/*
 * As defined by Member States
 */
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")

define "By Age Stratifier 3":
  case 
      when "Age In Years" >= 15 and "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, ':')

/**
 * HIV Elements
 */

/* General Data Elements */

// From Common

define "Community_testing":
  exists([Observation] O
    with [Encounter] E
      such that O.encounter.references(E) and exists(E.location.physicalType PT where PT ~  Concepts."Community-level testing") 
  where (O.status in { 'final', 'amended' }
  and O.code ~ Concepts."Rapid diagnostic test for HIV - HIV.B.DE82"
  and O.issued after start of "Measurement Period"
  and O.issued before end of "Measurement Period"))

/*@triggeredBy Encounter with location = facility level testing*/
define "Facility_testing":
  exists([Observation] O
    with [Encounter] E
      such that O.encounter.references(E) and exists(E.location.physicalType PT where PT ~  Concepts."Facility-level testing")
  where (O.status in { 'final', 'amended' }
  and O.code ~ Concepts."Rapid diagnostic test for HIV - HIV.B.DE82"
  and O.issued after start of "Measurement Period"
  and O.issued before end of "Measurement Period")
  )

define setting:
  case
    when Community_testing then Concepts."Community-level testing"
    when Facility_testing then Concepts."Facility-level testing"
    else null
  end

/* End of Date/time of suspected exposure to HIV C.DE9 */

/*
@dataElement: HIV.C.DE10 - Currently on PrEP
@activity: HIV.C3 Capture or update client history
@description: The client is currently taking PrEP. Oral pre-exposure prophylaxis (PrEP) of HIV is the use of ARV drugs by people who are not infected with HIV to block the acquisition of HIV.
*/

/*@triggeredBy Encounter with location = community level testing*/

define "Currently on PrEP":
  [MedicationStatement] MS
    where MS.status = 'completed'
    and exists(MS.reasonCode C where C ~ Concepts."Currently on PrEP")
    and MS.medication ~ Concepts."PrEP for HIV prevention"

/* End of Current PrEP regimen */

/*
@dataElement: HIV.C.DE18 - TDF + FTC
@activity: HIV.C3 Capture or update client history
@description: Treated with tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) pre-exposure prophylaxis (PrEP) regimen (oral PrEP)
*/

define "TDF + FTC C.DE18":
  "Currently on PrEP" MS
  where MS.medication ~ Concepts."TDF + FTC - HIV.C.DE18"

/* End of Other PrEP dosing type */

/*
@dataElement: HIV.C.DE18 - TDF + FTC
@activity: HIV.C3 Capture or update client history
@description: Treated with tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) pre-exposure prophylaxis (PrEP) regimen (oral PrEP)
*/

define "TDF + FTC C.DE18":
  exists (Elements."TDF + FTC C.DE18" MS
  where MS.status = 'completed' and MS.effective.toInterval() during "Measurement Period")

/* End of TDF + FTC C.DE18 */

/*
@dataElement: HIV.C.DE19 - TDF
@activity: HIV.C3 Capture or update client history
@description: Treated with single-agent tenofovir disoproxil fumarate (TDF) pre-exposure prophylaxis (PrEP) regimen (oral PrEP)
*/

define "TDF C.DE19":
  "Currently on PrEP" MS
  where MS.medication ~ Concepts."TDF - HIV.C.DE19"

/* End of TDF + FTC C.DE18 */

/*
@dataElement: HIV.C.DE19 - TDF
@activity: HIV.C3 Capture or update client history
@description: Treated with single-agent tenofovir disoproxil fumarate (TDF) pre-exposure prophylaxis (PrEP) regimen (oral PrEP)
*/

define "TDF C.DE19":
  exists (Elements."TDF C.DE19" MS
  where MS.status = 'completed' and MS.effective.toInterval() during "Measurement Period")

/* End of TDF C.DE19 */

/*
@dataElement: HIV.C.DE20 - TDF + 3TC
@activity: HIV.C3 Capture or update client history
@description: Treated with tenofovir disoproxil fumarate (TDF) and lamivudine (3TC) pre-exposure prophylaxis (PrEP) regimen (oral PrEP)
*/

define "TDF + 3TC C.DE20":
  "Currently on PrEP" MS
  where MS.medication ~ Concepts."TDF + 3TC - HIV.C.DE20"

/* End of TDF C.DE19 */

/*
@dataElement: HIV.C.DE20 - TDF + 3TC
@activity: HIV.C3 Capture or update client history
@description: Treated with tenofovir disoproxil fumarate (TDF) and lamivudine (3TC) pre-exposure prophylaxis (PrEP) regimen (oral PrEP)
*/

define "TDF + 3TC C.DE20":
  exists (Elements."TDF + 3TC C.DE20" MS
  where MS.status = 'completed' and MS.effective.toInterval() during "Measurement Period")

/* End of TDF + 3TC C.DE20 */

/*
@dataElement: HIV.C.DE21 - Other TDF-based regimen
@activity: HIV.C3 Capture or update client history
@description: Treated with other tenofovir disoproxil fumarate (TDF)-based regimen (oral PrEP)
*/

define "Other TDF-based regimen":
  "Currently on PrEP" MS
  where MS.medication ~ Concepts."Other TDF-based regimen"

/* End of TDF + 3TC C.DE20 */

/*
@dataElement: HIV.C.DE21 - Other TDF-based regimen
@activity: HIV.C3 Capture or update client history
@description: Treated with other tenofovir disoproxil fumarate (TDF)-based regimen (oral PrEP)
*/

define "Other TDF-based regimen":
  exists (Elements."Other TDF-based regimen" MS
  where MS.status = 'completed' and MS.effective.toInterval() during "Measurement Period")

/* End of Other TDF-based regimen */

/*
@dataElement: HIV.C.DE22 - Dapivirine vaginal ring DVR
@activity: HIV.C3 Capture or update client history
@description: Dapivirine vaginal ring (DVR) for HIV prevention
*/

define "Dapivirine vaginal ring DVR C.DE22":
  "Currently on PrEP" MS
  where MS.medication ~ Concepts."Dapivirine vaginal ring DVR - HIV.C.DE22"

/* End of Other TDF-based regimen */

/*
@dataElement: HIV.C.DE22 - Dapivirine vaginal ring DVR
@activity: HIV.C3 Capture or update client history
@description: Dapivirine vaginal ring (DVR) for HIV prevention
*/

define "Dapivirine vaginal ring DVR C.DE22":
  exists (Elements."Dapivirine vaginal ring DVR C.DE22" MS
  where MS.status = 'completed' and MS.effective.toInterval() during "Measurement Period")

/*
@dataElement: HIV.C.DE23 - CAB-LA
@activity: HIV.C3 Capture or update client history
@description: Long-acting injectable cabotegravir
*/

define "CAB-LA C.DE23":
  "Currently on PrEP" MS
  where MS.medication ~ Concepts."CAB-LA - HIV.C.DE23"

/*
@dataElement: HIV.C.DE23 - CAB-LA
@activity: HIV.C3 Capture or update client history
@description: Long-acting injectable cabotegravir
*/

define "CAB-LA C.DE23":
  exists (Elements."CAB-LA C.DE23" MS
  where MS.status = 'completed' and MS.effective.toInterval() during "Measurement Period")

define prep_product:
  List<String>{
    if "TDF + FTC C.DE18" or "TDF C.DE19" or "TDF + 3TC C.DE20" or "Other TDF-based regimen" then 'PREP Product Oral' else null,
    if "Dapivirine vaginal ring DVR C.DE22" then 'PREP Product long-acting device' else null,
    if "CAB-LA C.DE23" then 'PREP Product long-acting injectable' else null
  }

//provider type not provided?

define "Stratification":
 HIE."By Administrative Gender Stratifier".code 
  + ':' + HIE."By Age Stratifier 3"
+ ':' + HIE."By Geographic Region Stratifier"
+ Combine(HIE.patientGroups, ':') 
 + ':' + HIE."setting".code
+ Combine(HIE.prep_product, ':')

define "PREP Prescription":
  [MedicationRequest] MR
    where MR.status = 'completed'
    and MR.intent = 'order'
    and (MR.medication as CodeableConcept in Concepts."PrEP product prescribed Choices"
    or MR.medication as CodeableConcept in Concepts."Current PrEP regimen Choices")

define "Measure Population":
   Sum(
    (
      collapse (HE."PREP Prescription" MR
      return HIC."Prescription Relevant Period"( MR ) intersect "Measurement Period"
      )
    ) PREPUseInterval
      return days between start of PREPUseInterval and end of PREPUseInterval
  )

define function ToString(value AdministrativeGender): value.value

define function ToString(value string): value.value

define function ToString(value AddressUse): value.value

define function ToString(value ObservationStatus): value.value

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 instant): value.value

/*
@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 MedicationStatementStatus): value.value

define function ToString(value MedicationRequestStatus): value.value

define function ToString(value MedicationRequestIntent): value.value

define function "Prescription Relevant Period"(prescription FHIR.MedicationRequest):
  if (
    prescription.authoredOn is not null and prescription.dispenseRequest is not null
      and prescription.dispenseRequest.expectedSupplyDuration is not null
  )
  then Interval[
    date from prescription.authoredOn,
    date from prescription.authoredOn + System.Quantity{ value: GetDurationInDays(prescription.dispenseRequest.expectedSupplyDuration), unit: 'days' }
  ]
  else null

define function ToDateTime(value dateTime): value.value

//VERIFIED


//DRAFT

//need to add Time to start ART (within 7, 30 or 90 days of diagnosis, as per country guidelines)
//need to add Disaggregation by time since diagnosis
  


/* 
* DAK has codes for HAART misspecified 
* ICD-10 Z92.2	Other prophylactic chemotherapy		
* LOINC "54825-5	"	On scheduled pain medication regimen in last 7 days
*
* Should discuss 
*/







/*
* Kenya EMR defined as HIV positive condition
* Will need to discuss if produce flags through conditions for concepts to use in indicator calculation such as HIV positive and On ART
* However, we have moved forward with a more prescriptive approach 
* Inevitably our approach requires that certain data elements be available
*/

/*
 * HIV Treatment during the measurement period
 * uses dosage and dispensation amount to estimate last day of medication
 * medication should be dispensed before end of measurement period
 * medication should last until after 28 days after the end of the measurement period
 * This takes into account lost to follow up
 */

/*
*define "HIV Treatment during the measurement period":
*   [MedicationDispense] MD
*    where MD.status in { 'final', 'amended', 'corrected' }
*    and MD.medication ~ 'Antiretroviral'
*    and MD.whenHandedOver before end of "Measurement Period"
*    and (MD.whenHandedOver + MD.dosageInstruction[0].timing.repeat.duration.value * MedicationDispense.quantity.value) after (measurementPeriod.end - 28 days)
*/ 

/*
* Immunization defines HAART as
*  exists([MedicationAdministration] A where ExtractMedicationCode(A.medication) in IMMZc."ARV Drugs" and A.status = 'in-progress')
* I believe this is the incorrect resource unless they mean to say that medication is given during a medical encounter
* would like to discuss 
*/ 

/** 
 * Patient Deceased During Measurement Period
 * Immunization defines this as true when is a boolean. This may have the effect of deleting a person from indicators in all calculations
 * Should intend to use when patient.deceased FHIR boolean was updated to TRUE if no other date is available
 * Kenya EMR example does not account for when deceased is just a boolean
 */


/*
define "PREP Prescription Days":
  Sum(
    (
      collapse (
        [MedicationRequest] MR
          where MR.status = 'completed'
          and MR.intent = 'order'
          and MR.medication ~ Concepts."PrEP for HIV prevention"
        return WComV2."Prescription Relevant Period"( MR ) intersect "Measurement Period"
      )
    ) PREPUseInterval
      return days between start of PREPUseInterval and end of PREPUseInterval
  )
*/


define function GetDurationInDays(value FHIR.Duration): // returns Decimal:
    case value.code.value
      when 'a' then value.value * 365.0
      when 'mo' then value.value.value * 30.0
      when 'wk' then value.value.value * 7.0
      when 'd' then value.value.value
      when 'h' then value.value.value / 24.0
      when 'min' then value.value.value / 60.0 / 24.0
      when 's' then value.value.value / 60.0 / 60.0 / 24.0
      when 'ms' then value.value.value / 60.0 / 60.0 / 24.0 / 1000.0
      else Message(1000, true, 'Undefined', 'Error', 'Unsupported duration unit ' + value.code.value)
    end

define function ToDecimal(value decimal): value.value

/*
 * NOTE: Modeled as a Continuous Variable measure because this is an estimated denominator proportion measure
 */

define function "Measure Observation"(Patient "Patient"):
  1