[MOBY-dev] [moby] Re: problems with retrieveService() in Perl API
Mark Wilkinson
markw at illuminae.com
Fri Feb 10 16:33:34 UTC 2006
Does that mean we don't need a phone call today?
M
On Fri, 2006-02-10 at 10:36 -0500, Frank Gibbons wrote:
> OK, so there is a problem with SOAP::Lite 0.67. I downgraded my
> installation to 0.60 (which by the way, is reported here
> (http://soaplite.com/download.html) as being the recommended stable
> release, and now at least I can retrieveService details sufficiently to
> build a service instance. If upgraded back to 0.67, and the problem
> re-appears, so I'm downgrading to 0.60, where I will stay.
>
> However, as I discovered, when a user simply installs SOAP::Lite from CPAN,
> they may get quite a different version than 0.60 (I got 0.67), in which
> case, the message gets sent out correctly on the wire, but is perceived as
> empty by MOBY Central. I don't know much about the details of packaging
> SOAP requests, and you can read the gory details below for yourselves, but
> it appears that SOAP::Lite 0.60 and SOAP::Lite 0.67 do not understand each
> other. The clue was given by the User-Agent and SOAPServer lines, showing
> that my request was sent using SOAP::Lite/Perl/0.67, and the error message
> sent in response was generated by SOAP::Lite/Perl/0.60
>
> So, mystery solved. I'll put a check for SOAP::Lite's version, and a
> warning for this into the Makefile, until we can figure out what the real
> solution to this problem is.
>
> Thanks to Mark & Pieter for their help and suggestions.
>
> -Frank
> ================================== SOAP::Lite +trace output
> ============================
>
> SOAP::Transport::HTTP::Client::send_receive: POST
> http://mips.gsf.de/cgi-bin/proj/planet/moby/MOBY-Central.pl HTTP/1.1
> Accept: text/xml
> Accept: multipart/*
> Accept: application/soap
> User-Agent: SOAP::Lite/Perl/0.67
> Content-Length: 1539
> Content-Type: text/xml; charset=utf-8
> SOAPAction: "http://mips.gsf.de/MOBY/Central#retrieveService"
>
> <?xml version="1.0" encoding="UTF-8"?><soap:Envelope
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"
> xmlns:xsd="http://www.w3.org/2001/XMLSchema"
> soap:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"
> xmlns:soap="http://schemas.xmlsoap.org/soap/envelope/"><soap:Body><retrieveService
> xmlns="http://mips.gsf.de/MOBY/Central"><c-gensym6 xsi:type="xsd:anyURI">
> <retrieveService>
> <Service authURI="www.watdb.nl" serviceName="getWAtDBIdByPOAcc"
> lsid="urn:lsid:biomoby.org:serviceinstance:www.watdb.nl,getWAtDBIdByPOAcc">
> <serviceType>Retrieval</serviceType>
> <authoritative>1</authoritative>
> <Category>moby</Category>
> <Description><![CDATA[Returns a list of WAtDB mutantline ids with
> a certain PO accession number]]></Description>
> <contactEmail>paulien.adamse at wur.nl</contactEmail>
> <signatureURL/>
> <URL>http://www.watdb.nl/moby-live/cgi-bin/MOBY/Services/Watdb_mobyservices.py</URL>
> <Input>
> <Simple articleName="">
> <objectType
> lsid="urn:lsid:biomoby.org:objectclass:Object">Object</objectType>
> <Namespace
> lsid="urn:lsid:biomoby.org:namespacetype:PO_acc">PO_acc</Namespace>
> </Simple>
> </Input>
> <Output>
> <Simple articleName="">
> <objectType
> lsid="urn:lsid:biomoby.org:objectclass:Object">Object</objectType>
> <Namespace
> lsid="urn:lsid:biomoby.org:namespacetype:WAtDB_id">WAtDB_id</Namespace>
> </Simple>
> </Output>
> <secondaryArticles>
> </secondaryArticles>
> </Service>
> </retrieveService></c-gensym6></retrieveService></soap:Body></soap:Envelope>
> SOAP::Transport::HTTP::Client::send_receive: HTTP::Response=HASH(0x8906a8c)
> SOAP::Transport::HTTP::Client::send_receive: HTTP/1.1 500 Internal Server Error
> Connection: close
> Date: Fri, 10 Feb 2006 15:31:05 GMT
> Server: Apache
> Content-Length: 559
> Content-Type: text/xml; charset=utf-8
> Client-Date: Fri, 10 Feb 2006 15:29:58 GMT
> Client-Peer: 146.107.217.142:80
> Client-Response-Num: 1
> SOAPServer: SOAP::Lite/Perl/0.60
>
> <?xml version="1.0" encoding="UTF-8"?><SOAP-ENV:Envelope
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xmlns:SOAP-ENC="http://schemas.xmlsoap.org/soap/encoding/"
> xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/"
> xmlns:xsd="http://www.w3.org/2001/XMLSchema"
> SOAP-ENV:encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"><SOAP-ENV:Body><SOAP-ENV:Fault><faultcode>SOAP-ENV:Server</faultcode><faultstring>Empty
> String at /home/users/plant/lib/perl/MOBY/Central.pm line 2457
> </faultstring></SOAP-ENV:Fault></SOAP-ENV:Body></SOAP-ENV:Envelope>
> SOAP::Deserializer::deserialize: ()
> SOAP::Parser::decode: ()
> SOAP::SOM::new: ()
> SOAP::SOM::DESTROY: ()
>
> Connection to MOBY Central at URI 'http://mips.gsf.de/MOBY/Central' died
> because:
> SOAP-ENV:Server : Empty String at
> /home/users/plant/lib/perl/MOBY/Central.pm line 2457
>
> ERROR ERROR ERROR
>
>
>
> At 09:56 AM 2/10/2006, you wrote:
> >At 05:57 AM 2/10/2006, you wrote:
> > >for that one, but that gave me the same results. I currently running
> > >on SOAP::Lite 0.66 with custom patches, but I'm going to try 0.67
> > >today... If you reinstalled Perl, did you also reinstall SOAP::Lite?
> > >If yes which version? In case it's 0.60+ you might have an "anyURI"
> > >problem.
> >
> >Yes, when I re-installed the interpreter (built from source 5.8.6), I
> >reinstalled all of the modules too, from CPAN. I have SOAP::Lite version
> >0.67 installed. What is the "anyURI" problem you mention?
> >
> >Thanks for the response, Pieter.
> >
> >-Frank
> >
> >
> >PhD, Computational Biologist,
> >Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
> >Tel: 617-432-3555 Fax:
> >617-432-3557 http://llama.med.harvard.edu/~fgibbons
> >
> >_______________________________________________
> >MOBY-dev mailing list
> >MOBY-dev at biomoby.org
> >http://biomoby.org/mailman/listinfo/moby-dev
>
> PhD, Computational Biologist,
> Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
> Tel: 617-432-3555 Fax:
> 617-432-3557 http://llama.med.harvard.edu/~fgibbons
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-dev
--
--
...his last words were 'Hey guys! Watch this!'
--
Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274
"For most of this century we have viewed communications as a conduit,
a pipe between physical locations on the planet.
What's happened now is that the conduit has become so big and interesting
that communication has become more than a conduit,
it has become a destination in its own right..."
Paul Saffo - Director, Institute for the Future
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