edu.mayo.informatics.lexgrid.convert.directConversions.mrmap
Class MRMAP2LexGrid

java.lang.Object
  extended by edu.mayo.informatics.lexgrid.convert.directConversions.mrmap.MRMAP2LexGrid

public class MRMAP2LexGrid
extends java.lang.Object

Author:
Scott Bauer

Field Summary
static java.lang.String APROX_ASSOC_NAME
           
static java.lang.String ASSOC_NAME
           
static java.lang.String CODING_SCHEME_NAME
           
static java.lang.String CODING_SCHEME_URI
           
static java.lang.String FROMRSAB
           
static java.lang.String FROMVSAB
           
static boolean ISMAP
           
static java.lang.String MAPSETNAME
           
static java.lang.String MAPSETVERSION
           
static java.lang.String REPRESENTS_VERSION
           
static java.lang.String SOS
           
static java.lang.String TORSAB
           
static java.lang.String TOVSAB
           
static java.lang.String URIPREFIX
           
 
Constructor Summary
MRMAP2LexGrid(LgMessageDirectorIF messages, java.lang.String mrSatPath, java.lang.String mrMapPath)
           
MRMAP2LexGrid(LgMessageDirectorIF messages, java.lang.String mrSatPath, java.lang.String mrMapPath, java.lang.String sourceCodingScheme, java.lang.String sourceVersion, java.lang.String sourceURI, java.lang.String targetCodingScheme, java.lang.String targetVersion, java.lang.String targetURI)
           
MRMAP2LexGrid(LgMessageDirectorIF messages, java.lang.String mrSatPath, java.lang.String mrMapPath, 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)
           
 
Method Summary
protected  AssociationPredicate addTargetToExistingSource(MrMap map, AssociationPredicate predicate, java.lang.String sourceEntityCodeNamespace, java.lang.String targetEntityCodeNamespace)
           
protected  AssociationTarget createAssociationTarget(MrMap map, java.lang.String targetEntityCodeNamespace)
           
protected  CodingScheme createMrMapScheme(Relations rel, java.lang.String codingSchemeName, java.lang.String codingSchemeVersion, java.lang.String codingSchemeURI, java.lang.String sourceSchemeName, java.lang.String sourceSchemeVersion, java.lang.String sourceSchemeURI, java.lang.String targetSchemeName, java.lang.String targetSchemeVersion, java.lang.String targetSchemeURI)
           
protected  AssociationSource createNewAssociationSourceWithTarget(MrMap map, java.lang.String targetEntityCodeNamespace)
           
protected  AssociationData createTargetData(MrMap map)
           
 java.util.List<AssociationQualification> getAssociationQualifiers(MrMap map)
           
 CodingScheme[] loadToRevision()
           
protected  AssociationPredicate processMrMapBean(java.lang.String path, java.lang.String sourceSchemeNamespace, java.lang.String targetSchemeNamespace, java.lang.String currentRelation)
           
protected  MrMap processMrMapRow(java.lang.String[] mapRow)
           
 CodingScheme[] processMrMapToLexGrid()
           
protected  java.util.HashMap<java.lang.String,Relations> processMrSatBean(java.lang.String sPath, java.lang.String mPath)
           
protected  MrSat processMrSatRow(java.lang.String[] mapRow, int lineCount)
           
protected  void processMrSatToRelation(MrSat metaData, Relations relation)
           
protected  java.util.HashMap<java.lang.String,Relations> processRelationsContainers(java.lang.String mapPath)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

ASSOC_NAME

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

APROX_ASSOC_NAME

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

ISMAP

public static final boolean ISMAP
See Also:
Constant Field Values

URIPREFIX

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

TORSAB

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

TOVSAB

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

FROMRSAB

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

FROMVSAB

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

MAPSETVERSION

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

SOS

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

MAPSETNAME

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

CODING_SCHEME_NAME

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

CODING_SCHEME_URI

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

REPRESENTS_VERSION

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

MRMAP2LexGrid

public MRMAP2LexGrid(LgMessageDirectorIF messages,
                     java.lang.String mrSatPath,
                     java.lang.String mrMapPath)

MRMAP2LexGrid

public MRMAP2LexGrid(LgMessageDirectorIF messages,
                     java.lang.String mrSatPath,
                     java.lang.String mrMapPath,
                     java.lang.String sourceCodingScheme,
                     java.lang.String sourceVersion,
                     java.lang.String sourceURI,
                     java.lang.String targetCodingScheme,
                     java.lang.String targetVersion,
                     java.lang.String targetURI)

MRMAP2LexGrid

public MRMAP2LexGrid(LgMessageDirectorIF messages,
                     java.lang.String mrSatPath,
                     java.lang.String mrMapPath,
                     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)
Method Detail

loadToRevision

public CodingScheme[] loadToRevision()
                              throws LBRevisionException
Throws:
LBRevisionException

processMrMapToLexGrid

public CodingScheme[] processMrMapToLexGrid()

processMrSatBean

protected java.util.HashMap<java.lang.String,Relations> processMrSatBean(java.lang.String sPath,
                                                                         java.lang.String mPath)
                                                                  throws java.lang.SecurityException,
                                                                         java.lang.IllegalArgumentException,
                                                                         java.lang.NoSuchFieldException,
                                                                         java.lang.IllegalAccessException,
                                                                         java.io.FileNotFoundException
Throws:
java.lang.SecurityException
java.lang.IllegalArgumentException
java.lang.NoSuchFieldException
java.lang.IllegalAccessException
java.io.FileNotFoundException

processMrSatToRelation

protected void processMrSatToRelation(MrSat metaData,
                                      Relations relation)

processMrMapBean

protected AssociationPredicate processMrMapBean(java.lang.String path,
                                                java.lang.String sourceSchemeNamespace,
                                                java.lang.String targetSchemeNamespace,
                                                java.lang.String currentRelation)
                                         throws java.lang.Exception
Throws:
java.lang.Exception

processRelationsContainers

protected java.util.HashMap<java.lang.String,Relations> processRelationsContainers(java.lang.String mapPath)
                                                                            throws java.io.IOException
Throws:
java.io.IOException

createNewAssociationSourceWithTarget

protected AssociationSource createNewAssociationSourceWithTarget(MrMap map,
                                                                 java.lang.String targetEntityCodeNamespace)
                                                          throws LBParameterException,
                                                                 java.lang.IndexOutOfBoundsException,
                                                                 java.lang.IllegalArgumentException,
                                                                 java.lang.IllegalAccessException,
                                                                 java.lang.ClassNotFoundException
Throws:
LBParameterException
java.lang.IndexOutOfBoundsException
java.lang.IllegalArgumentException
java.lang.IllegalAccessException
java.lang.ClassNotFoundException

createAssociationTarget

protected AssociationTarget createAssociationTarget(MrMap map,
                                                    java.lang.String targetEntityCodeNamespace)
                                             throws LBParameterException,
                                                    java.lang.IllegalArgumentException,
                                                    java.lang.IllegalAccessException,
                                                    java.lang.ClassNotFoundException
Throws:
LBParameterException
java.lang.IllegalArgumentException
java.lang.IllegalAccessException
java.lang.ClassNotFoundException

createTargetData

protected AssociationData createTargetData(MrMap map)

getAssociationQualifiers

public java.util.List<AssociationQualification> getAssociationQualifiers(MrMap map)
                                                                  throws java.lang.IllegalArgumentException,
                                                                         java.lang.IllegalAccessException,
                                                                         java.lang.ClassNotFoundException
Throws:
java.lang.IllegalArgumentException
java.lang.IllegalAccessException
java.lang.ClassNotFoundException

addTargetToExistingSource

protected AssociationPredicate addTargetToExistingSource(MrMap map,
                                                         AssociationPredicate predicate,
                                                         java.lang.String sourceEntityCodeNamespace,
                                                         java.lang.String targetEntityCodeNamespace)
                                                  throws java.lang.IndexOutOfBoundsException,
                                                         LBParameterException,
                                                         java.lang.IllegalArgumentException,
                                                         java.lang.IllegalAccessException,
                                                         java.lang.ClassNotFoundException
Throws:
java.lang.IndexOutOfBoundsException
LBParameterException
java.lang.IllegalArgumentException
java.lang.IllegalAccessException
java.lang.ClassNotFoundException

createMrMapScheme

protected CodingScheme createMrMapScheme(Relations rel,
                                         java.lang.String codingSchemeName,
                                         java.lang.String codingSchemeVersion,
                                         java.lang.String codingSchemeURI,
                                         java.lang.String sourceSchemeName,
                                         java.lang.String sourceSchemeVersion,
                                         java.lang.String sourceSchemeURI,
                                         java.lang.String targetSchemeName,
                                         java.lang.String targetSchemeVersion,
                                         java.lang.String targetSchemeURI)

processMrMapRow

protected MrMap processMrMapRow(java.lang.String[] mapRow)
                         throws java.lang.SecurityException,
                                java.lang.NoSuchFieldException,
                                java.lang.IllegalArgumentException,
                                java.lang.IllegalAccessException
Throws:
java.lang.SecurityException
java.lang.NoSuchFieldException
java.lang.IllegalArgumentException
java.lang.IllegalAccessException

processMrSatRow

protected MrSat processMrSatRow(java.lang.String[] mapRow,
                                int lineCount)
                         throws java.lang.SecurityException,
                                java.lang.NoSuchFieldException,
                                java.lang.IllegalArgumentException,
                                java.lang.IllegalAccessException
Throws:
java.lang.SecurityException
java.lang.NoSuchFieldException
java.lang.IllegalArgumentException
java.lang.IllegalAccessException

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.