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 Refused stopped treatment */

/*
@dataElement: HIV.H.DE47 - On ART
@activity: HIV.H3 Record outreach and result
@description: Client is currently taking ART 
*/

define "On ART H.DE47":
    [MedicationStatement] MS
    where exists(MS.reasonCode C where C ~ Concepts."On ART - HIV.H.DE47")
    sort by start of effective.toInterval()

/* End of Refused stopped treatment */

/*
@dataElement: HIV.H.DE47 - On ART
@activity: HIV.H3 Record outreach and result
@description: Client is currently taking ART 
*/
define "On ART H.DE47":
  exists(Elements."On ART H.DE47" ART
   where ART.effective.toInterval() during "Measurement Period"
   )

/* End of Time to start ART */

/*
@dataElement: HIV.D.DE387 - Viral load test result
@activity: HIV.D20 Diagnostics
@description: Result from the viral load test in number of copies/mL
*/

define "Viral load test result D.DE387":
  [Observation: Concepts."Viral load test result - HIV.D.DE387"] O
    where O.status in { 'final', 'amended', 'corrected' }

/* End of Date of baseline CD4 count test D.DE368 */

/*
@dataElement: HIV.D.DE387 - Viral load test result
@activity: HIV.D20 Diagnostics
@description: Result from the viral load test in number of copies/mL
*/

define "Viral load test result D.DE387":
  Elements."Viral load test result D.DE387" O
    where O.effective.toInterval() during "Measurement Period"

define "viral load sample collection":
  [Procedure] P
  where P.status = 'completed'
  and P.code ~ ConceptsCustom."viral load test"

// HIV Testing
define "Elevated Viral load test during Measurement Period":
  "Viral load test result D.DE387" VL
    with Elements."viral load sample collection" P 
    such that VL.partOf.references(P) and P.performed.toInterval() during "Measurement Period"
    where VL.value > 1000 
    sort by start of effective.toInterval()

/**
 * Numerator
 * 
 * Definition: Number of people living with HIV on ART who received a follow-up VL test three months after a VL test result of ≥1000 copies/mL during the reporting period*
 * Calculation: COUNT of clients with "HIV status"='HIV-positive' AND "On ART"=True AND "Date of viral load sample collection" within reporting period AND "Viral load test result" GREATER THAN 1000 copies/mL AND follow-up "Date of viral load sample collection" LESS THAN 3 months AFTER elevated viral load result
 */

define "Numerator":
  HIE."Has HIV-positive Status"
  and HIE."On ART H.DE47"
  and 
    exists(HIE."Elevated Viral load test during Measurement Period")
  and 
    exists(
      HE."viral load sample collection" VL
      where (months between (start of First(HIE."Elevated Viral load test during Measurement Period").issued.toInterval()) and (date from start of VL.performed.toInterval() ) < 3 months)
      
      
    )

/**
 * Denominator
 *
 * Definition: Number of people living with HIV on ART with VL ≥1000 copies/mL during the reporting period
 * Calculation: COUNT of clients with "HIV status"='HIV-positive' AND "On ART"=True AND "Date of viral load sample collection" within reporting period AND "Viral load test result" GREATER THAN 1000 copies/mL
 */

define "Denominator":
  HIE."Has HIV-positive Status"
  and HIE."On ART H.DE47"
  and 
    exists(HIE."Elevated Viral load test during Measurement Period")

/* Populations */

/*
 *Initial Population
 */

define "Initial Population":
  true

/*
@dataElement: HIV.A.DE18 - Gender
@activity: HIV.A6.1 Review sociodemographic data with client | HIV.A5 Create new client record
@description: Gender of the client
*/

/*
 * By Administrative Gender of Patient Stratifier
 * Need to expand codes
 */

define "By Administrative Gender Stratifier":
  case 
      when Patient.gender = 'male' then Concepts."Male"
      when Patient.gender = 'female' then Concepts."Female"
      when Patient.gender = 'transgender female' then Concepts."Transgender female"
      when Patient.gender = 'transgender male' then Concepts."Transgender male"
      else Concepts."Other - HIV.A.DE23"
  end

/* End of Visit date A.DE3 */

/*
@dataElement: HIV.A.DE17 - Age
@activity: HIV.A6.1 Review sociodemographic data with client | HIV.A5 Create new client record
@description: Calculated age (number of years) of the client based on date of birth
*/
define "Age In Years":
  AgeInYearsAt(start of "Measurement Period")

/*
 * By Age Stratifiers
 * Age (0–4, 5–9, 10–14, 15–19, 20–24, 25–49, 50+ years)
 * 
 */
define "By Age Stratifier 2":
  case 
      when "Age In Years" <= 4 then '0-4'
      when "Age In Years" <= 9 then '5-9'
      when "Age In Years" <= 14 then '10–14'
      when "Age In Years" <= 19 then '15–19'
      when "Age In Years" <= 24 then '20–24'
      when "Age In Years" <= 49 then '25–49'
      when "Age In Years" >= 50 then '50+'
      else null
  end

// Geographic Region
define "By Geographic Region Stratifier":
    First(Patient.address A where A.use in { 'home' }).state

/* End of Key population member B.DE49 */

/*
@dataElement: HIV.B.DE50 - Key population member type
@activity: HIV.B6 Capture or update client history
@description: The type of key population that the client is included in
*/
define "Key population member type Observation":
  [Observation: Concepts."Key population member - HIV.B.DE49"] O
    where O.status in { 'final', 'amended', 'corrected' }
    and exists(O.category OC where OC ~ ConceptsCustom."social-history")

define "Key population member type Observation":
  Elements."Key population member type Observation" O
    where O.effective.toInterval() before end of "Measurement Period"
    or O.issued before end of "Measurement Period"

// Stratifier
define patientGroups:
  "Key population member type Observation" O
  return Combine(O.code.coding.code, ':')

/* End of Current ART regimen */

/*
@dataElement: HIV.D.DE77 - Preferred first-line ART regimen
@activity: HIV.D8 Capture or update client history
@description: The preferred first-line ART regimen for the client according to WHO (or national) guidelines
*/

define "Preferred first-line ART regimen":
[MedicationStatement] MS
    where MS.status = 'completed'
    and MS.medication ~ Concepts."Preferred first-line ART regimen"

/* End of Preferred first-line ART regimen */

/*
@dataElement: HIV.D.DE78 - Alternative first-line ART regimen
@activity: HIV.D8 Capture or update client history
@description: The alternative first-line ART regimen for the client according to WHO (or national) guidelines
*/

define "Alternative first-line ART regimen":
  [MedicationStatement] MS
    where MS.status = 'completed'
    and MS.medication ~ Concepts."Alternative first-line ART regimen"

/* End of Alternative first-line ART regimen */

/*
@dataElement: HIV.D.DE79 - First-line ART regimen under special circumstances
@activity: HIV.D8 Capture or update client history
@description: The first-line ART regimen for the client under special circumstances according to WHO (or national) guidelines
*/

define "First-line ART regimen under special circumstances":
    [MedicationStatement] MS
    where MS.status = 'completed'
    and MS.medication ~ Concepts."First-line ART regimen under special circumstances"

/* End of First-line ART regimen under special circumstances */

/*
@dataElement: HIV.D.DE80 - Preferred second-line ART regimen
@activity: HIV.D8 Capture or update client history
@description: The preferred second-line ART regimen for the client according to WHO (or national) guidelines
*/

define "Preferred second-line ART regimen":
    [MedicationStatement] MS
    where MS.status = 'completed'
    and MS.medication ~ Concepts."Preferred second-line ART regimen"

/* End of Preferred second-line ART regimen */

/*
@dataElement: HIV.D.DE81 - Alternative second-line ART regimen
@activity: HIV.D8 Capture or update client history
@description: The alternative second-line ART regimen for the client according to WHO (or national) guidelines
*/

define "Alternative second-line ART regimen":
    [MedicationStatement] MS
    where MS.status = 'completed'
    and MS.medication ~ Concepts."Alternative second-line ART regimen"

/* End of Restarting ART */

/*
@dataElement: HIV.D.DE75 - Current ART regimen
@activity: HIV.D8 Capture or update client history
@description: The current ART regimen the client is taking
*/

define "Current ART regimen":
  case 
      when exists(Elements."Preferred first-line ART regimen" MS where MS.effective.toInterval() during "Measurement Period") then Concepts."Preferred first-line ART regimen"
      when exists(Elements."Alternative first-line ART regimen" MS where MS.effective.toInterval() during "Measurement Period") then Concepts."Alternative first-line ART regimen"
      when exists(Elements."First-line ART regimen under special circumstances" MS where MS.effective.toInterval() during "Measurement Period") then Concepts."First-line ART regimen under special circumstances"
      when exists(Elements."Preferred second-line ART regimen" MS where MS.effective.toInterval() during "Measurement Period") then Concepts."Preferred second-line ART regimen"
      when exists(Elements."Alternative second-line ART regimen" MS where MS.effective.toInterval() during "Measurement Period") then Concepts."Alternative second-line ART regimen"
      else null
  end

/* End of Dates of substitution within third-line regimen */

/*
@dataElement: HIV.D.DE496 - Enhanced adherence counselling provided
@activity: HIV.D24 Counsel
@description: Enhanced adherence counselling was provided to the client during the visit
*/
 
define "Enhanced adherence counselling provided":
  [Communication] C
  where C.topic ~ Concepts."Enhanced adherence counselling provided"

/* End of Dates of substitution within third-line regimen */

/*
@dataElement: HIV.D.DE496 - Enhanced adherence counselling provided
@activity: HIV.D24 Counsel
@description: Enhanced adherence counselling was provided to the client during the visit
*/

define "Enhanced adherence counselling provided":
  exists (Elements."Enhanced adherence counselling provided" C
  where C.received.toInterval() during "Measurement Period"
  )

define "Enhanced adherence counselling provided Disaggregation":
  case 
      when "Enhanced adherence counselling provided" then Concepts."Enhanced adherence counselling provided"
      else null
  end

define "Stratification":
 HIE."By Administrative Gender Stratifier".code 
  + ':' + HIE."By Age Stratifier 2"
+ ':' + HIE."By Geographic Region Stratifier"
+ Combine(HIE.patientGroups, ':')
+ HIE."Current ART regimen".code 
+ HIE."Enhanced adherence counselling provided Disaggregation".code

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

define function ToString(value ProcedureStatus): value.value

/*
@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, '/'))

define function ToString(value string): value.value

define function ToInteger(value integer): value.value

/*
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 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

define function ToString(value AdministrativeGender): value.value

define function ToString(value AddressUse): value.value

define function ToString(value MedicationStatementStatus): value.value