Cannot delete Plate

[atarkowska]

2013-05-30 09:21:35,601 INFO  [          ome.services.graphs.GraphState] (3-thread-5) Failed to process Plate/Well/WellSample/Image: 1135 due to GraphException: Image:1135 improperly linked by 1 objects
2013-05-30 09:21:35,601 INFO  [                 org.perf4j.TimingLogger] (3-thread-5) start[1369902095595] time[6] tag[omero.delete.step.9]
2013-05-30 09:21:35,602 INFO  [      omero.cmd.graphs.DeleteI.@77d7ec06] (3-thread-5) Cancelled
2013-05-30 09:21:35,602 INFO  [                 org.perf4j.TimingLogger] (3-thread-5) start[1369902095595] time[7] tag[omero.request.step.9]
2013-05-30 09:21:35,602 INFO  [                 org.perf4j.TimingLogger] (3-thread-5) start[1369902095517] time[84] tag[omero.request]
2013-05-30 09:21:35,603 INFO  [                 org.perf4j.TimingLogger] (3-thread-5) start[1369902095500] time[102] tag[omero.call.exception]
2013-05-30 09:21:35,603 INFO  [        ome.services.util.ServiceHandler] (3-thread-5)  Excp:	omero.cmd.HandleI$Cancel: STEP ERR
2013-05-30 09:21:35,603 WARN  [              ome.services.util.Executor] (3-thread-5) Logins left: 1
2013-05-30 09:21:35,603 INFO  [                 org.perf4j.TimingLogger] (3-thread-5) start[1369902095500] time[103] tag[omero.request.tx]
2013-05-30 09:21:35,604 INFO  [ ome.services.blitz.fire.SessionManagerI] (l.Server-2) Found session locally: 49095709-8326-49e9-a4c5-1c70aafad46e
2013-05-30 09:21:35,605 INFO  [ ome.services.blitz.fire.SessionManagerI] (l.Server-2) Rejoining session ServiceFactoryI(session-15fb645e-e7f0-47d9-9e79-890e8c39e8c2/49095709-8326-49e9-a4c5-1c70aafad46e) (agent=OMERO.web)
2013-05-30 09:21:35,608 INFO  [        omero.cmd.basic.DoAllI.@379330f7] (l.Server-7) Add callback: .AKmgHM\"RIqyM*AEG\"md/9cf76cad-8b56-4aee-9fb0-daeb00b3ca0e
2013-05-30 09:21:35,609 INFO  [        omero.cmd.basic.DoAllI.@379330f7] (l.Server-9) getResponse: omero.cmd.GraphConstraintERR@846e08a
2013-05-30 09:21:35,609 INFO  [        omero.cmd.basic.DoAllI.@379330f7] (l.Server-9) getStatus: omero.cmd.Status@2e0b5c4a
2013-05-30 09:21:35,610 INFO  [        omero.cmd.basic.DoAllI.@379330f7] (l.Server-9) getResponse: omero.cmd.GraphConstraintERR@846e08a
2013-05-30 09:21:35,610 INFO  [                      omero.cmd.SessionI] (l.Server-9) Unregistered servant:49095709-8326-49e9-a4c5-1c70aafad46e/IHandle753bc370-42c2-4275-a634-1c8451132922(omero.cmd._HandleTie@b487554c)
2013-05-30 09:21:35,610 INFO  [        omero.cmd.basic.DoAllI.@379330f7] (l.Server-9) Closing...

[jamoore]

Thanks Ola. Can you please also provide:

• which file
• which server
• which client
• which version/build

[atarkowska]

user-7@gretzky, both clients, plates only, build 291

[jamoore]

Thanks, but knowing specific plates (ids on gretzky as well as fileset under /ome/data_repo or similar) is really important. I also forgot to ask which group, which is also important to find the data.

[pwalczysko]

The plate which I cannot delete:

• user-4,
• group read-write-1
• gretzky
• file /Volumes/mac-hd/Users/petr/Demo 4_2 import/bd-pathway/2009-05-01_000/Experiment.exp
• ID : 6
• Insight OMERO.insight-5.0.0-alpha4-180-a0aab67-dirty-ice33-b292-mac

[pwalczysko]

Suspected workflow with the abvoementioned plate:

• create a new folder, called Demo 4_2
• put a varied mix of files into it, including dv, dv.log, bd-pathway plate,
• import the whole Demo 4_2 folder
• plate goes under plates, the rest goes into newly created dataset Demo 4_2 import
• I have tried to delete Demo 4_2 import dataset and it took ages
• cancelled twice
• then was successful

[mtbcarroll]

on gretzky as user-8 I can't delete my plate ID 151

[atarkowska]

I think I gave enought information to run the following query as user-7 is a member of one group only:

omero=# select plate.id, plate.name, plate.permissions, experimentergroup.id, experimentergroup.name

from plate, experimenter, experimentergroup

omero-# where plate.owner_id = experimenter.id

omero-# and plate.group_id=experimentergroup.id

and experimenter.omename = 'user-7';

id | name | permissions | id | name

----+----------------------------------------------------------------------------------------------------------------------+-------------+----+-----------

53 | /Users/ola/OMERO/images/perkinelmer-operetta/P004-CC Edu-pHH32009-02-03T17_36_29-Measurement1/Images/Index.idx.xml | -120 | 9 | private-1

52 | /Users/ola/OMERO/images/ome-xml/testImportPlate/testImportPlateMultiplePlateAcquisitions1508.ome | -120 | 9 | private-1

7 | /Volumes/ome/data_repo/test_images_good/cellworx/hms/plate1/plate1.HTD | -120 | 9 | private-1

5 | /Volumes/ome/data_repo/test_images_good/cellworx/hms/plate1/TIFF/plate1.HTD | -120 | 9 | private-1

4 | /Volumes/ome/data_repo/test_images_good/cellomics/MFGTMP_081128200001_A02f239d1.C01 | -120 | 9 | private-1

3 | /Volumes/ome/data_repo/test_images_good/cellomics/MFGTMP_081222130005_E07f00d0.C01 | -120 | 9 | private-1

[jamoore]

Unfortunately, Ola, as we've seen those things can change. Further testing of chgrp or admin etc. can change what you were seeing. It's always best to capture as much of what you saw as possible, so that 1) no one else has to search for the info and 2) if anything changes, it's clear what was going on at the time.

[jamoore]

PR filed : ​https://github.com/openmicroscopy/openmicroscopy/pull/1225

[jmoore <josh@…>]

(In [b331a205e491f0b3c0bdb78569c8e000b16dd747/ome.git] on branch develop) Fix Plate delete (Fix #11009, See #10776)

fc6b8340236c006c64043c22296268bddb11ea14 removed the
"+WS" suffix from Image, which broke plate delete.
Essentially, the Image subgraph was not being processed
but just the image table itself.

[Josh Moore <josh@…>]

(In [7cb6bff0114b30a3525504dc02bb966f123284f3/ome.git] on branch develop) Merge pull request #1225 from joshmoore/11009-plate-delete

Fix Plate delete (Fix #11009, See #10776)