[Pdbwiki-devel] PHP upgrade

[Dan Bolser]

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
> --
>