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

[Josh Moore]

Hi Eilidh,

On Tue, Dec 5, 2017 at 10:51 PM, Eilidh Troup <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
>
> 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
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