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java.lang.Objectedu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon.UMLSBaseCode
edu.mayo.informatics.lexgrid.convert.directConversions.MetaThesaurusToSQL
public class MetaThesaurusToSQL
A tool to load the LexGrid SQL table from UMLS - using the CUI's as the concept codes.
Nested Class Summary | |
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protected class |
MetaThesaurusToSQL.QualifierHolder
Inner class to track keyed references to source qualifiers. |
Nested classes/interfaces inherited from class edu.mayo.informatics.lexgrid.convert.directConversions.UmlsCommon.UMLSBaseCode |
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UMLSBaseCode.Association, UMLSBaseCode.AssociationQualification, UMLSBaseCode.AssociationSorter, UMLSBaseCode.CodeHolder, UMLSBaseCode.ConceptPresentation, UMLSBaseCode.ConceptPresentationSorter, UMLSBaseCode.SABString |
Field Summary |
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Constructor Summary | |
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MetaThesaurusToSQL(java.lang.String sqlServer,
java.lang.String sqlDriver,
java.lang.String sqlUserName,
java.lang.String sqlPassword,
java.lang.String tablePrefix,
java.lang.String umlsServer,
java.lang.String umlsDriver,
java.lang.String umlsUserName,
java.lang.String umlsPassword,
LoaderPreferences loadPrefs,
java.net.URI manifestLocation,
boolean enforceIntegrity,
boolean rootRecalcOnly,
LgMessageDirectorIF director)
Class to convert from UMLS to SQL. |
Method Summary | |
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protected boolean |
addConceptAssociationToConceptsHelper(java.lang.String currentCodingScheme,
java.lang.String sourceCode,
java.lang.String association,
java.lang.String targetCode,
java.lang.String sourceOfAssociation,
java.lang.String roleGroup,
java.lang.String forwardName,
java.lang.String reverseName,
int count)
Add a code to code association. |
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 |
getCodingSchemeName()
|
protected java.lang.String[] |
getHierAssocNames(java.lang.String codeSystemName)
Returns the names of the hierarchical associations in use for the LexGrid code system of the given name. |
protected java.lang.String |
getPresentationFromAUI(java.lang.String codingSchemeName,
java.lang.String code,
java.lang.String aui)
Gets the Presentation ID (for example, T1) given a specific AUI, Code, and Coding Scheme Name first level nodes in hierarchical associations. |
protected int |
loadContext(UMLSBaseCode.AssociationQualification aq,
boolean constructHCD,
java.lang.String rela,
int totalCount)
Adds qualification to concepts and associations in the LexGrid repository. |
protected void |
loadRelations(java.lang.String codingSchemeName)
High level method with responsibility to map relationship content from UMLS RRF-based format to LexGrid model. |
protected int |
loadRelationsHelper(UMLSBaseCode.Association assoc,
java.lang.String codingSchemeName)
Carry out the mapping of relationships from UMLS RRF-based format to LexGrid model. |
static void |
main(java.lang.String[] args)
|
protected void |
populateSupportedAssociations()
Detect and register association information to the array of supported associations maintained by the loader. |
protected void |
qualifyConceptPresentation(java.lang.String code,
java.lang.String aui,
java.lang.String codingSchemeName,
java.lang.String qualifierName,
java.lang.String qualifierValue)
Add context qualifiers to text presentations for matching concepts (Overrides UMLSBAaseCode method). |
protected void |
rebuildRootNodes()
Remove and rebuild navigable relations from special endpoint nodes '@' and '@@' to first level nodes in hierarchical associations. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public MetaThesaurusToSQL(java.lang.String sqlServer, java.lang.String sqlDriver, java.lang.String sqlUserName, java.lang.String sqlPassword, java.lang.String tablePrefix, java.lang.String umlsServer, java.lang.String umlsDriver, java.lang.String umlsUserName, java.lang.String umlsPassword, LoaderPreferences loadPrefs, java.net.URI manifestLocation, boolean enforceIntegrity, boolean rootRecalcOnly, LgMessageDirectorIF director) throws java.lang.Exception
sqlServer
- location of SQL serversqlDriver
- SQL driver classsqlUserName
- user name for server authenticationsqlPassword
- password for server authenticationumlsServer
- location of UMLS serverumlsDriver
- UMLS driver classumlsUserName
- user name for server authenticationumlsPassword
- password for server authenticationloadPrefs
- loader peferencesmanifestLocation
- manifest locationenforceIntegrity
- enforce foreign key constraints on tablesrootRecalcOnly
- recalculate root nodes onlydirector
- message director for log output
java.lang.Exception
Method Detail |
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protected int loadContext(UMLSBaseCode.AssociationQualification aq, boolean constructHCD, java.lang.String rela, int totalCount) throws java.sql.SQLException
loadContext
in class UMLSBaseCode
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.
java.sql.SQLException
public static void main(java.lang.String[] args) throws java.lang.Exception
java.lang.Exception
public java.lang.String getCodingSchemeName()
protected boolean addConceptAssociationToConceptsHelper(java.lang.String currentCodingScheme, java.lang.String sourceCode, java.lang.String association, java.lang.String targetCode, java.lang.String sourceOfAssociation, java.lang.String roleGroup, java.lang.String forwardName, java.lang.String reverseName, int count) throws java.sql.SQLException
currentCodingScheme
- sourceCode
- association
- targetCode
- sourceOfAssociation
- forwardName
- reverseName
- count
-
java.sql.SQLException
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
qualifyConceptPresentation
in class UMLSBaseCode
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.
java.sql.SQLException
protected java.lang.String getPresentationFromAUI(java.lang.String codingSchemeName, java.lang.String code, java.lang.String aui) throws java.sql.SQLException
codingSchemeName
- The LexGrid code system name.code
- The code (CUI) to look foraui
- The AUI within the given code
java.sql.SQLException
protected void buildRootNodes(java.lang.String codingSchemeName) throws java.sql.SQLException
codingSchemeName
- The LexGrid code system name.
java.sql.SQLException
protected java.lang.String[] getHierAssocNames(java.lang.String codeSystemName) throws java.sql.SQLException
getHierAssocNames
in class UMLSBaseCode
codeSystemName
-
java.sql.SQLException
- If an error occurs resolving from the source.protected void loadRelations(java.lang.String codingSchemeName) throws java.sql.SQLException
codingSchemeName
-
java.sql.SQLException
protected int loadRelationsHelper(UMLSBaseCode.Association assoc, java.lang.String codingSchemeName) throws java.sql.SQLException
assoc
- codingSchemeName
-
java.sql.SQLException
protected void populateSupportedAssociations() throws java.sql.SQLException
java.sql.SQLException
protected void rebuildRootNodes() throws java.sql.SQLException
java.sql.SQLException
|
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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