map "http://worldhealthorganization.github.io/smart-ot/StructureMap/AFROMRCIFQuestionnaireToLogicalModel" = "AFROMRCIFQuestionnaireToLogicalModel"

uses "http://hl7.org/fhir/StructureDefinition/QuestionnaireResponse" alias QuestionnaireResponse as source
uses "http://worldhealthorganization.github.io/smart-ot/StructureDefinition/AFROMRCIF" alias MeaslesLogicalModel as target

group MRCIFQuestionnaireToLogicalModel(source qr : QuestionnaireResponse, target measlesLm : AFROMRCIF) {
  qr.item as item where linkId.value in ('investigationForm') -> measlesLm as measlesLm then mapInvestigationForm(item, measlesLm) "set Investigation form";
}

group mapInvestigationForm(source investigationForm, target measlesLm : AFROMRCIF) {
  investigationForm.item as qrReportingSource where linkId.value in ('reportingSource') -> measlesLm.ReportingSource as lmReportingSource then mapReportingSource(qrReportingSource, lmReportingSource) "set Reporting Source";
  investigationForm.item as qrDemographics where linkId.value in ('demographics') -> measlesLm.Demographics as lmDemographics then mapDemographics(qrDemographics, lmDemographics) "set Demographics";
  investigationForm.item as qrVaccinationStatus where linkId.value in ('vaccinationStatus') -> measlesLm.VaccinationStatus as lmVaccinationStatus then mapVaccinationStatus(qrVaccinationStatus, lmVaccinationStatus) "set Vaccination Status";
  investigationForm.item as qrClinical where linkId.value in ('clinical') -> measlesLm.Clinical as lmClinical then mapClinical(qrClinical, lmClinical) "set Clinical";
  investigationForm.item as qrLaboratoryResults where linkId.value in ('laboratoryResults') -> measlesLm.LaboratoryResults as lmLaboratoryResults then mapLaboratoryResults(qrLaboratoryResults, lmLaboratoryResults) "set Laboratory Results";
  investigationForm.item as qrCaseInvestigation where linkId.value in ('qrCaseInvestigation') -> measlesLm.qrCaseInvestigation as lmCaseInvestigation then mapCaseInvestigation(qrCaseInvestigation, lmCaseInvestigation) "set Contact Tracing";
  investigationForm.item as qrClassification where linkId.value in ('classification') -> measlesLm.Classification as lmClassification then mapClassification(qrClassification, lmClassification) "set Classification";
}

group mapReportingSource(source qrReportingSource, target lmReportingSource : SOTMeaslesReportingSource) {
  qrReportingSource.item as item then {
    item.answer first as caseId where item.linkId = 'caseID' then {
      caseId.value as value -> lmReportingSource.UniqueId = value "set01";
    } "set";
    qrReportingSource.item as qrReportingInstitution where linkId.value in ('reportingInstitution') -> lmReportingSource as lmReportingSource then mapReportingInstitution(qrReportingInstitution, lmReportingSource) "set reporting institution";
    item.answer first as dateReportedNational where item.linkId = 'DateReportedNational' then {
      dateReportedNational.value as value -> lmReportingSource.DateReportedNational = value "set date reported national";
    } "set date reported national";
  } "set reporting source";
}

group mapReportingInstitution(source qrReportingInstitution, target lmReportingSource : SOTMeaslesReportingSource) {
  qrReportingInstitution.item as item then {
    item.answer first as reportingFacility where item.linkId = 'reportingFacility' then {
      reportingFacility.value as healthFacilityName -> lmReportingSource.HealthServiceName = healthFacilityName "set health facility name";
    } "set health facility name";
    qrReportingInstitution -> create('Address') as lmAddress then {
      item.answer first as country where item.linkId = 'country' then {
        country.value as countryValue -> lmAddress.country = countryValue "set country";
      } "set country";
      item.answer first as municipality where item.linkId = 'municipality' then {
        municipality.value as cityValue -> lmAddress.city = cityValue "set city";
      } "set city  ";
      item.answer first as state where item.linkId = 'state' then {
        state.value as stateValue -> lmAddress.state = stateValue "set state";
      } "set state";
      item.answer first as locality where item.linkId = 'locality' then {
        locality.value as localityValue -> lmAddress.line = localityValue "set locality";
      } "set locality";
      qrReportingInstitution -> lmReportingSource.PlaceOfReporting = lmAddress "assign address";
    } "set address";
  } "set reporting institution";
}

group mapDemographics(source qrDemographics, target lmDemographics : SOTMeaslesDemographic) {
  qrDemographics.item as item then {
    item.answer first as name where item.linkId = 'name' then {
      name.value as nameValue ->  create('HumanName') as lmName,  lmName.family = nameValue,  lmDemographics.Name = lmName "set name";
    } "set name";
    // adapt address to be separate mappings
    item.answer first as address where item.linkId = 'address' then {
      address.value as value ->  create('Address') as lmAddress,  lmAddress.text = value,  lmDemographics.PlaceOfResidence = lmAddress "set address";
    } "set address";
    item.answer first as location where item.linkId = 'localityType' then {
      location.value as value -> lmDemographics.LocalityType = value "set Locality Type";
    } "set Locality Type";
    item.answer first as sex where item.linkId = 'sex' then {
      sex.value as value -> lmDemographics.Sex = value "set sex";
    } "set sex";
    item.answer first as DoB where item.linkId = 'DoB' then {
      DoB.value as value -> lmDemographics.DateOfBirth = value "set DoB";
    } "set DoB";
    item.answer first as ageOnset where item.linkId = 'ageOnset' then {
      ageOnset.value as value ->  create('Quantity') as lmAgeOnset,  lmAgeOnset.value = value,  lmDemographics.Age = lmAgeOnset "set ageOnset";
    } "set ageOnset";
  } "set demographics";
}

group mapVaccinationStatus(source qrVaccinationStatus, target lmVaccinationStatus : SOTMeaslesVaccinationStatus) {
  qrVaccinationStatus.item as item then {
    item.answer first as lastDoseDate where item.linkId = 'lastDoseDate' then {
      lastDoseDate.value as value -> lmVaccinationStatus.LastDoseDate = value "set Last Dose Date";
    } "set last dose date";
    item.answer first as noOfDoses where item.linkId = 'noOfDoses' then {
      noOfDoses.value as value -> lmVaccinationStatus.NumberOfDoses = value "set number of doses";
    } "set";
    item.answer first as vaccineType where item.linkId = 'vaccineType' then {
      vaccineType.value as value -> lmVaccinationStatus.VaccineType = value "set vaccine type";
    } "set";
  } "set";
}

group mapClinical(source qrClinical, target lmClinical : SOTMeaslesClinical) {
  qrClinical.item as item then {
    item.answer first as fever where item.linkId = 'fever' then {
      fever.value as value -> lmClinical.Fever = value "set Fever";
    } "set";
    item.answer first as rash where item.linkId = 'rash' then {
      rash.value as value -> lmClinical.Rash = value "set Rash";
    } "set";
    item.answer first as cough where item.linkId = 'cough' then {
      cough.value as value -> lmClinical.Cough = value "set Cough";
    } "set";
    item.answer first as conjunctivitis where item.linkId = 'conjunctivitis' then {
      conjunctivitis.value as value -> lmClinical.Conjunctivitis = value "set Conjunctivitis";
    } "set";
    item.answer first as coryza where item.linkId = 'coryza' then {
      coryza.value as value -> lmClinical.Coryza = value "set Coryza";
    } "set";
    item.answer first as lymphadenopathy where item.linkId = 'lymphadenopathy' then {
      lymphadenopathy.value as value -> lmClinical.Lymphadenopathy = value "set Lymphadenopathy";
    } "set";
    item.answer first as jointPain where item.linkId = 'jointPain' then {
      jointPain.value as value -> lmClinical.JointPain = value "set Arthralgia";
    } "set";
    item.answer first as admitted where item.linkId = 'admitted' then {
      admitted.value as value -> lmClinical.HistoryOfHospitalization = value "set Hospitalized";
    } "set";
    item.answer first as admittedHCFName where item.linkId = 'admittedHCFName' then {
      admittedHCFName.value as value -> lmClinical.HospitalName = value "set Hospital Name";
    } "set";
    item.answer first as outcome where item.linkId = 'outcome' then {
      outcome.value as value -> lmClinical.Outcome = value "set Outcome";
    } "set";
    item.answer first as answer where item.linkId = 'travelledOutside' then {
      answer.value as value -> lmClinical.travelledOutside = value "set specify virus";
    } "set";
    item.answer first as answer where item.linkId = 'infectionSetting' then {
      answer.value as value -> lmClinical.specifyInfectionSetting = value "set specify virus";
    } "set";
  } "set clinical";
}

group mapLaboratoryResults(source qrLaboratoryResults, target lmLaboratoryResults : LaboratoryResultsLogicalModel) {
  qrLaboratoryResults.item as item then {
    item.answer first as answer where item.linkId = 'sampleType' then {
      answer.value as value -> lmLaboratoryResults.SampleType = value "set SampleType";
    } "set";
    item.answer first as answer where item.linkId = 'collectionDate' then {
      answer.value as value -> lmLaboratoryResults.SpecimenCollectionDate = value "set SpecimenCollectionDate";
    } "set";
    item.answer first as answer where item.linkId = 'labName' then {
      answer.value as value -> lmLaboratoryResults.LabName = value "set Shipment Date";
    } "set";
    item.answer first as answer where item.linkId = 'specimenSentDate' then {
      answer.value as value -> lmLaboratoryResults.SpecimenSentDate = value "set SpecimenSentDate";
    } "set";
    item.answer first as answer where item.linkId = 'specimenReceivedDate' then {
      answer.value as value -> lmLaboratoryResults.SpecimenRecdDate = value "set SpecimenRecdDate";
    } "set";
    item.answer first as answer where item.linkId = 'testPerformed' then {
      answer.value as value -> lmLaboratoryResults.TypeOfTest = value "set TypeOfTest";
    } "set";
    item.answer first as answer where item.linkId = 'result' then {
      answer.value as value -> lmLaboratoryResults.Results = value "set Results";
    } "set";
    item.answer first as answer where item.linkId = 'specifyVirus' then {
      answer.value as value -> lmLaboratoryResults.ViralGenotype = value "set specify virus";
    } "set";
  } "set labs";
}

group mapCaseInvestigation(source qrCaseInvestigation, target lmCaseInvestigation : SOTMeaslesCaseInvestigation) {
  qrCaseInvestigation.item as item then {
    item.answer first as dateOfConsultation where item.linkId = 'DateOfConsultation' then {
      dateOfConsultation.value as value -> lmReportingSource.DateOfConsultation = value "set date of consultation";
    } "set date of consultation";
    item.answer first as dateReportedLocal where item.linkId = 'dateReported' then {
      dateReportedLocal.value as value -> lmReportingSource.DateReportedLocal = value "set date reported local";
    } "set date reported local";
    item.answer first as rashOnsetDate where item.linkId = 'rashOnsetDate' then {
      rashOnsetDate.value as value -> lmClinical.RashOnsetDate = value "set Rash Onset Date";
    } "set";
  } "set contact tracing";
}

group mapClassification(source qrClassification, target lmClassification : ClassificationLogicalModel) {
  qrClassification.item as item then {
    item.answer first as answer where item.linkId = 'finalClassification' then {
      answer.value as value -> lmClassification.FinalClassification = value "set finalClassification";
    } "set";
    item.answer first as reportedBy where item.linkId = 'reportedBy' then {
      reportedBy.value as value -> lmClassification.ReportedBy = value "set case ID";
    } "set case ID";
  } "set classification";
}