@Test
public void checkReferenceMoleculeAndClassUsage() throws Exception {
MySQLAdaptor dba =
new MySQLAdaptor("reactomedev.oicr.on.ca", "gk_central", "authortool", "**REMOVED**");
// Collection<GKInstance> c =
// dba.fetchInstancesByClass(ReactomeJavaConstants.ReferenceGroupCount);
// System.out.println("Total ReferenceMolecule: " + c.size());
Collection<GKInstance> c1 =
dba.fetchInstancesByClass(ReactomeJavaConstants.ReferenceMoleculeClass);
System.out.println("Total ReferenceMoleculeClass: " + c1.size());
Set<GKInstance> all = new HashSet<GKInstance>();
// all.addAll(c);
all.addAll(c1);
System.out.println("ReferenceMolecule\tReferrers");
for (GKInstance inst : all) {
Collection<?> refAtts = inst.getSchemClass().getReferers();
Set<GKInstance> allReferrers = new HashSet<GKInstance>();
for (Iterator<?> it1 = refAtts.iterator(); it1.hasNext(); ) {
GKSchemaAttribute att = (GKSchemaAttribute) it1.next();
Collection<GKInstance> referrers = inst.getReferers(att);
if (referrers != null) allReferrers.addAll(referrers);
}
if (allReferrers.size() > 0) {
System.out.println(inst + "\t" + join(allReferrers));
}
}
}
/**
* 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());
}
}
}
/**
* Sets up lists of instances that are different between database and local instances. If
* uncheckableList is null, then the "difference" between database and local will be used to
* generate these lists. If uncheckableList contains something, then the contents of the list
* (assumed to be of type GKInstance) will be taken instead.
*
* @param fileAdaptor
* @param dbAdaptor
* @param uncheckableList
*/
public void setAdaptors(
XMLFileAdaptor fileAdaptor, MySQLAdaptor dbAdaptor, List uncheckableList) {
try {
this.fileAdaptor = fileAdaptor;
this.dbAdaptor = dbAdaptor;
typeMap = new HashMap();
if (uncheckableList != null) {
// Create a "fake" syncMap if a list of instances
// already exists.
syncMap = new HashMap();
syncMap.put(CHANGED_KEY, uncheckableList);
// Create the corresponding "fake" type map. This
// is needed so that the correct actions are assigned
// to these instances, e.g. "update from db".
GKInstance uncheckableInstance;
for (Iterator it = uncheckableList.iterator(); it.hasNext(); ) {
uncheckableInstance = (GKInstance) it.next();
typeMap.put(uncheckableInstance, NEW_CHANGE_IN_DB_KEY);
}
} else // The usual case
// Create a syncMap based on the discrepancies
// between local and database instances.
syncMap = synchronize(fileAdaptor, dbAdaptor);
if (syncMap.size() == 0) isSame = true;
else {
isSame = false;
JPanel mapPane = createDisplayMapPane();
getContentPane().add(mapPane, BorderLayout.CENTER);
setTitle(
"Synchronization Results vs. " + dbAdaptor.getDBName() + "@" + dbAdaptor.getDBHost());
}
} catch (Exception e) {
System.err.println("SynchronizationPane.setAdaptors(): " + e);
e.printStackTrace();
}
}
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);
}
public void check() throws Exception {
if (dba == null)
throw new IllegalStateException("InstanceReferenceChecker.check(): No database specified.");
GKSchema schema = (GKSchema) dba.getSchema();
Set instanceAtts = new HashSet();
GKSchemaAttribute att = null;
for (Iterator it = schema.getOriginalAttributes().iterator(); it.hasNext(); ) {
att = (GKSchemaAttribute) it.next();
if (att.isInstanceTypeAttribute()) {
instanceAtts.add(att);
}
}
System.out.println("Instance Atts: " + instanceAtts.size());
Connection conn = dba.getConnection();
Statement stat = conn.createStatement();
ResultSet resultSet = null;
GKSchemaClass cls = null;
Map attMap = new HashMap();
Map tableNameMap = new HashMap();
String query = null;
for (Iterator it = instanceAtts.iterator(); it.hasNext(); ) {
att = (GKSchemaAttribute) it.next();
cls = (GKSchemaClass) att.getOrigin();
System.out.println("Checking " + att.getName() + " in " + cls.getName() + "...");
String tableName = null;
if (!att.isMultiple()) {
tableName = cls.getName();
} else {
tableName = cls.getName() + "_2_" + att.getName();
}
query =
"SELECT distinct " + att.getName() + ", " + att.getName() + "_class FROM " + tableName;
resultSet = stat.executeQuery(query);
while (resultSet.next()) {
long dbID = resultSet.getLong(1);
String clsName = resultSet.getString(2);
if (dbID == 0 && clsName == null) {
// errorMessage.append("0, null occur for " + att.getName() + " in " + tableName);
// errorMessage.append("\n");
continue;
}
Long dbIDLong = new Long(dbID);
String tmpCls = (String) attMap.get(dbIDLong);
if (tmpCls != null && !tmpCls.equals(clsName)) {
errorMessage.append(dbID + ", " + tmpCls + " in ");
errorMessage.append(tableNameMap.get(dbIDLong) + " is different from ");
errorMessage.append(tableName);
errorMessage.append("\n");
} else {
attMap.put(dbIDLong, clsName);
tableNameMap.put(dbIDLong, tableName);
}
}
resultSet.close();
}
stat.close();
System.out.println("The size of the map: " + attMap.size());
// Check DB_ID in the database
query = "SELECT _class FROM DatabaseObject WHERE DB_ID = ?";
PreparedStatement prepStat = conn.prepareStatement(query);
int c = 0;
// Set notInSet = new HashSet();
for (Iterator it = attMap.keySet().iterator(); it.hasNext(); ) {
Long dbID = (Long) it.next();
prepStat.setLong(1, dbID.longValue());
resultSet = prepStat.executeQuery();
c = 0;
while (resultSet.next()) {
c++;
String clsName = resultSet.getString(1);
String tmpClsName = (String) attMap.get(dbID);
if (!tmpClsName.equals(clsName)) {
errorMessage.append(dbID + ", " + tmpClsName);
errorMessage.append(" in " + tableNameMap.get(dbID));
errorMessage.append(" is different in DatabaseObject (");
errorMessage.append(clsName);
errorMessage.append(")\n");
}
}
if (c == 0) {
errorMessage.append(dbID + ", " + attMap.get(dbID));
errorMessage.append(" in " + tableNameMap.get(dbID));
errorMessage.append(" is not in the DatabaseObject");
errorMessage.append("\n");
} else if (c > 1) {
errorMessage.append(dbID + " occurs in more than once in DatabaseObject");
errorMessage.append("\n");
}
resultSet.close();
}
prepStat.close();
// Print out an empty line
System.out.println();
if (errorMessage.length() == 0) {
System.out.println("Nothing Wrong!");
} else {
FileWriter fileWriter = new FileWriter("error.txt");
BufferedWriter writer = new BufferedWriter(fileWriter);
writer.write(errorMessage.toString());
writer.close();
fileWriter.close();
System.out.println("Done. See errors in error.txt.");
}
}
private void convertReactomeToGPML(Long dbID, String outputFileName) throws Exception {
GKInstance pathway = adaptor.fetchInstance(dbID);
convertReactomeToGPML(pathway, outputFileName);
}
