/* * 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())); } } } } } }
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