org.biopax.paxtools.persistence.level2
Class HiRDBConnect

java.lang.Object
  org.biopax.paxtools.persistence.level2.HiRDBConnect

public class HiRDBConnect
extends java.lang.Object

RDB hibernation connect class

Field Summary

boolean	bPrintTime
boolean	bShowSQL
static java.lang.String	PUNAME_MYSQL
static java.lang.String	PUNAME_POSTGRESQL

Constructor Summary

HiRDBConnect()
contructor

HiRDBConnect(java.lang.String puName, java.lang.String connectionURL, java.lang.String user, java.lang.String password, java.lang.String indexBase)
contructor

Method Summary

boolean	buildDDL(java.lang.String outpuFilePath) build DDL
javax.persistence.EntityManager	createEntityManager()
boolean	deleteOWL(java.lang.String key) delete owl data
boolean	downloadOWL(java.lang.String key, java.io.OutputStream oStream) download owl data
java.lang.Class	getAnalyzer() text analyzer for lucene
java.lang.String	getConnectionURL() connection URL (JDBC path)
BioPAXElement	getElementByRDFID(javax.persistence.EntityManager em, java.lang.String rdfID) get element by rdf:ID
java.lang.String	getIndexBase() index base
java.lang.String	getPassword() database user password
java.lang.String	getPUName() persistence unit name
java.lang.String	getUser() database user
boolean	isSetupOK()
java.util.Set<java.lang.String>	listOWL() list owl data
void	setConnectionURL(java.lang.String value) connection URL (JDBC path)
void	setIndexBase(java.lang.String value) index base
void	setPassword(java.lang.String value) database user password
void	setPUName(java.lang.String value) persistence unit name
boolean	setup() setup before upload / download
void	setUser(java.lang.String value) database user
boolean	uploadOWL(java.lang.String keyName, java.io.InputStream iStream) upload owl data

Methods inherited from class java.lang.Object

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

Field Detail

PUNAME_POSTGRESQL

public static final java.lang.String PUNAME_POSTGRESQL

See Also:

Constant Field Values

PUNAME_MYSQL

public static final java.lang.String PUNAME_MYSQL

See Also:

Constant Field Values

bPrintTime

public boolean bPrintTime

bShowSQL

public boolean bShowSQL

Constructor Detail

HiRDBConnect

public HiRDBConnect()

contructor

HiRDBConnect

public HiRDBConnect(java.lang.String puName,
                    java.lang.String connectionURL,
                    java.lang.String user,
                    java.lang.String password,
                    java.lang.String indexBase)

contructor

Parameters:

puName - persistence unit name. "PaxtoolsForPostgreSQL" / "PaxtoolsForMySQL"

connectionURL - jdbc connection path. e.g. "jdbc:postgresql://localhost/PAXTOOLS"

user - jdbc user

password - jdbc password

indexBase - Lucene index base directory path

Method Detail

getPUName

public java.lang.String getPUName()

persistence unit name

setPUName

public void setPUName(java.lang.String value)

persistence unit name

getConnectionURL

public java.lang.String getConnectionURL()

connection URL (JDBC path)

setConnectionURL

public void setConnectionURL(java.lang.String value)

connection URL (JDBC path)

setUser

public void setUser(java.lang.String value)

database user

getUser

public java.lang.String getUser()

database user

setPassword

public void setPassword(java.lang.String value)

database user password

getPassword

public java.lang.String getPassword()

database user password

setIndexBase

public void setIndexBase(java.lang.String value)

index base

getIndexBase

public java.lang.String getIndexBase()

index base

getAnalyzer

public java.lang.Class getAnalyzer()

text analyzer for lucene

buildDDL

public boolean buildDDL(java.lang.String outpuFilePath)

build DDL

Parameters:

outputFilePath - DDL file path for output

setup

public boolean setup()

setup before upload / download

Returns:

true is OK

isSetupOK

public boolean isSetupOK()

uploadOWL

public boolean uploadOWL(java.lang.String keyName,
                         java.io.InputStream iStream)

upload owl data

Parameters:

keyName - key of OWL data. e.g. ordinary it may be owl file name.

iStream - input stream of owl data.

Returns:

true is OK

listOWL

public java.util.Set<java.lang.String> listOWL()

list owl data

Parameters:

oStream - output stream.

Returns:

true is OK

downloadOWL

public boolean downloadOWL(java.lang.String key,
                           java.io.OutputStream oStream)

download owl data

Parameters:

key - key of OWL data. e.g. ordinary it may be owl file name.

oStream - output stream of owl data.

Returns:

true is OK

deleteOWL

public boolean deleteOWL(java.lang.String key)

delete owl data

Parameters:

key - key of OWL data. e.g. ordinary it may be owl file name.

Returns:

true is OK

createEntityManager

public javax.persistence.EntityManager createEntityManager()

getElementByRDFID

public BioPAXElement getElementByRDFID(javax.persistence.EntityManager em,
                                       java.lang.String rdfID)

get element by rdf:ID

Parameters:

em - entity manager

rdfID - rdf:ID

Returns:

BioPAXElement