add-add'l-USCDI-extensions.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# add addl USCDI element extensions and tags to SD\n",
    "\n",
    "1. get list of data elements that are add'l USCDI\n",
    "2. read SD from resources-yaml folder\n",
    "3. create a copy\n",
    "4. find elements based on the addl USCDI elements list\n",
    "   1. add USCDI extension\n",
    "   2. add add'l USCDI tag ( in unicode ) to short\n",
    "      1. if short does not exist, add short from base resource - todo - not needed for this set\n",
    "   3. sort keys in element\n",
    "   4. save copy "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "('2023-10-20',\n",
       " PosixPath('/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml'),\n",
       " PosixPath('/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml-copy'))"
      ]
     },
     "execution_count": 9,
     "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",
    "\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",
    "today = datetime.today().strftime('%Y-%m-%d')\n",
    "today, in_path, out_path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['Patient.telecom',\n",
       " 'Patient.communication',\n",
       " 'Patient.extension:race',\n",
       " 'Patient.extension:ethnicity',\n",
       " 'Patient.extension:tribalAffiliation',\n",
       " 'Patient.extension:sex',\n",
       " 'Patient.extension:genderIdentity',\n",
       " 'Patient.deceased[x]',\n",
       " 'Patient.address.use',\n",
       " 'Patient.address.period',\n",
       " 'Patient.name.use',\n",
       " 'Patient.name.period',\n",
       " 'Patient.name.suffix',\n",
       " 'ServiceRequest.reasonCode',\n",
       " 'ServiceRequest.reasonReference',\n",
       " 'Procedure.reasonCode',\n",
       " 'Procedure.reasonReference',\n",
       " 'MedicationRequest.reasonCode',\n",
       " 'MedicationRequest.reasonReference',\n",
       " 'MedicationRequest.extension:medicationAdherence',\n",
       " 'Procedure.basedOn',\n",
       " 'DocumentReference.category:uscore',\n",
       " 'Observation.derivedFrom',\n",
       " 'Specimen.collection',\n",
       " 'Specimen.collection.bodySite',\n",
       " 'Specimen.condition']"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# get csv file of add'l uscdi elements using pandas\n",
    "import pandas as pd\n",
    "additional_uscdi = Path(my_path) / 'data/additional-uscdi-requirements.csv'\n",
    "df = pd.read_csv(additional_uscdi)\n",
    "\n",
    "#list the FHIR Element column\n",
    "addl_uscdi_elements = df['FHIR Element'].tolist()\n",
    "addl_uscdi_elements = [x.split(' or ') for x in addl_uscdi_elements[1:]]\n",
    "addl_uscdi_elements = [item for sublist in addl_uscdi_elements for item in sublist]\n",
    "# addl_uscdi_elements = list(set(addl_uscdi_elements))\n",
    "addl_uscdi_elements"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-specimen.yml***********\n",
      "☞ ☞ ☞ Type = Specimen\n",
      "☞ ☞ ☞ element 0: Specimen\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Specimen.identifier\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Specimen.type\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Specimen.subject\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 4: Specimen.collection\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 5: Specimen.collection.bodySite\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 6: Specimen.condition\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-care-experience-preference.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ element 0: Observation\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Observation.category:us-core\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Observation.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Observation.derivedFrom\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-treatment-intervention-preference.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ element 0: Observation\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Observation.category:us-core\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Observation.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Observation.derivedFrom\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-location.yml***********\n",
      "☞ ☞ ☞ Type = Location\n",
      "☞ ☞ ☞ element 0: Location\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Location.identifier\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Location.status\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Location.name\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 4: Location.type\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 5: Location.telecom\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 6: Location.address\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 7: Location.address.line\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 8: Location.address.city\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 9: Location.address.state\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 10: Location.address.postalCode\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 11: Location.managingOrganization\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-uscore-medicationstatement.yml***********\n",
      "☞ ☞ ☞ Type = MedicationStatement\n",
      "☞ ☞ ☞ element 0: MedicationStatement\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: MedicationStatement.extension:med-adherence\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: MedicationStatement.basedOn\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: MedicationStatement.status\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 4: MedicationStatement.medication[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 5: MedicationStatement.subject\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 6: MedicationStatement.effective[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 7: MedicationStatement.dateAsserted\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 8: MedicationStatement.informationSource\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 9: MedicationStatement.reasonCode\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 10: MedicationStatement.reasonReference\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 11: MedicationStatement.dosage\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 12: MedicationStatement.dosage.text\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 13: MedicationStatement.dosage.timing\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 14: MedicationStatement.dosage.doseAndRate\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 15: MedicationStatement.dosage.doseAndRate.dose[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-medication-adherence.yml***********\n",
      "☞ ☞ ☞ Type = Extension\n",
      "☞ ☞ ☞ element 0: Extension\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Extension.extension\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Extension.extension:medicationAdherence\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Extension.extension:medicationAdherence.url\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 4: Extension.extension:medicationAdherence.value[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 5: Extension.extension:dateAsserted\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 6: Extension.extension:dateAsserted.url\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 7: Extension.extension:dateAsserted.value[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 8: Extension.extension:informationSource\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 9: Extension.extension:informationSource.url\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 10: Extension.extension:informationSource.value[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 11: Extension.url\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 12: Extension.value[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-patient.yml***********\n",
      "☞ ☞ ☞ Type = Patient\n",
      "☞ ☞ ☞ element 0: Patient\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Patient.extension:race\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Patient.extension:ethnicity\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Patient.extension:tribalAffiliation\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 4: Patient.extension:birthsex\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 5: Patient.extension:sex\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 6: Patient.extension:genderIdentity\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 7: Patient.identifier\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 8: Patient.identifier.system\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 9: Patient.identifier.value\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 10: Patient.name\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 11: Patient.name.use\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗element not found in base SD - look at the datatype in the path Patient.name.use\n",
      "parent_element_path = Patient.name datatype_element_path = use\n",
      "datatype = HumanName\n",
      "type = HumanName, path = HumanName.use\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 12: Patient.name.family\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 13: Patient.name.given\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 14: Patient.name.suffix\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗element not found in base SD - look at the datatype in the path Patient.name.suffix\n",
      "parent_element_path = Patient.name datatype_element_path = suffix\n",
      "datatype = HumanName\n",
      "type = HumanName, path = HumanName.suffix\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 15: Patient.name.period\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗element not found in base SD - look at the datatype in the path Patient.name.period\n",
      "parent_element_path = Patient.name datatype_element_path = period\n",
      "datatype = HumanName\n",
      "type = HumanName, path = HumanName.period\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 16: Patient.telecom\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 17: Patient.telecom.system\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 18: Patient.telecom.value\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 19: Patient.telecom.use\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 20: Patient.gender\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 21: Patient.birthDate\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 22: Patient.deceased[x]\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 23: Patient.address\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 24: Patient.address.use\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗element not found in base SD - look at the datatype in the path Patient.address.use\n",
      "parent_element_path = Patient.address datatype_element_path = use\n",
      "datatype = Address\n",
      "type = Address, path = Address.use\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 25: Patient.address.line\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 26: Patient.address.city\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 27: Patient.address.state\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 28: Patient.address.postalCode\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 29: Patient.address.period\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗element not found in base SD - look at the datatype in the path Patient.address.period\n",
      "parent_element_path = Patient.address datatype_element_path = period\n",
      "datatype = Address\n",
      "type = Address, path = Address.period\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 30: Patient.communication\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 31: Patient.communication.language\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-average-blood-pressure.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ element 0: Observation\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Observation.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Observation.effective[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Observation.component\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 4: Observation.component:systolic\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 5: Observation.component:systolic.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 6: Observation.component:systolic.valueQuantity\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 7: Observation.component:systolic.valueQuantity.value\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 8: Observation.component:systolic.valueQuantity.unit\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 9: Observation.component:systolic.valueQuantity.system\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 10: Observation.component:systolic.valueQuantity.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 11: Observation.component:diastolic\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 12: Observation.component:diastolic.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 13: Observation.component:diastolic.valueQuantity\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 14: Observation.component:diastolic.valueQuantity.value\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 15: Observation.component:diastolic.valueQuantity.unit\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 16: Observation.component:diastolic.valueQuantity.system\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 17: Observation.component:diastolic.valueQuantity.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-observation-lab.yml***********\n",
      "☞ ☞ ☞ Type = Observation\n",
      "☞ ☞ ☞ element 0: Observation.category:us-core\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Observation.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Observation.value[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Observation.interpretation\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 4: Observation.specimen\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 5: Observation.referenceRange\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n",
      "***********/Users/ehaas/Documents/FHIR/USCDI4-Sandbox/input/resources-yaml/StructureDefinition-us-core-procedure.yml***********\n",
      "☞ ☞ ☞ Type = Procedure\n",
      "☞ ☞ ☞ element 0: Procedure\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 1: Procedure.basedOn\n",
      "❗❗❗add the USCDI extension\n",
      "❗❗❗add the short element from the base\n",
      "❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 2: Procedure.status\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 3: Procedure.code\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 4: Procedure.subject\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 5: Procedure.encounter\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "☞ ☞ ☞ element 6: Procedure.performed[x]\n",
      "❗❗❗ done with element\n",
      "----------\n",
      "❗❗❗ done with SD\n",
      "----------------------------------------\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "def get_shorty(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['id'] == element_path:\n",
    "                return element['short']\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",
    "\n",
    "\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",
    "    for i, element in enumerate(r['differential']['element']):\n",
    "        try:\n",
    "            print(f\"☞ ☞ ☞ element {i}: {element['id']}\")\n",
    "            if element['id'] in addl_uscdi_elements:\n",
    "                print('❗❗❗add the USCDI extension')\n",
    "                r_copy['differential']['element'][i][\"extension\"] = [{\n",
    "                    \"url\": \"http://hl7.org/fhir/us/core/StructureDefinition/uscdi-requirement\",\n",
    "                    \"valueBoolean\": True\n",
    "                }]\n",
    "                if 'short' in element.keys():\n",
    "                    shorty = element['short']\n",
    "                else:\n",
    "                    print(\"❗❗❗add the short element from the base\")\n",
    "                    shorty = get_shorty(r['type'], element['path'])\n",
    "\n",
    "                print(\"❗❗❗add the '𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜:' tag to short\")\n",
    "                r_copy['differential']['element'][i][\"short\"] = f\"𝗔𝗗𝗗𝗜𝗧𝗜𝗢𝗡𝗔𝗟 𝗨𝗦𝗖𝗗𝗜: {shorty}\"\n",
    "                \n",
    "            print('❗❗❗ done with element')\n",
    "            print('-'*10)\n",
    "\n",
    "        except Exception as e:\n",
    "            print(\"Exception: {}\".format(type(e).__name__))\n",
    "            print(\"Exception message: {}\".format(e))\n",
    "            print('-'*10)\n",
    "\n",
    "    print('❗❗❗ done with SD')\n",
    "    print('-'*40)\n",
    "    print('\\n')\n",
    "\n",
    "    # custom sort the keys in the elements using fhir.resources\n",
    "    r_copy = StructureDefinition.parse_obj(r_copy)\n",
    "\n",
    "\n",
    "    # save the copy to out_path using Pathlib\n",
    "    copyfile = out_path / sd.name\n",
    "    copyfile.write_text(r_copy.yaml(indent=2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "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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