feat: Finish integration of genome browser (#102) (#104)

bihealth · Oct 2, 2023 · a2f8282 · a2f8282
1 parent b2411a6
commit a2f8282
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Showing 5 changed files with 84 additions and 97 deletions.
diff --git a/frontend/src/components/GenomeBrowser.vue b/frontend/src/components/GenomeBrowser.vue
@@ -2,14 +2,12 @@
 import igv from 'igv'
 import { onMounted, ref, watch } from 'vue'
 
-// import { genCaseTrack, publicTracks } from '@/components/GenomeBrowser.tracks'
+import { publicTracks } from '@/lib/genomeBrowserTracks'
 
 /** Alias for Genome Browser type. */
 type GenomeBrowser = any
 
 export interface Props {
-  // Case UUID
-  caseUuid: string
   // Genome build, e.g., "hg19" or "b37"
   genome: string
   // Locus to go to, e.g., "chr1:1,900,000-2,000,000"
@@ -19,36 +17,37 @@ export interface Props {
 // Define the props.
 const props = defineProps<Props>()
 
-// The <div> to show the browser in.
+/** The <div> to show the browser in. */
 const genomeBrowserDivRef = ref(null)
-// Set on IGV browser creation.
+/** Set on IGV browser creation. */
 const igvBrowser = ref(null)
 
+/**
+ * Translate genome build names from GRCh37/GRCh38 to hg19/hg38.
+ *
+ * @param value The genome build name.
+ * @returns The translated genome build name. (hg19/hg38)
+ */
 const translateGenome = (value: any) => {
   if (value === 'GRCh37') {
     return 'hg19'
   } else if (value === 'GRCh38') {
-    return 'b38'
+    return 'hg38'
   } else {
     return value
   }
 }
 
-// Conditionally add case tracks.
-// const addCaseTracks = (browser: GenomeBrowser) => {
-//   if (props.caseUuid) {
-//     console.log(genCaseTrack(props.caseUuid))
-//     browser.loadTrack(genCaseTrack(props.caseUuid))
-//   }
-// }
-
-// Add all tracks.
-// const addTracks = (browser: any) => {
-//   addCaseTracks(browser)
-//   for (const track of publicTracks) {
-//     browser.loadTrack(track)
-//   }
-// }
+/**
+ * Add public tracks.
+ *
+ * @param browser The IGV browser.
+ */
+const addTracks = (browser: any) => {
+  for (const track of publicTracks) {
+    browser.loadTrack(track)
+  }
+}
 
 // Watch changes to the genome (requires full reload).
 watch(
@@ -59,20 +58,9 @@ watch(
       .then((browser: GenomeBrowser) => {
         browser.search(props.locus)
       })
-    // .then((browser: GenomeBrowser) => {
-    // addTracks(browser)
-    // })
-  }
-)
-
-// Watch changes to the case (requires track reload).
-watch(
-  () => props.caseUuid,
-  () => {
-    if (igvBrowser.value) {
-      ;(igvBrowser.value! as GenomeBrowser).removeTrackByName('Case SVs')
-      // addCaseTracks(igvBrowser.value)
-    }
+      .then((browser: GenomeBrowser) => {
+        addTracks(browser)
+      })
   }
 )
 
@@ -95,7 +83,7 @@ onMounted(() => {
     })
     .then((browser: GenomeBrowser) => {
       igvBrowser.value = browser
-      // addTracks(browser)
+      addTracks(browser)
       if (props.locus) {
         ;(igvBrowser.value! as GenomeBrowser).search(props.locus)
       }

diff --git a/frontend/src/components/__tests__/GenomeBrowser.spec.ts b/frontend/src/components/__tests__/GenomeBrowser.spec.ts
@@ -5,17 +5,29 @@ import { setupMountedComponents } from '@/lib/test-utils'
 import GenomeBrowser from '../GenomeBrowser.vue'
 
 describe.concurrent('GenomeBrowser', async () => {
-  it('renders the GenomeBrowser', async () => {
+  it('renders the GenomeBrowser with the hg19 genome', async () => {
     const { wrapper } = setupMountedComponents(
       { component: GenomeBrowser, template: false },
       {
         props: {
-          caseUuid: 'your_case_uuid',
           genome: 'hg19',
           locus: 'chr17:41246243-41246243'
         }
       }
     )
     expect(wrapper.exists()).toBe(true)
   })
+
+  it('renders the GenomeBrowser with the hg38 genome', async () => {
+    const { wrapper } = setupMountedComponents(
+      { component: GenomeBrowser, template: false },
+      {
+        props: {
+          genome: 'hg38',
+          locus: 'chr17:41246243-41246243'
+        }
+      }
+    )
+    expect(wrapper.exists()).toBe(true)
+  })
 })
diff --git a/frontend/src/lib/__tests__/genomeBrowserTracks.spec.ts b/frontend/src/lib/__tests__/genomeBrowserTracks.spec.ts
@@ -0,0 +1,45 @@
+import { describe, expect, it } from 'vitest'
+
+import { publicTracks } from '../genomeBrowserTracks'
+
+describe('publicTracks', () => {
+  it('should have at least one track', () => {
+    expect(publicTracks.length).toBeGreaterThan(0)
+  })
+
+  it('should have a name for each track', () => {
+    publicTracks.forEach((track) => {
+      expect(track.name).toBeDefined()
+    })
+  })
+
+  it('should have a sourceType for each track', () => {
+    publicTracks.forEach((track) => {
+      expect(track.sourceType).toBeDefined()
+    })
+  })
+
+  it('should have a format for each track', () => {
+    publicTracks.forEach((track) => {
+      expect(track.format).toBeDefined()
+    })
+  })
+
+  it('should have a visibilityWindow for each track', () => {
+    publicTracks.forEach((track) => {
+      expect(track.visibilityWindow).toBeDefined()
+    })
+  })
+
+  it('should have a url for each track', () => {
+    publicTracks.forEach((track) => {
+      expect(track.url).toBeDefined()
+    })
+  })
+
+  it('should have a color for each track', () => {
+    publicTracks.forEach((track) => {
+      expect(track.color).toBeDefined()
+    })
+  })
+})
diff --git a/...nd/src/components/GenomeBrowser.tracks.ts → frontend/src/lib/genomeBrowserTracks.ts b/...nd/src/components/GenomeBrowser.tracks.ts → frontend/src/lib/genomeBrowserTracks.ts
@@ -22,33 +22,6 @@ const curatedMmsTrack = {
   color: 'red'
 }
 
-// const clinvarTrack = {
-//   name: 'ClinVar SVs',
-//   sourceType: 'custom',
-//   visibilityWindow,
-//   height: 100,
-//   displayMode: 'SQUISHED',
-//   source: {
-//     url: `/svs/worker/clinvar/grch37/?min_pathogenicity=likely-pathogenic&chromosome=$CHR&begin=$START&end=$END`,
-//     method: 'GET',
-//     contentType: 'application/json',
-//     mappings: {
-//       chr: 'chromosome',
-//       start: 'begin',
-//     },
-//     queryable: true,
-//   },
-//   format: 'annotation',
-//   colorBy: 'pathogenicity',
-//   colorTable: {
-//     pathogenic: 'red',
-//     'likely-pathogenic': 'orange',
-//     uncertain: 'blue',
-//     'likely-benign': 'gray',
-//     benign: 'light gray',
-//   },
-// }
-
 const duplicationTrack = {
   name: 'UCSC Segmental Duplications',
   sourceType: 'annotation',
@@ -90,10 +63,6 @@ const fixTrack = {
 }
 
 const bgDbTracks = [
-  // {
-  //   title: 'In-House SVs',
-  //   token: 'inhouse',
-  // },
   {
     title: 'gnomad-SV',
     token: 'gnomad'
@@ -122,38 +91,12 @@ const bgDbTracks = [
     color: 'black'
   }
 })
+
 export const publicTracks = [
   duplicationTrack,
   repeatsTrack,
   altTrack,
   fixTrack,
   hescTadTrack,
   curatedMmsTrack
-  // clinvarTrack,
 ].concat(bgDbTracks)
-
-export const genCaseTrack = (caseUuid: string) => ({
-  order: -1,
-  height: '200',
-  name: 'Case SVs',
-  sourceType: 'custom',
-  visibilityWindow,
-  source: {
-    url: `/svs/ajax/fetch-variants/${caseUuid}/?chromosome=$CHR&start=$START&end=$END`,
-    // url: `https://varfish.bihealth.org/svs/ajax/fetch-variants/7a538a72-f8fb-4d71-a08b-6045f1e983dc/?chromosome=chr15&start=16989370.8&end=26828561.7`,
-    method: 'GET',
-    contentType: 'application/json',
-    mappings: {
-      chr: 'chromosome'
-    },
-    queryable: true
-  },
-  format: 'annotation',
-  colorBy: 'sv_type',
-  colorTable: {
-    DEL: 'red',
-    DUP: 'green',
-    INV: 'blue',
-    '*': 'black'
-  }
-})
diff --git a/frontend/src/views/SvDetailView.vue b/frontend/src/views/SvDetailView.vue
@@ -135,7 +135,6 @@ const genomeReleaseRef = ref(props.genomeRelease)
           <h2>Genome Browser</h2>
           <v-divider />
           <GenomeBrowser
-            :case-uuid="'case-uuid'"
             :genome="genomeRelease === 'grch37' ? 'hg19' : 'b38'"
             :locus="svLocus(svInfoStore.currentSvRecord) as string"
           />