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Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
jamesagnew 2018-02-02 13:20:09 -05:00
parent 351a2fc2f1 efc812bf56
commit 371be03b0f
5 changed files with 414 additions and 137 deletions
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6
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParameterUtil.java
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@ -192,10 +192,10 @@ public class ParameterUtil {
} }
public static Object fromInteger(Class<?> theType, IntegerDt theArgument) { public static Object fromInteger(Class<?> theType, IntegerDt theArgument) {
if (theArgument == null) {
return null;
}
if (theType.equals(Integer.class)) { if (theType.equals(Integer.class)) {
if (theArgument == null) {
return null;
}
return theArgument.getValue(); return theArgument.getValue();
} }
IPrimitiveType<?> retVal = (IPrimitiveType<?>) ReflectionUtil.newInstance(theType); IPrimitiveType<?> retVal = (IPrimitiveType<?>) ReflectionUtil.newInstance(theType);

268
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/Enumeration.java
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@ -1,134 +1,134 @@
package org.hl7.fhir.dstu3.model; package org.hl7.fhir.dstu3.model;
import java.io.IOException; import java.io.IOException;
import java.io.ObjectInput; import java.io.ObjectInput;
import java.io.ObjectOutput; import java.io.ObjectOutput;
import org.hl7.fhir.instance.model.api.IBaseEnumeration; import org.hl7.fhir.instance.model.api.IBaseEnumeration;
import ca.uhn.fhir.model.api.annotation.DatatypeDef; import ca.uhn.fhir.model.api.annotation.DatatypeDef;
/* /*
Copyright (c) 2011+, HL7, Inc Copyright (c) 2011+, HL7, Inc
All rights reserved. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met: are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this * Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer. list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice, * Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution. and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to * Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific endorse or promote products derived from this software without specific
prior written permission. prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE. POSSIBILITY OF SUCH DAMAGE.
*/ */
/** /**
* Primitive type "code" in FHIR, where the code is tied to an enumerated list of possible values * Primitive type "code" in FHIR, where the code is tied to an enumerated list of possible values
* *
*/ */
@DatatypeDef(name = "code", isSpecialization = true) @DatatypeDef(name = "code", isSpecialization = true)
public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements IBaseEnumeration<T> { public class Enumeration<T extends Enum<?>> extends PrimitiveType<T> implements IBaseEnumeration<T> {
private static final long serialVersionUID = 1L; private static final long serialVersionUID = 1L;
private EnumFactory<T> myEnumFactory; private EnumFactory<T> myEnumFactory;
/** /**
* Constructor * Constructor
* *
* @deprecated This no-arg constructor is provided for serialization only - Do not use * @deprecated This no-arg constructor is provided for serialization only - Do not use
*/ */
@Deprecated @Deprecated
public Enumeration() { public Enumeration() {
// nothing super();
} }
/** /**
* Constructor * Constructor
*/ */
public Enumeration(EnumFactory<T> theEnumFactory) { public Enumeration(EnumFactory<T> theEnumFactory) {
if (theEnumFactory == null) if (theEnumFactory == null)
throw new IllegalArgumentException("An enumeration factory must be provided"); throw new IllegalArgumentException("An enumeration factory must be provided");
myEnumFactory = theEnumFactory; myEnumFactory = theEnumFactory;
} }
/** /**
* Constructor * Constructor
*/ */
public Enumeration(EnumFactory<T> theEnumFactory, String theValue) { public Enumeration(EnumFactory<T> theEnumFactory, String theValue) {
if (theEnumFactory == null) if (theEnumFactory == null)
throw new IllegalArgumentException("An enumeration factory must be provided"); throw new IllegalArgumentException("An enumeration factory must be provided");
myEnumFactory = theEnumFactory; myEnumFactory = theEnumFactory;
setValueAsString(theValue); setValueAsString(theValue);
} }
/** /**
* Constructor * Constructor
*/ */
public Enumeration(EnumFactory<T> theEnumFactory, T theValue) { public Enumeration(EnumFactory<T> theEnumFactory, T theValue) {
if (theEnumFactory == null) if (theEnumFactory == null)
throw new IllegalArgumentException("An enumeration factory must be provided"); throw new IllegalArgumentException("An enumeration factory must be provided");
myEnumFactory = theEnumFactory; myEnumFactory = theEnumFactory;
setValue(theValue); setValue(theValue);
} }
@Override @Override
public Enumeration<T> copy() { public Enumeration<T> copy() {
return new Enumeration<T>(myEnumFactory, getValue()); return new Enumeration<T>(myEnumFactory, getValue());
} }
@Override @Override
protected String encode(T theValue) { protected String encode(T theValue) {
return myEnumFactory.toCode(theValue); return myEnumFactory.toCode(theValue);
} }
public String fhirType() { public String fhirType() {
return "code"; return "code";
} }
/** /**
* Provides the enum factory which binds this enumeration to a specific ValueSet * Provides the enum factory which binds this enumeration to a specific ValueSet
*/ */
public EnumFactory<T> getEnumFactory() { public EnumFactory<T> getEnumFactory() {
return myEnumFactory; return myEnumFactory;
} }
@Override @Override
protected T parse(String theValue) { protected T parse(String theValue) {
if (myEnumFactory != null) { if (myEnumFactory != null) {
return myEnumFactory.fromCode(theValue); return myEnumFactory.fromCode(theValue);
} }
return null; return null;
} }
@SuppressWarnings("unchecked") @SuppressWarnings("unchecked")
@Override @Override
public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException { public void readExternal(ObjectInput theIn) throws IOException, ClassNotFoundException {
myEnumFactory = (EnumFactory<T>) theIn.readObject(); myEnumFactory = (EnumFactory<T>) theIn.readObject();
super.readExternal(theIn); super.readExternal(theIn);
} }
public String toSystem() { public String toSystem() {
return getEnumFactory().toSystem(getValue()); return getEnumFactory().toSystem(getValue());
} }
@Override @Override
public void writeExternal(ObjectOutput theOut) throws IOException { public void writeExternal(ObjectOutput theOut) throws IOException {
theOut.writeObject(myEnumFactory); theOut.writeObject(myEnumFactory);
super.writeExternal(theOut); super.writeExternal(theOut);
} }
} }

4
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -728,6 +728,7 @@ public class JsonParserDstu3Test {
Observation obs = new Observation(); Observation obs = new Observation();
obs.setId("1"); obs.setId("1");
obs.getMeta().addProfile("http://profile"); obs.getMeta().addProfile("http://profile");
obs.setStatus(ObservationStatus.FINAL);
Extension ext = obs.addExtension(); Extension ext = obs.addExtension();
ext.setUrl("http://exturl").setValue(new StringType("ext_url_value")); ext.setUrl("http://exturl").setValue(new StringType("ext_url_value"));
@ -758,6 +759,9 @@ public class JsonParserDstu3Test {
assertEquals(1, obs.getExtension().size()); assertEquals(1, obs.getExtension().size());
assertEquals("http://exturl", obs.getExtension().get(0).getUrl()); assertEquals("http://exturl", obs.getExtension().get(0).getUrl());
assertEquals("ext_url_value", ((StringType) obs.getExtension().get(0).getValue()).getValue()); assertEquals("ext_url_value", ((StringType) obs.getExtension().get(0).getValue()).getValue());
assertEquals("final", obs.getStatusElement().getValueAsString());
assertEquals(ObservationStatus.FINAL, obs.getStatusElement().getValue());
} }
@Test @Test

267
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/PlainProviderR4Test.java Normal file
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@ -0,0 +1,267 @@
package ca.uhn.fhir.rest.server;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.Count;
import ca.uhn.fhir.rest.annotation.*;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.util.PortUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.CloseableHttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.impl.client.CloseableHttpClient;
import org.apache.http.impl.client.HttpClientBuilder;
import org.apache.http.impl.conn.PoolingHttpClientConnectionManager;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.servlet.ServletHandler;
import org.eclipse.jetty.servlet.ServletHolder;
import org.hamcrest.core.IsEqual;
import org.hamcrest.core.StringStartsWith;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.TimeUnit;
import static org.junit.Assert.*;
public class PlainProviderR4Test {
private static FhirContext ourCtx = FhirContext.forR4();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(PlainProviderR4Test.class);
private CloseableHttpClient myClient;
private int myPort;
private RestfulServer myRestfulServer;
private Server myServer;
@After
public void after() throws Exception {
myServer.stop();
}
@Before
public void before() throws Exception {
myPort = PortUtil.findFreePort();
myServer = new Server(myPort);
ServletHandler proxyHandler = new ServletHandler();
ServletHolder servletHolder = new ServletHolder();
myRestfulServer = new RestfulServer(ourCtx);
servletHolder.setServlet(myRestfulServer);
proxyHandler.addServletWithMapping(servletHolder, "/fhir/context/*");
myServer.setHandler(proxyHandler);
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
myClient = builder.build();
}
@Test
public void testGlobalHistory() throws Exception {
GlobalHistoryProvider provider = new GlobalHistoryProvider();
myRestfulServer.setProviders(provider);
myServer.start();
String baseUri = "http://localhost:" + myPort + "/fhir/context";
HttpResponse status = myClient.execute(new HttpGet(baseUri + "/_history?_since=2012-01-02T00%3A01%3A02&_count=12"));
String responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
ourLog.info("Response was:\n{}", responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
assertEquals(3, bundle.getEntry().size());
assertThat(provider.myLastSince.getValueAsString(), StringStartsWith.startsWith("2012-01-02T00:01:02"));
assertThat(provider.myLastCount.getValueAsString(), IsEqual.equalTo("12"));
status = myClient.execute(new HttpGet(baseUri + "/_history?&_count=12"));
responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(200, status.getStatusLine().getStatusCode());
bundle = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
assertEquals(3, bundle.getEntry().size());
assertNull(provider.myLastSince);
assertThat(provider.myLastCount.getValueAsString(), IsEqual.equalTo("12"));
status =myClient.execute(new HttpGet(baseUri + "/_history?_since=2012-01-02T00%3A01%3A02"));
responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(200, status.getStatusLine().getStatusCode());
bundle = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
assertEquals(3, bundle.getEntry().size());
assertThat(provider.myLastSince.getValueAsString(), StringStartsWith.startsWith("2012-01-02T00:01:02"));
assertNull(provider.myLastCount);
}
@Test
public void testGlobalHistoryNoParams() throws Exception {
GlobalHistoryProvider provider = new GlobalHistoryProvider();
myRestfulServer.setProviders(provider);
myServer.start();
String baseUri = "http://localhost:" + myPort + "/fhir/context";
CloseableHttpResponse status = myClient.execute(new HttpGet(baseUri + "/_history"));
String responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
assertEquals(200, status.getStatusLine().getStatusCode());
Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
assertEquals(3, bundle.getEntry().size());
assertNull(provider.myLastSince);
assertNull(provider.myLastCount);
}
@Test
public void testSearchByParamIdentifier() throws Exception {
myRestfulServer.setProviders(new SearchProvider());
myServer.start();
String baseUri = "http://localhost:" + myPort + "/fhir/context";
String uri = baseUri + "/Patient?identifier=urn:hapitest:mrns%7C00001";
HttpGet httpGet = new HttpGet(uri);
try (CloseableHttpResponse status = myClient.execute(httpGet)) {
String responseContent = IOUtils.toString(status.getEntity().getContent());
IOUtils.closeQuietly(status.getEntity().getContent());
ourLog.info("Response was:\n{}", responseContent);
assertEquals(200, status.getStatusLine().getStatusCode());
Bundle bundle = ourCtx.newXmlParser().parseResource(Bundle.class, responseContent);
assertEquals(1, bundle.getEntry().size());
Patient patient = (Patient) bundle.getEntry().get(0).getResource();
assertEquals("PatientOne", patient.getName().get(0).getGiven().get(0).getValue());
assertEquals(uri.replace(":hapitest:", "%3Ahapitest%3A"), bundle.getLink("self").getUrl());
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
private static Organization createOrganization() {
Organization retVal = new Organization();
retVal.setId("1");
retVal.addIdentifier();
retVal.getIdentifier().get(0).setUse(Identifier.IdentifierUse.OFFICIAL);
retVal.getIdentifier().get(0).setSystem(("urn:hapitest:mrns"));
retVal.getIdentifier().get(0).setValue("00001");
retVal.setName("Test Org");
return retVal;
}
private static Patient createPatient() {
Patient patient = new Patient();
patient.setId("1");
patient.addIdentifier();
patient.getIdentifier().get(0).setUse(Identifier.IdentifierUse.OFFICIAL);
patient.getIdentifier().get(0).setSystem(("urn:hapitest:mrns"));
patient.getIdentifier().get(0).setValue("00001");
patient.addName();
patient.getName().get(0).setFamily("Test");
patient.getName().get(0).addGiven("PatientOne");
patient.getGenderElement().setValueAsString("male");
return patient;
}
public static class GlobalHistoryProvider {
private IntegerType myLastCount;
private InstantType myLastSince;
@History
public List<IBaseResource> getGlobalHistory(@Since InstantType theSince, @Count IntegerType theCount) {
myLastSince = theSince;
myLastCount = theCount;
ArrayList<IBaseResource> retVal = new ArrayList<>();
Resource p = createPatient();
p.setId(new IdType("1"));
p.getMeta().setVersionId("A");
p.getMeta().getLastUpdatedElement().setValueAsString("2012-01-01T01:00:01");
retVal.add(p);
p = createPatient();
p.setId(new IdType("1"));
p.getMeta().setVersionId("B");
p.getMeta().getLastUpdatedElement().setValueAsString("2012-01-01T01:00:03");
retVal.add(p);
p = createOrganization();
p.setId(new IdType("1"));
p.getMeta().setVersionId("A");
p.getMeta().getLastUpdatedElement().setValueAsString("2013-01-01T01:00:01");
retVal.add(p);
return retVal;
}
}
public static class SearchProvider {
@Search(type = Patient.class)
public Patient findPatient(@RequiredParam(name = Patient.SP_IDENTIFIER) TokenParam theIdentifier) {
for (Patient next : getIdToPatient().values()) {
for (Identifier nextId : next.getIdentifier()) {
if (nextId.getSystem().equals(theIdentifier.getSystem()) && nextId.getValue().equals(theIdentifier.getValue())) {
return next;
}
}
}
return null;
}
public Map<String, Patient> getIdToPatient() {
Map<String, Patient> idToPatient = new HashMap<>();
{
Patient patient = createPatient();
idToPatient.put("1", patient);
}
{
Patient patient = new Patient();
patient.getIdentifier().add(new Identifier());
patient.getIdentifier().get(0).setUse(Identifier.IdentifierUse.OFFICIAL);
patient.getIdentifier().get(0).setSystem(("urn:hapitest:mrns"));
patient.getIdentifier().get(0).setValue("00002");
patient.getName().add(new HumanName());
patient.getName().get(0).setFamily("Test");
patient.getName().get(0).addGiven("PatientTwo");
patient.getGenderElement().setValueAsString("female");
idToPatient.put("2", patient);
}
return idToPatient;
}
/**
* Retrieve the resource by its identifier
*
* @param theId
* The resource identity
* @return The resource
*/
@Read(type = Patient.class)
public Patient getPatientById(@IdParam IdType theId) {
return getIdToPatient().get(theId.getValue());
}
}
}

6
src/changes/changes.xml
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@ -109,6 +109,12 @@
<![CDATA[<code>application/json+fhir</code>]]>. <![CDATA[<code>application/json+fhir</code>]]>.
Thanks to John Grimes for reporting! Thanks to John Grimes for reporting!
</action> </action>
<action type="fix">
Fixed a regression in server where a count parameter in the form
<![CDATA[<code>@Count IntegerType theCount</code>]]>
caused an exception if the client made a request with
no count parameter included. Thanks to Viviana Sanz for reporting!
</action>
</release> </release>
<release version="3.2.0" date="2018-01-13"> <release version="3.2.0" date="2018-01-13">
<action type="add"> <action type="add">