examples/fhirBundle.ipynb

{
 "cells": [
  {
   "cell_type": "code",
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   "outputs": [],
   "source": [
    "# First"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
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     "text": [
      "{'resourceType': 'Bundle', 'id': '0f2b637d-20e6-4fdf-8407-6932c0646553', 'meta': {'lastUpdated': '2023-09-09T16:17:01.064+00:00'}, 'type': 'searchset', 'link': [{'relation': 'self', 'url': 'https://hapi.fhir.org/baseR4/Observation?_count=15&_pretty=true'}, {'relation': 'next', 'url': 'https://hapi.fhir.org/baseR4?_getpages=0f2b637d-20e6-4fdf-8407-6932c0646553&_getpagesoffset=15&_count=15&_pretty=true&_bundletype=searchset'}], 'entry': [{'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553960', 'resource': {'resourceType': 'Observation', 'id': '9553960', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'vital-signs', 'display': 'vital-signs'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '8302-2', 'display': 'Body Height'}], 'text': 'Body Height'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 165.7289413395679, 'unit': 'cm', 'system': 'http://unitsofmeasure.org', 'code': 'cm'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553961', 'resource': {'resourceType': 'Observation', 'id': '9553961', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'vital-signs', 'display': 'vital-signs'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '72514-3', 'display': 'Pain severity - 0-10 verbal numeric rating [Score] - Reported'}], 'text': 'Pain severity - 0-10 verbal numeric rating [Score] - Reported'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 1.132947772785426, 'unit': '{score}', 'system': 'http://unitsofmeasure.org', 'code': '{score}'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553962', 'resource': {'resourceType': 'Observation', 'id': '9553962', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'vital-signs', 'display': 'vital-signs'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '29463-7', 'display': 'Body Weight'}], 'text': 'Body Weight'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 76.60651584729521, 'unit': 'kg', 'system': 'http://unitsofmeasure.org', 'code': 'kg'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553963', 'resource': {'resourceType': 'Observation', 'id': '9553963', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'vital-signs', 'display': 'vital-signs'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '39156-5', 'display': 'Body Mass Index'}], 'text': 'Body Mass Index'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 27.891315497482815, 'unit': 'kg/m2', 'system': 'http://unitsofmeasure.org', 'code': 'kg/m2'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553964', 'resource': {'resourceType': 'Observation', 'id': '9553964', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'vital-signs', 'display': 'vital-signs'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '55284-4', 'display': 'Blood Pressure'}], 'text': 'Blood Pressure'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'component': [{'code': {'coding': [{'system': 'http://loinc.org', 'code': '8462-4', 'display': 'Diastolic Blood Pressure'}], 'text': 'Diastolic Blood Pressure'}, 'valueQuantity': {'value': 78.43492956103366, 'unit': 'mm[Hg]', 'system': 'http://unitsofmeasure.org', 'code': 'mm[Hg]'}}, {'code': {'coding': [{'system': 'http://loinc.org', 'code': '8480-6', 'display': 'Systolic Blood Pressure'}], 'text': 'Systolic Blood Pressure'}, 'valueQuantity': {'value': 100.41383500314066, 'unit': 'mm[Hg]', 'system': 'http://unitsofmeasure.org', 'code': 'mm[Hg]'}}]}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553965', 'resource': {'resourceType': 'Observation', 'id': '9553965', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '6690-2', 'display': 'Leukocytes [#/volume] in Blood by Automated count'}], 'text': 'Leukocytes [#/volume] in Blood by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 8.203273494862886, 'unit': '10*3/uL', 'system': 'http://unitsofmeasure.org', 'code': '10*3/uL'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553966', 'resource': {'resourceType': 'Observation', 'id': '9553966', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '789-8', 'display': 'Erythrocytes [#/volume] in Blood by Automated count'}], 'text': 'Erythrocytes [#/volume] in Blood by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 4.870496961407079, 'unit': '10*6/uL', 'system': 'http://unitsofmeasure.org', 'code': '10*6/uL'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553967', 'resource': {'resourceType': 'Observation', 'id': '9553967', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '718-7', 'display': 'Hemoglobin [Mass/volume] in Blood'}], 'text': 'Hemoglobin [Mass/volume] in Blood'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 15.19524152962212, 'unit': 'g/dL', 'system': 'http://unitsofmeasure.org', 'code': 'g/dL'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553968', 'resource': {'resourceType': 'Observation', 'id': '9553968', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '4544-3', 'display': 'Hematocrit [Volume Fraction] of Blood by Automated count'}], 'text': 'Hematocrit [Volume Fraction] of Blood by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 37.52002767252242, 'unit': '%', 'system': 'http://unitsofmeasure.org', 'code': '%'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553969', 'resource': {'resourceType': 'Observation', 'id': '9553969', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '787-2', 'display': 'MCV [Entitic volume] by Automated count'}], 'text': 'MCV [Entitic volume] by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 82.94408602122716, 'unit': 'fL', 'system': 'http://unitsofmeasure.org', 'code': 'fL'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553970', 'resource': {'resourceType': 'Observation', 'id': '9553970', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '785-6', 'display': 'MCH [Entitic mass] by Automated count'}], 'text': 'MCH [Entitic mass] by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 29.228471567998135, 'unit': 'pg', 'system': 'http://unitsofmeasure.org', 'code': 'pg'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553971', 'resource': {'resourceType': 'Observation', 'id': '9553971', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '786-4', 'display': 'MCHC [Mass/volume] by Automated count'}], 'text': 'MCHC [Mass/volume] by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 35.00537608262707, 'unit': 'g/dL', 'system': 'http://unitsofmeasure.org', 'code': 'g/dL'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553972', 'resource': {'resourceType': 'Observation', 'id': '9553972', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '21000-5', 'display': 'Erythrocyte distribution width [Entitic volume] by Automated count'}], 'text': 'Erythrocyte distribution width [Entitic volume] by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 42.49971033081575, 'unit': 'fL', 'system': 'http://unitsofmeasure.org', 'code': 'fL'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553973', 'resource': {'resourceType': 'Observation', 'id': '9553973', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '777-3', 'display': 'Platelets [#/volume] in Blood by Automated count'}], 'text': 'Platelets [#/volume] in Blood by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 333.60492944186444, 'unit': '10*3/uL', 'system': 'http://unitsofmeasure.org', 'code': '10*3/uL'}}, 'search': {'mode': 'match'}}, {'fullUrl': 'https://hapi.fhir.org/baseR4/Observation/9553974', 'resource': {'resourceType': 'Observation', 'id': '9553974', 'meta': {'versionId': '1', 'lastUpdated': '2023-04-11T05:33:43.752+00:00', 'source': '#TT52YEu7rBkKmFsg'}, 'status': 'final', 'category': [{'coding': [{'system': 'http://terminology.hl7.org/CodeSystem/observation-category', 'code': 'laboratory', 'display': 'laboratory'}]}], 'code': {'coding': [{'system': 'http://loinc.org', 'code': '32207-3', 'display': 'Platelet distribution width [Entitic volume] in Blood by Automated count'}], 'text': 'Platelet distribution width [Entitic volume] in Blood by Automated count'}, 'subject': {'reference': 'Patient/9553888'}, 'encounter': {'reference': 'Encounter/9553959'}, 'effectiveDateTime': '2012-06-12T14:53:27-04:00', 'issued': '2012-06-12T14:53:27.591-04:00', 'valueQuantity': {'value': 426.5982734290056, 'unit': 'fL', 'system': 'http://unitsofmeasure.org', 'code': 'fL'}}, 'search': {'mode': 'match'}}]}\n"
     ]
    }
   ],
   "source": [
    "from medprompt import MedPrompter, get_time_diff_from_today\n",
    "import json\n",
    "import os\n",
    "bundle_path = os.path.join(os.getcwd(), 'observation_bundle.json')\n",
    "prompt = MedPrompter()\n",
    "prompt.set_template(template_path=\"../src/medprompt/templates/\",\n",
    "                    template_name=\"observation_v1.jinja\")\n",
    "with open (bundle_path) as f:\n",
    "    data = json.load(f)\n",
    "    print(data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The Body Height before 4105 days was 165.7289413395679 cm. The Pain severity - 0-10 verbal numeric rating [Score] - Reported before 4105 days was 1.132947772785426 {score}. The Body Weight before 4105 days was 76.60651584729521 kg. The Body Mass Index before 4105 days was 27.891315497482815 kg/m2. The Blood Pressure before 4105 days was. The Leukocytes [#/volume] in Blood by Automated count before 4105 days was 8.203273494862886 10*3/uL. The Erythrocytes [#/volume] in Blood by Automated count before 4105 days was 4.870496961407079 10*6/uL. The Hemoglobin [Mass/volume] in Blood before 4105 days was 15.19524152962212 g/dL. The Hematocrit [Volume Fraction] of Blood by Automated count before 4105 days was 37.52002767252242 %. The MCV [Entitic volume] by Automated count before 4105 days was 82.94408602122716 fL. The MCH [Entitic mass] by Automated count before 4105 days was 29.228471567998135 pg. The MCHC [Mass/volume] by Automated count before 4105 days was 35.00537608262707 g/dL. The Erythrocyte distribution width [Entitic volume] by Automated count before 4105 days was 42.49971033081575 fL. The Platelets [#/volume] in Blood by Automated count before 4105 days was 333.60492944186444 10*3/uL. The Platelet distribution width [Entitic volume] in Blood by Automated count before 4105 days was 426.5982734290056 fL. "
     ]
    }
   ],
   "source": [
    "for entry in data['entry']:\n",
    "    input_object = entry['resource']\n",
    "    input_object[\"time_diff\"] = get_time_diff_from_today\n",
    "    output = prompt.generate_prompt(input_object).replace(\"\\n\", \" \")\n",
    "    print(output, end=\". \")\n"
   ]
  }
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