Java Code
/*
* Copyright: (c) 2004-2009 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.
*
* Except as contained in the copyright notice above, or as used to identify
* MFMER as the author of this software, the trade names, trademarks, service
* marks, or product names of the copyright holder shall not be used in
* advertising, promotion or otherwise in connection with this software without
* prior written authorization of the copyright holder.
*
* Licensed under the Eclipse Public License, Version 1.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.eclipse.org/legal/epl-v10.html
*
*/
package org.LexGrid.LexBIG.example;
import org.LexGrid.LexBIG.DataModel.Collections.LocalNameList;
import org.LexGrid.LexBIG.DataModel.Collections.ResolvedConceptReferenceList;
import org.LexGrid.LexBIG.DataModel.Core.AssociatedConcept;
import org.LexGrid.LexBIG.DataModel.Core.Association;
import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeSummary;
import org.LexGrid.LexBIG.DataModel.Core.CodingSchemeVersionOrTag;
import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference;
import org.LexGrid.LexBIG.Exceptions.LBException;
import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl;
import org.LexGrid.LexBIG.LexBIGService.LexBIGService;
import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.PropertyType;
import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet.SearchDesignationOption;
import org.LexGrid.LexBIG.Utility.ConvenienceMethods;
import org.LexGrid.LexBIG.Utility.LBConstants.SortableProperties;
import org.LexGrid.commonTypes.EntityDescription;
/**
* Example showing how to find all endpoints of a named association for which
* the given term matches as source or target.
*
* Note: the match algorithm applied to the term is the standard lucene query
* syntax.
*/
public class FindRelatedNodesForTermAndAssoc {
public FindRelatedNodesForTermAndAssoc() {
super();
}
/**
* Entry point for processing.
*
* @param args
*/
public static void main(String[] args) {
if (args.length < 2) {
System.out
.println("Example: FindRelatedNodesForTermAndAssoc \"lung\" \"Anatomic_Structure_Is_Physical_Part_Of\"");
return;
}
;
try {
String term = args[0];
String assoc = args[1];
new FindRelatedNodesForTermAndAssoc().run(term, assoc);
} catch (Exception e) {
Util.displayAndLogError("REQUEST FAILED !!!", e);
}
}
public void run(String term, String assoc) throws LBException {
CodingSchemeSummary css = Util.promptForCodeSystem();
if (css != null) {
LexBIGService lbSvc = LexBIGServiceImpl.defaultInstance();
String scheme = css.getCodingSchemeURI();
CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
csvt.setVersion(css.getRepresentsVersion());
printSources(term, assoc, lbSvc, scheme, csvt);
printTargets(term, assoc, lbSvc, scheme, csvt);
}
}
/**
* Display association sources for which the given term participates as
* target.
*
* @param term
* @param assoc
* @param lbSvc
* @param scheme
* @param csvt
* @throws LBException
*/
protected void printSources(String term, String assoc, LexBIGService lbSvc, String scheme,
CodingSchemeVersionOrTag csvt) throws LBException {
// Find all nodes that the term matches.
ResolvedConceptReferenceList nodeList = lbSvc.getNodeSet(scheme, csvt, null).restrictToMatchingDesignations(
term, SearchDesignationOption.PREFERRED_ONLY, "LuceneQuery", null).resolveToList(
ConvenienceMethods.createSortOptionList(new String[] { SortableProperties.code.name() }), null,
new PropertyType[] { PropertyType.PRESENTATION }, 1024);
// For each node, find and print related sources ...
int nodeCount = nodeList.getResolvedConceptReferenceCount();
for (int i = 0; i < nodeCount; i++) {
ResolvedConceptReference node = (ResolvedConceptReference) nodeList.getResolvedConceptReference(i);
// Get a graph of relationships for which the node
// participate as a target.
ResolvedConceptReferenceList matches = lbSvc.getNodeGraph(scheme, csvt, null).restrictToAssociations(
ConvenienceMethods.createNameAndValueList(assoc), null).resolveAsList(node, false, true, 1, 1,
new LocalNameList(), null, null, 1024);
int matchCount = matches.getResolvedConceptReferenceCount();
if (matchCount > 0) {
Util.displayMessage('\n' + node.getConceptCode() + '/' + node.getEntityDescription().getContent());
for (int j = 0; j < matchCount; j++) {
ResolvedConceptReference match = (ResolvedConceptReference) matches.getResolvedConceptReference(j);
Association a = match.getTargetOf().getAssociation(0);
AssociatedConcept[] acl = a.getAssociatedConcepts().getAssociatedConcept();
String aName = a.getDirectionalName();
for (int k = 0; k < acl.length; k++) {
AssociatedConcept ac = acl[k];
EntityDescription ed = ac.getEntityDescription();
Util.displayMessage('\t' + (aName == null ? "[R]" + a.getAssociationName() : aName) + ": "
+ ac.getConceptCode() + '/' + (ed == null ? "**No Description**" : ed.getContent()));
}
}
}
}
}
/**
* Display association targets for which the given term participates as
* source.
*
* @param term
* @param assoc
* @param lbSvc
* @param scheme
* @param csvt
* @throws LBException
*/
protected void printTargets(String term, String assoc, LexBIGService lbSvc, String scheme,
CodingSchemeVersionOrTag csvt) throws LBException {
// Find all nodes that the term matches.
ResolvedConceptReferenceList nodeList = lbSvc.getNodeSet(scheme, csvt, null).restrictToMatchingDesignations(
term, SearchDesignationOption.PREFERRED_ONLY, "LuceneQuery", null).resolveToList(
ConvenienceMethods.createSortOptionList(new String[] { SortableProperties.code.name() }), null,
new PropertyType[] { PropertyType.PRESENTATION }, 1024);
// For each node, find and print related targets ...
int nodeCount = nodeList.getResolvedConceptReferenceCount();
for (int i = 0; i < nodeCount; i++) {
ResolvedConceptReference node = (ResolvedConceptReference) nodeList.getResolvedConceptReference(i);
// Get a graph of relationships for which the node
// participate as a source.
ResolvedConceptReferenceList matches = lbSvc.getNodeGraph(scheme, csvt, null).restrictToAssociations(
ConvenienceMethods.createNameAndValueList(assoc), null).resolveAsList(node, true, false, 1, 1,
new LocalNameList(), null, null, 1024);
int matchCount = matches.getResolvedConceptReferenceCount();
if (matchCount > 0) {
Util.displayMessage('\n' + node.getConceptCode() + '/' + node.getEntityDescription().getContent());
for (int j = 0; j < matchCount; j++) {
ResolvedConceptReference match = (ResolvedConceptReference) matches.getResolvedConceptReference(j);
Association a = match.getSourceOf().getAssociation(0);
AssociatedConcept[] acl = a.getAssociatedConcepts().getAssociatedConcept();
String aName = a.getDirectionalName();
for (int k = 0; k < acl.length; k++) {
AssociatedConcept ac = acl[k];
EntityDescription ed = ac.getEntityDescription();
Util.displayMessage('\t' + (aName == null ? a.getAssociationName() : aName) + ": "
+ ac.getConceptCode() + '/' + (ed == null ? "**No Description**" : ed.getContent()));
}
}
}
}
}
}
