MappingFIle.yml

---
name: AT-coreprofile-mapping

applicability: true

actions:
 - name: Apply to AT Core Profiles
   profiles:
   - profile: https://fhir.hl7.at/r5-core-main/StructureDefinition-at-core-patient.html
     applicability: Patient

 - name: KeepResources
   keep_resources:
     - Patient
     - Encounter
     - Condition
     - Procedure
     - Observation
     - DiagnosticReport
     - CarePlan
     - MedicationRequest

 - name: create AT-Patient
   create_resource: 
    - resourceType: Patient
      based_on:
        resource: Patient
      fields:
        - location: Patient.id
          value: $getField([Patient.id])
        - location: Patient.meta
          value: $getField([Patient.meta[0]])
        - location: Patient.text
          value: $getField([Patient.text])
        - location: Patient.identifier
          value: $getField([Patient.identifier]) 
        - location: Patient.active
          value: $getField([Patient.active])
        - location: Patient.name.family
          value: $getField([Patient.name.family])
        - location: Patient.name.given
          value: $getField([Patient.name.given])
        - location: Patient.name.prefix
          value: $getField([Patient.name.prefix])
        - location: Patient.telecom
          value: $getField([Patient.telecom])
        - location: Patient.gender
          value: $getField([Patient.gender])
        - location: Patient.birthDate
          value: $getField([Patient.birthDate])
        - location: Patient.address.use
          value: "home"
        - location: Patient.address.line
          value: $getField([Patient.address.line])
        - location: Patient.address.city
          value: $getField([Patient.address.city])
        - location: Patient.address.state
          value: $getField([Patient.address.state])
        - location: Patient.address.postalCode
          value: $getField([Patient.address.postalCode])
        - location: Patient.address.country
          value: $getField([Patient.address.country])
        - location: Patient.maritalStatus
          value: $getField([Patient.maritalStatus])
        - location: Patient.multipleBirth[x]
          value: $getField([Patient.multipleBirth[x]])
        - location: Patient.photo
          value:
              contentType: "image/jpeg"
              url: "https://thispersondoesnotexist.tools/"
        - location: Patient.contact
          value: $getField([Patient.contact])
        - location: Patient.communication.language.coding
          value:
              system: "urn:ietf:bcp:47"
              code: "de"
        - location: Patient.communication.preferred
          value: "true"

 - name: applyBoolean
   execute_script:
     - apply_to: bundle
       function_name: applyBoolean
       function: |
        function applyBoolean(bundle) {
            bundle.entry.forEach(entry => {
                if (entry.resource.resourceType === "Patient") {
                    if (entry.resource.multipleBirthBoolean != "undefined") {
                        bundle.entry.filter(e => e.resource.resourceType === "Patient")
                            .forEach(patientEntry => {
                                patientEntry.resource.multipleBirthBoolean = entry.resource.multipleBirthBoolean;
                                if (entry.resource.multipleBirthBoolean){
                                   patientEntry.resource.multipleBirthInteger = entry.resource.multipleBirthInteger;
                                }
                            });
                    }
                    if (entry.resource.deceasedBoolean != "undefined") {
                        bundle.entry.filter(e => e.resource.resourceType === "Patient")
                            .forEach(patientEntry => {
                                patientEntry.resource.deceased = entry.resource.deceased;
                                  if (entry.resource.deceasedBoolean){
                                   patientEntry.resource.deceasedDateTime = entry.resource.deceasedDateTime;
                                }
                            });
                    }
                }
            });
            return bundle;
        }

 - name: applyIdentifier
   execute_script:
     - apply_to: resource
       function_name: applyIdentifier
       function: |
        function applyIdentifier(resource, bundle) {
            if (resource.resourceType === "Patient") {
                const BufferedReader = Java.type("java.io.BufferedReader");
                const FileReader = Java.type("java.io.FileReader");
                const Math = Java.type("java.lang.Math");

                // Read the JSON file content
                const reader = new BufferedReader(new FileReader("src/main/resources/templates/mappings/AT-identifier.json"));
                const jsonContent = reader.lines().toArray().join("");
                reader.close();

                const jsonObject = JSON.parse(jsonContent);

                const getRandomNumber = (min, max) => Math.floor(Math.random() * (max - min + 1)) + min;

                const SocialSecurityNumber = { ...jsonObject[0], value: getRandomNumber(1e9, 1e10 - 1).toString() };
                const PatientInternalIdentifier = { ...jsonObject[2], value: getRandomNumber(Math.pow(4, 3), Math.pow(4, 4) - 1).toString() };

                resource.identifier = [SocialSecurityNumber, jsonObject[1], PatientInternalIdentifier];

                return resource;
            }
        }


 - name: applyExtensions
   execute_script:
     - apply_to: resource
       function_name: applyExtensions
       function: |
        function applyExtensions(resource, bundle) {
            const BufferedReader = Java.type("java.io.BufferedReader");
            const FileReader = Java.type("java.io.FileReader");
            const ArrayList = Java.type("java.util.ArrayList");
            const Math = Java.type("java.lang.Math");

            if (resource.resourceType === "Patient") {
                const data = new ArrayList();
                
                // Read JSON content from the extensions file
                const readJsonFile = (filePath) => {
                    const reader = new BufferedReader(new FileReader(filePath));
                    const content = reader.lines().toArray().join("");
                    reader.close();
                    return JSON.parse(content);
                };

                const jsonObject = readJsonFile("src/main/resources/templates/mappings/AT-extensions.json");
                const [PatientReligion, citizenship] = jsonObject;

                // Read CSV content and populate data
                const readCsvFile = (filePath) => {
                    const reader = new BufferedReader(new FileReader(filePath));
                    const lines = reader.lines().toArray();
                    reader.close();
                    return lines.map(line => line.split(","));
                };

                const religionData = readCsvFile("src/main/resources/AT-religion.csv");

                // Select religion based on random number
                const randomNumber = Math.random() * 100;
                let chosenReligion = "Römisch-Katholisch";
                let chosenReligionCode = 101;
                let cumulativePercentage = 0;

                for (const [code, name, percentage] of religionData) {
                    cumulativePercentage += parseFloat(percentage);
                    if (randomNumber <= cumulativePercentage) {
                        chosenReligionCode = code;
                        chosenReligion = name;
                        break;
                    }
                }

                PatientReligion.extension[0].valueCodeableConcept.coding[0].code = chosenReligionCode;
                PatientReligion.extension[0].valueCodeableConcept.coding[0].display = chosenReligion;

                resource.extension = [PatientReligion, citizenship];
            }

            return resource;
        }


 - name: replaceUSCorePatient
   execute_script:
     - apply_to: bundle
       function_name: replaceUSCorePatient
       function: |
          function replaceUSCorePatient(bundle) {
              const patientEntries = bundle.entry.filter(entry => entry.resource.resourceType === "Patient");

              bundle.entry.forEach((entry, index) => {
                  if (entry.resource.resourceType === "Patient") {
                      const nextPatientIndex = patientEntries.indexOf(entry) + 1;

                      if (nextPatientIndex < patientEntries.length) {
                          entry.resource = patientEntries[nextPatientIndex].resource;
                      } else {
                          bundle.entry.splice(index, 1);
                      }
                  }
              });

              return bundle;
          }