chore: Various test updates (#38) (#45)

frontend/src/api/__tests__/annonars.spec.ts

@@ -43,6 +43,19 @@ describe.concurrent('Annonars Client', () => {
     expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1VariantInfo))
   })
 
+  it('do removes chr prefix from chromosome if genome release is grch38', async () => {
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('chr')) {
+        return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
+      }
+      return Promise.resolve(JSON.stringify({ status: 400 }))
+    })
+
+    const client = new AnnonarsClient()
+    const result = await client.fetchVariantInfo('grch38', 'chr17', 43044295, 'A', 'G')
+    expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1VariantInfo))
+  })
+
   it('fails to fetch variant info with wrong variant', async () => {
     fetchMocker.mockResponse((req) => {
       if (req.url.includes('alternative=G')) {

frontend/src/api/__tests__/utils.spec.ts

@@ -61,6 +61,11 @@ describe('separateIt method', () => {
     const result = separateIt(123456789.12345)
     expect(result).toBe(' 123 456 789 ')
   })
+
+  it('should handle values less then 0', () => {
+    const result = separateIt(0.0134)
+    expect(result).toBe('0 ')
+  })
 })
 
 describe('isVariantMt method', () => {

frontend/src/components/VariantDetails/VariantValidator.vue

@@ -145,6 +145,7 @@ const activeIdentifier = ref<string>('')
               <tbody>
                 <tr
                   v-if="
+                    data.primary_assembly_loci &&
                     data.primary_assembly_loci.grch37 &&
                     data.primary_assembly_loci.grch37.hgvs_genomic_description
                   "
@@ -153,15 +154,16 @@ const activeIdentifier = ref<string>('')
                     {{ data.primary_assembly_loci.grch37.hgvs_genomic_description }}
                   </td>
                   <td>
-                    GRCh37:{{ data.primary_assembly_loci.grch37.vcf.chr }}:{{
-                      data.primary_assembly_loci.grch37.vcf.pos
-                    }}:{{ data.primary_assembly_loci.grch37.vcf.ref }}:{{
-                      data.primary_assembly_loci.grch37.vcf.alt
+                    GRCh37:{{ data.primary_assembly_loci.grch37?.vcf?.chr }}:{{
+                      data.primary_assembly_loci.grch37?.vcf?.pos
+                    }}:{{ data.primary_assembly_loci.grch37?.vcf?.ref }}:{{
+                      data.primary_assembly_loci.grch37?.vcf?.alt
                     }}
                   </td>
                 </tr>
                 <tr
                   v-if="
+                    data.primary_assembly_loci &&
                     data.primary_assembly_loci.grch38 &&
                     data.primary_assembly_loci.grch38.hgvs_genomic_description
                   "
@@ -170,10 +172,10 @@ const activeIdentifier = ref<string>('')
                     {{ data.primary_assembly_loci.grch38.hgvs_genomic_description }}
                   </td>
                   <td>
-                    GRCh38:{{ data.primary_assembly_loci.grch38.vcf.chr }}:{{
-                      data.primary_assembly_loci.grch38.vcf.pos
-                    }}:{{ data.primary_assembly_loci.grch38.vcf.ref }}:{{
-                      data.primary_assembly_loci.grch38.vcf.alt
+                    GRCh38:{{ data.primary_assembly_loci.grch38?.vcf?.chr }}:{{
+                      data.primary_assembly_loci.grch38?.vcf?.pos
+                    }}:{{ data.primary_assembly_loci.grch38?.vcf?.ref }}:{{
+                      data.primary_assembly_loci.grch38?.vcf?.alt
                     }}
                   </td>
                 </tr>

frontend/src/components/__tests__/ClinVar.spec.ts

@@ -52,8 +52,20 @@ describe.concurrent('ClinVar', async () => {
     const wrapper = makeWrapper(clinVarInfo)
     expect(wrapper.text()).toContain('Note that REEV is using a local copy of Clinvar')
     expect(wrapper.text()).toContain('VCV000041833')
-    const starts = wrapper.findAll('.mdi-star-outline')
-    expect(starts.length).toBe(5)
+    const starsOutline = wrapper.findAll('.mdi-star-outline')
+    expect(starsOutline.length).toBe(5)
+  })
+
+  it('renders the ClinVar info with stars', async () => {
+    const clinVarInfoStars = structuredClone(clinVarInfo)
+    clinVarInfoStars.summary_clinvar_gold_stars = 3
+    const wrapper = makeWrapper(clinVarInfoStars)
+    expect(wrapper.text()).toContain('Note that REEV is using a local copy of Clinvar')
+    expect(wrapper.text()).toContain('VCV000041833')
+    const stars = wrapper.findAll('.mdi-star-outline')
+    expect(stars.length).toBe(2)
+    const starsOutline = wrapper.findAll('.mdi-star-outline')
+    expect(starsOutline.length).toBe(2)
   })
 
   it('renders the ClinVar info (not found)', async () => {

frontend/src/components/__tests__/FreqsAutosomal.spec.ts

@@ -34,7 +34,7 @@ const smallVariantInfo = {
   hgnc_id: 'HGNC:1100'
 }
 
-const makeWrapper = (variantData: Object) => {
+const makeWrapper = (variantData: Object | null) => {
   return mount(FreqsAutosomal, {
     props: {
       smallVar: smallVariantInfo,
@@ -59,7 +59,7 @@ describe.concurrent('FreqsAutosomal', async () => {
   })
 
   it('renders the FreqsAutosomal info with no data', async () => {
-    const wrapper = makeWrapper({})
+    const wrapper = makeWrapper(null)
     expect(wrapper.text()).toContain('gnomAD Genomes')
     expect(wrapper.text()).toContain('No allele frequency information available in local database.')
   })

frontend/src/components/__tests__/FreqsMitochondrial.spec.ts

@@ -52,11 +52,11 @@ const variantInfo = {
   }
 }
 
-const makeWrapper = () => {
+const makeWrapper = (variantData: Object) => {
   return mount(FreqsMitochondrial, {
     props: {
       smallVar: smallVariantInfo,
-      varAnnos: variantInfo
+      varAnnos: variantData
     },
     global: {
       plugins: [vuetify, router, createTestingPinia({ createSpy: vi.fn() })],
@@ -69,10 +69,37 @@ const makeWrapper = () => {
 
 describe.concurrent('FreqsMitochondrial', async () => {
   it('renders the FreqsMitochondrial info', async () => {
-    const wrapper = makeWrapper()
+    const wrapper = makeWrapper(variantInfo)
     expect(wrapper.html()).toContain('HelixMTdb')
     expect(wrapper.html()).toContain('gnomAD-MT')
     const table = wrapper.find('table')
     expect(table.exists()).toBe(true)
   })
+
+  it('renders the FreqsMitochondrial info with no helixmtdb', async () => {
+    const variantInfoNoHelixmtdb: any = structuredClone(variantInfo)
+    variantInfoNoHelixmtdb.helixmtdb = {}
+    const wrapper = makeWrapper(variantInfoNoHelixmtdb)
+    expect(wrapper.html()).toContain('HelixMTdb')
+    expect(wrapper.html()).toContain('gnomAD-MT')
+    const table = wrapper.find('table')
+    expect(table.exists()).toBe(true)
+  })
+
+  it('renders the FreqsMitochondrial info with no gnomad-mtdna', async () => {
+    const variantInfoNoGnomad: any = structuredClone(variantInfo)
+    variantInfoNoGnomad['gnomad-mtdna'] = {}
+    const wrapper = makeWrapper(variantInfoNoGnomad)
+    expect(wrapper.html()).toContain('HelixMTdb')
+    expect(wrapper.html()).toContain('gnomAD-MT')
+    const table = wrapper.find('table')
+    expect(table.exists()).toBe(true)
+  })
+
+  it.skip('renders the FreqsMitochondrial info with invalid data', async () => {
+    const wrapper = makeWrapper(smallVariantInfo)
+    console.log(wrapper.html())
+    const alertIcon = wrapper.find('.mdi-alert-circle-outline')
+    expect(alertIcon.exists()).toBe(true)
+  })
 })

frontend/src/components/__tests__/VariantFreqs.spec.ts

@@ -11,6 +11,7 @@ import * as directives from 'vuetify/directives'
 
 import VariantFreqs from '@/components/VariantDetails/VariantFreqs.vue'
 import VariantDetailsFreqsAutosomal from '@/components/VariantDetails/FreqsAutosomal.vue'
+import VariantDetailsFreqsMitochondrial from '@/components/VariantDetails/FreqsMitochondrial.vue'
 import * as BRCA1VariantInfo from '@/assets/__tests__/BRCA1VariantInfo.json'
 
 const vuetify = createVuetify({
@@ -35,10 +36,19 @@ const smallVariantInfo = {
   hgnc_id: 'HGNC:1100'
 }
 
-const makeWrapper = () => {
+const smallVariantInfoMitochondrial = {
+  release: 'grch37',
+  chromosome: 'chrM',
+  start: '70',
+  end: '70',
+  reference: 'G',
+  alternative: 'A',
+  hgnc_id: 'HGNC:1100'
+}
+const makeWrapper = (variantInfo: Object) => {
   return mount(VariantFreqs, {
     props: {
-      smallVar: smallVariantInfo,
+      smallVar: variantInfo,
       varAnnos: BRCA1VariantInfo
     },
     global: {
@@ -52,8 +62,14 @@ const makeWrapper = () => {
 
 describe.concurrent('VariantFreqs', async () => {
   it('renders the VariantFreqs info', async () => {
-    const wrapper = makeWrapper()
+    const wrapper = makeWrapper(smallVariantInfo)
     const freqsAutosomal = wrapper.findComponent(VariantDetailsFreqsAutosomal)
     expect(freqsAutosomal.exists()).toBe(true)
   })
+
+  it('renders the VariantFreqs info for Mitochondrial Variants', async () => {
+    const wrapper = makeWrapper(smallVariantInfoMitochondrial)
+    const freqsAutosomal = wrapper.findComponent(VariantDetailsFreqsMitochondrial)
+    expect(freqsAutosomal.exists()).toBe(true)
+  })
 })

frontend/src/components/__tests__/VariantTools.spec.ts

@@ -55,5 +55,7 @@ describe.concurrent('VariantTools', async () => {
     expect(wrapper.text()).toContain('External Resources')
     expect(wrapper.text()).toContain('IGV')
     expect(wrapper.text()).toContain('Precomputed Scores')
+    const launchIcons = wrapper.findAll('.mdi-launch')
+    expect(launchIcons.length).toBe(8)
   })
 })

frontend/src/components/__tests__/VariantValidator.spec.ts

@@ -49,13 +49,30 @@ const makeWrapper = () => {
   })
 }
 
-// Mock fetch
-global.fetch = vi.fn((): any =>
-  Promise.resolve({ json: () => Promise.resolve(VariantValidatorInfo) })
-)
-
 describe.concurrent('VariantValidator', async () => {
   it('renders the VariantValidator info', async () => {
+    // Mock fetch
+    global.fetch = vi.fn((): any =>
+      Promise.resolve({ ok: true, json: () => Promise.resolve(VariantValidatorInfo) })
+    )
+    const wrapper = makeWrapper()
+    expect(wrapper.text()).toContain('to submit the variant to VariantValidator.org.')
+
+    const submitButton = wrapper.find('button')
+    expect(submitButton.exists()).toBe(true)
+    submitButton.trigger('click')
+    await nextTick()
+    expect(wrapper.text()).toContain('Loading ...')
+    const icon = wrapper.find('.v-progress-circular')
+    expect(icon.exists()).toBe(true)
+    await nextTick()
+  })
+
+  it('renders the VariantValidator info with error', async () => {
+    // Mock fetch
+    global.fetch = vi.fn((): any =>
+      Promise.resolve({ ok: false, json: () => Promise.resolve({ foo: 'foo' }) })
+    )
     const wrapper = makeWrapper()
     expect(wrapper.text()).toContain('to submit the variant to VariantValidator.org.')
 

frontend/src/stores/__tests__/genesList.spec.ts

@@ -14,7 +14,12 @@ const exampleGenesList = {
       score: 0.75,
       data: {
         hgnc_id: 'HGNC:3333',
-        symbol: 'EMP1'
+        symbol: 'EMP1',
+        name: 'epithelial membrane protein 1',
+        alias_symbol: ['TMP', 'CL-20'],
+        alias_name: [],
+        ensembl_gene_id: 'ENSG00000134531',
+        ncbi_gene_id: '2012'
       }
     },
     {
@@ -80,6 +85,24 @@ describe.concurrent('geneInfo Store', () => {
     expect(store.genesList).toBe(null)
   })
 
+  it('should fail to load data with invalid fetchGenes response', async () => {
+    // Disable error logging
+    vi.spyOn(console, 'error').mockImplementation(() => {})
+    const store = useGenesListStore()
+    fetchMocker.mockResponseOnce(JSON.stringify({ genes: [] }))
+
+    await store.loadData({ q: 'EMP', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+
+    expect(console.error).toHaveBeenCalled()
+    expect(console.error).toHaveBeenCalledWith(
+      'There was an error while searching for genes.',
+      new Error('No data returned from API.')
+    )
+    expect(store.storeState).toBe(StoreState.Error)
+    expect(store.query).toBe(null)
+    expect(store.genesList).toBe(null)
+  })
+
   it('should not load data if gene symbol is the same', async () => {
     const store = useGenesListStore()
     fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
@@ -95,7 +118,7 @@ describe.concurrent('geneInfo Store', () => {
     expect(fetchMocker.mock.calls.length).toBe(1)
   })
 
-  it('should redirect if the searchTerm has match', async () => {
+  it('should redirect if the searchTerm matched symbol', async () => {
     const store = useGenesListStore()
     fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
 
@@ -108,4 +131,49 @@ describe.concurrent('geneInfo Store', () => {
 
     expect(fetchMocker.mock.calls.length).toBe(1)
   })
+
+  it('should redirect if the searchTerm matched hgnc_id', async () => {
+    const store = useGenesListStore()
+    fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+
+    await store.loadData({ q: 'HGNC:3333', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+
+    expect(store.storeState).toBe(StoreState.Redirect)
+    expect(store.redirectHgncId).toBe('HGNC:3333')
+    expect(store.query).toBe('q=HGNC:3333&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol')
+    expect(store.genesList).toEqual(exampleGenesList.genes)
+
+    expect(fetchMocker.mock.calls.length).toBe(1)
+  })
+
+  it('should redirect if the searchTerm matched ensembl_gene_id', async () => {
+    const store = useGenesListStore()
+    fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+
+    await store.loadData({
+      q: 'ENSG00000134531',
+      fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol'
+    })
+
+    expect(store.storeState).toBe(StoreState.Redirect)
+    expect(store.redirectHgncId).toBe('HGNC:3333')
+    expect(store.query).toBe('q=ENSG00000134531&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol')
+    expect(store.genesList).toEqual(exampleGenesList.genes)
+
+    expect(fetchMocker.mock.calls.length).toBe(1)
+  })
+
+  it('should redirect if the searchTerm matched ncbi_gene_id', async () => {
+    const store = useGenesListStore()
+    fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+
+    await store.loadData({ q: '2012', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+
+    expect(store.storeState).toBe(StoreState.Redirect)
+    expect(store.redirectHgncId).toBe('HGNC:3333')
+    expect(store.query).toBe('q=2012&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol')
+    expect(store.genesList).toEqual(exampleGenesList.genes)
+
+    expect(fetchMocker.mock.calls.length).toBe(1)
+  })
 })

frontend/src/stores/__tests__/misc.spec.ts

@@ -30,4 +30,14 @@ describe.concurrent('miscInfo Store', () => {
     expect(store.storeState).toBe(StoreState.Active)
     expect(store.appVersion).toBe('v0.0.0')
   })
+
+  it('should handle error', async () => {
+    const store = useMiscStore()
+    fetchMocker.mockRejectOnce('error')
+
+    await store.initialize()
+
+    expect(store.storeState).toBe(StoreState.Error)
+    expect(store.appVersion).toBe(null)
+  })
 })