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java.lang.Objectorg.LexGrid.LexBIG.Impl.Extensions.AbstractExtendable
org.LexGrid.LexBIG.Impl.loaders.BaseLoader
org.LexGrid.LexBIG.Impl.loaders.MetaDataLoaderImpl
public class MetaDataLoaderImpl
Class to load OBO files.
Nested Class Summary |
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Nested classes/interfaces inherited from class org.LexGrid.LexBIG.Impl.loaders.BaseLoader |
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BaseLoader.DoConversion |
Field Summary |
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Fields inherited from class org.LexGrid.LexBIG.Impl.loaders.BaseLoader |
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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.MetaData_Loader |
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description, name |
Constructor Summary | |
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MetaDataLoaderImpl()
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Method Summary | |
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protected ExtensionDescription |
buildExtensionDescription()
Builds the extension description. |
protected OptionHolder |
declareAllowedOptions(OptionHolder holder)
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protected URNVersionPair[] |
doLoad()
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void |
loadAuxiliaryData(java.util.Map<java.lang.Object,java.lang.Object> source,
AbsoluteCodingSchemeVersionReference codingSchemeVersion,
boolean overwrite,
boolean stopOnErrors,
boolean async)
Load auxiliary (non-LexGrid) metadata from the given map into a searchable metadata index within the LexBIG system. |
void |
loadAuxiliaryData(java.net.URI source,
AbsoluteCodingSchemeVersionReference codingSchemeVersion,
boolean overwrite,
boolean stopOnErrors,
boolean async)
Load auxiliary (non-LexGrid) metadata from the specified XML file into a searchable metadata index within the LexBIG system. |
void |
loadLexGridManifest(CodingSchemeManifest source,
AbsoluteCodingSchemeVersionReference codingSchemeURNVersion,
boolean stopOnErrors,
boolean async)
Loads metadata specified by the given manifest to a previously loaded coding scheme in the LexBIG repository. |
void |
loadLexGridManifest(java.net.URI source,
AbsoluteCodingSchemeVersionReference codingSchemeURNVersion,
boolean stopOnErrors,
boolean async)
Loads metadata specified by the given manifest to a previously loaded coding scheme in the LexBIG repository. |
void |
validateAuxiliaryData(java.net.URI source,
AbsoluteCodingSchemeVersionReference codingSchemeVersion,
int validationLevel)
Validate content for a candidate resource without performing a load. |
void |
validateLexGridManifest(java.net.URI source,
AbsoluteCodingSchemeVersionReference codingSchemeVersion,
int validationLevel)
Validate content for a candidate resource without performing a load. |
Methods inherited from class org.LexGrid.LexBIG.Impl.Extensions.AbstractExtendable |
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getExtensionDescription |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface org.LexGrid.LexBIG.Extensions.Load.Loader |
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clearLog, getCodingSchemeManifest, getCodingSchemeManifestURI, getCodingSchemeReferences, getLoaderPreferences, getLog, getOntologyFormat, getOptions, getStatus, load, setCodingSchemeManifest, setCodingSchemeManifestURI, setLoaderPreferences, setLoaderPreferences |
Methods inherited from interface org.LexGrid.LexBIG.Extensions.Extendable |
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getDescription, getName, getProvider, getVersion |
Constructor Detail |
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public MetaDataLoaderImpl()
Method Detail |
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protected ExtensionDescription buildExtensionDescription()
AbstractExtendable
buildExtensionDescription
in class AbstractExtendable
public void validateAuxiliaryData(java.net.URI source, AbsoluteCodingSchemeVersionReference codingSchemeVersion, int validationLevel) throws LBParameterException
MetaData_Loader
validateAuxiliaryData
in interface MetaData_Loader
source
- URI of the XML-based auxiliary metadata file to check.codingSchemeVersion
- The target coding scheme name and version.validationLevel
- Supported levels of validation include:
0 = Verify the XML is well formed.
LBParameterException
public void loadAuxiliaryData(java.net.URI source, AbsoluteCodingSchemeVersionReference codingSchemeVersion, boolean overwrite, boolean stopOnErrors, boolean async) throws LBParameterException, LBInvocationException
MetaData_Loader
loadAuxiliaryData
in interface MetaData_Loader
source
- URI of the XML file containing custom metadata.codingSchemeVersion
- The target coding scheme name and version.overwrite
- If true, existing metadata for the scheme will be erased.
If false, new metadata will be appended to existing metadata.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
public void loadAuxiliaryData(java.util.Map<java.lang.Object,java.lang.Object> source, AbsoluteCodingSchemeVersionReference codingSchemeVersion, boolean overwrite, boolean stopOnErrors, boolean async) throws LBException
MetaData_Loader
loadAuxiliaryData
in interface MetaData_Loader
source
- Map defining custom metadata. All keys and values are
evaluated as strings when inserted to the index.codingSchemeVersion
- The target coding scheme name and version.overwrite
- If true, existing metadata for the scheme will be erased.
If false, new metadata will be appended to existing metadata.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.
LBException
- If resources cannot be accessed or another load operation is
already in progress.public void loadLexGridManifest(CodingSchemeManifest source, AbsoluteCodingSchemeVersionReference codingSchemeURNVersion, boolean stopOnErrors, boolean async) throws LBException
MetaData_Loader
loadLexGridManifest
in interface MetaData_Loader
source
- The manifest to apply.codingSchemeURNVersion
- The target coding scheme name and version.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.
LBException
- If resources cannot be accessed or another load operation is
already in progress.public void loadLexGridManifest(java.net.URI source, AbsoluteCodingSchemeVersionReference codingSchemeURNVersion, boolean stopOnErrors, boolean async) throws LBException
MetaData_Loader
loadLexGridManifest
in interface MetaData_Loader
source
- URI of the xml file containing the manifest definition.codingSchemeURNVersion
- The target coding scheme name and version.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.
LBException
- If resources cannot be accessed or another load operation is
already in progress.public void validateLexGridManifest(java.net.URI source, AbsoluteCodingSchemeVersionReference codingSchemeVersion, int validationLevel) throws LBException
MetaData_Loader
validateLexGridManifest
in interface MetaData_Loader
source
- URI of the XML-based manifest file to check.codingSchemeVersion
- The target coding scheme name and version.validationLevel
- Supported levels of validation include:
0 = Verify the XML is well formed.
1 = Verify the XML is valid in context of the
LexGrid Manifest Schema.
LBException
protected OptionHolder declareAllowedOptions(OptionHolder holder)
declareAllowedOptions
in class BaseLoader
protected URNVersionPair[] doLoad() throws CodingSchemeAlreadyLoadedException
doLoad
in class BaseLoader
CodingSchemeAlreadyLoadedException
|
Copyright: (c) 2004-2006 Mayo Foundation for Medical Education and Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the triple-shield Mayo logo are trademarks and service marks of MFMER. | ||||||||
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