edu.emory.cci.aiw.i2b2etl.dsb

Class I2B2DataSourceBackendForPhenotype

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.I2B2DataSourceBackendForPhenotype

All Implemented Interfaces:

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

public final class I2B2DataSourceBackendForPhenotype
extends org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend

Author:

Andrew Post, Nita Deshpande

Field Summary

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

username

Constructor Summary

Constructors

Constructor and Description
I2B2DataSourceBackendForPhenotype()

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)
String	getDiagnosisCodesRootFullName()
org.protempa.proposition.value.GranularityFactory	getGranularityFactory()
String	getIcd10DiagnosisCodesRootFullName()
String	getIcd10ProcedureCodesRootFullName()
String	getIcd9ProcedureCodesRootFullName()
String	getKeyType()
String	getLabsRootFullName()
String	getMedicationOrdersRootFullName()
Long	getResultInstanceId()
org.protempa.KeySetSpec[]	getSelectedKeySetSpecs()
org.protempa.proposition.value.UnitFactory	getUnitFactory()
String	getVitalsRootFullName()
void	initialize(org.protempa.backend.BackendInstanceSpec config)
protected org.protempa.backend.dsb.relationaldb.EntitySpec[]	primitiveParameterSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey)
void	setDiagnosisCodesRootFullName(String diagnosisCodesRootFullName)
void	setIcd10DiagnosisCodesRootFullName(String icd10DiagnosisCodesRootFullName)
void	setIcd10ProcedureCodesRootFullName(String icd10ProcedureCodesRootFullName)
void	setIcd9ProcedureCodesRootFullName(String icd9ProcedureCodesRootFullName)
void	setLabsRootFullName(String labsRootFullName)
void	setMedicationOrdersRootFullName(String medicationOrdersRootFullName)
void	setResultInstanceId(Long resultInstanceId)
void	setVitalsRootFullName(String vitalsRootFullName)

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

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

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

I2B2DataSourceBackendForPhenotype

public I2B2DataSourceBackendForPhenotype()

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

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

setLabsRootFullName

public void setLabsRootFullName(String labsRootFullName)

getLabsRootFullName

public String getLabsRootFullName()

getVitalsRootFullName

public String getVitalsRootFullName()

setVitalsRootFullName

public void setVitalsRootFullName(String vitalsRootFullName)

getDiagnosisCodesRootFullName

public String getDiagnosisCodesRootFullName()

setDiagnosisCodesRootFullName

public void setDiagnosisCodesRootFullName(String diagnosisCodesRootFullName)

getMedicationOrdersRootFullName

public String getMedicationOrdersRootFullName()

setMedicationOrdersRootFullName

public void setMedicationOrdersRootFullName(String medicationOrdersRootFullName)

getIcd9ProcedureCodesRootFullName

public String getIcd9ProcedureCodesRootFullName()

setIcd9ProcedureCodesRootFullName

public void setIcd9ProcedureCodesRootFullName(String icd9ProcedureCodesRootFullName)

getIcd10DiagnosisCodesRootFullName

public String getIcd10DiagnosisCodesRootFullName()

setIcd10DiagnosisCodesRootFullName

public void setIcd10DiagnosisCodesRootFullName(String icd10DiagnosisCodesRootFullName)

getIcd10ProcedureCodesRootFullName

public String getIcd10ProcedureCodesRootFullName()

setIcd10ProcedureCodesRootFullName

public void setIcd10ProcedureCodesRootFullName(String icd10ProcedureCodesRootFullName)