package ca.uhn.fhir.narrative;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import java.util.Date;
import org.hamcrest.core.StringContains;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.TemporalPrecisionEnum;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.NarrativeDt;
import ca.uhn.fhir.model.dstu2.composite.PeriodDt;
import ca.uhn.fhir.model.dstu2.composite.QuantityDt;
import ca.uhn.fhir.model.dstu2.composite.ResourceReferenceDt;
import ca.uhn.fhir.model.dstu2.composite.SimpleQuantityDt;
import ca.uhn.fhir.model.dstu2.resource.DiagnosticReport;
import ca.uhn.fhir.model.dstu2.resource.Encounter;
import ca.uhn.fhir.model.dstu2.resource.Medication;
import ca.uhn.fhir.model.dstu2.resource.MedicationOrder;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.model.dstu2.resource.OperationOutcome;
import ca.uhn.fhir.model.dstu2.resource.Parameters;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.dstu2.valueset.DiagnosticReportStatusEnum;
import ca.uhn.fhir.model.dstu2.valueset.EncounterClassEnum;
import ca.uhn.fhir.model.dstu2.valueset.MedicationOrderStatusEnum;
import ca.uhn.fhir.model.dstu2.valueset.ObservationStatusEnum;
import ca.uhn.fhir.model.primitive.DateTimeDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.util.TestUtil;
public class DefaultThymeleafNarrativeGeneratorDstu2Test {
private static FhirContext ourCtx = FhirContext.forDstu2();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(DefaultThymeleafNarrativeGeneratorDstu2Test.class);
private DefaultThymeleafNarrativeGenerator myGen;
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Before
public void before() {
myGen = new DefaultThymeleafNarrativeGenerator();
myGen.setUseHapiServerConformanceNarrative(true);
myGen.setIgnoreFailures(false);
myGen.setIgnoreMissingTemplates(false);
ourCtx.setNarrativeGenerator(myGen);
}
@Test
public void testGeneratePatient() throws DataFormatException {
Patient value = new Patient();
value.addIdentifier().setSystem("urn:names").setValue("123456");
value.addName().addFamily("blow").addGiven("joe").addGiven((String) null).addGiven("john");
value.getAddressFirstRep().addLine("123 Fake Street").addLine("Unit 1");
value.getAddressFirstRep().setCity("Toronto").setState("ON").setCountry("Canada");
value.setBirthDate(new Date(), TemporalPrecisionEnum.DAY);
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(ourCtx, value, narrative);
String output = narrative.getDiv().getValueAsString();
ourLog.info(output);
assertThat(output, StringContains.containsString("<div class=\"hapiHeaderText\">joe john <b>BLOW </b></div>"));
}
@Test
public void testUnsupportedType() throws DataFormatException {
myGen.setIgnoreMissingTemplates(true);
Parameters value = new Parameters();
value.setId("123");
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(ourCtx, value, narrative);
String output = narrative.getDiv().getValueAsString();
ourLog.info(output);
assertThat(output, not(containsString("narrative")));
}
@Test(expected=DataFormatException.class)
public void testUnsupportedTypeDontIgnore() throws DataFormatException {
myGen.setIgnoreMissingTemplates(false);
Parameters value = new Parameters();
value.setId("123");
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(ourCtx, value, narrative);
}
@Test
@Ignore
public void testGenerateEncounter() throws DataFormatException {
Encounter enc = new Encounter();
enc.addIdentifier().setSystem("urn:visits").setValue("1234567");
enc.setClassElement(EncounterClassEnum.AMBULATORY);
enc.setPeriod(new PeriodDt().setStart(new DateTimeDt("2001-01-02T11:11:00")));
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(ourCtx, enc, narrative);
assertEquals("", narrative.getDivAsString());
}
@Test
public void testGenerateOperationOutcome() {
//@formatter:off
String parse = "<OperationOutcome xmlns=\"http://hl7.org/fhir\">\n" +
" <issue>\n" +
" <severity value=\"error\"/>\n" +
" <diagnostics value=\"ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method
ca.uhn.fhir.rest.server.exceptions.InternalErrorException: Failed to call access method
at ca.uhn.fhir.rest.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:199)
at ca.uhn.fhir.rest.method.HistoryMethodBinding.invokeServer(HistoryMethodBinding.java:162)
at ca.uhn.fhir.rest.method.BaseResourceReturningMethodBinding.invokeServer(BaseResourceReturningMethodBinding.java:228)
at ca.uhn.fhir.rest.method.HistoryMethodBinding.invokeServer(HistoryMethodBinding.java:1)
at ca.uhn.fhir.rest.server.RestfulServer.handleRequest(RestfulServer.java:534)
at ca.uhn.fhir.rest.server.RestfulServer.doGet(RestfulServer.java:141)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:687)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:790)
at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.ebaysf.web.cors.CORSFilter.handleNonCORS(CORSFilter.java:437)
at org.ebaysf.web.cors.CORSFilter.doFilter(CORSFilter.java:172)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:357)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:260)
at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:188)
at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:191)
at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:168)
at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:189)
at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:288)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:206)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:136)
at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:114)
at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:838)
at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:113)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:115)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:55)
at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:135)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:564)
at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:544)
at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.reflect.InvocationTargetException
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at ca.uhn.fhir.rest.method.BaseMethodBinding.invokeServerMethod(BaseMethodBinding.java:194)
... 40 more
Caused by: java.lang.NumberFormatException: For input string: "3cb9a027-9e02-488d-8d01-952553d6be4e"
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Long.parseLong(Long.java:441)
at java.lang.Long.parseLong(Long.java:483)
at ca.uhn.fhir.model.primitive.IdDt.getIdPartAsLong(IdDt.java:194)
at ca.uhn.fhir.jpa.provider.JpaResourceProvider.getHistoryForResourceInstance(JpaResourceProvider.java:81)
... 45 more
\"/>\n" +
" </issue>\n" +
" <issue>\n" +
" <severity value=\"warning\"/>\n" +
" <diagnostics value=\"YThis is a warning\"/>\n" +
" </issue>\n" +
"</OperationOutcome>";
//@formatter:on
OperationOutcome oo = ourCtx.newXmlParser().parseResource(OperationOutcome.class, parse);
// String output = gen.generateTitle(oo);
// ourLog.info(output);
// assertEquals("Operation Outcome (2 issues)", output);
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(ourCtx, oo, narrative);
String output = narrative.getDiv().getValueAsString();
ourLog.info(output);
assertThat(output, containsString("<td><pre>YThis is a warning</pre></td>"));
}
@Test
public void testGenerateDiagnosticReportWithObservations() throws DataFormatException {
DiagnosticReport value = new DiagnosticReport();
value.getIssuedElement().setValueAsString("2011-02-22T11:13:00");
value.setStatus(DiagnosticReportStatusEnum.FINAL);
value.getCode().setText("Some & Diagnostic Report");
{
Observation obs = new Observation();
obs.getCode().addCoding().setCode("1938HB").setDisplay("Hemoglobin");
obs.setValue(new QuantityDt(null, 2.223, "mg/L"));
obs.addReferenceRange().setLow(new SimpleQuantityDt(2.20)).setHigh(new SimpleQuantityDt(2.99));
obs.setStatus(ObservationStatusEnum.FINAL);
obs.setComments("This is a result comment");
ResourceReferenceDt result = value.addResult();
result.setResource(obs);
}
{
Observation obs = new Observation();
obs.setValue(new StringDt("HELLO!"));
value.addResult().setResource(obs);
}
{
Observation obs = new Observation();
obs.setCode(new CodeableConceptDt("AA", "BB"));
value.addResult().setResource(obs);
}
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(ourCtx, value, narrative);
String output = narrative.getDiv().getValueAsString();
ourLog.info(output);
assertThat(output, StringContains.containsString("<div class=\"hapiHeaderText\"> Some & Diagnostic Report </div>"));
// Now try it with the parser
output = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(value);
ourLog.info(output);
assertThat(output, StringContains.containsString("<div class=\"hapiHeaderText\"> Some & Diagnostic Report </div>"));
}
@Test
@Ignore
public void testGenerateMedicationPrescription() {
MedicationOrder mp = new MedicationOrder();
mp.setId("12345");
Medication med = new Medication();
med.getCode().setText("ciproflaxin");
ResourceReferenceDt medRef = new ResourceReferenceDt(med);
mp.setMedication(medRef);
mp.setStatus(MedicationOrderStatusEnum.ACTIVE);
mp.setDateWritten(new DateTimeDt("2014-09-01"));
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(ourCtx, mp, narrative);
assertTrue("Expected medication name of ciprofloaxin within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ciprofloaxin") > -1);
assertTrue("Expected string status of ACTIVE within narrative: " + narrative.getDiv().toString(), narrative.getDiv().toString().indexOf("ACTIVE") > -1);
}
@Test
public void testGenerateMedication() {
Medication med = new Medication();
med.getCode().setText("ciproflaxin");
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(ourCtx, med, narrative);
String string = narrative.getDiv().toString();
assertThat(string, containsString("ciproflaxin"));
}
}