Package org.bridgedb.sql

Class SQLListener

java.lang.Object

org.bridgedb.sql.SQLBase

org.bridgedb.sql.SQLListener

All Implemented Interfaces:

MappingListener

Direct Known Subclasses:

SQLIdMapper

public class SQLListener
extends SQLBase
implements MappingListener

This is the root class of the SQL stack. It handles the creation of all the tables and handles all inserts, except those only required for URL and UriSpaces See CreateSQLTables method for an explanation of the tables.

Author:

Christian

Field Summary

Fields

Modifier and Type	Field	Description
protected String	autoIncrement
protected static int	FULLNAME_LENGTH
static String	ID_COLUMN_NAME
protected static int	ID_LENGTH
static String	MAPPING_SET_ID_COLUMN_NAME
static String	MAPPING_SET_TABLE_NAME
protected static int	MAPPING_URI_LENGTH
protected static String	SOURCE_DATASOURCE_COLUMN_NAME
static int	SQL_COMPAT_VERSION
protected static int	SYSCODE_LENGTH
protected static String	TARGET_DATASOURCE_COLUMN_NAME

Fields inherited from class org.bridgedb.sql.SQLBase

possibleOpenConnection, sqlAccess

Constructor Summary

Constructors

Constructor	Description
SQLListener(boolean dropTables)

Method Summary

Modifier and Type	Method	Description
void	closeInput()	Closes the input, flushing any links into storage.
protected void	createMappingSetTable()
protected void	createSQLTables()	Excecutes several SQL statements to create the tables and indexes in the database.
protected void	dropSQLTables()	Excecutes several SQL statements to drop the tables
protected void	dropTable(String name)	Drops a single table if it exists.
protected int	getAutoInc()
protected String	getDataSourceKey(DataSource dataSource)
void	insertLink(String sourceId, String targetId, int mappingSet, boolean symetric)	Inserts a mapping into the system.
void	putProperty(String key, String value)
int	registerMappingSet(DataSource source, DataSource target, boolean symetric)	Loads all the meta data for a Mapping Set.

Methods inherited from class org.bridgedb.sql.SQLBase

close, closeConnection, commitTransaction, createPreparedStatement, createStatement, insertEscpaeCharacters, rollbackTransaction, startTransaction

Methods inherited from class java.lang.Object

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

Field Detail

SQL_COMPAT_VERSION

public static final int SQL_COMPAT_VERSION

See Also:

Constant Field Values

SYSCODE_LENGTH

protected static final int SYSCODE_LENGTH

See Also:

Constant Field Values

FULLNAME_LENGTH

protected static final int FULLNAME_LENGTH

See Also:

Constant Field Values

ID_LENGTH

protected static final int ID_LENGTH

See Also:

Constant Field Values

MAPPING_URI_LENGTH

protected static final int MAPPING_URI_LENGTH

See Also:

Constant Field Values

MAPPING_SET_TABLE_NAME

public static final String MAPPING_SET_TABLE_NAME

See Also:

Constant Field Values

ID_COLUMN_NAME

public static final String ID_COLUMN_NAME

See Also:

Constant Field Values

MAPPING_SET_ID_COLUMN_NAME

public static final String MAPPING_SET_ID_COLUMN_NAME

See Also:

Constant Field Values

SOURCE_DATASOURCE_COLUMN_NAME

protected static final String SOURCE_DATASOURCE_COLUMN_NAME

See Also:

Constant Field Values

TARGET_DATASOURCE_COLUMN_NAME

protected static final String TARGET_DATASOURCE_COLUMN_NAME

See Also:

Constant Field Values

autoIncrement

protected final String autoIncrement

Constructor Detail

SQLListener

public SQLListener(boolean dropTables)
            throws BridgeDBException

Throws:

BridgeDBException

Method Detail

registerMappingSet

public int registerMappingSet(DataSource source,
                              DataSource target,
                              boolean symetric)
                       throws BridgeDBException

Description copied from interface: MappingListener

Loads all the meta data for a Mapping Set.

Specified by:

registerMappingSet in interface MappingListener

Parameters:

source - The SysCode of DataSource part of the source xref/url

target - The SysCode of DataSource part of the target xref/url

symetric - Flag to say if mapping should be loaded one way of both ways. Creates two mapping sets this one and the inverse with one number higher.

Returns:

Id of the forward mappingSet.

Throws:

BridgeDBException - - if something goes wrong Always thrown by the URI based version as it requires extra parameters to register a mapping Set.

getDataSourceKey

protected final String getDataSourceKey(DataSource dataSource)

getAutoInc

protected final int getAutoInc()
                        throws BridgeDBException

Throws:

BridgeDBException

closeInput

public void closeInput()
                throws BridgeDBException

Description copied from interface: MappingListener

Closes the input, flushing any links into storage.

May also update any cashed counts ext.

This method and URLListener method are intended to be duplicates of each other.

Specified by:

closeInput in interface MappingListener

Throws:

BridgeDBException - - if something goes wrong

insertLink

public void insertLink(String sourceId,
                       String targetId,
                       int mappingSet,
                       boolean symetric)
                throws BridgeDBException

Description copied from interface: MappingListener

Inserts a mapping into the system.

Implementatins may buffer the inserts, so closeInput must be called after the last insert or inserts may be lost.

No checking can be done that the DataSource part of the Xrefs match the declaration.

For speed, the implemented methods is also not required to check that the MappingsSet exists nor that the mapping Set's semantic setting matches that in the insert call.

Specified by:

insertLink in interface MappingListener

Parameters:

sourceId - ID of the source xref

targetId - ID of the target xref

mappingSet - The ID of the mapping set to be inserted into.

symetric - If true the inverse mapping will be inserted into the mapping set one number higher.

Throws:

BridgeDBException - - if something goes wrong

dropSQLTables

protected void dropSQLTables()
                      throws BridgeDBException

Excecutes several SQL statements to drop the tables

Throws:

BridgeDBException - - if something goes wrong

dropTable

protected void dropTable(String name)
                  throws BridgeDBException

Drops a single table if it exists.

Virtuosos appears not to have the if exists syntax so errors are assumed to be table not found.

Parameters:

name - - name of the table

Throws:

BridgeDBException - - if something goes wrong

createSQLTables

protected void createSQLTables()
                        throws BridgeDBException

Excecutes several SQL statements to create the tables and indexes in the database.

Table "info" is a control table used by all database version of BridgeDB, inlcuing none OPS ones. If verifies that database is called with the code that matches the schema version.

Table DataSource holds the org.bridgedb.DataSource registry between deployments of the service. The whole table is loaded into the DataSource.class regisrty in the constructor.

Throws:

BridgeDBException - - if something goes wrong

See Also:

Table "mapping" holds the Id part of the mapping. (The DataSource part is handled by MappingSet) The "id" field is purely for provenace tracking. Ie getting a particular mapping based on its Id. Mappings are only looked up in one direction, so ids are specically source and target. "mappingSetId" is a foreign key to the "mappingSet" table. Table "mappingSet" holds the DataSource part of each Mapping. Specifically it holds the SysCodes for which org.bridgedb.DataSource objects can be looked up. The Ops version will also map SysCodes to UriSpace(s). "predicate" is purely for provenace. (but could be used for Ops Profiles) "isTransitive" is a flag set at the time of loading to identify mappinSet generated using transativity of other sets. Currently only used by OPS to draw a different line in the graphviz but could be used by lenses. "mappingCount" is a precomputed value @see countLinks() method. Table "properties" underpins bridgeDB properties methods. "isPublic" field dettermines if the key will be returned by the getKeys() method.

createMappingSetTable

protected void createMappingSetTable()
                              throws BridgeDBException

Throws:

BridgeDBException

putProperty

public void putProperty(String key,
                        String value)
                 throws BridgeDBException

Throws:

BridgeDBException