Boolean returnCode;
FHIR_API_Wrapper temp;
globalMap.put("FHIR", temp=new FHIR_API_Wrapper());

returnCode = ((FHIR_API_Wrapper) globalMap.get("FHIR")).doPatient(toJava1.cPatId, toJava1.cBirthDate, toJava1.cDeceased, toJava1.cGender, toJava1.sourceFlag, toJava1.lastRowFlag);
or
returnCode = ((FHIR_API_Wrapper) globalMap.get("FHIR")).addEncounterToPatient(patFall.cPatId, patFall.FallNr, patFall.RecId,patFall.anfang, patFall.ende, "p70");

bundle = new Bundle();
bundleCounter++;
bundle.setType(Bundle.BundleType.TRANSACTION);
bundle.setId(String.valueOf(bundleCounter));
bdlMap.put(String.valueOf(bundleCounter), bundle);

Patient patient = new Patient();
IdDt patRand=IdDt.newRandomUuid();
patient.setId(cPatId); // argument from method call
patientRandMap.put(cPatId,patRand.getValueAsString());
patientCounter++;

Meta m= new Meta();
m.addProfile("https://fhir.bbmri.de/StructureDefinition/Patient");
patient.setMeta(m);

switch (geschlecht){
case "male": patient.setGender(AdministrativeGender.MALE); break;
case "female": patient.setGender(AdministrativeGender.FEMALE); break;
default: patient.setGender(AdministrativeGender.UNKNOWN);
}

patient.setId(cPatId);

if(geburtsDatum!=null)
  patient.setBirthDate(geburtsDatum);

if(sterbeDatum!=null)
  patient.setDeceased(new DateTimeType(sterbeDatum));

patientMap.put(patient.getId(),patient);
System.err.println("size after addition: "+patientMap.size());

bundle.addEntry()
   .setFullUrl(patRand.getValueAsString())
   .setResource(patient)
   .getRequest()
   .setUrl("Patient/"+patient.getId())
   .setMethod(HTTPVerb.PUT);

patientToBundle.put(patient.getId(), bundle.getId());

Condition condition = new Condition();
condition
   .getCode()
   .addCoding()
   .setSystem("http://fhir.de/CodeSystem/dimdi/icd-10-gm")
   .setVersion("2016")
   .setCode(code)
   .setDisplay(display.trim());
condition.setId(recId);
if(obEncId!=null)
  condition.setEncounter(new Reference("Encounter/fn"+obEncId));
if(onset!=null)
  condition.setOnset(new DateTimeType(onset));
if(abatement!=null)
  condition.setAbatement(new DateTimeType(abatement));
condition.getClinicalStatus()
   .addCoding()
   .setSystem("http://terminology.hl7.org/CodeSystem/condition-clinical")
   .setCode("resolved");

condition.setSubject(new Reference("Patient/"+patientMap.get(obPatId).getId()));

Bundle lookedUpBundle=bdlMap.get(patientToBundle.get(obPatId));

lookedUpBundle.addEntry()
   .setResource(condition)
   .setFullUrl(IdDt.newRandomUuid().getValueAsString())
   .getRequest()
   .setUrl("Condition/"+condition.getId())
   .setMethod(HTTPVerb.PUT);

System.err.println("condition added.");

FhirContext ctx = FhirContext.forR4();

// Create a client and PUT the transaction to the server
IGenericClient client = ctx.newRestfulGenericClient("http://FHIRSERVER:8080/fhir");

// Create an HTTP basic auth interceptor
String username = "admin";
String password = "psw";
IClientInterceptor authInterceptor = new BasicAuthInterceptor(username, password);
client.registerInterceptor(authInterceptor);

System.err.println("number of bundles: "+bdlMap.size());
for (Bundle bdlIt : bdlMap.values()) {
  System.out.println(ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(bdlIt));
  Bundle resp = client.transaction().withBundle(bdlIt).execute();
  System.out.println(ctx.newJsonParser().setPrettyPrint(true).encodeResourceToString(resp));
}

@ResourceDef(name="Specimen", profile="https://fhir.bbmri.de/StructureDefinition/Specimen")

public class GBASpecimen extends Specimen {

private static final long serialVersionUID = 1L;

/**
* Each extension is defined in a field. Any valid HAPI Data Type
* can be used for the field type. Note that the [name=""] attribute
* in the @Child annotation needs to match the name for the bean accessor
* and mutator methods.
*/
@Child(name="temperatureCC")
@Extension(url="https://fhir.bbmri.de/StructureDefinition/StorageTemperature", definedLocally=true, isModifier=false)
@Description(shortDefinition="The temperature")
private CodeableConcept myTemperatureCC;
@Child(name="orgaRef")
@Extension(url="https://fhir.bbmri.de/StructureDefinition/Custodian", definedLocally=true, isModifier=false)
@Description(shortDefinition="The custodian")
private Reference myOrgaRef;
@Child(name="diagnoseCC")
@Extension(url="https://fhir.bbmri.de/StructureDefinition/SampleDiagnosis", definedLocally=true, isModifier=false)
@Description(shortDefinition="SampleDiagnosis")
private CodeableConcept mySampleDiagnosisCC;
@Child(name="typeIBDWCC")
@Extension(url="http://ibdw.de/fhir/StructureDefinition/SampleType", definedLocally=true, isModifier=false)
@Description(shortDefinition="SampleType")
private CodeableConcept myTypeIBDWCC;


/**
* It is important to override the isEmpty() method, adding a check for any
* newly added fields.
*/
@Override
public boolean isEmpty() {
   return super.isEmpty()
   && ElementUtil.isEmpty(myTemperatureCC)
   && ElementUtil.isEmpty(myOrgaRef)
   && ElementUtil.isEmpty(mySampleDiagnosisCC)
   && ElementUtil.isEmpty(myTypeIBDWCC);
}

/********
* Accessors and mutators follow
*
* IMPORTANT:
* Each extension is required to have an getter/accessor and a setter/mutator.
* You are highly recommended to create getters which create instances if they
* do not already exist, since this is how the rest of the HAPI FHIR API works.
********/


/** Getter for CC */
public CodeableConcept getTemperatureCC() {
if (myTemperatureCC == null) {
  myTemperatureCC = new CodeableConcept();
}
return this.myTemperatureCC;
}

public CodeableConcept getSampleDiagnosisCC() {
if (mySampleDiagnosisCC == null) {
  mySampleDiagnosisCC = new CodeableConcept();
}
return this.mySampleDiagnosisCC;
}

public CodeableConcept getTypeIBDWCC() {
if (myTypeIBDWCC == null) {
  myTypeIBDWCC = new CodeableConcept();
}
return this.myTypeIBDWCC;
}

public Reference getOrgaRef() {
if (myOrgaRef == null) {
  myOrgaRef = new Reference();
}
return this.myOrgaRef;
}

@Override
public ResourceType getResourceType(){
return ResourceType.Specimen;

}

@Override
public FhirVersionEnum getStructureFhirVersionEnum() {
return FhirVersionEnum.R4;
}
}