WIP

varfish-org · Sep 27, 2022 · 774adf7 · 774adf7
1 parent 253e0c6
commit 774adf7
Showing 1 changed file with 72 additions and 68 deletions.
diff --git a/varfish/vueapp/src/components/SubmissionList.vue b/varfish/vueapp/src/components/SubmissionList.vue
@@ -380,6 +380,7 @@ export default {
       fetchError: false,
       rawModalUserAnnotations: null,
       rawModalUserAnnotationsCount: 0,
+      modalUserAnnotations: [],
       selectedSmallVariants: [],
     }
   },
@@ -411,74 +412,6 @@ export default {
         this.applySubmissionListSortOrder(value)
       },
     },
-
-    /**
-     * Return filtered data to display in the annotated variant modal.
-     */
-    modalUserAnnotations() {
-      const c = 300000000 // longer than longest chromosome
-      const ua = this.rawModalUserAnnotations
-      if (!ua) {
-        return []
-      }
-
-      const smallVariants = Object.values(ua.smallVariants)
-        .map((smallVar) => {
-          const flags = ua.smallVariantFlags[smallVar.variantId] || []
-          const rating = ua.acmgCriteriaRating[smallVar.variantId] || []
-          const comments = ua.smallVariantComments[smallVar.variantId] || []
-          return { ...smallVar, flags, rating, comments }
-        })
-        .filter((smallVar) => {
-          if (this.individualFilter) {
-            if (
-              !smallVar.caseNames.some((s) => s.includes(this.individualFilter))
-            ) {
-              return false
-            }
-          }
-          if (this.modalIncludeAll) {
-            return true
-          } else if (
-            this.modalIncludeComments &&
-            smallVar.comments.length > 0
-          ) {
-            return true
-          } else if (
-            this.modalIncludeCandidates &&
-            smallVar.flags.some((x) => x.flag_candidate)
-          ) {
-            return true
-          } else if (
-            this.modalIncludeFinalCausatives &&
-            smallVar.flags.some((x) => x.flag_final_causative)
-          ) {
-            return true
-          } else if (
-            this.modalIncludeAcmg3 &&
-            this.getAcmgRating(smallVar) >= 3
-          ) {
-            return true
-          } else if (
-            this.modalIncludeAcmg4 &&
-            this.getAcmgRating(smallVar) >= 4
-          ) {
-            return true
-          } else if (
-            this.modalIncludeAcmg5 &&
-            this.getAcmgRating(smallVar) >= 5
-          ) {
-            return true
-          } else {
-            return false
-          }
-        })
-      smallVariants.sort(
-        (a, b) =>
-          a.chromosome_no * c + a.start - (b.chromosome_no * c + b.start)
-      )
-      return smallVariants
-    },
   },
   methods: {
     ...mapActions('clinvarExport', [
@@ -492,6 +425,7 @@ export default {
      */
     fetchRawModalUserAnnotations() {
       if (this.familyUuid) {
+        this.modalUserAnnotations.splice(0, this.modalUserAnnotations.length)
         this.fetchError = false
         this.loadingVariants = true
         Vue.set(this, 'rawModalUserAnnotations', null)
@@ -556,6 +490,8 @@ export default {
               'rawModalUserAnnotationsCount',
               Object.keys(smallVariants).length
             )
+            const userAnnotations = this._computeUserAnnotations(this.rawModalUserAnnotations)
+            Array.prototype.push.apply(this.modalUserAnnotations, userAnnotations);
             this.loadingVariants = false
           })
           .catch((error) => {
@@ -566,6 +502,74 @@ export default {
       }
     },
 
+
+    /**
+     * Return filtered data to display in the annotated variant modal.
+     */
+    _computeUserAnnotations(ua) {
+      const c = 300000000 // longer than longest chromosome
+      if (!ua) {
+        return []
+      }
+
+      const smallVariants = Object.values(ua.smallVariants)
+        .map((smallVar) => {
+          const flags = ua.smallVariantFlags[smallVar.variantId] || []
+          const rating = ua.acmgCriteriaRating[smallVar.variantId] || []
+          const comments = ua.smallVariantComments[smallVar.variantId] || []
+          return { ...smallVar, flags, rating, comments }
+        })
+        .filter((smallVar) => {
+          if (this.individualFilter) {
+            if (
+              !smallVar.caseNames.some((s) => s.includes(this.individualFilter))
+            ) {
+              return false
+            }
+          }
+          if (this.modalIncludeAll) {
+            return true
+          } else if (
+            this.modalIncludeComments &&
+            smallVar.comments.length > 0
+          ) {
+            return true
+          } else if (
+            this.modalIncludeCandidates &&
+            smallVar.flags.some((x) => x.flag_candidate)
+          ) {
+            return true
+          } else if (
+            this.modalIncludeFinalCausatives &&
+            smallVar.flags.some((x) => x.flag_final_causative)
+          ) {
+            return true
+          } else if (
+            this.modalIncludeAcmg3 &&
+            this.getAcmgRating(smallVar) >= 3
+          ) {
+            return true
+          } else if (
+            this.modalIncludeAcmg4 &&
+            this.getAcmgRating(smallVar) >= 4
+          ) {
+            return true
+          } else if (
+            this.modalIncludeAcmg5 &&
+            this.getAcmgRating(smallVar) >= 5
+          ) {
+            return true
+          } else {
+            return false
+          }
+        })
+      smallVariants.sort(
+        (a, b) =>
+          a.chromosome_no * c + a.start - (b.chromosome_no * c + b.start)
+      )
+      return smallVariants
+    },
+
     toggleData(name) {
       this.$set(this, name, !this[name])
     },