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 java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;
import org.LexGrid.LexBIG.DataModel.Collections.AssociatedConceptList;
import org.LexGrid.LexBIG.DataModel.Collections.AssociationList;
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.ConceptReference;
import org.LexGrid.LexBIG.DataModel.Core.ResolvedConceptReference;
import org.LexGrid.LexBIG.Exceptions.LBException;
import org.LexGrid.LexBIG.Exceptions.LBResourceUnavailableException;
import org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods;
import org.LexGrid.LexBIG.Extensions.Generic.LexBIGServiceConvenienceMethods.HierarchyPathResolveOption;
import org.LexGrid.LexBIG.Impl.LexBIGServiceImpl;
import org.LexGrid.LexBIG.LexBIGService.CodedNodeGraph;
import org.LexGrid.LexBIG.LexBIGService.CodedNodeSet;
import org.LexGrid.LexBIG.LexBIGService.LexBIGService;
import org.LexGrid.LexBIG.Utility.Constructors;
import org.LexGrid.codingSchemes.CodingScheme;
import org.LexGrid.commonTypes.EntityDescription;
import org.LexGrid.naming.SupportedHierarchy;
import org.apache.commons.lang.StringUtils;
/**
* Attempts to provide a tree, based on a focus code, that includes the
* following information:
*
*
* - All paths from the hierarchy root to one or more focus codes.
* - Immediate children of every node in path to root
* - Indicator to show whether any unexpanded node can be further expanded
*
*
* This example accepts two parameters... The first parameter is required, and
* must contain at least one code in a comma-delimited list. A tree is produced
* for each code. Time to produce the tree for each code is printed in
* milliseconds. In order to factor out costs of startup and shutdown, resolving
* multiple codes may offer a better overall estimate performance.
*
* The second parameter is optional, and can indicate a hierarchy ID to navigate
* when resolving child nodes. If not provided, "is_a" is assumed.
*/
public class BuildTreeForCode {
LocalNameList noopList_ = Constructors.createLocalNameList("_noop_");
public BuildTreeForCode() {
super();
}
/**
* Entry point for processing.
*
* @param args
*/
public static void main(String[] args) {
if (args.length < 1) {
System.out.println("Example: BuildTreeForCode \"C0000,C0001\"");
return;
}
try {
// Prompt for a coding scheme to run against...
CodingSchemeSummary css = Util.promptForCodeSystem();
if (css != null) {
// Declare common service classes for processing ...
LexBIGService lbsvc = LexBIGServiceImpl.defaultInstance();
LexBIGServiceConvenienceMethods lbscm = (LexBIGServiceConvenienceMethods) lbsvc
.getGenericExtension("LexBIGServiceConvenienceMethods");
// Pull the URI and version from the selected value ...
String scheme = css.getCodingSchemeURI();
CodingSchemeVersionOrTag csvt = new CodingSchemeVersionOrTag();
// For any given ontology, we know the hierarchy
// information. But to keep the code as generic
// as possible and protect against changes, we
// resolve the supported hierarchy info from the
// coding scheme...
String hierarchyID = args.length > 1 ? args[1] : "is_a";
SupportedHierarchy hierarchyDefn = getSupportedHierarchy(lbsvc, scheme, csvt, hierarchyID);
// Loop through each provided code.
// The time to produce the tree for each code is printed in
// milliseconds. In order to factor out costs of startup
// and shutdown, resolving multiple codes may offer a
// better overall estimate performance.
String[] codes = args[0].split(",");
for (String code : codes)
new BuildTreeForCode().run(lbsvc, lbscm, scheme, csvt, hierarchyDefn, code);
}
} catch (Exception e) {
Util.displayAndLogError("REQUEST FAILED !!!", e);
}
}
/**
* Prints the tree for an individual code.
*/
public void run(LexBIGService lbsvc, LexBIGServiceConvenienceMethods lbscm, String scheme,
CodingSchemeVersionOrTag csvt, SupportedHierarchy hierarchyDefn, String focusCode) throws LBException {
// Print a header and define a new tree for the code being processed.
Util.displayMessage("============================================================");
Util.displayMessage("Focus code: " + focusCode);
Util.displayMessage("============================================================");
TreeItem ti = new TreeItem("<Root>", "Root node");
long ms = System.currentTimeMillis();
int pathsResolved = 0;
try {
// Resolve 'is_a' hierarchy info. This example will
// need to make some calls outside of what is covered
// by existing convenience methods, but we use the
// registered hierarchy to prevent need to hard code
// relationship and direction info used on lookup ...
String hierarchyID = hierarchyDefn.getLocalId();
String[] associationsToNavigate = hierarchyDefn.getAssociationNames();
boolean associationsNavigatedFwd = hierarchyDefn.getIsForwardNavigable();
// Identify the set of all codes on path from root
// to the focus code ...
Map<String, EntityDescription> codesToDescriptions = new HashMap<String, EntityDescription>();
AssociationList pathsFromRoot = getPathsFromRoot(lbsvc, lbscm, scheme, csvt, hierarchyID, focusCode,
codesToDescriptions);
// Typically there will be one path, but handle multiple just in
// case. Each path from root provides a 'backbone', from focus
// code to root, for additional nodes to hang off of in our
// printout. For every backbone node, one level of children is
// printed, along with an indication of whether those nodes can
// be expanded.
for (Iterator<Association> paths = pathsFromRoot.iterateAssociation(); paths.hasNext();) {
addPathFromRoot(ti, lbsvc, lbscm, scheme, csvt, paths.next(), associationsToNavigate,
associationsNavigatedFwd, codesToDescriptions);
pathsResolved++;
}
} finally {
System.out.println("Run time (milliseconds): " + (System.currentTimeMillis() - ms) + " to resolve "
+ pathsResolved + " paths from root.");
}
// Print the result ..
printTree(ti, focusCode, 0);
}
/**
* The given path represents a multi-tier association with associated
* concepts and targets. This method expands the association content and
* adds results to the given tree item, recursing as necessary to process
* each level in the path.
*
* Nodes in the association acts as the backbone for the display. For each
* backbone node, additional children are resolved one level deep along with
* an indication of further expandability.
*/
protected void addPathFromRoot(TreeItem ti, LexBIGService lbsvc, LexBIGServiceConvenienceMethods lbscm,
String scheme, CodingSchemeVersionOrTag csvt, Association path, String[] associationsToNavigate,
boolean associationsNavigatedFwd, Map<String, EntityDescription> codesToDescriptions) throws LBException {
// First, add the branch point from the path ...
ConceptReference branchRoot = path.getAssociationReference();
String branchCode = branchRoot.getCode();
String branchCodeDescription = codesToDescriptions.containsKey(branchCode) ? codesToDescriptions
.get(branchCode).getContent() : getCodeDescription(lbsvc, scheme, csvt, branchCode);
TreeItem branchPoint = new TreeItem(branchCode, branchCodeDescription);
String branchNavText = getDirectionalLabel(lbscm, scheme, csvt, path, associationsNavigatedFwd);
// Now process elements in the branch ...
AssociatedConceptList concepts = path.getAssociatedConcepts();
for (int i = 0; i < concepts.getAssociatedConceptCount(); i++) {
// Add all immediate leafs in the branch, and indication of
// sub-nodes. Do not process codes already in the backbone here;
// they will be printed in the recursive call ...
AssociatedConcept concept = concepts.getAssociatedConcept(i);
String code = concept.getCode();
TreeItem branchItem = new TreeItem(code, getCodeDescription(concept));
branchPoint.addChild(branchNavText, branchItem);
addChildren(branchItem, lbsvc, lbscm, scheme, csvt, code, codesToDescriptions.keySet(),
associationsToNavigate, associationsNavigatedFwd);
// Recurse to process the remainder of the backbone ...
AssociationList nextLevel = concept.getSourceOf();
if (nextLevel != null) {
if (nextLevel.getAssociationCount() != 0) {
// More levels left to process ...
for (int j = 0; j < nextLevel.getAssociationCount(); j++)
addPathFromRoot(branchPoint, lbsvc, lbscm, scheme, csvt, nextLevel.getAssociation(j),
associationsToNavigate, associationsNavigatedFwd, codesToDescriptions);
} else {
// End of the line ...
// Always add immediate children ot the focus code.
addChildren(branchItem, lbsvc, lbscm, scheme, csvt, concept.getCode(), Collections.EMPTY_SET,
associationsToNavigate, associationsNavigatedFwd);
}
}
}
// Add the populated tree item to those tracked from root.
ti.addChild(branchNavText, branchPoint);
}
/**
* Populate child nodes for a single branch of the tree, and indicates
* whether further expansion (to grandchildren) is possible.
*/
protected void addChildren(TreeItem ti, LexBIGService lbsvc, LexBIGServiceConvenienceMethods lbscm, String scheme,
CodingSchemeVersionOrTag csvt, String branchRootCode, Set<String> codesToExclude,
String[] associationsToNavigate, boolean associationsNavigatedFwd) throws LBException {
// Resolve the next branch, representing children of the given
// code, navigated according to the provided relationship and
// direction. Resolve the children as a code graph, looking 2
// levels deep but leaving the final level unresolved.
CodedNodeGraph cng = lbsvc.getNodeGraph(scheme, csvt, null);
ConceptReference focus = Constructors.createConceptReference(branchRootCode, scheme);
cng = cng.restrictToAssociations(Constructors.createNameAndValueList(associationsToNavigate), null);
ResolvedConceptReferenceList branch = cng.resolveAsList(focus, associationsNavigatedFwd,
!associationsNavigatedFwd, -1, 2, noopList_, null, null, null, -1, true);
// The resolved branch will be represented by the first node in
// the resolved list. The node will be subdivided by source or
// target associations (depending on direction). The associated
// nodes define the children.
for (Iterator<ResolvedConceptReference> nodes = branch.iterateResolvedConceptReference(); nodes.hasNext();) {
ResolvedConceptReference node = nodes.next();
AssociationList childAssociationList = associationsNavigatedFwd ? node.getSourceOf() : node.getTargetOf();
// Process each association defining children ...
for (Iterator<Association> pathsToChildren = childAssociationList.iterateAssociation(); pathsToChildren
.hasNext();) {
Association child = pathsToChildren.next();
String childNavText = getDirectionalLabel(lbscm, scheme, csvt, child, associationsNavigatedFwd);
// Each association may have multiple children ...
AssociatedConceptList branchItemList = child.getAssociatedConcepts();
for (Iterator<AssociatedConcept> branchNodes = branchItemList.iterateAssociatedConcept(); branchNodes
.hasNext();) {
AssociatedConcept branchItemNode = branchNodes.next();
String branchItemCode = branchItemNode.getCode();
// Add here if not in the list of excluded codes.
// This is also where we look to see if another level
// was indicated to be available. If so, mark the
// entry with a '+' to indicate it can be expanded.
if (!codesToExclude.contains(branchItemCode)) {
TreeItem childItem = new TreeItem(branchItemCode, getCodeDescription(branchItemNode));
AssociationList grandchildBranch = associationsNavigatedFwd ? branchItemNode.getSourceOf()
: branchItemNode.getTargetOf();
if (grandchildBranch != null)
childItem.expandable = true;
ti.addChild(childNavText, childItem);
}
}
}
}
}
/**
* Prints the given tree item, recursing through all branches.
*
* @param ti
*/
protected void printTree(TreeItem ti, String focusCode, int depth) {
StringBuffer indent = new StringBuffer();
for (int i = 0; i < depth * 2; i++)
indent.append("| ");
StringBuffer codeAndText = new StringBuffer(indent).append(focusCode.equals(ti.code) ? ">>>>" : "").append(
ti.code).append(':').append(ti.text.length() > 64 ? ti.text.substring(0, 62) + "..." : ti.text).append(
ti.expandable ? " [+]" : "");
Util.displayMessage(codeAndText.toString());
indent.append("| ");
for (String association : ti.assocToChildMap.keySet()) {
Util.displayMessage(indent.toString() + association);
List<TreeItem> children = ti.assocToChildMap.get(association);
Collections.sort(children);
for (TreeItem childItem : children)
printTree(childItem, focusCode, depth + 1);
}
}
// /////////////////////////////////////////////////////
// Helper Methods
// /////////////////////////////////////////////////////
/**
* Returns the entity description for the given code.
*/
protected String getCodeDescription(LexBIGService lbsvc, String scheme, CodingSchemeVersionOrTag csvt, String code)
throws LBException {
CodedNodeSet cns = lbsvc.getCodingSchemeConcepts(scheme, csvt);
cns = cns.restrictToCodes(Constructors.createConceptReferenceList(code, scheme));
ResolvedConceptReferenceList rcrl = cns.resolveToList(null, noopList_, null, 1);
if (rcrl.getResolvedConceptReferenceCount() > 0) {
EntityDescription desc = rcrl.getResolvedConceptReference(0).getEntityDescription();
if (desc != null)
return desc.getContent();
}
return "<Not assigned>";
}
/**
* Returns the entity description for the given resolved concept reference.
*/
protected String getCodeDescription(ResolvedConceptReference ref) throws LBException {
EntityDescription desc = ref.getEntityDescription();
if (desc != null)
return desc.getContent();
return "<Not assigned>";
}
/**
* Returns the label to display for the given association and directional
* indicator.
*/
protected String getDirectionalLabel(LexBIGServiceConvenienceMethods lbscm, String scheme,
CodingSchemeVersionOrTag csvt, Association assoc, boolean navigatedFwd) throws LBException {
String assocLabel = navigatedFwd ? lbscm.getAssociationForwardName(assoc.getAssociationName(), scheme, csvt)
: lbscm.getAssociationReverseName(assoc.getAssociationName(), scheme, csvt);
if (StringUtils.isBlank(assocLabel))
assocLabel = (navigatedFwd ? "" : "[Inverse]") + assoc.getAssociationName();
return assocLabel;
}
/**
* Resolves one or more paths from the hierarchy root to the given code
* through a list of connected associations defined by the hierarchy.
*/
protected AssociationList getPathsFromRoot(LexBIGService lbsvc, LexBIGServiceConvenienceMethods lbscm,
String scheme, CodingSchemeVersionOrTag csvt, String hierarchyID, String focusCode,
Map<String, EntityDescription> codesToDescriptions) throws LBException {
// Get paths from the focus code to the root from the
// convenience method. All paths are resolved. If only
// one path is required, it would be possible to use
// HierarchyPathResolveOption.ONE to reduce processing
// and improve overall performance.
AssociationList pathToRoot = lbscm.getHierarchyPathToRoot(scheme, csvt, null, focusCode, false,
HierarchyPathResolveOption.ALL, null);
// But for purposes of this example we need to display info
// in order coming from root direction. Process the paths to root
// recursively to reverse the order for processing ...
AssociationList pathFromRoot = new AssociationList();
for (int i = pathToRoot.getAssociationCount() - 1; i >= 0; i--)
reverseAssoc(lbsvc, lbscm, scheme, csvt, pathToRoot.getAssociation(i), pathFromRoot, codesToDescriptions);
return pathFromRoot;
}
/**
* Returns a description of the hierarchy defined by the given coding scheme
* and matching the specified ID.
*/
protected static SupportedHierarchy getSupportedHierarchy(LexBIGService lbsvc, String scheme,
CodingSchemeVersionOrTag csvt, String hierarchyID) throws LBException {
CodingScheme cs = lbsvc.resolveCodingScheme(scheme, csvt);
if (cs == null) {
throw new LBResourceUnavailableException("Coding scheme not found: " + scheme);
}
for (SupportedHierarchy h : cs.getMappings().getSupportedHierarchy())
if (h.getLocalId().equals(hierarchyID))
return h;
throw new LBResourceUnavailableException("Hierarchy not defined: " + hierarchyID);
}
/**
* Recursive call to reverse order of the given association list, adding
* results to the given list. In context of this program we use this
* technique to determine the path from root, starting from the path to root
* provided by the standard convenience method.
*/
protected AssociationList reverseAssoc(LexBIGService lbsvc, LexBIGServiceConvenienceMethods lbscm, String scheme,
CodingSchemeVersionOrTag csvt, Association assoc, AssociationList addTo,
Map<String, EntityDescription> codeToEntityDescriptionMap) throws LBException {
ConceptReference acRef = assoc.getAssociationReference();
AssociatedConcept acFromRef = new AssociatedConcept();
acFromRef.setCodingSchemeName(acRef.getCodingSchemeName());
acFromRef.setConceptCode(acRef.getConceptCode());
AssociationList acSources = new AssociationList();
acFromRef.setIsNavigable(Boolean.TRUE);
acFromRef.setSourceOf(acSources);
// Use cached description if available (should be cached
// for all but original root) ...
if (codeToEntityDescriptionMap.containsKey(acRef.getConceptCode()))
acFromRef.setEntityDescription(codeToEntityDescriptionMap.get(acRef.getConceptCode()));
// Otherwise retrieve on demand ...
else
acFromRef.setEntityDescription(Constructors.createEntityDescription(getCodeDescription(lbsvc, scheme, csvt,
acRef.getConceptCode())));
AssociatedConceptList acl = assoc.getAssociatedConcepts();
for (AssociatedConcept ac : acl.getAssociatedConcept()) {
// Create reverse association (same non-directional name)
Association rAssoc = new Association();
rAssoc.setAssociationName(assoc.getAssociationName());
// On reverse, old associated concept is new reference point.
ConceptReference ref = new ConceptReference();
ref.setCodingSchemeName(ac.getCodingSchemeName());
ref.setConceptCode(ac.getConceptCode());
rAssoc.setAssociationReference(ref);
// And old reference is new associated concept.
AssociatedConceptList rAcl = new AssociatedConceptList();
rAcl.addAssociatedConcept(acFromRef);
rAssoc.setAssociatedConcepts(rAcl);
// Set reverse directional name, if available.
String dirName = assoc.getDirectionalName();
if (dirName != null)
try {
rAssoc.setDirectionalName(lbscm.isForwardName(scheme, csvt, dirName) ? lbscm
.getAssociationReverseName(assoc.getAssociationName(), scheme, csvt) : lbscm
.getAssociationReverseName(assoc.getAssociationName(), scheme, csvt));
} catch (LBException e) {
}
// Save code desc for future reference when setting up
// concept references in recursive calls ...
codeToEntityDescriptionMap.put(ac.getConceptCode(), ac.getEntityDescription());
AssociationList sourceOf = ac.getSourceOf();
if (sourceOf != null)
for (Association sourceAssoc : sourceOf.getAssociation()) {
AssociationList pos = reverseAssoc(lbsvc, lbscm, scheme, csvt, sourceAssoc, addTo,
codeToEntityDescriptionMap);
pos.addAssociation(rAssoc);
}
else
addTo.addAssociation(rAssoc);
}
return acSources;
}
// /////////////////////////////////////////////////////
// Helper classes
// /////////////////////////////////////////////////////
/**
* Inner class to hold tree items for printout.
*/
protected class TreeItem implements Comparable<TreeItem> {
public String code = null;
public String text = null;
public boolean expandable = false;
public Map<String, List<TreeItem>> assocToChildMap = new TreeMap<String, List<TreeItem>>();
public boolean equals(Object o) {
return o instanceof TreeItem && code.compareTo(((TreeItem) o).code) == 0;
}
public int compareTo(TreeItem ti) {
String c1 = code;
String c2 = ti.code;
if (c1.startsWith("@"))
return 1;
if (c2.startsWith("@"))
return -1;
return c1.compareTo(c2);
}
public TreeItem(String code, String text) {
super();
this.code = code;
this.text = text;
}
public void addAll(String assocText, List<TreeItem> children) {
for (TreeItem item : children)
addChild(assocText, item);
}
public void addChild(String assocText, TreeItem child) {
List<TreeItem> children = assocToChildMap.get(assocText);
if (children == null) {
children = new ArrayList<TreeItem>();
assocToChildMap.put(assocText, children);
}
int i;
if ((i = children.indexOf(child)) >= 0) {
TreeItem existingTreeItem = children.get(i);
for (String assoc : child.assocToChildMap.keySet()) {
List<TreeItem> toAdd = child.assocToChildMap.get(assoc);
if (!toAdd.isEmpty()) {
existingTreeItem.addAll(assoc, toAdd);
existingTreeItem.expandable = false;
}
}
} else
children.add(child);
}
}
}
