Merge branch 'main' into version_2.6

CHANGELOG.md

@@ -1,6 +1,10 @@
+
 ## [2.6]
-### Changed 
-- Expand the output of validate endpoint to return the link for downloading json file containing evantual submission errors
+### Added
+- An endpoint `/apitest-status` that returns a response containing the status of a test submission, with link to the eventual json file with the submissions data errors
+- An endpoint `/status` that returns a response containing the status of a submission (submitted, processing, processed, error), with eventual error details
+### Changed
+- Renamed `/validate` endpoint to `/apitest`
 
 ## [2.5.2]
 ### Fixed

README.md

@@ -23,9 +23,9 @@ Transforms csv submission files (Variant.csv and CaseData.csv) into a json submi
 
 Proxy endpoint to the ClinVar submissions API (dry-run): https://submit.ncbi.nlm.nih.gov/api/v1/submissions/?dry-run=true. Requires a valid API key and a json file containing a submission object. If the request is valid (and the json submission object is validated) returns a response with code 200 and json body with the message value "success".
 
-### validate
+### apitest
 
-Proxy endpoint to the ClinVar validate API endpoint: "https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions". Requires a valid API key and a json file containing a submission object. If the json submission document is valid returns a submission ID which can be used for a real submission. If the json submission document is not validated, the endpoint returns a list of errors which will help fixing the document.
+Proxy endpoint to the validation API endpoint: (apitest) "https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions". Requires a valid API key and a json file containing a submission object. If the json submission document is valid returns a submission ID which can be used for a real submission. If the json submission document is not validated, the endpoint returns a list of errors which will help fixing the document.
 
 ## Running the application using Docker-compose
 An example containing a demo setup for the app is included in the docker-compose file. Start the docker-compose demo using this command:

preClinVar/constants.py

@@ -1,4 +1,5 @@
-DRY_RUN_SUBMISSION_URL = "https://submit.ncbi.nlm.nih.gov/api/v1/submissions/?dry-run=true"
+SUBMISSION_URL = "https://submit.ncbi.nlm.nih.gov/api/v1/submissions"
+DRY_RUN_SUBMISSION_URL = f"{SUBMISSION_URL}/?dry-run=true"
 VALIDATE_SUBMISSION_URL = "https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions"
 
 CLNSIG_TERMS = [

preClinVar/main.py

@@ -10,7 +10,7 @@
 
 from preClinVar.__version__ import VERSION
 from preClinVar.build import build_header, build_submission
-from preClinVar.constants import DRY_RUN_SUBMISSION_URL, VALIDATE_SUBMISSION_URL
+from preClinVar.constants import DRY_RUN_SUBMISSION_URL, SUBMISSION_URL, VALIDATE_SUBMISSION_URL
 from preClinVar.file_parser import csv_lines, file_fields_to_submission, tsv_lines
 from preClinVar.validate import validate_submission
 
@@ -33,16 +33,32 @@ async def root():
     return {"message": f"preClinVar v{VERSION} is up and running!"}
 
 
-@app.post("/validate")
-async def validate(api_key: str = Form(), json_file: UploadFile = File(...)) -> JSONResponse:
-    """A proxy to the apitest submission ClinVar API endpoint. Returns the ID of the submission and the data summary report with eventual errors."""
+@app.post("/apitest-status")
+async def apitest_status(api_key: str = Form(), submission_id: str = Form()) -> JSONResponse:
+    """Returns the status (validation) of a test submission to the apitest endpoint."""
+
+    # Create a submission header
+    header = build_header(api_key)
+
+    apitest_actions_url = f"{VALIDATE_SUBMISSION_URL}/{submission_id}/actions/"
+    apitest_actions_resp = requests.get(apitest_actions_url, headers=header)
+
+    return JSONResponse(
+        status_code=apitest_actions_resp.status_code,
+        content=apitest_actions_resp.json(),
+    )
+
+
+@app.post("/apitest")
+async def apitest(api_key: str = Form(), json_file: UploadFile = File(...)):
+    """A proxy to the apitest ClinVar API endpoint"""
     # Create a submission header
     header = build_header(api_key)
 
     # Get json file content as dict:
     submission_obj = json.load(json_file.file)
 
-    # And use it as data in a POST request to API
+    # And use it in POST request to API
     data = {
         "actions": [
             {
@@ -52,23 +68,10 @@ async def validate(api_key: str = Form(), json_file: UploadFile = File(...)) ->
             }
         ]
     }
-    apitest_resp = requests.post(VALIDATE_SUBMISSION_URL, data=json.dumps(data), headers=header)
-    apitest_json: dict = apitest_resp.json()
-
-    # If submission was created, return eventual link for downloading json file with data-specific errors
-    if apitest_resp.status_code == 201:
-
-        apitest_actions_url = f"{VALIDATE_SUBMISSION_URL}/{apitest_json.get('id')}/actions/"
-        apitest_actions_resp = requests.get(apitest_actions_url, headers=header)
-
-        return JSONResponse(
-            status_code=apitest_actions_resp.status_code,
-            content=apitest_actions_resp.json(),
-        )
-
+    resp = requests.post(VALIDATE_SUBMISSION_URL, data=json.dumps(data), headers=header)
     return JSONResponse(
-        status_code=apitest_resp.status_code,
-        content=apitest_json,
+        status_code=resp.status_code,
+        content=resp.json(),
     )
 
 
@@ -214,3 +217,19 @@ async def csv_2_json(
         status_code=400,
         content={"message": f"Created json file contains validation errors: {valid_results[1]}"},
     )
+
+
+@app.post("/status")
+async def status(api_key: str = Form(), submission_id: str = Form()) -> JSONResponse:
+    """Returns the status (validation) of a submission."""
+
+    # Create a submission header
+    header = build_header(api_key)
+
+    actions_url = f"{SUBMISSION_URL}/{submission_id}/actions/"
+    actions_resp = requests.get(actions_url, headers=header)
+
+    return JSONResponse(
+        status_code=actions_resp.status_code,
+        content=actions_resp.json(),
+    )

tests/test_main.py

@@ -7,7 +7,7 @@
 from fastapi.testclient import TestClient
 
 from preClinVar.__version__ import VERSION
-from preClinVar.constants import DRY_RUN_SUBMISSION_URL, VALIDATE_SUBMISSION_URL
+from preClinVar.constants import DRY_RUN_SUBMISSION_URL, SUBMISSION_URL, VALIDATE_SUBMISSION_URL
 from preClinVar.demo import (
     casedata_old_csv,
     casedata_old_csv_path,
@@ -290,8 +290,8 @@ def test_dry_run():
 
 
 @responses.activate
-def test_validate_wrong_api_key():
-    """Test the validate API proxy endpoint without a valid ClinVar API key"""
+def test_apitest_wrong_api_key():
+    """Test the apitest API proxy endpoint without a valid ClinVar API key"""
 
     # GIVEN a json submission file
     json_file = {"json_file": open(subm_json_path, "rb")}
@@ -304,25 +304,39 @@ def test_validate_wrong_api_key():
         status=401,  # The ClinVar API returs code 201 when request is successful (created)
     )
 
-    response = client.post("/validate", data={"api_key": DEMO_API_KEY}, files=json_file)
+    response = client.post("/apitest", data={"api_key": DEMO_API_KEY}, files=json_file)
 
     # THEN the ClinVar API should return "unauthorized"
     assert response.status_code == 401  # Not authorized
     assert response.json()["message"] == "No valid API key provided"
 
 
 @responses.activate
-def test_validate_error():
-    """Test the validated API proxy endpoint (with a mocked ClinVar API response)"""
+def test_apitest():
+    """Tests the endpoint apitest, a proxy to ClinVar apitest, with a mocked ClinVar API response."""
 
-    # GIVEN a mocked POST response from CLinVar apitest endpoint
+    # GIVEN a json submission file
+    json_file = {"json_file": open(subm_json_path, "rb")}
+
+    # AND a mocked ClinVar API
     responses.add(
         responses.POST,
         VALIDATE_SUBMISSION_URL,
         json={"id": DEMO_SUBMISSION_ID},
-        status=201,  # The ClinVar API returns code 201 when request is successful (created)
+        status=201,  # The ClinVar API returs code 201 when request is successful (created)
     )
 
+    response = client.post("/apitest", data={"api_key": DEMO_API_KEY}, files=json_file)
+
+    # THEN the ClinVar API proxy should return "success"
+    assert response.status_code == 201  # Created
+    assert response.json()["id"] == DEMO_SUBMISSION_ID
+
+
+@responses.activate
+def test_apitest_status():
+    """Test the endpoint that sends GET requests to the apitest actions ClinVar endpoint."""
+
     # GIVEN a mocked error response from apitest actions endpoint
     actions: list[dict] = [
         {
@@ -353,15 +367,47 @@ def test_validate_error():
         responses.GET,
         f"{VALIDATE_SUBMISSION_URL}/{DEMO_SUBMISSION_ID}/actions/",
         json={"actions": actions},
-        status=200,  # The ClinVar API returns code 201 when request is successful (created)
+        status=200,
     )
 
-    # GIVEN a json submission file
-    json_file = {"json_file": open(subm_json_path, "rb")}
-
-    response = client.post("/validate", data={"api_key": DEMO_API_KEY}, files=json_file)
+    # GIVEN a call to the apitest_status endpoint
+    response = client.post(
+        "/apitest-status", data={"api_key": DEMO_API_KEY, "submission_id": DEMO_SUBMISSION_ID}
+    )
 
-    # THEN the ClinVar API proxy should return the expected data
+    # THEN the response should contain the provided actions
     assert response.status_code == 200
     assert response.json()["actions"][0]["id"]
     assert response.json()["actions"][0]["responses"][0]["files"]
+
+
+@responses.activate
+def test_status_submitted():
+    """Test the status endpoint, proxy to the https://submit.ncbi.nlm.nih.gov/api/v1/submissions/SUBnnnnnn/actions ClinVar endpoint."""
+
+    # GIVEN a mocked submitted response from ClinVar:
+    actions: list[dict] = [
+        {
+            "id": f"{DEMO_SUBMISSION_ID}-1",
+            "responses": [],
+            "status": "submitted",
+            "targetDb": "clinvar",
+            "updated": "2024-04-26T13:39:24.384085Z",
+        }
+    ]
+
+    responses.add(
+        responses.GET,
+        f"{SUBMISSION_URL}/{DEMO_SUBMISSION_ID}/actions/",
+        json={"actions": actions},
+        status=200,
+    )
+
+    # GIVEN a call to the status endpoint
+    response = client.post(
+        "/status", data={"api_key": DEMO_API_KEY, "submission_id": DEMO_SUBMISSION_ID}
+    )
+
+    # THEN the response should contain the provided status
+    assert response.status_code == 200
+    assert response.json()["actions"][0]["status"] == "submitted"