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

This commit is contained in:
jamesagnew 2019-04-28 11:17:18 -04:00
parent c1bf6d0b3c 828df1528f
commit ddf12e7c28
9 changed files with 187 additions and 45 deletions
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64
hapi-fhir-base/src/main/java/ca/uhn/fhir/util/BundleUtil.java
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@ -11,9 +11,9 @@ 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.
@ -24,6 +24,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.util.ArrayList;
import java.util.List;
import java.util.Objects;
import org.apache.commons.lang3.tuple.Pair;
import org.hl7.fhir.instance.model.api.*;
@ -50,7 +51,7 @@ public class BundleUtil {
BaseRuntimeChildDefinition relChild = relDef.getChildByName("relation");
List<IBase> relValues = relChild.getAccessor().getValues(nextLink);
for (IBase next : relValues) {
IPrimitiveType<?> nextValue = (IPrimitiveType<?>)next;
IPrimitiveType<?> nextValue = (IPrimitiveType<?>) next;
if (theLinkRelation.equals(nextValue.getValueAsString())) {
isRightRel = true;
}
@ -64,7 +65,7 @@ public class BundleUtil {
BaseRuntimeChildDefinition urlChild = linkDef.getChildByName("url");
List<IBase> values = urlChild.getAccessor().getValues(nextLink);
for (IBase nextUrl : values) {
IPrimitiveType<?> nextValue = (IPrimitiveType<?>)nextUrl;
IPrimitiveType<?> nextValue = (IPrimitiveType<?>) nextUrl;
if (isNotBlank(nextValue.getValueAsString())) {
return nextValue.getValueAsString();
}
@ -83,35 +84,35 @@ public class BundleUtil {
BaseRuntimeElementCompositeDefinition<?> entryChildElem = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
BaseRuntimeChildDefinition requestChild = entryChildElem.getChildByName("request");
BaseRuntimeElementCompositeDefinition<?> requestDef = (BaseRuntimeElementCompositeDefinition<?>) requestChild.getChildByName("request");
BaseRuntimeChildDefinition urlChild = requestDef.getChildByName("url");
List<Pair<String, IBaseResource>> retVal = new ArrayList<>(entries.size());
for (IBase nextEntry : entries) {
String url = null;
IBaseResource resource = null;
for (IBase nextEntryValue : requestChild.getAccessor().getValues(nextEntry)) {
for (IBase nextUrlValue : urlChild.getAccessor().getValues(nextEntryValue)) {
url = ((IPrimitiveType<String>)nextUrlValue).getValue();
url = ((IPrimitiveType<String>) nextUrlValue).getValue();
}
}
// Should return 0..1 only
for (IBase nextValue : resourceChild.getAccessor().getValues(nextEntry)) {
resource = (IBaseResource) nextValue;
}
retVal.add(Pair.of(url, resource));
}
return retVal;
return retVal;
}
public static String getBundleType(FhirContext theContext, IBaseBundle theBundle) {
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
BaseRuntimeChildDefinition entryChild = def.getChildByName("type");
@ -147,13 +148,13 @@ public class BundleUtil {
List<IBase> entries = entryChild.getAccessor().getValues(theBundle);
BaseRuntimeElementCompositeDefinition<?> entryChildElem = (BaseRuntimeElementCompositeDefinition<?>) entryChild.getChildByName("entry");
BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
BaseRuntimeChildDefinition requestChild = entryChildElem.getChildByName("request");
BaseRuntimeElementCompositeDefinition<?> requestElem = (BaseRuntimeElementCompositeDefinition<?>) requestChild.getChildByName("request");
BaseRuntimeElementCompositeDefinition<?> requestElem = (BaseRuntimeElementCompositeDefinition<?>) requestChild.getChildByName("request");
BaseRuntimeChildDefinition urlChild = requestElem.getChildByName("url");
BaseRuntimeChildDefinition methodChild = requestElem.getChildByName("method");
for (IBase nextEntry : entries) {
IBaseResource resource = null;
String url = null;
@ -164,39 +165,40 @@ public class BundleUtil {
}
for (IBase nextRequest : requestChild.getAccessor().getValues(nextEntry)) {
for (IBase nextUrl : urlChild.getAccessor().getValues(nextRequest)) {
url = ((IPrimitiveType<?>)nextUrl).getValueAsString();
url = ((IPrimitiveType<?>) nextUrl).getValueAsString();
}
for (IBase nextUrl : methodChild.getAccessor().getValues(nextRequest)) {
String methodString = ((IPrimitiveType<?>)nextUrl).getValueAsString();
String methodString = ((IPrimitiveType<?>) nextUrl).getValueAsString();
if (isNotBlank(methodString)) {
requestType = RequestTypeEnum.valueOf(methodString);
}
}
}
/*
/*
* All 3 might be null - That's ok because we still want to know the
* order in the original bundle.
*/
retVal.add(new BundleEntryParts(requestType, url, resource));
}
return retVal;
}
/**
* Extract all of the resources from a given bundle
*/
public static List<IBaseResource> toListOfResources(FhirContext theContext, IBaseBundle theBundle) {
return toListOfResourcesOfType(theContext, theBundle, null);
return toListOfResourcesOfType(theContext, theBundle, IBaseResource.class);
}
/**
* Extract all of the resources of a given type from a given bundle
* Extract all of the resources of a given type from a given bundle
*/
@SuppressWarnings("unchecked")
public static <T extends IBaseResource> List<T> toListOfResourcesOfType(FhirContext theContext, IBaseBundle theBundle, Class<T> theTypeToInclude) {
Objects.requireNonNull(theTypeToInclude, "ResourceType must not be null");
List<T> retVal = new ArrayList<>();
RuntimeResourceDefinition def = theContext.getResourceDefinition(theBundle);
@ -207,36 +209,36 @@ public class BundleUtil {
BaseRuntimeChildDefinition resourceChild = entryChildElem.getChildByName("resource");
for (IBase nextEntry : entries) {
for (IBase next : resourceChild.getAccessor().getValues(nextEntry)) {
if (theTypeToInclude != null && !theTypeToInclude.isAssignableFrom(next.getClass())) {
continue;
if (theTypeToInclude.isAssignableFrom(next.getClass())) {
retVal.add((T) next);
}
retVal.add((T) next);
}
}
return retVal;
}
public static class BundleEntryParts
{
public static class BundleEntryParts {
private final RequestTypeEnum myRequestType;
private final IBaseResource myResource;
private final String myUrl;
BundleEntryParts(RequestTypeEnum theRequestType, String theUrl, IBaseResource theResource) {
super();
myRequestType = theRequestType;
myUrl = theUrl;
myResource = theResource;
}
public RequestTypeEnum getRequestType() {
return myRequestType;
}
public IBaseResource getResource() {
return myResource;
}
public String getUrl() {
return myUrl;
}
}
}

2
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
View File

@ -114,3 +114,5 @@ ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoConceptMapDstu3.matchesFound=Matches fo
ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoConceptMapDstu3.noMatchesFound=No matches found!
ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoConceptMapR4.matchesFound=Matches found!
ca.uhn.fhir.jpa.dao.r4.FhirResourceDaoConceptMapR4.noMatchesFound=No matches found!
ca.uhn.fhir.jpa.util.jsonpatch.JsonPatchUtils.failedToApplyPatch=Failed to apply JSON patch to {0}: {1}

6
hapi-fhir-jpaserver-base/pom.xml
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@ -529,6 +529,12 @@
<artifactId>guava-testlib</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>org.jetbrains</groupId>
<artifactId>annotations</artifactId>
<version>16.0.3</version>
<scope>compile</scope>
</dependency>
</dependencies>

25
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/jsonpatch/JsonPatchUtils.java
View File

@ -21,6 +21,9 @@ package ca.uhn.fhir.jpa.util.jsonpatch;
*/
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.StrictErrorHandler;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.fasterxml.jackson.core.JsonFactory;
import com.fasterxml.jackson.core.JsonParser;
@ -29,13 +32,15 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import com.github.fge.jsonpatch.JsonPatch;
import com.github.fge.jsonpatch.JsonPatchException;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.intellij.lang.annotations.Language;
import java.io.IOException;
import java.io.StringReader;
import static org.apache.commons.lang3.StringUtils.defaultString;
public class JsonPatchUtils {
public static <T extends IBaseResource> T apply(FhirContext theCtx, T theResourceToUpdate, String thePatchBody) {
public static <T extends IBaseResource> T apply(FhirContext theCtx, T theResourceToUpdate, @Language("JSON") String thePatchBody) {
// Parse the patch
ObjectMapper mapper = new ObjectMapper();
mapper.configure(JsonParser.Feature.INCLUDE_SOURCE_IN_LOCATION, false);
@ -54,7 +59,21 @@ public class JsonPatchUtils {
@SuppressWarnings("unchecked")
Class<T> clazz = (Class<T>) theResourceToUpdate.getClass();
T retVal = theCtx.newJsonParser().parseResource(clazz, mapper.writeValueAsString(after));
String postPatchedContent = mapper.writeValueAsString(after);
IParser fhirJsonParser = theCtx.newJsonParser();
fhirJsonParser.setParserErrorHandler(new StrictErrorHandler());
T retVal;
try {
retVal = fhirJsonParser.parseResource(clazz, postPatchedContent);
} catch (DataFormatException e) {
String resourceId = theResourceToUpdate.getIdElement().toUnqualifiedVersionless().getValue();
String resourceType = theCtx.getResourceDefinition(theResourceToUpdate).getName();
resourceId = defaultString(resourceId, resourceType);
String msg = theCtx.getLocalizer().getMessage(JsonPatchUtils.class, "failedToApplyPatch", resourceId, e.getMessage());
throw new InvalidRequestException(msg);
}
return retVal;
} catch (IOException | JsonPatchException theE) {

50
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/PatchProviderR4Test.java
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@ -7,10 +7,14 @@ import org.apache.http.client.methods.HttpPatch;
import org.apache.http.entity.ContentType;
import org.apache.http.entity.StringEntity;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Media;
import org.hl7.fhir.r4.model.Observation;
import org.hl7.fhir.r4.model.Patient;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import static org.hamcrest.CoreMatchers.containsString;
@ -19,6 +23,51 @@ import static org.junit.Assert.assertThat;
public class PatchProviderR4Test extends BaseResourceProviderR4Test {
private static final Logger ourLog = LoggerFactory.getLogger(PatchProviderR4Test.class);
@Test
public void testPatchAddArray() throws IOException {
IIdType id;
{
Media media = new Media();
media.setId("465eb73a-bce3-423a-b86e-5d0d267638f4");
media.setDuration(100L);
myMediaDao.update(media);
Observation obs = new Observation();
obs.addIdentifier().setSystem("urn:system").setValue("0");
id = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
}
String patchText = "[ " +
" {" +
" \"op\": \"add\"," +
" \"path\": \"/derivedFrom\"," +
" \"value\": [" +
" {\"reference\": \"/Media/465eb73a-bce3-423a-b86e-5d0d267638f4\"}" +
" ]" +
" } " +
"]";
HttpPatch patch = new HttpPatch(ourServerBase + "/Observation/" + id.getIdPart());
patch.setEntity(new StringEntity(patchText, ContentType.parse(Constants.CT_JSON_PATCH + Constants.CHARSET_UTF8_CTSUFFIX)));
patch.addHeader(Constants.HEADER_PREFER, Constants.HEADER_PREFER_RETURN + "=" + Constants.HEADER_PREFER_RETURN_REPRESENTATION);
patch.addHeader(Constants.HEADER_ACCEPT, Constants.CT_FHIR_JSON);
CloseableHttpResponse response = ourHttpClient.execute(patch);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String responseString = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info("Response:\n{}", responseString);
assertThat(responseString, containsString("\"derivedFrom\":[{\"reference\":\"Media/465eb73a-bce3-423a-b86e-5d0d267638f4\"}]"));
} finally {
response.close();
}
}
@Test
public void testPatchUsingJsonPatch() throws Exception {
String methodName = "testPatchUsingJsonPatch";
@ -186,5 +235,4 @@ public class PatchProviderR4Test extends BaseResourceProviderR4Test {
}
}

61
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/jsonpatch/JsonPatchUtilsTest.java
View File

@ -11,8 +11,7 @@ import org.springframework.transaction.PlatformTransactionManager;
import static org.hamcrest.CoreMatchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import static org.junit.Assert.*;
public class JsonPatchUtilsTest extends BaseJpaTest {
@ -48,12 +47,12 @@ public class JsonPatchUtilsTest extends BaseJpaTest {
public void testInvalidPatchSyntaxError() {
// Quotes are incorrect in the "value" body
String patchText = "[ {\n" +
" \"comment\": \"add image to examination\",\n" +
" \"patch\": [ {\n" +
" \"op\": \"foo\",\n" +
" \"path\": \"/derivedFrom/-\",\n" +
" \"value\": [{\"reference\": \"/Media/465eb73a-bce3-423a-b86e-5d0d267638f4\"}]\n" +
String patchText = "[ {" +
" \"comment\": \"add image to examination\"," +
" \"patch\": [ {" +
" \"op\": \"foo\"," +
" \"path\": \"/derivedFrom/-\"," +
" \"value\": [{\"reference\": \"/Media/465eb73a-bce3-423a-b86e-5d0d267638f4\"}]" +
" } ]\n" +
" } ]";
@ -69,6 +68,52 @@ public class JsonPatchUtilsTest extends BaseJpaTest {
}
@Test
public void testPatchAddArray() {
String patchText = "[ " +
" {" +
" \"op\": \"add\"," +
" \"path\": \"/derivedFrom\"," +
" \"value\": [" +
" {\"reference\": \"/Media/465eb73a-bce3-423a-b86e-5d0d267638f4\"}" +
" ]" +
" } " +
"]";
Observation toUpdate = new Observation();
toUpdate = JsonPatchUtils.apply(ourCtx, toUpdate, patchText);
String outcome = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(toUpdate);
ourLog.info(outcome);
assertThat(outcome, containsString("\"reference\": \"Media/465eb73a-bce3-423a-b86e-5d0d267638f4\""));
}
@Test
public void testPatchAddInvalidElement() {
String patchText = "[ " +
" {" +
" \"op\": \"add\"," +
" \"path\": \"/derivedFromXXX\"," +
" \"value\": [" +
" {\"reference\": \"/Media/465eb73a-bce3-423a-b86e-5d0d267638f4\"}" +
" ]" +
" } " +
"]";
Observation toUpdate = new Observation();
try {
JsonPatchUtils.apply(ourCtx, toUpdate, patchText);
fail();
} catch (InvalidRequestException e) {
assertEquals("Failed to apply JSON patch to Observation: Unknown element 'derivedFromXXX' found during parse", e.getMessage());
}
}
@Override
protected FhirContext getContext() {
return ourCtx;

14
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/util/BundleUtilTest.java
View File

@ -2,10 +2,13 @@ package ca.uhn.fhir.util;
import ca.uhn.fhir.context.FhirContext;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Patient;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.Test;
import java.util.List;
public class BundleUtilTest {
private static FhirContext ourCtx = FhirContext.forR4();
@ -38,6 +41,17 @@ public class BundleUtilTest {
Assert.assertEquals(null, BundleUtil.getTotal(ourCtx, b));
}
@Test
public void toListOfResourcesOfTypeTest() {
Bundle bundle = new Bundle();
for (int i = 0; i < 5; i++) {
bundle.addEntry(new Bundle.BundleEntryComponent().setResource(new Patient()));
}
List<Patient> list = BundleUtil.toListOfResourcesOfType(ourCtx, bundle, Patient.class);
Assert.assertEquals(5, list.size());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();

3
pom.xml
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@ -544,7 +544,8 @@
<jaxb_core_version>2.3.0.1</jaxb_core_version>
<jaxb_runtime_version>2.3.1</jaxb_runtime_version>
<jersey_version>2.25.1</jersey_version>
<jetty_version>9.4.17.v20190418</jetty_version>
<!-- 9.4.17 seems to have issues -->
<jetty_version>9.4.14.v20181114</jetty_version>
<jsr305_version>3.0.2</jsr305_version>
<!--<hibernate_version>5.2.10.Final</hibernate_version>-->
<hibernate_version>5.4.2.Final</hibernate_version>

7
src/changes/changes.xml
View File

@ -19,7 +19,7 @@
<li>Spring-Data (JPA): 2.1.3.RELEASE -&gt; 2.1.6.RELEASE</li>
<li>Caffeine (JPA): 2.6.2 -&gt; 2.7.0</li>
<li>JANSI (CLI): 1.16 -&gt; 1.17.1</li>
<li>Jetty (CLI): 9.4.14.v20181114 -&gt; 9.4.17.v20190418</li>
<!--<li>Jetty (CLI): 9.4.14.v20181114 -&gt; 9.4.17.v20190418</li>-->
</ul>
]]>
</action>
@ -181,6 +181,11 @@
<action type="fix">
Ensure that database cursors are closed immediately after performing a FHIR search.
</action>
<action type="add">
When performing a JSON Patch in JPA server, the post-patched document is now validated to
ensure that the patch was valid for the candidate resource. This means that invalid patches
are caught and not just silently ignored.
</action>
<action type="add">
Expunges are now done in batches in multiple threads. Both the number of expunge threads and batch size are configurable
in DaoConfig.