[MOBY-l] [moby] Re: MOBY tutorial - Taverna
Edward Kawas
edward.kawas at gmail.com
Tue Nov 21 20:58:40 UTC 2006
Hmm,
I will look into it, but when I actually call the webservice, I use an XML
string that is created by
http://www.jdom.org/docs/apidocs/org/jdom/output/Format.html#getPrettyFormat()
and the method states that it includes the declaration.
Eddie
> -----Original Message-----
> From: Paul Gordon [mailto:gordonp at ucalgary.ca]
> Sent: Tuesday, November 21, 2006 12:51 PM
> To: Edward Kawas
> Cc: moby-l at lists.open-bio.org; 'Mark Wilkinson'
> Subject: Re: [MOBY-l] [moby] Re: MOBY tutorial - Taverna
>
> 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/"
> <http://schemas.xmlsoap.org/soap/encoding/> ><?xml
> version="1.0"><moby:MOBY
>
> instead of the current:
>
> <ns1:arg0 xsi:type="soapenc:string"
> xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"
> <http://schemas.xmlsoap.org/soap/encoding/> ><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/>
> <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>
> <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>
> <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/>
> <http://schemas.xmlsoap.org/soap/encoding/>
> <http://schemas.xmlsoap.org/soap/encoding/>
> xmlns:ns1="http://biomoby.org/"
> <http://biomoby.org/> <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/>
> <http://schemas.xmlsoap.org/soap/encoding/>
> <http://schemas.xmlsoap.org/soap/encoding/> ><moby:MOBY
>
> xmlns:moby="http://www.biomoby.org/moby">
> <http://www.biomoby.org/moby">>
> <http://www.biomoby.org/moby">> ;
> <moby:mobyContent>
> <moby:mobyData moby:queryID="1">
> <moby:Simple
> moby:articleName="inseq">
> <AminoAcidSequence
> xmlns="http://www.biomoby.org/moby"
> <http://www.biomoby.org/moby">
> <http://www.biomoby.org/moby"> ;
> namespace="NCBI_gi" id="15898917"
> articleName="">
> <String namespace=""
> id=""
>
> articleName="SequenceString">MPGGFILAIDEGTTSARAII
>
>
>
> YNQDLEVLGIGQYDFPQHYPSPGYVEHNPDEIWNAQMLAIKEAMKKAKIESRQVAGIGVTNQ
> RETTILWDAISGKPIYNA
> IVWQDRRTSNITDWLKENYFGMIKDKTGLIPDPYFSGSKIKWILDNLPNVRSKAEKGE>
> IKFGTIDTYLIWKLTNGKIHVTDYSNASRTMLFNINKLEWDREILELLKIPESILPEVRPSS
>
>
>
> DIYGYTEVLGSSIPISGDAGDQQAALFGQVAYDMGEVKSTYGTGSFILMNIGSNPIFSENLL
>
> TTIAWGLESKRVTYALEGSIFITGAAVQWFRDGLRAIDASDDIEPLAASVPDTGGVYFVPAF
>
> VGLGAPYWDPYARGLIIGITRGTTKAHIARAILESIAYQNRDVIEIMEKESGTKINILKVDG
>
> GGAKDNLLMQFQADILGIRVVRPKVMETASMGVAMLAGLAINYWNSLNELKQKWTVDKEFIP
> SINKEERERRYNAWKEAVKRSLGWEKSLGSK</String>
> <Integer namespace=""
> id=""
> articleName="Length">499</Integer>
> </AminoAcidSequence>
> </moby:Simple>
> </moby:mobyData>
> </moby:mobyContent>
>
> </moby:MOBY></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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