[MOBY-dev] gbrowse_moby and bioMoby Python webservices

Fri Dec 10 15:13:52 UTC 2004

Now the Python API has been fixed I get some results with my service.
Great! But the output is not what it should be. Anybody got an idea what
is wrong with it? At the moment the "content" also contains the result,
but it should be visible for Namespace and Id as well.

The function is called getWAtDBIdByPOAcc
The function can be called with namespace PO_acc    id 9054

I could realy use some feedback.

Thanks in advance
(and have a nice weekend...)

Paulien Adamse

-----Original Message-----
From: moby-dev-bounces at portal.open-bio.org
[mailto:moby-dev-bounces at portal.open-bio.org] On Behalf Of Fiers, Mark
Sent: vrijdag 10 december 2004 15:29
To: Core developer announcements
Subject: Re: [MOBY-dev] gbrowse_moby and bioMoby Python webservices

Thank you very much!!!!!

It almost works. I had to make one small change (after some searching);
The Body class you've written is identified by a getattr in the module
in question. This does not work since the <body> tag send by
gbrowse_moby is in lowercase. I've worked aroud this by changing 'class
Body:' to 'class body:'.  (is it possible to define __getattr__() on
module level??? That would be a nice way to circumvent this problem)

Concerning Mark's question if gbrowse_moby sends incorrectly formatted
messages? The <body> tag is as far as I understand not a valid soap tag
and apparantly also not part of bioMoby XML. So, I would say that it is
still open for discussion, I'm not an expert on the subject.

Cheers
Mark

Yan Wong wrote:

>
> I've solved the problem and posted corrections to the CVS.
>
> See changelog for listed modifications.
>
> Here are the following steps to do to update your bioMoby Python 
> server API:
>
> In your bioMoby python package directory:
>
> -First update your ZSI library with the ZSI library provided by this
> package:
> cd packages
> tar jxvf ZSI-1.5.0-patched-2
> cd ZSI-1.5.0-patched-2
> python setup.py install (with your fancy options if you have)
>
> -Update your bioMoby Python library
> python setup.py install  (with options)
>
> -Update your scripts by applying the rules:
> however, you'll have to change some things in your script:
>
> BEFORE:
>
> from ZSI import dispatch
> dispatch.AsCGI()
>
> NOW:
>
> from ZSI import dispatch
> from bioMoby.webservice import TCBioMoby
>
> dispatch.AsCGI(typesmodule=TCBioMoby)
>
> or with mod_python:
>
> dispatch.AsHandler(modules=myModule,), request=req,
> typesmodule=TCBioMoby)
>
> TCBioMoby contains a class that serialize/deserialize the content 
> inside the tag Body  into a MobyContent Object.
>
> This will allow a Python webservice to deal with gbrowse_moby.
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://www.biomoby.org/mailman/listinfo/moby-dev
>

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