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

This commit is contained in:
James Agnew 2018-01-28 14:02:53 -06:00
parent f976b7bf7e 2e4f80d7a3
commit 044b9f584a
27 changed files with 623 additions and 613 deletions
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4
hapi-fhir-base/src/main/java/ca/uhn/fhir/i18n/HapiLocalizer.java
View File

@ -17,9 +17,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.parser;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

42
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/annotation/TagListParam.java
View File

@ -1,42 +0,0 @@
package ca.uhn.fhir.rest.annotation;
/*
* #%L
* HAPI FHIR - Core Library
* %%
* Copyright (C) 2014 - 2018 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.lang.annotation.ElementType;
import java.lang.annotation.Retention;
import java.lang.annotation.RetentionPolicy;
import java.lang.annotation.Target;
import ca.uhn.fhir.model.api.TagList;
/**
* Parameter annotation for the {@link TagList} parameter in a {@link GetTags},
* {@link AddTags}, or {@link DeleteTags} method.
*
* @see GetTags
* @see AddTags
* @see DeleteTags
*/
@Target(value = ElementType.PARAMETER)
@Retention(RetentionPolicy.RUNTIME)
public @interface TagListParam {
// nothing
}

60
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/param/ParameterUtil.java
View File

@ -1,7 +1,28 @@
package ca.uhn.fhir.rest.param;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.RuntimeSearchParam;
import ca.uhn.fhir.model.api.IQueryParameterAnd;
import ca.uhn.fhir.model.api.IQueryParameterOr;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.binder.QueryParameterAndBinder;
import ca.uhn.fhir.util.ReflectionUtil;
import ca.uhn.fhir.util.UrlUtil;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import java.lang.annotation.Annotation;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
/*
* #%L
* HAPI FHIR - Core Library
@ -11,9 +32,9 @@ import java.lang.reflect.Method;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@ -21,29 +42,9 @@ import java.lang.reflect.Method;
* limitations under the License.
* #L%
*/
import java.util.*;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.context.*;
import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.IntegerDt;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.TagListParam;
import ca.uhn.fhir.rest.api.QualifiedParamList;
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.param.binder.QueryParameterAndBinder;
import ca.uhn.fhir.util.ReflectionUtil;
import ca.uhn.fhir.util.UrlUtil;
public class ParameterUtil {
private static final String LABEL = "label=\"";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ParameterUtil.class);
private static final String SCHEME = "scheme=\"";
@SuppressWarnings("unchecked")
public static <T extends IIdType> T convertIdToType(IIdType value, Class<T> theIdParamType) {
if (value != null && !theIdParamType.isAssignableFrom(value.getClass())) {
@ -179,8 +180,7 @@ public class ParameterUtil {
public static Integer findParamAnnotationIndex(Method theMethod, Class<?> toFind) {
int paramIndex = 0;
for (Annotation[] annotations : theMethod.getParameterAnnotations()) {
for (int annotationIndex = 0; annotationIndex < annotations.length; annotationIndex++) {
Annotation nextAnnotation = annotations[annotationIndex];
for (Annotation nextAnnotation : annotations) {
Class<? extends Annotation> class1 = nextAnnotation.annotationType();
if (toFind.isAssignableFrom(class1)) {
return paramIndex;
@ -191,10 +191,6 @@ public class ParameterUtil {
return null;
}
public static Integer findTagListParameterIndex(Method theMethod) {
return findParamAnnotationIndex(theMethod, TagListParam.class);
}
public static Object fromInteger(Class<?> theType, IntegerDt theArgument) {
if (theType.equals(Integer.class)) {
if (theArgument == null) {
@ -271,12 +267,8 @@ public class ParameterUtil {
};
}
static List<String> splitParameterString(String theInput, boolean theUnescapeComponents) {
return splitParameterString(theInput, ',', theUnescapeComponents);
}
static List<String> splitParameterString(String theInput, char theDelimiter, boolean theUnescapeComponents) {
ArrayList<String> retVal = new ArrayList<String>();
ArrayList<String> retVal = new ArrayList<>();
if (theInput != null) {
StringBuilder b = new StringBuilder();
for (int i = 0; i < theInput.length(); i++) {
@ -335,7 +327,7 @@ public class ParameterUtil {
*/
public static String unescape(String theValue) {
if (theValue == null) {
return theValue;
return null;
}
if (theValue.indexOf('\\') == -1) {
return theValue;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.dao;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/EncodedResource.java
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@ -1,5 +1,25 @@
package ca.uhn.fhir.jpa.dao;
/*-
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2018 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import ca.uhn.fhir.jpa.entity.ResourceEncodingEnum;
class EncodedResource {

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/BaseHasResource.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceHistoryTable.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/ResourceTable.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.entity;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/config/TestR4Config.java
View File

@ -7,6 +7,7 @@ import net.ttddyy.dsproxy.listener.ThreadQueryCountHolder;
import net.ttddyy.dsproxy.support.ProxyDataSourceBuilder;
import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hibernate.query.criteria.LiteralHandlingMode;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Lazy;
@ -133,6 +134,8 @@ public class TestR4Config extends BaseJavaConfigR4 {
extraProperties.put("hibernate.search.default.directory_provider", "ram");
extraProperties.put("hibernate.search.lucene_version", "LUCENE_CURRENT");
extraProperties.put("hibernate.search.autoregister_listeners", "true");
extraProperties.put("hibernate.criteria.literal_handling_mode", LiteralHandlingMode.BIND);
return extraProperties;
}

31
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/BaseJpaTest.java
View File

@ -49,6 +49,11 @@ public abstract class BaseJpaTest {
protected ArrayList<IServerInterceptor> myServerInterceptorList;
protected IRequestOperationCallback myRequestOperationCallback = mock(IRequestOperationCallback.class);
@After
public final void afterPerformCleanup() {
BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(false);
}
@Before
public void beforeCreateSrd() {
mySrd = mock(ServletRequestDetails.class, Mockito.RETURNS_DEEP_STUBS);
@ -58,11 +63,6 @@ public abstract class BaseJpaTest {
when(mySrd.getUserData()).thenReturn(new HashMap<>());
}
@After
public final void afterPerformCleanup() {
BaseHapiFhirResourceDao.setDisableIncrementOnUpdateForUnitTest(false);
}
protected abstract FhirContext getContext();
/**
@ -159,11 +159,24 @@ public abstract class BaseJpaTest {
protected List<IIdType> toUnqualifiedVersionlessIds(IBundleProvider theFound) {
List<IIdType> retVal = new ArrayList<IIdType>();
int size = theFound.size();
Integer size = theFound.size();
StopWatch sw = new StopWatch();
while (size == null) {
int timeout = 20000;
if (sw.getMillis() > timeout) {
fail("Waited over "+timeout+"ms for search");
}
try {
Thread.sleep(100);
} catch (InterruptedException theE) {
//ignore
}
}
ourLog.info("Found {} results", size);
List<IBaseResource> resources = theFound.getResources(0, size);
for (IBaseResource next : resources) {
retVal.add((IIdType) next.getIdElement().toUnqualifiedVersionless());
retVal.add(next.getIdElement().toUnqualifiedVersionless());
}
return retVal;
}
@ -171,7 +184,7 @@ public abstract class BaseJpaTest {
protected List<IIdType> toUnqualifiedVersionlessIds(List<IBaseResource> theFound) {
List<IIdType> retVal = new ArrayList<IIdType>();
for (IBaseResource next : theFound) {
retVal.add((IIdType) next.getIdElement().toUnqualifiedVersionless());
retVal.add(next.getIdElement().toUnqualifiedVersionless());
}
return retVal;
}
@ -210,7 +223,7 @@ public abstract class BaseJpaTest {
}
@AfterClass
public static void afterClassShutdownDerby() throws SQLException {
public static void afterClassShutdownDerby() {
// DriverManager.getConnection("jdbc:derby:;shutdown=true");
// try {
// DriverManager.getConnection("jdbc:derby:memory:myUnitTestDB;drop=true");

523
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/SystemProviderR4Test.java
View File

@ -48,118 +48,28 @@ import ca.uhn.fhir.validation.ResultSeverityEnum;
public class SystemProviderR4Test extends BaseJpaR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderR4Test.class);
private static RestfulServer myRestServer;
private static IGenericClient ourClient;
private static FhirContext ourCtx;
private static CloseableHttpClient ourHttpClient;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(SystemProviderR4Test.class);
private static Server ourServer;
private static String ourServerBase;
private SimpleRequestHeaderInterceptor mySimpleHeaderInterceptor;
@Test
public void testTransactionWithInlineConditionalUrl() throws Exception {
myDaoConfig.setAllowInlineMatchUrlReferences(true);
Patient p = new Patient();
p.addName().setFamily("van de Heuvelcx85ioqWJbI").addGiven("Pietercx85ioqWJbI");
myPatientDao.create(p, mySrd);
Organization o = new Organization();
o.addIdentifier().setSystem("urn:oid:2.16.840.1.113883.2.4.6.1").setValue("07-8975469");
myOrganizationDao.create(o, mySrd);
//@formatter:off
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
" <id value=\"20160113160203\"/>\n" +
" <type value=\"transaction\"/>\n" +
" <entry>\n" +
" <fullUrl value=\"urn:uuid:c72aa430-2ddc-456e-7a09-dea8264671d8\"/>\n" +
" <resource>\n" +
" <Encounter>\n" +
" <identifier>\n" +
" <use value=\"official\"/>\n" +
" <system value=\"http://healthcare.example.org/identifiers/encounter\"/>\n" +
" <value value=\"845962.8975469\"/>\n" +
" </identifier>\n" +
" <status value=\"in-progress\"/>\n" +
" <class value=\"inpatient\"/>\n" +
" <patient>\n" +
" <reference value=\"Patient?family=van%20de%20Heuvelcx85ioqWJbI&amp;given=Pietercx85ioqWJbI\"/>\n" +
" </patient>\n" +
" <serviceProvider>\n" +
" <reference value=\"Organization?identifier=urn:oid:2.16.840.1.113883.2.4.6.1|07-8975469\"/>\n" +
" </serviceProvider>\n" +
" </Encounter>\n" +
" </resource>\n" +
" <request>\n" +
" <method value=\"POST\"/>\n" +
" <url value=\"Encounter\"/>\n" +
" </request>\n" +
" </entry>\n" +
"</Bundle>";
//@formatter:off
HttpPost req = new HttpPost(ourServerBase);
req.setEntity(new StringEntity(input, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
assertThat(encoded, containsString("transaction-response"));
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
@SuppressWarnings("deprecation")
@After
public void after() {
myRestServer.setUseBrowserFriendlyContentTypes(true);
ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
}
@Test
public void testTransactionDeleteWithDuplicateDeletes() throws Exception {
myDaoConfig.setAllowInlineMatchUrlReferences(true);
Patient p = new Patient();
p.addName().setFamily("van de Heuvelcx85ioqWJbI").addGiven("Pietercx85ioqWJbI");
IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
ourClient.read().resource(Patient.class).withId(id);
Bundle inputBundle = new Bundle();
inputBundle.setType(BundleType.TRANSACTION);
inputBundle.addEntry().getRequest().setMethod(HTTPVerb.DELETE).setUrl(id.getValue());
inputBundle.addEntry().getRequest().setMethod(HTTPVerb.DELETE).setUrl(id.getValue());
inputBundle.addEntry().getRequest().setMethod(HTTPVerb.DELETE).setUrl("Patient?name=Pietercx85ioqWJbI");
String input = myFhirCtx.newXmlParser().encodeResourceToString(inputBundle);
HttpPost req = new HttpPost(ourServerBase + "?_pretty=true");
req.setEntity(new StringEntity(input, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
assertThat(encoded, containsString("transaction-response"));
Bundle response = myFhirCtx.newXmlParser().parseResource(Bundle.class, encoded);
assertEquals(3, response.getEntry().size());
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
try {
ourClient.read().resource(Patient.class).withId(id).execute();
fail();
} catch (ResourceGoneException e) {
// good
}
@Before
public void before() {
mySimpleHeaderInterceptor = new SimpleRequestHeaderInterceptor();
ourClient.registerInterceptor(mySimpleHeaderInterceptor);
}
@Before
public void beforeStartServer() throws Exception {
if (myRestServer == null) {
@ -213,101 +123,6 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
myRestServer.setPagingProvider(myPagingProvider);
}
@Before
public void before() {
mySimpleHeaderInterceptor = new SimpleRequestHeaderInterceptor();
ourClient.registerInterceptor(mySimpleHeaderInterceptor);
}
@SuppressWarnings("deprecation")
@After
public void after() {
myRestServer.setUseBrowserFriendlyContentTypes(true);
ourClient.unregisterInterceptor(mySimpleHeaderInterceptor);
}
@SuppressWarnings("deprecation")
@Test
public void testResponseUsesCorrectContentType() throws Exception {
myRestServer.setUseBrowserFriendlyContentTypes(true);
myRestServer.setDefaultResponseEncoding(EncodingEnum.JSON);
HttpGet get = new HttpGet(ourServerBase);
// get.addHeader("Accept", "application/xml, text/html");
CloseableHttpResponse http = ourHttpClient.execute(get);
assertThat(http.getFirstHeader("Content-Type").getValue(), containsString("application/fhir+json"));
}
/**
* FOrmat has changed, source is no longer valid
*/
@Test
@Ignore
public void testValidateUsingIncomingResources() throws Exception {
FhirInstanceValidator val = new FhirInstanceValidator(myValidationSupport);
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
interceptor.addValidatorModule(val);
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setAddResponseHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
myRestServer.registerInterceptor(interceptor);
try {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/questionnaire-sdc-profile-example-ussg-fht.xml");
String bundleStr = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
HttpPost req = new HttpPost(ourServerBase);
req.setEntity(new StringEntity(bundleStr, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
//@formatter:off
assertThat(encoded, containsString("Questionnaire/54127-6/_history/"));
//@formatter:on
for (Header next : resp.getHeaders(RequestValidatingInterceptor.DEFAULT_RESPONSE_HEADER_NAME)) {
ourLog.info(next.toString());
}
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
} finally {
myRestServer.unregisterInterceptor(interceptor);
}
}
@Test
public void testEverythingReturnsCorrectFormatInPagingLink() throws Exception {
myRestServer.setDefaultResponseEncoding(EncodingEnum.JSON);
myRestServer.setPagingProvider(new FifoMemoryPagingProvider(1).setDefaultPageSize(10));
ResponseHighlighterInterceptor interceptor = new ResponseHighlighterInterceptor();
myRestServer.registerInterceptor(interceptor);
for (int i = 0; i < 11; i++) {
Patient p = new Patient();
p.addName().setFamily("Name" + i);
ourClient.create().resource(p).execute();
}
HttpGet get = new HttpGet(ourServerBase + "/Patient/$everything");
get.addHeader("Accept", "application/xml, text/html");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, containsString("_format=json"));
assertEquals(200, http.getStatusLine().getStatusCode());
} finally {
http.close();
}
myRestServer.unregisterInterceptor(interceptor);
}
@Test
public void testEverythingReturnsCorrectBundleType() throws Exception {
myRestServer.setDefaultResponseEncoding(EncodingEnum.JSON);
@ -339,7 +154,36 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
myRestServer.unregisterInterceptor(interceptor);
}
@Test
public void testEverythingReturnsCorrectFormatInPagingLink() throws Exception {
myRestServer.setDefaultResponseEncoding(EncodingEnum.JSON);
myRestServer.setPagingProvider(new FifoMemoryPagingProvider(1).setDefaultPageSize(10));
ResponseHighlighterInterceptor interceptor = new ResponseHighlighterInterceptor();
myRestServer.registerInterceptor(interceptor);
for (int i = 0; i < 11; i++) {
Patient p = new Patient();
p.addName().setFamily("Name" + i);
ourClient.create().resource(p).execute();
}
HttpGet get = new HttpGet(ourServerBase + "/Patient/$everything");
get.addHeader("Accept", "application/xml, text/html");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String response = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(response);
assertThat(response, containsString("_format=json"));
assertEquals(200, http.getStatusLine().getStatusCode());
} finally {
http.close();
}
myRestServer.unregisterInterceptor(interceptor);
}
@Test
public void testEverythingType() throws Exception {
HttpGet get = new HttpGet(ourServerBase + "/Patient/$everything");
@ -350,6 +194,12 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
http.close();
}
}
@Test
public void testGetOperationDefinition() {
OperationDefinition op = ourClient.read(OperationDefinition.class, "-s-get-resource-counts");
assertEquals("get-resource-counts", op.getCode());
}
@Test
public void testMarkResourcesForReindexing() throws Exception {
@ -374,7 +224,19 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
}
}
@SuppressWarnings("deprecation")
@Test
public void testResponseUsesCorrectContentType() throws Exception {
myRestServer.setUseBrowserFriendlyContentTypes(true);
myRestServer.setDefaultResponseEncoding(EncodingEnum.JSON);
HttpGet get = new HttpGet(ourServerBase);
// get.addHeader("Accept", "application/xml, text/html");
CloseableHttpResponse http = ourHttpClient.execute(get);
assertThat(http.getFirstHeader("Content-Type").getValue(), containsString("application/fhir+json"));
}
@Transactional(propagation = Propagation.NEVER)
@Test
public void testSuggestKeywords() throws Exception {
@ -458,11 +320,106 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
}
}
@Test
public void testTransactionCount() throws Exception {
for (int i = 0; i < 20; i++) {
Patient p = new Patient();
p.addName().setFamily("PATIENT_" + i);
myPatientDao.create(p, mySrd);
}
Bundle req = new Bundle();
req.setType(BundleType.TRANSACTION);
req.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl("Patient?_summary=count");
Bundle resp = ourClient.transaction().withBundle(req).execute();
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(1, resp.getEntry().size());
Bundle respSub = (Bundle) resp.getEntry().get(0).getResource();
assertEquals(20, respSub.getTotal());
assertEquals(0, respSub.getEntry().size());
}
@Test
public void testGetOperationDefinition() {
OperationDefinition op = ourClient.read(OperationDefinition.class, "-s-get-resource-counts");
assertEquals("get-resource-counts", op.getCode());
public void testTransactionCreateWithPreferHeader() throws Exception {
Patient p = new Patient();
p.setActive(true);
Bundle req;
Bundle resp;
// No prefer header
req = new Bundle();
req.setType(BundleType.TRANSACTION);
req.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
resp = ourClient.transaction().withBundle(req).execute();
assertEquals(null, resp.getEntry().get(0).getResource());
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
// Prefer return=minimal
mySimpleHeaderInterceptor.setHeaderName(Constants.HEADER_PREFER);
mySimpleHeaderInterceptor.setHeaderValue(Constants.HEADER_PREFER_RETURN + "=" + Constants.HEADER_PREFER_RETURN_MINIMAL);
req = new Bundle();
req.setType(BundleType.TRANSACTION);
req.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
resp = ourClient.transaction().withBundle(req).execute();
assertEquals(null, resp.getEntry().get(0).getResource());
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
// Prefer return=representation
mySimpleHeaderInterceptor.setHeaderName(Constants.HEADER_PREFER);
mySimpleHeaderInterceptor.setHeaderValue(Constants.HEADER_PREFER_RETURN + "=" + Constants.HEADER_PREFER_RETURN_REPRESENTATION);
req = new Bundle();
req.setType(BundleType.TRANSACTION);
req.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
resp = ourClient.transaction().withBundle(req).execute();
assertEquals(Patient.class, resp.getEntry().get(0).getResource().getClass());
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
}
@Test
public void testTransactionDeleteWithDuplicateDeletes() throws Exception {
myDaoConfig.setAllowInlineMatchUrlReferences(true);
Patient p = new Patient();
p.addName().setFamily("van de Heuvelcx85ioqWJbI").addGiven("Pietercx85ioqWJbI");
IIdType id = myPatientDao.create(p, mySrd).getId().toUnqualifiedVersionless();
ourClient.read().resource(Patient.class).withId(id);
Bundle inputBundle = new Bundle();
inputBundle.setType(BundleType.TRANSACTION);
inputBundle.addEntry().getRequest().setMethod(HTTPVerb.DELETE).setUrl(id.getValue());
inputBundle.addEntry().getRequest().setMethod(HTTPVerb.DELETE).setUrl(id.getValue());
inputBundle.addEntry().getRequest().setMethod(HTTPVerb.DELETE).setUrl("Patient?name=Pietercx85ioqWJbI");
String input = myFhirCtx.newXmlParser().encodeResourceToString(inputBundle);
HttpPost req = new HttpPost(ourServerBase + "?_pretty=true");
req.setEntity(new StringEntity(input, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
assertThat(encoded, containsString("transaction-response"));
Bundle response = myFhirCtx.newXmlParser().parseResource(Bundle.class, encoded);
assertEquals(3, response.getEntry().size());
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
try {
ourClient.read().resource(Patient.class).withId(id).execute();
fail();
} catch (ResourceGoneException e) {
// good
}
}
@Test
@ -473,23 +430,6 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
ourLog.info(response);
}
@Test
public void testTransactionWithIncompleteBundle() throws Exception {
Patient patient = new Patient();
patient.setGender(AdministrativeGender.MALE);
Bundle bundle = new Bundle();
bundle.setType(BundleType.TRANSACTION);
bundle.addEntry().setResource(patient);
try {
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
fail();
} catch (InvalidRequestException e) {
assertThat(e.toString(), containsString("missing or invalid HTTP Verb"));
}
}
@Test
public void testTransactionFromBundle2() throws Exception {
@ -607,61 +547,118 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
}
@Test
public void testTransactionCount() throws Exception {
for (int i = 0; i < 20; i++) {
Patient p = new Patient();
p.addName().setFamily("PATIENT_" + i);
myPatientDao.create(p, mySrd);
public void testTransactionWithIncompleteBundle() throws Exception {
Patient patient = new Patient();
patient.setGender(AdministrativeGender.MALE);
Bundle bundle = new Bundle();
bundle.setType(BundleType.TRANSACTION);
bundle.addEntry().setResource(patient);
try {
ourClient.transaction().withBundle(bundle).prettyPrint().execute();
fail();
} catch (InvalidRequestException e) {
assertThat(e.toString(), containsString("missing or invalid HTTP Verb"));
}
Bundle req = new Bundle();
req.setType(BundleType.TRANSACTION);
req.addEntry().getRequest().setMethod(HTTPVerb.GET).setUrl("Patient?_summary=count");
Bundle resp = ourClient.transaction().withBundle(req).execute();
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(resp));
assertEquals(1, resp.getEntry().size());
Bundle respSub = (Bundle) resp.getEntry().get(0).getResource();
assertEquals(20, respSub.getTotal());
assertEquals(0, respSub.getEntry().size());
}
@Test
public void testTransactionCreateWithPreferHeader() throws Exception {
public void testTransactionWithInlineConditionalUrl() throws Exception {
myDaoConfig.setAllowInlineMatchUrlReferences(true);
Patient p = new Patient();
p.setActive(true);
p.addName().setFamily("van de Heuvelcx85ioqWJbI").addGiven("Pietercx85ioqWJbI");
myPatientDao.create(p, mySrd);
Bundle req;
Bundle resp;
// No prefer header
req = new Bundle();
req.setType(BundleType.TRANSACTION);
req.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
resp = ourClient.transaction().withBundle(req).execute();
assertEquals(null, resp.getEntry().get(0).getResource());
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
Organization o = new Organization();
o.addIdentifier().setSystem("urn:oid:2.16.840.1.113883.2.4.6.1").setValue("07-8975469");
myOrganizationDao.create(o, mySrd);
// Prefer return=minimal
mySimpleHeaderInterceptor.setHeaderName(Constants.HEADER_PREFER);
mySimpleHeaderInterceptor.setHeaderValue(Constants.HEADER_PREFER_RETURN + "=" + Constants.HEADER_PREFER_RETURN_MINIMAL);
req = new Bundle();
req.setType(BundleType.TRANSACTION);
req.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
resp = ourClient.transaction().withBundle(req).execute();
assertEquals(null, resp.getEntry().get(0).getResource());
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
// Prefer return=representation
mySimpleHeaderInterceptor.setHeaderName(Constants.HEADER_PREFER);
mySimpleHeaderInterceptor.setHeaderValue(Constants.HEADER_PREFER_RETURN + "=" + Constants.HEADER_PREFER_RETURN_REPRESENTATION);
req = new Bundle();
req.setType(BundleType.TRANSACTION);
req.addEntry().setResource(p).getRequest().setMethod(HTTPVerb.POST).setUrl("Patient");
resp = ourClient.transaction().withBundle(req).execute();
assertEquals(Patient.class, resp.getEntry().get(0).getResource().getClass());
assertEquals("201 Created", resp.getEntry().get(0).getResponse().getStatus());
//@formatter:off
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">\n" +
" <id value=\"20160113160203\"/>\n" +
" <type value=\"transaction\"/>\n" +
" <entry>\n" +
" <fullUrl value=\"urn:uuid:c72aa430-2ddc-456e-7a09-dea8264671d8\"/>\n" +
" <resource>\n" +
" <Encounter>\n" +
" <identifier>\n" +
" <use value=\"official\"/>\n" +
" <system value=\"http://healthcare.example.org/identifiers/encounter\"/>\n" +
" <value value=\"845962.8975469\"/>\n" +
" </identifier>\n" +
" <status value=\"in-progress\"/>\n" +
" <class value=\"inpatient\"/>\n" +
" <patient>\n" +
" <reference value=\"Patient?family=van%20de%20Heuvelcx85ioqWJbI&amp;given=Pietercx85ioqWJbI\"/>\n" +
" </patient>\n" +
" <serviceProvider>\n" +
" <reference value=\"Organization?identifier=urn:oid:2.16.840.1.113883.2.4.6.1|07-8975469\"/>\n" +
" </serviceProvider>\n" +
" </Encounter>\n" +
" </resource>\n" +
" <request>\n" +
" <method value=\"POST\"/>\n" +
" <url value=\"Encounter\"/>\n" +
" </request>\n" +
" </entry>\n" +
"</Bundle>";
//@formatter:off
HttpPost req = new HttpPost(ourServerBase);
req.setEntity(new StringEntity(input, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
assertThat(encoded, containsString("transaction-response"));
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
}
/**
* FOrmat has changed, source is no longer valid
*/
@Test
@Ignore
public void testValidateUsingIncomingResources() throws Exception {
FhirInstanceValidator val = new FhirInstanceValidator(myValidationSupport);
RequestValidatingInterceptor interceptor = new RequestValidatingInterceptor();
interceptor.addValidatorModule(val);
interceptor.setFailOnSeverity(ResultSeverityEnum.ERROR);
interceptor.setAddResponseHeaderOnSeverity(ResultSeverityEnum.INFORMATION);
myRestServer.registerInterceptor(interceptor);
try {
InputStream bundleRes = SystemProviderDstu2Test.class.getResourceAsStream("/questionnaire-sdc-profile-example-ussg-fht.xml");
String bundleStr = IOUtils.toString(bundleRes, StandardCharsets.UTF_8);
HttpPost req = new HttpPost(ourServerBase);
req.setEntity(new StringEntity(bundleStr, ContentType.parse(Constants.CT_FHIR_XML + "; charset=utf-8")));
CloseableHttpResponse resp = ourHttpClient.execute(req);
try {
String encoded = IOUtils.toString(resp.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(encoded);
//@formatter:off
assertThat(encoded, containsString("Questionnaire/54127-6/_history/"));
//@formatter:on
for (Header next : resp.getHeaders(RequestValidatingInterceptor.DEFAULT_RESPONSE_HEADER_NAME)) {
ourLog.info(next.toString());
}
} finally {
IOUtils.closeQuietly(resp.getEntity().getContent());
}
} finally {
myRestServer.unregisterInterceptor(interceptor);
}
}
@AfterClass

10
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/RestfulServer.java
View File

@ -875,12 +875,14 @@ public class RestfulServer extends HttpServlet implements IRestfulServer<Servlet
for (int i = getInterceptors().size() - 1; i >= 0; i--) {
IServerInterceptor next = getInterceptors().get(i);
next.processingCompletedNormally(requestDetails);
try {
next.processingCompletedNormally(requestDetails);
} catch (Throwable t) {
ourLog.error("Failure in interceptor method", t);
}
}
if (outputStreamOrWriter != null) {
outputStreamOrWriter.close();
}
IOUtils.closeQuietly(outputStreamOrWriter);
} catch (NotModifiedException | AuthenticationException e) {

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/IAuthRuleBuilderRuleOpClassifierFinished.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/OperationRule.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleBuilder.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/interceptor/auth/RuleImplConditional.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.rest.server.interceptor.auth;
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
*
* http://www.apache.org/licenses/LICENSE-2.0
*
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

55
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/AddTagsMethodBinding.java
View File

@ -1,55 +0,0 @@
package ca.uhn.fhir.rest.server.method;
import java.io.IOException;
/*
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2018 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.lang.reflect.Method;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.AddTags;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.IRestfulServer;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
class AddTagsMethodBinding extends BaseAddOrDeleteTagsMethodBinding {
public AddTagsMethodBinding(Method theMethod, FhirContext theContext, Object theProvider, AddTags theAnnotation) {
super(theMethod, theContext, theProvider, theAnnotation.type());
}
@Override
protected boolean isDelete() {
return false;
}
@Override
public RestOperationTypeEnum getRestOperationType() {
return RestOperationTypeEnum.ADD_TAGS;
}
@Override
public Object invokeServer(IRestfulServer<?> theServer, RequestDetails theRequest) throws BaseServerResponseException, IOException {
return null;
}
}

117
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseAddOrDeleteTagsMethodBinding.java
View File

@ -1,117 +0,0 @@
package ca.uhn.fhir.rest.server.method;
/*-
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2018 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.lang.reflect.Method;
import java.lang.reflect.Modifier;
import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.context.ConfigurationException;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.TagList;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.TagListParam;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.param.ParameterUtil;
import ca.uhn.fhir.rest.server.IResourceProvider;
abstract class BaseAddOrDeleteTagsMethodBinding extends BaseMethodBinding<Void> {
private Class<? extends IBaseResource> myType;
private Integer myIdParamIndex;
private String myResourceName;
private Integer myTagListParamIndex;
public BaseAddOrDeleteTagsMethodBinding(Method theMethod, FhirContext theContext, Object theProvider, Class<? extends IBaseResource> theTypeFromMethodAnnotation) {
super(theMethod, theContext, theProvider);
if (theProvider instanceof IResourceProvider) {
myType = ((IResourceProvider) theProvider).getResourceType();
} else {
myType = theTypeFromMethodAnnotation;
}
if (Modifier.isInterface(myType.getModifiers())) {
throw new ConfigurationException("Method '" + theMethod.getName() + "' does not specify a resource type, but has an @" + IdParam.class.getSimpleName()
+ " parameter. Please specity a resource type in the method annotation on this method");
}
myResourceName = theContext.getResourceDefinition(myType).getName();
myIdParamIndex = ParameterUtil.findIdParameterIndex(theMethod, getContext());
myTagListParamIndex = ParameterUtil.findTagListParameterIndex(theMethod);
if (myIdParamIndex == null) {
throw new ConfigurationException("Method '" + theMethod.getName() + "' does not have an @" + IdParam.class.getSimpleName() + " parameter.");
}
if (myTagListParamIndex == null) {
throw new ConfigurationException("Method '" + theMethod.getName() + "' does not have a parameter of type " + TagList.class.getSimpleName() + ", or paramater is not annotated with the @"
+ TagListParam.class.getSimpleName() + " annotation");
}
}
@Override
public String getResourceName() {
return myResourceName;
}
@Override
public RestOperationTypeEnum getRestOperationType() {
return null;
}
protected abstract boolean isDelete();
@Override
public boolean incomingServerRequestMatchesMethod(RequestDetails theRequest) {
if (theRequest.getRequestType() != RequestTypeEnum.POST) {
return false;
}
if (!Constants.PARAM_TAGS.equals(theRequest.getOperation())) {
return false;
}
if (!myResourceName.equals(theRequest.getResourceName())) {
return false;
}
if (theRequest.getId() == null) {
return false;
}
if (isDelete()) {
if (Constants.PARAM_DELETE.equals(theRequest.getSecondaryOperation()) == false) {
return false;
}
} else {
if (theRequest.getSecondaryOperation() != null) {
return false;
}
}
return true;
}
}

4
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/BaseMethodBinding.java
View File

@ -494,10 +494,6 @@ public abstract class BaseMethodBinding<T> {
return new HistoryMethodBinding(theMethod, theContext, theProvider);
} else if (validate != null) {
return new ValidateMethodBindingDstu2Plus(returnType, returnTypeFromRp, theMethod, theContext, theProvider, validate);
} else if (addTags != null) {
return new AddTagsMethodBinding(theMethod, theContext, theProvider, addTags);
} else if (deleteTags != null) {
return new DeleteTagsMethodBinding(theMethod, theContext, theProvider, deleteTags);
} else if (transaction != null) {
return new TransactionMethodBinding(theMethod, theContext, theProvider);
} else if (operation != null) {

55
hapi-fhir-server/src/main/java/ca/uhn/fhir/rest/server/method/DeleteTagsMethodBinding.java
View File

@ -1,55 +0,0 @@
package ca.uhn.fhir.rest.server.method;
import java.io.IOException;
/*
* #%L
* HAPI FHIR - Server Framework
* %%
* Copyright (C) 2014 - 2018 University Health Network
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.lang.reflect.Method;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.rest.annotation.DeleteTags;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.api.server.IRestfulServer;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
public class DeleteTagsMethodBinding extends BaseAddOrDeleteTagsMethodBinding {
public DeleteTagsMethodBinding(Method theMethod, FhirContext theContext, Object theProvider, DeleteTags theDeleteTags) {
super(theMethod, theContext, theProvider, theDeleteTags.type());
}
@Override
protected boolean isDelete() {
return true;
}
@Override
public RestOperationTypeEnum getRestOperationType() {
return RestOperationTypeEnum.DELETE_TAGS;
}
@Override
public Object invokeServer(IRestfulServer<?> theServer, RequestDetails theRequest) throws BaseServerResponseException, IOException {
return null;
}
}

26
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/ServerMimetypeR4Test.java
View File

@ -6,6 +6,7 @@ import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import java.io.IOException;
import java.net.URI;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
@ -272,8 +273,31 @@ public class ServerMimetypeR4Test {
assertEquals(Constants.CT_FHIR_XML_NEW, status.getFirstHeader("content-type").getValue().replaceAll(";.*", ""));
}
/**
* See #837
*/
@Test
public void testResponseContentTypes() throws IOException {
assertEquals("application/fhir+json", readAndReturnContentType("application/fhir+json"));
assertEquals("application/fhir+xml", readAndReturnContentType(null));
assertEquals("application/json+fhir", readAndReturnContentType("application/json+fhir"));
assertEquals("application/json+fhir", readAndReturnContentType("application/json"));
assertEquals("application/fhir+json", readAndReturnContentType("application/fhir+json,application/json;q=0.9"));
}
private String readAndReturnContentType(String theAccept) throws IOException {
HttpGet httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient");
if (theAccept != null) {
httpGet.addHeader(Constants.HEADER_ACCEPT, theAccept);
}
HttpResponse status = ourClient.execute(httpGet);
String contentType = status.getEntity().getContentType().getValue();
IOUtils.closeQuietly(status.getEntity().getContent());
contentType = contentType.replaceAll(";.*","");
return contentType;
}
@Test
public void testSearchWithFormatJsonSimple() throws Exception {

2
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/interceptor/ExceptionHandlingInterceptorTest.java
View File

@ -84,7 +84,7 @@ public class ExceptionHandlingInterceptorTest {
}
}
@AfterClass
public static void afterClassClearContext() throws Exception {

189
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/rest/server/interceptor/InterceptorThrowingExceptionR4Test.java Normal file
View File

@ -0,0 +1,189 @@
package ca.uhn.fhir.rest.server.interceptor;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.api.AddProfileTagEnum;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Read;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.IResourceProvider;
import ca.uhn.fhir.rest.server.RestfulServer;
import ca.uhn.fhir.rest.server.interceptor.auth.AuthorizationInterceptor;
import ca.uhn.fhir.rest.server.interceptor.auth.IAuthRule;
import ca.uhn.fhir.rest.server.interceptor.auth.PolicyEnum;
import ca.uhn.fhir.rest.server.interceptor.auth.RuleBuilder;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.PortUtil;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.http.HttpEntity;
import org.apache.http.HttpResponse;
import org.apache.http.client.methods.HttpGet;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
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.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.*;
import java.util.concurrent.TimeUnit;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.contains;
import static org.junit.Assert.*;
public class InterceptorThrowingExceptionR4Test {
private static final String ERR403 = "{\"resourceType\":\"OperationOutcome\",\"issue\":[{\"severity\":\"error\",\"code\":\"processing\",\"diagnostics\":\"Access denied by default policy (no applicable rules)\"}]}";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(InterceptorThrowingExceptionR4Test.class);
private static CloseableHttpClient ourClient;
private static String ourConditionalCreateId;
private static FhirContext ourCtx = FhirContext.forR4();
private static boolean ourHitMethod;
private static int ourPort;
private static List<Resource> ourReturn;
private static Server ourServer;
private static RestfulServer ourServlet;
@Before
public void before() {
ourCtx.setAddProfileTagWhenEncoding(AddProfileTagEnum.NEVER);
for (IServerInterceptor next : new ArrayList<>(ourServlet.getInterceptors())) {
ourServlet.unregisterInterceptor(next);
}
ourServlet.setTenantIdentificationStrategy(null);
ourReturn = null;
ourHitMethod = false;
ourConditionalCreateId = "1123";
}
private Resource createPatient(Integer theId) {
Patient retVal = new Patient();
if (theId != null) {
retVal.setId(new IdType("Patient", (long) theId));
}
retVal.addName().setFamily("FAM");
return retVal;
}
private String extractResponseAndClose(HttpResponse status) throws IOException {
if (status.getEntity() == null) {
return null;
}
String responseContent;
responseContent = IOUtils.toString(status.getEntity().getContent(), StandardCharsets.UTF_8);
IOUtils.closeQuietly(status.getEntity().getContent());
return responseContent;
}
@Test
public void testFailureInProcessingCompletedNormally() throws Exception {
final List<Integer> hit = new ArrayList<>();
ourServlet.registerInterceptor(new InterceptorAdapter(){
@Override
public void processingCompletedNormally(ServletRequestDetails theRequestDetails) {
hit.add(1);
throw new NullPointerException();
}
});
ourServlet.registerInterceptor(new InterceptorAdapter(){
@Override
public void processingCompletedNormally(ServletRequestDetails theRequestDetails) {
hit.add(2);
throw new NullPointerException();
}
});
ourServlet.registerInterceptor(new InterceptorAdapter(){
@Override
public void processingCompletedNormally(ServletRequestDetails theRequestDetails) {
hit.add(3);
throw new NullPointerException();
}
});
HttpGet httpGet;
HttpResponse status;
String response;
ourReturn = Collections.singletonList(createPatient(2));
ourHitMethod = false;
httpGet = new HttpGet("http://localhost:" + ourPort + "/Patient/1");
status = ourClient.execute(httpGet);
response = extractResponseAndClose(status);
assertEquals(200, status.getStatusLine().getStatusCode());
assertThat(response, containsString("FAM"));
assertTrue(ourHitMethod);
ourLog.info("Hit: {}", hit);
assertThat(hit, contains(3,2,1));
}
@AfterClass
public static void afterClassClearContext() throws Exception {
ourServer.stop();
TestUtil.clearAllStaticFieldsForUnitTest();
}
@BeforeClass
public static void beforeClass() throws Exception {
ourPort = PortUtil.findFreePort();
try {
ourServer = new Server(ourPort);
} catch (Exception e) {
ourLog.error("FAILED", e);
throw e;
}
DummyPatientResourceProvider patProvider = new DummyPatientResourceProvider();
ServletHandler proxyHandler = new ServletHandler();
ourServlet = new RestfulServer(ourCtx);
ourServlet.setFhirContext(ourCtx);
ourServlet.setResourceProviders(patProvider);
ServletHolder servletHolder = new ServletHolder(ourServlet);
proxyHandler.addServletWithMapping(servletHolder, "/*");
ourServer.setHandler(proxyHandler);
ourServer.start();
PoolingHttpClientConnectionManager connectionManager = new PoolingHttpClientConnectionManager(5000, TimeUnit.MILLISECONDS);
HttpClientBuilder builder = HttpClientBuilder.create();
builder.setConnectionManager(connectionManager);
ourClient = builder.build();
}
public static class DummyPatientResourceProvider implements IResourceProvider {
@Override
public Class<? extends IBaseResource> getResourceType() {
return Patient.class;
}
@Read(version = true)
public Patient read(@IdParam IdType theId) {
ourHitMethod = true;
return (Patient) ourReturn.get(0);
}
}
}

33
pom.xml
View File

@ -409,8 +409,9 @@
<!-- Dependency Versions -->
<derby_version>10.14.1.0</derby_version>
<jersey_version>2.25.1</jersey_version>
<jetty_version>9.4.6.v20170531</jetty_version>
<hibernate_version>5.2.10.Final</hibernate_version>
<jetty_version>9.4.8.v20171121</jetty_version>
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.2.12.Final</hibernate_version>
<hibernate_validator_version>5.4.1.Final</hibernate_validator_version>
<!-- Update lucene version when you update hibernate-search version -->
<hibernate_search_version>5.7.1.Final</hibernate_search_version>
@ -419,9 +420,9 @@
<maven_license_plugin_version>1.8</maven_license_plugin_version>
<phloc_schematron_version>2.7.1</phloc_schematron_version>
<phloc_commons_version>4.4.11</phloc_commons_version>
<spring_version>5.0.0.RELEASE</spring_version>
<spring_version>5.0.3.RELEASE</spring_version>
<spring-boot.version>1.5.6.RELEASE</spring-boot.version>
<thymeleaf-version>3.0.7.RELEASE</thymeleaf-version>
<thymeleaf-version>3.0.9.RELEASE</thymeleaf-version>
<!-- We are aiming to still work on a very old version of SLF4j even though we depend on the newest, just to be nice to users of the API. This version is tested in the hapi-fhir-cobertura. -->
<slf4j_target_version>1.6.0</slf4j_target_version>
@ -798,6 +799,21 @@
<artifactId>jetty-servlets</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-io</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-continuation</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-security</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-servlet</artifactId>
@ -818,6 +834,11 @@
<artifactId>jetty-webapp</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty</groupId>
<artifactId>jetty-xml</artifactId>
<version>${jetty_version}</version>
</dependency>
<dependency>
<groupId>org.eclipse.jetty.websocket</groupId>
<artifactId>websocket-api</artifactId>
@ -1114,7 +1135,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<version>2.10</version>
<version>3.0.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
@ -1210,7 +1231,7 @@
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>versions-maven-plugin</artifactId>
<version>2.2</version>
<version>2.5</version>
</plugin>
<plugin>
<groupId>org.eclipse.jetty</groupId>

22
src/changes/changes.xml
View File

@ -8,6 +8,17 @@
<body>
<release version="3.3.0" date="TBD">
<action type="add">
The version of a few dependencies have been bumped to the
latest versions (dependent HAPI modules listed in brackets):
<![CDATA[
<ul>
<li>Hibernate (JPA): 5.2.10.Final -&gt; 5.2.12.Final</li>
<li>Spring (JPA): 5.0.0 -&gt; 5.0.3</li>
<li>Thymeleaf (Web Tespage Overlay): 3.0.7.RELEASE -&gt; 3.0.9.RELEASE</li>
</ul>
]]>
</action>
<action type="add">
This release corrects an inefficiency in the JPA Server, but requires a schema
change in order to update. Prior to this version of HAPI FHIR, a CLOB column
containing the complete resource body was stored in two
@ -32,6 +43,17 @@
Fix an issue where the JPA server crashed while attempting to normalize string values
containing Korean text. Thanks to GitHub user @JoonggeonLee for reporting!
</action>
<action type="fix">
An issue was solved where it was possible for server interceptors
to have both processingCompletedNormally and handleException called
if the stream.close() method threw an exception. Thanks to Carlos
Eduardo Lara Augusto for investigating!
</action>
<action type="remove" issue="831">
The <![CDATA[<code>@TagListParam</code>]]> annotation has been removed. This
annotation had no use after DSTU1 but never got deleted and was misleading. Thanks
to Angelo Kastroulis for reporting!
</action>
<action type="add">
A new method overload has been added to IServerInterceptor:
<![CDATA[