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Task #9926 (closed)

Opened 11 years ago

Closed 11 years ago

Last modified 11 years ago

Bug: Insight crash for image that is okay in webclient

Reported by: cblackburn Owned by: jburel
Priority: major Milestone: OMERO-4.4.7
Component: Insight Version: n.a.
Keywords: n.a. Cc: wmoore, bpindelski, s.loynton@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2013-02-12 (5)

Description (last modified by cblackburn)

Using web start Insight on howe I get a crash if I try to select the following image:

user: user-3 
group: read-annotate-1 
dataset: avi (id=61)
image: Level003-DB-089.avi

This was initially put down to bad data but checking the same image with the webclient I can select the image and view it with no problems.

Exception attached in comment.

Change History (10)

comment:1 Changed 11 years ago by cblackburn

Exception:

java.lang.Exception: Abnormal termination due to an uncaught exception.
java.lang.NoSuchMethodError: net.n3.nanoxml.IXMLElement.getChildrenNamed(Ljava/lang/String;)Ljava/util/ArrayList;
	at org.openmicroscopy.shoola.agents.util.editorpreview.PreviewModel.parseXmlDescription(PreviewModel.java:95)
	at org.openmicroscopy.shoola.agents.util.editorpreview.PreviewModel.<init>(PreviewModel.java:143)
	at org.openmicroscopy.shoola.agents.util.editorpreview.PreviewPanel.setDescriptionXml(PreviewPanel.java:358)
	at org.openmicroscopy.shoola.agents.util.editorpreview.PreviewPanel.<init>(PreviewPanel.java:341)
	at org.openmicroscopy.shoola.agents.metadata.editor.DocComponent.formatTootTip(DocComponent.java:389)
	at org.openmicroscopy.shoola.agents.metadata.editor.DocComponent.initComponents(DocComponent.java:591)
	at org.openmicroscopy.shoola.agents.metadata.editor.DocComponent.<init>(DocComponent.java:743)
	at org.openmicroscopy.shoola.agents.metadata.editor.DocComponent.<init>(DocComponent.java:755)
	at org.openmicroscopy.shoola.agents.metadata.editor.AnnotationDataUI.layoutAttachments(AnnotationDataUI.java:601)
	at org.openmicroscopy.shoola.agents.metadata.editor.AnnotationDataUI.buildUI(AnnotationDataUI.java:845)
	at org.openmicroscopy.shoola.agents.metadata.editor.GeneralPaneUI.layoutUI(GeneralPaneUI.java:285)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorUI.layoutUI(EditorUI.java:276)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorComponent.setStructuredDataResults(EditorComponent.java:192)
	at org.openmicroscopy.shoola.agents.metadata.view.MetadataViewerComponent.setMetadata(MetadataViewerComponent.java:304)
	at org.openmicroscopy.shoola.agents.metadata.StructuredDataLoader.handleResult(StructuredDataLoader.java:102)
	at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:90)
	at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:702)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:663)
	at java.awt.EventQueue$2.run(EventQueue.java:661)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:672)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Abnormal termination due to an uncaught exception.
java.lang.NoSuchMethodError: net.n3.nanoxml.IXMLElement.getChildrenNamed(Ljava/lang/String;)Ljava/util/ArrayList;
	at org.openmicroscopy.shoola.agents.util.editorpreview.PreviewModel.parseXmlDescription(PreviewModel.java:95)
	at org.openmicroscopy.shoola.agents.util.editorpreview.PreviewModel.<init>(PreviewModel.java:143)
	at org.openmicroscopy.shoola.agents.util.editorpreview.PreviewPanel.setDescriptionXml(PreviewPanel.java:358)
	at org.openmicroscopy.shoola.agents.util.editorpreview.PreviewPanel.<init>(PreviewPanel.java:341)
	at org.openmicroscopy.shoola.agents.metadata.editor.DocComponent.formatTootTip(DocComponent.java:389)
	at org.openmicroscopy.shoola.agents.metadata.editor.DocComponent.initComponents(DocComponent.java:591)
	at org.openmicroscopy.shoola.agents.metadata.editor.DocComponent.<init>(DocComponent.java:743)
	at org.openmicroscopy.shoola.agents.metadata.editor.DocComponent.<init>(DocComponent.java:755)
	at org.openmicroscopy.shoola.agents.metadata.editor.AnnotationDataUI.layoutAttachments(AnnotationDataUI.java:601)
	at org.openmicroscopy.shoola.agents.metadata.editor.AnnotationDataUI.buildUI(AnnotationDataUI.java:845)
	at org.openmicroscopy.shoola.agents.metadata.editor.GeneralPaneUI.layoutUI(GeneralPaneUI.java:285)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorUI.layoutUI(EditorUI.java:276)
	at org.openmicroscopy.shoola.agents.metadata.editor.EditorComponent.setStructuredDataResults(EditorComponent.java:192)
	at org.openmicroscopy.shoola.agents.metadata.view.MetadataViewerComponent.setMetadata(MetadataViewerComponent.java:304)
	at org.openmicroscopy.shoola.agents.metadata.StructuredDataLoader.handleResult(StructuredDataLoader.java:102)
	at org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:90)
	at org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:702)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:663)
	at java.awt.EventQueue$2.run(EventQueue.java:661)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:672)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Exception in thread "AWT-EventQueue-0"

	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:189)
	at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:287)
	at org.openmicroscopy.shoola.env.AbnormalExitHandler.doTermination(AbnormalExitHandler.java:146)
	at org.openmicroscopy.shoola.env.AbnormalExitHandler.terminate(AbnormalExitHandler.java:84)
	at org.openmicroscopy.shoola.env.AWTExceptionHanlder.handle(AWTExceptionHanlder.java:99)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at java.awt.EventDispatchThread.handleException(EventDispatchThread.java:412)
	at java.awt.EventDispatchThread.processException(EventDispatchThread.java:318)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:312)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

comment:2 Changed 11 years ago by cblackburn

  • Description modified (diff)

comment:3 Changed 11 years ago by jburel

Nothing to do with the image, but annotation related to it and the parser used by the editor.

comment:4 Changed 11 years ago by jburel

  • Resolution set to duplicate
  • Status changed from new to closed

see #9881

comment:5 Changed 11 years ago by jburel

  • Cc wmoore bpindelski added
  • Resolution duplicate deleted
  • Status changed from closed to reopened

The problem is due to the fact that the jars ordering described in the ivy file is not the order used when using insight/webstart. Basically it is important to have jhotdraw in the class path before nanoxml (library used by the editor) since jhotdraw uses a different version of nanoxml.

Will: how long will it take to get rid of nanoxml since the editor is no longer under development. We also need to check what we can do for the webstart build. (might be quicker)

comment:6 Changed 11 years ago by jmoore

Should be quite straight-forward to put the jhotdraw jar earlier. We're already doing something similar for other jars:

~/git $ git grep -A 18 "def insight"  components/tools/OmeroWeb/omeroweb/webstart/views.py 
components/tools/OmeroWeb/omeroweb/webstart/views.py:def insight(request):
components/tools/OmeroWeb/omeroweb/webstart/views.py-    t = template_loader.get_template('webstart/insight.xml')
components/tools/OmeroWeb/omeroweb/webstart/views.py-    
components/tools/OmeroWeb/omeroweb/webstart/views.py-    codebase = request.build_absolute_uri(settings.STATIC_URL+'webstart/jars/')
components/tools/OmeroWeb/omeroweb/webstart/views.py-    href = request.build_absolute_uri(reverse("webstart_insight"))
components/tools/OmeroWeb/omeroweb/webstart/views.py-
components/tools/OmeroWeb/omeroweb/webstart/views.py-    pattern = os.path.abspath(os.path.join(settings.OMERO_HOME, "lib", "insight",  "*.jar").replace('\\','/'))
components/tools/OmeroWeb/omeroweb/webstart/views.py-    jarlist = glob(pattern)
components/tools/OmeroWeb/omeroweb/webstart/views.py-    jarlist = [os.path.basename(x) for x in jarlist]
components/tools/OmeroWeb/omeroweb/webstart/views.py-
components/tools/OmeroWeb/omeroweb/webstart/views.py-    # ticket:9478 put insight jar at the start of the list if available
components/tools/OmeroWeb/omeroweb/webstart/views.py-    # This can be configured via omero.web.webstart_jar to point to a
components/tools/OmeroWeb/omeroweb/webstart/views.py-    # custom value.
components/tools/OmeroWeb/omeroweb/webstart/views.py-    idx = jarlist.index(settings.WEBSTART_JAR)
components/tools/OmeroWeb/omeroweb/webstart/views.py-    if idx > 0:
components/tools/OmeroWeb/omeroweb/webstart/views.py-        jarlist.pop(idx)
components/tools/OmeroWeb/omeroweb/webstart/views.py-        jarlist.insert(0, settings.WEBSTART_JAR)
components/tools/OmeroWeb/omeroweb/webstart/views.py-
components/tools/OmeroWeb/omeroweb/webstart/views.py-    context = {'codebase': codebase, 'href': href, 'jarlist': jarlist,

comment:7 Changed 11 years ago by jburel

  • Cc s.loynton@… added

comment:8 Changed 11 years ago by jburel

  • Milestone changed from Unscheduled to OMERO-4.5
  • Resolution set to fixed
  • Sprint set to 2013-02-12 (5)
  • Status changed from reopened to closed

comment:9 Changed 11 years ago by jburel <j.burel@…>

(In [757ecd4febf3ca515904edf9c5613d903240c97b/ome.git] on branch develop) Re-order jar so nano-xml is always the last one (see #9926)

comment:10 Changed 11 years ago by Josh Moore <josh@…>

(In [8512d512680aa7c6d35c967d07c24df73514ebdb/ome.git] on branch develop) Merge pull request #675 from jburel/rebased/develop/webstart

Re-order jar so nano-xml is always the last one (see #9926) (rebased onto develop)

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