org.LexGrid.LexBIG.Impl.loaders
Class OBOLoaderImpl
java.lang.Object
org.LexGrid.LexBIG.Impl.Extensions.AbstractExtendable
org.LexGrid.LexBIG.Impl.loaders.BaseLoader
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
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 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 |
OBOLoaderImpl
public OBOLoaderImpl()
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