hapi_fhir.ipynb

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   "source": [
    "![hapi fhir logo](images/hapi_fhir_banner.png)"
   ]
  },
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   "outputs": [],
   "source": [
    "from fhirclient import client\n",
    "import json\n",
    "import requests"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5fcec681-274a-4bdb-b576-7709fd1e120b",
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   "source": [
    "# settings\n",
    "%run util.py"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6b1b75e6-6641-4463-aefa-7b2cfeb0ebb3",
   "metadata": {},
   "source": [
    "### Check If HAPI Is Live\n",
    "\n",
    "check every available resource for a 200 status code"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "20fca573-2e6f-42c2-8a5a-94108bf57450",
   "metadata": {},
   "outputs": [],
   "source": [
    "print(is_hapi_live())"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "48172346-a366-438b-9b9b-f5ffaea05e9f",
   "metadata": {},
   "source": [
    "### Swagger Page"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "cb587bd6-1efc-4eae-a959-ff4a4160f94c",
   "metadata": {},
   "outputs": [],
   "source": [
    "# open the swagger web page to view all endpoints\n",
    "open_swagger()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2c49c504-b75b-4e6d-ae94-2f452b3a9581",
   "metadata": {},
   "source": [
    "### Get Resource List"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   "outputs": [],
   "source": [
    "# get resource list from hapi fhir running instance\n",
    "\n",
    "resources = get_resource_list()\n",
    "print(f\"There are {len(resources)} resources available\")\n",
    "print(\"The available resources are: \")\n",
    "\n",
    "idx = 0\n",
    "for resource in resources:\n",
    "    print(f\"{idx}. {resource}\")\n",
    "    idx += 1\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4a8c5db7-2f09-4125-9fb0-3842fe97320c",
   "metadata": {},
   "source": [
    "## Basic Functions"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bed91136-1210-4d11-ba72-da6f8bc6e89e",
   "metadata": {},
   "source": [
    "### Check index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "88e6ac2b-9f12-4dd5-84ad-c760830dabd0",
   "metadata": {},
   "outputs": [],
   "source": [
    "# test that getting index by name works\n",
    "observation_index = get_resource_index(\"observation\")\n",
    "patient_index = get_resource_index(\"PaTiEnT\")\n",
    "\n",
    "print(f\"\\nThe list index for Patient is {patient_index}\")\n"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "78fc9a1e-f928-4cf1-99e7-692e361970e2",
   "metadata": {},
   "source": [
    "### Get resource using index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "53ae44ff-2710-4027-b28c-c0bc0ffbe600",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Get resource using the index\n",
    "\n",
    "all_observations = get_json(resource=resources[observation_index])\n",
    "all_patients = get_json(resource=resources[patient_index])\n",
    "all_observations_json = json.loads(all_observations)\n",
    "\n",
    "print(f\"Observation keys: {all_observations_json.keys()}\")\n",
    "\n",
    "for k,v in all_observations_json.items():\n",
    "    print(f\"\\nkey: {k}\\nvalue: {v}\\n\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "601e59a5-b39c-4e6f-b978-51294098b34e",
   "metadata": {},
   "source": [
    "### Print JSON"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b33366a4-09db-40d8-b9a3-d982a0048f93",
   "metadata": {},
   "outputs": [],
   "source": [
    "\n",
    "all_patients_json = json.loads(all_patients)\n",
    "print(all_patients_json.keys())\n",
    "\n",
    "print(\"PATIENT\")\n",
    "for elem in all_patients_json['entry']:\n",
    "    print(f\"\\n{elem}\")"
   ]
  }
 ],
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