[Pdbwiki-devel] PHP upgrade

[Jose M. Duarte]

We've replaced the main page with a message that the site is under
maintenance. There's a new .htaccess pointing to index.html instead of
index.php so simply use the full URL pdbwiki.org/index.php to access the
mediawiki site.

Jose



2010/1/11 Dan Bolser <dan.bolser at gmail.com>

> 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
> >>
> >>
> >
>
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