org.LexGrid.LexBIG.Impl.loaders
Class MrmapRRFLoader

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.MrmapRRFLoader
All Implemented Interfaces:
java.io.Serializable, Extendable, Loader, MrMap_Loader, StatusReporter

public class MrmapRRFLoader
extends BaseLoader
implements MrMap_Loader

Loader class for MrMap and MrSat RRF files resulting in a mapping coding scheme or schemes depending on the content of these files.

Author:
Scott Bauer
See Also:
Serialized Form

Nested Class Summary
 
Nested classes/interfaces inherited from class org.LexGrid.LexBIG.Impl.loaders.BaseLoader
BaseLoader.DoConversion
 
Field Summary
static java.lang.String MANIFEST_URI
           
static java.lang.String MRSAT_URI
           
static java.lang.String VALIDATE
           
 
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.MrMap_Loader
description, name
 
Constructor Summary
MrmapRRFLoader()
           
 
Method Summary
protected  ExtensionDescription buildExtensionDescription()
          Builds the extension description.
protected  OptionHolder declareAllowedOptions(OptionHolder holder)
           
protected  URNVersionPair[] doLoad()
           
 OntologyFormat getOntologyFormat()
          Return the ontology format the loader can handle
 void load(java.net.URI mrMapsource, java.net.URI mrSatSource, java.lang.String nameForMappingScheme, java.lang.String nameForMappingVersion, java.lang.String nameforMappingURI, boolean stopOnErrors, boolean async)
           
 void load(java.net.URI mrMapsource, java.net.URI mrSatSource, java.lang.String nameForMappingScheme, java.lang.String nameForMappingVersion, java.lang.String nameforMappingURI, java.lang.String sourceScheme, java.lang.String sourceVersion, java.lang.String sourceURI, java.lang.String targetScheme, java.lang.String targetVersion, java.lang.String targetURI, boolean stopOnErrors, boolean async)
          User designated target Scheme URI.
static void main(java.lang.String[] args)
           
 void validate(java.lang.String source, 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, finalize, 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
 

Field Detail

VALIDATE

public static final java.lang.String VALIDATE
See Also:
Constant Field Values

MRSAT_URI

public static final java.lang.String MRSAT_URI
See Also:
Constant Field Values

MANIFEST_URI

public static final java.lang.String MANIFEST_URI
See Also:
Constant Field Values
Constructor Detail

MrmapRRFLoader

public MrmapRRFLoader()
Method Detail

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

buildExtensionDescription

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

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

main

public static void main(java.lang.String[] args)
Parameters:
args -

load

public void load(java.net.URI mrMapsource,
                 java.net.URI mrSatSource,
                 java.lang.String nameForMappingScheme,
                 java.lang.String nameForMappingVersion,
                 java.lang.String nameforMappingURI,
                 boolean stopOnErrors,
                 boolean async)
          throws LBException
Throws:
LBException

load

public void load(java.net.URI mrMapsource,
                 java.net.URI mrSatSource,
                 java.lang.String nameForMappingScheme,
                 java.lang.String nameForMappingVersion,
                 java.lang.String nameforMappingURI,
                 java.lang.String sourceScheme,
                 java.lang.String sourceVersion,
                 java.lang.String sourceURI,
                 java.lang.String targetScheme,
                 java.lang.String targetVersion,
                 java.lang.String targetURI,
                 boolean stopOnErrors,
                 boolean async)
          throws LBException
Description copied from interface: MrMap_Loader
User designated target Scheme URI. Non-resolving default used if null. 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 MrMap_Loader
Parameters:
mrMapsource - String representation of the path to corresponding to the RRF file.
mrSatSource - String representation of the path to corresponding to the RRF file.
nameForMappingScheme - User designated Mapping Scheme identifier. Default used if null.
nameForMappingVersion - User designated Mapping Scheme Version. Default used if null.
nameforMappingURI - User designated Mapping Scheme URI. Non-resolving default used if null.
sourceScheme - User designated source scheme identifier which can a local scheme to to which mappings resolve. Non resolving default created if null.
sourceVersion - User designated source scheme Version. Default used if null. Dependent on valid user defined source scheme identifier
sourceURI - User designated source scheme URI. Non-resolving default used if null.
targetScheme - User designated target scheme identifier which can a local scheme to to which mappings resolve. Non resolving default created if null. Dependent on valid user defined source scheme identifier.
targetVersion - User designated target scheme Version. Default used if null.
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:
LBException

validate

public void validate(java.lang.String source,
                     int validationLevel)
              throws LBException
Description copied from interface: MrMap_Loader
Validate content for a candidate resource without performing a load. Returns without exception if validation succeeds.

Specified by:
validate in interface MrMap_Loader
Parameters:
source - URI corresponding to the XML file.
validationLevel - Supported levels of validation include: 0 = Verify XML is well formed. 1 = Verify XML is valid.
Throws:
LBException

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

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.