@Test
public void testTwoInclude() throws Exception {
HttpGet httpGet =
new HttpGet(
"http://localhost:"
+ ourPort
+ "/Patient?name=Hello&_include=foo&_include=bar&_pretty=true");
HttpResponse status = ourClient.execute(httpGet);
String responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
ourLog.info(responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
assertEquals(1, bundle.size());
Patient p = bundle.getResources(Patient.class).get(0);
assertEquals(2, p.getName().size());
assertEquals("Hello", p.getId().getIdPart());
Set<String> values = new HashSet<String>();
values.add(p.getName().get(0).getFamilyFirstRep().getValue());
values.add(p.getName().get(1).getFamilyFirstRep().getValue());
assertThat(values, containsInAnyOrder("foo", "bar"));
}
@Test
public void testIIncludedResourcesNonContainedInExtensionJson() throws Exception {
HttpGet httpGet =
new HttpGet(
"http://localhost:" + ourPort + "/Patient?_query=extInclude&_pretty=true&_format=json");
HttpResponse status = ourClient.execute(httpGet);
String responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(200, status.getStatusLine().getStatusCode());
Bundle bundle = ourCtx.newJsonParser().parseBundle(responseContent);
ourLog.info(responseContent);
assertEquals(3, bundle.size());
assertEquals(
new IdDt("Patient/p1"),
bundle.toListOfResources().get(0).getId().toUnqualifiedVersionless());
assertEquals(
new IdDt("Patient/p2"),
bundle.toListOfResources().get(1).getId().toUnqualifiedVersionless());
assertEquals(
new IdDt("Organization/o1"),
bundle.toListOfResources().get(2).getId().toUnqualifiedVersionless());
assertEquals(
BundleEntrySearchModeEnum.INCLUDE,
bundle.getEntries().get(2).getSearchMode().getValueAsEnum());
Patient p1 = (Patient) bundle.toListOfResources().get(0);
assertEquals(0, p1.getContained().getContainedResources().size());
Patient p2 = (Patient) bundle.toListOfResources().get(1);
assertEquals(0, p2.getContained().getContainedResources().size());
}
@Test
public void testSchematronResourceValidator() throws IOException {
String res =
IOUtils.toString(
getClass().getClassLoader().getResourceAsStream("patient-example-dicom.json"));
Patient p = ourCtx.newJsonParser().parseResource(Patient.class, res);
FhirValidator val = ourCtx.newValidator();
val.setValidateAgainstStandardSchema(false);
val.setValidateAgainstStandardSchematron(true);
ValidationResult validationResult = val.validateWithResult(p);
assertTrue(validationResult.isSuccessful());
p.getTelecomFirstRep().setValue("123-4567");
validationResult = val.validateWithResult(p);
assertFalse(validationResult.isSuccessful());
OperationOutcome operationOutcome = (OperationOutcome) validationResult.toOperationOutcome();
ourLog.info(
ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome));
assertEquals(1, operationOutcome.getIssue().size());
assertThat(operationOutcome.getIssueFirstRep().getDiagnostics(), containsString("cpt-2:"));
p.getTelecomFirstRep().setSystem(ContactPointSystemEnum.EMAIL);
validationResult = val.validateWithResult(p);
assertTrue(validationResult.isSuccessful());
}
@Test
public void testTransaction() throws Exception {
String retVal = ourCtx.newXmlParser().encodeBundleToString(new Bundle());
ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
when(ourHttpClient.execute(capt.capture())).thenReturn(ourHttpResponse);
when(ourHttpResponse.getStatusLine())
.thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
when(ourHttpResponse.getEntity().getContentType())
.thenReturn(new BasicHeader("content-type", Constants.CT_ATOM_XML + "; charset=UTF-8"));
when(ourHttpResponse.getEntity().getContent())
.thenReturn(new ReaderInputStream(new StringReader(retVal), Charset.forName("UTF-8")));
Patient p1 = new Patient();
p1.addIdentifier().setSystem("urn:system").setValue("value");
IGenericClient client = ourCtx.newRestfulGenericClient("http://foo");
client.transaction().withResources(Arrays.asList((IBaseResource) p1)).execute();
HttpUriRequest value = capt.getValue();
assertTrue("Expected request of type POST on long params list", value instanceof HttpPost);
HttpPost post = (HttpPost) value;
String body = IOUtils.toString(post.getEntity().getContent());
IOUtils.closeQuietly(post.getEntity().getContent());
ourLog.info(body);
assertThat(
body, Matchers.containsString("<type value=\"" + BundleTypeEnum.TRANSACTION.getCode()));
}
/**
* 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;
}
@SuppressWarnings("deprecation")
@Test
public void testSchemaResourceValidator() throws IOException {
String res =
IOUtils.toString(
getClass().getClassLoader().getResourceAsStream("patient-example-dicom.json"));
Patient p = ourCtx.newJsonParser().parseResource(Patient.class, res);
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p));
FhirValidator val = ourCtx.newValidator();
val.setValidateAgainstStandardSchema(true);
val.setValidateAgainstStandardSchematron(false);
val.validate(p);
p.getAnimal().getBreed().setText("The Breed");
try {
val.validate(p);
fail();
} catch (ValidationFailureException e) {
OperationOutcome operationOutcome = (OperationOutcome) e.getOperationOutcome();
ourLog.info(
ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(operationOutcome));
assertEquals(1, operationOutcome.getIssue().size());
assertThat(
operationOutcome.getIssueFirstRep().getDetailsElement().getValue(),
containsString("cvc-complex-type"));
}
}
/** See issue #50 */
@Test
public void testOutOfBoundsDate() {
Patient p = new Patient();
p.setBirthDate(new DateDt("2000-15-31"));
String encoded = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(encoded);
assertThat(encoded, StringContains.containsString("2000-15-31"));
p = ourCtx.newXmlParser().parseResource(Patient.class, encoded);
assertEquals("2000-15-31", p.getBirthDateElement().getValueAsString());
assertEquals("2001-03-31", new SimpleDateFormat("yyyy-MM-dd").format(p.getBirthDate()));
ValidationResult result = ourCtx.newValidator().validateWithResult(p);
String resultString =
ourCtx
.newXmlParser()
.setPrettyPrint(true)
.encodeResourceToString(result.toOperationOutcome());
ourLog.info(resultString);
assertEquals(2, ((OperationOutcome) result.toOperationOutcome()).getIssue().size());
assertThat(resultString, StringContains.containsString("2000-15-31"));
}
private Patient newPatient(String familyName, String givenName, Date date) {
Log.d(TAG, "creating new patient");
Patient p = new Patient();
p.addName().addFamily(familyName).addGiven(givenName);
p.setBirthDate(new DateDt(date));
return p;
}
@Search()
public Patient search(@Elements Set<String> theElements) {
ourLastElements = theElements;
Patient patient = new Patient();
patient.setId("Patient/1/_history/1");
patient.getText().setDiv("<div>THE DIV</div>");
patient.addName().addFamily("FAMILY");
patient.setMaritalStatus(MaritalStatusCodesEnum.D);
return patient;
}
@Test
public void testForceConformanceCheck() throws Exception {
Conformance conf = new Conformance();
conf.setFhirVersion("0.5.0");
final String confResource = myCtx.newXmlParser().encodeResourceToString(conf);
ArgumentCaptor<HttpUriRequest> capt = ArgumentCaptor.forClass(HttpUriRequest.class);
when(myHttpResponse.getStatusLine())
.thenReturn(new BasicStatusLine(new ProtocolVersion("HTTP", 1, 1), 200, "OK"));
when(myHttpResponse.getEntity().getContentType())
.thenReturn(new BasicHeader("content-type", Constants.CT_FHIR_XML + "; charset=UTF-8"));
when(myHttpResponse.getEntity().getContent())
.thenAnswer(
new Answer<InputStream>() {
@Override
public InputStream answer(InvocationOnMock theInvocation) throws Throwable {
if (myFirstResponse) {
myFirstResponse = false;
return new ReaderInputStream(
new StringReader(confResource), Charset.forName("UTF-8"));
} else {
Patient resource = new Patient();
resource.addName().addFamily().setValue("FAM");
return new ReaderInputStream(
new StringReader(myCtx.newXmlParser().encodeResourceToString(resource)),
Charset.forName("UTF-8"));
}
}
});
when(myHttpClient.execute(capt.capture())).thenReturn(myHttpResponse);
myCtx.getRestfulClientFactory().setServerValidationMode(ServerValidationModeEnum.ONCE);
IGenericClient client = myCtx.newRestfulGenericClient("http://foo");
client.registerInterceptor(new BasicAuthInterceptor("USER", "PASS"));
client.forceConformanceCheck();
assertEquals(1, capt.getAllValues().size());
Patient pt = (Patient) client.read(new UriDt("http://foo/Patient/123"));
assertEquals("FAM", pt.getNameFirstRep().getFamilyAsSingleString());
assertEquals(2, capt.getAllValues().size());
Header auth = capt.getAllValues().get(0).getFirstHeader("Authorization");
assertNotNull(auth);
assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
auth = capt.getAllValues().get(1).getFirstHeader("Authorization");
assertNotNull(auth);
assertEquals("Basic VVNFUjpQQVNT", auth.getValue());
}
@Test
public void testNoIncludes() throws Exception {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient?name=Hello");
HttpResponse status = ourClient.execute(httpGet);
String responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(200, status.getStatusLine().getStatusCode());
Bundle bundle = ourCtx.newXmlParser().parseBundle(responseContent);
assertEquals(1, bundle.size());
Patient p = bundle.getResources(Patient.class).get(0);
assertEquals(0, p.getName().size());
assertEquals("Hello", p.getId().getIdPart());
}
private Device initializeDevice(Patient p) {
log("Initializing device");
Device d = newDevice();
d.setManufacturer(deviceInfo.getManufacturerName());
d.setModel(deviceInfo.getModelNumber());
d.setVersion(deviceInfo.getFirmwareRevision());
NarrativeDt n = getNarrative(d);
n.setDiv(
n.getDiv()
.getValueAsString()
.substring(5, n.getDiv().getValueAsString().length() - 6)
.concat("<strong>Serial Number: </strong>")
.concat(deviceInfo.getSerialNumber())
.concat("<br /><strong>Name: </strong>")
.concat(deviceInfo.getName())
.concat("<br /><strong>MAC Address: </strong>")
.concat(deviceInfo.getAddress()));
d.setText(n);
CodeableConceptDt type = new CodeableConceptDt();
// TODO find valid url
type.addCoding()
.setCode("15-102")
.setDisplay("Glukose-Analysegerät")
.setSystem("http://umdns.org");
d.setType(type);
d.setPatient(newResourceReference(p.getId()));
d.setIdentifier(Arrays.asList(getIdentifier("/devices/", "" + deviceInfo.getSysID())));
log("Initializing device done");
return d;
}
/**
* @notice In Fhir model, {@link Patient} has a collection of names, while in this extension
* table, {@link PersonComplement}, there is only one name for each {@link Person}.
*/
@Override
public IResourceEntity constructEntityFromResource(IResource resource) {
super.constructEntityFromResource(resource);
if (resource instanceof Patient) {
Patient patient = (Patient) resource;
Iterator<HumanNameDt> iterator = patient.getName().iterator();
// while(iterator.hasNext()){
if (iterator.hasNext()) {
HumanNameDt next = iterator.next();
this.givenName1 =
next.getGiven()
.get(0)
.getValue(); // the next method was not advancing to the next element, then the need
// to use the get(index) method
if (next.getGiven().size()
> 1) // TODO add unit tests, to assure this won't be changed to hasNext
this.givenName2 = next.getGiven().get(1).getValue();
Iterator<StringDt> family = next.getFamily().iterator();
this.familyName = "";
while (family.hasNext()) {
this.familyName = this.familyName.concat(family.next().getValue() + " ");
}
if (next.getSuffix().iterator().hasNext())
this.suffixName = next.getSuffix().iterator().next().getValue();
if (next.getPrefix().iterator().hasNext())
this.prefixName = next.getPrefix().iterator().next().getValue();
}
// }
this.active = patient.getActive();
// MARITAL STATUS
//
// this.maritalStatus.setId(OmopConceptMapping.getInstance().get(OmopConceptMapping.MARITAL_STATUS, patient.getMaritalStatus().getText()));
} else {
ourLog.error(
"There was not possible to construct the entity ? using the resource ?. It should be used the resource ?.",
this.getClass().getSimpleName(),
resource.getResourceName(),
getResourceType());
}
return this;
}
@Override
public Patient getRelatedResource() {
Patient patient = (Patient) super.getRelatedResource();
patient.addName().addFamily(this.familyName).addGiven(this.givenName1);
if (this.givenName2 != null) patient.getName().get(0).addGiven(this.givenName2);
boolean active = this.active != null ? this.active : false;
patient.setActive(active);
// MARITAL STATUS
// MaritalStatusCodesEnum[] values = MaritalStatusCodesEnum.values();
// for (int i = 0; i < values.length; i++) {
// if(values[i].equals(this.maritalStatus.getName())){
// patient.setMaritalStatus(values[i]);
// break;
// }
// }
// or patient.setMaritalStatus(MaritalStatusCodesEnum.valueOf(""));
return patient;
}
@Search
public List<Patient> findPatient(
@RequiredParam(name = Patient.SP_NAME) StringDt theName,
@IncludeParam(allow = {"foo", "bar"}) Set<Include> theIncludes) {
ArrayList<Patient> retVal = new ArrayList<Patient>();
Patient p = new Patient();
p.addIdentifier().setSystem("foo").setValue("bar");
p.setId(theName.getValue());
if (theIncludes != null) {
for (Include next : theIncludes) {
p.addName().addFamily().setValue(next.getValue());
}
}
retVal.add(p);
return retVal;
}
@Test
public void testOneIncludeJson() throws Exception {
HttpGet httpGet =
new HttpGet(
"http://localhost:" + ourPort + "/Patient?name=Hello&_include=foo&_format=json");
HttpResponse status = ourClient.execute(httpGet);
String responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(200, status.getStatusLine().getStatusCode());
ourLog.info(responseContent);
Bundle bundle = ourCtx.newJsonParser().parseBundle(responseContent);
assertEquals(1, bundle.size());
Patient p = bundle.getResources(Patient.class).get(0);
assertEquals(1, p.getName().size());
assertEquals("Hello", p.getId().getIdPart());
assertEquals("foo", p.getName().get(0).getFamilyFirstRep().getValue());
}
@Search(queryName = "containedInclude")
public List<Patient> containedInclude() {
Organization o1 = new Organization();
o1.getNameElement().setValue("o1");
Patient p1 = new Patient();
p1.setId("p1");
p1.addIdentifier().setValue("p1");
p1.getManagingOrganization().setResource(o1);
Patient p2 = new Patient();
p2.setId("p2");
p2.addIdentifier().setValue("p2");
p2.getManagingOrganization().setResource(o1);
return Arrays.asList(p1, p2);
}
@Search(queryName = "extInclude")
public List<Patient> extInclude() {
Organization o1 = new Organization();
o1.getNameElement().setValue("o1");
o1.setId("o1");
Patient p1 = new Patient();
p1.setId("p1");
p1.addIdentifier().setValue("p1");
p1.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
Patient p2 = new Patient();
p2.setId("p2");
p2.addIdentifier().setValue("p2");
p2.addUndeclaredExtension(false, "http://foo", new ResourceReferenceDt(o1));
return Arrays.asList(p1, p2);
}
private Observation initializeObservation(
Patient p, DeviceMetric metric, GlucoseRecord r, QuantityDt qdt) {
log("Initializing observation");
Observation o = newObservation(qdt);
o.setCode(createCode(r.unit));
o.setSubject(newResourceReference(p.getId()));
o.setDevice(newResourceReference(metric.getId()));
// set date and time for observation
DateTimeDt dt = new DateTimeDt();
dt.setValue(r.time.getTime());
o.setEffective(dt);
o.setIdentifier(
Arrays.asList(
getIdentifier(
"/devices/".concat("" + deviceInfo.getSysID()), "" + r.getSequenceNumber())));
// set narrative
o.setText(getNarrative(o));
log("Initializing observation done");
return o;
}
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);
}
