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

[Edward Kawas]

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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