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 the hierarchical relationships
* for a specific code, ancestors or descendants, within a fixed distance.
*
* This program accepts two parameters, indicating the code and distance. The
* first parameter is the code (required). The second parameter is the distance
* (optional). If 1, immediate children are displayed. If 2, grandchildren are
* displayed, etc. If absent or < 0, all downstream branches are displayed.
*
* 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 ListHierarchyByCode {
final static int DEFAULT_DISTANCE = -1;
public ListHierarchyByCode() {
super();
}
/**
* Entry point for processing.
*
* @param args
*/
public static void main(String[] args) {
if (args.length < 1) {
System.out.println("Example: ListHierarchyByCode \"C0000\" 2");
return;
}
;
try {
String code = args[0];
int distance = args.length == 1 ? DEFAULT_DISTANCE : Integer.parseInt(args[1]);
new ListHierarchyByCode().run(code, distance);
} catch (NumberFormatException nfe) {
System.out.println("Parameter 2 must indicate a number representing maximum distance to display.\n"
+ "Example: ListHierarchyByCode \"C0000\" 2");
return;
} catch (Exception e) {
Util.displayAndLogError("REQUEST FAILED !!!", e);
}
}
public void run(String code, int maxDistance) throws LBException {
CodingSchemeSummary css = Util.promptForCodeSystem();
long ms = System.currentTimeMillis();
try {
if (css != null) {
LexBIGService lbSvc = LexBIGServiceImpl.defaultInstance();
LexBIGServiceConvenienceMethods lbscm = (LexBIGServiceConvenienceMethods) lbSvc
.getGenericExtension("LexBIGServiceConvenienceMethods");
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 and levels ...
String[] hierarchyIDs = lbscm.getHierarchyIDs(scheme, csvt);
for (int i = 0; i < hierarchyIDs.length; i++) {
String hierarchyID = hierarchyIDs[i];
String reportedDistance = maxDistance >= 0 ? Integer.toString(maxDistance) : "ALL";
Util.displayMessage("------------------------------------------------------------");
Util.displayMessage("Hierarchy ID: " + hierarchyID);
Util.displayMessage("------------------------------------------------------------");
Util.displayMessage("Paths to ancestors (distance <= " + reportedDistance + ") ...");
printLevelPrev(lbscm, scheme, csvt, hierarchyID, code, maxDistance, 0);
Util.displayMessage("");
Util.displayMessage("Paths to descendants (distance <= " + reportedDistance + ") ...");
printLevelNext(lbscm, scheme, csvt, hierarchyID, code, maxDistance, 0);
Util.displayMessage("");
}
}
} finally {
System.out.println("Run time (ms): " + (System.currentTimeMillis() - ms));
}
}
/**
* Displays ancestors for a code within the specified hierarchy up to the
* given distance or until paths to root nodes are exhausted, recursing as
* necessary.
*
* @param lbcsm
* @param scheme
* @param csvt
* @param hierarchyID
* @param code
* @param maxDistance
* @param currentDistance
* @throws LBException
*/
protected void printLevelPrev(LexBIGServiceConvenienceMethods lbscm, String scheme, CodingSchemeVersionOrTag csvt,
String hierarchyID, String code, int maxDistance, int currentDistance) throws LBException {
if (maxDistance < 0 || currentDistance < maxDistance) {
StringBuffer indent = new StringBuffer();
for (int i = 0; i <= currentDistance; i++)
indent.append(" ");
AssociationList associations = lbscm.getHierarchyLevelPrev(scheme, csvt, hierarchyID, code, false, null);
for (int i = 0; i < associations.getAssociationCount(); i++) {
Association assoc = associations.getAssociation(i);
AssociatedConceptList concepts = assoc.getAssociatedConcepts();
for (int j = 0; j < concepts.getAssociatedConceptCount(); j++) {
AssociatedConcept concept = concepts.getAssociatedConcept(j);
String prevCode = concept.getConceptCode();
String prevDesc = concept.getEntityDescription() == null ? "NO DESCRIPTION" : concept
.getEntityDescription().getContent();
Util.displayMessage(indent + assoc.getDirectionalName() + "<-" + prevCode + ":" + prevDesc);
printLevelPrev(lbscm, scheme, csvt, hierarchyID, prevCode, maxDistance, currentDistance + 1);
}
}
}
}
/**
* Displays descendants for a code within the specified hierarchy up to the
* given distance or until all paths to leaf nodes is exhausted, recursing
* as necessary.
*
* @param lbscm
* @param scheme
* @param csvt
* @param hierarchyID
* @param code
* @param maxDistance
* @param currentDistance
* @throws LBException
*/
protected void printLevelNext(LexBIGServiceConvenienceMethods lbscm, String scheme, CodingSchemeVersionOrTag csvt,
String hierarchyID, String code, int maxDistance, int currentDistance) throws LBException {
if (maxDistance < 0 || currentDistance < maxDistance) {
StringBuffer indent = new StringBuffer();
for (int i = 0; i <= currentDistance; i++)
indent.append(" ");
AssociationList associations = lbscm.getHierarchyLevelNext(scheme, csvt, hierarchyID, code, false, null);
for (int i = 0; i < associations.getAssociationCount(); i++) {
Association assoc = associations.getAssociation(i);
AssociatedConceptList concepts = assoc.getAssociatedConcepts();
for (int j = 0; j < concepts.getAssociatedConceptCount(); j++) {
AssociatedConcept concept = concepts.getAssociatedConcept(j);
String nextCode = concept.getConceptCode();
String nextDesc = concept.getEntityDescription().getContent();
Util.displayMessage(indent + assoc.getDirectionalName() + "->" + nextCode + ":" + nextDesc);
printLevelNext(lbscm, scheme, csvt, hierarchyID, nextCode, maxDistance, currentDistance + 1);
}
}
}
}
}
