add-add'l-reference-subject.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# add addl optional references to subject in SD\n",
    "\n",
    "1. get list of SD that have subject element\n",
    "2. read SD from resources-yaml folder\n",
    "\n",
    "   1. add ms extension to Patient reference of subject element\n",
    "   2. find other reference types from base\n",
    "   3. add to Subject element in profile\n",
    "   4. save as yaml (sort keys)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 49,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('2023-11-03',\n",
       " PosixPath('/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml'),\n",
       " PosixPath('/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml-copy'))"
      ]
     },
     "execution_count": 49,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from yaml import load as yload, dump as ydump, Loader\n",
    "from json import loads, dumps\n",
    "from pathlib import Path\n",
    "from copy import deepcopy\n",
    "from datetime import datetime\n",
    "from fhir.resources.structuredefinition import StructureDefinition\n",
    "from pprint import pprint\n",
    "\n",
    "# my_path = r'/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input'\n",
    "my_path = r'/Users/ehaas/Documents/FHIR/US-Core/input'\n",
    "in_path = Path(my_path) / 'resources-yaml'\n",
    "out_path = Path(my_path) / 'resources-yaml-copy'\n",
    "out_path.mkdir(parents=True, exist_ok=True)\n",
    "#create out_path using pathlib Path.mkdir(parents=True, exist_ok=True)\n",
    "\n",
    "R4_path = Path(r'/Users/ehaas/.fhir/packages/hl7.fhir.r4.core#4.0.1/package')\n",
    "\n",
    "Types = ['CarePlan',\n",
    "'CareTeam',\n",
    "'Condition',\n",
    "'DiagnosticReport',\n",
    "'DocumentReference',\n",
    "'Encounter',\n",
    "'Goal',\n",
    "'MedicationDispense',\n",
    "'MedicationRequest',\n",
    "'Observation',\n",
    "'Observation',\n",
    "'Procedure',\n",
    "'QuestionnaireResponse',\n",
    "'ServiceRequest',\n",
    "'Specimen',\n",
    "]\n",
    "\n",
    "_targetProfile = [\n",
    "        {\n",
    "        \"extension\": [\n",
    "            {\n",
    "                \"url\": \"http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support\",\n",
    "                \"valueBoolean\": True\n",
    "            }\n",
    "            ]\n",
    "        },\n",
    "    ]\n",
    "\n",
    "today = datetime.today().strftime('%Y-%m-%d')\n",
    "today, in_path, out_path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 50,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-sex.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-specimen.yml***********\n",
      "☞ ☞ ☞ Type = Specimen\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Substance', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Specimen.subject', 'path': 'Specimen.subject', \"\n",
      " \"'short': 'The patient where the specimen came from.', 'type': [{'code': \"\n",
      " \"'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Substance', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-observation-pregnancystatus.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-observation-occupation.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-observation-sexual-orientation.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'Observation.subject'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-birthsex.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-care-experience-preference.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-careplan.yml***********\n",
      "☞ ☞ ☞ Type = CarePlan\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'CarePlan.subject', 'path': 'CarePlan.subject', \"\n",
      " \"'definition': 'Who care plan is for.', 'requirements': 'Identifies the \"\n",
      " \"patient or group whose intended care is described by the plan.', 'type': \"\n",
      " \"[{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'CarePlan.subject'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-diagnosticreport-note.yml***********\n",
      "☞ ☞ ☞ Type = DiagnosticReport\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'DiagnosticReport.subject', 'path': \"\n",
      " \"'DiagnosticReport.subject', 'min': 1, 'type': [{'code': 'Reference', \"\n",
      " \"'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-provenance.yml***********\n",
      "☞ ☞ ☞ Type = Provenance\n",
      "❗❗❗Type Provenance not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-blood-pressure.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-condition-encounter-diagnosis.yml***********\n",
      "☞ ☞ ☞ Type = Condition\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Condition.subject', 'path': 'Condition.subject', \"\n",
      " \"'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'Condition.patient'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-heart-rate.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-medication.yml***********\n",
      "☞ ☞ ☞ Type = Medication\n",
      "❗❗❗Type Medication not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-coverage.yml***********\n",
      "☞ ☞ ☞ Type = Coverage\n",
      "❗❗❗Type Coverage not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-pediatric-weight-for-height.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-questionnaireresponse.yml***********\n",
      "☞ ☞ ☞ Type = QuestionnaireResponse\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Resource']\n",
      "(\"☞ ☞ ☞ subject = {'id': 'QuestionnaireResponse.subject', 'path': \"\n",
      " \"'QuestionnaireResponse.subject', 'comment': '-', 'min': 1, 'type': [{'code': \"\n",
      " \"'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Resource'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-treatment-intervention-preference.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-implantable-device.yml***********\n",
      "☞ ☞ ☞ Type = Device\n",
      "❗❗❗Type Device not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-head-occipital-frontal-circumference-percentile.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-direct.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-location.yml***********\n",
      "☞ ☞ ☞ Type = Location\n",
      "❗❗❗Type Location not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-head-circumference.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-pulse-oximetry.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-servicerequest.yml***********\n",
      "☞ ☞ ☞ Type = ServiceRequest\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Location', 'http://hl7.org/fhir/StructureDefinition/Device']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'ServiceRequest.subject', 'path': \"\n",
      " \"'ServiceRequest.subject', 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-medication-adherence.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-bmi.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-immunization.yml***********\n",
      "☞ ☞ ☞ Type = Immunization\n",
      "❗❗❗Type Immunization not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-practitionerrole.yml***********\n",
      "☞ ☞ ☞ Type = PractitionerRole\n",
      "❗❗❗Type PractitionerRole not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-patient.yml***********\n",
      "☞ ☞ ☞ Type = Patient\n",
      "❗❗❗Type Patient not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-tribal-affiliation.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-race.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-allergyintolerance.yml***********\n",
      "☞ ☞ ☞ Type = AllergyIntolerance\n",
      "❗❗❗Type AllergyIntolerance not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-organization.yml***********\n",
      "☞ ☞ ☞ Type = Organization\n",
      "❗❗❗Type Organization not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-uscdi-requirements.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-medicationrequest.yml***********\n",
      "☞ ☞ ☞ Type = MedicationRequest\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'MedicationRequest.subject', 'path': \"\n",
      " \"'MedicationRequest.subject', 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'MedicationOrder.patient'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-ethnicity.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-average-blood-pressure.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-vital-signs.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-simple-observation.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-observation-lab.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-medicationdispense.yml***********\n",
      "☞ ☞ ☞ Type = MedicationDispense\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'MedicationDispense.subject', 'path': \"\n",
      " \"'MedicationDispense.subject', 'min': 1, 'type': [{'code': 'Reference', \"\n",
      " \"'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-careteam.yml***********\n",
      "☞ ☞ ☞ Type = CareTeam\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'CareTeam.subject', 'path': 'CareTeam.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'CarePlan.subject'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-genderidentity.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-procedure.yml***********\n",
      "☞ ☞ ☞ Type = Procedure\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Procedure.subject', 'path': 'Procedure.subject', \"\n",
      " \"'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'Procedure.subject'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-documentreference.yml***********\n",
      "☞ ☞ ☞ Type = DocumentReference\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Practitioner', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'DocumentReference.subject', 'path': \"\n",
      " \"'DocumentReference.subject', 'min': 1, 'type': [{'code': 'Reference', \"\n",
      " \"'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Practitioner', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-jurisdiction.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-observation-clinical-result.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-body-height.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-encounter.yml***********\n",
      "☞ ☞ ☞ Type = Encounter\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Encounter.subject', 'path': 'Encounter.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-body-temperature.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-smokingstatus.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'Observation.subject'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-body-weight.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-respiratory-rate.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-diagnosticreport-lab.yml***********\n",
      "☞ ☞ ☞ Type = DiagnosticReport\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'DiagnosticReport.subject', 'path': \"\n",
      " \"'DiagnosticReport.subject', 'min': 1, 'type': [{'code': 'Reference', \"\n",
      " \"'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-extension-questionnaire-uri.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "❗❗❗Type Extension not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-observation-pregnancyintent.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-relatedperson.yml***********\n",
      "☞ ☞ ☞ Type = RelatedPerson\n",
      "❗❗❗Type RelatedPerson not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-condition-problems-health-concerns.yml***********\n",
      "☞ ☞ ☞ Type = Condition\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Condition.subject', 'path': 'Condition.subject', \"\n",
      " \"'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'Condition.patient'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-goal.yml***********\n",
      "☞ ☞ ☞ Type = Goal\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Organization']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Goal.subject', 'path': 'Goal.subject', 'type': \"\n",
      " \"[{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Organization'], '_targetProfile': \"\n",
      " \"[{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True, 'mapping': [{'identity': \"\n",
      " \"'argonaut-dq-dstu2', 'map': 'Goal.subject'}]}\")\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-practitioner.yml***********\n",
      "☞ ☞ ☞ Type = Practitioner\n",
      "❗❗❗Type Practitioner not in Types\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-pediatric-bmi-for-age.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "❗❗❗No subject element\n",
      "***********/Users/ehaas/Documents/FHIR/US-Core/input/resources-yaml/StructureDefinition-us-core-observation-screening-assessment.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ subject ref types = ['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient']\n",
      "☞ ☞ ☞ subject R4 types = ['http://hl7.org/fhir/StructureDefinition/Patient', 'http://hl7.org/fhir/StructureDefinition/Group', 'http://hl7.org/fhir/StructureDefinition/Device', 'http://hl7.org/fhir/StructureDefinition/Location']\n",
      "❗❗❗target_Profile http://hl7.org/fhir/StructureDefinition/Patient is Patient\n",
      "(\"☞ ☞ ☞ subject = {'id': 'Observation.subject', 'path': 'Observation.subject', \"\n",
      " \"'min': 1, 'type': [{'code': 'Reference', 'targetProfile': \"\n",
      " \"['http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Group', \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/Device', \"\n",
      " \"'http://hl7.org/fhir/us/core/StructureDefinition/us-core-location'], \"\n",
      " \"'_targetProfile': [{'extension': [{'url': \"\n",
      " \"'http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support', \"\n",
      " \"'valueBoolean': True}]}]}], 'mustSupport': True}\")\n"
     ]
    }
   ],
   "source": [
    "def get_targetProfile(r_type, element_path):\n",
    "    for sd_base in R4_path.glob(f'StructureDefinition*-{r_type}.json'):\n",
    "        try:\n",
    "            r_base = loads(sd_base.read_text())\n",
    "        except Exception as e:\n",
    "            print(\"Exception: {}\".format(type(e).__name__))\n",
    "            print(\"Exception message: {}\".format(e))\n",
    "        # print(f\"======{sd_base}, {r_base['type']}======\")\n",
    "        for element in r_base['differential']['element']:\n",
    "            if element['path'] == element_path:\n",
    "                return element[\"type\"][0][\"targetProfile\"]\n",
    "                              \n",
    "        # print(f'❗❗❗element not found in base SD - look at the datatype in the path {element_path}')\n",
    "        # #use the penultimate element in element_path to find the datatype in the base SD\n",
    "        # parent_element_path = element_path.rsplit('.', 1)[0]\n",
    "        # #use the last two element in element_path to find the datatype element in the base SD\n",
    "        # datatype_element_path = element_path.split('.', )[-1]\n",
    "\n",
    "        # print(f\"parent_element_path = {parent_element_path} datatype_element_path = {datatype_element_path}\")\n",
    "\n",
    "        # #get the datatype\n",
    "        # for element in r_base['differential']['element']:\n",
    "        #     if element['id'] == parent_element_path:\n",
    "        #         for type in element['type']:\n",
    "        #             print(f\"datatype = {type['code']}\")\n",
    "        #             #get the datatype SD short and compare to the shorty\n",
    "        #             path = f\"{type['code']}.{datatype_element_path}\"\n",
    "        #             print(f\"type = {type['code']}, path = {path}\")\n",
    "        #             return get_shorty(type['code'], (f\"{type['code']}.{datatype_element_path}\"),)\n",
    "\n",
    "target_list = []\n",
    "# read StructureDefinitions from resources-yaml folder using pathlib\n",
    "for sd in in_path.glob('Struct*.yml'):\n",
    "    print(f\"***********{sd}***********\")\n",
    "    r = yload(sd.read_text(), Loader=Loader)\n",
    "    r_copy = deepcopy(r)\n",
    "    print(f\"☞ ☞ ☞ Type = {r['type']}\")\n",
    "    if r['type'] not in Types:\n",
    "        print(f\"❗❗❗Type {r['type']} not in Types\")\n",
    "        continue\n",
    "    try:\n",
    "        subject = (element for element in r['differential']['element']\n",
    "                        if element['path'].split('.')[-1] == 'subject').__next__()\n",
    "        print(f'☞ ☞ ☞ subject ref types = {subject[\"type\"][0][\"targetProfile\"]}')\n",
    "        R4_targetProfile = get_targetProfile(r_type=r['type'], element_path=subject['path'])\n",
    "        print(f'☞ ☞ ☞ subject R4 types = {R4_targetProfile}')\n",
    "        for target_Profile in R4_targetProfile:\n",
    "            if target_Profile == 'http://hl7.org/fhir/StructureDefinition/Patient':\n",
    "                print(f\"❗❗❗target_Profile {target_Profile} is Patient\")\n",
    "                continue\n",
    "            if target_Profile == 'http://hl7.org/fhir/StructureDefinition/Location':\n",
    "                subject[\"type\"][0][\"targetProfile\"].append('http://hl7.org/fhir/us/core/StructureDefinition/us-core-location')\n",
    "                continue\n",
    "            subject[\"type\"][0][\"targetProfile\"].append(target_Profile)\n",
    "        subject[\"type\"][0][\"_targetProfile\"] = _targetProfile  \n",
    "        target_list = target_list  + (R4_targetProfile)\n",
    "\n",
    "    except StopIteration:\n",
    "        print(f\"❗❗❗No subject element\")\n",
    "        continue\n",
    "    pprint(f\"☞ ☞ ☞ subject = {subject}\")\n",
    "    # custom sort the keys in the elements using fhir.resources\n",
    "    r = StructureDefinition.parse_obj(r)\n",
    "    # print(r.json(indent=4))\n",
    "        # save the copy to out_path using Pathlib\n",
    "    copyfile = out_path / sd.name\n",
    "    copyfile.write_text(r.yaml(indent=2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash -s \"$in_path\" \"$out_path\"\n",
    "##### DO THIS ONLY when you want to overwrite resources-yaml folder with resources-yaml-copy ####\n",
    "\n",
    "cp $2/Struct*.yml $1"
   ]
  }
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