Merge branch 'rel_6_4' into nd-4123-bulk-export-stuck-in-finalize-state
This commit is contained in:
nathaniel.doef
commit
87df691fc2
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@ -0,0 +1,3 @@
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type: fix
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issue: 4486
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title: "Previously, some MDM links of type `POSSIBLE_MATCH` were saved with unnormalized score values. This has been fixed."
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@ -0,0 +1,5 @@
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---
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type: fix
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issue: 4491
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title: "Batch2 Jobs in the FINALIZE state can now be
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cancelled."
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@ -0,0 +1,8 @@
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---
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type: fix
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issue: 4491
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title: "Moved batch2 reduction step logic to the messaging queue.
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Before it was executed during the maintenance run directly.
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This resulted in bugs with multiple reduction steps kicking
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off for long running jobs.
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"
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@ -150,6 +150,9 @@ public class IdHelperService implements IIdHelperService<JpaPid> {
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assert myDontCheckActiveTransactionForUnitTest || TransactionSynchronizationManager.isSynchronizationActive();
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assert theRequestPartitionId != null;
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if (theResourceId.contains("/")) {
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theResourceId = theResourceId.substring(theResourceId.indexOf("/") + 1);
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}
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IdDt id = new IdDt(theResourceType, theResourceId);
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Map<String, List<IResourceLookup<JpaPid>>> matches = translateForcedIdToPids(theRequestPartitionId,
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Collections.singletonList(id),
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@ -73,11 +73,9 @@ public class MdmLinkDaoSvc<P extends IResourcePersistentId, M extends IMdmLink<P
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mdmLink.setEidMatch(theMatchOutcome.isEidMatch() | mdmLink.isEidMatchPresent());
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mdmLink.setHadToCreateNewGoldenResource(theMatchOutcome.isCreatedNewResource() | mdmLink.getHadToCreateNewGoldenResource());
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mdmLink.setMdmSourceType(myFhirContext.getResourceType(theSourceResource));
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if (mdmLink.getScore() != null) {
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mdmLink.setScore(Math.max(theMatchOutcome.score, mdmLink.getScore()));
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} else {
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mdmLink.setScore(theMatchOutcome.score);
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}
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setScoreProperties(theMatchOutcome, mdmLink);
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// Add partition for the mdm link if it's available in the source resource
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RequestPartitionId partitionId = (RequestPartitionId) theSourceResource.getUserData(Constants.RESOURCE_PARTITION_ID);
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if (partitionId != null && partitionId.getFirstPartitionIdOrNull() != null) {
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@ -91,6 +89,24 @@ public class MdmLinkDaoSvc<P extends IResourcePersistentId, M extends IMdmLink<P
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return mdmLink;
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}
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private void setScoreProperties(MdmMatchOutcome theMatchOutcome, M mdmLink) {
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if (theMatchOutcome.getScore() != null) {
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mdmLink.setScore( mdmLink.getScore() != null
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? Math.max(theMatchOutcome.getNormalizedScore(), mdmLink.getScore())
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: theMatchOutcome.getNormalizedScore() );
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}
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if (theMatchOutcome.getVector() != null) {
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mdmLink.setVector( mdmLink.getVector() != null
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? Math.max(theMatchOutcome.getVector(), mdmLink.getVector())
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: theMatchOutcome.getVector() );
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}
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mdmLink.setRuleCount( mdmLink.getRuleCount() != null
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? Math.max(theMatchOutcome.getMdmRuleCount(), mdmLink.getRuleCount())
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: theMatchOutcome.getMdmRuleCount() );
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}
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@Nonnull
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public M getOrCreateMdmLinkByGoldenResourceAndSourceResource(
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IAnyResource theGoldenResource, IAnyResource theSourceResource
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@ -127,7 +143,6 @@ public class MdmLinkDaoSvc<P extends IResourcePersistentId, M extends IMdmLink<P
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* @param theSourceResourcePid The ResourcepersistenceId of the Source resource
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* @return The {@link IMdmLink} entity that matches these criteria if exists
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*/
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@SuppressWarnings("unchecked")
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public Optional<M> getLinkByGoldenResourcePidAndSourceResourcePid(P theGoldenResourcePid, P theSourceResourcePid) {
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if (theSourceResourcePid == null || theGoldenResourcePid == null) {
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return Optional.empty();
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@ -94,7 +94,7 @@ public class MdmMatchLinkSvc {
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private void handleMdmWithMultipleCandidates(IAnyResource theResource, CandidateList theCandidateList, MdmTransactionContext theMdmTransactionContext) {
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MatchedGoldenResourceCandidate firstMatch = theCandidateList.getFirstMatch();
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IResourcePersistentId sampleGoldenResourcePid = firstMatch.getCandidateGoldenResourcePid();
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IResourcePersistentId<?> sampleGoldenResourcePid = firstMatch.getCandidateGoldenResourcePid();
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boolean allSameGoldenResource = theCandidateList.stream()
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.allMatch(candidate -> candidate.getCandidateGoldenResourcePid().equals(sampleGoldenResourcePid));
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@ -105,17 +105,7 @@ public class MdmMatchLinkSvc {
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log(theMdmTransactionContext, "MDM received multiple match candidates, that were linked to different Golden Resources. Setting POSSIBLE_DUPLICATES and POSSIBLE_MATCHES.");
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//Set them all as POSSIBLE_MATCH
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List<IAnyResource> goldenResources = new ArrayList<>();
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for (MatchedGoldenResourceCandidate matchedGoldenResourceCandidate : theCandidateList.getCandidates()) {
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IAnyResource goldenResource = myMdmGoldenResourceFindingSvc
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.getGoldenResourceFromMatchedGoldenResourceCandidate(matchedGoldenResourceCandidate, theMdmTransactionContext.getResourceType());
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MdmMatchOutcome outcome = new MdmMatchOutcome(matchedGoldenResourceCandidate.getMatchResult().vector,
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matchedGoldenResourceCandidate.getMatchResult().getNormalizedScore());
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outcome.setMatchResultEnum(MdmMatchResultEnum.POSSIBLE_MATCH);
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outcome.setEidMatch(theCandidateList.isEidMatch());
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myMdmLinkSvc.updateLink(goldenResource, theResource, outcome, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
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goldenResources.add(goldenResource);
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}
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List<IAnyResource> goldenResources = createPossibleMatches(theResource, theCandidateList, theMdmTransactionContext);
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//Set all GoldenResources as POSSIBLE_DUPLICATE of the last GoldenResource.
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IAnyResource firstGoldenResource = goldenResources.get(0);
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@ -129,6 +119,26 @@ public class MdmMatchLinkSvc {
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}
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}
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private List<IAnyResource> createPossibleMatches(IAnyResource theResource, CandidateList theCandidateList, MdmTransactionContext theMdmTransactionContext) {
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List<IAnyResource> goldenResources = new ArrayList<>();
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for (MatchedGoldenResourceCandidate matchedGoldenResourceCandidate : theCandidateList.getCandidates()) {
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IAnyResource goldenResource = myMdmGoldenResourceFindingSvc
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.getGoldenResourceFromMatchedGoldenResourceCandidate(matchedGoldenResourceCandidate, theMdmTransactionContext.getResourceType());
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MdmMatchOutcome outcome = new MdmMatchOutcome(matchedGoldenResourceCandidate.getMatchResult().getVector(),
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matchedGoldenResourceCandidate.getMatchResult().getScore())
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.setMdmRuleCount( matchedGoldenResourceCandidate.getMatchResult().getMdmRuleCount());
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outcome.setMatchResultEnum(MdmMatchResultEnum.POSSIBLE_MATCH);
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outcome.setEidMatch(theCandidateList.isEidMatch());
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myMdmLinkSvc.updateLink(goldenResource, theResource, outcome, MdmLinkSourceEnum.AUTO, theMdmTransactionContext);
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goldenResources.add(goldenResource);
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}
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return goldenResources;
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}
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private void handleMdmWithNoCandidates(IAnyResource theResource, MdmTransactionContext theMdmTransactionContext) {
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log(theMdmTransactionContext, String.format("There were no matched candidates for MDM, creating a new %s Golden Resource.", theResource.getIdElement().getResourceType()));
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IAnyResource newGoldenResource = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(theResource, theMdmTransactionContext);
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@ -100,7 +100,6 @@ public class MdmLinkDaoSvcTest extends BaseMdmR4Test {
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mdmLink.setUpdated(new Date());
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mdmLink.setGoldenResourcePersistenceId(JpaPid.fromId(thePatientPid));
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mdmLink.setSourcePersistenceId(runInTransaction(()->myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), patient)));
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MdmLink saved= myMdmLinkDao.save(mdmLink);
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return saved;
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return myMdmLinkDao.save(mdmLink);
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}
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}
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@ -10,6 +10,7 @@ import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
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import ca.uhn.fhir.model.primitive.IdDt;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
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import ca.uhn.fhir.test.utilities.RangeTestHelper;
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import ca.uhn.fhir.util.ParametersUtil;
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import ca.uhn.fhir.util.StopWatch;
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import org.apache.commons.lang3.StringUtils;
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@ -377,7 +378,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
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List<Parameters.ParametersParameterComponent> list = getParametersByName(result, "link");
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assertThat(list, hasSize(4));
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List<Parameters.ParametersParameterComponent> part = list.get(3).getPart();
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assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, goldenResourceId.getValue(), patientId.getValue(), MdmMatchResultEnum.MATCH, "false", "false", "2");
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assertMdmLink(MDM_LINK_PROPERTY_COUNT, part, goldenResourceId.getValue(), patientId.getValue(), MdmMatchResultEnum.MATCH, "false", "false", ".666");
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}
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@Test
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@ -459,7 +460,7 @@ public class MdmProviderQueryLinkR4Test extends BaseLinkR4Test {
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assertThat(thePart.get(5).getValue().primitiveValue(), is(theNewGoldenResource));
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assertThat(thePart.get(6).getName(), is("score"));
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assertThat(thePart.get(6).getValue().primitiveValue(), is(theScore));
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RangeTestHelper.checkInRange(theScore, thePart.get(6).getValue().primitiveValue());
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}
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}
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|
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@ -16,6 +16,7 @@ import java.util.List;
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import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.MATCH;
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import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.NO_MATCH;
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import static ca.uhn.fhir.mdm.api.MdmMatchResultEnum.POSSIBLE_MATCH;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
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import static org.junit.jupiter.api.Assertions.assertNotEquals;
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@ -52,6 +53,23 @@ class MdmLinkUpdaterSvcImplTest extends BaseMdmR4Test {
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assertLinksMatchedByEid(false, false);
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}
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@Test
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public void testUpdateLinkPossibleMatchSavesNormalizedScore() {
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final Patient goldenPatient = createGoldenPatient(buildJanePatient());
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final Patient patient1 = createPatient(buildJanePatient());
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buildUpdateLinkMdmTransactionContext();
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MdmMatchOutcome matchOutcome = new MdmMatchOutcome(61L, 5.0).setMdmRuleCount(6).setMatchResultEnum(POSSIBLE_MATCH);
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myMdmLinkDaoSvc.createOrUpdateLinkEntity(goldenPatient, patient1, matchOutcome, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
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final List<MdmLink> targets = myMdmLinkDaoSvc.findMdmLinksByGoldenResource(goldenPatient);
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assertFalse(targets.isEmpty());
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assertEquals(1, targets.size());
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final MdmLink mdmLink = targets.get(0);
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assertEquals(matchOutcome.getNormalizedScore(), mdmLink.getScore());
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}
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@Test
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public void testUpdateLinkMatchAfterVersionChange() {
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myMdmSettings.getMdmRules().setVersion("1");
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|
|
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@ -95,6 +95,7 @@ public abstract class BaseResourceProviderDstu3Test extends BaseJpaDstu3Test {
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myPort = myServer.getPort();
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myServerBase = myServer.getBaseUrl();
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myClient = myServer.getFhirClient();
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myClient.setEncoding(EncodingEnum.JSON);
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myRestServer = myServer.getRestfulServer();
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myClient.getInterceptorService().unregisterInterceptorsIf(t -> t instanceof LoggingInterceptor);
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|
|
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|
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@ -430,7 +430,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
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|
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String respString = myClient.transaction().withBundle(input).prettyPrint().execute();
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||||
ourLog.debug(respString);
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Bundle bundle = myFhirContext.newXmlParser().parseResource(Bundle.class, respString);
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Bundle bundle = myFhirContext.newJsonParser().parseResource(Bundle.class, respString);
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IdType id = new IdType(bundle.getEntry().get(0).getResponse().getLocation());
|
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|
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Basic basic = myClient.read().resource(Basic.class).withId(id).execute();
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|
|
@ -1098,7 +1098,7 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
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//@formatter:on
|
||||
fail();
|
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} catch (PreconditionFailedException e) {
|
||||
assertEquals("HTTP 412 Precondition Failed: " + Msg.code(962) + "Failed to DELETE resource with match URL \"Patient?identifier=testDeleteConditionalMultiple\" because this search matched 2 resources",
|
||||
assertEquals("HTTP 412 Precondition Failed: " + Msg.code(962) + "Failed to DELETE resource with match URL \"Patient?identifier=testDeleteConditionalMultiple&_format=json\" because this search matched 2 resources",
|
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e.getMessage());
|
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}
|
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|
||||
|
|
|
|||
|
|
@ -34,6 +34,8 @@ 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.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.ValueSource;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
|
@ -45,11 +47,13 @@ import java.util.ArrayList;
|
|||
import java.util.Iterator;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.concurrent.atomic.AtomicBoolean;
|
||||
import java.util.concurrent.atomic.AtomicInteger;
|
||||
|
||||
import static ca.uhn.fhir.batch2.config.BaseBatch2Config.CHANNEL_NAME;
|
||||
import static ca.uhn.fhir.batch2.coordinator.WorkChunkProcessor.MAX_CHUNK_ERROR_COUNT;
|
||||
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;
|
||||
|
|
@ -216,9 +220,44 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
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|||
myLastStepLatch.awaitExpected();
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testJobDefinitionWithReductionStepIT() throws InterruptedException {
|
||||
private void createThreeStepReductionJob(
|
||||
String theJobId,
|
||||
IJobStepWorker<TestJobParameters, VoidModel, FirstStepOutput> theFirstStep,
|
||||
IJobStepWorker<TestJobParameters, FirstStepOutput, SecondStepOutput> theSecondStep,
|
||||
IReductionStepWorker<TestJobParameters, SecondStepOutput, ReductionStepOutput> theReductionsStep
|
||||
) {
|
||||
// create job definition (it's the test method's name)
|
||||
JobDefinition<? extends IModelJson> jd = JobDefinition.newBuilder()
|
||||
.setJobDefinitionId(theJobId)
|
||||
.setJobDescription("test job")
|
||||
.setJobDefinitionVersion(TEST_JOB_VERSION)
|
||||
.setParametersType(TestJobParameters.class)
|
||||
.gatedExecution()
|
||||
.addFirstStep(
|
||||
FIRST_STEP_ID,
|
||||
"Test first step",
|
||||
FirstStepOutput.class,
|
||||
theFirstStep
|
||||
)
|
||||
.addIntermediateStep("SECOND",
|
||||
"Second step",
|
||||
SecondStepOutput.class,
|
||||
theSecondStep)
|
||||
.addFinalReducerStep(
|
||||
LAST_STEP_ID,
|
||||
"Test last step",
|
||||
ReductionStepOutput.class,
|
||||
theReductionsStep
|
||||
)
|
||||
.build();
|
||||
myJobDefinitionRegistry.addJobDefinition(jd);
|
||||
}
|
||||
|
||||
@ParameterizedTest
|
||||
@ValueSource(booleans = { true, false })
|
||||
public void testJobDefinitionWithReductionStepIT(boolean theDelayReductionStepBool) throws InterruptedException {
|
||||
// setup
|
||||
String jobId = new Exception().getStackTrace()[0].getMethodName() + "_" + theDelayReductionStepBool;
|
||||
String testInfo = "test";
|
||||
AtomicInteger secondStepInt = new AtomicInteger();
|
||||
|
||||
|
|
@ -235,6 +274,7 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
|
|||
SecondStepOutput output = new SecondStepOutput();
|
||||
output.setValue(testInfo + secondStepInt.getAndIncrement());
|
||||
sink.accept(output);
|
||||
|
||||
return RunOutcome.SUCCESS;
|
||||
};
|
||||
|
||||
|
|
@ -243,63 +283,66 @@ public class Batch2CoordinatorIT extends BaseJpaR4Test {
|
|||
|
||||
private final ArrayList<SecondStepOutput> myOutput = new ArrayList<>();
|
||||
|
||||
private final AtomicBoolean myBoolean = new AtomicBoolean();
|
||||
|
||||
private final AtomicInteger mySecondGate = new AtomicInteger();
|
||||
|
||||
@Override
|
||||
public ChunkOutcome consume(ChunkExecutionDetails<TestJobParameters, SecondStepOutput> theChunkDetails) {
|
||||
myOutput.add(theChunkDetails.getData());
|
||||
// 1 because we know 2 packets are coming.
|
||||
// we'll fire the second maintenance run on the second packet
|
||||
// which should cause multiple maintenance runs to run simultaneously
|
||||
if (theDelayReductionStepBool && mySecondGate.getAndIncrement() == 1) {
|
||||
ourLog.info("SECOND FORCED MAINTENANCE PASS FORCED");
|
||||
myBatch2JobHelper.forceRunMaintenancePass();
|
||||
}
|
||||
return ChunkOutcome.SUCCESS();
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
@Override
|
||||
public RunOutcome run(@Nonnull StepExecutionDetails<TestJobParameters, SecondStepOutput> theStepExecutionDetails,
|
||||
@Nonnull IJobDataSink<ReductionStepOutput> theDataSink) throws JobExecutionFailedException {
|
||||
theDataSink.accept(new ReductionStepOutput(myOutput));
|
||||
callLatch(myLastStepLatch, theStepExecutionDetails);
|
||||
public RunOutcome run(
|
||||
@Nonnull StepExecutionDetails<TestJobParameters, SecondStepOutput> theStepExecutionDetails,
|
||||
@Nonnull IJobDataSink<ReductionStepOutput> theDataSink
|
||||
) throws JobExecutionFailedException {
|
||||
boolean isRunAlready = myBoolean.getAndSet(true);
|
||||
assertFalse(isRunAlready, "Reduction step should only be called once!");
|
||||
|
||||
complete(theStepExecutionDetails, theDataSink);
|
||||
return RunOutcome.SUCCESS;
|
||||
}
|
||||
};
|
||||
|
||||
// create 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
|
||||
)
|
||||
.addIntermediateStep("SECOND",
|
||||
"Second step",
|
||||
SecondStepOutput.class,
|
||||
second)
|
||||
.addFinalReducerStep(
|
||||
LAST_STEP_ID,
|
||||
"Test last step",
|
||||
ReductionStepOutput.class,
|
||||
last
|
||||
)
|
||||
.build();
|
||||
myJobDefinitionRegistry.addJobDefinition(jd);
|
||||
private void complete(
|
||||
@Nonnull StepExecutionDetails<TestJobParameters, SecondStepOutput> theStepExecutionDetails,
|
||||
@Nonnull IJobDataSink<ReductionStepOutput> theDataSink
|
||||
) {
|
||||
assertTrue(myBoolean.get());
|
||||
theDataSink.accept(new ReductionStepOutput(myOutput));
|
||||
callLatch(myLastStepLatch, theStepExecutionDetails);
|
||||
}
|
||||
};
|
||||
createThreeStepReductionJob(jobId, first, second, last);
|
||||
|
||||
// run test
|
||||
JobInstanceStartRequest request = buildRequest(jobId);
|
||||
myFirstStepLatch.setExpectedCount(1);
|
||||
Batch2JobStartResponse startResponse = myJobCoordinator.startInstance(request);
|
||||
|
||||
String instanceId = startResponse.getJobId();
|
||||
myFirstStepLatch.awaitExpected();
|
||||
|
||||
assertNotNull(instanceId);
|
||||
|
||||
myBatch2JobHelper.awaitGatedStepId(FIRST_STEP_ID, instanceId);
|
||||
|
||||
// wait for last step to finish
|
||||
ourLog.info("Setting last step latch");
|
||||
myLastStepLatch.setExpectedCount(1);
|
||||
|
||||
// waiting
|
||||
myBatch2JobHelper.awaitJobCompletion(instanceId);
|
||||
myLastStepLatch.awaitExpected();
|
||||
ourLog.info("awaited the last step");
|
||||
|
||||
// verify
|
||||
Optional<JobInstance> instanceOp = myJobPersistence.fetchInstance(instanceId);
|
||||
|
|
|
|||
|
|
@ -47,8 +47,8 @@ public class DiffProviderR4Test extends BaseResourceProviderR4Test {
|
|||
|
||||
Assertions.assertEquals("replace", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "type"));
|
||||
Assertions.assertEquals("Patient.text.div", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "path"));
|
||||
Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
|
||||
Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody/></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "value"));
|
||||
Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody></tbody></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "previousValue"));
|
||||
Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody></tbody></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 0, "operation", "value"));
|
||||
|
||||
Assertions.assertEquals("insert", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 1, "operation", "type"));
|
||||
Assertions.assertEquals("Patient.name", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 1, "operation", "path"));
|
||||
|
|
@ -86,8 +86,8 @@ public class DiffProviderR4Test extends BaseResourceProviderR4Test {
|
|||
|
||||
Assertions.assertEquals("replace", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "type"));
|
||||
Assertions.assertEquals("Patient.text.div", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "path"));
|
||||
Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody/></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "previousValue"));
|
||||
Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody/></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "value"));
|
||||
Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><table class=\"hapiPropertyTable\"><tbody></tbody></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "previousValue"));
|
||||
Assertions.assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"><div class=\"hapiHeaderText\"><b>SMITH </b></div><table class=\"hapiPropertyTable\"><tbody></tbody></table></div>", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 2, "operation", "value"));
|
||||
|
||||
Assertions.assertEquals("insert", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 3, "operation", "type"));
|
||||
Assertions.assertEquals("Patient.name", FhirPatchApplyR4Test.extractPartValuePrimitive(diff, 3, "operation", "path"));
|
||||
|
|
|
|||
|
|
@ -764,6 +764,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
|
|||
public void testUpdateResourceAfterReadOperationAndNoChangesShouldNotChangeVersion(){
|
||||
// Create Patient
|
||||
Patient patient = new Patient();
|
||||
patient.getText().setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">hello</div>");
|
||||
|
||||
patient = (Patient) myClient.create().resource(patient).execute().getResource();
|
||||
assertEquals(1, patient.getIdElement().getVersionIdPartAsLong());
|
||||
|
||||
|
|
|
|||
|
|
@ -477,6 +477,7 @@ public class TerminologySvcImplR4Test extends BaseTermR4Test {
|
|||
myCodeSystemDao.update(codeSystem, mySrd);
|
||||
|
||||
await().until(() -> {
|
||||
myBatch2JobHelper.runMaintenancePass();
|
||||
myTerminologyDeferredStorageSvc.saveAllDeferred();
|
||||
return myTerminologyDeferredStorageSvc.isStorageQueueEmpty(true);
|
||||
}, equalTo(true));
|
||||
|
|
|
|||
|
|
@ -227,19 +227,12 @@ public class ResourceProviderR5Test extends BaseResourceProviderR5Test {
|
|||
try (CloseableHttpResponse resp = ourHttpClient.execute(post)) {
|
||||
String respString = IOUtils.toString(resp.getEntity().getContent(), Charsets.UTF_8);
|
||||
ourLog.debug(respString);
|
||||
// assertEquals(200, resp.getStatusLine().getStatusCode());
|
||||
assertEquals(200, resp.getStatusLine().getStatusCode());
|
||||
|
||||
// As of 2023-01-26, the above line was restored.
|
||||
// As of 2021-12-28, the R5 structures return a version string that isn't
|
||||
// actually in the fhirVersion ValueSet. If this stops being the case this
|
||||
// test will fail and the line above should be restored
|
||||
OperationOutcome oo = myFhirCtx.newJsonParser().parseResource(OperationOutcome.class, respString);
|
||||
assertEquals(1, oo.getIssue().size());
|
||||
// assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("is not in the value set 'FHIRVersion'"));
|
||||
//As of 2022-10-06, the error is now that RequestGroup is not in the resourcetypes valueset, (though it is).
|
||||
|
||||
//TODO JA: I'm not sure if i have to update this valueset somewhere? the linked valueset _does_ contain the resource type.
|
||||
assertThat(oo.getIssue().get(0).getDiagnostics(), containsString("is not in the value set 'Resource Types'"));
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -71,7 +71,6 @@ public class Batch2JobHelper {
|
|||
return awaitJobHasStatusWithoutMaintenancePass(theBatchJobId, StatusEnum.COMPLETED);
|
||||
}
|
||||
|
||||
|
||||
public JobInstance awaitJobCancelled(String theBatchJobId) {
|
||||
return awaitJobHasStatus(theBatchJobId, StatusEnum.CANCELLED);
|
||||
}
|
||||
|
|
@ -106,7 +105,6 @@ public class Batch2JobHelper {
|
|||
return myJobCoordinator.getInstance(theBatchJobId);
|
||||
}
|
||||
|
||||
|
||||
public JobInstance awaitJobawaitJobHasStatusWithoutMaintenancePass(String theBatchJobId, int theSecondsToWait, StatusEnum... theExpectedStatus) {
|
||||
assert !TransactionSynchronizationManager.isActualTransactionActive();
|
||||
|
||||
|
|
@ -168,7 +166,6 @@ public class Batch2JobHelper {
|
|||
public long getCombinedRecordsProcessed(String theJobId) {
|
||||
JobInstance job = myJobCoordinator.getInstance(theJobId);
|
||||
return job.getCombinedRecordsProcessed();
|
||||
|
||||
}
|
||||
|
||||
public void awaitAllJobsOfJobDefinitionIdToComplete(String theJobDefinitionId) {
|
||||
|
|
@ -243,6 +240,14 @@ public class Batch2JobHelper {
|
|||
myJobMaintenanceService.runMaintenancePass();
|
||||
}
|
||||
|
||||
/**
|
||||
* Forces a run of the maintenance pass without waiting for
|
||||
* the semaphore to release
|
||||
*/
|
||||
public void forceRunMaintenancePass() {
|
||||
myJobMaintenanceService.forceMaintenancePass();
|
||||
}
|
||||
|
||||
public void cancelAllJobsAndAwaitCancellation() {
|
||||
List<JobInstance> instances = myJobPersistence.fetchInstances(1000, 0);
|
||||
for (JobInstance next : instances) {
|
||||
|
|
|
|||
|
|
@ -36,13 +36,13 @@ public final class MdmMatchOutcome {
|
|||
/**
|
||||
* A bitmap that indicates which rules matched
|
||||
*/
|
||||
public final Long vector;
|
||||
private final Long vector;
|
||||
|
||||
/**
|
||||
* The sum of all scores for all rules evaluated. Similarity rules add the similarity score (between 0.0 and 1.0) whereas
|
||||
* matcher rules add either a 0.0 or 1.0.
|
||||
*/
|
||||
public final Double score;
|
||||
private final Double score;
|
||||
|
||||
/**
|
||||
* Did the MDM match operation result in creating a new golden resource resource?
|
||||
|
|
@ -134,6 +134,10 @@ public final class MdmMatchOutcome {
|
|||
return this;
|
||||
}
|
||||
|
||||
public Double getScore() { return score; }
|
||||
|
||||
public Long getVector() { return vector; }
|
||||
|
||||
/**
|
||||
* Gets normalized score that is in the range from zero to one
|
||||
*
|
||||
|
|
|
|||
|
|
@ -89,12 +89,12 @@ public class MdmResourceMatcherSvc {
|
|||
|
||||
MdmMatchOutcome match(IBaseResource theLeftResource, IBaseResource theRightResource) {
|
||||
MdmMatchOutcome matchResult = getMatchOutcome(theLeftResource, theRightResource);
|
||||
MdmMatchResultEnum matchResultEnum = myMdmRulesJson.getMatchResult(matchResult.vector);
|
||||
MdmMatchResultEnum matchResultEnum = myMdmRulesJson.getMatchResult(matchResult.getVector());
|
||||
matchResult.setMatchResultEnum(matchResultEnum);
|
||||
if (ourLog.isDebugEnabled()) {
|
||||
ourLog.debug("{} {}: {}", matchResult.getMatchResultEnum(), theRightResource.getIdElement().toUnqualifiedVersionless(), matchResult);
|
||||
if (ourLog.isTraceEnabled()) {
|
||||
ourLog.trace("Field matcher results:\n{}", myMdmRulesJson.getDetailedFieldMatchResultWithSuccessInformation(matchResult.vector));
|
||||
ourLog.trace("Field matcher results:\n{}", myMdmRulesJson.getDetailedFieldMatchResultWithSuccessInformation(matchResult.getVector()));
|
||||
}
|
||||
}
|
||||
return matchResult;
|
||||
|
|
@ -133,8 +133,8 @@ public class MdmResourceMatcherSvc {
|
|||
ourLog.trace("Matcher {} is valid for resource type: {}. Evaluating match.", fieldComparator.getName(), resourceType);
|
||||
MdmMatchEvaluation matchEvaluation = fieldComparator.match(theLeftResource, theRightResource);
|
||||
if (matchEvaluation.match) {
|
||||
vector |= (1 << i);
|
||||
ourLog.trace("Match: Successfully matched matcher {} with score {}.", fieldComparator.getName(), matchEvaluation.score);
|
||||
vector |= (1L << i);
|
||||
ourLog.trace("Match: Successfully matched matcher {} with score {}. New vector: {}", fieldComparator.getName(), matchEvaluation.score, vector);
|
||||
} else {
|
||||
ourLog.trace("No match: Matcher {} did not match (score: {}).", fieldComparator.getName(), matchEvaluation.score);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -43,8 +43,8 @@ public abstract class BaseR4Test {
|
|||
}
|
||||
|
||||
protected void assertMatchResult(MdmMatchResultEnum theExpectedMatchEnum, long theExpectedVector, double theExpectedScore, boolean theExpectedNewGoldenResource, boolean theExpectedEidMatch, MdmMatchOutcome theMatchResult) {
|
||||
assertEquals(theExpectedScore, theMatchResult.score, 0.001);
|
||||
assertEquals(theExpectedVector, theMatchResult.vector);
|
||||
assertEquals(theExpectedScore, theMatchResult.getScore(), 0.001);
|
||||
assertEquals(theExpectedVector, theMatchResult.getVector());
|
||||
assertEquals(theExpectedEidMatch, theMatchResult.isEidMatch());
|
||||
assertEquals(theExpectedNewGoldenResource, theMatchResult.isCreatedNewResource());
|
||||
assertEquals(theExpectedMatchEnum, theMatchResult.getMatchResultEnum());
|
||||
|
|
|
|||
|
|
@ -0,0 +1,37 @@
|
|||
package ca.uhn.fhir.batch2.jobs.export;
|
||||
|
||||
import ca.uhn.fhir.batch2.model.StatusEnum;
|
||||
import ca.uhn.fhir.jpa.api.svc.IBatch2JobRunner;
|
||||
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
|
||||
import org.slf4j.Logger;
|
||||
|
||||
import static org.slf4j.LoggerFactory.getLogger;
|
||||
|
||||
public class BulkExportUtil {
|
||||
private static final Logger ourLog = getLogger(BulkExportUtil.class);
|
||||
|
||||
private BulkExportUtil() {
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Converts Batch2 StatusEnum -> BulkExportJobStatusEnum
|
||||
*/
|
||||
public static BulkExportJobStatusEnum fromBatchStatus(StatusEnum status) {
|
||||
switch (status) {
|
||||
case QUEUED:
|
||||
case FINALIZE:
|
||||
return BulkExportJobStatusEnum.SUBMITTED;
|
||||
case COMPLETED :
|
||||
return BulkExportJobStatusEnum.COMPLETE;
|
||||
case IN_PROGRESS:
|
||||
return BulkExportJobStatusEnum.BUILDING;
|
||||
default:
|
||||
ourLog.warn("Unrecognized status {}; treating as FAILED/CANCELLED/ERRORED", status.name());
|
||||
case FAILED:
|
||||
case CANCELLED:
|
||||
case ERRORED:
|
||||
return BulkExportJobStatusEnum.ERROR;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -22,10 +22,10 @@ package ca.uhn.fhir.batch2.jobs.services;
|
|||
|
||||
import ca.uhn.fhir.batch2.api.IJobCoordinator;
|
||||
import ca.uhn.fhir.batch2.api.JobOperationResultJson;
|
||||
import ca.uhn.fhir.batch2.jobs.export.BulkExportUtil;
|
||||
import ca.uhn.fhir.batch2.jobs.export.models.BulkExportJobParameters;
|
||||
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.i18n.Msg;
|
||||
import ca.uhn.fhir.jpa.api.model.Batch2JobInfo;
|
||||
import ca.uhn.fhir.jpa.api.model.Batch2JobOperationResult;
|
||||
|
|
@ -33,7 +33,6 @@ import ca.uhn.fhir.jpa.api.model.BulkExportParameters;
|
|||
import ca.uhn.fhir.jpa.api.svc.IBatch2JobRunner;
|
||||
import ca.uhn.fhir.jpa.batch.models.Batch2BaseJobParameters;
|
||||
import ca.uhn.fhir.jpa.batch.models.Batch2JobStartResponse;
|
||||
import ca.uhn.fhir.jpa.bulk.export.model.BulkExportJobStatusEnum;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.util.Batch2JobDefinitionConstants;
|
||||
import org.slf4j.Logger;
|
||||
|
|
@ -97,7 +96,10 @@ public class Batch2JobRunnerImpl implements IBatch2JobRunner {
|
|||
private Batch2JobInfo fromJobInstanceToBatch2JobInfo(@Nonnull JobInstance theInstance) {
|
||||
Batch2JobInfo info = new Batch2JobInfo();
|
||||
info.setJobId(theInstance.getInstanceId());
|
||||
info.setStatus(fromBatchStatus(theInstance.getStatus()));
|
||||
// should convert this to a more generic enum for all batch2 (which is what it seems like)
|
||||
// or use the status enum only (combine with bulk export enum)
|
||||
// on the Batch2JobInfo
|
||||
info.setStatus(BulkExportUtil.fromBatchStatus(theInstance.getStatus()));
|
||||
info.setCancelled(theInstance.isCancelled());
|
||||
info.setStartTime(theInstance.getStartTime());
|
||||
info.setEndTime(theInstance.getEndTime());
|
||||
|
|
@ -106,22 +108,6 @@ public class Batch2JobRunnerImpl implements IBatch2JobRunner {
|
|||
return info;
|
||||
}
|
||||
|
||||
public static BulkExportJobStatusEnum fromBatchStatus(StatusEnum status) {
|
||||
switch (status) {
|
||||
case QUEUED:
|
||||
return BulkExportJobStatusEnum.SUBMITTED;
|
||||
case COMPLETED :
|
||||
return BulkExportJobStatusEnum.COMPLETE;
|
||||
case IN_PROGRESS:
|
||||
return BulkExportJobStatusEnum.BUILDING;
|
||||
case FAILED:
|
||||
case CANCELLED:
|
||||
case ERRORED:
|
||||
default:
|
||||
return BulkExportJobStatusEnum.ERROR;
|
||||
}
|
||||
}
|
||||
|
||||
private Batch2JobStartResponse startBatch2BulkExportJob(BulkExportParameters theParameters) {
|
||||
JobInstanceStartRequest request = createStartRequest(theParameters);
|
||||
request.setParameters(BulkExportJobParameters.createFromExportJobParameters(theParameters));
|
||||
|
|
|
|||
|
|
@ -20,6 +20,8 @@ package ca.uhn.fhir.batch2.api;
|
|||
* #L%
|
||||
*/
|
||||
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
|
||||
public interface IJobMaintenanceService {
|
||||
/**
|
||||
* Do not wait for the next scheduled time for maintenance. Trigger it immediately.
|
||||
|
|
@ -29,4 +31,10 @@ public interface IJobMaintenanceService {
|
|||
|
||||
void runMaintenancePass();
|
||||
|
||||
/**
|
||||
* Forces a second maintenance run.
|
||||
* Only to be used in tests to simulate a long running maintenance step
|
||||
*/
|
||||
@VisibleForTesting
|
||||
void forceMaintenancePass();
|
||||
}
|
||||
|
|
|
|||
|
|
@ -28,8 +28,8 @@ import ca.uhn.fhir.batch2.model.JobInstance;
|
|||
import ca.uhn.fhir.batch2.model.JobWorkCursor;
|
||||
import ca.uhn.fhir.batch2.model.WorkChunk;
|
||||
import ca.uhn.fhir.batch2.progress.JobInstanceStatusUpdater;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import ca.uhn.fhir.model.api.IModelJson;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import org.slf4j.Logger;
|
||||
|
||||
import javax.annotation.Nonnull;
|
||||
|
|
@ -53,7 +53,7 @@ public class JobStepExecutor<PT extends IModelJson, IT extends IModelJson, OT ex
|
|||
JobStepExecutor(@Nonnull IJobPersistence theJobPersistence,
|
||||
@Nonnull BatchJobSender theBatchJobSender,
|
||||
@Nonnull JobInstance theInstance,
|
||||
@Nonnull WorkChunk theWorkChunk,
|
||||
WorkChunk theWorkChunk,
|
||||
@Nonnull JobWorkCursor<PT, IT, OT> theCursor,
|
||||
@Nonnull WorkChunkProcessor theExecutor, IJobMaintenanceService theJobMaintenanceService) {
|
||||
myJobPersistence = theJobPersistence;
|
||||
|
|
|
|||
|
|
@ -46,7 +46,7 @@ public class JobStepExecutorFactory {
|
|||
myJobMaintenanceService = theJobMaintenanceService;
|
||||
}
|
||||
|
||||
public <PT extends IModelJson, IT extends IModelJson, OT extends IModelJson> JobStepExecutor<PT,IT,OT> newJobStepExecutor(@Nonnull JobInstance theInstance, @Nonnull WorkChunk theWorkChunk, @Nonnull JobWorkCursor<PT, IT, OT> theCursor) {
|
||||
public <PT extends IModelJson, IT extends IModelJson, OT extends IModelJson> JobStepExecutor<PT,IT,OT> newJobStepExecutor(@Nonnull JobInstance theInstance, WorkChunk theWorkChunk, @Nonnull JobWorkCursor<PT, IT, OT> theCursor) {
|
||||
return new JobStepExecutor<>(myJobPersistence, myBatchJobSender, theInstance, theWorkChunk, theCursor, myJobStepExecutorSvc, myJobMaintenanceService);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -28,8 +28,8 @@ import ca.uhn.fhir.batch2.model.JobDefinitionStep;
|
|||
import ca.uhn.fhir.batch2.model.JobInstance;
|
||||
import ca.uhn.fhir.batch2.model.StatusEnum;
|
||||
import ca.uhn.fhir.batch2.model.WorkChunk;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import ca.uhn.fhir.model.api.IModelJson;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import org.slf4j.Logger;
|
||||
|
||||
import java.util.ArrayList;
|
||||
|
|
@ -55,10 +55,14 @@ public class ReductionStepExecutor {
|
|||
) {
|
||||
IReductionStepWorker<PT, IT, OT> reductionStepWorker = (IReductionStepWorker<PT, IT, OT>) theStep.getJobStepWorker();
|
||||
|
||||
// we mark it first so that no other maintenance passes will pick this job up!
|
||||
// if we shut down mid process, though, it will be stuck in FINALIZE forever :(
|
||||
if (!myJobPersistence.markInstanceAsStatus(theInstance.getInstanceId(), StatusEnum.FINALIZE)) {
|
||||
ourLog.warn("JobInstance[{}] is already in FINALIZE state, no reducer action performed.", theInstance.getInstanceId());
|
||||
ourLog.warn(
|
||||
"JobInstance[{}] is already in FINALIZE state. In memory status is {}. Reduction step will not rerun!"
|
||||
+ " This could be a long running reduction job resulting in the processed msg not being acknowledge,"
|
||||
+ " or the result of a failed process or server restarting.",
|
||||
theInstance.getInstanceId(),
|
||||
theInstance.getStatus().name()
|
||||
);
|
||||
return false;
|
||||
}
|
||||
theInstance.setStatus(StatusEnum.FINALIZE);
|
||||
|
|
@ -106,6 +110,8 @@ public class ReductionStepExecutor {
|
|||
break;
|
||||
|
||||
case FAIL:
|
||||
// non-idempotent; but failed chunks will be
|
||||
// ignored on a second runthrough of reduction step
|
||||
myJobPersistence.markWorkChunkAsFailed(chunk.getId(),
|
||||
"Step worker failed to process work chunk " + chunk.getId());
|
||||
retval = false;
|
||||
|
|
|
|||
|
|
@ -32,8 +32,9 @@ import ca.uhn.fhir.batch2.model.JobWorkNotificationJsonMessage;
|
|||
import ca.uhn.fhir.batch2.model.StatusEnum;
|
||||
import ca.uhn.fhir.batch2.model.WorkChunk;
|
||||
import ca.uhn.fhir.batch2.progress.JobInstanceStatusUpdater;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import ca.uhn.fhir.batch2.util.Batch2Constants;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.slf4j.Logger;
|
||||
import org.springframework.messaging.Message;
|
||||
|
|
@ -75,17 +76,28 @@ class WorkChannelMessageHandler implements MessageHandler {
|
|||
|
||||
String chunkId = workNotification.getChunkId();
|
||||
Validate.notNull(chunkId);
|
||||
Optional<WorkChunk> chunkOpt = myJobPersistence.fetchWorkChunkSetStartTimeAndMarkInProgress(chunkId);
|
||||
if (chunkOpt.isEmpty()) {
|
||||
ourLog.error("Unable to find chunk with ID {} - Aborting", chunkId);
|
||||
return;
|
||||
|
||||
boolean isReductionWorkNotification = Batch2Constants.REDUCTION_STEP_CHUNK_ID_PLACEHOLDER.equals(chunkId);
|
||||
|
||||
JobWorkCursor<?, ?, ?> cursor = null;
|
||||
WorkChunk workChunk = null;
|
||||
if (!isReductionWorkNotification) {
|
||||
Optional<WorkChunk> chunkOpt = myJobPersistence.fetchWorkChunkSetStartTimeAndMarkInProgress(chunkId);
|
||||
if (chunkOpt.isEmpty()) {
|
||||
ourLog.error("Unable to find chunk with ID {} - Aborting", chunkId);
|
||||
return;
|
||||
}
|
||||
workChunk = chunkOpt.get();
|
||||
ourLog.debug("Worker picked up chunk. [chunkId={}, stepId={}, startTime={}]", chunkId, workChunk.getTargetStepId(), workChunk.getStartTime());
|
||||
|
||||
cursor = buildCursorFromNotification(workNotification);
|
||||
|
||||
Validate.isTrue(workChunk.getTargetStepId().equals(cursor.getCurrentStepId()), "Chunk %s has target step %s but expected %s", chunkId, workChunk.getTargetStepId(), cursor.getCurrentStepId());
|
||||
} else {
|
||||
ourLog.debug("Processing reduction step work notification. No associated workchunks.");
|
||||
|
||||
cursor = buildCursorFromNotification(workNotification);
|
||||
}
|
||||
WorkChunk workChunk = chunkOpt.get();
|
||||
ourLog.debug("Worker picked up chunk. [chunkId={}, stepId={}, startTime={}]", chunkId, workChunk.getTargetStepId(), workChunk.getStartTime());
|
||||
|
||||
JobWorkCursor<?, ?, ?> cursor = buildCursorFromNotification(workNotification);
|
||||
|
||||
Validate.isTrue(workChunk.getTargetStepId().equals(cursor.getCurrentStepId()), "Chunk %s has target step %s but expected %s", chunkId, workChunk.getTargetStepId(), cursor.getCurrentStepId());
|
||||
|
||||
Optional<JobInstance> instanceOpt = myJobPersistence.fetchInstance(workNotification.getInstanceId());
|
||||
JobInstance instance = instanceOpt.orElseThrow(() -> new InternalErrorException("Unknown instance: " + workNotification.getInstanceId()));
|
||||
|
|
|
|||
|
|
@ -32,13 +32,12 @@ 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.WorkChunk;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import ca.uhn.fhir.model.api.IModelJson;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.slf4j.Logger;
|
||||
|
||||
import javax.annotation.Nullable;
|
||||
|
||||
import java.util.Optional;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
|
|
@ -102,7 +101,7 @@ public class WorkChunkProcessor {
|
|||
boolean success = myReductionStepExecutor.executeReductionStep(theInstance, step, inputType, parameters);
|
||||
|
||||
if (success) {
|
||||
// Now call call the normal step executor
|
||||
// Now call the normal step executor
|
||||
// the data sink stores the report on the instance (i.e. not chunks).
|
||||
// Assume the OT (report) data is smaller than the list of all IT data
|
||||
|
||||
|
|
@ -113,7 +112,6 @@ public class WorkChunkProcessor {
|
|||
}
|
||||
|
||||
return new JobStepExecutorOutput<>(success, dataSink);
|
||||
|
||||
} else {
|
||||
// all other kinds of steps
|
||||
Validate.notNull(theWorkChunk);
|
||||
|
|
|
|||
|
|
@ -35,7 +35,7 @@ import org.slf4j.Logger;
|
|||
import javax.annotation.Nonnull;
|
||||
import java.util.Date;
|
||||
|
||||
import static ca.uhn.fhir.batch2.config.Batch2Constants.BATCH_START_DATE;
|
||||
import static ca.uhn.fhir.batch2.util.Batch2Constants.BATCH_START_DATE;
|
||||
|
||||
public class GenerateRangeChunksStep<PT extends PartitionedUrlListJobParameters> implements IFirstJobStepWorker<PT, PartitionedUrlChunkRangeJson> {
|
||||
private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
|
||||
|
|
|
|||
|
|
@ -22,7 +22,6 @@ package ca.uhn.fhir.batch2.maintenance;
|
|||
|
||||
import ca.uhn.fhir.batch2.api.IJobPersistence;
|
||||
import ca.uhn.fhir.batch2.channel.BatchJobSender;
|
||||
import ca.uhn.fhir.batch2.coordinator.JobStepExecutorOutput;
|
||||
import ca.uhn.fhir.batch2.coordinator.WorkChunkProcessor;
|
||||
import ca.uhn.fhir.batch2.model.JobInstance;
|
||||
import ca.uhn.fhir.batch2.model.JobWorkCursor;
|
||||
|
|
@ -30,11 +29,11 @@ import ca.uhn.fhir.batch2.model.JobWorkNotification;
|
|||
import ca.uhn.fhir.batch2.model.StatusEnum;
|
||||
import ca.uhn.fhir.batch2.progress.JobInstanceProgressCalculator;
|
||||
import ca.uhn.fhir.batch2.progress.JobInstanceStatusUpdater;
|
||||
import ca.uhn.fhir.batch2.util.Batch2Constants;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import org.apache.commons.lang3.time.DateUtils;
|
||||
import org.slf4j.Logger;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
public class JobInstanceProcessor {
|
||||
|
|
@ -125,6 +124,8 @@ public class JobInstanceProcessor {
|
|||
|
||||
private void triggerGatedExecutions() {
|
||||
if (!myInstance.isRunning()) {
|
||||
ourLog.debug("JobInstance {} is not in a \"running\" state. Status {}",
|
||||
myInstance.getInstanceId(), myInstance.getStatus().name());
|
||||
return;
|
||||
}
|
||||
|
||||
|
|
@ -136,9 +137,12 @@ public class JobInstanceProcessor {
|
|||
|
||||
// final step
|
||||
if (jobWorkCursor.isFinalStep() && !jobWorkCursor.isReductionStep()) {
|
||||
ourLog.debug("Job instance {} is in final step and it's not a reducer step", myInstance.getInstanceId());
|
||||
return;
|
||||
}
|
||||
|
||||
// we should not be sending a second reduction step
|
||||
// to the queue if it's in finalize status
|
||||
if (jobWorkCursor.isReductionStep() && myInstance.getStatus() == StatusEnum.FINALIZE) {
|
||||
ourLog.warn("Job instance {} is still finalizing - a second reduction job will not be started.", myInstance.getInstanceId());
|
||||
return;
|
||||
|
|
@ -179,16 +183,13 @@ public class JobInstanceProcessor {
|
|||
myJobPersistence.updateInstance(myInstance);
|
||||
}
|
||||
|
||||
private void processReductionStep(JobWorkCursor<?, ?, ?> jobWorkCursor) {
|
||||
// do execution of the final step now
|
||||
// (ie, we won't send to job workers)
|
||||
JobStepExecutorOutput<?, ?, ?> result = myJobExecutorSvc.doExecution(
|
||||
JobWorkCursor.fromJobDefinitionAndRequestedStepId(myInstance.getJobDefinition(), jobWorkCursor.nextStep.getStepId()),
|
||||
private void processReductionStep(JobWorkCursor<?, ?, ?> theWorkCursor) {
|
||||
JobWorkNotification workNotification = new JobWorkNotification(
|
||||
myInstance,
|
||||
null);
|
||||
if (!result.isSuccessful()) {
|
||||
myInstance.setEndTime(new Date());
|
||||
myJobInstanceStatusUpdater.setFailed(myInstance);
|
||||
}
|
||||
theWorkCursor.nextStep.getStepId(),
|
||||
Batch2Constants.REDUCTION_STEP_CHUNK_ID_PLACEHOLDER // chunk id; we don't need it
|
||||
);
|
||||
ourLog.debug("Submitting a Work Notification for a job reduction step. No associated work chunk ids are available.");
|
||||
myBatchJobSender.sendWorkChannelMessage(workNotification);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -179,6 +179,16 @@ public class JobMaintenanceServiceImpl implements IJobMaintenanceService, IHasSc
|
|||
return myRunMaintenanceSemaphore.getQueueLength();
|
||||
}
|
||||
|
||||
@VisibleForTesting
|
||||
public void forceMaintenancePass() {
|
||||
// to simulate a long running job!
|
||||
ourLog.info(
|
||||
"Forcing a maintenance pass run; semaphore at {}",
|
||||
getQueueLength()
|
||||
);
|
||||
doMaintenancePass();
|
||||
}
|
||||
|
||||
@Override
|
||||
public void runMaintenancePass() {
|
||||
if (!myRunMaintenanceSemaphore.tryAcquire()) {
|
||||
|
|
@ -204,6 +214,7 @@ public class JobMaintenanceServiceImpl implements IJobMaintenanceService, IHasSc
|
|||
myJobDefinitionRegistry.setJobDefinition(instance);
|
||||
JobInstanceProcessor jobInstanceProcessor = new JobInstanceProcessor(myJobPersistence,
|
||||
myBatchJobSender, instance, progressAccumulator, myJobExecutorSvc);
|
||||
ourLog.debug("Triggering maintenance process for instance {} in status {}", instance.getInstanceId(), instance.getStatus().name());
|
||||
jobInstanceProcessor.process();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -24,6 +24,7 @@ import ca.uhn.fhir.batch2.api.IJobInstance;
|
|||
import ca.uhn.fhir.jpa.util.JsonDateDeserializer;
|
||||
import ca.uhn.fhir.jpa.util.JsonDateSerializer;
|
||||
import ca.uhn.fhir.model.api.IModelJson;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import com.fasterxml.jackson.annotation.JsonIgnore;
|
||||
import com.fasterxml.jackson.annotation.JsonProperty;
|
||||
import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
|
||||
|
|
@ -32,7 +33,6 @@ import org.apache.commons.lang3.builder.ToStringBuilder;
|
|||
import org.apache.commons.lang3.builder.ToStringStyle;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.Objects;
|
||||
|
||||
import static org.apache.commons.lang3.StringUtils.isBlank;
|
||||
|
||||
|
|
@ -359,10 +359,24 @@ public class JobInstance extends JobInstanceStartRequest implements IModelJson,
|
|||
}
|
||||
|
||||
/**
|
||||
* Returns true if the job instance is in {@link StatusEnum#IN_PROGRESS} and is not cancelled
|
||||
* Returns true if the job instance is in:
|
||||
* {@link StatusEnum#IN_PROGRESS}
|
||||
* {@link StatusEnum#FINALIZE}
|
||||
* and is not cancelled
|
||||
*/
|
||||
public boolean isRunning() {
|
||||
return getStatus() == StatusEnum.IN_PROGRESS && !isCancelled();
|
||||
if (isCancelled()) {
|
||||
return false;
|
||||
}
|
||||
|
||||
switch (getStatus()) {
|
||||
case IN_PROGRESS:
|
||||
case FINALIZE:
|
||||
return true;
|
||||
default:
|
||||
Logs.getBatchTroubleshootingLog().debug("Status {} is considered \"not running\"", getStatus().name());
|
||||
}
|
||||
return false;
|
||||
}
|
||||
|
||||
public boolean isFinished() {
|
||||
|
|
@ -376,7 +390,7 @@ public class JobInstance extends JobInstanceStartRequest implements IModelJson,
|
|||
}
|
||||
|
||||
public boolean isPendingCancellationRequest() {
|
||||
return myCancelled && (myStatus == StatusEnum.QUEUED || myStatus == StatusEnum.IN_PROGRESS);
|
||||
return myCancelled && myStatus.isCancellable();
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -34,51 +34,53 @@ public enum StatusEnum {
|
|||
/**
|
||||
* Task is waiting to execute and should begin with no intervention required.
|
||||
*/
|
||||
QUEUED(true, false),
|
||||
QUEUED(true, false, true),
|
||||
|
||||
/**
|
||||
* Task is current executing
|
||||
*/
|
||||
IN_PROGRESS(true, false),
|
||||
IN_PROGRESS(true, false, true),
|
||||
|
||||
/**
|
||||
* For reduction steps
|
||||
*/
|
||||
FINALIZE(true, false),
|
||||
FINALIZE(true, false, true),
|
||||
|
||||
/**
|
||||
* Task completed successfully
|
||||
*/
|
||||
COMPLETED(false, true),
|
||||
COMPLETED(false, true, false),
|
||||
|
||||
/**
|
||||
* Task execution resulted in an error but the error may be transient (or transient status is unknown).
|
||||
* Retrying may result in success.
|
||||
*/
|
||||
ERRORED(true, true),
|
||||
ERRORED(true, true, false),
|
||||
|
||||
/**
|
||||
* Task has failed and is known to be unrecoverable. There is no reason to believe that retrying will
|
||||
* result in a different outcome.
|
||||
*/
|
||||
FAILED(true, true),
|
||||
FAILED(true, true, false),
|
||||
|
||||
/**
|
||||
* Task has been cancelled.
|
||||
*/
|
||||
CANCELLED(true, true);
|
||||
CANCELLED(true, true, false);
|
||||
|
||||
private static final Logger ourLog = Logs.getBatchTroubleshootingLog();
|
||||
|
||||
private final boolean myIncomplete;
|
||||
private final boolean myEnded;
|
||||
private final boolean myIsCancellable;
|
||||
private static StatusEnum[] ourIncompleteStatuses;
|
||||
private static Set<StatusEnum> ourEndedStatuses;
|
||||
private static Set<StatusEnum> ourNotEndedStatuses;
|
||||
|
||||
StatusEnum(boolean theIncomplete, boolean theEnded) {
|
||||
StatusEnum(boolean theIncomplete, boolean theEnded, boolean theIsCancellable) {
|
||||
myIncomplete = theIncomplete;
|
||||
myEnded = theEnded;
|
||||
myIsCancellable = theIsCancellable;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -186,4 +188,8 @@ public enum StatusEnum {
|
|||
public boolean isIncomplete() {
|
||||
return myIncomplete;
|
||||
}
|
||||
|
||||
public boolean isCancellable() {
|
||||
return myIsCancellable;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
package ca.uhn.fhir.batch2.config;
|
||||
package ca.uhn.fhir.batch2.util;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
|
|
@ -30,4 +30,10 @@ public class Batch2Constants {
|
|||
* date when performing operations that pull resources by time windows.
|
||||
*/
|
||||
public static final Date BATCH_START_DATE = new InstantType("2000-01-01T00:00:00Z").getValue();
|
||||
|
||||
/**
|
||||
* This is a placeholder chunkid for the reduction step to allow it to be
|
||||
* used in the message handling
|
||||
*/
|
||||
public static final String REDUCTION_STEP_CHUNK_ID_PLACEHOLDER = "REDUCTION";
|
||||
}
|
||||
|
|
@ -26,7 +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.batch2.api.VoidModel;
|
||||
import ca.uhn.fhir.batch2.config.Batch2Constants;
|
||||
import ca.uhn.fhir.batch2.util.Batch2Constants;
|
||||
import ca.uhn.fhir.mdm.batch2.clear.MdmClearJobParameters;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
|
|
|||
|
|
@ -369,9 +369,10 @@ public class BulkDataExportProvider {
|
|||
myFhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToWriter(oo, response.getWriter());
|
||||
response.getWriter().close();
|
||||
break;
|
||||
default:
|
||||
ourLog.warn("Unrecognized status encountered: {}. Treating as BUILDING/SUBMITTED", info.getStatus().name());
|
||||
case BUILDING:
|
||||
case SUBMITTED:
|
||||
default:
|
||||
if (theRequestDetails.getRequestType() == RequestTypeEnum.DELETE) {
|
||||
handleDeleteRequest(theJobId, response, info.getStatus());
|
||||
} else {
|
||||
|
|
|
|||
|
|
@ -2217,7 +2217,7 @@ public class JsonParserDstu3Test {
|
|||
|
||||
input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div></div>\"}}";
|
||||
basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
|
||||
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"/>", basic.getText().getDivAsString());
|
||||
assertEquals("<div xmlns=\"http://www.w3.org/1999/xhtml\"></div>", basic.getText().getDivAsString());
|
||||
|
||||
input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div> </div>\"}}";
|
||||
basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
|
||||
|
|
|
|||
|
|
@ -447,4 +447,9 @@ public final class HapiWorkerContext extends I18nBase implements IWorkerContext
|
|||
public IWorkerContext setPackageTracker(IWorkerContextManager.IPackageLoadingTracker theIPackageLoadingTracker) {
|
||||
throw new UnsupportedOperationException(Msg.code(220));
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getSpecUrl() {
|
||||
throw new UnsupportedOperationException(Msg.code(2260));
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -122,7 +122,6 @@ resource.Questionnaire=org.hl7.fhir.r5.model.Questionnaire
|
|||
resource.QuestionnaireResponse=org.hl7.fhir.r5.model.QuestionnaireResponse
|
||||
resource.RegulatedAuthorization=org.hl7.fhir.r5.model.RegulatedAuthorization
|
||||
resource.RelatedPerson=org.hl7.fhir.r5.model.RelatedPerson
|
||||
resource.RequestGroup=org.hl7.fhir.r5.model.RequestGroup
|
||||
resource.RequestOrchestration=org.hl7.fhir.r5.model.RequestOrchestration
|
||||
resource.Requirements=org.hl7.fhir.r5.model.Requirements
|
||||
resource.ResearchStudy=org.hl7.fhir.r5.model.ResearchStudy
|
||||
|
|
|
|||
|
|
@ -0,0 +1,82 @@
|
|||
package ca.uhn.fhir.test.utilities;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR Test Utilities
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2023 Smile CDR, Inc.
|
||||
* %%
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.both;
|
||||
import static org.hamcrest.Matchers.greaterThanOrEqualTo;
|
||||
import static org.hamcrest.Matchers.is;
|
||||
import static org.hamcrest.Matchers.lessThanOrEqualTo;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
|
||||
public class RangeTestHelper {
|
||||
|
||||
public static final double THOUSANDTH = .001d;
|
||||
|
||||
|
||||
public static void checkInRange(double base, double value) {
|
||||
checkInRange(base, THOUSANDTH, value);
|
||||
}
|
||||
|
||||
public static void checkInRange(double theBase, double theRange, double theValue) {
|
||||
double lowerBound = theBase - theRange;
|
||||
double upperBound = theBase + theRange;
|
||||
checkWithinBounds(lowerBound, upperBound, theValue);
|
||||
}
|
||||
|
||||
public static void checkInRange(String theBase, String theValue) {
|
||||
// ease tests
|
||||
if (theBase == null && theValue == null) {
|
||||
return;
|
||||
}
|
||||
|
||||
double value = Double.parseDouble(theValue);
|
||||
double base = Double.parseDouble(theBase);
|
||||
checkInRange(base, THOUSANDTH, value);
|
||||
}
|
||||
|
||||
public static void checkInRange(String theBase, double theRange, String theValue) {
|
||||
// ease tests
|
||||
if (theBase == null && theValue == null) {
|
||||
return;
|
||||
}
|
||||
|
||||
double value = Double.parseDouble(theValue);
|
||||
double base = Double.parseDouble(theBase);
|
||||
checkInRange(base, theRange, value);
|
||||
}
|
||||
|
||||
public static void checkWithinBounds(double theLowerBound, double theUpperBound, double theValue) {
|
||||
assertThat(theValue, is(both(greaterThanOrEqualTo(theLowerBound)).and(lessThanOrEqualTo(theUpperBound))));
|
||||
}
|
||||
|
||||
public static void checkWithinBounds(String theLowerBound, String theUpperBound, String theValue) {
|
||||
assertNotNull(theLowerBound, "theLowerBound");
|
||||
assertNotNull(theUpperBound, "theUpperBound");
|
||||
assertNotNull(theValue, "theValue");
|
||||
double lowerBound = Double.parseDouble(theLowerBound);
|
||||
double upperBound = Double.parseDouble(theUpperBound);
|
||||
double value = Double.parseDouble(theValue);
|
||||
checkWithinBounds(lowerBound, upperBound, value);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,163 @@
|
|||
package ca.uhn.fhir.test.utilities;
|
||||
|
||||
import org.junit.jupiter.api.Nested;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertThrows;
|
||||
|
||||
class RangeTestHelperTest {
|
||||
|
||||
|
||||
@Nested
|
||||
public class DefaultRange {
|
||||
|
||||
@Test
|
||||
void checkInRange() {
|
||||
RangeTestHelper.checkInRange(.83d, .829999999d);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkLower() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkInRange(.91, .83)
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkHigher() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkInRange(.26, .25)
|
||||
);
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class WithinBounds {
|
||||
|
||||
@Test
|
||||
void checkInRange() {
|
||||
RangeTestHelper.checkWithinBounds(.91001, .91002, .910013);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkLower() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkWithinBounds(.91001, .91002, .9013)
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkHigher() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkWithinBounds(.87, .88, .9)
|
||||
);
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class PassingStrings {
|
||||
@Test
|
||||
void checkInRange() {
|
||||
RangeTestHelper.checkWithinBounds(".91001", ".91002", ".910013");
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkLower() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkWithinBounds(".91001", ".91002", ".9013")
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkHigher() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkWithinBounds(".87", ".88", ".9")
|
||||
);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class PassingStrings {
|
||||
|
||||
@Test
|
||||
void checkInRange() {
|
||||
RangeTestHelper.checkInRange("0.83", "0.829999999");
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkLower() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkInRange(".91", ".83")
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkHigher() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkInRange(".26", "0.25")
|
||||
);
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class ProvidedRange {
|
||||
|
||||
@Test
|
||||
void checkInRange() {
|
||||
// equals to higher bound
|
||||
RangeTestHelper.checkInRange(.83, .1, .83);
|
||||
RangeTestHelper.checkInRange(.831, .02, .833);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkLower() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkInRange(.84, .01, .82)
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkHigher() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkInRange(.2511,.0001, .2513)
|
||||
);
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class PassingStrings {
|
||||
|
||||
@Test
|
||||
void checkInRange() {
|
||||
RangeTestHelper.checkInRange(".82", .01, ".83");
|
||||
RangeTestHelper.checkInRange(".83d", .829999999d, ".8312d");
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkLower() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkInRange(".91", .02, ".83")
|
||||
);
|
||||
}
|
||||
|
||||
@Test
|
||||
void checkHigher() {
|
||||
AssertionError thrown = assertThrows(
|
||||
AssertionError.class,
|
||||
() -> RangeTestHelper.checkInRange(".26", .03, "0.3")
|
||||
);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
@ -171,6 +171,13 @@ public class VersionSpecificWorkerContextWrapper extends I18nBase implements IWo
|
|||
throw new UnsupportedOperationException(Msg.code(2114));
|
||||
}
|
||||
|
||||
@Override
|
||||
public String getSpecUrl() {
|
||||
|
||||
return "";
|
||||
|
||||
}
|
||||
|
||||
@Override
|
||||
public PackageInformation getPackageForUrl(String s) {
|
||||
throw new UnsupportedOperationException(Msg.code(2109));
|
||||
|
|
|
|||
6
pom.xml
6
pom.xml
|
|
@ -861,9 +861,11 @@
|
|||
</license>
|
||||
</licenses>
|
||||
|
||||
<properties>
|
||||
<properties>
|
||||
<fhir_core_version>5.6.881</fhir_core_version>
|
||||
<ucum_version>1.0.3</ucum_version>
|
||||
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
|
||||
|
||||
<fhir_core_version>5.6.84</fhir_core_version>
|
||||
<ucum_version>1.0.3</ucum_version>
|
||||
|
||||
<surefire_jvm_args>-Dfile.encoding=UTF-8 -Xmx2048m</surefire_jvm_args>
|
||||
|
|
|
|||
Loading…
Reference in New Issue