phenote.dataadapter
Class OntologyDataAdapter2

java.lang.Object
  phenote.dataadapter.OntologyDataAdapter2

public class OntologyDataAdapter2
extends java.lang.Object

is this really a data adapter? - OntologyLoader? this isnt a data adapter it doesnt load & commit character data - just loads ontologies. rename OntologyLoader for now can stay in dataadapter package this is specifically a OboFileLoader - other kinds of ontology loading may com along i'm working on refactoring this to work with the new terminology definitions

Method Summary

boolean	checkForLocalFileExists(phenote.config.xml.OntologyFileDocument.OntologyFile ontology)
boolean	checkForLocalFileExists(java.lang.String filename)
boolean	checkForUpdate(phenote.config.xml.OntologyFileDocument.OntologyFile ontologyFile)
boolean	copyOntologyToDotPhenote(java.net.URL localUrl, java.lang.String filename)
void	downloadUpdate(java.lang.String ontology)
static OntologyDataAdapter2	getInstance() synchronized so cant reload an ontology while ontologies are being initialized getInstance calls initOntologies - in other words you have to call getInstance to initialize the ontologies
java.net.URL	getLocalFile(java.lang.String handle)
long	getOboDate(java.net.URL oboUrl)
static void	initialize() just calls getInstance - but more intuitive for initialization
void	initOntologies()
void	initOntologies(boolean updateAll)
void	reloadOntologies() The ontology has been determined to be out of date (by quartz) and thus directed to reload itself from its file - in other words there is a new obo file to load in place of old one
static void	reset()

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static OntologyDataAdapter2 getInstance()

synchronized so cant reload an ontology while ontologies are being initialized getInstance calls initOntologies - in other words you have to call getInstance to initialize the ontologies

reset

public static void reset()

initialize

public static void initialize()

just calls getInstance - but more intuitive for initialization

initOntologies

public void initOntologies()

initOntologies

public void initOntologies(boolean updateAll)

getOboDate

public long getOboDate(java.net.URL oboUrl)
                throws OntologyException

Throws:

OntologyException

reloadOntologies

public void reloadOntologies()
                      throws OntologyException

The ontology has been determined to be out of date (by quartz) and thus directed to reload itself from its file - in other words there is a new obo file to load in place of old one

Throws:

OntologyException

checkForUpdate

public boolean checkForUpdate(phenote.config.xml.OntologyFileDocument.OntologyFile ontologyFile)
                       throws OntologyException

Returns:

A flag indicating if the given ontology has an update available

Throws:

OntologyException

downloadUpdate

public void downloadUpdate(java.lang.String ontology)
                    throws OntologyException

Throws:

OntologyException

getLocalFile

public java.net.URL getLocalFile(java.lang.String handle)
                          throws OntologyException

Throws:

OntologyException

checkForLocalFileExists

public boolean checkForLocalFileExists(phenote.config.xml.OntologyFileDocument.OntologyFile ontology)

checkForLocalFileExists

public boolean checkForLocalFileExists(java.lang.String filename)

copyOntologyToDotPhenote

public boolean copyOntologyToDotPhenote(java.net.URL localUrl,
                                        java.lang.String filename)