edu.emory.cci.aiw.i2b2etl.dsb

Class I2B2DataSourceBackend

java.lang.Object

org.protempa.backend.AbstractBackend<org.protempa.backend.DataSourceBackendUpdatedEvent>

org.protempa.backend.dsb.AbstractDataSourceBackend

org.protempa.backend.AbstractCommonsDataSourceBackend

org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

edu.emory.cci.aiw.i2b2etl.dsb.I2B2DataSourceBackend

All Implemented Interfaces:

org.protempa.backend.Backend<org.protempa.backend.DataSourceBackendUpdatedEvent>, org.protempa.backend.dsb.DataSourceBackend

public final class I2B2DataSourceBackend
extends org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

Author:

Andrew Post

Field Summary

Fields inherited from class org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

username

Constructor Summary

Constructors

Constructor and Description
I2B2DataSourceBackend()

Method Summary

Modifier and Type	Method and Description
protected org.protempa.backend.dsb.relationaldb.EntitySpec[]	constantSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey)
protected org.protempa.backend.dsb.relationaldb.EntitySpec[]	eventSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey)
org.protempa.proposition.value.GranularityFactory	getGranularityFactory()
String	getKeyType()
Long	getResultInstanceId()
org.protempa.KeySetSpec[]	getSelectedKeySetSpecs()
org.protempa.proposition.value.UnitFactory	getUnitFactory()
void	initialize(org.protempa.backend.BackendInstanceSpec config)
protected org.protempa.backend.dsb.relationaldb.EntitySpec[]	primitiveParameterSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey)
void	setResultInstanceId(Long resultInstanceId)
protected org.protempa.backend.dsb.relationaldb.StagingSpec[]	stagedSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey)

Methods inherited from class org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

close, deleteAllKeys, getConnectionSpecInstance, getDatabaseAPI, getDatabaseId, getDefaultKeyIdColumn, getDefaultKeyIdJoinKey, getDefaultKeyIdTable, getKeyLoaderKeyIdColumn, getKeyLoaderKeyIdJoinKey, getKeyLoaderKeyIdSchema, getKeyLoaderKeyIdTable, getMappingsFactory, getPassword, getQueryThreadCount, getQueryTimeout, getSchemaName, getUsername, isDryRun, isInKeySetMode, parseDatabaseAPI, parseDryRun, parseMappingsFactory, readPropositions, setDatabaseAPI, setDatabaseId, setDefaultKeyIdColumn, setDefaultKeyIdJoinKey, setDefaultKeyIdTable, setDryRun, setKeyLoaderKeyIdColumn, setKeyLoaderKeyIdJoinKey, setKeyLoaderKeyIdSchema, setKeyLoaderKeyIdTable, setMappingsFactory, setPassword, setQueryThreadCount, setQueryTimeout, setSchemaName, setUsername, validateConfiguration, validateData, writeKeys

Methods inherited from class org.protempa.backend.AbstractCommonsDataSourceBackend

getDataSourceBackendId, getDisplayName, getId, nameForErrors, parseGranularityFactory, parseUnitFactory, setDataSourceBackendId, setId, setKeyType

Methods inherited from class org.protempa.backend.dsb.AbstractDataSourceBackend

getKeyIdComparator, getKeyTypeDisplayName, getKeyTypePluralDisplayName, getSourceSystem, setGranularityFactory, setKeyIdComparator, setUnitFactory

Methods inherited from class org.protempa.backend.AbstractBackend

addBackendListener, fireBackendUpdated, fireEvent, fireUnrecoverableError, getConfigurationsId, removeBackendListener, setEventListeners

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.protempa.backend.Backend

addBackendListener, getConfigurationsId, removeBackendListener, setEventListeners

Constructor Detail

I2B2DataSourceBackend

public I2B2DataSourceBackend()

Method Detail

initialize

public void initialize(org.protempa.backend.BackendInstanceSpec config)
                throws org.protempa.backend.BackendInitializationException

Specified by:

initialize in interface org.protempa.backend.Backend<org.protempa.backend.DataSourceBackendUpdatedEvent>

Overrides:

initialize in class org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

Throws:

org.protempa.backend.BackendInitializationException

constantSpecs

protected org.protempa.backend.dsb.relationaldb.EntitySpec[] constantSpecs(String keyIdSchema,
                                                                           String keyIdTable,
                                                                           String keyIdColumn,
                                                                           String keyIdJoinKey)
                                                                    throws IOException

Specified by:

constantSpecs in class org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

Throws:

IOException

eventSpecs

protected org.protempa.backend.dsb.relationaldb.EntitySpec[] eventSpecs(String keyIdSchema,
                                                                        String keyIdTable,
                                                                        String keyIdColumn,
                                                                        String keyIdJoinKey)
                                                                 throws IOException

Specified by:

eventSpecs in class org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

Throws:

IOException

primitiveParameterSpecs

protected org.protempa.backend.dsb.relationaldb.EntitySpec[] primitiveParameterSpecs(String keyIdSchema,
                                                                                     String keyIdTable,
                                                                                     String keyIdColumn,
                                                                                     String keyIdJoinKey)
                                                                              throws IOException

Specified by:

primitiveParameterSpecs in class org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

Throws:

IOException

stagedSpecs

protected org.protempa.backend.dsb.relationaldb.StagingSpec[] stagedSpecs(String keyIdSchema,
                                                                          String keyIdTable,
                                                                          String keyIdColumn,
                                                                          String keyIdJoinKey)
                                                                   throws IOException

Specified by:

stagedSpecs in class org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

Throws:

IOException

getGranularityFactory

public org.protempa.proposition.value.GranularityFactory getGranularityFactory()

Specified by:

getGranularityFactory in interface org.protempa.backend.dsb.DataSourceBackend

Overrides:

getGranularityFactory in class org.protempa.backend.dsb.AbstractDataSourceBackend

getUnitFactory

public org.protempa.proposition.value.UnitFactory getUnitFactory()

Specified by:

getUnitFactory in interface org.protempa.backend.dsb.DataSourceBackend

Overrides:

getUnitFactory in class org.protempa.backend.dsb.AbstractDataSourceBackend

setResultInstanceId

public void setResultInstanceId(Long resultInstanceId)

getResultInstanceId

public Long getResultInstanceId()

getSelectedKeySetSpecs

public org.protempa.KeySetSpec[] getSelectedKeySetSpecs()
                                                 throws org.protempa.DataSourceReadException

Specified by:

getSelectedKeySetSpecs in interface org.protempa.backend.dsb.DataSourceBackend

Overrides:

getSelectedKeySetSpecs in class org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

Throws:

org.protempa.DataSourceReadException

getKeyType

public String getKeyType()

Specified by:

getKeyType in interface org.protempa.backend.dsb.DataSourceBackend

Overrides:

getKeyType in class org.protempa.backend.AbstractCommonsDataSourceBackend