public Throwable fhir(SparseArray<GlucoseRecord> records) {
try {
Patient p = getPatient();
Log.d(TAG, "converting glucoserecrods to observations now");
Device d = initializeDevice(p);
// do conditional update here so the device is updated if needed
String ident = getConditionalUrl(d, d.getIdentifierFirstRep());
String a = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(d);
IdDt id = (IdDt) client.update().resource(d).conditionalByUrl(ident).execute().getId();
d.setId(id);
DeviceMetric metric = initializeDeviceMetric(d);
metric.setId(
client
.create()
.resource(metric)
.conditionalByUrl(getConditionalUrl(metric, metric.getIdentifier()))
.execute()
.getId());
for (int i = 0; i < records.size(); i++) {
int j = records.keyAt(i);
GlucoseRecord r = records.get(j);
Log.d(TAG, "creating quantity");
QuantityDt qdt = initializeQuantityDt(r);
Observation o = initializeObservation(p, metric, r, qdt);
Log.d(TAG, "submitting to server...");
// client.update().resource(o).conditionalByUrl("Observation?identifier=http://...%7Cid").encodedJson().execute();
IdDt did =
(IdDt)
client
.update()
.resource(o)
.conditionalByUrl(getConditionalUrl(o, o.getIdentifierFirstRep()))
.execute()
.getId();
o.setId(did);
String s = ctx.newXmlParser().setPrettyPrint(true).encodeResourceToString(o);
Log.d(TAG, "... done");
}
} catch (Throwable e) {
return e;
}
return null;
}
/**
* Invokes the given search Url and writes the results to a file in the specified job folder.
*
* @param searchUrl
* @param serverBase
* @param jobDir
* @param fileName
* @throws IOException
*/
private int retrieveAndStoreData(
String searchUrl, String serverBase, File jobDir, String fileName) throws IOException {
int numRecords = 0;
final String url = urlEncodeQueryParams(searchUrl);
LOG.info(
"retrieveAndStoreData, serverBase: {} searchUrl: {} encoded query: {}",
serverBase,
searchUrl,
url);
final ServerAuthorization serverAuthorization =
AuthorizationUtil.findServerAuthorization(serverAuthorizations, serverBase);
BearerTokenAuthInterceptor authInterceptor = null;
if (serverAuthorization != null) {
// register authorization interceptor with the client
LOG.info("assigning bearing token interceptor, {}", serverAuthorization.getAccessToken());
authInterceptor = new BearerTokenAuthInterceptor(serverAuthorization.getAccessToken());
fhirRestClient.registerInterceptor(authInterceptor);
}
try {
// Perform a search
final Bundle searchResults =
fhirRestClient.search().byUrl(url).returnBundle(Bundle.class).execute();
// Split the bundle into its component resources
final SearchResultSplitter resultSplitter = new SearchResultSplitter();
final List<Resource> resources = resultSplitter.splitBundle(searchResults);
final File dataFile = createDataSourceFile(jobDir, fileName);
writeData(dataFile, resources, serverBase, true);
numRecords = resources.size();
// retrieve other pages of search results
Bundle nextResults = searchResults;
while (nextResults.getLink(Bundle.LINK_NEXT) != null) {
nextResults = fhirRestClient.loadPage().next(nextResults).execute();
List<Resource> nextResources = resultSplitter.splitBundle(nextResults);
writeData(dataFile, nextResources, serverBase, false);
numRecords += nextResources.size();
}
} finally {
if (authInterceptor != null) {
// unregister authorization interceptor with the client
fhirRestClient.unregisterInterceptor(authInterceptor);
}
}
return numRecords;
}
/**
* gets Patient from the server if existing. else creates a new one.
*
* @return
*/
private Patient getPatient() {
Log.d(TAG, "looking for patient");
Patient p =
this.newPatient(patient.getLastname(), patient.getFirstName(), patient.getDateOfBirth());
p.setText(getNarrative(p));
p.setIdentifier(
Arrays.asList(
new IdentifierDt()
.setSystem(SYSTEM_URL.concat("/patients/"))
.setValue(
patient
.getLastname()
.concat(patient.getFirstName())
.concat(
SimpleDateFormat.getDateInstance(DateFormat.SHORT)
.format(patient.getDateOfBirth())))));
IdDt patientId =
(IdDt)
client
.create()
.resource(p)
.conditionalByUrl(getConditionalUrl(p, p.getIdentifierFirstRep()))
.execute()
.getId();
p.setId(patientId);
return p;
}
@Test
public void testSearchByIdUsingClient() throws Exception {
IGenericClient client = ourCtx.newRestfulGenericClient("http://localhost:" + ourPort);
Bundle bundle =
client
.search()
.forResource("Patient")
.where(BaseResource.RES_ID.matches().value("aaa"))
.execute();
assertEquals(1, bundle.getEntries().size());
Patient p = bundle.getResources(Patient.class).get(0);
assertEquals("idaaa", p.getNameFirstRep().getFamilyAsSingleString());
assertEquals("IDAAA (identifier123)", bundle.getEntries().get(0).getTitle().getValue());
}
public void process(Bundle bundle) {
Bundle response = null;
RecordMatchResultsBuilder respBuilder;
if (BundleType.MESSAGE.equals(bundle.getType())) {
// Create a CSV data source for FRIL
final File jobDir = newRunDir(workDir);
final List<BundleEntryComponent> bundleEntries = bundle.getEntry();
try {
// The first entry is supposed to be the MessageHeader
// This will force an exception if not true.
final MessageHeader msgHdr = (MessageHeader) bundleEntries.get(0).getResource();
// This log statement keeps above from getting optimized out
LOG.trace("msg hdr id {}", msgHdr.getId());
Parameters masterQryParams = null;
Parameters queryQryParams = null;
String masterSearchUrl = null;
String querySearchUrl = null;
String masterServerBase = null;
String queryServerBase = null;
String resourceType = "Patient";
boolean isDeduplication = true;
// Find the Parameters resources that contain the search parameters
// and use those to construct search Urls
for (BundleEntryComponent entry : bundleEntries) {
Resource r = entry.getResource();
LOG.debug("Found Resource type: " + r.getResourceType().toString());
if (ResourceType.Parameters.equals(r.getResourceType())) {
Parameters params = (Parameters) r;
List<ParametersParameterComponent> paramList = params.getParameter();
// Now look for the parameter with name, resourceType.
ParametersParameterComponent p = ParametersUtil.findByName(paramList, RESOURCE_TYPE);
if (p != null) {
resourceType = p.getValue().toString();
}
// Find parameter that distinguishes between master and query sets
p = ParametersUtil.findByName(paramList, "type");
if (p != null) {
String val = p.getValue().toString();
if (val.equalsIgnoreCase(MASTER)) {
masterQryParams = params;
masterSearchUrl = buildSearchUrl(params);
masterServerBase = getServerBase(resourceType, masterQryParams);
} else if (val.equalsIgnoreCase(QUERY)) {
queryQryParams = params;
querySearchUrl = buildSearchUrl(params);
queryServerBase = getServerBase(resourceType, queryQryParams);
}
}
}
}
if (masterSearchUrl == null) {
final String errMsg =
"Required Parameter for master record set is missing, bundle: " + bundle.getId();
LOG.warn(errMsg);
// Construct and return an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
response = respBuilder.build();
getProducer().sendBody(getProducerEndpointUri(), response);
return;
}
LoggingInterceptor loggingInterceptor = null;
if (LOG.isDebugEnabled()) {
loggingInterceptor = new LoggingInterceptor(true);
fhirRestClient.registerInterceptor(loggingInterceptor);
}
int numMasterRecs = 0;
try {
// Retrieve the data associated with the search urls
numMasterRecs = retrieveAndStoreData(masterSearchUrl, masterServerBase, jobDir, "master");
if (querySearchUrl != null) {
isDeduplication = false;
retrieveAndStoreData(querySearchUrl, queryServerBase, jobDir, "query");
}
} catch (BaseServerResponseException e) {
final String errMsg =
String.format(
"Error response from server. code: %d, %s", e.getStatusCode(), e.getMessage());
LOG.warn(errMsg);
// Construct and return an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
response = respBuilder.build();
getProducer().sendBody(getProducerEndpointUri(), response);
return;
} catch (Exception e) {
final String errMsg = String.format("Unable to retrieve messages: %s", e.getMessage());
LOG.warn(errMsg, e);
// Construct and return an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
response = respBuilder.build();
getProducer().sendBody(getProducerEndpointUri(), response);
return;
} finally {
if (loggingInterceptor != null) {
fhirRestClient.unregisterInterceptor(loggingInterceptor);
}
}
// if no records were returned for the master record set query
if (numMasterRecs == 0) {
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.OK);
respBuilder.outcomeDetailText("No Records Found in Master Record Set");
response = respBuilder.build();
} else {
final File configFile = prepareMatchingRuleConfiguration(isDeduplication, jobDir);
// Perform the Match Operation
LOG.debug("About to Start FRIL w/ config {}", configFile.getAbsolutePath());
final int numMatches = findMatches(isDeduplication, configFile);
LOG.info("FRIL Number of Matches: {}", numMatches);
if (numMatches == 0) {
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.OK);
respBuilder.outcomeDetailText("No Matches Found");
response = respBuilder.build();
} else if (numMatches > 0) {
// Find the name of the file containing duplicates from the config
// file
final File dupsFile = getDuplicatesFile(configFile);
// Ensure the duplicates file exists
if (!dupsFile.exists()) {
final String errMsg = "Unable to find duplicates file";
LOG.error(errMsg + " at " + dupsFile.getAbsolutePath());
throw new FileNotFoundException(errMsg);
}
// Construct results
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.OK);
respBuilder.outcomeDetailText("Deduplication Complete");
respBuilder.duplicates(dupsFile);
response = respBuilder.build();
} else {
final String errMsg = "Unknown Processing Error";
LOG.error("{} bundleId: {}", errMsg, bundle.getId());
// Construct an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
response = respBuilder.build();
}
}
} catch (Exception e) {
final String errMsg = "Unexpected Error";
LOG.error("Processing bundle: {}", bundle.getId(), e);
// Construct an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
try {
response = respBuilder.build();
} catch (IOException ioe) {
// only so many times we can attempt to send a response; log error
LOG.error("Unable to Send Error Response. request bundle: {}", bundle.getId(), ioe);
}
}
if (deleteJobResults) {
// Delete the Job Results folder and content
deleteFolder(jobDir);
}
} else {
final String errMsg = "Unsupported Bundle type: " + bundle.getType().toString();
LOG.info("{} msgId: {}", errMsg, bundle.getId());
// Construct an error result
respBuilder = new RecordMatchResultsBuilder(bundle, ResponseType.FATALERROR);
respBuilder.outcomeIssueDiagnostics(errMsg);
try {
response = respBuilder.build();
} catch (IOException e) {
// only so many times we can attempt to send a response; log error
LOG.error("Unable to Send Error Response. request bundle: {}", bundle.getId());
}
}
// Send the response back to the requester
if (response != null) {
getProducer().sendBody(getProducerEndpointUri(), response);
} else {
LOG.error("Null Response for request! bundleId: {}", bundle.getId());
}
}
@SuppressWarnings({"unchecked", "rawtypes"})
@Before
public void before() throws Exception {
myFhirCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.NEVER);
myFhirCtx.getRestfulClientFactory().setSocketTimeout(1200 * 1000);
if (ourServer == null) {
ourPort = RandomServerPortProvider.findFreePort();
ourRestServer = new RestfulServer(myFhirCtx);
ourServerBase = "http://localhost:" + ourPort + "/fhir/context";
ourRestServer.setResourceProviders((List) myResourceProviders);
ourRestServer
.getFhirContext()
.setNarrativeGenerator(new DefaultThymeleafNarrativeGenerator());
myTerminologyUploaderProvider = myAppCtx.getBean(TerminologyUploaderProviderDstu3.class);
ourRestServer.setPlainProviders(mySystemProvider, myTerminologyUploaderProvider);
JpaConformanceProviderDstu3 confProvider =
new JpaConformanceProviderDstu3(ourRestServer, mySystemDao, myDaoConfig);
confProvider.setImplementationDescription("THIS IS THE DESC");
ourRestServer.setServerConformanceProvider(confProvider);
ourRestServer.setPagingProvider(myAppCtx.getBean(DatabaseBackedPagingProvider.class));
Server server = new Server(ourPort);
ServletContextHandler proxyHandler = new ServletContextHandler();
proxyHandler.setContextPath("/");
ServletHolder servletHolder = new ServletHolder();
servletHolder.setServlet(ourRestServer);
proxyHandler.addServlet(servletHolder, "/fhir/context/*");
ourWebApplicationContext = new GenericWebApplicationContext();
ourWebApplicationContext.setParent(myAppCtx);
ourWebApplicationContext.refresh();
// ContextLoaderListener loaderListener = new ContextLoaderListener(webApplicationContext);
// loaderListener.initWebApplicationContext(mock(ServletContext.class));
//
proxyHandler
.getServletContext()
.setAttribute(
WebApplicationContext.ROOT_WEB_APPLICATION_CONTEXT_ATTRIBUTE,
ourWebApplicationContext);
DispatcherServlet dispatcherServlet = new DispatcherServlet();
// dispatcherServlet.setApplicationContext(webApplicationContext);
dispatcherServlet.setContextClass(AnnotationConfigWebApplicationContext.class);
ServletHolder subsServletHolder = new ServletHolder();
subsServletHolder.setServlet(dispatcherServlet);
subsServletHolder.setInitParameter(
ContextLoader.CONFIG_LOCATION_PARAM, WebsocketDstu3Config.class.getName());
proxyHandler.addServlet(subsServletHolder, "/*");
// Register a CORS filter
CorsConfiguration config = new CorsConfiguration();
CorsInterceptor corsInterceptor = new CorsInterceptor(config);
config.addAllowedHeader("x-fhir-starter");
config.addAllowedHeader("Origin");
config.addAllowedHeader("Accept");
config.addAllowedHeader("X-Requested-With");
config.addAllowedHeader("Content-Type");
config.addAllowedHeader("Access-Control-Request-Method");
config.addAllowedHeader("Access-Control-Request-Headers");
config.addAllowedOrigin("*");
config.addExposedHeader("Location");
config.addExposedHeader("Content-Location");
config.setAllowedMethods(Arrays.asList("GET", "POST", "PUT", "DELETE", "OPTIONS"));
ourRestServer.registerInterceptor(corsInterceptor);
server.setHandler(proxyHandler);
server.start();
WebApplicationContext wac =
WebApplicationContextUtils.getWebApplicationContext(
subsServletHolder.getServlet().getServletConfig().getServletContext());
myValidationSupport = wac.getBean(JpaValidationSupportChainDstu3.class);
ourClient = myFhirCtx.newRestfulGenericClient(ourServerBase);
ourClient.registerInterceptor(new LoggingInterceptor(true));
PoolingHttpClientConnectionManager connectionManager =
new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourHttpClient = builder.build();
ourServer = server;
}
}
public static void establishScene() {
initScrollData();
Main.hLeft = new VBox(20);
Main.hLeft.setEffect(new DropShadow());
Main.hLeft.setAlignment(Pos.CENTER);
Main.hLeft.setBackground(new Background(Main.myBG));
Main.hLeft.setMinHeight(Main.height);
Main.hLeft.setMinWidth(Main.width / 2 - 100);
Main.hRight = new VBox(18);
Main.hRight.setAlignment(Pos.TOP_CENTER);
Main.hRight.setMinHeight(Main.height);
Main.hRight.setMinWidth(Main.width / 2 + 100);
Main.hRight.setPadding(new Insets(20, 0, 0, 20));
// Create Dividers
VBox stats = new VBox(10);
stats.setAlignment(Pos.CENTER);
// Patient Portal
Image pp = new Image("file:src/docketdoc/res/PD_Logo.png");
ImageView pap = new ImageView(pp);
VBox patientPortal = new VBox();
patientPortal.setAlignment(Pos.CENTER);
patientPortal.setPadding(new Insets(10, 10, 10, 10));
// Label
Label lp = new Label("Patient Portal");
lp.setStyle("-fx-font: 25px Futura;" + "-fx-text-fill: #66CDAA;");
patientPortal.getChildren().addAll(pap, lp);
// Search Patient
TextField searchTF = new TextField();
searchTF.setStyle(
"-fx-max-height: 50px;"
+ "-fx-max-width: 200px;"
+ "-fx-text-fill: #505050;"
+ "-fx-font: 12px Futura;"
+ "-fx-prompt-text-fill: #505050;");
searchTF.setPromptText("First Name");
TextField searchTFlast = new TextField();
searchTFlast.setStyle(
"-fx-max-height: 50px;"
+ "-fx-max-width: 200px;"
+ "-fx-text-fill: #505050;"
+ "-fx-font: 12px Futura;"
+ "-fx-prompt-text-fill: #505050;");
searchTFlast.setPromptText("Last Name");
// Interact Button
Button searchName = new Button("Search Name");
searchName.setStyle(
"-fx-background-radius: 0;"
+ "-fx-font: 16px Futura;"
+ "-fx-font-weight: bold;"
+ "-fx-text-fill: white;"
+ "-fx-background-color: #FF7F50;");
// Hover animation.
searchName.setOnMouseEntered(
e -> {
searchName.setOpacity(.5);
});
searchName.setOnMouseExited(
e -> {
searchName.setOpacity(2);
});
// Button Search for Name
searchName.setOnAction(
e -> {
/* ------------------------------------ */
/* Search patiend directory by FHIR API */
/* ------------------------------------ */
new FhirContext();
// Create a client (only needed once)
FhirContext ctx = FhirContext.forDstu2();
IGenericClient client =
ctx.newRestfulGenericClient("http://fhir2.healthintersections.com.au/open");
String search = new String(searchTF.getText() + " " + searchTFlast.getText());
// Invoke the client
Bundle bundle =
client
.search()
.forResource(Patient.class)
.where(Patient.NAME.matchesExactly().value(search))
.encodedJson()
.execute();
System.out.println("patients count=" + bundle.size());
List<Patient> list = bundle.getResources(Patient.class);
for (Patient p : list) {
namess = p.getNameFirstRep().getText();
agess = p.getBirthDateElement().toHumanDisplay();
sexess = p.getGender();
}
// Add to grid then display
// Update Name
nameShow = new Label(namess.toUpperCase());
namePat.getChildren().remove(nameShow);
patientData.getChildren().remove(namePat);
nameShow.setStyle("-fx-font: 15px Futura;" + "-fx-text-fill: #ff0080;");
namePat.getChildren().addAll(nameShow);
patientData.getChildren().add(namePat);
// Update Age
ageShow = new Label(agess.toUpperCase());
agePat.getChildren().remove(ageShow);
patientData.getChildren().remove(agePat);
ageShow.setStyle("-fx-font: 15px Futura;" + "-fx-text-fill: #ff0080;");
agePat.getChildren().addAll(ageShow);
patientData.getChildren().add(agePat);
// Update Sex
sexShow = new Label(sexess.toUpperCase());
sexPat.getChildren().remove(sexShow);
patientData.getChildren().remove(sexPat);
sexShow.setStyle("-fx-font: 15px Futura;" + "-fx-text-fill: #ff0080;");
sexPat.getChildren().addAll(sexShow);
patientData.getChildren().add(sexPat);
addScrollData();
searchTF.setText(null);
searchTFlast.setText(null);
});
/* ----------------------------------------- */
/* Right Side contained within a scroll Pane */
/* ----------------------------------------- */
patientData = new VBox(10);
// Name Divisors
pname = new Label("NAME:\t");
pname.setStyle("-fx-font: 15px Futura;" + "-fx-text-fill: #66CDAA;" + "-fx-font-weight: bold;");
namePat = new HBox(10);
namePat.getChildren().addAll(pname, nameShow);
// Age Divisors
page = new Label("DOB:\t");
page.setStyle("-fx-font: 15px Futura;" + "-fx-text-fill: #66CDAA;" + "-fx-font-weight: bold;");
agePat = new HBox(10);
agePat.getChildren().addAll(page, ageShow);
// Gender Divisors
psex = new Label("SEX:\t\t");
psex.setStyle("-fx-font: 15px Futura;" + "-fx-text-fill: #66CDAA;" + "-fx-font-weight: bold;");
sexPat = new HBox(10);
sexPat.getChildren().addAll(psex, sexShow);
patientData.getChildren().addAll(namePat, agePat, sexPat);
// Scrolls
scrollSocial.setContent(soScroll);
scrollMedical.setContent(medScroll);
scrollHistory.setContent(hisScroll);
// Add search results to right side
Main.hRight.getChildren().addAll(patientData, scrollMedical, scrollSocial, hisScroll);
// Add elements to Left Side
stats.getChildren().addAll(patientPortal, searchTF, searchTFlast, searchName);
// Set Main stage to home scene
Main.hLeft.getChildren().addAll(stats);
Main.containHome = new HBox();
Main.containHome.getChildren().addAll(Main.hLeft, Main.hRight);
Main.homeScene = new Scene(Main.containHome);
}