define "Initial Population":
  "Encounter With Pharyngitis or Tonsillitis With Antibiotic" EncounterWithPharyngitis
    where AgeInYearsAt(date from start of "Measurement Period") >= 3
    return EncounterWithPharyngitis

define "Denominator":
  "Initial Population"

define "Denominator Exclusions":
  "Encounters and Assessments with Hospice Patient"
    union Antibiotic."Encounter with Comorbid Condition History" ( "Encounter With Pharyngitis or Tonsillitis With Antibiotic", ( [ConditionEncounterDiagnosis: "Comorbid Conditions for Respiratory Conditions"] ).verified ( ) )
    union Antibiotic."Encounter with Antibiotic Medication History" ( "Encounter With Pharyngitis or Tonsillitis With Antibiotic", ( [MedicationRequest: "Antibiotic Medications for Pharyngitis"] ).isMedicationActive ( ) )
    union Antibiotic."Encounter with Competing Diagnosis History" ( "Encounter With Pharyngitis or Tonsillitis With Antibiotic", ( [ConditionEncounterDiagnosis: "Competing Conditions for Respiratory Conditions"] ).verified ( ) )

define "Numerator":
  from
    "Group A Streptococcus Lab Test With Result" GroupAStreptococcusTest,
    "Encounter With Pharyngitis or Tonsillitis With Antibiotic" EncounterWithPharyngitis
    where GroupAStreptococcusTest.effective.toInterval ( ) starts during day of Interval[( end of EncounterWithPharyngitis.period ) - 3 days, ( end of EncounterWithPharyngitis.period ) + 3 days]
    return EncounterWithPharyngitis

define "Encounter With Pharyngitis or Tonsillitis With Antibiotic":
  from
    "Encounter With Antibiotic Ordered Within Three Days" VisitWithAntibiotic,
    "Pharyngitis or Tonsillitis" AcutePharyngitisTonsillitis
    where AcutePharyngitisTonsillitis.prevalenceInterval ( ) starts during day of VisitWithAntibiotic.period
    return VisitWithAntibiotic

define "Encounter With Pharyngitis or Tonsillitis With Antibiotic":
  from
    "Encounter With Antibiotic Ordered Within Three Days" VisitWithAntibiotic,
    "Pharyngitis or Tonsillitis" AcutePharyngitisTonsillitis
    where AcutePharyngitisTonsillitis.prevalenceInterval ( ) starts during day of VisitWithAntibiotic.period
    return VisitWithAntibiotic

define "Encounter With Pharyngitis or Tonsillitis With Antibiotic":
  from
    "Encounter With Antibiotic Ordered Within Three Days" VisitWithAntibiotic,
    "Pharyngitis or Tonsillitis" AcutePharyngitisTonsillitis
    where AcutePharyngitisTonsillitis.prevalenceInterval ( ) starts during day of VisitWithAntibiotic.period
    return VisitWithAntibiotic

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 "Group A Streptococcus Lab Test With Result":
  ( ( [LaboratoryResultObservation: "Group A Streptococcus Test"] ).isLaboratoryTestPerformed ( ) ) GroupAStreptococcusTest
    where GroupAStreptococcusTest.value is not null

define "Qualifying Encounters":
  ( ( [Encounter: "Emergency Department Evaluation and Management Visit"]
      union [Encounter: "Home Healthcare Services"]
      union [Encounter: "Medical Disability Exam"]
      union [Encounter: "Office Visit"]
      union [Encounter: "Telephone Visits"]
      union [Encounter: "Virtual Encounter"]
      union [Encounter: "Outpatient Consultation"]
      union [Encounter: "Preventive Care Services Established Office Visit, 18 and Up"]
      union [Encounter: "Preventive Care Services Group Counseling"]
      union ( [Encounter] E
          where exists ( ( E.type ) T
              where T ~ "Unlisted preventive medicine service"
          )
      )
      union [Encounter: "Preventive Care Services, Initial Office Visit, 0 to 17"]
      union [Encounter: "Preventive Care Services Individual Counseling"]
      union [Encounter: "Preventive Care Services Initial Office Visit, 18 and Up"]
      union [Encounter: "Preventive Care, Established Office Visit, 0 to 17"]
  ).isEncounterPerformed ( ) ) ValidEncounter
    where ValidEncounter.period ends during day of Interval[( start of "Measurement Period" ), ( end of "Measurement Period" ) - 3 days]

define "Encounter With Antibiotic Ordered Within Three Days":
  "Qualifying Encounters" EDOrAmbulatoryVisit
    with ( ( [MedicationRequest: "Antibiotic Medications for Pharyngitis"] ).isMedicationOrder ( ) ) AntibioticOrdered
      such that EDOrAmbulatoryVisit.period.toInterval ( ) starts 3 days or less on or before day of AntibioticOrdered.authoredOn

define "Pharyngitis or Tonsillitis":
  ( [ConditionEncounterDiagnosis: "Acute Pharyngitis"]
      union [ConditionEncounterDiagnosis: "Acute Tonsillitis"]
  ).verified ( )

define "Encounter With Pharyngitis or Tonsillitis With Antibiotic":
  from
    "Encounter With Antibiotic Ordered Within Three Days" VisitWithAntibiotic,
    "Pharyngitis or Tonsillitis" AcutePharyngitisTonsillitis
    where AcutePharyngitisTonsillitis.prevalenceInterval ( ) starts during day of VisitWithAntibiotic.period
    return VisitWithAntibiotic

define "Numerator":
  from
    "Group A Streptococcus Lab Test With Result" GroupAStreptococcusTest,
    "Encounter With Pharyngitis or Tonsillitis With Antibiotic" EncounterWithPharyngitis
    where GroupAStreptococcusTest.effective.toInterval ( ) starts during day of Interval[( end of EncounterWithPharyngitis.period ) - 3 days, ( end of EncounterWithPharyngitis.period ) + 3 days]
    return EncounterWithPharyngitis

define "Initial Population":
  "Encounter With Pharyngitis or Tonsillitis With Antibiotic" EncounterWithPharyngitis
    where AgeInYearsAt(date from start of "Measurement Period") >= 3
    return EncounterWithPharyngitis

define "Denominator":
  "Initial Population"

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

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

define "Encounters and Assessments with Hospice Patient":
  "Initial Population" EligibleEncounters
    where Hospice."Has Hospice Services"

define "Denominator Exclusions":
  "Encounters and Assessments with Hospice Patient"
    union Antibiotic."Encounter with Comorbid Condition History" ( "Encounter With Pharyngitis or Tonsillitis With Antibiotic", ( [ConditionEncounterDiagnosis: "Comorbid Conditions for Respiratory Conditions"] ).verified ( ) )
    union Antibiotic."Encounter with Antibiotic Medication History" ( "Encounter With Pharyngitis or Tonsillitis With Antibiotic", ( [MedicationRequest: "Antibiotic Medications for Pharyngitis"] ).isMedicationActive ( ) )
    union Antibiotic."Encounter with Competing Diagnosis History" ( "Encounter With Pharyngitis or Tonsillitis With Antibiotic", ( [ConditionEncounterDiagnosis: "Competing Conditions for Respiratory Conditions"] ).verified ( ) )

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

define function ToString(value uri): 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
        }

/*
@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: 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

/*
@description: Returns an interval representing the normalized prevalence period of a given Condition.
@comment: Uses the ToInterval and ToAbatementInterval functions to determine the widest potential interval from
onset to abatement as specified in the given Condition. If the condition is active, or has an abatement date the resulting 
interval will have a closed ending boundary. Otherwise, the resulting interval will have an open ending boundary.
*/
define fluent function prevalenceInterval(condition Choice<"ConditionEncounterDiagnosis", "ConditionProblemsHealthConcerns">):
if condition.clinicalStatus ~ "active"
  or condition.clinicalStatus ~ "recurrence"
  or condition.clinicalStatus ~ "relapse" then
  Interval[start of condition.onset.toInterval(), end of condition.abatementInterval()]
else
    (end of condition.abatementInterval()) abatementDate
    return if abatementDate is null then
      Interval[start of condition.onset.toInterval(), abatementDate)
    else
      Interval[start of condition.onset.toInterval(), abatementDate]

/*
@description: Returns an interval representing the normalized abatement of a given Condition.
@comment: If the abatement element of the Condition is represented as a DateTime, the result
is an interval beginning and ending on that DateTime.
If the abatement is represented as a Quantity, the quantity is expected to be a calendar-duration and is interpreted as the age of the patient. The
result is an interval from the date the patient turned that age to immediately before one year later.
If the abatement is represented as a Quantity Interval, the quantities are expected to be calendar-durations and are interpreted as an age range during
which the abatement occurred. The result is an interval from the date the patient turned the starting age of the quantity interval, and ending immediately
before one year later than the date the patient turned the ending age of the quantity interval.
*/
define fluent function abatementInterval(condition Choice<"ConditionEncounterDiagnosis", "ConditionProblemsHealthConcerns">):
	if condition.abatement is DateTime then
	  Interval[condition.abatement as DateTime, condition.abatement as DateTime]
	else if condition.abatement is Quantity then
		Interval[Patient.birthDate + (condition.abatement as Quantity),
			Patient.birthDate + (condition.abatement as Quantity) + 1 year)
	else if condition.abatement is Interval<Quantity> then
	  Interval[Patient.birthDate + (condition.abatement.low as Quantity),
		  Patient.birthDate + (condition.abatement.high as Quantity) + 1 year)
	else if condition.abatement is Interval<DateTime> then
	  Interval[condition.abatement.low, condition.abatement.high)
	else null as Interval<DateTime>

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

//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'

//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'}

//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"
      )

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

//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'

//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'}

define function "Encounter with Comorbid Condition History"(episodes List<Encounter>, comorbidConditions List<ConditionEncounterDiagnosis>):
  episodes episode
      with comorbidConditions comcondition
        such that date from start of comcondition.prevalenceInterval() during Interval[date from start of episode.period - 1 year, date from start of episode.period]
      return episode

define function "Encounter with Antibiotic Medication History"(episodes List<Encounter>, antibioticMedications List<MedicationRequest>):
   episodes episode
    with antibioticMedications ActiveMedication
      such that ActiveMedication.medicationRequestPeriod() overlaps day of Interval[date from start of episode.period  - 30 days, date from start of episode.period - 1 day]

define function "Encounter with Competing Diagnosis History"(episodes List<Encounter>, competingConditions List<ConditionEncounterDiagnosis>):
  episodes episode
      with competingConditions competcondition
        such that competcondition.prevalenceInterval() starts 3 days or less on or after day of start of episode.period
      return episode