[Pdbwiki-devel] PHP upgrade

[Dan Bolser]

Also, the captcha seems borked.



2010/1/11 Dan Bolser <dan.bolser at gmail.com>:
> Sorry Jose, I noticed further problems too, and started to debug...
>
> I svn upped DPL, but its still broken :(
>
> I re-applied my patch, but the list of images seems broken.
>
> 2010/1/11 Jose M. Duarte <jose.m.duarte at gmail.com>:
>> Wow thanks a lot for taking care of this Dan!
>>
>> Right, I went to check and the main page was displaying well except for the
>> lists of latest discussions, structures etc (all DPL dependent). Then I
>> tried purging it and it now broke completely again. I'm getting:
>>
>> Warning: Parameter 3 to ExtDynamicPageList2::dplTag() expected to be a
>> reference, value given in
>> /home/member/hstehr/public_html/pdbwiki/mediawiki-1.15/includes/parser/Parser.php
>> on line 3243
>>
>> Have you upgraded also DPL to the latest version? I 'm not quite sure what
>> you've done already, you seemed to have applied a patch, does that mean that
>> we are already running the latest DPL?
>>
>> Jose
>>
>>
>>
>> 2010/1/11 Dan Bolser <dan.bolser at gmail.com>
>>>
>>> Hi All,
>>>
>>> I just got this message (below) from Jeff, and indeed I found PDBWiki
>>> to be broken.
>>>
>>> I logged in and hit 'svn update' in the mediawiki directory, however,
>>> this didn't resolve the problem.
>>>
>>> I fixed the function as described by Jeff (below), but I'm still
>>> seeing problems with the Jmol extension:
>>>
>>> Warning: Parameter 1 to Jmol::hParserBeforeStrip() expected to be a
>>> reference, value given in
>>>
>>> /home/member/hstehr/public_html/pdbwiki/mediawiki-1.15/extensions/StubManager/StubManager.php
>>> on line 783
>>>
>>> Warning: Parameter 1 to Jmol::hParserBeforeStrip() expected to be a
>>> reference, value given in
>>>
>>> /home/member/hstehr/public_html/pdbwiki/mediawiki-1.15/extensions/StubManager/StubManager.php
>>> on line 783
>>> MediaWiki internal error.
>>>
>>>
>>> Since we don't really use Jmol in PDBWiki, I decided to just disable
>>> it (for speed rather than anything else). However, we could try to
>>> update it (via svn?) or just fix it in a similar way.
>>>
>>> After disabling the Jmol extension, PDBWiki seems fine (although
>>> additional testing is advised ;-)
>>>
>>>
>>> Oh... I Just noticed additional warnings:
>>>
>>>  "Warning: Parameter 3 to ExtDynamicPageList2::dplTag() expected to be
>>> a reference, value given in
>>>
>>> /home/member/hstehr/public_html/pdbwiki/mediawiki-1.15/includes/parser/Parser.php
>>> on line 3243
>>>
>>>
>>> Lets try the above fix (as DPL is essential to PDBWiki)...
>>>
>>> diff -u ./DynamicPageList/DynamicPageList2.php~
>>> ./DynamicPageList/DynamicPageList2.php
>>> --- ./DynamicPageList/DynamicPageList2.php~     2009-03-04
>>> 09:56:47.000000000 -0500
>>> +++ ./DynamicPageList/DynamicPageList2.php      2010-01-11
>>> 04:31:28.000000000 -0500
>>> @@ -848,7 +848,7 @@
>>>
>>>
>>> //-------------------------------------------------------------------------------------
>>> ENTRY parser TAG
>>>     // The callback function wrapper for converting the input text to
>>> HTML output
>>> -    public static function dplTag( $input, $params, &$parser ) {
>>> +    public static function dplTag( $input, $params, $parser ) {
>>>         // entry point for user tag <dpl>
>>>         // create list and do a recursive parse of the output
>>>
>>>
>>> Right, that seems to have cracked it.
>>>
>>> Thanks for the heads up Jeff,
>>>
>>>
>>> All the best,
>>> Dan.
>>>
>>>
>>>
>>>
>>> 2010/1/9 J.W. Bizzaro <jeff at bioinformatics.org>:
>>> > (CC'd Dan -- FYI)
>>> >
>>> > Upon upgrading to PHP 5.3.1 (Apache needed to be upgraded), this is the
>>> > warning in MediaWiki:
>>> >
>>> > Warning: Parameter 1 to Language::getMagic() expected to be a reference,
>>> > value given in
>>> > /home/httpd/mediawiki/mediawiki-1.15.0/includes/StubObject.php on line
>>> > 58
>>> >
>>> > The function is here:
>>> >
>>> >  languages/Language.php
>>> >
>>> > I removed the pass-by-reference (&), and all seems to be working.
>>> >
>>> > I read in a forum that MediaWiki 1.15.1 also fixes the problem.  So, if
>>> > we
>>> > still have problems, an upgrade to 1.15.1 would be in order.
>>> >
>>> > Jeff
>>> >
>>> > Martin Kucej wrote:
>>> >>
>>> >> PHP 5.3 had some changes in OO programming. I can see an error message
>>> >> in
>>> >> our Wiki.
>>> >> Martin
>>> >>
>>> >>
>>> >>
>>> >>
>>> >
>>> > --
>>> > J.W. Bizzaro
>>> > Bioinformatics Organization, Inc. (Bioinformatics.Org)
>>> > E-mail: jeff at bioinformatics.org
>>> > Phone:  +1 978 621 8258
>>> > --
>>> >
>>>
>>> _______________________________________________
>>> Pdbwiki-devel mailing list
>>> Pdbwiki-devel at bioinformatics.org
>>> http://www.bioinformatics.org/mailman/listinfo/pdbwiki-devel
>>> http://www.pdbwiki.org
>>
>>
>