Merge branch 'main' into fix/61-handle-an0

jsstevenson · web-flow · commit 03d1710eb3d1 · 2026-02-19T15:04:40.000-05:00
diff --git a/.ebextensions/01_download_data.config b/.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
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -18,7 +18,6 @@ jobs:
     env:
       REGISTRY: ghcr.io
       IMAGE_NAME: ${{ github.repository }}
-      ANYVLM_VERSION: ${{ github.event.release.tag_name }}
 
     steps:
       - name: Checkout repository
@@ -48,8 +47,6 @@ jobs:
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
-          build-args: |
-            ANYVLM_VERSION=${{ env.ANYVLM_VERSION }}
 
       - name: Generate artifact attestation
         uses: actions/attest-build-provenance@v3
diff --git a/Dockerfile b/Dockerfile
@@ -4,10 +4,6 @@ LABEL org.opencontainers.image.source=https://github.com/genomicmedlab/anyvlm
 LABEL org.opencontainers.image.description="AnyVLM container image"
 LABEL org.opencontainers.image.licenses=Apache-2.0
 
-ARG ANYVLM_VERSION
-RUN echo "Building AnyVLM version: ${ANYVLM_VERSION}"
-ENV SETUPTOOLS_SCM_PRETEND_VERSION_FOR_ANYVLM=${ANYVLM_VERSION}
-
 RUN apt-get update && \
     apt-get install -y libpq-dev gcc && \
     rm -rf /var/lib/apt/lists/*
@@ -17,7 +13,7 @@ WORKDIR /app
 COPY pyproject.toml .
 COPY src ./src
 
-RUN pip install --upgrade pip setuptools setuptools_scm
+RUN pip install --upgrade pip setuptools
 RUN pip install --no-cache-dir .
 
 EXPOSE 8000
diff --git a/Makefile b/Makefile
@@ -21,8 +21,6 @@ else
 endif
 XRM=xargs -0${_XRM_R} rm
 
-# Provide version for container builds
-export ANYVLM_VERSION := $(shell git describe --tags --abbrev=0 2>/dev/null || echo 0.0.0)
 
 ############################################################################
 #= BASIC USAGE
diff --git a/README.md b/README.md
@@ -32,20 +32,20 @@ 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=22&start=44389414&referenceBases=A&alternateBases=G"
+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:
 
 ```json
-{"beaconHandovers":[{"handoverType":{"id":"GREGoR-NCH","label":"GREGoR AnyVLM Reference"},"url":"https://variants.gregorconsortium.org/"}],"meta":{"apiVersion":"v1.0","beaconId":"org.anyvlm.gregor","returnedSchemas":[{"entityType":"genomicVariant","schema":"ga4gh-beacon-variant-v2.0.0"}]},"responseSummary":{"exists":true,"numTotalResults":2},"response":{"resultSets":[{"exists":true,"id":"GREGoR-NCH Homozygous","results":[],"resultsCount":2,"setType":"genomicVariant"},{"exists":true,"id":"GREGoR-NCH Heterozygous","results":[],"resultsCount":0,"setType":"genomicVariant"},{"exists":true,"id":"GREGoR-NCH Hemizygous","results":[],"resultsCount":0,"setType":"genomicVariant"}]}}
+{"beaconHandovers":[{"handoverType":{"id":"CUSTOM:GREGoR-NCH","label":"GREGoR AnyVLM Reference"},"url":"https://variants.gregorconsortium.org/","note":null}],"meta":{"apiVersion":"v1.0","beaconId":"org.anyvlm.gregor","returnedSchemas":[{"entityType":"genomicVariant","schema":"ga4gh-beacon-variant-v2.0.0"}]},"responseSummary":{"exists":true,"numTotalResults":34},"response":{"resultSets":[{"exists":true,"id":"CUSTOM:GREGoR-NCH Homozygous","results":[],"resultsCount":0,"setType":"genomicVariant"},{"exists":true,"id":"CUSTOM:GREGoR-NCH Heterozygous","results":[],"resultsCount":34,"setType":"genomicVariant"},{"exists":true,"id":"CUSTOM:GREGoR-NCH Hemizygous","results":[],"resultsCount":0,"setType":"genomicVariant"},{"exists":false,"id":"CUSTOM:GREGoR-NCH Unknown","results":[],"resultsCount":0,"setType":"genomicVariant"}]}}
 ```
 
 See the [usage](https://anyvlm.readthedocs.org/en/stable/usage.html) page in the documentation for more information.
diff --git a/compose.dev.yaml b/compose.dev.yaml
@@ -2,9 +2,6 @@ services:
   anyvlm:
     build:
       context: .
-      args:
-        # NOTE: Makefile sets this to ANYVLM_VERSION=$(git describe --tags --abbrev=0 2>/dev/null || echo 0.0.0)
-        ANYVLM_VERSION: ${ANYVLM_VERSION:?ANYVLM_VERSION must be set to the AnyVLM version being used}
     depends_on:
       anyvlm_db:
         required: true
diff --git a/docs/source/configuration/docker_compose.rst b/docs/source/configuration/docker_compose.rst
@@ -22,10 +22,6 @@ The Docker Compose configuration is split across multiple files to separate conc
 * ``compose.dev.yaml``
    Defines AnyVLM-specific development services, including FastAPI and PostgreSQL services built from local Dockerfiles. This file is intended for developers working on the AnyVLM codebase.
 
-   .. note::
-
-      ``compose.dev.yaml`` and the ``Dockerfile`` expect ``ANYVLM_VERSION`` to be set to the AnyVLM version being used (for example, ``1.0.0``) when running Docker Compose or building the image directly. This is handled automatically when using the Makefile.
-
 * ``compose.anyvar.yaml``
    Defines the services required to run the AnyVar REST service and its dependencies. This file is optional and is provided as a convenience for users who do not already have AnyVar running.
 
diff --git a/docs/source/getting_started/docker_compose.rst b/docs/source/getting_started/docker_compose.rst
@@ -58,6 +58,6 @@ Full stack with AnyVar
 
 .. code-block:: console
 
-   % ANYVLM_VERSION=0.0.0 docker compose -f compose.dev.yaml -f compose.anyvar.yaml up --build
+   % docker compose -f compose.dev.yaml -f compose.anyvar.yaml up --build
 
 Once the containers are running, visit `http://127.0.0.1:8080 <http://127.0.0.1:8080>`_ to view the interactive Swagger UI and confirm the service is responding.
diff --git a/docs/source/usage.rst b/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
 ----------
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,5 +1,6 @@
 [project]
 name = "anyvlm"
+version="1.0.0-rc2"
 authors = [
   { name="biocommons contributors", email="biocommons-dev@googlegroups.com" },
 ]
@@ -31,7 +32,6 @@ dependencies = [
     "pysam==0.23.0",  # see https://github.com/ga4gh/vrs-python/issues/560
     "pyyaml",
 ]
-dynamic = ["version"]
 
 [project.optional-dependencies]
 test = [
@@ -70,16 +70,10 @@ Source = "https://github.com/genomicmedlab/anyvlm/"
 [project.scripts]
 anyvlm = "anyvlm.cli:_cli"
 
-
 [build-system]
-requires = [
-    "setuptools >= 65.3",
-    "setuptools_scm >= 8"
-]
+requires = ["setuptools >= 65.3"]
 build-backend = "setuptools.build_meta"
 
-[tool.setuptools_scm]
-
 [tool.pytest.ini_options]
 addopts = "--cov=anyvlm --cov-report term-missing"
 testpaths = ["tests"]
diff --git a/src/anyvlm/main.py b/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],
diff --git a/src/anyvlm/schemas/common.py b/src/anyvlm/schemas/common.py
@@ -1,14 +1,17 @@
 """Define REST API schemas"""
 
-from enum import Enum
+from enum import StrEnum
 from typing import Literal
 
+from anyvar.restapi.schema import ImplMetadata
+from ga4gh.va_spec import VASPEC_VERSION
+from ga4gh.vrs import VRS_VERSION
 from pydantic import BaseModel
 
 from anyvlm import __version__
 
 
-class ServiceEnvironment(str, Enum):
+class ServiceEnvironment(StrEnum):
     """Define current runtime environment."""
 
     LOCAL = "local"
@@ -36,6 +39,13 @@ class ServiceType(BaseModel):
 SERVICE_DESCRIPTION = "An AnyVLM instance"
 
 
+class SpecMetadata(BaseModel):
+    """Define substructure for reporting specification metadata."""
+
+    vrs_version: str = VRS_VERSION
+    vaspec_version: str = VASPEC_VERSION
+
+
 class ServiceInfo(BaseModel):
     """Define response structure for GA4GH /service_info endpoint."""
 
@@ -54,3 +64,5 @@ class ServiceInfo(BaseModel):
     updatedAt: Literal["2025-06-01T00:00:00Z"] = "2025-06-01T00:00:00Z"  # noqa: N815
     environment: ServiceEnvironment
     version: str = __version__
+    spec_metadata: SpecMetadata = SpecMetadata()
+    impl_metadata: ImplMetadata = ImplMetadata()
diff --git a/tests/unit/test_restapi.py b/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:
@@ -29,3 +29,7 @@ def test_service_info(restapi_client: TestClient, test_data_dir: Path):
     resolver = jsonschema.RefResolver.from_schema(spec)
     data = response.json()
     jsonschema.validate(instance=data, schema=resp_schema, resolver=resolver)
+
+    assert data["spec_metadata"]["vrs_version"] is not None
+    assert data["spec_metadata"]["vaspec_version"] is not None
+    assert data["impl_metadata"]["vrs_python_version"] is not None
diff --git a/tests/unit/test_variant_counts_endpoint.py b/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")
diff --git a/tests/unit/test_vcf_upload_endpoint.py b/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,
                 )
