org.hl7.fhir.instance.model.api.IBaseResource Java Examples

@Test
public void convertEncounter20() throws IOException {
	// encounter format of HAPI FHIR 2.0
	String oldContent = AllTests.getResourceAsString("/rsc/json/EncounterFormat20.json");
	assertFalse(FindingsFormatUtil.isCurrentFindingsFormat(oldContent));

	Optional<String> newContent = FindingsFormatUtil.convertToCurrentFindingsFormat(oldContent);
	assertTrue(newContent.isPresent());

	IBaseResource resource = AllTests.getJsonParser().parseResource(newContent.get());
	assertTrue(resource instanceof Encounter);
	Encounter encounter = (Encounter) resource;

	// indication changed to diagnosis
	List<DiagnosisComponent> diagnosis = encounter.getDiagnosis();
	assertNotNull(diagnosis);
	assertFalse(diagnosis.isEmpty());
	DiagnosisComponent component = diagnosis.get(0);
	Reference conditionRef = component.getCondition();
	assertNotNull(conditionRef);
	assertTrue(conditionRef.getReference().contains("CONDITIONA"));
	// patient changed to subject
	Reference subjectRef = encounter.getSubject();
	assertNotNull(subjectRef);
	assertTrue(subjectRef.getReference().contains("PATIENTID"));
}
 

/***
 * Update existing CodeSystems with the codes in all ValueSet resources.
 * System level CodeSystem update operation
 *
 * @return FHIR OperationOutcome detailing the success or failure of the operation
 */
@Operation(name = "$updateCodeSystems", idempotent = true)
public OperationOutcome updateCodeSystems()
{
    IBundleProvider valuesets = this.valueSetDao.search(new SearchParameterMap());
    OperationOutcome response = new OperationOutcome();

    OperationOutcome outcome;
    for (IBaseResource valueSet : valuesets.getResources(0, valuesets.size()))
    {
        outcome = this.performCodeSystemUpdate((ValueSet) valueSet);
        if (outcome.hasIssue())
        {
            for (OperationOutcome.OperationOutcomeIssueComponent issue : outcome.getIssue())
            {
                response.addIssue(issue);
            }
        }
    }

    return response;
}
 

@Override
public ReferenceResolution lookup(Object appInfo, IBaseResource context, IBaseReference reference) throws FHIRException {
  try {
    if (reference.getReferenceElement().isLocal()) {
      if (!(context instanceof DomainResource))
        return null;
      for (Resource r : ((DomainResource) context).getContained()) {
        if (('#' + r.getId()).equals(reference.getReferenceElement().getValue())) {
          return new ReferenceResolution(context, r);
        }
      }
    } else {
      String[] parts = reference.getReferenceElement().getValue().split("/");
      String filename = TestingUtilities.resourceNameToFile(parts[0].toLowerCase() + '-' + parts[1].toLowerCase() + ".xml");
      if (new File(filename).exists())
        return new ReferenceResolution(null, new XmlParser().parse(new FileInputStream(filename)));
    }
    return null;
  } catch (Exception e) {
    throw new FHIRException(e);
  }
}
 

private void processSearchSimple(ObjectValue target, Field field, boolean inheritedList, String suffix) throws EGraphQLException, FHIRException {
  if (services == null)
    throw new EGraphQLException("Resource Referencing services not provided");
  List<IBaseResource> list = new ArrayList<>();
  services.listResources(appInfo, field.getName().substring(0, field.getName().length() - 4), field.getArguments(), list);
  Argument arg = null;
  ObjectValue obj = null;

  List<Resource> vl = filterResources(field.argument("fhirpath"), list);
  if (!vl.isEmpty()) {
    arg = target.addField(field.getAlias() + suffix, listStatus(field, true));
    for (Resource v : vl) {
      obj = new ObjectValue();
      arg.addValue(obj);
      processObject(v, v, obj, field.getSelectionSet(), inheritedList, suffix);
    }
  }
}
 

@Override
public Optional<BigDecimal> getNumericValue(){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		if (FindingsScriptingUtil.hasScript(this)) {
			FindingsScriptingUtil.evaluate(this);
			resource = loadResource();
		}
		return accessor.getNumericValue((DomainResource) resource.get());
	}
	return Optional.empty();
}
 

@Override
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
  try {
    if (type.equals("Condition")) 
      matches.add(new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "condition-example.xml")));
    else if (type.equals("Patient")) {
      matches.add(new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "patient-example.xml")));
      matches.add(new XmlParser().parse(TestingUtilities.loadTestResourceStream("r5", "patient-example-xds.xml")));
    }
  } catch (Exception e) {
    throw new FHIRException(e);
  }
}
 

@Override
public void setPatientId(String patientId){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.setPatientId((DomainResource) resource.get(), patientId);
		saveResource(resource.get());
	}
	
	getEntity().setPatientId(patientId);
}
 

@Override
public Optional<String> getStart(){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		return accessor.getStart((DomainResource) resource.get());
	}
	return Optional.empty();
}
 

private Iterable<org.hl7.fhir.r4.model.Library> resolveLibraries(List< IBaseResource > resourceList) {
    List<org.hl7.fhir.r4.model.Library> ret = new ArrayList<>();
    for (IBaseResource res : resourceList) {
        Class<?> clazz = res.getClass();
        ret.add((org.hl7.fhir.r4.model.Library)clazz.cast(res));
    }
    return ret;
}
 

@Override
public Optional<LocalDateTime> getEndTime(){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		return accessor.getEndTime((DomainResource) resource.get());
	}
	return Optional.empty();
}
 

@Override
public void listResources(Object appInfo, String type, List<Argument> searchParams, List<IBaseResource> matches) throws FHIRException {
  try {
    if (type.equals("Condition"))
      matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("condition-example.xml"))));
    else if (type.equals("Patient")) {
      matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("patient-example.xml"))));
      matches.add(new XmlParser().parse(new FileInputStream(TestingUtilities.resourceNameToFile("patient-example-xds.xml"))));
    }
  } catch (Exception e) {
    throw new FHIRException(e);
  }
}
 

/**
 * Method to fetch a CodeSystem based on a provided URL. Tries to fetch it
 * from remote server. If it succeeds, it caches it in our global cache.
 *
 * @param theContext FHIR Context
 * @param theSystem The CodeSystem URL
 * @return Returns the retrieved FHIR Resource object or null
 */
@Override
public final CodeSystem fetchCodeSystem(
        final FhirContext theContext, final String theSystem) {
    logD(
            "CareConnectValidator asked to fetch Code System: %s%n",
            theSystem);


    if (!isSupported(theSystem)) {
        log.trace("  Returning null as it's an HL7 one");
        return null;
    }

    CodeSystem newCS;

    if (cachedResource.get(theSystem) == null) {
        log.trace(" Not cached");
        IBaseResource response = fetchURL(theSystem);
        if (response != null) {
            log.trace("  Retrieved");
            cachedResource.put(theSystem, (CodeSystem) response);
            log.trace("   Cached");
        }
    }
    if (cachedResource.get(theSystem) == null && cachedResource.get(theSystem) instanceof CodeSystem) {
        log.trace("  Couldn't fetch it, so returning null");
        return null;
    } else {
        log.trace(" Provided from cache");
        return newCS = (CodeSystem) cachedResource.get(theSystem);

    }
    //return newCS;
}
 

/**
 * Method to fetch a remote StructureDefinition resource.
 *
 * Caches results.
 *
 * @param theCtx FHIR Context
 * @param theUrl The URL to fetch from
 * @return The StructureDefinition resource or null
 */
@Override
public final StructureDefinition fetchStructureDefinition(
        final FhirContext theCtx,
        final String theUrl) {
    logD(
            "CareConnectValidator asked to fetch StructureDefinition: %s%n",
            theUrl);

    if (!isSupported(theUrl)) {
        log.trace("  Returning null as it's an HL7 one");
        return null;
    }

    if (cachedResource.get(theUrl) == null) {
        IBaseResource response = fetchURL(theUrl);
        log.trace("  About to parse response into a StructureDefinition");

        cachedResource.put(theUrl, CareConnectProfileFix.fixProfile((StructureDefinition) response));
        logD("  StructureDefinition now added to the cache: %s%n", theUrl);
    } else {
        logD("  This URL was already loaded: %s%n", theUrl);
    }
    StructureDefinition sd
            = (StructureDefinition)
            cachedResource.get(theUrl);
    return sd;
}
 

@Override
public void setStart(String start){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.setStart((DomainResource) resource.get(), start);
		saveResource(resource.get());
	}
}
 

private DomainResource fetchCodeSystemOrValueSet(FhirContext theContext, String theSystem, boolean codeSystem) {
  synchronized (this) {
    logW("******* CareConnect fetchCodeSystemOrValueSet: system="+theSystem);

    Map<String, IBaseResource> codeSystems = cachedResource;

    return null;
  }
}
 

public void setType(List<ICoding> coding){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.setType((DomainResource) resource.get(), coding);
		saveResource(resource.get());
	}
}
 

/**
 * Method to fetch a CodeSystem based on a provided URL. Tries to fetch it
 * from remote server. If it succeeds, it caches it in our global cache.
 *
 * @param theContext FHIR Context
 * @param theSystem The CodeSystem URL
 * @return Returns the retrieved FHIR Resource object or null
 */
@Override
public final CodeSystem fetchCodeSystem(
        final FhirContext theContext, final String theSystem) {
    logD(
            "MyInstanceValidator asked to fetch Code System: %s%n",
            theSystem);


    if (!isSupported(theSystem)) {
        log.trace("  Returning null as it's an HL7 one");
        return null;
    }

    CodeSystem newCS;

    if (cachedResource.get(theSystem) == null) {
        log.trace(" Not cached");
        IBaseResource response = fetchURL(theSystem);
        if (response != null) {
            log.trace("  Retrieved");
            cachedResource.put(theSystem, (CodeSystem) response);
            log.trace("   Cached");
        }
    }
    if (cachedResource.get(theSystem) == null && cachedResource.get(theSystem) instanceof CodeSystem) {
        log.trace("  Couldn't fetch it, so returning null");
        return null;
    } else {
        log.trace(" Provided from cache");
        return newCS = (CodeSystem) cachedResource.get(theSystem);

    }
    //return newCS;
}
 

@Override
public void setFacilityType(ICoding coding){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.setFacilityType((DomainResource) resource.get(), coding);
		saveResource(resource.get());
	}
	
}
 

/**
 * Retrieves the ID from the given resource instance
 */
public static IdType of(IBaseResource theResouce) {
  if (theResouce == null) {
    throw new NullPointerException("theResource can not be null");
  } else {
    IIdType retVal = theResouce.getIdElement();
    if (retVal == null) {
      return null;
    } else if (retVal instanceof IdType) {
      return (IdType) retVal;
    } else {
      return new IdType(retVal.getValue());
    }
  }
}
 

public List<ICoding> getType(){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		return accessor.getType((DomainResource) resource.get());
	}
	return new ArrayList<>();
}
 

public synchronized Collection<Object> resolveResourceList(List<IBaseResource> resourceList) {
    List<Object> ret = new ArrayList<>();
    for (IBaseResource res : resourceList) {
        Class<?> clazz = res.getClass();
        ret.add(clazz.cast(res));
    }
    // ret.addAll(resourceList);
    return ret;
}
 

@Override
public void setDocumentClass(ICoding coding){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.setDocumentClass((DomainResource) resource.get(), coding);
		saveResource(resource.get());
	}
}
 

@Override
public void setCoding(List<ICoding> coding){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.setCoding((DomainResource) resource.get(), coding);
		saveResource(resource.get());
	}
}
 

private Iterable<org.hl7.fhir.dstu3.model.Library> resolveLibraries(List< IBaseResource > resourceList) {
    List<org.hl7.fhir.dstu3.model.Library> ret = new ArrayList<>();
    for (IBaseResource res : resourceList) {
        Class<?> clazz = res.getClass();
        ret.add((org.hl7.fhir.dstu3.model.Library)clazz.cast(res));
    }
    return ret;
}
 

@Override
public void setCategory(ObservationCategory category){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.setCategory((DomainResource) resource.get(), category);
		saveResource(resource.get());
	}
}
 

@Override
public void addComponent(ObservationComponent component){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.addComponent((DomainResource) resource.get(), component);
		saveResource(resource.get());
	}
}
 

@Override
public void updateComponent(ObservationComponent component){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.updateComponent((DomainResource) resource.get(), component);
		saveResource(resource.get());
	}
}
 

@Override
public List<ICoding> getCoding(){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		return accessor.getCoding((DomainResource) resource.get());
	}
	return Collections.emptyList();
}
 

@Override
public void setEndTime(LocalDateTime time){
	Optional<IBaseResource> resource = loadResource();
	if (resource.isPresent()) {
		accessor.setEndTime((DomainResource) resource.get(), time);
		saveResource(resource.get());
	}
}
 

/**
 * Method to fetch a remote StructureDefinition resource.
 *
 * Caches results.
 *
 * @param theCtx FHIR Context
 * @param theUrl The URL to fetch from
 * @return The StructureDefinition resource or null
 */
@Override
public final StructureDefinition fetchStructureDefinition(
        final FhirContext theCtx,
        final String theUrl) {
    logD(
            "MyInstanceValidator asked to fetch StructureDefinition: %s%n",
            theUrl);

    if (!isSupported(theUrl)) {
        log.trace("  Returning null as it's an HL7 one");
        return null;
    }

    if (cachedResource.get(theUrl) == null) {
        IBaseResource response = fetchURL(theUrl);
        log.trace("  About to parse response into a StructureDefinition");

        cachedResource.put(theUrl, (StructureDefinition) response);
        logD("  StructureDefinition now added to the cache: %s%n", theUrl);
    } else {
        logD("  This URL was already loaded: %s%n", theUrl);
    }
    StructureDefinition sd
            = (StructureDefinition)
            cachedResource.get(theUrl);
    return sd;
}