Package ca.uhn.fhir.jpa.dao

Class BaseHapiFhirDao<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>

All Implemented Interfaces:

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

Direct Known Subclasses:

BaseHapiFhirResourceDao

@Repository
public abstract class BaseHapiFhirDao<T extends org.hl7.fhir.instance.model.api.IBaseResource>
extends BaseStorageResourceDao<T>
implements IDao, IJpaDao<T>, org.springframework.context.ApplicationContextAware

TODO: JA - This class has only one subclass now. Historically it was a common ancestor for BaseHapiFhirSystemDao and BaseHapiFhirResourceDao but I've untangled the former from this hierarchy in order to simplify moving common functionality for resource DAOs into the hapi-fhir-storage project. This class should be merged into BaseHapiFhirResourceDao, but that should be done in its own dedicated PR since it'll be a noisy change.

Field Summary

Fields

Modifier and Type	Field	Description
static final long	INDEX_STATUS_INDEXED
static final long	INDEX_STATUS_INDEXING_FAILED
protected final CodingSpy	myCodingSpy
protected DaoRegistry	myDaoRegistry
protected DeleteConflictService	myDeleteConflictService
protected javax.persistence.EntityManager	myEntityManager
protected IForcedIdDao	myForcedIdDao
protected IIdHelperService<JpaPid>	myIdHelperService
protected InMemoryResourceMatcher	myInMemoryResourceMatcher
protected ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster	myInterceptorBroadcaster
protected IJpaStorageResourceParser	myJpaStorageResourceParser
protected PartitionSettings	myPartitionSettings
protected IResourceHistoryTableDao	myResourceHistoryTableDao
protected IResourceLinkDao	myResourceLinkDao
protected IResourceTableDao	myResourceTableDao
protected IResourceTagDao	myResourceTagDao
protected ISearchCoordinatorSvc<JpaPid>	mySearchCoordinatorSvc
protected ITermReadSvc	myTerminologySvc
static final String	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, myFhirContext, myResourceVersionSvc, mySearchParamRegistry, myStorageSettings, 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
BaseHapiFhirDao()

Method Summary

Modifier and Type	Method	Description
protected void	addPidToResource(IResourceLookup<JpaPid> theEntity, org.hl7.fhir.instance.model.api.IBaseResource theResource)
static String	decodeResource(byte[] theResourceBytes, ResourceEncodingEnum theResourceEncoding)
static String	encodeResource(org.hl7.fhir.instance.model.api.IBaseResource theResource, ResourceEncodingEnum theEncoding, List<String> theExcludeElements, ca.uhn.fhir.context.FhirContext theContext)
protected org.springframework.context.ApplicationContext	getApplicationContext()
ca.uhn.fhir.context.FhirContext	getContext()
protected ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster	getInterceptorBroadcaster()
JpaStorageSettings	getStorageSettings()
protected TagDefinition	getTagOrNull(ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails, TagTypeEnum theTagType, String theScheme, String theTerm, String theLabel, String theVersion, Boolean theUserSelected)	null will only be returned if the scheme and tag are both blank
boolean	isLogicalReference(org.hl7.fhir.instance.model.api.IIdType theId)
static String	parseContentTextIntoWords(ca.uhn.fhir.context.FhirContext theContext, org.hl7.fhir.instance.model.api.IBaseResource theResource)
void	populateFullTextFields(ca.uhn.fhir.context.FhirContext theContext, org.hl7.fhir.instance.model.api.IBaseResource theResource, ResourceTable theEntity, ResourceIndexedSearchParams theNewParams)
protected ca.uhn.fhir.jpa.dao.EncodedResource	populateResourceIntoEntity(ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails, ca.uhn.fhir.rest.api.server.RequestDetails theRequest, org.hl7.fhir.instance.model.api.IBaseResource theResource, ResourceTable theEntity, boolean thePerformIndexing)	Returns true if the resource has changed (either the contents or the tags)
protected void	postDelete(ResourceTable theEntity)	Subclasses may override to provide behaviour.
protected void	postPersist(ResourceTable theEntity, T theResource, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)	Subclasses may override to provide behaviour.
protected void	postUpdate(ResourceTable theEntity, T theResource, ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)	Subclasses may override to provide behaviour.
BaseHasResource	readEntity(org.hl7.fhir.instance.model.api.IIdType theValueId, ca.uhn.fhir.rest.api.server.RequestDetails theRequest)
void	setApplicationContext(org.springframework.context.ApplicationContext theApplicationContext)
void	setContext(ca.uhn.fhir.context.FhirContext theContext)
void	setDaoSearchParamSynchronizer(DaoSearchParamSynchronizer theDaoSearchParamSynchronizer)
static void	setDisableIncrementOnUpdateForUnitTest(boolean theDisableIncrementOnUpdateForUnitTest)
void	setEntityManager(javax.persistence.EntityManager theEntityManager)
void	setExternallyStoredResourceServiceRegistryForUnitTest(ExternallyStoredResourceServiceRegistry theExternallyStoredResourceServiceRegistry)
void	setJpaStorageResourceParserForUnitTest(IJpaStorageResourceParser theJpaStorageResourceParser)	Do not call this method outside of unit tests
void	setPartitionSettingsForUnitTest(PartitionSettings thePartitionSettings)
void	setResourceHistoryTableDao(IResourceHistoryTableDao theResourceHistoryTableDao)
void	setSearchParamPresenceSvc(ISearchParamPresenceSvc theSearchParamPresenceSvc)
void	setSearchParamWithInlineReferencesExtractor(SearchParamWithInlineReferencesExtractor theSearchParamWithInlineReferencesExtractor)
void	setStorageSettingsForUnitTest(JpaStorageSettings theStorageSettings)
static void	setValidationDisabledForUnitTest(boolean theValidationDisabledForUnitTest)	Do not call this method outside of unit tests
protected boolean	shouldDroppedTagBeRemovedOnUpdate(ca.uhn.fhir.rest.api.server.RequestDetails theRequest, ResourceTag theTag)	This method is called when an update to an existing resource detects that the resource supplied for update is missing a tag/profile/security label that the currently persisted resource holds.
void	start()
static MemoryCacheService.TagDefinitionCacheKey	toTagDefinitionMemoryCacheKey(TagTypeEnum theTagType, String theScheme, String theTerm, String theVersion, Boolean theUserSelected)
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)
IBasePersistedResource	updateHistoryEntity(ca.uhn.fhir.rest.api.server.RequestDetails theRequest, T theResource, IBasePersistedResource theEntity, IBasePersistedResource theHistoryEntity, org.hl7.fhir.instance.model.api.IIdType theResourceId, ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails, boolean isUpdatingCurrent)
DaoMethodOutcome	updateInternal(ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails, T theResource, String theMatchUrl, boolean thePerformIndexing, boolean theForceUpdateVersion, IBasePersistedResource theEntity, org.hl7.fhir.instance.model.api.IIdType theResourceId, org.hl7.fhir.instance.model.api.IBaseResource theOldResource, ca.uhn.fhir.rest.api.RestOperationTypeEnum theOperationType, ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails)
protected void	validateMetaCount(int theMetaCount)
protected void	validateResourceForStorage(T theResource, ResourceTable theEntityToSave)	This method is invoked immediately before storing a new resource, or an update to an existing resource to allow the DAO to ensure that it is valid for persistence.

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

deleteExpunge, doUpdateForUpdateOrPatch, getDeleteExpungeJobSubmitter, getMatchResourceUrlService, getResourceName, getResourceType, getStorageResourceParser, getTransactionService, patch, patchInTransaction, readEntityLatestVersion, readEntityLatestVersion, validateResourceType

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

clearRequestAsProcessingSubRequest, createErrorOperationOutcome, createInfoOperationOutcome, createInfoOperationOutcome, createMethodOutcomeForResourceId, createOperationOutcome, createResourceGoneException, doCallHooks, extractReferencesToAutoVersion, markRequestAsProcessingSubRequest, populateOperationOutcomeForUpdate, preProcessResourceForStorage, preProcessResourceForStorage, setSearchParamRegistry, toMethodOutcome, toMethodOutcomeLazy, translateRawParameters

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.IFhirResourceDao

create, create, create, create, create, delete, delete, delete, deleteByUrl, deleteByUrl, deletePidList, deletePidList, expunge, expunge, expunge, forceExpungeInExistingTransaction, getCurrentVersionId, history, history, history, metaAddOperation, metaDeleteOperation, metaGetOperation, metaGetOperation, read, read, read, readByPid, readByPid, reindex, reindex, removeTag, removeTag, search, search, search, searchForIds, searchForIds, translateRawParameters, update, update, update, update, update, update, validate, validateCriteriaAndReturnResourceDefinition

Field Details

INDEX_STATUS_INDEXED

public static final long INDEX_STATUS_INDEXED

See Also:

• Constant Field Values

INDEX_STATUS_INDEXING_FAILED

public static final long INDEX_STATUS_INDEXING_FAILED

See Also:

• Constant Field Values

NS_JPA_PROFILE

public static final String NS_JPA_PROFILE

See Also:

• Constant Field Values

myEntityManager

protected javax.persistence.EntityManager myEntityManager

myIdHelperService

@Autowired
protected IIdHelperService<JpaPid> myIdHelperService

myForcedIdDao

@Autowired
protected IForcedIdDao myForcedIdDao

mySearchCoordinatorSvc

@Autowired
protected ISearchCoordinatorSvc<JpaPid> mySearchCoordinatorSvc

myTerminologySvc

@Autowired
protected ITermReadSvc myTerminologySvc

myResourceHistoryTableDao

@Autowired
protected IResourceHistoryTableDao myResourceHistoryTableDao

myResourceTableDao

@Autowired
protected IResourceTableDao myResourceTableDao

myResourceLinkDao

@Autowired
protected IResourceLinkDao myResourceLinkDao

myResourceTagDao

@Autowired
protected IResourceTagDao myResourceTagDao

myDeleteConflictService

@Autowired
protected DeleteConflictService myDeleteConflictService

myInterceptorBroadcaster

@Autowired
protected ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster myInterceptorBroadcaster

myDaoRegistry

@Autowired
protected DaoRegistry myDaoRegistry

myInMemoryResourceMatcher

@Autowired
protected InMemoryResourceMatcher myInMemoryResourceMatcher

myJpaStorageResourceParser

@Autowired
protected IJpaStorageResourceParser myJpaStorageResourceParser

myPartitionSettings

@Autowired
protected PartitionSettings myPartitionSettings

myCodingSpy

protected final CodingSpy myCodingSpy

Constructor Details

BaseHapiFhirDao

public BaseHapiFhirDao()

Method Details

setExternallyStoredResourceServiceRegistryForUnitTest

public void setExternallyStoredResourceServiceRegistryForUnitTest(ExternallyStoredResourceServiceRegistry theExternallyStoredResourceServiceRegistry)

setSearchParamPresenceSvc

public void setSearchParamPresenceSvc(ISearchParamPresenceSvc theSearchParamPresenceSvc)

getInterceptorBroadcaster

protected ca.uhn.fhir.interceptor.api.IInterceptorBroadcaster getInterceptorBroadcaster()

Specified by:

getInterceptorBroadcaster in class BaseStorageDao

getApplicationContext

protected org.springframework.context.ApplicationContext getApplicationContext()

setApplicationContext

public void setApplicationContext(@Nonnull
 org.springframework.context.ApplicationContext theApplicationContext)
                           throws org.springframework.beans.BeansException

Specified by:

setApplicationContext in interface org.springframework.context.ApplicationContextAware

Throws:

org.springframework.beans.BeansException

getStorageSettings

public JpaStorageSettings getStorageSettings()

Specified by:

getStorageSettings in class BaseStorageDao

getContext

public ca.uhn.fhir.context.FhirContext getContext()

Specified by:

getContext in interface IDao

Specified by:

getContext in class BaseStorageDao

setContext

@Autowired
public void setContext(ca.uhn.fhir.context.FhirContext theContext)

getTagOrNull

protected TagDefinition getTagOrNull(ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails,
 TagTypeEnum theTagType,
 String theScheme,
 String theTerm,
 String theLabel,
 String theVersion,
 Boolean theUserSelected)

null will only be returned if the scheme and tag are both blank

isLogicalReference

public boolean isLogicalReference(org.hl7.fhir.instance.model.api.IIdType theId)

populateResourceIntoEntity

protected ca.uhn.fhir.jpa.dao.EncodedResource populateResourceIntoEntity(ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequest,
 org.hl7.fhir.instance.model.api.IBaseResource theResource,
 ResourceTable theEntity,
 boolean thePerformIndexing)

Returns true if the resource has changed (either the contents or the tags)

postDelete

protected void postDelete(ResourceTable theEntity)

Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database

Parameters:

theEntity - The resource

postPersist

protected void postPersist(ResourceTable theEntity,
 T theResource,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Subclasses may override to provide behaviour. Called when a resource has been inserted into the database for the first time.

Parameters:

theEntity - The entity being updated (Do not modify the entity! Undefined behaviour will occur!)

theResource - The resource being persisted

theRequestDetails - The request details, needed for partition support

postUpdate

protected void postUpdate(ResourceTable theEntity,
 T theResource,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails)

Subclasses may override to provide behaviour. Called when a pre-existing resource has been updated in the database

Parameters:

theEntity - The resource

theResource - The resource being persisted

theRequestDetails - The request details, needed for partition support

readEntity

public BaseHasResource readEntity(org.hl7.fhir.instance.model.api.IIdType theValueId,
 ca.uhn.fhir.rest.api.server.RequestDetails theRequest)

Specified by:

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

shouldDroppedTagBeRemovedOnUpdate

protected boolean shouldDroppedTagBeRemovedOnUpdate(ca.uhn.fhir.rest.api.server.RequestDetails theRequest,
 ResourceTag theTag)

This method is called when an update to an existing resource detects that the resource supplied for update is missing a tag/profile/security label that the currently persisted resource holds.

The default implementation removes any profile declarations, but leaves tags and security labels in place. Subclasses may choose to override and change this behaviour.

See Updates to Tags, Profiles, and Security Labels for a description of the logic that the default behaviour follows.

Parameters:

theTag - The tag

Returns:

Returns true if the tag should be removed

setEntityManager

public void setEntityManager(javax.persistence.EntityManager theEntityManager)

setSearchParamWithInlineReferencesExtractor

public void setSearchParamWithInlineReferencesExtractor(SearchParamWithInlineReferencesExtractor theSearchParamWithInlineReferencesExtractor)

setResourceHistoryTableDao

public void setResourceHistoryTableDao(IResourceHistoryTableDao theResourceHistoryTableDao)

setDaoSearchParamSynchronizer

public void setDaoSearchParamSynchronizer(DaoSearchParamSynchronizer theDaoSearchParamSynchronizer)

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>

updateHistoryEntity

public IBasePersistedResource updateHistoryEntity(ca.uhn.fhir.rest.api.server.RequestDetails theRequest,
 T theResource,
 IBasePersistedResource theEntity,
 IBasePersistedResource theHistoryEntity,
 org.hl7.fhir.instance.model.api.IIdType theResourceId,
 ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails,
 boolean isUpdatingCurrent)

updateInternal

public DaoMethodOutcome updateInternal(ca.uhn.fhir.rest.api.server.RequestDetails theRequestDetails,
 T theResource,
 String theMatchUrl,
 boolean thePerformIndexing,
 boolean theForceUpdateVersion,
 IBasePersistedResource theEntity,
 org.hl7.fhir.instance.model.api.IIdType theResourceId,
 @Nullable
 org.hl7.fhir.instance.model.api.IBaseResource theOldResource,
 ca.uhn.fhir.rest.api.RestOperationTypeEnum theOperationType,
 ca.uhn.fhir.rest.api.server.storage.TransactionDetails theTransactionDetails)

Specified by:

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

addPidToResource

protected void addPidToResource(IResourceLookup<JpaPid> theEntity,
 org.hl7.fhir.instance.model.api.IBaseResource theResource)

validateMetaCount

protected void validateMetaCount(int theMetaCount)

validateResourceForStorage

protected void validateResourceForStorage(T theResource,
 ResourceTable theEntityToSave)

This method is invoked immediately before storing a new resource, or an update to an existing resource to allow the DAO to ensure that it is valid for persistence. By default, checks for the "subsetted" tag and rejects resources which have it. Subclasses should call the superclass implementation to preserve this check.

Parameters:

theResource - The resource that is about to be persisted

theEntityToSave - TODO

start

@PostConstruct
public void start()

setStorageSettingsForUnitTest

public void setStorageSettingsForUnitTest(JpaStorageSettings theStorageSettings)

populateFullTextFields

public void populateFullTextFields(ca.uhn.fhir.context.FhirContext theContext,
 org.hl7.fhir.instance.model.api.IBaseResource theResource,
 ResourceTable theEntity,
 ResourceIndexedSearchParams theNewParams)

setPartitionSettingsForUnitTest

public void setPartitionSettingsForUnitTest(PartitionSettings thePartitionSettings)

setJpaStorageResourceParserForUnitTest

public void setJpaStorageResourceParserForUnitTest(IJpaStorageResourceParser theJpaStorageResourceParser)

Do not call this method outside of unit tests

toTagDefinitionMemoryCacheKey

@Nonnull
public static MemoryCacheService.TagDefinitionCacheKey toTagDefinitionMemoryCacheKey(TagTypeEnum theTagType,
 String theScheme,
 String theTerm,
 String theVersion,
 Boolean theUserSelected)

parseContentTextIntoWords

public static String parseContentTextIntoWords(ca.uhn.fhir.context.FhirContext theContext,
 org.hl7.fhir.instance.model.api.IBaseResource theResource)

decodeResource

public static String decodeResource(byte[] theResourceBytes,
 ResourceEncodingEnum theResourceEncoding)

encodeResource

public static String encodeResource(org.hl7.fhir.instance.model.api.IBaseResource theResource,
 ResourceEncodingEnum theEncoding,
 List<String> theExcludeElements,
 ca.uhn.fhir.context.FhirContext theContext)

setDisableIncrementOnUpdateForUnitTest

public static void setDisableIncrementOnUpdateForUnitTest(boolean theDisableIncrementOnUpdateForUnitTest)

setValidationDisabledForUnitTest

public static void setValidationDisabledForUnitTest(boolean theValidationDisabledForUnitTest)

Do not call this method outside of unit tests