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enola-dkfzenola-dkfz
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Merge pull request #188 from samply/develop_ehds2_cql
Add EHDS2 CQL to develop branch
2 parents 49be488 + a9279d1 commit 62aaa02

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‎resources/cql/EHDS2_IN_INITIAL_POPULATION

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define InInitialPopulation:

‎resources/cql/EHDS2_OBSERVATION

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define ObservationList:
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if InInitialPopulation then [Observation] else {} as List<Observation>
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// Return the value in the given system for the given Observation
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define function ObservationValueCode(observation FHIR.Observation, system_var String):
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(observation.value as CodeableConcept).coding.where(system = system_var).code.first()
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// Check to see if there are any Observation resources with the
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// given system/value pair.
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define function ExistsObservationValueCode(system_var String, code_var String):
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exists from [Observation] O
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where ObservationValueCode(O, system_var) = code_var
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// Return the value associated with the extension with the given URL for the given Observation
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define function BaseObservationExtensionValue(observation FHIR.Observation, url_var String):
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observation.extension.where(url = url_var).value
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// Return the value of the Observation extension with the given URL
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define function ObservationExtensionValue(observation FHIR.Observation, url_var String):
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SensibleString(BaseObservationExtensionValue(observation, url_var))
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define function ExistsObservationExtensionValue(url_var String, value_var String):
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exists from [Observation] O
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where ObservationExtensionValue(O, url_var) = value_var
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// Return the pathogen type for the given Observation
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define function PathogenCode(observation FHIR.Observation):
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ObservationValueCode(observation, 'https://ecdc.amr/pathogen-codes')
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// Check to see if there are any Observation resources with the
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// given pathogen type.
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define function ExistsPathogenCode(code_var String):
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ExistsObservationValueCode('https://ecdc.amr/pathogen-codes', code_var)
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// Return the antibiotic type for the given Observation
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define function AntibioticCode(observation FHIR.Observation):
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ObservationValueCode(observation, 'https://ecdc.amr/antibiotic-codes')
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// Check to see if there are any Observation resources with the
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// given antibiotic type.
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define function ExistsAntibioticCode(code_var String):
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ExistsObservationValueCode('https://ecdc.amr/antibiotic-codes', code_var)
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// Return the resistance type for the given Observation
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define function SirCode(observation FHIR.Observation):
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ObservationValueCode(observation, 'https://ecdc.amr/sir-codes')
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// Check to see if there are any Observation resources with the
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// given resistance type.
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define function ExistsSirCode(code_var String):
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ExistsObservationValueCode('https://ecdc.amr/sir-codes', code_var)
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// Return the data source for the given Observation
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define function DataSource(observation FHIR.Observation):
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ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationDataSource')
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// Check to see if there are any Observation resources with the
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// given data source.
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define function ExistsDataSource(value_var String):
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ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationDataSource', value_var)
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// Return the isolate ID for the given Observation
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define function IsolateId(observation FHIR.Observation):
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ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationIsolateId')
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// Check to see if there are any Observation resources with the
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// given isolate ID.
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define function ExistsIsolateId(value_var String):
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ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationIsolateId', value_var)
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// Return the patient type for the given Observation
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define function PatientType(observation FHIR.Observation):
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ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationPatientType')
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// Check to see if there are any Observation resources with the
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// given patient type.
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define function ExistsPatientType(value_var String):
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ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationPatientType', value_var)
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// Return the reference guidelines SIR for the given Observation
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define function ReferenceGuidelinesSir(observation FHIR.Observation):
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ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationReferenceGuidelinesSIR')
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// Check to see if there are any Observation resources with the
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// given reference guidelines SIR.
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define function ExistsReferenceGuidelinesSir(value_var String):
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ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationReferenceGuidelinesSIR', value_var)
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// Return the reporting country for the given Observation
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define function ReportingCountry(observation FHIR.Observation):
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ObservationExtensionValue(observation, 'https://ecdc.amr/fhir/StructureDefinition/ObservationReportingCountry')
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// Check to see if there are any Observation resources with the
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// given reporting country.
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define function ExistsReportingCountry(value_var String):
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ExistsObservationExtensionValue('https://ecdc.amr/fhir/StructureDefinition/ObservationReportingCountry', value_var)
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// Return the year from the date used for statistics
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define function YearDateUsedForStatistics(observation FHIR.Observation):
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year from observation.issued
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// Return the month from the date used for statistics
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define function MonthDateUsedForStatistics(observation FHIR.Observation):
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month from observation.issued
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// Return the year-month from the date used for statistics
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define function YearMonthDateUsedForStatistics(observation FHIR.Observation):
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ToString(YearDateUsedForStatistics(observation)) + '-' + ToString(MonthDateUsedForStatistics(observation))
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// Return the the date valid from
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define function DateValidFrom(observation FHIR.Observation):
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ToDate(observation.effective as dateTime)
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// Return the year from the date valid from
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define function YearDateValidFrom(observation FHIR.Observation):
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year from DateValidFrom(observation)
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// Return the month from the date valid from
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define function MonthDateValidFrom(observation FHIR.Observation):
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month from DateValidFrom(observation)
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// Return the year-month from the date valid from
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define function YearMonthDateValidFrom(observation FHIR.Observation):
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ToString(YearDateValidFrom(observation)) + '-' + ToString(MonthDateValidFrom(observation))
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‎resources/cql/EHDS2_PATIENT

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// Return the value of the Patient extension with the given URL.
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// Return "Unknown" if not available or empty.
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define function PatientExtensionValue(url_var String):
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SensibleString(Patient.extension.where(url = url_var).value)
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// Return gender of patient
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define Gender:
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SensibleString(Patient.gender)
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// Return age of patient, as an integer
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define AgeInYears:
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ToInteger(PatientExtensionValue('https://ecdc.amr/fhir/StructureDefinition/PatientAge'))
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// Round patient age to the nearest multiple of 10 (i/p for a histogram).
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// Return result as a string
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define AgeClass:
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ToString((AgeInYears div 10) * 10)
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// Return ID of hospital associated with patient
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define HospitalId:
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PatientExtensionValue('https://ecdc.amr/fhir/StructureDefinition/PatientHospitalId')
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// Return hospital unit type associated with patient
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define HospitalUnitType:
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PatientExtensionValue('https://ecdc.amr/fhir/StructureDefinition/PatientHospitalUnitType')
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// Return laboratory code associated with patient
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define LaboratoryCode:
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PatientExtensionValue('https://ecdc.amr/fhir/StructureDefinition/PatientLaboratoryCode')
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‎resources/cql/EHDS2_SPECIMEN

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define SpecimenList:
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if InInitialPopulation then [Specimen] else {} as List<Specimen>
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// Return the isolate ID for the given Specimen
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define function SpecimenIsolateId(specimen FHIR.Specimen):
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SensibleString(specimen.id)
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// Check to see if there are any Specimen resources with the
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// given isolate ID.
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define function ExistsSpecimenIsolateId(id_var String):
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exists from [Specimen] S
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where SpecimenIsolateId(S) = id_var
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‎resources/cql/EHDS2_UTIL

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// Return "val" if the supplied string value is sensible.
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// Return "Unknown" if null or empty.
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define function SensibleString(val String):
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if (val is null or val = '' or val = '-')
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then 'Unkown'
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else val
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