chore: correctly applying prettier style (#1096)

A path was missing in the package.json.
varfish-org · Aug 1, 2023 · b12c3ac · b12c3ac
1 parent bfec8a8
commit b12c3ac
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Showing 96 changed files with 500 additions and 496 deletions.
diff --git a/cases/vueapp/src/api/cases.js b/cases/vueapp/src/api/cases.js
@@ -4,7 +4,7 @@ export default {
   async listCase(
     csrfToken,
     projectUuid,
-    { pageNo, pageSize, orderBy, orderDir, queryString }
+    { pageNo, pageSize, orderBy, orderDir, queryString },
   ) {
     let queryArr = []
     if (pageNo !== undefined) {
@@ -29,7 +29,7 @@ export default {
     const queryStr = queryArr.length ? '?' + queryArr.join('&') : ''
     const response = await apiFetch(
       csrfToken,
-      `/cases/ajax/case/list/${projectUuid}/${queryStr}`
+      `/cases/ajax/case/list/${projectUuid}/${queryStr}`,
     )
     return await response.json()
   },
@@ -39,7 +39,7 @@ export default {
       csrfToken,
       `/cases/ajax/case/retrieve-update/${caseUuid}/`,
       'GET',
-      payload
+      payload,
     )
     return await response.json()
   },
@@ -49,15 +49,15 @@ export default {
       csrfToken,
       `/cases/ajax/case/retrieve-update/${caseUuid}/`,
       'PATCH',
-      payload
+      payload,
     )
     return await response.json()
   },
 
   async loadProjectQcValues(csrfToken, projectUuid) {
     const response = await apiFetch(
       csrfToken,
-      `/variants/ajax/project/qc/${projectUuid}/`
+      `/variants/ajax/project/qc/${projectUuid}/`,
     )
     return await response.json()
   },
@@ -86,7 +86,7 @@ export default {
     const response = await apiFetch(
       csrfToken,
       `/cases/ajax/case-comment/list-create/${caseUuid}/`,
-      'GET'
+      'GET',
     )
     return await response.json()
   },
@@ -96,7 +96,7 @@ export default {
       csrfToken,
       `/cases/ajax/case-comment/list-create/${caseUuid}/`,
       'POST',
-      payload
+      payload,
     )
     return await response.json()
   },
@@ -105,7 +105,7 @@ export default {
     const response = await apiFetch(
       csrfToken,
       `/cases/ajax/case-comment/retrieve-update-destroy/${caseCommentUuid}/`,
-      'GET'
+      'GET',
     )
     return await response.json()
   },
@@ -115,7 +115,7 @@ export default {
       csrfToken,
       `/cases/ajax/case-comment/retrieve-update-destroy/${caseCommentUuid}/`,
       'PATCH',
-      payload
+      payload,
     )
     return await response.json()
   },
@@ -124,15 +124,15 @@ export default {
     await apiFetch(
       csrfToken,
       `/cases/ajax/case-comment/retrieve-update-destroy/${caseCommentUuid}/`,
-      'DELETE'
+      'DELETE',
     )
   },
 
   async listCasePhenotypeTerms(csrfToken, caseUuid) {
     const response = await apiFetch(
       csrfToken,
       `/cases/ajax/case-phenotype-terms/list-create/${caseUuid}/`,
-      'GET'
+      'GET',
     )
     return await response.json()
   },
@@ -142,7 +142,7 @@ export default {
       csrfToken,
       `/cases/ajax/case-phenotype-terms/list-create/${caseUuid}/`,
       'POST',
-      payload
+      payload,
     )
     return await response.json()
   },
@@ -151,7 +151,7 @@ export default {
     const response = await apiFetch(
       csrfToken,
       `/cases/ajax/case-phenotype-terms/retrieve-update-destroy/${casePhenotypeTermsUuid}/`,
-      'GET'
+      'GET',
     )
     return await response.json()
   },
@@ -161,7 +161,7 @@ export default {
       csrfToken,
       `/cases/ajax/case-phenotype-terms/retrieve-update-destroy/${casePhenotypeTermsUuid}/`,
       'PATCH',
-      payload
+      payload,
     )
     return await response.json()
   },
@@ -170,62 +170,62 @@ export default {
     await apiFetch(
       csrfToken,
       `/cases/ajax/case-phenotype-terms/retrieve-update-destroy/${casePhenotypeTermsUuid}/`,
-      'DELETE'
+      'DELETE',
     )
   },
 
   async fetchAnnotationReleaseInfos(csrfToken, caseUuid) {
     const response = await apiFetch(
       csrfToken,
-      `/cases/api/annotation-release-info/list/${caseUuid}/`
+      `/cases/api/annotation-release-info/list/${caseUuid}/`,
     )
     return await response.json()
   },
 
   async fetchSvAnnotationReleaseInfos(csrfToken, caseUuid) {
     const response = await apiFetch(
       csrfToken,
-      `/cases/api/sv-annotation-release-info/list/${caseUuid}/`
+      `/cases/api/sv-annotation-release-info/list/${caseUuid}/`,
     )
     return await response.json()
   },
 
   async fetchCaseGeneAnnotation(csrfToken, caseUuid) {
     const response = await apiFetch(
       csrfToken,
-      `/cases/api/case-gene-annotation/list/${caseUuid}/`
+      `/cases/api/case-gene-annotation/list/${caseUuid}/`,
     )
     return await response.json()
   },
 
   async fetchCaseAlignmentStats(csrfToken, caseUuid) {
     const response = await apiFetch(
       csrfToken,
-      `/cases/api/case-alignment-stats/list/${caseUuid}/`
+      `/cases/api/case-alignment-stats/list/${caseUuid}/`,
     )
     return await response.json()
   },
 
   async fetchCaseVariantStats(csrfToken, caseUuid) {
     const response = await apiFetch(
       csrfToken,
-      `/cases/api/case-variant-stats/list/${caseUuid}/`
+      `/cases/api/case-variant-stats/list/${caseUuid}/`,
     )
     return await response.json()
   },
 
   async fetchCaseRelatedness(csrfToken, caseUuid) {
     const response = await apiFetch(
       csrfToken,
-      `/cases/api/case-relatedness/list/${caseUuid}/`
+      `/cases/api/case-relatedness/list/${caseUuid}/`,
     )
     return await response.json()
   },
 
   async fetchPermissions(csrfToken, projectUuid) {
     const response = await apiFetch(
       csrfToken,
-      `/cases/ajax/user-permissions/${projectUuid}/`
+      `/cases/ajax/user-permissions/${projectUuid}/`,
     )
     return await response.json()
   },

diff --git a/cases/vueapp/src/common.js b/cases/vueapp/src/common.js
@@ -35,14 +35,14 @@ export const connectTopRowControls = () => {
         updateUserSetting(
           casesStore.appContext.csrf_token,
           'vueapp.filtration_inline_help',
-          newValue
+          newValue,
         )
       }
       const elem = $('#vueapp-filtration-inline-help')
       if (elem) {
         elem.prop('checked', newValue)
       }
-    }
+    },
   )
   watch(
     () => casesStore.complexityMode,
@@ -51,22 +51,22 @@ export const connectTopRowControls = () => {
         updateUserSetting(
           casesStore.appContext.csrf_token,
           'vueapp.filtration_complexity_mode',
-          newValue
+          newValue,
         )
       }
       const elem = $('#vueapp-filtration-complexity-mode')
       if (elem && elem.val(newValue)) {
         elem.val(newValue).change()
       }
-    }
+    },
   )
 
   // Vice versa.
   onMounted(() => {
     const handleUpdate = () => {
       const casesStore = useCasesStore()
       casesStore.showInlineHelp = $('#vueapp-filtration-inline-help').prop(
-        'checked'
+        'checked',
       )
       casesStore.complexityMode = $('#vueapp-filtration-complexity-mode').val()
     }
@@ -89,7 +89,7 @@ export const tsTvRatio = (entry) => {
 export const downloadFile = (
   filename,
   contents,
-  mimeType = 'application/octet-stream'
+  mimeType = 'application/octet-stream',
 ) => {
   const element = document.createElement('a')
   element.setAttribute('href', 'data:' + mimeType + ';base64,' + btoa(contents))

diff --git a/cases/vueapp/src/components/CaseDetail.vue b/cases/vueapp/src/components/CaseDetail.vue
@@ -43,7 +43,7 @@ casesStore.initializeRes.then(() => {
           if (newParams.case && newParams.case !== oldParams.case) {
             caseDetailsStore.initialize(caseUuidRef.value)
           }
-        }
+        },
       )
     })
     .catch((err) => {
@@ -75,7 +75,7 @@ const handleEditQueryPresetsClicked = async () => {
     allPresets.map((p) => ({
       value: p.sodar_uuid,
       label: p.label,
-    }))
+    })),
   )
 
   try {
@@ -301,11 +301,11 @@ const handleUpdateCasePhenotypeTermsClicked = async ({
     let origTerms = []
     if (casePhenotypeTermsUuid) {
       const casePhenotypeTerms = caseDetailsStore.getCasePhenotypeTerms(
-        casePhenotypeTermsUuid
+        casePhenotypeTermsUuid,
       )
       if (!casePhenotypeTerms) {
         throw new Error(
-          `Could not fetch case phenotype terms ${casePhenotypeTermsUuid}`
+          `Could not fetch case phenotype terms ${casePhenotypeTermsUuid}`,
         )
       }
       origTerms = casePhenotypeTerms.terms
@@ -326,7 +326,7 @@ const handleUpdateCasePhenotypeTermsClicked = async ({
         {
           individual,
           terms,
-        }
+        },
       )
     }
 

diff --git a/cases/vueapp/src/components/CaseDetailCardAnnotations.vue b/cases/vueapp/src/components/CaseDetailCardAnnotations.vue
@@ -40,11 +40,11 @@ const buildComputedAnnoCountByFlag = (theList) => {
 }
 
 const varAnnoCountByFlag = buildComputedAnnoCountByFlag(
-  caseDetailsStore.varAnnoList
+  caseDetailsStore.varAnnoList,
 )
 
 const svAnnoCountByFlag = buildComputedAnnoCountByFlag(
-  caseDetailsStore.svrAnnoList
+  caseDetailsStore.svrAnnoList,
 )
 </script>
 

diff --git a/cases/vueapp/src/components/CaseDetailCardQueries.vue b/cases/vueapp/src/components/CaseDetailCardQueries.vue
@@ -28,15 +28,15 @@ watch(
     try {
       const presetSet = await queryPresetsApi.retrievePresetSet(
         csrfToken,
-        newValue
+        newValue,
       )
       presetSetLabel.value = presetSet.label
     } catch (err) {
       console.error('Problem retrieving preset set', err)
     } finally {
       presetSetLoading.value = false
     }
-  }
+  },
 )
 </script>
 

diff --git a/cases/vueapp/src/components/CaseDetailCardTerms.vue b/cases/vueapp/src/components/CaseDetailCardTerms.vue
@@ -74,7 +74,7 @@ watch(
   () => termLabels.value,
   (_newValue, _oldValue) => {
     fetchTermLabels()
-  }
+  },
 )
 
 onMounted(() => {

diff --git a/cases/vueapp/src/components/CaseDetailCardVariantQc.vue b/cases/vueapp/src/components/CaseDetailCardVariantQc.vue
@@ -14,7 +14,7 @@ const tsTv = (member) => {
   ) {
     const stats = caseDetailsStore.caseVariantStats[member.name]
     return (stats.ontarget_transitions / stats.ontarget_transversions).toFixed(
-      2
+      2,
     )
   } else {
     return 0
@@ -49,15 +49,15 @@ const tsTv = (member) => {
                 {{
                   formatLargeInt(
                     caseDetailsStore.caseVariantStats[member.name]
-                      .ontarget_transitions
+                      .ontarget_transitions,
                   )
                 }}
               </td>
               <td class="text-right">
                 {{
                   formatLargeInt(
                     caseDetailsStore.caseVariantStats[member.name]
-                      .ontarget_transversions
+                      .ontarget_transversions,
                   )
                 }}
               </td>
@@ -71,7 +71,7 @@ const tsTv = (member) => {
                 v-else
                 class="text-right text-danger font-weight-bold"
                 :title="`Ts/Tv ratio should be within 2.0-2.9 but is ${tsTv(
-                  member
+                  member,
                 )}`"
               >
                 <i-bi-exclamation-circle />

diff --git a/cases/vueapp/src/components/CaseDetailContent.vue b/cases/vueapp/src/components/CaseDetailContent.vue
@@ -31,7 +31,7 @@ const currentTab = ref('overview')
 const caseDetailsStore = useCaseDetailsStore()
 
 const annosLoading = computed(
-  () => caseDetailsStore.varAnnos === null || caseDetailsStore.svAnnos === null
+  () => caseDetailsStore.varAnnos === null || caseDetailsStore.svAnnos === null,
 )
 const annoCount = computed(() => {
   if (annosLoading) {

diff --git a/cases/vueapp/src/components/CaseDetailPaneAnnotations.vue b/cases/vueapp/src/components/CaseDetailPaneAnnotations.vue
@@ -45,7 +45,7 @@ const showModal = ({ gridRow, gridApi, smallVariant }) => {
     gridRow,
     gridApi,
     smallVariant,
-    'refseq'
+    'refseq',
   )
 }
 
@@ -55,7 +55,7 @@ onMounted(async () => {
   const csrfToken = casesStore.appContext.csrfToken
   const apiQueryResults = await variantsApi.listCaseVariantsUserAnnotated(
     csrfToken,
-    caseDetailsStore.caseObj.sodar_uuid
+    caseDetailsStore.caseObj.sodar_uuid,
   )
   filterQueryStore.queryResults = apiQueryResults.rows
 })