Merge pull request #115 from geneontology/gocam_model_integration

Gocam model integration

app/routers/models.py

@@ -1,10 +1,13 @@
 """Model API router."""
 
 import logging
+from http.client import HTTPException
+from pprint import pprint
 from typing import List
 
 import requests
 from fastapi import APIRouter, Path, Query
+from gocam.translation.minerva_wrapper import MinervaWrapper
 from oaklib.implementations.sparql.sparql_implementation import SparqlImplementation
 from oaklib.resource import OntologyResource
 
@@ -20,6 +23,48 @@
 logger = logging.getLogger()
 
 
+@router.get(
+    "/api/gocam-model/{id}",
+    tags=["models"],
+    description="Returns model details in gocam-py format based on a GO-CAM model ID.",
+)
+async def get_gocam_model_by_id_in_gocam_py_format(
+    id: str = Path(
+        ...,
+        description="A GO-CAM identifier (e.g. 581e072c00000820, 581e072c00000295, 5900dc7400000968)",
+        example="581e072c00000295",
+    )
+) -> dict:
+    """
+    Returns model details in gocam-py format based on a GO-CAM model ID.
+
+    :param id: A GO-CAM identifier (e.g. 581e072c00000820, 581e072c00000295, 5900dc7400000968)
+    :return: model details in gocam-py format based on a GO-CAM model ID.
+    """
+    mw = MinervaWrapper()
+    stripped_ids = []
+    if id.startswith("gomodel:"):
+        model_id = id.replace("gomodel:", "")
+        stripped_ids.append(model_id)
+    else:
+        stripped_ids.append(id)
+    for stripped_id in stripped_ids:
+        path_to_s3 = "https://go-public.s3.amazonaws.com/files/go-cam/%s.json" % stripped_id
+        print(path_to_s3)
+        try:
+            response = requests.get(path_to_s3, timeout=30, headers={"User-Agent": USER_AGENT})
+            print(response.json())
+            response.raise_for_status()
+            if response.status_code == 403 or response.status_code == 404:
+                raise DataNotFoundException("GO-CAM model not found.")
+            data = response.json()
+            gocam_reposnse = mw.minerva_object_to_model(data)  # convert minerva object to gocam model
+            pprint(gocam_reposnse)
+            return gocam_reposnse.model_dump()
+        except Exception as e:
+            raise HTTPException(status_code=500, detail=f"Unexpected error: {e}") from e
+
+
 @router.get("/api/models/go", tags=["models"], description="Returns go term details based on a GO-CAM model ID.")
 async def get_goterms_by_model_id(
     gocams: List[str] = Query(
@@ -313,7 +358,7 @@ async def get_pmid_by_model_id(
 
 @router.get(
     "/api/go-cam/{id}", tags=["models"], description="Returns model details based on a GO-CAM model ID in JSON format."
-)
+)  # note: this is the endpoint that is currently used by gocam-py to for use in CTX export.
 async def get_model_details_by_model_id_json(
     id: str = Path(
         ...,

app/utils/sparql_utils.py

@@ -1,5 +1,20 @@
 """Utils for SPARQL queries."""
 
+from typing import Any
+
+from fastapi.responses import ORJSONResponse
+
+
+def create_response(data: Any):
+    """
+    Create a response with the given data.
+
+    :param data:
+    :return:
+    """
+    return ORJSONResponse(content=data.dict())
+
+
 SEPARATOR = "|"  # separator for splitting values
 
 

pyproject.toml

@@ -28,6 +28,7 @@ go-deploy = ">=0.4.1"
 biothings-client = "^0.3.0"
 email-validator = "^2.0.0.post2"
 bmt = "^1.1.2"
+gocam = "^0.2.0"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=7.4.0"

tests/unit/test_models_endpoints.py

@@ -8,6 +8,7 @@
 from requests import HTTPError
 
 from app.main import app
+from tests.integration.step_defs.bioentity_function_steps import response_code
 
 logging.basicConfig(filename="combined_access_error.log", level=logging.INFO, format="%(asctime)s - %(message)s")
 logger = logging.getLogger()
@@ -151,6 +152,16 @@ def test_get_model_details_by_model_id_json(self):
             self.assertGreater(len(response.json().get("individuals")), 0)
             self.assertGreater(len(response.json().get("facts")), 0)
 
+    def test_get_model_details_by_model_id_json_gocam_py(self):
+        """
+        Test the endpoint to retrieve model details by model ID in JSON format from the S3 bucket, check for success.
+
+        :return: None
+        """
+        for id in go_cam_ids:
+            response = test_client.get(f"/api/gocam-model/{id}")
+            self.assertEqual(response.status_code, 200)
+            self.assertEqual(response.json().get("id"), "gomodel:" + id.replace("gomodel:", ""))
 
     def test_get_model_details_by_model_id_not_found_json(self):
         """