Package com.ibm.fhir.persistence.jdbc.impl

Class FHIRPersistenceJDBCImpl

java.lang.Object

com.ibm.fhir.persistence.jdbc.impl.FHIRPersistenceJDBCImpl

All Implemented Interfaces:

FHIRPersistence, SchemaNameSupplier

public class FHIRPersistenceJDBCImpl
extends Object
implements FHIRPersistence, SchemaNameSupplier

The JDBC implementation of the FHIRPersistence interface, providing implementations for CRUD APIs and search.

Field Summary

Fields

Modifier and Type	Field	Description
static String	TRX_SYNCH_REG_JNDI_NAME
protected static String	TXN_JNDI_NAME
protected Boolean	updateCreateEnabled
protected UserTransaction	userTransaction

Constructor Summary

Constructors

Constructor	Description
FHIRPersistenceJDBCImpl(FHIRPersistenceJDBCCache cache)	Constructor for use when running as web application in WLP.
FHIRPersistenceJDBCImpl(Properties configProps, IConnectionProvider cp, FHIRConfigProvider configProvider, FHIRPersistenceJDBCCache cache)	Constructor for use when running standalone, outside of any web container.
FHIRPersistenceJDBCImpl(Properties configProps, IConnectionProvider cp, FHIRPersistenceJDBCCache cache)	Constructor for use when running standalone, outside of any web container.

Method Summary

Modifier and Type	Method	Description
protected void	addCanonicalCompositeParam(List<ExtractedParameterValue> allParameters)	Augment the given allParameters list with ibm-internal parameters that represent the relationship between the url and version parameters.
protected void	addCompartmentParams(List<ExtractedParameterValue> allParameters, Resource fhirResource)	Augment the given allParameters list with ibm-internal parameters that represent relationships between the fhirResource to its compartments.
protected Action	buildActionChain()	Build a chain of actions we want to apply to new connections.
protected List<Resource>	buildSortedResourceDTOList(ResourceDAO resourceDao, Class<? extends Resource> resourceType, List<Long> sortedIdList)	This method takes the passed list of sorted Resource ids, acquires the ResourceDTO corresponding to each id, and returns those ResourceDTOs in a List, sorted according to the input sorted ids.
List<ResourceChangeLogRecord>	changes(int resourceCount, Instant fromLastModified, Long afterResourceId, String resourceTypeName)	Fetch up to resourceCount records from the RESOURCE_CHANGE_LOG table
protected List<Resource>	convertResourceDTOList(List<Resource> resourceDTOList, Class<? extends Resource> resourceType, List<String> elements)	Converts the passed Resource Data Transfer Object collection to a collection of FHIR Resource objects.
protected <T extends Resource> List<T>	convertResourceDTOList(List<Resource> resourceDTOList, Class<T> resourceType)	Converts the passed Resource Data Transfer Object collection to a collection of FHIR Resource objects.
protected List<Resource>	convertResourceDTOListOld(List<Resource> resourceDTOList, Class<? extends Resource> resourceType)	Converts the passed Resource Data Transfer Object collection to a collection of FHIR Resource objects.
<T extends Resource> SingleResourceResult<T>	create(FHIRPersistenceContext context, T resource)	Stores a new FHIR Resource in the datastore.
<T extends Resource> SingleResourceResult<T>	delete(FHIRPersistenceContext context, Class<T> resourceType, String logicalId)	Deletes the specified FHIR Resource from the datastore.
void	doCachePrefill(Connection connection)	Prefill the caches
ResourceEraseRecord	erase(EraseDTO eraseDto)	Erases part or a whole of a resource in the data layer
ResourcePayload	fetchResourcePayloads(Class<? extends Resource> resourceType, Instant fromLastModified, Instant toLastModified, Function<ResourcePayload,Boolean> processor)	Special function for high speed export of resource payloads.
String	generateResourceId()	Generates a resource ID.
OperationOutcome	getHealth()	Returns an OperationOutcome indicating the current status of the persistence store / backend
String	getSchemaForRequestContext(Connection connection)	Get the schema name for the current request context
FHIRPersistenceTransaction	getTransaction()	Returns a FHIRPersistenceTransaction object associated with the persistence layer implementation in use.
<T extends Resource> MultiResourceResult<T>	history(FHIRPersistenceContext context, Class<T> resourceType, String logicalId)	Retrieves all of the versions of the specified FHIR Resource.
boolean	isDeleteSupported()	Returns true iff the persistence layer implementation supports the "delete" operation.
boolean	isReindexSupported()	Returns true iff the persistence layer implementation supports the "reindex" special operation
boolean	isTransactional()	Returns true iff the persistence layer implementation supports transactions.
MultiResourceResult<Resource>	newSearch(FHIRPersistenceContext context, Class<? extends Resource> resourceType)	Search query implementation based on the 1385 new query builder.
void	persistResourceTokenValueRecords(Collection<ResourceTokenValueRec> records, Collection<ResourceProfileRec> profileRecs, Collection<ResourceTokenValueRec> tagRecs, Collection<ResourceTokenValueRec> securityRecs)	Called just prior to commit so that we can persist all the token value records that have been accumulated during the transaction.
<T extends Resource> SingleResourceResult<T>	read(FHIRPersistenceContext context, Class<T> resourceType, String logicalId)	Retrieves the most recent version of a FHIR Resource from the datastore.
int	reindex(FHIRPersistenceContext context, OperationOutcome.Builder operationOutcomeResult, Instant tstamp, List<Long> indexIds, String resourceLogicalId)	Initiates reindexing for either a specified list of index IDs, or a randomly chosen resource.
List<Long>	retrieveIndex(int count, Instant notModifiedAfter, Long afterIndexId, String resourceTypeName)	Retrieves a list of index IDs available for reindexing.
protected UserTransaction	retrieveUserTransaction(String jndiName)	Retrieves (via a JNDI lookup) a reference to the UserTransaction.
MultiResourceResult<Resource>	search(FHIRPersistenceContext context, Class<? extends Resource> resourceType)	Performs a search on the specified target resource type using the specified search parameters.
<T extends Resource> SingleResourceResult<T>	update(FHIRPersistenceContext context, String logicalId, T resource)	Updates an existing FHIR Resource by storing a new version in the datastore.
<T extends Resource> void	updateParameters(ResourceIndexRecord rir, Class<T> resourceTypeClass, Resource existingResourceDTO, ReindexResourceDAO reindexDAO, OperationOutcome.Builder operationOutcomeResult)	Update the parameters for the resource described by the given DTO
<T extends Resource> SingleResourceResult<T>	vread(FHIRPersistenceContext context, Class<T> resourceType, String logicalId, String versionId)	Retrieves a specific version of a FHIR Resource from the datastore.

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.ibm.fhir.persistence.FHIRPersistence

isChangesSupported

Field Detail

TXN_JNDI_NAME

protected static final String TXN_JNDI_NAME

See Also:

Constant Field Values

TRX_SYNCH_REG_JNDI_NAME

public static final String TRX_SYNCH_REG_JNDI_NAME

See Also:

Constant Field Values

userTransaction

protected UserTransaction userTransaction

updateCreateEnabled

protected Boolean updateCreateEnabled

Constructor Detail

FHIRPersistenceJDBCImpl

public FHIRPersistenceJDBCImpl(FHIRPersistenceJDBCCache cache)
                        throws Exception

Constructor for use when running as web application in WLP.

Throws:

Exception

FHIRPersistenceJDBCImpl

public FHIRPersistenceJDBCImpl(Properties configProps,
                               IConnectionProvider cp,
                               FHIRPersistenceJDBCCache cache)
                        throws Exception

Constructor for use when running standalone, outside of any web container. The IConnectionProvider should be a pooling implementation which supports an ITransactionProvider. Uses the default adapter for reading FHIR configurations, which works OK for unit-tests.

Parameters:

configProps -

cp -

Throws:

Exception

FHIRPersistenceJDBCImpl

public FHIRPersistenceJDBCImpl(Properties configProps,
                               IConnectionProvider cp,
                               FHIRConfigProvider configProvider,
                               FHIRPersistenceJDBCCache cache)
                        throws Exception

Constructor for use when running standalone, outside of any web container. The IConnectionProvider should be a pooling implementation which supports an ITransactionProvider.

Parameters:

configProps -

cp -

configProvider - adapter to provide access to FHIR configuration

Throws:

Exception

Method Detail

buildActionChain

protected Action buildActionChain()

Build a chain of actions we want to apply to new connections. Current the only action we need is setting the tenant if we're in multi-tenant mode.

Returns:

the chain of actions to be applied

create

public <T extends Resource> SingleResourceResult<T> create(FHIRPersistenceContext context,
                                                           T resource)
                                                    throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Stores a new FHIR Resource in the datastore.

Specified by:

create in interface FHIRPersistence

Parameters:

context - the FHIRPersistenceContext instance associated with the current request

resource - the FHIR Resource instance to be created in the datastore

Returns:

a SingleResourceResult with a copy of resource with Meta fields updated by the persistence layer and/or an OperationOutcome with hints, warnings, or errors related to the interaction

Throws:

FHIRPersistenceException

update

public <T extends Resource> SingleResourceResult<T> update(FHIRPersistenceContext context,
                                                           String logicalId,
                                                           T resource)
                                                    throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Updates an existing FHIR Resource by storing a new version in the datastore.

Specified by:

update in interface FHIRPersistence

Parameters:

context - the FHIRPersistenceContext instance associated with the current request

logicalId - the logical id of the FHIR Resource to be updated

resource - the new contents of the FHIR Resource to be stored

Returns:

a SingleResourceResult with a copy of resource with fields updated by the persistence layer and/or an OperationOutcome with hints, warnings, or errors related to the interaction

Throws:

FHIRPersistenceException

search

public MultiResourceResult<Resource> search(FHIRPersistenceContext context,
                                            Class<? extends Resource> resourceType)
                                     throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Performs a search on the specified target resource type using the specified search parameters.

Specified by:

search in interface FHIRPersistence

Parameters:

context - the FHIRPersistenceContext instance associated with the current request

resourceType - the resource type which is the target of the search

Returns:

a MultiResourceResult with the list of FHIR Resources in the search result set and/or an OperationOutcome with hints, warnings, or errors related to the interaction

Throws:

FHIRPersistenceException

newSearch

public MultiResourceResult<Resource> newSearch(FHIRPersistenceContext context,
                                               Class<? extends Resource> resourceType)
                                        throws FHIRPersistenceException

Search query implementation based on the 1385 new query builder.

Parameters:

context -

resourceType -

Returns:

Throws:

FHIRPersistenceException

delete

public <T extends Resource> SingleResourceResult<T> delete(FHIRPersistenceContext context,
                                                           Class<T> resourceType,
                                                           String logicalId)
                                                    throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Deletes the specified FHIR Resource from the datastore.

Specified by:

delete in interface FHIRPersistence

Parameters:

context - the FHIRPersistenceContext instance associated with the current request

resourceType - The type of FHIR Resource to be deleted.

logicalId - the logical id of the FHIR Resource to be deleted

Returns:

a SingleResourceResult with the FHIR Resource that was deleted or null if the specified resource doesn't exist and/or an OperationOutcome with hints, warnings, or errors related to the interaction

Throws:

FHIRPersistenceException

read

public <T extends Resource> SingleResourceResult<T> read(FHIRPersistenceContext context,
                                                         Class<T> resourceType,
                                                         String logicalId)
                                                  throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Retrieves the most recent version of a FHIR Resource from the datastore.

Specified by:

read in interface FHIRPersistence

Parameters:

context - the FHIRPersistenceContext instance associated with the current request

resourceType - the resource type of the Resource instance to be retrieved

logicalId - the logical id of the Resource instance to be retrieved

Returns:

a SingleResourceResult with the FHIR Resource that was retrieved from the datastore and/or an OperationOutcome with hints, warnings, or errors related to the interaction

Throws:

FHIRPersistenceResourceDeletedException - if the resource being read is currently in a deleted state and FHIRPersistenceContext.includeDeleted() is set to false

FHIRPersistenceException

history

public <T extends Resource> MultiResourceResult<T> history(FHIRPersistenceContext context,
                                                           Class<T> resourceType,
                                                           String logicalId)
                                                    throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Retrieves all of the versions of the specified FHIR Resource.

Specified by:

history in interface FHIRPersistence

Parameters:

context - the FHIRPersistenceContext instance associated with the current request

resourceType - the resource type of the Resource instances to be retrieved

logicalId - the logical id of the Resource instances to be retrieved

Returns:

a MultiResourceResult with a list containing the available versions of the specified FHIR Resource and/or an OperationOutcome with hints, warnings, or errors related to the interaction

Throws:

FHIRPersistenceException

vread

public <T extends Resource> SingleResourceResult<T> vread(FHIRPersistenceContext context,
                                                          Class<T> resourceType,
                                                          String logicalId,
                                                          String versionId)
                                                   throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Retrieves a specific version of a FHIR Resource from the datastore.

Specified by:

vread in interface FHIRPersistence

Parameters:

context - the FHIRPersistenceContext instance associated with the current request

resourceType - the resource type of the Resource instance to be retrieved

logicalId - the logical id of the Resource instance to be retrieved

versionId - the version of the Resource instance to be retrieved

Returns:

a SingleResourceResult with the FHIR Resource that was retrieved from the datastore and/or an OperationOutcome with hints, warnings, or errors related to the interaction

Throws:

FHIRPersistenceResourceDeletedException - if the resource being read is currently in a deleted state and FHIRPersistenceContext.includeDeleted() is set to false

FHIRPersistenceException

buildSortedResourceDTOList

protected List<Resource> buildSortedResourceDTOList(ResourceDAO resourceDao,
                                                    Class<? extends Resource> resourceType,
                                                    List<Long> sortedIdList)
                                             throws FHIRException,
                                                    FHIRPersistenceException,
                                                    IOException

This method takes the passed list of sorted Resource ids, acquires the ResourceDTO corresponding to each id, and returns those ResourceDTOs in a List, sorted according to the input sorted ids.

Parameters:

resourceDao - - The resource DAO.

resourceType - - The type of Resource that each id in the passed list represents.

sortedIdList - - A list of Resource ids representing the proper sort order for the list of Resources to be returned.

Returns:

List - A list of ResourcesDTOs of the passed resourceType, sorted according the order of ids in the passed sortedIdList.

Throws:

FHIRPersistenceException

IOException

FHIRException

convertResourceDTOList

protected List<Resource> convertResourceDTOList(List<Resource> resourceDTOList,
                                                Class<? extends Resource> resourceType,
                                                List<String> elements)
                                         throws FHIRException,
                                                IOException

Converts the passed Resource Data Transfer Object collection to a collection of FHIR Resource objects.

Parameters:

resourceDTOList -

resourceType -

Returns:

Throws:

FHIRException

IOException

addCompartmentParams

protected void addCompartmentParams(List<ExtractedParameterValue> allParameters,
                                    Resource fhirResource)
                             throws FHIRSearchException

Augment the given allParameters list with ibm-internal parameters that represent relationships between the fhirResource to its compartments. These parameter values are subsequently used to improve the performance of compartment-based FHIR search queries. See CompartmentUtil.makeCompartmentParamName(String) for details on how the parameter name is composed for each relationship.

Parameters:

allParameters -

Throws:

FHIRSearchException

addCanonicalCompositeParam

protected void addCanonicalCompositeParam(List<ExtractedParameterValue> allParameters)
                                   throws FHIRSearchException

Augment the given allParameters list with ibm-internal parameters that represent the relationship between the url and version parameters. These parameter values are subsequently used in canonical reference searches. See CompartmentUtil.makeCompartmentParamName(String) for details on how the parameter name is composed.

Parameters:

allParameters -

Throws:

FHIRSearchException

getHealth

public OperationOutcome getHealth()
                           throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Returns an OperationOutcome indicating the current status of the persistence store / backend

Specified by:

getHealth in interface FHIRPersistence

Returns:

An OperationOutcome with a list of 0 or more OperationalOutcomeIssue indicating the status of the underlying datastore

Throws:

FHIRPersistenceException

retrieveUserTransaction

protected UserTransaction retrieveUserTransaction(String jndiName)

Retrieves (via a JNDI lookup) a reference to the UserTransaction. If the JNDI lookup fails, we'll assume that we're not running inside the container.

convertResourceDTOList

protected <T extends Resource> List<T> convertResourceDTOList(List<Resource> resourceDTOList,
                                                              Class<T> resourceType)
                                                       throws FHIRException,
                                                              IOException

Converts the passed Resource Data Transfer Object collection to a collection of FHIR Resource objects.

Parameters:

resourceDTOList -

resourceType -

Returns:

Throws:

FHIRException

IOException

convertResourceDTOListOld

protected List<Resource> convertResourceDTOListOld(List<Resource> resourceDTOList,
                                                   Class<? extends Resource> resourceType)
                                            throws FHIRException,
                                                   IOException

Converts the passed Resource Data Transfer Object collection to a collection of FHIR Resource objects.

Parameters:

resourceDTOList -

resourceType -

Returns:

Throws:

FHIRException

IOException

isTransactional

public boolean isTransactional()

Description copied from interface: FHIRPersistence

Returns true iff the persistence layer implementation supports transactions.

Specified by:

isTransactional in interface FHIRPersistence

getTransaction

public FHIRPersistenceTransaction getTransaction()

Description copied from interface: FHIRPersistence

Returns a FHIRPersistenceTransaction object associated with the persistence layer implementation in use. This can then be used to control transactional boundaries.

Specified by:

getTransaction in interface FHIRPersistence

isDeleteSupported

public boolean isDeleteSupported()

Description copied from interface: FHIRPersistence

Returns true iff the persistence layer implementation supports the "delete" operation.

Specified by:

isDeleteSupported in interface FHIRPersistence

getSchemaForRequestContext

public String getSchemaForRequestContext(Connection connection)
                                  throws FHIRPersistenceDBConnectException

Description copied from interface: SchemaNameSupplier

Get the schema name for the current request context

Specified by:

getSchemaForRequestContext in interface SchemaNameSupplier

Parameters:

connection - the connection for which we want to obtain the schema name

Returns:

the main schema name to use for the given connection

Throws:

FHIRPersistenceDBConnectException

doCachePrefill

public void doCachePrefill(Connection connection)
                    throws FHIRPersistenceException

Prefill the caches

Throws:

FHIRPersistenceException

isReindexSupported

public boolean isReindexSupported()

Description copied from interface: FHIRPersistence

Returns true iff the persistence layer implementation supports the "reindex" special operation

Specified by:

isReindexSupported in interface FHIRPersistence

Returns:

reindex

public int reindex(FHIRPersistenceContext context,
                   OperationOutcome.Builder operationOutcomeResult,
                   Instant tstamp,
                   List<Long> indexIds,
                   String resourceLogicalId)
            throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Initiates reindexing for either a specified list of index IDs, or a randomly chosen resource. The number of resources processed is returned. This can be used by a controller to continue processing until everything is complete.

Specified by:

reindex in interface FHIRPersistence

Parameters:

context - the FHIRPersistenceContext instance associated with the current request.

operationOutcomeResult - accumulate issues in this OperationOutcome.Builder

tstamp - only reindex resources with a reindex_tstamp less than this

indexIds - list of index IDs of resources to reindex, or null

resourceLogicalId - resourceType/logicalId value of a specific resource to reindex, or null; this parameter is ignored if the indexIds parameter value is non-null

Returns:

count of the number of resources reindexed by this call

Throws:

FHIRPersistenceException

updateParameters

public <T extends Resource> void updateParameters(ResourceIndexRecord rir,
                                                  Class<T> resourceTypeClass,
                                                  Resource existingResourceDTO,
                                                  ReindexResourceDAO reindexDAO,
                                                  OperationOutcome.Builder operationOutcomeResult)
                                           throws Exception

Update the parameters for the resource described by the given DTO

Type Parameters:

T -

Parameters:

rir - the resource index record

resourceTypeClass - the resource type class

existingResourceDTO - the existing resource DTO

reindexDAO - the reindex resource DAO

operationOutcomeResult - the operation outcome result

Throws:

Exception

generateResourceId

public String generateResourceId()

Description copied from interface: FHIRPersistence

Generates a resource ID.

Specified by:

generateResourceId in interface FHIRPersistence

Returns:

resource ID

persistResourceTokenValueRecords

public void persistResourceTokenValueRecords(Collection<ResourceTokenValueRec> records,
                                             Collection<ResourceProfileRec> profileRecs,
                                             Collection<ResourceTokenValueRec> tagRecs,
                                             Collection<ResourceTokenValueRec> securityRecs)
                                      throws FHIRPersistenceException

Called just prior to commit so that we can persist all the token value records that have been accumulated during the transaction. This collection therefore contains multiple resource types, which have to be processed separately.

Parameters:

records -

profileRecs -

tagRecs -

securityRecs -

Throws:

FHIRPersistenceException

fetchResourcePayloads

public ResourcePayload fetchResourcePayloads(Class<? extends Resource> resourceType,
                                             Instant fromLastModified,
                                             Instant toLastModified,
                                             Function<ResourcePayload,Boolean> processor)
                                      throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Special function for high speed export of resource payloads. The process function must process the InputStream before returning. Result processing will be stopped if the process function returns Boolean FALSE.

Specified by:

fetchResourcePayloads in interface FHIRPersistence

Parameters:

resourceType - the resource type which is the target of the search

fromLastModified - start reading from this timestamp

toLastModified - do not read beyond this timestamp

processor - function to process each payload record

Returns:

the last ResourcePayload processed, or null if no data was found

Throws:

FHIRPersistenceException

changes

public List<ResourceChangeLogRecord> changes(int resourceCount,
                                             Instant fromLastModified,
                                             Long afterResourceId,
                                             String resourceTypeName)
                                      throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Fetch up to resourceCount records from the RESOURCE_CHANGE_LOG table

Specified by:

changes in interface FHIRPersistence

Parameters:

resourceCount - the max number of resource change records to fetch

fromLastModified - filter records with record.lastUpdate >= fromLastModified. Optional.

afterResourceId - filter records with record.resourceId > afterResourceId. Optional.

resourceTypeName - filter records with record.resourceType = resourceTypeName. Optional.

Returns:

a list containing up to resourceCount elements describing resources which have changed

Throws:

FHIRPersistenceException

erase

public ResourceEraseRecord erase(EraseDTO eraseDto)
                          throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Erases part or a whole of a resource in the data layer

Specified by:

erase in interface FHIRPersistence

Parameters:

eraseDto - the details of the user input

Returns:

a record indicating the success or partial success of the erase

Throws:

FHIRPersistenceException

retrieveIndex

public List<Long> retrieveIndex(int count,
                                Instant notModifiedAfter,
                                Long afterIndexId,
                                String resourceTypeName)
                         throws FHIRPersistenceException

Description copied from interface: FHIRPersistence

Retrieves a list of index IDs available for reindexing.

Specified by:

retrieveIndex in interface FHIRPersistence

Parameters:

count - the maximum nuber of index IDs to retrieve

notModifiedAfter - only retrieve index IDs for resources not last updated after the specified timestamp

afterIndexId - retrieve index IDs starting after this specified index ID, or null to start with first index ID

resourceTypeName - the resource type of index IDs to return, or null

Returns:

list of index IDs available for reindexing

Throws:

FHIRPersistenceException