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

Method Summary

Modifier and Type	Method	Description
protected Action	buildActionChain()	Build a chain of actions we want to apply to new connections.
protected List<Resource>	buildSortedFhirResources(ResourceDAO resourceDao, FHIRPersistenceContext context, Class<? extends Resource> resourceType, List<Long> sortedIdList, List<String> elements)	This method takes the passed list of sorted Resource ids, acquires the Resource corresponding to each id, and returns those Resources in a List, sorted according to the input sorted ids.
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.
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	isTransactional()	Returns true iff the persistence layer implementation supports transactions.
<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.
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> 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

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()
                        throws Exception

Constructor for use when running as web application in WLP.

Throws:

Exception

FHIRPersistenceJDBCImpl

public FHIRPersistenceJDBCImpl(Properties configProps,
                               IConnectionProvider cp)
                        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)
                        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

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

buildSortedFhirResources

protected List<Resource> buildSortedFhirResources(ResourceDAO resourceDao,
                                                  FHIRPersistenceContext context,
                                                  Class<? extends Resource> resourceType,
                                                  List<Long> sortedIdList,
                                                  List<String> elements)
                                           throws FHIRException,
                                                  FHIRPersistenceException,
                                                  IOException

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

Parameters:

context - - The FHIR persistence context for the current request.

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.

elements - - An optional list of element names to include in the resources. If null, filtering will be skipped.

Returns:

List - A list of Resources 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

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

generateResourceId

public String generateResourceId()

Description copied from interface: FHIRPersistence

Generates a resource ID.

Specified by:

generateResourceId in interface FHIRPersistence

Returns:

resource ID