define "Initial Population":
  "Qualifying Encounters During Measurement Period"
    union "Encounters with Patient Hospital Locations"

define "Initial Population":
  "Qualifying Encounters During Measurement Period"
    union "Encounters with Patient Hospital Locations"

/*
@description: Returns the Location resource specified by the given reference.
*/
define fluent function getLocation(reference Reference):
  singleton from (
    [Location] L where reference.references(L)
  )

/*
@description: Converts the given [Period](https://hl7.org/fhir/datatypes.html#Period)
value to a CQL DateTime Interval
@comment: If the start value of the given period is unspecified, the starting
boundary of the resulting interval will be open (meaning the start of the interval
is unknown, as opposed to interpreted as the beginning of time).
*/
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]

/*
@description: Converts the given FHIR [CodeableConcept](https://hl7.org/fhir/datatypes.html#CodeableConcept) value to a CQL Concept.
*/
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
        }

/*
@description: Converts the given FHIR [Coding](https://hl7.org/fhir/datatypes.html#Coding) value to a CQL Code.
*/
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 ToString(value uri): value.value

// ----------------------------------------------------------------------
// Core encounter logic
// ----------------------------------------------------------------------

// Encounters with NHSN class codes (IMP, ACUTE, NONAC, SS)





define "Encounters with NHSN Inpatient Class":
  [Encounter] Enc
    where Enc.class ~ QICoreCommon."inpatient encounter"
      or Enc.class ~ QICoreCommon."inpatient acute"
      or Enc.class ~ QICoreCommon."inpatient non-acute"
      or Enc.class ~ QICoreCommon."short stay"

define "Qualifying Encounters During Measurement Period":
  ( [Encounter: "Encounter Inpatient"]
    union [Encounter: "Emergency Department Visit"]
    union [Encounter: "Observation Services"]
    union "Encounters with NHSN Inpatient Class"
    union [Encounter: class ~ "emergency"]
    union [Encounter: class ~ "observation encounter"] ) QualifyingEncounters
    where QualifyingEncounters.status in { 'in-progress', 'finished', 'triaged', 'onleave', 'entered-in-error' }
      and QualifyingEncounters.period overlaps "Measurement Period"

define "Encounters":
  [Encounter]

define "Encounters with Patient Hospital Locations":
  "Encounters" Ens
    where exists ( Ens.location EncounterLocation
        where EncounterLocation.period overlaps Ens.period
          and EncounterLocation.location.getLocation ( ).type in "Inpatient, Emergency, and Observation Locations"
    )
      and Ens.status in { 'in-progress', 'finished', 'triaged', 'onleave', 'entered-in-error' }
      and Ens.period overlaps "Measurement Period"

define "Initial Population":
  "Qualifying Encounters During Measurement Period"
    union "Encounters with Patient Hospital Locations"

// Coverage SDE – tuples of Coverage data


define "SDE Coverage":
  [Coverage] Coverages
    where exists ( "Initial Population" IP
        where Coverages.period overlaps IP.period
    )
    return {
      id: Coverages.id,
      meta: Coverages.meta,
      status: Coverages.status,
      type: Coverages.type,
      policyHolder: Coverages.policyHolder,
      subscriber: Coverages.subscriber,
      subscriberId: Coverages.subscriberId,
      beneficiary: Coverages.beneficiary,
      dependent: Coverages.dependent,
      relationship: Coverages.relationship,
      period: Coverages.period,
      payor: Coverages.payor,
      class: Coverages.class,
      order: Coverages.order,
      network: Coverages.network,
      subrogation: Coverages.subrogation,
      contract: Coverages.contract
    }

// Encounter SDEs


define "SDE Encounter":
  "Encounters" Ens
    where not "CheckIP"(Ens)
      and exists ( "Initial Population" IP
          where Ens.period overlaps IP.period
      )
    return {
      id: Ens.id,
      meta: Ens.meta,
      identifier: Ens.identifier,
      status: Ens.status,
      statusHistory: Ens.statusHistory,
      class: Ens.class,
      classHistory: Ens.classHistory,
      type: Ens.type,
      serviceType: Ens.serviceType,
      priority: Ens.priority,
      subject: Ens.subject,
      period: Ens.period,
      length: Ens.length,
      reasonCode: Ens.reasonCode,
      reasonReference: Ens.reasonReference,
      diagnosis: Ens.diagnosis,
      account: Ens.account,
      hospitalization: Ens.hospitalization,
      location: Ens.location,
      partOf: Ens.partOf
    }

// Procedure SDE


define "SDE Procedure":
  [Procedure] Procedures
    where exists ( "Initial Population" IP
        where "Normalize Interval"(Procedures.performed) overlaps IP.period
    )
    return {
      id: Procedures.id,
      meta: Procedures.meta,
      extension: Procedures.extension,
      basedOn: Procedures.basedOn,
      partOf: Procedures.partOf,
      status: Procedures.status,
      category: Procedures.category,
      code: Procedures.code,
      subject: Procedures.subject,
      encounter: Procedures.encounter,
      performed: Procedures.performed,
      location: Procedures.location,
      reasonCode: Procedures.reasonCode,
      reasonReference: Procedures.reasonReference,
      bodySite: Procedures.bodySite
    }

// Device SDE – tuples of Device data


define "SDE Device":
  [Device] Devices
    where exists ( "Initial Population" )
    return {
      id: Devices.id,
      meta: Devices.meta,
      extension: Devices.extension,
      status: Devices.status,
      expirationDate: Devices.expirationDate,
      lotNumber: Devices.lotNumber,
      serialNumber: Devices.serialNumber,
      modelNumber: Devices.modelNumber,
      partNumber: Devices.partNumber,
      type: Devices.type,
      patient: Devices.patient,
      parent: Devices.parent
    }

define "SDE Observation Vital Signs Category":
  [USCoreVitalSignsProfile] Obs
    where exists ( "Initial Population" IP
        where "Normalize Interval"(Obs.effective) overlaps IP.period
    )
    return {
      id: Obs.id,
      meta: Obs.meta,
      extension: Obs.extension,
      partOf: Obs.partOf,
      status: Obs.status,
      category: Obs.category,
      code: Obs.code,
      subject: Obs.subject,
      encounter: Obs.encounter,
      effective: Obs.effective,
      issued: Obs.issued,
      value: Obs.value,
      dataAbsentReason: Obs.dataAbsentReason,
      interpretation: Obs.interpretation,
      bodySite: Obs.bodySite,
      method: Obs.method,
      specimen: Obs.specimen,
      referenceRange: Obs.referenceRange,
      hasMember: Obs.hasMember,
      derivedFrom: Obs.derivedFrom,
      component: Obs.component
    }

define "SDE DiagnosticReport Others":
  [DiagnosticReportNote] dr
    where not ( exists ( dr.category Category
          where Category ~ "Radiology"
      )
        or exists ( dr.category Category
            where Category ~ "Pathology"
        )
        or exists ( dr.category Category
            where Category ~ "Cardiology"
        )
    )
      and exists ( "Initial Population" IP
          where "Normalize Interval"(dr.effective) overlaps IP.period
      )
    return {
      id: dr.id,
      meta: dr.meta,
      extension: dr.extension,
      basedOn: dr.basedOn,
      status: dr.status,
      category: dr.category,
      code: dr.code,
      subject: dr.subject,
      encounter: dr.encounter,
      effective: dr.effective,
      issued: dr.issued,
      specimen: dr.specimen,
      result: dr.result,
      conclusion: dr.conclusion,
      conclusionCode: dr.conclusionCode
    }

define "SDE Specimens":
  [USCoreSpecimenProfile] sp
    where exists ( "Initial Population" IP
        where "Normalize Interval"(sp.collection.collected) overlaps IP.period
    )
    return {
      id: sp.id,
      type: sp.type
    }

define "SDE Medication Administration Not Done":
  [MedicationAdministrationNotDone] MedAdministrations
    where exists ( "Initial Population" IP
        where "Normalize Interval"(MedAdministrations.effective) overlaps IP.period
    )
    return {
      id: MedAdministrations.id,
      meta: MedAdministrations.meta,
      instantiates: MedAdministrations.instantiates,
      partOf: MedAdministrations.partOf,
      status: MedAdministrations.status,
      statusReason: MedAdministrations.statusReason,
      category: MedAdministrations.category,
      medication: MedAdministrations.medication,
      subject: MedAdministrations.subject,
      context: MedAdministrations.context,
      supportingInformation: MedAdministrations.supportingInformation,
      effective: MedAdministrations.effective,
      performer: MedAdministrations.performer,
      reasonCode: MedAdministrations.reasonCode,
      reasonReference: MedAdministrations.reasonReference,
      request: MedAdministrations.request,
      device: MedAdministrations.device,
      note: MedAdministrations.note,
      dosage: MedAdministrations.dosage
    }

// SDE Medication Not Requested - negation requests (doNotPerform is true)


define "SDE Medication Not Requested":
  [MedicationNotRequested] MedNotRequests
    where exists ( "Initial Population" IP
        where MedNotRequests.authoredOn during IP.period
    )
    return {
      id: MedNotRequests.id,
      meta: MedNotRequests.meta,
      status: MedNotRequests.status,
      statusReason: MedNotRequests.statusReason,
      intent: MedNotRequests.intent,
      category: MedNotRequests.category,
      priority: MedNotRequests.priority,
      doNotPerform: MedNotRequests.doNotPerform,
      reported: MedNotRequests.reported,
      medication: MedNotRequests.medication,
      subject: MedNotRequests.subject,
      encounter: MedNotRequests.encounter,
      authoredOn: MedNotRequests.authoredOn,
      requester: MedNotRequests.requester,
      recorder: MedNotRequests.recorder,
      reasonCode: MedNotRequests.reasonCode,
      reasonReference: MedNotRequests.reasonReference,
      instantiatesCanonical: MedNotRequests.instantiatesCanonical,
      instantiatesUri: MedNotRequests.instantiatesUri,
      courseOfTherapyType: MedNotRequests.courseOfTherapyType,
      dosageInstruction: MedNotRequests.dosageInstruction
    }

define "Initial Population":
  "Qualifying Encounters During Measurement Period"
    union "Encounters with Patient Hospital Locations"

// ServiceRequest SDE - regular requests (doNotPerform is false or absent)


define "SDE Service Request Base":
  [ServiceRequest] ServiceRequests
    where exists ( "Initial Population" IP
        where ServiceRequests.authoredOn during IP.period
    )
    return {
      id: ServiceRequests.id,
      meta: ServiceRequests.meta,
      instantiatesCanonical: ServiceRequests.instantiatesCanonical,
      instantiatesUri: ServiceRequests.instantiatesUri,
      basedOn: ServiceRequests.basedOn,
      replaces: ServiceRequests.replaces,
      requisition: ServiceRequests.requisition,
      status: ServiceRequests.status,
      intent: ServiceRequests.intent,
      category: ServiceRequests.category,
      priority: ServiceRequests.priority,
      //doNotPerform: ServiceRequests.doNotPerform,
      
      code: ServiceRequests.code,
      orderDetail: ServiceRequests.orderDetail,
      quantity: ServiceRequests.quantity,
      subject: ServiceRequests.subject,
      encounter: ServiceRequests.encounter,
      occurrence: ServiceRequests.occurrence,
      asNeeded: ServiceRequests.asNeeded,
      authoredOn: ServiceRequests.authoredOn,
      requester: ServiceRequests.requester,
      performerType: ServiceRequests.performerType,
      performer: ServiceRequests.performer,
      locationCode: ServiceRequests.locationCode,
      reasonCode: ServiceRequests.reasonCode,
      reasonReference: ServiceRequests.reasonReference,
      insurance: ServiceRequests.insurance,
      bodySite: ServiceRequests.bodySite,
      note: ServiceRequests.note,
      patientInstruction: ServiceRequests.patientInstruction
    }

// ServiceNotRequested SDE - negation requests (doNotPerform is true)


define "SDE Service Not Requested":
  [ServiceNotRequested] ServiceNotReqs
    where exists ( "Initial Population" IP
        where ServiceNotReqs.authoredOn during IP.period
    )
    return {
      id: ServiceNotReqs.id,
      meta: ServiceNotReqs.meta,
      instantiatesCanonical: ServiceNotReqs.instantiatesCanonical,
      instantiatesUri: ServiceNotReqs.instantiatesUri,
      basedOn: ServiceNotReqs.basedOn,
      replaces: ServiceNotReqs.replaces,
      requisition: ServiceNotReqs.requisition,
      status: ServiceNotReqs.status,
      intent: ServiceNotReqs.intent,
      category: ServiceNotReqs.category,
      priority: ServiceNotReqs.priority,
      doNotPerform: ServiceNotReqs.doNotPerform,
      code: ServiceNotReqs.code,
      orderDetail: ServiceNotReqs.orderDetail,
      quantity: ServiceNotReqs.quantity,
      subject: ServiceNotReqs.subject,
      encounter: ServiceNotReqs.encounter,
      occurrence: ServiceNotReqs.occurrence,
      asNeeded: ServiceNotReqs.asNeeded,
      authoredOn: ServiceNotReqs.authoredOn,
      requester: ServiceNotReqs.requester,
      performerType: ServiceNotReqs.performerType,
      performer: ServiceNotReqs.performer,
      locationCode: ServiceNotReqs.locationCode,
      reasonCode: ServiceNotReqs.reasonCode,
      reasonReference: ServiceNotReqs.reasonReference,
      insurance: ServiceNotReqs.insurance,
      bodySite: ServiceNotReqs.bodySite,
      note: ServiceNotReqs.note,
      patientInstruction: ServiceNotReqs.patientInstruction
    }

// Combined SDE for all Service Requests (both regular and negation)


define "SDE Service Request":
  "SDE Service Request Base"
    union "SDE Service Not Requested"

// Survey is fixed category code in ObservationScreeningAssessment profile in QI-Core    


define "SDE Observation Survey":
  [ObservationScreeningAssessment] Obs
    where exists ( "Initial Population" IP
        where "Normalize Interval"(Obs.effective) overlaps IP.period
    )
    return {
      id: Obs.id,
      meta: Obs.meta,
      extension: Obs.extension,
      partOf: Obs.partOf,
      status: Obs.status,
      category: Obs.category,
      code: Obs.code,
      subject: Obs.subject,
      encounter: Obs.encounter,
      effective: Obs.effective,
      issued: Obs.issued,
      value: Obs.value,
      dataAbsentReason: Obs.dataAbsentReason,
      interpretation: Obs.interpretation,
      bodySite: Obs.bodySite,
      method: Obs.method,
      specimen: Obs.specimen,
      referenceRange: Obs.referenceRange,
      hasMember: Obs.hasMember,
      derivedFrom: Obs.derivedFrom,
      component: Obs.component
    }

// Minimal patient SDE


define "SDE Minimal Patient":
  [Patient] MinPt
    where exists ( "Initial Population" )
    return {
      id: MinPt.id,
      meta: MinPt.meta,
      extension: MinPt.extension,
      identifier: MinPt.identifier,
      active: MinPt.active,
      name: MinPt.name,
      telecom: MinPt.telecom,
      gender: MinPt.gender,
      birthDate: MinPt.birthDate,
      deceased: MinPt.deceased,
      address: MinPt.address,
      maritalStatus: MinPt.maritalStatus,
      multipleBirth: MinPt.multipleBirth,
      photo: MinPt.photo,
      contact: MinPt.contact,
      communication: MinPt.communication,
      generalPractitioner: MinPt.generalPractitioner,
      managingOrganization: MinPt.managingOrganization,
      link: MinPt.link
    }

define "SDE Medication":
  ( [MedicationRequest]
    union [MedicationAdministration] ) MedReqOrAdmin
    let medication: GetMedication(MedReqOrAdmin.medication as Reference)
    where medication is not null
      and exists ( "Initial Population" IP
          where Coalesce("Normalize Interval"(MedReqOrAdmin.effective), MedReqOrAdmin.authoredOn.toInterval()) overlaps IP.period
      )
    return {
      id: medication.id,
      meta: medication.meta,
      code: medication.code,
      status: medication.status,
      manufacturer: medication.manufacturer,
      form: medication.form,
      amount: medication.amount,
      ingredient: medication.ingredient,
      batch: medication.batch
    }

// SDE Medication Request - regular requests (doNotPerform is false or absent)


define "SDE Medication Request Base":
  [MedicationRequest] MedRequests
    where exists ( "Initial Population" IP
        where MedRequests.authoredOn during IP.period
    )
    return {
      id: MedRequests.id,
      meta: MedRequests.meta,
      status: MedRequests.status,
      statusReason: MedRequests.statusReason,
      intent: MedRequests.intent,
      category: MedRequests.category,
      priority: MedRequests.priority,
      //doNotPerform: MedRequests.doNotPerform,
      
      reported: MedRequests.reported,
      medication: MedRequests.medication,
      subject: MedRequests.subject,
      encounter: MedRequests.encounter,
      authoredOn: MedRequests.authoredOn,
      requester: MedRequests.requester,
      recorder: MedRequests.recorder,
      reasonCode: MedRequests.reasonCode,
      reasonReference: MedRequests.reasonReference,
      instantiatesCanonical: MedRequests.instantiatesCanonical,
      instantiatesUri: MedRequests.instantiatesUri,
      courseOfTherapyType: MedRequests.courseOfTherapyType,
      dosageInstruction: MedRequests.dosageInstruction
    }

// SDE Medication Not Requested - negation requests (doNotPerform is true)


define "SDE Medication Not Requested":
  [MedicationNotRequested] MedNotRequests
    where exists ( "Initial Population" IP
        where MedNotRequests.authoredOn during IP.period
    )
    return {
      id: MedNotRequests.id,
      meta: MedNotRequests.meta,
      status: MedNotRequests.status,
      statusReason: MedNotRequests.statusReason,
      intent: MedNotRequests.intent,
      category: MedNotRequests.category,
      priority: MedNotRequests.priority,
      doNotPerform: MedNotRequests.doNotPerform,
      reported: MedNotRequests.reported,
      medication: MedNotRequests.medication,
      subject: MedNotRequests.subject,
      encounter: MedNotRequests.encounter,
      authoredOn: MedNotRequests.authoredOn,
      requester: MedNotRequests.requester,
      recorder: MedNotRequests.recorder,
      reasonCode: MedNotRequests.reasonCode,
      reasonReference: MedNotRequests.reasonReference,
      instantiatesCanonical: MedNotRequests.instantiatesCanonical,
      instantiatesUri: MedNotRequests.instantiatesUri,
      courseOfTherapyType: MedNotRequests.courseOfTherapyType,
      dosageInstruction: MedNotRequests.dosageInstruction
    }

// Combined SDE for all Medication Requests (both regular and negation)


define "SDE Medication Request":
  "SDE Medication Request Base"
    union "SDE Medication Not Requested"

define "SDE IP Encounters":
  "Initial Population" IP
    return {
      id: IP.id,
      meta: IP.meta,
      identifier: IP.identifier,
      status: IP.status,
      statusHistory: IP.statusHistory,
      class: IP.class,
      classHistory: IP.classHistory,
      type: IP.type,
      serviceType: IP.serviceType,
      priority: IP.priority,
      subject: IP.subject,
      period: IP.period,
      length: IP.length,
      reasonCode: IP.reasonCode,
      reasonReference: IP.reasonReference,
      diagnosis: IP.diagnosis,
      account: IP.account,
      hospitalization: IP.hospitalization,
      location: IP.location,
      partOf: IP.partOf
    }

define "SDE Observation Simple":
  [SimpleObservation] Obs
    where ( exists ( Obs.category Category
          where Category ~ "social-history"
      )
        or exists ( Obs.category Category
            where Category ~ "imaging"
        )
        or exists ( Obs.category Category
            where Category ~ "procedure"
        )
    )
      and exists ( "Initial Population" IP
          where "Normalize Interval"(Obs.effective) overlaps IP.period
      )
    return {
      id: Obs.id,
      meta: Obs.meta,
      extension: Obs.extension,
      partOf: Obs.partOf,
      status: Obs.status,
      category: Obs.category,
      code: Obs.code,
      subject: Obs.subject,
      encounter: Obs.encounter,
      effective: Obs.effective,
      issued: Obs.issued,
      value: Obs.value,
      dataAbsentReason: Obs.dataAbsentReason,
      interpretation: Obs.interpretation,
      bodySite: Obs.bodySite,
      method: Obs.method,
      specimen: Obs.specimen,
      referenceRange: Obs.referenceRange,
      hasMember: Obs.hasMember,
      derivedFrom: Obs.derivedFrom,
      component: Obs.component
    }

// Observation SDEs


define "SDE Observation Lab Category":
  [LaboratoryResultObservation] Obs
    where exists ( "Initial Population" IP
        where "Normalize Interval"(Obs.effective) overlaps IP.period
    )
    return {
      id: Obs.id,
      meta: Obs.meta,
      extension: Obs.extension,
      partOf: Obs.partOf,
      status: Obs.status,
      category: Obs.category,
      code: Obs.code,
      subject: Obs.subject,
      encounter: Obs.encounter,
      effective: Obs.effective,
      issued: Obs.issued,
      value: Obs.value,
      dataAbsentReason: Obs.dataAbsentReason,
      interpretation: Obs.interpretation,
      bodySite: Obs.bodySite,
      method: Obs.method,
      specimen: Obs.specimen,
      referenceRange: Obs.referenceRange,
      hasMember: Obs.hasMember,
      derivedFrom: Obs.derivedFrom,
      component: Obs.component
    }

// ServiceNotRequested SDE - negation requests (doNotPerform is true)


define "SDE Service Not Requested":
  [ServiceNotRequested] ServiceNotReqs
    where exists ( "Initial Population" IP
        where ServiceNotReqs.authoredOn during IP.period
    )
    return {
      id: ServiceNotReqs.id,
      meta: ServiceNotReqs.meta,
      instantiatesCanonical: ServiceNotReqs.instantiatesCanonical,
      instantiatesUri: ServiceNotReqs.instantiatesUri,
      basedOn: ServiceNotReqs.basedOn,
      replaces: ServiceNotReqs.replaces,
      requisition: ServiceNotReqs.requisition,
      status: ServiceNotReqs.status,
      intent: ServiceNotReqs.intent,
      category: ServiceNotReqs.category,
      priority: ServiceNotReqs.priority,
      doNotPerform: ServiceNotReqs.doNotPerform,
      code: ServiceNotReqs.code,
      orderDetail: ServiceNotReqs.orderDetail,
      quantity: ServiceNotReqs.quantity,
      subject: ServiceNotReqs.subject,
      encounter: ServiceNotReqs.encounter,
      occurrence: ServiceNotReqs.occurrence,
      asNeeded: ServiceNotReqs.asNeeded,
      authoredOn: ServiceNotReqs.authoredOn,
      requester: ServiceNotReqs.requester,
      performerType: ServiceNotReqs.performerType,
      performer: ServiceNotReqs.performer,
      locationCode: ServiceNotReqs.locationCode,
      reasonCode: ServiceNotReqs.reasonCode,
      reasonReference: ServiceNotReqs.reasonReference,
      insurance: ServiceNotReqs.insurance,
      bodySite: ServiceNotReqs.bodySite,
      note: ServiceNotReqs.note,
      patientInstruction: ServiceNotReqs.patientInstruction
    }

define "SDE Medication Administration Base":
  [MedicationAdministration] MedAdministrations
    where exists ( "Initial Population" IP
        where "Normalize Interval"(MedAdministrations.effective) overlaps IP.period
    )
    return {
      id: MedAdministrations.id,
      meta: MedAdministrations.meta,
      instantiates: MedAdministrations.instantiates,
      partOf: MedAdministrations.partOf,
      status: MedAdministrations.status,
      statusReason: MedAdministrations.statusReason,
      category: MedAdministrations.category,
      medication: MedAdministrations.medication,
      subject: MedAdministrations.subject,
      context: MedAdministrations.context,
      supportingInformation: MedAdministrations.supportingInformation,
      effective: MedAdministrations.effective,
      performer: MedAdministrations.performer,
      reasonCode: MedAdministrations.reasonCode,
      reasonReference: MedAdministrations.reasonReference,
      request: MedAdministrations.request,
      device: MedAdministrations.device,
      note: MedAdministrations.note,
      dosage: MedAdministrations.dosage
    }

define "SDE Medication Administration Not Done":
  [MedicationAdministrationNotDone] MedAdministrations
    where exists ( "Initial Population" IP
        where "Normalize Interval"(MedAdministrations.effective) overlaps IP.period
    )
    return {
      id: MedAdministrations.id,
      meta: MedAdministrations.meta,
      instantiates: MedAdministrations.instantiates,
      partOf: MedAdministrations.partOf,
      status: MedAdministrations.status,
      statusReason: MedAdministrations.statusReason,
      category: MedAdministrations.category,
      medication: MedAdministrations.medication,
      subject: MedAdministrations.subject,
      context: MedAdministrations.context,
      supportingInformation: MedAdministrations.supportingInformation,
      effective: MedAdministrations.effective,
      performer: MedAdministrations.performer,
      reasonCode: MedAdministrations.reasonCode,
      reasonReference: MedAdministrations.reasonReference,
      request: MedAdministrations.request,
      device: MedAdministrations.device,
      note: MedAdministrations.note,
      dosage: MedAdministrations.dosage
    }

// Medication SDEs


define "SDE Medication Administration":
  "SDE Medication Administration Base"
    union "SDE Medication Administration Not Done"

define "SDE Medication Administration Base":
  [MedicationAdministration] MedAdministrations
    where exists ( "Initial Population" IP
        where "Normalize Interval"(MedAdministrations.effective) overlaps IP.period
    )
    return {
      id: MedAdministrations.id,
      meta: MedAdministrations.meta,
      instantiates: MedAdministrations.instantiates,
      partOf: MedAdministrations.partOf,
      status: MedAdministrations.status,
      statusReason: MedAdministrations.statusReason,
      category: MedAdministrations.category,
      medication: MedAdministrations.medication,
      subject: MedAdministrations.subject,
      context: MedAdministrations.context,
      supportingInformation: MedAdministrations.supportingInformation,
      effective: MedAdministrations.effective,
      performer: MedAdministrations.performer,
      reasonCode: MedAdministrations.reasonCode,
      reasonReference: MedAdministrations.reasonReference,
      request: MedAdministrations.request,
      device: MedAdministrations.device,
      note: MedAdministrations.note,
      dosage: MedAdministrations.dosage
    }

// DiagnosticReport SDEs


define "SDE DiagnosticReport Lab":
  [DiagnosticReportLab] dr
    where exists ( "Initial Population" IP
        where "Normalize Interval"(dr.effective) overlaps IP.period
    )

// ----------------------------------------------------------------------
// Core retrieves
// ----------------------------------------------------------------------

// Locations from IP encounters





define "Get Locations from IP Encounters in Measurement Period":
  flatten ( "Initial Population" IP
      let locationElements: IP.location
      return locationElements LE
        let locationReference: LE.location
        return locationReference.getLocation ( )
  )

// Location SDE


define "SDE Location":
  "Get Locations from IP Encounters in Measurement Period" Locations
    where exists ( "Initial Population" )
      and Locations is not null
    return {
      id: Locations.id,
      meta: Locations.meta,
      extension: Locations.extension,
      status: Locations.status,
      operationalStatus: Locations.operationalStatus,
      name: Locations.name,
      alias: Locations.alias,
      description: Locations.description,
      mode: Locations.mode,
      type: Locations.type,
      telecom: Locations.telecom,
      address: Locations.address,
      physicalType: Locations.physicalType,
      position: Locations.position,
      managingOrganization: Locations.managingOrganization,
      partOf: Locations.partOf,
      hoursOfOperation: Locations.hoursOfOperation,
      availabilityExceptions: Locations.availabilityExceptions,
      endpoint: Locations.endpoint
    }

define "SDE DiagnosticReport Note":
  [DiagnosticReportNote] dr
    where ( exists ( dr.category Category
          where Category ~ "Radiology"
      )
        or exists ( dr.category Category
            where Category ~ "Pathology"
        )
        or exists ( dr.category Category
            where Category ~ "Cardiology"
        )
    )
      and exists ( "Initial Population" IP
          where "Normalize Interval"(dr.effective) overlaps IP.period
      )
    return {
      id: dr.id,
      meta: dr.meta,
      extension: dr.extension,
      basedOn: dr.basedOn,
      status: dr.status,
      category: dr.category,
      code: dr.code,
      subject: dr.subject,
      encounter: dr.encounter,
      effective: dr.effective,
      issued: dr.issued,
      specimen: dr.specimen,
      result: dr.result,
      conclusion: dr.conclusion,
      conclusionCode: dr.conclusionCode
    }

// SDE Medication Request - regular requests (doNotPerform is false or absent)


define "SDE Medication Request Base":
  [MedicationRequest] MedRequests
    where exists ( "Initial Population" IP
        where MedRequests.authoredOn during IP.period
    )
    return {
      id: MedRequests.id,
      meta: MedRequests.meta,
      status: MedRequests.status,
      statusReason: MedRequests.statusReason,
      intent: MedRequests.intent,
      category: MedRequests.category,
      priority: MedRequests.priority,
      //doNotPerform: MedRequests.doNotPerform,
      
      reported: MedRequests.reported,
      medication: MedRequests.medication,
      subject: MedRequests.subject,
      encounter: MedRequests.encounter,
      authoredOn: MedRequests.authoredOn,
      requester: MedRequests.requester,
      recorder: MedRequests.recorder,
      reasonCode: MedRequests.reasonCode,
      reasonReference: MedRequests.reasonReference,
      instantiatesCanonical: MedRequests.instantiatesCanonical,
      instantiatesUri: MedRequests.instantiatesUri,
      courseOfTherapyType: MedRequests.courseOfTherapyType,
      dosageInstruction: MedRequests.dosageInstruction
    }

// ----------------------------------------------------------------------
// SDEs
// ----------------------------------------------------------------------




define "SDE Condition Problems HealthConcerns":
  [ConditionProblemsHealthConcerns] Diagnosis
    where exists ( "Initial Population" IP
        where Diagnosis.prevalenceInterval ( ) overlaps day of IP.period
    )
    return {
      id: Diagnosis.id,
      meta: Diagnosis.meta,
      status: Diagnosis.clinicalStatus,
      verificationStatus: Diagnosis.verificationStatus,
      category: Diagnosis.category,
      severity: Diagnosis.severity,
      code: Diagnosis.code,
      bodySite: Diagnosis.bodySite,
      subject: Diagnosis.subject,
      encounterReferenceId: Diagnosis.encounter.reference.getId ( ),
      onset: Diagnosis.onset,
      stage: Diagnosis.stage,
      evidence: Diagnosis.evidence,
      note: Diagnosis.note
    }

define "SDE Condition Diagnosis":
  [ConditionEncounterDiagnosis] Diagnosis
    where exists ( "Initial Population" IP
        where Diagnosis.prevalenceInterval ( ) overlaps day of IP.period
    )
    return {
      id: Diagnosis.id,
      meta: Diagnosis.meta,
      status: Diagnosis.clinicalStatus,
      verificationStatus: Diagnosis.verificationStatus,
      category: Diagnosis.category,
      severity: Diagnosis.severity,
      code: Diagnosis.code,
      bodySite: Diagnosis.bodySite,
      subject: Diagnosis.subject,
      encounterReferenceId: Diagnosis.encounter.reference.getId ( ),
      onset: Diagnosis.onset,
      stage: Diagnosis.stage,
      evidence: Diagnosis.evidence,
      note: Diagnosis.note
    }

// ServiceRequest SDE - regular requests (doNotPerform is false or absent)


define "SDE Service Request Base":
  [ServiceRequest] ServiceRequests
    where exists ( "Initial Population" IP
        where ServiceRequests.authoredOn during IP.period
    )
    return {
      id: ServiceRequests.id,
      meta: ServiceRequests.meta,
      instantiatesCanonical: ServiceRequests.instantiatesCanonical,
      instantiatesUri: ServiceRequests.instantiatesUri,
      basedOn: ServiceRequests.basedOn,
      replaces: ServiceRequests.replaces,
      requisition: ServiceRequests.requisition,
      status: ServiceRequests.status,
      intent: ServiceRequests.intent,
      category: ServiceRequests.category,
      priority: ServiceRequests.priority,
      //doNotPerform: ServiceRequests.doNotPerform,
      
      code: ServiceRequests.code,
      orderDetail: ServiceRequests.orderDetail,
      quantity: ServiceRequests.quantity,
      subject: ServiceRequests.subject,
      encounter: ServiceRequests.encounter,
      occurrence: ServiceRequests.occurrence,
      asNeeded: ServiceRequests.asNeeded,
      authoredOn: ServiceRequests.authoredOn,
      requester: ServiceRequests.requester,
      performerType: ServiceRequests.performerType,
      performer: ServiceRequests.performer,
      locationCode: ServiceRequests.locationCode,
      reasonCode: ServiceRequests.reasonCode,
      reasonReference: ServiceRequests.reasonReference,
      insurance: ServiceRequests.insurance,
      bodySite: ServiceRequests.bodySite,
      note: ServiceRequests.note,
      patientInstruction: ServiceRequests.patientInstruction
    }

// ----------------------------------------------------------------------
// Helper functions
// ----------------------------------------------------------------------




define function "CheckIP"(encounter Encounter):
  exists ( "Initial Population" IP
      where encounter.id = IP.id
  )

// Former NHSNHelpers functions, adapted for QI Core


define function "Normalize Interval"(choice Choice<DateTime, Interval<DateTime>>):
  case
    when choice is DateTime then Interval[choice as DateTime, choice as DateTime]
    when choice is Interval<DateTime>then choice as Interval<DateTime>
    else null as Interval<DateTime>end

define function "GetMedication"(reference Reference):
  singleton from ( [Medication] Medication
      where reference.references ( Medication )
  )

/*
@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 Reference, resource Resource):
  resource.id = Last(Split(reference.reference, '/'))

/*
@description: Normalizes a value that is a choice of timing-valued types to an equivalent interval
@comment: Normalizes a choice type of DateTime, Quanitty, Interval<DateTime>, or Interval<Quantity> 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 QICore, allowing this function to be used across any resource.
The input can be provided as a DateTime, Quantity, Interval<DateTime> or Interval<Quantity>.
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 Quantity, the quantity is expected to be a calendar-duration interpreted as an Age,
and the result is a DateTime Interval beginning on the Date the patient turned that age and ending immediately before one year later.
If the input is a DateTime Interval, the result is the input.
If the input is a Quantity Interval, the quantities are expected to be calendar-durations interpreted as an Age, and the result
is a DateTime Interval beginning on the date the patient turned the age given as the start of the quantity interval, and ending
immediately before one year later than the date the patient turned the age given as the end of the quantity interval.
If the input is a Timing, an error will be thrown indicating that Timing calculations are not implemented. Any other input will reslt in a null DateTime Interval
*/
define fluent function toInterval(choice Choice<DateTime, Quantity, Interval<DateTime>, Interval<Quantity>, Timing>):
  case
	  when choice is DateTime then
    	Interval[choice as DateTime, choice as DateTime]
		when choice is Interval<DateTime> then
  		choice as Interval<DateTime>
		when choice is Quantity then
		  Interval[Patient.birthDate + (choice as Quantity),
			  Patient.birthDate + (choice as Quantity) + 1 year)
		when choice is Interval<Quantity> then
		  Interval[Patient.birthDate + (choice.low as Quantity),
			  Patient.birthDate + (choice.high as Quantity) + 1 year)
		when choice is Timing then
      Message(null, true, 'NOT_IMPLEMENTED', 'Error', 'Calculation of an interval from a Timing value is not supported') as Interval<DateTime>
		else
			null as Interval<DateTime>
	end

/*
@description: Returns an interval representing the normalized prevalence period of a given Condition.
@comment: Uses the ToInterval and ToAbatementInterval functions to determine the widest potential interval from
onset to abatement as specified in the given Condition. If the condition is active, or has an abatement date the resulting 
interval will have a closed ending boundary. Otherwise, the resulting interval will have an open ending boundary.
*/
define fluent function prevalenceInterval(condition Choice<"ConditionEncounterDiagnosis", "ConditionProblemsHealthConcerns">):
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.
@comment: If the abatement element of the Condition is represented as a DateTime, the result
is an interval beginning and ending on that DateTime.
If the abatement is represented as a Quantity, the quantity is expected to be a calendar-duration and is interpreted as the age of the patient. The
result is an interval from the date the patient turned that age to immediately before one year later.
If the abatement is represented as a Quantity Interval, the quantities are expected to be calendar-durations and are interpreted as an age range during
which the abatement occurred. The result is an interval from the date the patient turned the starting age of the quantity interval, and ending immediately
before one year later than the date the patient turned the ending age of the quantity interval.
*/
define fluent function abatementInterval(condition Choice<"ConditionEncounterDiagnosis", "ConditionProblemsHealthConcerns">):
	if condition.abatement is DateTime then
	  Interval[condition.abatement as DateTime, condition.abatement as DateTime]
	else if condition.abatement is Quantity then
		Interval[Patient.birthDate + (condition.abatement as Quantity),
			Patient.birthDate + (condition.abatement as Quantity) + 1 year)
	else if condition.abatement is Interval<Quantity> then
	  Interval[Patient.birthDate + (condition.abatement.low as Quantity),
		  Patient.birthDate + (condition.abatement.high as Quantity) + 1 year)
	else if condition.abatement is Interval<DateTime> then
	  Interval[condition.abatement.low, condition.abatement.high)
	else null as Interval<DateTime>

/*
@description: Returns the tail of the given uri (i.e. everything after the last slash in the URI).
@comment: This function can be used to determine the logical id of a given resource. It can be used in
a single-server environment to trace references. However, this function does not attempt to resolve
or distinguish the base of the given url, and so cannot be used safely in multi-server environments.
*/
define fluent function getId(uri String):
  Last(Split(uri, '/'))