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

Class ResourceDAOImpl

java.lang.Object

com.ibm.fhir.persistence.jdbc.dao.impl.FHIRDbDAOImpl

com.ibm.fhir.persistence.jdbc.dao.impl.ResourceDAOImpl

All Implemented Interfaces:

FHIRDbDAO, ResourceDAO

Direct Known Subclasses:

DerbyResourceDAO, EraseResourceDAO, PostgresResourceDAO, PostgresResourceNoProcDAO, ReindexResourceDAO

public class ResourceDAOImpl
extends FHIRDbDAOImpl
implements ResourceDAO

This Data Access Object implements the ResourceDAO interface for creating, updating, and retrieving rows in the IBM FHIR Server resource tables.

Field Summary

Fields

Modifier and Type	Field	Description
static String	DEFAULT_VALUE_REINDEX_TSTAMP
static int	IDX_DATA
static int	IDX_IS_DELETED
static int	IDX_LAST_UPDATED
static int	IDX_LOGICAL_ID
static int	IDX_LOGICAL_RESOURCE_ID
static int	IDX_RESOURCE_ID
static int	IDX_VERSION_ID

Constructor Summary

Constructors

Constructor	Description
ResourceDAOImpl(Connection c, String schemaName, FHIRDbFlavor flavor, FHIRPersistenceJDBCCache cache, IResourceReferenceDAO rrd)	Constructs a DAO instance for use outside a managed transaction (JEE) environment
ResourceDAOImpl(Connection c, String schemaName, FHIRDbFlavor flavor, TransactionSynchronizationRegistry trxSynchRegistry, FHIRPersistenceJDBCCache cache, IResourceReferenceDAO rrd, ParameterTransactionDataImpl ptdi)	Constructs a DAO instance suitable for acquiring connections from a JDBC Datasource object.

Method Summary

Modifier and Type	Method	Description
protected void	addResourceTypeCacheCandidate(String resourceType, Integer resourceTypeId)	Adds a resource type/ resource id pair to a candidate collection for population into the ResourceTypesCache.
protected boolean	checkIfNoneMatch(Integer ifNoneMatch, int currentVersionId)	Test for If-None-Match conditional create-on-update behavior.
protected Resource	createDTO(ResultSet resultSet)	Creates and returns a Resource DTO based on the contents of the passed ResultSet
protected void	deleteFromParameterTable(Connection conn, String tableName, long logicalResourceId)	Delete all parameters for the given resourceId from the named parameter value table
protected FHIRPersistenceJDBCCache	getCache()	Getter for access to the FHIRPersistenceJDBCCache from subclasses
protected IResourceReferenceDAO	getResourceReferenceDAO()	Getter for the IResourceReferenceDAO used by this ResourceDAO implementation
protected Integer	getResourceTypeIdFromCaches(String resourceType)	Get the value of the database id for the given resourceType from the cache.
protected String	getSearchByIdsSql(String resourceType)
protected ParameterTransactionDataImpl	getTransactionData()	Get the ParameterTransactionDataImpl held by this.
List<Resource>	history(String resourceType, String logicalId, Timestamp fromDateTime, int offset, int maxResults)	Reads and returns all versions of the Resource with the passed logicalId, ordered by descending version id.
int	historyCount(String resourceType, String logicalId, Timestamp fromDateTime)	Reads and returns the COUNT of all versions of the Resource with the passed logicalId.
Resource	insert(Resource resource, List<ExtractedParameterValue> parameters, String parameterHashB64, ParameterDAO parameterDao, Integer ifNoneMatch)	Inserts the passed Resource DTO and its associated search parameters to the appropriate FHIR resource tables.
Resource	read(String logicalId, String resourceType)	Reads and returns the latest version of the Resource with the passed logical id and resource type.
Map<String,Integer>	readAllResourceTypeNames()	Reads all rows in the resource_types table and returns the data as a Map
Integer	readResourceTypeId(String resourceType)	Reads the id associated with the name of the passed Resource type from the Resource_Types table.
List<Resource>	search(Select select)	Executes the search contained in the passed Select, using its encapsulated search string and bind variables.
List<Resource>	search(String sqlSelect)	Executes the passed fully-formed SQL Select statement and returns the results If no matching resources are found, an empty collection is returned.
List<Resource>	searchByIds(String resourceType, List<Long> resourceIds)	Searches for Resources that contain one of the passed ids.
int	searchCount(Select countQuery)	Executes a count query based on the data contained in the passed Select statement, using its encapsulated search string and bind variables.
int	searchCount(String sqlSelectCount)	Executes the passed fully-formed SQL Select COUNT statement and returns the integer count.
List<Long>	searchForIds(Select dataQuery)	This method supports the execution of a specialized query designed to return Resource ids, based on the contents of the passed select statement.
Map<Integer,List<Long>>	searchWholeSystem(Select wholeSystemQuery)	Executes the whole-system filter search contained in the passed Select, using its encapsulated search string and bind variables.
protected void	setInt(PreparedStatement ps, int index, Integer value)	Set an int parameter in the statement, handling null as required
void	setPersistenceContext(FHIRPersistenceContext context)	Sets the current persistence context
Resource	versionRead(String logicalId, String resourceType, int versionId)	Reads and returns the version of the Resource with the passed logical id, resource type, and version id.

Methods inherited from class com.ibm.fhir.persistence.jdbc.dao.impl.FHIRDbDAOImpl

buildExceptionWithIssue, buildFHIRPersistenceDBConnectException, cleanup, cleanup, createDTOs, getConnection, getFlavor, getSchemaName, getTranslator, isDb2Database, runCountQuery, runCountQuery, runQuery, runQuery, runQuery_STR_VALUES, severe, severe

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.jdbc.dao.api.FHIRDbDAO

getConnection, getFlavor, isDb2Database

Field Detail

DEFAULT_VALUE_REINDEX_TSTAMP

public static final String DEFAULT_VALUE_REINDEX_TSTAMP

See Also:

Constant Field Values

IDX_RESOURCE_ID

public static final int IDX_RESOURCE_ID

See Also:

Constant Field Values

IDX_LOGICAL_RESOURCE_ID

public static final int IDX_LOGICAL_RESOURCE_ID

See Also:

Constant Field Values

IDX_VERSION_ID

public static final int IDX_VERSION_ID

See Also:

Constant Field Values

IDX_LAST_UPDATED

public static final int IDX_LAST_UPDATED

See Also:

Constant Field Values

IDX_IS_DELETED

public static final int IDX_IS_DELETED

See Also:

Constant Field Values

IDX_DATA

public static final int IDX_DATA

See Also:

Constant Field Values

IDX_LOGICAL_ID

public static final int IDX_LOGICAL_ID

See Also:

Constant Field Values

Constructor Detail

ResourceDAOImpl

public ResourceDAOImpl(Connection c,
                       String schemaName,
                       FHIRDbFlavor flavor,
                       TransactionSynchronizationRegistry trxSynchRegistry,
                       FHIRPersistenceJDBCCache cache,
                       IResourceReferenceDAO rrd,
                       ParameterTransactionDataImpl ptdi)

Constructs a DAO instance suitable for acquiring connections from a JDBC Datasource object.

Parameters:

c -

schemaName -

flavor -

trxSyncRegistry -

ResourceDAOImpl

public ResourceDAOImpl(Connection c,
                       String schemaName,
                       FHIRDbFlavor flavor,
                       FHIRPersistenceJDBCCache cache,
                       IResourceReferenceDAO rrd)

Constructs a DAO instance for use outside a managed transaction (JEE) environment

Parameters:

c -

schemaName -

flavor -

Method Detail

getResourceReferenceDAO

protected IResourceReferenceDAO getResourceReferenceDAO()

Getter for the IResourceReferenceDAO used by this ResourceDAO implementation

Returns:

getTransactionData

protected ParameterTransactionDataImpl getTransactionData()

Get the ParameterTransactionDataImpl held by this.

Returns:

the transactionData object. Can be null.

read

public Resource read(String logicalId,
                     String resourceType)
              throws FHIRPersistenceDataAccessException,
                     FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Reads and returns the latest version of the Resource with the passed logical id and resource type. If no matching resource is found, null is returned.

Specified by:

read in interface ResourceDAO

Returns:

Resource - The most recent version of the Resource with the passed logical id and resource type, or null if not found.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

versionRead

public Resource versionRead(String logicalId,
                            String resourceType,
                            int versionId)
                     throws FHIRPersistenceDataAccessException,
                            FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Reads and returns the version of the Resource with the passed logical id, resource type, and version id. If no matching resource is found, null is returned.

Specified by:

versionRead in interface ResourceDAO

Returns:

Resource - The version of the Resource with the passed logical id, resource type, and version id or null if not found.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

createDTO

protected Resource createDTO(ResultSet resultSet)
                      throws FHIRPersistenceDataAccessException

Creates and returns a Resource DTO based on the contents of the passed ResultSet

Overrides:

createDTO in class FHIRDbDAOImpl

Parameters:

resultSet - A ResultSet containing FHIR persistent object data.

Returns:

Resource - A Resource DTO

Throws:

FHIRPersistenceDataAccessException

history

public List<Resource> history(String resourceType,
                              String logicalId,
                              Timestamp fromDateTime,
                              int offset,
                              int maxResults)
                       throws FHIRPersistenceDataAccessException,
                              FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Reads and returns all versions of the Resource with the passed logicalId, ordered by descending version id. If non-null, the passed fromDateTime is used to limit the returned Resource versions to those that were updated after the fromDateTime.

Specified by:

history in interface ResourceDAO

Parameters:

resourceType - - The name of a FHIR Resource type

logicalId - - The logical id of a FHIR Resource

fromDateTime - - The starting date/time of the version history.

Returns:

List - An ordered list of Resource versions.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

historyCount

public int historyCount(String resourceType,
                        String logicalId,
                        Timestamp fromDateTime)
                 throws FHIRPersistenceDataAccessException,
                        FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Reads and returns the COUNT of all versions of the Resource with the passed logicalId. If non-null, the passed fromDateTime is used to limit the count of Resource versions to those that were updated after the fromDateTime.

Specified by:

historyCount in interface ResourceDAO

Parameters:

resourceType - - The name of a FHIR Resource type

logicalId - - The logical id of a FHIR Resource

fromDateTime - - The starting date/time of the version history.

Returns:

int - The count of Resource versions.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

setPersistenceContext

public void setPersistenceContext(FHIRPersistenceContext context)

Description copied from interface: ResourceDAO

Sets the current persistence context

Specified by:

setPersistenceContext in interface ResourceDAO

readAllResourceTypeNames

public Map<String,Integer> readAllResourceTypeNames()
                                                   throws FHIRPersistenceDBConnectException,
                                                          FHIRPersistenceDataAccessException

Description copied from interface: ResourceDAO

Reads all rows in the resource_types table and returns the data as a Map

Specified by:

readAllResourceTypeNames in interface ResourceDAO

Returns:

Map - A map containing key=parameter-name, value=parameter-name-id

Throws:

FHIRPersistenceDBConnectException

FHIRPersistenceDataAccessException

readResourceTypeId

public Integer readResourceTypeId(String resourceType)
                           throws FHIRPersistenceDBConnectException,
                                  FHIRPersistenceDataAccessException

Description copied from interface: ResourceDAO

Reads the id associated with the name of the passed Resource type from the Resource_Types table. If the id for the passed name is not present in the database, an id is generated, persisted, and returned.

Specified by:

readResourceTypeId in interface ResourceDAO

Returns:

Integer - the id associated with the name of the passed Resource type.

Throws:

FHIRPersistenceDBConnectException

FHIRPersistenceDataAccessException

addResourceTypeCacheCandidate

protected void addResourceTypeCacheCandidate(String resourceType,
                                             Integer resourceTypeId)
                                      throws FHIRPersistenceException

Adds a resource type/ resource id pair to a candidate collection for population into the ResourceTypesCache. This pair must be present as a row in the FHIR DB RESOURCE_TYPES table.

Parameters:

resourceType - A valid FHIR resource type.

resourceTypeId - The corresponding id for the resource type.

Throws:

FHIRPersistenceException

getResourceTypeIdFromCaches

protected Integer getResourceTypeIdFromCaches(String resourceType)

Get the value of the database id for the given resourceType from the cache. Expects that the cache has already been primed with this resource type. The cache is made up of two maps: one shared, the other private to this transaction. Ids in the latter are promoted to the shared map when the current transaction is committed.

Parameters:

resourceType -

Returns:

checkIfNoneMatch

protected boolean checkIfNoneMatch(Integer ifNoneMatch,
                                   int currentVersionId)

Test for If-None-Match conditional create-on-update behavior. The If-None-Match header value is encoded by the REST layer (minimizes propagation of user input) using the following rules

   If-None-Match: null then ifNoneMatch = null
   If-None-Match: * then ifNoneMatch = 0
 

Other values such as W/"1" are intentionally unsupported because their behavior may be unintuitive, especially around deleted resources.

Parameters:

ifNoneMatch - the encoded If-None-Match header value

currentVersionId - the current version of the resource to compare with

Returns:

insert

public Resource insert(Resource resource,
                       List<ExtractedParameterValue> parameters,
                       String parameterHashB64,
                       ParameterDAO parameterDao,
                       Integer ifNoneMatch)
                throws FHIRPersistenceException

Description copied from interface: ResourceDAO

Inserts the passed Resource DTO and its associated search parameters to the appropriate FHIR resource tables. After insert, the generated primary key is acquired and set in the Resource object.

Specified by:

insert in interface ResourceDAO

Parameters:

resource - A Resource Data Transfer Object

parameters - A collection of search parameters to be persisted along with the passed Resource

parameterHashB64 - Base64 encoded SHA-256 hash of parameters

parameterDao - The Parameter DAO

ifNoneMatch - 0 for conditional create-on-update behavior; otherwise null

Returns:

Resource The Resource DTO

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

FHIRPersistenceVersionIdMismatchException

FHIRPersistenceException

search

public List<Resource> search(String sqlSelect)
                      throws FHIRPersistenceDataAccessException,
                             FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Executes the passed fully-formed SQL Select statement and returns the results If no matching resources are found, an empty collection is returned.

Specified by:

search in interface ResourceDAO

Parameters:

sqlSelect - - A fully formed SQL select statement.

Returns:

List - A List of Resources that satisfy the passed SQL query string.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

searchByIds

public List<Resource> searchByIds(String resourceType,
                                  List<Long> resourceIds)
                           throws FHIRPersistenceDataAccessException,
                                  FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Searches for Resources that contain one of the passed ids.

Specified by:

searchByIds in interface ResourceDAO

Parameters:

resourceType - - The type of the FHIR Resource

resourceIds - - A List of resource ids.

Returns:

List - A List of resources matching the the passed list of ids.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

getSearchByIdsSql

protected String getSearchByIdsSql(String resourceType)

searchCount

public int searchCount(String sqlSelectCount)
                throws FHIRPersistenceDataAccessException,
                       FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Executes the passed fully-formed SQL Select COUNT statement and returns the integer count.

Specified by:

searchCount in interface ResourceDAO

Returns:

int - The count of resources that fulfill the passed SQL select statement.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

getCache

protected FHIRPersistenceJDBCCache getCache()

Getter for access to the FHIRPersistenceJDBCCache from subclasses

Returns:

searchCount

public int searchCount(Select countQuery)
                throws FHIRPersistenceDataAccessException,
                       FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Executes a count query based on the data contained in the passed Select statement, using its encapsulated search string and bind variables.

Specified by:

searchCount in interface ResourceDAO

Parameters:

countQuery - - Contains a search string and (optionally) bind variables.

Returns:

int A count of FHIR Resources satisfying the passed search.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

search

public List<Resource> search(Select select)
                      throws FHIRPersistenceDataAccessException,
                             FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Executes the search contained in the passed Select, using its encapsulated search string and bind variables.

Specified by:

search in interface ResourceDAO

Parameters:

select - - Contains a search query and (optionally) bind variables.

Returns:

List A list of FHIR Resources satisfying the passed search.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

searchForIds

public List<Long> searchForIds(Select dataQuery)
                        throws FHIRPersistenceDataAccessException,
                               FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

This method supports the execution of a specialized query designed to return Resource ids, based on the contents of the passed select statement. Note that the first column to be selected MUST be the Resource.id column.

Specified by:

searchForIds in interface ResourceDAO

Returns:

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

deleteFromParameterTable

protected void deleteFromParameterTable(Connection conn,
                                        String tableName,
                                        long logicalResourceId)
                                 throws SQLException

Delete all parameters for the given resourceId from the named parameter value table

Parameters:

conn -

tableName -

logicalResourceId -

Throws:

SQLException

searchWholeSystem

public Map<Integer,List<Long>> searchWholeSystem(Select wholeSystemQuery)
                                                throws FHIRPersistenceDataAccessException,
                                                       FHIRPersistenceDBConnectException

Description copied from interface: ResourceDAO

Executes the whole-system filter search contained in the passed Select, using its encapsulated search string and bind variables.

Specified by:

searchWholeSystem in interface ResourceDAO

Parameters:

wholeSystemQuery - - Contains a search query and (optionally) bind variables.

Returns:

Map> A map of FHIR resource type ID to list of logical resource IDs satisfying the passed search.

Throws:

FHIRPersistenceDataAccessException

FHIRPersistenceDBConnectException

setInt

protected void setInt(PreparedStatement ps,
                      int index,
                      Integer value)
               throws SQLException

Set an int parameter in the statement, handling null as required

Parameters:

ps -

index -

value -

Throws:

SQLException