forked from bioclipse/bioclipse.ds
/
DSView.java
1621 lines (1309 loc) · 55.6 KB
/
DSView.java
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/* *****************************************************************************
* Copyright (c) 2009-2010 Ola Spjuth.
* All rights reserved. This program and the accompanying materials
* are made available under the terms of the Eclipse Public License v1.0
* which accompanies this distribution, and is available at
* http://www.eclipse.org/legal/epl-v10.html
*
* Contributors:
* Ola Spjuth - initial API and implementation
******************************************************************************/
package net.bioclipse.ds.ui.views;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import net.bioclipse.cdk.business.ICDKManager;
import net.bioclipse.cdk.domain.CDKMolecule;
import net.bioclipse.cdk.domain.ICDKMolecule;
import net.bioclipse.cdk.jchempaint.editor.JChemPaintEditor;
import net.bioclipse.cdk.ui.sdfeditor.editor.MultiPageMoleculesEditorPart;
import net.bioclipse.core.business.BioclipseException;
import net.bioclipse.core.util.LogUtils;
import net.bioclipse.ds.report.AbstractTestReportModel;
import net.bioclipse.ds.ui.Activator;
import net.bioclipse.ds.business.IDSManager;
import net.bioclipse.ds.model.Endpoint;
import net.bioclipse.ds.model.IDSTest;
import net.bioclipse.ds.model.ITestResult;
import net.bioclipse.ds.model.TestRun;
import net.bioclipse.ds.model.result.SimpleResult;
import net.bioclipse.ds.report.DSSingleReportModel;
import net.bioclipse.ds.report.StatusHelper;
import net.bioclipse.ds.ui.DSContextProvider;
import net.bioclipse.ds.ui.ImageHelper;
import net.bioclipse.ds.ui.VotingConsensus;
import net.bioclipse.jobs.BioclipseJob;
import net.bioclipse.jobs.BioclipseJobUpdateHook;
import org.apache.log4j.Logger;
import org.eclipse.swt.events.PaintEvent;
import org.eclipse.swt.events.PaintListener;
import org.eclipse.swt.graphics.Image;
import org.eclipse.swt.layout.GridData;
import org.eclipse.swt.layout.GridLayout;
import org.eclipse.swt.widgets.Canvas;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Display;
import org.eclipse.swt.widgets.Text;
import org.eclipse.ui.help.IWorkbenchHelpSystem;
import org.eclipse.ui.part.*;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.IStatus;
import org.eclipse.core.runtime.Status;
import org.eclipse.core.runtime.jobs.IJobChangeEvent;
import org.eclipse.core.runtime.jobs.IJobChangeListener;
import org.eclipse.core.runtime.jobs.Job;
import org.eclipse.help.IContextProvider;
import org.eclipse.jface.util.IPropertyChangeListener;
import org.eclipse.jface.util.PropertyChangeEvent;
import org.eclipse.jface.viewers.*;
import org.eclipse.jface.action.*;
import org.eclipse.jface.dialogs.IPageChangedListener;
import org.eclipse.jface.dialogs.MessageDialog;
import org.eclipse.jface.dialogs.PageChangedEvent;
import org.eclipse.ui.*;
import org.eclipse.swt.widgets.Menu;
import org.eclipse.swt.SWT;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.IAtomContainer;
/**
*
* @author ola
*
*/
public class DSView extends ViewPart implements IPartListener2, IPropertyChangeListener {
private static final Logger logger = Logger.getLogger(DSView.class);
public static final String VIEW_ID="net.bioclipse.ds.ui.views.DSView";
private static Image questImg;
private static Image warnImg;
private static Image crossImg;
private static Image checkImg;
private static Image wheelImg;
private static Image equalImg;
private TreeViewer viewer;
private Action runAction;
//Kepp track of existing mappings from editor to TestRun
private Map<ICDKMolecule, List<TestRun>> molTestMap;
//Kepp track of existing mappings from molecule to TestRun
private Map<ICDKMolecule, IPropertyChangeListener> molListenerMap;
//The active test runs. Initializes upon test run, and updates on editor switch
private List<TestRun> activeTestRuns;
//Tracks the state in the view. True if a run has been made.
private boolean executed;
private Action clearAction;
private Action excludeAction;
private Action includeAction;
private Action expandAllAction;
private Action collapseAllAction;
private Action refreshAction;
private List<BioclipseJob<List<ITestResult>>> runningJobs;
/**
* Used to store and set selection for a new run
*/
private IStructuredSelection storedSelection;
private String selectedProperty;
private Action autoRunAction;
private boolean autorun;
//The currently shown image in consensusView
private Image consensusImage;
private Text consensusText;
private Canvas consensusCanvas;
private Action helpAction;
private IContextProvider contextProvider;
private static DSView instance;
/**
* The constructor.
*/
public DSView() {
}
/*
* Getters and setters
*/
public static DSView getInstance(){
return instance;
}
public List<BioclipseJob<List<ITestResult>>> getRunningJobs() {
return runningJobs;
}
public boolean isExecuted() {
return executed;
}
public void setExecuted( boolean executed ) {
this.executed = executed;
}
public void setAutorun( boolean autorun ) {
this.autorun = autorun;
}
public boolean isAutorun() {
return autorun;
}
/*
* Methods
*/
/**
* This is a callback that will allow us
* to create the viewer and initialize it.
*/
public void createPartControl(Composite parent) {
DSView.instance=this;
GridLayout gridLayout = new GridLayout();
gridLayout.numColumns = 1;
parent.setLayout(gridLayout);
viewer = new TreeViewer(parent, SWT.BORDER | SWT.MULTI | SWT.H_SCROLL | SWT.V_SCROLL);
ColumnViewerToolTipSupport.enableFor(viewer);
viewer.setContentProvider(new DSViewContentProvider());
// viewer.setLabelProvider(new DecoratingLabelProvider(new DSViewLabelProvider(),new DSViewDecorator()));
viewer.setLabelProvider(new DSViewLabelProvider());
// viewer.setSorter(new ViewerSorter());
viewer.addFilter( new HideNotVisbleFilter() );
viewer.addSelectionChangedListener( new ISelectionChangedListener(){
public void selectionChanged( SelectionChangedEvent event ) {
updateActionStates();
Object obj = ((IStructuredSelection)event.getSelection()).getFirstElement();
if ( obj instanceof ITestResult ) {
ITestResult tr = (ITestResult) obj;
selectedProperty=tr.getResultProperty();
}
}
});
GridData gridData = new GridData(GridData.FILL, GridData.FILL, true, true);
viewer.getTree().setLayoutData(gridData);
viewer.setInput(new String[]{"Initializing..."});
// Create the help context id for the viewer's control
PlatformUI.getWorkbench().getHelpSystem().setHelp(viewer.getControl(), VIEW_ID);
makeActions();
hookContextMenu();
contributeToActionBars();
//Create the ConsensusSection at the bottom of View
Composite consensusComposite=new Composite(parent,SWT.BORDER);
GridData gridData2 = new GridData(GridData.FILL, GridData.END, true, false);
gridData2.heightHint=50;
consensusComposite.setLayoutData(gridData2);
GridLayout gridLayout2 = new GridLayout(2, false);
gridLayout2.marginLeft=0;
gridLayout2.marginWidth=0;
gridLayout2.marginBottom=10;
gridLayout2.marginTop=0;
gridLayout2.marginRight=0;
gridLayout2.marginHeight=0;
consensusComposite.setLayout(gridLayout2);
//Create components of consensusComposite
consensusText=new Text(consensusComposite,SWT.BORDER);
GridData gridData3 = new GridData(GridData.FILL, GridData.BEGINNING, true, true);
gridData3.heightHint=40;
consensusText.setLayoutData(gridData3);
//Initialize and cache consensus images
questImg= Activator.getImageDecriptor( "icons48/question.png" ).createImage();
warnImg= Activator.getImageDecriptor( "icons48/warn.png" ).createImage();
crossImg= Activator.getImageDecriptor( "icons48/cross.png" ).createImage();
checkImg= Activator.getImageDecriptor( "icons48/check.png" ).createImage();
wheelImg= Activator.getImageDecriptor( "icons48/wheel.png" ).createImage();
equalImg= Activator.getImageDecriptor( "icons48/equal.png" ).createImage();
//Start off with a question-image
consensusImage=questImg;
consensusCanvas = new Canvas(consensusComposite,SWT.NO_REDRAW_RESIZE);
consensusCanvas.addPaintListener(new PaintListener() {
public void paintControl(PaintEvent e) {
e.gc.drawImage(consensusImage,0,1);
}
});
GridData gridData4 = new GridData(GridData.END, GridData.BEGINNING, false, false);
gridData4.widthHint=50;
gridData4.heightHint=50;
gridData4.minimumHeight=50;
gridData4.minimumWidth=50;
consensusCanvas.setLayoutData(gridData4);
//Initialize instance variables
molTestMap=new HashMap<ICDKMolecule, List<TestRun>>();
molListenerMap=new HashMap<ICDKMolecule, IPropertyChangeListener>();
runningJobs=new ArrayList<BioclipseJob<List<ITestResult>>>();
//Turn off autorun by default
setAutorun( false );
updateActionStates();
Job job=new Job("Initializing decision support tests"){
@Override
protected IStatus run( IProgressMonitor monitor ) {
IDSManager ds = net.bioclipse.ds.Activator.getDefault().getJavaManager();
try {
monitor.beginTask( "Initializing decision support tests", ds.getTests().size()+1 );
monitor.worked( 1 );
for (String testID : ds.getTests()){
IDSTest test = ds.getTest( testID );
monitor.subTask( "Initializing test: " + testID );
test.initialize( monitor );
}
Display.getDefault().asyncExec( new Runnable(){
public void run() {
//Init viewer with available endpoints
IDSManager ds = net.bioclipse.ds.Activator.getDefault().getJavaManager();
try {
viewer.setInput(ds.getFullEndpoints().toArray());
viewer.expandAll();
} catch ( BioclipseException e ) {
LogUtils.handleException( e, logger, Activator.PLUGIN_ID );
viewer.setInput(new String[]{"Error initializing tests"});
}
updateConsensusView();
updateActionStates();
//Listen for part lifecycle events to react on editors
getSite().getWorkbenchWindow().getPartService().addPartListener(DSView.getInstance());
//Make viewer post selection to Eclipse
getSite().setSelectionProvider(viewer);
//If editor is open, react on it
if (getSite()==null) return;
if (getSite().getWorkbenchWindow()==null) return;
if (getSite().getWorkbenchWindow().getActivePage()==null) return;
IEditorPart openEditor = getSite().getWorkbenchWindow()
.getActivePage().getActiveEditor();
if (openEditor!=null){
activateEditor(openEditor);
if (isAutorun()){
// doRunAllTests();
//TODO: Implement
}
}
}
});
} catch ( Exception e1 ) {
LogUtils.handleException( e1, logger, Activator.PLUGIN_ID );
Display.getDefault().asyncExec( new Runnable(){
public void run() {
viewer.setInput(new String[]{"Error initializing tests"});
}
});
return new Status(IStatus.ERROR, Activator.PLUGIN_ID,
"All tests could not be initalized: " + e1.getMessage());
}
monitor.done();
return Status.OK_STATUS;
}
};
job.setUser( false );
job.schedule();
}
private void updateConsensusView() {
if (activeTestRuns==null){
consensusText.setText( "Not run");
consensusImage=questImg;
consensusCanvas.update();
consensusCanvas.redraw();
return;
}
boolean running=false;
boolean notStarted=false;
//If we have any tests running or not started, do not do consensus
for (TestRun tr : activeTestRuns){
if (tr.getStatus()==TestRun.RUNNING)
running=true;
else if (tr.getStatus()==TestRun.NOT_STARTED)
notStarted=true;
}
if(notStarted){
consensusText.setText( "Tests not started");
consensusImage=questImg;
}
else if (running){
consensusText.setText( "Tests running...");
consensusImage=wheelImg;
}
else{
int res=VotingConsensus.getConsensusFromTestRuns(activeTestRuns);
if (res==ITestResult.POSITIVE){
consensusText.setText( "Consensus: POSITIVE");
consensusImage=warnImg;
}
else if (res==ITestResult.NEGATIVE){
consensusText.setText( "Consensus: NEGATIVE");
consensusImage=checkImg;
}
else if (res==ITestResult.INCONCLUSIVE){
consensusText.setText( "Consensus: INCONCLUSIVE");
consensusImage=equalImg;
}
}
consensusCanvas.update();
consensusCanvas.redraw();
}
/**
* Clean up part listener
*/
@Override
public void dispose() {
super.dispose();
getSite().getWorkbenchWindow().getPartService().removePartListener(this);
//unregister all listeners
for (ICDKMolecule mole : molListenerMap.keySet()){
IPropertyChangeListener li = molListenerMap.get( mole );
if ( mole instanceof JChemPaintEditor ) {
JChemPaintEditor jcp = (JChemPaintEditor) mole;
jcp.removePropertyChangedListener( li);
}
}
molListenerMap.clear();
molListenerMap=null;
}
private void hookContextMenu() {
MenuManager menuMgr = new MenuManager("#PopupMenu", "net.bioclipse.ds.context");
menuMgr.setRemoveAllWhenShown(true);
menuMgr.addMenuListener(new IMenuListener() {
public void menuAboutToShow(IMenuManager manager) {
updateActionStates();
DSView.this.fillContextMenu(manager);
}
});
Menu menu = menuMgr.createContextMenu(viewer.getControl());
viewer.getControl().setMenu(menu);
getSite().registerContextMenu(menuMgr, viewer);
}
private void contributeToActionBars() {
IActionBars bars = getViewSite().getActionBars();
fillLocalPullDown(bars.getMenuManager());
fillLocalToolBar(bars.getToolBarManager());
}
private void fillLocalPullDown(IMenuManager manager) {
}
private void fillContextMenu(IMenuManager manager) {
manager.add(runAction);
manager.add(clearAction);
manager.add(new Separator());
manager.add(includeAction);
manager.add(excludeAction);
manager.add(new Separator());
manager.add(refreshAction);
manager.add(new Separator(IWorkbenchActionConstants.MB_ADDITIONS));
}
private void fillLocalToolBar(IToolBarManager manager) {
manager.add(autoRunAction);
manager.add(runAction);
manager.add(clearAction);
manager.add(new Separator());
manager.add(includeAction);
manager.add(excludeAction);
manager.add(new Separator());
manager.add(expandAllAction);
manager.add(collapseAllAction);
manager.add(new Separator());
manager.add(helpAction);
manager.add(new Separator(IWorkbenchActionConstants.MB_ADDITIONS));
}
private void updateActionStates() {
if (activeTestRuns!=null && activeTestRuns.size()>0)
runAction.setEnabled( true );
else
runAction.setEnabled( false );
if (isAutorun()){
autoRunAction.setImageDescriptor( Activator.getImageDecriptor( "icons/fastforward_dis2.png" ));
}else{
autoRunAction.setImageDescriptor(Activator.getImageDecriptor( "icons/fastforward.png" ));
}
boolean testSelected=false;
for (Object obj : ((IStructuredSelection)viewer.getSelection()).toList()){
if ( obj instanceof TestRun ) {
testSelected=true;
}
else if ( obj instanceof IDSTest ) {
testSelected=true;
}
}
if (testSelected){
includeAction.setEnabled( true );
excludeAction.setEnabled( true );
}
else{
includeAction.setEnabled( false );
excludeAction.setEnabled( false );
}
}
private void makeActions() {
runAction = new Action() {
public void run() {
doRunAllTests();
}
};
runAction.setText("Run all Tests");
runAction.setToolTipText("Runs the Decision Support Tests " +
"on the active molecule(s)");
runAction.setImageDescriptor(Activator.getImageDecriptor( "icons/smallRun.gif" ));
runAction.setDisabledImageDescriptor( Activator.getImageDecriptor( "icons/smallRun_dis.gif" ));
autoRunAction = new Action() {
public void run() {
setAutorun( !autorun);
updateActionStates();
if (autorun){
// setAutoRunPropListener();
doRunAllTests();
}else{
// clearAutoRunPropListener();
}
}
};
autoRunAction.setText("Toggle AutoTest");
autoRunAction.setToolTipText("Turns on/off automatic running of tests on structural changes");
autoRunAction.setImageDescriptor(Activator.getImageDecriptor( "icons/fastforward.png" ));
autoRunAction.setDisabledImageDescriptor( Activator.getImageDecriptor( "icons/fastforward_dis2.png" ));
clearAction = new Action() {
public void run() {
doClearAllTests();
}
};
clearAction.setText("Clear all Tests");
clearAction.setToolTipText("Clear all active tests");
clearAction.setImageDescriptor(Activator.getImageDecriptor( "icons/broom.png" ));
excludeAction = new Action() {
public void run() {
doExcludeSelectedTests();
}
};
excludeAction.setText("Exclude test");
excludeAction.setToolTipText("Exclude selected test(s)");
excludeAction.setImageDescriptor(Activator.getImageDecriptor( "icons/item_delete.gif" ));
excludeAction.setDisabledImageDescriptor(Activator.getImageDecriptor( "icons/item_delete_dis.gif" ));
includeAction = new Action() {
public void run() {
doIncludeSelectedTests();
}
};
includeAction.setText("Include test");
includeAction.setToolTipText("Include selected test(s)");
includeAction.setImageDescriptor(Activator.getImageDecriptor( "icons/item_add.gif" ));
includeAction.setDisabledImageDescriptor(Activator.getImageDecriptor( "icons/item_add_dis.gif" ));
collapseAllAction = new Action() {
public void run() {
viewer.collapseAll();
}
};
collapseAllAction.setText("Collapse all");
collapseAllAction.setToolTipText("Collapse all tests");
collapseAllAction.setImageDescriptor(Activator.getImageDecriptor( "icons/collapseall.gif" ));
expandAllAction = new Action() {
public void run() {
viewer.expandAll();
}
};
expandAllAction.setText("Expand all");
expandAllAction.setToolTipText("Expand all tests to reveal hits");
expandAllAction.setImageDescriptor(Activator.getImageDecriptor( "icons/expandall.gif" ));
refreshAction = new Action() {
public void run() {
viewer.refresh();
}
};
refreshAction.setText("Refresh");
refreshAction.setToolTipText("Force a refresh of all tests' status");
refreshAction.setImageDescriptor(Activator.getImageDecriptor( "icons/refresh2.png" ));
helpAction = new Action() {
public void run() {
IWorkbenchHelpSystem helpSystem = PlatformUI.getWorkbench()
.getHelpSystem();
helpSystem.displayHelpResource("/" + Activator.PLUGIN_ID +
"/html/maintopic.html");
}
};
helpAction.setText("Help");
helpAction.setToolTipText("Open help for teh Decision Support");
helpAction.setImageDescriptor(Activator.getImageDecriptor( "icons/help.gif" ));
}
protected void doIncludeSelectedTests() {
IStructuredSelection sel = (IStructuredSelection)viewer.getSelection();
for (Object obj : sel.toList()){
if ( obj instanceof IDSTest ) {
IDSTest dstest = (IDSTest) obj;
dstest.setExcluded( false );
viewer.refresh(dstest);
}
else if ( obj instanceof TestRun ) {
TestRun testrun = (TestRun) obj;
testrun.setStatus( TestRun.NOT_STARTED);
testrun.getTest().setExcluded( false );
viewer.refresh(testrun);
}
}
}
protected void doExcludeSelectedTests() {
IStructuredSelection sel = (IStructuredSelection)viewer.getSelection();
for (Object obj : sel.toList()){
if ( obj instanceof IDSTest ) {
IDSTest dstest = (IDSTest) obj;
dstest.setExcluded( true );
viewer.refresh(dstest);
}
else if ( obj instanceof TestRun ) {
TestRun testrun = (TestRun) obj;
testrun.setStatus( TestRun.EXCLUDED);
testrun.getTest().setExcluded( true );
if (testrun.getMatches()!=null)
testrun.getMatches().clear();
viewer.refresh(testrun);
}
}
}
protected void doClearAllTests() {
IEditorPart editor = PlatformUI.getWorkbench().getActiveWorkbenchWindow()
.getActivePage().getActiveEditor();
JChemPaintEditor jcp = getJCPfromActiveEditor();
if (jcp != null){
doClearAndSetUpNewTestRuns( jcp.getCDKMolecule() );
}else{
logger.warn( "ClearAllTests NOT IMPLEMENTED FOR EDITOR: " + editor );
}
}
private void doRunAllTests() {
logger.debug("Running tests...");
if (activeTestRuns==null || activeTestRuns.size()<=0){
showMessage( "No active testruns to run" );
return;
}
//Store active selection
storedSelection=(IStructuredSelection) viewer.getSelection();
//Get the molecule from the editor
JChemPaintEditor jcp = getJCPfromActiveEditor();
if (jcp==null){
showError("The current editor is not supported to run DS tests on.");
return;
}
final ICDKMolecule mol=jcp.getCDKMolecule();
//Cancel all running tests
for (BioclipseJob<List<ITestResult>> job : runningJobs){
//Ask job to cancel
job.cancel();
logger.debug("Job: " + job.getName() + " asked to cancel.");
}
//Wait for all running jobs to cancel
for (BioclipseJob<List<ITestResult>> job : runningJobs){
logger.debug("Waiting for Job: " + job.getName() + " to finish...");
try {
job.join();
} catch ( InterruptedException e ) {
}
logger.debug("Job: " + job.getName() + " finished.");
}
//We need to clear previous tests if already run
if (isExecuted()==true){
doClearAndSetUpNewTestRuns( mol );
// partActivated( jcp );
viewer.refresh();
}
setExecuted( true );
IDSManager ds=net.bioclipse.ds.Activator.getDefault().getJavaManager();
for (final TestRun tr : activeTestRuns){
if (tr.getTest().getTestErrorMessage().length()<1){
if (tr.getStatus()==TestRun.EXCLUDED || tr.getTest().isExcluded()){
viewer.refresh(tr);
logger.debug( "===== Test: " + tr + " skipped since excluded.");
}
else{
//Start by cloning the molecule. This is to avoid threading
//issues in CDK.
try {
IAtomContainer clonedAC=(IAtomContainer) mol
.getAtomContainer().clone();
ICDKMolecule clonedMol=new CDKMolecule(clonedAC);
preprocessClonedMol(clonedMol);
logger.debug( "== Testrun: " + tr.getTest().getName() + " started" );
tr.setStatus( TestRun.RUNNING );
tr.setMolecule( clonedMol );
viewer.refresh(tr);
viewer.setExpandedState( tr, true );
runTestAsJobs( clonedMol, ds, tr , mol);
} catch ( CloneNotSupportedException e ) {
LogUtils.handleException( e, logger, Activator.PLUGIN_ID);
}
}
}
else{
logger.debug("The test: " + tr.getTest() + " has an error so not run.");
}
}
logger.debug( "===== All testruns started" );
}
/**
* Preprocess the molecule:
*
* a) Remove explicit hydrogens
*
* @param clonedMol
*/
private void preprocessClonedMol( ICDKMolecule clonedMol ) {
ICDKManager cdk = net.bioclipse.cdk.business.Activator
.getDefault().getJavaCDKManager();
cdk.removeExplicitHydrogens( clonedMol );
}
private void runTestAsJobs( final ICDKMolecule clonedMol, IDSManager ds,
final TestRun tr, final ICDKMolecule originalMol) {
try {
//Start up a job with the test
BioclipseJob<List<ITestResult>> job =
ds.runTest( tr.getTest().getId(), clonedMol,
new BioclipseJobUpdateHook<List<ITestResult>>(tr.getTest().getName()));
job.addJobChangeListener( new IJobChangeListener(){
public void aboutToRun( IJobChangeEvent event ) {
}
public void awake( IJobChangeEvent event ) {
}
@SuppressWarnings("unchecked")
public void done( IJobChangeEvent event ) {
final BioclipseJob<List<ITestResult>> job=(BioclipseJob<List<ITestResult>>) event.getJob();
List<ITestResult> result = null;
try{
result = job.getReturnValue();
}catch(ClassCastException e){
result=new ArrayList<ITestResult>();
result.add( new SimpleResult( e.getMessage(), SimpleResult.ERROR ) );
}
final List<ITestResult> matches = result;
//Update viewer in SWT thread
Display.getDefault().asyncExec( new Runnable(){
public void run() {
logger.debug("Matcher '" + tr.getTest().getName()
+ "' finished with " + matches.size() + " hits");
//Copy properties from result into original molecule
//from the cloned
for (Object obj : clonedMol.getAtomContainer()
.getProperties().keySet()){
// System.out.println("OBJ found: " + obj);
// System.out.println("Existing: " + originalMol.getAtomContainer().getProperties());
if (!originalMol.getAtomContainer()
.getProperties().containsKey( obj )){
originalMol.getAtomContainer()
.getProperties().put(
obj, clonedMol.getAtomContainer()
.getProperties().get( obj ) );
// System.out.println("DS-RES set on:" + clonedMol.getAtomContainer().hashCode() + "="+ clonedMol.getAtomContainer()
// .getProperties().get( obj ));
}
}
//We also need to clone any ISubStructureMatches Atoms in AC since they are based on a clone
// for (ITestResult result : matches){
// if ( result instanceof SubStructureMatch) {
// SubStructureMatch ssmatch = (SubStructureMatch) result;
// IAtomContainer matchAC = ssmatch.getAtomContainer();
// IAtomContainer newAC=new NNAtomContainer();
// for (IAtom matchedAtom : matchAC.atoms()){
// int clonedAtomno=clonedMol.getAtomContainer().getAtomNumber( matchedAtom );
// IAtom newAtom = originalMol.getAtomContainer().getAtom( clonedAtomno );
// newAC.addAtom( newAtom );
// }
// ssmatch.setAtomContainer( newAC );
// }
// }
for (ITestResult result : matches){
result.setTestRun( tr );
tr.addResult(result);
}
tr.setMatches( matches );
// logger.debug( "===== " + tr + " finished" );
if (tr.getTest().getTestErrorMessage()!="")
tr.setStatus( TestRun.ERROR );
else
tr.setStatus( TestRun.FINISHED );
viewer.refresh( tr );
viewer.setExpandedState( tr, true );
updateConsensusView();
//We need to turn on external generators
IEditorPart part = getSite().getWorkbenchWindow().getActivePage().getActiveEditor();
if ( part instanceof JChemPaintEditor ) {
JChemPaintEditor jcp=(JChemPaintEditor)part;
jcp.getWidget().setUseExtensionGenerators( true );
//manually update jcpeditor
jcp.update();
}else if ( part instanceof MultiPageMoleculesEditorPart ) {
MultiPageMoleculesEditorPart mpe = (MultiPageMoleculesEditorPart)part;
mpe.getMoleculesPage().setUseExtensionGenerators( true );
mpe.getMoleculesPage().refresh();
}
//If we previously stored a selection, set it now
selectIfStoredSelection(tr);
//This job is done, remove from list of running jobs
getRunningJobs().remove( job );
}
});
}
public void running( IJobChangeEvent event ) {
}
public void scheduled( IJobChangeEvent event ) {
}
public void sleeping( IJobChangeEvent event ) {
}}
);
job.schedule();
//Store ref to job in list
runningJobs.add(job);
} catch ( Exception e ) {
logger.error( "Error running test: " + tr.getTest() +
": " + e.getMessage());
LogUtils.debugTrace( logger, e );
tr.setStatus( TestRun.ERROR );
viewer.refresh( tr );
updateConsensusView();
}
}
private void selectIfStoredSelection(TestRun tr) {
if (storedSelection==null) return;
for (Object obj : storedSelection.toList()){
//Select this testrun if same id as stored one
if ( obj instanceof TestRun ) {
TestRun storedtr = (TestRun) obj;
if (storedtr.getTest().getId().equals( tr.getTest().getId() )){
viewer.setSelection( new StructuredSelection(tr) );
}
}
//If this testrun has no matches, do not try to select them
else if (tr.getMatches()==null || tr.getMatches().size()<=0)
return;
//Select the first ITestResult if it has same TestRun.Test as stored
else if ( obj instanceof ITestResult ) {
ITestResult storedtres=(ITestResult)obj;
if (storedtres.getTestRun().getTest().getId().equals( tr.getTest().getId() )){
// viewer.setSelection( new StructuredSelection(tr.getMatches().get( 0 )) );
//TODO: fire explicit property to make this highlight?
}
}
}
}
private void showMessage(String message) {
MessageDialog.openInformation(
viewer.getControl().getShell(),
"Decision support",
message);
}
private void showError(String message) {
MessageDialog.openError(
viewer.getControl().getShell(),
"Decision support",
message);
}
/**
* Passing the focus request to the viewer's control.
*/
public void setFocus() {
viewer.getControl().setFocus();
}
private void updateView() {
viewer.refresh();
// viewer.expandToLevel( 1 );
viewer.expandAll();
updateActionStates();
//Also update consensus part
updateConsensusView();
}
/**
* Wait for all jobs to finish, then return ReportModel
* @return
*/
public DSSingleReportModel waitAndReturnReportModel(){
//Wait for all jobs to finish
for (BioclipseJob<List<ITestResult>> job : runningJobs){
logger.debug("Waiting for Job: " + job.getName() + " to finish...");
try {
job.join();
} catch ( InterruptedException e ) {