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

[Paul Gordon]

The missing bit is the XML declaration for the MOBY payload, not the one 
for the SOAP envelope.

So, the message should look like:

<ns1:arg0 xsi:type="soapenc:string" 
xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/">&lt?xml 
version="1.0"&gt;&lt;moby:MOBY

instead of the current:

<ns1:arg0 xsi:type="soapenc:string" 
xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/">&lt;moby:MOBY
> Sorry, but the declaration that you are talking about (the one missing) is the
> one inside the soap message?
>
> Eddie
>
>   
>> -----Original Message-----
>> From: Paul Gordon [mailto:gordonp at ucalgary.ca] 
>> Sent: Tuesday, November 21, 2006 12:44 PM
>> To: Edward Kawas
>> Cc: moby-l at lists.open-bio.org; Mark Wilkinson
>> Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna
>>
>> 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/" 
>> <http://schemas.xmlsoap.org/soap/envelope/>  
>> xmlns:xsd="http://www.w3.org/2001/XMLSchema" 
>> <http://www.w3.org/2001/XMLSchema>  
>> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
>> <http://www.w3.org/2001/XMLSchema-instance> 
>>     
>>> <soapenv:Body><ns1:ConvertAAtoFASTA_AA 
>>>       
>> soapenv:encodingStyle="http://schemas.xmlsoap.org/soap/encodin
>> g/" <http://schemas.xmlsoap.org/soap/encoding/>  
>> xmlns:ns1="http://biomoby.org/" <http://biomoby.org/> 
>>     
>>> <ns1:arg0 xsi:type="soapenc:string" 
>>>       
>> xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/" 
>> <http://schemas.xmlsoap.org/soap/encoding/> >&lt;moby:MOBY 
>> xmlns:moby=&quot;http://www.biomoby.org/moby&quot;&gt 
>> <http://www.biomoby.org/moby">> ;
>>   &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 
>> <http://www.biomoby.org/moby"> ; 
>> 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;MPGGFILAIDEGTTSARAII
>>     
> YNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAIKEAMKKAKIESRQVAGIGVTNQRETTILWDAISGKPIYNA
> IVWQDRRTSNITDWLKENYFGMIKDKTGLIPDPYFSGSKIKWILDNLPNVRSKAEKGE>
> IKFGTIDTYLIWKLTNGKIHVTDYSNASRTMLFNINKLEWDREILELLKIPESILPEVRPSS
>   
>> DIYGYTEVLGSSIPISGDAGDQQAALFGQVAYDMGEVKSTYGTGSFILMNIGSNPIFSENLL
>> TTIAWGLESKRVTYALEGSIFITGAAVQWFRDGLRAIDASDDIEPLAASVPDTGGVYFVPAF
>> VGLGAPYWDPYARGLIIGITRGTTKAHIARAILESIAYQNRDVIEIMEKESGTKINILKVDG
>> GGAKDNLLMQFQADILGIRVVRPKVMETASMGVAMLAGLAINYWNSLNELKQKWTVDKEFIP
>> SINKEERERRYNAWKEAVKRSLGWEKSLGSK&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></soape
>> nv: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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>> 		    
>>
>> 	
>> 	
>> 	  
>>
>>
>>
>>     
>
>
>