edu.mayo.informatics.lexgrid.convert.directConversions
Class UMLSToSQL

java.lang.Object
  extended by edu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon.UMLSBaseCode
      extended by edu.mayo.informatics.lexgrid.convert.directConversions.UMLSToSQL

public class UMLSToSQL
extends UMLSBaseCode

A tool to load the LexGrid SQL table from UMLS.

Version:
subversion $Revision: 9147 $ checked in on $Date: 2008-07-11 21:20:31 +0000 (Fri, 11 Jul 2008) $
Author:
Dan Armbrust, Jesse Erdmann, Thomas Johnson, Kevin Peterson, Deepak Sharma

Nested Class Summary
 
Nested classes/interfaces inherited from class edu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon.UMLSBaseCode
UMLSBaseCode.Association, UMLSBaseCode.AssociationQualification, UMLSBaseCode.AssociationSorter, UMLSBaseCode.CodeHolder, UMLSBaseCode.ConceptPresentation, UMLSBaseCode.ConceptPresentationSorter, UMLSBaseCode.SABString
 
Field Summary
 
Fields inherited from class edu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon.UMLSBaseCode
associationQualifierRUI_, auiToCodeCache_, batchSize, defaultLanguage_, entryStateId_, getAllAssocQualifiersFromRRF_, getAssocInstance_, getAssocQualifier_, getAssocQualifierFromRRF_, getAUIFromPresentation_, getCodeForCUI_, getCodeForCUINoAUI_, getPresentationRank_, getPropIds_, getSource_, getUMLSRoot_, insertIntoAssociations, insertIntoCodingScheme, insertIntoCodingSchemeMultiAttributes, insertIntoCodingSchemeSupportedAttributes, insertIntoConceptsMultiAttributes, insertIntoEntities, insertIntoEntityAssociationsToEntity, insertIntoEntityAssociationsToEntityQualifier, insertIntoEntityProperty, insertIntoEntityPropertyLinks, insertIntoEntityPropertyMultiAttributes, insertIntoEntityType, insertIntoEntryState, insertIntoRelations, isoMap, loadedAssociations_, loadPrefs_, log, manifestLocation_, manifestNameChange_, messages_, mrconsoRepresentationalMap_, MRRANK_, sabToCodeSystem_, schemeToHierNames_, sqlConnection_, sqlModifier_, sqlTableUtility_, stc_, supportedAssociationQualifiers_, supportedAssociations_, supportedCodingSchemes_, supportedHierarchies_, supportedLanguages_, supportedPropertyLinks_, supportedPropertyQualifiers_, supportedPropertyTypes_, supportedSources_, umlsConnection_, umlsConnection2_, umlsSqlModifier_
 
Constructor Summary
UMLSToSQL(java.lang.String sqlServer, java.lang.String sqlDriver, java.lang.String sqlUserName, java.lang.String sqlPassword, java.lang.String sqlTablePrefix, java.lang.String umlsServer, java.lang.String umlsDriver, java.lang.String umlsUserName, java.lang.String umlsPassword, java.lang.String codingScheme, LoaderPreferences loadPrefs, java.net.URI manifestLocation, boolean enforceIntegrity, LgMessageDirectorIF director)
          Class to convert from UMLS to SQL.
 
Method Summary
protected  void buildRootNodes(java.lang.String codingSchemeName)
          Build navigable relations from special endpoint nodes '@' and '@@' to first level nodes in hierarchical associations.
 java.lang.String getLoadedCodingSchemeName()
           
 
Methods inherited from class edu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon.UMLSBaseCode
addAssociationToAssociations, addConceptToConcepts, addConceptToConceptsMultiAttributes, addConceptToEntityPropertyMultiAttributes, addEntityAssociationQualifierToEntityAssociation, addEntityAssociationToEntity, addEntityType, addEntryState, addRelationToRelations, addToCodingScheme, addToEntityProperty, buildRootNode, closeConnections, closeLoadStatements, generateUniqueKey, generateUniqueKey, get5DigitRandom, getCodingSchemeNameFromManifest, getExpandedForm, getHierAssocNames, getHierRelas, getHierRels, getIsoMap, getISOString, getRegisteredNameFromManifest, getRelaNames, getRelationInverseName, getRelationSABs, getSHA1, getSourceVersionString, initIsoMap, initLoadStatements, initMRCONSOTTYMAP, insertIntoCodingSchemeSupportedAttributes, insertIntoConceptPropertyLinks, isHierarchicalAssociation, isHierarchicalName, isLoaded, isLoaded, loadContext, loadDefaultSupportedNamespace, loadLoaderPreferences, loadMRRANK, loadSupportedAssociationQualifiers, loadSupportedLanguages, loadSupportedProperties, loadSupportedPropertyLinks, loadSupportedPropertyQualifiers, loadSupportedSources, makeConnections, mapCodeSystemNameToSAB, mapCUIToCode, mapCUIToCodeWithAUI, mapRela, mapSABToCodeSystemName, mapSupportedAssociationsHelper, mapVSABtoRSAB, markLoaded, markLoaded, qualifyConceptPresentation, toCommaDelimitedWithQuotes, updateApproxNumberOfConcepts
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

UMLSToSQL

public UMLSToSQL(java.lang.String sqlServer,
                 java.lang.String sqlDriver,
                 java.lang.String sqlUserName,
                 java.lang.String sqlPassword,
                 java.lang.String sqlTablePrefix,
                 java.lang.String umlsServer,
                 java.lang.String umlsDriver,
                 java.lang.String umlsUserName,
                 java.lang.String umlsPassword,
                 java.lang.String codingScheme,
                 LoaderPreferences loadPrefs,
                 java.net.URI manifestLocation,
                 boolean enforceIntegrity,
                 LgMessageDirectorIF director)
          throws java.lang.Exception
Class to convert from UMLS to SQL.

Parameters:
sqlServer - location of SQL server
sqlDriver - SQL driver class
sqlUserName - username for server authentication
sqlPassword - password for server authentication
sqlTablePrefix - table prefix to use for generated files
umlsServer - location of UMLS server
umlsDriver - UMLS driver class
umlsUserName - username for server authentication
umlsPassword - password for server authentication
codingScheme - CodingScheme to be converted
loadPrefs - Loader Preferences
manifestLocation - location of Manifest file
enforceIntegrity - enforce foreign key constraints on tables
director - message director for log output
Throws:
java.lang.Exception
Method Detail

getLoadedCodingSchemeName

public java.lang.String getLoadedCodingSchemeName()

buildRootNodes

protected void buildRootNodes(java.lang.String codingSchemeName)
                       throws java.sql.SQLException
Build navigable relations from special endpoint nodes '@' and '@@' to first level nodes in hierarchical associations.

Parameters:
codingSchemeName - The LexGrid code system name.
Throws:
java.sql.SQLException

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