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 Established on ART */

/*
@dataElement: HIV.D.DE43 - ART start type
@activity: HIV.D8 Capture or update client history
@description: Whether the client is ART naive or is restarting ART
*/

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

/* End of ART start type */

/*
@dataElement: HIV.D.DE44 - First-time user of ART
@activity: HIV.D8 Capture or update client history
@description: Client is ART naive, having never taken ART to treat HIV before
*/

define "First-time user of ART":
  "ART start type" MS
      where exists(MS.reasonCode C where C ~ Concepts."First-time user of ART")

/* 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 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"

/* End of Presumptive TB D.DE945 */

/*
@dataElement: HIV.D.DE952 - Date of TB diagnosis
@activity: HIV.D8 Capture or update client history
@description: The date when the diagnosis was established
*/

define "Date of TB diagnosis":
  [Observation: Concepts."Diagnosed TB"] C
  return C.effective.toInterval()

/* End of Presumptive TB D.DE945 */

/*
@dataElement: HIV.D.DE952 - Date of TB diagnosis
@activity: HIV.D8 Capture or update client history
@description: The date when the diagnosis was established
*/

define "Date of TB diagnosis":
  exists(Elements."Date of TB diagnosis" C where C during "Measurement Period")

/* End of TB diagnostic test date */

/*
@dataElement: HIV.D.DE1001 - TB treatment start date
@activity: HIV.D8 Capture or update client history
@description: The date on which the client start or restarted tuberculosis (TB) treatment
*/

define "TB treatment start date":
  [MedicationStatement] MS
    where exists(MS.reasonCode C where C ~ ConceptsCustom."tb treatment")
    return (start of MS.effective.toInterval())

/* End of TB diagnostic test date */

/*
@dataElement: HIV.D.DE1001 - TB treatment start date
@activity: HIV.D8 Capture or update client history
@description: The date on which the client start or restarted tuberculosis (TB) treatment
*/

define "TB treatment start date":
  exists(Elements."TB treatment start date" MS where MS during "Measurement Period")

/**
 * Numerator
 * 
 * Definition: Number of people living with HIV newly initiated on ART who were diagnosed with TB and who started treatment for active TB disease
 * Calculation: COUNT of clients with "HIV status"='HIV-positive' AND with "ART start type"='First-time user of ART' AND with "ART start date" in the reporting period AND "TB screening date" in the reporting period AND "TB screening result"='Screen positive for TB' AND a "TB diagnostic test category" is NOT NULL AND with a "TB diagnostic test date" in the reporting period AND "Date of TB diagnosis" AND "TB treatment start date" in the reporting period
 */

define "Numerator":
  HIE."Has HIV-positive Status"
  and (start of First(HE."First-time user of ART").effective.toInterval() during "Measurement Period")
  //related the two since we want a positive observation from a specific diagnostic test.
  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"
  )
  and HIE."Date of TB diagnosis"
  and HIE."TB treatment start date"

/**
 * Denominator
 *
 * Definition: Number of people living with HIV newly initiated on ART who were diagnosed with active TB disease
 * Calculation: COUNT of clients with "HIV status"='HIV-positive' AND with "ART start type"='First-time user of ART' AND with "ART start date" in the reporting period AND "TB screening date" in the reporting period AND "TB screening result"='Screen positive for TB' AND a "TB diagnostic test category" is NOT NULL AND with a "TB diagnostic test date" in the reporting period AND "Date of TB diagnosis" in the reporting period
 */

define "Denominator":
  HIE."Has HIV-positive Status"
  and (start of First(HE."First-time user of ART").effective.toInterval() during "Measurement Period")
  //related the two since we want a positive observation from a specific diagnostic test.
  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"
  )
  and HIE."Date of TB diagnosis"

/* 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

define "Stratification":
 HIE."By Administrative Gender Stratifier".code 
  + ':' + HIE."By Age Stratifier 2"
+ ':' + 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 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