feat: Integrate cada prio web service (#213)

backend/app/api/internal/endpoints/proxy.py

@@ -46,6 +46,10 @@ async def reverse_proxy(request: Request) -> Response:
         backend_url = settings.BACKEND_PREFIX_NGINX + url.path.replace("/internal/proxy/nginx", "")
     elif url.path.startswith(f"{settings.INTERNAL_STR}/proxy/dotty"):
         backend_url = settings.BACKEND_PREFIX_DOTTY + url.path.replace("/internal/proxy/dotty", "")
+    elif url.path.startswith(f"{settings.INTERNAL_STR}/proxy/cada-prio"):
+        backend_url = settings.BACKEND_PREFIX_CADA_PRIO + url.path.replace(
+            "/internal/proxy/cada-prio", ""
+        )
 
     if backend_url:
         client = httpx.AsyncClient()

backend/app/core/config.py

@@ -93,6 +93,8 @@ def assemble_cors_origins(cls, v: str | list[str]) -> list[str] | str:  # pragma
     BACKEND_PREFIX_NGINX: str = "http://nginx:80"
     #: Prefix for the backend of dotty service.
     BACKEND_PREFIX_DOTTY: str = "http://dotty:8080"
+    #: Prefix for the backend of cada-prio service.
+    BACKEND_PREFIX_CADA_PRIO: str = "http://cada-prio:8080"
 
     #: URL to REDIS service.
     REDIS_URL: str = "redis://redis:6379"

backend/env.dev

@@ -17,6 +17,7 @@ BACKEND_PREFIX_MEHARI=http://localhost:3002
 BACKEND_PREFIX_VIGUNO=http://localhost:3003
 BACKEND_PREFIX_NGINX=http://localhost:3004
 BACKEND_PREFIX_DOTTY=http://localhost:3005
+BACKEND_PREFIX_CADA_PRIORI=http://localhost:3006
 
 # Access to redis as it runs Docker Compose.
 REDIS_URL=redis://localhost:3030

backend/tests/api/internal/test_proxy.py

@@ -87,6 +87,21 @@ async def test_proxy_dotty(monkeypatch: MonkeyPatch, httpx_mock: HTTPXMock, clie
     assert response.text == "Mocked response"
 
 
+@pytest.mark.asyncio
+async def test_proxy_cada_prio(monkeypatch: MonkeyPatch, httpx_mock: HTTPXMock, client: TestClient):
+    """Test proxying to cada-prio backend."""
+    monkeypatch.setattr(settings, "BACKEND_PREFIX_CADA_PRIO", f"http://{MOCKED_BACKEND_HOST}")
+    httpx_mock.add_response(
+        url=f"http://{MOCKED_BACKEND_HOST}/{MOCKED_URL_TOKEN}",
+        method="GET",
+        text="Mocked response",
+    )
+
+    response = client.get(f"/internal/proxy/cada-prio/{MOCKED_URL_TOKEN}")
+    assert response.status_code == 200
+    assert response.text == "Mocked response"
+
+
 @pytest.mark.asyncio
 async def test_invalid_proxy_route(client: TestClient):
     """Test invalid proxy route."""

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

@@ -0,0 +1,42 @@
+import { beforeEach, describe, expect, it, vi } from 'vitest'
+import createFetchMock from 'vitest-fetch-mock'
+
+import { CadaPrioClient } from '@/api/cadaprio'
+
+const fetchMocker = createFetchMock(vi)
+
+describe.concurrent('Cada Prio Client', () => {
+  beforeEach(() => {
+    fetchMocker.enableMocks()
+    fetchMocker.resetMocks()
+  })
+
+  it('fetches gene impact correctly', async () => {
+    fetchMocker.mockResponseOnce(JSON.stringify({ result: 'pathogenic' }))
+
+    const client = new CadaPrioClient()
+    const result = await client.predictGeneImpact(['HP:0000001'])
+    expect(JSON.stringify(result)).toEqual(JSON.stringify({ result: 'pathogenic' }))
+  })
+
+  it('fetches gene impact correctly with gene symbols', async () => {
+    fetchMocker.mockResponseOnce(JSON.stringify({ result: 'pathogenic' }))
+
+    const client = new CadaPrioClient()
+    const result = await client.predictGeneImpact(['HP:0000001'], ['BRCA1'])
+    expect(JSON.stringify(result)).toEqual(JSON.stringify({ result: 'pathogenic' }))
+  })
+
+  it('fails to fetch gene impact with wrong HPO terms', async () => {
+    fetchMocker.mockResponse((req) => {
+      if (req.url.includes('hpo_terms=HP:0000001')) {
+        return Promise.resolve(JSON.stringify({ result: 'pathogenic' }))
+      }
+      return Promise.resolve(JSON.stringify({ status: 400 }))
+    })
+
+    const client = new CadaPrioClient()
+    const result = await client.predictGeneImpact(['123'])
+    expect(JSON.stringify(result)).toEqual(JSON.stringify({ status: 400 }))
+  })
+})

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

@@ -3,6 +3,7 @@ import { describe, expect, it } from 'vitest'
 import {
   API_INTERNAL_BASE_PREFIX,
   API_INTERNAL_BASE_PREFIX_ANNONARS,
+  API_INTERNAL_BASE_PREFIX_CADA_PRIO,
   API_INTERNAL_BASE_PREFIX_MEHARI,
   API_INTERNAL_BASE_PREFIX_NGINX
 } from '@/api/common'
@@ -31,4 +32,10 @@ describe.concurrent('API_BASE_PREFIX constants', () => {
     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', () => {
+    const originalMode = import.meta.env.MODE
+    expect(API_INTERNAL_BASE_PREFIX_CADA_PRIO).toBe('/internal/proxy/cada-prio')
+    import.meta.env.MODE = originalMode
+  })
 })

frontend/src/api/cadaprio.ts

@@ -0,0 +1,23 @@
+import { API_INTERNAL_BASE_PREFIX_CADA_PRIO } from './common'
+
+const API_BASE_URL = `${API_INTERNAL_BASE_PREFIX_CADA_PRIO}/`
+
+export class CadaPrioClient {
+  private apiBaseUrl: string
+  private csrfToken: string | null
+
+  constructor(apiBaseUrl?: string, csrfToken?: string) {
+    this.apiBaseUrl = apiBaseUrl ?? API_BASE_URL
+    this.csrfToken = csrfToken ?? null
+  }
+
+  async predictGeneImpact(hpoTerms: string[], geneSymbols?: string[]): Promise<any> {
+    const geneSuffix = geneSymbols ? `&gene_symbols=${geneSymbols.join(',')}` : ''
+    const url = `${this.apiBaseUrl}api/v1/predict?hpo_terms=${hpoTerms.join(',')}${geneSuffix}`
+
+    const response = await fetch(url, {
+      method: 'GET'
+    })
+    return await response.json()
+  }
+}

frontend/src/api/common.ts

@@ -4,4 +4,5 @@ export const API_INTERNAL_BASE_PREFIX_MEHARI = '/internal/proxy/mehari'
 export const API_INTERNAL_BASE_PREFIX_VIGUNO = '/internal/proxy/viguno'
 export const API_INTERNAL_BASE_PREFIX_NGINX = '/internal/proxy/nginx'
 export const API_INTERNAL_BASE_PREFIX_DOTTY = '/internal/proxy/dotty'
+export const API_INTERNAL_BASE_PREFIX_CADA_PRIO = '/internal/proxy/cada-prio'
 export const API_V1_BASE_PREFIX = '/api/v1/'