define "HIV Status Positive Condition":
  [Condition: Concepts."HIV-positive - HIV.B.DE116"] C
    where C.clinicalStatus ~ ConceptsCustom."active"
      and exists(C.category CC where CC ~ ConceptsCustom."encounter-diagnosis")
    sort by start of onset.toInterval()

define "HIV Status Positive Condition":
  Elements."HIV Status Positive Condition" C
  where C.onset before end of "Measurement Period"

/* End of HIV-inconclusive */

/*
@dataElement: HIV.B.DE115 - HIV status
@activity: HIV.B7 Test for HIV using testing algorithm
@description: HIV status reported after applying the national HIV testing algorithm. No single HIV test can provide an HIV-positive diagnosis.
*/
define "HIV Status Observation":
  [Observation: Concepts."HIV status"] O
    where O.status in { 'final', 'amended', 'corrected' }

define "HIV Status Positive Observation":
"HIV Status Observation" O
    where O.value ~ Concepts."HIV-positive - HIV.B.DE116"
      sort by start of effective.toInterval()

define "HIV Status Positive Observation":
  Elements."HIV Status Positive Observation" O
  where O.issued before end of "Measurement Period"
  or O.effective.toInterval() starts before end of "Measurement Period"

define "Has HIV-positive Status":
  exists "HIV Status Positive Condition"
  or exists "HIV Status Positive Observation"

/* End of Newly on ART during labour and delivery */

/*
@dataElement: HIV.E.DE46 - Delivery date
@activity: HIV.E1 Capture or update mother's history
@description: Date on which the woman delivered
*/
define "Live Birth Delivery":
  [Observation: Concepts."Live birth"] O
    where O.status in { 'final', 'amended', 'corrected' }

/* End of Newly on ART during labour and delivery */

/*
@dataElement: HIV.E.DE46 - Delivery date
@activity: HIV.E1 Capture or update mother's history
@description: Date on which the woman delivered
*/
define "Live Birth Delivery":
  Elements."Live Birth Delivery" O
    where O.effective.toInterval() during "Measurement Period"

/* End of Serodiscordant partner D.DE37 */

/*
@dataElement: HIV.D.DE38 - On ART
@activity: HIV.D8 Capture or update client history
@description: Client is currently taking ART
*/

define "On ART D.DE38":
    [MedicationStatement] MS
    where exists(MS.reasonCode C where C ~ Concepts."On ART - HIV.D.DE38")
    sort by start of effective.toInterval()

/* End of Facility-level testing */

/*
@dataElement: HIV.B.DE29 - Currently pregnant
@activity: HIV.B6 Capture or update client history
@description: Client is currently pregnant
*/

define "Currently pregnant B.DE29":
  [Condition: Concepts."Currently pregnant - HIV.B.DE29"] C
  sort by start of prevalenceInterval()

/**
 * Numerator
 * 
 * Definition: Number of HIV-positive pregnant women who delivered during the reporting period and received ART during pregnancy and/or at labour and delivery
 * Calculation: COUNT of women with "HIV status"='HIV-positive' AND "Delivery date" in the reporting period AND (("On ART"=True at labour and delivery) OR ("On ART"=True during pregnancy, for this pregnancy))
 */


define "Numerator":
  HIE."Has HIV-positive Status" and
  exists(HIE."Live Birth Delivery" BirthDelivery
    where BirthDelivery.effective.toInterval() during "Measurement Period"
  ) and 
  exists ( 
    HE."On ART D.DE38" A 
    where A.effective.toInterval() during First(HIE."Live Birth Delivery" BirthDelivery
    where BirthDelivery.effective.toInterval() during "Measurement Period").effective.toInterval()
    or 
    A.effective.toInterval() during First(HE."Currently pregnant B.DE29" C 
    where C.prevalenceInterval() during "Measurement Period").prevalenceInterval()
  
  )

/* End of Other E.DE70 */

/*
@dataElement: HIV.E.DE85 - ANC contact date
@activity: HIV.E1 Capture or update mother's history
@description: The date and time of the client's ANC contact (in the ANC DAK this is called 'Contact date')
*/

define "Antenatal care contact":
  [Encounter] E
    where E.type.coding.code contains ConceptsCustom."Antenatal care contact".code

/* End of Facility-level testing */

/*
@dataElement: HIV.B.DE29 - Currently pregnant
@activity: HIV.B6 Capture or update client history
@description: Client is currently pregnant
*/

define "Currently pregnant B.DE29":
  Elements."Currently pregnant B.DE29" C
    where C.prevalenceInterval() during "Measurement Period"

/* End of Reporting date */


/*
 * Custom elements and logic for use DT and IND CQL Libraries
 */

 define "ANC within pregnancy":
  Elements."Antenatal care contact" E
  where E.period.toInterval() during First("Currently pregnant B.DE29").prevalenceInterval()

define "Has Delivery in Health Facility":
  exists (
    "Live Birth Delivery" O
      where O.value is CodeableConcept
        and O.value as CodeableConcept = Concepts."Health facility"
  )

/**
 * Denominator
 *
 * Definition: a) Programme-based/service delivery denominator | Number of HIV-positive pregnant women who delivered during the reporting period and attended ANC or had a facility-based delivery | b) Population-based denominator | Number of HIV-positive pregnant women who delivered during the reporting period
 * Calculation: Programme-based/service delivery denominator: | COUNT of women with "HIV status"='HIV-positive' AND "Delivery date" in the reporting period AND (had an "ANC contact date" during reporting period OR "Place of delivery" was a 'Health facility') |  | Population-based denominator: | *Number of HIV-positive pregnant women who delivered during the reporting period
 */

define "Denominator":
  HIE."Has HIV-positive Status" and
  exists(HIE."Live Birth Delivery" BirthDelivery
    where BirthDelivery.effective.toInterval() during "Measurement Period"
  )and 
  (First(HIE."ANC within pregnancy").period.toInterval() during "Measurement Period"
  or
    HIE."Has Delivery in Health Facility")

/* Populations */

/*
 *Initial Population
 */

define "Initial Population":
  true

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
        }

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 ToDateTime(value dateTime): value.value

define function ToString(value ObservationStatus): value.value

define function ToDateTime(value instant): value.value

/*
@description: Returns an interval representing the normalized prevalence period of a given Condition resource.
@comment: Uses the toInterval and toAbatementInterval functions to determine the widest potential interval from
onset to abatement as specified in the given Condition.
*/
define fluent function prevalenceInterval(condition Condition):
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 resource.
@comment: NOTE: Due to the complexity of determining an interval from a String, this function will throw
a run-time exception if used with a Condition instance that has a String as the abatement value.
*/
define fluent function abatementInterval(condition Condition):
  if condition.abatement is FHIR.dateTime then
    Interval[FHIRHelpers.ToDateTime(condition.abatement as FHIR.dateTime), FHIRHelpers.ToDateTime(condition.abatement as FHIR.dateTime)]
  else if condition.abatement is FHIR.Period then
    FHIRHelpers.ToInterval(condition.abatement as FHIR.Period)
  else if condition.abatement 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 if condition.abatement is FHIR.Age then
    Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(condition.abatement as FHIR.Age),
      FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(condition.abatement as FHIR.Age) + 1 year)
  else if condition.abatement is FHIR.Range then
    Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((condition.abatement as FHIR.Range).low),
      FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((condition.abatement as FHIR.Range).high) + 1 year)
  else if condition.abatement is FHIR.boolean then
    Interval[end of condition.onset.toInterval(), condition.recordedDate)
  else 
    null

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 ToDate(value date): value.value

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

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

/*
From FHIRCommon 4.1.0:
*/

/*
@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

define function ToString(value string): value.value