public class OBOLoaderImpl extends BaseLoader implements OBO_Loader
BaseLoader.DoConversion
ASYNC_OPTION, FAIL_ON_ERROR_OPTION, inUse, LOADER_POST_PROCESSOR_OPTION, LOADER_PREFERENCE_FILE_OPTION, MANIFEST_FILE_OPTION, SUPPLEMENT_OPTION
description, name
Constructor and Description |
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OBOLoaderImpl() |
Modifier and Type | Method and Description |
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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.
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addBooleanOptionValue, baseLoad, buildRootNode, clearLog, constructVersionPairsFromCodingSchemes, createCachingMessageDirectorIF, createDefaultInserter, createDefaultInserter, doesOptionExist, doIndex, doPostProcessing, doRegister, 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
getExtensionDescription
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
clearLog, getCodingSchemeManifest, getCodingSchemeManifestURI, getCodingSchemeReferences, getLoaderPreferences, getLog, getOptions, getStatus, load, setCodingSchemeManifest, setCodingSchemeManifestURI, setLoaderPreferences, setLoaderPreferences
getDescription, getName, getProvider, getVersion
public java.lang.String getOBOVersion()
getOBOVersion
in interface OBO_Loader
protected ExtensionDescription buildExtensionDescription()
AbstractExtendable
buildExtensionDescription
in class AbstractExtendable
public void validate(java.net.URI uri, java.net.URI metaSource, int validationLevel) throws LBParameterException
OBO_Loader
validate
in interface OBO_Loader
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.LBParameterException
public void load(java.net.URI uri, java.net.URI metaSource, boolean stopOnErrors, boolean async) throws LBParameterException, LBInvocationException
OBO_Loader
load
in interface OBO_Loader
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.LBParameterException
LBInvocationException
protected OptionHolder declareAllowedOptions(OptionHolder holder)
declareAllowedOptions
in class BaseLoader
protected URNVersionPair[] doLoad() throws java.lang.Exception
doLoad
in class BaseLoader
java.lang.Exception
public OntologyFormat getOntologyFormat()
Loader
getOntologyFormat
in interface Loader
getOntologyFormat
in class BaseLoader
public void finalize() throws java.lang.Throwable
finalize
in class java.lang.Object
java.lang.Throwable