defineStore(
const res = await variantsApi.listAcmgRating(
csrfToken.value,
caseUuid.value,
- smallVariant$
+ smallVariant$,
)
if (res.length) {
acmgRating.value = res[0]
@@ -103,7 +103,7 @@ export const useVariantAcmgRatingStore = defineStore(
csrfToken.value,
caseUuid.value,
smallVariant,
- { ...smallVariant, ...payload }
+ { ...smallVariant, ...payload },
)
} finally {
serverInteractions.value -= 1
@@ -132,7 +132,7 @@ export const useVariantAcmgRatingStore = defineStore(
{
...smallVariant,
...payload,
- }
+ },
)
} finally {
serverInteractions.value -= 1
@@ -156,7 +156,7 @@ export const useVariantAcmgRatingStore = defineStore(
try {
await variantsApi.deleteAcmgRating(
csrfToken.value,
- acmgRating.value.sodar_uuid
+ acmgRating.value.sodar_uuid,
)
} finally {
serverInteractions.value -= 1
@@ -205,5 +205,5 @@ export const useVariantAcmgRatingStore = defineStore(
deleteAcmgRating,
getAcmgRating,
}
- }
+ },
)
diff --git a/variants/vueapp/src/stores/variantComments.js b/variants/vueapp/src/stores/variantComments.js
index 1ab074776..f551b8628 100644
--- a/variants/vueapp/src/stores/variantComments.js
+++ b/variants/vueapp/src/stores/variantComments.js
@@ -50,7 +50,7 @@ export const useVariantCommentsStore = defineStore('variantComments', () => {
try {
const res = await variantsApi.listComment(csrfToken.value, caseUuid.value)
caseComments.value = Object.fromEntries(
- res.map((comments) => [comments.sodar_uuid, comments])
+ res.map((comments) => [comments.sodar_uuid, comments]),
)
} catch (err) {
storeState.value = StoreState.error
@@ -71,7 +71,7 @@ export const useVariantCommentsStore = defineStore('variantComments', () => {
comments.value = await variantsApi.listComment(
csrfToken.value,
caseUuid.value,
- smallVariant$
+ smallVariant$,
)
} catch (err) {
storeState.value = StoreState.error
@@ -94,7 +94,7 @@ export const useVariantCommentsStore = defineStore('variantComments', () => {
csrfToken.value,
caseUuid.value,
smallVariant,
- { ...smallVariant, text }
+ { ...smallVariant, text },
)
} finally {
serverInteractions.value -= 1
@@ -146,7 +146,7 @@ export const useVariantCommentsStore = defineStore('variantComments', () => {
delete caseComments.value[commentUuid]
comments.value = comments.value.filter(
- (comment) => comment.sodar_uuid !== commentUuid
+ (comment) => comment.sodar_uuid !== commentUuid,
)
}
diff --git a/variants/vueapp/src/stores/variantDetails.js b/variants/vueapp/src/stores/variantDetails.js
index fd30bd30c..45118db59 100644
--- a/variants/vueapp/src/stores/variantDetails.js
+++ b/variants/vueapp/src/stores/variantDetails.js
@@ -61,7 +61,7 @@ export const useVariantDetailsStore = defineStore('variantDetails', () => {
smallVariantRecord$.chromosome,
smallVariantRecord$.start,
smallVariantRecord$.reference,
- smallVariantRecord$.alternative
+ smallVariantRecord$.alternative,
)
.then((result) => {
varAnnos.value = result.result
@@ -73,7 +73,7 @@ export const useVariantDetailsStore = defineStore('variantDetails', () => {
smallVariantRecord$.start,
smallVariantRecord$.reference,
smallVariantRecord$.alternative,
- hgncId
+ hgncId,
)
.then((result) => {
txCsq.value = result.result
@@ -82,7 +82,7 @@ export const useVariantDetailsStore = defineStore('variantDetails', () => {
.retrieveVariantDetails(
csrfToken.value,
database.value,
- smallVariant.value
+ smallVariant.value,
)
.then((res) => {
fetched.value = true
diff --git a/variants/vueapp/src/stores/variantFlags.js b/variants/vueapp/src/stores/variantFlags.js
index a79151a57..573991b8e 100644
--- a/variants/vueapp/src/stores/variantFlags.js
+++ b/variants/vueapp/src/stores/variantFlags.js
@@ -70,7 +70,7 @@ export const useVariantFlagsStore = defineStore('variantFlags', () => {
try {
const res = await variantsApi.listFlags(csrfToken.value, caseUuid.value)
caseFlags.value = Object.fromEntries(
- res.map((flags) => [flags.sodar_uuid, flags])
+ res.map((flags) => [flags.sodar_uuid, flags]),
)
} catch (err) {
storeState.value = StoreState.error
@@ -91,7 +91,7 @@ export const useVariantFlagsStore = defineStore('variantFlags', () => {
const res = await variantsApi.listFlags(
csrfToken.value,
caseUuid.value,
- smallVariant$
+ smallVariant$,
)
if (res.length) {
flags.value = res[0]
@@ -119,7 +119,7 @@ export const useVariantFlagsStore = defineStore('variantFlags', () => {
csrfToken.value,
caseUuid.value,
smallVariant,
- { ...smallVariant, ...payload }
+ { ...smallVariant, ...payload },
)
} finally {
serverInteractions.value -= 1
@@ -148,7 +148,7 @@ export const useVariantFlagsStore = defineStore('variantFlags', () => {
{
...smallVariant,
...payload,
- }
+ },
)
} finally {
serverInteractions.value -= 1