[MOBY-dev] Updates to MOBY Central

[Edward Kawas]

Pieter,

Okay, I have committed a fix.

It should be backwards compatible.

Let me know if this works for you!

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx
Sent: Thursday, February 08, 2007 2:16 PM
To: Core developer announcements
Subject: Re: [MOBY-dev] Updates to MOBY Central


On  08 Feb 2007, at 22:47, Mark Wilkinson wrote:

> Hmmmm... that DUMP subroutine has always been a bit "odd" compared  
> to the
> rest of the API (actually... is it even IN the API?).

Yeah it's bit of a weird one, but it's also extremely useful for  
duplicating a Central :).

> I guess if it is
> causing problems now then it should be fixed properly.
>
> M
>
>
>
>
>
> On Thu, 08 Feb 2007 12:58:02 -0800, Edward Kawas  
> <edward.kawas at gmail.com>
> wrote:
>
>> Hi Pieter,
>>
>> You are right. The serializer (MOBY::SOAP::Serializer) expects a  
>> string.
>> I
>> have fixed it, but I think that my patch is very sub optimal. What  
>> I did
>> was
>> wrap the code contained in
>>
>> do {
>> ...
>> } if $_[1] =~ /^(?:method|response)$/;
>>
>> With:
>> do {
>>   do {
>>    ...
>>   } unless ref($_[3]) =~ /ARRAY/;
>> } if $_[1] =~ /^(?:method|response)$/;
>>
>> This seems to work, i.e. I see something in the soap trace. However,
>> when I
>> attempt to use the array ref, things don't work for me ... I am
>> wondering if
>> I should encode the strings in the array!?!

I guess. If the BioMOBY Perl libs are not encoding the strings in the  
array and the new serializer is not doing that either it must cause  
trouble with not escaped characters...

I'll try to dig further tomorrow.

Cheers,

Pi

>>
>> Thoughts anyone?
>>
>> Eddie
>>
>>
>>
>>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org
>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter  
>> Neerincx
>> Sent: Thursday, February 08, 2007 12:01 PM
>> To: Core developer announcements
>> Subject: Re: [MOBY-dev] Updates to MOBY Central
>>
>> Hi Eddie,
>>
>> I think I ran into a small problem. When I use
>> MOBY::Client::Central::DUMP I get the following error:
>> -------------------
>> Connection to MOBY Central at 'http://mobycentral.icapture.ubc.ca/
>> MOBY/Central' died because:
>>          String value expected instead of ARRAY reference
>>
>>   ERROR ERROR ERROR
>> -------------------
>>
>> This happens both with:
>> * Old BioMOBY libs with S::L 0.60 connecting to updated BioMOBY
>> Central with S::L 0.69
>> * New BioMOBY libs with S::L 0.69 connecting to updated BioMOBY
>> Central with S::L 0.69
>>
>> I'm suspecting the following line to be the cruel-pit:
>>
>> MOBY::Central.pm line 3139 sub DUMP_MySQL:  return [@response];
>>
>> I'm guessing your new S::L (de-)serializer expects an XML string
>> instead of the array ref... Is that possible?
>>
>> Cheers,
>>
>> Pi in update mode :)
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>
> -- 
> Using Opera's revolutionary e-mail client: http://www.opera.com/mail/
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev

Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1038
Dreijenlaan 3
6703 HA Wageningen
phone: 0317-484 706
fax: 0317-483 584
mobile: 06-143 66 783
pieter.neerincx at wur.nl

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev