[MOBY-dev] Updates to MOBY Central

[Pieter Neerincx]

On 9-Feb-2007, at 12:12 AM, Edward Kawas wrote:

> Pieter,
>
> Okay, I have committed a fix.
>
> It should be backwards compatible.
>
> Let me know if this works for you!

It does :).

Thanks!

Pi


>
> 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 :)
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>>
>>
>>
>> -- 
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>
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Wageningen University and Research centre (WUR)
Laboratory of Bioinformatics
Transitorium (building 312) room 1034
Dreijenlaan 3
6703 HA Wageningen
The Netherlands
phone: 0317-483 060
fax: 0317-483 584
mobile: 06-143 66 783
pieter.neerincx at wur.nl