feat: add notebook for submitting civic assertions via prod api

analysis/civic/prod_submission.ipynb

@@ -0,0 +1,122 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import json\n",
+    "import os\n",
+    "import sys\n",
+    "from pathlib import Path\n",
+    "\n",
+    "module_path = os.path.abspath(os.path.join(\"../\"))\n",
+    "if module_path not in sys.path:\n",
+    "    sys.path.append(module_path)\n",
+    "from utils import dry_run_test_api, submit  # noqa: E402"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with Path(\"assertion_onco.json\").open() as f:\n",
+    "  onco_sub = json.load(f)\n",
+    "\n",
+    "assert dry_run_test_api(onco_sub).status_code == 204"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with Path(\"batch_assertions_clinical_impact.json\").open() as f:\n",
+    "  clin_impact_sub = None\n",
+    "  _data = json.load(f)\n",
+    "  _subs = _data[\"clinicalImpactSubmission\"]\n",
+    "\n",
+    "  for _sub in _subs:\n",
+    "    if _sub[\"localKey\"] == \"civic.AID:7\":\n",
+    "      clin_impact_sub = {\"clinicalImpactSubmission\": [_sub]}\n",
+    "      break\n",
+    "\n",
+    "assert dry_run_test_api(clin_impact_sub).status_code == 204"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "201"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "onco_sub_resp = submit(onco_sub)\n",
+    "onco_sub_resp.status_code"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "201"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "clin_impact_sub_resp = submit(clin_impact_sub)\n",
+    "clin_impact_sub_resp.status_code"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "venv",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

analysis/utils.py

@@ -10,10 +10,26 @@
 
 load_dotenv()
 
+CLINVAR_API = "https://submit.ncbi.nlm.nih.gov/api/v1/submissions/"
 TEST_URL = "https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions"
 HEADERS = {"Content-type": "application/json", "SP-API-KEY": environ["CLINVAR_API_KEY"]}
 
 
+def submit(submission: list[dict]) -> requests.Response:
+    """Create submission via ClinVar Submission API
+
+    :param submission: ClinVar submission
+    :return: Response from ClinVar Submission API
+    """
+    payload = {
+        "actions": [
+            {"type": "AddData", "targetDb": "clinvar", "data": {"content": submission}}
+        ]
+    }
+
+    return requests.post(CLINVAR_API, headers=HEADERS, json=payload, timeout=5)
+
+
 def dry_run_test_api(submission: list[dict]) -> requests.Response:
     """Perform a dry run using ClinVar Submission Test API