org.LexGrid.LexBIG.Impl.loaders
Class OBOLoaderImpl

java.lang.Object
  extended by org.LexGrid.LexBIG.Impl.Extensions.AbstractExtendable
      extended by org.LexGrid.LexBIG.Impl.loaders.BaseLoader
          extended by org.LexGrid.LexBIG.Impl.loaders.OBOLoaderImpl
All Implemented Interfaces:
java.io.Serializable, Extendable, Loader, OBO_Loader, StatusReporter

public class OBOLoaderImpl
extends BaseLoader
implements OBO_Loader

Class to load OBO files.

Version:
subversion $Revision: $ checked in on $Date: $
Author:
Dan Armbrust, Jesse Erdmann
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class org.LexGrid.LexBIG.Impl.loaders.BaseLoader
BaseLoader.DoConversion
 
Field Summary
 
Fields inherited from class org.LexGrid.LexBIG.Impl.loaders.BaseLoader
ASYNC_OPTION, FAIL_ON_ERROR_OPTION, inUse, LOADER_POST_PROCESSOR_OPTION, LOADER_PREFERENCE_FILE_OPTION, MANIFEST_FILE_OPTION, SUPPLEMENT_OPTION
 
Fields inherited from interface org.LexGrid.LexBIG.Extensions.Load.OBO_Loader
description, name
 
Constructor Summary
OBOLoaderImpl()
           
 
Method Summary
protected  ExtensionDescription buildExtensionDescription()
          Builds the extension description.
protected  OptionHolder declareAllowedOptions(OptionHolder holder)
           
protected  URNVersionPair[] doLoad()
           
 void finalize()
           
 java.lang.String getOBOVersion()
           
 OntologyFormat getOntologyFormat()
          Return the ontology format the loader can handle
 void load(java.net.URI uri, java.net.URI metaSource, boolean stopOnErrors, boolean async)
          Load content from a candidate resource.
 void validate(java.net.URI uri, java.net.URI metaSource, int validationLevel)
          Validate content for a candidate resource without performing a load.
 
Methods inherited from class org.LexGrid.LexBIG.Impl.loaders.BaseLoader
addBooleanOptionValue, baseLoad, buildRootNode, clearLog, constructVersionPairsFromCodingSchemes, createCachingMessageDirectorIF, createDefaultInserter, createDefaultInserter, doesOptionExist, doIndex, doPostProcessing, doTransitiveAndIndex, doTransitiveTable, getAbsoluteCodingSchemeVersionReferenceFromOptionString, getCodingSchemeManifest, getCodingSchemeManifestURI, getCodingSchemeReferences, getDescription, getLoaderPreferences, getLog, getLogger, getManifestUtil, getMessageDirector, getName, getOptions, getPostProcessor, getProvider, getResourceUri, getStatus, getStringFromURI, getVersion, isDoApplyPostLoadManifest, isDoComputeTransitiveClosure, isDoIndexing, isDoRegister, isDoRemoveOnFailure, isInUse, load, lock, persistCodingSchemeToDatabase, persistCodingSchemeToDatabase, register, register, setCachingMessageDirectorIF, setCodingSchemeManifest, setCodingSchemeManifestURI, setCodingSchemeReferences, setDoApplyPostLoadManifest, setDoComputeTransitiveClosure, setDoIndexing, setDoRegister, setDoRemoveOnFailure, setInUse, setLoaderPreferences, setLoaderPreferences, setManifestUtil, setOptions, setResourceUri, setStatus, unlock, urnVersionPairToAbsoluteCodingSchemeVersionReference
 
Methods inherited from class org.LexGrid.LexBIG.Impl.Extensions.AbstractExtendable
getExtensionDescription
 
Methods inherited from class java.lang.Object
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 
Methods inherited from interface org.LexGrid.LexBIG.Extensions.Load.Loader
clearLog, getCodingSchemeManifest, getCodingSchemeManifestURI, getCodingSchemeReferences, getLoaderPreferences, getLog, getOptions, getStatus, load, setCodingSchemeManifest, setCodingSchemeManifestURI, setLoaderPreferences, setLoaderPreferences
 
Methods inherited from interface org.LexGrid.LexBIG.Extensions.Extendable
getDescription, getName, getProvider, getVersion
 

Constructor Detail

OBOLoaderImpl

public OBOLoaderImpl()
Method Detail

getOBOVersion

public java.lang.String getOBOVersion()
Specified by:
getOBOVersion in interface OBO_Loader

buildExtensionDescription

protected ExtensionDescription buildExtensionDescription()
Description copied from class: AbstractExtendable
Builds the extension description.

Specified by:
buildExtensionDescription in class AbstractExtendable
Returns:
the extension description

validate

public void validate(java.net.URI uri,
                     java.net.URI metaSource,
                     int validationLevel)
              throws LBParameterException
Description copied from interface: OBO_Loader
Validate content for a candidate resource without performing a load. Returns without exception if validation succeeds.

Specified by:
validate in interface OBO_Loader
Parameters:
uri - URI corresponding to the OBO file.
metaSource - URI corresponding to the OBO metadata XML file. Optional.
validationLevel - Supported levels of validation include: 0 = Verify the source file conforms to the OBO format, and the metadata file conforms to the OBO metadata format.
Throws:
LBParameterException

load

public void load(java.net.URI uri,
                 java.net.URI metaSource,
                 boolean stopOnErrors,
                 boolean async)
          throws LBParameterException,
                 LBInvocationException
Description copied from interface: OBO_Loader
Load content from a candidate resource. This will also result in implicit generation of standard indices required by the LexBIG runtime. An exception is raised if resources cannot be accessed or another load operation is already in progress.

Specified by:
load in interface OBO_Loader
Parameters:
uri - URI corresponding to the OBO file.
metaSource - URI corresponding to the OBO metadata XML file. Optional.
stopOnErrors - True means stop if any load error is detected. False means attempt to load what can be loaded if recoverable errors are encountered.
async - Flag controlling whether load occurs in the calling thread. If true, the load will occur in a separate asynchronous process. If false, this method blocks until the load operation completes or fails. Regardless of setting, the getStatus and getLog calls are used to fetch results.
Throws:
LBParameterException
LBInvocationException

declareAllowedOptions

protected OptionHolder declareAllowedOptions(OptionHolder holder)
Specified by:
declareAllowedOptions in class BaseLoader

doLoad

protected URNVersionPair[] doLoad()
                           throws java.lang.Exception
Specified by:
doLoad in class BaseLoader
Throws:
java.lang.Exception

getOntologyFormat

public OntologyFormat getOntologyFormat()
Description copied from interface: Loader
Return the ontology format the loader can handle

Specified by:
getOntologyFormat in interface Loader
Overrides:
getOntologyFormat in class BaseLoader

finalize

public void finalize()
              throws java.lang.Throwable
Overrides:
finalize in class java.lang.Object
Throws:
java.lang.Throwable

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