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"

/* On ART - includes "On ART - HIV.B.DE47" and "On ART - HIV.B.DE48" */
define "ART Medication Statement":
  [MedicationStatement: Concepts."ART regimen Choices"] MS
  sort by start of effective.toInterval()

// HIV Status

// ART Status

define "ART Medication Statement":
  Elements."ART Medication Statement" MS
  where MS.effective.toInterval() during "Measurement Period"
  sort by start of effective.toInterval()

define "On ART":
  exists "ART Medication Statement"

/* End of C reactive protein test result */

/*
@dataElement: HIV.D.DE1028 - TPT regimen type
@activity: HIV.D4 Screen for TB
@description: Type of TPT regimen the client is currently on
*/
define "TPT regimen":
  [MedicationStatement: Concepts."TPT regimen type Choices"] MS
    where MS.status in { 'active', 'completed' }

define "TB preventive treatment TPT completed in measurement period":
  Elements."TPT regimen" MS
    where start of MS.effective.toInterval() in "Measurement Period"
      and MS.status = 'completed'

/**
 * Numerator
 * 
 * Definition: Number of ART patients who completed a course of TPT during the reporting period
 * Calculation: COUNT of clients with "HIV status"='HIV-positive' AND "On ART"=True AND "TB preventive treatment (TPT) start date" in the previous period AND "TB preventive treatment (TPT) status"='Completed'
 */

define "Numerator":
 HIE."Has HIV-positive Status" and HIE."On ART" and exists(HIE."TB preventive treatment TPT completed in measurement period")

/* End of Date of TB diagnosis */

/*
@dataElement: HIV.D.DE954 - TB preventive treatment TPT start date
@activity: HIV.D8 Capture or update client history
@description: The date on which the client began taking TPT
*/
// TODO: Replace placeholder with relevant CQL logic
define "TB preventive treatment TPT start date":
  "TPT regimen" MS
  return start of MS.effective.toInterval()

define "TB preventive treatment TPT start date in previous measurement period":
  Elements."TB preventive treatment TPT start date" D
    where D before (end of "Measurement Period" - duration in days of "Measurement Period")
    and D after (start of "Measurement Period" - duration in days of "Measurement Period")

/**
 * Denominator
 *
 * Definition: Number of ART patients who initiated any course of TPT during the previous reporting period
 * Calculation: COUNT of clients with "HIV status"='HIV-positive' AND "On ART"=True AND "TB preventive treatment (TPT) start date" in the prior reporting period
 */

define "Denominator":
 HIE."Has HIV-positive Status" and HIE."On ART" and exists(HIE."TB preventive treatment TPT start date in previous measurement period")

/**
 * Indicator Definition
 */ 

/* 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

define "TPT regimen":
  Elements."TPT regimen" MS
    where MS.effective.toInterval() during "Measurement Period"

define "TPT regimen type":
  "TPT regimen" MS
  return Common.ExtractMedicationCode(MS.medication)

define "ART Duration in Months":
  "ART Medication Statement" MS
  return duration in months of MS.effective.toInterval()

define "By ART initiation":
  case
    when Sum("ART Duration in Months") < 12 then '<12 months on ART'
    when Sum("ART Duration in Months") >= 12 then '12+ months on ART'
    else 'Unknown'
  end

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

/*
 * Combined stratifiers
 */
define "Stratification":
  HIE."By Administrative Gender Stratifier".code 
    + ':' + HIE."By Age Stratifier"
    + ':' + Combine(HIE."TPT regimen type".coding.code)
    + ':' + HIE."By ART initiation"
	  + ':' + HIE."By Geographic Region Stratifier"

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 string): value.value

define function ToString(value MedicationStatementStatus): value.value

define function ToString(value AdministrativeGender): value.value

/**
 * @description Takes a choice between a Medication and a CodeableConcept and returns just the code of the medication
 */
define function ExtractMedicationCode(choice Choice<FHIR.CodeableConcept, FHIR.Reference>):
  case
	  when choice is FHIR.CodeableConcept then
    	choice as FHIR.CodeableConcept
    when choice is FHIR.Reference then
      First([Medication] M 
        where M.id = Last(Split(choice.reference, '/'))
        return M.code as FHIR.CodeableConcept)
    else
      Message(null as FHIR.CodeableConcept, true, '1', 'Error', 'Cannot compute a medication code') // TODO: I'm sure that this is supported somehow?
  end

define function ToString(value AddressUse): value.value