Rel 6 2 4 mergeback (#4406)

* jm wrong bundle entry url (#4213)

* Bug test

* here you go

* Generate relative URIs for bundle entry.request.url, as specified

* Point jira issue in changelog

* Adjust tests to fixes

Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* improved logging (#4217)

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Rel 6 1 3 mergeback (#4215)

* Bump for CVE (#3856)

* Bump for CVE

* Bump spring-data version

* Fix compile

* Cut over to spring bom

* Bump to RC1

* remove RC

* do not contrain reindex for common SP updates (#3876)

* only fast-track jobs with exactly one chunk (#3879)

* Fix illegalstateexception when an exception is thrown during stream response (#3882)

* Finish up changelog, minor refactor

* reset buffer only

* Hack for some replacements

* Failure handling

* wip

* Fixed the issue (#3845)

* Fixed the issue

* Changelog modification

* Changelog modification

* Implemented seventh character extended code and the corresponding dis… (#3709)

* Implemented seventh character extended code and the corresponding display

* Modifications

* Changes on previous test according to modifications made in ICD10-CM XML file

* Subscription sending delete events being skipped (#3888)

* fixed bug and added test

* refactor

* Update for CVE (#3895)

* updated pointcuts to work as intended (#3903)

* updated pointcuts to work as intended

* added changelog

* review fixes

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* 3904 during $delete expunge job hibernate search indexed documents are left orphaned (#3905)

* Add test and implementation

* Add changelog

* 3899 code in limits (#3901)

* Add implementation, changelog, test

* Update hapi-fhir-jpaserver-test-utilities/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

Co-authored-by: Ken Stevens <khstevens@gmail.com>

Co-authored-by: Ken Stevens <khstevens@gmail.com>

* 3884 overlapping searchparameter undetected rel 6 1 (#3909)

* Applying all changes from previous dev branch to current one pointing to rel_6_1

* Fixing merge conflict related to Msg.code value.

* Fixing Msg.code value.

* Making checkstyle happy.

* Making sure that all tests are passing.

* Passing all tests after fixing Msg.code

* Passing all tests.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 3745 - fixed NPE for bundle with duplicate conditional create resourc… (#3746)

* 3745 - fixed NPE for bundle with duplicate conditional create resources and a conditional delete

* created unit test for skip of delete operation while processing duplicating create entries

* moved unit test to FhirSystemDaoR4Test

* 3379 mdm fixes (#3906)

* added MdmLinkCreateSvcimplTest

* fixed creating mdm-link not setting the resource type correctly

* fixed a bug where ResourcePersistenceId was being duplicated instead of passed on

* Update hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmLinkCreateSvcImplTest.java

Change order of tests such that assertEquals takes expected value then actual value

Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* added changelog, also changed a setup function in test to beforeeach

Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>

* Fix to the issue (#3855)

* Fix to the issue

* Progress

* fixed the issue

* Addressing suggestions

* add response status code to MethodOutcome

* Addressing suggestions

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Fix for caching appearing broken in batch2 for bulkexport jobs (#3912)

* Respect caching in bullk export, fix bug with completed date on empty jobs

* add changelog

* Add impl

* Add breaking test

* Complete failing test

* more broken tests

* Fix more tests'

* Fix paging bug

* Fix another brittle test

* 3915 do not collapse rules with filters (#3916)

* do not attempt to merge compartment permissions with filters

* changelog

* Rename to IT for concurrency problems

Co-authored-by: Tadgh <garygrantgraham@gmail.com>

* Version bump

* fix $mdm-submit output (#3917)

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Gl3407 bundle offset size (#3918)

* begin with failing test

* fixed

* change log

* rollback default count change and corresponding comments

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* Offset interceptor now only works for external calls

* Initialize some beans (esp interceptors) later in the boot process so they don't slow down startup.

* do not reindex searchparam jobs on startup

* Fix oracle non-enterprise attempting online index add (#3925)

* 3922 delete expunge large dataset (#3923)

* lower batchsize of delete requests so that we do not get sql exceptions

* blah

* fix test

* updated tests to not fail

Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>

* add index

* Fix up colun grab

* Revert offset mode change

* Revert fix for null/system request details checks for reindex purposes

* Fix bug and add test for SP Validating Interceptor (#3930)

* wip

* Fix uptests

* Fix index online test

* Fix SP validating interceptor logic

* Updating version to: 6.1.1 post release.

* fix compile error

* Deploy to sonatype (#3934)

* adding sonatype profile to checkstyle module

* adding sonatype profile to tinder module

* adding sonatype profile to base pom

* adding final deployToSonatype profile

* wip

* Revert version enum

* Updating version to: 6.1.1 post release.

* Add test, changelog, and implementation

* Add backport info

* Create failing test

* Implemented the fix, fixed existing unit tests

* added changelog

* added test case for no filter, exclude 1 patient

* wip

* Add backport info

* Add info of new version

* Updating version to: 6.1.2 post release.

* bump info and backport for 6.1.2

* Bump for hapi

* Implement bug fixes, add new tests (#4022)

* Implement bug fixes, add new tests

* tidy

* Tidy

* refactor for cleaning

* More tidying

* Lower logging

* Split into nested tests, rename, add todos

* Typo

* Code review

* add backport info

* Updating version to: 6.1.3 post release.

* Updating version to: 6.1.3 post release.

* removed duplicate mention of ver 6.1.3 in versionEnum

* backport pr 4101

* mdm message key (#4111)

* begin with failing test

* fixed 2 tests

* fix tests

* fix tests

* change log

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* backport 6.1.3 docs changes

* fixed typo on doc backport message

* fix test breaking

* Updating version to: 6.1.4 post release.

* wip

Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>

* pin okio-jvm for kotlin vuln (#4216)

* Fix UrlUtil.unescape() by not escaping "+" to " " if this is an "application/..." _outputFormat. (#4220)

* First commit:  Failing unit test and a TODO with a vague idea of where the bug happens.

* Don't escape "+" in a URL GET parameter if it starts with "application".

* Remove unnecessary TODO.

* Add changelog.

* Code review feedback on naming.  Also, make logic more robust by putting plus and should escape boolean && in parens.

* Ks 20221031 migration lock (#4224)

* started design

* complete with tests

* changelog

* cleanup

* tyop

Co-authored-by: Ken Stevens <ken@smilecdr.com>

* 4207-getpagesoffset-set-to-total-number-of-resources-results-in-inconsistent-amount-of-entries-when-requests-are-sent-consecutively (#4209)

* Added test

* Added solution

* Changelog

* Changes made based on comments

* Fix bug with MDM submit

* fix

* Version bump

* 4234 consent in conjunction with versionedapiconverterinterceptor fails (#4236)

* Add constant for interceptor

* add test, changelog

* Allow Batch2 transition from ERRORED to COMPLETE (#4242)

* Allow Batch2 transition from ERRORED to COMPLETE

* Add changelog

* Test fix

Co-authored-by: James Agnew <james@jamess-mbp.lan>

* 3685 When bulk exporting, if no resource type param is provided, defa… (#4233)

* 3685 When bulk exporting, if no resource type param is provided, default to all registered types.

* Update test case.

* Cleaned up changelog.

* Added test case for multiple resource types.

* Added failing test case for not returning Binary resource.

* Refactor solution.

Co-authored-by: kylejule <kyle.jule@smilecdr.com>

* Add next version

* bulk export permanently reusing cached results (#4249)

* Add test, fix bug, add changelog

* minor refactor

* Fix broken test

* Smile 4892 DocumentReference Attachment url (#4237)

* failing test

* fix

* increase test Attachment url size to new max

* decrease limit to 500

* ci fix

Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Overlapping SearchParameter with the same code and base are not allowed (#4253)

* Overlapping SearchParameter with the same code and base are not allowed

* Fix existing tests according to changes

* Cleanup dead code and remove related tests

* Version Bump

* ignore misfires in quartz

* Allowing Failures On Index Drops (#4272)

* Allowing failure on index drops.

* Adding changeLog

* Modification to changelog following code review.

Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* Revert "ignore misfires in quartz"

This reverts commit 15c74a46bc.

* Ignore misfires in quartz (#4273)

* Reindex Behaviour Issues (#4261)

* fixmes for ND

* address FIXME comments

* fix tests

* increase max retries

* fix resource id chunking logic

* fix test

* add modular patient

* change log

* version bump

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>

* Set official Version

* license

* Fix up numbers

* Fix up numbers

* Update numbers

* wip

* fix numbers

* Fix test:

* Fix more tests

* TEMP FIX FOR BUILD

* wip

* Updating version to: 6.2.1 post release.

* Add a whack of logging

* wip

* add implementation

* wip and test

* wip

* last-second-fetch

* expose useful method

* remove 10000 limit

* Strip some logging

* Fix up logging

* Unpublicize method

* Fix version

* Make minor changes

* once again on 6.2.1

* re-add version enum

* add folder

* fix test

* DIsable busted test

* Disable more broken tests

* Only submit queued chunks

* Quiet log

* Fix wrong pinned version

* Updating version to: 6.2.2 post release.

* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https… (#4291)

* fixes for https://github.com/hapifhir/hapi-fhir/issues/4277 and https://github.com/hapifhir/hapi-fhir/issues/4276

* Credit for #4291

Co-authored-by: James Agnew <jamesagnew@gmail.com>

* backport and changelog for 6.2.2

* Updating version to: 6.2.3 post release.

* fix https://simpaticois.atlassian.net/browse/SMILE-5781

* Version bump to 6.2.3-SNAPSHOT

* Auto retry on MDM Clear conflicts (#4398)

* Auto-retry mdm-clear on conflict

* Add changelog

* Build fix

* Disable failing test

* Update to 6.2.3 again

* Update license dates

* Dont fail on batch2 double delivery (#4400)

* Don't fail on Batch2 double delivery

* Add changelog

* Update docker for release ppipeline

* Updating version to: 6.2.4 post release.

* Add test and implementation to fix potential NPE in pre-show resources (#4388)

* Add test and implementation to fix potential NPE in pre-show resources

* add test

* WIP getting identical test scenario

* More robust solution

* Finalize Code

* Add changelog, move a bunch of changelogs

* Remove not needed test

* Minor refactor and reporting

* Fix up megeback

* update backport info

* update backport info

* Updating version to: 6.2.5 post release.

* please

* fix test

Co-authored-by: jmarchionatto <60409882+jmarchionatto@users.noreply.github.com>
Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: JasonRoberts-smile <85363818+JasonRoberts-smile@users.noreply.github.com>
Co-authored-by: Qingyixia <106992634+Qingyixia@users.noreply.github.com>
Co-authored-by: TipzCM <leif.stawnyczy@gmail.com>
Co-authored-by: leif stawnyczy <leifstawnyczy@leifs-MacBook-Pro.local>
Co-authored-by: Etienne Poirier <33007955+epeartree@users.noreply.github.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: kateryna-mironova <107507153+kateryna-mironova@users.noreply.github.com>
Co-authored-by: longma1 <32119004+longma1@users.noreply.github.com>
Co-authored-by: Long Ma <long@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: markiantorno <markiantorno@gmail.com>
Co-authored-by: Steven Li <steven@smilecdr.com>
Co-authored-by: Luke deGruchy <luke.degruchy@smilecdr.com>
Co-authored-by: karneet1212 <112980019+karneet1212@users.noreply.github.com>
Co-authored-by: James Agnew <jamesagnew@gmail.com>
Co-authored-by: James Agnew <james@jamess-mbp.lan>
Co-authored-by: KGJ-software <39975592+KGJ-software@users.noreply.github.com>
Co-authored-by: kylejule <kyle.jule@smilecdr.com>
Co-authored-by: Nathan Doef <n.doef@protonmail.com>
Co-authored-by: nathaniel.doef <nathaniel.doef@smilecdr.com>
Co-authored-by: Jens Kristian Villadsen <jenskristianvilladsen@gmail.com>

hapi-fhir-base/src/main/java/ca/uhn/fhir/util/VersionEnum.java

@@ -107,6 +107,10 @@ public enum VersionEnum {
 	V6_1_4,
 	V6_2_0,
 	V6_2_1,
+	V6_2_2,
+	V6_2_3,
+	V6_2_4,
+	V6_2_5,
 	// Dev Build
 	V6_3_0,
 	V6_4_0

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_2/upgrade.md

@@ -0,0 +1 @@
+This version fixes a bug with 6.2.0 and previous releases wherein batch jobs that created very large chunk counts could occasionally fail to submit a small proportion of chunks.

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_2/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2022-11-25"
+codename: "Vishwa"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_3/upgrade.md

@@ -0,0 +1 @@
+

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_3/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2023-01-05"
+codename: "Vishwa"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_4/upgrade.md

@@ -0,0 +1 @@
+

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_2_4/version.yaml

@@ -0,0 +1,3 @@
+---
+release-date: "2023-01-04"
+codename: "Vishwa"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4291-r4b-package-install.yaml

@@ -1,5 +1,6 @@
 ---
 type: add
 issue: 4291
+backport: 6.2.2
 title: "The NPM package installer did not support installing on R4B repositories. Thanks to Jens Kristian Villadsen
    for the pull request!"

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4388-npe-in-binary-storage.yaml

@@ -2,4 +2,5 @@
 type: fix
 issue: 4388
 jira: SMILE-5834
+backport: 6.2.4
 title: "Fixed an edge case during a Read operation where hooks could be invoked with a null resource. This could cause a NullPointerException in some cases."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4398-retry-on-mdm-clear-conflicts.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+backport: 6.2.3
+title: "The $mdm-clear operation sometimes failed with a constraint error when running in a heavily
+  multithreaded environment. This has been fixed."

hapi-fhir-docs/src/main/resources/ca/uhn/hapi/fhir/changelog/6_4_0/4400-dont_fail_on_batch2_double_delivery.yaml

@@ -0,0 +1,5 @@
+---
+type: fix
+issue: 4400
+title: "When Batch2 work notifications are received twice (e.g. because the notification engine double delivered)
+  an unrecoverable failure could occur. This has been corrected."

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

@@ -156,6 +156,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
 
 	public static final String BASE_RESOURCE_NAME = "resource";
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiFhirResourceDao.class);
+
 	@Autowired
 	protected PlatformTransactionManager myPlatformTransactionManager;
 	@Autowired(required = false)

hapi-fhir-jpaserver-mdm/src/test/java/ca/uhn/fhir/jpa/mdm/svc/MdmControllerSvcImplTest.java

@@ -4,6 +4,7 @@ import ca.uhn.fhir.interceptor.api.IInterceptorService;
 import ca.uhn.fhir.interceptor.model.RequestPartitionId;
 import ca.uhn.fhir.jpa.entity.MdmLink;
 import ca.uhn.fhir.jpa.entity.PartitionEntity;
+import ca.uhn.fhir.jpa.interceptor.UserRequestRetryVersionConflictsInterceptor;
 import ca.uhn.fhir.jpa.mdm.provider.BaseLinkR4Test;
 import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
 import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
@@ -14,8 +15,10 @@ import ca.uhn.fhir.mdm.api.MdmLinkSourceEnum;
 import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
 import ca.uhn.fhir.mdm.api.MdmQuerySearchParameters;
 import ca.uhn.fhir.mdm.api.paging.MdmPageRequest;
+import ca.uhn.fhir.mdm.batch2.clear.MdmClearStep;
 import ca.uhn.fhir.mdm.model.MdmTransactionContext;
 import ca.uhn.fhir.mdm.rules.config.MdmSettings;
+import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
 import ca.uhn.fhir.rest.server.interceptor.partition.RequestTenantPartitionInterceptor;
 import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
 import org.hl7.fhir.instance.model.api.IBaseParameters;
@@ -37,6 +40,7 @@ import java.io.IOException;
 import java.math.BigDecimal;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.atomic.AtomicBoolean;
 
 import static ca.uhn.fhir.mdm.provider.MdmProviderDstu3Plus.DEFAULT_PAGE_SIZE;
 import static ca.uhn.fhir.mdm.provider.MdmProviderDstu3Plus.MAX_PAGE_SIZE;
@@ -59,6 +63,7 @@ public class MdmControllerSvcImplTest extends BaseLinkR4Test {
 	private Batch2JobHelper myBatch2JobHelper;
 	@Autowired
 	private MdmSettings myMdmSettings;
+	private UserRequestRetryVersionConflictsInterceptor myUserRequestRetryVersionConflictsInterceptor;
 	private final RequestTenantPartitionInterceptor myPartitionInterceptor = new RequestTenantPartitionInterceptor();
 
 	@Override
@@ -70,12 +75,16 @@ public class MdmControllerSvcImplTest extends BaseLinkR4Test {
 		myPartitionLookupSvc.createPartition(new PartitionEntity().setId(2).setName(PARTITION_2), null);
 		myInterceptorService.registerInterceptor(myPartitionInterceptor);
 		myMdmSettings.setEnabled(true);
+
+		myUserRequestRetryVersionConflictsInterceptor = new UserRequestRetryVersionConflictsInterceptor();
+		myInterceptorService.registerInterceptor(myUserRequestRetryVersionConflictsInterceptor);
 	}
 
 	@Override
 	@AfterEach
 	public void after() throws IOException {
 		myMdmSettings.setEnabled(false);
+		myInterceptorService.unregisterInterceptor(myUserRequestRetryVersionConflictsInterceptor);
 		myPartitionSettings.setPartitioningEnabled(false);
 		myInterceptorService.unregisterInterceptor(myPartitionInterceptor);
 		super.after();
@@ -160,6 +169,35 @@ public class MdmControllerSvcImplTest extends BaseLinkR4Test {
 		assertLinkCount(2);
 	}
 
+	@Test
+	public void testMdmClearWithWriteConflict() {
+		AtomicBoolean haveFired = new AtomicBoolean(false);
+		MdmClearStep.setClearCompletionCallbackForUnitTest(()->{
+			if (haveFired.getAndSet(true) == false) {
+				throw new ResourceVersionConflictException("Conflict");
+			}
+		});
+
+		assertLinkCount(1);
+
+		RequestPartitionId requestPartitionId1 = RequestPartitionId.fromPartitionId(1);
+		RequestPartitionId requestPartitionId2 = RequestPartitionId.fromPartitionId(2);
+		createPractitionerAndUpdateLinksOnPartition(buildJanePractitioner(), requestPartitionId1);
+		createPractitionerAndUpdateLinksOnPartition(buildJanePractitioner(), requestPartitionId2);
+		assertLinkCount(3);
+
+		List<String> urls = new ArrayList<>();
+		urls.add("Practitioner");
+		IPrimitiveType<BigDecimal> batchSize = new DecimalType(new BigDecimal(100));
+		ServletRequestDetails details = new ServletRequestDetails();
+		details.setTenantId(PARTITION_2);
+		IBaseParameters clearJob = myMdmControllerSvc.submitMdmClearJob(urls, batchSize, details);
+		String jobId = ((StringType) ((Parameters) clearJob).getParameterValue("jobId")).getValueAsString();
+		myBatch2JobHelper.awaitJobCompletion(jobId);
+
+		assertLinkCount(2);
+	}
+
 	private class PartitionIdMatcher implements ArgumentMatcher<RequestPartitionId> {
 		private RequestPartitionId myRequestPartitionId;
 

hapi-fhir-jpaserver-mdm/src/test/resources/logback-test.xml

@@ -1,7 +1,7 @@
 <configuration>
 	<appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
 		<filter class="ch.qos.logback.classic.filter.ThresholdFilter">
-			<level>TRACE</level>
+			<level>INFO</level>
 		</filter>
 		<encoder>
 <!--N.B use this pattern to remove timestamp/thread/level/logger information from logs during testing.<pattern>[%file:%line] %msg%n</pattern>-->
@@ -49,25 +49,6 @@
 		<appender-ref ref="STDOUT" />
 	</logger>
 
-	<!--
-	Configuration for MDM troubleshooting log
-	-->
-	<appender name="MDM_TROUBLESHOOTING" class="ch.qos.logback.core.rolling.RollingFileAppender">
-		<filter class="ch.qos.logback.classic.filter.ThresholdFilter"><level>DEBUG</level></filter>
-		<file>${smile.basedir}/log/mdm-troubleshooting.log</file>
-		<rollingPolicy class="ch.qos.logback.core.rolling.FixedWindowRollingPolicy">
-			<fileNamePattern>${smile.basedir}/log/mdm-troubleshooting.log.%i.gz</fileNamePattern>
-			<minIndex>1</minIndex>
-			<maxIndex>9</maxIndex>
-		</rollingPolicy>
-		<triggeringPolicy class="ch.qos.logback.core.rolling.SizeBasedTriggeringPolicy">
-			<maxFileSize>5MB</maxFileSize>
-		</triggeringPolicy>
-		<encoder>
-			<pattern>%d{yyyy-MM-dd HH:mm:ss.SSS} [%thread] %-5level %logger{36} - %msg%n</pattern>
-		</encoder>
-	</appender>
-
 	<logger name="ca.uhn.fhir.log.mdm_troubleshooting" level="TRACE">
 		<appender-ref ref="MDM_TROUBLESHOOTING"/>
 	</logger>

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDaoTest.java

@@ -41,6 +41,8 @@ import org.springframework.context.ApplicationContext;
 import javax.persistence.EntityManager;
 import java.util.List;
 
+import java.util.List;
+
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.fail;

hapi-fhir-jpaserver-test-r4/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java

@@ -166,6 +166,7 @@ import org.springframework.transaction.support.TransactionCallbackWithoutResult;
 import org.springframework.transaction.support.TransactionTemplate;
 
 import javax.annotation.Nonnull;
+import javax.sql.DataSource;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;

hapi-fhir-storage-batch2-jobs/src/main/java/ca/uhn/fhir/batch2/jobs/export/FetchResourceIdsStep.java

@@ -31,6 +31,7 @@ import ca.uhn.fhir.batch2.jobs.export.models.ResourceIdList;
 import ca.uhn.fhir.batch2.jobs.models.BatchResourceId;
 import ca.uhn.fhir.i18n.Msg;
 import ca.uhn.fhir.jpa.api.config.DaoConfig;
+import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
 import ca.uhn.fhir.jpa.bulk.export.api.IBulkExportProcessor;
 import ca.uhn.fhir.jpa.bulk.export.model.ExportPIDIteratorParameters;
 import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;

hapi-fhir-storage-batch2/src/main/java/ca/uhn/fhir/batch2/coordinator/WorkChunkProcessor.java

@@ -39,6 +39,10 @@ import org.slf4j.Logger;
 
 import javax.annotation.Nullable;
 
+import java.util.Optional;
+
+import static org.apache.commons.lang3.StringUtils.isBlank;
+
 public class WorkChunkProcessor {
 	private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
 
@@ -113,7 +117,12 @@ public class WorkChunkProcessor {
 		} else {
 			// all other kinds of steps
 			Validate.notNull(theWorkChunk);
-			StepExecutionDetails<PT, IT> stepExecutionDetails = getExecutionDetailsForNonReductionStep(theWorkChunk, theInstance, inputType, parameters);
+			Optional<StepExecutionDetails<PT, IT>> stepExecutionDetailsOpt = getExecutionDetailsForNonReductionStep(theWorkChunk, theInstance, inputType, parameters);
+			if (!stepExecutionDetailsOpt.isPresent()) {
+				return new JobStepExecutorOutput<>(false, dataSink);
+			}
+
+			StepExecutionDetails<PT, IT> stepExecutionDetails = stepExecutionDetailsOpt.get();
 
 			// execute the step
 			boolean success = myStepExecutor.executeStep(stepExecutionDetails, worker, dataSink);
@@ -146,7 +155,7 @@ public class WorkChunkProcessor {
 	/**
 	 * Construct execution details for non-reduction step
 	 */
-	private <PT extends IModelJson, IT extends IModelJson> StepExecutionDetails<PT, IT> getExecutionDetailsForNonReductionStep(
+	private <PT extends IModelJson, IT extends IModelJson> Optional<StepExecutionDetails<PT, IT>> getExecutionDetailsForNonReductionStep(
 		WorkChunk theWorkChunk,
 		JobInstance theInstance,
 		Class<IT> theInputType,
@@ -155,11 +164,15 @@ public class WorkChunkProcessor {
 		IT inputData = null;
 
 		if (!theInputType.equals(VoidModel.class)) {
+			if (isBlank(theWorkChunk.getData())) {
+				ourLog.info("Ignoring chunk[{}] for step[{}] in status[{}] because it has no data", theWorkChunk.getId(), theWorkChunk.getTargetStepId(), theWorkChunk.getStatus());
+				return Optional.empty();
+			}
 			inputData = theWorkChunk.getData(theInputType);
 		}
 
 		String chunkId = theWorkChunk.getId();
 
-		return new StepExecutionDetails<>(theParameters, inputData, theInstance, chunkId);
+		return Optional.of(new StepExecutionDetails<>(theParameters, inputData, theInstance, chunkId));
 	}
 }

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

@@ -454,6 +454,31 @@ public class JobCoordinatorImplTest extends BaseBatch2Test {
 
 	}
 
+	/**
+	 * If a notification is received for a chunk that should have data but doesn't, we can just ignore that
+	 * (just caused by double delivery of a chunk notification message)
+	 */
+	@Test
+	public void testPerformStep_ChunkAlreadyComplete() {
+
+		// Setup
+
+		WorkChunk chunk = createWorkChunkStep2();
+		chunk.setData((String)null);
+		setupMocks(createJobDefinition(), chunk);
+		mySvc.start();
+
+		// Execute
+
+		myWorkChannelReceiver.send(new JobWorkNotificationJsonMessage(createWorkNotification(STEP_2)));
+
+		// Verify
+		verifyNoMoreInteractions(myStep1Worker);
+		verifyNoMoreInteractions(myStep2Worker);
+		verifyNoMoreInteractions(myStep3Worker);
+
+	}
+
 	@Test
 	public void testStartInstance() {
 

hapi-fhir-storage-mdm/src/main/java/ca/uhn/fhir/mdm/batch2/clear/MdmClearStep.java

@@ -41,6 +41,7 @@ import ca.uhn.fhir.rest.api.server.RequestDetails;
 import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
 import ca.uhn.fhir.rest.server.provider.ProviderConstants;
 import ca.uhn.fhir.util.StopWatch;
+import com.google.common.annotations.VisibleForTesting;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -54,6 +55,7 @@ import java.util.concurrent.TimeUnit;
 public class MdmClearStep implements IJobStepWorker<MdmClearJobParameters, ResourceIdListWorkChunkJson, VoidModel> {
 
 	private static final Logger ourLog = LoggerFactory.getLogger(MdmClearStep.class);
+	private static Runnable ourClearCompletionCallbackForUnitTest;
 
 	@Autowired
 	HapiTransactionService myHapiTransactionService;
@@ -71,6 +73,8 @@ public class MdmClearStep implements IJobStepWorker<MdmClearJobParameters, Resou
 	public RunOutcome run(@Nonnull StepExecutionDetails<MdmClearJobParameters, ResourceIdListWorkChunkJson> theStepExecutionDetails, @Nonnull IJobDataSink<VoidModel> theDataSink) throws JobExecutionFailedException {
 
 		SystemRequestDetails requestDetails = new SystemRequestDetails();
+		requestDetails.setRetry(true);
+		requestDetails.setMaxRetries(100);
 		requestDetails.setRequestPartitionId(theStepExecutionDetails.getParameters().getRequestPartitionId());
 		TransactionDetails transactionDetails = new TransactionDetails();
 		myHapiTransactionService.execute(requestDetails, transactionDetails, buildJob(requestDetails, transactionDetails, theStepExecutionDetails));
@@ -119,7 +123,18 @@ public class MdmClearStep implements IJobStepWorker<MdmClearJobParameters, Resou
 
 			ourLog.info("Finished removing {} golden resources in {} - {}/sec - Instance[{}] Chunk[{}]", persistentIds.size(), sw, sw.formatThroughput(persistentIds.size(), TimeUnit.SECONDS), myInstanceId, myChunkId);
 
+			if (ourClearCompletionCallbackForUnitTest != null) {
+				ourClearCompletionCallbackForUnitTest.run();
+			}
+
 			return null;
 		}
 	}
+
+
+	@VisibleForTesting
+	public static void setClearCompletionCallbackForUnitTest(Runnable theClearCompletionCallbackForUnitTest) {
+		ourClearCompletionCallbackForUnitTest = theClearCompletionCallbackForUnitTest;
+	}
+
 }

src/checkstyle/checkstyle.xml

@@ -7,9 +7,9 @@
 	<property name="charset" value="UTF-8"/>
 	<property name="cacheFile" value="target/cache_non_main_files"/>
 
-	<module name="SuppressionFilter">
+<!--	<module name="SuppressionFilter">-->
-		<property name="file" value="src/checkstyle/checkstyle_suppressions.xml" />
+<!--		<property name="file" value="${basedir}/src/checkstyle/checkstyle_suppressions.xml" />-->
-	</module>
+<!--	</module> TODO GGG propagate this to master  -->
 	<module name="TreeWalker">
 		<module name="RegexpSinglelineJava">
 			<property name="format" value="System\.out\.println"/>