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

define "Denominator":
  "Initial Population"

define "Denominator Exclusions":
  "Encounter Less Than Two Days"
    union "Encounter With Comfort Measures During Day Of Or Day After Arrival"
    union "Encounter With Thrombolytic Therapy Given Prior To Arrival Or During Hospitalization"

define "Denominator Exceptions":
  "Encounter With Documented Reason For No Antithrombotic Ordered Or Administered Day Of Or Day After Hospital Arrival"
    union "Encounter With Pharmacological Contraindications For Antithrombotic Therapy Given Day Of Or Day After Hospital Arrival"
    union "Encounter With An INR Greater Than 3.5"

define "Numerator":
  "Encounter With Antithrombotic Therapy"

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 Antithrombotic Therapy":
  TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
    with ["MedicationAdministration": "Antithrombotic Therapy for Ischemic Stroke"] Antithrombotic
      such that Antithrombotic.status in { 'in-progress', 'completed' }
        and Antithrombotic.effective.toInterval ( ) starts during day of ( start of IschemicStrokeEncounter.hospitalizationWithObservation ( ) ).calendarDayOfOrDayAfter ( )

define "Numerator":
  "Encounter With Antithrombotic Therapy"

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

define "Denominator":
  "Initial Population"

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

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

define "Encounter Less Than Two Days":
  TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
    where IschemicStrokeEncounter.hospitalizationWithObservation ( ).lengthInDays ( ) < 2

define "Encounter With Comfort Measures During Day Of Or Day After Arrival":
  TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
    with TJC."Intervention Comfort Measures" ComfortMeasure
      such that Coalesce(start of ComfortMeasure.performed.toInterval(), ComfortMeasure.authoredOn) during day of ( start of IschemicStrokeEncounter.hospitalizationWithObservation ( ) ).calendarDayOfOrDayAfter ( )

define "Thrombolytic Therapy Medication Or Procedures":
  ( ["MedicationAdministration": "Thrombolytic tPA Therapy"] ThrombolyticMedication
      where ThrombolyticMedication.status in { 'in-progress', 'completed' }
      return {
        id: ThrombolyticMedication.id,
        effective: ThrombolyticMedication.effective
      }
  )
    union ( ["Procedure": "Intravenous or Intraarterial Thrombolytic tPA Therapy"] ThrombolyticProcedure
        where ThrombolyticProcedure.status = 'completed'
        return {
          id: ThrombolyticProcedure.id,
          effective: ThrombolyticProcedure.performed
        }
    )

define "Encounter With Thrombolytic Therapy Medication Or Procedures":
  TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
    with "Thrombolytic Therapy Medication Or Procedures" ThrombolyticTherapy
      such that ThrombolyticTherapy.effective.toInterval ( ) starts during Interval[start of IschemicStrokeEncounter.hospitalizationWithObservation ( ) - 24 hours, end of IschemicStrokeEncounter.hospitalizationWithObservation ( ) )

define "Encounter With Thrombolytic Therapy Prior To Arrival":
  TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
    where exists ( ( IschemicStrokeEncounter.encounterDiagnosis ( ) ) EncounterDiagnosis
        where EncounterDiagnosis.code in "Intravenous or Intraarterial Thrombolytic tPA Therapy Prior to Arrival"
    )

define "Encounter With Thrombolytic Therapy Documented As Already Given":
  ( TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
      where exists [ConditionProblemsHealthConcerns: "Intravenous or Intraarterial Thrombolytic tPA Therapy Prior to Arrival"] PriorTPA
        where PriorTPA.recordedDate during IschemicStrokeEncounter.hospitalizationWithObservation ( )
          and PriorTPA.verificationStatus is not null implies ( PriorTPA.verificationStatus !~ Status."refuted"
            and PriorTPA.verificationStatus !~ Status."entered-in-error" 
        )
  )
    union TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
      where exists ( ( IschemicStrokeEncounter.encounterDiagnosis ( ) ) EncounterDiagnosis
          where EncounterDiagnosis.code in "Intravenous or Intraarterial Thrombolytic tPA Therapy Prior to Arrival"
      )

define "Encounter With Thrombolytic Therapy Given Prior To Arrival Or During Hospitalization":
  "Encounter With Thrombolytic Therapy Medication Or Procedures"
    union "Encounter With Thrombolytic Therapy Prior To Arrival"
    union "Encounter With Thrombolytic Therapy Documented As Already Given"

define "Denominator Exclusions":
  "Encounter Less Than Two Days"
    union "Encounter With Comfort Measures During Day Of Or Day After Arrival"
    union "Encounter With Thrombolytic Therapy Given Prior To Arrival Or During Hospitalization"

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

define "Reason For Not Ordering Antithrombotic":
  ( ["MedicationNotRequested": "Antithrombotic Therapy for Ischemic Stroke"] NoAntithromboticOrder
      where ( NoAntithromboticOrder.reasonCode in "Medical Reason for Not Providing Treatment"
          or NoAntithromboticOrder.reasonCode in "Patient Refusal"
      )
        and NoAntithromboticOrder.status in { 'active', 'completed' }
        and NoAntithromboticOrder.intent in { 'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order' }
      return {
        id: NoAntithromboticOrder.id,
        authoredOn: NoAntithromboticOrder.authoredOn
      }
  )
    union ( ["MedicationRequest": "Antithrombotic Therapy for Ischemic Stroke"] MedReqAntithrombotic
        with ["TaskRejected"] TaskReject
          such that TaskReject.focus.references ( MedReqAntithrombotic )
            and ( TaskReject.statusReason in "Medical Reason for Not Providing Treatment"
                or TaskReject.statusReason in "Patient Refusal"
            )
            and ( MedReqAntithrombotic.status in { 'active', 'completed' }
                and TaskReject.code ~ USQualityCoreCommon."Fulfill"
            )
        return {
          id: MedReqAntithrombotic.id,
          authoredOn: MedReqAntithrombotic.authoredOn
        }
    )

define "Reason For Not Administering Antithrombotic":
  ["MedicationAdministrationNotDone": "Antithrombotic Therapy for Ischemic Stroke"] MedicationAdm
    where ( MedicationAdm.statusReason in "Medical Reason for Not Providing Treatment"
        or MedicationAdm.statusReason in "Patient Refusal"
    )
    return {
      id: MedicationAdm.id,
      authoredOn: MedicationAdm.effective
    }

define "Documented Reason For No Antithrombotic Ordered Or Administered":
  "Reason For Not Ordering Antithrombotic"
    union "Reason For Not Administering Antithrombotic"

define "Encounter With Documented Reason For No Antithrombotic Ordered Or Administered Day Of Or Day After Hospital Arrival":
  TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
    with "Documented Reason For No Antithrombotic Ordered Or Administered" NoAntithrombotic
      such that NoAntithrombotic.authoredOn during day of ( start of IschemicStrokeEncounter.hospitalizationWithObservation ( ) ).calendarDayOfOrDayAfter ( )

define "Encounter With Pharmacological Contraindications For Antithrombotic Therapy Given Day Of Or Day After Hospital Arrival":
  TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
    with ["MedicationAdministration": "Pharmacological Contraindications For Antithrombotic Therapy"] PharmacologicalContraindications
      such that PharmacologicalContraindications.status in { 'in-progress', 'completed' }
        and PharmacologicalContraindications.effective.toInterval ( ) starts during day of ( start of IschemicStrokeEncounter.hospitalizationWithObservation ( ) ).calendarDayOfOrDayAfter ( )

define "Encounter With An INR Greater Than 3.5":
  TJC."Ischemic Stroke Encounter" IschemicStrokeEncounter
    with ["LaboratoryResultObservation": "INR"] INR
      such that INR.value as Quantity > 3.5
        and INR.status in { 'final', 'amended', 'corrected' }
        and INR.issued during day of ( start of IschemicStrokeEncounter.hospitalizationWithObservation ( ) ).calendarDayOfOrDayAfter ( )

define "Denominator Exceptions":
  "Encounter With Documented Reason For No Antithrombotic Ordered Or Administered Day Of Or Day After Hospital Arrival"
    union "Encounter With Pharmacological Contraindications For Antithrombotic Therapy Given Day Of Or Day After Hospital Arrival"
    union "Encounter With An INR Greater Than 3.5"

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 fluent function calendarDayOfOrDayAfter(StartValue DateTime):
  Interval [date from (StartValue), date from (StartValue) + 1 day]

/*
@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: 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

/*
 @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: 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: Calculates the difference in calendar days between the start and end of the given interval.
*/
define fluent function lengthInDays(Value Interval<DateTime> ):
  difference in days between start of Value and end of Value

/*  
@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: 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
    }

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 MedicationAdministrationStatus): 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 EncounterStatus): value.value

define function ToString(value ServiceRequestStatus): value.value

define function ToString(value ServiceRequestIntent): value.value

define function ToString(value ProcedureStatus): value.value

define function ToString(value MedicationRequestStatus): value.value

define function ToString(value MedicationRequestIntent): value.value

define function ToString(value ObservationStatus): value.value