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

private ValueSet importValueSet(String value, List<ValueSetExpansionParameterComponent> params, Parameters expParams) throws ETooCostly, TerminologyServiceException, FileNotFoundException, IOException, FHIRFormatError {
  if (value == null)
    throw new TerminologyServiceException("unable to find value set with no identity");
  ValueSet vs = context.fetchResource(ValueSet.class, value);
  if (vs == null)
    throw new TerminologyServiceException("Unable to find imported value set " + value);
  ValueSetExpansionOutcome vso = new ValueSetExpanderSimple(context).expand(vs, expParams);
  if (vso.getError() != null)
    throw new TerminologyServiceException("Unable to expand imported value set: " + vso.getError());
  if (vs.hasVersion())
    if (!existsInParams(params, "version", new UriType(vs.getUrl() + "|" + vs.getVersion())))
      params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
  for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
    if (!existsInParams(params, p.getName(), p.getValue()))
      params.add(p);
  }
  canBeHeirarchy = false; // if we're importing a value set, we have to be combining, so we won't try for a heirarchy
  return vso.getValueset();
}
 

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();
}
 

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();
}
 

private void doServerIncludeCodes(ConceptSetComponent inc, boolean heirarchical, List<ValueSetExpansionParameterComponent> params, List<ValueSet> imports, Parameters expParams) throws FHIRException {
  ValueSetExpansionOutcome vso = context.expandVS(inc, heirarchical);
  if (vso.getError() != null)
    throw new TerminologyServiceException("Unable to expand imported value set: " + vso.getError());
  ValueSet vs = vso.getValueset();
  if (vs.hasVersion())
    if (!existsInParams(params, "version", new UriType(vs.getUrl() + "|" + vs.getVersion())))
      params.add(new ValueSetExpansionParameterComponent().setName("version").setValue(new UriType(vs.getUrl() + "|" + vs.getVersion())));
  for (ValueSetExpansionParameterComponent p : vso.getValueset().getExpansion().getParameter()) {
    if (!existsInParams(params, p.getName(), p.getValue()))
      params.add(p);
  }
  for (ValueSetExpansionContainsComponent cc : vs.getExpansion().getContains()) {
    addCodeAndDescendents(cc, null, expParams, imports);
  }
}
 

private void includeCodes(ConceptSetComponent inc, List<ValueSetExpansionParameterComponent> params, Parameters expParams, boolean heirarchical) throws ETooCostly, FileNotFoundException, IOException, FHIRException {
  inc.checkNoModifiers("Compose.include", "expanding");
  List<ValueSet> imports = new ArrayList<ValueSet>();
  for (UriType imp : inc.getValueSet()) {
    imports.add(importValueSet(imp.getValue(), params, expParams));
  }

  if (!inc.hasSystem()) {
    if (imports.isEmpty()) // though this is not supposed to be the case
      return;
    ValueSet base = imports.get(0);
    imports.remove(0);
    base.checkNoModifiers("Imported ValueSet", "expanding");
    copyImportContains(base.getExpansion().getContains(), null, expParams, imports);
  } else {
    CodeSystem cs = context.fetchCodeSystem(inc.getSystem());
    if ((cs == null || cs.getContent() != CodeSystemContentMode.COMPLETE)) {
      doServerIncludeCodes(inc, heirarchical, params, imports, expParams);
    } else {
      doInternalIncludeCodes(inc, params, expParams, imports, cs);
    }
  }
}
 

@Test
public void testCreateAndReadInTenantA() {
  ourLog.info("Base URL is: " + HapiProperties.getServerAddress());

  // Create tenant A
  ourClientTenantInterceptor.setTenantId("DEFAULT");
  ourClient
    .operation()
    .onServer()
    .named(ProviderConstants.PARTITION_MANAGEMENT_CREATE_PARTITION)
    .withParameter(Parameters.class, ProviderConstants.PARTITION_MANAGEMENT_PARTITION_ID, new IntegerType(1))
    .andParameter(ProviderConstants.PARTITION_MANAGEMENT_PARTITION_NAME, new CodeType("TENANT-A"))
    .execute();


  ourClientTenantInterceptor.setTenantId("TENANT-A");
  Patient pt = new Patient();
  pt.addName().setFamily("Family A");
  ourClient.create().resource(pt).execute().getId();

  Bundle searchResult = ourClient.search().forResource(Patient.class).returnBundle(Bundle.class).cacheControl(new CacheControlDirective().setNoCache(true)).execute();
  assertEquals(1, searchResult.getEntry().size());
  Patient pt2 = (Patient) searchResult.getEntry().get(0).getResource();
  assertEquals("Family A", pt2.getName().get(0).getFamily());
}
 

@Test
public void testCreateAndReadInTenantB() {
  ourLog.info("Base URL is: " + HapiProperties.getServerAddress());

  // Create tenant A
  ourClientTenantInterceptor.setTenantId("DEFAULT");
  ourClient
    .operation()
    .onServer()
    .named(ProviderConstants.PARTITION_MANAGEMENT_CREATE_PARTITION)
    .withParameter(Parameters.class, ProviderConstants.PARTITION_MANAGEMENT_PARTITION_ID, new IntegerType(2))
    .andParameter(ProviderConstants.PARTITION_MANAGEMENT_PARTITION_NAME, new CodeType("TENANT-B"))
    .execute();


  ourClientTenantInterceptor.setTenantId("TENANT-B");
  Patient pt = new Patient();
  pt.addName().setFamily("Family B");
  ourClient.create().resource(pt).execute().getId();

  Bundle searchResult = ourClient.search().forResource(Patient.class).returnBundle(Bundle.class).cacheControl(new CacheControlDirective().setNoCache(true)).execute();
  assertEquals(1, searchResult.getEntry().size());
  Patient pt2 = (Patient) searchResult.getEntry().get(0).getResource();
  assertEquals("Family B", pt2.getName().get(0).getFamily());
}
 

@Operation(name = "$get-elm", idempotent = true, type = Library.class)
public Parameters getElm(@IdParam IdType theId, @OptionalParam(name="format") String format) {
    Library theResource = this.libraryResourceProvider.getDao().read(theId);
    // this.formatCql(theResource);

    ModelManager modelManager = this.getModelManager();
    LibraryManager libraryManager = this.getLibraryManager(modelManager);

    String elm = "";
    CqlTranslator translator = this.dataRequirementsProvider.getTranslator(theResource, libraryManager, modelManager);
    if (translator != null) {
        if (format.equals("json")) {
            elm = translator.toJson();
        }
        else {
            elm = translator.toXml();
        }
    }
    Parameters p = new Parameters();
    p.addParameter().setValue(new StringType(elm));
    return p;
}
 

private void addEvaluatedResourcesToParameters(Bundle contained, Parameters parameters) {
    Map<String, Resource> resourceMap = new HashMap<>();
    if (contained.hasEntry()) {
        for (Bundle.BundleEntryComponent entry : contained.getEntry()) {
            if (entry.hasResource() && !(entry.getResource() instanceof ListResource)) {
                if (!resourceMap.containsKey(entry.getResource().getIdElement().getValue())) {
                    parameters.addParameter(new Parameters.ParametersParameterComponent().setName("resource")
                            .setResource(entry.getResource()));

                    resourceMap.put(entry.getResource().getIdElement().getValue(), entry.getResource());

                    resolveReferences(entry.getResource(), parameters, resourceMap);
                }
            }
        }
    }
}
 

private void resolveReferences(Resource resource, Parameters parameters, Map<String, Resource> resourceMap) {
    List<IBase> values;
    for (BaseRuntimeChildDefinition child : this.measureResourceProvider.getContext().getResourceDefinition(resource).getChildren()) {
        values = child.getAccessor().getValues(resource);
        if (values == null || values.isEmpty()) {
            continue;
        }

        else if (values.get(0) instanceof Reference
                && ((Reference) values.get(0)).getReferenceElement().hasResourceType()
                && ((Reference) values.get(0)).getReferenceElement().hasIdPart()) {
            Resource fetchedResource = (Resource) registry
                    .getResourceDao(((Reference) values.get(0)).getReferenceElement().getResourceType())
                    .read(new IdType(((Reference) values.get(0)).getReferenceElement().getIdPart()));

            if (!resourceMap.containsKey(fetchedResource.getIdElement().getValue())) {
                parameters.addParameter(new Parameters.ParametersParameterComponent().setName("resource")
                        .setResource(fetchedResource));

                resourceMap.put(fetchedResource.getIdElement().getValue(), fetchedResource);
            }
        }
    }
}
 

@Override
public ValueSetExpansionOutcome expand(ValueSet source, Parameters expParams) throws ETooCostly, IOException {
  String cacheKey = makeCacheKey(source, expParams);
	if (expansions.containsKey(cacheKey))
		return expansions.get(cacheKey);
	ValueSetExpander vse = new ValueSetExpanderSimple(context);
	ValueSetExpansionOutcome vso = vse.expand(source, expParams);
	if (vso.getError() != null) {
	  // well, we'll see if the designated server can expand it, and if it can, we'll cache it locally
		vso = context.expandVS(source, false, expParams == null || !expParams.getParameterBool("excludeNested"));
		if (cacheFolder != null) {
		  FileOutputStream s = new FileOutputStream(Utilities.path(cacheFolder, makeFileName(source.getUrl())));
		  context.newXmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, vso.getValueset());
		  s.close();
		}
	}
	if (vso.getValueset() != null)
	  expansions.put(cacheKey, vso);
	return vso;
}
 

private String makeCacheKey(ValueSet source, Parameters expParams) throws IOException {
  if (expParams == null)
    return source.getUrl();
  JsonParser p = new JsonParser();
  String r = p.composeString(expParams);
  return source.getUrl() + " " + r.hashCode(); 
}
 

@Operation(name = "$get-narrative", idempotent = true, type = Library.class)
public Parameters getNarrative(@IdParam IdType theId) {
    Library theResource = this.libraryResourceProvider.getDao().read(theId);
    Narrative n = this.narrativeProvider.getNarrative(this.libraryResourceProvider.getContext(), theResource);
    Parameters p = new Parameters();
    p.addParameter().setValue(new StringType(n.getDivAsString()));
    return p;
}
 

@Operation(name = "$get-narrative", idempotent = true, type = Measure.class)
public Parameters getNarrative(@IdParam IdType theId) {
    Measure theResource = this.measureResourceProvider.getDao().read(theId);
    CqfMeasure cqfMeasure = this.dataRequirementsProvider.createCqfMeasure(theResource, this.libraryResolutionProvider);
    Narrative n = this.narrativeProvider.getNarrative(this.measureResourceProvider.getContext(), cqfMeasure);
    Parameters p = new Parameters();
    p.addParameter().setValue(new StringType(n.getDivAsString()));
    return p;
}
 

public static IWorkerContext context() {
  if (fcontext == null) {
    FilesystemPackageCacheManager pcm;
    try {
      pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
      fcontext = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.core", "4.0.0"));
      fcontext.setUcumService(new UcumEssenceService(TestingUtilities.resourceNameToFile("ucum", "ucum-essence.xml")));
      fcontext.setExpansionProfile(new Parameters());
    } catch (Exception e) {
      throw new Error(e);
    }

  }
  return fcontext;
}
 

@Operation(name = "$collect-data", idempotent = true, type = Measure.class)
public Parameters collectData(@IdParam IdType theId, @RequiredParam(name = "periodStart") String periodStart,
        @RequiredParam(name = "periodEnd") String periodEnd, @OptionalParam(name = "patient") String patientRef,
        @OptionalParam(name = "practitioner") String practitionerRef,
        @OptionalParam(name = "lastReceivedOn") String lastReceivedOn) throws FHIRException {
    // TODO: Spec says that the periods are not required, but I am not sure what to
    // do when they aren't supplied so I made them required
    MeasureReport report = evaluateMeasure(theId, periodStart, periodEnd, null, null, patientRef, null,
            practitionerRef, lastReceivedOn, null, null, null);
    report.setGroup(null);

    Parameters parameters = new Parameters();

    parameters.addParameter(
            new Parameters.ParametersParameterComponent().setName("measurereport").setResource(report));

    if (report.hasContained()) {
        for (Resource contained : report.getContained()) {
            if (contained instanceof Bundle) {
                addEvaluatedResourcesToParameters((Bundle) contained, parameters);
            }
        }
    }

    // TODO: need a way to resolve referenced resources within the evaluated
    // resources
    // Should be able to use _include search with * wildcard, but HAPI doesn't
    // support that

    return parameters;
}
 

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();
}
 

private void copyImportContains(List<ValueSetExpansionContainsComponent> list, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filter) throws FHIRException {
  for (ValueSetExpansionContainsComponent c : list) {
    c.checkNoModifiers("Imported Expansion in Code System", "expanding");
    ValueSetExpansionContainsComponent np = addCode(c.getSystem(), c.getCode(), c.getDisplay(), parent, null, expParams, c.getAbstract(), c.getInactive(), filter);
    copyImportContains(c.getContains(), np, expParams, filter);
  }
}
 

private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params, Parameters expParams, List<ValueSet> filters) throws ETooCostly, FHIRException {
  if (expand != null) {
    if (expand.getContains().size() > maxExpansionSize)
      throw new ETooCostly("Too many codes to display (>" + Integer.toString(expand.getContains().size()) + ")");
    for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
      if (!existsInParams(params, p.getName(), p.getValue()))
        params.add(p);
    }

    copyImportContains(expand.getContains(), null, expParams, filters);
  }
}
 

private void addCodeAndDescendents(ValueSetExpansionContainsComponent focus, ValueSetExpansionContainsComponent parent, Parameters expParams, List<ValueSet> filters)  throws FHIRException {
  focus.checkNoModifiers("Expansion.contains", "expanding");
  ValueSetExpansionContainsComponent np = addCode(focus.getSystem(), focus.getCode(), focus.getDisplay(), parent, 
       convert(focus.getDesignation()), expParams, focus.getAbstract(), focus.getInactive(), filters);
  for (ValueSetExpansionContainsComponent c : focus.getContains())
    addCodeAndDescendents(focus, np, expParams, filters);
}
 

private Parameters makeDefaultExpansion() {
  Parameters res = new Parameters();
  res.addParameter("excludeNested", true);
  res.addParameter("includeDesignations", false);
  return res;
}
 

@Override
public Parameters lookupCode(Map<String, String> params) {
  return client.lookupCode(params);
}
 

@Override
public Parameters validateVS(Parameters pin) {
  return client.operateType(ValueSet.class, "validate-code", pin);
}
 

@Override
public Parameters validateCS(Parameters pin) {
  return client.operateType(CodeSystem.class, "validate-code", pin);
}
 

@Override
public ValueSet expandValueset(ValueSet vs, Parameters p, Map<String, String> params) {
  return client.expandValueset(vs, p, params);
}
 

/**
* 
* @param source the value set definition to expand
* @param profile a profile affecting the outcome. If you don't supply a profile, the default internal expansion profile will be used.
*  
* @return
* @throws ETooCostly
* @throws FileNotFoundException
* @throws IOException
*/
 public ValueSetExpansionOutcome expand(ValueSet source, Parameters parameters) throws ETooCostly, FileNotFoundException, IOException;
 

public Parameters lookupCode(Map<String, String> params) throws FHIRException; 

public Parameters validateVS(Parameters pin) throws FHIRException;