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Revert Jetty upgrade, and improve patch error messages

This commit is contained in:
James Agnew 2019-04-26 11:21:42 -04:00
parent 9e9a1ed06d
commit 685adf7754
7 changed files with 140 additions and 14 deletions
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2
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
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@ -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
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@ -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
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@ -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;

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
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@ -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>
</release>
<release version="3.7.0" date="2019-02-06" description="Gale">
<action type="add">