define "Qualifying Colonoscopy Procedure Performed":
  ["Procedure": "Colonoscopy"] ColonoscopyPerformed
    where ColonoscopyPerformed.status in { 'completed', 'in-progress' }

define "Qualifying Stool-based Test with Positive Result":
  [Observation: "Colorectal Screening"] ColorectalScreening
    where ColorectalScreening.status in { 'final', 'amended', 'corrected' }
      and ColorectalScreening.value in { 'Positive', 'positive' }
      and ColorectalScreening.effective.toInterval ( ) during day of "Measurement Period"

define "Index Positive Stool-based Test":
  First("Qualifying Stool-based Test with Positive Result" IndexColorectalScreening
      sort by effective
  )

define "Has Follow-up Colonoscopy Within 180 Days of the Index Positive Stool-based Test":
  exists ( "Qualifying Colonoscopy Procedure Performed" ColonoscopyProcedure
      where ColonoscopyProcedure.performed starts 180 days or less on or after "Index Positive Stool-based Test".effective
  )

define "Numerator":
  "Has Follow-up Colonoscopy Within 180 Days of the Index Positive Stool-based Test"

define "Initial Population":
	/***
	Patients aged between 45 and 75 years with at least 1 qualifying stool-based screening with positive result during the measurement period.
	***/
  
  AgeInYearsAt("Index Positive Stool-based Test".effective) in Interval[45, 75]
    and exists ( "Qualifying Stool-based Test with Positive Result" )

define "Denominator":
  "Initial Population"

define "Qualifying Hospital Encounter":
  ( ["Encounter": "Encounter Inpatient"]
    union ["Encounter": "Emergency Department Evaluation and Management Visit"] ) HospitalEncounter
    where HospitalEncounter.status = 'finished'
      and HospitalEncounter.period during "Measurement Period"

define "Index Positive Stool-based Test Done During Hospitalization":
  "Qualifying Hospital Encounter" QualifyingHospitalEncounter
    with "Index Positive Stool-based Test" IndexScreening
      such that IndexScreening.effective.toInterval ( ) starts during day of QualifyingHospitalEncounter.period

define "Had Index Positive Stool-based Test Conducted in Hospital or Emergency Department":
  exists ( "Index Positive Stool-based Test Done During Hospitalization" )

define "Had Positive Stool-based Test Within 365 Days Prior to Index Positive Stool-based Test Result Date":
  exists ( [Observation: "Colorectal Screening"] ColorectalScreening
      where ColorectalScreening.status in { 'final', 'amended', 'corrected' }
        and ColorectalScreening.value in { 'Positive', 'positive' }
        and ColorectalScreening.effective.toInterval ( ) starts 365 days or less before "Index Positive Stool-based Test".effective
  )

define "Had Colorectal Cancer Prior to Index Positive Stool-based Test Result Date":
  exists ( [Condition: "Malignant Neoplasm of Colon"] ColorectalCancerCondition
      where ( ColorectalCancerCondition.clinicalStatus ~ "active"
          or ColorectalCancerCondition.clinicalStatus ~ "recurrence"
          or ColorectalCancerCondition.clinicalStatus ~ "relapse"
      )
        and ColorectalCancerCondition.verificationStatus ~ "confirmed"
        and ColorectalCancerCondition.recordedDate before "Index Positive Stool-based Test".effective
  )

define "Had Total Colectomy Performed Prior to Index Positive Stool-based Test Result Date":
  exists ( [Procedure: "Total Colectomy"] TotalColectomyProcedure
      where TotalColectomyProcedure.status = 'completed'
        and TotalColectomyProcedure.performed ends on or before "Index Positive Stool-based Test".effective
  )

define "Had Hospice Care Within 365 Days Prior to or 180 Days After Index Positive Stool-based Test Result Date":
  exists ( ["Encounter": "Encounter Inpatient"] HospitalEncounter
      where HospitalEncounter.status = 'finished'
        and HospitalEncounter.hospitalization.dischargeDisposition ~ "Discharge to home for hospice care (procedure)"
        and ( HospitalEncounter.period ends 365 days or less on or before "Index Positive Stool-based Test".effective
            or HospitalEncounter.period starts 180 days or less on or after "Index Positive Stool-based Test".effective
        )
  )
    or exists ( [ServiceRequest: "Hospice Care"] HospiceServiceOrder
        where HospiceServiceOrder.intent = 'order'
          and ( HospiceServiceOrder.authoredOn 365 days or less on or before "Index Positive Stool-based Test".effective
              or HospiceServiceOrder.authoredOn 180 days or less on or after "Index Positive Stool-based Test".effective
          )
    )
    or exists ( ( ["Encounter": "Hospice Encounter"]
        union ["Encounter": "Hospice Care Ambulatory"] ) HospiceEncounter
        where HospiceEncounter.status = 'finished'
          and ( HospiceEncounter.period ends 365 days or less on or before "Index Positive Stool-based Test".effective
              or HospiceEncounter.period starts 180 days or less on or after "Index Positive Stool-based Test".effective
          )
    )

define "Had Palliative Care Within 365 Days Prior to or 180 Days After Index Positive Stool-based Test Result Date":
  exists ( ["Procedure": "Palliative Care"] PalliativeCareProcedure
      where PalliativeCareProcedure.status = 'completed'
        and PalliativeCareProcedure.performed ends 365 days or less on or before "Index Positive Stool-based Test".effective
        or PalliativeCareProcedure.performed starts 180 days or less on or after "Index Positive Stool-based Test".effective
  )
    or exists ( [ServiceRequest: "Palliative Care"] PalliativeCareService
        where PalliativeCareService.intent = 'order'
          and ( PalliativeCareService.authoredOn 365 days or less on or before "Index Positive Stool-based Test".effective
              or PalliativeCareService.authoredOn 180 days or less on or after "Index Positive Stool-based Test".effective
          )
    )
    or exists ( ["Encounter": "Palliative Care Encounter"] PalliativeCareEncounter
        where PalliativeCareEncounter.status = 'finished'
          and ( PalliativeCareEncounter.period ends 365 days or less on or before "Index Positive Stool-based Test".effective
              or PalliativeCareEncounter.period starts 180 days or less on or after "Index Positive Stool-based Test".effective
          )
    )

define "Denominator Exclusions":
  "Had Index Positive Stool-based Test Conducted in Hospital or Emergency Department"
    or "Had Positive Stool-based Test Within 365 Days Prior to Index Positive Stool-based Test Result Date"
    or "Had Colorectal Cancer Prior to Index Positive Stool-based Test Result Date"
    or "Had Total Colectomy Performed Prior to Index Positive Stool-based Test Result Date"
    or "Had Hospice Care Within 365 Days Prior to or 180 Days After Index Positive Stool-based Test Result Date"
    or "Had Palliative Care Within 365 Days Prior to or 180 Days After Index Positive Stool-based Test Result Date"

define "Has Colonoscopy Procedure Performed Within 3 Years Prior to the Index Positive Stool-based Test":
  exists ( "Qualifying Colonoscopy Procedure Performed" ColonoscopyProcedure
      where ColonoscopyProcedure.performed starts 3 years or less before "Index Positive Stool-based Test".effective
  )

define "Patient Deceased Within 180 Days of the Index Positive Stool-based Test":
  Patient.deceased.toInterval ( ) starts 180 days or less on or after "Index Positive Stool-based Test".effective

define "Denominator Exceptions":
  "Has Colonoscopy Procedure Performed Within 3 Years Prior to the Index Positive Stool-based Test"
    or "Patient Deceased Within 180 Days of the Index Positive Stool-based Test"

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

define "Qualifying Colonoscopy Procedure Performed":
  ["Procedure": "Colonoscopy"] ColonoscopyPerformed
    where ColonoscopyPerformed.status in { 'completed', 'in-progress' }

define "Qualifying Stool-based Test with Positive Result":
  [Observation: "Colorectal Screening"] ColorectalScreening
    where ColorectalScreening.status in { 'final', 'amended', 'corrected' }
      and ColorectalScreening.value in { 'Positive', 'positive' }
      and ColorectalScreening.effective.toInterval ( ) during day of "Measurement Period"

define "Index Positive Stool-based Test":
  First("Qualifying Stool-based Test with Positive Result" IndexColorectalScreening
      sort by effective
  )

define "Has Follow-up Colonoscopy Within 180 Days of the Index Positive Stool-based Test":
  exists ( "Qualifying Colonoscopy Procedure Performed" ColonoscopyProcedure
      where ColonoscopyProcedure.performed starts 180 days or less on or after "Index Positive Stool-based Test".effective
  )

define "Numerator":
  "Has Follow-up Colonoscopy Within 180 Days of the Index Positive Stool-based Test"

define "Initial Population":
	/***
	Patients aged between 45 and 75 years with at least 1 qualifying stool-based screening with positive result during the measurement period.
	***/
  
  AgeInYearsAt("Index Positive Stool-based Test".effective) in Interval[45, 75]
    and exists ( "Qualifying Stool-based Test with Positive Result" )

define "Denominator":
  "Initial Population"

define "Qualifying Hospital Encounter":
  ( ["Encounter": "Encounter Inpatient"]
    union ["Encounter": "Emergency Department Evaluation and Management Visit"] ) HospitalEncounter
    where HospitalEncounter.status = 'finished'
      and HospitalEncounter.period during "Measurement Period"

define "Index Positive Stool-based Test Done During Hospitalization":
  "Qualifying Hospital Encounter" QualifyingHospitalEncounter
    with "Index Positive Stool-based Test" IndexScreening
      such that IndexScreening.effective.toInterval ( ) starts during day of QualifyingHospitalEncounter.period

define "Had Index Positive Stool-based Test Conducted in Hospital or Emergency Department":
  exists ( "Index Positive Stool-based Test Done During Hospitalization" )

define "Had Positive Stool-based Test Within 365 Days Prior to Index Positive Stool-based Test Result Date":
  exists ( [Observation: "Colorectal Screening"] ColorectalScreening
      where ColorectalScreening.status in { 'final', 'amended', 'corrected' }
        and ColorectalScreening.value in { 'Positive', 'positive' }
        and ColorectalScreening.effective.toInterval ( ) starts 365 days or less before "Index Positive Stool-based Test".effective
  )

define "Had Colorectal Cancer Prior to Index Positive Stool-based Test Result Date":
  exists ( [Condition: "Malignant Neoplasm of Colon"] ColorectalCancerCondition
      where ( ColorectalCancerCondition.clinicalStatus ~ "active"
          or ColorectalCancerCondition.clinicalStatus ~ "recurrence"
          or ColorectalCancerCondition.clinicalStatus ~ "relapse"
      )
        and ColorectalCancerCondition.verificationStatus ~ "confirmed"
        and ColorectalCancerCondition.recordedDate before "Index Positive Stool-based Test".effective
  )

define "Had Total Colectomy Performed Prior to Index Positive Stool-based Test Result Date":
  exists ( [Procedure: "Total Colectomy"] TotalColectomyProcedure
      where TotalColectomyProcedure.status = 'completed'
        and TotalColectomyProcedure.performed ends on or before "Index Positive Stool-based Test".effective
  )

define "Had Hospice Care Within 365 Days Prior to or 180 Days After Index Positive Stool-based Test Result Date":
  exists ( ["Encounter": "Encounter Inpatient"] HospitalEncounter
      where HospitalEncounter.status = 'finished'
        and HospitalEncounter.hospitalization.dischargeDisposition ~ "Discharge to home for hospice care (procedure)"
        and ( HospitalEncounter.period ends 365 days or less on or before "Index Positive Stool-based Test".effective
            or HospitalEncounter.period starts 180 days or less on or after "Index Positive Stool-based Test".effective
        )
  )
    or exists ( [ServiceRequest: "Hospice Care"] HospiceServiceOrder
        where HospiceServiceOrder.intent = 'order'
          and ( HospiceServiceOrder.authoredOn 365 days or less on or before "Index Positive Stool-based Test".effective
              or HospiceServiceOrder.authoredOn 180 days or less on or after "Index Positive Stool-based Test".effective
          )
    )
    or exists ( ( ["Encounter": "Hospice Encounter"]
        union ["Encounter": "Hospice Care Ambulatory"] ) HospiceEncounter
        where HospiceEncounter.status = 'finished'
          and ( HospiceEncounter.period ends 365 days or less on or before "Index Positive Stool-based Test".effective
              or HospiceEncounter.period starts 180 days or less on or after "Index Positive Stool-based Test".effective
          )
    )

define "Had Palliative Care Within 365 Days Prior to or 180 Days After Index Positive Stool-based Test Result Date":
  exists ( ["Procedure": "Palliative Care"] PalliativeCareProcedure
      where PalliativeCareProcedure.status = 'completed'
        and PalliativeCareProcedure.performed ends 365 days or less on or before "Index Positive Stool-based Test".effective
        or PalliativeCareProcedure.performed starts 180 days or less on or after "Index Positive Stool-based Test".effective
  )
    or exists ( [ServiceRequest: "Palliative Care"] PalliativeCareService
        where PalliativeCareService.intent = 'order'
          and ( PalliativeCareService.authoredOn 365 days or less on or before "Index Positive Stool-based Test".effective
              or PalliativeCareService.authoredOn 180 days or less on or after "Index Positive Stool-based Test".effective
          )
    )
    or exists ( ["Encounter": "Palliative Care Encounter"] PalliativeCareEncounter
        where PalliativeCareEncounter.status = 'finished'
          and ( PalliativeCareEncounter.period ends 365 days or less on or before "Index Positive Stool-based Test".effective
              or PalliativeCareEncounter.period starts 180 days or less on or after "Index Positive Stool-based Test".effective
          )
    )

define "Denominator Exclusions":
  "Had Index Positive Stool-based Test Conducted in Hospital or Emergency Department"
    or "Had Positive Stool-based Test Within 365 Days Prior to Index Positive Stool-based Test Result Date"
    or "Had Colorectal Cancer Prior to Index Positive Stool-based Test Result Date"
    or "Had Total Colectomy Performed Prior to Index Positive Stool-based Test Result Date"
    or "Had Hospice Care Within 365 Days Prior to or 180 Days After Index Positive Stool-based Test Result Date"
    or "Had Palliative Care Within 365 Days Prior to or 180 Days After Index Positive Stool-based Test Result Date"

define "Has Colonoscopy Procedure Performed Within 3 Years Prior to the Index Positive Stool-based Test":
  exists ( "Qualifying Colonoscopy Procedure Performed" ColonoscopyProcedure
      where ColonoscopyProcedure.performed starts 3 years or less before "Index Positive Stool-based Test".effective
  )

define "Patient Deceased Within 180 Days of the Index Positive Stool-based Test":
  Patient.deceased.toInterval ( ) starts 180 days or less on or after "Index Positive Stool-based Test".effective

define "Denominator Exceptions":
  "Has Colonoscopy Procedure Performed Within 3 Years Prior to the Index Positive Stool-based Test"
    or "Patient Deceased Within 180 Days of the Index Positive Stool-based Test"

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