[ome-users] In-place import from CIFS share fails with permission error

[Simon Li]

Hi Brian

Could you give us some details about your OMERO system, including:
- Operating system and version
- How you installed OMERO (e.g. manually, scripted, instructions on one of our web-pages)
- How you're starting/stopping OMERO (e.g. manually, systemd, upstart)
- Disk volume mount options

Thanks, Simon

On 11 January 2018 at 17:54, Brian Dunnette <dunn0172 at umn.edu<mailto:dunn0172 at umn.edu>> wrote:
Mark-

It appears that the svs file is owned by the omero system user; however, though I ran the chmod/chgrp commands from the inplace-import document (and my umask is 0002), the permissions on new import directories and their files don't seem to be set correctly:

[omero at nunstudy-omero ~]$ umask
0002
[inplace_user at nunstudy-omero 11-43-02.765]$ umask
0002

# Change-group script
chgrp inplace_user /omero/ManagedRepository
chmod g+rws /omero/ManagedRepository
chmod g+rws /omero/ManagedRepository/*
chmod g+rws /omero/ManagedRepository/*/*
chmod g+rws /omero/ManagedRepository/*/*/*
chmod g+rws /omero/ManagedRepository/*/*/*/*
chgrp inplace_user /omero/ManagedRepository/*
chgrp inplace_user /omero/ManagedRepository/*/*
chgrp inplace_user /omero/ManagedRepository/*/*/*
chgrp inplace_user /omero/ManagedRepository/*/*/*/*

[inplace_user at nunstudy-omero 11]$ omero import -- --transfer=ln_s /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs
...
11:43:03.083 [main] INFO  o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs
11:43:03.105 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs
11:43:03.106 [main] ERROR o.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs
java.lang.RuntimeException:
---------------------------------------------------
Check failed: /omero/ManagedRepository/dunn0172admin_3/2018-01/11/11-43-02.765/562.svs cannot be modified locally!
You likely do not have access to the ManagedRepository for in-place import.
Aborting...

[inplace_user at nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0172admin_3/2018-01/
total 0
drwxrwsr-x 4 omero inplace_user 26 Jan 11 11:40 .
drwxrwsr-x 3 omero inplace_user 21 Jan 10 11:22 ..
drwxrwsr-x 3 omero inplace_user 26 Jan 10 11:22 10
drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 11

[inplace_user at nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0172admin_3/2018-01/11/
total 0
drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 .
drwxrwsr-x 4 omero inplace_user 26 Jan 11 11:40 ..
drwxrwxr-x 2 omero inplace_user 21 Jan 11 11:40 11-40-49.349
drwxr-sr-x 2 omero inplace_user 21 Jan 11 11:43 11-43-02.765

[inplace_user at nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0172admin_3/2018-01/11/11-43-02.765/
total 4
drwxr-sr-x 2 omero inplace_user 21 Jan 11 11:43 .
drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 ..
-rw-r--r-- 1 omero inplace_user 36 Jan 11 11:43 562.svs


Suggestions?

Thanks,


Brian Dunnette

Digital Imaging & Info Tech

Lab Medicine and Pathology<http://pathology.umn.edu>

University of Minnesota

dunn0172 at umn.edu<mailto:dunn0172 at umn.edu>
(612) 424-8187<tel:(612)%20424-8187> (Mobile)
(612) 624-6176<tel:(612)%20624-6176> (Office)
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On Thu, Jan 11, 2018 at 4:35 AM, Mark Carroll <m.t.b.carroll at dundee.ac.uk<mailto:m.t.b.carroll at dundee.ac.uk>> wrote:
Dear Brian,

We're attempting to do an in-place import of SVS files from a CIFS share
into our new OMERO 5.3.5 install, and followed the in-place import guide
(set up the inplace_user user & group, gave them ownership of the
ManagedRepository, verified that inplace_user can create a directory in
ManagedRepository and the omero system user can delete it).

    Check failed:
    /omero/ManagedRepository/dunn0172admin_3/2018-01/10/11-15-14.918/561.svs
    cannot be modified locally!

    You likely do not have access to the ManagedRepository for in-place
    import.

Is this file owned by the omero system user? Is the inplace_user able to:

* append to it?
* delete it?
* create another file in that same
/omero/ManagedRepository/dunn0172admin_3/2018-01/10/11-15-14.918/ directory?

-- Mark

The University of Dundee is a registered Scottish Charity, No: SC015096
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