/**
ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
License:
ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
EXHIBIT A. CPAL version 1.0
The contents of this file are subject to the CPAL 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://isa-tools.org/licenses/ISAcreator-license.html.
The License is based on the Mozilla Public License version 1.1 but Sections
14 and 15 have been added to cover use of software over a computer network and
provide for limited attribution for the Original Developer. In addition, Exhibit
A has been modified to be consistent with Exhibit B.
Software distributed under the License is distributed on an AS IS basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
the specific language governing rights and limitations under the License.
The Original Code is ISAcreator.
The Original Developer is the Initial Developer. The Initial Developer of the
Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com;
Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com;
http://www.isa-tools.org). All portions of the code written by the ISA Team are
Copyright (c) 2007-2011 ISA Team. All Rights Reserved.
EXHIBIT B. Attribution Information
Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team
Attribution Phrase: Developed by the ISA Team
Attribution URL: http://www.isa-tools.org
Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png
Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL.
Sponsors:
The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone).
*/
package org.isatools.isacreator.ontologybrowsingutils;
import org.isatools.isacreator.configuration.Ontology;
import org.isatools.isacreator.configuration.OntologyBranch;
import org.isatools.isacreator.configuration.RecommendedOntology;
import org.isatools.isacreator.ontologymanager.BioPortal4Client;
import org.isatools.isacreator.ontologymanager.OntologyService;
import org.isatools.isacreator.ontologymanager.common.OntologyTerm;
import org.isatools.isacreator.ontologymanager.utils.OntologyUtils;
import org.isatools.isacreator.utils.StringProcessing;
import javax.swing.*;
import javax.swing.event.*;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.DefaultTreeModel;
import javax.swing.tree.TreePath;
import java.awt.*;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.List;
import java.util.Map;
/**
* Created by the ISA team
*
* @author Eamonn Maguire (eamonnmag@gmail.com)
* <p/>
* Date: 16/05/2011
* Time: 15:46
*/
public class WSOntologyTreeCreator implements OntologyTreeCreator, TreeSelectionListener, TreeModelListener, TreeExpansionListener, TreeSubject {
private List<TreeObserver> observers;
private DefaultMutableTreeNode rootNode;
private DefaultTreeModel treeModel;
private Map<String, RecommendedOntology> ontologies;
private Container browser;
private static BioPortal4Client bioportalClient;
private JTree tree;
public WSOntologyTreeCreator(Container browser, JTree tree) {
this.browser = browser;
this.tree = tree;
observers = new ArrayList<TreeObserver>();
bioportalClient = new BioPortal4Client();
}
public DefaultMutableTreeNode createTree(Map<String, RecommendedOntology> ontologies) throws FileNotFoundException {
this.ontologies = ontologies;
rootNode = new DefaultMutableTreeNode(ontologies.size() + " recommended ontologies");
treeModel = new DefaultTreeModel(rootNode);
treeModel.addTreeModelListener(this);
tree.setModel(treeModel);
tree.addTreeExpansionListener(this);
tree.addTreeSelectionListener(this);
initiateOntologyVisualization();
return rootNode;
}
private void initiateOntologyVisualization() {
// instead of visualising just one ontology, we need to visualise all that have been selected to browse on, if they have branches
// specified...or maybe should allow to browse the whole ontology as well.
try {
browser.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
for (String ontology : ontologies.keySet()) {
RecommendedOntology recommendedOntology = ontologies.get(ontology);
// if ontology has no branch specified, query the whole ontology.
Map<String, OntologyTerm> rootTerms;
String nodeLabel = recommendedOntology.getOntology().getOntologyDisplayLabel();
if (recommendedOntology.getBranchToSearchUnder() != null) {
nodeLabel += " under " + recommendedOntology.getBranchToSearchUnder().getBranchName();
String branchIdentifier = recommendedOntology.getBranchToSearchUnder().getBranchIdentifier();
if (StringProcessing.isURL(branchIdentifier)) {
branchIdentifier = OntologyUtils.getModifiedBranchIdentifier(branchIdentifier, "#");
}
rootTerms = bioportalClient.getTermChildren(branchIdentifier, recommendedOntology.getOntology().getOntologyAbbreviation());
} else {
rootTerms = bioportalClient.getOntologyRoots(recommendedOntology.getOntology().getOntologyAbbreviation());
}
DefaultMutableTreeNode ontologyNode = new DefaultMutableTreeNode(nodeLabel);
rootNode.add(ontologyNode);
boolean addedTerms = false;
// update the tree
for (String termId : rootTerms.keySet()) {
if (termId != null && !termId.equalsIgnoreCase("")) {
addedTerms = true;
addTermToTree(ontologyNode, rootTerms.get(termId), recommendedOntology.getOntology());
}
}
if (recommendedOntology.getOntology().getOntologyAbbreviation().equalsIgnoreCase("newt")) {
addInformationToTree(ontologyNode, "NEWT cannot be loaded from the Ontology lookup service");
}
if (!addedTerms) {
addInformationToTree(ontologyNode, "Problem loading " + recommendedOntology.getOntology().getOntologyAbbreviation() + " (version "
+ recommendedOntology.getOntology().getOntologyVersion() + ") from BioPortal!");
}
}
updateTree();
} catch (Exception e) {
addInformationToTree(rootNode, "No connection available...!");
updateTree();
} finally {
browser.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
}
}
public void updateTree() {
DefaultMutableTreeNode root = (DefaultMutableTreeNode) treeModel.getRoot();
TreePath path = new TreePath(root.getPath());
tree.collapsePath(path);
tree.expandPath(path);
}
/**
* Method to preload the next level of the ontology so that we know which nodes are leaves and which are
* nodes at any given level.
*
* @param termAccession - accession of term to load children for
* @param parentTerm - the parent node of the term being searched for.
*/
private void preloadNextOntologyLevel(String termAccession, DefaultMutableTreeNode parentTerm) {
browser.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR));
Ontology ontology = extractOntologyFromNode(parentTerm);
Map<String, OntologyTerm> termChildren = bioportalClient.getTermChildren(termAccession, ontology.getOntologyAbbreviation());
// add the level of non visible nodes
for (String accession : termChildren.keySet()) {
addTermToTree(parentTerm, termChildren.get(accession), ontology);
}
browser.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
}
private Ontology extractOntologyFromNode(DefaultMutableTreeNode node) {
if (node.getUserObject() instanceof OntologyTreeItem) {
OntologyTreeItem termNode = (OntologyTreeItem) node.getUserObject();
return termNode.getOntology();
}
return null;
}
private void addInformationToTree(DefaultMutableTreeNode parent, String information) {
DefaultMutableTreeNode childNode =
new DefaultMutableTreeNode(information);
if (parent == null) {
parent = rootNode;
}
treeModel.insertNodeInto(childNode, parent, parent.getChildCount());
}
private void addTermToTree(DefaultMutableTreeNode parent, OntologyTerm ontologyTerm, Ontology ontology) {
if (ontologyTerm != null) {
DefaultMutableTreeNode childNode =
new DefaultMutableTreeNode(new OntologyTreeItem(
new OntologyBranch(ontologyTerm.getOntologyTermAccession(), ontologyTerm.getOntologyTermName()), ontology));
if (parent == null) {
parent = rootNode;
}
treeModel.insertNodeInto(childNode, parent, parent.getChildCount());
}
}
public void treeExpanded(TreeExpansionEvent treeExpansionEvent) {
// get selected node
DefaultMutableTreeNode node = (DefaultMutableTreeNode) treeExpansionEvent.getPath().getLastPathComponent();
if (node == null) {
return;
}
// add next level of nodes if not already added
final Enumeration<DefaultMutableTreeNode> treeNodeEnumeration = node.children();
while (treeNodeEnumeration.hasMoreElements()) {
DefaultMutableTreeNode treeNode = treeNodeEnumeration.nextElement();
if (treeNode.getUserObject() instanceof OntologyTreeItem) {
if (treeNode.getChildCount() == 0) {
OntologyTreeItem currentTerm = (OntologyTreeItem) treeNode.getUserObject();
preloadNextOntologyLevel(currentTerm.getBranch().getBranchIdentifier(), treeNode);
}
}
}
}
public void expandTreeToReachTerm(OntologyTerm term) {
Enumeration treeVisitor = rootNode.breadthFirstEnumeration();
Ontology ontology = new Ontology("", term.getOntologyVersionId(), term.getOntologySourceInformation().getSourceName(), term.getOntologySourceInformation().getSourceDescription());
Map<String, OntologyTerm> nodeParentsFromRoot = bioportalClient.getAllTermParents(term.getOntologyTermAccession(), term.getOntologySourceInformation().getSourceVersion());
TreePath lastPath = null;
for (OntologyTerm node : nodeParentsFromRoot.values()) {
while (treeVisitor.hasMoreElements()) {
DefaultMutableTreeNode visitingNode = (DefaultMutableTreeNode) treeVisitor.nextElement();
if (visitingNode.getUserObject() instanceof OntologyTreeItem) {
OntologyTreeItem termNode = (OntologyTreeItem) visitingNode.getUserObject();
if (termNode.getBranch().getBranchName().toLowerCase().equalsIgnoreCase(node.getOntologyTermName())
|| termNode.getBranch().getBranchIdentifier().equalsIgnoreCase(node.getOntologyTermAccession())) {
TreePath pathToNode = new TreePath(visitingNode.getPath());
tree.expandPath(pathToNode);
tree.setSelectionPath(pathToNode);
lastPath = pathToNode;
break;
}
}
}
}
if (lastPath != null) {
tree.scrollPathToVisible(lastPath);
tree.repaint();
}
}
public void valueChanged(TreeSelectionEvent treeSelectionEvent) {
// get selected node
DefaultMutableTreeNode node = (DefaultMutableTreeNode) treeSelectionEvent.getPath().getLastPathComponent();
if (node == null) {
return;
}
// get node data object
if (node.getUserObject() instanceof OntologyTreeItem) {
OntologyTreeItem ontologyTerm = (OntologyTreeItem) node.getUserObject();
// tell the observers that an item has been selected.
notifyObservers();
// load the children and the meta data, unless the term is the 'no roots defined' dummy term
if (ontologyTerm != null && !ontologyTerm.getBranch().getBranchIdentifier().equalsIgnoreCase("No Root Terms Defined!")) {
// load children only for leaf nodes and those that have not been marked as processed
if (node.isLeaf() && node.getAllowsChildren()) {
// load children. if no children, set allowsChildren to false
Map<String, OntologyTerm> termChildren = bioportalClient.getTermChildren(ontologyTerm.getBranch().getBranchIdentifier(),
ontologyTerm.getOntology().getOntologyAbbreviation());
if (termChildren.size() > 0) {
node.setAllowsChildren(true);
}
}
} else {
rootNode.removeAllChildren();
treeModel.reload();
}
}
}
public void treeNodesChanged(TreeModelEvent treeModelEvent) {
}
public void treeNodesInserted(TreeModelEvent treeModelEvent) {
}
public void treeNodesRemoved(TreeModelEvent treeModelEvent) {
}
public void treeStructureChanged(TreeModelEvent treeModelEvent) {
}
public void treeCollapsed(TreeExpansionEvent treeExpansionEvent) {
}
public void notifyObservers() {
for (TreeObserver observer : observers) {
observer.notifyOfSelection();
}
}
public void registerObserver(TreeObserver observer) {
if (observer != null) {
observers.add(observer);
}
}
public void unregisterObserver(TreeObserver observer) {
if (observer != null) {
if (observers.contains(observer)) {
observers.remove(observer);
}
}
}
public void setBrowser(Container browser) {
this.browser = browser;
}
}