[ome-users] Using Bio-formats through Python

[Steve Bennett]

Hi Josh,
  Thanks for the reply.

> Most of OMERO could be thought of as an Ice-based (therefore)
> Python-accessible wrapper around Bio-Formats, so there are definitely bits
> of code we can point you to in terms of writing an Ice interface. It all
> very much depends on how you intend to deploy it, etc. OMERO.web for
> example which is also Django-based, connects to OMERO (ultimately) via an
> API defined in these Ice files:
>

>
> https://github.com/openmicroscopy/openmicroscopy/tree/master/components/blitz/resources/omero/
>
> I.E, for whatever actions you want to take on the Bio-Formats that you are
> wrapping with Ice, you'll want to have minimally a method, if not a
> service, that provides the functionality which would then need to be
> implemented in Java.
>

Great, thanks. I'll do some reading up on Ice and that code to see whether
using it, or pipes, makes more sense. I suspect the latter, as very little
communication is needed between the Django app and Bio-formats. Perhaps
something as little as "Open this file, and write out the metadata you find
as JSON to this pipe."


>
>  * How many instances of Bio-Formats should be running and on how many
> servers?
>

Just one per deployment.


>  * Do they need to be started/stopped?
>

I had imagined that Bio-Formats was just a .jar instantiated as needed, but
obviously not. There wouldn't be any inherent problem with having a service
running in the background, other than its incremental effect on the whole
system complexity.


>  * What kind of security, etc. is needed? (i.e. would a firewall protect
> them)
>

Not really an issue, as it would be running on the same server as MyTardis
(which is generally firewalled, of course).

Steve
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