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

[Brian Dunnette]

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
(612) 424-8187 (Mobile)
(612) 624-6176 (Office)
-----
The information transmitted in this e-mail is intended only for the person
or entity to which it is addressed and may contain confidential and/or
privileged material, including 'protected health information'. If you are
not the intended recipient, you are hereby notified that any review,
retransmission, dissemination, distribution, or copying of this message is
strictly prohibited. If you have received this communication in error,
please destroy and delete this message from any computer and contact us
immediately by return e-mail.

On Thu, Jan 11, 2018 at 4:35 AM, Mark Carroll <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
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20180111/dbb0742b/attachment.html>