Java Code Examples for org.hl7.fhir.r4.model.Bundle.BundleEntryComponent#setResource()

@Override
public Bundle search(Object appInfo, String type, List<Argument> searchParams) throws FHIRException {
  try {
    Bundle bnd = new Bundle();
    BundleLinkComponent bl = bnd.addLink();
    bl.setRelation("next");
    bl.setUrl("http://test.fhir.org/r4/Patient?_format=text/xhtml&search-id=77c97e03-8a6c-415f-a63d-11c80cf73f&&active=true&_sort=_id&search-offset=50&_count=50");
    bl = bnd.addLink();
    bl.setRelation("self");
    bl.setUrl("http://test.fhir.org/r4/Patient?_format=text/xhtml&search-id=77c97e03-8a6c-415f-a63d-11c80cf73f&&active=true&_sort=_id&search-offset=0&_count=50");
    BundleEntryComponent be = bnd.addEntry();
    be.setFullUrl("http://hl7.org/fhir/Patient/example");
    be.setResource(new XmlParser().parse(new FileInputStream(Utilities.path(TestingUtilities.resourceNameToFile("patient-example.xml")))));
    be = bnd.addEntry();
    be.setFullUrl("http://hl7.org/fhir/Patient/example");
    be.setResource(new XmlParser().parse(new FileInputStream(Utilities.path(TestingUtilities.resourceNameToFile("patient-example-xds.xml")))));
    be.getSearch().setScore(0.5);
    be.getSearch().setMode(SearchEntryMode.MATCH);
    bnd.setTotal(50);
    return bnd;
  } catch (Exception e) {
    throw new FHIRException(e);
  }
}
 

/**
 * Helper function to create an Entry for the given Resource within the given Bundle. Sets the
 * resourceID to a random UUID, sets the entry's fullURL to that resourceID, and adds the entry to
 * the bundle.
 *
 * @param bundle   The Bundle to add the Entry to
 * @param resource Resource the new Entry should contain
 * @param resourceID The Resource ID to assign
 * @return the created Entry
 */
private static BundleEntryComponent newEntry(Bundle bundle, Resource resource,
    String resourceID) {
  BundleEntryComponent entry = bundle.addEntry();

  resource.setId(resourceID);
  entry.setFullUrl(getUrlPrefix(resource.fhirType()) + resourceID);
  entry.setResource(resource);

  if (TRANSACTION_BUNDLE) {
    BundleEntryRequestComponent request = entry.getRequest();
    request.setMethod(HTTPVerb.POST);
    request.setUrl(resource.getResourceType().name());
    entry.setRequest(request);
  }

  return entry;
}
 

private static void sendFile(FHIRToolingClient client, File f, int size, IniFile ini) throws FHIRFormatError, FileNotFoundException, IOException {
  long ms = System.currentTimeMillis();
  System.out.print("Loading "+f.getName()+".. ");
  IParser parser = f.getName().endsWith(".json") ? new JsonParser() : new XmlParser();
  Resource res = parser.parse(new FileInputStream(f));
  System.out.println("  done: ("+Long.toString(System.currentTimeMillis()-ms)+" ms)");
  
  if (res instanceof Bundle) {
    Bundle bnd = (Bundle) res;
    int cursor = ini.hasProperty("progress", f.getName()) ? ini.getIntegerProperty("progress", f.getName()) : 0;
    while (cursor < bnd.getEntry().size()) {
      Bundle bt = new Bundle();
      bt.setType(BundleType.BATCH);     
      bt.setId(UUID.randomUUID().toString().toLowerCase());
      for (int i = cursor; i < Math.min(bnd.getEntry().size(), cursor+size); i++) {
        BundleEntryComponent be = bt.addEntry();
        be.setResource(bnd.getEntry().get(i).getResource());
        be.getRequest().setMethod(HTTPVerb.PUT);
        be.getRequest().setUrl(be.getResource().getResourceType().toString()+"/"+be.getResource().getId());
      }
      System.out.print(f.getName()+" ("+cursor+"/"+bnd.getEntry().size()+"): ");
      ms = System.currentTimeMillis();
      Bundle resp = client.transaction(bt);

      int ncursor = cursor+size;
      for (int i = 0; i < resp.getEntry().size(); i++) {
        BundleEntryComponent t = resp.getEntry().get(i);
        if (!t.getResponse().getStatus().startsWith("2")) { 
          System.out.println("failed status at "+Integer.toString(i)+": "+t.getResponse().getStatus());
          ncursor = cursor+i-1;
          break;
        }
      }
      cursor = ncursor;
      System.out.println("  .. done: ("+Long.toString(System.currentTimeMillis()-ms)+" ms) "+SimpleDateFormat.getInstance().format(new Date()));
      ini.setIntegerProperty("progress", f.getName(), cursor, null);
      ini.save();
    }
    ini.setBooleanProperty("finished", f.getName(), true, null);
    ini.save();
  } else {
    client.update(res);
    ini.setBooleanProperty("finished", f.getName(), true, null);
    ini.save();
  }    
}
 

@SuppressWarnings("unchecked")
private void createBundle(){
	try {
		Date now = new Date();
		
		this.bundle = new Bundle();
		bundle.setId("BundleFromPractitioner");
		bundle.setMeta(new Meta().setLastUpdated(now).setProfile(Collections.singletonList(
			new CanonicalType("http://fhir.ch/ig/ch-crl/StructureDefinition/ch-crl-bundle"))));
		bundle.setType(BundleType.DOCUMENT);
		
		BundleEntryComponent compositionEntry = bundle.addEntry();
		Composition composition = new Composition();
		compositionEntry.setResource(composition);
		composition.setId("CompFromPractitioner");
		composition.setMeta(new Meta().setLastUpdated(now)
			.setProfile(Collections.singletonList(new CanonicalType(
				"http://fhir.ch/ig/ch-crl/StructureDefinition/ch-crl-composition"))));
		composition.setStatus(CompositionStatus.FINAL);
		composition.setType(new CodeableConcept(
			new Coding("http://loinc.org", "72134-0", "Cancer event report")));
		composition.setDate(now);
		composition.setTitle("Report to the Cancer Registry");
		
		BundleEntryComponent subjectEntry = bundle.addEntry();
		IFhirTransformer<Patient, IPatient> patientTransformer =
			(IFhirTransformer<Patient, IPatient>) FhirTransformersHolder
				.getTransformerFor(Patient.class, IPatient.class);
		Patient subject = patientTransformer.getFhirObject(patient)
			.orElseThrow(() -> new IllegalStateException("Could not create subject"));
		subject.getExtension().clear();
		fixAhvIdentifier(subject);
		
		subjectEntry.setResource(subject);
		
		BundleEntryComponent practitionerEntry = bundle.addEntry();
		IFhirTransformer<Practitioner, IMandator> practitionerTransformer =
			(IFhirTransformer<Practitioner, IMandator>) FhirTransformersHolder
				.getTransformerFor(Practitioner.class, IMandator.class);
		Practitioner practitioner = practitionerTransformer.getFhirObject(author)
			.orElseThrow(() -> new IllegalStateException("Could not create autor"));
		practitioner.getExtension().clear();
		practitioner.getIdentifier().clear();
		practitionerEntry.setResource(practitioner);
		
		BundleEntryComponent documentReferenceEntry = bundle.addEntry();
		DocumentReference documentReference = new DocumentReference();
		documentReferenceEntry.setResource(documentReference);
		documentReference.setId(document.getId());
		DocumentReferenceContentComponent content = documentReference.addContent();
		content.setAttachment(new Attachment().setContentType("application/pdf")
			.setData(IOUtils.toByteArray(document.getContent())));
		
		composition.setSubject(new Reference(subject));
		composition.setAuthor(Collections.singletonList(new Reference(practitioner)));
		SectionComponent section = composition.addSection();
		section.addEntry(new Reference(documentReference));
	} catch (IOException e) {
		LoggerFactory.getLogger(getClass()).error("Error creating FHIR bundle", e);
		throw new IllegalStateException("Error creating FHIR bundle", e);
	}
}