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.AssociatedConceptList;
import org.LexGrid.LexBIG.DataModel.Collections.AssociationList;
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.Exceptions.LBException;
import org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods;
import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl;
import org.LexGrid.LexBIG.LexBIGService.LexBIGService;
/**
* Example showing how to determine and display paths from a given concept back
* to defined root nodes through any hierarchies registered for the coding
* scheme.
*
* This program accepts one parameter (required), indicating the code to
* evaluate.
*
* BACKGROUND: From a database perspective, LexBIG stores relationships
* internally in a forward direction, source to target. Due to differences in
* source formats, however, a wide variety of associations may be used ('PAR',
* 'CHD', 'isa', 'hasSubtype', etc). In addition, the direction of navigation
* may vary ('isa' expands in a reverse direction whereas 'hasSubtype' expands
* in a forward direction.
*
* The intent of the getHierarchy* methods on the
* LexBIGServiceConvenienceMethods interface is to simplify the process of
* hierarchy discovery and navigation. These methods significantly reduce the
* need to understand conventions for root nodes, associations, and direction of
* navigation for a specific source format.
*
*/
public class ListHierarchyPathToRoot {
public ListHierarchyPathToRoot() {
super();
}
/**
* Entry point for processing.
*
* @param args
*/
public static void main(String[] args) {
if (args.length < 1) {
System.out.println("Example: ListHierarchyPathToRoot \"C0000\"");
return;
}
;
try {
String code = args[0];
new ListHierarchyPathToRoot().run(code);
} catch (Exception e) {
Util.displayAndLogError("REQUEST FAILED !!!", e);
}
}
public void run(String code) throws LBException {
CodingSchemeSummary css = Util.promptForCodeSystem();
long ms = System.currentTimeMillis();
try {
if (css != null) {
LexBIGService lbSvc = LexBIGServiceImpl.defaultInstance();
LexBIGServiceConvenienceMethods lbscm = (LexBIGServiceConvenienceMethods) lbSvc
.getGenericExtension("LexBIGServiceConvenienceMethods");
// Fetch the description for the specified code.
// Not required to find path to root, just nice to display.
String scheme = css.getCodingSchemeURI();
CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
csvt.setVersion(css.getRepresentsVersion());
String desc = null;
try {
desc = lbscm.createCodeNodeSet(new String[] { code }, scheme, csvt).resolveToList(null, null, null,
1).getResolvedConceptReference(0).getEntityDescription().getContent();
} catch (Exception e) {
desc = "<not found>";
}
Util.displayMessage("============================================================");
Util.displayMessage("Focus code: " + code + ":" + desc);
Util.displayMessage("============================================================");
// Iterate through all hierarchies ...
String[] hierarchyIDs = lbscm.getHierarchyIDs(scheme, csvt);
for (int i = 0; i < hierarchyIDs.length; i++) {
String hierarchyID = hierarchyIDs[i];
Util.displayMessage("------------------------------------------------------------");
Util.displayMessage("Hierarchy ID: " + hierarchyID);
Util.displayMessage("------------------------------------------------------------");
AssociationList associations = lbscm.getHierarchyPathToRoot(scheme, csvt, hierarchyID, code, false,
LexBIGServiceConvenienceMethods.HierarchyPathResolveOption.ALL, null);
for (int j = 0; j < associations.getAssociationCount(); j++) {
Association association = associations.getAssociation(j);
printChain(association, 0);
}
Util.displayMessage("");
}
}
} finally {
System.out.println("Run time (ms): " + (System.currentTimeMillis() - ms));
}
}
/**
* Displays the given concept chain, taking into account any branches that
* might be imbedded.
*
* @param assoc
* @param depth
* @throws LBException
*/
protected void printChain(Association assoc, int depth) throws LBException {
StringBuffer indent = new StringBuffer();
for (int i = 0; i <= depth; i++)
indent.append(" ");
AssociatedConceptList concepts = assoc.getAssociatedConcepts();
for (int i = 0; i < concepts.getAssociatedConceptCount(); i++) {
// Print focus of this branch ...
AssociatedConcept concept = concepts.getAssociatedConcept(i);
Util.displayMessage(new StringBuffer(indent).append(assoc.getAssociationName()).append("->").append(
concept.getConceptCode()).append(':').append(
concept.getEntityDescription() == null ? "NO DESCRIPTION" : concept.getEntityDescription()
.getContent()).toString());
// Find and recurse printing for next batch ...
AssociationList nextLevel = concept.getSourceOf();
if (nextLevel != null && nextLevel.getAssociationCount() != 0)
for (int j = 0; j < nextLevel.getAssociationCount(); j++)
printChain(nextLevel.getAssociation(j), depth + 1);
}
}
}
