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Added in CQL for decision table for measles to test out the entire process. Updated tools based on SOPs. Updated sushi-config to load the CQL into the FSH library files.
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‎input/cql/IMMZCommon.cql

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library IMMZCommon
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using FHIR version '4.0.1'
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include FHIRHelpers version '4.0.1'
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/**
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* @description Fetches a singleton protocol applied from an immunization
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* @comment The protocol list from the immunization
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*/
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define function Only(protocols List<FHIR.Immunization.ProtocolApplied>):
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singleton from protocols
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/**
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* @description Fetches a singleton protocol applied from an immunization
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* @comment The protocol list from the immunization
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*/
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define fluent function only(protocols List<FHIR.Immunization.ProtocolApplied>):
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singleton from protocols
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/**
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* @description Takes the date choice of a date/string choice (for Immunization date)
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*/
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define function ToDate(choice Choice<FHIR.date, FHIR.string>):
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case
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when choice is FHIR.date then
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choice as FHIR.date
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else
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Message(null as FHIR.date, true, '1', 'Error', 'Cannot compute a date from a String value')
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end
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/**
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* @description Takes the date choice of a date/string choice (for Immunization date)
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*/
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define function ToDateTime(choice Choice<FHIR.dateTime, FHIR.string>):
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case
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when choice is FHIR.dateTime then
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choice as FHIR.dateTime
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else
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Message(null as FHIR.dateTime, true, '1', 'Error', 'Cannot compute a date from a String value')
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end
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/**
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* @description Takes a choice of FHIR.string and FHIR.positiveInt and ensures the result is a FHIR.positiveInt
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*/
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define function ToPositiveInt(choice Choice<FHIR.positiveInt, FHIR.string>):
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case
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when choice is FHIR.positiveInt then
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choice as FHIR.positiveInt
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else
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Message(null as FHIR.positiveInt, true, '1', 'Error', 'Cannot compute a positive from a String value') // TODO: I'm sure that this is supported somehow?
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end
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/**
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* @description Takes a choice between a Medication and a CodeableConcept and returns just the code of the medication
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*/
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define function ExtractMedicationCode(choice Choice<FHIR.CodeableConcept, FHIR.Reference>):
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case
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when choice is FHIR.CodeableConcept then
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choice as FHIR.CodeableConcept
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when choice is FHIR.Reference then
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First([Medication] M
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where M.id = Last(Split(choice.reference, '/'))
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return M.code as FHIR.CodeableConcept)
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else
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Message(null as FHIR.CodeableConcept, true, '1', 'Error', 'Cannot compute a medication code') // TODO: I'm sure that this is supported somehow?
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end
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/**
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* @description Takes a choice between a Medication and a CodeableConcept and returns just the code of the medication
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*/
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define function ExtractMedicationInitiationDate(choice Choice<FHIR.dateTime, FHIR.Period>):
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case
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when choice is FHIR.Period then
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start of (choice as FHIR.Period)
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when choice is FHIR.dateTime then
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choice as FHIR.dateTime
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else
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Message(null as FHIR.dateTime, true, '1', 'Error', 'Cannot compute medication treatment initiation date') // TODO: I'm sure that this is supported somehow?
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end
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‎input/cql/IMMZConcepts.cql

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library IMMZConcepts
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codesystem "IMMZC": 'http://smart.who.int/immunizations/CodeSystem/IMMZ.C'
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codesystem "IMMZD": 'http://smart.who.int/immunizations/CodeSystem/IMMZ.D'
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codesystem "IMMZZ": 'http://smart.who.int/immunizations/CodeSystem/IMMZ.Z'
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//WHO ATC IPS Valueset
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valueset "WHO ATC": 'http://hl7.org/fhir/uv/ips/ValueSet/whoatc-uv-ips'
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// General use ValueSets
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// Vaccine Value Sets
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valueset "Live Attenuated": 'http://smart.who.int/immunizations/ValueSet/IMMZ.Z.LiveAttenuated'
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valueset "MCV Vaccine": 'http://smart.who.int/immunizations/ValueSet/IMMZ.Z.DE9'
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valueset "BCG Vaccine": 'http://smart.who.int/immunizations/ValueSet/IMMZ.Z.DE1'
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valueset "Cholera Vaccine": 'http://smart.who.int/immunizations/ValueSet/IMMZ.Z.DE2'

‎input/cql/IMMZD2DTMeaslesElements.cql

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/*
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* Library: IMMZD2DTMeaslesElements
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*/
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library IMMZD2DTMeaslesElements
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using FHIR version '4.0.1'
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include FHIRHelpers version '4.0.1'
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include WHOConcepts
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include WHOCommon called WC
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include WHOElements called WE
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include IMMZCommon called Common
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include IMMZConcepts called Concepts
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include IMMZElements called Elements
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context Patient
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/*
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@internal: MCV containing Doses Administered to Patient
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*/
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define "MCV Doses Administered to Patient":
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Elements."Doses Administered to Patient" I
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where
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I.vaccineCode in Concepts."MCV Vaccine"
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and I.isSubpotent is not true
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/*
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@internal: MCV containing Doses Administered to Patient that are in the Primary series
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*/
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define "MCV Primary Series Doses Administered to Patient":
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"MCV Doses Administered to Patient" I
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where
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exists( I.protocolApplied pa where pa.series = 'Primary series' )
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/*
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@internal: Number of MCV Primary Series doses
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*/
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define "Number of MCV Primary Series Doses Administered":
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Count("MCV Primary Series Doses Administered to Patient")
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/*
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@input: No measles primary series doses were administered
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@pseudocode: Count of vaccines administered (where "Vaccine type" = "Measles-containing vaccines" and "Type of dose" = "Primary series") = 0
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*/
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define "No measles primary series doses were administered":
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"Number of MCV Primary Series Doses Administered" = 0
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/*
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@input: MCV1 was administered
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@pseudocode: Count of vaccines administered (where "Vaccine type" = "Measles-containing vaccines" and "Type of dose" = "Primary series") = 1
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*/
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define "MCV1 was administered":
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"Number of MCV Primary Series Doses Administered" = 1
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/*
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@input: MCV2 was administered
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@pseudocode: Count of vaccines administered (where "Vaccine type" = "Measles-containing vaccines" and "Type of dose" = "Primary series") = 2
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*/
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define "MCV2 was administered":
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"Number of MCV Primary Series Doses Administered" = 2
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‎input/cql/IMMZD2DTMeaslesEncounterElements.cql

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/*
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* Library: IMMZD2DTMeaslesEncounterElements
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*/
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library IMMZD2DTMeaslesEncounterElements
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using FHIR version '4.0.1'
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include FHIRHelpers version '4.0.1'
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include WHOConcepts
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include WHOCommon called WC
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include WHOElements called WE
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include IMMZCommon called Common
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include IMMZConcepts called Concepts
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include IMMZEncounterElements called Encounter
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include IMMZD2DTMeaslesElements called MeaslesElements
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parameter Today Date default Today()
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parameter EncounterId String
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context Patient
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/*
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@internal: MCV containing Doses Administered to Patient
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*/
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define "MCV Doses Administered to Patient":
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Encounter."Doses Administered to Patient" I
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where
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I.occurrence.toInterval() on or before Today
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/*
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@internal: MCV containing Doses Administered to Patient that are in the Primary series
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*/
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define "MCV Primary Series Doses Administered to Patient":
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MeaslesElements."MCV Primary Series Doses Administered to Patient" I
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where
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I.occurrence.toInterval() on or before Today
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/*
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@internal: Number of MCV Primary Series doses
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*/
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define "Number of MCV Primary Series Doses Administered":
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Count("MCV Primary Series Doses Administered to Patient")
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/*
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@input: No measles primary series doses were administered
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@pseudocode: Count of vaccines administered (where "Vaccine type" = "Measles-containing vaccines" and "Type of dose" = "Primary series") = 0
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*/
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define "No measles primary series doses were administered":
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"Number of MCV Primary Series Doses Administered" = 0
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/*
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@input: MCV1 was administered
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@pseudocode: Count of vaccines administered (where "Vaccine type" = "Measles-containing vaccines" and "Type of dose" = "Primary series") = 1
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*/
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define "MCV1 was administered":
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"Number of MCV Primary Series Doses Administered" = 1
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/*
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@input: MCV2 was administered
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@pseudocode: Count of vaccines administered (where "Vaccine type" = "Measles-containing vaccines" and "Type of dose" = "Primary series") = 2
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*/
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define "MCV2 was administered":
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"Number of MCV Primary Series Doses Administered" = 2
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