org.hl7.fhir.dstu3.model.Resource Java Examples

public void seeResource(String url, Resource r) throws FHIRException {
   if (r instanceof StructureDefinition)
     seeProfile(url, (StructureDefinition) r);
   else if (r instanceof ValueSet)
     seeValueSet(url, (ValueSet) r);
   else if (r instanceof CodeSystem)
     seeCodeSystem(url, (CodeSystem) r);
   else if (r instanceof OperationDefinition)
     seeOperationDefinition(url, (OperationDefinition) r);
   else if (r instanceof ConceptMap)
     maps.put(((ConceptMap) r).getUrl(), (ConceptMap) r);
   else if (r instanceof StructureMap)
     transforms.put(((StructureMap) r).getUrl(), (StructureMap) r);
   else if (r instanceof NamingSystem)
   	systems.add((NamingSystem) r);
}
 

public StructureDefinition getProfile(StructureDefinition source, String url) {
	StructureDefinition profile = null;
	String code = null;
	if (url.startsWith("#")) {
		profile = source;
		code = url.substring(1);
	} else if (context != null) {
		String[] parts = url.split("\\#");
		profile = context.fetchResource(StructureDefinition.class, parts[0]);
    code = parts.length == 1 ? null : parts[1];
	}  	  
	if (profile == null)
		return null;
	if (code == null)
		return profile;
	for (Resource r : profile.getContained()) {
		if (r instanceof StructureDefinition && r.getId().equals(code))
			return (StructureDefinition) r;
	}
	return null;
}
 

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).composePlainText(oo.getText().getDiv()), TerminologyServiceErrorClass.UNKNOWN));
      } else {
        ValueSet vs = (ValueSet) r; 
        expansions.put(vs.getUrl(), new ValueSetExpansionOutcome(vs));
      }
      } finally {
        IOUtils.closeQuietly(is);
      }
    }
  }
}
 

/**
 * Helper function to create an Entry for the given Resource within the given Bundle.
 * Sets the entry's fullURL to 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);
  if (Boolean.parseBoolean(Config.get("exporter.fhir.bulk_data"))) {
    entry.setFullUrl(resource.fhirType() + "/" + resourceID);
  } else {
    entry.setFullUrl("urn:uuid:" + 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;
}
 

public XhtmlNode generateDocumentNarrative(Bundle feed) {
  /*
   When the document is presented for human consumption, applications must present the collated narrative portions of the following resources in order:
   * The Composition resource
   * The Subject resource
   * Resources referenced in the section.content
   */
  XhtmlNode root = new XhtmlNode(NodeType.Element, "div");
  Composition comp = (Composition) feed.getEntry().get(0).getResource();
  root.getChildNodes().add(comp.getText().getDiv());
  Resource subject = ResourceUtilities.getById(feed, null, comp.getSubject().getReference());
  if (subject != null && subject instanceof DomainResource) {
    root.hr();
    root.getChildNodes().add(((DomainResource)subject).getText().getDiv());
  }
  List<SectionComponent> sections = comp.getSection();
  renderSections(feed, root, sections, 1);
  return root;
}
 

public void executeRoundTrip(String[] args) throws IOException, FHIRException {
	FileInputStream in;
	File source = new CSFile(args[1]);
	File dest = new CSFile(args[2]);
	if (args.length >= 4) {
		Utilities.copyFile(args[1], args[3]);
	}

	if (!source.exists())        
		throw new FHIRException("Source File \""+source.getAbsolutePath()+"\" not found");
	in = new CSFileInputStream(source);
	XmlParser p = new XmlParser();
	JsonParser parser = new JsonParser();
	JsonParser pj = parser;
	Resource rf = p.parse(in);
	ByteArrayOutputStream json = new ByteArrayOutputStream();
	parser.setOutputStyle(OutputStyle.PRETTY);
	parser.compose(json, rf);
	json.close();
	TextFile.stringToFile(new String(json.toByteArray()), Utilities.changeFileExt(dest.getAbsolutePath(), ".json"));
	rf = pj.parse(new ByteArrayInputStream(json.toByteArray()));
	FileOutputStream s = new FileOutputStream(dest);
	new XmlParser().compose(s, rf, true);
	s.close();
}
 

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 ValueSet expandValueset(ValueSet source, ExpansionProfile profile) {
  List<Header> headers = null;
  Parameters p = new Parameters();
  p.addParameter().setName("valueSet").setResource(source);
  if (profile != null)
    p.addParameter().setName("profile").setResource(profile);
  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 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();
}
 

protected Resource parseResourceContained(XmlPullParser xpp) throws IOException, FHIRFormatError, XmlPullParserException  {
	next(xpp);
	int eventType = nextNoWhitespace(xpp);
	if (eventType == XmlPullParser.START_TAG) { 
		Resource r = (Resource) parseResource(xpp);
		nextNoWhitespace(xpp);
		next(xpp);
		return r;
	} else {
		unknownContent(xpp);
		return null;
	}
}
 

/**
 * Compose a resource to a stream, possibly using pretty presentation for a human reader, and maybe a different choice in the xhtml narrative (used in the spec in one place, but should not be used in production)
 * @ 
 */
public void compose(OutputStream stream, Resource resource, boolean htmlPretty)  throws IOException {
	XMLWriter writer = new XMLWriter(stream, "UTF-8");
	writer.setPretty(style == OutputStyle.PRETTY);
	writer.start();
	compose(writer, resource, htmlPretty);
	writer.end();
}
 

public List<Resource> searchQuestionnaireResponse(FhirContext ctx,

                                                      @OptionalParam(name = QuestionnaireResponse.SP_IDENTIFIER) TokenParam identifier,
                                                      @OptionalParam(name= QuestionnaireResponse.SP_RES_ID) StringParam id,
                                                      @OptionalParam(name= QuestionnaireResponse.SP_QUESTIONNAIRE) ReferenceParam questionnaire,
                                                      @OptionalParam(name = QuestionnaireResponse.SP_PATIENT) ReferenceParam patient,
                                                      @IncludeParam(allow= {"*"}) Set<Include> includes

    );
 

@Search
public List<Resource> searchPerson(HttpServletRequest theRequest,
                                   @OptionalParam(name= Person.SP_NAME) StringParam name,
                                   @OptionalParam(name = Person.SP_IDENTIFIER) TokenParam identifier,
                                   @OptionalParam(name = Person.SP_EMAIL) TokenParam email,
                                   @OptionalParam(name = Person.SP_PHONE) TokenParam phone
 ) {
    return personDao.search(ctx,name, identifier, email, phone);
}
 

@Search
public List<Resource> search(HttpServletRequest theRequest,
                             @OptionalParam(name = Task.SP_PATIENT) ReferenceParam patient
        , @OptionalParam(name = Task.SP_IDENTIFIER) TokenParam identifier
        , @OptionalParam(name = Task.SP_RES_ID) StringParam id
        , @OptionalParam(name = Task.SP_OWNER) ReferenceParam owner
        , @OptionalParam(name = Task.SP_REQUESTER) ReferenceParam requester
        , @OptionalParam(name = Task.SP_STATUS) TokenParam status
        , @OptionalParam(name = Task.SP_CODE) TokenParam code
) {
    return taskDao.search(ctx,patient, identifier,id, owner, requester,status, code);
}
 

/**
 * Compose a resource to a stream, possibly using pretty presentation for a human reader (used in the spec, for example, but not normally in production)
 * @ 
 */
@Override
public void compose(OutputStream stream, Resource resource)  throws IOException {
	XMLWriter writer = new XMLWriter(stream, "UTF-8");
	writer.setPretty(style == OutputStyle.PRETTY);
	writer.start();
	compose(writer, resource, writer.isPretty());
	writer.end();
}
 

@Search
public List<Resource> searchQuestionnaire(HttpServletRequest theRequest,
                                          @OptionalParam(name = QuestionnaireResponse.SP_IDENTIFIER) TokenParam identifier,
                                          @OptionalParam(name = QuestionnaireResponse.SP_RES_ID) StringParam id,
                                          @OptionalParam(name = QuestionnaireResponse.SP_QUESTIONNAIRE) ReferenceParam questionnaire,
                                          @OptionalParam(name = QuestionnaireResponse.SP_PATIENT) ReferenceParam patient,
                                          @IncludeParam(allow = {"*"}) Set<Include> includes
) {
    return formDao.searchQuestionnaireResponse(ctx, identifier, id, questionnaire, patient, includes);
}
 

private StructureDefinition findContainedProfile(String url, SnapShotGenerationTestsContext context) throws DefinitionException, FHIRException {
  for (Resource r : context.tests.getContained()) {
    if (r instanceof StructureDefinition) {
      StructureDefinition sd = (StructureDefinition) r;
      if (sd.getUrl().equals(url)) {
        StructureDefinition p = sd.copy();
        ProfileUtilities pu = new ProfileUtilities(TestingUtilities.context, null, null);
        pu.setIds(p, false);
        pu.generateSnapshot(getSD(p.getBaseDefinition(), context), p, p.getUrl(), p.getName());
        return p;
      }
    }
  }
  return null;
}
 

public Resource fetchFixture(String id) {
  if (fixtures.containsKey(id))
    return fixtures.get(id);

  for (TestScriptFixtureComponent ds : tests.getFixture()) {
    if (id.equals(ds.getId()))
      throw new Error("not done yet");
  }
  for (Resource r : tests.getContained()) {
    if (id.equals(r.getId()))
      return r;
  }
  return null;
}
 

@Override
public List<Base> performSearch(Object appContext, String url) {
  List<Base> results = new ArrayList<Base>();
  String[] parts = url.split("\\?");
  if (parts.length == 2 && parts[0].substring(1).equals("PractitionerRole")) {
    String[] vals = parts[1].split("\\=");
    if (vals.length == 2 && vals[0].equals("practitioner"))
    for (Resource r : extras) {
      if (r instanceof PractitionerRole && ((PractitionerRole) r).getPractitioner().getReference().equals("Practitioner/"+vals[1])) {
        results.add(r);
      }
    }
  }
  return results;
}
 

public void executeCanonicalXml(String[] args) throws FHIRException, IOException {
	FileInputStream in;
	File source = new CSFile(args[1]);
	File dest = new CSFile(args[2]);

	if (!source.exists())        
		throw new FHIRException("Source File \""+source.getAbsolutePath()+"\" not found");
	in = new CSFileInputStream(source);
	XmlParser p = new XmlParser();
	Resource rf = p.parse(in);
	XmlParser cxml = new XmlParser();
	cxml.setOutputStyle(OutputStyle.NORMAL);
	cxml.compose(new FileOutputStream(dest), rf);
}
 

@Override
public List<Base> executeFunction(Object appContext, String functionName, List<List<Base>> parameters) {
  if ("fixture".equals(functionName)) {
    String id = fp.convertToString(parameters.get(0));
    Resource res = fetchFixture(id);
    if (res != null) {
      List<Base> list = new ArrayList<Base>();
      list.add(res);
      return list;
    }
  }
  return null;
}
 

private void resolveFixtures(SnapShotGenerationTestsContext context) {
  if (context.fixtures == null) {
    context.fixtures = new HashMap<>();
    for (TestScriptFixtureComponent fd : context.tests.getFixture()) {
      Resource r = TestingUtilities.context.fetchResource(Resource.class, fd.getResource().getReference());
      context.fixtures.put(fd.getId(), r);
    }
  }
}
 

List<Resource> search(
        FhirContext ctx,
        @OptionalParam(name = Claim.SP_PATIENT) ReferenceParam patient
        , @OptionalParam(name = Claim.SP_IDENTIFIER) TokenParam identifier
        , @OptionalParam(name = Claim.SP_RES_ID) StringParam id
        , @OptionalParam(name = Claim.SP_USE) TokenParam use
        , @OptionalParam(name = "status") TokenParam status
);
 

/**
 * @param resourceFormat
 * @param options
 * @return
 */
protected <T extends Resource> ResourceRequest<T> issueResourceRequest(String resourceFormat, HttpUriRequest request, byte[] payload, List<Header> headers) {
  configureFhirRequest(request, resourceFormat, headers);
  HttpResponse response = null;
  if(request instanceof HttpEntityEnclosingRequest && payload != null) {
    response = sendPayload((HttpEntityEnclosingRequestBase)request, payload, proxy);
  } else if (request instanceof HttpEntityEnclosingRequest && payload == null){
    throw new EFhirClientException("PUT and POST requests require a non-null payload");
  } else {
    response = sendRequest(request);
  }
  T resource = unmarshalReference(response, resourceFormat);
  return new ResourceRequest<T>(resource, response.getStatusLine().getStatusCode(), getLocationHeader(response));
}
 

private static void unbundle(String src) throws FHIRFormatError, FileNotFoundException, IOException {
  String folder = Utilities.getDirectoryForFile(src);
  Bundle bnd = (Bundle) new JsonParser().parse(new FileInputStream(src));
  for (BundleEntryComponent be : bnd.getEntry()) {
    Resource r = be.getResource();
    if (r != null) {
      String tgt = Utilities.path(folder, r.fhirType()+"-"+r.getId()+".json");
      new JsonParser().compose(new FileOutputStream(tgt), r);
    }
  }
}
 

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 boolean hasSource(String sourceId) {
  for (TestScriptFixtureComponent ds : tests.getFixture()) {
    if (sourceId.equals(ds.getId()))
      return true;
  }
  for (Resource r : tests.getContained()) {
    if (sourceId.equals(r.getId()))
      return true;
  }
  return false;
}
 

public <T extends Resource> String nameForClass(Class<T> resourceClass) {
  if (resourceClass == null)
    return null;
	String res = resourceClass.getSimpleName();
	if (res.equals("List_"))
		return "List";
	else
		return res;
}
 

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();
}
 

List<Resource> search (FhirContext ctx,
               @OptionalParam(name= Observation.SP_CATEGORY) TokenParam category,
               @OptionalParam(name= Observation.SP_CODE) TokenOrListParam codes,
               @OptionalParam(name= Observation.SP_DATE) DateRangeParam effectiveDate,
               @OptionalParam(name = Observation.SP_PATIENT) ReferenceParam patient
, @OptionalParam(name = Observation.SP_IDENTIFIER) TokenParam identifier
, @OptionalParam(name= Observation.SP_RES_ID) StringParam id
, @OptionalParam(name = Observation.SP_SUBJECT) ReferenceParam subject

, @IncludeParam(allow = { "Observation.related" ,  "*" }) Set<Include> includes
);