[Pdbwiki-devel] PHP upgrade

[Dan Bolser]

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
>> > --
>> >
>>
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>
>