/** Split objects into normal and disease components */
private void splitObjects() {
normalIds = new HashSet<Long>();
diseaseIds = new HashSet<Long>();
RenderablePathway diagram = (RenderablePathway) getRenderable();
if (pathway == null || diagram.getReactomeDiagramId() == null) return;
try {
GKInstance pdInst = adaptor.fetchInstance(diagram.getReactomeDiagramId());
// Get the disease pathway instance
List<GKInstance> pathways =
pdInst.getAttributeValuesList(ReactomeJavaConstants.representedPathway);
GKInstance diseasePathway = null;
GKInstance normalPathway = null;
GKInstance disease = (GKInstance) pathway.getAttributeValue(ReactomeJavaConstants.disease);
if (disease == null && contains(pathway, pathways)) {
normalPathway = pathway;
} else {
diseasePathway = pathway;
// There should be a normal pathway contained by a disease pathway
List<?> subPathways = diseasePathway.getAttributeValuesList(ReactomeJavaConstants.hasEvent);
for (Object obj : subPathways) {
GKInstance subPathway = (GKInstance) obj;
disease = (GKInstance) subPathway.getAttributeValue(ReactomeJavaConstants.disease);
if (disease == null && contains(subPathway, pathways)) {
normalPathway = subPathway;
break;
}
}
}
if (normalPathway != null) {
// Get all disease related objects
Set<GKInstance> normalEvents = InstanceUtilities.grepPathwayEventComponents(normalPathway);
for (GKInstance inst : normalEvents) normalIds.add(inst.getDBID());
Set<GKInstance> normalEntities = InstanceUtilities.grepPathwayParticipants(normalPathway);
for (GKInstance inst : normalEntities) normalIds.add(inst.getDBID());
if (diseasePathway != null) {
Set<GKInstance> allEvents = InstanceUtilities.grepPathwayEventComponents(diseasePathway);
allEvents.removeAll(normalEvents);
for (GKInstance inst : allEvents) {
diseaseIds.add(inst.getDBID());
// Want to make sure disease pathways are connected to objects
if (inst.getSchemClass().isa(ReactomeJavaConstants.ReactionlikeEvent)) {
Set<GKInstance> rxtEntities = InstanceUtilities.getReactionParticipants(inst);
for (GKInstance rxtEntity : rxtEntities) {
diseaseIds.add(rxtEntity.getDBID());
}
}
}
// Set<GKInstance> allEntities =
// InstanceUtilities.grepPathwayParticipants(diseasePathway);
// allEntities.removeAll(normalEntities);
// for (GKInstance inst : allEntities)
// diseaseIds.add(inst.getDBID());
}
}
splitComponents();
} catch (Exception e) {
e.printStackTrace();
}
}
/**
* Overlay a single disease reaction onto a normal reaction.
*
* @param normalReaction
* @param diseaseReaction
* @param overlaidObjects
*/
private void overlayDiseaseReaction(HyperEdge normalReaction, GKInstance diseaseReaction)
throws Exception {
// Make a copy of the HyperEdge for future process that is related to Vertex and JSON generation
HyperEdge reactionCopy = normalReaction.shallowCopy();
reactionCopy.setReactomeId(diseaseReaction.getDBID());
reactionCopy.setDisplayName(diseaseReaction.getDisplayName());
reactionCopy.setLineColor(DefaultRenderConstants.DEFAULT_DISEASE_BACKGROUND);
displayedObject.addComponent(reactionCopy);
overlaidObjects.add(reactionCopy);
// Want to handle inputs, outputs and catalysts since regulators can
// be ignored
List<Node> nodes = new ArrayList<Node>();
nodes.addAll(normalReaction.getInputNodes());
nodes.addAll(normalReaction.getOutputNodes());
nodes.addAll(normalReaction.getHelperNodes());
// List objects not listed in the disease reaction as crossed objects
Set<GKInstance> participants = InstanceUtilities.getReactionParticipants(diseaseReaction);
Set<Long> diseaseIds = new HashSet<Long>();
for (GKInstance participant : participants) {
diseaseIds.add(participant.getDBID());
if (participant.getSchemClass().isValidAttribute(ReactomeJavaConstants.hasMember)) {
List<GKInstance> list = participant.getAttributeValuesList(ReactomeJavaConstants.hasMember);
if (list != null && list.size() > 0) {
for (GKInstance inst : list) diseaseIds.add(inst.getDBID());
}
}
if (participant.getSchemClass().isValidAttribute(ReactomeJavaConstants.hasCandidate)) {
List<GKInstance> list =
participant.getAttributeValuesList(ReactomeJavaConstants.hasCandidate);
if (list != null && list.size() > 0) {
for (GKInstance inst : list) diseaseIds.add(inst.getDBID());
}
}
}
Set<GKInstance> lofInstances = new HashSet<GKInstance>();
Map<Node, GKInstance> normalToDiseaseEntity =
mapMutatedToNormalNodes(diseaseReaction, normalReaction, nodes, lofInstances);
for (Node node : nodes) {
if (!diseaseIds.contains(node.getReactomeId())) {
// Check if it should be mapped to a normal entity
GKInstance diseaseEntity = normalToDiseaseEntity.get(node);
if (diseaseEntity == null) crossedObjects.add(node); // Just crossed out
else {
Node diseaseNode =
replaceNormalNode(node, diseaseEntity, contains(diseaseEntity, lofInstances));
if (diseaseNode == null) continue; // Just in case
// Re-link to diseaseNode
ConnectInfo connectInfo = reactionCopy.getConnectInfo();
List<?> widgets = connectInfo.getConnectWidgets();
for (Object obj : widgets) {
ConnectWidget widget = (ConnectWidget) obj;
if (widget.getConnectedNode() == node) widget.replaceConnectedNode(diseaseNode);
}
}
} else overlaidObjects.add(node);
}
}
private void clearDeleteRecord() {
if (deleteList != null) {
java.util.List list = deleteList.getSelection();
if (list.size() > 0) {
try {
java.util.List dbIDs = new ArrayList(list.size());
for (Iterator it = list.iterator(); it.hasNext(); ) {
GKInstance instance = (GKInstance) it.next();
dbIDs.add(instance.getDBID());
}
fileAdaptor.clearDeleteRecord(dbIDs);
} catch (IOException e) {
System.err.println("SynchronizationDialog.clearDeleteRecord(): " + e);
e.printStackTrace();
}
deleteList.deleteInstances(list);
// Check if deleteList needs to be removed
if (deleteList.getDisplayedInstances().size() == 0) {
centerPane.remove(deleteList);
centerPane.validate();
centerPane.repaint();
}
}
}
}
public void randomlyMapDiseaseNodesToNormalNodes(
Map<Node, GKInstance> normalToDiseaseEntity,
Collection<GKInstance> mapped,
List<GKInstance> diseaseInputs,
List<Node> normalNodes) {
if (diseaseInputs != null && diseaseInputs.size() > 0) {
normalNodes.removeAll(normalToDiseaseEntity.keySet());
if (normalNodes.size() > 0) {
for (GKInstance input : diseaseInputs) {
// if (mapped.contains(input))
if (contains(input, mapped)) continue; // it has been mapped already
// Check if it has been used based on DB_ID
Node matched = null;
for (Node node : normalNodes) {
if (node.getReactomeId().equals(input.getDBID())) {
matched = node;
break;
}
}
if (matched == null)
// Just pick up the first node
matched = normalNodes.get(0);
normalToDiseaseEntity.put(matched, input);
normalNodes.remove(matched);
if (normalNodes.size() == 0) break;
}
}
}
}
/**
* Some of disease reactions may not be drawn in the pathway diagram (e.g. LoF or GoF reactions).
* These reactions should be overlaid onto their normalReaction counterparts, which are encoded by
* their normalReaction attributes.
*
* @param diseaseIds
*/
private void overlayDiseaseReactions(Set<Long> diseaseIds) {
// Get the list of all drawing objects for checking
Map<Long, Renderable> idToObject = new HashMap<Long, Renderable>();
List<Renderable> components = displayedObject.getComponents();
if (components == null || components.size() == 0) return;
for (Renderable r : components) {
if (r.getReactomeId() == null) continue;
idToObject.put(r.getReactomeId(), r);
}
try {
normalToDiseaseNode = new HashMap<Node, Node>();
for (Long diseaseId : diseaseIds) {
if (idToObject.containsKey(diseaseId)) continue;
// Have to copy the normal reactions to draw
GKInstance inst = adaptor.fetchInstance(diseaseId);
if (inst.getSchemClass().isa(ReactomeJavaConstants.ReactionlikeEvent)) {
List<GKInstance> normalReactions =
inst.getAttributeValuesList(ReactomeJavaConstants.normalReaction);
if (normalReactions != null && normalReactions.size() > 0) {
for (GKInstance normalRxt : normalReactions) {
Renderable r = idToObject.get(normalRxt.getDBID());
if (r instanceof HyperEdge) overlayDiseaseReaction((HyperEdge) r, inst);
}
}
}
}
return;
} catch (Exception e) {
e.printStackTrace();
}
}
private Node replaceNormalNode(
Node normalNode, GKInstance diseaseEntity, Boolean needDashedBorder) {
Node diseaseNode = normalToDiseaseNode.get(normalNode);
if (diseaseNode != null) return diseaseNode;
try {
// If a node exists already, it should use
for (Renderable r : diseaseComps) {
if (diseaseEntity.getDBID().equals(r.getReactomeId()) && r instanceof Node) {
// This is rather arbitrary: if two nodes are very close,
// use the existing one.
int dx = Math.abs(r.getPosition().x - normalNode.getPosition().x);
int dy = Math.abs(r.getPosition().y - normalNode.getPosition().y);
if (dx < 10 && dy < 10) {
// We don't need to create a new Node if it exists already
normalToDiseaseNode.put(normalNode, (Node) r);
overlaidObjects.add(r); // Add it to overlaid object to cover edges
return (Node) r;
}
}
}
diseaseNode = normalNode.getClass().newInstance();
RenderUtility.copyRenderInfo(normalNode, diseaseNode);
// The following should NOT be called since NodeAttachment is
// related to disease entity only.
// TODO: Need to support this. Currently it is not supported!!! See example
// in PI3/AKT cancer pathway.
// diseaseNode.setNodeAttachmentsLocally(node.getNodeAttachments());
diseaseNode.setDisplayName(diseaseEntity.getDisplayName());
diseaseNode.setReactomeId(diseaseEntity.getDBID());
diseaseNode.invalidateBounds();
diseaseNode.setRenderer(normalNode.getRenderer());
diseaseNode.setLineColor(DefaultRenderConstants.DEFAULT_DISEASE_BACKGROUND);
diseaseNode.setNeedDashedBorder(needDashedBorder);
RenderUtility.hideCompartmentInNodeName(diseaseNode);
overlaidObjects.add(diseaseNode);
displayedObject.addComponent(diseaseNode);
normalToDiseaseNode.put(normalNode, diseaseNode);
return diseaseNode;
} catch (Exception e) {
e.printStackTrace();
}
return null;
}
private void convertReactomeToGPML(GKInstance pathway, String outputFileName) throws Exception {
Long dbID = pathway.getDBID();
System.out.println("converting pathway #" + dbID + " " + pathway.getDisplayName() + "...");
Document doc = r2gConverter.convertPathway(pathway);
XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
outputter.output(doc, new FileOutputStream(outputFileName));
/*
// Test loading using JDOM and validation
SAXBuilder builder = new SAXBuilder(true);
builder.setFeature("http://apache.org/xml/features/validation/schema", true);
builder.setProperty("http://apache.org/xml/properties/schema/external-schemaLocation",
"http://genmapp.org/GPML/2008a http://svn.bigcat.unimaas.nl/pathvisio/trunk/GPML2008a.xsd");
doc = builder.build(new File(outputFileName));
*/
}
/**
* This method is used to dump all human pathway diagrams into a specified directory.
*
* @param dir
* @throws Exception
*/
public void dumpHumanPathwayDiagrams(File dir) throws Exception {
Collection<?> diagrams = adaptor.fetchInstancesByClass(ReactomeJavaConstants.PathwayDiagram);
SchemaClass cls = adaptor.fetchSchema().getClassByName(ReactomeJavaConstants.PathwayDiagram);
SchemaAttribute att = cls.getAttribute(ReactomeJavaConstants.representedPathway);
adaptor.loadInstanceAttributeValues(diagrams, att);
// Group all human pathways
for (Iterator<?> it = diagrams.iterator(); it.hasNext(); ) {
GKInstance diagram = (GKInstance) it.next();
GKInstance pathway =
(GKInstance) diagram.getAttributeValue(ReactomeJavaConstants.representedPathway);
GKInstance species = (GKInstance) pathway.getAttributeValue(ReactomeJavaConstants.species);
if (species == null) continue;
if (species.getDBID().equals(48887L)) {
String fileName = getFileName(pathway);
File file = new File(dir, fileName);
convertReactomeToGPML(pathway, file.getAbsolutePath());
}
}
}
public boolean shouldEscape(GKInstance inst) {
if (!needEscapePermissioin) return false;
if (needEscape && escapedDbIds.contains(inst.getDBID())) {
if (cutoffDate != null) {
try {
// Check if the latest IEs is later than the cutoff date
GKInstance latestIE = InstanceUtilities.getLatestIEFromInstance(inst);
// Just in case
if (latestIE == null) return true;
String ieDateValue = (String) latestIE.getAttributeValue(ReactomeJavaConstants.dateTime);
// Have to make sure default date instance is used!
DateFormat df = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.S");
Date ieDate = df.parse(ieDateValue);
return !ieDate.after(cutoffDate);
} catch (Exception e) {
// Don't want to show a GUI here. Just generate error message silently.
System.err.println("QAEscapeHelper.shouldEscape(): " + e);
e.printStackTrace();
return false;
}
} else return true;
}
return false;
}
private void showComparison() {
// Find the instance that can be used for comparision. This instance
// should be chosen from changedList or localHasUnexpInstance
GKInstance instance = null;
if (changedList != null) { // Check changedList first
List selection = changedList.getSelection();
if (selection.size() > 0) instance = (GKInstance) selection.get(0);
}
if (instance == null && localHasMoreIEList != null) {
List selection = localHasMoreIEList.getSelection();
if (selection.size() > 0) instance = (GKInstance) selection.get(0);
}
if (instance == null) return;
final InstanceComparisonPane comparisonPane = new InstanceComparisonPane();
// Fine tune comparison pane for making comparisons with
// database
comparisonPane.setSaveDialogHideUnusedButtons(true);
comparisonPane.setSaveDialogSaveAsNewBtnFirst(false);
comparisonPane.setSaveDialogSaveAsNewBtnTitle(
"Create new local instance and put merge into that");
comparisonPane.setSaveDialogReplaceFirstBtnTitle(
"Overwrite existing instance with merge (recommended)");
comparisonPane.setCloseAfterSaving(true);
try {
String clsName = instance.getSchemClass().getName();
Long instanceId = instance.getDBID();
final GKInstance localCopy = fileAdaptor.fetchInstance(clsName, instanceId);
dbAdaptor.setUseCache(false);
// final GKInstance dbCopy = dbAdaptor.fetchInstance(clsName, instanceId);
// The class type might be changed locally or remotely. So not clsName should be used
// to fetch database instance. Otherwise, null exception will be thrown. The same thing
// is done also in creating synchronization result.
final GKInstance dbCopy = dbAdaptor.fetchInstance(instanceId);
dbAdaptor.setUseCache(true);
comparisonPane.setInstances(localCopy, dbCopy);
String title =
"Comparing Instances \""
+ instance.getDisplayName()
+ "\" in the local and DB repositories";
JDialog parentDialog = (JDialog) SwingUtilities.getAncestorOfClass(JDialog.class, centerPane);
final JDialog dialog = new JDialog(parentDialog, title);
// Try to update the list automatically
dialog.addWindowListener(
new WindowAdapter() {
public void windowClosed(WindowEvent e) {
handleMergeResult(localCopy, dbCopy, comparisonPane);
// To prevent double calling. It is called again when parentDialog is closed.
dialog.removeWindowListener(this);
}
});
dialog.getContentPane().add(comparisonPane, BorderLayout.CENTER);
dialog.setModal(true);
dialog.setSize(800, 600);
GKApplicationUtilities.center(dialog);
dialog.setVisible(true);
// Update synchronization dialog panels depending on user
// choice.
if (comparisonPane.getSaveMergeOption() == InstanceComparisonPane.SAVE_AS_NEW) {
GKInstance merged = comparisonPane.getMerged();
if (newList == null) {
List list = new ArrayList();
list.add(merged);
newList = initInstanceListPane(list, "Instances created locally: " + list.size());
} else newList.addInstance(merged);
} else if (comparisonPane.getSaveMergeOption() == InstanceComparisonPane.OVERWRITE_FIRST) {
dbAdaptor.setUseCache(false);
GKInstance remoteCopy = dbAdaptor.fetchInstance(instance.getDBID());
dbAdaptor.setUseCache(true);
if (remoteCopy != null) {
InstanceComparer comparer = new InstanceComparer();
int reply = comparer.compare(instance, remoteCopy);
if (reply == InstanceComparer.LOCAL_HAS_MORE_IE) {
if (localHasMoreIEList == null) {
List list = new ArrayList();
list.add(instance);
localHasMoreIEList =
initInstanceListPane(
list, "Local instances having unexpected InstanceEdits: " + list.size());
} else localHasMoreIEList.addInstance(instance);
} else if (reply == InstanceComparer.IS_IDENTICAL) {
// Merge has made local and database copies
// identical - don't need to check in anymore
changedList.deleteInstance(instance);
} else if (reply != InstanceComparer.NEW_CHANGE_IN_LOCAL) {
// Merge has produced a conflict
typeMap.put(mapCompareResultToString(reply), instance);
} else
// The user should now be allowed to commit this
// instance, because it will now have changed.
commitToDBAction.setEnabled(true);
JOptionPane.showMessageDialog(
parentDialog,
"Merge successful, you will need to check the merged instance into the database.\n\n",
"Merge OK",
JOptionPane.INFORMATION_MESSAGE);
}
}
} catch (Exception e1) {
System.err.println("Synchronization.createDisplayMapPane(): " + e1);
e1.printStackTrace();
JOptionPane.showMessageDialog(
this,
"Error in comparing: " + instance.toString(),
"Error in Comparing",
JOptionPane.ERROR_MESSAGE);
}
}
private void updateFromDB() {
InstanceListPane touchedList = null;
// Find out which instances have been selected in all relevant lists
// Update the attribute values for changed list.
try {
if (changedList != null) {
java.util.List list = new ArrayList(changedList.getSelection()); // To support it.remove()
// Use a new ArrayList.
if (list != null && list.size() > 0) {
for (Iterator it = list.iterator(); it.hasNext(); ) {
GKInstance instance = (GKInstance) it.next();
// Fetch GKInstance based on its DB_ID since SchemaClass might be changed.
GKInstance localCopy = fileAdaptor.fetchInstance(instance.getDBID());
dbAdaptor.setUseCache(false);
GKInstance dbCopy = dbAdaptor.fetchInstance(instance.getDBID());
dbAdaptor.setUseCache(true);
if (SynchronizationManager.getManager().updateFromDB(localCopy, dbCopy, this)) {
AttributeEditManager.getManager().attributeEdit(localCopy);
fileAdaptor.removeDirtyFlag(localCopy);
} else it.remove(); // Remove from the list
}
// Remove all selected instances
changedList.deleteInstances(list);
touchedList = changedList;
}
}
if (localHasMoreIEList != null && localHasMoreIEList.getSelection().size() > 0) {
List list = new ArrayList(localHasMoreIEList.getSelection());
for (Iterator it = list.iterator(); it.hasNext(); ) {
GKInstance localCopy = (GKInstance) it.next();
dbAdaptor.setUseCache(false);
GKInstance dbCopy = dbAdaptor.fetchInstance(localCopy.getDBID());
dbAdaptor.setUseCache(true);
if (SynchronizationManager.getManager().updateFromDB(localCopy, dbCopy, this)) {
AttributeEditManager.getManager().attributeEdit(localCopy);
fileAdaptor.removeDirtyFlag(localCopy);
} else it.remove(); // Remove from the list, if it it cancelled by the user.
}
localHasMoreIEList.deleteInstances(list);
touchedList = localHasMoreIEList;
}
// Delete the local copy for deleteInDBList.
if (deleteInDBList != null) {
java.util.List list = deleteInDBList.getSelection();
if (list != null && list.size() > 0) {
for (Iterator it = list.iterator(); it.hasNext(); ) {
GKInstance instance = (GKInstance) it.next();
fileAdaptor.deleteInstance(instance);
}
}
deleteInDBList.deleteInstances(list);
touchedList = deleteInDBList;
}
// Get another copy for the local repository
if (deleteList != null) {
java.util.List<?> list = deleteList.getSelection();
if (list != null && list.size() > 0) {
Map<SchemaClass, Set<GKInstance>> checkOutMap =
new HashMap<SchemaClass, Set<GKInstance>>(); // All checked out Instances
for (Iterator<?> it = list.iterator(); it.hasNext(); ) {
GKInstance instance = (GKInstance) it.next();
Map<SchemaClass, List<GKInstance>> schemaMap =
InstanceUtilities.listDownloadableInstances(instance);
// Have to merge schemaMap to checkOutMap
for (SchemaClass key : schemaMap.keySet()) {
List<GKInstance> list1 = schemaMap.get(key);
if (list1 != null && list1.size() > 0) {
Set<GKInstance> list2 = checkOutMap.get(key);
if (list2 == null) {
list2 = new HashSet<GKInstance>();
checkOutMap.put(key, list2);
}
// Remove first to avoid any duplication
list2.addAll(list1);
}
}
}
fileAdaptor.store(checkOutMap);
InstanceUtilities.clearShellFlags(checkOutMap);
// There are maybe more than selected instances after checking out
List<GKInstance> checkedOut = new ArrayList<GKInstance>();
for (Set<GKInstance> set : checkOutMap.values()) {
checkedOut.addAll(set);
}
deleteList.deleteInstances(checkedOut);
// deleteList.deleteInstances(list);
// Need to clear out these deletion records
List<Long> dbIds = new ArrayList<Long>();
for (GKInstance inst : checkedOut) dbIds.add(inst.getDBID());
fileAdaptor.clearDeleteRecord(dbIds);
touchedList = deleteList;
}
}
} catch (Exception e) {
System.err.println("SynchronizationDialog.updateFromDB(): " + e);
e.printStackTrace();
}
updateInstanceList(touchedList);
}
/**
* In case where MySQLAdaptor cache is turned off, GKInstances having the same DB_IDs from the
* database are different during different queries. Using this helper method to check if a
* GKInstance is contained in a Collection<GKInstance> created in different time point.
*
* @param inst
* @param c
* @return
*/
private boolean contains(GKInstance inst, Collection<GKInstance> c) {
for (GKInstance inst1 : c) {
if (inst1.getDBID().equals(inst.getDBID())) return true;
}
return false;
}