[MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES forregistry hosts

Tue Feb 6 15:48:40 UTC 2007

Hi Romina,

I can confirm that calling services running S::L 0.69 from a client  
running S::L 0.55 is succesful.  .69 to .69 is obviously OK also.  What I  
have not yet successfully tested is calling a service from a .69 client to  
an earlier version on the server-side.  The way to do that would be to use  
gbrowse_moby on the mobycentral machine, but I don't know what versions of  
Perl anyone else is running so I can't reliably do that experiment...  can  
anyone try one of their Perl services from gbrowse-moby on a server with  
perl 0.60 or less?

MOBY Central itself seems fine... and Java invocations of services seem  
fine also (largely because the Java libraries don't use the WSDL from MOBY  
Central to create their connections... there may be a lesson in there  
somewhere!  Ugh... WSDL!!)

M

On Tue, 06 Feb 2007 07:38:59 -0800, Romina Royo <rroyo at lsi.upc.edu> wrote:

> Hello again,
>
> Mark, I just called your service and it did work.
>
> Eddy, if those are some of the errors you fixed yesterday I might be
> doing something wrong. Let me re-check everything and if the errors are
> still there I'll send you more details about the code I'm using.
>
> Thank you very much!
> Romina
>
>
>
> mark wilkinson wrote:
>> Hmmmm... Well that's a bit of a disaster!
>>
>> Could you check what happens when you call one of my services (eg  
>> MOBYSHoundGetGenbankff)?  I wonder if SOAP::Lite versions don't talk to  
>> each other properly (which would be a nightmare, but given our  
>> experiences yesterday, not surprising!)
>>
>> M
>>
>>
>> --
>> Mark Wilkinson
>> ...on the road!
>>
>>
>> -----Original Message-----
>> From: Romina Royo <rroyo at lsi.upc.edu>
>> Date: Tue, 06 Feb 2007 15:25:15
>> To:Core developer announcements <moby-dev at lists.open-bio.org>
>> Cc:mobydev <moby-dev at biomoby.org>
>> Subject: Re: [MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for
>>  registry hosts
>>
>> Hello,
>>
>> I updated the moby-live/Perl libraries from cvs and I installed
>> SOAP::Lite 0.69.
>>
>> Here are some of the results I got:
>>
>> - When executing a synchronous Perl service (function execute in
>> Client/Service.pm) I got this error:
>>
>> <SOAP-ENV:Fault><faultcode>SOAP-ENV:VersionMismatch</faultcode><faultstring>Wrong
>> SOAP version specified. Supported versions:
>>   1.1 (http://schemas.xmlsoap.org/soap/envelope/)
>>   1.2 (http://www.w3.org/2001/06/soap-envelope)
>> </faultstring></SOAP-ENV:Fault>
>>
>> mm.. I guess it is OK because the service provider might be using some
>> other SOAP version?
>>
>> - When doing the same test on one of our services (SOAP::Lite 0.69
>> installed on the service side). I got this error:
>>
>> <soap:Fault><faultcode>soap:Client</faultcode><faultstring>Application
>> failed during request deserialization:
>> xml declaration not at start of external entity at line 1, column 941,
>> byte 941 at
>> /usr/lib/perl5/site_perl/5.8.3/x86_64-linux-thread-multi/XML/Parser.pm
>> line 187
>> </faultstring></soap:Fault>
>>
>> - When executing a Java service:
>>   <soapenv:Fault>
>>    <faultcode>soapenv:Client</faultcode>
>>    <faultstring>org.jboss.axis.AxisFault: Version Mismatch</faultstring>
>>    <detail/>
>>   </soapenv:Fault>
>>
>> and again, it might be ok?
>>
>> - When trying to retrieve the wsdl of a 'moby-async' service (function
>> retrieveService) I got this error:
>>
>> Connection to MOBY Central at
>> 'http://mobycentral.icapture.ubc.ca/MOBY/Central'
>> died because:
>>         Can't use string ("<?xml version="1.0"?>
>>         <definiti") as a symbol ref while "strict refs" in use at
>> /usr/lib/perl5
>> /site_perl/5.8.5/MOBY/Central.pm line 3290, <IN> line 371.
>>
>>  ERROR ERROR ERROR
>>
>> The function retrieveService does work when the service is not
>> 'moby-async' though.
>>
>> - When executing an asynchronous service (function
>> Async/Service/execute) everything seems ok.
>>
>> Has anyone had similar problems? Any ideas?
>>
>> Thank you!
>> Romina
>>
>> Mark Wilkinson wrote:
>>
>>> Hi all,
>>>
>>> First off, apologies to anyone who was trying to get through to MOBY
>>> Central this afternoon - Eddie and I were making the changes necessary  
>>> to
>>> get it ready for SOAP::Lite 0.69 and the changes that worked perfectly  
>>> on
>>> the test server didn't work on the real MOBY Central... so it took a
>>> couple of hours of troubleshooting before we had it back up again.
>>>
>>> The good news is that it seems to work correctly with both Perl and  
>>> Java
>>> clients.  What we don't know is if it is backwards compatible with  
>>> earlier
>>> versions of the MOBY::Client::* libraries, in particular,
>>> MOBY::Client::Service.  I *think* it is, but we didn't have the
>>> opportunity to test it.  In any case, the API did not change, so if you
>>> just cvs update your client libraries everything should come back to  
>>> life
>>> if it isn't working.
>>>
>>> Upgrading to SOAP::Lite 0.69 was a nightmare!  The new SOAP::Lite  
>>> behaves
>>> subtly differently than the old one in several ways that we were not
>>> expecting.  Thankfully, Pieter and Eddie had done most of the
>>> trouble-shoting already, but it still threw us for a loop in some  
>>> places
>>> with incompatible SOAP version errors and a new auto-encoding of  
>>> strings
>>> by SOAP::Lite that we used to do in-code by ourselves (resulting in
>>> double-coded messages).
>>>
>>> Anyway, it's done now.  Please scream loudly if it doesn't work for  
>>> you!!
>>> I have backups of everything so if necessary we can roll-back quickly.
>>>
>>> All of this was done primarily to get us to be compatible with the new
>>> Asynchronous services API that use the Manchester WSRF::Lite modules  
>>> which
>>> depend on SOAP::Lite 0.69.  Can I ask the good folks at INB to test the
>>> code to see if it works for them v.v. Async services?  The database can
>>> now hold Category=moby-async (which reminds me, I need to update the
>>> database templates in the CVS...), and Eddie assures me that the code  
>>> will
>>> now provide correct WSDL for an Asych interface.  The myGrid folks have
>>> added moby-async as a valid service category into their ontology as  
>>> well,
>>> so in principle... it should all work... (touch wood!)
>>>
>>> *********************
>>> IMPORTANTLY this means that the new MOBY Central code will likely NOT  
>>> work
>>> on versions of SOAP::Lite prior to 0.69!!!  Keep this in mind if you  
>>> are
>>> running your own registry...
>>> *********************
>>>
>>> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll  
>>> try to
>>> make the changes to gbrowse_moby such that it can also invoke  
>>> asynchronous
>>> services.  I think the Async modules also need to be added to the  
>>> MANIFEST
>>> before they are installed by default, so I'll try to remember to do  
>>> that
>>> as well.
>>>
>>> Otherwise there were just some small changes to the test suite to  
>>> better
>>> clean-up the registry if something goes wrong during testing, and I
>>> cleaned-up the test database so that it also doesn't cause the test  
>>> suite
>>> to fail.  I will restart the test registry using the new codebase first
>>> thing in the morning so that the two are identical.
>>>
>>> We still haven't figured out why those namespace changes happened a  
>>> couple
>>> of days ago.  It coincided with the Gene Ontology curators making some
>>> additions to the Namespace list, so I suspect that there is a bug in  
>>> the
>>> interface I have given to them (which talks directly to the database
>>> without using the MOBY API), but exactly WHY this happened is still a
>>> mystery.  I've alerted Midori to the problem and she's going to  
>>> hold-off
>>> on making any more changes until we can figure out what is going wrong.
>>>
>>> That's all the news from MOBY Central!
>>>
>>> Let us know ASAP if you notice anything wrong.  It's been a rough ride
>>> today...
>>>
>>> Mark
>>>
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>
>>
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