Omero Server does not import images

[mamina]

Hello everybody,

I am using the Omero Virtual Appliance v. 5.0.4, running through VirtualBox.
Up to yesterday, I was able to load images without any issue, using Omero.Insight.
Suddenly, the uploads started failing for any file. I also tried to reboot the virtual machine, but the problem still persisted. More in detail, the file upload works perfectly, but the system fails while importing metadata.

I tried manually importing the images through the command line 'omero' tool:

omero import Att-1h-LPS100-40x_.tif

without success. Here the output of the process:

Using session d54a02fa-3ea1-43b0-9246-d3e173f21109 (root@localhost:4064). Idle timeout: 10.0 min. Current group: system
2014-09-09 07:28:28,057 1054 [ main] INFO ome.formats.importer.ImportConfig - OMERO Version: 5.0.4-ice34-b43
2014-09-09 07:28:28,106 1103 [ main] INFO ome.formats.importer.ImportConfig - Bioformats version: 5.0.4-ice34-b43 revision: a7c8d26 date: 1 September 2014
2014-09-09 07:28:28,133 1130 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-09-09 07:28:28,774 1771 [ main] INFO ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-09-09 07:28:29,518 2515 [ main] INFO ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 737ms. (744ms total) [0 unknowns]
2014-09-09 07:28:29,719 2716 [ main] ERROR ome.system.UpgradeCheck - Error reading from url: http://upgrade.openmicroscopy.org.uk?ve ... orporation "Server returned HTTP response code: 400 for URL: http://upgrade.openmicroscopy.org.uk?ve ... orporation"
2014-09-09 07:28:29,882 2879 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2014-09-09 07:28:30,981 3978 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2014-09-09 07:28:31,757 4754 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.0.4
2014-09-09 07:28:31,757 4754 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.0.4-ice34-b43
2014-09-09 07:28:31,758 4755 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 1.7.0_65
2014-09-09 07:28:31,758 4755 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2014-09-09 07:28:31,758 4755 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2014-09-09 07:28:31,758 4755 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 3.2.0-4-amd64
2014-09-09 07:28:32,008 5005 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2014-09-09 07:28:32,612 5609 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2014-09-09 07:28:32,646 5643 [ main] INFO ts.importer.transfers.UploadFileTransfer - Transferring /home/omero/Att-1h-LPS100-40x_.tif...
2014-09-09 07:28:32,715 5712 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/omero/Att-1h-LPS100-40x_.tif
2014-09-09 07:28:33,166 6163 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/omero/Att-1h-LPS100-40x_.tif
2014-09-09 07:28:33,236 6233 [ main] INFO ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2014-09-09 07:28:33,245 6242 [ main] ERROR ome.formats.importer.ImportLibrary - Error on import: Unknown job:3101
omero.ApiUsageException: null
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_65]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_65]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_65]
at java.lang.reflect.Constructor.newInstance(Constructor.java:526) ~[na:1.7.0_65]
at java.lang.Class.newInstance(Class.java:374) ~[na:1.7.0_65]
at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142) ~[ice.jar:na]
at IceInternal.BasicStream.throwException(BasicStream.java:1564) ~[ice.jar:na]
at IceInternal.Outgoing.throwUserException(Outgoing.java:443) ~[ice.jar:na]
at omero.grid._ImportProcessDelM.verifyUpload(_ImportProcessDelM.java:401) ~[blitz.jar:na]
at omero.grid.ImportProcessPrxHelper.verifyUpload(ImportProcessPrxHelper.java:1756) ~[blitz.jar:na]
at omero.grid.ImportProcessPrxHelper.verifyUpload(ImportProcessPrxHelper.java:1721) ~[blitz.jar:na]
at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:482) ~[blitz.jar:na]
at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) ~[blitz.jar:na]
at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) [blitz.jar:na]
at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:731) [blitz.jar:na]
2014-09-09 07:28:33,246 6243 [ main] INFO ome.formats.importer.ImportLibrary - Exiting on error

The issue seems to happen here:

ome.formats.importer.ImportLibrary - Error on import: Unknown job:3101

Any idea on how to solve the issue?

Best,

Marco

[jmoore]

Hi Marco,

Based on the IP addresses, I'm assuming that all of the following QA items are from you or someone you work with?

• https://www.openmicroscopy.org/qa2/qa/feedback/9522/
• https://www.openmicroscopy.org/qa2/qa/feedback/9523/
• https://www.openmicroscopy.org/qa2/qa/feedback/9524/

9525 and 9524 (the attempts to import) show the exception you mention, which I've never seen before and certainly looks quite dire. 9522 and 9523, though, give a clue:

Code: Select all

SQL state [XX001]; error code [0]; ERROR: could not read block 5 in file "base/16385/17477": read only 0 of 8192 bytes; nested exception is org.postgresql.util.PSQLException: ERROR: could not read block 5 in file "base/16385/17477": read only 0 of 8192 bytes
at ...


In other words, it looks like the disk for your VM is corrupted. Do you have a snapshot or backup that you can rollback to?

Cheers,
~Josh

[mamina]

Dear Josh

You are right, those are my reports.
I just downloaded the Omero virtual image yesterday, so I do not have a back-up since I am just testing the server.
I already removed the corrupted Virtual Machine and tried all over again (just a matter of one hour), and I got the same results.

Perhaps it is an issue with VirtualBox?
I am currently running it on top of Apple Os X 10.9.2. The virtual disk is physically hosted in a NTFS partition.

Best,

Marco

[jmoore]

Perhaps it is an issue with VirtualBox?

Possibly. What version are you using?
~Josh.

[mamina]

I am using VirtualBox 4.3.6.
I tried again, starting from the Omero Virtual Appliance, but hosting the virtual machine image on a HFS+ partition. It seems to work so far.

I will report later on further developments.

Best,

Marco

[mamina]

Ok, I haven't had any issue with the installation on HFS+ file system.
It looks like the NTFS partition + VirtualBox combo was causing some troubles.

Marco