Deprecate legacy endpoints

biothings_annotator/application/views/__init__.py

@@ -1,10 +1,8 @@
 from typing import Dict, List
 from biothings_annotator.application.views.annotator import (
     BatchCurieView,
-    CurieLegacyView,
     CurieView,
     StatusView,
-    TrapiLegacyView,
     TrapiView,
 )
 from biothings_annotator.application.views.metadata import MetadataView, VersionView
@@ -36,12 +34,6 @@ def build_routes() -> List[Dict]:
         "name": "curie_endpoint",
     }
 
-    curie_route_mirror = {
-        "handler": CurieLegacyView.as_view(),
-        "uri": r"/annotator/<curie:str>",
-        "name": "curie_endpoint_mirror",
-    }
-
     batch_curie_route = {
         "handler": BatchCurieView.as_view(),
         "uri": r"/curie/",
@@ -50,7 +42,6 @@ def build_routes() -> List[Dict]:
 
     # --- TRAPI ROUTES ---
     trapi_route_main = {"handler": TrapiView.as_view(), "uri": "/trapi/", "name": "trapi_endpoint"}
-    trapi_route_mirror = {"handler": TrapiLegacyView.as_view(), "uri": "/annotator/", "name": "trapi_endpoint_mirror"}
 
     # --- METADATA ROUTES ---
     metadata_route = {"handler": MetadataView.as_view(), "uri": "/metadata/openapi", "name": "metadata"}
@@ -65,10 +56,8 @@ def build_routes() -> List[Dict]:
         status_route_main,
         version_route_main,
         curie_route_main,
-        curie_route_mirror,
         batch_curie_route,
         trapi_route_main,
-        trapi_route_mirror,
         metadata_route,
     ]
     return route_collection

biothings_annotator/application/views/annotator.py

@@ -430,22 +430,3 @@ async def post(self, request: Request):
             }
             general_error_response = sanic.json(error_context, status=400)
             return general_error_response
-
-
-# --- Legacy Redirects ---
-# The /annotator endpoint has been deprcated so we setup these redirects:
-# GET /anotator/<CURIE_ID> -> /curie/<CURIE_ID> (Singular CURIE ID)
-# POST /anotator/ -> /trapi/
-class CurieLegacyView(HTTPMethodView):
-    @openapi.deprecated()
-    async def get(self, request: Request, curie: str):
-        redirect_response = response.redirect(f"/curie/{curie}", status=302)
-        return redirect_response
-
-
-class TrapiLegacyView(HTTPMethodView):
-    @openapi.deprecated()
-    async def post(self, request: Request):
-        trapi_view = TrapiView()
-        redirect_response = await trapi_view.post(request)
-        return redirect_response

tests/test_application_endpoints.py

@@ -96,6 +96,8 @@ async def test_status_get_failed_data_check(test_annotator: sanic.Sanic, endpoin
     Tests the Status endpoint GET when the data check fails
     Mocking the annotate_curie method to return a value that doesn't contain "NCBIGene:1017"
     """
+    endpoint = "/status/"
+
     # Mock the return value to simulate the data check failure
     with patch.object(Annotator, "annotate_curie", return_value={"_id": "some_other_id"}):
         request, response = await test_annotator.asgi_client.request(method="get", url=endpoint)
@@ -252,40 +254,35 @@ async def test_curie_get(temporary_data_storage: Union[str, Path], test_annotato
 @pytest.mark.unit
 @pytest.mark.asyncio(loop_scope="module")
 @pytest.mark.parametrize(
-    "endpoint, batch_curie",
+    "batch_curie",
     (
         [
-            "/curie/",
-            [
+            "NCBIGene:695",
+            "MONDO:0001222",
+            "DOID:6034",
+            "CHEMBL.COMPOUND:821",
+            "PUBCHEM.COMPOUND:3406",
+            "CHEBI:192712",
+            "CHEMBL.COMPOUND:3707246",
+        ],
+        {
+            "ids": [
                 "NCBIGene:695",
                 "MONDO:0001222",
                 "DOID:6034",
                 "CHEMBL.COMPOUND:821",
                 "PUBCHEM.COMPOUND:3406",
                 "CHEBI:192712",
                 "CHEMBL.COMPOUND:3707246",
-            ],
-        ],
-        [
-            "/curie/",
-            {
-                "ids": [
-                    "NCBIGene:695",
-                    "MONDO:0001222",
-                    "DOID:6034",
-                    "CHEMBL.COMPOUND:821",
-                    "PUBCHEM.COMPOUND:3406",
-                    "CHEBI:192712",
-                    "CHEMBL.COMPOUND:3707246",
-                ]
-            },
-        ],
+            ]
+        },
     ),
 )
-async def test_curie_post(test_annotator: sanic.Sanic, endpoint: str, batch_curie: Union[List, Dict]):
+async def test_curie_post(test_annotator: sanic.Sanic, batch_curie: Union[List, Dict]):
     """
     Tests the CURIE endpoint POST
     """
+    endpoint = "/curie/"
     if isinstance(batch_curie, list):
         curie_ids = set(batch_curie)
     elif isinstance(batch_curie, dict):
@@ -367,115 +364,3 @@ async def test_trapi_post(temporary_data_storage: Union[str, Path], test_annotat
                         assert identifier is not None
                         score = values.get("_score", None)
                         assert score is not None
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio(loop_scope="module")
-@pytest.mark.parametrize("data_store", ["expected_curie.json"])
-async def test_annotator_get_redirect(
-    temporary_data_storage: Union[str, Path], test_annotator: sanic.Sanic, data_store: Dict
-):
-    """
-    Tests the legacy endpoint /annotator with a redirect to the
-    /curie/ endpoint
-    """
-    data_file_path = temporary_data_storage.joinpath(data_store)
-    with open(str(data_file_path), "r", encoding="utf-8") as file_handle:
-        expected_curie_body = json.load(file_handle)
-
-    endpoint = "/annotator/"
-    curie_id = "NCBIGene:1017"
-    url = f"{endpoint}{curie_id}"
-    request, response = await test_annotator.asgi_client.request(method="get", url=url, follow_redirects=True)
-
-    assert request.method == "GET"
-    assert request.is_safe
-    assert request.query_string == ""
-    assert request.scheme == "http"
-    # assert request.server_path == url
-
-    response_body = response.json
-    response_body[curie_id][0].pop("_score")
-
-    assert response.json.keys() == expected_curie_body.keys()
-    response_curie_annotation = response.json.get(curie_id)
-    expected_curie_annotation = expected_curie_body.get(curie_id)
-
-    # Expected length of 1 response for one anootation
-    assert len(response_curie_annotation) == len(expected_curie_annotation)
-
-    # Verify structure without the content to avoid having to capture drifting changes
-    # in the responses over time. The structure should be more static
-    # ['query', 'HGNC', 'MIM', '_id', 'alias', 'go', 'interpro', 'name', 'pharos', 'summary', 'symbol', 'taxid', 'type_of_gene']
-    assert response_curie_annotation[0].keys() == expected_curie_annotation[0].keys()
-
-    assert response.http_version == "HTTP/1.1"
-    assert response.content_type == "application/json"
-    assert response.is_success
-    assert not response.is_error
-    assert response.is_closed
-    assert response.status_code == 200
-    assert response.encoding == "utf-8"
-
-
-@pytest.mark.unit
-@pytest.mark.asyncio(loop_scope="module")
-@pytest.mark.parametrize("data_store", ["trapi_request.json"])
-async def test_annotator_post_redirect(
-    temporary_data_storage: Union[str, Path], test_annotator: sanic.Sanic, data_store: Dict
-):
-    """
-    Tests the annotator redirect for the /trapi/ POST endpoint
-    """
-    data_file_path = temporary_data_storage.joinpath(data_store)
-    with open(str(data_file_path), "r", encoding="utf-8") as file_handle:
-        trapi_body = json.load(file_handle)
-
-    endpoint = "/annotator/"
-    request, response = await test_annotator.asgi_client.request(
-        method="post", url=endpoint, json=trapi_body, follow_redirects=True
-    )
-
-    assert request.method == "POST"
-    assert request.query_string == ""
-    assert request.scheme == "http"
-    assert request.server_path == endpoint
-
-    assert response.http_version == "HTTP/1.1"
-    assert response.content_type == "application/json"
-    assert response.is_success
-    assert not response.is_error
-    assert response.is_closed
-    assert response.status_code == 200
-    assert response.encoding == "utf-8"
-
-    node_set = set(trapi_body["message"]["knowledge_graph"]["nodes"].keys())
-
-    annotation = response.json
-    assert isinstance(annotation, dict)
-    for key, attribute in annotation.items():
-        assert key in node_set
-        if isinstance(attribute, dict):
-            attribute = [attribute]
-        assert isinstance(attribute, list)
-        for subattribute in attribute:
-            assert isinstance(subattribute, dict)
-            subattribute_collection = subattribute.get("attributes", None)
-
-            assert isinstance(subattribute_collection, list)
-            for subattributes in subattribute_collection:
-                assert subattributes["attribute_type_id"] == "biothings_annotations"
-                assert isinstance(subattributes["value"], list)
-                for values in subattributes["value"]:
-                    notfound = values.get("notfound", False)
-                    if notfound:
-                        curie_prefix, query = utils.parse_curie(key)
-                        assert values == {"query": query, "notfound": True}
-                    else:
-                        assert isinstance(values, dict)
-                        query = values.get("query", None)
-                        assert query is not None
-                        identifier = values.get("_id", None)
-                        assert identifier is not None
-                        score = values.get("_score", None)
-                        assert score is not None