map "http://example.org/StructureMap/MeaslesLabResultsMap" = "MeaslesLabResultsMap"

// Measles Lab Results QuestionnaireResponse to FHIR resources
// Maps to: Observation (Measles IgM), Observation (Rubella IgM), DiagnosticReport

uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
uses "http://hl7.org/fhir/StructureDefinition/Bundle" alias Bundle as target
uses "http://hl7.org/fhir/StructureDefinition/Observation" alias Observation as target
uses "http://hl7.org/fhir/StructureDefinition/DiagnosticReport" alias DiagnosticReport as target

group MeaslesLabResultsMap(source src : QuestionnaireResponse, target bundle : Bundle) {
  src -> bundle.id = uuid() "bundleId";
  src -> bundle.type = 'transaction' "bundleType";
  // Measles IgM Observation
  src -> bundle.entry as e then {
    src -> e.resource = create('Observation') as measlesObs then MapMeaslesIgM(src, measlesObs) "execMeaslesIgM";
    src ->  e.request as req,  req.method = 'POST',  req.url = 'Observation' "measlesObsReq";
  } "measlesIgMEntry";
  // Rubella IgM Observation
  src -> bundle.entry as e then {
    src -> e.resource = create('Observation') as rubellaObs then MapRubellaIgM(src, rubellaObs) "execRubellaIgM";
    src ->  e.request as req,  req.method = 'POST',  req.url = 'Observation' "rubellaObsReq";
  } "rubellaIgMEntry";
  // DiagnosticReport
  src -> bundle.entry as e then {
    src -> e.resource = create('DiagnosticReport') as report then MapLabDiagnosticReport(src, report) "execReport";
    src ->  e.request as req,  req.method = 'POST',  req.url = 'DiagnosticReport' "reportReq";
  } "diagnosticReportEntry";
}

group MapMeaslesIgM(source src : QuestionnaireResponse, target obs : Observation) {
  src -> obs.id = uuid() "obsId";
  src -> obs.status = 'final' "status";
  // LOINC code for Measles virus IgM Ab in Serum
  src -> obs.code as code then {
    src -> code.coding as coding then {
      src -> coding.system = 'http://loinc.org' "loincSys";
      src -> coding.code = '20479-4' "measlesIgMCode";
      src -> coding.display = 'Measles virus IgM Ab [Presence] in Serum' "measlesIgMDisplay";
    } "measlesIgMCoding";
    src -> code.text = 'Measles IgM' "obsText";
  } "codeBlock";
  src.subject as subj ->  obs.subject as ref,  ref.reference = ('Patient/' + subj.reference);
  // Lab ID as identifier
  src.item as item where linkId = '8732404074721' then {
    item.answer first as ans -> obs.identifier as id then {
      ans -> id.system = 'http://example.org/identifier/lab-id' "labIdSys";
      ans -> id.value = ans.valueString "labIdValue";
    } "labId";
  } "labIdItem";
  // Specimen sent date → effective period start
  src.item as item where linkId = '718251724172' then {
    item.answer first as ans -> obs.effective = ans.valueDate "effectiveDate";
  } "specimenSentDate";
  // Date specimen received → issued
  src.item as item where linkId = 'date-specimen-received' then {
    item.answer first as ans -> obs.issued = ans.valueDate "issued";
  } "receivedDate";
  // Specimen condition as note
  src.item as item where linkId = 'specimen-condition' then {
    item.answer first as ans ->  obs.note as note,  note.text = ('Specimen condition: ' + ans.valueCoding.display) "conditionNote";
  } "specimenCondition";
  // Measles IgM result → value
  src.item as item where linkId = 'measles-igm' then {
    item.answer first as ans -> obs.valueCodeableConcept as coding then {
      ans -> coding.coding as cod then {
        ans -> cod.system = 'http://example.org/CodeSystem/lab-result' "resultSys";
        ans -> cod.code = (ans.valueCoding.code) "resultCode";
        ans -> cod.display = (ans.valueCoding.display) "resultDisplay";
      } "resultCoding";
    } "measlesIgMResult";
    // Interpretation
    item.answer first as ans -> obs.interpretation as interp then {
      ans.valueCoding as val where code = 'Positive' ->  interp.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation',  cod.code = 'POS',  cod.display = 'Positive' "posInterp";
      ans.valueCoding as val where code = 'Negative' ->  interp.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation',  cod.code = 'NEG',  cod.display = 'Negative' "negInterp";
      ans.valueCoding as val where code = 'Indeterminate' ->  interp.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation',  cod.code = 'IND',  cod.display = 'Indeterminate' "indInterp";
    } "interpretation";
  } "measlesIgMItem";
  // Date results sent out
  src.item as item where linkId = 'date-lab-sent-results' then {
    item.answer first as ans -> obs.extension as ext then {
      ans -> ext.url = 'http://example.org/StructureDefinition/resultsSentDate' "extUrl";
      ans -> ext.valueDate = ans.valueDate "extValue";
    } "resultsSentExt";
  } "resultsSentDate";
  // Regional lab referral date
  src.item as item where linkId = '655865451155' then {
    item.answer first as ans -> obs.extension as ext then {
      ans -> ext.url = 'http://example.org/StructureDefinition/regionalLabDate' "extUrl";
      ans -> ext.valueDate = ans.valueDate "extValue";
    } "regionalLabExt";
  } "regionalLabDate";
  // Final classification as note
  src.item as item where linkId = 'final-classification' then {
    item.answer first as ans ->  obs.note as note,  note.text = ('Final classification: ' + ans.valueCoding.display) "classificationNote";
  } "finalClassification";
}

group MapRubellaIgM(source src : QuestionnaireResponse, target obs : Observation) {
  src -> obs.id = uuid() "obsId";
  src -> obs.status = 'final' "status";
  // LOINC code for Rubella virus IgM Ab in Serum
  src -> obs.code as code then {
    src -> code.coding as coding then {
      src -> coding.system = 'http://loinc.org' "loincSys";
      src -> coding.code = '22501-3' "rubellaIgMCode";
      src -> coding.display = 'Rubella virus IgM Ab [Presence] in Serum' "rubellaIgMDisplay";
    } "rubellaIgMCoding";
    src -> code.text = 'Rubella IgM' "obsText";
  } "codeBlock";
  src.subject as subj ->  obs.subject as ref,  ref.reference = ('Patient/' + subj.reference);
  // Lab ID as identifier
  src.item as item where linkId = '8732404074721' then {
    item.answer first as ans -> obs.identifier as id then {
      ans -> id.system = 'http://example.org/identifier/lab-id' "labIdSys";
      ans -> id.value = ans.valueString "labIdValue";
    } "labId";
  } "labIdItem";
  // Specimen received date → effective
  src.item as item where linkId = 'date-specimen-received' then {
    item.answer first as ans -> obs.effective = ans.valueDate "effectiveDate";
  } "receivedDate";
  // Rubella IgM result → value
  src.item as item where linkId = 'rubella-igm' then {
    item.answer first as ans -> obs.valueCodeableConcept as coding then {
      ans -> coding.coding as cod then {
        ans -> cod.system = 'http://example.org/CodeSystem/lab-result' "resultSys";
        ans -> cod.code = (ans.valueCoding.code) "resultCode";
        ans -> cod.display = (ans.valueCoding.display) "resultDisplay";
      } "resultCoding";
    } "rubellaIgMResult";
    // Interpretation
    item.answer first as ans -> obs.interpretation as interp then {
      ans.valueCoding as val where code = 'Positive' ->  interp.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation',  cod.code = 'POS',  cod.display = 'Positive' "posInterp";
      ans.valueCoding as val where code = 'Negative' ->  interp.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation',  cod.code = 'NEG',  cod.display = 'Negative' "negInterp";
      ans.valueCoding as val where code = 'Indeterminate' ->  interp.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/v3-ObservationInterpretation',  cod.code = 'IND',  cod.display = 'Indeterminate' "indInterp";
    } "interpretation";
  } "rubellaIgMItem";
  // Status: not done if absent
  src.item as item where linkId = 'rubella-igm' then {
    item where answer.empty() ->  obs.status = 'cancelled',  obs.dataAbsentReason as reason,  reason.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/data-absent-reason',  cod.code = 'not-performed' "notDone";
  } "rubellaNotDone";
}

group MapLabDiagnosticReport(source src : QuestionnaireResponse, target report : DiagnosticReport) {
  src -> report.id = uuid() "reportId";
  src -> report.status = 'final' "status";
  // Category: Laboratory
  src -> report.category as cat then {
    src -> cat.coding as coding then {
      src -> coding.system = 'http://terminology.hl7.org/CodeSystem/v2-0074' "catSys";
      src -> coding.code = 'LAB' "catCode";
      src -> coding.display = 'Laboratory' "catDisplay";
    } "catCoding";
  } "category";
  // Measles serology panel LOINC
  src -> report.code as code then {
    src -> code.coding as coding then {
      src -> coding.system = 'http://loinc.org' "loincSys";
      src -> coding.code = '41852-5' "panelCode";
      src -> coding.display = 'Microorganism or agent identified in Specimen' "panelDisplay";
    } "panelCoding";
    src -> code.text = 'Measles/Rubella Serology Panel' "codeText";
  } "codeBlock";
  src.subject as subj ->  report.subject as ref,  ref.reference = ('Patient/' + subj.reference);
  // Lab ID
  src.item as item where linkId = '8732404074721' then {
    item.answer first as ans -> report.identifier as id then {
      ans -> id.system = 'http://example.org/identifier/lab-id' "labIdSys";
      ans -> id.value = ans.valueString "labIdValue";
    } "labId";
  } "labIdItem";
  // Effective date from specimen received
  src.item as item where linkId = 'date-specimen-received' then {
    item.answer first as ans -> report.effective = ans.valueDate "effectiveDate";
  } "effectiveDate";
  // Issued date from results sent
  src.item as item where linkId = 'date-lab-sent-results' then {
    item.answer first as ans -> report.issued = ans.valueDate "issued";
  } "issuedDate";
  // Final classification as conclusion
  src.item as item where linkId = 'final-classification' then {
    item.answer first as ans -> report.conclusion = (ans.valueCoding.display) "conclusion";
    item.answer first as ans -> report.conclusionCode as code then {
      ans ->  code.coding as cod,  cod.system = 'http://example.org/CodeSystem/measles-classification',  cod.code = (ans.valueCoding.code),  cod.display = (ans.valueCoding.display) "conclusionCode";
    } "conclusionCode";
  } "classification";
}