[moby] [MOBY-dev] MOBY Central now breaks Java

Thu Dec 16 20:16:04 UTC 2004

Hi Paul, 

Are you certain that it is still malformed?  I think we fixed that
problem this morning.

... oh.... wait... it may be that you are hitting the test server.  Try
it again now that I have restarted it (yes, Phil, sometimes a restart
DOES solve the problem ;-) )

If it is still sending out malformed XML I would be surprised, since it
isn't breaking the Perl parsers...???

M

On Thu, 2004-12-16 at 11:23, Paul Gordon wrote:
> Hi everyone,
> 
>     MOBY Central code seems to have broken CentralImpl.java.  The 
> returned object after a findService call is not well-formed XML, so Axis 
> doesn't let you get very far with debugging.  I telneted to port 80 on 
> MOBY Central and POSTed a hand-crafted findService request.  You can see 
> the input and output below, but the gist of it is that the Perl parser 
> of the MOBY Central server seems to switch a string for a hash reference 
> somewhere internally while handling the SOAP payload.  I think this is a 
> bug in the server-side Perl. Are these errors due to the server code 
> transition currently taking place?
> 
> A second issue is that the MOBY Central Apache appends its 500 Error 
> page to the SOAP message, making it an invalid XML document.  Therefore 
> the real error never propagates to the client, but rather a parsing 
> error ooccurs.
> 
> Regards,
> 
> Paul
> 
> --------------------------------------
> 
> Input to mobycentral.cbr.nrc.ca:80
> 
> POST /cgi-bin/MOBY05/mobycentral.pl HTTP/1.0
> Content-length: 840
> 
> <?xml version="1.0"?>
> <soap:Envelope
> xmlns:soap="http://www.w3.org/2001/06/soap-envelope"
> soap:encodingStyle="http://www.w3.org/2001/06/soap-encoding">
> 
> <soap:Header>
> </soap:Header>
> 
> <soap:Body><findService 
> xmlns="http://mobycentral.cbr.nrc.ca/MOBY/Central"><inputObjects>
>      <Input>
>      <Simple xmlns="http://www.biomoby.org/moby">
>      <objectType>Object</objectType>
>      <Namespace>GO</Namespace>
>      </Simple></Input>
>      </inputObjects>
>      <outputObjects>
>      <Output>
>      </Output>
>      </outputObjects>
>      <serviceType></serviceType>
>      <Category>moby</Category>
>      <authURI></authURI>
>      <expandObjects>1</expandObjects>
>      <expandServices>1</expandServices>
>      <authoritative>0</authoritative>
>      <keywords>
>      </keywords>
>      </findService>
> </soap:Body>
> 
> </soap:Envelope>
> 
> I get the following error returned:
> 
> HTTP/1.1 500 Internal Server Error
> Date: Thu, 16 Dec 2004 19:11:59 GMT
> Server: Apache/1.3.29 (Unix) mod_perl/1.29
> SOAPServer: SOAP::Lite/Perl/0.60
> Content-Length: 626
> Connection: close
> Content-Type: text/xml; charset=utf-8
> 
> <?xml version="1.0" encoding="UTF-8"?><SOAP-ENV:Envelope 
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
> xmlns:SOAP-ENC="http://www.w3.org/2001/06/soap-encoding"
> xmlns:SOAP-ENV="http://www.w3.org/2001/06/soap-envelope"
> xmlns:xsd="http://www.w3.org/2001/XMLSchema"
> SOAP-ENV:encodingStyle="http://www.w3.org/2001/06/soap-encoding"><SOAP-ENV:Body><SOAP-ENV:Fault><faultcode>SOAP-ENV:Server</faultcode><faultstring>Entity: 
> line 1: error: Start tag expected, '<' not found
> HASH(0x16a76a0)
> ^
>  at /usr/local/lib/perl5/site_perl/5.8.0/MOBY/Central.pm line 2277
> </faultstring></SOAP-ENV:Fault></SOAP-ENV:Body></SOAP-ENV:Envelope><!DOCTYPE 
> HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">
> <HTML><HEAD>
> <TITLE>500 Internal Server Error</TITLE>
> </HEAD><BODY>
> <H1>Internal Server Error</H1>
> The server encountered an internal error or
> misconfiguration and was unable to complete
> your request.<P>
> Please contact the server administrator,
>  markw at illuminae.com and inform them of the time the error occurred,
> and anything you might have done that may have
> caused the error.<P>
> More information about this error may be available
> in the server error log.<P>
> <HR>
> <ADDRESS>Apache/1.3.29 Server at mobycentral.cbr.nrc.ca Port 80</ADDRESS>
> </BODY></HTML>
> 
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-- 
Mark Wilkinson
Assistant Professor (Bioinformatics)
Dept. Medical Genetics, UBC, Canada