org.hl7.fhir.r4.model.OperationOutcome Java Examples

public static String getErrorDescription(OperationOutcome error) {  
if (error.hasText() && error.getText().hasDiv())
	return new XhtmlComposer(XhtmlComposer.XML).composePlainText(error.getText().getDiv());

StringBuilder b = new StringBuilder();
for (OperationOutcomeIssueComponent t : error.getIssue())
	if (t.getSeverity() == IssueSeverity.ERROR)
		b.append("Error:" +t.getDetails()+"\r\n");
	else if (t.getSeverity() == IssueSeverity.FATAL)
		b.append("Fatal:" +t.getDetails()+"\r\n");
	else if (t.getSeverity() == IssueSeverity.WARNING)
		b.append("Warning:" +t.getDetails()+"\r\n");
	else if (t.getSeverity() == IssueSeverity.INFORMATION)
		b.append("Information:" +t.getDetails()+"\r\n");
return b.toString();
}
 

public static OperationOutcomeIssueComponent convertToIssue(ValidationMessage message, OperationOutcome op) {
  OperationOutcomeIssueComponent issue = new OperationOutcome.OperationOutcomeIssueComponent();
  issue.setCode(convert(message.getType()));
  
  if (message.getLocation() != null) {
    // message location has a fhirPath in it. We need to populate the expression
    issue.addExpression(message.getLocation());
  }
  // pass through line/col if they're present
  if (message.getLine() != 0)
    issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_LINE).setValue(new IntegerType(message.getLine()));
  if (message.getCol() != 0)
    issue.addExtension().setUrl(ToolingExtensions.EXT_ISSUE_COL).setValue(new IntegerType(message.getCol()));
  issue.setSeverity(convert(message.getLevel()));
  CodeableConcept c = new CodeableConcept();
  c.setText(message.getMessage());
  issue.setDetails(c);
  if (message.getSource() != null) {
    issue.getExtension().add(ToolingExtensions.makeIssueSource(message.getSource()));
  }
  return issue;
}
 

@Create
public MethodOutcome create(HttpServletRequest theRequest, @ResourceParam ObservationDefinition observationDefinition)

{
    log.info("create method is called");
    resourcePermissionProvider.checkPermission("create");
    MethodOutcome method = new MethodOutcome();

    OperationOutcome opOutcome = new OperationOutcome();

    method.setOperationOutcome(opOutcome);

    try {
        ObservationDefinition newObservationDefinition = observationDefinitionDao.create(ctx,observationDefinition, null);
        method.setCreated(true);
        method.setId(newObservationDefinition.getIdElement());
        method.setResource(newObservationDefinition);
    } catch (Exception ex) {
        log.info(ex.getMessage());
        ProviderResponseLibrary.handleException(method,ex);
    }
    return method;
}
 

public <T extends Resource> T vread(Class<T> resourceClass, String id, String version) {
	ResourceRequest<T> result = null;
	try {
		result = utils.issueGetResourceRequest(resourceAddress.resolveGetUriFromResourceClassAndIdAndVersion(resourceClass, id, version), getPreferredResourceFormat());
		result.addErrorStatus(410);//gone
		result.addErrorStatus(404);//unknown
		result.addErrorStatus(405);//unknown
		result.addSuccessStatus(200);//Only one for now
		if(result.isUnsuccessfulRequest()) {
			throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
		}
	} catch (Exception e) {
		handleException("An error has occurred while trying to read this version of the resource", e);
	}
	return result.getPayload();
}
 

public <T extends Resource> T getCanonical(Class<T> resourceClass, String canonicalURL) {
  ResourceRequest<T> result = null;
  try {
    result = utils.issueGetResourceRequest(resourceAddress.resolveGetUriFromResourceClassAndCanonical(resourceClass, canonicalURL), getPreferredResourceFormat());
    result.addErrorStatus(410);//gone
    result.addErrorStatus(404);//unknown
    result.addErrorStatus(405);//unknown
    result.addSuccessStatus(200);//Only one for now
    if(result.isUnsuccessfulRequest()) {
      throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
    }
  } catch (Exception e) {
    handleException("An error has occurred while trying to read this version of the resource", e);
  }
  Bundle bnd = (Bundle) result.getPayload();
  if (bnd.getEntry().size() == 0)
    throw new EFhirClientException("No matching resource found for canonical URL '"+canonicalURL+"'");
  if (bnd.getEntry().size() > 1)
    throw new EFhirClientException("Multiple matching resources found for canonical URL '"+canonicalURL+"'");
  return (T) bnd.getEntry().get(0).getResource();
}
 

@SuppressWarnings("unchecked")

public <T extends Resource> OperationOutcome validate(Class<T> resourceClass, T resource, String id) {
	ResourceRequest<T> result = null;
	try {
		result = utils.issuePostRequest(resourceAddress.resolveValidateUri(resourceClass, id), utils.getResourceAsByteArray(resource, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat());
		result.addErrorStatus(400);//gone
		result.addErrorStatus(422);//Unprocessable Entity
		result.addSuccessStatus(200);//OK
		if(result.isUnsuccessfulRequest()) {
			throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
		}
	} catch(Exception e) {
		handleException("An error has occurred while trying to validate this resource", e);
	}
	return (OperationOutcome)result.getPayload();
}
 

public ValueSet expandValueset(ValueSet source, Parameters expParams) {
  List<Header> headers = null;
  Parameters p = expParams == null ? new Parameters() : expParams.copy();
  p.addParameter().setName("valueSet").setResource(source);
  ResourceRequest<Resource> result = utils.issuePostRequest(resourceAddress.resolveOperationUri(ValueSet.class, "expand"), 
      utils.getResourceAsByteArray(p, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), headers);
  result.addErrorStatus(410);//gone
  result.addErrorStatus(404);//unknown
  result.addErrorStatus(405);
  result.addErrorStatus(422);//Unprocessable Entity
  result.addSuccessStatus(200);
  result.addSuccessStatus(201);
  if(result.isUnsuccessfulRequest()) {
    throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
  }
  return (ValueSet) result.getPayload();
}
 

/***
 * 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;
}
 

public ValueSet expandValueset(ValueSet source, Parameters expParams, Map<String, String> params) {
  List<Header> headers = null;
  Parameters p = expParams == null ? new Parameters() : expParams.copy();
  p.addParameter().setName("valueSet").setResource(source);
  for (String n : params.keySet())
    p.addParameter().setName(n).setValue(new StringType(params.get(n)));
  ResourceRequest<Resource> result = utils.issuePostRequest(resourceAddress.resolveOperationUri(ValueSet.class, "expand", params), 
      utils.getResourceAsByteArray(p, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), headers);
  result.addErrorStatus(410);//gone
  result.addErrorStatus(404);//unknown
  result.addErrorStatus(405);
  result.addErrorStatus(422);//Unprocessable Entity
  result.addSuccessStatus(200);
  result.addSuccessStatus(201);
  if(result.isUnsuccessfulRequest()) {
    throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
  }
  return (ValueSet) result.getPayload();
}
 

public ConceptMap initializeClosure(String name) {
  Parameters params = new Parameters();
  params.addParameter().setName("name").setValue(new StringType(name));
  List<Header> headers = null;
  ResourceRequest<Resource> result = utils.issuePostRequest(resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
      utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), headers);
  result.addErrorStatus(410);//gone
  result.addErrorStatus(404);//unknown
  result.addErrorStatus(405);
  result.addErrorStatus(422);//Unprocessable Entity
  result.addSuccessStatus(200);
  result.addSuccessStatus(201);
  if(result.isUnsuccessfulRequest()) {
    throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
  }
  return (ConceptMap) result.getPayload();
}
 

public ConceptMap updateClosure(String name, Coding coding) {
  Parameters params = new Parameters();
  params.addParameter().setName("name").setValue(new StringType(name));
  params.addParameter().setName("concept").setValue(coding);
  List<Header> headers = null;
  ResourceRequest<Resource> result = utils.issuePostRequest(resourceAddress.resolveOperationUri(null, "closure", new HashMap<String, String>()),
      utils.getResourceAsByteArray(params, false, isJson(getPreferredResourceFormat())), getPreferredResourceFormat(), headers);
  result.addErrorStatus(410);//gone
  result.addErrorStatus(404);//unknown
  result.addErrorStatus(405);
  result.addErrorStatus(422);//Unprocessable Entity
  result.addSuccessStatus(200);
  result.addSuccessStatus(201);
  if(result.isUnsuccessfulRequest()) {
    throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
  }
  return (ConceptMap) result.getPayload();
}
 

@Delete
public MethodOutcome delete
        (@IdParam IdType internalId) {
    resourcePermissionProvider.checkPermission("delete");
    MethodOutcome method = new MethodOutcome();

    try {
        OperationOutcome outcome = observationDefinitionDao.delete(ctx,internalId);
        method.setCreated(false);

        method.setResource(outcome);
    } catch (Exception ex) {
        log.info(ex.getMessage());
        ProviderResponseLibrary.handleException(method,ex);
    }

    return method;
}
 

@Read
public ObservationDefinition get
        (@IdParam IdType internalId) {
    resourcePermissionProvider.checkPermission("read");
    ObservationDefinition observationDefinition = observationDefinitionDao.read( ctx, internalId);

    if ( observationDefinition == null) {
        throw OperationOutcomeFactory.buildOperationOutcomeException(
                new ResourceNotFoundException("No ObservationDefinition/" + internalId.getIdPart()),
                 OperationOutcome.IssueType.NOTFOUND);
    }

    return observationDefinition;
}
 

public static boolean isAnError(OperationOutcome error) {
	for (OperationOutcomeIssueComponent t : error.getIssue())
		if (t.getSeverity() == IssueSeverity.ERROR)
			return true;
		else if (t.getSeverity() == IssueSeverity.FATAL)
			return true;
	return false;
}
 

@Override
public OperationOutcome delete(FhirContext ctx, IdType theId) {
    log.trace("Delete OperationDefinition = " + theId.getValue());

    ObservationDefinitionEntity observationDefinitionEntity = readEntity(ctx, theId);

    if (observationDefinitionEntity == null) return null;

    for (ObservationDefinitionIdentifier identifier : observationDefinitionEntity.getIdentifiers()) {
        em.remove(identifier);
    }
    em.remove(observationDefinitionEntity);
    return new OperationOutcome();

}
 

public static OperationOutcome createErrorOutcome(String display) {
    Coding code = new Coding().setDisplay(display);
    return new OperationOutcome().addIssue(
            new OperationOutcome.OperationOutcomeIssueComponent()
                    .setSeverity(OperationOutcome.IssueSeverity.ERROR)
                    .setCode(OperationOutcome.IssueType.PROCESSING)
                    .setDetails(new CodeableConcept().addCoding(code))
    );
}
 

/***
 * Update existing CodeSystems with the codes in the specified ValueSet.
 *
 * This is for development environment purposes to enable ValueSet expansion and validation
 * without complete CodeSystems.
 *
 * @param theId the id of the ValueSet
 * @return FHIR OperationOutcome detailing the success or failure of the operation
 */
@Operation(name = "$updateCodeSystems", idempotent = true, type = ValueSet.class)
public OperationOutcome updateCodeSystems(@IdParam IdType theId)
{
    ValueSet vs = this.valueSetDao.read(theId);

    OperationOutcomeBuilder responseBuilder = new OperationOutcomeBuilder();
    if (vs == null)
    {
        return responseBuilder.buildIssue("error", "notfound", "Unable to find Resource: " + theId.getId()).build();
    }

    return performCodeSystemUpdate(vs);
}
 

public OperationOutcome performCodeSystemUpdate(ValueSet vs)
{
    OperationOutcomeBuilder responseBuilder = new OperationOutcomeBuilder();

    List<String> codeSystems = new ArrayList<>();
    if (vs.hasCompose() && vs.getCompose().hasInclude())
    {
        CodeSystem codeSystem;
        for (ValueSet.ConceptSetComponent csc : vs.getCompose().getInclude())
        {
            if (!csc.hasSystem()) continue;

            codeSystem = getCodeSystemByUrl(csc.getSystem());

            if (!csc.hasConcept()) continue;

            updateCodeSystem(
                    codeSystem.setUrl(csc.getSystem()),
                    getUnionDistinctCodes(csc, codeSystem)
            );

            codeSystems.add(codeSystem.getUrl());
        }
    }

    return responseBuilder.buildIssue(
            "information",
            "informational",
            "Successfully updated the following CodeSystems: " + String.join(", ", codeSystems)
    ).build();
}
 

public OperationOutcomeBuilder buildIssue(String severity, String code, String details)
{
    complexProperty.addIssue(
            new OperationOutcome.OperationOutcomeIssueComponent()
                    .setSeverity(OperationOutcome.IssueSeverity.fromCode(severity))
                    .setCode(OperationOutcome.IssueType.fromCode(code))
                    .setDetails(new CodeableConcept().setText(details))
    );

    return this;
}
 

public Parameters lookupCode(Map<String, String> params) {
  ResourceRequest<Resource> result = utils.issueGetResourceRequest(resourceAddress.resolveOperationUri(CodeSystem.class, "lookup", params), getPreferredResourceFormat());
  result.addErrorStatus(410);//gone
  result.addErrorStatus(404);//unknown
  result.addErrorStatus(405);
  result.addErrorStatus(422);//Unprocessable Entity
  result.addSuccessStatus(200);
  result.addSuccessStatus(201);
  if(result.isUnsuccessfulRequest()) {
    throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
  }
  return (Parameters) result.getPayload();
}
 

public <T extends Resource> T read(Class<T> resourceClass, String id) {//TODO Change this to AddressableResource
	ResourceRequest<T> result = null;
	try {
		result = utils.issueGetResourceRequest(resourceAddress.resolveGetUriFromResourceClassAndId(resourceClass, id), getPreferredResourceFormat());
		result.addErrorStatus(410);//gone
		result.addErrorStatus(404);//unknown
		result.addSuccessStatus(200);//Only one for now
		if(result.isUnsuccessfulRequest()) {
			throw new EFhirClientException("Server returned error code " + result.getHttpStatus(), (OperationOutcome)result.getPayload());
		}
	} catch (Exception e) {
		handleException("An error has occurred while trying to read this resource", e);
	}
	return result.getPayload();
}
 

private void loadCache() throws FHIRFormatError, IOException {
  File[] files = new File(cacheFolder).listFiles();
  for (File f : files) {
    if (f.getName().endsWith(".xml")) {
      final FileInputStream is = new FileInputStream(f);
      try {	   
        Resource r = context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).parse(is);
        if (r instanceof OperationOutcome) {
          OperationOutcome oo = (OperationOutcome) r;
          expansions.put(ToolingExtensions.getExtension(oo,VS_ID_EXT).getValue().toString(),
              new ValueSetExpansionOutcome(new XhtmlComposer(XhtmlComposer.XML, false).composePlainText(oo.getText().getDiv()), TerminologyServiceErrorClass.UNKNOWN));
        } else if (r instanceof ValueSet) {
          ValueSet vs = (ValueSet) r;
          if (vs.hasExpansion())
            expansions.put(vs.getUrl(), new ValueSetExpansionOutcome(vs));
          else {
            canonicals.put(vs.getUrl(), vs);
            if (vs.hasVersion())
              canonicals.put(vs.getUrl()+"|"+vs.getVersion(), vs);
          }
        } else if (r instanceof MetadataResource) {
          MetadataResource md = (MetadataResource) r;
          canonicals.put(md.getUrl(), md);
          if (md.hasVersion())
            canonicals.put(md.getUrl()+"|"+md.getVersion(), md);
        }
      } finally {
        IOUtils.closeQuietly(is);
      }
    }
  }
}
 

public OperationOutcome getOutcome() {
  return outcome;
}
 

public EOperationOutcome(OperationOutcome outcome) {
  super();
  this.outcome = outcome;
}
 

public EFhirClientException(String message, List<OperationOutcome> serverErrors) {
	super(message);
	if(serverErrors != null && serverErrors.size() > 0) {
		errors.addAll(serverErrors);
	}
}
 

private boolean hasError(OperationOutcome oo) {
  for (OperationOutcomeIssueComponent t : oo.getIssue())
    if (t.getSeverity() == IssueSeverity.ERROR || t.getSeverity() == IssueSeverity.FATAL)
      return true;
  return false;
}
 

public OperationOutcomeBuilder()
{
    super(new OperationOutcome());
}
 

/**
 * Generate EFhirClientException indicating the cause of the exception
 * along with any OperationOutcome server error the server may have generated.
 * 
 * A default message of "One or more server side errors have occurred during this operation. Refer to e.getServerErrors() for additional details."
 * will be returned to users.
 * 
 * @param message
 * @param serverError
 */
public EFhirClientException(OperationOutcome serverError) {
	super("Error on the server: "+serverError.getText().getDiv().allText()+". Refer to e.getServerErrors() for additional details.");
	if(serverError != null) {
		errors.add(serverError);
	}
}
 

/**
 * Generate EFhirClientException which include a message indicating the cause of the exception
 * along with any OperationOutcome server error that may have resulted.
 * 
 * @param message
 * @param serverError
 */
public EFhirClientException(String message, OperationOutcome serverError) {
	super(message);
	if(serverError != null) {
		errors.add(serverError);
	}
}
 

/**
 * Method returns all OperationOutcome server errors that are 
 * associated with this exception.
 * 
 * @return
 */
public List<OperationOutcome> getServerErrors() {
	return errors;
}