Java Code Examples for org.hl7.fhir.dstu3.model.Bundle#setType()

private static void buildVitalSignsSet() throws FileNotFoundException, IOException, FHIRFormatError {
  Calendar base = Calendar.getInstance();
  base.add(Calendar.DAY_OF_MONTH, -1);
  Bundle b = new Bundle();
  b.setType(BundleType.COLLECTION);
  b.setId(UUID.randomUUID().toString().toLowerCase());
  
  vitals(b, base, 0, 80, 120, 95, 37.1);
  vitals(b, base, 35, 85, 140, 98, 36.9);
  vitals(b, base, 53, 75, 110, 96, 36.2);
  vitals(b, base, 59, 65, 100, 94, 35.5);
  vitals(b, base, 104, 60, 90, 90, 35.9);
  vitals(b, base, 109, 65, 100, 92, 36.5);
  vitals(b, base, 114, 70, 130, 94, 37.5);
  vitals(b, base, 120, 90, 150, 97, 37.3);
  vitals(b, base, 130, 95, 133, 97, 37.2);
  vitals(b, base, 150, 85, 125, 98, 37.1);
  
  new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("c:\\temp\\vitals.xml"), b);
}
 

public Bundle process(String sourceFile) throws FileNotFoundException, SAXException, IOException, ParserConfigurationException {
  this.definitions = sourceFile;
  log("Begin. Produce Loinc CDEs in "+dest+" from "+definitions);
  loadLoinc();
  log("LOINC loaded");

  now = DateTimeType.now();

  bundle = new Bundle();
  bundle.setType(BundleType.COLLECTION);
  bundle.setId("http://hl7.org/fhir/commondataelement/loinc");
  bundle.setMeta(new Meta().setLastUpdatedElement(InstantType.now()));

  processLoincCodes();
  return bundle;
}
 

/**
 * Export the hospital in FHIR STU3 format.
 */
public static void export(long stop) {
  if (Boolean.parseBoolean(Config.get("exporter.hospital.fhir_stu3.export"))) {

    Bundle bundle = new Bundle();
    if (Boolean.parseBoolean(Config.get("exporter.fhir.transaction_bundle"))) {
      bundle.setType(BundleType.TRANSACTION);
    } else {
      bundle.setType(BundleType.COLLECTION);
    }
    for (Provider h : Provider.getProviderList()) {
      // filter - exports only those hospitals in use
      Table<Integer, String, AtomicInteger> utilization = h.getUtilization();
      int totalEncounters = utilization.column(Provider.ENCOUNTERS).values().stream()
          .mapToInt(ai -> ai.get()).sum();
      if (totalEncounters > 0) {
        BundleEntryComponent entry = FhirStu3.provider(bundle, h);
        addHospitalExtensions(h, (Organization) entry.getResource());
      }
    }

    String bundleJson = FHIR_CTX.newJsonParser().setPrettyPrint(true)
        .encodeResourceToString(bundle);

    // get output folder
    List<String> folders = new ArrayList<>();
    folders.add("fhir_stu3");
    String baseDirectory = Config.get("exporter.baseDirectory");
    File f = Paths.get(baseDirectory, folders.toArray(new String[0])).toFile();
    f.mkdirs();
    Path outFilePath = f.toPath().resolve("hospitalInformation" + stop + ".json");

    try {
      Files.write(outFilePath, Collections.singleton(bundleJson), StandardOpenOption.CREATE_NEW);
    } catch (IOException e) {
      e.printStackTrace();
    }
  }
}
 

/**
*     

* @throws FHIRException
* @throws IOException
* @throws FileNotFoundException
*/
 public static void buildStatsSeries() throws FHIRException, IOException, FileNotFoundException {
   Bundle b = new Bundle();
   b.setType(BundleType.COLLECTION);
   b.setId(UUID.randomUUID().toString().toLowerCase());

   addAge(b, 5, 1, "18.3");
   addAge(b, 5, 2, "18.4");
   addAge(b, 5, 3, "18.6");
   addAge(b, 5, 4, "18.8");
   addAge(b, 5, 5, "19.0");
   addAge(b, 5, 6, "19.1");
   addAge(b, 5, 7, "19.3");
   addAge(b, 5, 8, "19.5");
   addAge(b, 5, 9, "19.6");
   addAge(b, 5,10, "19.8");
   addAge(b, 5,11, "20.0");
   addAge(b, 6, 0, "20.2");
   addAge(b, 6, 1, "20.3");
   addAge(b, 6, 2, "20.5");
   addAge(b, 6, 3, "20.7");
   addAge(b, 6, 4, "20.9");
   addAge(b, 6, 5, "21.0");
   addAge(b, 6, 6, "21.2");
   addAge(b, 6, 7, "21.4");
   addAge(b, 6, 8, "21.6");
   addAge(b, 6, 9, "21.8");
   addAge(b, 6,10, "22.0");
   addAge(b, 6,11, "22.2");
   addAge(b, 7, 0, "22.4");
   addAge(b, 7, 1, "22.6");
   addAge(b, 7, 2, "22.8");
   addAge(b, 7, 3, "23.0");
   addAge(b, 7, 4, "23.2");
   addAge(b, 7, 5, "23.4");
   addAge(b, 7, 6, "23.6");
   addAge(b, 7, 7, "23.9");
   addAge(b, 7, 8, "24.1");
   addAge(b, 7, 9, "24.3");
   addAge(b, 7,10, "24.5");
   addAge(b, 7,11, "24.8");
   addAge(b, 8, 0, "25.0");
   addAge(b, 8, 1, "25.3");
   addAge(b, 8, 2, "25.5");
   addAge(b, 8, 3, "25.8");
   addAge(b, 8, 4, "26.0");
   addAge(b, 8, 5, "26.3");
   addAge(b, 8, 6, "26.6");
   addAge(b, 8, 7, "26.8");
   addAge(b, 8, 8, "27.1");
   addAge(b, 8, 9, "27.4");
   addAge(b, 8,10, "27.6");
   addAge(b, 8,11, "27.9");
   addAge(b, 9, 0, "28.2");
   addAge(b, 9, 1, "28.5");
   addAge(b, 9, 2, "28.8");
   addAge(b, 9, 3, "29.1");
   addAge(b, 9, 4, "29.4");
   addAge(b, 9, 5, "29.7");
   addAge(b, 9, 6, "30.0");
   addAge(b, 9, 7, "30.3");
   addAge(b, 9, 8, "30.6");
   addAge(b, 9, 9, "30.9");
   addAge(b, 9, 10, "31.2");
   addAge(b, 9, 11, "31.5");
   addAge(b, 10, 0, "31.9");

 
   new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream("c:\\temp\\obs.xml"), b);
 }
 

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++) {
        if (i >=0 && i < bnd.getEntry().size()) {
          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();
  }    
}
 

/**
 * Convert the given Person into a FHIR Bundle, containing the Patient and the
 * associated entries from their health record.
 *
 * @param person Person to generate the FHIR from
 * @param stopTime Time the simulation ended
 * @return FHIR Bundle containing the Person's health record.
 */
public static Bundle convertToFHIR(Person person, long stopTime) {
  Bundle bundle = new Bundle();
  if (TRANSACTION_BUNDLE) {
    bundle.setType(BundleType.TRANSACTION);
  } else {
    bundle.setType(BundleType.COLLECTION);
  }

  BundleEntryComponent personEntry = basicInfo(person, bundle, stopTime);

  for (Encounter encounter : person.record.encounters) {
    BundleEntryComponent encounterEntry = encounter(person, personEntry, bundle, encounter);

    for (HealthRecord.Entry condition : encounter.conditions) {
      condition(personEntry, bundle, encounterEntry, condition);
    }

    for (HealthRecord.Entry allergy : encounter.allergies) {
      allergy(personEntry, bundle, encounterEntry, allergy);
    }

    for (Observation observation : encounter.observations) {
      // If the Observation contains an attachment, use a Media resource, since
      // Observation resources in stu3 don't support Attachments
      if (observation.value instanceof Attachment) {
        media(personEntry, bundle, encounterEntry, observation);
      } else {
        observation(personEntry, bundle, encounterEntry, observation);
      }
    }

    for (Procedure procedure : encounter.procedures) {
      procedure(personEntry, bundle, encounterEntry, procedure);
    }

    for (Medication medication : encounter.medications) {
      medication(personEntry, bundle, encounterEntry, medication);
    }

    for (HealthRecord.Entry immunization : encounter.immunizations) {
      immunization(personEntry, bundle, encounterEntry, immunization);
    }

    for (Report report : encounter.reports) {
      report(personEntry, bundle, encounterEntry, report);
    }

    for (CarePlan careplan : encounter.careplans) {
      careplan(personEntry, bundle, encounterEntry, careplan);
    }

    for (ImagingStudy imagingStudy : encounter.imagingStudies) {
      imagingStudy(personEntry, bundle, encounterEntry, imagingStudy);
    }

    for (HealthRecord.Device device : encounter.devices) {
      device(personEntry, bundle, device);
    }
    
    for (HealthRecord.Supply supply : encounter.supplies) {
      supplyDelivery(personEntry, bundle, supply, encounter);
    }
    
    // one claim per encounter
    BundleEntryComponent encounterClaim = encounterClaim(personEntry, bundle,
        encounterEntry, encounter.claim);

    explanationOfBenefit(personEntry,bundle,encounterEntry,person,
        encounterClaim, encounter);
  }
  return bundle;
}