diff --git a/frontend/src/api/__tests__/acmgSeqvar.spec.ts b/frontend/src/api/__tests__/acmgSeqvar.spec.ts
index 8a8b736c..8518e810 100644
--- a/frontend/src/api/__tests__/acmgSeqvar.spec.ts
+++ b/frontend/src/api/__tests__/acmgSeqvar.spec.ts
@@ -7,6 +7,7 @@ import { type AcmgRatingBackend } from '@/stores/seqvarAcmgRating'
const fetchMocker = createFetchMock(vi)
+// Test data
const seqVar = new SeqvarImpl('grch37', '1', 123, 'A', 'G')
const mockAcmgRating: AcmgRatingBackend = {
comment: 'exampleComment',
@@ -26,15 +27,19 @@ describe.concurrent('AcmgSeqVar Client', () => {
})
it('lists ACMG ratings correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify([mockAcmgRating]))
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.listAcmgRatings()
+ // assert:
expect(result).toEqual([mockAcmgRating])
})
it('fails to list ACMG ratings', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('acmgSeqvar/list')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -42,22 +47,28 @@ describe.concurrent('AcmgSeqVar Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.listAcmgRatings()
+ // assert:
expect(result).toEqual({ status: 500 })
})
it('fetches ACMG rating correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(mockAcmgRating))
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.fetchAcmgRating(seqVar)
+ // assert:
expect(result).toEqual(mockAcmgRating)
})
it('fails to fetch ACMG rating', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('acmgSeqvar/get')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -65,22 +76,28 @@ describe.concurrent('AcmgSeqVar Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.fetchAcmgRating(seqVar)
+ // assert:
expect(result).toEqual({ status: 500 })
})
it('saves ACMG rating correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(mockAcmgRating))
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.saveAcmgRating(seqVar, mockAcmgRating)
+ // assert:
expect(result).toEqual(mockAcmgRating)
})
it('fails to save ACMG rating', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('acmgSeqvar/create')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -88,22 +105,28 @@ describe.concurrent('AcmgSeqVar Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.saveAcmgRating(seqVar, mockAcmgRating)
+ // assert:
expect(result).toEqual({ status: 500 })
})
it('updates ACMG rating correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(mockAcmgRating))
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.updateAcmgRating(seqVar, mockAcmgRating)
+ // assert:
expect(result).toEqual(mockAcmgRating)
})
it('fails to update ACMG rating', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('acmgSeqvar/update')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -111,22 +134,28 @@ describe.concurrent('AcmgSeqVar Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.updateAcmgRating(seqVar, mockAcmgRating)
+ // assert:
expect(result).toEqual({ status: 500 })
})
it('deletes ACMG rating correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({}))
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.deleteAcmgRating(seqVar)
+ // assert:
expect(result).toEqual({})
})
it('fails to delete ACMG rating', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('acmgSeqvar/delete')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -134,9 +163,11 @@ describe.concurrent('AcmgSeqVar Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AcmgSeqVarClient()
const result = await client.deleteAcmgRating(seqVar)
+ // assert:
expect(result).toEqual({ status: 500 })
})
})
diff --git a/frontend/src/api/__tests__/annonars.spec.ts b/frontend/src/api/__tests__/annonars.spec.ts
index f6b8b3c8..a1f58bba 100644
--- a/frontend/src/api/__tests__/annonars.spec.ts
+++ b/frontend/src/api/__tests__/annonars.spec.ts
@@ -9,6 +9,7 @@ import { SeqvarImpl } from '@/lib/genomicVars'
const fetchMocker = createFetchMock(vi)
+// Test data
const seqVar = new SeqvarImpl('grch37', '1', 123, 'A', 'G')
describe.concurrent('Annonars Client', () => {
@@ -18,14 +19,19 @@ describe.concurrent('Annonars Client', () => {
})
it('fetches gene info correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify(BRCA1geneInfo))
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchGeneInfo('BRCA1')
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1geneInfo))
})
it('fails to fetch gene info with wrong HGNC id', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('hgnc_id=BRCA1')) {
return Promise.resolve(JSON.stringify(BRCA1geneInfo))
@@ -33,20 +39,28 @@ describe.concurrent('Annonars Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchGeneInfo('123')
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
})
it('fetches variant info correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify(BRCA1VariantInfo))
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchVariantInfo(seqVar)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1VariantInfo))
})
it('do removes chr prefix from chromosome if genome release is grch38', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('chr')) {
return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
@@ -54,12 +68,16 @@ describe.concurrent('Annonars Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchVariantInfo(seqVar)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1VariantInfo))
})
it('fails to fetch variant info with wrong variant', async () => {
+ // arrange:
const seqVarInvalid = new SeqvarImpl('grch37', '1', 123, 'A', 'T')
fetchMocker.mockResponse((req) => {
if (req.url.includes('alternative=G')) {
@@ -68,20 +86,28 @@ describe.concurrent('Annonars Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchVariantInfo(seqVarInvalid)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
})
it('fetches gene clinvar info correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify(BRCA1geneInfo))
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchGeneClinvarInfo('BRCA1')
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1geneInfo))
})
it('fails to fetch gene clinvar info with wrong HGNC id', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('hgnc_id=BRCA1')) {
return Promise.resolve(JSON.stringify(BRCA1geneInfo))
@@ -89,22 +115,30 @@ describe.concurrent('Annonars Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchGeneClinvarInfo('123')
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
})
it('fetches genes correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify(EMPSearchInfo))
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchGenes(
'q=BRCA1&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol'
)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(EMPSearchInfo))
})
it('fails to fetch genes with wrong query', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('q=BRCA1')) {
return Promise.resolve(JSON.stringify(EMPSearchInfo))
@@ -112,28 +146,39 @@ describe.concurrent('Annonars Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchGenes(
'q=BRCA2&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol'
)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
})
it('fetches gene infos correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(BRCA1geneInfo))
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchGeneInfos(['BRCA1', 'BRCA2'])
+
+ // assert:
expect(JSON.stringify(result)).toMatch(JSON.stringify(BRCA1geneInfo['genes']['HGNC:1100']))
})
it.fails('fails to fetch gene infos with wrong HGNC id', async () => {
+ // arrange:
fetchMocker.mockResponse(() => {
return Promise.resolve(JSON.stringify({ status: 500 }))
})
+ // act:
const client = new AnnonarsClient()
const result = await client.fetchGeneInfos(['123', 'BRCA2'])
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 500 }))
})
})
diff --git a/frontend/src/api/__tests__/auth.spec.ts b/frontend/src/api/__tests__/auth.spec.ts
index e3c57ddb..1385646c 100644
--- a/frontend/src/api/__tests__/auth.spec.ts
+++ b/frontend/src/api/__tests__/auth.spec.ts
@@ -12,38 +12,50 @@ describe.concurrent('AuthClient', () => {
})
it('should login successfully', async () => {
+ // arrange:
fetchMocker.mockResponseOnce('', { status: 204 })
+ // act:
const client = new AuthClient()
const result = await client.login('testuser', 'password123')
+ // assert:
expect(result).toBe(true)
})
it('should fail to login with incorrect credentials', async () => {
+ // arrange:
fetchMocker.mockResponseOnce('', { status: 401 })
+ // act:
const client = new AuthClient()
const result = await client.login('invaliduser', 'invalidpassword')
+ // assert:
expect(result).toBe(false)
})
it('should logout successfully', async () => {
+ // arrange:
fetchMocker.mockResponseOnce('Logout Successful', { status: 200 })
+ // act:
const client = new AuthClient()
const result = await client.logout()
+ // assert:
expect(result).toBe('Logout Successful')
})
it('should handle logout failure', async () => {
+ // arrange:
fetchMocker.mockResponseOnce('Logout Failed', { status: 500 })
+ // act:
const client = new AuthClient()
const result = await client.logout()
+ // assert:
expect(result).toBe('Logout Failed')
})
})
diff --git a/frontend/src/api/__tests__/bookmarks.spec.ts b/frontend/src/api/__tests__/bookmarks.spec.ts
index 450135c0..3ecda8d9 100644
--- a/frontend/src/api/__tests__/bookmarks.spec.ts
+++ b/frontend/src/api/__tests__/bookmarks.spec.ts
@@ -7,6 +7,7 @@ import { BookmarksClient } from '../bookmarks'
const fetchMocker = createFetchMock(vi)
+// Test data
const mockBookmarks: BookmarkData[] = [
{
user: '2c0a153e-5e8c-11ee-8c99-0242ac120002',
@@ -23,6 +24,7 @@ describe.concurrent('Bookmarks Client', () => {
})
it('fetches bookmarks correctly', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('users/me')) {
return Promise.resolve(JSON.stringify({ id: '2c0a153e-5e8c-11ee-8c99-0242ac120002' }))
@@ -31,13 +33,17 @@ describe.concurrent('Bookmarks Client', () => {
}
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+
+ // act:
const client = new BookmarksClient()
const result = await client.fetchBookmarks()
+ // assert:
expect(result).toEqual(mockBookmarks)
})
it('fails to fetch bookmarks', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('users/me')) {
return Promise.resolve(JSON.stringify({ id: '2c0a153e-5e8c-11ee-8c99-0242ac120002' }))
@@ -46,63 +52,84 @@ describe.concurrent('Bookmarks Client', () => {
}
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+
+ // act:
const client = new BookmarksClient()
const result = await client.fetchBookmarks()
+ // assert:
expect(result).toEqual({ status: 500 })
})
it('fetches bookmark correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(mockBookmarks[0]))
+ // act:
const client = new BookmarksClient()
const result = await client.fetchBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(result).toEqual(mockBookmarks[0])
})
it('fails to fetch bookmark', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({ detail: 'Internal Server Error' }), { status: 500 })
+ // act:
const client = new BookmarksClient()
const result = await client.fetchBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(result).toEqual({ detail: 'Internal Server Error' })
})
it('creates bookmark correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({}))
+ // act:
const client = new BookmarksClient()
const result = await client.createBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(result).toEqual({})
})
it('fails to create bookmark', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({ detail: 'Internal Server Error' }), { status: 500 })
+ // act:
const client = new BookmarksClient()
const result = await client.createBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(result).toEqual({ detail: 'Internal Server Error' })
})
it('deletes bookmark correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({}))
+ // act:
const client = new BookmarksClient()
const result = await client.deleteBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(result).toEqual({})
})
it('fails to delete bookmark', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({ detail: 'Internal Server Error' }), { status: 500 })
+ // act:
const client = new BookmarksClient()
const result = await client.deleteBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(result).toEqual({ detail: 'Internal Server Error' })
})
})
diff --git a/frontend/src/api/__tests__/cadaPrio.spec.ts b/frontend/src/api/__tests__/cadaPrio.spec.ts
index bf5de3fe..fa7b6cda 100644
--- a/frontend/src/api/__tests__/cadaPrio.spec.ts
+++ b/frontend/src/api/__tests__/cadaPrio.spec.ts
@@ -12,22 +12,31 @@ describe.concurrent('Cada Prio Client', () => {
})
it('fetches gene impact correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify({ result: 'pathogenic' }))
+ // act:
const client = new CadaPrioClient()
const result = await client.predictGeneImpact(['HP:0000001'])
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ result: 'pathogenic' }))
})
it('fetches gene impact correctly with gene symbols', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify({ result: 'pathogenic' }))
+ // act:
const client = new CadaPrioClient()
const result = await client.predictGeneImpact(['HP:0000001'], ['BRCA1'])
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ result: 'pathogenic' }))
})
it('fails to fetch gene impact with wrong HPO terms', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('hpo_terms=HP:0000001')) {
return Promise.resolve(JSON.stringify({ result: 'pathogenic' }))
@@ -35,8 +44,11 @@ describe.concurrent('Cada Prio Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new CadaPrioClient()
const result = await client.predictGeneImpact(['123'])
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
})
})
diff --git a/frontend/src/api/__tests__/caseinfo.spec.ts b/frontend/src/api/__tests__/caseinfo.spec.ts
index 5472e6a4..85683648 100644
--- a/frontend/src/api/__tests__/caseinfo.spec.ts
+++ b/frontend/src/api/__tests__/caseinfo.spec.ts
@@ -6,6 +6,7 @@ import { type Case, Ethnicity, Inheritance, Sex, Zygosity } from '@/stores/case'
const fetchMocker = createFetchMock(vi)
+// Test data
const mockCaseInfo: Case = {
pseudonym: '',
diseases: [],
@@ -26,15 +27,19 @@ describe.concurrent('CaseInfo Client', () => {
})
it('fetches case info correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(mockCaseInfo))
+ // act:
const client = new CaseInfoClient()
const result = await client.fetchCaseInfo()
+ // assert:
expect(result).toEqual(mockCaseInfo)
})
it('fails to fetch case info', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('caseinfo/get')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -42,22 +47,28 @@ describe.concurrent('CaseInfo Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new CaseInfoClient()
const result = await client.fetchCaseInfo()
+ // assert:
expect(result).toEqual({ status: 500 })
})
it('creates case info correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(mockCaseInfo))
+ // act:
const client = new CaseInfoClient()
const result = await client.createCaseInfo(mockCaseInfo)
+ // assert:
expect(result).toEqual(mockCaseInfo)
})
it('fails to create case info', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('caseinfo/create')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -65,22 +76,28 @@ describe.concurrent('CaseInfo Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new CaseInfoClient()
const result = await client.createCaseInfo(mockCaseInfo)
+ // assert:
expect(result).toEqual({ status: 500 })
})
it('updates case info correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(mockCaseInfo))
+ // act:
const client = new CaseInfoClient()
const result = await client.updateCaseInfo(mockCaseInfo)
+ // assert:
expect(result).toEqual(mockCaseInfo)
})
it('fails to update case info', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('caseinfo/update')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -88,22 +105,28 @@ describe.concurrent('CaseInfo Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new CaseInfoClient()
const result = await client.updateCaseInfo(mockCaseInfo)
+ // assert:
expect(result).toEqual({ status: 500 })
})
it('deletes case info correctly', async () => {
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({}))
+ // act:
const client = new CaseInfoClient()
const result = await client.deleteCaseInfo()
+ // assert:
expect(result).toEqual({})
})
it('fails to delete case info', async () => {
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('caseinfo/delete')) {
return Promise.resolve(JSON.stringify({ status: 500 }))
@@ -111,9 +134,11 @@ describe.concurrent('CaseInfo Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new CaseInfoClient()
const result = await client.deleteCaseInfo()
+ // assert:
expect(result).toEqual({ status: 500 })
})
})
diff --git a/frontend/src/api/__tests__/common.spec.ts b/frontend/src/api/__tests__/common.spec.ts
index 33af0d60..327b3848 100644
--- a/frontend/src/api/__tests__/common.spec.ts
+++ b/frontend/src/api/__tests__/common.spec.ts
@@ -10,31 +10,56 @@ import {
describe.concurrent('API_BASE_PREFIX constants', () => {
it('returns the correct API base prefix in production mode', () => {
+ // arrange:
const originalMode = import.meta.env.MODE
+
+ // act: nothing, only test check
+
+ // assert:
expect(API_INTERNAL_BASE_PREFIX).toBe('/internal/')
import.meta.env.MODE = originalMode
})
it('returns the correct API base prefix for annonars in production mode', () => {
+ // arrange:
const originalMode = import.meta.env.MODE
+
+ // act: nothing, only test check
+
+ // assert:
expect(API_INTERNAL_BASE_PREFIX_ANNONARS).toBe('/internal/proxy/annonars')
import.meta.env.MODE = originalMode
})
it('returns the correct API base prefix for mehari in production mode', () => {
+ // arrange:
const originalMode = import.meta.env.MODE
+
+ // act: nothing, only test check
+
+ // assert:
expect(API_INTERNAL_BASE_PREFIX_MEHARI).toBe('/internal/proxy/mehari')
import.meta.env.MODE = originalMode
})
it('returns the correct API base prefix for nginx in production mode', () => {
+ // arrange:
const originalMode = import.meta.env.MODE
+
+ // act: nothing, only test check
+
+ // assert:
expect(API_INTERNAL_BASE_PREFIX_NGINX).toBe('/internal/proxy/nginx')
import.meta.env.MODE = originalMode
})
it('returns the correct API base prefix for cada-prio in production mode', () => {
+ // arrange:
const originalMode = import.meta.env.MODE
+
+ // act: nothing, only test check
+
+ // assert:
expect(API_INTERNAL_BASE_PREFIX_CADA_PRIO).toBe('/internal/proxy/cada-prio')
import.meta.env.MODE = originalMode
})
diff --git a/frontend/src/api/__tests__/dotty.spec.ts b/frontend/src/api/__tests__/dotty.spec.ts
index c2692c12..670b300d 100644
--- a/frontend/src/api/__tests__/dotty.spec.ts
+++ b/frontend/src/api/__tests__/dotty.spec.ts
@@ -12,6 +12,7 @@ describe.concurrent('DottyClient', () => {
})
it('should resolve to SPDI successfully', async () => {
+ // arrange:
const mockData: DottyResponse = {
success: true,
value: {
@@ -24,13 +25,16 @@ describe.concurrent('DottyClient', () => {
}
fetchMocker.mockResponseOnce(JSON.stringify(mockData), { status: 200 })
+ // act:
const client = new DottyClient()
const result = await client.toSpdi('NM_000059.3:c.274G>A')
+ // assert:
expect(result).toEqual(mockData)
})
it('should load transcripts successfully', async () => {
+ // arrange:
const mockData = {
transcripts: {
'HGNC:1100': {
@@ -40,9 +44,11 @@ describe.concurrent('DottyClient', () => {
}
fetchMocker.mockResponseOnce(JSON.stringify(mockData), { status: 200 })
+ // act:
const client = new DottyClient()
const result = await client.fetchTranscripts('HGNC:1100', 'GRCh37')
+ // assert:
expect(result).toEqual(mockData)
})
})
diff --git a/frontend/src/api/__tests__/mehari.spec.ts b/frontend/src/api/__tests__/mehari.spec.ts
index 91a162fe..bc8b87c4 100644
--- a/frontend/src/api/__tests__/mehari.spec.ts
+++ b/frontend/src/api/__tests__/mehari.spec.ts
@@ -9,6 +9,7 @@ import { LinearStrucvarImpl } from '@/lib/genomicVars'
const fetchMocker = createFetchMock(vi)
+// Test data
const seqVar = new SeqvarImpl('grch37', '1', 123, 'A', 'G')
const strucVar = new LinearStrucvarImpl('DEL', 'grch37', 'chr17', 43044295, 43044297)
@@ -19,22 +20,31 @@ describe.concurrent('Mehari Client', () => {
})
it('fetches TxCsq info correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify(BRCA1TxInfo))
+ // act:
const client = new MehariClient()
const result = await client.retrieveSeqvarsCsq(seqVar, 'HGNC:1100')
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1TxInfo))
})
it('fetches TxCsq info correctly without HGNC id', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify(BRCA1TxInfo))
+ // act:
const client = new MehariClient()
const result = await client.retrieveSeqvarsCsq(seqVar)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1TxInfo))
})
it('fails to fetch variant info with wrong variant', async () => {
+ // arrange:
const seqVarInvalid = new SeqvarImpl('grch37', '1', 123, 'A', 'T')
fetchMocker.mockResponse((req) => {
if (req.url.includes('alternative=G')) {
@@ -43,20 +53,28 @@ describe.concurrent('Mehari Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new MehariClient()
const result = await client.retrieveSeqvarsCsq(seqVarInvalid)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
})
it('fetches Structur Variant info correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify(SVInfo))
+ // act:
const client = new MehariClient()
const result = await client.retrieveStrucvarsCsq(strucVar)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify(SVInfo))
})
it('fails to fetch variant info with wrong variant', async () => {
+ // arrange:
const strucVarInvalid = new LinearStrucvarImpl('DUP', 'grch37', 'chr17', 43044295, 43044297)
fetchMocker.mockResponse((req) => {
if (req.url.includes('DEL')) {
@@ -65,8 +83,11 @@ describe.concurrent('Mehari Client', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ // act:
const client = new MehariClient()
const result = await client.retrieveStrucvarsCsq(strucVarInvalid)
+
+ // assert:
expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
})
})
diff --git a/frontend/src/api/__tests__/misc.spec.ts b/frontend/src/api/__tests__/misc.spec.ts
index 48c95517..45e97193 100644
--- a/frontend/src/api/__tests__/misc.spec.ts
+++ b/frontend/src/api/__tests__/misc.spec.ts
@@ -12,10 +12,14 @@ describe.concurrent('Misc Client', () => {
})
it('fetches version info correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce('v0.0.0')
+ // act:
const client = new MiscClient()
const result = await client.fetchVersion()
+
+ // assert:
expect(result).toEqual('v0.0.0')
})
})
diff --git a/frontend/src/api/__tests__/settings.spec.ts b/frontend/src/api/__tests__/settings.spec.ts
index 7af17775..bc58056f 100644
--- a/frontend/src/api/__tests__/settings.spec.ts
+++ b/frontend/src/api/__tests__/settings.spec.ts
@@ -12,52 +12,76 @@ describe.concurrent('Settings Client', () => {
})
it('fetches version info correctly', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(
JSON.stringify({ matomo_host: 'https://matomo.example.com/', matomo_site_id: '1' })
)
+ // act:
const client = new SettingsClient()
const result = await client.fetchFrontendSettings()
+
+ // assert:
expect(result).toEqual({ matomo_host: 'https://matomo.example.com/', matomo_site_id: '1' })
})
it('handles different settings data', async () => {
+ // arrange:
const alternativeSettings = { theme: 'dark', language: 'en' }
fetchMocker.mockResponseOnce(JSON.stringify(alternativeSettings))
+ // act:
const client = new SettingsClient()
const result = await client.fetchFrontendSettings()
+
+ // assert:
expect(result).toEqual(alternativeSettings)
})
it('handles empty settings response', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify({}))
+ // act:
const client = new SettingsClient()
const result = await client.fetchFrontendSettings()
+
+ // assert:
expect(result).toEqual({})
})
it('handles null settings response', async () => {
+ // arrange:
fetchMocker.mockResponseOnce('null')
+ // act:
const client = new SettingsClient()
const result = await client.fetchFrontendSettings()
+
+ // assert:
expect(result).toBeNull()
})
it('handles server error when fetching settings', async () => {
+ // arrange:
const errorMessage = 'Internal Server Error' // The statusText for a 500 error
fetchMocker.mockResponseOnce(JSON.stringify({ msg: 'Internal server error' }), { status: 500 })
+ // act:
const client = new SettingsClient()
+
+ // assert:
await expect(client.fetchFrontendSettings()).rejects.toThrow(errorMessage)
})
it('handles network error when fetching settings', async () => {
+ // arrange:
fetchMocker.mockReject(new Error('Network Error'))
+ // act:
const client = new SettingsClient()
+
+ // assert:
await expect(client.fetchFrontendSettings()).rejects.toThrow('Network Error')
})
})
diff --git a/frontend/src/api/__tests__/users.spec.ts b/frontend/src/api/__tests__/users.spec.ts
index 69e1607c..47491f40 100644
--- a/frontend/src/api/__tests__/users.spec.ts
+++ b/frontend/src/api/__tests__/users.spec.ts
@@ -12,6 +12,7 @@ describe.concurrent('Users Client', () => {
})
it('should fetch current user profile successfully', async () => {
+ // arrange:
const userData = {
id: '1',
email: 'test@example.com',
@@ -21,17 +22,22 @@ describe.concurrent('Users Client', () => {
}
fetchMocker.mockResponseOnce(JSON.stringify(userData), { status: 200 })
+ // act:
const client = new UsersClient()
const result = await client.fetchCurrentUserProfile()
+ // assert:
expect(result).toEqual(userData)
})
it('should throw UnauthenticatedError when not authenticated', async () => {
+ // arrange:
fetchMocker.mockResponseOnce('', { status: 401 })
+ // act:
const client = new UsersClient()
+ // assert:
try {
await client.fetchCurrentUserProfile()
expect(true).toBe(false)
@@ -41,10 +47,13 @@ describe.concurrent('Users Client', () => {
})
it('should throw UnauthenticatedError on unexpected status', async () => {
+ // arrange:
fetchMocker.mockResponseOnce('', { status: 500 })
+ // act:
const client = new UsersClient()
+ // assert:
try {
await client.fetchCurrentUserProfile()
expect(true).toBe(false)
diff --git a/frontend/src/api/__tests__/utils.spec.ts b/frontend/src/api/__tests__/utils.spec.ts
index 85356deb..7e9c8c2d 100644
--- a/frontend/src/api/__tests__/utils.spec.ts
+++ b/frontend/src/api/__tests__/utils.spec.ts
@@ -14,50 +14,45 @@ describe.concurrent('Utils Client', () => {
})
it('sends a test email correctly', async () => {
- // Prepare the mock response
+ // arrange:
const mockResponse = { msg: 'Test email sent successfully' }
fetchMocker.mockResponseOnce(JSON.stringify(mockResponse))
- // Instantiate the client and perform the action
+ // act:
const client = new UtilsClient()
const email_to = 'test@example.com'
const result = await client.sendTestEmail(email_to)
- // Assert that the fetch was called correctly
+ // assert:
expect(fetchMocker).toHaveBeenCalledWith(
`${API_V1_BASE_PREFIX}utils/test-email/?email_to=${email_to}`,
{
method: 'POST'
}
)
-
- // Assert the response matches the expected result
expect(result).toEqual(mockResponse)
})
it('handles invalid email address error', async () => {
- // Prepare the mock response for an invalid email address
+ // arrange:
const mockErrorResponse = { msg: 'Invalid email address' }
fetchMocker.mockResponseOnce(JSON.stringify(mockErrorResponse), { status: 400 })
+ // act:
const client = new UtilsClient()
const invalidEmail = 'invalid-email'
- // Try-catch block to handle the expected error
+ // assert:
try {
await client.sendTestEmail(invalidEmail)
- // If no error is thrown, force the test to fail
expect(true).toBe(false)
} catch (error) {
- // Assert the fetch was called with the invalid email
expect(fetchMocker).toHaveBeenCalledWith(
expect.stringContaining(`email_to=${invalidEmail}`),
{
method: 'POST'
}
)
-
- // Assert the error message matches the expected result
expect(error).toEqual(
new AssertionError({ message: 'expected true to be false // Object.is equality' })
)
@@ -65,25 +60,22 @@ describe.concurrent('Utils Client', () => {
})
it('handles server error when sending an email', async () => {
- // Prepare the mock response for a server error
+ // arrange:
const mockServerErrorResponse = { msg: 'Internal server error' }
fetchMocker.mockResponseOnce(JSON.stringify(mockServerErrorResponse), { status: 500 })
+ // act:
const client = new UtilsClient()
const email_to = 'test@example.com'
- // Try-catch block to handle the expected error
+ // assert:
try {
await client.sendTestEmail(email_to)
- // If no error is thrown, force the test to fail
expect(true).toBe(false)
} catch (error) {
- // Assert the fetch was called correctly
expect(fetchMocker).toHaveBeenCalledWith(expect.stringContaining(`email_to=${email_to}`), {
method: 'POST'
})
-
- // Assert the error message matches the expected server error
expect(error).toEqual(
new AssertionError({ message: 'expected true to be false // Object.is equality' })
)
diff --git a/frontend/src/api/__tests__/viguno.spec.ts b/frontend/src/api/__tests__/viguno.spec.ts
index b8c9eaab..b023816f 100644
--- a/frontend/src/api/__tests__/viguno.spec.ts
+++ b/frontend/src/api/__tests__/viguno.spec.ts
@@ -12,136 +12,200 @@ describe.concurrent('Viguno Client', () => {
})
it('resolves OMIM term by ID correctly', async () => {
+ // arrange:
const mockOmimTerm = { id: 'OMIM:123456', name: 'Example Disease' }
fetchMocker.mockResponseOnce(JSON.stringify(mockOmimTerm))
+ // act:
const client = new VigunoClient()
const result = await client.resolveOmimTermById('123456')
+
+ // assert:
expect(result).toEqual(mockOmimTerm)
})
it('handles non-existent OMIM term ID', async () => {
+ // arrange:
const errorMessage = 'OMIM term not found'
fetchMocker.mockResponseOnce(JSON.stringify({ msg: errorMessage }), { status: 404 })
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.resolveOmimTermById('999999')).rejects.toThrow(errorMessage)
})
it('handles server error when resolving OMIM term by ID', async () => {
+ // arrange:
const errorMessage = 'Internal Server Error'
fetchMocker.mockResponseOnce(JSON.stringify({ msg: errorMessage }), { status: 500 })
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.resolveOmimTermById('123456')).rejects.toThrow(errorMessage)
})
it('handles network error when resolving OMIM term by ID', async () => {
+ // arrange:
fetchMocker.mockReject(new Error('Network Error'))
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.resolveOmimTermById('123456')).rejects.toThrow('Network Error')
})
it('returns a list of OMIM terms for a valid query', async () => {
+ // arrange:
const mockResponse = [
{ id: 'OMIM:123456', name: 'Example Disease 1' },
{ id: 'OMIM:234567', name: 'Example Disease 2' }
]
fetchMocker.mockResponseOnce(JSON.stringify(mockResponse))
+ // act:
const client = new VigunoClient()
const result = await client.queryOmimTermsByName('Example')
+
+ // assert:
expect(result).toEqual(mockResponse)
})
it('returns an empty list for a query with no results', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify([]))
+ // act:
const client = new VigunoClient()
const result = await client.queryOmimTermsByName('NonExistentDisease')
+
+ // assert:
expect(result).toEqual([])
})
it('handles server error for a query', async () => {
+ // arrange:
const errorMessage = 'Internal Server Error'
fetchMocker.mockResponseOnce(JSON.stringify({ msg: errorMessage }), { status: 500 })
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.queryOmimTermsByName('Example')).rejects.toThrow(errorMessage)
})
it('handles network error during a query', async () => {
+ // arrange:
fetchMocker.mockReject(new Error('Network Error'))
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.queryOmimTermsByName('Example')).rejects.toThrow('Network Error')
})
it('resolves HPO term by ID correctly', async () => {
+ // arrange:
const mockHpoTerm = { id: 'HP:0000118', name: 'Phenotypic abnormality' }
fetchMocker.mockResponseOnce(JSON.stringify(mockHpoTerm))
+ // act:
const client = new VigunoClient()
const result = await client.resolveHpoTermById('0000118')
+
+ // assert:
expect(result).toEqual(mockHpoTerm)
})
it('handles non-existent HPO term ID', async () => {
+ // arrange:
const errorMessage = 'HPO term not found'
fetchMocker.mockResponseOnce(JSON.stringify({ msg: errorMessage }), { status: 404 })
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.resolveHpoTermById('9999999')).rejects.toThrow(errorMessage)
})
it('handles server error when resolving HPO term by ID', async () => {
+ // arrange:
const errorMessage = 'Internal Server Error'
fetchMocker.mockResponseOnce(JSON.stringify({ msg: errorMessage }), { status: 500 })
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.resolveHpoTermById('0000118')).rejects.toThrow(errorMessage)
})
it('handles network error when resolving HPO term by ID', async () => {
+ // arrange:
fetchMocker.mockReject(new Error('Network Error'))
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.resolveHpoTermById('0000118')).rejects.toThrow('Network Error')
})
it('queries HPO terms by name correctly', async () => {
+ // arrange:
const mockHpoTerms = [
{ id: 'HP:0000118', name: 'Phenotypic abnormality' },
{ id: 'HP:0000152', name: 'Abnormality of head or neck' }
]
fetchMocker.mockResponseOnce(JSON.stringify(mockHpoTerms))
+ // act:
const client = new VigunoClient()
const result = await client.queryHpoTermsByName('Phenotypic')
+
+ // assert:
expect(result).toEqual(mockHpoTerms)
})
it('returns an empty list for a name query with no results', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify([]))
+ // act:
const client = new VigunoClient()
const result = await client.queryHpoTermsByName('NonExistentTerm')
+
+ // assert:
expect(result).toEqual([])
})
it('handles server error during name query', async () => {
+ // arrange:
const errorMessage = 'Internal Server Error'
fetchMocker.mockResponseOnce(JSON.stringify({ msg: errorMessage }), { status: 500 })
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.queryHpoTermsByName('Phenotypic')).rejects.toThrow(errorMessage)
})
it('handles network error during name query', async () => {
+ // arrange:
fetchMocker.mockReject(new Error('Network Error'))
+ // act:
const client = new VigunoClient()
+
+ // assert:
await expect(client.queryHpoTermsByName('Phenotypic')).rejects.toThrow('Network Error')
})
})
diff --git a/frontend/src/lib/__tests__/acmgSeqvar.spec.ts b/frontend/src/lib/__tests__/acmgSeqvar.spec.ts
index b6694c50..c64c3acd 100644
--- a/frontend/src/lib/__tests__/acmgSeqvar.spec.ts
+++ b/frontend/src/lib/__tests__/acmgSeqvar.spec.ts
@@ -10,7 +10,12 @@ import {
describe.concurrent('MultiSourceAcmgCriteriaState', () => {
it('should have correct default values', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+
+ // assert:
// Check keys of AcmgCriteriaState.criteriaStates
expect(Object.keys(AcmgCriteriaState.criteriaStates).length).toEqual(4)
expect(AcmgCriteriaState.criteriaStates).toHaveProperty(StateSource.Default)
@@ -36,119 +41,174 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should correctly get criteria state', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+
+ // assert:
expect(AcmgCriteriaState.getCriteriaState(AcmgCriteria.PVS1)).toEqual(
AcmgCriteriaState.criteriaStates[StateSource.Default][AcmgCriteria.PVS1]
)
})
it('should correctly get criteria state from interVar', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange:
const criteriaState = {
criteria: AcmgCriteria.PVS1,
presence: Presence.Present,
evidenceLevel: AcmgEvidenceLevel.PathogenicVeryStrong
}
+
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, Presence.Present)
+
+ // assert:
expect(AcmgCriteriaState.getCriteriaState(AcmgCriteria.PVS1)).toStrictEqual(criteriaState)
})
it('should correctly get criteria state from server', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange:
const criteriaState = {
criteria: AcmgCriteria.PVS1,
presence: Presence.Present,
evidenceLevel: AcmgEvidenceLevel.PathogenicVeryStrong
}
+
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.Server, AcmgCriteria.PVS1, Presence.Present)
+
+ // assert:
expect(AcmgCriteriaState.getCriteriaState(AcmgCriteria.PVS1)).toStrictEqual(criteriaState)
})
it('should correctly get criteria state from server and InterVar', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange:
const criteriaState = {
criteria: AcmgCriteria.PVS1,
presence: Presence.Absent,
evidenceLevel: AcmgEvidenceLevel.PathogenicVeryStrong
}
+
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, Presence.Present)
AcmgCriteriaState.setPresence(StateSource.Server, AcmgCriteria.PVS1, Presence.Absent)
+
+ // assert:
expect(AcmgCriteriaState.getCriteriaState(AcmgCriteria.PVS1)).toStrictEqual(criteriaState)
})
it('should correctly get criteria state with invalid request', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange:
const criteriaState = {
criteria: 'invalid' as AcmgCriteria,
presence: Presence.Unknown,
evidenceLevel: AcmgEvidenceLevel.NotSet
}
+
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+
+ // assert:
expect(AcmgCriteriaState.getCriteriaState('invalid' as AcmgCriteria)).toStrictEqual(
criteriaState
)
})
it('should correctly get criteria state from default source', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange:
const criteriaState = {
criteria: AcmgCriteria.PVS1,
presence: Presence.Unknown,
evidenceLevel: AcmgEvidenceLevel.PathogenicVeryStrong
}
+
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+
+ // assert:
expect(
AcmgCriteriaState.getCriteriaStateFromSource(AcmgCriteria.PVS1, StateSource.Default)
).toStrictEqual(criteriaState)
})
it('should correctly get criteria state from interVar source', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange:
const criteriaState = {
criteria: AcmgCriteria.PVS1,
presence: Presence.Present,
evidenceLevel: AcmgEvidenceLevel.NotSet
}
+
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, Presence.Present)
+
+ // assert:
expect(
AcmgCriteriaState.getCriteriaStateFromSource(AcmgCriteria.PVS1, StateSource.InterVar)
).toStrictEqual(criteriaState)
})
it('should correctly get criteria state from server source', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange:
const criteriaState = {
criteria: AcmgCriteria.PVS1,
presence: Presence.Present,
evidenceLevel: AcmgEvidenceLevel.NotSet
}
+
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.Server, AcmgCriteria.PVS1, Presence.Present)
+
+ // assert:
expect(
AcmgCriteriaState.getCriteriaStateFromSource(AcmgCriteria.PVS1, StateSource.Server)
).toStrictEqual(criteriaState)
})
it('should correctly get criteria state from user source', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange:
const criteriaState = {
criteria: AcmgCriteria.PVS1,
presence: Presence.Present,
evidenceLevel: AcmgEvidenceLevel.NotSet
}
+
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.User, AcmgCriteria.PVS1, Presence.Present)
+
+ // assert:
expect(
AcmgCriteriaState.getCriteriaStateFromSource(AcmgCriteria.PVS1, StateSource.User)
).toStrictEqual(criteriaState)
})
it('should throw error if getting invalid criteria from source', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+
+ // assert:
expect(() =>
AcmgCriteriaState.getCriteriaStateFromSource('invalid' as AcmgCriteria, StateSource.User)
).toThrowError()
})
it('should correctly set presence for InterVar', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, Presence.Present)
+
+ // assert:
expect(
AcmgCriteriaState.criteriaStates[StateSource.InterVar][AcmgCriteria.PVS1].presence
).toEqual(Presence.Present)
@@ -162,8 +222,13 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should correctly set presence for Server', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.Server, AcmgCriteria.PVS1, Presence.Present)
+
+ // assert:
expect(
AcmgCriteriaState.criteriaStates[StateSource.Server][AcmgCriteria.PVS1].presence
).toEqual(Presence.Present)
@@ -177,8 +242,13 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should correctly set presence for User', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.User, AcmgCriteria.PVS1, Presence.Present)
+
+ // assert:
expect(AcmgCriteriaState.criteriaStates[StateSource.User][AcmgCriteria.PVS1].presence).toEqual(
Presence.Present
)
@@ -192,13 +262,21 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should raise error for setting present for Default', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+
+ // assert:
expect(() =>
AcmgCriteriaState.setPresence(StateSource.Default, AcmgCriteria.PVS1, Presence.Present)
).toThrowError()
})
it('should correctly set absent presence for User', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.User, AcmgCriteria.PVS1, Presence.Absent)
expect(AcmgCriteriaState.criteriaStates[StateSource.User][AcmgCriteria.PVS1].presence).toEqual(
@@ -206,12 +284,17 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
)
// Set presence to absent
AcmgCriteriaState.setUserPresenceAbsent()
+
+ // assert:
expect(AcmgCriteriaState.criteriaStates[StateSource.User][AcmgCriteria.PVS1].presence).toEqual(
Presence.Absent
)
})
it('should correctly set interVar presence for User', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.User, AcmgCriteria.PVS1, Presence.Absent)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, Presence.Present)
@@ -220,12 +303,17 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
)
// Set presence to unknown
AcmgCriteriaState.setUserPresenceInterVar()
+
+ // assert:
expect(AcmgCriteriaState.criteriaStates[StateSource.User][AcmgCriteria.PVS1].presence).toEqual(
Presence.Present
)
})
it('should correctly set server presence for User', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.User, AcmgCriteria.PVS1, Presence.Absent)
AcmgCriteriaState.setPresence(StateSource.Server, AcmgCriteria.PVS1, Presence.Present)
@@ -234,18 +322,25 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
)
// Set presence to unknown
AcmgCriteriaState.setUserPresenceServer()
+
+ // assert:
expect(AcmgCriteriaState.criteriaStates[StateSource.User][AcmgCriteria.PVS1].presence).toEqual(
Presence.Present
)
})
it('should correctly set evidence level for user', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setEvidenceLevel(
StateSource.User,
AcmgCriteria.PVS1,
AcmgEvidenceLevel.PathogenicModerate
)
+
+ // assert:
expect(
AcmgCriteriaState.criteriaStates[StateSource.User][AcmgCriteria.PVS1].evidenceLevel
).toEqual(AcmgEvidenceLevel.PathogenicModerate)
@@ -259,12 +354,17 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should correctly set evidence level for server', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setEvidenceLevel(
StateSource.Server,
AcmgCriteria.PVS1,
AcmgEvidenceLevel.PathogenicModerate
)
+
+ // assert:
expect(
AcmgCriteriaState.criteriaStates[StateSource.Server][AcmgCriteria.PVS1].evidenceLevel
).toEqual(AcmgEvidenceLevel.PathogenicModerate)
@@ -278,12 +378,17 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should correctly set evidence level for interVar', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setEvidenceLevel(
StateSource.InterVar,
AcmgCriteria.PVS1,
AcmgEvidenceLevel.PathogenicModerate
)
+
+ // assert:
expect(
AcmgCriteriaState.criteriaStates[StateSource.InterVar][AcmgCriteria.PVS1].evidenceLevel
).toEqual(AcmgEvidenceLevel.PathogenicModerate)
@@ -297,7 +402,12 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should raise error for setting evidence level for Default', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+
+ // assert:
expect(() =>
AcmgCriteriaState.setEvidenceLevel(
StateSource.Default,
@@ -308,9 +418,13 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should correctly get States', () => {
- const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
+ // arrange: nothing, only test check
+ // act:
+ const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
const criteriaStates = AcmgCriteriaState.getStates()
+
+ // assert:
// Check keys of AcmgCriteriaState.criteriaStates
expect(Object.keys(criteriaStates).length).toEqual(4)
expect(criteriaStates).toHaveProperty(StateSource.Default)
@@ -336,6 +450,9 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
})
it('should correctly get evidence counts', () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, Presence.Present)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PS1, Presence.Present)
@@ -349,6 +466,7 @@ describe.concurrent('MultiSourceAcmgCriteriaState', () => {
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BS2, Presence.Present)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BS3, Presence.Present)
+ // assert:
expect(
AcmgCriteriaState.getActiveEvidenceCounts(AcmgEvidenceLevel.PathogenicVeryStrong)
).toEqual(1)
@@ -470,6 +588,9 @@ describe.concurrent(
`should return 'Pathogenic' for 'PVS1: %s, PS1: %s, PS2: %s, PM1: %s, PM2: %s, PM3: %s,
PM4: %s, PP1: %s, PP2: %s, PP3: %s, PP4: %s' with no confclicts`,
(pvs1, ps1, ps2, pm1, pm2, pm3, pp1, pp2, pp3, pp4) => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, pvs1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PS1, ps1)
@@ -481,6 +602,8 @@ describe.concurrent(
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PP2, pp2)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PP3, pp3)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PP4, pp4)
+
+ // assert:
expect(AcmgCriteriaState.getAcmgClass()).toEqual(['Pathogenic', false])
}
)
@@ -574,6 +697,9 @@ describe.concurrent(
`should return 'Likely pathogenic' for 'PVS1: %s, PS1: %s, PS2: %s, PM1: %s, PM2: %s, PM3: %s,
PM4: %s, PP1: %s, PP2: %s, PP3: %s, PP4: %s' with no confclicts`,
(pvs1, ps1, ps2, pm1, pm2, pm3, pp1, pp2, pp3, pp4) => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, pvs1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PS1, ps1)
@@ -585,6 +711,8 @@ describe.concurrent(
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PP2, pp2)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PP3, pp3)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PP4, pp4)
+
+ // assert:
expect(AcmgCriteriaState.getAcmgClass()).toEqual(['Likely pathogenic', false])
}
)
@@ -598,12 +726,17 @@ describe.concurrent(
])(
`should return 'Benign' for 'BA1: %s, BS1: %s, BS2: %s, BP1: %s, BP2: %s' with no confclicts`,
(ba1, bs1, bs2, bp1, bp2) => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BA1, ba1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BS1, bs1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BS2, bs2)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BP1, bp1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BP2, bp2)
+
+ // assert:
expect(AcmgCriteriaState.getAcmgClass()).toEqual(['Benign', false])
}
)
@@ -615,12 +748,17 @@ describe.concurrent(
`should return 'Likely benign' for 'BA1: %s, BS1: %s, BS2: %s, BP1: %s, BP2: %s' with no
confclicts`,
(ba1, bs1, bs2, bp1, bp2) => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BA1, ba1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BS1, bs1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BS2, bs2)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BP1, bp1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BP2, bp2)
+
+ // assert:
expect(AcmgCriteriaState.getAcmgClass()).toEqual(['Likely benign', false])
}
)
@@ -638,12 +776,17 @@ describe.concurrent(
`should return 'Uncertain significance' for 'PM1: %s, PP1: %s, PP2: %s, BS1: %s, BP1: %s'
with no confclicts`,
(pm1, pp1, pp2, bs1, bp1) => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PM1, pm1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PP1, pp1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PP2, pp2)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BS1, bs1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BP1, bp1)
+
+ // assert:
expect(AcmgCriteriaState.getAcmgClass()).toEqual(['Uncertain significance', false])
}
)
@@ -656,12 +799,17 @@ describe.concurrent(
`should return 'Conflicting' for 'PVS1: %s, PS1: %s, PS2: %s, BA1: %s, BS1: %s'
with confclicts`,
(pvs1, ps1, ps2, ba1, bs1) => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PVS1, pvs1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PS1, ps1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.PS2, ps2)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BA1, ba1)
AcmgCriteriaState.setPresence(StateSource.InterVar, AcmgCriteria.BS1, bs1)
+
+ // assert:
expect(AcmgCriteriaState.getAcmgClass()).toEqual(['Conflicting', true])
}
)
@@ -672,6 +820,9 @@ describe.concurrent(
'MultiSourceAcmgCriteriaState ACMG class computation with user override',
() => {
it(`should return 'Likely pathogenic' for PVS1 as Moderate and PS1`, () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
// Set PVS1 and PS1 to present
AcmgCriteriaState.setPresence(StateSource.User, AcmgCriteria.PVS1, Presence.Present)
@@ -685,11 +836,15 @@ describe.concurrent(
AcmgEvidenceLevel.PathogenicModerate
)
+ // assert:
// Expect to return 'Likely pathogenic'
expect(AcmgCriteriaState.getAcmgClass()).toEqual(['Likely pathogenic', false])
})
it(`should return 'Likely benign' for Ba1 as Strong and Bs1 as Supporting`, () => {
+ // arrange: nothing, only test check
+
+ // act:
const AcmgCriteriaState = new MultiSourceAcmgCriteriaState()
// Set Ba1 and Bs1 to present
AcmgCriteriaState.setPresence(StateSource.User, AcmgCriteria.BA1, Presence.Present)
@@ -709,6 +864,7 @@ describe.concurrent(
AcmgEvidenceLevel.BenignSupporting
)
+ // assert:
// Expect to return 'Likely benign'
expect(AcmgCriteriaState.getAcmgClass()).toEqual(['Likely benign', false])
})
diff --git a/frontend/src/lib/__tests__/genomeBuild.spec.ts b/frontend/src/lib/__tests__/genomeBuild.spec.ts
index 77f8f34b..6d73fe07 100644
--- a/frontend/src/lib/__tests__/genomeBuild.spec.ts
+++ b/frontend/src/lib/__tests__/genomeBuild.spec.ts
@@ -11,10 +11,18 @@ import {
describe.concurrent('constants', () => {
it('genomeBuildAliases should have the well-known keys', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(Object.keys(GENOME_BUILD_ALIASES)).toEqual(['hg19', 'grch37', 'hg38', 'grch38'])
})
it('CHROM_REFSEQ_37 should have the well-known keys', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(Object.keys(CHROM_REFSEQ_37)).toEqual([
'1',
'2',
@@ -45,6 +53,10 @@ describe.concurrent('constants', () => {
})
it('CHROM_REFSEQ_38 should have the well-known keys', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(Object.keys(CHROM_REFSEQ_38)).toEqual([
'1',
'2',
@@ -75,6 +87,10 @@ describe.concurrent('constants', () => {
})
it('CHROM_LENGTHS_37 should have the well-known keys', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(Object.keys(CHROM_LENGTHS_37)).toEqual([
'1',
'2',
@@ -105,6 +121,10 @@ describe.concurrent('constants', () => {
})
it('CHROM_LENGTHS_38 should have the well-known keys', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(Object.keys(CHROM_LENGTHS_38)).toEqual([
'1',
'2',
@@ -135,6 +155,10 @@ describe.concurrent('constants', () => {
})
it('lengths of 37 and 38 differ but not in chrMT', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(CHROM_LENGTHS_37.X).not.toEqual(CHROM_LENGTHS_38.X)
expect(CHROM_LENGTHS_37.Y).not.toEqual(CHROM_LENGTHS_38.Y)
expect(CHROM_LENGTHS_37.MT).toEqual(CHROM_LENGTHS_38.MT)
@@ -143,24 +167,44 @@ describe.concurrent('constants', () => {
describe.concurrent('refseqToGenomeBuild', () => {
it('should return grch37 for NC_000001.10', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(refseqToGenomeBuild('NC_000001.10')).toEqual('grch37')
})
it('should return grch38 for NC_000001.11', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(refseqToGenomeBuild('NC_000001.11')).toEqual('grch38')
})
it('should return grch38 for NC_012920.1', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(refseqToGenomeBuild('NC_012920.1')).toEqual('grch38')
})
it('should work case insensitive', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(refseqToGenomeBuild('nc_000001.10')).toEqual('grch37')
expect(refseqToGenomeBuild('nc_000001.11')).toEqual('grch38')
expect(refseqToGenomeBuild('nc_012920.1')).toEqual('grch38')
})
it('should throw an error for NC_000001.12', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(() => refseqToGenomeBuild('NC_000001.12')).toThrow(
'Unknown RefSeq identifier: NC_000001.12'
)
diff --git a/frontend/src/lib/__tests__/genomicVars.spec.ts b/frontend/src/lib/__tests__/genomicVars.spec.ts
index 7891ea46..85bf5e62 100644
--- a/frontend/src/lib/__tests__/genomicVars.spec.ts
+++ b/frontend/src/lib/__tests__/genomicVars.spec.ts
@@ -25,6 +25,10 @@ import {
describe.concurrent('regular expression REGEX_GNOMAD_VARIANT', () => {
it('should match variants with chromosome name only', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('chr1-100-AT-TG').toMatch(REGEX_GNOMAD_VARIANT)
expect('chr22-100-AT-TG').toMatch(REGEX_GNOMAD_VARIANT)
expect('chrX-100-AT-TG').toMatch(REGEX_GNOMAD_VARIANT)
@@ -46,6 +50,10 @@ describe.concurrent('regular expression REGEX_GNOMAD_VARIANT', () => {
})
it('should match variants with valid genome releases name', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('hg19-chr1-100-AT-TG').toMatch(REGEX_GNOMAD_VARIANT)
expect('hg19-chr22-100-AT-TG').toMatch(REGEX_GNOMAD_VARIANT)
expect('hg38-chrX-100-AT-TG').toMatch(REGEX_GNOMAD_VARIANT)
@@ -67,6 +75,10 @@ describe.concurrent('regular expression REGEX_GNOMAD_VARIANT', () => {
})
it('should match variants with invalid genome releases name', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('T2T-Y-100-AT-TG').toMatch(REGEX_GNOMAD_VARIANT)
expect('T2T-MT-100-AT-TG').toMatch(REGEX_GNOMAD_VARIANT)
@@ -82,6 +94,10 @@ describe.concurrent('regular expression REGEX_GNOMAD_VARIANT', () => {
describe.concurrent('regular expression REGEX_CANONICAL_SPDI', () => {
it('should match correctly formatted variants only', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('NC_000001.11:100:AT:TG').toMatch(REGEX_CANONICAL_SPDI)
expect('NC_999999.999:100:AT:TG').toMatch(REGEX_CANONICAL_SPDI)
expect('NC_000000.0:100:AT:TG').toMatch(REGEX_CANONICAL_SPDI)
@@ -103,6 +119,10 @@ describe.concurrent('regular expression REGEX_CANONICAL_SPDI', () => {
describe.concurrent('regular expression REGEX_RELAXED_SPDI', () => {
it('should match variants with chromosome name only', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('chr1:100:AT:TG').toMatch(REGEX_RELAXED_SPDI)
expect('chr22:100:AT:TG').toMatch(REGEX_RELAXED_SPDI)
expect('chrX:100:AT:TG').toMatch(REGEX_RELAXED_SPDI)
@@ -124,6 +144,10 @@ describe.concurrent('regular expression REGEX_RELAXED_SPDI', () => {
})
it('should match variants with valid genome releases name', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('hg19:chr1:100:AT:TG').toMatch(REGEX_RELAXED_SPDI)
expect('hg19:chr22:100:AT:TG').toMatch(REGEX_RELAXED_SPDI)
expect('hg38:chrX:100:AT:TG').toMatch(REGEX_RELAXED_SPDI)
@@ -145,6 +169,10 @@ describe.concurrent('regular expression REGEX_RELAXED_SPDI', () => {
})
it('should match variants with invalid genome releases name', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('T2T:Y:100:AT:TG').toMatch(REGEX_RELAXED_SPDI)
expect('T2T:MT:100:AT:TG').toMatch(REGEX_RELAXED_SPDI)
@@ -160,6 +188,10 @@ describe.concurrent('regular expression REGEX_RELAXED_SPDI', () => {
describe.concurrent('regular expression REGEX_DBSNP_ID', () => {
it('should match correctly formatted rs IDs only', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('rs1').toMatch(REGEX_DBSNP_ID)
expect('rs99999999999').toMatch(REGEX_DBSNP_ID)
expect('sr1').not.toMatch(REGEX_DBSNP_ID)
@@ -169,6 +201,10 @@ describe.concurrent('regular expression REGEX_DBSNP_ID', () => {
describe.concurrent('regular expression REGEX_CLINVAR_ID', () => {
it('should match correctly formatted IDs only', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('VCV000148363.2').toMatch(REGEX_CLINVAR_ID)
expect('VCV000000000.0').toMatch(REGEX_CLINVAR_ID)
expect('RCV000148363.2').toMatch(REGEX_CLINVAR_ID)
@@ -194,6 +230,10 @@ describe.concurrent('regular expression REGEX_CLINVAR_ID', () => {
describe.concurrent('regular expression REGEX_CNV_COLON', () => {
it('should match variants with chromosome name only', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('DEL:chr1:100:200').toMatch(REGEX_CNV_COLON)
expect('DEL:1:100:200').toMatch(REGEX_CNV_COLON)
expect('DUP:chr1:100:200').toMatch(REGEX_CNV_COLON)
@@ -210,6 +250,10 @@ describe.concurrent('regular expression REGEX_CNV_COLON', () => {
})
it('should match variants with valid genome releases name', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('DEL:GRCh37:chr1:100:200').toMatch(REGEX_CNV_COLON)
expect('DEL:GRCh38:1:100:200').toMatch(REGEX_CNV_COLON)
expect('DUP:hg19:chr1:100:200').toMatch(REGEX_CNV_COLON)
@@ -226,6 +270,10 @@ describe.concurrent('regular expression REGEX_CNV_COLON', () => {
})
it('should match variants with RefSeq identifiers', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('DEL:NC_000001.10:100:200').toMatch(REGEX_CNV_COLON)
expect('DEL:NC_000001.11:100:200').toMatch(REGEX_CNV_COLON)
expect('DUP:NC_000001.10:100:200').toMatch(REGEX_CNV_COLON)
@@ -242,6 +290,10 @@ describe.concurrent('regular expression REGEX_CNV_COLON', () => {
})
it('should match variants with invalid genome releases name', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('DEL:T2T:chr1:100:200').toMatch(REGEX_CNV_COLON)
expect('DEL:T2T:chr1:100:200'.match(REGEX_CNV_COLON)?.groups).toEqual({
@@ -257,6 +309,10 @@ describe.concurrent('regular expression REGEX_CNV_COLON', () => {
describe.concurrent('regular expression REGEX_CNV_HYPEN', () => {
it('should match variants with chromosome name only', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('DEL-chr1-100-200').toMatch(REGEX_CNV_HYPHEN)
expect('DEL-1-100-200').toMatch(REGEX_CNV_HYPHEN)
expect('DUP-chr1-100-200').toMatch(REGEX_CNV_HYPHEN)
@@ -273,6 +329,10 @@ describe.concurrent('regular expression REGEX_CNV_HYPEN', () => {
})
it('should match variants with valid genome releases name', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('DEL-GRCh37-chr1-100-200').toMatch(REGEX_CNV_HYPHEN)
expect('DEL-GRCh38-1-100-200').toMatch(REGEX_CNV_HYPHEN)
expect('DUP-hg19-chr1-100-200').toMatch(REGEX_CNV_HYPHEN)
@@ -289,6 +349,10 @@ describe.concurrent('regular expression REGEX_CNV_HYPEN', () => {
})
it('should match variants with RefSeq identifiers', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('DEL-NC_000001.10-100-200').toMatch(REGEX_CNV_HYPHEN)
expect('DEL-NC_000001.11-100-200').toMatch(REGEX_CNV_HYPHEN)
expect('DUP-NC_000001.10-100-200').toMatch(REGEX_CNV_HYPHEN)
@@ -305,6 +369,10 @@ describe.concurrent('regular expression REGEX_CNV_HYPEN', () => {
})
it('should match variants with invalid genome releases name', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('DEL-T2T-chr1-100-200').toMatch(REGEX_CNV_HYPHEN)
expect('DEL-T2T-chr1-100-200'.match(REGEX_CNV_HYPHEN)?.groups).toEqual({
@@ -320,6 +388,10 @@ describe.concurrent('regular expression REGEX_CNV_HYPEN', () => {
describe.concurrent('regular expression REGEX_CNV_ISCN_2020', () => {
it('should match valid strings', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect('arr[GRCh37] 2q12.2q13 (107132950_110427254)x1').toMatch(REGEX_CNV_ISCN_2020)
expect(
'arr[GRCh37] 2q12.2q13 (107132950_110427254)x1'.match(REGEX_CNV_ISCN_2020)?.groups
@@ -368,6 +440,7 @@ describe.concurrent('validateSequenceVariant()', () => {
['1', 249250621, 'AT'],
['1', 249250622, 'A']
])('throws on %s-%d-%s', (chrom, pos, del) => {
+ // arrange:
const variant = {
genomeBuild: 'grch37' as GenomeBuild,
chrom,
@@ -376,6 +449,10 @@ describe.concurrent('validateSequenceVariant()', () => {
ins: 'TG',
userRepr: 'TEST'
}
+
+ // act: nothing to do
+
+ // assert:
expect(() => validateSeqvar(variant)).toThrow()
})
@@ -383,6 +460,7 @@ describe.concurrent('validateSequenceVariant()', () => {
['1', 249250620, 'AT'],
['1', 249250621, 'A']
])('work on %s-%d-%s', (chrom, pos, del) => {
+ // arrange:
const variant = {
genomeBuild: 'grch37' as GenomeBuild,
chrom,
@@ -391,6 +469,10 @@ describe.concurrent('validateSequenceVariant()', () => {
ins: 'TG',
userRepr: 'TEST'
}
+
+ // act: nothing to do
+
+ // assert:
expect(validateSeqvar(variant)).toEqual(variant)
})
})
@@ -404,6 +486,10 @@ describe.concurrent('parseSeparatedSeqvar()', () => {
['m-100-at-tg', 'grch37', 'MT'],
['mt-100-at-tg', 'grch37', 'MT']
])('hyphen-separated result for %s', (variant, expectedGenomeRelease, expectedChrom) => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(parseSeparatedSeqvar(variant)).toEqual({
genomeBuild: expectedGenomeRelease,
chrom: expectedChrom,
@@ -422,6 +508,10 @@ describe.concurrent('parseSeparatedSeqvar()', () => {
['m:100:at:tg', 'grch37', 'MT'],
['mt:100:at:tg', 'grch37', 'MT']
])('colon-separated result for %s', (variant, expectedGenomeRelease, expectedChrom) => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(parseSeparatedSeqvar(variant)).toEqual({
genomeBuild: expectedGenomeRelease,
chrom: expectedChrom,
@@ -440,6 +530,10 @@ describe.concurrent('parseCanonicalSpdiSeqvar()', () => {
['NC_000023.10:100:AT:TG', 'grch37', 'X'],
['NC_012920.1:100:at:tg', 'grch37', 'MT']
])('result for %s', (variant, expectedGenomeRelease, expectedChrom) => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(parseCanonicalSpdiSeqvar(variant)).toEqual({
genomeBuild: expectedGenomeRelease,
chrom: expectedChrom,
@@ -453,6 +547,10 @@ describe.concurrent('parseCanonicalSpdiSeqvar()', () => {
describe.concurrent('parseSeparatedStrucvar()', () => {
it('parse DEL:1:100:200', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(parseSeparatedStrucvar('DEL:1:100:200')).toEqual({
chrom: '1',
copyNumber: undefined,
@@ -465,6 +563,10 @@ describe.concurrent('parseSeparatedStrucvar()', () => {
})
it('parse DEL:GRCh37:1:100:200', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(parseSeparatedStrucvar('DEL:1:100:200')).toEqual({
chrom: '1',
copyNumber: undefined,
@@ -477,6 +579,10 @@ describe.concurrent('parseSeparatedStrucvar()', () => {
})
it('parse DEL:NC_000001.11:100:200', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(parseSeparatedStrucvar('DEL:NC_000001.11:100:200')).toEqual({
chrom: '1',
copyNumber: undefined,
@@ -489,6 +595,10 @@ describe.concurrent('parseSeparatedStrucvar()', () => {
})
it('parse DUP-NC_000001.11-100-200', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(parseSeparatedStrucvar('DUP-NC_000001.11-100-200')).toEqual({
chrom: '1',
copyNumber: undefined,
@@ -501,20 +611,36 @@ describe.concurrent('parseSeparatedStrucvar()', () => {
})
it('throws when start > stop', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(() => parseSeparatedStrucvar('DEL:NC_000001.11:200:100')).toThrow()
})
it('throws when start > length', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(() => parseSeparatedStrucvar('DEL:NC_000001.11:249250621:249250621')).toThrow()
})
it('throws when stop > length', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(() => parseSeparatedStrucvar('DEL:NC_000001.11:1:249250623')).toThrow()
})
})
describe.concurrent('parseIscnCnv', () => {
it('should match valid strings', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(parseIscnCnv('arr[GRCh37] 2q12.2q13 (107132950_110427254)x1')).toEqual({
chrom: '2',
copyNumber: 1,
@@ -574,6 +700,10 @@ describe.concurrent('parseIscnCnv', () => {
})
it('should throw on invalid positions', () => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(() => parseSeparatedStrucvar('arr[GRCh37] 2q12.2q13 (200_100)x1')).toThrow()
expect(() => parseSeparatedStrucvar('arr[GRCh37] 2q12.2q13 (243199374_243199374)x1')).toThrow()
expect(() => parseSeparatedStrucvar('arr[GRCh37] 2q12.2q13 (1_243199374)x1')).toThrow()
@@ -586,11 +716,17 @@ describe.concurrent('parseIscnCnv', () => {
describe.concurrent('SeqvarImpl', () => {
it('should work properly with toName()', () => {
+ // arrange:
const variant = new SeqvarImpl('grch37', '1', 100, 'AT', 'TG')
+
+ // act: nothing to do
+
+ // assert:
expect(variant.toName()).toEqual('grch37-1-100-AT-TG')
})
it('should be constructable with seqvarImplFromSeqvar()', () => {
+ // arrange:
const seqvar: Seqvar = {
genomeBuild: 'grch37',
chrom: '1',
@@ -600,17 +736,27 @@ describe.concurrent('SeqvarImpl', () => {
userRepr: 'TEST'
}
const variant = seqvarImplFromSeqvar(seqvar)
+
+ // act: nothing to do
+
+ // assert:
expect(variant).toEqual(seqvar)
})
})
describe.concurrent('LinearStrucvarImpl', () => {
it('should work properly with toName()', () => {
+ // arrange:
const variant = new LinearStrucvarImpl('DEL', 'grch37', '1', 100, 200, undefined, undefined)
+
+ // act: nothing to do
+
+ // assert:
expect(variant.toName()).toEqual('DEL-grch37-1-100-200')
})
it('should be constructable with seqvarImplFromSeqvar()', () => {
+ // arrange:
const strucvar: LinearStrucvar = {
svType: 'DEL',
genomeBuild: 'grch37',
@@ -620,6 +766,10 @@ describe.concurrent('LinearStrucvarImpl', () => {
userRepr: 'DEL-grch37-1-100-200'
}
const variant = linearStrucvarImplFromLinearStrucvar(strucvar)
+
+ // act: nothing to do
+
+ // assert:
expect(variant).toEqual(strucvar)
})
})
diff --git a/frontend/src/lib/__tests__/query.spec.ts b/frontend/src/lib/__tests__/query.spec.ts
index 200e1267..4607d970 100644
--- a/frontend/src/lib/__tests__/query.spec.ts
+++ b/frontend/src/lib/__tests__/query.spec.ts
@@ -24,6 +24,7 @@ describe.concurrent('Variant lookup with dotty', () => {
})
it('should return a gene', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(
JSON.stringify({
success: true,
@@ -36,13 +37,20 @@ describe.concurrent('Variant lookup with dotty', () => {
})
)
+ // act:
const result = await lookupWithDotty(seqVar.userRepr, seqVar.genomeBuild)
+
+ // assert:
expect(result).toStrictEqual(seqVar)
})
it('should throw an error if dotty fails', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify({ success: false }))
+ // act: nothing to do
+
+ // assert:
await expect(lookupWithDotty(seqVar.userRepr, seqVar.genomeBuild)).rejects.toThrow()
})
})
@@ -64,6 +72,7 @@ describe.concurrent('Resolve seqvar from the given query', () => {
})
it('should return a gene', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(
JSON.stringify({
success: true,
@@ -76,7 +85,10 @@ describe.concurrent('Resolve seqvar from the given query', () => {
})
)
+ // act:
const result = await resolveSeqvar(seqVar.userRepr, seqVar.genomeBuild)
+
+ // assert:
expect(result).toStrictEqual(seqVar)
})
})
@@ -99,11 +111,15 @@ describe.concurrent('Resolve strucvar from the given query', () => {
})
it('should return a gene', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify({ success: true, value: strucVar }))
+ // act:
const result = resolveStrucvar(strucVar.userRepr, strucVar.genomeBuild)
const expected = structuredClone(strucVar)
expected.userRepr = 'DEL-GRCh37-17-41176312-41277500'
+
+ // assert:
expect(result).toStrictEqual(expected)
})
})
@@ -115,6 +131,7 @@ describe.concurrent('Gene lookup', () => {
})
it('should return a gene', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(
JSON.stringify({
success: true,
@@ -135,13 +152,20 @@ describe.concurrent('Gene lookup', () => {
})
)
+ // act:
const result = await lookupGene('BRCA1')
+
+ // assert:
expect(result).toContain('BRCA1')
})
it('should throw an error if dotty fails', async () => {
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify({ success: false }))
+ // act: nothing to do
+
+ // assert:
await expect(lookupGene('BRCA1')).rejects.toThrow()
})
})
diff --git a/frontend/src/lib/__tests__/testUtils.spec.ts b/frontend/src/lib/__tests__/testUtils.spec.ts
index 5b6bd725..87dc328a 100644
--- a/frontend/src/lib/__tests__/testUtils.spec.ts
+++ b/frontend/src/lib/__tests__/testUtils.spec.ts
@@ -2,59 +2,80 @@ import { describe, expect, it } from 'vitest'
import { setupMountedComponents } from '@/lib/testUtils'
+// Test data
const TestComponent = { template: 'Test
', __name: 'TestComponent' }
describe.concurrent('Test Utils - setupMountedComponents', async () => {
it('should mount component with template', async () => {
+ // arrange:
const { wrapper } = await setupMountedComponents(
{ component: TestComponent },
{ initialStoreState: { state: { count: 42 } } }
)
+ // act: nothing, only test rendering
+
+ // assert:
expect(wrapper.exists()).toBe(true)
})
it('should mount component without template', async () => {
+ // arrange:
const { wrapper } = await setupMountedComponents(
{ component: TestComponent },
{ initialStoreState: { count: 42 } }
)
+ // act: nothing, only test rendering
+
+ // assert:
expect(wrapper.exists()).toBe(true)
})
it('should mock router push method', async () => {
+ // arrange:
const { router } = await setupMountedComponents(
{ component: TestComponent },
{ initialStoreState: { count: 42 } }
)
+ // act:
router.push('/new-route')
+
+ // assert:
expect(router.push).toHaveBeenCalledWith('/new-route')
})
it('should create vuetify, router, and pinia instances', async () => {
+ // arrange:
const { wrapper, router, pinia } = await setupMountedComponents(
{ component: TestComponent },
{ initialStoreState: { count: 42 } }
)
+ // act: nothing, only test rendering
+
+ // assert:
expect(wrapper.exists()).toBe(true)
expect(router).toBeDefined()
expect(pinia).toBeDefined()
})
it('should set props when rendering without template', async () => {
+ // arrange:
const TestComponent = {
props: ['message'],
template: '{{ message }}
',
__name: 'TestComponent'
}
-
const { wrapper } = await setupMountedComponents(
{ component: TestComponent },
{ props: { message: 'Hello, Props!' } }
)
+
+ // act: nothing, only test rendering
+
+ // assert:
expect(wrapper.text()).toBe('Hello, Props!')
})
})
diff --git a/frontend/src/lib/__tests__/utils.spec.ts b/frontend/src/lib/__tests__/utils.spec.ts
index e2f3e73c..8ff12b9e 100644
--- a/frontend/src/lib/__tests__/utils.spec.ts
+++ b/frontend/src/lib/__tests__/utils.spec.ts
@@ -1,4 +1,4 @@
-import { describe, expect, it, test } from 'vitest'
+import { describe, expect, it } from 'vitest'
import { type GenomeBuild } from '@/lib/genomeBuilds'
import { type Seqvar } from '@/lib/genomicVars'
@@ -27,73 +27,133 @@ const seqVar: Seqvar = {
describe.concurrent('roundIt method', () => {
it('should round a positive value with default digits', () => {
+ // arrange: nothing to do
+
+ // act:
const result = roundIt(3.14159)
+
+ // assert:
expect(result).toBe('3.14')
})
it('should round a positive value with specified digits', () => {
+ // arrange: nothing to do
+
+ // act:
const result = roundIt(3.14159, 3)
+
+ // assert:
expect(result).toBe('3.142')
})
it('should handle zero value', () => {
+ // arrange: nothing to do
+
+ // act:
const result = roundIt(0)
+
+ // assert:
expect(result).toBe("0")
})
it('should handle NaN value', () => {
+ // arrange: nothing to do
+
+ // act:
const result = roundIt(NaN)
+
+ // assert:
expect(result).toBe("0")
})
it('should add label to title if provided', () => {
+ // arrange: nothing to do
+
+ // act:
const result = roundIt(5.6789, 2, 'Value')
+
+ // assert:
expect(result).toBe('5.68')
})
it('should handle negative value', () => {
+ // arrange: nothing to do
+
+ // act:
const result = roundIt(-10.12345)
+
+ // assert:
expect(result).toBe('-10.12')
})
})
describe.concurrent('separateIt method', () => {
it('should separate a positive value with default separator', () => {
+ // arrange: nothing to do
+
+ // act:
const result = separateIt(123456789)
+
+ // assert:
expect(result).toBe('123 456 789')
})
it('should separate a positive value with specified separator', () => {
+ // arrange: nothing to do
+
+ // act:
const result = separateIt(123456789, ',')
+
+ // assert:
expect(result).toBe('123,456,789')
})
it('should handle zero value', () => {
+ // arrange: nothing to do
+
+ // act:
const result = separateIt(0)
+
+ // assert:
expect(result).toBe('0')
})
it('should handle float value', () => {
+ // arrange: nothing to do
+
+ // act:
const result = separateIt(123456789.12345)
+
+ // assert:
expect(result).toBe('123 456 789')
})
it('should handle values less then 0', () => {
+ // arrange: nothing to do
+
+ // act:
const result = separateIt(0.0134)
+
+ // assert:
expect(result).toBe('0')
})
})
describe.concurrent('isVariantMt method', () => {
it('should return true if mitochondrial chromosome', () => {
+ // arrange:
seqVar.chrom = 'MT'
- const result_MT = isVariantMt(seqVar)
seqVar.chrom = 'M'
- const result_M = isVariantMt(seqVar)
seqVar.chrom = 'chrMT'
- const result_chrMT = isVariantMt(seqVar)
seqVar.chrom = 'chrM'
+
+ // act:
+ const result_MT = isVariantMt(seqVar)
+ const result_M = isVariantMt(seqVar)
+ const result_chrMT = isVariantMt(seqVar)
const result_chrM = isVariantMt(seqVar)
+
+ // assert:
expect(result_MT).toBe(true)
expect(result_M).toBe(true)
expect(result_chrMT).toBe(true)
@@ -101,65 +161,115 @@ describe.concurrent('isVariantMt method', () => {
})
it('should return false if not mitochondrial chromosome', () => {
+ // arrange:
seqVar.chrom = '1'
+
+ // act:
const result = isVariantMt(seqVar)
+
+ // assert:
expect(result).toBe(false)
})
})
describe.concurrent('isVariantMtHomopolymer method', () => {
it('should return true if mitochondrial homopolymer', () => {
+ // arrange:
seqVar.chrom = 'MT'
seqVar.pos = 70
+
+ // act:
const result = isVariantMtHomopolymer(seqVar)
+
+ // assert:
expect(result).toBe(true)
})
it('should return false if not mitochondrial homopolymer (chromosome)', () => {
+ // arrange:
seqVar.chrom = '1'
seqVar.pos = 70
+
+ // act:
const result = isVariantMtHomopolymer(seqVar)
+
+ // assert:
expect(result).toBe(false)
})
it('should return false if not mitochondrial homopolymer (position)', () => {
+ // arrange:
seqVar.chrom = 'MT'
seqVar.pos = 1
+
+ // act:
const result = isVariantMtHomopolymer(seqVar)
+
+ // assert:
expect(result).toBe(false)
})
})
describe.concurrent('removeCommasFromNumbers method', () => {
it('should remove commas from numbers', () => {
+ // arrange: nothing to do
+
+ // act:
const result = removeCommasFromNumbers('1,234,567,890')
+
+ // assert:
expect(result).toBe('1234567890')
})
it('should return the same string if no commas', () => {
+ // arrange: nothing to do
+
+ // act:
const result = removeCommasFromNumbers('1234567890')
+
+ // assert:
expect(result).toBe('1234567890')
})
it('should return the same string if empty', () => {
+ // arrange: nothing to do
+
+ // act:
const result = removeCommasFromNumbers('')
+
+ // assert:
expect(result).toBe('')
})
it('should not remove commas from strings', () => {
+ // arrange: nothing to do
+
+ // act:
const result = removeCommasFromNumbers('foo,foo,bar')
+
+ // assert:
expect(result).toBe('foo,foo,bar')
})
it('should not remove commas from numbers in strings', () => {
+ // arrange: nothing to do
+
+ // act:
const result = removeCommasFromNumbers('foo,1,234,567,890,bar')
+
+ // assert:
expect(result).toBe('foo,1234567890,bar')
})
})
describe.concurrent('infoFromQuery method', () => {
it('should return info from query', () => {
+ // arrange: nothing to do
+
+ // act:
const result = infoFromQuery('chr37:12345:A:G')
+
+ // assert:
expect(result).toEqual({
chromosome: 'chr37',
pos: '12345',
@@ -170,7 +280,12 @@ describe.concurrent('infoFromQuery method', () => {
})
it('should return empty object if no query', () => {
+ // arrange: nothing to do
+
+ // act:
const result = infoFromQuery('')
+
+ // assert:
expect(result).toEqual({
chromosome: '',
pos: undefined,
@@ -183,22 +298,31 @@ describe.concurrent('infoFromQuery method', () => {
describe.concurrent('copy method', () => {
it('should return a JSON object for given dict', () => {
+ // arrange: nothing to do
+
+ // act:
const result = copy({ foo: 'bar' })
+
+ // assert:
expect(result).toEqual({ foo: 'bar' })
})
})
describe.concurrent('extractDbnsfpMimDiseaseId', () => {
- test.each([
+ it.each([
['[MIM:616921] Dyskinesia, limb and orofacial, infantile-onset', '616921'],
['[MIM:616921] Dyskinesia, limb and orofacial, infantile-onset [recessive?]', '616921']
])('%s => %s', (lhs, rhs) => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(extractDbnsfpMimDiseaseId(lhs)).toEqual(rhs)
})
})
describe.concurrent('transformDbnsfpMimDiseaseId', () => {
- test.each([
+ it.each([
[
'[MIM:616921]Dyskinesia, limb and orofacial, infantile-onset',
'[MIM:616921] Dyskinesia, limb and orofacial, infantile-onset',
@@ -220,6 +344,10 @@ describe.concurrent('transformDbnsfpMimDiseaseId', () => {
false
]
])('should work correctly', (lhs, rhs, showTermIds) => {
+ // arrange: nothing to do
+ // act: nothing to do
+
+ // assert:
expect(transformDbnsfpMimDiseaseId(lhs, showTermIds)).toEqual(rhs)
})
})
diff --git a/frontend/src/stores/__tests__/bookmarks.spec.ts b/frontend/src/stores/__tests__/bookmarks.spec.ts
index c877ce9d..8f6a6021 100644
--- a/frontend/src/stores/__tests__/bookmarks.spec.ts
+++ b/frontend/src/stores/__tests__/bookmarks.spec.ts
@@ -15,13 +15,18 @@ describe.concurrent('User Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useBookmarksStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.bookmarks).toStrictEqual([])
})
it('should load bookmarks', async () => {
+ // arrange:
const mockBookmarks: BookmarkData[] = [
{
user: '2c0a153e-5e8c-11ee-8c99-0242ac120002',
@@ -30,93 +35,112 @@ describe.concurrent('User Store', () => {
id: '2c0a153e-5e8c-11ee-8c99-0242ac120001'
}
]
-
- const store = useBookmarksStore()
fetchMocker.mockResponse(JSON.stringify(mockBookmarks))
+ const store = useBookmarksStore()
+ // act:
await store.loadBookmarks()
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.bookmarks).toEqual(mockBookmarks)
})
it('should handle error when loading bookmarks', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
-
- const store = useBookmarksStore()
fetchMocker.mockReject(new Error('Internal Server Error'))
+ const store = useBookmarksStore()
+ // act:
await store.loadBookmarks()
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.bookmarks).toStrictEqual([])
})
it('should delete bookmark', async () => {
- const store = useBookmarksStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({}))
+ const store = useBookmarksStore()
+ // act:
await store.deleteBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.bookmarks).toStrictEqual({})
})
it('should handle error when deleting bookmark', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
-
- const store = useBookmarksStore()
fetchMocker.mockReject(new Error('Internal Server Error'))
+ const store = useBookmarksStore()
+ // act:
await store.deleteBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.bookmarks).toStrictEqual([])
})
it('should create bookmark', async () => {
- const store = useBookmarksStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({ bookmark: 'created' }))
+ const store = useBookmarksStore()
+ // act:
await store.createBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.bookmarks).toStrictEqual({ bookmark: 'created' })
})
it('should handle error when creating bookmark', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
-
- const store = useBookmarksStore()
fetchMocker.mockReject(new Error('Internal Server Error'))
+ const store = useBookmarksStore()
+ // act:
await store.createBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.bookmarks).toStrictEqual([])
})
it('should fetch bookmark', async () => {
+ // arrange:
+ fetchMocker.mockResponse(JSON.stringify({ bookmark: 'created' }))
const store = useBookmarksStore()
store.storeState = StoreState.Active
- fetchMocker.mockResponse(JSON.stringify({ bookmark: 'created' }))
+ // act:
const result = await store.fetchBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(result).toStrictEqual({ bookmark: 'created' })
})
it('should handle error when fetching bookmark', async () => {
+ // arrange:
+ fetchMocker.mockResponse(JSON.stringify({ detail: 'Internal Server Error' }), { status: 500 })
const store = useBookmarksStore()
store.storeState = StoreState.Active
- fetchMocker.mockResponse(JSON.stringify({ detail: 'Internal Server Error' }), { status: 500 })
+ // act:
await store.fetchBookmark('seqvar', 'HGNC:1100')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.bookmarks).toStrictEqual([])
})
diff --git a/frontend/src/stores/__tests__/cadaPrio.spec.ts b/frontend/src/stores/__tests__/cadaPrio.spec.ts
index 6f444e91..cb634c1c 100644
--- a/frontend/src/stores/__tests__/cadaPrio.spec.ts
+++ b/frontend/src/stores/__tests__/cadaPrio.spec.ts
@@ -15,31 +15,40 @@ describe.concurrent('Cada Prio Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useCadaPrioStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.geneRanking).toBe(null)
})
it('should predict gene impact', async () => {
- const store = useCadaPrioStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({ result: 'pathogenic' }))
+ const store = useCadaPrioStore()
+ // act:
await store.loadData(['HP:0000001'])
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.geneRanking).toStrictEqual({ result: 'pathogenic' })
})
it('should handle error when predicting gene impact', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
-
- const store = useCadaPrioStore()
fetchMocker.mockReject(new Error('Internal Server Error'))
+ const store = useCadaPrioStore()
+ // act:
await store.loadData(['HP:0000001'])
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.geneRanking).toBe(null)
})
diff --git a/frontend/src/stores/__tests__/geneInfo.spec.ts b/frontend/src/stores/__tests__/geneInfo.spec.ts
index 516c2eb1..157a681e 100644
--- a/frontend/src/stores/__tests__/geneInfo.spec.ts
+++ b/frontend/src/stores/__tests__/geneInfo.spec.ts
@@ -15,8 +15,12 @@ describe.concurrent('geneInfo Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useGeneInfoStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.hgncId).toBe(null)
expect(store.geneInfo).toBe(null)
@@ -25,13 +29,16 @@ describe.concurrent('geneInfo Store', () => {
})
it('should clear state', () => {
+ // arrange:
const store = useGeneInfoStore()
store.storeState = StoreState.Active
store.hgncId = 'BRCA1'
store.geneInfo = JSON.parse(JSON.stringify({ gene: 'info' }))
+ // act:
store.clearData()
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.hgncId).toBe(null)
expect(store.geneInfo).toBe(null)
@@ -40,6 +47,7 @@ describe.concurrent('geneInfo Store', () => {
})
it('should load data', async () => {
+ // arrange:
const store = useGeneInfoStore()
fetchMocker.mockResponse((req) => {
if (req.url.includes('info')) {
@@ -52,8 +60,11 @@ describe.concurrent('geneInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+
+ // act:
await store.loadData('HGNC:1100', 'GRCh37')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.hgncId).toBe('HGNC:1100')
expect(store.geneInfo).toEqual({ gene: 'info' })
@@ -62,6 +73,7 @@ describe.concurrent('geneInfo Store', () => {
})
it('should fail to load data with invalid request to gene info', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
const store = useGeneInfoStore()
@@ -76,8 +88,11 @@ describe.concurrent('geneInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+
+ // act:
await store.loadData('invalid', 'invalid')
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.hgncId).toBe(null)
expect(store.geneInfo).toBe(null)
@@ -86,6 +101,7 @@ describe.concurrent('geneInfo Store', () => {
})
it('should fail to load data with invalid request to clinvar info', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
const store = useGeneInfoStore()
@@ -100,8 +116,11 @@ describe.concurrent('geneInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+
+ // act:
await store.loadData('invalid', 'invalid')
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.hgncId).toBe(null)
expect(store.geneInfo).toBe(null)
@@ -110,19 +129,24 @@ describe.concurrent('geneInfo Store', () => {
})
it('should not load data if gene symbol is the same', async () => {
+ // arrange:
const store = useGeneInfoStore()
fetchMocker.mockResponse(JSON.stringify({ genes: { 'HGNC:1100': { gene: 'info' } } }))
+ // act:
await store.loadData('HGNC:1100', 'GRCh37')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.hgncId).toBe('HGNC:1100')
expect(store.geneInfo).toEqual({ gene: 'info' })
expect(store.geneClinvar).toEqual({ gene: 'info' })
expect(store.hgncId).toBe('HGNC:1100')
+ // act2:
await store.loadData('HGNC:1100', 'GRCh37')
+ // assert2:
expect(fetchMocker.mock.calls.length).toBe(4)
})
})
diff --git a/frontend/src/stores/__tests__/genesList.spec.ts b/frontend/src/stores/__tests__/genesList.spec.ts
index 2b400e2f..15f4526f 100644
--- a/frontend/src/stores/__tests__/genesList.spec.ts
+++ b/frontend/src/stores/__tests__/genesList.spec.ts
@@ -7,6 +7,7 @@ import { StoreState } from '../misc'
const fetchMocker = createFetchMock(vi)
+// Test data
const exampleGenesList = {
genes: [
{
@@ -39,8 +40,12 @@ describe.concurrent('geneInfo Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useGenesListStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.query).toBe(null)
expect(store.genesList).toBe(null)
@@ -48,50 +53,62 @@ describe.concurrent('geneInfo Store', () => {
})
it('should clear state', () => {
+ // arrange:
const store = useGenesListStore()
store.storeState = StoreState.Active
store.query = 'q=BRCA1&fields=symbol'
store.genesList = JSON.parse(JSON.stringify({ gene: 'info' }))
+ // act:
store.clearData()
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.query).toBe(null)
expect(store.genesList).toBe(null)
})
it('should load data', async () => {
- const store = useGenesListStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+ const store = useGenesListStore()
+ // act:
await store.loadData({ q: 'EMP', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.query).toBe('q=EMP&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol')
expect(store.genesList).toEqual(exampleGenesList.genes)
})
it('should fail to load data with invalid request', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useGenesListStore()
fetchMocker.mockResponseOnce(JSON.stringify({ foo: 'bar' }), { status: 400 })
+ const store = useGenesListStore()
+ // act:
await store.loadData({ q: 'XXX', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.query).toBe(null)
expect(store.genesList).toBe(null)
})
it('should fail to load data with invalid fetchGenes response', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useGenesListStore()
fetchMocker.mockResponseOnce(JSON.stringify({ genes: [] }))
+ const store = useGenesListStore()
+ // act:
await store.loadData({ q: 'EMP', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+ // assert:
expect(console.error).toHaveBeenCalled()
expect(console.error).toHaveBeenCalledWith(
'There was an error while searching for genes.',
@@ -103,76 +120,89 @@ describe.concurrent('geneInfo Store', () => {
})
it('should not load data if gene symbol is the same', async () => {
- const store = useGenesListStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+ const store = useGenesListStore()
+ // act:
await store.loadData({ q: 'EMP', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.query).toBe('q=EMP&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol')
expect(store.genesList).toEqual(exampleGenesList.genes)
+ // act2:
await store.loadData({ q: 'EMP', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+ // assert2:
expect(fetchMocker.mock.calls.length).toBe(1)
})
it('should redirect if the searchTerm matched symbol', async () => {
- const store = useGenesListStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+ const store = useGenesListStore()
+ // act:
await store.loadData({ q: 'EMP1', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+ // assert:
expect(store.storeState).toBe(StoreState.Redirect)
expect(store.redirectHgncId).toBe('HGNC:3333')
expect(store.query).toBe('q=EMP1&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 hgnc_id', async () => {
- const store = useGenesListStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+ const store = useGenesListStore()
+ // act:
await store.loadData({ q: 'HGNC:3333', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+ // assert:
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()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+ const store = useGenesListStore()
+ // act:
await store.loadData({
q: 'ENSG00000134531',
fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol'
})
+ // assert:
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()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(exampleGenesList))
+ const store = useGenesListStore()
+ // act:
await store.loadData({ q: '2012', fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol' })
+ // assert:
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)
})
})
diff --git a/frontend/src/stores/__tests__/misc.spec.ts b/frontend/src/stores/__tests__/misc.spec.ts
index c75eaf80..0cb1d789 100644
--- a/frontend/src/stores/__tests__/misc.spec.ts
+++ b/frontend/src/stores/__tests__/misc.spec.ts
@@ -14,30 +14,40 @@ describe.concurrent('miscInfo Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useMiscStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.appVersion).toBe(null)
})
it('should load data', async () => {
- const store = useMiscStore()
+ // arrange:
fetchMocker.mockResponseOnce('v0.0.0')
+ const store = useMiscStore()
+ // act:
await store.initialize()
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.appVersion).toBe('v0.0.0')
})
it('should handle error', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useMiscStore()
fetchMocker.mockRejectOnce(new Error('error'))
+ const store = useMiscStore()
+ // act:
await store.initialize()
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.appVersion).toBe(null)
})
diff --git a/frontend/src/stores/__tests__/seqvarAcmgRating.spec.ts b/frontend/src/stores/__tests__/seqvarAcmgRating.spec.ts
index 5fd7a4a3..bab8f68b 100644
--- a/frontend/src/stores/__tests__/seqvarAcmgRating.spec.ts
+++ b/frontend/src/stores/__tests__/seqvarAcmgRating.spec.ts
@@ -11,6 +11,7 @@ import { useSeqvarAcmgRatingStore } from '../seqvarAcmgRating'
const fetchMocker = createFetchMock(vi)
+// Test data
const seqvarInfo: Seqvar = {
genomeBuild: 'grch37',
chrom: '17',
@@ -57,8 +58,12 @@ describe.concurrent('geneInfo Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useSeqvarAcmgRatingStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.acmgRating).toStrictEqual(new MultiSourceAcmgCriteriaState())
expect(store.seqvar).toBe(null)
@@ -66,20 +71,23 @@ describe.concurrent('geneInfo Store', () => {
})
it('should clear state', () => {
+ // arrange:
const store = useSeqvarAcmgRatingStore()
store.storeState = StoreState.Active
store.acmgRating = JSON.parse(JSON.stringify({ acmg: 'rating' }))
store.seqvar = structuredClone(seqvarInfo)
+ // act:
store.clearData()
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.acmgRating).toStrictEqual(new MultiSourceAcmgCriteriaState())
expect(store.seqvar).toBe(null)
})
it('should correctly retrieve data for InterVar and Server', async () => {
- const store = useSeqvarAcmgRatingStore()
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('remote/acmg')) {
return Promise.resolve(JSON.stringify(ExampleInterVarResponse))
@@ -88,9 +96,12 @@ describe.concurrent('geneInfo Store', () => {
}
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ const store = useSeqvarAcmgRatingStore()
+ // act:
await store.fetchAcmgRating(structuredClone(seqvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
const expectedAcmgRating = new MultiSourceAcmgCriteriaState()
for (const [key, value] of Object.entries(ExampleInterVarResponse)) {
@@ -122,22 +133,25 @@ describe.concurrent('geneInfo Store', () => {
})
it('should fail to load data with invalid request', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useSeqvarAcmgRatingStore()
fetchMocker.mockResponseOnce(JSON.stringify({ foo: 'bar' }), { status: 400 })
+ const store = useSeqvarAcmgRatingStore()
+ // act:
await expect(
async () => await store.fetchAcmgRating(structuredClone(seqvarInfo))
).rejects.toThrow()
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.acmgRating).toStrictEqual(new MultiSourceAcmgCriteriaState())
expect(store.seqvar).toBe(null)
})
it('should not load data if small variant is the same', async () => {
- const store = useSeqvarAcmgRatingStore()
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('remote/acmg')) {
return Promise.resolve(JSON.stringify(ExampleInterVarResponse))
@@ -146,8 +160,12 @@ describe.concurrent('geneInfo Store', () => {
}
return Promise.resolve(JSON.stringify({ status: 400 }))
})
+ const store = useSeqvarAcmgRatingStore()
+
+ // act:
await store.fetchAcmgRating(structuredClone(seqvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
const expectedAcmgRating = new MultiSourceAcmgCriteriaState()
for (const [key, value] of Object.entries(ExampleInterVarResponse)) {
@@ -177,8 +195,10 @@ describe.concurrent('geneInfo Store', () => {
expect(store.acmgRating).toStrictEqual(expectedAcmgRating)
expect(store.seqvar).toStrictEqual(seqvarInfo)
+ // act2:
await store.fetchAcmgRating(structuredClone(seqvarInfo))
+ // assert2:
expect(fetchMocker.mock.calls.length).toBe(2)
})
})
diff --git a/frontend/src/stores/__tests__/strucvarAcmgRating.spec.ts b/frontend/src/stores/__tests__/strucvarAcmgRating.spec.ts
index 555dfe75..52ba66a6 100644
--- a/frontend/src/stores/__tests__/strucvarAcmgRating.spec.ts
+++ b/frontend/src/stores/__tests__/strucvarAcmgRating.spec.ts
@@ -17,6 +17,7 @@ import { useStrucvarAcmgRatingStore } from '../strucvarAcmgRating'
const fetchMocker = createFetchMock(vi)
+// Test data
const strucvarInfo: Strucvar = {
genomeBuild: 'grch37',
svType: 'DEL',
@@ -26,46 +27,6 @@ const strucvarInfo: Strucvar = {
userRepr: 'DEL-grch37-17-41176312-41277500'
}
-// const svRecord = {
-// svType: 'DEL',
-// chromosome: 'chr17',
-// start: '41176312',
-// end: '41277500',
-// release: 'grch37',
-// result: [
-// {
-// hgnc_id: 'HGNC:18315',
-// transcript_effects: [
-// 'transcript_variant',
-// 'exon_variant',
-// 'splice_region_variant',
-// 'intron_variant',
-// 'upstream_variant',
-// 'downstream_variant'
-// ]
-// },
-// {
-// hgnc_id: 'HGNC:20691',
-// transcript_effects: ['upstream_variant']
-// },
-// {
-// hgnc_id: 'HGNC:1100',
-// transcript_effects: [
-// 'transcript_variant',
-// 'exon_variant',
-// 'splice_region_variant',
-// 'intron_variant',
-// 'upstream_variant',
-// 'downstream_variant'
-// ]
-// },
-// {
-// hgnc_id: 'HGNC:16919',
-// transcript_effects: ['upstream_variant']
-// }
-// ]
-// }
-
const ExampleAutoCNVResponse = {
job: {
result: {
@@ -98,32 +59,42 @@ describe.concurrent('geneInfo Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useStrucvarAcmgRatingStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.acmgRating).toStrictEqual(new MultiSourceAcmgCriteriaCNVState('DEL'))
expect(store.strucvar).toBe(undefined)
})
it('should clear state', () => {
+ // arrange:
const store = useStrucvarAcmgRatingStore()
store.storeState = StoreState.Active
store.acmgRating = JSON.parse(JSON.stringify({ acmg: 'rating' }))
store.strucvar = structuredClone(strucvarInfo)
+ // act:
store.clearData()
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.acmgRating).toStrictEqual(new MultiSourceAcmgCriteriaCNVState('DEL'))
expect(store.strucvar).toBe(undefined)
})
it('should correctly retrieve data', async () => {
- const store = useStrucvarAcmgRatingStore()
+ // arrange:
fetchMocker.mockResponseOnce(JSON.stringify(ExampleAutoCNVResponse))
+ const store = useStrucvarAcmgRatingStore()
+ // act:
await store.fetchAcmgRating(structuredClone(strucvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
const expectedAcmgRating = new MultiSourceAcmgCriteriaCNVState('DEL')
for (const criteria of ACMG_CRITERIA_CNV_LOSS) {
@@ -168,23 +139,30 @@ describe.concurrent('geneInfo Store', () => {
})
it('should fail to load data with invalid request', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useStrucvarAcmgRatingStore()
fetchMocker.mockResponseOnce(JSON.stringify({ foo: 'bar' }), { status: 400 })
+ const store = useStrucvarAcmgRatingStore()
+ // act:
await store.fetchAcmgRating(structuredClone(strucvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.acmgRating).toStrictEqual(new MultiSourceAcmgCriteriaCNVState('DEL'))
expect(store.strucvar).toBe(undefined)
})
it('should not load data if structure variant is the same', async () => {
- const store = useStrucvarAcmgRatingStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify(ExampleAutoCNVResponse))
+ const store = useStrucvarAcmgRatingStore()
+
+ // act:
await store.fetchAcmgRating(structuredClone(strucvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
const expectedAcmgRating = new MultiSourceAcmgCriteriaCNVState('DEL')
for (const criteria of ACMG_CRITERIA_CNV_LOSS) {
@@ -227,8 +205,10 @@ describe.concurrent('geneInfo Store', () => {
expect(store.acmgRating).toStrictEqual(expectedAcmgRating)
expect(store.strucvar).toStrictEqual(structuredClone(strucvarInfo))
+ // act2:
await store.fetchAcmgRating(structuredClone(strucvarInfo))
+ // assert2:
expect(fetchMocker.mock.calls.length).toBe(1)
})
})
diff --git a/frontend/src/stores/__tests__/strucvarInfo.spec.ts b/frontend/src/stores/__tests__/strucvarInfo.spec.ts
index 6c565314..5da90a31 100644
--- a/frontend/src/stores/__tests__/strucvarInfo.spec.ts
+++ b/frontend/src/stores/__tests__/strucvarInfo.spec.ts
@@ -9,6 +9,7 @@ import { useStrucvarInfoStore } from '@/stores/strucvarInfo'
const fetchMocker = createFetchMock(vi)
+// Test data
const strucvarInfo: Strucvar = {
genomeBuild: 'grch37',
svType: 'DEL',
@@ -26,28 +27,35 @@ describe.concurrent('svInfo Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useStrucvarInfoStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.strucvar).toBe(undefined)
expect(store.genesInfos).toStrictEqual(undefined)
})
it('should clear state', () => {
+ // arrange:
const store = useStrucvarInfoStore()
store.storeState = StoreState.Active
store.strucvar = structuredClone(strucvarInfo)
store.genesInfos = JSON.parse(JSON.stringify([geneInfo['genes']['HGNC:1100']]))
+ // act:
store.clearData()
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.strucvar).toBe(undefined)
expect(store.genesInfos).toStrictEqual(undefined)
})
it('should load data', async () => {
- const store = useStrucvarInfoStore()
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('csq')) {
return Promise.resolve(JSON.stringify({ result: [{ hgnc_id: 'HGNC:1100' }] }))
@@ -55,19 +63,22 @@ describe.concurrent('svInfo Store', () => {
return Promise.resolve(JSON.stringify(geneInfo))
}
})
+ const store = useStrucvarInfoStore()
+
+ // act:
await store.loadData(structuredClone(strucvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.strucvar).toStrictEqual(strucvarInfo)
expect(store.genesInfos).toStrictEqual([geneInfo['genes']['HGNC:1100']])
})
it('should correctly handle errors', async () => {
+ // arrange:
// Disable console.error
const spy = vi.spyOn(console, 'error')
spy.mockImplementation(() => {})
-
- const store = useStrucvarInfoStore()
fetchMocker.mockResponse((req) => {
if (req.url.includes('csq')) {
return Promise.resolve(JSON.stringify({ status: 400 }))
@@ -75,8 +86,12 @@ describe.concurrent('svInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+ const store = useStrucvarInfoStore()
+
+ // act:
await store.loadData(structuredClone(strucvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.strucvar).toBe(undefined)
expect(store.genesInfos).toStrictEqual(undefined)
diff --git a/frontend/src/stores/__tests__/terms.spec.ts b/frontend/src/stores/__tests__/terms.spec.ts
index 22878eed..b6adf387 100644
--- a/frontend/src/stores/__tests__/terms.spec.ts
+++ b/frontend/src/stores/__tests__/terms.spec.ts
@@ -15,88 +15,113 @@ describe.concurrent('Terms Store', () => {
})
it('initial state', () => {
+ // arrange:
const store = useTermsStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.hpoTerms).toStrictEqual([])
expect(store.omimTerms).toStrictEqual([])
})
it('clears data', () => {
+ // arrange:
const store = useTermsStore()
store.hpoTerms = [{ term_id: 'HP:0000118', name: 'Phenotypic abnormality' }]
+ // act:
store.clearData()
+ // assert:
expect(store.hpoTerms).toStrictEqual([])
})
it('fetches HPO terms by name', async () => {
+ // arrange:
const mockHpoTerms = [{ term_id: 'HP:0000118', name: 'Phenotypic abnormality' }]
fetchMocker.mockResponseOnce(JSON.stringify({ result: mockHpoTerms }))
-
const store = useTermsStore()
+
+ // act:
await store.fetchHpoTerms('Phenotypic abnormality')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.hpoTerms).toEqual(mockHpoTerms)
})
it('fetches HPO term by ID', async () => {
+ // arrange:
const mockHpoTerms = [{ term_id: 'HP:0000118', name: 'Phenotypic abnormality' }]
fetchMocker.mockResponseOnce(JSON.stringify({ result: mockHpoTerms }))
+ // act:
const store = useTermsStore()
await store.fetchHpoTerms('HP:0000118')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.hpoTerms).toEqual(mockHpoTerms)
})
it('handles error when fetching HPO terms', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
fetchMocker.mockResponseOnce(JSON.stringify({}), { status: 500 })
-
const store = useTermsStore()
+
+ // act:
await store.fetchHpoTerms('InvalidQuery')
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.hpoTerms).toStrictEqual([])
})
it('fetches OMIM terms by name', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
const mockOmimTerms = [{ term_id: 'OMIM:123456', name: 'Example Disease' }]
fetchMocker.mockResponseOnce(JSON.stringify({ result: mockOmimTerms }))
-
const store = useTermsStore()
+
+ // act:
await store.fetchOmimTerms('Example Disease')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.omimTerms).toEqual(mockOmimTerms)
})
it('fetches OMIM term by ID', async () => {
+ // arrange:
const mockOmimTerm = { term_id: 'OMIM:123456', name: 'Example Disease' }
fetchMocker.mockResponseOnce(JSON.stringify({ result: mockOmimTerm }))
-
const store = useTermsStore()
+
+ // act:
await store.fetchOmimTerms('OMIM:123456')
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.omimTerms).toEqual([mockOmimTerm])
})
it('handles error when fetching OMIM terms', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
fetchMocker.mockResponseOnce(JSON.stringify({}), { status: 500 })
-
const store = useTermsStore()
+
+ // act:
await store.fetchOmimTerms('InvalidQuery')
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.omimTerms).toStrictEqual([])
})
diff --git a/frontend/src/stores/__tests__/user.spec.ts b/frontend/src/stores/__tests__/user.spec.ts
index e51c26d5..ed5131aa 100644
--- a/frontend/src/stores/__tests__/user.spec.ts
+++ b/frontend/src/stores/__tests__/user.spec.ts
@@ -15,14 +15,19 @@ describe.concurrent('User Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useUserStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.currentUser).toBe(undefined)
expect(store.isAuthenticated).toBe(false)
})
it('should load current user', async () => {
+ // arrange:
const mockUser: UserData = {
id: '1',
email: 'test@example.com',
@@ -31,40 +36,48 @@ describe.concurrent('User Store', () => {
is_verified: true,
oauth_accounts: []
}
-
- const store = useUserStore()
fetchMocker.mockResponse(JSON.stringify(mockUser))
+ const store = useUserStore()
+ // act:
await store.loadCurrentUser()
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.currentUser).toEqual(mockUser)
expect(store.isAuthenticated).toBe(true)
})
it('should handle unauthenticated error when loading current user', async () => {
- const store = useUserStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({ detail: 'Unauthenticated' }), { status: 401 })
+ const store = useUserStore()
+ // act:
await store.loadCurrentUser()
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.currentUser).toBe(null)
expect(store.isAuthenticated).toBe(false)
})
it('should handle other errors when loading current user', async () => {
- const store = useUserStore()
+ // arrange:
fetchMocker.mockResponse(JSON.stringify({ detail: 'Internal Server Error' }), { status: 500 })
+ const store = useUserStore()
+ // act:
await store.loadCurrentUser()
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.currentUser).toBe(null)
expect(store.isAuthenticated).toBe(false)
})
it('should initialize store', async () => {
+ // arrange:
const mockUser: UserData = {
id: '1',
email: 'test@example.com',
@@ -73,18 +86,20 @@ describe.concurrent('User Store', () => {
is_verified: true,
oauth_accounts: []
}
-
- const store = useUserStore()
fetchMocker.mockResponse(JSON.stringify(mockUser))
+ const store = useUserStore()
+ // act:
await store.initialize()
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.currentUser).toEqual(mockUser)
expect(store.isAuthenticated).toBe(true)
})
it('should not initialize store twice', async () => {
+ // arrange:
const mockUser: UserData = {
id: '1',
email: 'test@example.com',
@@ -93,15 +108,15 @@ describe.concurrent('User Store', () => {
is_verified: true,
oauth_accounts: []
}
-
- const store = useUserStore()
fetchMocker.mockResponse(JSON.stringify(mockUser))
+ const store = useUserStore()
+ // act:
await store.initialize()
const initialState = { ...store }
-
await store.initialize()
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.currentUser).toEqual(mockUser)
expect(store.isAuthenticated).toBe(true)
diff --git a/frontend/src/stores/__tests__/variantInfo.spec.ts b/frontend/src/stores/__tests__/variantInfo.spec.ts
index 24e37714..db203ea8 100644
--- a/frontend/src/stores/__tests__/variantInfo.spec.ts
+++ b/frontend/src/stores/__tests__/variantInfo.spec.ts
@@ -13,6 +13,7 @@ import { useSeqvarInfoStore } from '../seqvarInfo'
const fetchMocker = createFetchMock(vi)
+// Test data
const seqvarInfo: Seqvar = {
genomeBuild: 'grch37',
chrom: '17',
@@ -30,8 +31,12 @@ describe.concurrent('geneInfo Store', () => {
})
it('should have initial state', () => {
+ // arrange:
const store = useSeqvarInfoStore()
+ // act: nothing to do
+
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.seqvar).toBe(undefined)
expect(store.varAnnos).toBe(null)
@@ -41,6 +46,7 @@ describe.concurrent('geneInfo Store', () => {
})
it('should clear state', () => {
+ // arrange:
const store = useSeqvarInfoStore()
store.storeState = StoreState.Active
store.seqvar = structuredClone(seqvarInfo)
@@ -48,8 +54,10 @@ describe.concurrent('geneInfo Store', () => {
store.geneInfo = JSON.parse(JSON.stringify(BRCA1GeneInfo))
store.txCsq = JSON.parse(JSON.stringify(BRCA1TxInfo))
+ // act:
store.clearData()
+ // assert:
expect(store.storeState).toBe(StoreState.Initial)
expect(store.seqvar).toBe(undefined)
expect(store.varAnnos).toBe(null)
@@ -58,7 +66,7 @@ describe.concurrent('geneInfo Store', () => {
})
it('should load data', async () => {
- const store = useSeqvarInfoStore()
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('annos/variant')) {
return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
@@ -72,9 +80,12 @@ describe.concurrent('geneInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+ const store = useSeqvarInfoStore()
+ // act:
await store.loadData(structuredClone(seqvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.seqvar).toStrictEqual(seqvarInfo)
expect(store.varAnnos).toEqual(BRCA1VariantInfo.result)
@@ -83,13 +94,16 @@ describe.concurrent('geneInfo Store', () => {
})
it('should fail to load data with invalid request', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useSeqvarInfoStore()
fetchMocker.mockResponseOnce(JSON.stringify({ foo: 'bar' }), { status: 400 })
+ const store = useSeqvarInfoStore()
+ // act:
await store.loadData(structuredClone(seqvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Error)
expect(store.seqvar).toBe(undefined)
expect(store.varAnnos).toBe(null)
@@ -98,9 +112,9 @@ describe.concurrent('geneInfo Store', () => {
})
it('should handle loading data with invalid fetchVariantInfo response', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useSeqvarInfoStore()
fetchMocker.mockResponse((req) => {
if (req.url.includes('annos/variant')) {
return Promise.resolve(
@@ -116,9 +130,12 @@ describe.concurrent('geneInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+ const store = useSeqvarInfoStore()
+ // act:
await store.loadData(structuredClone(seqvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.seqvar).toStrictEqual(seqvarInfo)
expect(store.varAnnos).toStrictEqual({
@@ -133,9 +150,9 @@ describe.concurrent('geneInfo Store', () => {
})
it('should handle loading data with invalid retrieveSeqvarsCsq response', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useSeqvarInfoStore()
fetchMocker.mockResponse((req) => {
if (req.url.includes('annos/variant')) {
return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
@@ -149,21 +166,23 @@ describe.concurrent('geneInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+ const store = useSeqvarInfoStore()
+ // act:
await store.loadData(structuredClone(seqvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.seqvar).toStrictEqual(seqvarInfo)
-
expect(store.varAnnos).toStrictEqual(BRCA1VariantInfo.result)
expect(store.geneInfo).toEqual(null)
expect(store.txCsq).toStrictEqual([])
})
it('should fail to load data with invalid fetchGeneInfo response', async () => {
+ // arrange:
// Disable error logging
vi.spyOn(console, 'error').mockImplementation(() => {})
- const store = useSeqvarInfoStore()
fetchMocker.mockResponse((req) => {
if (req.url.includes('annos/variant')) {
return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
@@ -177,9 +196,12 @@ describe.concurrent('geneInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+ const store = useSeqvarInfoStore()
+ // act:
await store.loadData(structuredClone(seqvarInfo))
+ // assert:
expect(console.error).toHaveBeenCalled()
expect(console.error).toHaveBeenCalledWith(
'There was an error loading the variant data.',
@@ -193,7 +215,7 @@ describe.concurrent('geneInfo Store', () => {
})
it('should not load data if variant is the same', async () => {
- const store = useSeqvarInfoStore()
+ // arrange:
fetchMocker.mockResponse((req) => {
if (req.url.includes('annos/variant')) {
return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
@@ -207,17 +229,22 @@ describe.concurrent('geneInfo Store', () => {
return Promise.resolve(JSON.stringify({ status: 400 }))
}
})
+ const store = useSeqvarInfoStore()
+ // act:
await store.loadData(structuredClone(seqvarInfo))
+ // assert:
expect(store.storeState).toBe(StoreState.Active)
expect(store.seqvar).toStrictEqual(seqvarInfo)
expect(store.varAnnos).toEqual(BRCA1VariantInfo.result)
expect(store.geneInfo).toEqual(BRCA1GeneInfo.genes['HGNC:1100'])
expect(store.txCsq).toEqual(BRCA1TxInfo.result)
+ // act2:
await store.loadData(structuredClone(seqvarInfo))
+ // assert2:
expect(fetchMocker.mock.calls.length).toBe(5)
})
})