Package ca.uhn.fhir.jpa.dao

Class JpaResourceDaoCodeSystem<T extends org.hl7.fhir.instance.model.api.IBaseResource>

java.lang.Object

ca.uhn.fhir.jpa.dao.BaseStorageDao

ca.uhn.fhir.jpa.dao.BaseStorageResourceDao<T>

ca.uhn.fhir.jpa.dao.BaseHapiFhirDao<T>

ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao<T>

ca.uhn.fhir.jpa.dao.JpaResourceDaoCodeSystem<T>

All Implemented Interfaces:

IDao, IFhirResourceDao<T>, IFhirResourceDaoCodeSystem<T>, IJpaDao<T>, org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware

public class JpaResourceDaoCodeSystem<T extends org.hl7.fhir.instance.model.api.IBaseResource>
extends BaseHapiFhirResourceDao<T>
implements IFhirResourceDaoCodeSystem<T>

Nested Class Summary

Nested classes/interfaces inherited from interface ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoCodeSystem

IFhirResourceDaoCodeSystem.SubsumesResult

Field Summary

Fields

Modifier and Type	Field	Description
protected IIdHelperService	myIdHelperService
protected ITermDeferredStorageSvc	myTermDeferredStorageSvc
protected ITermCodeSystemStorageSvc	myTerminologyCodeSystemStorageSvc

Fields inherited from class ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao

BASE_RESOURCE_NAME, myInterceptorBroadcaster, myPlatformTransactionManager, mySearchDao, myTransactionService

Fields inherited from class ca.uhn.fhir.jpa.dao.BaseHapiFhirDao

cacheTagDefinitionDao, myCodingSpy, myDeleteConflictService, myEntityManager, myInMemoryResourceMatcher, myJpaStorageResourceParser, myPartitionSettings, myResourceHistoryCalculator, myResourceHistoryTableDao, myResourceLinkDao, myResourceTableDao, myResourceTagDao, myResourceTypeCacheSvc, mySearchCoordinatorSvc, myTerminologySvc, NS_JPA_PROFILE

Fields inherited from class ca.uhn.fhir.jpa.dao.BaseStorageResourceDao

STRICT_ERROR_HANDLER

Fields inherited from class ca.uhn.fhir.jpa.dao.BaseStorageDao

MESSAGE_KEY_DELETE_RESOURCE_ALREADY_DELETED, MESSAGE_KEY_DELETE_RESOURCE_NOT_EXISTING, myMetaTagSorter, myResourceVersionSvc, mySearchParamRegistry, myStorageSettings, OO_ISSUE_CODE_INFORMATIONAL, OO_SEVERITY_ERROR, OO_SEVERITY_INFO, OO_SEVERITY_WARN

Fields inherited from interface ca.uhn.fhir.jpa.api.dao.IDao

CURRENTLY_REINDEXING, RESOURCE_PID, RESOURCE_PID_KEY

Constructor Summary

Constructors

Constructor	Description
JpaResourceDaoCodeSystem()

Method Summary

Modifier and Type	Method	Description
static String	createVersionedSystemIfVersionIsPresent(String theCodeSystemUrl, String theVersion)
static ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult	doLookupCode(ca.uhn.fhir.context.FhirContext theFhirContext, FhirTerser theFhirTerser, ca.uhn.fhir.context.support.IValidationSupport theValidationSupport, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem, org.hl7.fhir.instance.model.api.IBaseCoding theCoding, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theDisplayLanguage, Collection<org.hl7.fhir.instance.model.api.IPrimitiveType<String>> thePropertyNames)
List<org.hl7.fhir.instance.model.api.IIdType>	findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem, ca.uhn.fhir.rest.api.server.RequestDetails theRequest)
ReindexJobStatus	getReindexJobStatus()
ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult	lookupCode(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem, org.hl7.fhir.instance.model.api.IBaseCoding theCoding, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)
ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult	lookupCode(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem, org.hl7.fhir.instance.model.api.IBaseCoding theCoding, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theDisplayLanguage, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)
ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult	lookupCode(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem, org.hl7.fhir.instance.model.api.IBaseCoding theCoding, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theDisplayLanguage, Collection<org.hl7.fhir.instance.model.api.IPrimitiveType<String>> thePropertyNames, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)
protected void	preDelete(T theResourceToDelete, ResourceTable theEntityToDelete, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)	Subclasses may override to provide behaviour.
ReindexOutcome	reindex(ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId thePid, ReindexParameters theReindexParameters, ca.uhn.fhir.rest.api.server.RequestDetails theRequest, ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails)	If there are more code systems to process than JpaStorageSettings.getDeferIndexingForCodesystemsOfSize(), then these codes will have their processing deferred (for a later time).
void	start()
IFhirResourceDaoCodeSystem.SubsumesResult	subsumes(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeA, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeB, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem, org.hl7.fhir.instance.model.api.IBaseCoding theCodingA, org.hl7.fhir.instance.model.api.IBaseCoding theCodingB, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)
ResourceTable	updateEntity(ca.uhn.fhir.rest.api.server.RequestDetails theRequest, org.hl7.fhir.instance.model.api.IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion, ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry)
ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult	validateCode(org.hl7.fhir.instance.model.api.IIdType theCodeSystemId, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeSystemUrl, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theVersion, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode, org.hl7.fhir.instance.model.api.IPrimitiveType<String> theDisplay, org.hl7.fhir.instance.model.api.IBaseCoding theCoding, org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConcept, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Methods inherited from class ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao

create, create, create, create, create, delete, delete, delete, deleteByUrl, deleteByUrl, deletePidList, doCreateForPost, doMetaAddOperation, doMetaDeleteOperation, doUpdateForUpdateOrPatch, expunge, expunge, expunge, fetchAllVersionsOfResources, forceExpungeInExistingTransaction, getDeleteExpungeJobSubmitter, getMatchResourceUrlService, getMatchUrlService, getMessageSanitized, getRequestPartitionHelperService, getResourceName, getResourceType, getStorageResourceParser, getTransactionService, history, history, history, invokeStoragePreAccessResources, invokeStoragePreShowResources, isPagingProviderDatabaseBacked, isResourceIdServerAssigned, metaAddOperation, metaDeleteOperation, metaGetOperation, metaGetOperation, postUpdateTransaction, read, read, read, readByPid, readByPid, readEntity, readEntityLatestVersion, readEntityLatestVersion, reindex, removeTag, removeTag, requestReindexForRelatedResources, search, search, search, searchForIds, searchForIdStream, searchForResourceIds, searchForResources, setIdHelperSvcForUnitTest, setOffsetAndCount, setRequestPartitionHelperService, setResourceType, setTransactionService, shouldSkipReindex, toMetaDt, update, update, update, update, update, update, updateEntityForDelete, validate, validateCriteriaAndReturnResourceDefinition, validatePartitionIdMatch

Methods inherited from class ca.uhn.fhir.jpa.dao.BaseHapiFhirDao

addPidToResource, decodeResource, getApplicationContext, getContext, getInterceptorBroadcaster, getStorageSettings, isLogicalReference, parseContentTextIntoWords, populateResourceIntoEntity, postDelete, postPersist, postUpdate, setApplicationContext, setContext, setDaoSearchParamSynchronizer, setDisableIncrementOnUpdateForUnitTest, setEntityManager, setExternallyStoredResourceServiceRegistryForUnitTest, setInterceptorBroadcasterForUnitTest, setJpaStorageResourceParserForUnitTest, setPartitionSettingsForUnitTest, setResourceHistoryCalculator, setResourceHistoryTableDao, setResourceTypeCacheSvc, setSearchParamPresenceSvc, setSearchParamWithInlineReferencesExtractor, setStorageSettingsForUnitTest, setValidationDisabledForUnitTest, shouldDroppedTagBeRemovedOnUpdate, updateHistoryEntity, updateInternal, updateTags, validateMetaCount, validateResourceForStorage

Methods inherited from class ca.uhn.fhir.jpa.dao.BaseStorageResourceDao

deleteExpunge, patch, patchInTransaction, validateResourceType

Methods inherited from class ca.uhn.fhir.jpa.dao.BaseStorageDao

addIssueToOperationOutcomeForAutoCreatedPlaceholder, clearRequestAsProcessingSubRequest, createErrorOperationOutcome, createInfoOperationOutcome, createInfoOperationOutcome, createMethodOutcomeForResourceId, createResourceGoneException, createWarnOperationOutcome, doCallHooks, extractReferencesToAutoVersion, extractReferencesToAvoidReplacement, markRequestAsProcessingSubRequest, populateOperationOutcomeForUpdate, preProcessResourceForStorage, preProcessResourceForStorage, setMyMetaTagSorter, setSearchParamRegistry, toMethodOutcome, toMethodOutcomeLazy, translateRawParameters, verifyResourceIdIsValid

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface ca.uhn.fhir.jpa.api.dao.IDao

getContext

Methods inherited from interface ca.uhn.fhir.jpa.api.dao.IFhirResourceDao

create, create, create, create, create, delete, delete, delete, deleteByUrl, deleteByUrl, deletePidList, deletePidList, expunge, expunge, expunge, fetchAllVersionsOfResources, forceExpungeInExistingTransaction, getCurrentVersionId, getResourceType, history, history, history, metaAddOperation, metaDeleteOperation, metaGetOperation, metaGetOperation, patch, patchInTransaction, read, read, read, readByPid, readByPid, readEntity, reindex, removeTag, removeTag, search, search, search, searchForIds, searchForIds, searchForIdStream, searchForResourceIds, searchForResources, translateRawParameters, update, update, update, update, update, update, validate, validateCriteriaAndReturnResourceDefinition

Field Details

myTerminologyCodeSystemStorageSvc

@Autowired
protected ITermCodeSystemStorageSvc myTerminologyCodeSystemStorageSvc

myIdHelperService

@Autowired
protected IIdHelperService myIdHelperService

myTermDeferredStorageSvc

@Autowired
protected ITermDeferredStorageSvc myTermDeferredStorageSvc

Constructor Details

JpaResourceDaoCodeSystem

public JpaResourceDaoCodeSystem()

Method Details

start

@PostConstruct
public void start()

Overrides:

start in class BaseHapiFhirResourceDao<T extends org.hl7.fhir.instance.model.api.IBaseResource>

findCodeSystemIdsContainingSystemAndCode

public List<org.hl7.fhir.instance.model.api.IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode,
 String theSystem,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequest)

Specified by:

findCodeSystemIdsContainingSystemAndCode in interface IFhirResourceDaoCodeSystem<T extends org.hl7.fhir.instance.model.api.IBaseResource>

lookupCode

@Nonnull
public ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult lookupCode(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem,
 org.hl7.fhir.instance.model.api.IBaseCoding theCoding,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Specified by:

lookupCode in interface IFhirResourceDaoCodeSystem<T extends org.hl7.fhir.instance.model.api.IBaseResource>

lookupCode

@Nonnull
public ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult lookupCode(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem,
 org.hl7.fhir.instance.model.api.IBaseCoding theCoding,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theDisplayLanguage,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Specified by:

lookupCode in interface IFhirResourceDaoCodeSystem<T extends org.hl7.fhir.instance.model.api.IBaseResource>

lookupCode

@Nonnull
public ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult lookupCode(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem,
 org.hl7.fhir.instance.model.api.IBaseCoding theCoding,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theDisplayLanguage,
 Collection<org.hl7.fhir.instance.model.api.IPrimitiveType<String>> thePropertyNames,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Specified by:

lookupCode in interface IFhirResourceDaoCodeSystem<T extends org.hl7.fhir.instance.model.api.IBaseResource>

subsumes

public IFhirResourceDaoCodeSystem.SubsumesResult subsumes(org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeA,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeB,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem,
 org.hl7.fhir.instance.model.api.IBaseCoding theCodingA,
 org.hl7.fhir.instance.model.api.IBaseCoding theCodingB,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Specified by:

subsumes in interface IFhirResourceDaoCodeSystem<T extends org.hl7.fhir.instance.model.api.IBaseResource>

preDelete

protected void preDelete(T theResourceToDelete,
 ResourceTable theEntityToDelete,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Description copied from class: BaseHapiFhirResourceDao

Subclasses may override to provide behaviour. Invoked within a delete transaction with the resource that is about to be deleted.

Overrides:

preDelete in class BaseHapiFhirResourceDao<T extends org.hl7.fhir.instance.model.api.IBaseResource>

reindex

public ReindexOutcome reindex(ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId thePid,
 ReindexParameters theReindexParameters,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequest,
 ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails)

If there are more code systems to process than JpaStorageSettings.getDeferIndexingForCodesystemsOfSize(), then these codes will have their processing deferred (for a later time). This can result in future reindex steps *skipping* these code systems (if they're still deferred) and thus incorrect expansions resulting. So we override the reindex method for CodeSystems specifically to force reindex batch jobs to wait until all code systems are processed before moving on.

Specified by:

reindex in interface IFhirResourceDao<T extends org.hl7.fhir.instance.model.api.IBaseResource>

Overrides:

reindex in class BaseHapiFhirResourceDao<T extends org.hl7.fhir.instance.model.api.IBaseResource>

getReindexJobStatus

public ReindexJobStatus getReindexJobStatus()

Specified by:

getReindexJobStatus in interface IFhirResourceDao<T extends org.hl7.fhir.instance.model.api.IBaseResource>

updateEntity

public ResourceTable updateEntity(ca.uhn.fhir.rest.api.server.RequestDetails theRequest,
 org.hl7.fhir.instance.model.api.IBaseResource theResource,
 IBasePersistedResource theEntity,
 Date theDeletedTimestampOrNull,
 boolean thePerformIndexing,
 boolean theUpdateVersion,
 ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails,
 boolean theForceUpdate,
 boolean theCreateNewHistoryEntry)

Specified by:

updateEntity in interface IJpaDao<T extends org.hl7.fhir.instance.model.api.IBaseResource>

Overrides:

updateEntity in class BaseHapiFhirDao<T extends org.hl7.fhir.instance.model.api.IBaseResource>

validateCode

@Nonnull
public ca.uhn.fhir.context.support.IValidationSupport.CodeValidationResult validateCode(org.hl7.fhir.instance.model.api.IIdType theCodeSystemId,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCodeSystemUrl,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theVersion,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theDisplay,
 org.hl7.fhir.instance.model.api.IBaseCoding theCoding,
 org.hl7.fhir.instance.model.api.IBaseDatatype theCodeableConcept,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Specified by:

validateCode in interface IFhirResourceDaoCodeSystem<T extends org.hl7.fhir.instance.model.api.IBaseResource>

doLookupCode

public static ca.uhn.fhir.context.support.IValidationSupport.LookupCodeResult doLookupCode(ca.uhn.fhir.context.FhirContext theFhirContext,
 FhirTerser theFhirTerser,
 ca.uhn.fhir.context.support.IValidationSupport theValidationSupport,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theCode,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theSystem,
 org.hl7.fhir.instance.model.api.IBaseCoding theCoding,
 org.hl7.fhir.instance.model.api.IPrimitiveType<String> theDisplayLanguage,
 Collection<org.hl7.fhir.instance.model.api.IPrimitiveType<String>> thePropertyNames)

createVersionedSystemIfVersionIsPresent

public static String createVersionedSystemIfVersionIsPresent(String theCodeSystemUrl,
 String theVersion)