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Code Issues Packages Projects Releases Wiki Activity

3770 fix batch2 failure loop (#3779) 

* 3770 fixing error handling

* some updates to error handling

* changelog

* blah

* bumping version

* fix test failures

* code review points

* review points

* add retry test

* assert counts in the test

* test fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
This commit is contained in:
TipzCM 2022-07-15 12:42:46 -04:00 committed by GitHub
parent ab4d9578e7
commit 0c644271ce
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
81 changed files with 454 additions and 117 deletions
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2
hapi-deployable-pom/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-android/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-batch/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

4
hapi-fhir-bom/pom.xml
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@ -3,14 +3,14 @@
<modelVersion>4.0.0</modelVersion>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-bom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<packaging>pom</packaging>
<name>HAPI FHIR BOM</name>
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-checkstyle/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-app/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-cli</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-cli/hapi-fhir-cli-jpaserver/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom</relativePath>
</parent>

2
hapi-fhir-cli/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-client-okhttp/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-client/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-converter/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-dist/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-docs/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

6
hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_1_0/3770-added-error-handling-for-batch2.yaml Normal file
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@ -0,0 +1,6 @@
---
type: fix
issue: 3770
title: "Batch2 will have a standard error handling that will fail the job if it fails
a chunk processing for more than 3 times.
Further, added better validation to reindex job to disallow bad urls."

2
hapi-fhir-jacoco/pom.xml
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@ -11,7 +11,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jaxrsserver-base/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpa/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-jpaserver-base/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

9
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/batch2/JpaJobPersistenceImpl.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.JobOperationResultJson;
import ca.uhn.fhir.batch2.coordinator.BatchWorkChunk;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.MarkWorkChunkAsErrorRequest;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.jpa.dao.data.IBatch2JobInstanceRepository;
@ -198,6 +199,14 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
myWorkChunkRepository.updateChunkStatusAndIncrementErrorCountForEndError(theChunkId, new Date(), theErrorMessage, StatusEnum.ERRORED);
}
@Override
public Optional<WorkChunk> markWorkChunkAsErroredAndIncrementErrorCount(MarkWorkChunkAsErrorRequest theParameters) {
markWorkChunkAsErroredAndIncrementErrorCount(theParameters.getChunkId(), theParameters.getErrorMsg());
Optional<Batch2WorkChunkEntity> op = myWorkChunkRepository.findById(theParameters.getChunkId());
return op.map(c -> toChunk(c, theParameters.isIncludeData()));
}
@Override
public void markWorkChunkAsFailed(String theChunkId, String theErrorMessage) {
myWorkChunkRepository.updateChunkStatusAndIncrementErrorCountForEndError(theChunkId, new Date(), theErrorMessage, StatusEnum.FAILED);

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

@ -27,6 +27,7 @@ class JpaJobPersistenceImplTest {
@InjectMocks
JpaJobPersistenceImpl mySvc;
@Test
void cancelSuccess() {
// setup

2
hapi-fhir-jpaserver-cql/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-mdm/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-model/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-searchparam/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-subscription/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-jpaserver-test-utilities/pom.xml
View File

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

14
hapi-fhir-jpaserver-test-utilities/src/main/java/ca/uhn/fhir/jpa/test/Batch2JobHelper.java
View File

@ -28,6 +28,9 @@ import org.awaitility.core.ConditionTimeoutException;
import org.hamcrest.Matchers;
import org.springframework.beans.factory.annotation.Autowired;
import java.time.Duration;
import java.util.concurrent.TimeUnit;
import java.util.Collection;
import java.util.List;
@ -71,6 +74,17 @@ public class Batch2JobHelper {
}, equalTo(StatusEnum.CANCELLED));
}
public JobInstance awaitJobHitsStatusInTime(String theId, int theSeconds, StatusEnum... theStatuses) {
await().atMost(theSeconds, TimeUnit.SECONDS)
.pollDelay(Duration.ofSeconds(10))
.until(() -> {
myJobMaintenanceService.runMaintenancePass();
return myJobCoordinator.getInstance(theId).getStatus();
}, Matchers.in(theStatuses));
return myJobCoordinator.getInstance(theId);
}
public void awaitJobInProgress(String theId) {
await().until(() -> {
myJobMaintenanceService.runMaintenancePass();

89
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/batch2/Batch2CoordinatorIT.java
View File

@ -7,6 +7,7 @@ import ca.uhn.fhir.batch2.api.IJobDataSink;
import ca.uhn.fhir.batch2.api.IJobMaintenanceService;
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.IJobStepWorker;
import ca.uhn.fhir.batch2.api.ILastJobStepWorker;
import ca.uhn.fhir.batch2.api.IReductionStepWorker;
import ca.uhn.fhir.batch2.api.JobExecutionFailedException;
import ca.uhn.fhir.batch2.api.RunOutcome;
@ -17,6 +18,11 @@ import ca.uhn.fhir.batch2.model.ChunkOutcome;
import ca.uhn.fhir.batch2.model.JobDefinition;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.batch2.model.JobWorkNotificationJsonMessage;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.jpa.subscription.channel.api.ChannelConsumerSettings;
import ca.uhn.fhir.jpa.subscription.channel.api.IChannelFactory;
import ca.uhn.fhir.jpa.subscription.channel.impl.LinkedBlockingChannel;
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
import ca.uhn.fhir.jpa.test.Batch2JobHelper;
import ca.uhn.fhir.model.api.IModelJson;
@ -24,11 +30,16 @@ import ca.uhn.fhir.util.JsonUtil;
import ca.uhn.test.concurrency.LatchTimedOutError;
import ca.uhn.test.concurrency.PointcutLatch;
import com.fasterxml.jackson.annotation.JsonProperty;
import org.junit.jupiter.api.AfterEach;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.messaging.Message;
import org.springframework.messaging.MessageChannel;
import org.springframework.messaging.MessageHandler;
import org.springframework.messaging.support.ExecutorChannelInterceptor;
import javax.annotation.Nonnull;
import java.util.ArrayList;
@ -39,6 +50,8 @@ import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.atomic.AtomicInteger;
import static ca.uhn.fhir.batch2.config.BaseBatch2Config.CHANNEL_NAME;
import static ca.uhn.fhir.batch2.coordinator.StepExecutionSvc.MAX_CHUNK_ERROR_COUNT;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
@ -58,6 +71,8 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
IJobMaintenanceService myJobMaintenanceService;
@Autowired
Batch2JobHelper myBatch2JobHelper;
@Autowired
private IChannelFactory myChannelFactory;
@Autowired
IJobPersistence myJobPersistence;
@ -65,6 +80,7 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
private final PointcutLatch myFirstStepLatch = new PointcutLatch("First Step");
private final PointcutLatch myLastStepLatch = new PointcutLatch("Last Step");
private IJobCompletionHandler<TestJobParameters> myCompletionHandler;
private LinkedBlockingChannel myWorkChannel;
private static RunOutcome callLatch(PointcutLatch theLatch, StepExecutionDetails<?, ?> theStep) {
theLatch.call(theStep);
@ -73,7 +89,13 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
@BeforeEach
public void before() {
myCompletionHandler = details -> {};
myCompletionHandler = details -> {};
myWorkChannel = (LinkedBlockingChannel) myChannelFactory.getOrCreateReceiver(CHANNEL_NAME, JobWorkNotificationJsonMessage.class, new ChannelConsumerSettings());
}
@AfterEach
public void after() {
myWorkChannel.clearInterceptorsForUnitTest();
}
@Test
@ -123,7 +145,6 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
myLastStepLatch.awaitExpected();
}
@Test
public void testFastTrack_Maintenance_do_not_both_call_CompletionHandler() throws InterruptedException {
IJobStepWorker<TestJobParameters, VoidModel, FirstStepOutput> firstStep = (step, sink) -> {
@ -189,7 +210,6 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
myLastStepLatch.awaitExpected();
}
@Test
public void testJobDefinitionWithReductionStepIT() throws InterruptedException {
// setup
@ -371,6 +391,69 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
myBatch2JobHelper.awaitJobCancelled(instanceId);
}
@Test
public void testStepRunFailure_continuouslyThrows_marksJobFailed() {
AtomicInteger interceptorCounter = new AtomicInteger();
myWorkChannel.addInterceptor(new ExecutorChannelInterceptor() {
@Override
public void afterMessageHandled(Message<?> message, MessageChannel channel, MessageHandler handler, Exception ex) {
if (ex != null) {
interceptorCounter.incrementAndGet();
ourLog.info("Work Channel Exception thrown: {}. Resending message", ex.getMessage());
channel.send(message);
}
}
});
// setup
AtomicInteger counter = new AtomicInteger();
// step 1
IJobStepWorker<TestJobParameters, VoidModel, FirstStepOutput> first = (step, sink) -> {
counter.getAndIncrement();
throw new RuntimeException("Exception");
};
// final step
ILastJobStepWorker<TestJobParameters, FirstStepOutput> last = (step, sink) -> {
fail("We should never hit this last step");
return RunOutcome.SUCCESS;
};
// job definition
String jobId = new Exception().getStackTrace()[0].getMethodName();
JobDefinition<? extends IModelJson> jd = JobDefinition.newBuilder()
.setJobDefinitionId(jobId)
.setJobDescription("test job")
.setJobDefinitionVersion(TEST_JOB_VERSION)
.setParametersType(TestJobParameters.class)
.gatedExecution()
.addFirstStep(
FIRST_STEP_ID,
"Test first step",
FirstStepOutput.class,
first
)
.addLastStep(
LAST_STEP_ID,
"Test last step",
last
)
.build();
myJobDefinitionRegistry.addJobDefinition(jd);
// test
JobInstanceStartRequest request = buildRequest(jobId);
myFirstStepLatch.setExpectedCount(1);
String instanceId = myJobCoordinator.startInstance(request);
JobInstance instance = myBatch2JobHelper.awaitJobHitsStatusInTime(instanceId,
12, // we want to wait a long time (2 min here) cause backoff is incremental
StatusEnum.FAILED, StatusEnum.ERRORED // error states
);
assertEquals(MAX_CHUNK_ERROR_COUNT + 1, counter.get());
assertEquals(MAX_CHUNK_ERROR_COUNT, interceptorCounter.get());
assertTrue(instance.getStatus() == StatusEnum.FAILED
|| instance.getStatus() == StatusEnum.ERRORED);
}
@Nonnull
private JobInstanceStartRequest buildRequest(String jobId) {
JobInstanceStartRequest request = new JobInstanceStartRequest();

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/bulk/imprt2/BulkImportR4Test.java
View File

@ -185,7 +185,7 @@ public class BulkImportR4Test extends BaseJpaR4Test {
assertNotNull(instance.getCreateTime());
assertNotNull(instance.getStartTime());
assertNull(instance.getEndTime());
assertThat(instance.getErrorMessage(), containsString("NullPointerException: This is an exception"));
assertThat(instance.getErrorMessage(), containsString("This is an exception"));
});
} finally {

2
hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/delete/job/ReindexJobTest.java
View File

@ -129,7 +129,7 @@ public class ReindexJobTest extends BaseJpaR4Test {
// Verify
assertEquals(StatusEnum.ERRORED, outcome.getStatus());
assertEquals("java.lang.NullPointerException: foo message", outcome.getErrorMessage());
assertEquals("foo message", outcome.getErrorMessage());
}
@Test

2
hapi-fhir-jpaserver-uhnfhirtest/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-server-mdm/pom.xml
View File

@ -7,7 +7,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server-openapi/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-autoconfigure/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-apache/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-apache</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-client-okhttp/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-client-okhttp</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/hapi-fhir-spring-boot-sample-server-jersey/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-sample-server-jersey</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-samples/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-spring-boot</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</parent>
<artifactId>hapi-fhir-spring-boot-samples</artifactId>

2
hapi-fhir-spring-boot/hapi-fhir-spring-boot-starter/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-spring-boot/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-sql-migrate/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

23
hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexJobParametersValidator.java
View File

@ -21,13 +21,19 @@ package ca.uhn.fhir.batch2.jobs.reindex;
*/
import ca.uhn.fhir.batch2.api.IJobParametersValidator;
import ca.uhn.fhir.batch2.jobs.parameters.PartitionedUrl;
import ca.uhn.fhir.batch2.jobs.parameters.UrlListValidator;
import ca.uhn.fhir.util.UrlUtil;
import org.jetbrains.annotations.NotNull;
import org.jetbrains.annotations.Nullable;
import java.util.ArrayList;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class ReindexJobParametersValidator implements IJobParametersValidator<ReindexJobParameters> {
private final UrlListValidator myUrlListValidator;
public ReindexJobParametersValidator(UrlListValidator theUrlListValidator) {
@ -37,6 +43,21 @@ public class ReindexJobParametersValidator implements IJobParametersValidator<Re
@Nullable
@Override
public List<String> validate(@NotNull ReindexJobParameters theParameters) {
return myUrlListValidator.validatePartitionedUrls(theParameters.getPartitionedUrls());
List<String> errors = myUrlListValidator.validatePartitionedUrls(theParameters.getPartitionedUrls());
if (errors == null || errors.isEmpty()) {
// only check if there's no other errors (new list to fix immutable issues)
errors = new ArrayList<>();
List<PartitionedUrl> urls = theParameters.getPartitionedUrls();
for (PartitionedUrl purl : urls) {
String url = purl.getUrl();
if (url.contains(" ") || url.contains("\n") || url.contains("\t")) {
errors.add("Invalid URL. URL cannot contain spaces : " + url);
}
}
}
return errors;
}
}

47
hapi-fhir-storage-batch2-jobs/src/test/java/ca/uhn/fhir/batch2/jobs/reindex/ReindexJobParametersValidatorTest.java Normal file
View File

@ -0,0 +1,47 @@
package ca.uhn.fhir.batch2.jobs.reindex;
import ca.uhn.fhir.batch2.jobs.parameters.UrlListValidator;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.mockito.InjectMocks;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
import org.springframework.beans.factory.annotation.Value;
import java.util.List;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertTrue;
@ExtendWith(MockitoExtension.class)
public class ReindexJobParametersValidatorTest {
@Mock
private UrlListValidator myListValidator;
@InjectMocks
private ReindexJobParametersValidator myValidator;
@ParameterizedTest
@ValueSource(strings = { "\n", " ", "\t" })
public void validate_urlWithSpace_fails(String theWhiteSpaceChar) {
List<String> errors = runTestWithUrl("Patient," + theWhiteSpaceChar + "Practitioner");
// verify
assertFalse(errors.isEmpty());
assertTrue(errors.get(0).contains("Invalid URL. URL cannot contain spaces"));
}
private List<String> runTestWithUrl(String theUrl) {
// setup
ReindexJobParameters parameters = new ReindexJobParameters();
parameters.addUrl(theUrl);
// test
List<String> errors = myValidator.validate(parameters);
return errors;
}
}

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

@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

19
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/api/IJobPersistence.java
View File

@ -22,6 +22,7 @@ package ca.uhn.fhir.batch2.api;
import ca.uhn.fhir.batch2.coordinator.BatchWorkChunk;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.MarkWorkChunkAsErrorRequest;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.model.WorkChunk;
@ -100,8 +101,26 @@ public interface IJobPersistence {
*
* @param theChunkId The chunk ID
*/
@Deprecated
void markWorkChunkAsErroredAndIncrementErrorCount(String theChunkId, String theErrorMessage);
/**
* Marks a given chunk as having errored (ie, may be recoverable)
*
* Returns the work chunk.
*
* NB: For backwards compatibility reasons, it could be an empty optional, but
* this doesn't mean it has no workchunk (just implementers are not updated)
*
* @param theParameters - the parameters for marking the workchunk with error
* @return - workchunk optional, if available.
*/
default Optional<WorkChunk> markWorkChunkAsErroredAndIncrementErrorCount(MarkWorkChunkAsErrorRequest theParameters) {
// old method - please override me
markWorkChunkAsErroredAndIncrementErrorCount(theParameters.getChunkId(), theParameters.getErrorMsg());
return Optional.empty(); // returning empty so as not to break implementers
}
/**
* Marks a given chunk as having failed (i.e. probably not recoverable)
*

29
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/StepExecutionSvc.java
View File

@ -36,6 +36,7 @@ import ca.uhn.fhir.batch2.model.JobDefinition;
import ca.uhn.fhir.batch2.model.JobDefinitionStep;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.JobWorkCursor;
import ca.uhn.fhir.batch2.model.MarkWorkChunkAsErrorRequest;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.i18n.Msg;
@ -48,10 +49,23 @@ import javax.annotation.Nullable;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
import java.util.Optional;
public class StepExecutionSvc {
private static final Logger ourLog = LoggerFactory.getLogger(StepExecutionSvc.class);
// TODO
/**
* This retry only works if your channel producer supports
* retries on message processing exceptions.
*
* What's more, we may one day want to have this configurable
* by the caller.
* But since this is not a feature of HAPI,
* this has not been done yet.
*/
public static final int MAX_CHUNK_ERROR_COUNT = 3;
private final IJobPersistence myJobPersistence;
private final BatchJobSender myBatchJobSender;
@ -303,7 +317,20 @@ public class StepExecutionSvc {
} catch (Exception e) {
ourLog.error("Failure executing job {} step {}", jobDefinitionId, targetStepId, e);
if (theStepExecutionDetails.hasAssociatedWorkChunk()) {
myJobPersistence.markWorkChunkAsErroredAndIncrementErrorCount(chunkId, e.toString());
MarkWorkChunkAsErrorRequest parameters = new MarkWorkChunkAsErrorRequest();
parameters.setChunkId(chunkId);
parameters.setErrorMsg(e.getMessage());
Optional<WorkChunk> updatedOp = myJobPersistence.markWorkChunkAsErroredAndIncrementErrorCount(parameters);
if (updatedOp.isPresent()) {
WorkChunk chunk = updatedOp.get();
// TODO - marking for posterity
// see comments on MAX_CHUNK_ERROR_COUNT
if (chunk.getErrorCount() > MAX_CHUNK_ERROR_COUNT) {
myJobPersistence.markWorkChunkAsFailed(chunkId, "Too many errors: " + chunk.getErrorCount());
return false;
}
}
}
throw new JobStepFailedException(Msg.code(2041) + e.getMessage(), e);
} catch (Throwable t) {

6
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/SynchronizedJobPersistenceWrapper.java
View File

@ -23,6 +23,7 @@ package ca.uhn.fhir.batch2.coordinator;
import ca.uhn.fhir.batch2.api.IJobPersistence;
import ca.uhn.fhir.batch2.api.JobOperationResultJson;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.MarkWorkChunkAsErrorRequest;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.model.WorkChunk;
@ -92,6 +93,11 @@ public class SynchronizedJobPersistenceWrapper implements IJobPersistence {
myWrap.markWorkChunkAsErroredAndIncrementErrorCount(theChunkId, theErrorMessage);
}
@Override
public Optional<WorkChunk> markWorkChunkAsErroredAndIncrementErrorCount(MarkWorkChunkAsErrorRequest theParameters) {
return myWrap.markWorkChunkAsErroredAndIncrementErrorCount(theParameters);
}
@Override
public synchronized void markWorkChunkAsFailed(String theChunkId, String theErrorMessage) {
myWrap.markWorkChunkAsFailed(theChunkId, theErrorMessage);

33
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/MarkWorkChunkAsErrorRequest.java Normal file
View File

@ -0,0 +1,33 @@
package ca.uhn.fhir.batch2.model;
public class MarkWorkChunkAsErrorRequest {
private String myChunkId;
private String myErrorMsg;
private boolean myIncludeData;
public String getChunkId() {
return myChunkId;
}
public void setChunkId(String theChunkId) {
myChunkId = theChunkId;
}
public String getErrorMsg() {
return myErrorMsg;
}
public void setErrorMsg(String theErrorMsg) {
myErrorMsg = theErrorMsg;
}
public boolean isIncludeData() {
return myIncludeData;
}
public void setIncludeData(boolean theIncludeData) {
myIncludeData = theIncludeData;
}
}

1
hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/model/StatusEnum.java
View File

@ -116,6 +116,7 @@ public enum StatusEnum {
retVal = ourNotEndedStatuses;
return retVal;
}
@Nonnull
private static void initializeStaticEndedStatuses() {
EnumSet<StatusEnum> endedSet = EnumSet.noneOf(StatusEnum.class);

8
hapi-fhir-storage-batch2/src/test/java/ca/uhn/fhir/batch2/coordinator/JobCoordinatorImplTest.java
View File

@ -12,6 +12,7 @@ import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.JobInstanceStartRequest;
import ca.uhn.fhir.batch2.model.JobWorkNotification;
import ca.uhn.fhir.batch2.model.JobWorkNotificationJsonMessage;
import ca.uhn.fhir.batch2.model.MarkWorkChunkAsErrorRequest;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.jpa.subscription.channel.api.IChannelReceiver;
@ -245,8 +246,11 @@ public class JobCoordinatorImplTest extends BaseBatch2Test {
assertEquals(PARAM_2_VALUE, params.getParam2());
assertEquals(PASSWORD_VALUE, params.getPassword());
verify(myJobInstancePersister, times(1)).markWorkChunkAsErroredAndIncrementErrorCount(eq(CHUNK_ID), myErrorMessageCaptor.capture());
assertEquals("java.lang.NullPointerException: This is an error message", myErrorMessageCaptor.getValue());
ArgumentCaptor<MarkWorkChunkAsErrorRequest> parametersArgumentCaptor = ArgumentCaptor.forClass(MarkWorkChunkAsErrorRequest.class);
verify(myJobInstancePersister, times(1)).markWorkChunkAsErroredAndIncrementErrorCount(parametersArgumentCaptor.capture());
MarkWorkChunkAsErrorRequest capturedParams = parametersArgumentCaptor.getValue();
assertEquals(CHUNK_ID, capturedParams.getChunkId());
assertEquals("This is an error message", capturedParams.getErrorMsg());
}
@Test

67
hapi-fhir-storage-batch2/src/test/java/ca/uhn/fhir/batch2/coordinator/StepExecutionSvcTest.java
View File

@ -19,6 +19,7 @@ import ca.uhn.fhir.batch2.model.JobDefinitionReductionStep;
import ca.uhn.fhir.batch2.model.JobDefinitionStep;
import ca.uhn.fhir.batch2.model.JobInstance;
import ca.uhn.fhir.batch2.model.JobWorkCursor;
import ca.uhn.fhir.batch2.model.MarkWorkChunkAsErrorRequest;
import ca.uhn.fhir.batch2.model.StatusEnum;
import ca.uhn.fhir.batch2.model.WorkChunk;
import ca.uhn.fhir.batch2.model.WorkChunkData;
@ -34,9 +35,12 @@ import org.mockito.junit.jupiter.MockitoExtension;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.atomic.AtomicInteger;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertFalse;
import static org.junit.jupiter.api.Assertions.assertNotNull;
import static org.junit.jupiter.api.Assertions.assertTrue;
import static org.junit.jupiter.api.Assertions.fail;
import static org.mockito.ArgumentMatchers.any;
@ -492,11 +496,70 @@ public class StepExecutionSvcTest {
fail("Expected Exception to be thrown");
} catch (JobStepFailedException jobStepFailedException) {
assertTrue(jobStepFailedException.getMessage().contains(msg));
} catch (Exception anythingElse) {
fail(anythingElse.getMessage());
}
}
@Test
public void doExecution_stepWorkerThrowsRandomExceptionForever_eventuallyMarksAsFailedAndReturnsFalse() {
// setup
int counter = 0;
AtomicInteger errorCounter = new AtomicInteger();
String errorMsg = "my Error Message";
JobInstance jobInstance = getTestJobInstance();
WorkChunk chunk = new WorkChunk();
chunk.setId("chunkId");
chunk.setData(new StepInputData());
JobWorkCursor<TestJobParameters, StepInputData, StepOutputData> workCursor = mock(JobWorkCursor.class);
JobDefinitionStep<TestJobParameters, StepInputData, StepOutputData> step = mockOutWorkCursor(StepType.INTERMEDIATE, workCursor, true, false);
// when
when(myNonReductionStep.run(any(), any()))
.thenThrow(new RuntimeException(errorMsg));
when(myJobPersistence.markWorkChunkAsErroredAndIncrementErrorCount(any(MarkWorkChunkAsErrorRequest.class)))
.thenAnswer((p) -> {
WorkChunk ec = new WorkChunk();
ec.setId(chunk.getId());
int count = errorCounter.getAndIncrement();
ec.setErrorCount(count);
return Optional.of(ec);
});
// test
Boolean processedOutcomeSuccessfully = null;
do {
try {
JobStepExecutorOutput<?, ?, ?> output = myExecutorSvc.doExecution(
workCursor,
jobInstance,
chunk
);
/*
* Getting a value here means we are no longer
* throwing exceptions. Which is the desired outcome.
* We just now need to ensure that this outcome is
* "false"
*/
processedOutcomeSuccessfully = output.isSuccessful();
} catch (JobStepFailedException ex) {
assertTrue(ex.getMessage().contains(errorMsg));
counter++;
}
/*
* +2 because...
* we check for > MAX_CHUNK_ERROR_COUNT (+1)
* we want it to run one extra time here (+1)
*/
} while (processedOutcomeSuccessfully == null && counter < StepExecutionSvc.MAX_CHUNK_ERROR_COUNT + 2);
// verify
assertNotNull(processedOutcomeSuccessfully);
// +1 because of the > MAX_CHUNK_ERROR_COUNT check
assertEquals(StepExecutionSvc.MAX_CHUNK_ERROR_COUNT + 1, counter);
assertFalse(processedOutcomeSuccessfully);
}
private void runExceptionThrowingTest(Exception theExceptionToThrow) {
// setup
JobInstance jobInstance = getTestJobInstance();

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

2
hapi-fhir-storage-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>
<modelVersion>4.0.0</modelVersion>

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

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/patch/XmlPatchUtils.java
View File

@ -1,7 +1,7 @@
package ca.uhn.fhir.jpa.patch;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.i18n.Msg;
import ca.uhn.fhir.rest.api.Constants;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import com.github.dnault.xmlpatch.Patcher;

5
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/channel/impl/LinkedBlockingChannel.java
View File

@ -24,6 +24,7 @@ import ca.uhn.fhir.jpa.subscription.channel.api.IChannelProducer;
import ca.uhn.fhir.jpa.subscription.channel.api.IChannelReceiver;
import org.springframework.messaging.support.ExecutorSubscribableChannel;
import java.util.ArrayList;
import java.util.concurrent.BlockingQueue;
import java.util.concurrent.LinkedBlockingQueue;
import java.util.concurrent.ThreadPoolExecutor;
@ -44,9 +45,7 @@ public class LinkedBlockingChannel extends ExecutorSubscribableChannel implement
}
public void clearInterceptorsForUnitTest() {
while (getInterceptors().size() > 0) {
removeInterceptor(0);
}
setInterceptors(new ArrayList<>());
}
@Override

66
hapi-fhir-storage/src/main/java/ca/uhn/fhir/jpa/subscription/channel/impl/LinkedBlockingChannelFactory.java
View File

@ -34,6 +34,7 @@ import org.apache.commons.lang3.concurrent.BasicThreadFactory;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.annotation.Nonnull;
import javax.annotation.PreDestroy;
import java.util.Collections;
import java.util.HashMap;
@ -76,41 +77,44 @@ public class LinkedBlockingChannelFactory implements IChannelFactory {
// TODO - does this need retry settings?
final String channelName = myChannelNamer.getChannelName(theChannelName, theChannelSettings);
return myChannels.computeIfAbsent(channelName, t -> {
return myChannels.computeIfAbsent(channelName, t -> buildLinkedBlockingChannel(theConcurrentConsumers, channelName));
}
String threadNamingPattern = channelName + "-%d";
@Nonnull
private LinkedBlockingChannel buildLinkedBlockingChannel(int theConcurrentConsumers, String channelName) {
String threadNamingPattern = channelName + "-%d";
ThreadFactory threadFactory = new BasicThreadFactory.Builder()
.namingPattern(threadNamingPattern)
.uncaughtExceptionHandler(uncaughtExceptionHandler(channelName))
.daemon(false)
.priority(Thread.NORM_PRIORITY)
.build();
ThreadFactory threadFactory = new BasicThreadFactory.Builder()
.namingPattern(threadNamingPattern)
.uncaughtExceptionHandler(uncaughtExceptionHandler(channelName))
.daemon(false)
.priority(Thread.NORM_PRIORITY)
.build();
LinkedBlockingQueue<Runnable> queue = new LinkedBlockingQueue<>(SubscriptionConstants.DELIVERY_EXECUTOR_QUEUE_SIZE);
RejectedExecutionHandler rejectedExecutionHandler = (theRunnable, theExecutor) -> {
ourLog.info("Note: Executor queue is full ({} elements), waiting for a slot to become available!", queue.size());
StopWatch sw = new StopWatch();
try {
queue.put(theRunnable);
} catch (InterruptedException e) {
Thread.currentThread().interrupt();
throw new RejectedExecutionException(Msg.code(568) + "Task " + theRunnable.toString() +
" rejected from " + e);
}
ourLog.info("Slot become available after {}ms", sw.getMillis());
};
ThreadPoolExecutor executor = new ThreadPoolExecutor(
theConcurrentConsumers,
theConcurrentConsumers,
0L,
TimeUnit.MILLISECONDS,
queue,
threadFactory,
rejectedExecutionHandler);
return new LinkedBlockingChannel(channelName, executor, queue);
LinkedBlockingQueue<Runnable> queue = new LinkedBlockingQueue<>(SubscriptionConstants.DELIVERY_EXECUTOR_QUEUE_SIZE);
RejectedExecutionHandler rejectedExecutionHandler = (theRunnable, theExecutor) -> {
ourLog.info("Note: Executor queue is full ({} elements), waiting for a slot to become available!", queue.size());
StopWatch sw = new StopWatch();
try {
queue.put(theRunnable);
} catch (InterruptedException e) {
Thread.currentThread().interrupt();
throw new RejectedExecutionException(Msg.code(568) + "Task " + theRunnable.toString() +
" rejected from " + e);
}
ourLog.info("Slot become available after {}ms", sw.getMillis());
};
ThreadPoolExecutor executor = new ThreadPoolExecutor(
theConcurrentConsumers,
theConcurrentConsumers,
0L,
TimeUnit.MILLISECONDS,
queue,
threadFactory,
rejectedExecutionHandler);
});
LinkedBlockingChannel retval = new LinkedBlockingChannel(channelName, executor, queue);
return retval;
}
private Thread.UncaughtExceptionHandler uncaughtExceptionHandler(String theChannelName) {

2
hapi-fhir-structures-dstu2.1/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-dstu3/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-hl7org-dstu2/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r4/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-structures-r5/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-test-utilities/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-testpage-overlay/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2.1/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu2/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-dstu3/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-r4/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation-resources-r5/pom.xml
View File

@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

2
hapi-fhir-validation/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent>

16
hapi-tinder-plugin/pom.xml
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@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>
@ -58,37 +58,37 @@
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-dstu3</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r4</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-structures-r5</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu2</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-dstu3</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-validation-resources-r4</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.apache.velocity</groupId>

2
hapi-tinder-test/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../pom.xml</relativePath>
</parent>

4
pom.xml
View File

@ -6,7 +6,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<packaging>pom</packaging>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<name>HAPI-FHIR</name>
<description>An open-source implementation of the FHIR specification in Java.</description>
<url>https://hapifhir.io</url>
@ -2015,7 +2015,7 @@
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir-checkstyle</artifactId>
<!-- Remember to bump this when you upgrade the version -->
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
</dependency>
</dependencies>
</plugin>

2
tests/hapi-fhir-base-test-jaxrsserver-kotlin/pom.xml
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@ -6,7 +6,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
tests/hapi-fhir-base-test-mindeps-client/pom.xml
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@ -4,7 +4,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>

2
tests/hapi-fhir-base-test-mindeps-server/pom.xml
View File

@ -5,7 +5,7 @@
<parent>
<groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-fhir</artifactId>
<version>6.1.0-PRE13-SNAPSHOT</version>
<version>6.1.0-PRE14-SNAPSHOT</version>
<relativePath>../../pom.xml</relativePath>
</parent>