Task #5662 (closed)
Bug: Ice.MarshalException on script execution (Win)
| Reported by: | jamoore | Owned by: | jamoore |
|---|---|---|---|
| Priority: | critical | Milestone: | OMERO-Beta4.3 |
| Component: | Scripting | Version: | n.a. |
| Keywords: | n.a. | Cc: | jburel, cxallan |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2011-06-02 (13) |
Description (last modified by jmoore)
I didn't expect Make Movie to work on Windows, but certainly didn't expect a MarshalException (see below)
What appears to be happening is that the byte array stored in the DB has become corrupted, causing the method to throw. There is already a try/catch block which returns null to force re-creation, but it's unclear why the existing params began throwing exceptions in the middle of testing this morning, after upgrade perhaps because of the new files, etc..
See: http://www.zeroc.com/forums/help-center/5315-ice-marshalexception-problem-w-icestorm.html
Update
The bytea's aren't corrupted but rather are being returned in a different format starting with PostgreSQL 9.0. Issuing ALTER DATABASE your_database SET bytea_output = 'escape'; corrected the problem. See:
- PostgreSQL problem with bytea
- bytea on windows perl client
- hibernate-not-loading postgresql-bytea consistently
- byte_output default => data corruption
- bytea_output default value change in 9.0 breaks Apache::Session::Postgres
- Inconsistent Loading of Bytea across platform
- pg_unescape_bytea Doesn't work using PostgreSQL 9.0
- http://www.postgresql.org/docs/9.0/static/datatype-binary.html
Change History (10)
comment:1 Changed 13 years ago by jmoore
- Description modified (diff)
- Summary changed from Bug: Ice.MarshalException on Make Movie to Bug: Ice.MarshalException on Make Movie (Win)
comment:2 Changed 13 years ago by jmoore
- Summary changed from Bug: Ice.MarshalException on Make Movie (Win) to Bug: Ice.MarshalException on script execution (Win)
Seems to be unrelated to Make Movie:
java.lang.Exception: java.lang.Exception: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot create a figure for the specified images.
at org.openmicroscopy.shoola.env.data.views.ProcessBatchCall.doStep(ProcessBatchCall.java:101)
at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
at java.lang.Thread.run(Thread.java:680)
Caused by: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data.
Cannot create a figure for the specified images.
at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:875)
at org.openmicroscopy.shoola.env.data.OMEROGateway.createFigure(OMEROGateway.java:6108)
at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.createFigure(OmeroImageServiceImpl.java:1370)
at org.openmicroscopy.shoola.env.data.views.calls.FigureCreator$1.initialize(FigureCreator.java:78)
at org.openmicroscopy.shoola.env.data.views.ProcessBatchCall.doStep(ProcessBatchCall.java:99)
... 6 more
Caused by: org.openmicroscopy.shoola.env.data.ProcessException: Cannot run script with ID:53
at org.openmicroscopy.shoola.env.data.OMEROGateway.runScript(OMEROGateway.java:514)
at org.openmicroscopy.shoola.env.data.OMEROGateway.createFigure(OMEROGateway.java:6029)
... 9 more
Caused by: omero.InternalException
serverStackTrace = "Ice.MarshalException
reason = (null)
at IceInternal.BasicStream.typeToClass(BasicStream.java:2403)
at IceInternal.BasicStream.findClass(BasicStream.java:2320)
at IceInternal.BasicStream.loadObjectFactory(BasicStream.java:2187)
at IceInternal.BasicStream.readObject(BasicStream.java:1540)
at Ice.InputStreamI.readObject(InputStreamI.java:179)
at omero.grid.ParamsHelper.parse(ParamsHelper.java:193)
at omero.grid.ParamsHelper.getParamsOrNull(ParamsHelper.java:103)
at omero.grid.ParamsHelper.getOrCreateParams(ParamsHelper.java:92)
at omero.grid.InteractiveProcessorI.params(InteractiveProcessorI.java:163)
at omero.grid.InteractiveProcessorI.execute(InteractiveProcessorI.java:224)
at ome.services.blitz.impl.ScriptI$1.call(ScriptI.java:124)
at ome.services.blitz.impl.ScriptI$1.call(ScriptI.java:110)
at ome.services.throttling.Callback2.run(Callback2.java:49)
at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80)
at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:155)
at ome.services.blitz.impl.ScriptI.runScript_async(ScriptI.java:110)
at omero.api._IScriptTie.runScript_async(_IScriptTie.java:127)
at omero.api._IScriptDisp.___runScript(_IScriptDisp.java:394)
at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:534)
at IceInternal.Incoming.invoke(Incoming.java:159)
at Ice.ConnectionI.invokeAll(ConnectionI.java:2037)
at Ice.ConnectionI.message(ConnectionI.java:972)
at IceInternal.ThreadPool.run(ThreadPool.java:577)
at IceInternal.ThreadPool.access$100(ThreadPool.java:12)
at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971)
"
serverExceptionClass = "Ice.MarshalException"
message = ""
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at java.lang.Class.newInstance0(Class.java:355)
at java.lang.Class.newInstance(Class.java:308)
at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
at IceInternal.BasicStream.throwException(BasicStream.java:1632)
at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
at omero.api._IScriptDelM.runScript(_IScriptDelM.java:508)
at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:662)
at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:634)
at org.openmicroscopy.shoola.env.data.OMEROGateway.runScript(OMEROGateway.java:511)
... 10 more
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:183)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:272)
at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:242)
at org.openmicroscopy.shoola.env.ui.ActivityComponent.showException(ActivityComponent.java:474)
at org.openmicroscopy.shoola.env.ui.ActivityComponent.actionPerformed(ActivityComponent.java:927)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
at java.awt.Component.processMouseEvent(Component.java:6374)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6139)
at java.awt.Container.processEvent(Container.java:2085)
at java.awt.Component.dispatchEventImpl(Component.java:4736)
at java.awt.Container.dispatchEventImpl(Container.java:2143)
at java.awt.Component.dispatchEvent(Component.java:4566)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
at java.awt.Container.dispatchEventImpl(Container.java:2129)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4566)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)
at java.awt.EventQueue.access$000(EventQueue.java:86)
at java.awt.EventQueue$1.run(EventQueue.java:639)
at java.awt.EventQueue$1.run(EventQueue.java:637)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:653)
at java.awt.EventQueue$2.run(EventQueue.java:651)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)
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)
comment:3 Changed 13 years ago by jmoore
- Owner set to jmoore
- Remaining Time set to 0.25
- Sprint set to 2011-06-02 (13)
- Status changed from new to accepted
comment:4 Changed 13 years ago by jmoore
- Description modified (diff)
comment:5 Changed 13 years ago by jmoore
Failing
2 | \omero\analysis_scripts\FLIM.py 51 | \omero\export_scripts\Batch_Image_Export.py 52 | \omero\export_scripts\Make_Movie.py 5 | \omero\figure_scripts\Movie_Figure.py 6 | \omero\figure_scripts\Movie_ROI_Figure.py 7 | \omero\figure_scripts\ROI_Split_Figure.py 8 | \omero\figure_scripts\Split_View_Figure.py 53 | \omero\figure_scripts\Thumbnail_Figure.py 12 | \omero\util_scripts\Channel_Offsets.py 13 | \omero\util_scripts\Combine_Images.py
Passing
10 | \omero\import_scripts\Populate_ROI.py 11 | \omero\setup_scripts\FLIM_initialise.py 14 | \omero\util_scripts\Images_From_ROIs.py
comment:6 Changed 13 years ago by jmoore
# Find the links which link the params to the ParseJob
~/git/dist $ bin/omero hql "select l.id from Job j join j.originalFileLinks l where l.child.id = 12"
# | Col1
---+------
0 | 201
1 | 203
(2 rows)
# Delete them to force a new parsing
~/git/dist $ bin/omero shell --login
In [2]: u = client.sf.getUpdateService()
In [4]: u.deleteObject(omero.model.JobOriginalFileLinkI(201, False))
In [5]: u.deleteObject(omero.model.JobOriginalFileLinkI(203, False))
# Get the params. Success!
~/git/dist $ bin/omero script params 12
id: 12
name: Channel_Offsets.py
version: 4.2.0
authors: William Moore, OME Team
institutions: University of Dundee
...
# Try to launch. Failure!
~/git/dist $ bin/omero script launch 12
...
omero.InternalException: exception ::omero::InternalException
{
serverStackTrace = Ice.MarshalException
...
# Try to get the params. Also failure!!!
~/git/dist $ bin/omero script params 12
...
omero.InternalException: exception ::omero::InternalException
{
serverStackTrace = Ice.MarshalException
comment:7 Changed 13 years ago by jmoore
In script form. The assertion at the bottom passes, i.e. the two byte arrays are the same:
script_id = 12
import Ice
from omero.rtypes import unwrap
u = client.sf.getUpdateService()
q = client.sf.getQueryService()
s = client.sf.getScriptService()
for result in unwrap(q.projection("select l.id from ParseJob j join j.originalFileLinks l where l.child.id = %s" % script_id, None)):
id = result[0]
print "Deleting %s..." % id
u.deleteObject(omero.model.JobOriginalFileLinkI(id, False))
def params(id):
rv = q.findByQuery("select j from ParseJob j join j.originalFileLinks l where l.child.id = %s" % id, None)
if rv is not None:
return rv
else:
print "No data"
def launch(id):
inputs = {}
proc = None
try:
proc = s.runScript(id, inputs, None)
except omero.InternalException, ie:
print "Got marshal exception"
if proc:
try:
cb = omero.scripts.ProcessCallbackI(client, proc)
while not cb.block(1000): # ms.
pass
cb.close()
rv = proc.getResults(0)
finally:
proc.close(False)
print "Results:", rv
s.getParams(script_id) # Create new
a = params(script_id) # Print out the newly created
b = launch(script_id) # Something happens here ?!?!?!
c = params(script_id) # Print out the value after the marshal exception
assert a.params == c.params
print "Identical"
comment:8 Changed 13 years ago by jmoore
- Description modified (diff)
comment:9 Changed 13 years ago by jmoore
- Cc cxallan added
- Description modified (diff)
- Priority changed from minor to critical
- Remaining Time changed from 0.25 to 0
- Resolution set to fixed
- Status changed from accepted to closed
comment:10 Changed 13 years ago by jmoore <josh@…>
(In [daf776cc460ec1c0aae15c7d29fc2955f96e626a/ome.git] on branch develop) Catching MarshalException in ParamsHelper (See #5662)
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java.lang.Exception: java.lang.Exception: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data. Cannot create a movie for image: 278 at org.openmicroscopy.shoola.env.data.views.ProcessBatchCall.doStep(ProcessBatchCall.java:101) at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226) at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165) at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274) at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91) at java.lang.Thread.run(Thread.java:680) Caused by: org.openmicroscopy.shoola.env.data.DSAccessException: Cannot access data. Cannot create a movie for image: 278 at org.openmicroscopy.shoola.env.data.OMEROGateway.handleException(OMEROGateway.java:875) at org.openmicroscopy.shoola.env.data.OMEROGateway.createMovie(OMEROGateway.java:5752) at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.createMovie(OmeroImageServiceImpl.java:1313) at org.openmicroscopy.shoola.env.data.views.calls.MovieCreator$1.initialize(MovieCreator.java:79) at org.openmicroscopy.shoola.env.data.views.ProcessBatchCall.doStep(ProcessBatchCall.java:99) ... 6 more Caused by: org.openmicroscopy.shoola.env.data.ProcessException: Cannot run script with ID:52 at org.openmicroscopy.shoola.env.data.OMEROGateway.runScript(OMEROGateway.java:514) at org.openmicroscopy.shoola.env.data.OMEROGateway.createMovie(OMEROGateway.java:5750) ... 9 more Caused by: omero.InternalException serverStackTrace = "Ice.MarshalException reason = (null) at IceInternal.BasicStream.typeToClass(BasicStream.java:2403) at IceInternal.BasicStream.findClass(BasicStream.java:2320) at IceInternal.BasicStream.loadObjectFactory(BasicStream.java:2187) at IceInternal.BasicStream.readObject(BasicStream.java:1540) at Ice.InputStreamI.readObject(InputStreamI.java:179) at omero.grid.ParamsHelper.parse(ParamsHelper.java:193) at omero.grid.ParamsHelper.getParamsOrNull(ParamsHelper.java:103) at omero.grid.ParamsHelper.getOrCreateParams(ParamsHelper.java:92) at omero.grid.InteractiveProcessorI.params(InteractiveProcessorI.java:163) at omero.grid.InteractiveProcessorI.execute(InteractiveProcessorI.java:224) at ome.services.blitz.impl.ScriptI$1.call(ScriptI.java:124) at ome.services.blitz.impl.ScriptI$1.call(ScriptI.java:110) at ome.services.throttling.Callback2.run(Callback2.java:49) at ome.services.throttling.InThreadThrottlingStrategy.safeRunnableCall(InThreadThrottlingStrategy.java:80) at ome.services.blitz.impl.AbstractAmdServant.safeRunnableCall(AbstractAmdServant.java:155) at ome.services.blitz.impl.ScriptI.runScript_async(ScriptI.java:110) at omero.api._IScriptTie.runScript_async(_IScriptTie.java:127) at omero.api._IScriptDisp.___runScript(_IScriptDisp.java:394) at omero.api._IScriptDisp.__dispatch(_IScriptDisp.java:534) at IceInternal.Incoming.invoke(Incoming.java:159) at Ice.ConnectionI.invokeAll(ConnectionI.java:2037) at Ice.ConnectionI.message(ConnectionI.java:972) at IceInternal.ThreadPool.run(ThreadPool.java:577) at IceInternal.ThreadPool.access$100(ThreadPool.java:12) at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:971) " serverExceptionClass = "Ice.MarshalException" message = "" at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) at java.lang.reflect.Constructor.newInstance(Constructor.java:513) at java.lang.Class.newInstance0(Class.java:355) at java.lang.Class.newInstance(Class.java:308) at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243) at IceInternal.BasicStream.throwException(BasicStream.java:1632) at IceInternal.Outgoing.throwUserException(Outgoing.java:442) at omero.api._IScriptDelM.runScript(_IScriptDelM.java:508) at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:662) at omero.api.IScriptPrxHelper.runScript(IScriptPrxHelper.java:634) at org.openmicroscopy.shoola.env.data.OMEROGateway.runScript(OMEROGateway.java:511) ... 10 more at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:183) at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:272) at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:242) at org.openmicroscopy.shoola.env.ui.ActivityComponent.showException(ActivityComponent.java:474) at org.openmicroscopy.shoola.env.ui.ActivityComponent.actionPerformed(ActivityComponent.java:927) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236) at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272) at java.awt.Component.processMouseEvent(Component.java:6374) at javax.swing.JComponent.processMouseEvent(JComponent.java:3267) at java.awt.Component.processEvent(Component.java:6139) at java.awt.Container.processEvent(Container.java:2085) at java.awt.Component.dispatchEventImpl(Component.java:4736) at java.awt.Container.dispatchEventImpl(Container.java:2143) at java.awt.Component.dispatchEvent(Component.java:4566) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212) at java.awt.Container.dispatchEventImpl(Container.java:2129) at java.awt.Window.dispatchEventImpl(Window.java:2478) at java.awt.Component.dispatchEvent(Component.java:4566) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680) at java.awt.EventQueue.access$000(EventQueue.java:86) at java.awt.EventQueue$1.run(EventQueue.java:639) at java.awt.EventQueue$1.run(EventQueue.java:637) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$2.run(EventQueue.java:653) at java.awt.EventQueue$2.run(EventQueue.java:651) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:650) 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)