Add get seeds notebook

client/Get Seeds.ipynb

@@ -0,0 +1,114 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "1b76234d-f32b-499e-a0df-f64d085e7a0a",
+   "metadata": {},
+   "source": [
+    "# Get seeds from FHIR server"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "43e12dca-2544-4674-ad69-6789c2b6bdcc",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from fhirpy import SyncFHIRClient\n",
+    "from fhirpy.base.exceptions import OperationOutcome\n",
+    "from collections import defaultdict\n",
+    "import json\n",
+    "import gzip"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7f79f578-4bb2-4bdc-94f6-4839ae45b51a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "SOURCE_BASE_URL = \"https://au-core.beda.software/fhir/\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b4cee225-2e53-4956-aab6-db477524cb3f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "source = SyncFHIRClient(SOURCE_BASE_URL)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b983fa5e-f4d5-4b98-beaf-fbd8faa61086",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "resources = defaultdict(list)\n",
+    "patients =  source.resources(\"Patient\").fetch_all()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5c29483b-11bb-433a-b1a8-191326301c6f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for patient in patients:\n",
+    "    for entry in patient.execute(\"$everything\", method=\"GET\")[\"entry\"]:\n",
+    "        resource = entry[\"resource\"]\n",
+    "        resources[resource[\"resourceType\"]].append(resource)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "44b8144f-b3f1-4129-9942-69055db3d350",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with gzip.open('seeds.ndjson.gz', 'wt') as file:\n",
+    "    for item in [item for sublist in resources.values() for item in sublist]:\n",
+    "        json.dump(item, file)\n",
+    "        file.write('\\n')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d97cbcaf-60d5-4731-a68e-798553915e22",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "len([item for sublist in resources.values() for item in sublist])"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.11.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}