Fix routing for VEP (#18)

APISpecification.yaml

@@ -3,7 +3,7 @@ info:
   title: Tools api
   version: 0.0.1
 paths:
-  /vep/config:
+  /api/tools/vep/config:
     get:
       parameters:
         - name: genome_id
@@ -18,7 +18,7 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/VepConfigResponse'
-  /vep/submission:
+  /api/tools/vep/submissions:
     post:
       requestBody:
         content:

app/blast/blast.py

@@ -1,6 +1,6 @@
 from contextlib import asynccontextmanager
 from urllib import response
-from fastapi import FastAPI, Response
+from fastapi import FastAPI, Response, APIRouter
 from fastapi.encoders import jsonable_encoder
 from fastapi.exceptions import RequestValidationError
 from fastapi.responses import JSONResponse
@@ -30,7 +30,6 @@
 
 app = FastAPI()
 
-
 # Override response for input payload validation error
 @app.exception_handler(RequestValidationError)
 async def validation_exception_handler(request, exc):
@@ -74,8 +73,8 @@ class DbType(str, Enum):
 
 
 class BlastParams(BaseModel, extra='allow'):
-    email: str | None = "[email protected]"
-    title: str | None = ""
+    email: str = "[email protected]"
+    title: str = ""
     program: Program
     database: DbType
 

app/main.py

@@ -19,7 +19,7 @@
 from starlette.middleware.cors import CORSMiddleware
 
 from blast.blast import app as blast_app
-from vep.routes import router
+from vep.routes import router as vep_router
 from core.config import API_PREFIX, ALLOWED_HOSTS, VERSION, PROJECT_NAME, DEBUG
 
 def get_application() -> FastAPI:
@@ -29,14 +29,14 @@ def get_application() -> FastAPI:
         CORSMiddleware,
         allow_origins=ALLOWED_HOSTS or ["*"],
         allow_credentials=True,
-        allow_methods=["GET"],
+        allow_methods=["POST", "GET"],
         allow_headers=["*"],
     )
 
-    application.include_router(router, prefix=API_PREFIX)
+    application.include_router(vep_router, prefix=API_PREFIX)
 
     return application
 
 
 app = get_application()
-app.mount("/blast", blast_app)
+app.mount("/api/tools/blast", blast_app)

app/tests/test_blast.py

@@ -3,13 +3,14 @@
 import pytest
 from app.blast.blast import get_db_path
 from app.main import app
+from core.config import API_PREFIX
 
 # Test config endpoint
 def test_read_config():
 	with TestClient(app) as client: #include @startup hook
 		with open('/data/blast_config.json') as f:
 			config = json.load(f)
-		response = client.get('/blast/config')
+		response = client.get(API_PREFIX + '/blast/config')
 		assert response.status_code == 200
 		assert response.json() == config
 
@@ -30,7 +31,7 @@ def test_get_db_path(blast_payload):
 # Test single BLAST job submission with a valid payload
 def test_blast_job(blast_payload):
 	with TestClient(app) as client:
-		response = client.post('/blast/job', json=blast_payload)
+		response = client.post(API_PREFIX + '/blast/job', json=blast_payload)
 		assert response.status_code == 200
 		resp = response.json()
 		assert 'submission_id' in resp
@@ -48,7 +49,7 @@ def test_blast_jobs(blast_payload):
 	with TestClient(app) as client:
 		blast_payload['genome_ids'].append(blast_payload['genome_ids'][0])
 		blast_payload['query_sequences'].append({'id': 2, 'value': 'MPIGSKERPTFKTRCNKADLGPI'})
-		response = client.post('/blast/job', json=blast_payload)
+		response = client.post(API_PREFIX + '/blast/job', json=blast_payload)
 		assert response.status_code == 200
 		resp = response.json()
 		assert 'submission_id' in resp
@@ -63,7 +64,7 @@ def test_blast_jobs(blast_payload):
 def test_blast_job_data_error(blast_payload):
 	with TestClient(app) as client:
 		del blast_payload['query_sequences']
-		response = client.post('/blast/job', json=blast_payload)
+		response = client.post(API_PREFIX + '/blast/job', json=blast_payload)
 		assert response.status_code == 422
 		resp = response.json()
 		assert 'error' in resp
@@ -74,7 +75,7 @@ def test_blast_job_jd_error(blast_payload):
 	with TestClient(app) as client:
 		# 'stype'='dna' is incompatible with 'program'='blastp'
 		blast_payload['parameters']['stype'] = 'dna'
-		response = client.post('/blast/job', json=blast_payload)
+		response = client.post(API_PREFIX + '/blast/job', json=blast_payload)
 		assert response.status_code == 200
 		resp = response.json()
 		assert 'jobs' in resp
@@ -87,7 +88,7 @@ def test_blast_job_jd_error(blast_payload):
 # Test BLAST job status endpoint
 def test_blast_job_status():
 	with TestClient(app) as client:
-		response = client.get('/blast/jobs/status/ncbiblast_ensembl-12345')
+		response = client.get(API_PREFIX + '/blast/jobs/status/ncbiblast_ensembl-12345')
 		assert response.status_code == 200
 		assert 'status' in response.json()
 
@@ -96,7 +97,7 @@ def test_blast_job_status():
 def test_blast_job_statuses():
 	with TestClient(app) as client:
 		job_ids = {'job_ids': ['ncbiblast-1234', 'ncbiblast-5678']}
-		response = client.post('/blast/jobs/status', json=job_ids)
+		response = client.post(API_PREFIX + '/blast/jobs/status', json=job_ids)
 		assert response.status_code == 200
 		resp = response.json()
 		assert 'statuses' in resp
@@ -107,13 +108,13 @@ def test_blast_job_statuses():
 # Test JD proxy error response
 def test_blast_proxy_error():
 	with TestClient(app) as client:
-		response = client.get('/blast/jobs/na/na')
+		response = client.get(API_PREFIX + '/blast/jobs/na/na')
 		assert response.status_code == 404
 		assert 'error' in response.json()
 
 # Test invalid endpoint error response
 def test_404_error():
 	with TestClient(app) as client:
-		response = client.get('/blast/invalid_path')
+		response = client.get(API_PREFIX + '/blast/invalid_path')
 		assert response.status_code == 404
 		assert response.json() == {'error': 'Invalid endpoint'}