define "Denominator Initial Population":
  [Location] L
    with Elements."Encounter During Measurement Period" E
     such that E.location.location.references(L)

define "Denominator":
  "Denominator Initial Population"

define function "Denominator Observation"(location Location):
  Sum(
    from (Parameters."Location Parameters"(location)) P, Parameters."Critical Access Hospital Parameters" H
      where P ~ H.parameter
      return all H.parameterEstimate
  ) * Elements."Patient Days"(location)

define "Numerator Initial Population":
  exists (Elements."Encounter During Measurement Period")

define "Numerator":
  "Numerator Initial Population"

define function "Numerator Observation"():
  Count(Elements."Catheter-Associated UTI")

/*
@description: CAUTI Risk Adjustment factors for Critical Access Hospitals
@comment: Source: https://www.cdc.gov/nhsn/2022rebaseline/tables/table-10.html
*/
define "Critical Access Hospital Parameters":
  List<Tuple {
    parameter String,
    parameterEstimate Decimal,
    standardError Decimal,
    pValue String
  }> {
    // Intercept
    Tuple {
      parameter: 'Intercept',
      parameterEstimate: -7.6495,
      standardError: 0.1492,
      pValue: '<0.0001'
    },

    // Average length of stay >= 6.5 days
    Tuple {
      parameter: 'Average length of stay >= 6.5',
      parameterEstimate: 0.4257,
      standardError: 0.1564,
      pValue: '0.0065'
    },

    // Average length of stay < 6.5 days
    Tuple {
      parameter: 'Average length of stay < 6.5 days',
      parameterEstimate: 0.0,
      standardError: 0.0,
      pValue: 'REFERENT'
    },

    // Proportion of total beds that are ICU < 0.16
    Tuple {
      parameter: 'Proportion of total beds that are ICU < 0.16',
      parameterEstimate: 0.4189,
      standardError: 0.1708,
      pValue: '0.0142'
    },

    // Proportion of total beds that are ICU >= 0.16
    Tuple {
      parameter: 'Proportion of total beds that are ICU >= 0.16',
      parameterEstimate: 0.0,
      standardError: 0.0,
      pValue: 'REFERENT'
    }
  }

/*
@description: Returns the characteristic codes for the given facility
*/
define function "Location Parameters"(location Location):
  {
    'Intercept',
    location.averageLengthOfStayParameter(),
    location.proportionOfBedsICUParameter()
  }

// These would need to access computed data for these characteristics for the location
define fluent function averageLengthOfStayParameter(location Location):
  'Average length of stay >= 6.5 days'

define fluent function proportionOfBedsICUParameter(location Location):
  'Proportion of total beds that are ICU < 0.16'

define "Encounter During Measurement Period":
  [Encounter] E
    where E.period during "Measurement Period"

define "Urine Culture With Bacterium":
  [Observation: "Urine Culture"] O
    where O.status = 'final'
      and exists (
        O.component C
          where C.code in "Bacterium Presence"
            and C.value >= 10000 '[CFU]/mL'
      )

define "UTI":
  "Urine Culture With Bacterium" U
    let 
      DOE: date from start of U.effective.toInterval(),
      IWP: Interval[DOE - 3 days, DOE + 3 days]
    where start of U.effective.toInterval() during "Measurement Period"
    return {
      urineCultureResult: U,
      dateOfEvent: DOE,
      infectionWindowPeriod: IWP
    }

define "Catheter Inserted Procedure":
  [Procedure: "Catheter Inserted"] P
    where P.status = 'completed'

define "Catheter Removed Procedure":
  [Procedure: "Catheter Removed"] P
    where P.status = 'completed'

define "Catheter Usage":
  "Catheter Inserted Procedure" I
    let catheterRemoved: 
      First(
        "Catheter Removed Procedure" R
          where R.performed.toInterval() starts after I.performed.toInterval()
          sort by start of performed.toInterval()
      )
    return Interval[
      date from start of I.performed.toInterval(), 
      date from start of catheterRemoved.performed.toInterval()
    ]

define "Catheter-Associated UTI":
  "UTI" U
    where exists (
        "Catheter Usage" Usage
          where start of Usage before U.dateOfEvent
            and end of Usage on or after U.dateOfEvent - 1 day
            and duration in days of Usage > 2
    )

define function "Patient Days"(location Location):
  Sum(
    "Encounter During Measurement Period" E
      where E.location.location.references(location)
      return all duration in days of E.period
  )

define "Denominator Initial Population":
  [Location] L
    with Elements."Encounter During Measurement Period" E
     such that E.location.location.references(L)

define "Numerator Initial Population":
  exists (Elements."Encounter During Measurement Period")

define "Numerator":
  "Numerator Initial Population"

define "Denominator":
  "Denominator Initial Population"

define function "Denominator Observation"(location Location):
  Sum(
    from (Parameters."Location Parameters"(location)) P, Parameters."Critical Access Hospital Parameters" H
      where P ~ H.parameter
      return all H.parameterEstimate
  ) * Elements."Patient Days"(location)

define function "Numerator Observation"():
  Count(Elements."Catheter-Associated UTI")

/*
@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, '/'))

/*
@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 fluent 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
      Message(null as Interval<DateTime>, true, 'NOT_IMPLEMENTED', 'Error', 'Calculation of an interval from a Timing value is not supported')
    when choice is FHIR.string then
      Message(null as Interval<DateTime>, true, 'NOT_IMPLEMENTED', 'Error', 'Calculation of an interval from a String value is not supported')
    else
      null as Interval<DateTime>
  end

/*
@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]

define function ToString(value string): value.value

define function ToString(value ObservationStatus): value.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
        }

/*
@description: Converts the given FHIR [Quantity](https://hl7.org/fhir/datatypes.html#Quantity) 
value to a CQL Quantity
@comment: If the given quantity has a comparator specified, a runtime error is raised. If the given quantity
has a system other than UCUM (i.e. `http://unitsofmeasure.org`) or CQL calendar units (i.e. `http://hl7.org/fhirpath/CodeSystem/calendar-units`)
an error is raised. For UCUM to calendar units, the `ToCalendarUnit` function is used.
@seealso: ToCalendarUnit
*/
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

/*
@description: Converts a UCUM definite duration unit to a CQL calendar duration
unit using conversions specified in the [quantities](https://cql.hl7.org/02-authorsguide.html#quantities) 
topic of the CQL specification.
@comment: Note that for durations above days (or weeks), the conversion is understood to be approximate
*/
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 ToDateTime(value dateTime): value.value

define function ToDateTime(value instant): value.value

define function ToDate(value date): value.value

define function ToString(value ProcedureStatus): value.value