add project files

.gitignore

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+.ipynb*
+__py*

README.md

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+# CSE 5810 Biomedical Informatics (Spring 2022)
+
+[![N|Solid](https://ddfoqzqsu0zvp.cloudfront.net/media/documents/school-of-engineering-wordmark-side-blue.png)](https://www.cse.uconn.edu/)
+
+---
+
+## Implementation Project Final Status
+### **Frank Zappulla**
+---
+
+#### Requirements
+
+- *For Windows Users Only* - [install WSL2](https://www.youtube.com/watch?v=n-J9438Mv-s&t=51s)
+    - This will give you a real linux terminal where you can use conda
+- Conda 
+    - If you don't have Conda, you should install [miniconda](https://docs.conda.io/en/latest/miniconda.html)
+- [Docker](https://docs.docker.com/get-docker/)
+
+---
+### Getting Started Instructions
+1. Start your local instance of [HAPI FHIR](https://github.uconn.edu/frz02001/HAPI_FHIR)
+2. clone this repository
+    - `git clone https://github.uconn.edu/frz02001/cse5810_implementation.git`
+3. Change directory into this repository
+    - `cd cse5810_implementation`
+4. Create your conda environment using the included yaml file
+    - `conda env create --file=hapi_fhir.yaml`
+5. Activate the conda environment you just created
+    - `conda activate hapi_fhir`
+6. Launch jupyter lab
+    - `jupyter lab`
+7. Copy and paste the url in the terminal into your browser
+8. Double click on the `hapi_fhir.ipynb` file to open the developer's notebook
+9. You should now be using the notebook that was demonstrated during class

config.py

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+
+app_id = 'my_web_app'
+api_base = 'http://localhost:8080/fhir'
+swagger_url = "http://hapi.fhir.org/baseR4/swagger-ui/#/"
+format_ = "_format=json"
+pretty = "_pretty=true"

hapi_fhir.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "48b1ba4f-ccb9-4889-840f-72440cd35d8a",
+   "metadata": {},
+   "source": [
+    "![hapi fhir logo](images/hapi_fhir_logo_new.jpeg)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "0342149e-30b3-466f-8140-ca74002b9568",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from fhirclient import client\n",
+    "import json\n",
+    "import requests"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "5fcec681-274a-4bdb-b576-7709fd1e120b",
+   "metadata": {},
+   "outputs": [],
+   "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": 5,
+   "id": "20fca573-2e6f-42c2-8a5a-94108bf57450",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "True\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(is_hapi_live())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "48172346-a366-438b-9b9b-f5ffaea05e9f",
+   "metadata": {},
+   "source": [
+    "### Swagger Page"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "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,
+   "id": "7685af34-5956-46ae-a2d7-caa2504d1299",
+   "metadata": {},
+   "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}\")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.9.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}