feat!: add prefix to api endpoints needed for deployment

.ebextensions/01_download_data.config

@@ -25,7 +25,7 @@ container_commands:
         test: test -f "/usr/local/share/seqrepo.tar.gz"
         command: "rm /usr/local/share/seqrepo.tar.gz"
 
-    04_install_package:
+    05_install_package:
         leader_only: true
         command: |
             set -euo pipefail

README.md

@@ -32,14 +32,14 @@ A set of Docker Compose resources are provided as part of the AnyVLM project. Se
 Given an available AnyVLM node, submit a VCF which contains allele frequency data:
 
 ```bash
-curl -X POST "http://localhost:8080/ingest_vcf?assembly=grch38" \
+curl -X POST "http://localhost:8080/anyvlm/ingest_vcf?assembly=grch38" \
   -F "file=@/path/to/variants.vcf.gz"
 ```
 
 Then, submit a query for allele frequency
 
 ```bash
-curl "http://localhost:8080/variant_counts?assemblyId=GRCh38&referenceName=7&start=140714556&referenceBases=A&alternateBases=T"
+curl "http://localhost:8080/anyvlm/variant_counts?assemblyId=GRCh38&referenceName=7&start=140714556&referenceBases=A&alternateBases=T"
 ```
 
 A successful query returns a response like the following:

docs/source/usage.rst

@@ -12,7 +12,7 @@ Given a VCF describing cohort-level allele frequency, submit a ``POST`` request
 
 .. code-block:: console
 
-   % curl -X POST "http://localhost:8080/ingest_vcf?assembly=grch38" \
+   % curl -X POST "http://localhost:8080/anyvlm/ingest_vcf?assembly=grch38" \
      -F "file=@/path/to/variants.vcf.gz"
 
 VCF Requirements
@@ -42,7 +42,7 @@ Issue a ``GET`` request to ``/variant_counts`` with arguments for reference sequ
 
 .. code-block:: console
 
-   % curl "http://localhost:8080/variant_counts?assemblyId=GRCh38&referenceName=22&start=10510105&referenceBases=T&alternateBases=A"
+   % curl "http://localhost:8080/anyvlm/variant_counts?assemblyId=GRCh38&referenceName=22&start=10510105&referenceBases=T&alternateBases=A"
 
 Parameters
 ----------

src/anyvlm/main.py

@@ -144,11 +144,14 @@ async def lifespan(app: FastAPI) -> AsyncGenerator:
     app.state.anyvlm_storage.close()
 
 
+API_PREFIX = "/anyvlm"
+
 app = FastAPI(
     title="AnyVLM",
     description=SERVICE_DESCRIPTION,
     version=__version__,
-    docs_url="/",
+    docs_url=API_PREFIX,
+    openapi_url=f"{API_PREFIX}/openapi.json",
     license={
         "name": "Apache 2.0",
         "url": "https://github.com/genomicmedlab/anyvlm/blob/main/LICENSE",
@@ -161,7 +164,7 @@ async def lifespan(app: FastAPI) -> AsyncGenerator:
     swagger_ui_parameters={"tryItOutEnabled": True},
     lifespan=lifespan,
 )
-app.include_router(vlm_router)
+app.include_router(vlm_router, prefix=API_PREFIX)
 
 
 @app.exception_handler(RequestValidationError)
@@ -188,7 +191,7 @@ async def validation_exception_handler(
 
 
 @app.get(
-    "/service-info",
+    f"{API_PREFIX}/service-info",
     summary="Get basic service information",
     description="Retrieve service metadata, such as versioning and contact info. Structured in conformance with the [GA4GH service info API specification](https://www.ga4gh.org/product/service-info/)",
     tags=[EndpointTag.META],

tests/unit/test_restapi.py

@@ -16,7 +16,7 @@ def restapi_client():
 
 
 def test_service_info(restapi_client: TestClient, test_data_dir: Path):
-    response = restapi_client.get("/service-info")
+    response = restapi_client.get("/anyvlm/service-info")
     response.raise_for_status()
 
     with (test_data_dir / "ga4gh-service-info" / "service-info.yaml").open() as f:

tests/unit/test_variant_counts_endpoint.py

@@ -16,7 +16,7 @@
     "referenceBases": TEST_VARIANT.ref,
     "alternateBases": TEST_VARIANT.alt,
 }
-ENDPOINT = "/variant_counts"
+ENDPOINT = "/anyvlm/variant_counts"
 
 
 @pytest.fixture(scope="session")

tests/unit/test_vcf_upload_endpoint.py

@@ -14,6 +14,7 @@
 # Constants for testing
 MAX_FILE_SIZE = 5 * 1024 * 1024 * 1024  # 5GB
 UPLOAD_CHUNK_SIZE = 1024 * 1024  # 1MB
+ENDPOINT = "/anyvlm/ingest_vcf"
 
 
 @pytest.fixture(scope="module")
@@ -160,14 +161,14 @@ class TestIngestVcfEndpoint:
 
     def test_endpoint_exists(self, client: TestClient):
         """Test that the endpoint exists and accepts POST."""
-        response = client.post("/ingest_vcf")
+        response = client.post(ENDPOINT)
         # Should not be 404
         assert response.status_code != 404
 
     def test_missing_file_parameter(self, client: TestClient):
         """Test request without file parameter."""
         response = client.post(
-            "/ingest_vcf",
+            ENDPOINT,
             params={"assembly": "GRCh38"},
         )
         assert response.status_code == 422  # Unprocessable Entity
@@ -177,7 +178,7 @@ def test_missing_assembly_parameter(self, client: TestClient, valid_vcf_gz: Path
         """Test request without assembly parameter."""
         with valid_vcf_gz.open("rb") as f:
             files = {"file": ("test.vcf.gz", f, "application/gzip")}
-            response = client.post("/ingest_vcf", files=files)
+            response = client.post(ENDPOINT, files=files)
 
         assert response.status_code == 422
         assert (
@@ -189,7 +190,7 @@ def test_invalid_assembly_value(self, client: TestClient, valid_vcf_gz: Path):
         with valid_vcf_gz.open("rb") as f:
             files = {"file": ("test.vcf.gz", f, "application/gzip")}
             response = client.post(
-                "/ingest_vcf",
+                ENDPOINT,
                 params={"assembly": "GRCh99"},  # Invalid
                 files=files,
             )
@@ -202,7 +203,7 @@ def test_invalid_file_extension(self, client: TestClient, valid_vcf_gz: Path):
             # Use .vcf extension (should be .vcf.gz)
             files = {"file": ("test.vcf", f, "application/gzip")}
             response = client.post(
-                "/ingest_vcf",
+                ENDPOINT,
                 params={"assembly": "GRCh38"},
                 files=files,
             )
@@ -219,7 +220,7 @@ def test_not_gzipped_file(self, client: TestClient):
         files = {"file": ("test.vcf.gz", io.BytesIO(content), "application/gzip")}
 
         response = client.post(
-            "/ingest_vcf",
+            ENDPOINT,
             params={"assembly": "GRCh38"},
             files=files,
         )
@@ -234,7 +235,7 @@ def test_not_a_vcf_file(self, client: TestClient, not_vcf_gz: Path):
         with not_vcf_gz.open("rb") as f:
             files = {"file": ("test.vcf.gz", f, "application/gzip")}
             response = client.post(
-                "/ingest_vcf",
+                ENDPOINT,
                 params={"assembly": "GRCh38"},
                 files=files,
             )
@@ -251,7 +252,7 @@ def test_vcf_missing_required_fields(
         with missing_fields_vcf_gz.open("rb") as f:
             files = {"file": ("test.vcf.gz", f, "application/gzip")}
             response = client.post(
-                "/ingest_vcf",
+                ENDPOINT,
                 params={"assembly": "GRCh38"},
                 files=files,
             )
@@ -275,7 +276,7 @@ def test_successful_upload_and_ingestion(
         with valid_vcf_gz.open("rb") as f:
             files = {"file": ("test.vcf.gz", f, "application/gzip")}
             response = client.post(
-                "/ingest_vcf",
+                ENDPOINT,
                 params={"assembly": "GRCh38"},
                 files=files,
             )
@@ -312,7 +313,7 @@ def test_ingestion_failure_propagates(
         with valid_vcf_gz.open("rb") as f:
             files = {"file": ("test.vcf.gz", f, "application/gzip")}
             response = client.post(
-                "/ingest_vcf",
+                ENDPOINT,
                 params={"assembly": "GRCh38"},
                 files=files,
             )
@@ -330,7 +331,7 @@ def test_temp_file_cleanup_on_success(self, client: TestClient, valid_vcf_gz: Pa
             with valid_vcf_gz.open("rb") as f:
                 files = {"file": ("test.vcf.gz", f, "application/gzip")}
                 response = client.post(
-                    "/ingest_vcf",
+                    ENDPOINT,
                     params={"assembly": "GRCh38"},
                     files=files,
                 )
@@ -350,7 +351,7 @@ def test_temp_file_cleanup_on_error(self, client: TestClient, valid_vcf_gz: Path
             with valid_vcf_gz.open("rb") as f:
                 files = {"file": ("test.vcf.gz", f, "application/gzip")}
                 response = client.post(
-                    "/ingest_vcf",
+                    ENDPOINT,
                     params={"assembly": "GRCh38"},
                     files=files,
                 )
@@ -372,7 +373,7 @@ def test_assembly_grch37_parameter(self, client: TestClient, valid_vcf_gz: Path)
             with valid_vcf_gz.open("rb") as f:
                 files = {"file": ("test.vcf.gz", f, "application/gzip")}
                 response = client.post(
-                    "/ingest_vcf",
+                    ENDPOINT,
                     params={"assembly": "GRCh37"},
                     files=files,
                 )