{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "PosixPath('/Users/ehaas/Documents/FHIR/davinci-ecdx/CDEX-Signatures/in_files/test_bundle.json')"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from json import loads, dumps, dump\n",
    "from pathlib import Path\n",
    "from jcs import canonicalize\n",
    "from yaml import dump as dumpy\n",
    "from IPython.display import display, Markdown\n",
    "\n",
    "out_file = 'canonical-fhir-document.json'\n",
    "in_file = '/Users/ehaas/Documents/FHIR/davinci-ecdx/CDEX-Signatures/in_files/test_bundle.json'\n",
    "path = Path() / in_file\n",
    "path"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Get Document"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'resourceType': 'Bundle',\n",
       " 'id': '12521',\n",
       " 'meta': {'versionId': '1', 'lastUpdated': '2022-02-15T15:53:19.296Z'},\n",
       " 'identifier': {'system': 'urn:ietf:rfc:3986',\n",
       "  'value': 'urn:uuid:0c3151bd-1cbf-4d64-b04d-cd9187a4c6e0'},\n",
       " 'type': 'document',\n",
       " 'timestamp': '2013-05-28T22:12:21Z',\n",
       " 'entry': [{'fullUrl': 'urn:uuid:541a72a8-df75-4484-ac89-ac4923f03b81',\n",
       "   'resource': {'resourceType': 'Observation',\n",
       "    'referenceRange': [{'text': 'this is my markdown file line 1 \\nstill line 1  \\nline2\\n\\nline3\\n- bullet 1 \\n- bullet 1.\\n\\n    code \"block\"\\n'}],\n",
       "    'meta': {'lastUpdated': '2013-05-05T16:13:03Z'},\n",
       "    'text': {'status': 'additional',\n",
       "     'div': '<div xmlns=\"http://www.w3.org/1999/xhtml\"> Acute Asthmatic attack. Was wheezing\\n\\n\\n\\n                        for days prior to admission. </div>'},\n",
       "    'status': 'final',\n",
       "    'code': {'coding': [{'system': 'http://loinc.org', 'code': '46241-6'}],\n",
       "     'text': 'Reason for admission'},\n",
       "    'subject': {'reference': 'urn:uuid:d546d85-2487-4ae5-a7b2-f7fa79811120',\n",
       "     'display': 'Eve Everywoman'},\n",
       "    'encounter': {'reference': 'urn:uuid:a16719d5-5267-4f69-913a-f29e4b800a14'}}}]}"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "my_dict = loads(path.read_text())\n",
    "my_dict"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### pop sig, id, meta if there"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'resourceType': 'Bundle',\n",
       " 'identifier': {'system': 'urn:ietf:rfc:3986',\n",
       "  'value': 'urn:uuid:0c3151bd-1cbf-4d64-b04d-cd9187a4c6e0'},\n",
       " 'type': 'document',\n",
       " 'timestamp': '2013-05-28T22:12:21Z',\n",
       " 'entry': [{'fullUrl': 'urn:uuid:541a72a8-df75-4484-ac89-ac4923f03b81',\n",
       "   'resource': {'resourceType': 'Observation',\n",
       "    'referenceRange': [{'text': 'this is my markdown file line 1 \\nstill line 1  \\nline2\\n\\nline3\\n- bullet 1 \\n- bullet 1.\\n\\n    code \"block\"\\n'}],\n",
       "    'meta': {'lastUpdated': '2013-05-05T16:13:03Z'},\n",
       "    'text': {'status': 'additional',\n",
       "     'div': '<div xmlns=\"http://www.w3.org/1999/xhtml\"> Acute Asthmatic attack. Was wheezing\\n\\n\\n\\n                        for days prior to admission. </div>'},\n",
       "    'status': 'final',\n",
       "    'code': {'coding': [{'system': 'http://loinc.org', 'code': '46241-6'}],\n",
       "     'text': 'Reason for admission'},\n",
       "    'subject': {'reference': 'urn:uuid:d546d85-2487-4ae5-a7b2-f7fa79811120',\n",
       "     'display': 'Eve Everywoman'},\n",
       "    'encounter': {'reference': 'urn:uuid:a16719d5-5267-4f69-913a-f29e4b800a14'}}}]}"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "try:\n",
    "    my_dict.pop(\"signature\")\n",
    "except KeyError:\n",
    "    pass\n",
    "\n",
    "# http://hl7.org/fhir/canonicalization/json  keep all\n",
    "# for http://hl7.org/fhir/canonicalization/json#static pop id meta and text elements first\n",
    "# my_dict.pop(\"text\") recursively\n",
    "\n",
    "# for http://hl7.org/fhir/canonicalization/json#document pop Bundle.id Bundle.meta elements first\n",
    "try:\n",
    "    my_dict.pop(\"id\")\n",
    "except KeyError:\n",
    "    pass\n",
    "try:\n",
    "    my_dict.pop(\"meta\")\n",
    "except KeyError:\n",
    "    pass\n",
    "\n",
    "my_dict"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### sort and remove white space"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "this is my markdown file line 1 \n",
       "still line 1  \n",
       "line2\n",
       "\n",
       "line3\n",
       "- bullet 1 \n",
       "- bullet 1.\n",
       "\n",
       "    code \"block\"\n"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "display(Markdown(my_dict['entry'][0]['resource']['referenceRange'][0]['text']))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "b'{\"entry\":[{\"fullUrl\":\"urn:uuid:541a72a8-df75-4484-ac89-ac4923f03b81\",\"resource\":{\"code\":{\"coding\":[{\"code\":\"46241-6\",\"system\":\"http://loinc.org\"}],\"text\":\"Reason for admission\"},\"encounter\":{\"reference\":\"urn:uuid:a16719d5-5267-4f69-913a-f29e4b800a14\"},\"meta\":{\"lastUpdated\":\"2013-05-05T16:13:03Z\"},\"referenceRange\":[{\"text\":\"this is my markdown file line 1 \\\\nstill line 1  \\\\nline2\\\\n\\\\nline3\\\\n- bullet 1 \\\\n- bullet 1.\\\\n\\\\n    code \\\\\"block\\\\\"\\\\n\"}],\"resourceType\":\"Observation\",\"status\":\"final\",\"subject\":{\"display\":\"Eve Everywoman\",\"reference\":\"urn:uuid:d546d85-2487-4ae5-a7b2-f7fa79811120\"},\"text\":{\"div\":\"<div xmlns=\\\\\"http://www.w3.org/1999/xhtml\\\\\"> Acute Asthmatic attack. Was wheezing\\\\n\\\\n\\\\n\\\\n                        for days prior to admission. </div>\",\"status\":\"additional\"}}}],\"identifier\":{\"system\":\"urn:ietf:rfc:3986\",\"value\":\"urn:uuid:0c3151bd-1cbf-4d64-b04d-cd9187a4c6e0\"},\"resourceType\":\"Bundle\",\"timestamp\":\"2013-05-28T22:12:21Z\",\"type\":\"document\"}'"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "canon_json = canonicalize(my_dict)\n",
    "canon_json"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Write to file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "955"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "\n",
    "out_path = Path() / out_file\n",
    "out_path.write_bytes(canon_json)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'entry': [{'fullUrl': 'urn:uuid:541a72a8-df75-4484-ac89-ac4923f03b81',\n",
       "   'resource': {'code': {'coding': [{'code': '46241-6',\n",
       "       'system': 'http://loinc.org'}],\n",
       "     'text': 'Reason for admission'},\n",
       "    'encounter': {'reference': 'urn:uuid:a16719d5-5267-4f69-913a-f29e4b800a14'},\n",
       "    'meta': {'lastUpdated': '2013-05-05T16:13:03Z'},\n",
       "    'referenceRange': [{'text': 'this is my markdown file line 1 \\nstill line 1  \\nline2\\n\\nline3\\n- bullet 1 \\n- bullet 1.\\n\\n    code \"block\"\\n'}],\n",
       "    'resourceType': 'Observation',\n",
       "    'status': 'final',\n",
       "    'subject': {'display': 'Eve Everywoman',\n",
       "     'reference': 'urn:uuid:d546d85-2487-4ae5-a7b2-f7fa79811120'},\n",
       "    'text': {'div': '<div xmlns=\"http://www.w3.org/1999/xhtml\"> Acute Asthmatic attack. Was wheezing\\n\\n\\n\\n                        for days prior to admission. </div>',\n",
       "     'status': 'additional'}}}],\n",
       " 'identifier': {'system': 'urn:ietf:rfc:3986',\n",
       "  'value': 'urn:uuid:0c3151bd-1cbf-4d64-b04d-cd9187a4c6e0'},\n",
       " 'resourceType': 'Bundle',\n",
       " 'timestamp': '2013-05-28T22:12:21Z',\n",
       " 'type': 'document'}"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "json_string = canon_json.decode('utf-8')\n",
    "data = loads(json_string)\n",
    "data\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\"> Acute Asthmatic attack. Was wheezing\\n\\n\\n\\n                        for days prior to admission. </div>\"\n"
     ]
    }
   ],
   "source": [
    "print(dumps(data['entry'][0]['resource']['text']['div'],indent=2))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "this is my markdown file line 1 \n",
       "still line 1  \n",
       "line2\n",
       "\n",
       "line3\n",
       "- bullet 1 \n",
       "- bullet 1.\n",
       "\n",
       "    code \"block\"\n"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "display(Markdown(data['entry'][0]['resource']['referenceRange'][0]['text']))"
   ]
  }
 ],
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  "kernelspec": {
   "display_name": "fhir_builds",
   "language": "python",
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
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   "file_extension": ".py",
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