library CRCSMCommonFunctions version '1.0.0'\r\n\r\nusing FHIR version '4.0.1'\r\n\r\ninclude CDSConnectCommonsforFHIRv401 version '1.0.0' called C3F\r\ninclude FHIRHelpers version '4.0.1' called FHIRHelpers\r\ninclude CSMCommonFunctions version '1.0.0' called CSMCommonFunctions\r\n\r\ncodesystem "FlagCode": 'http://cancerscreeningcds.github.io/crcsm-cds/CodeSystem/recommendation-flag-code-system'\r\n\r\ncode "OVERDUE" : 'overdue' from "FlagCode" display 'Overdue'\r\ncode "DUE" : 'due' from "FlagCode" display 'Due'\r\ncode "NOT DUE" : 'not-due' from "FlagCode" display 'Not due'\r\ncodesystem "cpg-activity-type-cs": 'http://hl7.org/fhir/uv/cpg/CodeSystem/cpg-activity-type-cs'\r\ncode "Record an inference": 'record-inference' from "cpg-activity-type-cs" display 'Record an inference'\r\n\r\n// TODO: move parameters to DataElements.cql\r\n// TODO: check overdue default against TEP input\r\nparameter "OverdueDefault" System.Quantity default 6 months\r\nparameter "DueDefault" System.Quantity default 3 months\r\nparameter "OverdueFollowup" System.Quantity default 90 days\r\n\r\ncontext Patient\r\n\r\n//------------------------------------------------------------------------------\r\n// Recommendation model\r\n//------------------------------------------------------------------------------\r\n\r\ndefine SourceDocumentationACS:\r\n {\r\n label: 'ACS'\r\n }\r\n\r\ndefine SourceDocumentationUSPSTF:\r\n {\r\n label: 'USPSTF'\r\n }\r\n\r\ndefine SourceDocumentationUSMSTF:\r\n {\r\n label: 'USMSTF'\r\n }\r\n\r\ndefine SourceDocumentationOther:\r\n {\r\n label: 'Other'\r\n } \r\n\r\n// TODO: do we really need event as a list in the output?\r\n// TODO: add handling for when repeat is null\r\ndefine function SetRecommendation( \r\n code System.Code,\r\n reason System.Code,\r\n documentation Tuple{label System.String},\r\n timingAge Tuple{value Decimal, code String},\r\n event System.DateTime,\r\n repeat Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}) \r\n returns Tuple {code System.Code,reason System.Code,documentation Tuple{label System.String},timingAge Tuple{value Decimal, code String},\r\n timingTiming Tuple{event List<System.String>,repeat Tuple{boundsPeriod Tuple{start System.String},frequency System.Integer,period System.Decimal,periodUnit System.String}},\r\n flag System.Code\r\n }: \r\n code C\r\n let startDate: if timingAge is not null then CalculateStartDateByAge(timingAge) else null,\r\n nextdue: if event is not null then event \r\n else CalculateNextDueByCodeAndInterval(ToConcept(C), startDate, repeat),\r\n timingTiming: {\r\n event: {ToString(nextdue)},\r\n repeat: {\r\n boundsPeriod: {\r\n start: if timingAge is not null then ToString(CalculateStartDateByAge(timingAge)) else null\r\n },\r\n frequency: repeat.frequency,\r\n period: repeat.period,\r\n periodUnit: repeat.periodUnit\r\n }\r\n },\r\n flag: EvaluateFlagDefault(nextdue) \r\n return \r\n Tuple {\r\n code: C,\r\n reason: reason,\r\n documentation: documentation,\r\n timingAge: timingAge,\r\n timingTiming: timingTiming,\r\n flag: flag\r\n }\r\n\r\ndefine function CalculateStartDateByAge(timingAge Tuple{value Decimal, code String}): \r\n Patient.birthDate + System.Quantity{value: (timingAge.value), unit: FHIRHelpers.ToCalendarUnit(timingAge.code)}\r\n\r\ndefine function SetFollowupRecommendation( \r\n code System.Code,\r\n reason System.Code,\r\n documentation Tuple{label System.String},\r\n event System.DateTime)\r\n returns Tuple {code System.Code,reason System.Code,documentation Tuple{label System.String},\r\n timingTiming Tuple{event List<System.String>},\r\n flag System.Code\r\n }: \r\n code C\r\n let nextdue: event,\r\n timingTiming: {\r\n event: {ToString(nextdue)}\r\n },\r\n flag: EvaluateFollowupFlag(nextdue) \r\n return \r\n Tuple {\r\n code: C,\r\n reason: reason,\r\n documentation: documentation,\r\n timingTiming: timingTiming,\r\n flag: flag\r\n } \r\n\r\n//------------------------------------------------------------------------------\r\n// Calculated next due date\r\n//------------------------------------------------------------------------------\r\n// +startDate, +repeat, +lastreport = use startDate if > lastreport else lastreport + repeat\r\n// +startDate, +repeat, -lastreport = use startDate\r\n// +startDate, -repeat, +lastreport = use startDate if > lastreport else no prediction (non-repeating and ?completed)\r\n// +startDate, -repeat, -lastreport = use startDate\r\n// -startDate, +repeat, +lastreport = use lastreport + repeat\r\n// -startDate, +repeat, -lastreport = use today\r\n// -startDate, -repeat, +lastreport = no prediction (non-repeating and ?completed)\r\n// -startDate, -repeat, -lastreport = use today\r\ndefine function CalculateNextDueByCodeAndInterval(code Concept, \r\n startDate DateTime,\r\n repeat Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}):\r\n code C\r\n //TODO: add last report lookup from observation for cases where report itself is not transmitted, only documented in a flowsheet\r\n let lastReport: MostRecentDiagnosticReportByCode(C)\r\n return\r\n case\r\n // +startDate, +repeat, +lastReport\r\n when startDate is not null and RepeatIsValid(repeat) and lastReport is not null then\r\n if startDate > FHIRHelpers.ToDateTime(lastReport.effective) as DateTime then startDate \r\n else date from AddIntervalToDateTime(FHIRHelpers.ToDateTime(lastReport.effective) as DateTime, repeat)\r\n // +startDate, +repeat, -lastReport\r\n when startDate is not null and RepeatIsValid(repeat) and lastReport is null then\r\n startDate\r\n // +startDate, -repeat, +lastReport\r\n when startDate is not null and repeat is null and lastReport is not null then\r\n if startDate > FHIRHelpers.ToDateTime(lastReport.effective) as DateTime then startDate else null\r\n // +startDate, -repeat, -lastReport\r\n when startDate is not null and repeat is null and lastReport is null then\r\n startDate\r\n // -startDate, +repeat, +lastReport\r\n when startDate is null and RepeatIsValid(repeat) and lastReport is not null then\r\n date from AddIntervalToDateTime(FHIRHelpers.ToDateTime(lastReport.effective) as DateTime, repeat)\r\n // -startDate, +repeat, -lastReport\r\n when startDate is null and RepeatIsValid(repeat) and lastReport is null then\r\n Today()\r\n // -startDate, -repeat, +lastReport\r\n when startDate is null and RepeatIsValid(repeat) is false and lastReport is not null then\r\n null\r\n // -startDate, -repeat, -lastReport\r\n when startDate is null and RepeatIsValid(repeat) is false and lastReport is null then\r\n Today()\r\n else null \r\n end\r\n\r\ndefine function RepeatIsValid(repeat Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}):\r\n repeat.frequency is not null and repeat.period is not null and repeat.periodUnit is not null\r\n\r\ndefine function AddIntervalToDateTime(startDateTime System.DateTime, \r\n repeat Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}):\r\n startDateTime + System.Quantity {\r\n value: (repeat.frequency * repeat.period) * 1.0,\r\n unit: FHIRHelpers.ToCalendarUnit(repeat.periodUnit)\r\n }\r\n\r\n//------------------------------------------------------------------------------\r\n// scheduled frequency\r\n//------------------------------------------------------------------------------\r\n\r\ndefine function EvaluateInterval(repeat Choice<FHIR.Timing.Repeat, Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}>):\r\n case\r\n when IntervalIsUnknown(repeat)\r\n then 'Unknown'\r\n when IntervalIsAnnual(repeat)\r\n then 'Annual'\r\n when IntervalIs3Years(repeat)\r\n then '3 years'\r\n when IntervalIs5Years(repeat)\r\n then '5 years'\r\n when IntervalIs10Years(repeat)\r\n then '10 years'\r\n else 'Other'\r\n end\r\n\r\ndefine function IntervalIsAnnual(repeat Choice<FHIR.Timing.Repeat, Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}>):\r\n if repeat.frequency.value = 1 and repeat.period.value = 1 and repeat.periodUnit.value = 'a' \r\n then true else false\r\n\r\ndefine function IntervalIs3Years(repeat Choice<FHIR.Timing.Repeat, Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}>):\r\n if repeat.frequency.value = 1 and repeat.period.value = 3 and repeat.periodUnit.value = 'a' \r\n then true else false\r\n\r\ndefine function IntervalIs5Years(repeat Choice<FHIR.Timing.Repeat, Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}>):\r\n if repeat.frequency.value = 1 and repeat.period.value = 5 and repeat.periodUnit.value = 'a' \r\n then true else false\r\n\r\ndefine function IntervalIs10Years(repeat Choice<FHIR.Timing.Repeat, Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}>):\r\n if repeat.frequency.value = 1 and repeat.period.value = 10 and repeat.periodUnit.value = 'a' \r\n then true else false\r\n\r\n define function IntervalIsUnknown(repeat Choice<FHIR.Timing.Repeat, Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}>):\r\n if repeat is null or repeat.frequency is null\r\n then true else false \r\n\r\n//------------------------------------------------------------------------------\r\n// flag due/overdue\r\n//------------------------------------------------------------------------------\r\n\r\n//TODO: use grace periods should be function arguments\r\ndefine function EvaluateFlag(repeat Choice<FHIR.Timing.Repeat, Tuple{frequency System.Integer,period System.Decimal,periodUnit System.String}>, \r\n nextDueDate DateTime):\r\n EvaluateFlagDefault(nextDueDate)\r\n\r\ndefine function EvaluateFlagDefault(nextDueDate DateTime):\r\n if nextDueDate < Today() - (OverdueDefault) then\r\n "OVERDUE"\r\n else if nextDueDate <= Today() + (DueDefault) and nextDueDate >= Today() - (OverdueDefault) then\r\n "DUE"\r\n else\r\n "NOT DUE"\r\n \r\ndefine function EvaluateFollowupFlag(nextDueDate DateTime):\r\n if nextDueDate < Today() - (OverdueFollowup) then\r\n "OVERDUE"\r\n else if nextDueDate <= Today() + (DueDefault) and nextDueDate >= Today() - (OverdueFollowup) then\r\n "DUE"\r\n else\r\n "NOT DUE" \r\n\r\n//------------------------------------------------------------------------------\r\n// Create extension\r\n//------------------------------------------------------------------------------\r\ndefine function CreateExtension(url String, coding Code):\r\n { \r\n url: url,\r\n valueCodeableConcept: {\r\n coding: { coding }\r\n } \r\n }\r\n\r\ndefine function CreateRecommendationFlagExtension(coding Code):\r\n {{ \r\n url: 'http://cancerscreeningcds.github.io/crcsm-cds/StructureDefinition/csm-recommendation-flag',\r\n valueCodeableConcept: {\r\n coding: { coding }\r\n } \r\n }}\r\n\r\n//------------------------------------------------------------------------------\r\n// Diagnostic Report Functions\r\n//------------------------------------------------------------------------------\r\n\r\ndefine function MostRecentDiagnosticReportByCode(code Concept):\r\n CSMCommonFunctions.MostRecentDiagnosticReport(DiagnosticReportsByCode(code))\r\n\r\ndefine function MostRecentDiagnosticReportByVS(vs System.ValueSet):\r\n CSMCommonFunctions.MostRecentDiagnosticReport(DiagnosticReportsByVS(vs))\r\n\r\n//TODO: determine if we need to look for non-test result, like specialty referral\r\ndefine function DiagnosticReportsByCode(concept Concept):\r\n [DiagnosticReport] R\r\n where R.code ~ concept \r\n\r\ndefine function DiagnosticReportsByVS(vs System.ValueSet):\r\n [DiagnosticReport: vs] R\r\n\r\n// Returns list of completed diagnostic reports matching code in a given lookback period\r\ndefine function CompletedDiagnosticReportsByLookback(term Concept, lookback System.Quantity):\r\n CSMCommonFunctions.CompletedDiagnosticReport(\r\n CSMCommonFunctions.LookBack(\r\n DiagnosticReportsByCode(term),\r\n lookback\r\n )\r\n )\r\n\r\n// Returns list of completed diagnostic reports matching value set in a given lookback period\r\ndefine function CompletedDiagnosticReportsByLookback(vs System.ValueSet, lookback System.Quantity):\r\n CSMCommonFunctions.CompletedDiagnosticReport(\r\n CSMCommonFunctions.LookBack(\r\n DiagnosticReportsByVS(vs),\r\n lookback\r\n )\r\n )\r\n\r\n//define function DiagnosticReportResultsByModality(DiagnosticReportList List<FHIR.DiagnosticReport>, ObsList List<FHIR.Observation>, modality System.ValueSet, result System.ValueSet):\r\n// DiagnosticReportList D\r\n// where\r\n// D.code in modality\r\n// and AnyTrue(CollateConclusionCodes(D, ObsList) C return C in result)\r\n\r\n//------------------------------------------------------------------------------\r\n// Observation Functions\r\n//------------------------------------------------------------------------------\r\n\r\n// Returns list of verified observations matching a direct reference code in a given lookback period\r\ndefine function VerifiedObservations(term Concept, lookback System.Quantity):\r\n C3F.Verified(\r\n C3F.ObservationLookBack(\r\n [Observation] O where O.code ~ term,\r\n lookback\r\n )\r\n )\r\n\r\n// Returns list of verified observations matching a value set in a given lookback period\r\ndefine function VerifiedObservations(vs System.ValueSet, lookback System.Quantity):\r\n C3F.Verified(\r\n C3F.ObservationLookBack(\r\n [Observation: vs],\r\n lookback\r\n )\r\n )\r\n\r\n\r\n//------------------------------------------------------------------------------\r\n// Service Request Functions\r\n//------------------------------------------------------------------------------\r\n\r\n//TODO: need for direct reference code?\r\ndefine function ActiveServiceRequestOrders(vs System.ValueSet):\r\n [ServiceRequest: vs] O\r\n where O.status in {'active'}\r\n and O.intent in {'order', 'original-order', 'reflex-order', 'filler-order', 'instance-order'}\r\n\r\n//------------------------------------------------------------------------------\r\n// Diagnostic report results\r\n//------------------------------------------------------------------------------\r\n// Aggregate result codes -\r\n// DiagnosticReport.conclusionCode[]\r\n// Observatio.value where DiagnosticReport.result[].reference = Observation\r\n// Observatio.value where Observation.basedOn = DiagnosticReport.basedOn (request)\r\n\r\n// if a DiagnosticReport.code has target code, then call original CollateConclusionCodes\r\n// if a DiagnosticReport.code does not have target code, then return values from matched Observations\r\ndefine function CollateConclusionCodes(D DiagnosticReport, ObsList List<Observation>, code System.Code):\r\n if FHIRHelpers.ToConcept(D.code) ~ code then\r\n CollateConclusionCodes(D, ObsList)\r\n else\r\n ValuesFromObservation(D, ObsList) \r\n\r\ndefine function CollateConclusionCodes(D DiagnosticReport, ObsList List<Observation>):\r\n D.conclusionCode union\r\n ValuesFromObservation(D, ObsList)\r\n\r\ndefine function ValuesFromObservation(D DiagnosticReport, ObsList List<Observation>):\r\n (ObsList) O\r\n where\r\n Exists( (D.result ) R where Last(Split(R.reference,'/')) = O.id ) or\r\n Exists( (O.basedOn) oB where AnyTrue((D.basedOn) dB return dB = oB ) )\r\n return O.value as FHIR.CodeableConcept\r\n\r\ndefine function ValueQuantityFromObservation(D DiagnosticReport, ObsList List<Observation>):\r\n (ObsList) O\r\n where\r\n Exists( (D.result ) R where Last(Split(R.reference,'/')) = O.id ) or\r\n Exists( (O.basedOn) oB where AnyTrue((D.basedOn) dB return dB = oB ) )\r\n return O.value as FHIR.Quantity
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