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

// Measles Case Report QuestionnaireResponse to FHIR resources
// Maps to: Patient, Encounter, Condition (Measles), Immunization (MR/Measles), Specimen

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/Patient" alias Patient as target
uses "http://hl7.org/fhir/StructureDefinition/Encounter" alias Encounter as target
uses "http://hl7.org/fhir/StructureDefinition/Condition" alias Condition as target
uses "http://hl7.org/fhir/StructureDefinition/Immunization" alias Immunization as target
uses "http://hl7.org/fhir/StructureDefinition/Specimen" alias Specimen as target

group MeaslesCaseReportMap(source src : QuestionnaireResponse, target bundle : Bundle) {
  src -> bundle.id = uuid() "bundleId";
  src -> bundle.type = 'transaction' "bundleType";
  src -> bundle.entry as e then {
    src -> e.resource = create('Patient') as patient then MapMeaslesPatient(src, patient) "execPatient";
    src ->  e.request as req,  req.method = 'PUT',  req.url = ('Patient/' + %src.subject.reference) "patientReq";
  } "patientEntry";
  src -> bundle.entry as e then {
    src -> e.resource = create('Encounter') as encounter then MapMeaslesEncounter(src, encounter) "execEncounter";
    src ->  e.request as req,  req.method = 'POST',  req.url = 'Encounter' "encounterReq";
  } "encounterEntry";
  src -> bundle.entry as e then {
    src -> e.resource = create('Condition') as condition then MapMeaslesCondition(src, condition) "execCondition";
    src ->  e.request as req,  req.method = 'POST',  req.url = 'Condition' "conditionReq";
  } "conditionEntry";
  src -> bundle.entry as e then {
    src -> e.resource = create('Immunization') as immunization then MapMeaslesImmunization(src, immunization) "execImmunization";
    src ->  e.request as req,  req.method = 'POST',  req.url = 'Immunization' "immunizationReq";
  } "immunizationEntry";
  src -> bundle.entry as e then {
    src -> e.resource = create('Specimen') as specimen then MapMeaslesSpecimen(src, specimen) "execSpecimen";
    src ->  e.request as req,  req.method = 'POST',  req.url = 'Specimen' "specimenReq";
  } "specimenEntry";
}

group MapMeaslesPatient(source src : QuestionnaireResponse, target patient : Patient) {
  src -> patient.id = uuid() "patientId";
  src.item as demographics where linkId = '670954892057' then {
    // Given name
    demographics.item as item where linkId = '873240407472' then {
      item.answer first as ans ->  patient.name as name,  name.given = ans.valueString "givenName";
    } "firstName";
    // Middle name
    demographics.item as item where linkId = '246751846436' then {
      item.answer first as ans ->  patient.name as name,  name.given = ans.valueString "middleName";
    } "middleName";
    // Family name
    demographics.item as item where linkId = '486402457213' then {
      item.answer first as ans ->  patient.name as name,  name.family = ans.valueString "familyName";
    } "familyName";
    // Gender
    demographics.item as item where linkId = '929966324957' then {
      item.answer first as ans -> patient.gender = (ans.valueCoding.code) "gender";
    } "gender";
    // Date of birth
    demographics.item as item where linkId = '257830485990' then {
      item.answer first as ans -> patient.birthDate = ans.valueDate "birthDate";
    } "birthDate";
    // Residence (Urban/Rural) as address use
    demographics.item as item where linkId = 'residence' then {
      item.answer first as ans -> patient.address as addr then {
        ans.valueCoding as val where code = 'Urban' ->  addr.use = 'home',  addr.type = 'physical' "urbanAddr";
        ans.valueCoding as val where code = 'Rural' ->  addr.use = 'home',  addr.type = 'physical',  addr.district = 'Rural' "ruralAddr";
      } "residenceType";
    } "residence";
    // Parent / Guardian
    demographics.item as item where linkId = 'parent' then {
      item.answer first as ans -> patient.contact as contact then {
        ans ->  contact.name as cname,  cname.text = ans.valueString "contactName";
      } "parentContact";
    } "parent";
    // Phone
    demographics.item as item where linkId = '754217593839' then {
      item.answer first as ans ->  patient.telecom as tel,  tel.system = 'phone',  tel.value = ans.valueString "phone";
    } "phone";
    // County/Sub-County/Ward address
    demographics.item as item where linkId = '242811643559' then {
      item.answer first as ans ->  patient.address as addr,  addr.line = ans.valueString "village";
    } "village";
    demographics.item as item where linkId = '946232932304' then {
      item.answer first as ans ->  patient.address as addr,  addr.district = ans.valueString "landmark";
    } "landmark";
    demographics.item as item where linkId = '424111786438' then {
      item.answer first as ans ->  patient.address as addr,  addr.line = ans.valueString "street";
    } "street";
  } "demographics";
}

group MapMeaslesEncounter(source src : QuestionnaireResponse, target encounter : Encounter) {
  src -> encounter.id = uuid() "encounterId";
  src -> encounter.status = 'finished' "status";
  src -> encounter.class as cls then {
    src -> cls.system = 'http://terminology.hl7.org/CodeSystem/v3-ActCode' "clsSys";
    src -> cls.code = 'AMB' "clsCode";
  } "class";
  src.subject as subj ->  encounter.subject as ref,  ref.reference = ('Patient/' + subj.reference);
  // EPID No from reporting site
  src.item as reportSite where linkId = '151479012557' then {
    reportSite.item as item where linkId = '992818778559' then {
      item.answer first as ans -> encounter.identifier as id then {
        ans -> id.system = 'http://example.org/identifier/epid' "epidSys";
        ans -> id.value = ans.valueString "epidValue";
      } "epidId";
    } "epidNo";
  } "reportSite";
  // Case information
  src.item as caseInfo where linkId = '216343227137' then {
    // Date first seen at facility → period start
    caseInfo.item as item where linkId = '554231819382' then {
      item.answer first as ans ->  encounter.period as period,  period.start = ans.valueDate "periodStart";
    } "firstSeen";
    // IP/OP number
    caseInfo.item as item where linkId = '755731625544' then {
      item.answer first as ans -> encounter.identifier as id then {
        ans -> id.system = 'http://example.org/identifier/ip-op' "ipopSys";
        ans -> id.value = ans.valueString "ipopValue";
      } "ipopId";
    } "ipopNo";
    // Hospitalization
    caseInfo.item as item where linkId = '483042281962' then {
      item.answer first as ans where valueCoding.code = 'yes' -> encounter.hospitalization as hosp then {
        ans ->  hosp.admitSource as src,  src.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/admit-source',  cod.code = 'hosp-trans' "admitSource";
      } "hospitalization";
    } "hospitalized";
    // Date of admission
    caseInfo.item as item where linkId = '340908984116' then {
      item.answer first as ans ->  encounter.period as period,  period.start = ans.valueDate "admitDate";
    } "admitDate";
    // Outcome → disposition
    caseInfo.item as item where linkId = '508745697175' then {
      item.answer first as ans -> encounter.hospitalization as hosp then {
        ans.valueCoding as val where code = 'Alive' ->  hosp.dischargeDisposition as disp,  disp.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/discharge-disposition',  cod.code = 'home' "alive";
        ans.valueCoding as val where code = 'Dead' ->  hosp.dischargeDisposition as disp,  disp.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/discharge-disposition',  cod.code = 'exp' "dead";
      } "outcomeDisp";
    } "outcome";
  } "caseInfo";
  // Case type (Case or Line List) as type
  src.item as clinicalHistory where linkId = '477144604557' then {
    clinicalHistory.item as item where linkId = '865158268604' then {
      item.answer first as ans -> encounter.type as type then {
        ans ->  type.coding as cod,  cod.system = 'http://example.org/CodeSystem/measles-case-type',  cod.code = (ans.valueCoding.code),  cod.display = (ans.valueCoding.display) "caseType";
      } "encounterType";
    } "caseOrLineList";
  } "clinicalHistory";
}

group MapMeaslesCondition(source src : QuestionnaireResponse, target condition : Condition) {
  src -> condition.id = uuid() "conditionId";
  // Measles SNOMED code
  src -> condition.code as code then {
    src -> code.coding as coding then {
      src -> coding.system = 'http://snomed.info/sct' "snomedSys";
      src -> coding.code = '14189004' "measlesCode";
      src -> coding.display = 'Measles' "measlesDisplay";
    } "measlesCoding";
    src -> code.text = 'Measles' "measlesText";
  } "codeBlock";
  src.subject as subj ->  condition.subject as ref,  ref.reference = ('Patient/' + subj.reference);
  src.item as clinicalHistory where linkId = '477144604557' then {
    // Date of onset of illness
    clinicalHistory.item as item where linkId = '728034137219' then {
      item.answer first as ans -> condition.onset = ans.valueDate "onsetDate";
    } "onsetDate";
    // Clinical symptoms as body site / note
    clinicalHistory.item as item where linkId = '745196148424' then {
      item.answer as ans ->  condition.note as note,  note.text = (ans.valueCoding.display) "symptomNote";
    } "symptoms";
    // Date of rash onset
    clinicalHistory.item as item where linkId = '576528567552' then {
      item.answer first as ans -> condition.extension as ext then {
        ans -> ext.url = 'http://example.org/StructureDefinition/rashOnsetDate' "extUrl";
        ans -> ext.valueDate = ans.valueDate "extValue";
      } "rashOnset";
    } "rashDate";
    // Type of rash
    clinicalHistory.item as item where linkId = '704922081985' then {
      item.answer first as ans ->  condition.note as note,  note.text = ('Rash type: ' + ans.valueCoding.display) "rashTypeNote";
    } "rashType";
    // Home visited for contact investigation
    clinicalHistory.item as item where linkId = '207408507040' then {
      item.answer first as ans ->  condition.note as note,  note.text = (iif(ans.valueCoding.code = 'yes', 'Home visited for contact investigation: Yes', 'Home visited for contact investigation: No')) "contactInvestNote";
    } "homeVisited";
    // Date of home visit
    clinicalHistory.item as item where linkId = '566661890668' then {
      item.answer first as ans -> condition.extension as ext then {
        ans -> ext.url = 'http://example.org/StructureDefinition/contactInvestigationDate' "extUrl";
        ans -> ext.valueDate = ans.valueDate "extValue";
      } "homeVisitExt";
    } "homeVisitDate";
  } "clinicalHistory";
  // Outcome → clinical status from case info
  src.item as caseInfo where linkId = '216343227137' then {
    caseInfo.item as item where linkId = '508745697175' then {
      item.answer first as ans -> condition.clinicalStatus as status then {
        ans.valueCoding as val where code = 'Dead' ->  status.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/condition-clinical',  cod.code = 'inactive' "deadStatus";
        ans.valueCoding as val where code = 'Alive' ->  status.coding as cod,  cod.system = 'http://terminology.hl7.org/CodeSystem/condition-clinical',  cod.code = 'active' "aliveStatus";
      } "clinicalStatus";
    } "outcome";
  } "caseInfoStatus";
}

group MapMeaslesImmunization(source src : QuestionnaireResponse, target immunization : Immunization) {
  src -> immunization.id = uuid() "immunizationId";
  src -> immunization.status = 'completed' "status";
  // MR / Measles vaccine code
  src -> immunization.vaccineCode as code then {
    src -> code.coding as coding then {
      src -> coding.system = 'http://hl7.org/fhir/sid/cvx' "cvxSys";
      src -> coding.code = '05' "measlesCode";
      src -> coding.display = 'Measles-Rubella (MR) Vaccine' "mrDisplay";
    } "mrCoding";
  } "vaccineCode";
  src.subject as subj ->  immunization.patient as ref,  ref.reference = ('Patient/' + subj.reference) "patient";
  src.item as vaccination where linkId = '736291402384' then {
    // Vaccination status
    vaccination.item as item where linkId = '517772812375' then {
      item.answer first as ans where valueCoding.code = 'no' -> immunization.status = 'not-done' "notVaccinated";
      item.answer first as ans where valueCoding.code = 'unknown' ->  immunization.statusReason as reason,  reason.text = 'Unknown vaccination status' "unknownStatus";
    } "vaccinationStatus";
    // Number of doses
    vaccination.item as item where linkId = '886125589225' then {
      item.answer first as ans -> immunization.protocolApplied as protocol then {
        ans -> protocol.doseNumber = ans.valueInteger "doseNumber";
      } "protocol";
    } "doses";
    // MR vaccination in last 30 days
    vaccination.item as item where linkId = '308128177300' then {
      item.answer first as ans -> immunization.extension as ext then {
        ans -> ext.url = 'http://example.org/StructureDefinition/vaccineLast30Days' "extUrl";
        ans -> ext.valueCoding = ans.valueCoding "extValue";
      } "last30DaysExt";
    } "last30Days";
    // Date of last vaccination
    vaccination.item as item where linkId = '544290619304' then {
      item.answer first as ans -> immunization.occurrenceDateTime = ans.valueDate "lastVaccDate";
    } "lastVaccDate";
  } "vaccination";
}

group MapMeaslesSpecimen(source src : QuestionnaireResponse, target specimen : Specimen) {
  src -> specimen.id = uuid() "specimenId";
  // Blood/Urine/Respiratory type (default to blood serum for measles serology)
  src -> specimen.type as type then {
    src -> type.coding as coding then {
      src -> coding.system = 'http://snomed.info/sct' "snomedSys";
      src -> coding.code = '119364003' "serumCode";
      src -> coding.display = 'Serum specimen' "serumDisplay";
    } "serumCoding";
  } "specimenType";
  src.subject as subj ->  specimen.subject as ref,  ref.reference = ('Patient/' + subj.reference);
  src.item as specimenCollection where linkId = '271053545237' then {
    // Specimen type(s) selected
    specimenCollection.item as item where linkId = '412689284625' then {
      item.answer as ans ->  specimen.note as note,  note.text = ('Specimen collected: ' + ans.valueCoding.display) "specimenNote";
    } "specimenTypes";
    // Date of specimen collection
    specimenCollection.item as item where linkId = '8962468583341' then {
      item.answer first as ans ->  specimen.collection as coll,  coll.collectedDateTime = ans.valueDate "collectionDate";
    } "collectionDate";
    // Date specimen sent to lab
    specimenCollection.item as item where linkId = '718251724172' then {
      item.answer first as ans -> specimen.processing as proc then {
        ans -> proc.description = 'Specimen sent to lab' "procDesc";
        ans -> proc.timeDateTime = ans.valueDate "procTime";
      } "sentToLab";
    } "sentToLabDate";
    // Other specimen types
    specimenCollection.item as item where linkId = '340507649387' then {
      item.answer first as ans ->  specimen.note as note,  note.text = ('Other specimen type: ' + ans.valueString) "otherSpecimenNote";
    } "otherSpecimen";
  } "specimenCollection";
}