edu.emory.cci.aiw.cvrg.eureka.etl.dsb

Class EurekaDataSourceBackend

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.cvrg.eureka.etl.dsb.EurekaDataSourceBackend

All Implemented Interfaces:

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

public final class EurekaDataSourceBackend
extends org.protempa.backend.dsb.relationaldb.RelationalDbDataSourceBackend
implements EurekaFileDataSourceBackend

Data source backend for Eureka!.

Author:

Andrew Post

Field Summary

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

username

Constructor Summary

Constructors

Constructor and Description
EurekaDataSourceBackend()

Method Summary

Modifier and Type	Method and Description
void	close()
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	getCptProcedureCodesRootFullName()
String	getDatabaseId()
String	getDiagnosisCodesRootFullName()
String	getFilename()
String	getIcd9ProcedureCodesRootFullName()
String	getKeyType()
String	getKeyTypeDisplayName()
String	getLabsRootFullName()
String	getMedicationOrdersRootFullName()
String	getSampleUrl()
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)
org.protempa.DataStreamingEventIterator<org.protempa.proposition.Proposition>	readPropositions(Set<String> keyIds, Set<String> propIds, org.protempa.backend.dsb.filter.Filter filters, org.protempa.dest.QueryResultsHandler queryResultsHandler)
void	setCptProcedureCodesRootFullName(String cptProcedureCodesRootFullName)
void	setDatabaseId(String databaseId)
void	setDiagnosisCodesRootFullName(String diagnosisCodesRootFullName)
void	setFilename(String filename)
void	setIcd9ProcedureCodesRootFullName(String icd9ProcedureCodesRootFullName)
void	setLabsRootFullName(String labsRootFullName)
void	setMedicationOrdersRootFullName(String medicationOrdersRootFullName)
void	setSampleUrl(String sampleUrl)
void	setVitalsRootFullName(String vitalsRootFullName)
protected org.protempa.backend.dsb.relationaldb.StagingSpec[]	stagedSpecs(String keyIdSchema, String keyIdTable, String keyIdColumn, String keyIdJoinKey)
org.protempa.backend.dsb.DataValidationEvent[]	validateData(org.protempa.KnowledgeSource knowledgeSource)

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

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

getGranularityFactory, getKeyIdComparator, getKeyTypePluralDisplayName, getSourceSystem, getUnitFactory, 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.dsb.DataSourceBackend

deleteAllKeys, getGranularityFactory, getKeyIdComparator, getKeyTypePluralDisplayName, getSelectedKeySetSpecs, getSourceSystem, getUnitFactory, validateConfiguration, writeKeys

Methods inherited from interface org.protempa.backend.Backend

addBackendListener, getConfigurationsId, getDisplayName, getId, removeBackendListener, setEventListeners

Constructor Detail

EurekaDataSourceBackend

public EurekaDataSourceBackend()

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

validateData

public org.protempa.backend.dsb.DataValidationEvent[] validateData(org.protempa.KnowledgeSource knowledgeSource)
                                                            throws org.protempa.backend.DataSourceBackendFailedDataValidationException,
                                                                   org.protempa.KnowledgeSourceReadException

Specified by:

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

Overrides:

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

Throws:

org.protempa.backend.DataSourceBackendFailedDataValidationException

org.protempa.KnowledgeSourceReadException

readPropositions

public org.protempa.DataStreamingEventIterator<org.protempa.proposition.Proposition> readPropositions(Set<String> keyIds,
                                                                                                      Set<String> propIds,
                                                                                                      org.protempa.backend.dsb.filter.Filter filters,
                                                                                                      org.protempa.dest.QueryResultsHandler queryResultsHandler)
                                                                                               throws org.protempa.DataSourceReadException

Specified by:

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

Overrides:

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

Throws:

org.protempa.DataSourceReadException

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

getKeyType

public String getKeyType()

Specified by:

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

Overrides:

getKeyType in class org.protempa.backend.AbstractCommonsDataSourceBackend

getKeyTypeDisplayName

public String getKeyTypeDisplayName()

Specified by:

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

Overrides:

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

getDatabaseId

public String getDatabaseId()

Overrides:

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

setDatabaseId

public void setDatabaseId(String databaseId)

Overrides:

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

setSampleUrl

public void setSampleUrl(String sampleUrl)

getSampleUrl

public String getSampleUrl()

setFilename

public void setFilename(String filename)

Specified by:

setFilename in interface EurekaFileDataSourceBackend

getFilename

public String getFilename()

Specified by:

getFilename in interface EurekaFileDataSourceBackend

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)

getCptProcedureCodesRootFullName

public String getCptProcedureCodesRootFullName()

setCptProcedureCodesRootFullName

public void setCptProcedureCodesRootFullName(String cptProcedureCodesRootFullName)

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

close

public void close()
           throws org.protempa.BackendCloseException

Specified by:

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

Overrides:

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

Throws:

org.protempa.BackendCloseException