[ome-users] In-place import from CIFS share fails with permission error
Brian Dunnette
dunn0172 at umn.edu
Thu Jan 11 21:13:18 GMT 2018
Simon-
Here are the details (to the best of my knowledge) of our server:
- We're running Red Hat Enterprise v7.4
- OMERO was installed based on the CentOS 7 doc here:
https://docs.openmicroscopy.org/omero/5.3.5/sysadmins/unix/server-centos7-ice36.html
- OMERO.admin is started via systemd, using the script from the docs (
https://docs.openmicroscopy.org/omero/5.3.5/_downloads/omero-systemd.service
)
Root, /home, /var, and /omero (the binary repository) are each their own
XFS volumes, while the images we're trying to import/link are on an eNAS
(mounted as the omero system user):
[dunn0172 at nunstudy-omero system]$ grep inplace /etc/passwd /etc/group
> /etc/passwd:inplace_user:x:1003:1003::/home/inplace_user:/bin/bash
> /etc/group:omero:x:1002:inplace_user
> /etc/group:inplace_user:x:1003:
>
> # /etc/fstab
> UUID=e96e0f81-c366-4c30-bc2b-3a6f47d54d13 / xfs defaults 0 0
> /dev/mapper/vg_os-home /home xfs defaults 0 0
> /dev/mapper/vg_os-var /var xfs defaults 0 0
> /dev/mapper/vg_os-swap swap swap defaults 0 0
> /dev/mapper/vg_os-omero /omero xfs defaults 0 0
> //files.umn.edu/ahc-ns /mnt/ahc-ns/ cifs
> credentials=/root/files.umn.edu.creds,dir_mode=0777,file_mode=0777,sec=ntlmssp,uid=1002,gid=1003
> 0 0
>
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)
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On Thu, Jan 11, 2018 at 12:34 PM, Simon Li <spli at dundee.ac.uk> wrote:
> 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> 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/dunn0
>>> 172admin_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/dunn0
>>> 172admin_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/dunn0
>>> 172admin_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
>>>
>>
>>
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>>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
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