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OMERO.editor crashes when importing example protocols

https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7647

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OMERO.editor crashes when importing example protocols

PostPosted: Tue Sep 30, 2014 2:20 pm
by Sethur
Hi,

when I try to import, e.g. Fluorophore-Conjugaton.cpe.xml, which is one of the example protocols provided within OMERO.editor (as a web download), OMERO.editor crashes with the following error:

Code: Select all
java.lang.Exception: Abnormal termination due to an uncaught exception.
java.lang.NoSuchMethodError: net.n3.nanoxml.IXMLElement.getChildren()Ljava/util/ArrayList;
   at org.openmicroscopy.shoola.agents.editor.model.CPEimport.createTreeModel(CPEimport.java:707)
   at org.openmicroscopy.shoola.agents.editor.model.TreeModelFactory.getTree(TreeModelFactory.java:101)
   at org.openmicroscopy.shoola.agents.editor.view.EditorModel.setFileToEdit(EditorModel.java:346)
   at org.openmicroscopy.shoola.agents.editor.view.EditorComponent.setFileToEdit(EditorComponent.java:300)
   at org.openmicroscopy.shoola.agents.editor.EditorAgent.openLocalFile(EditorAgent.java:208)
   at org.openmicroscopy.shoola.agents.editor.view.EditorComponent.openLocalFile(EditorComponent.java:327)
   at org.openmicroscopy.shoola.agents.editor.actions.OpenLocalFileAction.propertyChange(OpenLocalFileAction.java:123)
   at java.beans.PropertyChangeSupport.fire(Unknown Source)
   at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
   at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
   at java.awt.Component.firePropertyChange(Unknown Source)
   at org.openmicroscopy.shoola.util.ui.filechooser.FileChooser.acceptSelection(FileChooser.java:373)
   at org.openmicroscopy.shoola.util.ui.filechooser.CustomizedFileChooser.approveSelection(CustomizedFileChooser.java:373)
   at javax.swing.plaf.basic.BasicFileChooserUI$Handler.mouseClicked(Unknown Source)
   at sun.swing.FilePane$Handler.mouseClicked(Unknown Source)
   at java.awt.AWTEventMulticaster.mouseClicked(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$200(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.WaitDispatchSupport$2.run(Unknown Source)
   at java.awt.WaitDispatchSupport$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.awt.WaitDispatchSupport.enter(Unknown Source)
   at java.awt.Dialog.show(Unknown Source)
   at java.awt.Component.show(Unknown Source)
   at java.awt.Component.setVisible(Unknown Source)
   at java.awt.Window.setVisible(Unknown Source)
   at java.awt.Dialog.setVisible(Unknown Source)
   at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:557)
   at org.openmicroscopy.shoola.agents.editor.actions.OpenLocalFileAction.actionPerformed(OpenLocalFileAction.java:103)
   at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
   at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
   at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$200(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)
Abnormal termination due to an uncaught exception.
java.lang.NoSuchMethodError: net.n3.nanoxml.IXMLElement.getChildren()Ljava/util/ArrayList;
   at org.openmicroscopy.shoola.agents.editor.model.CPEimport.createTreeModel(CPEimport.java:707)
   at org.openmicroscopy.shoola.agents.editor.model.TreeModelFactory.getTree(TreeModelFactory.java:101)
   at org.openmicroscopy.shoola.agents.editor.view.EditorModel.setFileToEdit(EditorModel.java:346)
   at org.openmicroscopy.shoola.agents.editor.view.EditorComponent.setFileToEdit(EditorComponent.java:300)
   at org.openmicroscopy.shoola.agents.editor.EditorAgent.openLocalFile(EditorAgent.java:208)
   at org.openmicroscopy.shoola.agents.editor.view.EditorComponent.openLocalFile(EditorComponent.java:327)
   at org.openmicroscopy.shoola.agents.editor.actions.OpenLocalFileAction.propertyChange(OpenLocalFileAction.java:123)
   at java.beans.PropertyChangeSupport.fire(Unknown Source)
   at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
   at java.beans.PropertyChangeSupport.firePropertyChange(Unknown Source)
   at java.awt.Component.firePropertyChange(Unknown Source)
   at org.openmicroscopy.shoola.util.ui.filechooser.FileChooser.acceptSelection(FileChooser.java:373)
   at org.openmicroscopy.shoola.util.ui.filechooser.CustomizedFileChooser.approveSelection(CustomizedFileChooser.java:373)
   at javax.swing.plaf.basic.BasicFileChooserUI$Handler.mouseClicked(Unknown Source)
   at sun.swing.FilePane$Handler.mouseClicked(Unknown Source)
   at java.awt.AWTEventMulticaster.mouseClicked(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$200(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.WaitDispatchSupport$2.run(Unknown Source)
   at java.awt.WaitDispatchSupport$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.awt.WaitDispatchSupport.enter(Unknown Source)
   at java.awt.Dialog.show(Unknown Source)
   at java.awt.Component.show(Unknown Source)
   at java.awt.Component.setVisible(Unknown Source)
   at java.awt.Window.setVisible(Unknown Source)
   at java.awt.Dialog.setVisible(Unknown Source)
   at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:557)
   at org.openmicroscopy.shoola.agents.editor.actions.OpenLocalFileAction.actionPerformed(OpenLocalFileAction.java:103)
   at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
   at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
   at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$200(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)
Exception in thread "AWT-EventQueue-0"

   at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:191)
   at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:291)
   at org.openmicroscopy.shoola.env.AbnormalExitHandler.doTermination(AbnormalExitHandler.java:147)
   at org.openmicroscopy.shoola.env.AbnormalExitHandler.terminate(AbnormalExitHandler.java:85)
   at org.openmicroscopy.shoola.env.RootThreadGroup.uncaughtException(RootThreadGroup.java:69)
   at java.awt.EventDispatchThread.processException(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.WaitDispatchSupport$2.run(Unknown Source)
   at java.awt.WaitDispatchSupport$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.awt.WaitDispatchSupport.enter(Unknown Source)
   at java.awt.Dialog.show(Unknown Source)
   at java.awt.Component.show(Unknown Source)
   at java.awt.Component.setVisible(Unknown Source)
   at java.awt.Window.setVisible(Unknown Source)
   at java.awt.Dialog.setVisible(Unknown Source)
   at org.openmicroscopy.shoola.util.ui.UIUtilities.centerAndShow(UIUtilities.java:557)
   at org.openmicroscopy.shoola.agents.editor.actions.OpenLocalFileAction.actionPerformed(OpenLocalFileAction.java:103)
   at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
   at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
   at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
   at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
   at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
   at java.awt.Component.processMouseEvent(Unknown Source)
   at javax.swing.JComponent.processMouseEvent(Unknown Source)
   at java.awt.Component.processEvent(Unknown Source)
   at java.awt.Container.processEvent(Unknown Source)
   at java.awt.Component.dispatchEventImpl(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
   at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
   at java.awt.Container.dispatchEventImpl(Unknown Source)
   at java.awt.Window.dispatchEventImpl(Unknown Source)
   at java.awt.Component.dispatchEvent(Unknown Source)
   at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
   at java.awt.EventQueue.access$200(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.awt.EventQueue$3.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.awt.EventQueue$4.run(Unknown Source)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
   at java.awt.EventQueue.dispatchEvent(Unknown Source)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
   at java.awt.EventDispatchThread.run(Unknown Source)


This also happens with the FRAP example, so I assume it will happen with every example.

Any idea why this happens?

Cheers,

Tristan

Re: OMERO.editor crashes when importing example protocols

PostPosted: Wed Oct 01, 2014 12:35 pm
by jburel
hi Tristan
The error is due to a jar ordering issue in the classpath. (2 versions of nanoxml are conflicting.)
Did you start the editor via insight from Webstart or from the Desktop application?

Thanks
Jmarie

Re: OMERO.editor crashes when importing example protocols

PostPosted: Tue Oct 07, 2014 8:27 am
by Sethur
Hi Jean-Marie,

I started the editor via the button in OMERO.insight, but OMERO.editor also crashes on example protocol import when launched directly.

Cheers,

Tristan

Re: OMERO.editor crashes when importing example protocols

PostPosted: Wed Oct 08, 2014 1:55 pm
by jburel
Thanks Tristan for the information. It makes sense.

We have not actively worked on the editor for some time and we are planning to deprecate it.
Were you just evaluating the tool or were you planning to use it?

Regards
jmarie

Re: OMERO.editor crashes when importing example protocols

PostPosted: Thu Oct 09, 2014 10:52 am
by Sethur
Hi Jmarie,

I was evaluating the editor for practical use at the OICE. I think its functionality is actually quite useful, but people are usually lazy when it comes to properly documenting there experiments, so I'm not yet sure how much it would actually be used at our facility.

Nevertheless I wanted to teach users how to work with it. Did you have some alternative in mind after deprecating the editor? Would it be a lot of effort to get it working again with the current version of OMERO?

Cheers,

Tristan

Re: OMERO.editor crashes when importing example protocols

PostPosted: Sat Oct 11, 2014 8:34 pm
by jburel
Hi Tristan

We gathered some useful feedback while developing the editor at the time.
Often, users will start from a well-known protocol and modify a limited number of values.
In 5.1, we will introduce a Key-value annotation which could be used as "simplified Editor"
e.g. concentration 100ml,
Such annotation could also be used to record metadata not in the ome-model e.g. some detector settings
Any feedback welcome

Jmarie

Re: OMERO.editor crashes when importing example protocols

PostPosted: Mon Oct 13, 2014 9:19 am
by wmoore
Hi Tristan,

You might want to have a look at ISA tools: http://www.isa-tools.org/

I've not been following the project recently but I noticed several similarities between OMERO.editor and their approach when I was working on OMERO.editor. They use a tabular format with a column for each 'parameter'.

Re: OMERO.editor crashes when importing example protocols

PostPosted: Wed Oct 22, 2014 9:17 am
by Sethur
Hi Will,

thanks for pointing out isa-tools. I would suggest to remove OMERO.editor from the clients package if its not usable any longer.

Best,

Tristan

Re: OMERO.editor crashes when importing example protocols

PostPosted: Wed Oct 22, 2014 2:13 pm
by sbesson
Hi Tristan,

thanks for your input. We just removed the OMERO.editor from the clients with https://github.com/openmicroscopy/openm ... /pull/3113. This removal will be effective starting with the release of OMERO 5.1.0.

Sebastien
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