From sac at bioperl.org  Wed Jul  9 15:48:51 2008
From: sac at bioperl.org (Steve Chervitz)
Date: Wed, 9 Jul 2008 12:48:51 -0700
Subject: [DAS] [Root-l] Had to disable Cite PHP extension on the biodas
	wiki
In-Reply-To: <F0F25A15-AA09-42C0-B89A-82F9F2226D7C@bioteam.net>
References: <F0F25A15-AA09-42C0-B89A-82F9F2226D7C@bioteam.net>
Message-ID: <8f200b4c0807091248s4e33ca8eobf7c1da199c41fa@mail.gmail.com>

Hi Chris,

I originally set up the biodas wiki site and don't recall installing Cite or
SpecialCite, of if/whether it is still needed. Andreas also worked on the
wiki and may have more clues (added to the cc list).

Looks like the error is just for SpecialCite, so it may be possible to just
disable that and keep using Cite. Looking at the docs for SpecialCite, it
doesn't seem useful for the biodas wiki:

http://www.mediawiki.org/wiki/Extension:Cite/Special:Cite.php

Thanks,
Steve

On Tue, Jun 24, 2008 at 5:59 AM, Chris Dagdigian <chris at bioteam.net> wrote:

>
> Hi folks,
>
> Lincoln reported that www.biodas.org was down today and oddly enough all
> of our other mediawiki sites were functional. The error keeping the DAS site
> down was this:
>
>  [Tue Jun 24 08:48:17 2008] [error] [client 72.85.166.28] PHP Fatal error:
>>  Call to undefined function wfLoadExtensionMessages() in
>> /home/websites/cross-site-stuff/extensions/Cite/SpecialCite.php on line 37
>>
>>
> In order to bring the BioDAS wiki back online I had to make the following
> hackish changes:
>
> - Deleted the symbolic link to Cite in the biodas wiki extensions webroot
> - Commented out the Cite and SpecialCite includes in biodas
> LocalSettings.php
>
> That brought the site back at the expense of blowing away any functionality
> DAS was using that relied on the MediaWiki Citation extensions.
>
> Can someone who is familiar with the DAS wiki site and how it is configured
> touch base with me and or root-l at open-bio.org so we can bring your
> extensions back if needed?
>
> Regards,
> Chris
> OBF
>
>
> _______________________________________________
> Root-l mailing list
> Root-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/root-l
>

From ap3 at sanger.ac.uk  Wed Jul  9 16:12:09 2008
From: ap3 at sanger.ac.uk (Andreas Prlic)
Date: Wed, 9 Jul 2008 21:12:09 +0100 (BST)
Subject: [DAS] [Root-l] Had to disable Cite PHP extension on the biodas
	wiki
In-Reply-To: <8f200b4c0807091248s4e33ca8eobf7c1da199c41fa@mail.gmail.com>
References: <F0F25A15-AA09-42C0-B89A-82F9F2226D7C@bioteam.net>
	<8f200b4c0807091248s4e33ca8eobf7c1da199c41fa@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0807092107460.3699@cbi4b.internal.sanger.ac.uk>

Hi Steve,

the biojava site is using this to track referencews in pubmed, see
   http://biojava.org/wiki/BioJava:BioJavaInside

would it be possible to re-enable this again? I believe it is also 
used on biodas...
thanks!
Andreas
--------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                    Hinxton, Cambridge CB10 1SA, UK



On Wed, 9 Jul 2008, Steve Chervitz wrote:

> Hi Chris,
>
> I originally set up the biodas wiki site and don't recall installing Cite or
> SpecialCite, of if/whether it is still needed. Andreas also worked on the
> wiki and may have more clues (added to the cc list).
>
> Looks like the error is just for SpecialCite, so it may be possible to just
> disable that and keep using Cite. Looking at the docs for SpecialCite, it
> doesn't seem useful for the biodas wiki:
>
> http://www.mediawiki.org/wiki/Extension:Cite/Special:Cite.php
>
> Thanks,
> Steve
>
> On Tue, Jun 24, 2008 at 5:59 AM, Chris Dagdigian <chris at bioteam.net> wrote:
>
>>
>> Hi folks,
>>
>> Lincoln reported that www.biodas.org was down today and oddly enough all
>> of our other mediawiki sites were functional. The error keeping the DAS site
>> down was this:
>>
>>  [Tue Jun 24 08:48:17 2008] [error] [client 72.85.166.28] PHP Fatal error:
>>>  Call to undefined function wfLoadExtensionMessages() in
>>> /home/websites/cross-site-stuff/extensions/Cite/SpecialCite.php on line 37
>>>
>>>
>> In order to bring the BioDAS wiki back online I had to make the following
>> hackish changes:
>>
>> - Deleted the symbolic link to Cite in the biodas wiki extensions webroot
>> - Commented out the Cite and SpecialCite includes in biodas
>> LocalSettings.php
>>
>> That brought the site back at the expense of blowing away any functionality
>> DAS was using that relied on the MediaWiki Citation extensions.
>>
>> Can someone who is familiar with the DAS wiki site and how it is configured
>> touch base with me and or root-l at open-bio.org so we can bring your
>> extensions back if needed?
>>
>> Regards,
>> Chris
>> OBF
>>
>>
>> _______________________________________________
>> Root-l mailing list
>> Root-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/root-l
>>
>


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From mauricio at open-bio.org  Tue Jul 15 17:44:26 2008
From: mauricio at open-bio.org (Mauricio Herrera Cuadra)
Date: Tue, 15 Jul 2008 17:44:26 -0400
Subject: [DAS] [Root-l] Had to disable Cite PHP extension on the biodas
	wiki
In-Reply-To: <Pine.LNX.4.64.0807092107460.3699@cbi4b.internal.sanger.ac.uk>
References: <F0F25A15-AA09-42C0-B89A-82F9F2226D7C@bioteam.net>	<8f200b4c0807091248s4e33ca8eobf7c1da199c41fa@mail.gmail.com>
	<Pine.LNX.4.64.0807092107460.3699@cbi4b.internal.sanger.ac.uk>
Message-ID: <487D1A3A.10102@open-bio.org>

I just did a SVN update of cross-site-stuff/extensions/ directory and 
restored Cite symlinks from BioDAS and BioJava extensions/ webroots, 
also uncommented the Cite and SpecialCite requires in LocalSettings.php 
for both sites. Restarted Apache and sites seem to work fine (no errors 
in Apache logs). However, I'll need you guys to double check since you 
know your wikis best than I do.

Thanks,
Mauricio.


Andreas Prlic wrote:
> Hi Steve,
> 
> the biojava site is using this to track referencews in pubmed, see
>   http://biojava.org/wiki/BioJava:BioJavaInside
> 
> would it be possible to re-enable this again? I believe it is also used 
> on biodas...
> thanks!
> Andreas
> --------------------------------------------------
> 
> Andreas Prlic      Wellcome Trust Sanger Institute
>                    Hinxton, Cambridge CB10 1SA, UK
> 
> 
> 
> On Wed, 9 Jul 2008, Steve Chervitz wrote:
> 
>> Hi Chris,
>>
>> I originally set up the biodas wiki site and don't recall installing 
>> Cite or
>> SpecialCite, of if/whether it is still needed. Andreas also worked on the
>> wiki and may have more clues (added to the cc list).
>>
>> Looks like the error is just for SpecialCite, so it may be possible to 
>> just
>> disable that and keep using Cite. Looking at the docs for SpecialCite, it
>> doesn't seem useful for the biodas wiki:
>>
>> http://www.mediawiki.org/wiki/Extension:Cite/Special:Cite.php
>>
>> Thanks,
>> Steve
>>
>> On Tue, Jun 24, 2008 at 5:59 AM, Chris Dagdigian <chris at bioteam.net> 
>> wrote:
>>
>>>
>>> Hi folks,
>>>
>>> Lincoln reported that www.biodas.org was down today and oddly enough all
>>> of our other mediawiki sites were functional. The error keeping the 
>>> DAS site
>>> down was this:
>>>
>>>  [Tue Jun 24 08:48:17 2008] [error] [client 72.85.166.28] PHP Fatal 
>>> error:
>>>>  Call to undefined function wfLoadExtensionMessages() in
>>>> /home/websites/cross-site-stuff/extensions/Cite/SpecialCite.php on 
>>>> line 37
>>>>
>>>>
>>> In order to bring the BioDAS wiki back online I had to make the 
>>> following
>>> hackish changes:
>>>
>>> - Deleted the symbolic link to Cite in the biodas wiki extensions 
>>> webroot
>>> - Commented out the Cite and SpecialCite includes in biodas
>>> LocalSettings.php
>>>
>>> That brought the site back at the expense of blowing away any 
>>> functionality
>>> DAS was using that relied on the MediaWiki Citation extensions.
>>>
>>> Can someone who is familiar with the DAS wiki site and how it is 
>>> configured
>>> touch base with me and or root-l at open-bio.org so we can bring your
>>> extensions back if needed?
>>>
>>> Regards,
>>> Chris
>>> OBF
>>>
>>>
>>> _______________________________________________
>>> Root-l mailing list
>>> Root-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/root-l
>>>
>>
> 
>