define "Initial Population":
  TJC."Ischemic Stroke Encounter"

define "Denominator":
  "Encounter With A History Of Atrial Ablation"
    union "Encounter With Prior Or Present Diagnosis Of Atrial Fibrillation Or Flutter"

define "Denominator Exclusions":
  ( "Denominator" Encounter
      where Encounter.status = 'finished'
        and ( Encounter.hospitalization.dischargeDisposition in "Discharge To Acute Care Facility"
            or Encounter.hospitalization.dischargeDisposition in "Left Against Medical Advice"
            or Encounter.hospitalization.dischargeDisposition in "Patient Expired"
            or Encounter.hospitalization.dischargeDisposition in "Discharged to Home for Hospice Care"
            or Encounter.hospitalization.dischargeDisposition in "Discharged to Health Care Facility for Hospice Care"
        )
  )
    union "Encounter With Comfort Measures During Hospitalization For Patients With Documented Atrial Fibrillation Or Flutter"

define "Denominator Exceptions":
  "Denominator" Encounter
    with "Documented Reason For Not Giving Anticoagulant At Discharge" NoDischargeAnticoagulant
      such that NoDischargeAnticoagulant.authoredOn during Encounter.period

define "Numerator":
  "Denominator" Encounter
    with ["MedicationRequest": "Anticoagulant Therapy"] DischargeAnticoagulant
      such that DischargeAnticoagulant.status in { 'active', 'completed' }
        and DischargeAnticoagulant.intent in { 'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order' }
        and ( DischargeAnticoagulant.isCommunity ( )
            or DischargeAnticoagulant.isDischarge ( )
        )
        and DischargeAnticoagulant.authoredOn during Encounter.period
        and not exists ( ["TaskRejected"] TaskReject
            where TaskReject.focus.references ( DischargeAnticoagulant )
              and TaskReject.code ~ USQualityCoreCommon."Fulfill"
        )

define "Non Elective Inpatient Encounter With Age":
  ["Encounter": "Nonelective Inpatient Encounter"] NonElectiveEncounter
        where AgeInYearsAt(date from start of NonElectiveEncounter.period ) >= 18
         and NonElectiveEncounter.period ends during day of "Measurement Period"

define "Ischemic Stroke Encounter":
  "Non Elective Inpatient Encounter With Age" NonElectiveEncounterWithAge
   where NonElectiveEncounterWithAge.hasPrincipalDiagnosisOf("Ischemic Stroke" )

define "Intervention Comfort Measures":
  ( ["ServiceRequest": "Comfort Measures"] ComfortCare
    where ComfortCare.status in { 'active', 'completed', 'on-hold' }
      and ComfortCare.intent in { 'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order' }
  )  
  union ( ["Procedure": "Comfort Measures"] ComfortCarePerformed
        where ComfortCarePerformed.status in { 'completed', 'in-progress' }
  )

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

define "SDE Payer":
  [USQualityCore.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 "Encounter With A History Of Atrial Ablation":
  ( TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
      where exists ( ["Procedure": "Atrial Ablation"] AtrialAblationProcedure
          where AtrialAblationProcedure.status = 'completed'
            and AtrialAblationProcedure.performed.toInterval ( ) starts before start of IschemicStrokeEncounter.period
      )
  )
    union ( TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
        with ["ConditionProblemsHealthConcerns": "History of Atrial Ablation"] AtrialAblationDiagnosis
          such that AtrialAblationDiagnosis.verificationStatus is not null implies ( AtrialAblationDiagnosis.verificationStatus !~ Status."refuted"
              and AtrialAblationDiagnosis.verificationStatus !~ Status."entered-in-error"
          )
            and AtrialAblationDiagnosis.onset.toInterval ( ) starts before start of IschemicStrokeEncounter.period
    )
    union ( TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
        with ["SimpleObservation": "History of Atrial Ablation"] AtrialAblationObservation
          such that AtrialAblationObservation.status in { 'final', 'amended', 'corrected' }
            and AtrialAblationObservation.effective.earliest ( ) on or before end of IschemicStrokeEncounter.period
    )
    union ( TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
        with ["ConditionEncounterDiagnosis": "History of Atrial Ablation"] AtrialAblationEncDiagnosis
          such that AtrialAblationEncDiagnosis.verificationStatus is not null implies ( AtrialAblationEncDiagnosis.verificationStatus !~ Status."refuted"
              and AtrialAblationEncDiagnosis.verificationStatus !~ Status."entered-in-error"
          )
            and AtrialAblationEncDiagnosis.onset.toInterval ( ) starts before start of IschemicStrokeEncounter.period
    )

define "Encounter With Prior Or Present Diagnosis Of Atrial Fibrillation Or Flutter":
  ( TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
      with ["ConditionProblemsHealthConcerns": "Atrial Fibrillation or Flutter"] AtrialFibrillationFlutter
        such that AtrialFibrillationFlutter.verificationStatus is not null implies ( AtrialFibrillationFlutter.verificationStatus !~ Status."refuted"
            and AtrialFibrillationFlutter.verificationStatus !~ Status."entered-in-error"
        )
          and AtrialFibrillationFlutter.onset.toInterval ( ) starts on or before end of IschemicStrokeEncounter.period
  )
    union TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
      where exists ( ( IschemicStrokeEncounter.encounterDiagnosis ( ) ) EncounterDiagnosis
          where EncounterDiagnosis.code in "Atrial Fibrillation or Flutter"
      )

define "Denominator":
  "Encounter With A History Of Atrial Ablation"
    union "Encounter With Prior Or Present Diagnosis Of Atrial Fibrillation Or Flutter"

define "Numerator":
  "Denominator" Encounter
    with ["MedicationRequest": "Anticoagulant Therapy"] DischargeAnticoagulant
      such that DischargeAnticoagulant.status in { 'active', 'completed' }
        and DischargeAnticoagulant.intent in { 'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order' }
        and ( DischargeAnticoagulant.isCommunity ( )
            or DischargeAnticoagulant.isDischarge ( )
        )
        and DischargeAnticoagulant.authoredOn during Encounter.period
        and not exists ( ["TaskRejected"] TaskReject
            where TaskReject.focus.references ( DischargeAnticoagulant )
              and TaskReject.code ~ USQualityCoreCommon."Fulfill"
        )

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

define "Initial Population":
  TJC."Ischemic Stroke Encounter"

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

define "Encounter With Comfort Measures During Hospitalization For Patients With Documented Atrial Fibrillation Or Flutter":
  "Denominator" Encounter
    with TJC."Intervention Comfort Measures" ComfortMeasure
      such that Coalesce(start of ComfortMeasure.performed.toInterval(), ComfortMeasure.authoredOn) during Encounter.hospitalizationWithObservation ( )

define "Denominator Exclusions":
  ( "Denominator" Encounter
      where Encounter.status = 'finished'
        and ( Encounter.hospitalization.dischargeDisposition in "Discharge To Acute Care Facility"
            or Encounter.hospitalization.dischargeDisposition in "Left Against Medical Advice"
            or Encounter.hospitalization.dischargeDisposition in "Patient Expired"
            or Encounter.hospitalization.dischargeDisposition in "Discharged to Home for Hospice Care"
            or Encounter.hospitalization.dischargeDisposition in "Discharged to Health Care Facility for Hospice Care"
        )
  )
    union "Encounter With Comfort Measures During Hospitalization For Patients With Documented Atrial Fibrillation Or Flutter"

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

define "Documented Reason For Not Giving Anticoagulant At Discharge":
  ( ["MedicationNotRequested": "Anticoagulant Therapy"] NoAnticoagulant
      where ( NoAnticoagulant.reasonCode in "Medical Reason For Not Providing Treatment"
          or NoAnticoagulant.reasonCode in "Patient Refusal"
      )
        and ( NoAnticoagulant.isCommunity ( )
            or NoAnticoagulant.isDischarge ( )
        )
        and NoAnticoagulant.status in { 'active', 'completed' }
        and NoAnticoagulant.intent in { 'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order' }
  )
    union ( ["MedicationRequest": "Anticoagulant Therapy"] MedReqAntiCoagulant
        with ["TaskRejected"] TaskReject
          such that TaskReject.focus.references ( MedReqAntiCoagulant )
            and ( TaskReject.statusReason in "Medical Reason For Not Providing Treatment"
                or TaskReject.statusReason in "Patient Refusal"
            )
            and MedReqAntiCoagulant.status in { 'active', 'completed' }
            and TaskReject.code ~ USQualityCoreCommon."Fulfill"
    )

define "Denominator Exceptions":
  "Denominator" Encounter
    with "Documented Reason For Not Giving Anticoagulant At Discharge" NoDischargeAnticoagulant
      such that NoDischargeAnticoagulant.authoredOn during Encounter.period

/*
@description: Returns the single extension (if present) on the given resource with the specified url.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given resource with the specified url.
*/
define fluent function ext(domainResource DomainResource, url String):
  singleton from domainResource.exts(url)

/*
@description: Returns any extensions defined on the given resource with the specified url
*/
define fluent function exts(domainResource DomainResource, url String):
  domainResource.extension E
    where E.url = url
    return E

/*
@description: Returns true if any of the given references are to the given resource
@comment: Returns true if the `id` element of the given resource exactly equals the tail of any of the given references.
NOTE: This function assumes resources from the same source server.
*/
define fluent function references(references List<FHIR.Reference>, resource FHIR.Resource):
  exists (references R where R.references(resource))

/*
@description: Returns true if the given reference is to the given resource
@comment: Returns true if the `id` element of the given resource exactly equals the tail of the given reference.
NOTE: This function assumes resources from the same source server.
*/
define fluent function references(reference FHIR.Reference, resource FHIR.Resource):
  resource.id = Last(Split(reference.reference, '/'))

/*
@description: Returns true if the given code is in the given codeList
@comment: Returns true if the `code` is equivalent to any of the codes in the given `codeList`, false otherwise.
*/
define fluent function includesCode(codeList List<CodeableConcept>, code Concept):
  exists (codeList C where C ~ code)

/*
@description: Returns true if the given reference is to the given resourceId
@comment: Returns true if the `resourceId` parameter exactly equals the tail of the given reference.
NOTE: This function assumes resources from the same source server.
*/
define fluent function references(reference FHIR.Reference, resourceId String):
  resourceId = Last(Split(reference.reference, '/'))

/*
@description: Normalizes a value that is a choice of timing-valued types to an equivalent interval
@comment: Normalizes a choice type of FHIR.dateTime, FHIR.Period, FHIR.Timing, FHIR.instance, FHIR.string, FHIR.Age, or FHIR.Range 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 FHIR, allowing this function to be used across any resource.

The input can be provided as a dateTime, Period, Timing, instant, string, Age, or Range.
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 Period, the result is a DateTime Interval.
If the input is a Timing, an error is raised indicating a single interval cannot be computed from a Timing.
If the input is an instant, the result is a DateTime Interval beginning and ending on that instant.
If the input is a string, an error is raised indicating a single interval cannot be computed from a string.
If the input is an Age, the result is a DateTime Interval beginning when the patient was the given Age,
and ending immediately prior to when the patient was the given Age plus one year.
If the input is a Range, the result is a DateTime Interval beginning when the patient was the Age given
by the low end of the Range, and ending immediately prior to when the patient was the Age given by the
high end of the Range plus one year.

NOTE: Due to the
complexity of determining a single interval from a Timing or String type, this function will throw a run-time exception if it is used
with a Timing or String.
*/
define fluent function toInterval(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, 'NOT_IMPLEMENTED', 'Error', 'Calculation of an interval from a Timing value is not supported')
    when choice is FHIR.string then
      Message(null as Interval<DateTime>, true, 'NOT_IMPLEMENTED', 'Error', 'Calculation of an interval from a String value is not supported')
    else
      null as Interval<DateTime>
  end

/*
@description: Given an interval, return the starting point if the interval has a starting boundary specified,
otherwise, return the ending point
*/
define fluent function earliest(choice Choice<FHIR.dateTime, FHIR.Period, FHIR.Age, FHIR.Range>):
  (choice.toInterval()) period
    return
      if (period.hasStart()) then start of period
      else end of period

/*
@description: Given an interval, return true if the interval has a starting boundary specified
(i.e. the start of the interval is not null and not the minimum DateTime value)
*/
define fluent function hasStart(period Interval<DateTime>):
  not ( start of period is null
      or start of period = minimum DateTime
  )

/*
@description: Returns true if the given MedicationRequest has a category of Community
*/
define fluent function isCommunity(medicationRequest MedicationRequest):
  exists (medicationRequest.category C
    where C ~ Community
  )

/*
@description: Returns true if the given MedicationRequest has a category of Discharge
*/
define fluent function isDischarge(medicationRequest MedicationRequest):
  exists (medicationRequest.category C
    where C ~ Discharge
  )

/*
@description: Returns the single extension (if present) on the given element with the specified url.
@comment: This function uses singleton from to ensure that a run-time exception is thrown if there
is more than one extension on the given element with the specified url.
*/
define fluent function ext(element Element, url String):
  singleton from element.exts(url)

/*
@description: Returns any extensions defined on the given element with the specified url.
*/
define fluent function exts(element Element, url String):
  element.extension E
    where E.url = url
    return E

define function ToString(value string): value.value

define function ToString(value uri): value.value

define function ToDate(value date): 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 ToString(value ClaimStatus): value.value

define function ToString(value Use): 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 ProcedureStatus): value.value

define function ToDateTime(value dateTime): value.value

define function ToDateTime(value instant): 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 ObservationStatus): value.value

define function ToString(value MedicationRequestStatus): value.value

define function ToString(value MedicationRequestIntent): value.value

define function ToString(value EncounterStatus): value.value

define function ToString(value ServiceRequestStatus): value.value

define function ToString(value ServiceRequestIntent): value.value

/*
 @description: Returns the condition that is specified as the principal diagnosis for the encounter and has a code in the given valueSet.
 @comment: See the QICore 6 Authoring Patterns discussion on [Principal Diagnosis and Present on Admission](https://github.com/cqframework/CQL-Formatting-and-Usage-Wiki/wiki/Authoring-Patterns-QICore-v6.0.0#conditions-present-on-admission-and-principal-diagnoses) for more information
 */
 define fluent function hasPrincipalDiagnosisOf(encounter Encounter, valueSet System.ValueSet):
   (encounter.principalDiagnosis()) PD
     return PD.diagnosis in valueSet
       or PD.diagnosis.getCondition().code in valueSet

/*
@description: Returns the claim diagnosis element that is specified as the principal diagnosis for the encounter
 @comment: See the QICore 6 Authoring Patterns discussion on [Principal Diagnosis and Present on Admission](https://github.com/cqframework/CQL-Formatting-and-Usage-Wiki/wiki/Authoring-Patterns-QICore-v6.0.0#conditions-present-on-admission-and-principal-diagnoses) for more information
*/
define fluent function principalDiagnosis(encounter Encounter):
singleton from (
     (encounter.claimDiagnosis()) CD
       where CD.type.includesCode("Principal Diagnosis")
   )

/*
@description: Returns the claim diagnosis elements for the given encounter
@comment: See the QICore 6 Authoring Patterns discussion on [Principal Diagnosis and Present on Admission](https://github.com/cqframework/CQL-Formatting-and-Usage-Wiki/wiki/Authoring-Patterns-QICore-v6.0.0#conditions-present-on-admission-and-principal-diagnoses) for more information
*/
define fluent function claimDiagnosis(encounter Encounter):
  encounter E
    let 
      claim: ([Claim] C where C.status = 'active' and C.use = 'claim' and exists (C.item I where I.encounter.references(E))),
      claimItem: (claim.item I where I.encounter.references(E))
    return claim.diagnosis D where D.sequence in claimItem.diagnosisSequence

/*
@description: Returns the Condition resource for the given reference
*/
define fluent function getCondition(reference Reference):
  singleton from (([ConditionEncounterDiagnosis] union [ConditionProblemsHealthConcerns]) C where reference.references(C.id))

/*  
@description: Returns the Condition resources referenced by the diagnosis element of the Encounter  
*/
define fluent function encounterDiagnosis(Encounter Encounter ):
  Encounter.reasonReference D
    return singleton from (([ConditionEncounterDiagnosis] union [ConditionProblemsHealthConcerns]) C where D.references(C.id))

/*
@description: Hospitalization with Observation returns the total interval from the start of any immediately prior emergency department visit through the observation visit to the discharge of the given encounter
*/
define fluent function hospitalizationWithObservation(TheEncounter Encounter ):
  TheEncounter Visit
  		let ObsVisit: Last([Encounter: "Observation Services"] LastObs
  				where LastObs.status = 'finished'
            and LastObs.period ends 1 hour or less on or before start of Visit.period
  				sort by end of period
  			),
  			VisitStart: Coalesce(start of ObsVisit.period, start of Visit.period),
  			EDVisit: Last([Encounter: "Emergency Department Visit"] LastED
  				where LastED.status = 'finished'
            and LastED.period ends 1 hour or less on or before VisitStart
  				sort by end of period
  			)
  		return Interval[Coalesce(start of EDVisit.period, VisitStart), end of Visit.period]

/*
@description: Returns the sex element as defined for the USCore patient profile
*/
define fluent function sex(patient Patient):
  patient.ext('http://hl7.org/fhir/us/core/StructureDefinition/us-core-sex').value as FHIR.code

define fluent function ethnicity(patient Patient):
  (patient.ext('http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity')) E
    return {
      ombCategory: E.ext('ombCategory').value as FHIR.Coding,
      detailed: (E.exts('detailed')) d return d.value as FHIR.Coding,
      text: E.ext('text').value as FHIR.string
    }

define fluent function race(patient Patient):
  (patient.ext('http://hl7.org/fhir/us/core/StructureDefinition/us-core-race')) E
    return {
      ombCategory: (E.exts('ombCategory')) o return o.value as FHIR.Coding,
      detailed: (E.exts('detailed')) d return d.value as FHIR.Coding,
      text: E.ext('text').value as FHIR.string
    }