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 TB screening date */

/*
@dataElement: HIV.D.DE992 - TB diagnostic test category
@activity: HIV.D4 Screen for TB
@description: The type of diagnostic test performed to detect tuberculosis (TB) disease
*/

define "TB diagnostic test category":
  [Procedure] P
  where P.status = 'completed'
  and P.category ~ Concepts."TB diagnostic test category"

/* End of LF-LAM */

/*
@dataElement: HIV.D.DE994 - mWRD test for TB
@activity: HIV.D4 Screen for TB
@description: Client tested with a WHO-recommended molecular diagnostic test to detect Mycobacterium tuberculosis (MTB)
*/

define "mWRD test for TB":
  "TB diagnostic test category" P
  where P.code ~ Concepts."mWRD test for TB"

/* End of History of contact with a person with TB */

/*
@dataElement: HIV.D.DE986 - TB screening result
@activity: HIV.D4 Screen for TB
@description: Record the result of the tuberculosis (TB) screening
*/

define "TB screening result":
  [Observation: Concepts."TB screening result"] O
    where O.status in { 'final', 'amended', 'corrected' }

/* End of TB screening result */

/*
@dataElement: HIV.D.DE987 - Screen positive for TB
@activity: HIV.D4 Screen for TB
@description: Screening result was positive for tuberculosis (TB)
*/

define "Screen positive for TB":
  "TB screening result" O
  where O.value ~ Concepts."Screen positive for TB"

/**
 * Numerator
 * 
 * Definition: Number of people living with HIV and having TB symptoms who were tested using a rapid molecular test (for example, Xpert MTB/RIF) as a first test during the reporting period
 * Calculation: COUNT of clients with "HIV status"='HIV-positive' AND "TB screening date" in the reporting period AND "TB screening result"='Screen positive for TB' AND "TB diagnostic test category"='mWRD test for TB'
 */



define "Numerator":
  HIE."Has HIV-positive Status"
  and 
  //I related the two because otherwise a positive observation could come from another test type and be counted. 
  exists(
    HE."mWRD test for TB" P
    with HE."Screen positive for TB" O
      such that P.partOf.references(O)
    where P.performed.toInterval() during "Measurement Period"
  )

/**
 * Denominator
 *
 * Definition: Number of people living with HIV who are screened for TB and found to have symptoms during the reporting period
 * Calculation: COUNT of clients with "HIV status"='HIV-positive' AND "TB screening date" in the reporting period AND "TB screening result"='Screen positive for TB'
 */

define "Denominator":
  HIE."Has HIV-positive Status"
  and 
  exists(
    HE."TB diagnostic test category" P
    with HE."Screen positive for TB" O
      such that P.partOf.references(O)
    where P.performed.toInterval() 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
 * (0–4, 5–9, 10–14, 15–19, 20–24, 25–29, 30–34, 35–39, 40–44, 45–49, 50+ years)
 * 
 */
define "By Age Stratifier":
  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" <= 29 then '25–29'
      when "Age In Years" <= 34 then '30–34'
      when "Age In Years" <= 39 then '35–39'
      when "Age In Years" <= 44 then '40–44'
      when "Age In Years" <= 49 then '45–49'
      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 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()

/* 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 Currently pregnant B.DE29 */

/*
@dataElement: HIV.B.DE32 - Breastfeeding
@activity: HIV.B6 Capture or update client history
@description: Infant is being breastfed by mother
*/

define "Breastfeeding B.DE32":
  [Observation: Concepts."Breastfeeding - HIV.B.DE32"] O
    where O.status in { 'final', 'amended', 'corrected' }
      and O.value is true

/* End of Currently pregnant B.DE29 */

/*
@dataElement: HIV.B.DE32 - Breastfeeding
@activity: HIV.B6 Capture or update client history
@description: Infant is being breastfed by mother
*/

define "Breastfeeding B.DE32":
  Elements."Breastfeeding B.DE32" O
    where O.effective.toInterval() during "Measurement Period"

define "pregnancy stratifier":
  case
    when exists("Currently pregnant B.DE29") then Concepts."Currently pregnant - HIV.B.DE29"
    when exists("Breastfeeding B.DE32") then Concepts."Breastfeeding - HIV.B.DE32"
    else null
  end

define "Stratification":
 HIE."By Administrative Gender Stratifier".code 
  + ':' + HIE."By Age Stratifier"
+ ':' + HIE."By Geographic Region Stratifier"
+ Combine(HIE.patientGroups, ':')
+ HIE."pregnancy stratifier".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 ToString(value AdministrativeGender): value.value

define function ToString(value AddressUse): 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

define function ToBoolean(value boolean): value.value