// Jurisdiction of residence (jurisdiction of the patient)
define "Most recent physical home address":
  First(
    Patient.address A
      where A.use = 'home'
        and A.type = 'physical'
      sort by end of period desc
  )

define "Postal Code of Residence":
  "Most recent physical home address".postalCode

define "SDE Postal Code of Residence":
  SurveillanceDataElements."Postal Code of Residence"

define "State of Residence":
  "Most recent physical home address".state

define "SDE State of Residence":
  SurveillanceDataElements."State of Residence"

define "SDE Race":
  (flatten (
      Patient.extension Extension
        where Extension.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-race'
          return Extension.extension
    )) E
      where E.url = 'ombCategory'
        or E.url = 'detailed'
      return E.value as Coding

define "SDE Race":
  SDE."SDE Race"

define "SDE Sex":
  case
      when Patient.gender = 'male' then Code { code: 'M', system: 'http://hl7.org/fhir/v3/AdministrativeGender', display: 'Male' }
      when Patient.gender = 'female' then Code { code: 'F', system: 'http://hl7.org/fhir/v3/AdministrativeGender', display: 'Female' }
      else null
    end

define "SDE Sex":
  SDE."SDE Sex"

//Numerator
define "Patient Age 12 to 16 Years at Start of Measurement Period":
  AgeInYearsAt(start of "Measurement Period") in Interval[12, 16]

define "Qualifying Encounters During Measurement Period":
  (AC.QualifiedEncounters([Encounter: "Encounter to Screen for Depression"])
    union AC.QualifiedEncounters([Encounter: "Physical Therapy Evaluation"])
    union AC.QualifiedEncounters([Encounter: "Telephone Visits"])) QualifyingEnc 
    where FC.ToInterval(QualifyingEnc.period) during "Measurement Period"

define "Has Adolescent Depression Screening":
  ((AC.QualifiedObservations([Observation: "Adolescent Depression Screening Assessment"])) AdolescentScreening
    with "Qualifying Encounters During Measurement Period" QualifyingEnc
      such that "Screening Within 14 Days of Encounter"(AdolescentScreening, QualifyingEnc))

//Adolescent Numerator
define "Most Recent Adolescent Depression Screening":
  AC.MostRecent(("Has Adolescent Depression Screening"))

define "Most Recent Adolescent Screening Negative":
  ("Most Recent Adolescent Depression Screening" AdolescentScreening
    where AdolescentScreening.value ~ ToConcept("Depression Screening Negative")) is not null

define "Most Recent Adolescent Positive Depression Screening":
  "Most Recent Adolescent Depression Screening" RecentScreening
    where RecentScreening.value ~ ToConcept("Depression Screening Positive")

define "Follow Up Interventions For Positive Adolescent Depression Screening":
  (AC.QualifiedMedicationRequests([MedicationRequest: "Adolescent Depression Medications"])
    union AC.QualifiedServiceRequests([ServiceRequest: "Referral for Adolescent Depression"])
    union AC.QualifiedProcedures([Procedure: "Follow Up for Adolescent Depression"])) FollowUpInterventions
    let "Intervention Day": Coalesce(FC.ToInterval(FollowUpInterventions.authoredOn), FC.ToInterval(FollowUpInterventions.performed))
    with "Qualifying Encounters During Measurement Period" QualifyingEnc
      such that "Intervention Day" same day as QualifyingEnc.period
      or "Intervention Day" 2 days or less after day of end of FC.ToInterval(QualifyingEnc.period)

define "Most Recent Adolescent Depression Screening Positive and Follow Up Provided":
  ("Most Recent Adolescent Positive Depression Screening" RecentScreening
  let "Screening Day": Coalesce(FC.ToInterval(RecentScreening.effective), FC.ToInterval(RecentScreening.issued))
  with "Follow Up Interventions For Positive Adolescent Depression Screening" FollowUpInterventions
    such that "Screening Day" 14 days or less before start of Coalesce(FC.ToInterval(FollowUpInterventions.authoredOn), FC.ToInterval(FollowUpInterventions.performed))
  ) is not null

define "Patient Age 17 Years at Start of Measurement Period":
  AgeInYearsAt(start of "Measurement Period") = 17

define "Has Adult Depression Screening":
  ((AC.QualifiedObservations([Observation: "Adult Depression Screening Assessment"])) AdolescentScreening
    with "Qualifying Encounters During Measurement Period" QualifyingEnc
      such that "Screening Within 14 Days of Encounter"(AdolescentScreening, QualifyingEnc))

//Adult Numerator
define "Most Recent Adult Depression Screening":
  AC.MostRecent(("Has Adult Depression Screening"))

define "Most Recent Adult Screening Negative":
  ("Most Recent Adult Depression Screening" AdultScreening
    where AdultScreening.value ~ ToConcept("Depression Screening Negative")) is not null

define "Most Recent Adult Positive Depression Screening":
  "Most Recent Adult Depression Screening" RecentScreening
    where RecentScreening.value ~ ToConcept("Depression Screening Positive")

define "Follow Up Interventions For Positive Adult Depression Screening":
  ((AC.QualifiedMedicationRequests([MedicationRequest: "Adult Depression Medications"])
    union AC.QualifiedServiceRequests([ServiceRequest: "Referral for Adult Depression"])
    union AC.QualifiedProcedures([Procedure: "Follow Up for Adult Depression"]))) FollowUpInterventions
    let "Intervention Day": Coalesce(FC.ToInterval(FollowUpInterventions.authoredOn), FC.ToInterval(FollowUpInterventions.performed))
    with "Qualifying Encounters During Measurement Period" QualifyingEnc
      such that "Intervention Day" same day as QualifyingEnc.period
      or "Intervention Day" 2 days or less after day of end of FC.ToInterval(QualifyingEnc.period)

define "Most Recent Adult Depression Screening Positive and Follow Up Provided":
  ("Most Recent Adult Positive Depression Screening" RecentScreening
  let "Screening Day": Coalesce(FC.ToInterval(RecentScreening.effective), FC.ToInterval(RecentScreening.issued))
  with "Follow Up Interventions For Positive Adult Depression Screening" FollowUpInterventions
    such that "Screening Day" 14 days or less before start of Coalesce(FC.ToInterval(FollowUpInterventions.authoredOn), FC.ToInterval(FollowUpInterventions.performed))
  ) is not null

define "Patient Age 18 Years or Older at Start of Measurement Period":
  AgeInYearsAt(start of "Measurement Period") >= 18

define "Numerator":
  ( "Patient Age 12 to 16 Years at Start of Measurement Period"
      and ( "Most Recent Adolescent Screening Negative"
        or "Most Recent Adolescent Depression Screening Positive and Follow Up Provided" )
)
  or ( "Patient Age 17 Years at Start of Measurement Period"
    and ( "Most Recent Adolescent Screening Negative"
      or "Most Recent Adolescent Depression Screening Positive and Follow Up Provided"
      or "Most Recent Adult Screening Negative"
      or  "Most Recent Adult Depression Screening Positive and Follow Up Provided") 
  )
  or ( "Patient Age 18 Years or Older at Start of Measurement Period"
    and ( "Most Recent Adult Screening Negative"
      or "Most Recent Adult Depression Screening Positive and Follow Up Provided" ) )

define "Initial Population":
  AgeInYearsAt(start of "Measurement Period") >= 12
    and exists(
      "Qualifying Encounters During Measurement Period" E 
        where FC.ToInterval(E.period) during "Measurement Period"
    )

define "Denominator":
  "Initial Population"

define "SDE Payer":
  [Coverage: type in "Payer"] Payer
        return {
          code: Payer.type,
          period: Payer.period
        }

define "SDE Payer":
  SDE."SDE Payer"

// Jurisdiction of care (jurisdiction of the most recent encounter)
// TODO:
//define "Most recent address of care":

// NOTE: Included in eICR
// Occupational Data for Health - Past or Present Job
// http://hl7.org/fhir/us/odh/StructureDefinition-odh-PastOrPresentJob.html
// Observation: LOINC#11341-5, valueCodeableConcept in https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.7186

// Social Determinants of Health (SDOH)
// http://build.fhir.org/ig/HL7/fhir-sdoh-clinicalcare/StructureDefinition-SDOHCC-ObservationScreeningResponse.html
// Food insecurity risk: http://build.fhir.org/ig/HL7/fhir-sdoh-clinicalcare/Observation-SDOHCC-ObservationResponseHungerVitalSignQuestion3Example.html
// Observation: LOINC#88124-3, valueCodeableConcept in https://loinc.org/LL2510-7/ (At risk, No risk)
define "Food Insecurity Risk Status":
  First(
    [Observation: "Food insecurity risk [HVS]"] O
      sort by issued desc
  ).value as CodeableConcept

define "SDE Food Insecurity Risk Status":
  SurveillanceDataElements."Food Insecurity Risk Status"

define "SDE Ethnicity":
  (flatten (
      Patient.extension Extension
        where Extension.url = 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity'
          return Extension.extension
    )) E
      where E.url = 'ombCategory'
        or E.url = 'detailed'
      return E.value as Coding

define "SDE Ethnicity":
  SDE."SDE Ethnicity"

// Age
define "Age":
  AgeInYearsAt(end of "Measurement Period")

define "SDE Age":
  SurveillanceDataElements."Age"

//Denominator Exclusion 
define "History of Bipolar Diagnosis Before Qualifying Encounter": 
  (AC.QualifiedConditions([Condition: "Bipolar Disorder"])) BipolarDiagnosis 
  with "Qualifying Encounters During Measurement Period" QualifyingEnc
    such that FC.ToPrevalenceInterval(BipolarDiagnosis) starts before QualifyingEnc.period

define "Denominator Exclusions":
  exists("History of Bipolar Diagnosis Before Qualifying Encounter")

//Denominator Exception
define "Medical or Patient Reason for Not Screening Adolescent for Depression":
  AC.AbsentData([Observation: "Adolescent Depression Screening Assessment"], "Qualifying Encounters During Measurement Period", "Depression Screening Declined", "Medical Reason")

define "Medical or Patient Reason for Not Screening Adult for Depression":
  AC.AbsentData([Observation: "Adult Depression Screening Assessment"], "Qualifying Encounters During Measurement Period", "Depression Screening Declined", "Medical Reason")

define "Denominator Exceptions":
  (exists("Medical or Patient Reason for Not Screening Adolescent for Depression")
    and not exists("Has Adolescent Depression Screening"))
  or (exists("Medical or Patient Reason for Not Screening Adult for Depression")
    and not exists("Has Adult Depression Screening"))

define function ToString(value AddressUse): value.value

define function ToString(value AddressType): value.value

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 ToString(value uri): value.value

define function ToString(value AdministrativeGender): value.value

define function MostRecent(observations List<Observation>):
  Last(
    observations O
      sort by start of FC.ToInterval(effective)
  )

define function QualifiedObservations(value List<FHIR.Observation>):
  value Observation
		where (
      //registered | preliminary | final | amended | corrected | cancelled | entered-in-error | unknown
      Observation.status ~ 'final'
			or Observation.status ~ 'amended'
			or Observation.status ~ 'corrected'
		)

define function ToString(value ObservationStatus): value.value

/* Common Resource Qualifications and Negations */
define function QualifiedEncounters(value List<FHIR.Encounter>):
  value Encounter
    where (
      //planned | arrived | triaged | in-progress | onleave | finished | cancelled | entered-in-error | unknown
      Encounter.status ~ 'arrived'
      or Encounter.status ~ 'in-progress'
      or Encounter.status ~ 'finished'
      or Encounter.status ~ 'onleave'
      or Encounter.status ~ 'triaged'
    )

define function ToString(value EncounterStatus): value.value

/*
@description: Normalizes a value that is a choice of timing-valued types to an equivalent interval
@comment: Normalizes a choice type of FHIR.dateTime, FHIR.Period, FHIR.Timing, FHIR.instance, FHIR.string, FHIR.Age, or FHIR.Range 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 FHIR, allowing this function to be used across any resource.

The input can be provided as a dateTime, Period, Timing, instant, string, Age, or Range.
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 Period, the result is a DateTime Interval.
If the input is a Timing, an error is raised indicating a single interval cannot be computed from a Timing.
If the input is an instant, the result is a DateTime Interval beginning and ending on that instant.
If the input is a string, an error is raised indicating a single interval cannot be computed from a string.
If the input is an Age, the result is a DateTime Interval beginning when the patient was the given Age,
and ending immediately prior to when the patient was the given Age plus one year.
If the input is a Range, the result is a DateTime Interval beginning when the patient was the Age given
by the low end of the Range, and ending immediately prior to when the patient was the Age given by the
high end of the Range plus one year.

NOTE: Due to the
complexity of determining a single interval from a Timing or String type, this function will throw a run-time exception if it is used
with a Timing or String.
*/
define function ToInterval(choice Choice<FHIR.dateTime, FHIR.Period, FHIR.Timing, FHIR.instant, FHIR.string, FHIR.Age, FHIR.Range>):
  case
	  when choice is FHIR.dateTime then
    	Interval[FHIRHelpers.ToDateTime(choice as FHIR.dateTime), FHIRHelpers.ToDateTime(choice as FHIR.dateTime)]
		when choice is FHIR.Period then
  		FHIRHelpers.ToInterval(choice as FHIR.Period)
		when choice is FHIR.instant then
			Interval[FHIRHelpers.ToDateTime(choice as FHIR.instant), FHIRHelpers.ToDateTime(choice as FHIR.instant)]
		when choice is FHIR.Age then
		  Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(choice as FHIR.Age),
			  FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(choice as FHIR.Age) + 1 year)
		when choice is FHIR.Range then
		  Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((choice as FHIR.Range).low),
			  FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity((choice as FHIR.Range).high) + 1 year)
		when choice is FHIR.Timing then
			//Interval[FHIRHelpers.ToDateTime(choice as FHIR.timing), FHIRHelpers.ToDateTime(choice as FHIR.dateTime)]
		  Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute a single interval from a Timing type')
    when choice is FHIR.string then
      Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute an interval from a String value')
		else
			null as Interval<DateTime>
	end

define function ToDateTime(value dateTime): value.value

define function ToDateTime(value instant): value.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 "Screening Within 14 Days of Encounter"(observation FHIR.Observation, encounter FHIR.Encounter)
returns System.Boolean:
  Coalesce(end of FC.ToInterval(observation.effective), observation.issued) 14 days or less before day of start of encounter.period
    and observation.value is not null

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 QualifiedMedicationRequests(value List<FHIR.MedicationRequest>):
  value MedicationRequest
    where (
      //active | on-hold | cancelled | completed | entered-in-error | stopped | draft | unknown
      (MedicationRequest.status ~ 'active'
        or MedicationRequest.status ~ 'completed'
      )
        and (
          MedicationRequest.doNotPerform is null
          or MedicationRequest.doNotPerform = false
        )
        and MedicationRequest.intent ~ 'order'
    )

define function ToString(value MedicationRequestStatus): value.value

define function ToBoolean(value boolean): value.value

define function ToString(value MedicationRequestIntent): value.value

define function ToString(value string): value.value

define function QualifiedServiceRequests(value List<FHIR.ServiceRequest>):
  value ServiceRequest
    where (
      //draft | active | on-hold | revoked | completed | entered-in-error | unknown
      ServiceRequest.status ~ 'active'
      or ServiceRequest.status ~ 'completed'
      and ServiceRequest.intent ~ 'order'
    )
    and (
      ServiceRequest.doNotPerform is null
      or ServiceRequest.doNotPerform = false
    )

define function ToString(value ServiceRequestStatus): value.value

define function ToString(value ServiceRequestIntent): value.value

define function QualifiedProcedures(value List<FHIR.Procedure>):
  value Procedure
    where (
      //preparation | in-progress | not-done | on-hold | stopped | completed | entered-in-error | unknown
      Procedure.status ~ 'completed'
    )

define function ToString(value ProcedureStatus): value.value

define function QualifiedConditions(value List<FHIR.Condition>):
  value Condition
    where (
      FHIRHelpers.ToConcept(Condition.clinicalStatus) ~ FC."active"
    )
    and (
      FHIRHelpers.ToConcept(Condition.verificationStatus) ~ FC."confirmed"
    )

/*
@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 function ToPrevalenceInterval(condition Condition):
if condition.clinicalStatus ~ "active"
  or condition.clinicalStatus ~ "recurrence"
  or condition.clinicalStatus ~ "relapse" then
  Interval[start of ToInterval(condition.onset), end of ToAbatementInterval(condition)]
else
  Interval[start of ToInterval(condition.onset), end of ToAbatementInterval(condition))

/*
@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 function ToAbatementInterval(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, '1', 'Error', 'Cannot compute an interval from a String value')
	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 ToInterval(condition.onset), condition.recordedDate)
	else null

define function AbsentData(observation List<FHIR.Observation>, enc List<FHIR.Encounter>, code1 System.Code, valueset1 System.ValueSet)
returns List<FHIR.Observation>:
  (QualifiedObservations(observation)) Obs
    with enc QualifyingEnc
      such that Coalesce(end of FC.ToInterval(Obs.effective), end of FC.ToInterval(Obs.issued)) same day as end of QualifyingEnc.period
    where exists(
        Obs.component c where(
            c.code as CodeableConcept ~ code1
            or c.code as CodeableConcept in valueset1
        ))
      and not exists(Obs.component c where(c.value is not null))
      or (ResourceNotDone(Obs).value as FHIR.boolean = true
        and (ResourceNotDoneReason(Obs).value as CodeableConcept ~ code1
        or ResourceNotDoneReason(Obs).value as CodeableConcept in valueset1))

define function ResourceNotDone(notDone DomainResource):
  QICoreModifierExtension(notDone, 'qicore-notDone')

define function QICoreModifierExtension(domainResource DomainResource, url String):
  singleton from QICoreModifierExtensions(domainResource, url)

/* QI-CORE Extensions */

/*
NOTE: Extensions are not the preferred approach, but are used as a way to access
content that is defined by extensions but not yet surfaced in the
CQL model info.
*/
define function QICoreModifierExtensions(domainResource DomainResource, url String):
  domainResource.modifierExtension E
    where E.url = ('http://hl7.org/fhir/us/qicore/StructureDefinition/' + url)
    return E

define function ResourceNotDoneReason(notDoneReason DomainResource):
  QICoreExtension(notDoneReason, 'qicore-notDoneReason')

define function QICoreExtension(domainResource DomainResource, url String):
  singleton from QICoreExtensions(domainResource, url)

define function QICoreExtensions(domainResource DomainResource, url String):
  domainResource.extension E
    where E.url = ('http://hl7.org/fhir/us/qicore/StructureDefinition/' + url)
    return E