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Task #10380 (closed)

Opened 11 years ago

Closed 11 years ago

Last modified 11 years ago

BUG: Move does not work in FS

Reported by: pwalczysko Owned by: jamoore
Priority: critical Milestone: 5.0.0-beta1
Component: Client Version: n.a.
Keywords: FS Cc: fs@…, ux@…,
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: FS Demo 2

Description

Todays build on gretzky, works the same in Insight and Web.
The moving of projects and datasets works fine between groups.
What is not working is moving of images.

A)
If the image is within a project/dataset then these are moved without the image in them and the images end up in Orphaned folder in the source group.

B)
If the image is moved on it's own (without the project/dataset), then an error is produced both in Insight and web.
The error from Web is listed below.

STEP ERR stacktrace: ome.services.graphs.GraphException(message=No top-level item found: update FilesetImageLink set details.group.id = :grp where id = :id and details.group.id = :gid (id=7, grp=103)
at ome.services.chgrp.ChgrpStep.action(ChgrpStep.java:95)
at ome.services.graphs.GraphState.execute(GraphState.java:347)
at omero.cmd.graphs.ChgrpI.step(ChgrpI.java:155)
at omero.cmd.basic.DoAllI$X.step(DoAllI.java:100)
at omero.cmd.basic.DoAllI.step(DoAllI.java:301)
at omero.cmd.HandleI.steps(HandleI.java:435)
at omero.cmd.HandleI$1.doWork(HandleI.java:365)
at omero.cmd.HandleI$1.doWork(HandleI.java:363)
at sun.reflect.GeneratedMethodAccessor243.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:592)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at ome.services.util.Executor$Impl$Interceptor.invoke(Executor.java:518)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.security.basic.EventHandler.invoke(EventHandler.java:154)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.orm.hibernate3.HibernateInterceptor.invoke(HibernateInterceptor.java:111)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:108)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at ome.tools.hibernate.ProxyCleanupFilter$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 $Proxy65.doWork(Unknown Source)
at ome.services.util.Executor$Impl.execute(Executor.java:416)
at omero.cmd.HandleI.run(HandleI.java:359)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:417)
at ome.services.util.Executor$Impl$1.call(Executor.java:447)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:269)
at java.util.concurrent.FutureTask.run(FutureTask.java:123)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:651)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:676)
at java.lang.Thread.run(Thread.java:595)
, message: , step: 84, id: 81

Attachments (1)

move in Insight does not work.png​ (73.6 KB) - added by pwalczysko 11 years ago.

Download all attachments as: .zip

Change History (7)

Changed 11 years ago by pwalczysko

comment:1 Changed 11 years ago by pwalczysko

Insight log see below:

2013-02-13 12:04:52,259 INFO  [y.shoola.env.data.login.LoginServiceImpl] (entQueue-0) Logged onto OMERO at: gretzky.openmicroscopy.org.uk
User Name: user-1 -- Password: ***

2013-02-13 12:05:21,794 INFO  [       ome.formats.importer.ImportConfig] (hread-1160) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:05:21,794 INFO  [       ome.formats.importer.ImportConfig] (hread-1160) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:05:21,795 INFO  [   ome.formats.importer.ImportCandidates] (hread-1160) Depth: 4 Metadata Level: MINIMUM
2013-02-13 12:05:21,796 DEBUG [                  ome.scifio.io.Location] (hread-1160) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:05:22,121 INFO  [              loci.formats.FormatHandler] (hread-1160) APNGReader initializing /Users/petr/29-11-12/three1 Insight
2013-02-13 12:05:22,356 DEBUG [                  ome.scifio.io.Location] (hread-1160) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:05:22,356 INFO  [   ome.formats.importer.ImportCandidates] (hread-1160) 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 561ms. (561ms total) [0 unknowns]
2013-02-13 12:05:22,357 INFO  [       ome.formats.importer.ImportConfig] (hread-1160) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:05:22,357 INFO  [       ome.formats.importer.ImportConfig] (hread-1160) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:05:22,409 INFO  [       ome.formats.importer.ImportConfig] (hread-1160) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:05:22,409 INFO  [       ome.formats.importer.ImportConfig] (hread-1160) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:05:28,518 DEBUG [                  ome.scifio.io.Location] (hread-1160) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:05:28,530 DEBUG [                  ome.scifio.io.Location] (hread-1160) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:05:56,949 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:05:56,949 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:05:56,950 INFO  [   ome.formats.importer.ImportCandidates] (hread-1162) Depth: 4 Metadata Level: MINIMUM
2013-02-13 12:05:56,950 DEBUG [                  ome.scifio.io.Location] (hread-1162) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:05:57,272 INFO  [              loci.formats.FormatHandler] (hread-1162) APNGReader initializing /Users/petr/27-11-12/test3.png
2013-02-13 12:05:57,486 DEBUG [                  ome.scifio.io.Location] (hread-1162) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:05:57,486 INFO  [   ome.formats.importer.ImportCandidates] (hread-1162) 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 536ms. (536ms total) [0 unknowns]
2013-02-13 12:05:57,486 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:05:57,486 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:05:57,527 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:05:57,527 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:06:03,083 DEBUG [                  ome.scifio.io.Location] (hread-1162) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:06:03,096 DEBUG [                  ome.scifio.io.Location] (hread-1162) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:06:03,419 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:06:03,419 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:06:03,420 INFO  [   ome.formats.importer.ImportCandidates] (hread-1162) Depth: 4 Metadata Level: MINIMUM
2013-02-13 12:06:03,420 DEBUG [                  ome.scifio.io.Location] (hread-1162) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:06:03,459 INFO  [              loci.formats.FormatHandler] (hread-1162) APNGReader initializing /Users/petr/27-11-12/test.png
2013-02-13 12:06:03,664 DEBUG [                  ome.scifio.io.Location] (hread-1162) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:06:03,665 INFO  [   ome.formats.importer.ImportCandidates] (hread-1162) 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 244ms. (245ms total) [0 unknowns]
2013-02-13 12:06:03,665 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:06:03,665 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:06:03,679 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) OMERO Version: 4.4.4-1263-b6e4f9d-dirty-ice33-b163
2013-02-13 12:06:03,679 INFO  [       ome.formats.importer.ImportConfig] (hread-1162) Bioformats version: 4.5-DEV revision: 9df8519 date: 13 February 2013
2013-02-13 12:06:09,574 DEBUG [                  ome.scifio.io.Location] (hread-1162) Location.mapFile: embedded-stream.raw -> null
2013-02-13 12:06:09,587 DEBUG [                  ome.scifio.io.Location] (hread-1162) Location.mapFile: embedded-stream.raw -> null

comment:2 Changed 11 years ago by pwalczysko

  • Component changed from General to Client
  • Priority changed from minor to critical

comment:3 Changed 11 years ago by jmoore

  • Owner set to jmoore
  • Remaining Time set to 0.5

Just trying to reproduce now.

comment:4 Changed 11 years ago by jmoore

  • Remaining Time changed from 0.5 to 0.1

As long as it's clear that all the images contained in the fileset will be moved when the dataset is moved, then I have a workaround. Preparing a PR and then we can discuss there.

comment:5 Changed 11 years ago by jmoore

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

Nice happy PR number opened: ​https://github.com/openmicroscopy/openmicroscopy/pull/777

Moving conversation there.

comment:6 Changed 11 years ago by jmoore <josh@…>

(In [d9475c7a68f926f39a8b2d6e6124f33448f6acfa/ome.git] on branch develop) Move Image+FS rather than Image+Only with Datasets (Fix #10380)

Image+Only does not concern itself with fileset links or with
well sample links, therefore when the Dataset was moved, and
Fileset links found to the Image, the Image was left where it
was. Now, the links are followed and all the Images in the
Fileset are also moved.

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