define "SDE Race":
  (flatten (
      Patient.extension Extension
        where Extension.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race'
          return Extension.extension
    )) E
      where E.url = 'ombCategory'
        or E.url = 'detailed'
      return E.value as Coding

define "SDE Sex":
  case
      when Patient.gender = 'male' then Code { code: 'M', system: 'http://hl7.org/fhir/v3/AdministrativeGender', display: 'Male' }
      when Patient.gender = 'female' then Code { code: 'F', system: 'http://hl7.org/fhir/v3/AdministrativeGender', display: 'Female' }
      else null
    end

define "SDE Payer":
  [Coverage: type in "Payer"] Payer
        return {
          code: Payer.type,
          period: Payer.period
        }

define "SDE Ethnicity":
  (flatten (
      Patient.extension Extension
        where Extension.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity'
          return Extension.extension
    )) E
      where E.url = 'ombCategory'
        or E.url = 'detailed'
      return E.value as Coding

define "Most Recent Tobacco Use Screening Indicates Tobacco Non User":
  ( Last(["Observation": "Tobacco Use Screening"] TobaccoUseScreening
        where Global."Normalize Interval"(TobaccoUseScreening.effective)overlaps "Measurement Period"
        sort by start of Global."Normalize Interval"(effective)
    )) MostRecentTobaccoUseScreening
      where MostRecentTobaccoUseScreening.value in "Tobacco Non-User"

define "Most Recent Tobacco Use Screening Indicates Tobacco User":
  ( Last(["Observation": "Tobacco Use Screening"] TobaccoUseScreening
        where Global."Normalize Interval"(TobaccoUseScreening.effective)overlaps "Measurement Period"
        sort by start of Global."Normalize Interval"(effective)
    )) MostRecentTobaccoUseScreening
      where MostRecentTobaccoUseScreening.value in "Tobacco User"

// MedicationStatement is not available in R5, known publication issue
//define "Active Pharmacotherapy for Tobacco Cessation":
//  ["MedicationStatement": "Tobacco Use Cessation Pharmacotherapy"] TakingCessationPharmacotherapy
//      where Global."Normalize Interval" ( TakingCessationPharmacotherapy.effective ) overlaps after "Measurement Period"
//        and TakingCessationPharmacotherapy.status in { 'active', 'completed' }

define "Tobacco Cessation Counseling Given":
  ["Encounter": "Tobacco Use Cessation Counseling"] TobaccoCessationCounseling
      where TobaccoCessationCounseling.period during "Measurement Period"
        and TobaccoCessationCounseling.status = 'finished'

define "Tobacco Cessation Pharmacotherapy Ordered":
  ["MedicationRequest": "Tobacco Use Cessation Pharmacotherapy"] CessationPharmacotherapyOrdered
      where CessationPharmacotherapyOrdered.authoredOn during "Measurement Period"
        and CessationPharmacotherapyOrdered.status = 'active'

define "Numerator 3":
  "Most Recent Tobacco Use Screening Indicates Tobacco Non User" is not null
      or ( "Most Recent Tobacco Use Screening Indicates Tobacco User" is not null
          and ( exists "Tobacco Cessation Counseling Given"
              or exists "Tobacco Cessation Pharmacotherapy Ordered"
              //or exists "Active Pharmacotherapy for Tobacco Cessation"
          )
      )

define "Medical Reason for Not Screening for Tobacco Use":
  ["Observation": "Tobacco Use Screening"] NoTobaccoUseScreening
      where NoTobaccoUseScreening.issued during "Measurement Period"
        and "Not Done"(NoTobaccoUseScreening)
        and "Not Done Reason in Medical Reason"(NoTobaccoUseScreening)
        and NoTobaccoUseScreening.status = 'final'

//or exists "Active Pharmacotherapy for Tobacco Cessation"

define "Has Limited Life Expectancy":
  exists ( ["Condition"] LimitedLifeExpectancy
        where Global."Prevalence Period" ( LimitedLifeExpectancy ) overlaps after "Measurement Period"
          and LimitedLifeExpectancy.clinicalStatus ~ ToConcept(Global."active")
    )

define "Denominator Exceptions 1":
  exists "Medical Reason for Not Screening for Tobacco Use"
      or "Has Limited Life Expectancy"

define "Numerator 1":
  "Most Recent Tobacco Use Screening Indicates Tobacco Non User" is not null
      or "Most Recent Tobacco Use Screening Indicates Tobacco User" is not null

define "Numerator 2":
  exists "Tobacco Cessation Counseling Given"
      or exists "Tobacco Cessation Pharmacotherapy Ordered"

define "SDE Race":
  SDE."SDE Race"

define "SDE Sex":
  SDE."SDE Sex"

define "Office Based Visit During Measurement Period":
  ( ["Encounter": "Health behavior intervention, individual, face-to-face; initial 30 minutes"]
      union ["Encounter": "Health behavior assessment, or re-assessment (ie, health-focused clinical interview, behavioral observations, clinical decision making)"]
      union ["Encounter": "Home Healthcare Services"]
      union ["Encounter": "Occupational Therapy Evaluation"]
      union ["Encounter": "Office Visit"]
      union ["Encounter": "Ophthalmological Services"]
      union ["Encounter": "Physical Therapy Evaluation"]
      union ["Encounter": "Psych Visit - Diagnostic Evaluation"]
      union ["Encounter": "Psych Visit - Psychotherapy"]
      union ["Encounter": "Psychoanalysis"]
      union ["Encounter": "Speech and Hearing Evaluation"] ) OfficeBasedEncounter
      where OfficeBasedEncounter.period during "Measurement Period"
        and OfficeBasedEncounter.status = 'finished'

define "Preventive Visit During Measurement Period":
  ( ["Encounter": "Annual Wellness Visit"]
      union ["Encounter": "Preventive Care Services - Established Office Visit, 18 and Up"]
      union ["Encounter": "Preventive Care Services - Group Counseling"]
      union ["Encounter": "Preventive Care Services - Other"]
      union ["Encounter": "Preventive Care Services-Individual Counseling"]
      union ["Encounter": "Preventive Care Services-Initial Office Visit, 18 and Up"] ) PreventiveEncounter
      where PreventiveEncounter.period during "Measurement Period"
        and PreventiveEncounter.status = 'finished'

define "Initial Population":
  exists ( ["Patient"] BirthDate
        where Global."CalendarAgeInYearsAt" ( FHIRHelpers.ToDate ( BirthDate.birthDate ), start of "Measurement Period" ) >= 18
    )
      and ( Count("Office Based Visit During Measurement Period")>= 2
          or exists "Preventive Visit During Measurement Period"
      )

define "Denominator 3":
  "Initial Population"

define "Denominator 2":
  "Initial Population"
      and "Most Recent Tobacco Use Screening Indicates Tobacco User" is not null

define "SDE Payer":
  SDE."SDE Payer"

define "SDE Ethnicity":
  SDE."SDE Ethnicity"

define "Medical Reason for Not Counseling Tobacco User":
  ["Procedure": "Tobacco Use Cessation Counseling"] NoTobaccoCessationCounseling
      where Global."Normalize Interval" ( NoTobaccoCessationCounseling.performed ) starts during "Measurement Period"
        and ( ( NoTobaccoCessationCounseling.status = 'not-done'
              and NoTobaccoCessationCounseling.statusReason in "Medical Reason"
          )
            or ( "Not Done"(NoTobaccoCessationCounseling)
                and "Not Done Reason in Medical Reason"(NoTobaccoCessationCounseling)
            )
        )

define "Medical Reason for Not Ordering Tobacco Cessation Pharmacotherapy":
  ["MedicationRequest": "Tobacco Use Cessation Pharmacotherapy"] NoCessationPharmacotherapyOrdered
      where NoCessationPharmacotherapyOrdered.authoredOn during "Measurement Period"
        and NoCessationPharmacotherapyOrdered.status = 'completed'
        and ( ( "Not Done"(NoCessationPharmacotherapyOrdered)
              and "Not Done Reason in Medical Reason"(NoCessationPharmacotherapyOrdered)
          )
            or ( NoCessationPharmacotherapyOrdered.doNotPerform = true
                and NoCessationPharmacotherapyOrdered.statusReason in "Medical Reason"
            )
        )

define "Denominator Exceptions 2":
  exists "Medical Reason for Not Counseling Tobacco User"
      or exists "Medical Reason for Not Ordering Tobacco Cessation Pharmacotherapy"
      or "Has Limited Life Expectancy"

define "Denominator Exceptions 3":
  exists "Medical Reason for Not Screening for Tobacco Use"
      or exists "Medical Reason for Not Counseling Tobacco User"
      or exists "Medical Reason for Not Ordering Tobacco Cessation Pharmacotherapy"
      or "Has Limited Life Expectancy"

define "Denominator 1":
  "Initial Population"

define function "Not Done"(res DomainResource ):
  if ( res R
      where ( "GetModiferExtension"(R, 'http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-notDone').value = true )
  ) is not null then true
    else false

define function "GetModiferExtension"(res DomainResource, url String ):
  singleton from "GetModifierExtensions"(res, url)

define function "GetModifierExtensions"(res DomainResource, url String ):
  res.modifierExtension E
    where E.url = ( url )
    return E

define function "Not Done Reason in Medical Reason"(res DomainResource ):
  if ( res R
      where "GetModiferExtension"(R, 'http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-notDoneReason').value in "Medical Reason"
  ) is not null then true
    else false

/*
*
*    CQFMeasures Common Logic
*
*/

define function "Normalize Interval"(choice Choice<FHIR.dateTime, FHIR.Period, FHIR.Timing, FHIR.instant, FHIR.string, FHIR.Age, FHIR.Range>):
  case
	  when choice is FHIR.dateTime then
    	Interval[FHIRHelpers.ToDateTime(choice as FHIR.dateTime), FHIRHelpers.ToDateTime(choice as FHIR.dateTime)]
		when choice is FHIR.Period then
  		FHIRHelpers.ToInterval(choice as FHIR.Period)
		when choice is FHIR.instant then
			Interval[FHIRHelpers.ToDateTime(choice as FHIR.instant), FHIRHelpers.ToDateTime(choice as FHIR.instant)]
		when choice is FHIR.Age then
		  Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(choice as FHIR.Age),
			  FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(choice as FHIR.Age) + 1 year)
		when choice is FHIR.Range then
		  Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((choice as FHIR.Range).low),
			  FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((choice as FHIR.Range).high) + 1 year)
		when choice is FHIR.Timing then
		  Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute a single interval from a Timing type')
    when choice is FHIR.string then
      Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute an interval from a String value')
		else
			null as Interval<DateTime>
	end

define function "Prevalence Period"(condition Condition):
  Interval[start of "Normalize Interval"(condition.onset), end of "Normalize Abatement"(condition))

define function "Normalize Abatement"(condition Condition):
	if condition.abatement is FHIR.dateTime then
	  Interval[FHIRHelpers.ToDateTime(condition.abatement as FHIR.dateTime), FHIRHelpers.ToDateTime(condition.abatement as FHIR.dateTime)]
	else if condition.abatement is FHIR.Period then
	  FHIRHelpers.ToInterval(condition.abatement as FHIR.Period)
	else if condition.abatement is FHIR.string then
    Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute an interval from a String value')
	else if condition.abatement is FHIR.Age then
		Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(condition.abatement as FHIR.Age),
			FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(condition.abatement as FHIR.Age) + 1 year)
	else if condition.abatement is FHIR.Range then
	  Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((condition.abatement as FHIR.Range).low),
		  FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((condition.abatement as FHIR.Range).high) + 1 year)
	else if condition.abatement is FHIR.boolean then
	  Interval[end of "Normalize Interval"(condition.onset), condition.recordedDate)
	else null

define function "CalendarAgeInYearsAt"(BirthDateTime DateTime, AsOf DateTime):
	years between ToDate(BirthDateTime)and ToDate(AsOf)

define function "ToDate"(Value DateTime):
	DateTime(year from Value, month from Value, day from Value, 0, 0, 0, 0, timezoneoffset from Value)

define function ToDateTime(value dateTime): value.value

/*
@description: Converts the given [Period](https://hl7.org/fhir/datatypes.html#Period)
value to a CQL DateTime Interval
@comment: If the start value of the given period is unspecified, the starting
boundary of the resulting interval will be open (meaning the start of the interval
is unknown, as opposed to interpreted as the beginning of time).
*/
define function ToInterval(period FHIR.Period):
    if period is null then
        null
    else
        if period."start" is null then
            Interval(period."start".value, period."end".value]
        else
            Interval[period."start".value, period."end".value]

define function ToDateTime(value instant): value.value

define function ToDate(value date): value.value

/*
@description: Converts the given FHIR [Quantity](https://hl7.org/fhir/datatypes.html#Quantity) 
value to a CQL Quantity
@comment: If the given quantity has a comparator specified, a runtime error is raised. If the given quantity
has a system other than UCUM (i.e. `http://unitsofmeasure.org`) or CQL calendar units (i.e. `http://hl7.org/fhirpath/CodeSystem/calendar-units`)
an error is raised. For UCUM to calendar units, the `ToCalendarUnit` function is used.
@seealso: ToCalendarUnit
*/
define function ToQuantity(quantity FHIR.Quantity):
    case
        when quantity is null then null
        when quantity.value is null then null
        when quantity.comparator is not null then
            Message(null, true, 'FHIRHelpers.ToQuantity.ComparatorQuantityNotSupported', 'Error', 'FHIR Quantity value has a comparator and cannot be converted to a System.Quantity value.')
        when quantity.system is null or quantity.system.value = 'http://unitsofmeasure.org'
              or quantity.system.value = 'http://hl7.org/fhirpath/CodeSystem/calendar-units' then
            System.Quantity { value: quantity.value.value, unit: ToCalendarUnit(Coalesce(quantity.code.value, quantity.unit.value, '1')) }
        else
            Message(null, true, 'FHIRHelpers.ToQuantity.InvalidFHIRQuantity', 'Error', 'Invalid FHIR Quantity code: ' & quantity.unit.value & ' (' & quantity.system.value & '|' & quantity.code.value & ')')
    end

/*
@description: Converts a UCUM definite duration unit to a CQL calendar duration
unit using conversions specified in the [quantities](https://cql.hl7.org/02-authorsguide.html#quantities) 
topic of the CQL specification.
@comment: Note that for durations above days (or weeks), the conversion is understood to be approximate
*/
define function ToCalendarUnit(unit System.String):
    case unit
        when 'ms' then 'millisecond'
        when 's' then 'second'
        when 'min' then 'minute'
        when 'h' then 'hour'
        when 'd' then 'day'
        when 'wk' then 'week'
        when 'mo' then 'month'
        when 'a' then 'year'
        else unit
    end

define function ToString(value string): value.value

define function ToString(value EncounterStatus): value.value

/*
@description: Converts the given FHIR [CodeableConcept](https://hl7.org/fhir/datatypes.html#CodeableConcept) value to a CQL Concept.
*/
define function ToConcept(concept FHIR.CodeableConcept):
    if concept is null then
        null
    else
        System.Concept {
            codes: concept.coding C return ToCode(C),
            display: concept.text.value
        }

/*
@description: Converts the given FHIR [Coding](https://hl7.org/fhir/datatypes.html#Coding) value to a CQL Code.
*/
define function ToCode(coding FHIR.Coding):
    if coding is null then
        null
    else
        System.Code {
          code: coding.code.value,
          system: coding.system.value,
          version: coding.version.value,
          display: coding.display.value
        }

define function ToString(value MedicationRequestStatus): value.value

define function ToBoolean(value boolean): value.value

define function ToString(value uri): value.value

define function ToString(value base64Binary): value.value

define function ToString(value ObservationStatus): value.value

define function ToString(value AdministrativeGender): value.value

define function ToString(value ProcedureStatus): value.value