In-place importing as sysadmin

[ratamero]

Apologies for the delay - we've got another update from IT Services:

"I didn't have a copy of the Blitz-0.log, so I has to recreate by test server to capture one, which I've attached.

I've taken a bit of a look and it seems as though the error is being generated by the following:

https://github.com/openmicroscopy/openm ... .java#L223


When monitoring the SMB server while the in place import is taking happening the file is opened in a read only mode:

Locked files:
Pid Uid DenyMode Access R/W Oplock SharePath Name Time
--------------------------------------------------------------------------------------------------
30240 0 DENY_NONE 0x120089 RDONLY LEASE(RWH) /data/omerotest u1473606/RPE1Sec61gfp_16_11_17/RPE1-ser61bGFP_siRDNA_noco_wash1H_2_4_R3D.dv

However, is seems that OMERO is trying to do a write operation (the flush operation) on the file, which might be the cause of the permission denied error."


I've put the Blitz log at https://www.dropbox.com/s/9ui0ur0nsb9bn ... 0.log?dl=0

Any insight is appreciated!

best regards

Erick

[manics]

Hi Erick

I've reproduced your error in docker: https://gitlab.com/openmicroscopy/incub ... mba-server

Code: Select all

$ /opt/omero/server/O
MERO.server/bin/omero import --transfer=ln_s /mnt/hello.fake

...
2018-07-03 11:15:29,680 2412       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2018-07-03 11:15:30,303 3035       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2018-07-03 11:15:30,321 3053       [      main] INFO   s.importer.transfers.SymlinkFileTransfer - Transferring /mnt/hello.fake...
2018-07-03 11:15:30,405 3137       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /mnt/hello.fake
2018-07-03 11:15:30,552 3284       [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /mnt/hello.fake omero.ResourceError: null
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_161]
...
2018-07-03 11:15:30,558 3290       [      main] ERROR        ome.formats.importer.ImportLibrary - Error on import: cannot flush /OMERO/ManagedRepository/root_0/2018-07/03/11-15-29.834/hello.fake: java.io.IOException: Permission denied
omero.ResourceError: null
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_161]


Interestingly mounting the share read-only doesn't help either.

I've created a ticket to track this issue: https://trello.com/c/VQpgwU3e/463-smb-3 ... s-may-fail

[ratamero]

Thanks, Simon! I'll keep an eye on it. We'll stay off the in-place imports for the moment and temporarily use an older SMB version if absolutely necessary in the meantime.