[ome-devel] OMERO REST HTTP API ?

Wed Feb 4 10:36:33 GMT 2015

Hi Will,

I quickly hacked up something with Flask [Web framework], using the 
BlitzGateway, but if there is general interest, I might investigate 
using Django (I chose the Flask approach, as I'm more a friend of micro 
frameworks, and envisioned it just as 'another gateway' to talk to 
OMERO, not an expansion of the existing Web Gateway).
It's currently just a little prototype with very limited features, thus 
I have not published the source anywhere. (I just implemented everything 
I needed for a particular use case)

Thanks for the source link, I'll take a look at it.

I've discussed the 'append planes' problem some time ago [ 
http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-November/003066.html 
], and I'm well aware that it does not work with stock OMERO, this is 
why I'm using a patched version. As written in my posting, I'll take a 
look into producing a good solution, and submit it for consideration 
(for the time being I'm fine with my hack, but I'm aware that it's not 
the proper way).

Regards,
Christian

On 02/04/2015 11:12 AM, William Moore wrote:
> Hi Christian,
>
>   How are you planning to implement your REST API?
> Using the existing Django web framework?
>
> We have been discussing the development of a "complete" json OMERO API
> using Django, but haven't had the time to focus on it yet (or in the
> near future)
> since it is not a small task to "do it right".
>
> But we would be happy to help you as much as we can to avoid
> duplication of effort.
> It would be particularly useful if you could make your code available
> (E.g. github)
> so we can understand what you're working on.
>
> You already know about the web gateway, but there is also some work in this
> direction in
> https://github.com/openmicroscopy/openmicroscopy/blob/develop/components/tools/OmeroWeb/omeroweb/webclient/tree.py
> where we are using queryService projections. This is faster for getting
> data from the DB into json data since it avoids creating
> omero.model Objects etc.
> We're currently using this to populate the jsTree in web client.
>
> You say you want to "append planes to existing images". I don't know if
> we mentioned
> this before but it is not currently possible to add planes to an
> existing image
> since the pixel data of an image is immutable once it's been created.
> However, you could create a series of single-plane images then combine
> them into
> a new multi-plane image in one shot.
>
>   Cheers,
>
>     Will.
>
>
>
> On 3 Feb 2015, at 10:31, Christian Carsten Sachs <c.sachs at fz-juelich.de
> <mailto:c.sachs at fz-juelich.de>> wrote:
>
>> Hello Ola,
>>
>> thank you for your responses.
>> But when the image data comes from the camera, it is raw and does not
>> have any container (eg TIFF) OMERO could import, so the normal ways
>> won't work. My use case is rather non-standard ...
>> I think I will continue with the approach I had thought off, as to me it
>> appears to fit my project's overall needs best ...
>> [An API approach appears necessary, either directly or decoupled via an
>> REST API, because among other things, I want to append planes to
>> existing images, as mentioned in an earlier post of mine (which needs
>> modifications to OMERO aswell.)]
>>
>> Regards,
>> Christian
>>
>> On 02/03/2015 11:20 AM, Aleksandra Tarkowska (Staff) wrote:
>>> Dear Christian,
>>>
>>>
>>>
>>>
>>>> Instead did you try Command Line Importer or DropBox? We had few
>>>> questions
>>>> in the past asking about the code, allowing import, see one of them
>>>> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-September/0029
>>>> 8
>>>> 2.html
>>>> There are many options like target Dataset, etc.
>>>
>>> Link to the test file in above post is available under
>>> https://github.com/openmicroscopy/openmicroscopy/blob/dev_5_0/components/to
>>> ols/OmeroPy/test/integration/library.py
>>>
>>>
>>>
>>> Kind regards
>>> Ola
>>>
>>>
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