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Task #5516 (closed)

Opened 13 years ago

Closed 13 years ago

BUG: Scripts not running under windows insight/server

Reported by: bwzloranger Owned by: jamoore
Priority: blocker Milestone: OMERO-Beta4.3
Component: OmeroPy Version: n.a.
Keywords: n.a. Cc: jburel, wmoore, jamoore
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-06-02 (13)

Description

Went to scripts->Util->Channel offsets and received a dialog box indicating the script could not be run. Error message in insight as follows:

809942 ms since start (2011-05-24 11:20:42,617) ** ERROR **
 [thread: AWT-EventQueue-0][class: org.openmicroscopy.shoola.agents.metadata.ScriptLoader] -
 Data Retrieval Failure: org.openmicroscopy.shoola.env.data.ProcessException: Cannot load the script: 262
	at org.openmicroscopy.shoola.env.data.OMEROGateway.loadScript(OMEROGateway.java:5874)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.loadScript(OmeroImageServiceImpl.java:1360)
	at org.openmicroscopy.shoola.env.data.views.calls.ScriptsLoader$2.doCall(ScriptsLoader.java:97)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)
Caused by: omero.InternalException
    serverStackTrace = "Traceback (most recent call last):
                          File "c:\omero_dist\lib\python\omero\util\decorators.py", line 61, in exc_handler
                            rv = func(*args, **kwargs)
                          File "c:\omero_dist\lib\python\omero\processor.py", line 794, in parseJob
                            client = self.user_client("OMERO.parseJob")
                          File "c:\omero_dist\lib\python\omero\processor.py", line 690, in user_client
                            client = omero.client(args)
                          File "c:\omero_dist\lib\python\omero\__init__.py", line 28, in client
                            return omero.clients.BaseClient(*args, **kwargs)
                          File "c:\omero_dist\lib\python\omero\clients.py", line 109, in __init__
                            id.properties = Ice.createProperties(args)
                          File "C:\Ice-3.3.1\python\Ice.py", line 524, in createProperties
                            properties = IcePy.createProperties(args, defaults)
                        ValueError: list element must be a string
                        "
    serverExceptionClass = ""
    message = "Internal exception"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at java.lang.Class.newInstance0(Unknown Source)
	at java.lang.Class.newInstance(Unknown Source)
	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.getParams(_IScriptDelM.java:191)
	at omero.api.IScriptPrxHelper.getParams(IScriptPrxHelper.java:254)
	at omero.api.IScriptPrxHelper.getParams(IScriptPrxHelper.java:226)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.loadScript(OMEROGateway.java:5871)
	... 9 more
Data Retrieval Failure: org.openmicroscopy.shoola.env.data.ProcessException: Cannot load the script: 262
	at org.openmicroscopy.shoola.env.data.OMEROGateway.loadScript(OMEROGateway.java:5874)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.loadScript(OmeroImageServiceImpl.java:1360)
	at org.openmicroscopy.shoola.env.data.views.calls.ScriptsLoader$2.doCall(ScriptsLoader.java:97)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)
Caused by: omero.InternalException
    serverStackTrace = "Traceback (most recent call last):
                          File "c:\omero_dist\lib\python\omero\util\decorators.py", line 61, in exc_handler
                            rv = func(*args, **kwargs)
                          File "c:\omero_dist\lib\python\omero\processor.py", line 794, in parseJob
                            client = self.user_client("OMERO.parseJob")
                          File "c:\omero_dist\lib\python\omero\processor.py", line 690, in user_client
                            client = omero.client(args)
                          File "c:\omero_dist\lib\python\omero\__init__.py", line 28, in client
                            return omero.clients.BaseClient(*args, **kwargs)
                          File "c:\omero_dist\lib\python\omero\clients.py", line 109, in __init__
                            id.properties = Ice.createProperties(args)
                          File "C:\Ice-3.3.1\python\Ice.py", line 524, in createProperties
                            properties = IcePy.createProperties(args, defaults)
                        ValueError: list element must be a string
                        "
    serverExceptionClass = ""
    message = "Internal exception"
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
	at java.lang.reflect.Constructor.newInstance(Unknown Source)
	at java.lang.Class.newInstance0(Unknown Source)
	at java.lang.Class.newInstance(Unknown Source)
	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.getParams(_IScriptDelM.java:191)
	at omero.api.IScriptPrxHelper.getParams(IScriptPrxHelper.java:254)
	at omero.api.IScriptPrxHelper.getParams(IScriptPrxHelper.java:226)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.loadScript(OMEROGateway.java:5871)
	... 9 more
Exception in thread "AWT-EventQueue-0"

Change History (5)

comment:1 Changed 13 years ago by jmoore

  • Cc jmoore added
  • Component changed from General to OmeroPy
  • Owner changed from jmoore to bwzloranger

Brian can you modify the file "lib/python/omero/clients.py" and print out the contents of "args" on line 109 before calling "Ice.createProperties". This is probably unicode or similar being passed in.

comment:2 Changed 13 years ago by jmoore

If this was pixels 101, then the following might explain at least one scenario:

~/Downloads/5515/Logs $ grep 101 Blitz-0.log 
...
2011-05-24 11:09:43,892 INFO  [  ome.services.pixeldata.PixelDataThread] (2-thread-2) Creating PIXELDATA event for pixels id:101
2011-05-24 11:09:43,907 INFO  [                ome.io.nio.PixelsService] (l.Server-1) Missing pyramid:c:\OMERO\Pixels\101_pyramid
2011-05-24 11:09:44,610 INFO  [        ome.services.util.ServiceHandler] (l.Server-5)  Args:	[class ome.model.core.Image, (101), (), (), ome.parameters.Parameters@aafeff]
2011-05-24 11:09:44,657 INFO  [        ome.services.util.ServiceHandler] (l.Server-5)  Rslt:	{101=(ome.model.annotations.FileAnnotation:Id_151)}
2011-05-24 11:09:44,704 INFO  [        ome.services.util.ServiceHandler] (l.Server-4)  Args:	[101]
2011-05-24 11:09:44,751 INFO  [        ome.services.util.ServiceHandler] (l.Server-4)  Rslt:	ome.model.core.Pixels:Id_101
2011-05-24 11:09:44,767 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Args:	[101, 0]
2011-05-24 11:09:44,782 INFO  [        ome.services.util.ServiceHandler] (l.Server-8)  Rslt:	(ome.model.display.RenderingDef:Id_101)
2011-05-24 11:09:44,954 INFO  [        ome.services.util.ServiceHandler] (l.Server-1)  Rslt:	{102=[-1, -40, -1, ... 1 more], 103=[-1, -40, -1, ... 1 more], 101=[-1, -40, -1, ... 1 more], ... 1 more}
2011-05-24 11:09:52,563 INFO  [   ome.services.blitz.impl.DeleteHandleI] (3-thread-5) Deleting /Image:101
... This leads to the warning ...

~/Downloads/5515/Logs $ grep 101 PixelData-0.log 
2011-05-24 10:25:41,101 INFO  [             ome.io.nio.RomioPixelBuffer] (3-thread-1) Retrieving plane: 0x1x0
2011-05-24 10:25:43,101 INFO  [             ome.io.nio.RomioPixelBuffer] (3-thread-1) Retrieving plane: 0x1x0
2011-05-24 10:26:49,101 INFO  [             ome.io.nio.RomioPixelBuffer] (3-thread-1) Retrieving plane: 0x1x0
2011-05-24 10:28:31,101 INFO  [             ome.io.nio.RomioPixelBuffer] (3-thread-1) Retrieving plane: 0x2x0
2011-05-24 10:28:43,101 INFO  [             ome.io.nio.RomioPixelBuffer] (3-thread-1) Retrieving plane: 0x2x0
2011-05-24 10:28:46,101 INFO  [             ome.io.nio.RomioPixelBuffer] (3-thread-1) Retrieving plane: 0x2x0
2011-05-24 10:29:35,101 INFO  [             ome.io.nio.RomioPixelBuffer] (3-thread-1) Retrieving plane: 0x2x0
2011-05-24 10:30:07,101 INFO  [             ome.io.nio.RomioPixelBuffer] (3-thread-1) Retrieving plane: 0x2x0
2011-05-24 11:09:45,485 INFO  [e.io.bioformats.OmeroPixelsPyramidWriter] (3-thread-3) setId(c:\OMERO\Pixels\.101_pyramid7646151252646832883.tmp)
2011-05-24 11:13:31,240 INFO  [                ome.io.nio.PixelsService] (3-thread-3) SUCCESS -- Pyramid created for pixels id:101
2011-05-24 11:13:31,240 INFO  [e.io.bioformats.OmeroPixelsPyramidWriter] (3-thread-3) close(c:\OMERO\Pixels\.101_pyramid7646151252646832883.tmp)

comment:3 Changed 13 years ago by jmoore

Sorry, this was meant for #5515.

comment:4 Changed 13 years ago by jmoore

  • Owner changed from bwzloranger to jmoore
  • Remaining Time set to 0.1
  • Status changed from new to accepted

comment:5 Changed 13 years ago by jmoore <josh@…>

  • Remaining Time changed from 0.1 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

(In [7babe6ee7685ac3dd8790bab74d967525dfb36e5/ome.git] on branch develop) Encoding unicode args to Ice.createProperties to utf-8 (Fix #5516)

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