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Task #8855 (closed)

Opened 12 years ago

Closed 12 years ago

Bug: CLI import fails schema-2012-06 branch

Reported by: cblackburn Owned by: cblackburn
Priority: critical Milestone: OMERO-4.4
Component: Import Version: n.a.
Keywords: n.a. Cc: jamoore, cxallan
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: 2012-05-22 (15)

Description (last modified by cblackburn)

Trying to import a dv file fails. See output below.

Attachments (2)

Blitz-0.log (600.3 KB) - added by cblackburn 12 years ago.
master.err (5.4 KB) - added by cblackburn 12 years ago.

Download all attachments as: .zip

Change History (12)

comment:1 Changed 12 years ago by cblackburn

jrs-macbookpro-25031:dist cblackburn$ bin/omero import ../../../Images/dv/IAGFP-Noc01_R3D.dv
Previous session expired for root on localhost:4064
Server: [localhost]
Username: [root]
Password:
Created session f26b782d-6fb4-41de-8c83-2a68227945e1 (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
2012-05-17 15:33:18,639 0          [      main] INFO          ome.formats.importer.ImportConfig  - OMERO Version: 4.3.3-DEV-ice33
2012-05-17 15:33:18,642 3          [      main] INFO          ome.formats.importer.ImportConfig  - Bioformats version: 4.4-DEV revision: 3c17e2b date: 17 May 2012
2012-05-17 15:33:18,671 32         [      main] INFO   formats.importer.cli.CommandLineImporter  - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2012-05-17 15:33:18,989 350        [      main] INFO      ome.formats.importer.ImportCandidates  - Depth: 4 Metadata Level: MINIMUM
2012-05-17 15:33:19,804 1165       [      main] INFO      ome.formats.importer.ImportCandidates  - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 792ms. (815ms total) [0 unknowns]
2012-05-17 15:33:22,441 3802       [      main] WARN                    ome.system.UpgradeCheck  - UPGRADE AVAILABLE:Please upgrade to Beta-4.3.4 See http://trac.openmicroscopy.org.uk/omero for the latest version
2012-05-17 15:33:22,493 3854       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Attempting initial SSL connection to localhost:4064
2012-05-17 15:33:22,966 4327       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Insecure connection requested, falling back
2012-05-17 15:33:23,287 4648       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Server: 4.3.3
2012-05-17 15:33:23,288 4649       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Client: Beta4.3.3-DEV-ice33
2012-05-17 15:33:23,288 4649       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Java Version: 1.6.0_31
2012-05-17 15:33:23,288 4649       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - OS Name: Mac OS X
2012-05-17 15:33:23,288 4649       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - OS Arch: x86_64
2012-05-17 15:33:23,288 4649       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - OS Version: 10.6.8
2012-05-17 15:33:23,611 4972       [      main] WARN       ome.formats.enums.IQueryEnumProvider  - Enumeration 'Unknown' does not exist in 'class omero.model.Correction' setting to 'Other'
2012-05-17 15:33:23,619 4980       [      main] WARN       ome.formats.enums.IQueryEnumProvider  - Enumeration 'Unknown' does not exist in 'class omero.model.Immersion' setting to 'Other'
2012-05-17 15:33:23,670 5031       [      main] WARN       ome.formats.enums.IQueryEnumProvider  - Enumeration 'Unknown' does not exist in 'class omero.model.DetectorType' setting to 'Other'
2012-05-17 15:33:23,774 5135       [      main] INFO         ome.formats.importer.ImportLibrary  - File format: Deltavision
2012-05-17 15:33:23,775 5136       [      main] INFO         ome.formats.importer.ImportLibrary  - Base reader: loci.formats.in.DeltavisionReader
2012-05-17 15:33:23,775 5136       [      main] INFO         ome.formats.importer.ImportLibrary  - Metadata only import? false
2012-05-17 15:33:23,775 5136       [      main] INFO         ome.formats.importer.ImportLibrary  - Archiving enabled? false
2012-05-17 15:33:23,775 5136       [      main] INFO         ome.formats.importer.ImportLibrary  - Container metadata only import? false
2012-05-17 15:33:23,775 5136       [      main] INFO         ome.formats.importer.ImportLibrary  - Reader is not of HCS domain, use metafile: true
2012-05-17 15:33:24,389 5750       [      main] ERROR     ome.formats.importer.cli.ErrorHandler  - INTERNAL_EXCEPTION: /Users/cblackburn/Work/repos/ome/dist/../../../Images/dv/IAGFP-Noc01_R3D.dv
omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Write-method not permitted.
                        	at ome.io.nio.RomioPixelBuffer.throwIfReadOnly(RomioPixelBuffer.java:109)
                        	at ome.io.nio.RomioPixelBuffer.setRegion(RomioPixelBuffer.java:604)
                        	at ome.io.nio.RomioPixelBuffer.setTile(RomioPixelBuffer.java:882)
                        	at ome.services.RawPixelsBean.setTile(RawPixelsBean.java:777)
                        	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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:165)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy90.setTile(Unknown Source)
                        	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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy90.setTile(Unknown Source)
                        	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 ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
                        	at ome.services.throttling.Callback.run(Callback.java:56)
                        	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
                        	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:137)
                        	at ome.services.blitz.impl.RawPixelsStoreI.setTile_async(RawPixelsStoreI.java:268)
                        	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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at omero.cmd.CallContext.invoke(CallContext.java:59)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy91.setTile_async(Unknown Source)
                        	at omero.api._RawPixelsStoreTie.setTile_async(_RawPixelsStoreTie.java:309)
                        	at omero.api._RawPixelsStoreDisp.___setTile(_RawPixelsStoreDisp.java:862)
                        	at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1321)
                        	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 = "ome.conditions.ApiUsageException"
    message = "Write-method not permitted."
	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._RawPixelsStoreDelM.setTile(_RawPixelsStoreDelM.java:1774)
	at omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2435)
	at omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2407)
	at ome.formats.OMEROMetadataStoreClient.setTile(OMEROMetadataStoreClient.java:2540)
	at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:900)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:812)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:572)
	at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:288)
	at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:141)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:395)

omero.ApiUsageException
    serverStackTrace = "ome.conditions.ApiUsageException: Write-method not permitted.
                        	at ome.io.nio.RomioPixelBuffer.throwIfReadOnly(RomioPixelBuffer.java:109)
                        	at ome.io.nio.RomioPixelBuffer.setRegion(RomioPixelBuffer.java:604)
                        	at ome.io.nio.RomioPixelBuffer.setTile(RomioPixelBuffer.java:882)
                        	at ome.services.RawPixelsBean.setTile(RawPixelsBean.java:777)
                        	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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.security.basic.EventHandler.invoke(EventHandler.java:165)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.SessionHandler.doStateful(SessionHandler.java:182)
                        	at ome.tools.hibernate.SessionHandler.invoke(SessionHandler.java:166)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:231)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.util.ServiceHandler.invoke(ServiceHandler.java:116)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy90.setTile(Unknown Source)
                        	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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at ome.security.basic.BasicSecurityWiring.invoke(BasicSecurityWiring.java:98)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at ome.services.blitz.fire.AopContextInitializer.invoke(AopContextInitializer.java:43)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy90.setTile(Unknown Source)
                        	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 ome.services.blitz.util.IceMethodInvoker.invoke(IceMethodInvoker.java:179)
                        	at ome.services.throttling.Callback.run(Callback.java:56)
                        	at ome.services.throttling.InThreadThrottlingStrategy.callInvokerOnRawArgs(InThreadThrottlingStrategy.java:56)
                        	at ome.services.blitz.impl.AbstractAmdServant.callInvokerOnRawArgs(AbstractAmdServant.java:137)
                        	at ome.services.blitz.impl.RawPixelsStoreI.setTile_async(RawPixelsStoreI.java:268)
                        	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 org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
                        	at omero.cmd.CallContext.invoke(CallContext.java:59)
                        	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
                        	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
                        	at $Proxy91.setTile_async(Unknown Source)
                        	at omero.api._RawPixelsStoreTie.setTile_async(_RawPixelsStoreTie.java:309)
                        	at omero.api._RawPixelsStoreDisp.___setTile(_RawPixelsStoreDisp.java:862)
                        	at omero.api._RawPixelsStoreDisp.__dispatch(_RawPixelsStoreDisp.java:1321)
                        	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 = "ome.conditions.ApiUsageException"
    message = "Write-method not permitted."
	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._RawPixelsStoreDelM.setTile(_RawPixelsStoreDelM.java:1774)
	at omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2435)
	at omero.api.RawPixelsStorePrxHelper.setTile(RawPixelsStorePrxHelper.java:2407)
	at ome.formats.OMEROMetadataStoreClient.setTile(OMEROMetadataStoreClient.java:2540)
	at ome.formats.importer.ImportLibrary.writeDataTileBased(ImportLibrary.java:900)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:812)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:572)
	at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:288)
	at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:141)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:395)
2012-05-17 15:33:24,452 5813       [      main] INFO         ome.formats.importer.ImportLibrary  - Exiting on error

comment:2 Changed 12 years ago by cblackburn

  • Description modified (diff)
  • Owner set to jmoore

This error has only arisen today with changes to this branch as tests that were previously passing are now failing if an import is needed.

Last edited 12 years ago by cblackburn (previous) (diff)

comment:3 Changed 12 years ago by jmoore

  • Cc jmoore cxallan added

The only thing that I know of that might have happened on this code path is the changes to initializeServices (was origin/develop merged back in?). If that gets called and the RawPixelsStore were to be closed and then re-opened, then the file-on-disk server-side would be corrupted.

comment:4 Changed 12 years ago by jmoore

  • Owner jmoore deleted

Removing my name since I won't be able to look at this until Wed. at the earliest.

comment:5 Changed 12 years ago by jmoore

  • Owner set to cblackburn

Colin, passing back to you to retry with the latest. (Do you remember what sha this happened on?) For me it's working:

@schema-2012-06 ~/git $ dist/bin/omero import ~/NoBackup/SampleImages/IAGFP-Noc01_R3D.dv
Using session 0cda6f08-c11d-428f-aeb1-010c0af5479f (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
2012-05-18 11:41:15,695 0          [      main] INFO          ome.formats.importer.ImportConfig  - OMERO Version: 4.3.3-DEV-ice33
...
2012-05-18 11:41:19,553 3858       [      main] INFO         ome.formats.importer.ImportLibrary  - Reader is not of HCS domain, use metafile: true
2012-05-18 11:41:21,926 6231       [      main] INFO   ormats.importer.cli.LoggingImportMonitor  - IMPORT_DONE
Imported pixels:
612
2012-05-18 11:41:21,926 6231       [      main] INFO      ome.formats.importer.cli.ErrorHandler  - Number of errors: 0

@schema-2012-06 ~/git $ git log -n 1
commit c05ad115162e5a56de7242fc85af095e0e2654bd
Author: jmoore <josh@glencoesoftware.com>
Date:   Thu May 17 11:40:59 2012 +0200

    Fix use of 'PlateAcquisitions' in test

If you are still getting it with the latest sha1, it'd be helpful if you could attach a clean Blitz-0.log, master.out and master.err.

comment:6 Changed 12 years ago by cblackburn

Okay, I'll retest.

comment:7 Changed 12 years ago by cblackburn

Okay, slightly baffling retest.

Can't recreate with: a33f248 Fix 2012-06 => 2010-06 downgrade in ExporterTest

Problem appears with: 25adfbf bioformats: move to latest origin/2012-06

(git submodule update done each time)

However, if I then remove the logs and restart the import works!

I've attached the logs from a failure on 25adfbf

Changed 12 years ago by cblackburn

Changed 12 years ago by cblackburn

comment:8 Changed 12 years ago by cblackburn

master.out is empty.

comment:9 Changed 12 years ago by cblackburn

With the latest schema branch I was able to reproduce this by simply having old logs present under var/log If I emptied that directory imports worked fine! Restart with logs in place and imports failed. Since the restart following the kernel panic I have been unable to recreate this error. So it may just have been something screwed up on my system. Unless there is anything obvious in the logs this ticket can probably be closed?

comment:10 Changed 12 years ago by jmoore

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

Colin: it could well be OS/FS related. So, if you are no longer seeing it (and it was dependent on the presence of server logs?!?!) then yes, let's assume this was just you. If it comes back, let us know.

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

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