chore: extending test coverage (#38) (#40)

backend/Pipfile

@@ -20,6 +20,7 @@ pytest = "*"
 pytest-asyncio = "*"
 pytest-cov = "*"
 pytest-httpx = "*"
+pytest-subprocess = "*"
 sphinx = "*"
 sphinx-rtd-theme = "*"
 starlette = "*"

backend/app/main.py

@@ -31,7 +31,7 @@
 #: The REEV version from the file (``None`` if to load dynamically from git)
 REEV_VERSION = None
 # Try to obtain version from file, otherwise keep it at ``None``
-if os.path.exists(VERSION_FILE):
+if os.path.exists(VERSION_FILE):  # pragma: no cover
     with open(VERSION_FILE) as f:
         REEV_VERSION = f.read().strip() or None
 

backend/tests/test_main.py

@@ -74,3 +74,48 @@ async def test_invalid_proxy_route(monkeypatch, httpx_mock):
     response = client.get("/proxy/some-other-path")
     assert response.status_code == 404
     assert response.text == "Reverse proxy route not found"
+
+
+@pytest.mark.asyncio
+async def test_version(monkeypatch):
+    """Test version endpoint."""
+    monkeypatch.setattr(main, "REEV_VERSION", "1.2.3")
+    response = client.get("/version")
+    assert response.status_code == 200
+    assert response.text == "1.2.3"
+
+
+@pytest.mark.asyncio
+async def test_version_no_version(monkeypatch, fp):
+    """Test version endpoint with no version."""
+    monkeypatch.setattr(main, "REEV_VERSION", None)
+    # We mock the output of ``git describe`` as subprocesses will be triggered
+    # internally.
+    fp.register(["git", "describe", "--tags", "--dirty"], stdout="v0.0.0-16-g7a4205d-dirty")
+    response = client.get("/version")
+
+    assert response.status_code == 200
+    assert response.text == "v0.0.0-16-g7a4205d-dirty"
+
+
+@pytest.mark.asyncio
+async def test_variantvalidator(monkeypatch, httpx_mock):
+    """Test variant validator endpoint."""
+    variantvalidator_url = "https://rest.variantvalidator.org/VariantValidator/variantvalidator"
+    httpx_mock.add_response(
+        url=f"{variantvalidator_url}/{MOCKED_URL_TOKEN}",
+        method="GET",
+        text="Mocked response",
+    )
+
+    response = client.get(f"/variantvalidator/{MOCKED_URL_TOKEN}")
+    assert response.status_code == 200
+    assert response.text == "Mocked response"
+
+
+@pytest.mark.asyncio
+async def test_favicon():
+    """Test favicon endpoint."""
+    response = client.get("/favicon.ico")
+    assert response.status_code == 200
+    assert response.headers["content-type"] == "image/vnd.microsoft.icon"

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

@@ -3,10 +3,12 @@ import createFetchMock from 'vitest-fetch-mock'
 
 import { AnnonarsClient } from '../annonars'
 import * as BRCA1geneInfo from '@/assets/__tests__/BRCA1GeneInfo.json'
+import * as BRCA1VariantInfo from '@/assets/__tests__/BRCA1VariantInfo.json'
+import * as EMPSearchInfo from '@/assets/__tests__/EMPSearchInfo.json'
 
 const fetchMocker = createFetchMock(vi)
 
-describe('Annonars Client', () => {
+describe.concurrent('Annonars Client', () => {
   beforeEach(() => {
     fetchMocker.enableMocks()
     fetchMocker.resetMocks()
@@ -20,9 +22,9 @@ describe('Annonars Client', () => {
     expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1geneInfo))
   })
 
-  it('fails to fetch gene info with wrong hgnc-id', async () => {
+  it('fails to fetch gene info with wrong HGNC id', async () => {
     fetchMocker.mockResponse((req) => {
-      if (req.url.includes('hgnc-id=BRCA1')) {
+      if (req.url.includes('hgnc_id=BRCA1')) {
         return Promise.resolve(JSON.stringify(BRCA1geneInfo))
       }
       return Promise.resolve(JSON.stringify({ status: 400 }))
@@ -32,4 +34,50 @@ describe('Annonars Client', () => {
     const result = await client.fetchGeneInfo('123')
     expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
   })
+
+  it('fetches variant info correctly', async () => {
+    fetchMocker.mockResponseOnce(JSON.stringify(BRCA1VariantInfo))
+
+    const client = new AnnonarsClient()
+    const result = await client.fetchVariantInfo('grch37', 'chr17', 43044295, 'A', 'G')
+    expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1VariantInfo))
+  })
+
+  it('fails to fetch variant info with wrong variant', async () => {
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('alternative=G')) {
+        return Promise.resolve(JSON.stringify(BRCA1VariantInfo))
+      }
+      return Promise.resolve(JSON.stringify({ status: 400 }))
+    })
+
+    const client = new AnnonarsClient()
+    const result = await client.fetchVariantInfo('grch37', 'chr17', 43044295, 'A', 'T')
+    expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
+  })
+
+  it('fetches genes correctly', async () => {
+    fetchMocker.mockResponseOnce(JSON.stringify(EMPSearchInfo))
+
+    const client = new AnnonarsClient()
+    const result = await client.fetchGenes(
+      'q=BRCA1&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol'
+    )
+    expect(JSON.stringify(result)).toEqual(JSON.stringify(EMPSearchInfo))
+  })
+
+  it('fails to fetch genes with wrong query', async () => {
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('q=BRCA1')) {
+        return Promise.resolve(JSON.stringify(EMPSearchInfo))
+      }
+      return Promise.resolve(JSON.stringify({ status: 400 }))
+    })
+
+    const client = new AnnonarsClient()
+    const result = await client.fetchGenes(
+      'q=BRCA2&fields=hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol'
+    )
+    expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
+  })
 })

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

@@ -1,8 +1,14 @@
 import { describe, it, expect } from 'vitest'
 
-import { API_BASE_PREFIX_ANNONARS, API_BASE_PREFIX_MEHARI } from '../common'
+import { API_BASE_PREFIX, API_BASE_PREFIX_ANNONARS, API_BASE_PREFIX_MEHARI } from '../common'
+
+describe.concurrent('API_BASE_PREFIX constants', () => {
+  it('returns the correct API base prefix in production mode', () => {
+    const originalMode = import.meta.env.MODE
+    expect(API_BASE_PREFIX).toBe('/')
+    import.meta.env.MODE = originalMode
+  })
 
-describe('API_BASE_PREFIX constants', () => {
   it('returns the correct API base prefix for annonars in production mode', () => {
     const originalMode = import.meta.env.MODE
     expect(API_BASE_PREFIX_ANNONARS).toBe('/proxy/annonars')

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

@@ -0,0 +1,43 @@
+import { beforeEach, describe, it, expect, vi } from 'vitest'
+import createFetchMock from 'vitest-fetch-mock'
+
+import { MehariClient } from '../mehari'
+import * as BRCA1TxInfo from '@/assets/__tests__/BRCA1TxInfo.json'
+
+const fetchMocker = createFetchMock(vi)
+
+describe.concurrent('Mehari Client', () => {
+  beforeEach(() => {
+    fetchMocker.enableMocks()
+    fetchMocker.resetMocks()
+  })
+
+  it('fetches TxCsq info correctly', async () => {
+    fetchMocker.mockResponseOnce(JSON.stringify(BRCA1TxInfo))
+
+    const client = new MehariClient()
+    const result = await client.retrieveTxCsq('grch37', 'chr17', 43044295, 'A', 'G', 'HGNC:1100')
+    expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1TxInfo))
+  })
+
+  it('fetches TxCsq info correctly without HGNC id', async () => {
+    fetchMocker.mockResponseOnce(JSON.stringify(BRCA1TxInfo))
+
+    const client = new MehariClient()
+    const result = await client.retrieveTxCsq('grch37', 'chr17', 43044295, 'A', 'G')
+    expect(JSON.stringify(result)).toEqual(JSON.stringify(BRCA1TxInfo))
+  })
+
+  it('fails to fetch variant info with wrong variant', async () => {
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('alternative=G')) {
+        return Promise.resolve(JSON.stringify(BRCA1TxInfo))
+      }
+      return Promise.resolve(JSON.stringify({ status: 400 }))
+    })
+
+    const client = new MehariClient()
+    const result = await client.retrieveTxCsq('grch37', 'chr17', 43044295, 'A', 'T')
+    expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
+  })
+})

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

@@ -5,7 +5,7 @@ import { MiscClient } from '../misc'
 
 const fetchMocker = createFetchMock(vi)
 
-describe('Misc Client', () => {
+describe.concurrent('Misc Client', () => {
   beforeEach(() => {
     fetchMocker.enableMocks()
     fetchMocker.resetMocks()

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

@@ -1,8 +1,15 @@
 import { describe, it, expect } from 'vitest'
 
-import { roundIt, search } from '../utils'
+import {
+  roundIt,
+  separateIt,
+  isVariantMt,
+  isVariantMtHomopolymer,
+  search,
+  infoFromQuery
+} from '../utils'
 
-describe('roundIt method', () => {
+describe.concurrent('roundIt method', () => {
   it('should round a positive value with default digits', () => {
     const result = roundIt(3.14159)
     expect(result).toBe('<abbr title="3.14159">3.14</abbr>')
@@ -34,8 +41,70 @@ describe('roundIt method', () => {
   })
 })
 
+describe('separateIt method', () => {
+  it('should separate a positive value with default separator', () => {
+    const result = separateIt(123456789)
+    expect(result).toBe(' 123 456 789 ')
+  })
+
+  it('should separate a positive value with specified separator', () => {
+    const result = separateIt(123456789, ',')
+    expect(result).toBe(',123,456,789,')
+  })
+
+  it('should handle zero value', () => {
+    const result = separateIt(0)
+    expect(result).toBe('0 ')
+  })
+
+  it('should handle float value', () => {
+    const result = separateIt(123456789.12345)
+    expect(result).toBe(' 123 456 789 ')
+  })
+})
+
+describe('isVariantMt method', () => {
+  it('should return true if mitochondrial chromosome', () => {
+    const result_MT = isVariantMt({ chromosome: 'MT' })
+    const result_M = isVariantMt({ chromosome: 'M' })
+    const result_chrMT = isVariantMt({ chromosome: 'chrMT' })
+    const result_chrM = isVariantMt({ chromosome: 'chrM' })
+    expect(result_MT).toBe(true)
+    expect(result_M).toBe(true)
+    expect(result_chrMT).toBe(true)
+    expect(result_chrM).toBe(true)
+  })
+
+  it('should return false if not mitochondrial chromosome', () => {
+    const result = isVariantMt({ chromosome: '1' })
+    expect(result).toBe(false)
+  })
+})
+
+describe('isVariantMtHomopolymer method', () => {
+  it('should return true if mitochondrial homopolymer', () => {
+    const result = isVariantMtHomopolymer({ chromosome: 'MT', start: 70 })
+    expect(result).toBe(true)
+  })
+
+  it('should return false if not mitochondrial homopolymer (chromosome)', () => {
+    const result = isVariantMtHomopolymer({ chromosome: '1', start: 70 })
+    expect(result).toBe(false)
+  })
+
+  it('should return false if not mitochondrial homopolymer (position)', () => {
+    const result = isVariantMtHomopolymer({ chromosome: 'MT', start: 1 })
+    expect(result).toBe(false)
+  })
+
+  it('should return false for NaN', () => {
+    const result = isVariantMtHomopolymer(NaN)
+    expect(result).toBe(false)
+  })
+})
+
 describe('search method', () => {
-  it('should return route location if match', () => {
+  it('should return "gene" route location for HGNC queries', () => {
     const result = search('HGNC:1100', 'ghcr37')
     expect(result).toEqual({
       name: 'gene',
@@ -46,6 +115,52 @@ describe('search method', () => {
     })
   })
 
+  it('should return "variant" route location for Variant queries', () => {
+    const result = search('chr37:12345:A:G', 'ghcr37')
+    expect(result).toEqual({
+      name: 'variant',
+      params: {
+        searchTerm: 'chr37:12345:A:G',
+        genomeRelease: 'ghcr37'
+      }
+    })
+  })
+
+  it('should return "genes" route location for general queries', () => {
+    const result = search('TP53', 'ghcr37')
+    expect(result).toEqual({
+      name: 'genes',
+      query: {
+        q: 'TP53',
+        fields: 'hgnc_id,ensembl_gene_id,ncbi_gene_id,symbol'
+      }
+    })
+  })
+})
+
+describe('infoFromQuery method', () => {
+  it('should return info from query', () => {
+    const result = infoFromQuery('chr37:12345:A:G')
+    expect(result).toEqual({
+      chromosome: 'chr37',
+      pos: '12345',
+      reference: 'A',
+      alternative: 'G',
+      hgnc_id: undefined
+    })
+  })
+
+  it('should return empty object if no query', () => {
+    const result = infoFromQuery('')
+    expect(result).toEqual({
+      chromosome: '',
+      pos: undefined,
+      reference: undefined,
+      alternative: undefined,
+      hgnc_id: undefined
+    })
+  })
+
   it('should return null if no entry', () => {
     const result = search('', 'foo37')
     expect(result).toBe(null)

frontend/src/api/utils.ts

@@ -58,7 +58,7 @@ export const isVariantMt = (smallVar: any): boolean => {
  * @param smallVar Small variant to check.
  * @returns whether the position is in a mitochondrial homopolymer
  */
-export const isVariantMtHomopolymer = (smallVar: any): any => {
+export const isVariantMtHomopolymer = (smallVar: any): boolean => {
   if (!smallVar) {
     return false
   }
@@ -75,6 +75,8 @@ export const isVariantMtHomopolymer = (smallVar: any): any => {
   }
   if (isVariantMt(smallVar)) {
     return positionCheck(start) || positionCheck(end)
+  } else {
+    return false
   }
 }
 
@@ -141,7 +143,6 @@ export const search = (searchTerm: string, genomeRelease: string) => {
       return routeLocation
     }
   }
-  return null
 }
 
 /**