[MOBY-l] [moby] Re: MOBY tutorial - Taverna

[Paul Gordon]

Good old System.println() on the servlet side :-)

Printing request
<?xml version="1.0" encoding="UTF-8"?><soapenv:Envelope 
xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/" 
xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><soapenv:Body><ns1:ConvertAAtoFASTA_AA 
soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/" 
xmlns:ns1="http://biomoby.org/"><ns1:arg0 xsi:type="soapenc:string" 
xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/">&lt;moby:MOBY 
xmlns:moby=&quot;http://www.biomoby.org/moby&quot;&gt;
  &lt;moby:mobyContent&gt;
    &lt;moby:mobyData moby:queryID=&quot;1&quot;&gt;
      &lt;moby:Simple moby:articleName=&quot;inseq&quot;&gt;
        &lt;AminoAcidSequence 
xmlns=&quot;http://www.biomoby.org/moby&quot; 
namespace=&quot;NCBI_gi&quot; id=&quot;15898917&quot; 
articleName=&quot;&quot;&gt;
          &lt;String namespace=&quot;&quot; id=&quot;&quot; 
articleName=&quot;SequenceString&quot;&gt;MPGGFILAIDEGTTSARAIIYNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAIKEAMKKAKIESRQVAGIGVTNQRETTILWDAISGKPIYNAIVWQDRRTSNITDWLKENYFGMIKDKTGLIPDPYFSGSKIKWILDNLPNVRSKAEKGEIKFGTIDTYLIWKLTNGKIHVTDYSNASRTMLFNINKLEWDREILELLKIPESILPEVRPSSDIYGYTEVLGSSIPISGDAGDQQAALFGQVAYDMGEVKSTYGTGSFILMNIGSNPIFSENLLTTIAWGLESKRVTYALEGSIFITGAAVQWFRDGLRAIDASDDIEPLAASVPDTGGVYFVPAFVGLGAPYWDPYARGLIIGITRGTTKAHIARAILESIAYQNRDVIEIMEKESGTKINILKVDGGGAKDNLLMQFQADILGIRVVRPKVMETASMGVAMLAGLAINYWNSLNELKQKWTVDKEFIPSINKEERERRYNAWKEAVKRSLGWEKSLGSK&lt;/String&gt;
          &lt;Integer namespace=&quot;&quot; id=&quot;&quot; 
articleName=&quot;Length&quot;&gt;499&lt;/Integer&gt;
        &lt;/AminoAcidSequence&gt;
      &lt;/moby:Simple&gt;
    &lt;/moby:mobyData&gt;
  &lt;/moby:mobyContent&gt;
&lt;/moby:MOBY&gt;</ns1:arg0></ns1:ConvertAAtoFASTA_AA></soapenv:Body></soapenv:Envelope>

> Hi Paul,
>
> The plugin should be outputting the xml declaration. How did you determine that
> it wasn't?
>
> Thanks,
>
> Eddie
>
>   
>> -----Original Message-----
>> From: moby-l-bounces at lists.open-bio.org 
>> [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Paul Gordon
>> Sent: Tuesday, November 21, 2006 12:25 PM
>> To: markw at illuminae.com
>> Cc: moby-l at lists.open-bio.org
>> Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna
>>
>> In that case, I think Taverna (or the BioMOBY plugin?)  needs 
>> a little tinkering.  I'm not sure if it always omits the XML 
>> declaration on submission, but is certainly seems to if I 
>> load my own sample XML input (which does have the declaration).
>>     
>>> On Tue, 2006-11-21 at 12:17 -0700, Paul Gordon wrote:
>>>
>>>   
>>>       
>>>> Perhaps I am wrong, but the MOBY API specifically says that this 
>>>> declaration is required, no?  That's why we have to 
>>>>         
>> string-encode or
>>     
>>>> base64 encode, etc. the SOAP contents (since processing 
>>>>         
>> instructions 
>>     
>>>> starting with "xml" are not allowed in the contents of an XML 
>>>> document)?  If not, I'll get rid of the warning message...
>>>>
>>>>     
>>>>         
>>> That is correct.  It does.
>>>
>>> M
>>>
>>>
>>>
>>>   
>>>       
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>>     
>
>
>