testing scripts for updating USCDI extensions

functional-status-assessments/compare_tables.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/ehaas/.pyenv/versions/3.10.2/envs/jupyter/lib/python3.10/site-packages/openpyxl/styles/stylesheet.py:226: UserWarning: Workbook contains no default style, apply openpyxl's default\n",
+      "  warn(\"Workbook contains no default style, apply openpyxl's default\")\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "(187, 6)"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from pandas import read_excel\n",
+    "from pandas import DataFrame\n",
+    "from pandas import merge\n",
+    "\n",
+    "# Read the excel file\n",
+    "df1 = read_excel('/Users/ehaas/Downloads/FunctionalStatusClinicalAssessment.xlsx', sheet_name='Expansion List', skiprows=13)\n",
+    "\n",
+    "df1.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 31,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/ehaas/.pyenv/versions/3.10.2/envs/jupyter/lib/python3.10/site-packages/openpyxl/styles/stylesheet.py:226: UserWarning: Workbook contains no default style, apply openpyxl's default\n",
+      "  warn(\"Workbook contains no default style, apply openpyxl's default\")\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "(148, 6)"
+      ]
+     },
+     "execution_count": 31,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df2 = read_excel('WalkingOrAmbulationLocomotionADLIADL.xlsx', sheet_name='Expansion List', skiprows=13)\n",
+    "\n",
+    "df2.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 32,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(17, 7)"
+      ]
+     },
+     "execution_count": 32,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Merge the two dataframes\n",
+    "\n",
+    "df3 = df1.merge(df2, indicator=True, how='outer')\n",
+    "df3[df3['_merge'] == 'both'].shape"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "jupyter",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.2"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

input/data/additional-uscdi-requirements.csv

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+Additional USCDI Requirements,Profile,FHIR Element
+KEEP ME HERE ,KEEP ME HERE ,KEEP ME HERE 
+Contact Detail,[US Core Patient Profile],Patient.telecom
+A Communication Language,[US Core Patient Profile],Patient.communication
+A Race,[US Core Patient Profile],Patient.extension:race
+An Ethnicity,[US Core Patient Profile],Patient.extension:ethnicity
+A Tribal Affiliation,[US Core Patient Profile],Patient.extension:tribalAffiliation
+A Sex,[US Core Patient Profile],Patient.extension:sex
+Gender Identity,[US Core Patient Profile],Patient.extension:genderIdentity
+Date Of Death,[US Core Patient Profile],Patient.deceased[x]
+Previous Address,[US Core Patient Profile],Patient.address.use or Patient.address.period
+Previous Name,[US Core Patient Profile],Patient.name.use or Patient.name.period
+Suffix,[US Core Patient Profile],Patient.name.suffix
+A Reason Or Indication For Referral Or Consultation,[US Core ServiceRequest Profile],ServiceRequest.reasonCode
+A Reason Or Indication For Referral Or Consultation,[US Core ServiceRequest Profile],ServiceRequest.reasonReference
+The Reason Or Indication For The Prescription,[US Core MedicationRequest Profile],MedicationRequest.reasonCode
+The Reason Or Indication For The Prescription,[US Core MedicationRequest Profile],MedicationRequest.reasonReference
+Medication Adherence,[US Core MedicationRequest Profile],MedicationRequest.extension:medicationAdherence
+A Reference To The Request For The Procedure,[US Core Procedure Profile],Procedure.basedOn
+US Core Document Category,[US Core DocumentReference Profile],DocumentReference.category:uscore
+"References To An Associated Survey, Assessment, Or Screening Tool",[US Core Simple Observation Profile],Observation.derivedFrom
+Specimen Source Site,[US Core Specimen Profile],Specimen.collection.bodySite
+Specimen Condition Acceptability,[US Core Specimen Profile],Specimen.condition

input/resources-yaml-copy/StructureDefinition-us-core-average-blood-pressure.yml

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+resourceType: StructureDefinition
+id: us-core-average-blood-pressure
+url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-average-blood-pressure
+name: USCoreAverageBloodPressureProfile
+title: US Core Average Blood Pressure Profile
+status: active
+experimental: false
+date: 2023-10-11
+description: To promote interoperability and adoption through common implementation,
+  this profile sets minimum expectations for the Observation resource to record, search,
+  and fetch average diastolic and systolic blood pressure observations with standard
+  LOINC codes and UCUM units of measure. It is based on the US Core Vital Signs Profile
+  and identifies which *additional* core elements, extensions, vocabularies, and value
+  sets  **SHALL** be present and constrains the way the elements are used when using
+  the profile.  It provides the floor for standards development for specific use cases.
+fhirVersion: 4.0.1
+kind: resource
+abstract: false
+type: Observation
+baseDefinition: http://hl7.org/fhir/us/core/StructureDefinition/us-core-vital-signs
+derivation: constraint
+differential:
+  element:
+  - id: Observation
+    path: Observation
+    short: US Core Average Blood Pressure Profile
+    definition: \-
+    comment: \-
+  - id: Observation.code
+    path: Observation.code
+    short: Average Blood Pressure
+    type:
+    - code: CodeableConcept
+    patternCodeableConcept:
+      coding:
+      - system: http://loinc.org
+        code: 96607-7
+    mustSupport: true
+  - id: Observation.effective[x]
+    path: Observation.effective[x]
+    short: clinically relevant time-period for the average of blood pressure (BP)
+      readings
+    type:
+    - extension:
+      - url: http://hl7.org/fhir/StructureDefinition/elementdefinition-type-must-support
+        valueBoolean: true
+      code: Period
+    mustSupport: true
+  - id: Observation.component
+    path: Observation.component
+    slicing:
+      discriminator:
+      - type: pattern
+        path: code
+      ordered: false
+      rules: open
+    short: Component observations
+    min: 2
+    max: '*'
+    mustSupport: true
+  - id: Observation.component:systolic
+    path: Observation.component
+    sliceName: systolic
+    short: Average Systolic Blood Pressure
+    min: 1
+    max: '1'
+    mustSupport: true
+  - id: Observation.component:systolic.code
+    path: Observation.component.code
+    short: Average Systolic Blood Pressure Code
+    min: 1
+    max: '1'
+    patternCodeableConcept:
+      coding:
+      - system: http://loinc.org
+        code: 96608-5
+    mustSupport: true
+  - id: Observation.component:systolic.valueQuantity
+    path: Observation.component.valueQuantity
+    short: Vital Sign Component Value
+    type:
+    - code: Quantity
+    mustSupport: true
+  - id: Observation.component:systolic.valueQuantity.value
+    path: Observation.component.valueQuantity.value
+    short: Numerical value (with implicit precision)
+    min: 1
+    max: '1'
+    type:
+    - code: decimal
+    mustSupport: true
+  - id: Observation.component:systolic.valueQuantity.unit
+    path: Observation.component.valueQuantity.unit
+    short: Unit representation
+    min: 1
+    max: '1'
+    type:
+    - code: string
+    mustSupport: true
+  - id: Observation.component:systolic.valueQuantity.system
+    path: Observation.component.valueQuantity.system
+    short: System that defines coded unit form
+    min: 1
+    max: '1'
+    type:
+    - code: uri
+    fixedUri: http://unitsofmeasure.org
+    mustSupport: true
+  - id: Observation.component:systolic.valueQuantity.code
+    path: Observation.component.valueQuantity.code
+    short: Coded form of the unit
+    min: 1
+    max: '1'
+    type:
+    - code: code
+    fixedCode: mm[Hg]
+    mustSupport: true
+  - id: Observation.component:diastolic
+    path: Observation.component
+    sliceName: diastolic
+    short: Average Diastolic Blood Pressure
+    min: 1
+    max: '1'
+    mustSupport: true
+  - id: Observation.component:diastolic.code
+    path: Observation.component.code
+    short: Average Diastolic Blood Pressure Code
+    min: 1
+    max: '1'
+    patternCodeableConcept:
+      coding:
+      - system: http://loinc.org
+        code: 96609-3
+    mustSupport: true
+  - id: Observation.component:diastolic.valueQuantity
+    path: Observation.component.valueQuantity
+    short: Vital Sign Component Value
+    type:
+    - code: Quantity
+    mustSupport: true
+  - id: Observation.component:diastolic.valueQuantity.value
+    path: Observation.component.valueQuantity.value
+    short: Numerical value (with implicit precision)
+    min: 1
+    max: '1'
+    type:
+    - code: decimal
+    mustSupport: true
+  - id: Observation.component:diastolic.valueQuantity.unit
+    path: Observation.component.valueQuantity.unit
+    short: Unit representation
+    min: 1
+    max: '1'
+    type:
+    - code: string
+    mustSupport: true
+  - id: Observation.component:diastolic.valueQuantity.system
+    path: Observation.component.valueQuantity.system
+    short: System that defines coded unit form
+    min: 1
+    max: '1'
+    type:
+    - code: uri
+    fixedUri: http://unitsofmeasure.org
+    mustSupport: true
+  - id: Observation.component:diastolic.valueQuantity.code
+    path: Observation.component.valueQuantity.code
+    short: Coded form of the unit
+    min: 1
+    max: '1'
+    type:
+    - code: code
+    fixedCode: mm[Hg]
+    mustSupport: true

input/resources-yaml-copy/StructureDefinition-us-core-care-experience-preference.yml

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+resourceType: StructureDefinition
+id: us-core-care-experience-preference
+url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-care-experience-preference
+name: USCoreCareExperiencePreferenceProfile
+title: US Core Care Experience Preference Profile
+status: active
+experimental: false
+date: 2023-10-11
+description: To promote interoperability and adoption through common implementation,
+  this profile sets minimum expectations for the Observation resource to record, search,
+  and fetch for a patient's care experience preferences. It is based on the US Core
+  Simple Profile and identifies which *additional* core elements, extensions, vocabularies,
+  and value sets **SHALL** be present and constrains the way the elements are used
+  when using the profile. It provides the floor for standards development for specific
+  use cases.
+copyright: Used by permission of HL7 International, all rights reserved Creative Commons
+  License
+fhirVersion: 4.0.1
+kind: resource
+abstract: false
+type: Observation
+baseDefinition: http://hl7.org/fhir/us/core/StructureDefinition/us-core-simple-observation
+derivation: constraint
+differential:
+  element:
+  - id: Observation
+    path: Observation
+    short: US Core Care Experience Preference Profile
+    definition: \-
+    comment: \-
+  - id: Observation.category:us-core
+    path: Observation.category
+    sliceName: us-core
+    min: 0
+    max: '1'
+    patternCodeableConcept:
+      coding:
+      - system: http://hl7.org/fhir/us/core/CodeSystem/us-core-category
+        code: care-experience-preference
+    mustSupport: true
+  - id: Observation.code
+    path: Observation.code
+    short: Care experience preferences code
+    type:
+    - code: CodeableConcept
+    patternCodeableConcept:
+      coding:
+      - system: http://loinc.org
+        code: 95541-9
+    mustSupport: true
+  - id: Observation.derivedFrom
+    extension:
+    - url: http://hl7.org/fhir/us/core/StructureDefinition/us-core-uscdi
+      valueBoolean: true
+    path: Observation.derivedFrom
+    short: "\U0001D5D4\U0001D5D7\U0001D5D7'\U0001D5DF \U0001D5E8\U0001D5E6\U0001D5D6\U0001D5D7\U0001D5DC:
+      US Core Profiles or other resource the observation is made from"
+    definition: US Core Observations, DocumentReference, QuestionnaireResponse or
+      other resource from which this observation value is derived.
+    type:
+    - code: Reference
+      targetProfile:
+      - http://hl7.org/fhir/us/core/StructureDefinition/us-core-documentreference
+      - http://hl7.org/fhir/StructureDefinition/Observation
+      - http://hl7.org/fhir/us/core/StructureDefinition/us-core-questionnaireresponse
+      - http://hl7.org/fhir/StructureDefinition/ImagingStudy
+      - http://hl7.org/fhir/StructureDefinition/Media
+      - http://hl7.org/fhir/StructureDefinition/MolecularSequence