[ome-devel] Plan for transferring data from one OMERO to another

[Eilidh Troup]

Hi Josh,

Thanks very much. This is a screenshot from running the script in OMERO.insight. I’d like the text entered in the password to be hidden, like this *****.

Eilidh 



> On 7 Dec 2017, at 14:39, Josh Moore <josh at glencoesoftware.com> wrote:
> 
> Hi Eilidh,
> 
> On Tue, Dec 5, 2017 at 10:51 PM, Eilidh Troup <e.troup at epcc.ed.ac.uk <mailto:e.troup at epcc.ed.ac.uk>> wrote:
>> Hi Josh,
>> 
>> Thanks for your help. I can now transfer an image from one OMERO to another
>> : )
> 
> Congratulations.
> 
> 
>> I’ve put the latest version of the script at
>> https://github.com/SynthSys/omero-user-scripts/blob/master/Export_to_other_omero.py <https://github.com/SynthSys/omero-user-scripts/blob/master/Export_to_other_omero.py>
>> 
>> I’ve got more questions though:
>> How can I find the managed repository directory? (Something like
>> omero.managed.dir, Default: ${omero.data.dir}/ManagedRepository ?)
> 
> In [2]: client.sf.getConfigService().getConfigValue("omero.managed.dir")
> 
> 
>> How can I hide the password text entry?
> 
> Where are you seeing password text entry?
> 
> 
>> How can I get the newly created image id? It is printed to stdout as
>> "Image:920" for example, but I don't know how to get hold of that number in
>> my script.
> 
> You can use something like:
> 
>   import sys
>   old_stdout = sys.stdout
>   sys.stdout = open(temporary_file_name, "w")
>   try:
>       # do import
>   finally:
>       sys.stdout = old_stdout
> 
> 
>> Also, the docker script you sent didn’t quite work (don’t worry about it
>> though, I got what I needed from your example) - I got this error when I ran
>> the python script:
>> 
>> bash-4.2$ python /gist/export_to_remote_omero.py
>> Traceback (most recent call last):
> ...
>> ::Glacier2::PermissionDeniedException
>> {
>>    reason = internal server error
>> }
> 
> Alright. If you'd like to investigate further, we'll need the server logs.
> 
> 
>> Thanks,
>> Eilidh
> 
> All the best,
> ~Josh
> 
> 
>> On 10 Nov 2017, at 09:22, Josh Moore <josh at glencoesoftware.com> wrote:
>> 
>> Hi Elidh,
>> 
>> On Thu, Nov 9, 2017 at 5:07 PM, Eilidh Troup <e.troup at epcc.ed.ac.uk> wrote:
>> 
>> Hi,
>> 
>> I’ve run into a similar problem as last time.
>> 
>> 
>> Turns out, there's a similar solution.
>> 
>> I’ve written a script that
>> will upload an image to a remote OMERO server, but only from the python
>> command line, and not from within a script running in a local OMERO. As
>> before, the script will work from the command line or from with OMERO when
>> transferring the image to the local OMERO server. When I try to import an
>> image on the remote server, I get the following error:
>> 
>> ...
>> 
>> 
>> The code, and full error output are below.
>> I’ve also put it into a different script on gist that demonstrates the error
>> by running it from within OMERO as a script.
>> https://gist.github.com/eilidh-t/e763dab7d4f3515cc85b0b6ddfb8d9f4
>> 
>> 
>> I've update your script:
>> https://gist.github.com/joshmoore/0c2e5319d8d5ae7f79ee82e3e68b721b
>> 
>> The most important change is:
>> 
>>   del os.environ["ICE_CONFIG"] before importing
>> 
>> which does the equivalent of `Ice.Config=/dev/null` but for the import
>> process. Likely, that should be done closer to the top.
>> 
>> Other changes include:
>> 
>> * use ome.cli.CLI rather than calling subprocess (simplicity)
>> * only register the script if it doesn't exist (less test mess)
>> * pass a key to not store the root's password (security)
>> * adding a warning about the security whole that this script could
>> cause (security)
>> 
>> My general workflow was:
>> 
>> * docker-compose up -d
>> * docker-compose exec omero1 bash
>> * cd /opt/omero/server/OMERO.server
>> * export PYTHONPATH=lib/python
>> * python /gist/export_to_remote_omero.py
>> 
>> If I needed to change the script, I deleted the uploaded file from
>> lib/script/export_to_remote_omero.py and re-ran.
>> 
>> Thanks for your help with this,
>> Eilidh
>> 
>> 
>> 
>> Let us know if that works for you.
>> ~J
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>> 
>> 
>> 
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>> 
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>> 
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk <mailto:ome-devel at lists.openmicroscopy.org.uk>
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20171208/975decd2/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PastedGraphic-2.png
Type: image/png
Size: 71931 bytes
Desc: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20171208/975decd2/attachment.png>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: not available
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20171208/975decd2/attachment.ksh>