edu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon
Class UMLSBaseCode

java.lang.Object
  extended by edu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon.UMLSBaseCode
Direct Known Subclasses:
MetaThesaurusToSQL, UMLSToSQL

Deprecated.

@Deprecated
public class UMLSBaseCode
extends java.lang.Object

Common Code for RRF/UMLS based loaders. Here are the table use details for the UMLS converter Used tables: MRCONSO.RRF MRREL.RRF MRSAB.RRF MRDEF.RRF MRSTY.RRF MRSAT.RRF MRDOC.RRF MRRANK.RRF MRHIER.RRF Conditionally referenced: MRHIER.RRF (for contextual links) Unused tables: AMBIGLUI.RRF AMBIGSUI.RRF MRAUI.RRF MRCOC.RRF MRCOLS.RRF MRCUI.RRF MRCXT.RRF MRFILES.RRF MRHIST.RRF MRMAP.RRF MRSMAP.RRF MRXNS_ENG.RRF MRXNW_ENG.RRF MRXW_BAQ.RRF MRXW_CZE.RRF MRXW_DAN.RRF MRXW_DUT.RRF MRXW_ENG.RRF MRXW_FIN.RRF MRXW_FRE.RRF MRXW_GER.RRF MRXW_HEB.RRF MRXW_HUN.RRF MRXW_ITA.RRF MRXW_JPN.RRF MRXW_NOR.RRF MRXW_POR.RRF MRXW_RUS.RRF MRXW_SPA.RRF MRXW_SWE.RRF There are a couple of unused tables that I probably should be using - but I'm just not loading that info yet - such as the history. I'm not sure about the map tables - I'll need to look into them more at some future point. Here is the breakdown for the NCI MetaThesaurus: Used tables: MRCONSO.RRF MRREL.RRF MRSAB.RRF MRDEF.RRF MRSTY.RRF MRRANK.RRF Unused tables: MRCOC.RRF MRCOLS.RRF MRDOC.RRF MRFILES.RRF Here, I think that the only one that I'm not using that I maybe should be is the MRCOC file - I'll have to look at this again at some point. Differences/issues I can remember (though there may have been more): While loading from the UMLS: For most terminologies, I could get the Language from the LAT column in the MRCONSO file. In Snomed, I had to do a query on the MRSAT table and pull the language out of the ATV column. In the UMLS - when we load things, we are loading based on terminology concept codes, not CUI's - so to get the preferred text for a code in a terminology (per language) required reading all presentations for a code from a terminology, and then doing a sort taking into account 4 different columns, each with various values that mean preferred in different terminologies In the NCI MetaThesaurus, since we are loading it using the CUI's as the concept codes, I can just use the IsPref column to determine the preferred text. I think that all of the other differences in the UMLS loader versus the NCI MetaThesaurus loader are due to loading based on CUI's instead of concept codes.

Version:
subversion $Revision: 9636 $ checked in on $Date: 2008-08-20 16:32:48 +0000 (Wed, 20 Aug 2008) $
Author:
Dan Armbrust, Jesse Erdmann, Thomas Johnson, Kevin Peterson, Deepak Sharma, Sridhar Dwarkanath

Nested Class Summary
 class UMLSBaseCode.Association
          Deprecated.  
 class UMLSBaseCode.AssociationQualification
          Deprecated.  
 class UMLSBaseCode.AssociationSorter
          Deprecated.  
 class UMLSBaseCode.CodeHolder
          Deprecated.  
 class UMLSBaseCode.ConceptPresentation
          Deprecated.  
 class UMLSBaseCode.ConceptPresentationSorter
          Deprecated.  
 class UMLSBaseCode.SABString
          Deprecated. Inner class defining a string optionally qualified by SAB and providing corresponding equality methods, etc, to support use and comparison in various collections.
 
Field Summary
protected  java.util.HashSet associationQualifierRUI_
          Deprecated.  
protected  org.apache.commons.collections.map.LRUMap auiToCodeCache_
          Deprecated.  
protected  int batchSize
          Deprecated.  
protected  java.lang.String defaultLanguage_
          Deprecated.  
protected static int entryStateId_
          Deprecated.  
protected  java.sql.PreparedStatement getAllAssocQualifiersFromRRF_
          Deprecated.  
protected  java.sql.PreparedStatement getAssocInstance_
          Deprecated.  
protected  java.sql.PreparedStatement getAssocQualifier_
          Deprecated.  
protected  java.sql.PreparedStatement getAssocQualifierFromRRF_
          Deprecated.  
protected  java.sql.PreparedStatement getAUIFromPresentation_
          Deprecated.  
protected  java.sql.PreparedStatement getCodeForCUI_
          Deprecated.  
protected  java.sql.PreparedStatement getCodeForCUINoAUI_
          Deprecated.  
protected  java.sql.PreparedStatement getPresentationRank_
          Deprecated.  
protected  java.sql.PreparedStatement getPropIds_
          Deprecated.  
protected  java.sql.PreparedStatement getSource_
          Deprecated.  
protected  java.sql.PreparedStatement getUMLSRoot_
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoAssociations
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoCodingScheme
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoCodingSchemeMultiAttributes
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoCodingSchemeSupportedAttributes
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoConceptsMultiAttributes
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoEntities
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoEntityAssociationsToEntity
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoEntityAssociationsToEntityQualifier
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoEntityProperty
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoEntityPropertyLinks
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoEntityPropertyMultiAttributes
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoEntityType
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoEntryState
          Deprecated.  
protected  java.sql.PreparedStatement insertIntoRelations
          Deprecated.  
protected  java.util.Hashtable isoMap
          Deprecated.  
protected  java.util.HashSet loadedAssociations_
          Deprecated.  
protected  LoaderPreferences loadPrefs_
          Deprecated.  
protected static org.apache.log4j.Logger log
          Deprecated.  
protected  java.net.URI manifestLocation_
          Deprecated.  
 boolean manifestNameChange_
          Deprecated.  
protected  LgMessageDirectorIF messages_
          Deprecated.  
protected  java.util.Hashtable mrconsoRepresentationalMap_
          Deprecated.  
protected  java.util.HashMap MRRANK_
          Deprecated.  
protected  java.util.Hashtable sabToCodeSystem_
          Deprecated.  
protected  java.util.Map schemeToHierNames_
          Deprecated.  
protected  java.sql.Connection sqlConnection_
          Deprecated.  
protected  GenericSQLModifier sqlModifier_
          Deprecated.  
protected  SQLTableUtilities sqlTableUtility_
          Deprecated.  
protected  SQLTableConstants stc_
          Deprecated.  
protected  java.util.HashSet supportedAssociationQualifiers_
          Deprecated.  
protected  UMLSBaseCode.Association[] supportedAssociations_
          Deprecated.  
protected  java.util.HashSet supportedCodingSchemes_
          Deprecated.  
protected  java.util.HashSet supportedHierarchies_
          Deprecated.  
protected  java.util.HashSet supportedLanguages_
          Deprecated.  
protected  java.util.HashSet supportedPropertyLinks_
          Deprecated.  
protected  java.util.HashSet supportedPropertyQualifiers_
          Deprecated.  
protected  java.util.HashSet supportedPropertyTypes_
          Deprecated.  
protected  java.util.HashSet supportedSources_
          Deprecated.  
protected  java.sql.Connection umlsConnection_
          Deprecated.  
protected  java.sql.Connection umlsConnection2_
          Deprecated.  
protected  GenericSQLModifier umlsSqlModifier_
          Deprecated.  
 
Constructor Summary
UMLSBaseCode()
          Deprecated.  
 
Method Summary
protected  void addAssociationToAssociations(java.lang.String codingSchemeName, java.lang.String relationName, java.lang.String association, java.lang.String forwardName, java.lang.String reverseName, java.lang.String inverse, java.lang.Boolean isNavigable, java.lang.Boolean isTransitive, java.lang.Boolean isAntiTransitive, java.lang.Boolean isSymmetric, java.lang.Boolean isAntiSymmetric, java.lang.Boolean isReflexive, java.lang.Boolean isAntiReflexive, java.lang.Boolean isFunctional, java.lang.Boolean isReverseFunctional, java.lang.Boolean isTranslationAssociation, java.lang.String targetCodingScheme, java.lang.String entityDescription)
          Deprecated.  
protected  void addConceptToConcepts(java.lang.String codingSchemeName, java.lang.String conceptCode, java.lang.Boolean firstRelease, java.lang.Boolean modifiedInRelease, java.lang.Boolean deprecated, java.lang.Boolean isActive, java.lang.Boolean isDefined, java.lang.Boolean isInferred, java.lang.String conceptStatus, java.lang.Boolean isAnonymous, java.lang.String entityDescription)
          Deprecated.  
protected  void addConceptToConceptsMultiAttributes(java.lang.String codingSchemeName, java.lang.String conceptCode, java.lang.String attributeName, java.lang.String attributeValue)
          Deprecated.  
protected  void addConceptToEntityPropertyMultiAttributes(java.lang.String codingSchemeName, java.lang.String entityType, java.lang.String conceptCode, java.lang.String propertyId, java.lang.String typeName, java.lang.String attributeValue, java.lang.String val1, java.lang.String val2)
          Deprecated.  
protected  void addEntityAssociationQualifierToEntityAssociation(java.lang.String codingSchemeName, java.lang.String multiAttributesKey, java.lang.String qualifierName, java.lang.String qualifierValue)
          Deprecated.  
protected  void addEntityAssociationToEntity(java.lang.String codingSchemeName, java.lang.String sourceCodingSchemeName, java.lang.String sourceEntityType, java.lang.String sourceConceptCode, java.lang.String relationName, java.lang.String association, java.lang.String targetCodingSchemeName, java.lang.String targetEntityType, java.lang.String targetConceptCode, java.lang.String multiAttributesKey, java.lang.Boolean firstVersion, java.lang.Boolean lastVersion)
          Deprecated.  
protected  void addEntityType(java.lang.String codingSchemeName, java.lang.String entityCodeNamespace, java.lang.String entityCode, java.lang.String entityType)
          Deprecated.  
protected  void addEntryState(int entryStateId, java.lang.String entryType, java.lang.String owner, java.lang.String status, java.lang.String effectiveDate, java.lang.String expirationDate, java.lang.String revisionId, java.lang.String prevRevisionId, java.lang.String changeType, int relativeOrder)
          Deprecated.  
protected  void addRelationToRelations(java.lang.String codingSchemeName, java.lang.String relationName, java.lang.Boolean isNative, java.lang.String entityDescription)
          Deprecated.  
protected  void addToCodingScheme(java.lang.String codingSchemeName, java.lang.String registeredName, java.lang.String representsVersion, java.lang.String formalName, java.lang.String language, int approxNumConcepts, java.lang.Boolean isActive, int entryStateId, java.lang.String releaseURI, java.lang.String entityDescription, java.lang.String copyright)
          Deprecated.  
protected  void addToEntityProperty(java.lang.String codingSchemeName, java.lang.String entityType, java.lang.String conceptCode, java.lang.String propertyId, java.lang.String propertyType, java.lang.String propertyName, java.lang.String language, java.lang.String presentationFormat, java.lang.Boolean isPreferred, java.lang.String degreeOfFidelity, java.lang.Boolean matchIfNoContext, java.lang.String representationForm, java.lang.String propertyValue)
          Deprecated.  
protected  void buildRootNode(java.lang.String codingSchemeName, boolean isMeta, UMLSBaseCode.SABString[] dirNames, java.lang.String lgRelationContainerName)
          Deprecated. Build relations to an artificial root ('@') or tail ('@@') node to assist with navigation of one or more associations.
protected  void closeConnections()
          Deprecated.  
protected  void closeLoadStatements()
          Deprecated.  
protected  java.lang.String generateUniqueKey(int seed)
          Deprecated. Generates a unique but random key, using the given integer as seed.
protected  java.lang.String generateUniqueKey(java.lang.String[] basis)
          Deprecated. Generates a unique but reproducible key based on the given base of string values.
protected  java.lang.String get5DigitRandom()
          Deprecated.  
protected  java.lang.String getCodingSchemeNameFromManifest(java.lang.String defaultCodingSchemeName)
          Deprecated. Helper method to check if the Coding Scheme Name is changed in the Manifest.
protected  java.lang.String getExpandedForm(java.lang.String rrfName, java.lang.String rrfField)
          Deprecated. Return the detailed name of the given RRF name; null if not available.
protected  java.lang.String[] getHierAssocNames(java.lang.String codeSystemName)
          Deprecated. Returns the names of the hierarchical associations in use for the LexGrid code system of the given name.
protected  UMLSBaseCode.SABString[] getHierRelas()
          Deprecated. Relation names in the RRF (RELA field) for hierarchical associations specific to the source distribution.
protected  UMLSBaseCode.SABString[] getHierRels()
          Deprecated. Standard names (REL field in the RRF) for hierarchical associations in the UMLS.
static java.util.Hashtable getIsoMap()
          Deprecated.  
protected  java.lang.String getISOString(java.lang.String UMLSCodingSchemeName)
          Deprecated.  
protected  java.lang.String getRegisteredNameFromManifest(java.lang.String defaultRegisteredName)
          Deprecated. Helper method to check if the Registered name is changed in the Manifest.
protected  UMLSBaseCode.SABString[] getRelaNames(UMLSBaseCode.SABString[] relNames)
          Deprecated. Resolve source-assigned relation names corresponding to the given array of standard UMLS relation names (e.g. resolve 'part_of' for 'PAR').
protected  java.lang.String getRelationInverseName(java.lang.String rrfName, java.lang.String rrfField)
          Deprecated. Return the inverse name of the given RRF-based relation; null if not available.
protected  UMLSBaseCode.SABString[] getRelationSABs(java.lang.String[] rrfNames, java.lang.String rrfField)
          Deprecated. Resolve UMLS source abbreviations corresponding to the given array of source-defined relation names (e.g. resolved from MRREL).
protected  java.security.MessageDigest getSHA1()
          Deprecated. Returns a message digest to be used for fixed-length key generation. s
protected  java.lang.String getSourceVersionString(java.lang.String fallbackString)
          Deprecated.  
protected  void initIsoMap()
          Deprecated.  
protected  void initLoadStatements()
          Deprecated.  
protected  void initMRCONSOTTYMAP()
          Deprecated.  
protected  void insertIntoCodingSchemeSupportedAttributes(java.lang.String codingSchemeName, java.lang.String supportedAttributeTag, java.lang.String id, java.lang.String urn, java.lang.String value, java.lang.String assemblyRule, java.lang.String agentRole)
          Deprecated.  
protected  void insertIntoConceptPropertyLinks(java.lang.String codingSchemeName, java.lang.String entityType, java.lang.String conceptCode, java.lang.String sourcePropertyId, java.lang.String link, java.lang.String targetPropertyId)
          Deprecated.  
protected  boolean isHierarchicalAssociation(UMLSBaseCode.Association assoc, java.lang.String codingSchemeName)
          Deprecated. Indicates whether the given association is used to represent hierarchical relationships in the source being processed.
protected  boolean isHierarchicalName(java.lang.String name, java.lang.String codeSystemName)
          Deprecated. Indicates whether the given name is used to represent hierarchical relationships in the source being processed.
protected  boolean isLoaded(java.lang.String name, java.lang.String codingSchemeName, java.lang.String relationsContainerName)
          Deprecated. Indicates if the given association name matches those currently loaded for the given coding scheme and relations container.
protected  boolean isLoaded(UMLSBaseCode.Association assoc, java.lang.String codingSchemeName, java.lang.String relationsContainerName)
          Deprecated. Indicates if the given association matches those currently loaded for the given coding scheme and relations container.
protected  int loadContext(UMLSBaseCode.AssociationQualification aq, boolean constructHCD, java.lang.String rela, int totalCount)
          Deprecated. Adds qualification to concepts and associations in the LexGrid repository.
protected  void loadDefaultSupportedNamespace(java.lang.String codingSchemeName)
          Deprecated.  
protected  void loadLoaderPreferences()
          Deprecated.  
protected  void loadMRRANK()
          Deprecated.  
protected  void loadSupportedAssociationQualifiers(java.lang.String codingSchemeName)
          Deprecated.  
protected  void loadSupportedLanguages(java.lang.String codingSchemeName)
          Deprecated.  
protected  void loadSupportedProperties(java.lang.String codingSchemeName)
          Deprecated.  
protected  void loadSupportedPropertyLinks(java.lang.String codingSchemeName)
          Deprecated.  
protected  void loadSupportedPropertyQualifiers(java.lang.String codingSchemeName)
          Deprecated.  
protected  void loadSupportedSources(java.lang.String codingSchemeName)
          Deprecated.  
protected  void makeConnections(java.lang.String umlsServer, java.lang.String umlsDriver, java.lang.String umlsUserName, java.lang.String umlsPassword, java.lang.String sqlServer, java.lang.String sqlDriver, java.lang.String sqlUserName, java.lang.String sqlPassword, java.lang.String tablePrefix, boolean enforceIntegrity)
          Deprecated.  
protected  java.lang.String mapCodeSystemNameToSAB(java.lang.String codeSystemName)
          Deprecated. Map from the coding scheme name used for identification in the LexGrid model to the UMLS source abbreviation (SAB).
protected  UMLSBaseCode.CodeHolder[] mapCUIToCode(java.lang.String cui, java.lang.String aui, java.lang.String sab)
          Deprecated.  
protected  UMLSBaseCode.CodeHolder[] mapCUIToCodeWithAUI(java.lang.String cui, java.lang.String aui)
          Deprecated.  
protected  java.lang.String mapRela(java.lang.String rrfName)
          Deprecated. Maps from the given UMLS-provided relationship name to a pre-designated LexGrid association name (e.g. map from 'inverse_isa' to 'hasSubtype'), if available.
protected  java.lang.String mapSABToCodeSystemName(java.lang.String sab)
          Deprecated. Map from the UMLS source abbreviation (SAB) to the coding scheme name used for identification in the LexGrid model.
protected  UMLSBaseCode.Association mapSupportedAssociationsHelper(java.lang.String rrfName, java.lang.String rrfSAB, java.lang.String rrfDirFlag, java.lang.String rrfField, java.util.Map map)
          Deprecated. Map the provided information to a new Association and add, if new, add to the given hashtable.
protected  java.lang.String mapVSABtoRSAB(java.lang.String vsab)
          Deprecated.  
protected  void markLoaded(java.lang.String name, java.lang.String codingSchemeName, java.lang.String relationsContainerName)
          Deprecated. Sets an indication that the given association has been loaded for the given coding scheme and relations container.
protected  void markLoaded(UMLSBaseCode.Association assoc, java.lang.String codingSchemeName, java.lang.String relationsContainerName)
          Deprecated. Sets an indication that the given association has been loaded for the given coding scheme and relations container.
protected  void qualifyConceptPresentation(java.lang.String code, java.lang.String aui, java.lang.String codingSchemeName, java.lang.String qualifierName, java.lang.String qualifierValue)
          Deprecated. Add context qualifiers to text presentations for matching concepts.
protected  java.lang.String toCommaDelimitedWithQuotes(java.lang.String[] strings)
          Deprecated. Converts the given string array to a single string, separating each value by comma and embedding quotes before and after each value.
protected  void updateApproxNumberOfConcepts(int count, java.lang.String codingSchemeName)
          Deprecated.  
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

log

protected static org.apache.log4j.Logger log
Deprecated. 

umlsConnection_

protected java.sql.Connection umlsConnection_
Deprecated. 

umlsConnection2_

protected java.sql.Connection umlsConnection2_
Deprecated. 

sqlConnection_

protected java.sql.Connection sqlConnection_
Deprecated. 

sqlTableUtility_

protected SQLTableUtilities sqlTableUtility_
Deprecated. 

stc_

protected SQLTableConstants stc_
Deprecated. 

umlsSqlModifier_

protected GenericSQLModifier umlsSqlModifier_
Deprecated. 

sqlModifier_

protected GenericSQLModifier sqlModifier_
Deprecated. 

batchSize

protected final int batchSize
Deprecated. 

isoMap

protected java.util.Hashtable isoMap
Deprecated. 

loadedAssociations_

protected java.util.HashSet loadedAssociations_
Deprecated. 

supportedCodingSchemes_

protected java.util.HashSet supportedCodingSchemes_
Deprecated. 

supportedAssociations_

protected UMLSBaseCode.Association[] supportedAssociations_
Deprecated. 

supportedAssociationQualifiers_

protected java.util.HashSet supportedAssociationQualifiers_
Deprecated. 

supportedPropertyTypes_

protected java.util.HashSet supportedPropertyTypes_
Deprecated. 

supportedPropertyLinks_

protected java.util.HashSet supportedPropertyLinks_
Deprecated. 

supportedPropertyQualifiers_

protected java.util.HashSet supportedPropertyQualifiers_
Deprecated. 

supportedSources_

protected java.util.HashSet supportedSources_
Deprecated. 

supportedLanguages_

protected java.util.HashSet supportedLanguages_
Deprecated. 

supportedHierarchies_

protected java.util.HashSet supportedHierarchies_
Deprecated. 

associationQualifierRUI_

protected java.util.HashSet associationQualifierRUI_
Deprecated. 

MRRANK_

protected java.util.HashMap MRRANK_
Deprecated. 

defaultLanguage_

protected java.lang.String defaultLanguage_
Deprecated. 

mrconsoRepresentationalMap_

protected java.util.Hashtable mrconsoRepresentationalMap_
Deprecated. 

sabToCodeSystem_

protected java.util.Hashtable sabToCodeSystem_
Deprecated. 

insertIntoCodingScheme

protected java.sql.PreparedStatement insertIntoCodingScheme
Deprecated. 

insertIntoCodingSchemeMultiAttributes

protected java.sql.PreparedStatement insertIntoCodingSchemeMultiAttributes
Deprecated. 

insertIntoEntityProperty

protected java.sql.PreparedStatement insertIntoEntityProperty
Deprecated. 

insertIntoEntityPropertyMultiAttributes

protected java.sql.PreparedStatement insertIntoEntityPropertyMultiAttributes
Deprecated. 

insertIntoEntities

protected java.sql.PreparedStatement insertIntoEntities
Deprecated. 

insertIntoEntryState

protected java.sql.PreparedStatement insertIntoEntryState
Deprecated. 

insertIntoEntityType

protected java.sql.PreparedStatement insertIntoEntityType
Deprecated. 

insertIntoConceptsMultiAttributes

protected java.sql.PreparedStatement insertIntoConceptsMultiAttributes
Deprecated. 

insertIntoRelations

protected java.sql.PreparedStatement insertIntoRelations
Deprecated. 

insertIntoAssociations

protected java.sql.PreparedStatement insertIntoAssociations
Deprecated. 

insertIntoEntityAssociationsToEntity

protected java.sql.PreparedStatement insertIntoEntityAssociationsToEntity
Deprecated. 

insertIntoEntityAssociationsToEntityQualifier

protected java.sql.PreparedStatement insertIntoEntityAssociationsToEntityQualifier
Deprecated. 

insertIntoEntityPropertyLinks

protected java.sql.PreparedStatement insertIntoEntityPropertyLinks
Deprecated. 

insertIntoCodingSchemeSupportedAttributes

protected java.sql.PreparedStatement insertIntoCodingSchemeSupportedAttributes
Deprecated. 

getCodeForCUI_

protected java.sql.PreparedStatement getCodeForCUI_
Deprecated. 

getCodeForCUINoAUI_

protected java.sql.PreparedStatement getCodeForCUINoAUI_
Deprecated. 

getSource_

protected java.sql.PreparedStatement getSource_
Deprecated. 

getUMLSRoot_

protected java.sql.PreparedStatement getUMLSRoot_
Deprecated. 

getAssocInstance_

protected java.sql.PreparedStatement getAssocInstance_
Deprecated. 

getAssocQualifier_

protected java.sql.PreparedStatement getAssocQualifier_
Deprecated. 

getAllAssocQualifiersFromRRF_

protected java.sql.PreparedStatement getAllAssocQualifiersFromRRF_
Deprecated. 

getAssocQualifierFromRRF_

protected java.sql.PreparedStatement getAssocQualifierFromRRF_
Deprecated. 

getAUIFromPresentation_

protected java.sql.PreparedStatement getAUIFromPresentation_
Deprecated. 

getPresentationRank_

protected java.sql.PreparedStatement getPresentationRank_
Deprecated. 

getPropIds_

protected java.sql.PreparedStatement getPropIds_
Deprecated. 

auiToCodeCache_

protected org.apache.commons.collections.map.LRUMap auiToCodeCache_
Deprecated. 

messages_

protected LgMessageDirectorIF messages_
Deprecated. 

loadPrefs_

protected LoaderPreferences loadPrefs_
Deprecated. 

manifestLocation_

protected java.net.URI manifestLocation_
Deprecated. 

manifestNameChange_

public boolean manifestNameChange_
Deprecated. 

entryStateId_

protected static int entryStateId_
Deprecated. 

schemeToHierNames_

protected java.util.Map schemeToHierNames_
Deprecated. 
Constructor Detail

UMLSBaseCode

public UMLSBaseCode()
Deprecated. 
Method Detail

makeConnections

protected void makeConnections(java.lang.String umlsServer,
                               java.lang.String umlsDriver,
                               java.lang.String umlsUserName,
                               java.lang.String umlsPassword,
                               java.lang.String sqlServer,
                               java.lang.String sqlDriver,
                               java.lang.String sqlUserName,
                               java.lang.String sqlPassword,
                               java.lang.String tablePrefix,
                               boolean enforceIntegrity)
                        throws java.lang.Exception
Deprecated. 
Throws:
java.lang.Exception

initMRCONSOTTYMAP

protected void initMRCONSOTTYMAP()
Deprecated. 

addToCodingScheme

protected void addToCodingScheme(java.lang.String codingSchemeName,
                                 java.lang.String registeredName,
                                 java.lang.String representsVersion,
                                 java.lang.String formalName,
                                 java.lang.String language,
                                 int approxNumConcepts,
                                 java.lang.Boolean isActive,
                                 int entryStateId,
                                 java.lang.String releaseURI,
                                 java.lang.String entityDescription,
                                 java.lang.String copyright)
                          throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addToEntityProperty

protected void addToEntityProperty(java.lang.String codingSchemeName,
                                   java.lang.String entityType,
                                   java.lang.String conceptCode,
                                   java.lang.String propertyId,
                                   java.lang.String propertyType,
                                   java.lang.String propertyName,
                                   java.lang.String language,
                                   java.lang.String presentationFormat,
                                   java.lang.Boolean isPreferred,
                                   java.lang.String degreeOfFidelity,
                                   java.lang.Boolean matchIfNoContext,
                                   java.lang.String representationForm,
                                   java.lang.String propertyValue)
                            throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addConceptToEntityPropertyMultiAttributes

protected void addConceptToEntityPropertyMultiAttributes(java.lang.String codingSchemeName,
                                                         java.lang.String entityType,
                                                         java.lang.String conceptCode,
                                                         java.lang.String propertyId,
                                                         java.lang.String typeName,
                                                         java.lang.String attributeValue,
                                                         java.lang.String val1,
                                                         java.lang.String val2)
                                                  throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addConceptToConceptsMultiAttributes

protected void addConceptToConceptsMultiAttributes(java.lang.String codingSchemeName,
                                                   java.lang.String conceptCode,
                                                   java.lang.String attributeName,
                                                   java.lang.String attributeValue)
                                            throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addAssociationToAssociations

protected void addAssociationToAssociations(java.lang.String codingSchemeName,
                                            java.lang.String relationName,
                                            java.lang.String association,
                                            java.lang.String forwardName,
                                            java.lang.String reverseName,
                                            java.lang.String inverse,
                                            java.lang.Boolean isNavigable,
                                            java.lang.Boolean isTransitive,
                                            java.lang.Boolean isAntiTransitive,
                                            java.lang.Boolean isSymmetric,
                                            java.lang.Boolean isAntiSymmetric,
                                            java.lang.Boolean isReflexive,
                                            java.lang.Boolean isAntiReflexive,
                                            java.lang.Boolean isFunctional,
                                            java.lang.Boolean isReverseFunctional,
                                            java.lang.Boolean isTranslationAssociation,
                                            java.lang.String targetCodingScheme,
                                            java.lang.String entityDescription)
                                     throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addEntityAssociationToEntity

protected void addEntityAssociationToEntity(java.lang.String codingSchemeName,
                                            java.lang.String sourceCodingSchemeName,
                                            java.lang.String sourceEntityType,
                                            java.lang.String sourceConceptCode,
                                            java.lang.String relationName,
                                            java.lang.String association,
                                            java.lang.String targetCodingSchemeName,
                                            java.lang.String targetEntityType,
                                            java.lang.String targetConceptCode,
                                            java.lang.String multiAttributesKey,
                                            java.lang.Boolean firstVersion,
                                            java.lang.Boolean lastVersion)
                                     throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addEntityAssociationQualifierToEntityAssociation

protected void addEntityAssociationQualifierToEntityAssociation(java.lang.String codingSchemeName,
                                                                java.lang.String multiAttributesKey,
                                                                java.lang.String qualifierName,
                                                                java.lang.String qualifierValue)
                                                         throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addRelationToRelations

protected void addRelationToRelations(java.lang.String codingSchemeName,
                                      java.lang.String relationName,
                                      java.lang.Boolean isNative,
                                      java.lang.String entityDescription)
                               throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addConceptToConcepts

protected void addConceptToConcepts(java.lang.String codingSchemeName,
                                    java.lang.String conceptCode,
                                    java.lang.Boolean firstRelease,
                                    java.lang.Boolean modifiedInRelease,
                                    java.lang.Boolean deprecated,
                                    java.lang.Boolean isActive,
                                    java.lang.Boolean isDefined,
                                    java.lang.Boolean isInferred,
                                    java.lang.String conceptStatus,
                                    java.lang.Boolean isAnonymous,
                                    java.lang.String entityDescription)
                             throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addEntityType

protected void addEntityType(java.lang.String codingSchemeName,
                             java.lang.String entityCodeNamespace,
                             java.lang.String entityCode,
                             java.lang.String entityType)
                      throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

addEntryState

protected void addEntryState(int entryStateId,
                             java.lang.String entryType,
                             java.lang.String owner,
                             java.lang.String status,
                             java.lang.String effectiveDate,
                             java.lang.String expirationDate,
                             java.lang.String revisionId,
                             java.lang.String prevRevisionId,
                             java.lang.String changeType,
                             int relativeOrder)
                      throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

getIsoMap

public static java.util.Hashtable getIsoMap()
                                     throws java.lang.Exception
Deprecated. 
Throws:
java.lang.Exception

initIsoMap

protected void initIsoMap()
Deprecated. 

updateApproxNumberOfConcepts

protected void updateApproxNumberOfConcepts(int count,
                                            java.lang.String codingSchemeName)
Deprecated. 

getISOString

protected java.lang.String getISOString(java.lang.String UMLSCodingSchemeName)
                                 throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

mapVSABtoRSAB

protected java.lang.String mapVSABtoRSAB(java.lang.String vsab)
                                  throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

loadSupportedPropertyLinks

protected void loadSupportedPropertyLinks(java.lang.String codingSchemeName)
                                   throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

loadSupportedProperties

protected void loadSupportedProperties(java.lang.String codingSchemeName)
                                throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

loadSupportedPropertyQualifiers

protected void loadSupportedPropertyQualifiers(java.lang.String codingSchemeName)
                                        throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

loadSupportedAssociationQualifiers

protected void loadSupportedAssociationQualifiers(java.lang.String codingSchemeName)
                                           throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

loadSupportedSources

protected void loadSupportedSources(java.lang.String codingSchemeName)
                             throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

loadSupportedLanguages

protected void loadSupportedLanguages(java.lang.String codingSchemeName)
                               throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

insertIntoConceptPropertyLinks

protected void insertIntoConceptPropertyLinks(java.lang.String codingSchemeName,
                                              java.lang.String entityType,
                                              java.lang.String conceptCode,
                                              java.lang.String sourcePropertyId,
                                              java.lang.String link,
                                              java.lang.String targetPropertyId)
                                       throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

insertIntoCodingSchemeSupportedAttributes

protected void insertIntoCodingSchemeSupportedAttributes(java.lang.String codingSchemeName,
                                                         java.lang.String supportedAttributeTag,
                                                         java.lang.String id,
                                                         java.lang.String urn,
                                                         java.lang.String value,
                                                         java.lang.String assemblyRule,
                                                         java.lang.String agentRole)
                                                  throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

initLoadStatements

protected void initLoadStatements()
                           throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

qualifyConceptPresentation

protected void qualifyConceptPresentation(java.lang.String code,
                                          java.lang.String aui,
                                          java.lang.String codingSchemeName,
                                          java.lang.String qualifierName,
                                          java.lang.String qualifierValue)
                                   throws java.sql.SQLException
Deprecated. 
Add context qualifiers to text presentations for matching concepts.

Parameters:
code - The code of the concept to qualify.
aui - The AUI identifying specific context text to be matched.
codingSchemeName - The coding scheme container the code to be qualified.
qualifierName - The qualifier name (e.g. 'HCD').
qualifierValue - The qualifier value.
Throws:
java.sql.SQLException

loadContext

protected int loadContext(UMLSBaseCode.AssociationQualification aq,
                          boolean constructHCD,
                          java.lang.String rela,
                          int totalCount)
                   throws java.sql.SQLException
Deprecated. 
Adds qualification to concepts and associations in the LexGrid repository.

Parameters:
aq - Qualification information from the UMLS source.
constructHCD - Indicates whether artificial context values should be constructed if not provided in the UMLS information.
rela - The relationship attribute defined by UMLS (can be empty or null).
totalCount - The total number of context links qualified previously.
Returns:
The number of contextual links qualified in the repository for the given UMLS info.
Throws:
java.sql.SQLException

mapCUIToCode

protected UMLSBaseCode.CodeHolder[] mapCUIToCode(java.lang.String cui,
                                                 java.lang.String aui,
                                                 java.lang.String sab)
                                          throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

mapCUIToCodeWithAUI

protected UMLSBaseCode.CodeHolder[] mapCUIToCodeWithAUI(java.lang.String cui,
                                                        java.lang.String aui)
                                                 throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

getSourceVersionString

protected java.lang.String getSourceVersionString(java.lang.String fallbackString)
Deprecated. 

closeLoadStatements

protected void closeLoadStatements()
                            throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

closeConnections

protected void closeConnections()
                         throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

buildRootNode

protected void buildRootNode(java.lang.String codingSchemeName,
                             boolean isMeta,
                             UMLSBaseCode.SABString[] dirNames,
                             java.lang.String lgRelationContainerName)
                      throws java.sql.SQLException
Deprecated. 
Build relations to an artificial root ('@') or tail ('@@') node to assist with navigation of one or more associations. If building a root node, nodes acting as source but not as target are connected to the '@' node. If building a tail node, nodes acting as target but not source are connected to the '@@' node. Therefore, '@' becomes the ultimate source node and '@@' the ultimate target node for navigation.

Parameters:
codingSchemeName - The LexGrid code system name being loaded.
isMeta - True if the LexGrid code system is to represent multiple UMLS ontologies, acting as a single meta-ontology; false if the code system represents a single UMLS ontology. If true, LexGrid concept codes and association references are defined in terms of UMLS CUI instead of native codes from the source ontology. In addition, relations for meta distributions are interpreted as intra-scheme, whereas relations for individual coding systems are allowed to cross coding scheme boundaries.
dirNames - The names of UMLS directional relations to be evaluated, optionally qualified by SAB. Roots are evaluated for participation as source or target for the given names.
lgRelationContainerName - The LexGrid relations container defining the associations to be evaluated, or null to match any relations for the code system.
Throws:
java.sql.SQLException

getExpandedForm

protected java.lang.String getExpandedForm(java.lang.String rrfName,
                                           java.lang.String rrfField)
                                    throws java.sql.SQLException
Deprecated. 
Return the detailed name of the given RRF name; null if not available.

Parameters:
rrfName - The UMLS relation name.
rrfField - The UMLS field (e.g. 'RELA' or 'REL').
Returns:
String
Throws:
java.sql.SQLException

getHierRelas

protected UMLSBaseCode.SABString[] getHierRelas()
                                         throws java.sql.SQLException
Deprecated. 
Relation names in the RRF (RELA field) for hierarchical associations specific to the source distribution.

Returns:
String[]
Throws:
java.sql.SQLException - If an error occurs resolving from the source.

getHierRels

protected UMLSBaseCode.SABString[] getHierRels()
                                        throws java.sql.SQLException
Deprecated. 
Standard names (REL field in the RRF) for hierarchical associations in the UMLS.

Returns:
String[]
Throws:
java.sql.SQLException - If an error occurs resolving from the source.

getHierAssocNames

protected java.lang.String[] getHierAssocNames(java.lang.String codeSystemName)
                                        throws java.sql.SQLException
Deprecated. 
Returns the names of the hierarchical associations in use for the LexGrid code system of the given name.

Parameters:
codeSystemName -
Returns:
String[]
Throws:
java.sql.SQLException - If an error occurs resolving from the source.

getRelaNames

protected UMLSBaseCode.SABString[] getRelaNames(UMLSBaseCode.SABString[] relNames)
                                         throws java.sql.SQLException
Deprecated. 
Resolve source-assigned relation names corresponding to the given array of standard UMLS relation names (e.g. resolve 'part_of' for 'PAR').

Parameters:
relNames - SABString[]
Returns:
String[]
Throws:
java.sql.SQLException - If an error occurs resolving from the source.

getRelationSABs

protected UMLSBaseCode.SABString[] getRelationSABs(java.lang.String[] rrfNames,
                                                   java.lang.String rrfField)
                                            throws java.sql.SQLException
Deprecated. 
Resolve UMLS source abbreviations corresponding to the given array of source-defined relation names (e.g. resolved from MRREL).

Parameters:
rrfNames - String[]
rrfField - 'RELA' or 'REL'.
Returns:
SABString[] Array of corresponding SAB-qualified relation names.
Throws:
java.sql.SQLException - If an error occurs resolving from the source.

getRelationInverseName

protected java.lang.String getRelationInverseName(java.lang.String rrfName,
                                                  java.lang.String rrfField)
                                           throws java.sql.SQLException
Deprecated. 
Return the inverse name of the given RRF-based relation; null if not available.

Parameters:
rrfName - The UMLS relation name.
rrfField - 'RELA' or 'REL'.
Returns:
String
Throws:
java.sql.SQLException

isHierarchicalAssociation

protected boolean isHierarchicalAssociation(UMLSBaseCode.Association assoc,
                                            java.lang.String codingSchemeName)
                                     throws java.sql.SQLException
Deprecated. 
Indicates whether the given association is used to represent hierarchical relationships in the source being processed.

Parameters:
assoc - Association object to check; not null.
codingSchemeName - Name of the LexGrid coding scheme containing the association; null to match any coding scheme.
Returns:
true if representing hierarchical relations; false otherwise.
Throws:
java.sql.SQLException - If an error occurs resolving from the source.

isHierarchicalName

protected boolean isHierarchicalName(java.lang.String name,
                                     java.lang.String codeSystemName)
                              throws java.sql.SQLException
Deprecated. 
Indicates whether the given name is used to represent hierarchical relationships in the source being processed.

Parameters:
dirName - Directional name of the association to check.
codeSystemName - Name of the LexGrid coding scheme containing the association; null to match any coding scheme.
Returns:
true if the name represents hierarchical definitions; false if not.
Throws:
java.sql.SQLException - If an error occurs resolving from the source.

isLoaded

protected boolean isLoaded(UMLSBaseCode.Association assoc,
                           java.lang.String codingSchemeName,
                           java.lang.String relationsContainerName)
                    throws java.sql.SQLException
Deprecated. 
Indicates if the given association matches those currently loaded for the given coding scheme and relations container.

Parameters:
assoc -
codingSchemeName -
relationsContainerName -
Returns:
true if loaded; false if not.
Throws:
java.sql.SQLException

isLoaded

protected boolean isLoaded(java.lang.String name,
                           java.lang.String codingSchemeName,
                           java.lang.String relationsContainerName)
                    throws java.sql.SQLException
Deprecated. 
Indicates if the given association name matches those currently loaded for the given coding scheme and relations container.

Parameters:
name -
codingSchemeName -
relationsContainerName -
Returns:
true if loaded; false if not.
Throws:
java.sql.SQLException

markLoaded

protected void markLoaded(UMLSBaseCode.Association assoc,
                          java.lang.String codingSchemeName,
                          java.lang.String relationsContainerName)
                   throws java.sql.SQLException
Deprecated. 
Sets an indication that the given association has been loaded for the given coding scheme and relations container.

Parameters:
assoc -
codingSchemeName -
relationsContainerName -
Throws:
java.sql.SQLException

markLoaded

protected void markLoaded(java.lang.String name,
                          java.lang.String codingSchemeName,
                          java.lang.String relationsContainerName)
                   throws java.sql.SQLException
Deprecated. 
Sets an indication that the given association has been loaded for the given coding scheme and relations container.

Parameters:
name -
codingSchemeName -
relationsContainerName -
Throws:
java.sql.SQLException

mapSABToCodeSystemName

protected java.lang.String mapSABToCodeSystemName(java.lang.String sab)
                                           throws java.sql.SQLException
Deprecated. 
Map from the UMLS source abbreviation (SAB) to the coding scheme name used for identification in the LexGrid model.

Parameters:
sab -
Returns:
String
Throws:
java.sql.SQLException

mapCodeSystemNameToSAB

protected java.lang.String mapCodeSystemNameToSAB(java.lang.String codeSystemName)
                                           throws java.sql.SQLException
Deprecated. 
Map from the coding scheme name used for identification in the LexGrid model to the UMLS source abbreviation (SAB).

Parameters:
codeSystemName -
Returns:
String
Throws:
java.sql.SQLException

mapSupportedAssociationsHelper

protected UMLSBaseCode.Association mapSupportedAssociationsHelper(java.lang.String rrfName,
                                                                  java.lang.String rrfSAB,
                                                                  java.lang.String rrfDirFlag,
                                                                  java.lang.String rrfField,
                                                                  java.util.Map map)
                                                           throws java.sql.SQLException
Deprecated. 
Map the provided information to a new Association and add, if new, add to the given hashtable.

Parameters:
rrfName - The name of the relationship as provided by the UMLS.
rrfSAB - The source abbreviation of the UMLS code system.
rrfDirFlag - The UMLS directional flag. Y indicates that this is the direction of the RELA relationship in its source; N indicates that it is not; otherwise indicates that it is not important or has not yet been determined. (If blank RELA, we interpret as 'N', based on empirical review of meta files).
rrfField - Indicates whether the association name is defined as a standard UMLS relation ('REL') or source-provided label ('RELA').
map - A Map of Associations, keyed by SAB-qualified name.
Returns:
The mapped Association.
Throws:
java.sql.SQLException

mapRela

protected java.lang.String mapRela(java.lang.String rrfName)
Deprecated. 
Maps from the given UMLS-provided relationship name to a pre-designated LexGrid association name (e.g. map from 'inverse_isa' to 'hasSubtype'), if available. Otherwise, return the rela unmodified.

Parameters:
rrfName -
Returns:
The mapped value.

toCommaDelimitedWithQuotes

protected java.lang.String toCommaDelimitedWithQuotes(java.lang.String[] strings)
Deprecated. 
Converts the given string array to a single string, separating each value by comma and embedding quotes before and after each value.

Parameters:
strings -
Returns:
String

getSHA1

protected java.security.MessageDigest getSHA1()
Deprecated. 
Returns a message digest to be used for fixed-length key generation. s


generateUniqueKey

protected java.lang.String generateUniqueKey(java.lang.String[] basis)
Deprecated. 
Generates a unique but reproducible key based on the given base of string values.

Parameters:
components -
Returns:
A unique string based on 20-byte output from a SHA-1 message digest.
Throws:
java.sql.SQLException

generateUniqueKey

protected java.lang.String generateUniqueKey(int seed)
Deprecated. 
Generates a unique but random key, using the given integer as seed.

Parameters:
seed -
Returns:
String

get5DigitRandom

protected java.lang.String get5DigitRandom()
Deprecated. 

loadLoaderPreferences

protected void loadLoaderPreferences()
Deprecated. 

getRegisteredNameFromManifest

protected java.lang.String getRegisteredNameFromManifest(java.lang.String defaultRegisteredName)
Deprecated. 
Helper method to check if the Registered name is changed in the Manifest. Because this is done pre-load, we need to check.

Parameters:
defaultRegisteredName - The default to return if the manifest does not override it
Returns:
The Registered Name

getCodingSchemeNameFromManifest

protected java.lang.String getCodingSchemeNameFromManifest(java.lang.String defaultCodingSchemeName)
Deprecated. 
Helper method to check if the Coding Scheme Name is changed in the Manifest. Because this is done pre-load, we need to check.

Parameters:
defaultCodingSchemeName - The default to return if the manifest does not override it
Returns:
The CodingScheme Name

loadMRRANK

protected void loadMRRANK()
Deprecated. 

loadDefaultSupportedNamespace

protected void loadDefaultSupportedNamespace(java.lang.String codingSchemeName)
                                      throws java.sql.SQLException
Deprecated. 
Throws:
java.sql.SQLException

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