[moby] [MOBY-dev] questions about gbrowse-moby

Wed Jan 12 08:57:53 UTC 2005

I have almost solve the problem.

Last night, I setup a test_python_echo service on my webserver and trace
the HTTP transactions.

The service returns a message in an object with namespace="Global_keyword"

As input, the service receives a

<body><![CDATA[<?xml version="1.0" ?>
<moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
        <moby:mobyContent>
                <moby:mobyData moby:queryID="1">
                        <moby:Simple>
                                <moby:Object moby:id="Hallo Welt"
moby:namespace="Global_Keyword"/>
                        </moby:Simple>
                </moby:mobyData>
        </moby:mobyContent>
</moby:MOBY>
]]></body>

As output I give him:

<body><![CDATA[<?xml version="1.0" ?>
<moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
        <moby:mobyContent>
                <moby:mobyData moby:queryID="1">
                        <moby:Simple>
                                <moby:Object moby:id="Hallo Welt"
moby:namespace="Global_Keyword"/>
                        </moby:Simple>
                </moby:mobyData>
        </moby:mobyContent>
</moby:MOBY>
]]></body>

this is the raw xml returned:
'<?xml version="1.0" ?>\n<moby:MOBY
xmlns:moby="http://www.biomoby.org/moby">\n\t<moby:mobyContent>\n\t\t<moby:mobyData
moby:queryID="1">\n\t\t\t<moby:Simple>\n\t\t\t\t<moby:Object
moby:id="Hallo Welt"
moby:namespace="Global_Keyword"/>\n\t\t\t</moby:Simple>\n\t\t</moby:mobyData>\n\t</moby:mobyContent>\n</moby:MOBY>\n'

But still no success :(

I think I am going to look into the code of gbrowse-moby and make other
test s to see what's wrong...

> Hi Yan!
>
>
>> The question I have is What kind of SOAP messages does gbrowse_moby
send
>> to query services?
>> Is there any source of gbrowse_moby?
>
> gbrowse_moby is part of the Gbrowse codebase, and you can get it by
checking-out Gbrowse (gmod.sourceforge.net).  At the moment there is no
way to install gbrowse_moby without installing the rest of gbrowse, but I
do plan on adding a Makefile "switch" sometime soon...  What you should do
is go through the Gbrowse Makefile/make process and then rather than doing
the "make install" step, just look in the cgi-bin folder and you will find
the "maked" gbrowse_moby source code.
>
> It looks like your problem is here:
>
> xmlns:moby="http://www.biomoby.org/moby"><moby:mobyContent><moby:mobyData
>
> You are not escaping the '<' before your mobyContent and mobyData
tags...
>
> I think that is the problem (just by a quick eyeball analysis...)
>
> Let me know if that does not work and I'll investigate further.
>
> M
>
>
>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at biomoby.org
>> http://www.biomoby.org/mailman/listinfo/moby-dev
> --
> Mark Wilkinson
> Assistant Professor (Bioinformatics)
> Dept. Medical Genetics, UBC, Canada
>
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