Fix requests in proxy endpoints and parsing of observedIn

CHANGELOG.md

@@ -11,3 +11,4 @@
 - Tests and coverage GitHub workflow
 - Updated submission schema in resources following new release of schema by ClinVar (draft-07)
 - Proxy endpoint to interrogate the submission dry run endpoint of ClinVar API
+- Proxy endpoint to interrogate the submission validate endpoint of ClinVar API

preClinVar/constants.py

@@ -1,3 +1,2 @@
 DRY_RUN_SUBMISSION_URL = "https://submit.ncbi.nlm.nih.gov/api/v1/submissions/?dry-run=true"
-
 VALIDATE_SUBMISSION_URL = "https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions"

preClinVar/demo/submission.json

@@ -23,6 +23,13 @@
       },
       "localID": "1d9ce6ebf2f82d913cfbe20c5085947b",
       "localKey": "1d9ce6ebf2f82d913cfbe20c5085947b",
+      "observedIn": [
+        {
+          "affectedStatus": "yes",
+          "alleleOrigin": "germline",
+          "collectionMethod": "clinical testing"
+        }
+      ],
       "recordStatus": "novel",
       "releaseStatus": "public",
       "variantSet": {
@@ -61,6 +68,13 @@
       },
       "localID": "69b138a4c5caf211d796a59a7b46e40d",
       "localKey": "69b138a4c5caf211d796a59a7b46e40d",
+      "observedIn": [
+        {
+          "affectedStatus": "yes",
+          "alleleOrigin": "germline",
+          "collectionMethod": "clinical testing"
+        }
+      ],
       "recordStatus": "novel",
       "releaseStatus": "public",
       "variantSet": {
@@ -99,6 +113,13 @@
       },
       "localID": "e1bdbf66cd8df98d0d6874a9c4a0d7bc",
       "localKey": "e1bdbf66cd8df98d0d6874a9c4a0d7bc",
+      "observedIn": [
+        {
+          "affectedStatus": "yes",
+          "alleleOrigin": "germline",
+          "collectionMethod": "clinical testing"
+        }
+      ],
       "recordStatus": "novel",
       "releaseStatus": "public",
       "variantSet": {
@@ -137,6 +158,13 @@
       },
       "localID": "ace28c419a620040c49be5ec9cb7ba37",
       "localKey": "ace28c419a620040c49be5ec9cb7ba37",
+      "observedIn": [
+        {
+          "affectedStatus": "yes",
+          "alleleOrigin": "germline",
+          "collectionMethod": "clinical testing"
+        }
+      ],
       "recordStatus": "novel",
       "releaseStatus": "public",
       "variantSet": {

preClinVar/main.py

@@ -7,7 +7,7 @@
 from fastapi import FastAPI, File, Query, UploadFile
 from fastapi.responses import JSONResponse
 from preClinVar.build import build_header
-from preClinVar.constants import DRY_RUN_SUBMISSION_URL
+from preClinVar.constants import DRY_RUN_SUBMISSION_URL, VALIDATE_SUBMISSION_URL
 from preClinVar.parse import csv_fields_to_submission, csv_lines
 from preClinVar.validate import validate_submission
 from pydantic import BaseModel, Field
@@ -31,19 +31,41 @@ async def root():
     return {"message": "preClinVar is up and running!"}
 
 
+@app.post("/validate")
+async def validate(
+    api_key: str = Query(max_length=64, min_length=64), json_file: UploadFile = File(...)
+):
+    """A proxy to the validate submission 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 in POST request to API
+    data = {
+        "actions": [{"type": "AddData", "targetDb": "clinvar", "data": {"content": submission_obj}}]
+    }
+    resp = requests.post(VALIDATE_SUBMISSION_URL, data=json.dumps(data), headers=header)
+    return resp.json()
+
+
 @app.post("/dry-run")
 async def dry_run(
     api_key: str = Query(max_length=64, min_length=64), json_file: UploadFile = File(...)
 ):
-    """Dry-run a ClinVar submission by sending a test to the ClinVar API"""
+    """A proxy to the dry run submission 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 in POST request to API
-    resp = requests.post(DRY_RUN_SUBMISSION_URL, json=submission_obj, headers=header)
+    data = {
+        "actions": [{"type": "AddData", "targetDb": "clinvar", "data": {"content": submission_obj}}]
+    }
+    resp = requests.post(DRY_RUN_SUBMISSION_URL, data=json.dumps(data), headers=header)
     return resp.json()
 
 

preClinVar/parse.py

@@ -114,6 +114,8 @@ def set_item_observed_in(item, casedata_dict):
     if casedata_dict.get("Clinical features"):
         obs_in["clinicalFeatures"] = casedata_dict.get("Clinical features").split(";")
 
+    item["observedIn"] = [obs_in]
+
     # NOT parsing the following key/values for now:
     # clinicalFeaturesComment
     # numberOfIndividuals

tests/test_main.py

@@ -44,3 +44,14 @@ def test_dry_run_wrong_api_key():
     response = client.post(url, files=json_file)
     assert response.status_code == 200
     assert response.json()["message"] == "No valid API key provided"
+
+
+def test_validate_wrong_api_key():
+    """Test endpoint that sends a request to the ClinVar dry run API endpoint"""
+    json_file = {"json_file": open(subm_json_path, "rb")}
+
+    url = "?api_key=".join(["/validate", DEMO_API_KEY])
+
+    response = client.post(url, files=json_file)
+    assert response.status_code == 200
+    assert response.json()["message"] == "No valid API key provided"