bundler/STU3_Bundler.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Script to bundle all resources in folder as a batch, transaction, collection, or message\n",
    "\n",
    "- python version 3.6+\n",
    "- get data from folder\n",
    "- bundle\n",
    "- validate and save"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 237,
   "metadata": {},
   "outputs": [],
   "source": [
    "from json import load, dumps, loads\n",
    "from IPython import display as D\n",
    "from requests import get, post, put\n",
    "from IPython.display import display, Markdown, HTML\n",
    "from fhirclient.models import bundle as B\n",
    "import fhirclient.models.fhirdate as D\n",
    "import os, uuid\n",
    "from datetime import datetime\n",
    "\n",
    "bundle_id = 'indv-report08'\n",
    "bundle_type = 'transaction'"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "###  write to file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 238,
   "metadata": {},
   "outputs": [],
   "source": [
    "def write_file(r): # write file\n",
    "    #out_path = '/Users/ehaas/Documents/FHIR/Davinci-DEQM/source/examples/'  # append forward slash\n",
    "    out_path ='r3'\n",
    "    with open(f'{out_path}/Bundle-{bundle_id}.json', 'w') as f:\n",
    "        f.write(r)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### open json file and return as dict"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 239,
   "metadata": {},
   "outputs": [],
   "source": [
    "def open_file(f_name): # get files\n",
    "    with open(f'{in_path}/{f_name}') as f:\n",
    "        r = f.read()\n",
    "        return(loads(r))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get files in current path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 240,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['Coverage-coverage01.json', 'Encounter-encounter01.json', 'Location-location01.json', 'MeasureReport-indv-measurereport01.json', 'Organization-organization01.json', 'Organization-organization02.json', 'Patient-patient01.json', 'Practitioner-practitioner01.json', 'Task-task01.json']\n"
     ]
    }
   ],
   "source": [
    "in_path = 'r3'\n",
    "files = [x for x in os.listdir(in_path) if x.endswith(\".json\") and not x.startswith(\"Bundle\")]\n",
    "print(files)\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### create Bundle 'b'  change the id for unique Bundles!!!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 241,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'id': 'indv-report08', 'type': 'transaction', 'resourceType': 'Bundle'}"
      ]
     },
     "execution_count": 241,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "b = B.Bundle()\n",
    "b.id =  bundle_id\n",
    "b.type = bundle_type\n",
    "#b.foo = D.FHIRDate(f'{datetime.utcnow().isoformat()}Z')\n",
    "b.as_json()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Add resources to bundle\n",
    "\n",
    "#### Create a mapping of ids to uuids\n",
    "\n",
    "- get id from resource\n",
    "- map to uuid (create a dict of {urn, (old_ref)})\n",
    "- remove id element\n",
    "- replace all old refs in bundle with new urns\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 242,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\n",
      "   \"id\": \"indv-report08\",\n",
      "   \"entry\": [\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2c897e-0bf3-11ea-b0f6-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"Coverage\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"lastUpdated\": \"2019-02-11T14:19:25.000+00:00\",\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/davinci-deqm/STU3/StructureDefinition/coverage-deqm\"\n",
      "               ],\n",
      "               \"versionId\": \"2\"\n",
      "            },\n",
      "            \"beneficiary\": {\n",
      "               \"reference\": \"urn:uuid:fa2cd76e-0bf3-11ea-a780-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"payor\": [\n",
      "               {\n",
      "                  \"reference\": \"Organization/organization04\"\n",
      "               }\n",
      "            ],\n",
      "            \"policyHolder\": {\n",
      "               \"reference\": \"urn:uuid:fa2cd76e-0bf3-11ea-a780-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"relationship\": {\n",
      "               \"coding\": [\n",
      "                  {\n",
      "                     \"code\": \"self\"\n",
      "                  }\n",
      "               ]\n",
      "            },\n",
      "            \"status\": \"active\",\n",
      "            \"subscriber\": {\n",
      "               \"reference\": \"urn:uuid:fa2cd76e-0bf3-11ea-a780-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"subscriberId\": \"A123456789\",\n",
      "            \"resourceType\": \"Coverage\"\n",
      "         }\n",
      "      },\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2c897f-0bf3-11ea-a089-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"Encounter\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-encounter\"\n",
      "               ]\n",
      "            },\n",
      "            \"class\": {\n",
      "               \"code\": \"IMP\",\n",
      "               \"display\": \"inpatient encounter\",\n",
      "               \"system\": \"http://hl7.org/fhir/v3/ActCode\"\n",
      "            },\n",
      "            \"hospitalization\": {\n",
      "               \"dischargeDisposition\": {\n",
      "                  \"coding\": [\n",
      "                     {\n",
      "                        \"code\": \"home\",\n",
      "                        \"display\": \"Home\",\n",
      "                        \"system\": \"http://hl7.org/fhir/discharge-disposition\"\n",
      "                     }\n",
      "                  ]\n",
      "               }\n",
      "            },\n",
      "            \"period\": {\n",
      "               \"end\": \"2018-05-29T11:00:00-04:00\",\n",
      "               \"start\": \"2018-05-29T11:00:00-04:00\"\n",
      "            },\n",
      "            \"status\": \"finished\",\n",
      "            \"subject\": {\n",
      "               \"display\": \"Natalie Huff Walter\",\n",
      "               \"reference\": \"urn:uuid:fa2cd76e-0bf3-11ea-a780-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"type\": [\n",
      "               {\n",
      "                  \"coding\": [\n",
      "                     {\n",
      "                        \"code\": \"56876005\",\n",
      "                        \"display\": \"Drug rehabilitation and detoxification\",\n",
      "                        \"system\": \"http://snomed.info/sct\"\n",
      "                     }\n",
      "                  ]\n",
      "               }\n",
      "            ],\n",
      "            \"resourceType\": \"Encounter\"\n",
      "         }\n",
      "      },\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2cb078-0bf3-11ea-85c4-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"Location\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-location\"\n",
      "               ]\n",
      "            },\n",
      "            \"address\": {\n",
      "               \"city\": \"Somerset\",\n",
      "               \"country\": \"USA\",\n",
      "               \"line\": [\n",
      "                  \"102 Heritage Dr.\"\n",
      "               ],\n",
      "               \"postalCode\": \"08873\",\n",
      "               \"state\": \"NJ\"\n",
      "            },\n",
      "            \"name\": \"DaVinciClinic01\",\n",
      "            \"resourceType\": \"Location\"\n",
      "         }\n",
      "      },\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2cb079-0bf3-11ea-80db-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"MeasureReport\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/davinci-deqm/STU3/StructureDefinition/indv-measurereport-deqm\"\n",
      "               ]\n",
      "            },\n",
      "            \"extension\": [\n",
      "               {\n",
      "                  \"url\": \"http://hl7.org/fhir/us/davinci-deqm/STU3/StructureDefinition/extension-certificationIdentifier\",\n",
      "                  \"valueIdentifier\": {\n",
      "                     \"system\": \"urn:oid:2.16.840.1.113883.3.2074.1\",\n",
      "                     \"value\": \"0015HQN9BD3304E\"\n",
      "                  }\n",
      "               },\n",
      "               {\n",
      "                  \"url\": \"http://hl7.org/fhir/us/davinci-deqm/STU3/StructureDefinition/extension-reportingVendor\",\n",
      "                  \"valueReference\": {\n",
      "                     \"reference\": \"urn:uuid:fa2cd76d-0bf3-11ea-b21b-4ccc6a181ed3\"\n",
      "                  }\n",
      "               }\n",
      "            ],\n",
      "            \"date\": \"2018-09-05T16:59:52.404Z\",\n",
      "            \"evaluatedResources\": {\n",
      "               \"extension\": [\n",
      "                  {\n",
      "                     \"url\": \"http://hl7.org/fhir/us/davinci-deqm/STU3/StructureDefinition/extension-referenceAny\",\n",
      "                     \"valueReference\": {\n",
      "                        \"reference\": \"urn:uuid:fa2d2552-0bf3-11ea-b67e-4ccc6a181ed3\"\n",
      "                     }\n",
      "                  }\n",
      "               ]\n",
      "            },\n",
      "            \"group\": [\n",
      "               {\n",
      "                  \"identifier\": {\n",
      "                     \"system\": \"http://www.acme.org/groups\",\n",
      "                     \"value\": \"112\"\n",
      "                  },\n",
      "                  \"measureScore\": 100,\n",
      "                  \"population\": [\n",
      "                     {\n",
      "                        \"code\": {\n",
      "                           \"coding\": [\n",
      "                              {\n",
      "                                 \"code\": \"initial-population\",\n",
      "                                 \"display\": \"Initial Population\",\n",
      "                                 \"system\": \"http://hl7.org/fhir/measure-population\"\n",
      "                              }\n",
      "                           ]\n",
      "                        },\n",
      "                        \"identifier\": {\n",
      "                           \"system\": \"http://www.acme.org/populations\",\n",
      "                           \"value\": \"11234\"\n",
      "                        }\n",
      "                     }\n",
      "                  ]\n",
      "               }\n",
      "            ],\n",
      "            \"measure\": {\n",
      "               \"reference\": \"https://ncqa.org/fhir/ig/Measure/measure-mrp\"\n",
      "            },\n",
      "            \"patient\": {\n",
      "               \"reference\": \"urn:uuid:fa2cd76e-0bf3-11ea-a780-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"period\": {\n",
      "               \"end\": \"2018-09-01\",\n",
      "               \"start\": \"2018-08-01\"\n",
      "            },\n",
      "            \"reportingOrganization\": {\n",
      "               \"reference\": \"urn:uuid:fa2cd76c-0bf3-11ea-84b7-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"status\": \"complete\",\n",
      "            \"type\": \"individual\",\n",
      "            \"resourceType\": \"MeasureReport\"\n",
      "         }\n",
      "      },\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2cd76c-0bf3-11ea-84b7-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"Organization\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"lastUpdated\": \"2019-02-21T01:47:54.000+00:00\",\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/davinci-deqm/STU3/StructureDefinition/organization-deqm\"\n",
      "               ],\n",
      "               \"versionId\": \"4\"\n",
      "            },\n",
      "            \"active\": true,\n",
      "            \"address\": [\n",
      "               {\n",
      "                  \"city\": \"Warwick\",\n",
      "                  \"country\": \"USA\",\n",
      "                  \"line\": [\n",
      "                     \"73 Lakewood Street\"\n",
      "                  ],\n",
      "                  \"postalCode\": \"02886\",\n",
      "                  \"state\": \"RI\"\n",
      "               }\n",
      "            ],\n",
      "            \"identifier\": [\n",
      "               {\n",
      "                  \"assigner\": {\n",
      "                     \"display\": \"www.irs.gov\"\n",
      "                  },\n",
      "                  \"system\": \"urn:oid:2.16.840.1.113883.4.4\",\n",
      "                  \"type\": {\n",
      "                     \"coding\": [\n",
      "                        {\n",
      "                           \"code\": \"TAX\",\n",
      "                           \"display\": \"Tax ID number\",\n",
      "                           \"system\": \"http://hl7.org/fhir/v2/0203\"\n",
      "                        }\n",
      "                     ]\n",
      "                  },\n",
      "                  \"use\": \"official\",\n",
      "                  \"value\": \"123456789\"\n",
      "               }\n",
      "            ],\n",
      "            \"name\": \"DaVinciHospital01\",\n",
      "            \"telecom\": [\n",
      "               {\n",
      "                  \"system\": \"phone\",\n",
      "                  \"value\": \"(+1) 401-555-1212\"\n",
      "               }\n",
      "            ],\n",
      "            \"type\": [\n",
      "               {\n",
      "                  \"coding\": [\n",
      "                     {\n",
      "                        \"code\": \"prov\",\n",
      "                        \"display\": \"Healthcare Provider\",\n",
      "                        \"system\": \"http://hl7.org/fhir/organization-type\"\n",
      "                     }\n",
      "                  ]\n",
      "               }\n",
      "            ],\n",
      "            \"resourceType\": \"Organization\"\n",
      "         }\n",
      "      },\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2cd76d-0bf3-11ea-b21b-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"Organization\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"lastUpdated\": \"2019-03-06T19:03:03.000+00:00\",\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/davinci-deqm/STU3/StructureDefinition/organization-deqm\"\n",
      "               ],\n",
      "               \"versionId\": \"3\"\n",
      "            },\n",
      "            \"active\": true,\n",
      "            \"address\": [\n",
      "               {\n",
      "                  \"city\": \"Englewood\",\n",
      "                  \"country\": \"USA\",\n",
      "                  \"line\": [\n",
      "                     \"3 Sherwood St.\"\n",
      "                  ],\n",
      "                  \"postalCode\": \"07631\",\n",
      "                  \"state\": \"NJ\"\n",
      "               }\n",
      "            ],\n",
      "            \"identifier\": [\n",
      "               {\n",
      "                  \"assigner\": {\n",
      "                     \"display\": \"www.irs.gov\"\n",
      "                  },\n",
      "                  \"system\": \"urn:oid:2.16.840.1.113883.4.4\",\n",
      "                  \"type\": {\n",
      "                     \"coding\": [\n",
      "                        {\n",
      "                           \"code\": \"TAX\",\n",
      "                           \"display\": \"Tax ID number\",\n",
      "                           \"system\": \"http://hl7.org/fhir/v2/0203\"\n",
      "                        }\n",
      "                     ]\n",
      "                  },\n",
      "                  \"use\": \"official\",\n",
      "                  \"value\": \"234567891\"\n",
      "               }\n",
      "            ],\n",
      "            \"name\": \"DaVinciHospital02\",\n",
      "            \"telecom\": [\n",
      "               {\n",
      "                  \"system\": \"phone\",\n",
      "                  \"value\": \"(+1) 551-555-1212\"\n",
      "               }\n",
      "            ],\n",
      "            \"type\": [\n",
      "               {\n",
      "                  \"coding\": [\n",
      "                     {\n",
      "                        \"code\": \"prov\",\n",
      "                        \"display\": \"Healthcare Provider\",\n",
      "                        \"system\": \"http://hl7.org/fhir/organization-type\"\n",
      "                     }\n",
      "                  ]\n",
      "               }\n",
      "            ],\n",
      "            \"resourceType\": \"Organization\"\n",
      "         }\n",
      "      },\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2cd76e-0bf3-11ea-a780-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"Patient\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"lastUpdated\": \"2019-02-11T14:19:25.000+00:00\",\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-patient\"\n",
      "               ],\n",
      "               \"versionId\": \"5\"\n",
      "            },\n",
      "            \"extension\": [\n",
      "               {\n",
      "                  \"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex\",\n",
      "                  \"valueCode\": \"M\"\n",
      "               },\n",
      "               {\n",
      "                  \"extension\": [\n",
      "                     {\n",
      "                        \"url\": \"ombCategory\",\n",
      "                        \"valueCoding\": {\n",
      "                           \"code\": \"2106-3\",\n",
      "                           \"display\": \"White\",\n",
      "                           \"system\": \"urn:oid:2.16.840.1.113883.6.238\"\n",
      "                        }\n",
      "                     },\n",
      "                     {\n",
      "                        \"url\": \"text\",\n",
      "                        \"valueString\": \"White\"\n",
      "                     }\n",
      "                  ],\n",
      "                  \"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race\"\n",
      "               },\n",
      "               {\n",
      "                  \"extension\": [\n",
      "                     {\n",
      "                        \"url\": \"ombCategory\",\n",
      "                        \"valueCoding\": {\n",
      "                           \"code\": \"2186-5\",\n",
      "                           \"display\": \"Not Hispanic or Latino\",\n",
      "                           \"system\": \"urn:oid:2.16.840.1.113883.6.238\"\n",
      "                        }\n",
      "                     },\n",
      "                     {\n",
      "                        \"url\": \"text\",\n",
      "                        \"valueString\": \"Not Hispanic or Latino\"\n",
      "                     }\n",
      "                  ],\n",
      "                  \"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity\"\n",
      "               }\n",
      "            ],\n",
      "            \"active\": true,\n",
      "            \"address\": [\n",
      "               {\n",
      "                  \"city\": \"Thornton\",\n",
      "                  \"country\": \"USA\",\n",
      "                  \"line\": [\n",
      "                     \"7496 Beaver Ridge Ave\"\n",
      "                  ],\n",
      "                  \"postalCode\": \"07003\",\n",
      "                  \"state\": \"NJ\",\n",
      "                  \"use\": \"home\"\n",
      "               }\n",
      "            ],\n",
      "            \"birthDate\": \"1946-12-16\",\n",
      "            \"communication\": [\n",
      "               {\n",
      "                  \"language\": {\n",
      "                     \"coding\": [\n",
      "                        {\n",
      "                           \"code\": \"en-US\",\n",
      "                           \"display\": \"US English\",\n",
      "                           \"system\": \"urn:ietf:bcp:47\"\n",
      "                        }\n",
      "                     ]\n",
      "                  },\n",
      "                  \"preferred\": true\n",
      "               }\n",
      "            ],\n",
      "            \"deceasedBoolean\": false,\n",
      "            \"gender\": \"male\",\n",
      "            \"identifier\": [\n",
      "               {\n",
      "                  \"system\": \"http://hospital.davinci.org\",\n",
      "                  \"type\": {\n",
      "                     \"coding\": [\n",
      "                        {\n",
      "                           \"code\": \"MR\",\n",
      "                           \"display\": \"Medical record number\",\n",
      "                           \"system\": \"http://hl7.org/fhir/v2/0203\"\n",
      "                        }\n",
      "                     ]\n",
      "                  },\n",
      "                  \"use\": \"usual\",\n",
      "                  \"value\": \"12345\"\n",
      "               }\n",
      "            ],\n",
      "            \"managingOrganization\": {\n",
      "               \"reference\": \"urn:uuid:fa2cd76c-0bf3-11ea-84b7-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"maritalStatus\": {\n",
      "               \"coding\": [\n",
      "                  {\n",
      "                     \"code\": \"M\",\n",
      "                     \"display\": \"Married\",\n",
      "                     \"system\": \"http://hl7.org/fhir/v3/MaritalStatus\"\n",
      "                  }\n",
      "               ]\n",
      "            },\n",
      "            \"name\": [\n",
      "               {\n",
      "                  \"family\": \"Webster\",\n",
      "                  \"given\": [\n",
      "                     \"Jairo\"\n",
      "                  ],\n",
      "                  \"use\": \"official\"\n",
      "               }\n",
      "            ],\n",
      "            \"resourceType\": \"Patient\"\n",
      "         }\n",
      "      },\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2cfe62-0bf3-11ea-ac6e-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"Practitioner\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"lastUpdated\": \"2019-03-06T19:03:03.000+00:00\",\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/davinci-deqm/STU3/StructureDefinition/practitioner-deqm\"\n",
      "               ],\n",
      "               \"versionId\": \"4\"\n",
      "            },\n",
      "            \"active\": true,\n",
      "            \"gender\": \"male\",\n",
      "            \"identifier\": [\n",
      "               {\n",
      "                  \"system\": \"http://hl7.org/fhir/sid/us-npi\",\n",
      "                  \"type\": {\n",
      "                     \"coding\": [\n",
      "                        {\n",
      "                           \"code\": \"PRN\",\n",
      "                           \"display\": \"Provider number\",\n",
      "                           \"system\": \"http://hl7.org/fhir/v2/0203\"\n",
      "                        }\n",
      "                     ]\n",
      "                  },\n",
      "                  \"use\": \"official\",\n",
      "                  \"value\": \"456789123\"\n",
      "               }\n",
      "            ],\n",
      "            \"name\": [\n",
      "               {\n",
      "                  \"family\": \"Hale\",\n",
      "                  \"given\": [\n",
      "                     \"Cody\"\n",
      "                  ],\n",
      "                  \"suffix\": [\n",
      "                     \"MD\"\n",
      "                  ]\n",
      "               }\n",
      "            ],\n",
      "            \"resourceType\": \"Practitioner\"\n",
      "         }\n",
      "      },\n",
      "      {\n",
      "         \"fullUrl\": \"urn:uuid:fa2d2552-0bf3-11ea-b67e-4ccc6a181ed3\",\n",
      "         \"request\": {\n",
      "            \"method\": \"POST\",\n",
      "            \"url\": \"Task\"\n",
      "         },\n",
      "         \"resource\": {\n",
      "            \"meta\": {\n",
      "               \"profile\": [\n",
      "                  \"http://hl7.org/fhir/us/hedis/StructureDefinition/hedis-task\"\n",
      "               ]\n",
      "            },\n",
      "            \"authoredOn\": \"2018-09-25T14:24:23.584Z\",\n",
      "            \"code\": {\n",
      "               \"coding\": [\n",
      "                  {\n",
      "                     \"code\": \"1111F\",\n",
      "                     \"display\": \"Medication Reconciliation\",\n",
      "                     \"system\": \"http://www.ama-assn.org/go/cpt\"\n",
      "                  }\n",
      "               ]\n",
      "            },\n",
      "            \"context\": {\n",
      "               \"reference\": \"urn:uuid:fa2c897f-0bf3-11ea-a089-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"executionPeriod\": {\n",
      "               \"end\": \"2017-06-11\",\n",
      "               \"start\": \"2017-06-11\"\n",
      "            },\n",
      "            \"for\": {\n",
      "               \"reference\": \"urn:uuid:fa2cd76e-0bf3-11ea-a780-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"identifier\": [\n",
      "               {\n",
      "                  \"system\": \"http://www.acme.org/tasks\",\n",
      "                  \"value\": \"19009\"\n",
      "               }\n",
      "            ],\n",
      "            \"intent\": \"plan\",\n",
      "            \"owner\": {\n",
      "               \"reference\": \"urn:uuid:fa2cfe62-0bf3-11ea-ac6e-4ccc6a181ed3\"\n",
      "            },\n",
      "            \"priority\": \"routine\",\n",
      "            \"status\": \"completed\",\n",
      "            \"resourceType\": \"Task\"\n",
      "         }\n",
      "      }\n",
      "   ],\n",
      "   \"type\": \"transaction\",\n",
      "   \"resourceType\": \"Bundle\"\n",
      "}\n"
     ]
    }
   ],
   "source": [
    "b.entry = []\n",
    "ref_map = {}\n",
    "for i in files:\n",
    "    r =open_file(i)\n",
    "    # remove text adn id elements from Bundle\n",
    "    r.pop('text', None) # remove text elements from Bundle\n",
    "    old_id = r.pop('id',None) # remove text elements from Bundle\n",
    "    new_urn = uuid.uuid1().urn # new urn for resource\n",
    "    ref_map[new_urn] = f'{r[\"resourceType\"]}/{old_id}'\n",
    "    # print( id_map , '\\n')\n",
    "    e = B.BundleEntry(dict\n",
    "        (\n",
    "        resource = r,\n",
    "        fullUrl = new_urn,\n",
    "        )\n",
    "      )\n",
    "    if bundle_type in ['transaction', 'batch']:\n",
    "        e.request = B.BundleEntryRequest(dict\n",
    "                    (\n",
    "                    method = 'POST',\n",
    "                    url = r['resourceType']\n",
    "                    )\n",
    "                    )\n",
    "    \n",
    "    b.entry.append(e)\n",
    "\n",
    "b_json = dumps(b.as_json(),indent =3)\n",
    "# print(b_json)\n",
    "for new_ref, old_ref in ref_map.items():\n",
    "    b_json = b_json.replace(old_ref,new_ref)\n",
    "print(b_json)    \n",
    "write_file(b_json)"
   ]
  }
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