fix: OMIM id extraction for link-out (#260)

bihealth · Dec 10, 2023 · f362311 · f362311
1 parent 374377a
commit f362311
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Showing 3 changed files with 62 additions and 19 deletions.
diff --git a/frontend/src/components/GeneDetails/ConditionsCard.vue b/frontend/src/components/GeneDetails/ConditionsCard.vue
@@ -4,6 +4,7 @@ import { computed, ref } from 'vue'
 
 import type { HpoTerm } from '@/api/viguno'
 import CadaRanking from '@/components/GeneDetails/ConditionsCard/CadaRanking.vue'
+import { extractDbnsfpMimDiseaseId, transformDbnsfpMimDiseaseId } from '@/lib/utils'
 
 export interface Props {
   geneInfo: any
@@ -23,20 +24,6 @@ const showTermIds = ref<boolean>(false)
 /** Whether to show terms as hyperlinks. */
 const showTermLinks = ref<boolean>(true)
 
-/** Extract MIM disease ID from dbSNFP string */
-const extractMimDiseaseId = (id: string) => {
-  return id.split('[')[1].split(']')[0]
-}
-
-/** Transforms MIM disease ID from dbNSFP depending on `showTermIds.value` */
-const transformMimDiseaseId = (id: string) => {
-  if (showTermIds.value) {
-    return id.replace(']', '] ')
-  } else {
-    return id.split(']')[1].trim()
-  }
-}
-
 // -- code for expanded / collapsed card --------------------------------------
 
 /** Whether the card is expanded. */
@@ -153,15 +140,15 @@ const hpoTermsToShow = computed<HpoTerm[]>(() => {
                 <template v-if="idx > 0"> , </template>
                 <template v-if="showTermLinks">
                   <a
-                    :href="`https://www.omim.org/entry/${extractMimDiseaseId(disease)}`"
+                    :href="`https://www.omim.org/entry/${extractDbnsfpMimDiseaseId(disease)}`"
                     target="_blank"
                   >
                     <v-icon>mdi-launch</v-icon>
-                    {{ transformMimDiseaseId(disease) }}
+                    {{ transformDbnsfpMimDiseaseId(disease, showTermIds) }}
                   </a>
                 </template>
                 <template v-else>
-                  {{ transformMimDiseaseId(disease) }}
+                  {{ transformDbnsfpMimDiseaseId(disease, showTermIds) }}
                 </template>
               </template>
             </div>

diff --git a/frontend/src/lib/__tests__/utils.spec.ts b/frontend/src/lib/__tests__/utils.spec.ts
@@ -1,16 +1,18 @@
-import { describe, expect, it } from 'vitest'
+import { describe, expect, it, test } from 'vitest'
 
 import { type GenomeBuild } from '@/lib/genomeBuilds'
 import { type Seqvar } from '@/lib/genomicVars'
 
 import {
   copy,
+  extractDbnsfpMimDiseaseId,
   infoFromQuery,
   isVariantMt,
   isVariantMtHomopolymer,
   removeCommasFromNumbers,
   roundIt,
-  separateIt
+  separateIt,
+  transformDbnsfpMimDiseaseId
 } from '../utils'
 
 /** Example Sequence variant. */
@@ -185,3 +187,39 @@ describe.concurrent('copy method', () => {
     expect(result).toEqual({ foo: 'bar' })
   })
 })
+
+describe.concurrent('extractDbnsfpMimDiseaseId', () => {
+  test.each([
+    ['[MIM:616921] Dyskinesia, limb and orofacial, infantile-onset', '616921'],
+    ['[MIM:616921] Dyskinesia, limb and orofacial, infantile-onset [recessive?]', '616921']
+  ])('%s => %s', (lhs, rhs) => {
+    expect(extractDbnsfpMimDiseaseId(lhs)).toEqual(rhs)
+  })
+})
+
+describe.concurrent('transformDbnsfpMimDiseaseId', () => {
+  test.each([
+    [
+      '[MIM:616921]Dyskinesia, limb and orofacial, infantile-onset',
+      '[MIM:616921] Dyskinesia, limb and orofacial, infantile-onset',
+      true
+    ],
+    [
+      '[MIM:616921]Dyskinesia, limb and orofacial, infantile-onset [recessive?]',
+      '[MIM:616921] Dyskinesia, limb and orofacial, infantile-onset [recessive?]',
+      true
+    ],
+    [
+      '[MIM:616921]Dyskinesia, limb and orofacial, infantile-onset',
+      'Dyskinesia, limb and orofacial, infantile-onset',
+      false
+    ],
+    [
+      '[MIM:616921]Dyskinesia, limb and orofacial, infantile-onset [recessive?]',
+      'Dyskinesia, limb and orofacial, infantile-onset [recessive?]',
+      false
+    ]
+  ])('should work correctly', (lhs, rhs, showTermIds) => {
+    expect(transformDbnsfpMimDiseaseId(lhs, showTermIds)).toEqual(rhs)
+  })
+})
diff --git a/frontend/src/lib/utils.ts b/frontend/src/lib/utils.ts
@@ -226,3 +226,21 @@ export const bookmarkTo = (bookmark: BookmarkData): RouteLocationRaw => {
       }
   }
 }
+
+/**
+ * Extract MIM disease ID from dbSNFP string
+ */
+export const extractDbnsfpMimDiseaseId = (id: string) => {
+  return id.split('[')[1].split(']', 1)[0].replace('MIM:', '')
+}
+
+/**
+ * Transforms MIM disease ID from dbNSFP depending on `showTermIds.value`
+ */
+export const transformDbnsfpMimDiseaseId = (id: string, showTermIds: boolean) => {
+  if (showTermIds) {
+    return id.replace(']', '] ')
+  } else {
+    return id.split(']').splice(1).join(']').trim()
+  }
+}