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Always apply new search params to any resource reindexing

This commit is contained in:
James Agnew 2018-12-14 13:43:25 -05:00
parent 11b8304cb4
commit f978bc3039
6 changed files with 79 additions and 15 deletions
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6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -174,20 +174,14 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao,
@Autowired
private ISearchDao mySearchDao;
@Autowired
private ISearchParamExtractor mySearchParamExtractor;
@Autowired
private ISearchParamPresenceSvc mySearchParamPresenceSvc;
//@Autowired
//private ISearchResultDao mySearchResultDao;
@Autowired
private IResourceIndexedCompositeStringUniqueDao myResourceIndexedCompositeStringUniqueDao;
@Autowired
private BeanFactory beanFactory;
@Autowired
private DaoRegistry myDaoRegistry;
@Autowired
private SearchParamExtractorService mySearchParamExtractorService;
@Autowired
private SearchParamWithInlineReferencesExtractor mySearchParamWithInlineReferencesExtractor;
@Autowired
private DatabaseSearchParamSynchronizer myDatabaseSearchParamSynchronizer;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/IResourceReindexingSvc.java
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@ -58,4 +58,6 @@ public interface IResourceReindexingSvc {
* to be used by unit tests.
*/
void cancelAndPurgeAllJobs();
int countReindexJobs();
}

30
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/reindex/ResourceReindexingSvcImpl.java
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@ -30,11 +30,11 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.IResourceHistoryTableDao;
import ca.uhn.fhir.jpa.dao.data.IResourceReindexJobDao;
import ca.uhn.fhir.jpa.dao.data.IResourceTableDao;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.entity.ResourceReindexJobEntity;
import ca.uhn.fhir.jpa.model.entity.ForcedId;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.ResourceGoneException;
import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
import ca.uhn.fhir.util.StopWatch;
import com.google.common.annotations.VisibleForTesting;
@ -203,7 +203,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
return null;
}
private Integer doReindexingPassInsideLock() {
private int doReindexingPassInsideLock() {
expungeJobsMarkedAsDeleted();
return runReindexJobs();
}
@ -232,14 +232,17 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
expungeJobsMarkedAsDeleted();
}
@Autowired
private ISearchParamRegistry mySearchParamRegistry;
private int runReindexJobs() {
Collection<ResourceReindexJobEntity> jobs = myTxTemplate.execute(t -> myReindexJobDao.findAll(PageRequest.of(0, 10), false));
assert jobs != null;
Collection<ResourceReindexJobEntity> jobs = getResourceReindexJobEntities();
if (jobs.size() > 0) {
ourLog.info("Running {} reindex jobs: {}", jobs.size(), jobs);
} else {
ourLog.debug("Running {} reindex jobs: {}", jobs.size(), jobs);
return 0;
}
int count = 0;
@ -255,6 +258,17 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
return count;
}
@Override
public int countReindexJobs() {
return getResourceReindexJobEntities().size();
}
private Collection<ResourceReindexJobEntity> getResourceReindexJobEntities() {
Collection<ResourceReindexJobEntity> jobs = myTxTemplate.execute(t -> myReindexJobDao.findAll(PageRequest.of(0, 10), false));
assert jobs != null;
return jobs;
}
private void markJobAsDeleted(ResourceReindexJobEntity theJob) {
ourLog.info("Marking reindexing job ID[{}] as deleted", theJob.getId());
myTxTemplate.execute(t -> {
@ -274,6 +288,10 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
StopWatch sw = new StopWatch();
AtomicInteger counter = new AtomicInteger();
if (theJob.getThresholdLow() == null) {
mySearchParamRegistry.forceRefresh();
}
// Calculate range
Date low = theJob.getThresholdLow() != null ? theJob.getThresholdLow() : BEGINNING_OF_TIME;
Date high = theJob.getThresholdHigh();
@ -461,7 +479,7 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceTable.getResourceType());
long expectedVersion = resourceTable.getVersion();
IBaseResource resource = dao.read(resourceTable.getIdDt().toVersionless(), null,true);
IBaseResource resource = dao.read(resourceTable.getIdDt().toVersionless(), null, true);
if (resource == null) {
throw new InternalErrorException("Could not find resource version " + resourceTable.getIdDt().toUnqualified().getValue() + " in database");
}

46
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
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@ -10,6 +10,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import com.google.common.collect.Lists;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
@ -23,6 +24,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import java.util.stream.Collectors;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
@ -583,6 +585,50 @@ public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
}
}
/**
* Check that a custom ValueSet against a custom CodeSystem expands correctly
*/
@Test
public void testCustomValueSetExpansion() {
CodeSystem cs= new CodeSystem();
cs.setUrl("http://codesystems-r-us");
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
IIdType csId = myCodeSystemDao.create(cs).getId().toUnqualifiedVersionless();
TermCodeSystemVersion version = new TermCodeSystemVersion();
version.getConcepts().add(new TermConcept(version, "A"));
version.getConcepts().add(new TermConcept(version, "B"));
version.getConcepts().add(new TermConcept(version, "C"));
version.getConcepts().add(new TermConcept(version, "D"));
runInTransaction(()->{
ResourceTable resTable = myEntityManager.find(ResourceTable.class, csId.getIdPartAsLong());
version.setResource(resTable);
myTermSvc.storeNewCodeSystemVersion(csId.getIdPartAsLong(), cs.getUrl(), "My System", version);
});
org.hl7.fhir.dstu3.model.ValueSet vs = new org.hl7.fhir.dstu3.model.ValueSet();
vs.setUrl("http://valuesets-r-us");
vs.getCompose()
.addInclude()
.setSystem(cs.getUrl())
.addConcept(new org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent().setCode("A"))
.addConcept(new org.hl7.fhir.dstu3.model.ValueSet.ConceptReferenceComponent().setCode("C"));
myValueSetDao.create(vs);
org.hl7.fhir.dstu3.model.ValueSet expansion = myValueSetDao.expandByIdentifier(vs.getUrl(), null);
List<String> expansionCodes = expansion
.getExpansion()
.getContains()
.stream()
.map(t -> t.getCode())
.sorted()
.collect(Collectors.toList());
assertEquals(Lists.newArrayList("A","C"), expansionCodes);
}
public static List<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
List<String> retVal = new ArrayList<>();

5
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/registry/BaseSearchParamRegistry.java
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@ -57,10 +57,9 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
@Autowired
private ModelConfig myModelConfig;
private volatile long myLastRefresh;
private ApplicationContext myApplicationContext;
private ISearchParamProvider mySearchParamProvider;
public BaseSearchParamRegistry(ISearchParamProvider theSearchParamProvider) {
BaseSearchParamRegistry(ISearchParamProvider theSearchParamProvider) {
super();
mySearchParamProvider = theSearchParamProvider;
}
@ -128,7 +127,7 @@ public abstract class BaseSearchParamRegistry<SP extends IBaseResource> implemen
return Collections.unmodifiableList(retVal);
}
public Map<String, Map<String, RuntimeSearchParam>> getBuiltInSearchParams() {
private Map<String, Map<String, RuntimeSearchParam>> getBuiltInSearchParams() {
return myBuiltInSearchParams;
}

5
src/changes/changes.xml
View File

@ -151,6 +151,11 @@
encounters new extensions. Thanks to Heinz-Dieter Conradi for the
pull request!
</action>
<action type="fix">
Under some circumstances, when a custom search parameter was added to the JPA server
resources could start reindexing before the new search parameter had been saved, meaning that
it was not applied to all resources. This has been corrected.
</action>
</release>
<release version="3.6.0" date="2018-11-12" description="Food">
<action type="add">