Add type parameter to resource reindexing operation (#1921)
* Add type parameter to resource reindexing operation * Add changelog * CLean up reindexing
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@ -0,0 +1,5 @@
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---
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type: add
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issue: 1921
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title: "A new optional `type` parameter has been added to the `$mark-all-resources-for-reindexing` operation, allowing
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resources of a specific type to be marked."
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@ -28,6 +28,7 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
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@ -62,6 +63,8 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
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@Autowired
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protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
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@Autowired
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protected ITermDeferredStorageSvc myTermDeferredStorageSvc;
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@Autowired
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private ITermCodeSystemDao myCsDao;
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@Autowired
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private IValidationSupport myValidationSupport;
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@ -134,7 +137,7 @@ public class FhirResourceDaoCodeSystemDstu3 extends BaseHapiFhirResourceDao<Code
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if (isNotBlank(codeSystemUrl)) {
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TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
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if (persCs != null) {
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myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
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myTermDeferredStorageSvc.deleteCodeSystem(persCs);
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}
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}
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}
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@ -28,6 +28,7 @@ import ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
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@ -65,6 +66,8 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
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protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc;
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@Autowired
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private FhirContext myFhirContext;
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@Autowired
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protected ITermDeferredStorageSvc myTermDeferredStorageSvc;
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@Override
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public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
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@ -132,7 +135,7 @@ public class FhirResourceDaoCodeSystemR4 extends BaseHapiFhirResourceDao<CodeSys
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if (isNotBlank(codeSystemUrl)) {
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TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
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if (persCs != null) {
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myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
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myTermDeferredStorageSvc.deleteCodeSystem(persCs);
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}
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}
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}
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@ -29,6 +29,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.index.IdHelperService;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
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@ -67,6 +68,8 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
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private IValidationSupport myValidationSupport;
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@Autowired
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private FhirContext myFhirContext;
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@Autowired
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protected ITermDeferredStorageSvc myTermDeferredStorageSvc;
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@Override
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public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, RequestDetails theRequest) {
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@ -134,7 +137,7 @@ public class FhirResourceDaoCodeSystemR5 extends BaseHapiFhirResourceDao<CodeSys
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if (isNotBlank(codeSystemUrl)) {
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TermCodeSystem persCs = myCsDao.findByCodeSystemUri(codeSystemUrl);
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if (persCs != null) {
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myTerminologyCodeSystemStorageSvc.deleteCodeSystem(persCs);
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myTermDeferredStorageSvc.deleteCodeSystem(persCs);
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}
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}
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}
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@ -27,14 +27,23 @@ import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IPrimitiveType;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public abstract class BaseJpaSystemProviderDstu2Plus<T, MT> extends BaseJpaSystemProvider<T, MT> {
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@Operation(name = MARK_ALL_RESOURCES_FOR_REINDEXING, idempotent = true, returnParameters = {
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@OperationParam(name = "status")
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})
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public IBaseResource markAllResourcesForReindexing() {
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public IBaseResource markAllResourcesForReindexing(
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@OperationParam(name="type", min = 0, max = 1, typeName = "code") IPrimitiveType<String> theType
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) {
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if (theType != null && isNotBlank(theType.getValueAsString())) {
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getResourceReindexingSvc().markAllResourcesForReindexing(theType.getValueAsString());
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} else {
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getResourceReindexingSvc().markAllResourcesForReindexing();
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}
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IBaseParameters retVal = ParametersUtil.newInstance(getContext());
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@ -37,7 +37,9 @@ import ca.uhn.fhir.jpa.model.sched.HapiJob;
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import ca.uhn.fhir.jpa.model.sched.ISchedulerService;
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import ca.uhn.fhir.jpa.model.sched.ScheduledJobDefinition;
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import ca.uhn.fhir.jpa.searchparam.registry.ISearchParamRegistry;
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import ca.uhn.fhir.parser.DataFormatException;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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import ca.uhn.fhir.util.StopWatch;
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import com.google.common.annotations.VisibleForTesting;
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@ -188,8 +190,14 @@ public class ResourceReindexingSvcImpl implements IResourceReindexingSvc {
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@Override
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@Transactional(Transactional.TxType.REQUIRED)
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public Long markAllResourcesForReindexing(String theType) {
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String typeDesc;
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if (isNotBlank(theType)) {
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try {
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myContext.getResourceType(theType);
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} catch (DataFormatException e) {
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throw new InvalidRequestException("Unknown resource type: " + theType);
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}
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myReindexJobDao.markAllOfTypeAsDeleted(theType);
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typeDesc = theType;
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} else {
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@ -40,7 +40,6 @@ import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import ca.uhn.fhir.jpa.entity.TermConceptProperty;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc;
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import ca.uhn.fhir.jpa.term.api.ITermDeferredStorageSvc;
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@ -49,6 +48,7 @@ import ca.uhn.fhir.jpa.term.api.ITermVersionAdapterSvc;
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import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
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import ca.uhn.fhir.rest.api.Constants;
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import ca.uhn.fhir.rest.api.server.RequestDetails;
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import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
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import ca.uhn.fhir.util.ObjectUtil;
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@ -199,23 +199,30 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
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}
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@Override
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@Transactional(propagation = Propagation.NEVER)
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public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
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ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
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TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
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txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
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txTemplate.executeWithoutResult(t -> {
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myEntityManager.flush();
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TermCodeSystem cs = myCodeSystemDao.findById(theCodeSystem.getPid()).orElseThrow(IllegalStateException::new);
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cs.setCurrentVersion(null);
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myCodeSystemDao.save(cs);
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myCodeSystemDao.flush();
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});
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List<TermCodeSystemVersion> codeSystemVersions = myCodeSystemVersionDao.findByCodeSystemPid(theCodeSystem.getPid());
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for (TermCodeSystemVersion next : codeSystemVersions) {
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deleteCodeSystemVersion(next.getPid());
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}
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txTemplate.executeWithoutResult(t -> {
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myCodeSystemVersionDao.deleteForCodeSystem(theCodeSystem);
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myCodeSystemDao.delete(theCodeSystem);
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myEntityManager.flush();
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});
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}
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/**
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@ -679,27 +686,30 @@ public class TermCodeSystemStorageSvcImpl implements ITermCodeSystemStorageSvc {
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}
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@SuppressWarnings("ConstantConditions")
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private <T> void doDelete(String theDescriptor, Supplier<Slice<Long>> theLoader, Supplier<Integer> theCounter, IHapiJpaRepository<T> theDao) {
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TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
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txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
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int count;
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ourLog.info(" * Deleting {}", theDescriptor);
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int totalCount = theCounter.get();
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int totalCount = txTemplate.execute(t -> theCounter.get());
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StopWatch sw = new StopWatch();
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count = 0;
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while (true) {
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Slice<Long> link = theLoader.get();
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Slice<Long> link = txTemplate.execute(t -> theLoader.get());
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if (!link.hasContent()) {
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break;
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}
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TransactionTemplate txTemplate = new TransactionTemplate(myTransactionManager);
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txTemplate.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
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txTemplate.execute(t -> {
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link.forEach(id -> theDao.deleteByPid(id));
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return null;
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});
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count += link.getNumberOfElements();
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ourLog.info(" * {} {} deleted - {}/sec - ETA: {}", count, theDescriptor, sw.formatThroughput(count, TimeUnit.SECONDS), sw.getEstimatedTimeRemaining(count, totalCount));
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ourLog.info(" * {} {} deleted ({}/{}) remaining - {}/sec - ETA: {}", count, theDescriptor, count, totalCount, sw.formatThroughput(count, TimeUnit.SECONDS), sw.getEstimatedTimeRemaining(count, totalCount));
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}
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theDao.flush();
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}
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@ -21,8 +21,10 @@ package ca.uhn.fhir.jpa.term;
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*/
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import ca.uhn.fhir.jpa.model.sched.HapiJob;
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@ -50,6 +52,7 @@ import javax.annotation.PostConstruct;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.List;
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import java.util.UUID;
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public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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@ -57,8 +60,11 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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@Autowired
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protected ITermConceptDao myConceptDao;
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@Autowired
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protected ITermCodeSystemDao myCodeSystemDao;
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@Autowired
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protected PlatformTransactionManager myTransactionMgr;
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private boolean myProcessDeferred = true;
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private List<TermCodeSystem> myCodeSystemsToDelete = Collections.synchronizedList(new ArrayList<>());
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private List<TermConcept> myDeferredConcepts = Collections.synchronizedList(new ArrayList<>());
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private List<ValueSet> myDeferredValueSets = Collections.synchronizedList(new ArrayList<>());
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private List<ConceptMap> myDeferredConceptMaps = Collections.synchronizedList(new ArrayList<>());
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@ -98,6 +104,14 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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myDeferredValueSets.addAll(theValueSets);
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}
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@Override
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@Transactional
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public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
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theCodeSystem.setCodeSystemUri("urn:uuid:" + UUID.randomUUID().toString());
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myCodeSystemDao.save(theCodeSystem);
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myCodeSystemsToDelete.add(theCodeSystem);
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}
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@Override
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public void saveAllDeferred() {
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while (!isStorageQueueEmpty()) {
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@ -194,7 +208,8 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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if (!isDeferredConcepts() &&
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!isConceptLinksToSaveLater() &&
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!isDeferredValueSets() &&
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!isDeferredConceptMaps()) {
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!isDeferredConceptMaps() &&
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!isDeferredCodeSystemDeletions()) {
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return;
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}
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@ -213,6 +228,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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return null;
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});
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}
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if (isDeferredConceptMaps()) {
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tt.execute(t -> {
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processDeferredConceptMaps();
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@ -220,8 +236,18 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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});
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}
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if (isDeferredCodeSystemDeletions()) {
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processDeferredCodeSystemDeletions();
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}
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}
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}
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private void processDeferredCodeSystemDeletions() {
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for (TermCodeSystem next : myCodeSystemsToDelete) {
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myCodeSystemStorageSvc.deleteCodeSystem(next);
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}
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myCodeSystemsToDelete.clear();
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}
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@Override
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public boolean isStorageQueueEmpty() {
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@ -231,6 +257,7 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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retVal &= !isConceptLinksToSaveLater();
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retVal &= !isDeferredValueSets();
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retVal &= !isDeferredConceptMaps();
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retVal &= !isDeferredCodeSystemDeletions();
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return retVal;
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}
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@ -249,6 +276,10 @@ public class TermDeferredStorageSvcImpl implements ITermDeferredStorageSvc {
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return isDeferredConcepts() || isConceptLinksToSaveLater();
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}
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private boolean isDeferredCodeSystemDeletions() {
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return !myCodeSystemsToDelete.isEmpty();
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}
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private boolean isDeferredConcepts() {
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return !myDeferredConcepts.isEmpty();
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}
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@ -20,6 +20,7 @@ package ca.uhn.fhir.jpa.term.api;
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* #L%
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*/
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import org.hl7.fhir.r4.model.ConceptMap;
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@ -51,8 +52,11 @@ public interface ITermDeferredStorageSvc {
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void addValueSetsToStorageQueue(List<ValueSet> theValueSets);
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void deleteCodeSystem(TermCodeSystem theCodeSystem);
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/**
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* This is mostly here for unit tests - Saves any and all deferred concepts and links
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*/
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void saveAllDeferred();
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}
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@ -3,23 +3,20 @@ package ca.uhn.fhir.jpa.dao.r4;
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import ca.uhn.fhir.jpa.term.TermReindexingSvcImpl;
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import ca.uhn.fhir.util.TestUtil;
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import org.apache.commons.io.IOUtils;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.CodeSystem;
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import org.junit.AfterClass;
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import org.junit.Test;
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import java.nio.charset.StandardCharsets;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertNotEquals;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertNull;
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public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
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@AfterClass
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public static void afterClassClearContext() {
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TestUtil.clearAllStaticFieldsForUnitTest();
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TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
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}
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@Test
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public void testIndexContained() throws Exception {
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TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
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@ -36,5 +33,51 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
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}
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@Test
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public void testDeleteLargeCompleteCodeSystem() {
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CodeSystem cs = new CodeSystem();
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cs.setContent(CodeSystem.CodeSystemContentMode.COMPLETE);
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cs.setUrl("http://foo");
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for (int i = 0; i < 222; i++) {
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cs.addConcept().setCode("CODE" + i);
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}
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IIdType id = myCodeSystemDao.create(cs).getId().toUnqualifiedVersionless();
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myTerminologyDeferredStorageSvc.saveDeferred();
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myTerminologyDeferredStorageSvc.saveDeferred();
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runInTransaction(() -> {
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assertEquals(1, myTermCodeSystemDao.count());
|
||||
assertNotNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
|
||||
assertEquals(1, myTermCodeSystemVersionDao.count());
|
||||
assertEquals(222, myTermConceptDao.count());
|
||||
});
|
||||
|
||||
myCodeSystemDao.delete(id);
|
||||
|
||||
// Nothing is deleted initially but the URI is changed so it can't be found
|
||||
runInTransaction(() -> {
|
||||
assertEquals(1, myTermCodeSystemDao.count());
|
||||
assertNull(myTermCodeSystemDao.findByCodeSystemUri("http://foo"));
|
||||
assertEquals(1, myTermCodeSystemVersionDao.count());
|
||||
assertEquals(222, myTermConceptDao.count());
|
||||
});
|
||||
|
||||
// Now the background scheduler will do its thing
|
||||
myTerminologyDeferredStorageSvc.saveDeferred();
|
||||
runInTransaction(() -> {
|
||||
assertEquals(0, myTermCodeSystemDao.count());
|
||||
assertEquals(0, myTermCodeSystemVersionDao.count());
|
||||
assertEquals(0, myTermConceptDao.count());
|
||||
});
|
||||
|
||||
}
|
||||
|
||||
@AfterClass
|
||||
public static void afterClassClearContext() {
|
||||
TestUtil.clearAllStaticFieldsForUnitTest();
|
||||
TermReindexingSvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
|
@ -233,7 +233,6 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
|
|||
assertEquals(200, http.getStatusLine().getStatusCode());
|
||||
} finally {
|
||||
IOUtils.closeQuietly(http);
|
||||
;
|
||||
}
|
||||
|
||||
get = new HttpGet(ourServerBase + "/$perform-reindexing-pass");
|
||||
|
@ -249,6 +248,30 @@ public class SystemProviderR4Test extends BaseJpaR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMarkResourcesForReindexingTyped() throws Exception {
|
||||
HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing?type=Patient");
|
||||
CloseableHttpResponse http = ourHttpClient.execute(get);
|
||||
try {
|
||||
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
|
||||
ourLog.info(output);
|
||||
assertEquals(200, http.getStatusLine().getStatusCode());
|
||||
} finally {
|
||||
IOUtils.closeQuietly(http);
|
||||
}
|
||||
|
||||
get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing?type=FOO");
|
||||
http = ourHttpClient.execute(get);
|
||||
try {
|
||||
String output = IOUtils.toString(http.getEntity().getContent(), StandardCharsets.UTF_8);
|
||||
ourLog.info(output);
|
||||
assertEquals(400, http.getStatusLine().getStatusCode());
|
||||
} finally {
|
||||
IOUtils.closeQuietly(http);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@SuppressWarnings("deprecation")
|
||||
@Test
|
||||
public void testResponseUsesCorrectContentType() throws Exception {
|
||||
|
|
Loading…
Reference in New Issue