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)
Change History (12)
comment:1 Changed 12 years ago by cblackburn
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.
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.