Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #12703 (closed)

Opened 9 years ago

Closed 9 years ago

Last modified 9 years ago

BUG: bd-pathway fails on import

Reported by: pwalczysko Owned by: mlinkert
Priority: blocker Milestone: 5.1.0-m4
Component: Bio-Formats Version: 5.1.0-m1
Keywords: n.a. Cc: ux@…, ajpatterson, mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: n.a.

Description

In importer (started from Insight)

test_images_good/bd-pathway (import whole folder)

Fails at Failed to import Metadata stage.

Combination of clients and servers where the bug appears or does not appear

  • m3 server (seabass 14064) & m3 client -> NO BUG
  • trout merge (4064) from today (12 Jan) & today's build client -> BUG PRESENT
  • trout lates (14064) & Friday's (09 Jan) build client -> NO BUG
  • trout merge (4064) & Fridays build client -> BUG PRESENT

Not sure if units or formats problem, feel free to reassign pleasse.

java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: error-on-init
Parameters: {message=For input string: "-merge-deploy/ManagedRepository/user-4_5/2015-01/12/11-36-01", stacktrace=java.lang.NumberFormatException: For input string: "-merge-deploy/ManagedRepository/user-4_5/2015-01/12/11-36-01"
	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
	at java.lang.Integer.parseInt(Integer.java:492)
	at java.lang.Integer.parseInt(Integer.java:527)
	at loci.formats.in.BDReader.initFile(BDReader.java:422)
	at loci.formats.FormatReader.setId(FormatReader.java:1404)
	at loci.formats.ImageReader.setId(ImageReader.java:835)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.Memoizer.setId(Memoizer.java:627)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:403)
	at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:620)
	at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:225)
	at omero.cmd.HandleI.steps(HandleI.java:427)
	at omero.cmd.HandleI$1.doWork(HandleI.java:365)
	at omero.cmd.HandleI$1.doWork(HandleI.java:361)
	at sun.reflect.GeneratedMethodAccessor293.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
	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 com.sun.proxy.$Proxy72.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:457)
	at omero.cmd.HandleI.run(HandleI.java:359)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
	at ome.services.util.Executor$Impl$1.call(Executor.java:498)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:744)
}

	at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:628)
	at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:301)
	at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
	at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
	at IceInternal.Incoming.invoke(Incoming.java:222)
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
	at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
	at Ice.ConnectionI.message(ConnectionI.java:1213)
	at IceInternal.ThreadPool.run(ThreadPool.java:321)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:695)

	at org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:677)
	at ome.formats.importer.ImportLibrary.notifyObservers(ImportLibrary.java:234)
	at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:634)
	at omero.cmd.CmdCallbackI.finished(CmdCallbackI.java:301)
	at omero.cmd._CmdCallbackDisp.___finished(_CmdCallbackDisp.java:118)
	at omero.cmd._CmdCallbackDisp.__dispatch(_CmdCallbackDisp.java:145)
	at IceInternal.Incoming.invoke(Incoming.java:222)
	at Ice.ConnectionI.invokeAll(ConnectionI.java:2482)
	at Ice.ConnectionI.dispatch(ConnectionI.java:1258)
	at Ice.ConnectionI.message(ConnectionI.java:1213)
	at IceInternal.ThreadPool.run(ThreadPool.java:321)
	at IceInternal.ThreadPool.access$300(ThreadPool.java:12)
	at IceInternal.ThreadPool$EventHandlerThread.run(ThreadPool.java:693)
	at java.lang.Thread.run(Thread.java:695)
Caused by: java.lang.RuntimeException: Failure response on import!
Category: ::omero::grid::ImportRequest
Name: error-on-init
Parameters: {message=For input string: "-merge-deploy/ManagedRepository/user-4_5/2015-01/12/11-36-01", stacktrace=java.lang.NumberFormatException: For input string: "-merge-deploy/ManagedRepository/user-4_5/2015-01/12/11-36-01"
	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
	at java.lang.Integer.parseInt(Integer.java:492)
	at java.lang.Integer.parseInt(Integer.java:527)
	at loci.formats.in.BDReader.initFile(BDReader.java:422)
	at loci.formats.FormatReader.setId(FormatReader.java:1404)
	at loci.formats.ImageReader.setId(ImageReader.java:835)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.Memoizer.setId(Memoizer.java:627)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at ome.services.blitz.repo.CheckedPath.bfSetId(CheckedPath.java:403)
	at ome.services.blitz.repo.ManagedImportRequestI.open(ManagedImportRequestI.java:620)
	at ome.services.blitz.repo.ManagedImportRequestI.init(ManagedImportRequestI.java:225)
	at omero.cmd.HandleI.steps(HandleI.java:427)
	at omero.cmd.HandleI$1.doWork(HandleI.java:365)
	at omero.cmd.HandleI$1.doWork(HandleI.java:361)
	at sun.reflect.GeneratedMethodAccessor293.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:606)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
	at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:576)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
	at ome.tools.hibernate.ProxyCleanupFilter$Interceptor.invoke(ProxyCleanupFilter.java:241)
	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 com.sun.proxy.$Proxy72.doWork(Unknown Source)
	at ome.services.util.Executor$Impl.execute(Executor.java:457)
	at omero.cmd.HandleI.run(HandleI.java:359)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
	at ome.services.util.Executor$Impl$1.call(Executor.java:498)
	at java.util.concurrent.FutureTask.run(FutureTask.java:262)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
	at java.lang.Thread.run(Thread.java:744)
}

	at ome.formats.importer.ImportLibrary$ImportCallback.onFinished(ImportLibrary.java:628)
	... 11 more

Change History (2)

comment:1 Changed 9 years ago by mlinkert

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

This was introduced in ​https://github.com/openmicroscopy/bioformats/pull/1522 opened yesterday, and is fixed in ​https://github.com/openmicroscopy/bioformats/commit/56ea5990b038e98713107e6292b61e88ba13f752 (just added to that PR). Feel free to re-open or comment on the PR if tomorrow's merge build doesn't work.

comment:2 Changed 9 years ago by Melissa Linkert <melissa@…>

  • Remaining Time set to 0

(In [56ea5990b038e98713107e6292b61e88ba13f752/bioformats.git] on branch develop) BD Pathway: only use relative paths when determining well labels

Fixes #12703.

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

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.63762 sec.)

© 2000-2014 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 3.0 Unported License
OME source code is available under the GNU General public license or through commercial license from Glencoe Software

We're Hiring!