Package org.bridgedb.sql

Class SQLIdMapper

java.lang.Object

org.bridgedb.sql.SQLBase

org.bridgedb.sql.SQLListener

org.bridgedb.sql.SQLIdMapper

All Implemented Interfaces:

IDMapper, IDMapperCapabilities, MappingListener

public class SQLIdMapper
extends SQLListener
implements IDMapper, IDMapperCapabilities

Builds on the SQLListener to implement the Standard BridgeDB functions of IDMapper and IDMapperCapabilities. This Allows the OPS version to function as any other BridgeDB implementation

Author:

Christian

Field Summary

Fields

Modifier and Type	Field	Description
protected CodeMapper	codeMapper	Map between IdSysCodePair and Xref or DataSources
protected static int	DEFAULT_LIMIT

Fields inherited from class org.bridgedb.sql.SQLListener

autoIncrement, FULLNAME_LENGTH, ID_COLUMN_NAME, ID_LENGTH, MAPPING_SET_ID_COLUMN_NAME, MAPPING_SET_TABLE_NAME, MAPPING_URI_LENGTH, SOURCE_DATASOURCE_COLUMN_NAME, SQL_COMPAT_VERSION, SYSCODE_LENGTH, TARGET_DATASOURCE_COLUMN_NAME

Fields inherited from class org.bridgedb.sql.SQLBase

possibleOpenConnection, sqlAccess

Constructor Summary

Constructors

Constructor	Description
SQLIdMapper(boolean dropTables, CodeMapper codeMapper)

Method Summary

Modifier and Type	Method	Description
protected void	appendLimitConditions(StringBuilder query, Integer position, Integer limit)	Adds the limit condition if this is the support method for limitng the number of results.
protected void	appendMappingJoinMapping(StringBuilder query)
protected void	appendSourceIdSysCodePair(StringBuilder query, IdSysCodePair ref)	Add a condition to the query that only mappings with a specific source IdSysCodePair should be used.
protected void	appendSourceXref(StringBuilder query, String id, String sysCode)	Add a condition to the query that only mappings with a specific source Xref should be used.
protected void	appendTopConditions(StringBuilder query, Integer position, Integer limit)	Adds the top condition if this is the support method for limitng the number of results.
protected boolean	badXref(Xref ref)	Check if the Xref is invalid in some way.
void	close()
Set<Xref>	freeSearch(String text, int limit)
IDMapperCapabilities	getCapabilities()
Set<String>	getKeys()
String	getProperty(String key)
Set<DataSource>	getSupportedSrcDataSources()
Set<DataSource>	getSupportedTgtDataSources()
protected boolean	IdSysCodePairExists(IdSysCodePair ref)
boolean	isConnected()
boolean	isFreeSearchSupported()
boolean	isMappingSupported(DataSource src, DataSource tgt)
Map<Xref,Set<Xref>>	mapID(Collection<Xref> srcXrefs, DataSource... tgtDataSources)
Set<Xref>	mapID(Xref xref, DataSource tgtDataSource)	Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.
Set<Xref>	mapID(Xref xref, DataSource... tgtDataSources)
protected String	toCode(DataSource tgtDataSource)
protected String[]	toCodes(DataSource[] tgtDataSources)
protected IdSysCodePair	toIdSysCodePair(Xref xref)
protected Set<Xref>	toXrefs(Set<IdSysCodePair> pairs)
boolean	xrefExists(Xref xref)

Methods inherited from class org.bridgedb.sql.SQLListener

closeInput, createMappingSetTable, createSQLTables, dropSQLTables, dropTable, getAutoInc, getDataSourceKey, insertLink, putProperty, registerMappingSet

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

DEFAULT_LIMIT

protected static final int DEFAULT_LIMIT

See Also:

Constant Field Values

codeMapper

protected final CodeMapper codeMapper

Map between IdSysCodePair and Xref or DataSources

Constructor Detail

SQLIdMapper

public SQLIdMapper(boolean dropTables,
                   CodeMapper codeMapper)
            throws BridgeDBException

Throws:

BridgeDBException

Method Detail

mapID

public Map<Xref,Set<Xref>> mapID(Collection<Xref> srcXrefs,
                                       DataSource... tgtDataSources)
                                throws IDMapperException

Specified by:

mapID in interface IDMapper

Throws:

IDMapperException

mapID

public Set<Xref> mapID(Xref xref,
                       DataSource... tgtDataSources)
                throws BridgeDBException

Specified by:

mapID in interface IDMapper

Throws:

BridgeDBException

mapID

public Set<Xref> mapID(Xref xref,
                       DataSource tgtDataSource)
                throws BridgeDBException

Get all cross-references for the given entity, restricting the result to contain only references from the given set of data sources.

Parameters:

xref - the entity to get cross-references for.

tgtDataSource - target ID types/data source. Can not be null

Returns:

A Set containing the cross references, or an empty Set when no cross references could be found. This method does not return null.

Throws:

BridgeDBException - if the mapping service is (temporarily) unavailable

xrefExists

public boolean xrefExists(Xref xref)
                   throws BridgeDBException

Specified by:

xrefExists in interface IDMapper

Throws:

BridgeDBException

IdSysCodePairExists

protected boolean IdSysCodePairExists(IdSysCodePair ref)
                               throws BridgeDBException

Throws:

BridgeDBException

freeSearch

public Set<Xref> freeSearch(String text,
                            int limit)
                     throws BridgeDBException

Specified by:

freeSearch in interface IDMapper

Throws:

BridgeDBException

getCapabilities

public IDMapperCapabilities getCapabilities()

Specified by:

getCapabilities in interface IDMapper

close

public void close()

Specified by:

close in interface IDMapper

isConnected

public boolean isConnected()

Specified by:

isConnected in interface IDMapper

isFreeSearchSupported

public boolean isFreeSearchSupported()

Specified by:

isFreeSearchSupported in interface IDMapperCapabilities

getSupportedSrcDataSources

public Set<DataSource> getSupportedSrcDataSources()
                                           throws BridgeDBException

Specified by:

getSupportedSrcDataSources in interface IDMapperCapabilities

Throws:

BridgeDBException

getSupportedTgtDataSources

public Set<DataSource> getSupportedTgtDataSources()
                                           throws BridgeDBException

Specified by:

getSupportedTgtDataSources in interface IDMapperCapabilities

Throws:

BridgeDBException

isMappingSupported

public boolean isMappingSupported(DataSource src,
                                  DataSource tgt)
                           throws BridgeDBException

Specified by:

isMappingSupported in interface IDMapperCapabilities

Throws:

BridgeDBException

getProperty

public String getProperty(String key)

Specified by:

getProperty in interface IDMapperCapabilities

getKeys

public Set<String> getKeys()

Specified by:

getKeys in interface IDMapperCapabilities

badXref

protected final boolean badXref(Xref ref)

Check if the Xref is invalid in some way.

For example if it is null or if either the Id or DataSource part is null.

Parameters:

ref - - the xref to check

Returns:

if the xref whether or not the xref is valid

appendSourceIdSysCodePair

protected final void appendSourceIdSysCodePair(StringBuilder query,
                                               IdSysCodePair ref)

Add a condition to the query that only mappings with a specific source IdSysCodePair should be used.

Parameters:

query - Query to add to.

ref - IdSysCodePair that forms the base of the condition.

appendSourceXref

protected final void appendSourceXref(StringBuilder query,
                                      String id,
                                      String sysCode)

Add a condition to the query that only mappings with a specific source Xref should be used.

Parameters:

query - Query to add to.

id - - identifier of the Xref

sysCode - - system code of the source database of the Xref

appendLimitConditions

protected void appendLimitConditions(StringBuilder query,
                                     Integer position,
                                     Integer limit)

Adds the limit condition if this is the support method for limitng the number of results.

System such as MYSQL use a Limit clause at the end of the query. Where applicable this is added here.

Parameters:

query - Query to add Limit to

position - The offset of the fragment of results to return

limit - The size of the fragment of results to return

appendTopConditions

protected void appendTopConditions(StringBuilder query,
                                   Integer position,
                                   Integer limit)

Adds the top condition if this is the support method for limitng the number of results.

System such as Virtuosos use a Top clause directly after the select. Where applicable this is added here.

Parameters:

query - Query to add TOP to

position - The offset of the fragment of results to return

limit - The size of the fragment of results to return

appendMappingJoinMapping

protected final void appendMappingJoinMapping(StringBuilder query)

toCodes

protected final String[] toCodes(DataSource[] tgtDataSources)

toIdSysCodePair

protected final IdSysCodePair toIdSysCodePair(Xref xref)
                                       throws BridgeDBException

Throws:

BridgeDBException

toXrefs

protected final Set<Xref> toXrefs(Set<IdSysCodePair> pairs)
                           throws BridgeDBException

Throws:

BridgeDBException

toCode

protected final String toCode(DataSource tgtDataSource)