[Pdbwiki-devel] PHP upgrade

[Jose M. Duarte]

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
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> http://www.bioinformatics.org/mailman/listinfo/pdbwiki-devel
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>
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