MATGlobalCommonFunctions_FHIR4-4.0.000.cql

library MATGlobalCommonFunctions_FHIR4 version '4.0.000'

using FHIR version '4.0.0'

include FHIRHelpers version '4.0.0' called FHIRHelpers

codesystem "LOINC": 'http://loinc.org'
codesystem "SNOMEDCT": 'http://snomed.info/sct/731000124108'
codesystem "RoleCode": 'http://hl7.org/fhir/v3/RoleCode'
codesystem "Diagnosis Role": 'http://terminology.hl7.org/CodeSystem/diagnosis-role'
codesystem "RequestIntent": 'http://terminology.hl7.org/CodeSystem/request-intent'
codesystem "MedicationRequestCategory": 'http://terminology.hl7.org/CodeSystem/medicationrequest-category'
codesystem "ConditionClinicalStatusCodes": 'http://terminology.hl7.org/CodeSystem/condition-clinical'
codesystem "ConditionVerificationStatusCodes": 'http://terminology.hl7.org/CodeSystem/condition-verification'

valueset "Encounter Inpatient": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.666.5.307'
valueset "Emergency Department Visit": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113883.3.117.1.7.1.292'
valueset "Observation Services": 'http://cts.nlm.nih.gov/fhir/ValueSet/2.16.840.1.113762.1.4.1111.143'

code "Birthdate": '21112-8' from "LOINC" display 'Birth date'
code "Dead": '419099009' from "SNOMEDCT" display 'Dead'
code "ER": 'ER' from "RoleCode" display 'Emergency room'
code "ICU": 'ICU' from "RoleCode" display 'Intensive care unit'
code "Billing": 'billing' from "Diagnosis Role" display 'Billing'

// Condition Clinical Status Codes - Consider value sets for these
code "active": 'active' from "ConditionClinicalStatusCodes"
code "recurrence": 'recurrence' from "ConditionClinicalStatusCodes"
code "relapse": 'relapse' from "ConditionClinicalStatusCodes"
code "inactive": 'inactive' from "ConditionClinicalStatusCodes"
code "remission": 'remission' from "ConditionClinicalStatusCodes"
code "resolved": 'resolved' from "ConditionClinicalStatusCodes"

// Condition Verification Status Codes - Consider value sets for these
code "unconfirmed": 'unconfirmed' from ConditionVerificationStatusCodes
code "provisional": 'provisional' from ConditionVerificationStatusCodes
code "differential": 'differential' from ConditionVerificationStatusCodes
code "confirmed": 'confirmed' from ConditionVerificationStatusCodes
code "refuted": 'refuted' from ConditionVerificationStatusCodes
code "entered-in-error": 'entered-in-error' from ConditionVerificationStatusCodes

parameter "Measurement Period" Interval<DateTime>

context Patient

define "Inpatient Encounter":
	[Encounter: "Encounter Inpatient"] EncounterInpatient
		where EncounterInpatient.status = 'finished'
		    and "LengthInDays"(EncounterInpatient.period) <= 120
			and EncounterInpatient.period ends during "Measurement Period"

define function "ToDate"(Value DateTime):
	DateTime(year from Value, month from Value, day from Value, 0, 0, 0, 0, timezone from Value)

define function "CalendarAgeInDaysAt"(BirthDateTime DateTime, AsOf DateTime):
	days between ToDate(BirthDateTime)and ToDate(AsOf)

define function "CalendarAgeInDays"(BirthDateTime DateTime):
	CalendarAgeInDaysAt(BirthDateTime, Today())

define function "CalendarAgeInMonthsAt"(BirthDateTime DateTime, AsOf DateTime):
	months between ToDate(BirthDateTime)and ToDate(AsOf)

define function "CalendarAgeInMonths"(BirthDateTime DateTime):
	CalendarAgeInMonthsAt(BirthDateTime, Today())

define function "CalendarAgeInYearsAt"(BirthDateTime DateTime, AsOf DateTime):
	years between ToDate(BirthDateTime)and ToDate(AsOf)

define function "CalendarAgeInYears"(BirthDateTime DateTime):
	CalendarAgeInYearsAt(BirthDateTime, Today())

define function "LengthInDays"(Value Interval<DateTime>):
	difference in days between start of Value and end of Value

define function "ED Visit"(TheEncounter FHIR.Encounter):
    singleton from (
        [Encounter: "Emergency Department Visit"] EDVisit
            where EDVisit.status = 'finished'
                and EDVisit.period ends 1 hour or less on or before start of FHIRHelpers.ToInterval(TheEncounter.period)
    )

define function "Hospitalization"(TheEncounter FHIR.Encounter):
	( "ED Visit"(TheEncounter) ) X
    return
        if X is null then TheEncounter.period
        else Interval[start of FHIRHelpers.ToInterval(X.period), end of FHIRHelpers.ToInterval(TheEncounter.period)]

define function "Hospitalization Locations"(TheEncounter FHIR.Encounter):
	( "ED Visit"(TheEncounter) ) EDEncounter
    return
        if EDEncounter is null then TheEncounter.location
        else flatten { EDEncounter.location, TheEncounter.location }

define function "Hospitalization Length of Stay"(TheEncounter FHIR.Encounter):
	LengthInDays("Hospitalization"(TheEncounter))

define function "Hospital Admission Time"(TheEncounter FHIR.Encounter):
	start of "Hospitalization"(TheEncounter)

define function "Hospital Discharge Time"(TheEncounter FHIR.Encounter):
	end of FHIRHelpers.ToInterval(TheEncounter.period)

define function "Hospital Arrival Time"(TheEncounter FHIR.Encounter):
	start of FHIRHelpers.ToInterval(First(
	    ( "Hospitalization Locations"(TheEncounter) ) HospitalLocation
			sort by start of FHIRHelpers.ToInterval(period)
	).period)

define function "HospitalizationWithObservation"(TheEncounter FHIR.Encounter):
	TheEncounter Visit
		let ObsVisit: Last([Encounter: "Observation Services"] LastObs
				where LastObs.period ends 1 hour or less on or before start of Visit.period
				sort by end of period
			),
			VisitStart: Coalesce(start of ObsVisit.period, start of Visit.period),
			EDVisit: Last([Encounter: "Emergency Department Visit"] LastED
				where LastED.period ends 1 hour or less on or before VisitStart
				sort by end of period
			)
		return Interval[Coalesce(start of EDVisit.period, VisitStart), end of Visit.period]

define function "HospitalizationWithObservationLengthofStay"(Encounter FHIR.Encounter):
	"LengthInDays"("HospitalizationWithObservation"(Encounter))

// TODO - fix these (must fetch Location resources and compare id to reference)
/*define function "Hospital Departure Time"(TheEncounter FHIR.Encounter):
	end of FHIRHelpers.ToInterval(Last(
	    ( "Hospitalization Locations"(TheEncounter) ) HospitalLocation
			sort by start of FHIRHelpers.ToInterval(period)
	).period)

define function "Emergency Department Arrival Time"(TheEncounter FHIR.Encounter):
	start of FHIRHelpers.ToInterval((
	    singleton from (
	        ( "Hospitalization Locations"(TheEncounter) ) HospitalLocation
				where HospitalLocation.type ~ "ER"
		)
	).period)

define function "First Inpatient Intensive Care Unit"(TheEncounter FHIR.Encounter):
	First(
	    ( TheEncounter.location ) HospitalLocation
			where HospitalLocation.type ~ "ICU"
				and HospitalLocation.period during TheEncounter.period
			sort by start of FHIRHelpers.ToInterval(period)
	)*/

/*
*
*    CQFMeasures Common Logic
*
*/

define function "Normalize Onset"(onset Choice<FHIR.dateTime, FHIR.Age, FHIR.Period, FHIR.Range, FHIR.string>):
  if onset is FHIR.dateTime then
	  Interval[FHIRHelpers.ToDateTime(onset as FHIR.dateTime), FHIRHelpers.ToDateTime(onset as FHIR.dateTime)]
	else if onset is FHIR.Period then
	  FHIRHelpers.ToInterval(onset as FHIR.Period)
	else if onset is FHIR.Age then
	  Interval[FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(onset as FHIR.Age),
		  FHIRHelpers.ToDate(Patient.birthDate) + FHIRHelpers.ToQuantity(onset as FHIR.Age) + 1 year)
	else null

define function "Normalize Abatement"(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.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.boolean then
	  Interval[end of "Normalize Onset"(condition.onset), condition.recordedDate)
	else null

define function "Prevalence Period"(condition Condition):
  Interval[start of "Normalize Onset"(condition.onset), end of "Normalize Abatement"(condition))

define function "Normalize Interval"(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.Timing then
		  Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute a single interval from a Timing type')
		when choice is FHIR.instant then
			Interval[FHIRHelpers.ToDateTime(choice as FHIR.instant), FHIRHelpers.ToDateTime(choice as FHIR.instant)]
    when choice is FHIR.string then
      Message(null as Interval<DateTime>, true, '1', 'Error', 'Cannot compute an interval from a String value')
		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)
		else null as Interval<DateTime>
	end

define function "GetId"(uri String):
	Last(Split(uri, '/'))


define function "EncounterDiagnosis"(Encounter Encounter):
  Encounter.diagnosis D
    return singleton from ([Condition] C where C.id = "GetId"(D.condition.reference))

// Returns the condition that is specified as the principal diagnosis for the encounter
// TODO: BTR 2019-07-30: Shouldn't need the FHIRHelpers reference here, investigate
define function "PrincipalDiagnosis"(Encounter Encounter):
	(singleton from (Encounter.diagnosis D where FHIRHelpers.ToInteger(D.rank) = 1)) PD
		return singleton from ([Condition] C where C.id = "GetId"(PD.condition.reference))

// Returns the location for the given location reference
define function GetLocation(reference Reference):
  singleton from (
    [Location] L where L.id = GetId(reference.reference)
  )

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

define function "GetExtension"(domainResource DomainResource, url String):
  singleton from "GetExtensions"(domainResource, url)

/*
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 "GetBaseExtensions"(domainResource DomainResource, url String):
  domainResource.extension E
	  where E.url = ('http://hl7.org/fhir/StructureDefinition/' + url)
		return E

define function "GetBaseExtension"(domainResource DomainResource, url String):
  singleton from "GetBaseExtensions"(domainResource, url)

/*
NOTE: Provenance is not the preferred approach, this is provided only as an illustration
for what using Provenance could look like, and is not a tested pattern
*/
define function "GetProvenance"(resource Resource):
  singleton from ([Provenance: target in resource.id])

define function "GetMedicationCode"(request MedicationRequest):
  if request.medication is CodeableConcept then
	  request.medication as CodeableConcept
	else
	  (singleton from ([Medication] M where M.id = GetId((request.medication as Reference).reference))).code