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hapi-fhir
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Code Issues Packages Projects Releases Wiki Activity

Improve batch2 error handling (#3482) 

* Improve batch2 error handling

* Build fixes

* Work on reindexing

* Test fixes

* Account for gzipped contents

* License header updates

* Register VS operations on public server

* Test fix

* Build fix

* Remove animal sniffer plugin

* Compile fix
This commit is contained in:
James Agnew 2022-03-26 17:40:12 -04:00 committed by GitHub
parent 625ed936e9
commit b833c13a3c
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41 changed files with 633 additions and 187 deletions
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4
README.md
View File

@ -10,8 +10,10 @@ HAPI FHIR - Java API for HL7 FHIR Clients and Servers
| :---: | :---: | :---: |
| [![Build Status][Badge-AzurePipelineMaster]][Link-AzurePipelinesMaster] | [![Build Status][Badge-AzureReleaseSnapshot]][Link-AzurePipelinesSnapshot] | [![Release Artifacts][Badge-MavenCentral]][Link-MavenCentral] |
## Test Coverage
## Coverage and Quality
[![codecov][Badge-CodeCov]][Link-CodeCov]
[![Language grade: Java](https://img.shields.io/lgtm/grade/java/g/hapifhir/hapi-fhir.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/hapifhir/hapi-fhir/context:java)
## Documentation and wiki

25
hapi-deployable-pom/pom.xml
View File

@ -18,27 +18,6 @@
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
<executions>
<execution>
<id>check-java-api</id>
<phase>test</phase>
<inherited>true</inherited>
<goals>
<goal>check</goal>
</goals>
<configuration>
<signature>
<groupId>org.codehaus.mojo.signature</groupId>
<artifactId>java18</artifactId>
<version>1.0</version>
</signature>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>
@ -196,7 +175,7 @@
</links>
<additionalparam>-Xdoclint:none</additionalparam>
<additionalJOption>-Xdoclint:none</additionalJOption>
<source>8</source>
<source>11</source>
</configuration>
</reportSet>
</reportSets>
@ -220,7 +199,7 @@
<verbose>false</verbose>
<debug>false</debug>
<additionalJOption>-Xdoclint:none</additionalJOption>
<source>8</source>
<source>11</source>
</configuration>
<executions>
<execution>

5
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/api/IBaseInterceptorService.java
View File

@ -91,4 +91,9 @@ public interface IBaseInterceptorService<POINTCUT extends IPointcut> extends IBa
* Unregisters all interceptors that are indicated by the given callback function returning <code>true</code>
*/
void unregisterInterceptorsIf(Predicate<Object> theShouldUnregisterFunction);
/**
* Unregisters all anonymous interceptors (i.e. all interceptors registered with <code>registerAnonymousInterceptor</code>)
*/
void unregisterAllAnonymousInterceptors();
}

63
hapi-fhir-base/src/main/java/ca/uhn/fhir/interceptor/executor/BaseInterceptorService.java
View File

@ -163,6 +163,13 @@ public abstract class BaseInterceptorService<POINTCUT extends IPointcut> impleme
}
}
@Override
public void unregisterAllAnonymousInterceptors() {
synchronized (myRegistryMutex) {
unregisterInterceptorsIf(t -> true, myAnonymousInvokers);
}
}
@Override
public void unregisterInterceptorsIf(Predicate<Object> theShouldUnregisterFunction) {
unregisterInterceptorsIf(theShouldUnregisterFunction, myGlobalInvokers);
@ -170,7 +177,9 @@ public abstract class BaseInterceptorService<POINTCUT extends IPointcut> impleme
}
private void unregisterInterceptorsIf(Predicate<Object> theShouldUnregisterFunction, ListMultimap<POINTCUT, BaseInvoker> theGlobalInvokers) {
theGlobalInvokers.entries().removeIf(t -> theShouldUnregisterFunction.test(t.getValue().getInterceptor()));
synchronized (myRegistryMutex) {
theGlobalInvokers.entries().removeIf(t -> theShouldUnregisterFunction.test(t.getValue().getInterceptor()));
}
}
@Override
@ -476,6 +485,32 @@ public abstract class BaseInterceptorService<POINTCUT extends IPointcut> impleme
protected abstract Optional<HookDescriptor> scanForHook(Method nextMethod);
protected static <T extends Annotation> Optional<T> findAnnotation(AnnotatedElement theObject, Class<T> theHookClass) {
T annotation;
if (theObject instanceof Method) {
annotation = MethodUtils.getAnnotation((Method) theObject, theHookClass, true, true);
} else {
annotation = theObject.getAnnotation(theHookClass);
}
return Optional.ofNullable(annotation);
}
private static int determineOrder(Class<?> theInterceptorClass) {
int typeOrder = Interceptor.DEFAULT_ORDER;
Optional<Interceptor> typeOrderAnnotation = findAnnotation(theInterceptorClass, Interceptor.class);
if (typeOrderAnnotation.isPresent()) {
typeOrder = typeOrderAnnotation.get().order();
}
return typeOrder;
}
private static String toErrorString(List<String> theParameterTypes) {
return theParameterTypes
.stream()
.sorted()
.collect(Collectors.joining(","));
}
protected abstract static class BaseInvoker implements Comparable<BaseInvoker> {
private final int myOrder;
@ -605,30 +640,4 @@ public abstract class BaseInterceptorService<POINTCUT extends IPointcut> impleme
}
protected static <T extends Annotation> Optional<T> findAnnotation(AnnotatedElement theObject, Class<T> theHookClass) {
T annotation;
if (theObject instanceof Method) {
annotation = MethodUtils.getAnnotation((Method) theObject, theHookClass, true, true);
} else {
annotation = theObject.getAnnotation(theHookClass);
}
return Optional.ofNullable(annotation);
}
private static int determineOrder(Class<?> theInterceptorClass) {
int typeOrder = Interceptor.DEFAULT_ORDER;
Optional<Interceptor> typeOrderAnnotation = findAnnotation(theInterceptorClass, Interceptor.class);
if (typeOrderAnnotation.isPresent()) {
typeOrder = typeOrderAnnotation.get().order();
}
return typeOrder;
}
private static String toErrorString(List<String> theParameterTypes) {
return theParameterTypes
.stream()
.sorted()
.collect(Collectors.joining(","));
}
}

51
hapi-fhir-cli/hapi-fhir-cli-api/src/main/java/ca/uhn/fhir/cli/BulkImportCommand.java
View File

@ -20,8 +20,8 @@ package ca.uhn.fhir.cli;
* #L%
*/
import ca.uhn.fhir.batch2.jobs.imprt.BulkImportFileServlet;
import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
import ca.uhn.fhir.batch2.jobs.imprt.BulkImportFileServlet;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
@ -32,8 +32,12 @@ import ca.uhn.fhir.util.ParametersUtil;
import org.apache.commons.cli.CommandLine;
import org.apache.commons.cli.Options;
import org.apache.commons.cli.ParseException;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOCase;
import org.apache.commons.io.LineIterator;
import org.apache.commons.io.file.PathUtils;
import org.apache.commons.io.filefilter.FileFileFilter;
import org.apache.commons.io.filefilter.IOFileFilter;
import org.apache.commons.io.filefilter.SuffixFileFilter;
import org.eclipse.jetty.server.Connector;
import org.eclipse.jetty.server.Server;
import org.eclipse.jetty.server.ServerConnector;
@ -47,12 +51,20 @@ import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import java.io.File;
import java.io.FileReader;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.nio.charset.StandardCharsets;
import java.nio.file.FileVisitOption;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Locale;
import java.util.concurrent.ExecutionException;
import java.util.zip.GZIPInputStream;
public class BulkImportCommand extends BaseCommand {
@ -86,7 +98,7 @@ public class BulkImportCommand extends BaseCommand {
addFhirVersionOption(options);
addRequiredOption(options, null, PORT, PORT, "The port to listen on. If set to 0, an available free port will be selected.");
addOptionalOption(options, null, SOURCE_BASE, "base url", "The URL to advertise as the base URL for accessing the files (i.e. this is the address that this command will declare that it is listening on). If not present, the server will default to \"http://localhost:[port]\" which will only work if the server is on the same host.");
addRequiredOption(options, null, SOURCE_DIRECTORY, "directory", "The source directory. This directory will be scanned for files with an extension of .json or .ndjson and any files in this directory will be assumed to be NDJSON and uploaded. This command will read the first resource from each file to verify its resource type, and will assume that all resources in the file are of the same type.");
addRequiredOption(options, null, SOURCE_DIRECTORY, "directory", "The source directory. This directory will be scanned for files with an extensions of .json, .ndjson, .json.gz and .ndjson.gz, and any files in this directory will be assumed to be NDJSON and uploaded. This command will read the first resource from each file to verify its resource type, and will assume that all resources in the file are of the same type.");
addRequiredOption(options, null, TARGET_BASE, "base url", "The base URL of the target FHIR server.");
addBasicAuthOption(options);
return options;
@ -169,7 +181,18 @@ public class BulkImportCommand extends BaseCommand {
myServlet = new BulkImportFileServlet();
for (File t : files) {
BulkImportFileServlet.IFileSupplier fileSupplier = () -> new FileReader(t);
BulkImportFileServlet.IFileSupplier fileSupplier = new BulkImportFileServlet.IFileSupplier() {
@Override
public boolean isGzip() {
return t.getName().toLowerCase(Locale.ROOT).endsWith(".gz");
}
@Override
public InputStream get() throws IOException {
return new FileInputStream(t);
}
};
indexes.add(myServlet.registerFile(fileSupplier));
}
@ -195,18 +218,28 @@ public class BulkImportCommand extends BaseCommand {
private void scanDirectoryForJsonFiles(String baseDirectory, List<String> types, List<File> files) {
try {
File directory = new File(baseDirectory);
FileUtils
.streamFiles(directory, false, "json", "ndjson", "JSON", "NDJSON")
final String[] extensions = new String[]{".json", ".ndjson", ".json.gz", ".ndjson.gz"};
final IOFileFilter filter = FileFileFilter.INSTANCE.and(new SuffixFileFilter(extensions, IOCase.INSENSITIVE));
PathUtils
.walk(directory.toPath(), filter, 1, false, FileVisitOption.FOLLOW_LINKS)
.map(Path::toFile)
.filter(t -> t.isFile())
.filter(t -> t.exists())
.forEach(t -> files.add(t));
if (files.isEmpty()) {
throw new CommandFailureException(Msg.code(2058) + "No .json/.ndjson files found in directory: " + directory.getAbsolutePath());
throw new CommandFailureException(Msg.code(2058) + "No files found in directory \"" + directory.getAbsolutePath() + "\". Allowed extensions: " + Arrays.asList(extensions));
}
FhirContext ctx = getFhirContext();
for (File next : files) {
try (Reader reader = new FileReader(next)) {
try (InputStream nextIs = new FileInputStream(next)) {
InputStream is;
if (next.getName().toLowerCase(Locale.ROOT).endsWith(".gz")) {
is = new GZIPInputStream(nextIs);
} else {
is = nextIs;
}
Reader reader = new InputStreamReader(is, StandardCharsets.UTF_8);
LineIterator lineIterator = new LineIterator(reader);
String firstLine = lineIterator.next();
IBaseResource resource = ctx.newJsonParser().parseResource(firstLine);

50
hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/BulkImportCommandTest.java
View File

@ -25,12 +25,16 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.Writer;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.zip.GZIPOutputStream;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.Matchers.equalTo;
@ -111,6 +115,40 @@ public class BulkImportCommandTest {
assertEquals(fileContents1, fetchFile(jobParameters.getNdJsonUrls().get(1)));
}
@Test
public void testBulkImport_GzippedFile() throws IOException {
String fileContents1 = "{\"resourceType\":\"Observation\"}\n{\"resourceType\":\"Observation\"}";
String fileContents2 = "{\"resourceType\":\"Patient\"}\n{\"resourceType\":\"Patient\"}";
writeNdJsonFileToTempDirectory(fileContents1, "file1.json.gz");
writeNdJsonFileToTempDirectory(fileContents2, "file2.json.gz");
when(myJobCoordinator.startInstance(any())).thenReturn("THE-JOB-ID");
// Start the command in a separate thread
new Thread(() -> App.main(new String[]{
BulkImportCommand.BULK_IMPORT,
"--" + BaseCommand.FHIR_VERSION_PARAM_LONGOPT, "r4",
"--" + BulkImportCommand.PORT, "0",
"--" + BulkImportCommand.SOURCE_DIRECTORY, myTempDir.toAbsolutePath().toString(),
"--" + BulkImportCommand.TARGET_BASE, myRestfulServerExtension.getBaseUrl()
})).start();
ourLog.info("Waiting for initiation requests");
await().until(() -> myRestfulServerExtension.getRequestContentTypes().size(), equalTo(2));
ourLog.info("Initiation requests complete");
verify(myJobCoordinator, timeout(10000).times(1)).startInstance(myStartCaptor.capture());
JobInstanceStartRequest startRequest = myStartCaptor.getValue();
BulkImportJobParameters jobParameters = startRequest.getParameters(BulkImportJobParameters.class);
// Reverse order because Patient should be first
assertEquals(2, jobParameters.getNdJsonUrls().size());
assertEquals(fileContents2, fetchFile(jobParameters.getNdJsonUrls().get(0)));
assertEquals(fileContents1, fetchFile(jobParameters.getNdJsonUrls().get(1)));
}
private String fetchFile(String url) throws IOException {
String outcome;
try (CloseableHttpResponse response = myHttpClientExtension.getClient().execute(new HttpGet(url))) {
@ -120,9 +158,15 @@ public class BulkImportCommandTest {
return outcome;
}
private void writeNdJsonFileToTempDirectory(String fileContents1, String fileName) throws IOException {
try (Writer w = new FileWriter(new File(myTempDir.toFile(), fileName))) {
w.append(fileContents1);
private void writeNdJsonFileToTempDirectory(String theContents, String theFileName) throws IOException {
try (FileOutputStream fos = new FileOutputStream(new File(myTempDir.toFile(), theFileName), false)) {
OutputStream os = fos;
if (theFileName.endsWith(".gz")) {
os = new GZIPOutputStream(os);
}
try (Writer w = new OutputStreamWriter(os)) {
w.append(theContents);
}
}
}

7
hapi-fhir-docs/pom.xml
View File

@ -126,13 +126,6 @@
<build>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>

7
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_0_0/3482-streamline-presence-updates.yaml Normal file
View File

@ -0,0 +1,7 @@
---
type: perf
issue: 3482
title: "When updating or reindexing a resource on a JPA server where indexing search param presence is
enabled (i.e. support for the `:missing` modifier), updates will try to reuse existing database rows
where possible instead of deleting one row and adding another. This should cause a slight performance
boost systems with this feature enabled."

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
View File

@ -355,7 +355,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
}
}
// Populate the resource with it's actual final stored ID from the entity
// Populate the resource with its actual final stored ID from the entity
theResource.setId(entity.getIdDt());
// Pre-cache the resource ID

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -1,5 +1,6 @@
package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.model.ExpungeOptions;
import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
@ -193,6 +194,11 @@ public abstract class BaseHapiFhirSystemDao<T extends IBaseBundle, MT> extends B
preFetchIndexes(entityIds, "tags", "myTags", null);
}
entityIds = loadedResourceTableEntries.stream().map(t->t.getId()).collect(Collectors.toList());
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.ENABLED) {
preFetchIndexes(entityIds, "searchParamPresence", "mySearchParamPresents", null);
}
new QueryChunker<ResourceTable>().chunk(loadedResourceTableEntries, SearchBuilder.getMaximumPageSize() / 2, entries -> {
Map<Long, ResourceTable> entities = entries

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ISearchParamPresentDao.java
View File

@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresentEntity;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Modifying;
import org.springframework.data.jpa.repository.Query;
@ -29,13 +29,13 @@ import java.util.List;
* #L%
*/
public interface ISearchParamPresentDao extends JpaRepository<SearchParamPresent, Long>, IHapiFhirJpaRepository {
public interface ISearchParamPresentDao extends JpaRepository<SearchParamPresentEntity, Long>, IHapiFhirJpaRepository {
@Query("SELECT s FROM SearchParamPresent s WHERE s.myResource = :res")
List<SearchParamPresent> findAllForResource(@Param("res") ResourceTable theResource);
@Query("SELECT s FROM SearchParamPresentEntity s WHERE s.myResource = :res")
List<SearchParamPresentEntity> findAllForResource(@Param("res") ResourceTable theResource);
@Modifying
@Query("delete from SearchParamPresent t WHERE t.myResourcePid = :resid")
@Query("delete from SearchParamPresentEntity t WHERE t.myResourcePid = :resid")
void deleteByResourceId(@Param("resid") Long theResourcePid);
}

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

@ -65,7 +65,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresentEntity;
import ca.uhn.fhir.jpa.model.entity.TagDefinition;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.rest.server.util.CompositeInterceptorBroadcaster;
@ -133,7 +133,7 @@ public class ExpungeEverythingService {
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageVersionResourceEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageVersionEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(NpmPackageEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SearchParamPresent.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(SearchParamPresentEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(BulkImportJobFileEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(BulkImportJobEntity.class));
counter.addAndGet(expungeEverythingByTypeWithoutPurging(ForcedId.class));

46
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/index/DaoResourceLinkResolver.java
View File

@ -35,7 +35,6 @@ import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.model.cross.IResourceLookup;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.extractor.IResourceLinkResolver;
import ca.uhn.fhir.jpa.util.MemoryCacheService;
import ca.uhn.fhir.mdm.util.CanonicalIdentifier;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
@ -62,6 +61,7 @@ import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.nio.charset.StandardCharsets;
import java.util.Date;
import java.util.List;
import java.util.Optional;
@ -80,11 +80,23 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
@Override
public IResourceLookup findTargetResource(@Nonnull RequestPartitionId theRequestPartitionId, RuntimeSearchParam theSearchParam, String theSourcePath, IIdType theSourceResourceId, String theResourceType, Class<? extends IBaseResource> theType, IBaseReference theReference, RequestDetails theRequest, TransactionDetails theTransactionDetails) {
ResourcePersistentId persistentId = null;
if (theTransactionDetails != null) {
ResourcePersistentId resolvedResourceId = theTransactionDetails.getResolvedResourceId(theSourceResourceId);
if (resolvedResourceId != null && resolvedResourceId.getIdAsLong() != null && resolvedResourceId.getAssociatedResourceId() != null) {
persistentId = resolvedResourceId;
}
}
IResourceLookup resolvedResource;
String idPart = theSourceResourceId.getIdPart();
try {
resolvedResource = myIdHelperService.resolveResourceIdentity(theRequestPartitionId, theResourceType, idPart);
ourLog.trace("Translated {}/{} to resource PID {}", theType, idPart, resolvedResource);
if (persistentId == null) {
resolvedResource = myIdHelperService.resolveResourceIdentity(theRequestPartitionId, theResourceType, idPart);
ourLog.trace("Translated {}/{} to resource PID {}", theType, idPart, resolvedResource);
} else {
resolvedResource = new ResourceLookupPersistentIdWrapper(persistentId);
}
} catch (ResourceNotFoundException e) {
Optional<ResourceTable> createdTableOpt = createPlaceholderTargetIfConfiguredToDoSo(theType, theReference, idPart, theRequest, theTransactionDetails);
@ -113,6 +125,12 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
throw new InvalidRequestException(Msg.code(1096) + "Resource " + resName + "/" + idPart + " is deleted, specified in path: " + theSourcePath);
}
if (persistentId == null) {
persistentId = new ResourcePersistentId(resolvedResource.getResourceId());
persistentId.setAssociatedResourceId(theSourceResourceId);
theTransactionDetails.addResolvedResourceId(theSourceResourceId, persistentId);
}
if (!theSearchParam.hasTargets() && theSearchParam.getTargets().contains(theResourceType)) {
return null;
}
@ -271,4 +289,26 @@ public class DaoResourceLinkResolver implements IResourceLinkResolver {
myDaoRegistry.getDaoOrThrowException(theType);
}
private static class ResourceLookupPersistentIdWrapper implements IResourceLookup {
private final ResourcePersistentId myPersistentId;
public ResourceLookupPersistentIdWrapper(ResourcePersistentId thePersistentId) {
myPersistentId = thePersistentId;
}
@Override
public String getResourceType() {
return myPersistentId.getAssociatedResourceId().getResourceType();
}
@Override
public Long getResourceId() {
return myPersistentId.getIdAsLong();
}
@Override
public Date getDeleted() {
return null;
}
}
}

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/predicate/BasePredicateBuilder.java
View File

@ -29,7 +29,7 @@ import ca.uhn.fhir.jpa.dao.predicate.querystack.QueryStack;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.BasePartitionable;
import ca.uhn.fhir.jpa.model.entity.BaseResourceIndexedSearchParam;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresentEntity;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.param.ParamPrefixEnum;
@ -78,10 +78,10 @@ abstract class BasePredicateBuilder {
}
void addPredicateParamMissingForReference(String theResourceName, String theParamName, boolean theMissing, RequestPartitionId theRequestPartitionId) {
From<?, SearchParamPresent> paramPresentJoin = myQueryStack.createJoin(SearchBuilderJoinEnum.PRESENCE, null);
From<?, SearchParamPresentEntity> paramPresentJoin = myQueryStack.createJoin(SearchBuilderJoinEnum.PRESENCE, null);
Expression<Long> hashPresence = paramPresentJoin.get("myHashPresence").as(Long.class);
Long hash = SearchParamPresent.calculateHashPresence(myPartitionSettings, theRequestPartitionId, theResourceName, theParamName, !theMissing);
Long hash = SearchParamPresentEntity.calculateHashPresence(myPartitionSettings, theRequestPartitionId, theResourceName, theParamName, !theMissing);
List<Predicate> predicates = new ArrayList<>();
predicates.add(myCriteriaBuilder.equal(hashPresence, hash));

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/migrate/tasks/HapiFhirJpaMigrationTasks.java
View File

@ -37,7 +37,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamQuantity;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamUri;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresentEntity;
import ca.uhn.fhir.util.VersionEnum;
import java.util.Arrays;
@ -1608,7 +1608,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
Boolean present = columnToBoolean(t.get("SP_PRESENT"));
String resType = (String) t.get("RES_TYPE");
String paramName = (String) t.get("PARAM_NAME");
Long hash = SearchParamPresent.calculateHashPresence(new PartitionSettings(), (RequestPartitionId) null, resType, paramName, present);
Long hash = SearchParamPresentEntity.calculateHashPresence(new PartitionSettings(), (RequestPartitionId) null, resType, paramName, present);
consolidateSearchParamPresenceIndexesTask.executeSql("HFJ_RES_PARAM_PRESENT", "update HFJ_RES_PARAM_PRESENT set HASH_PRESENCE = ? where PID = ?", hash, pid);
});
version.addTask(consolidateSearchParamPresenceIndexesTask);

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/builder/predicate/SearchParamPresentPredicateBuilder.java
View File

@ -22,7 +22,7 @@ package ca.uhn.fhir.jpa.search.builder.predicate;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresentEntity;
import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
import com.healthmarketscience.sqlbuilder.BinaryCondition;
import com.healthmarketscience.sqlbuilder.Condition;
@ -53,7 +53,7 @@ public class SearchParamPresentPredicateBuilder extends BaseJoiningPredicateBuil
public Condition createPredicateParamMissingForReference(String theResourceName, String theParamName, boolean theMissing, RequestPartitionId theRequestPartitionId) {
Long hash = SearchParamPresent.calculateHashPresence(myPartitionSettings, theRequestPartitionId, theResourceName, theParamName, !theMissing);
Long hash = SearchParamPresentEntity.calculateHashPresence(myPartitionSettings, theRequestPartitionId, theResourceName, theParamName, !theMissing);
BinaryCondition predicate = BinaryCondition.equalTo(myColumnHashPresence, generatePlaceholder(hash));
return combineWithRequestPartitionIdPredicate(theRequestPartitionId, predicate);
}

41
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/sp/SearchParamPresenceSvcImpl.java
View File

@ -24,7 +24,7 @@ import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ISearchParamPresentDao;
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresentEntity;
import ca.uhn.fhir.jpa.util.AddRemoveCount;
import com.google.common.annotations.VisibleForTesting;
import org.springframework.beans.factory.annotation.Autowired;
@ -54,8 +54,7 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
}
@Override
public AddRemoveCount
updatePresence(ResourceTable theResource, Map<String, Boolean> theParamNameToPresence) {
public AddRemoveCount updatePresence(ResourceTable theResource, Map<String, Boolean> theParamNameToPresence) {
AddRemoveCount retVal = new AddRemoveCount();
if (myDaoConfig.getIndexMissingFields() == DaoConfig.IndexEnabledEnum.DISABLED) {
return retVal;
@ -64,19 +63,18 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
Map<String, Boolean> presenceMap = new HashMap<>(theParamNameToPresence);
// Find existing entries
Collection<SearchParamPresent> existing;
existing = mySearchParamPresentDao.findAllForResource(theResource);
Map<Long, SearchParamPresent> existingHashToPresence = new HashMap<>();
for (SearchParamPresent nextExistingEntity : existing) {
Collection<SearchParamPresentEntity> existing = theResource.getSearchParamPresents();
Map<Long, SearchParamPresentEntity> existingHashToPresence = new HashMap<>();
for (SearchParamPresentEntity nextExistingEntity : existing) {
existingHashToPresence.put(nextExistingEntity.getHashPresence(), nextExistingEntity);
}
// Find newly wanted set of entries
Map<Long, SearchParamPresent> newHashToPresence = new HashMap<>();
Map<Long, SearchParamPresentEntity> newHashToPresence = new HashMap<>();
for (Entry<String, Boolean> next : presenceMap.entrySet()) {
String paramName = next.getKey();
SearchParamPresent present = new SearchParamPresent();
SearchParamPresentEntity present = new SearchParamPresentEntity();
present.setPartitionSettings(myPartitionSettings);
present.setResource(theResource);
present.setParamName(paramName);
@ -88,22 +86,33 @@ public class SearchParamPresenceSvcImpl implements ISearchParamPresenceSvc {
}
// Delete any that should be deleted
List<SearchParamPresent> toDelete = new ArrayList<>();
for (Entry<Long, SearchParamPresent> nextEntry : existingHashToPresence.entrySet()) {
List<SearchParamPresentEntity> toDelete = new ArrayList<>();
for (Entry<Long, SearchParamPresentEntity> nextEntry : existingHashToPresence.entrySet()) {
if (newHashToPresence.containsKey(nextEntry.getKey()) == false) {
toDelete.add(nextEntry.getValue());
}
}
mySearchParamPresentDao.deleteAll(toDelete);
retVal.addToRemoveCount(toDelete.size());
// Add any that should be added
List<SearchParamPresent> toAdd = new ArrayList<>();
for (Entry<Long, SearchParamPresent> nextEntry : newHashToPresence.entrySet()) {
List<SearchParamPresentEntity> toAdd = new ArrayList<>();
for (Entry<Long, SearchParamPresentEntity> nextEntry : newHashToPresence.entrySet()) {
if (existingHashToPresence.containsKey(nextEntry.getKey()) == false) {
toAdd.add(nextEntry.getValue());
}
}
// Try to reuse any entities we can
while (toDelete.size() > 0 && toAdd.size() > 0) {
SearchParamPresentEntity nextToDelete = toDelete.remove(toDelete.size() - 1);
SearchParamPresentEntity nextToAdd = toAdd.remove(toAdd.size() - 1);
nextToDelete.updateValues(nextToAdd);
mySearchParamPresentDao.save(nextToDelete);
retVal.addToAddCount(1);
retVal.addToRemoveCount(1);
}
mySearchParamPresentDao.deleteAll(toDelete);
retVal.addToRemoveCount(toDelete.size());
mySearchParamPresentDao.saveAll(toAdd);
retVal.addToRemoveCount(toAdd.size());

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImplTest.java
View File

@ -8,6 +8,7 @@ import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.jpa.dao.data.IBatch2JobInstanceRepository;
import ca.uhn.fhir.jpa.dao.data.IBatch2WorkChunkRepository;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
import ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity;
import ca.uhn.fhir.util.JsonUtil;

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/bulk/imprt2/BulkImportR4Test.java
View File

@ -203,7 +203,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
int fileCount = 3;
List<String> indexes = addFiles(fileCount - 1);
indexes.add(myBulkImportFileServlet.registerFile(() -> new StringReader("{\"resourceType\":\"Foo\"}")));
indexes.add(myBulkImportFileServlet.registerFileByContents("{\"resourceType\":\"Foo\"}"));
BulkImportJobParameters parameters = new BulkImportJobParameters();
for (String next : indexes) {
@ -378,7 +378,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
builder.append("\n");
builder.append("\n");
String index = myBulkImportFileServlet.registerFile(() -> new StringReader(builder.toString()));
String index = myBulkImportFileServlet.registerFileByContents(builder.toString());
retVal.add(index);
}
return retVal;

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java
View File

@ -3557,7 +3557,10 @@ public class FhirResourceDaoDstu3SearchNoFtTest extends BaseJpaDstu3Test {
myCaptureQueriesListener.clear();
myObservationDao.update(obs);
assertEquals(2, myCaptureQueriesListener.countUpdateQueries());
assertEquals(10, myCaptureQueriesListener.countSelectQueries());
assertEquals(5, myCaptureQueriesListener.countUpdateQueries());
assertEquals(1, myCaptureQueriesListener.countInsertQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
String unformattedSql = myCaptureQueriesListener.getUpdateQueriesForCurrentThread().get(0).getSql(true, false);
assertThat(unformattedSql, stringContainsInOrder(
"SRC_PATH='Observation.performer'",

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PartitioningSqlR4Test.java
View File

@ -19,7 +19,7 @@ import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.model.entity.ResourceLink;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.model.entity.ResourceTag;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresent;
import ca.uhn.fhir.jpa.model.entity.SearchParamPresentEntity;
import ca.uhn.fhir.jpa.model.util.JpaConstants;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
@ -442,7 +442,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
assertEquals(myPartitionDate, resourceLinks.get(0).getPartitionId().getPartitionDate());
// HFJ_RES_PARAM_PRESENT
List<SearchParamPresent> presents = mySearchParamPresentDao.findAllForResource(resourceTable);
List<SearchParamPresentEntity> presents = mySearchParamPresentDao.findAllForResource(resourceTable);
assertEquals(3, presents.size());
assertEquals(myPartitionId, presents.get(0).getPartitionId().getPartitionId().intValue());
assertEquals(myPartitionDate, presents.get(0).getPartitionId().getPartitionDate());
@ -529,7 +529,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
assertEquals(myPartitionDate, resourceLinks.get(0).getPartitionId().getPartitionDate());
// HFJ_RES_PARAM_PRESENT
List<SearchParamPresent> presents = mySearchParamPresentDao.findAllForResource(resourceTable);
List<SearchParamPresentEntity> presents = mySearchParamPresentDao.findAllForResource(resourceTable);
assertEquals(3, presents.size());
assertEquals(null, presents.get(0).getPartitionId().getPartitionId());
assertEquals(myPartitionDate, presents.get(0).getPartitionId().getPartitionDate());

69
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
View File

@ -3,11 +3,18 @@ package ca.uhn.fhir.jpa.delete.job;
import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexAppCtx;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexJobParameters;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.interceptor.api.HookParams;
import ca.uhn.fhir.interceptor.api.IAnonymousInterceptor;
import ca.uhn.fhir.interceptor.api.IPointcut;
import ca.uhn.fhir.interceptor.api.Pointcut;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Observation;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
import org.springframework.beans.factory.annotation.Autowired;
@ -29,6 +36,11 @@ public class ReindexJobTest extends BaseJpaR4Test {
myReindexTestHelper = new ReindexTestHelper(myFhirContext, myDaoRegistry, mySearchParamRegistry);
}
@AfterEach
public void after() {
myInterceptorRegistry.unregisterAllAnonymousInterceptors();
}
@Test
public void testReindex_ByUrl() {
// setup
@ -92,4 +104,61 @@ public class ReindexJobTest extends BaseJpaR4Test {
assertThat(myReindexTestHelper.getAlleleObservationIds(), hasSize(50));
}
@Test
public void testReindex_ExceptionThrownDuringWrite() {
// setup
myReindexTestHelper.createObservationWithAlleleExtension(Observation.ObservationStatus.FINAL);
myReindexTestHelper.createAlleleSearchParameter();
mySearchParamRegistry.forceRefresh();
// Throw an exception during reindex
IAnonymousInterceptor exceptionThrowingInterceptor = (pointcut, args) -> {
throw new NullPointerException("foo message");
};
myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.JPA_PERFTRACE_INFO, exceptionThrowingInterceptor);
// execute
JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
startRequest.setParameters(new ReindexJobParameters());
String id = myJobCoordinator.startInstance(startRequest);
JobInstance outcome = myBatch2JobHelper.awaitJobFailure(id);
// Verify
assertEquals(StatusEnum.ERRORED, outcome.getStatus());
assertEquals("java.lang.NullPointerException: foo message", outcome.getErrorMessage());
}
@Test
public void testReindex_FailureThrownDuringWrite() {
// setup
myReindexTestHelper.createObservationWithAlleleExtension(Observation.ObservationStatus.FINAL);
myReindexTestHelper.createAlleleSearchParameter();
mySearchParamRegistry.forceRefresh();
// Throw an error (will be treated as unrecoverable) during reindex
IAnonymousInterceptor exceptionThrowingInterceptor = (pointcut, args) -> {
throw new Error("foo message");
};
myInterceptorRegistry.registerAnonymousInterceptor(Pointcut.JPA_PERFTRACE_INFO, exceptionThrowingInterceptor);
// execute
JobInstanceStartRequest startRequest = new JobInstanceStartRequest();
startRequest.setJobDefinitionId(ReindexAppCtx.JOB_REINDEX);
startRequest.setParameters(new ReindexJobParameters());
String id = myJobCoordinator.startInstance(startRequest);
JobInstance outcome = myBatch2JobHelper.awaitJobFailure(id);
// Verify
assertEquals(StatusEnum.FAILED, outcome.getStatus());
assertEquals("java.lang.Error: foo message", outcome.getErrorMessage());
}
}

105
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/reindex/ReindexStepTest.java
View File

@ -5,9 +5,15 @@ import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.VoidModel;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexChunkIds;
import ca.uhn.fhir.batch2.jobs.reindex.ReindexStep;
import ca.uhn.fhir.jpa.api.config.DaoConfig;
import ca.uhn.fhir.jpa.dao.r4.BaseJpaR4Test;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.SearchParameter;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.Test;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
@ -31,6 +37,11 @@ public class ReindexStepTest extends BaseJpaR4Test {
@Captor
private ArgumentCaptor<String> myErrorCaptor;
@AfterEach
public void after() {
myDaoConfig.setIndexMissingFields(new DaoConfig().getIndexMissingFields());
}
@Test
public void testReindex_NoActionNeeded() {
@ -59,6 +70,36 @@ public class ReindexStepTest extends BaseJpaR4Test {
}
@Test
public void testReindex_NoActionNeeded_IndexMissingFieldsEnabled() {
// Setup
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON")).getIdPartAsLong();
Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS")).getIdPartAsLong();
ReindexChunkIds data = new ReindexChunkIds();
data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id0.toString()));
data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id1.toString()));
// Execute
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id");
// Verify
assertEquals(2, outcome.getRecordsProcessed());
assertEquals(6, myCaptureQueriesListener.logSelectQueries().size());
assertEquals(0, myCaptureQueriesListener.countInsertQueries());
assertEquals(0, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(1, myCaptureQueriesListener.getCommitCount());
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
}
@Test
public void testReindex_IndexesWereMissing() {
@ -93,6 +134,70 @@ public class ReindexStepTest extends BaseJpaR4Test {
}
@Test
public void testReindex_IndexesAddedAndRemoved_IndexMissingFieldsEnabled() {
// Setup
myDaoConfig.setIndexMissingFields(DaoConfig.IndexEnabledEnum.ENABLED);
IIdType orgId = createOrganization(withId("ORG"));
Long id0 = createPatient(withActiveTrue(), withFamily("SIMPSON"), withOrganization(orgId)).getIdPartAsLong();
Long id1 = createPatient(withActiveTrue(), withFamily("FLANDERS"), withOrganization(orgId)).getIdPartAsLong();
ReindexChunkIds data = new ReindexChunkIds();
data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id0.toString()));
data.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(id1.toString()));
SearchParameter sp = new SearchParameter();
sp.setType(Enumerations.SearchParamType.STRING);
sp.addBase("Patient");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setCode("family2");
sp.setExpression("Patient.name.family");
mySearchParameterDao.create(sp);
sp = new SearchParameter();
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.addBase("Patient");
sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
sp.setCode(Patient.SP_ORGANIZATION + "2");
sp.setExpression("Patient.managingOrganization");
mySearchParameterDao.create(sp);
sp = new SearchParameter();
sp.setType(Enumerations.SearchParamType.STRING);
sp.addBase("Patient");
sp.setStatus(Enumerations.PublicationStatus.RETIRED);
sp.setCode("family");
sp.setExpression("Patient.name.family");
mySearchParameterDao.create(sp);
sp = new SearchParameter();
sp.setType(Enumerations.SearchParamType.REFERENCE);
sp.addBase("Patient");
sp.setStatus(Enumerations.PublicationStatus.RETIRED);
sp.setCode(Patient.SP_ORGANIZATION);
sp.setExpression("Patient.managingOrganization");
mySearchParameterDao.create(sp);
mySearchParamRegistry.forceRefresh();
// Execute
myCaptureQueriesListener.clear();
RunOutcome outcome = myReindexStep.doReindex(data, myDataSink, "index-id", "chunk-id");
// Verify
assertEquals(2, outcome.getRecordsProcessed());
assertEquals(10, myCaptureQueriesListener.logSelectQueries().size());
assertEquals(0, myCaptureQueriesListener.countInsertQueries());
assertEquals(4, myCaptureQueriesListener.countUpdateQueries());
assertEquals(0, myCaptureQueriesListener.countDeleteQueries());
assertEquals(1, myCaptureQueriesListener.getCommitCount());
assertEquals(0, myCaptureQueriesListener.getRollbackCount());
}
@Test
public void testReindex_OneResourceReindexFailedButOthersSucceeded() {

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/util/Batch2JobHelper.java
View File

@ -2,11 +2,11 @@ package ca.uhn.fhir.jpa.util;
import ca.uhn.fhir.batch2.api.IJobCleanerService;
import ca.uhn.fhir.batch2.api.IJobCoordinator;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.StatusEnum;
import org.hamcrest.Matchers;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.concurrent.TimeUnit;
import static org.awaitility.Awaitility.await;
import static org.hamcrest.Matchers.equalTo;
@ -25,4 +25,12 @@ public class Batch2JobHelper {
}, equalTo(StatusEnum.COMPLETED));
}
public JobInstance awaitJobFailure(String theId) {
await().until(() -> {
myJobCleanerService.runCleanupPass();
return myJobCoordinator.getInstance(theId).getStatus();
}, Matchers.anyOf(equalTo(StatusEnum.ERRORED),equalTo(StatusEnum.FAILED)));
return myJobCoordinator.getInstance(theId);
}
}

9
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ResourceTable.java
View File

@ -264,7 +264,7 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
@OptimisticLock(excluded = true)
private Collection<SearchParamPresent> mySearchParamPresents;
private Collection<SearchParamPresentEntity> mySearchParamPresents;
@OneToMany(mappedBy = "myResource", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
@OptimisticLock(excluded = true)
@ -775,4 +775,11 @@ public class ResourceTable extends BaseHasResource implements Serializable, IBas
public void setLuceneIndexData(ExtendedLuceneIndexData theLuceneIndexData) {
myLuceneIndexData = theLuceneIndexData;
}
public Collection<SearchParamPresentEntity> getSearchParamPresents() {
if (mySearchParamPresents == null) {
mySearchParamPresents = new ArrayList<>();
}
return mySearchParamPresents;
}
}

16
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/SearchParamPresent.java → hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/SearchParamPresentEntity.java
View File

@ -34,7 +34,7 @@ import java.io.Serializable;
@Index(name = "IDX_RESPARMPRESENT_RESID", columnList = "RES_ID"),
@Index(name = "IDX_RESPARMPRESENT_HASHPRES", columnList = "HASH_PRESENCE")
})
public class SearchParamPresent extends BasePartitionable implements Serializable {
public class SearchParamPresentEntity extends BasePartitionable implements Serializable {
private static final long serialVersionUID = 1L;
@ -60,7 +60,7 @@ public class SearchParamPresent extends BasePartitionable implements Serializabl
/**
* Constructor
*/
public SearchParamPresent() {
public SearchParamPresentEntity() {
super();
}
@ -126,6 +126,18 @@ public class SearchParamPresent extends BasePartitionable implements Serializabl
myPartitionSettings = thePartitionSettings;
}
/**
* Copy all mutable values from the given source
*/
public void updateValues(SearchParamPresentEntity theSource) {
super.setPartitionId(theSource.getPartitionId());
setResource(theSource.getResource());
setPartitionSettings(theSource.getPartitionSettings());
setHashPresence(theSource.getHashPresence());
setParamName(theSource.getParamName());
setPresent(theSource.isPresent());
}
public static long calculateHashPresence(PartitionSettings thePartitionSettings, PartitionablePartitionId theRequestPartitionId, String theResourceType, String theParamName, Boolean thePresent) {
RequestPartitionId requestPartitionId = PartitionablePartitionId.toRequestPartitionId(theRequestPartitionId);
return calculateHashPresence(thePartitionSettings, requestPartitionId, theResourceType, theParamName, thePresent);

13
hapi-fhir-jpaserver-uhnfhirtest/src/main/java/ca/uhn/fhirtest/TestRestfulServer.java
View File

@ -16,6 +16,7 @@ import ca.uhn.fhir.jpa.provider.JpaCapabilityStatementProvider;
import ca.uhn.fhir.jpa.provider.JpaConformanceProviderDstu2;
import ca.uhn.fhir.jpa.provider.JpaSystemProviderDstu2;
import ca.uhn.fhir.jpa.provider.TerminologyUploaderProvider;
import ca.uhn.fhir.jpa.provider.ValueSetOperationProvider;
import ca.uhn.fhir.jpa.provider.dstu3.JpaConformanceProviderDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3;
import ca.uhn.fhir.jpa.provider.r4.JpaSystemProviderR4;
@ -265,20 +266,12 @@ public class TestRestfulServer extends RestfulServer {
registerInterceptor(cascadingDeleteInterceptor);
/*
* Bulk Export
* Register some providers
*/
registerProvider(myAppCtx.getBean(BulkDataExportProvider.class));
/*
* $reindex
*/
registerProvider(myAppCtx.getBean(ReindexProvider.class));
/*
* $diff operation
*/
registerProvider(myAppCtx.getBean(DiffProvider.class));
registerProvider(myAppCtx.getBean(ValueSetOperationProvider.class));
/*
* OpenAPI

7
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
View File

@ -63,13 +63,6 @@
<build>
<pluginManagement>
<plugins>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.basepom.maven</groupId>
<artifactId>duplicate-finder-maven-plugin</artifactId>

43
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/imprt/BulkImportFileServlet.java
View File

@ -26,6 +26,7 @@ import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.ReaderInputStream;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -34,7 +35,11 @@ import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.Map;
import java.util.UUID;
@ -46,8 +51,8 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
public class BulkImportFileServlet extends HttpServlet {
private static final long serialVersionUID = 8302513561762436076L;
public static final String INDEX_PARAM = "index";
private static final long serialVersionUID = 8302513561762436076L;
private static final Logger ourLog = LoggerFactory.getLogger(BulkImportFileServlet.class);
private final Map<String, IFileSupplier> myFileIds = new HashMap<>();
@ -93,8 +98,17 @@ public class BulkImportFileServlet extends HttpServlet {
theResponse.addHeader(Constants.HEADER_CONTENT_TYPE, CT_FHIR_NDJSON + CHARSET_UTF8_CTSUFFIX);
IFileSupplier supplier = myFileIds.get(indexParam);
try (Reader reader = supplier.get()) {
IOUtils.copy(reader, theResponse.getWriter());
if (supplier.isGzip()) {
theResponse.addHeader(Constants.HEADER_CONTENT_ENCODING, Constants.ENCODING_GZIP);
}
try (Reader reader = new InputStreamReader(supplier.get())) {
String string = IOUtils.toString(reader);
ourLog.info(string);
}
try (InputStream reader = supplier.get()) {
IOUtils.copy(reader, theResponse.getOutputStream());
}
}
@ -112,10 +126,29 @@ public class BulkImportFileServlet extends HttpServlet {
return index;
}
@FunctionalInterface
/**
* Mostly intended for unit tests, registers a file
* using raw file contents.
*/
public String registerFileByContents(String theFileContents) {
return registerFile(new IFileSupplier() {
@Override
public boolean isGzip() {
return false;
}
@Override
public InputStream get() {
return new ReaderInputStream(new StringReader(theFileContents), StandardCharsets.UTF_8);
}
});
}
public interface IFileSupplier {
Reader get() throws IOException;
boolean isGzip();
InputStream get() throws IOException;
}

27
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/LoadIdsStep.java
View File

@ -26,9 +26,7 @@ import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
import ca.uhn.fhir.batch2.api.RunOutcome;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.svc.IResourceReindexSvc;
import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
@ -39,6 +37,7 @@ import java.util.Collection;
import java.util.Date;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
@ -48,12 +47,6 @@ public class LoadIdsStep implements IJobStepWorker<ReindexJobParameters, Reindex
@Autowired
private IResourceReindexSvc myResourceReindexSvc;
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
private MatchUrlService myMatchUrlService;
@Nonnull
@Override
public RunOutcome run(@Nonnull StepExecutionDetails<ReindexJobParameters, ReindexChunkRange> theStepExecutionDetails, @Nonnull IJobDataSink<ReindexChunkIds> theDataSink) throws JobExecutionFailedException {
@ -67,7 +60,7 @@ public class LoadIdsStep implements IJobStepWorker<ReindexJobParameters, Reindex
Date nextStart = start;
RequestPartitionId requestPartitionId = theStepExecutionDetails.getParameters().getRequestPartitionId();
Set<ReindexChunkIds.Id> idBuffer = new HashSet<>();
Set<ReindexChunkIds.Id> idBuffer = new LinkedHashSet<>();
long previousLastTime = 0L;
int totalIdsFound = 0;
int chunkCount = 0;
@ -84,13 +77,6 @@ public class LoadIdsStep implements IJobStepWorker<ReindexJobParameters, Reindex
ourLog.info("Found {} IDs from {} to {}", nextChunk.getIds().size(), nextStart, nextChunk.getLastDate());
// If we get the same last time twice in a row, we've clearly reached the end
if (nextChunk.getLastDate().getTime() == previousLastTime) {
ourLog.info("Matching final timestamp of {}, loading is completed", new Date(previousLastTime));
break;
}
previousLastTime = nextChunk.getLastDate().getTime();
for (int i = 0; i < nextChunk.getIds().size(); i++) {
ReindexChunkIds.Id nextId = new ReindexChunkIds.Id();
nextId.setResourceType(nextChunk.getResourceTypes().get(i));
@ -98,9 +84,16 @@ public class LoadIdsStep implements IJobStepWorker<ReindexJobParameters, Reindex
idBuffer.add(nextId);
}
// If we get the same last time twice in a row, we've clearly reached the end
if (nextChunk.getLastDate().getTime() == previousLastTime) {
ourLog.info("Matching final timestamp of {}, loading is completed", new Date(previousLastTime));
break;
}
previousLastTime = nextChunk.getLastDate().getTime();
nextStart = nextChunk.getLastDate();
if (idBuffer.size() >= 1000) {
while (idBuffer.size() >= 1000) {
List<ReindexChunkIds.Id> submissionIds = new ArrayList<>();
for (Iterator<ReindexChunkIds.Id> iter = idBuffer.iterator(); iter.hasNext(); ) {

16
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexChunkIds.java
View File

@ -24,6 +24,8 @@ import ca.uhn.fhir.model.api.IModelJson;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import java.util.ArrayList;
import java.util.List;
@ -40,6 +42,13 @@ public class ReindexChunkIds implements IModelJson {
return myIds;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("ids", myIds)
.toString();
}
public static class Id implements IModelJson {
@ -48,6 +57,13 @@ public class ReindexChunkIds implements IModelJson {
@JsonProperty("id")
private String myId;
@Override
public String toString() {
// We put a space in here and not a "/" since this is a PID, not
// a resource ID
return "[" + myResourceType + " " + myId + "]";
}
public String getResourceType() {
return myResourceType;
}

6
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexChunkRange.java
View File

@ -63,8 +63,9 @@ public class ReindexChunkRange implements IModelJson {
return myStart;
}
public void setStart(@Nonnull Date theStart) {
public ReindexChunkRange setStart(@Nonnull Date theStart) {
myStart = theStart;
return this;
}
@Nonnull
@ -72,8 +73,9 @@ public class ReindexChunkRange implements IModelJson {
return myEnd;
}
public void setEnd(@Nonnull Date theEnd) {
public ReindexChunkRange setEnd(@Nonnull Date theEnd) {
myEnd = theEnd;
return this;
}
}

3
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexStep.java
View File

@ -30,7 +30,6 @@ import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.api.svc.IIdHelperService;
import ca.uhn.fhir.jpa.api.svc.IResourceReindexSvc;
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
import ca.uhn.fhir.parser.DataFormatException;
@ -56,8 +55,6 @@ public class ReindexStep implements IJobStepWorker<ReindexJobParameters, Reindex
@Autowired
private HapiTransactionService myHapiTransactionService;
@Autowired
private IResourceReindexSvc myResourceReindexSvc;
@Autowired
private IFhirSystemDao<?, ?> mySystemDao;
@Autowired
private DaoRegistry myDaoRegistry;

2
hapi-fhir-storage-batch2-jobs/src/test/java/ca/uhn/fhir/batch2/jobs/imprt/BulkImportFileServletTest.java
View File

@ -36,7 +36,7 @@ public class BulkImportFileServletTest {
public void testDownloadFile() throws IOException {
String input = "{\"resourceType\":\"Patient\", \"id\": \"A\", \"active\": true}\n" +
"{\"resourceType\":\"Patient\", \"id\": \"B\", \"active\": false}";
String index = mySvc.registerFile(() -> new StringReader(input));
String index = mySvc.registerFileByContents(input);
CloseableHttpClient client = myServletExtension.getHttpClient();

6
hapi-fhir-storage-batch2-jobs/src/test/java/ca/uhn/fhir/batch2/jobs/imprt/FetchFilesStepTest.java
View File

@ -42,7 +42,7 @@ public class FetchFilesStepTest {
// Setup
String index = myBulkImportFileServlet.registerFile(() -> new StringReader("{\"resourceType\":\"Patient\"}"));
String index = myBulkImportFileServlet.registerFileByContents("{\"resourceType\":\"Patient\"}");
BulkImportJobParameters parameters = new BulkImportJobParameters()
.addNdJsonUrl(myHttpServletExtension.getBaseUrl() + "/download?index=" + index)
@ -71,7 +71,7 @@ public class FetchFilesStepTest {
b.append("{\"resourceType\":\"Patient\"}").append("\n");
}
String resource = b.toString();
String index = myBulkImportFileServlet.registerFile(() -> new StringReader(resource));
String index = myBulkImportFileServlet.registerFileByContents(resource);
BulkImportJobParameters parameters = new BulkImportJobParameters()
.addNdJsonUrl(myHttpServletExtension.getBaseUrl() + "/download?index=" + index)
@ -93,7 +93,7 @@ public class FetchFilesStepTest {
// Setup
String index = myBulkImportFileServlet.registerFile(() -> new StringReader("{\"resourceType\":\"Patient\"}"));
String index = myBulkImportFileServlet.registerFileByContents("{\"resourceType\":\"Patient\"}");
BulkImportJobParameters parameters = new BulkImportJobParameters()
.addNdJsonUrl(myHttpServletExtension.getBaseUrl() + "/download?index=" + index)

98
hapi-fhir-storage-batch2-jobs/src/test/java/ca/uhn/fhir/batch2/jobs/reindex/LoadIdsStepTest.java Normal file
View File

@ -0,0 +1,98 @@
package ca.uhn.fhir.batch2.jobs.reindex;
import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.StepExecutionDetails;
import ca.uhn.fhir.jpa.api.svc.IResourceReindexSvc;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import org.hl7.fhir.r4.model.InstantType;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import javax.annotation.Nonnull;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.mockito.ArgumentMatchers.eq;
import static org.mockito.ArgumentMatchers.isNull;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import static org.mockito.Mockito.when;
@ExtendWith(MockitoExtension.class)
public class LoadIdsStepTest {
public static final Date DATE_1 = new InstantType("2022-01-01T00:00:00Z").getValue();
public static final Date DATE_2 = new InstantType("2022-01-02T00:00:00Z").getValue();
public static final Date DATE_3 = new InstantType("2022-01-03T00:00:00Z").getValue();
public static final Date DATE_4 = new InstantType("2022-01-04T00:00:00Z").getValue();
public static final Date DATE_END = new InstantType("2022-02-01T00:00:00Z").getValue();
@Mock
private IResourceReindexSvc myResourceReindexSvc;
@Mock
private IJobDataSink<ReindexChunkIds> mySink;
@InjectMocks
private LoadIdsStep mySvc;
@Captor
private ArgumentCaptor<ReindexChunkIds> myChunkIdsCaptor;
@Test
public void testGenerateSteps() {
ReindexJobParameters parameters = new ReindexJobParameters();
ReindexChunkRange range = new ReindexChunkRange()
.setStart(DATE_1)
.setEnd(DATE_END);
String instanceId = "instance-id";
String chunkId = "chunk-id";
StepExecutionDetails<ReindexJobParameters, ReindexChunkRange> details = new StepExecutionDetails<>(parameters, range, instanceId, chunkId);
// First Execution
when(myResourceReindexSvc.fetchResourceIdsPage(eq(DATE_1), eq(DATE_END), isNull(), isNull()))
.thenReturn(createIdChunk(0L, 20000L, DATE_2));
when(myResourceReindexSvc.fetchResourceIdsPage(eq(DATE_2), eq(DATE_END), isNull(), isNull()))
.thenReturn(createIdChunk(20000L, 40000L, DATE_3));
when(myResourceReindexSvc.fetchResourceIdsPage(eq(DATE_3), eq(DATE_END), isNull(), isNull()))
.thenReturn(createIdChunk(40000L, 40040L, DATE_3));
mySvc.run(details, mySink);
verify(mySink, times(41)).accept(myChunkIdsCaptor.capture());
for (int i = 0; i < 40; i++) {
assertEquals(createIdChunk(i * 1000, (i * 1000) + 1000).toString(), myChunkIdsCaptor.getAllValues().get(i).toString());
}
assertEquals(createIdChunk(40000, 40040).toString(), myChunkIdsCaptor.getAllValues().get(40).toString());
}
@Nonnull
private ReindexChunkIds createIdChunk(int theLow, int theHigh) {
ReindexChunkIds retVal = new ReindexChunkIds();
for (int i = theLow; i < theHigh; i++) {
retVal.getIds().add(new ReindexChunkIds.Id().setResourceType("Patient").setId(Integer.toString(i)));
}
return retVal;
}
@Nonnull
private IResourceReindexSvc.IdChunk createIdChunk(long idLow, long idHigh, Date lastDate) {
List<ResourcePersistentId> ids = new ArrayList<>();
List<String> resourceTypes = new ArrayList<>();
for (long i = idLow; i < idHigh; i++) {
ids.add(new ResourcePersistentId(i));
resourceTypes.add("Patient");
}
IResourceReindexSvc.IdChunk chunk = new IResourceReindexSvc.IdChunk(ids, resourceTypes, lastDate);
return chunk;
}
}

2
hapi-fhir-storage-batch2/pom.xml
View File

@ -14,7 +14,7 @@
<packaging>jar</packaging>
<name>HAPI FHIR JPA Server - Batch2 Task Processor</name>
<description></description>
<description>Batch2 is a framework for managing and executing long running "batch" jobs</description>
<dependencies>

4
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/JobCoordinatorImpl.java
View File

@ -218,6 +218,10 @@ public class JobCoordinatorImpl extends BaseJobService implements IJobCoordinato
ourLog.error("Failure executing job {} step {}", jobDefinitionId, targetStepId, e);
myJobPersistence.markWorkChunkAsErroredAndIncrementErrorCount(chunkId, e.toString());
throw new JobExecutionFailedException(Msg.code(2041) + e.getMessage(), e);
} catch (Throwable t) {
ourLog.error("Unexpected failure executing job {} step {}", jobDefinitionId, targetStepId, t);
myJobPersistence.markWorkChunkAsFailed(chunkId, t.toString());
return false;
}
int recordsProcessed = outcome.getRecordsProcessed();

1
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/impl/SynchronizedJobPersistenceWrapper.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.WorkChunk;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;

7
hapi-fhir-test-utilities/pom.xml
View File

@ -167,13 +167,6 @@
<argLine>@{argLine} ${surefire_jvm_args}</argLine>
</configuration>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
<resources>
<resource>

23
pom.xml
View File

@ -852,8 +852,10 @@
<fontawesomeVersion>5.4.1</fontawesomeVersion>
<maven.compiler.source>11</maven.compiler.source>
<maven.compiler.target>11</maven.compiler.target>
<maven.compiler.release>11</maven.compiler.release>
<maven.compiler.testSource>17</maven.compiler.testSource>
<maven.compiler.testTarget>17</maven.compiler.testTarget>
<maven.compiler.testRelease>17</maven.compiler.testRelease>
</properties>
<dependencyManagement>
@ -2055,7 +2057,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<version>3.10.1</version>
<configuration>
<forceJavacCompilerUse>true</forceJavacCompilerUse>
<encoding>UTF-8</encoding>
@ -2143,11 +2145,6 @@
<artifactId>buildnumber-maven-plugin</artifactId>
<version>1.4</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
<version>1.20</version>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>cobertura-maven-plugin</artifactId>
@ -2319,10 +2316,10 @@
<version>3.5.4</version>
</requireMavenVersion>
<requireJavaVersion>
<version>11</version>
<version>17</version>
<message>
HAPI FHIR is still targeting JDK 8 for published binaries, but we require JDK 11
to build and test this library.
HAPI FHIR is targeting JDK 11 for published binaries,
but we require JDK 17 to build and test this library.
</message>
</requireJavaVersion>
</rules>
@ -2976,13 +2973,6 @@
<execution><id>validate</id><phase>none</phase></execution>
</executions>
</plugin>
<plugin>
<groupId>org.codehaus.mojo</groupId>
<artifactId>animal-sniffer-maven-plugin</artifactId>
<executions>
<execution><id>check-java-api</id><phase>none</phase></execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
@ -3008,6 +2998,7 @@
<configuration>
<source>17</source>
<target>17</target>
<release>17</release>
<testSource>17</testSource>
<testTarget>17</testTarget>
</configuration>