define "Initial Population":
  AgeInYearsAt(date from 
    end of "Measurement Period"
  ) in Interval[16, 24]
    and Patient.sex = '248152002'
    and exists ( "Qualifying Encounters" )
    and ( ( "Has Assessments Identifying Sexual Activity" )
        or ( "Has Diagnoses Identifying Sexual Activity" )
        or ( "Has Active Contraceptive Medications" )
        or ( "Has Ordered Contraceptive Medications" )
        or ( "Has Laboratory Tests Identifying Sexual Activity" )
        or ( "Has Diagnostic Studies Identifying Sexual Activity" )
        or ( "Has Procedures Identifying Sexual Activity" )
    )

define "Denominator":
  "Initial Population"

define "Denominator Exclusions":
  Hospice."Has Hospice Services"
    or ( ( "Has Pregnancy Test Exclusion" )
        and not ( "Has Assessments Identifying Sexual Activity" )
        and not ( "Has Diagnoses Identifying Sexual Activity" )
        and not ( "Has Active Contraceptive Medications" )
        and not ( "Has Ordered Contraceptive Medications" )
        and not ( "Has Laboratory Tests Identifying Sexual Activity But Not Pregnancy" )
        and not ( "Has Diagnostic Studies Identifying Sexual Activity" )
        and not ( "Has Procedures Identifying Sexual Activity" )
    )

define "Numerator":
  exists ( ( ( [LaboratoryResultObservation: "Chlamydia Screening"] ).isLaboratoryTestPerformed ( ) ) ChlamydiaTest
      where ChlamydiaTest.effective.latest ( ) during day of "Measurement Period"
        and ChlamydiaTest.value is not null
  )

define "Stratification 1":
  AgeInYearsAt(date from 
    end of "Measurement Period"
  ) in Interval[16, 20]

define "Stratification 2":
  AgeInYearsAt(date from 
    end of "Measurement Period"
  ) in Interval[21, 24]

define "Has Hospice Services":
  exists ((([Encounter: "Encounter Inpatient"]).isEncounterPerformed()) InpatientEncounter
      where (InpatientEncounter.hospitalization.dischargeDisposition ~ "Discharge to home for hospice care (procedure)"
          or InpatientEncounter.hospitalization.dischargeDisposition ~ "Discharge to healthcare facility for hospice care (procedure)"
      )
        and InpatientEncounter.period ends during day of "Measurement Period"
  )
    or exists ((([Encounter: "Hospice Encounter"]).isEncounterPerformed()) HospiceEncounter
        where HospiceEncounter.period overlaps day of "Measurement Period"
    )
    or exists ((([ObservationScreeningAssessment: "Hospice care [Minimum Data Set]"]).isAssessmentPerformed()) HospiceAssessment
        where HospiceAssessment.value ~ "Yes (qualifier value)"
          and HospiceAssessment.effective.toInterval() overlaps day of "Measurement Period"
    )
    or exists ((([ServiceRequest: "Hospice Care Ambulatory"]).isInterventionOrder()) HospiceOrder
        where HospiceOrder.authoredOn during day of "Measurement Period"
    )
    or exists ((([Procedure: "Hospice Care Ambulatory"]).isInterventionPerformed()) HospicePerformed
        where HospicePerformed.performed.toInterval() overlaps day of "Measurement Period"
    )
    or exists ((([ConditionProblemsHealthConcerns: "Hospice Diagnosis"]
        union [ConditionEncounterDiagnosis: "Hospice Diagnosis"]).verified()) HospiceCareDiagnosis
        where HospiceCareDiagnosis.prevalenceInterval() overlaps day of "Measurement Period"
    )

define "SDE Sex":
  case
    when Patient.sex = '248153007' then "Male (finding)"
    when Patient.sex = '248152002' then "Female (finding)"
    else null
  end

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

define "SDE Ethnicity":
  Patient.ethnicity E
    return Tuple {
      codes: { E.ombCategory } union E.detailed,
      display: E.text
    }

define "SDE Race":
  Patient.race R
    return Tuple {
      codes: R.ombCategory union R.detailed,
      display: R.text
    }

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

define "Numerator":
  exists ( ( ( [LaboratoryResultObservation: "Chlamydia Screening"] ).isLaboratoryTestPerformed ( ) ) ChlamydiaTest
      where ChlamydiaTest.effective.latest ( ) during day of "Measurement Period"
        and ChlamydiaTest.value is not null
  )

define "Stratification 2":
  AgeInYearsAt(date from 
    end of "Measurement Period"
  ) in Interval[21, 24]

define "Stratification 1":
  AgeInYearsAt(date from 
    end of "Measurement Period"
  ) in Interval[16, 20]

define "Qualifying Encounters":
  ( ( [Encounter: "Office Visit"]
      union [Encounter: "Preventive Care Services Established Office Visit, 18 and Up"]
      union [Encounter: "Preventive Care Services Initial Office Visit, 18 and Up"]
      union [Encounter: "Preventive Care Services, Initial Office Visit, 0 to 17"]
      union [Encounter: "Preventive Care, Established Office Visit, 0 to 17"]
      union [Encounter: "Home Healthcare Services"]
      union [Encounter: "Telephone Visits"]
      union [Encounter: "Virtual Encounter"]
  ).isEncounterPerformed ( ) ) ValidEncounters
    where ValidEncounters.period during day of "Measurement Period"

define "Has Assessments Identifying Sexual Activity":
  exists ( ( ( [ObservationScreeningAssessment: "Have you ever had vaginal intercourse [PhenX]"] ).isAssessmentPerformed ( ) ) SexualActivityAssessment
      where SexualActivityAssessment.value ~ "Yes (qualifier value)"
        and SexualActivityAssessment.effective.toInterval ( ) on or before end of "Measurement Period"
  )

define "Has Diagnoses Identifying Sexual Activity":
  exists ( ( ( [ConditionEncounterDiagnosis: "Diagnoses Used to Indicate Sexual Activity"]
        union [ConditionProblemsHealthConcerns: "Diagnoses Used to Indicate Sexual Activity"]
        union [ConditionEncounterDiagnosis: "HIV"]
        union [ConditionProblemsHealthConcerns: "HIV"]
        union [ConditionEncounterDiagnosis: "Complications of Pregnancy, Childbirth and the Puerperium"]
        union [ConditionProblemsHealthConcerns: "Complications of Pregnancy, Childbirth and the Puerperium"]
    ).verified ( ) ) SexualActivityDiagnosis
      where SexualActivityDiagnosis.prevalenceInterval ( ) overlaps "Measurement Period"
  )

define "Has Active Contraceptive Medications":
  exists ( ( [MedicationRequest: "Contraceptive Medications"] ).isMedicationActive ( ) ) ActiveContraceptives
    where ActiveContraceptives.medicationRequestPeriod ( ) overlaps "Measurement Period"

define "Has Ordered Contraceptive Medications":
  exists ( ( [MedicationRequest: "Contraceptive Medications"] ).isMedicationOrder ( ) ) OrderedContraceptives
    where OrderedContraceptives.authoredOn.toInterval ( ) during day of "Measurement Period"

define "Has Laboratory Tests Identifying Sexual Activity But Not Pregnancy":
  exists ( ( [ServiceRequest: "Pap Test"]
      union [ServiceRequest: "Lab Tests During Pregnancy"]
      union [ServiceRequest: "Lab Tests for Sexually Transmitted Infections"]
  ).isLaboratoryTestOrder ( ) ) LabOrders
    where LabOrders.authoredOn.toInterval ( ) during day of "Measurement Period"

define "Has Laboratory Tests Identifying Sexual Activity":
  exists ( ( ( [ServiceRequest: "Pregnancy Test"] ).isLaboratoryTestOrder ( ) ) PregnancyTest
      where PregnancyTest.authoredOn.toInterval ( ) during day of "Measurement Period"
  )
    or "Has Laboratory Tests Identifying Sexual Activity But Not Pregnancy"

define "Has Diagnostic Studies Identifying Sexual Activity":
  exists ( ( [ServiceRequest: "Diagnostic Studies During Pregnancy"] ).isDiagnosticStudyOrder ( ) ) SexualActivityDiagnostics
    where SexualActivityDiagnostics.authoredOn.toInterval ( ) during day of "Measurement Period"

define "Has Procedures Identifying Sexual Activity":
  exists ( ( [Procedure: "Procedures Used to Indicate Sexual Activity"] ).isProcedurePerformed ( ) ) ProceduresForSexualActivity
    where ProceduresForSexualActivity.performed.toInterval ( ) during day of "Measurement Period"

define "Initial Population":
  AgeInYearsAt(date from 
    end of "Measurement Period"
  ) in Interval[16, 24]
    and Patient.sex = '248152002'
    and exists ( "Qualifying Encounters" )
    and ( ( "Has Assessments Identifying Sexual Activity" )
        or ( "Has Diagnoses Identifying Sexual Activity" )
        or ( "Has Active Contraceptive Medications" )
        or ( "Has Ordered Contraceptive Medications" )
        or ( "Has Laboratory Tests Identifying Sexual Activity" )
        or ( "Has Diagnostic Studies Identifying Sexual Activity" )
        or ( "Has Procedures Identifying Sexual Activity" )
    )

define "Denominator":
  "Initial Population"

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

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

define "Has Pregnancy Test Exclusion":
  exists ( ( ( ( [ServiceRequest: "Pregnancy Test"] ).isLaboratoryTestOrder ( ) ) PregnancyTest
        with ( ( [ServiceRequest: "XRay Study"] ).isDiagnosticStudyOrder ( ) ) XrayOrder
          such that XrayOrder.authoredOn.toInterval ( ) occurs 6 days or less on or after day of PregnancyTest.authoredOn.toInterval ( )
        where PregnancyTest.authoredOn.toInterval ( ) during "Measurement Period"
    )
      union ( ( [ServiceRequest: "Pregnancy Test"] ).isLaboratoryTestOrder ( ) ) PregnancyTestOrder
        with ( ( [MedicationRequest: "Isotretinoin"] ).isMedicationOrder ( ) ) AccutaneOrder
          such that AccutaneOrder.authoredOn.toInterval ( ) occurs 6 days or less on or after day of PregnancyTestOrder.authoredOn.toInterval ( )
        where PregnancyTestOrder.authoredOn.toInterval ( ) during "Measurement Period"
  )

define "Denominator Exclusions":
  Hospice."Has Hospice Services"
    or ( ( "Has Pregnancy Test Exclusion" )
        and not ( "Has Assessments Identifying Sexual Activity" )
        and not ( "Has Diagnoses Identifying Sexual Activity" )
        and not ( "Has Active Contraceptive Medications" )
        and not ( "Has Ordered Contraceptive Medications" )
        and not ( "Has Laboratory Tests Identifying Sexual Activity But Not Pregnancy" )
        and not ( "Has Diagnostic Studies Identifying Sexual Activity" )
        and not ( "Has Procedures Identifying Sexual Activity" )
    )

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

define fluent function medicationRequestPeriod(Request "MedicationRequest"):
  Request R
    let
      dosage: singleton from R.dosageInstruction,
      doseAndRate: singleton from dosage.doseAndRate,
      timing: dosage.timing,
      frequency: Coalesce(timing.repeat.frequencyMax, timing.repeat.frequency),
      period: Quantity(timing.repeat.period, timing.repeat.periodUnit),
      doseRange: doseAndRate.dose,
      doseQuantity: doseAndRate.dose,
      dose: Coalesce(end of doseRange, doseQuantity),
      dosesPerDay: Coalesce(ToDaily(frequency, period), Count(timing.repeat.timeOfDay), 1.0),
      boundsPeriod: timing.repeat.bounds as Interval<DateTime>,
      daysSupply: (convert R.dispenseRequest.expectedSupplyDuration to days).value,
      quantity: R.dispenseRequest.quantity,
      refills: Coalesce(R.dispenseRequest.numberOfRepeatsAllowed, 0),
      startDate:
        Coalesce(
          date from start of boundsPeriod,
          date from R.authoredOn,
          date from start of R.dispenseRequest.validityPeriod
        ),
      totalDaysSupplied: Coalesce(daysSupply, quantity.value / (dose.value * dosesPerDay)) * (1 + refills)
    return
      if startDate is not null and totalDaysSupplied is not null then
        Interval[startDate, startDate + Quantity(totalDaysSupplied - 1, 'day') ]
      else if startDate is not null and boundsPeriod."high" is not null then
        Interval[startDate, date from end of boundsPeriod]
      else
        null

/**********************************************************************/
/* Functions in this region are copied from opioid-mme-r4             */
/**********************************************************************/

define function Quantity(value Decimal, unit String):
  if value is not null then
    System.Quantity { value: value, unit: unit }
  else
    null

/*
 Goal is to get to number of days
 Two broad approaches to the calculation:
  1) Based on supply and frequency, calculate the number of expected days the medication will cover/has covered
  2) Based on relevant period, determine a covered interval and calculate the length of that interval in days
This topic covers several use cases and illustrates how to calculate Cumulative
Medication Duration for each type of medication resource using the supply and
frequency approach.
*/

/*
  For the first approach, we need to get from frequency to a frequency/day
  So we define ToDaily
*/

/*
  Calculates daily frequency given frequency within a period
*/
define function ToDaily(frequency System.Integer, period System.Quantity):
  case period.unit
    when 'h' then frequency * (24.0 / period.value)
    when 'min' then frequency * (24.0 / period.value) * 60
    when 's' then frequency * (24.0 / period.value) * 60 * 60
    when 'd' then frequency * (24.0 / period.value) / 24
    when 'wk' then frequency * (24.0 / period.value) / (24 * 7)
    when 'mo' then frequency * (24.0 / period.value) / (24 * 30) /* assuming 30 days in month */
    when 'a' then frequency * (24.0 / period.value) / (24 * 365) /* assuming 365 days in year */
    when 'hour' then frequency * (24.0 / period.value)
    when 'minute' then frequency * (24.0 / period.value) * 60
    when 'second' then frequency * (24.0 / period.value) * 60 * 60
    when 'day' then frequency * (24.0 / period.value) / 24
    when 'week' then frequency * (24.0 / period.value) / (24 * 7)
    when 'month' then frequency * (24.0 / period.value) / (24 * 30) /* assuming 30 days in month */
    when 'year' then frequency * (24.0 / period.value) / (24 * 365) /* assuming 365 days in year */
    when 'hours' then frequency * (24.0 / period.value)
    when 'minutes' then frequency * (24.0 / period.value) * 60
    when 'seconds' then frequency * (24.0 / period.value) * 60 * 60
    when 'days' then frequency * (24.0 / period.value) / 24
    when 'weeks' then frequency * (24.0 / period.value) / (24 * 7)
    when 'months' then frequency * (24.0 / period.value) / (24 * 30) /* assuming 30 days in month */
    when 'years' then frequency * (24.0 / period.value) / (24 * 365) /* assuming 365 days in year */
    else Message(null, true, 'CMDLogic.ToDaily.UnknownUnit', ErrorLevel, 'Unknown unit ' & period.unit)
  end

/*
@description: Given an interval, returns the ending point if the interval has an ending boundary specified,
otherwise, returns the starting point
*/
define fluent function latest(choice Choice<DateTime, Quantity, Interval<DateTime>, Interval<Quantity>> ):
  (choice.toInterval()) period
    return
      if (period."hasEnd"()) then end of period
      else start of period

/*
@description: Given an interval, returns true if the interval has an ending boundary specified
(i.e. the end of the interval is not null and not the maximum DateTime value)
*/
define fluent function hasEnd(period Interval<DateTime> ):
  not (
    end of period is null
      or end of period = maximum DateTime
  )

/*
@description: Normalizes a value that is a choice of timing-valued types to an equivalent interval
@comment: Normalizes a choice type of DateTime, Quanitty, Interval<DateTime>, or Interval<Quantity> types
to an equivalent interval. This selection of choice types is a superset of the majority of choice types that are used as possible
representations for timing-valued elements in QICore, allowing this function to be used across any resource.
The input can be provided as a DateTime, Quantity, Interval<DateTime> or Interval<Quantity>.
The intent of this function is to provide a clear and concise mechanism to treat single
elements that have multiple possible representations as intervals so that logic doesn't have to account
for the variability. More complex calculations (such as medication request period or dispense period
calculation) need specific guidance and consideration. That guidance may make use of this function, but
the focus of this function is on single element calculations where the semantics are unambiguous.
If the input is a DateTime, the result a DateTime Interval beginning and ending on that DateTime.
If the input is a Quantity, the quantity is expected to be a calendar-duration interpreted as an Age,
and the result is a DateTime Interval beginning on the Date the patient turned that age and ending immediately before one year later.
If the input is a DateTime Interval, the result is the input.
If the input is a Quantity Interval, the quantities are expected to be calendar-durations interpreted as an Age, and the result
is a DateTime Interval beginning on the date the patient turned the age given as the start of the quantity interval, and ending
immediately before one year later than the date the patient turned the age given as the end of the quantity interval.
If the input is a Timing, an error will be thrown indicating that Timing calculations are not implemented. Any other input will reslt in a null DateTime Interval
*/
define fluent function toInterval(choice Choice<DateTime, Quantity, Interval<DateTime>, Interval<Quantity>, Timing>):
  case
	  when choice is DateTime then
    	Interval[choice as DateTime, choice as DateTime]
		when choice is Interval<DateTime> then
  		choice as Interval<DateTime>
		when choice is Quantity then
		  Interval[Patient.birthDate + (choice as Quantity),
			  Patient.birthDate + (choice as Quantity) + 1 year)
		when choice is Interval<Quantity> then
		  Interval[Patient.birthDate + (choice.low as Quantity),
			  Patient.birthDate + (choice.high as Quantity) + 1 year)
		when choice is Timing then
      Message(null, true, 'NOT_IMPLEMENTED', 'Error', 'Calculation of an interval from a Timing value is not supported') as Interval<DateTime>
		else
			null as Interval<DateTime>
	end

define function ToString(value uri): 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]

/*
@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
        }

//Laboratory Test, Performed
define fluent function isLaboratoryTestPerformed(Obs List<LaboratoryResultObservation>):
  Obs O
    where O.status in { 'final', 'amended', 'corrected' }

//Encounter, Performed
//General usage unless required otherwise by measure intent (e.g., follow-up encounters)
define fluent function isEncounterPerformed(Enc List<Encounter>):
  Enc E
    where E.status = 'finished'

//Assessment, Performed
define fluent function isAssessmentPerformed(Obs List<ObservationScreeningAssessment>):
  Obs O
    where O.status in { 'final', 'amended', 'corrected' }

//This library contains functions used to constrain FHIR resource elements for measures authored by NCQA, based on QICore 6.0.0 resources including IG and authoring patterns. The functions may appear similar to some QICoreCommon functions but differ in that they have constraints that are relevant for measures authored by NCQA.

//Condition
//Returns conditions in the given list that either have no verification status or have a verification status of confirmed, unconfirmed, provisional, or differential
define fluent function verified(conditions List<Choice<ConditionProblemsHealthConcerns, ConditionEncounterDiagnosis>>):
  conditions C
    where C.verificationStatus is not null implies
      (C.verificationStatus ~ "confirmed"
        or C.verificationStatus ~ "unconfirmed"
        or C.verificationStatus ~ "provisional"
        or C.verificationStatus ~ "differential"
      )

//Medication, Active
define fluent function isMedicationActive(MedicationRequest List<MedicationRequest>):
  MedicationRequest M
    where M.status = 'active'
      and M.intent in {'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order'}

//Medication, Order
define fluent function isMedicationOrder(MedicationRequest List<MedicationRequest>):
  MedicationRequest M
    where M.status in { 'active', 'completed' }
    and M.intent in {'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order'}

//Laboratory Test, Order
define fluent function isLaboratoryTestOrder(ServiceRequest List<ServiceRequest>):
  ServiceRequest S
    where S.status in { 'active', 'completed' }
      and S.intent in {'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order'}

//Diagnostic Study, Order
define fluent function isDiagnosticStudyOrder(ServiceRequest List<ServiceRequest>):
  ServiceRequest S
    where S.status in { 'active', 'completed' }
      and S.intent in {'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order'}

//Procedure, Performed
define fluent function isProcedurePerformed(Proc List<Procedure>):
  Proc P
    where P.status ~ 'completed'

//Intervention, Order
define fluent function isInterventionOrder(ServiceRequest List<ServiceRequest>):
  ServiceRequest S
    where S.status in { 'active', 'completed' }
      and S.intent in {'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order'}

//Intervention, Performed
define fluent function isInterventionPerformed(Proc List<Procedure>):
  Proc P
    where P.status ~ 'completed'