Hi all,
Recently, I e-mailed the list with problems getting Jmol to run on MediaWiki.
Fortunately, I had a really great response and have now got Jmol working on
MediaWiki. It did require me charting new territories in RHEL4.0 (namely
downloaded CentOS rpm files to get updated releases of MySQL and PHP). Thanks
to all that responded.
I now have a new problem! I'm suspicious that it is not actually a Jmol
problem (so apologies if I'm posting off-topic), but rather a MediaWiki or Php
problem, however, I'm not knowledgeable enough in either to be certain where
the issue is. Specifically, I cannot upload **any** files other than the
standard set (jpg, png, etc). I've tried all the standard changes to the
LocalSettings.php file, but it appears to have absolutely 'bob-all' effect.
The versions I'm running are:
* MediaWiki: 1.11.0
* PHP: 5.1.6 (apache2handler)
* MySQL: 5.0.48
A copy of my LocalSettings.php file is listed below. It's a bit of a mess at
the end, but that's because I've been busy trying every combination under the
big bright thing in the sky.
Has anyone else had the same problem with MediaWiki 1.11, with the above
releases of MySQL and Php? If so, tips, tricks for a Php-newbie like me would
be hugely appreciated!
------------------------------------
<?php
# This file was automatically generated by the MediaWiki installer.
# If you make manual changes, please keep track in case you need to
# recreate them later.
#
# See includes/DefaultSettings.php for all configurable settings
# and their default values, but don't forget to make changes in _this_
# file, not there.
# If you customize your file layout, set $IP to the directory that contains
# the other MediaWiki files. It will be used as a base to locate files.
if( defined( 'MW_INSTALL_PATH' ) ) {
$IP = MW_INSTALL_PATH;
} else {
$IP = dirname( __FILE__ );
}
$path = array( $IP, "$IP/includes", "$IP/languages" );
set_include_path( implode( PATH_SEPARATOR, $path ) );
require_once( "includes/DefaultSettings.php" );
require_once( "extensions/FileProtocolLinks.php" );
# If PHP's memory limit is very low, some operations may fail.
ini_set( 'memory_limit', '20M' );
if ( $wgCommandLineMode ) {
if ( isset( $_SERVER ) && array_key_exists( 'REQUEST_METHOD', $_SERVER
) ) {
die( "This script must be run from the command line\n" );
}
} elseif ( empty( $wgNoOutputBuffer ) ) {
## Compress output if the browser supports it
if( !ini_get( 'zlib.output_compression' ) ) @ob_start( 'ob_gzhandler' );
}
$wgSitename = "Kwiki";
$wgScriptPath = "/wiki";
$wgScript = "$wgScriptPath/index.php";
$wgRedirectScript = "$wgScriptPath/redirect.php";
$wgShowExceptionDetails = true;
## For more information on customizing the URLs please see:
## http://meta.wikimedia.org/wiki/Eliminating_index.php_from_the_url
## If using PHP as a CGI module, the ?title= style usually must be used.
$wgArticlePath = "$wgScript/$1";
# $wgArticlePath = "$wgScript?title=$1";
$wgStylePath = "$wgScriptPath/skins";
$wgStyleDirectory = "$IP/skins";
##$wgLogo = "$wgStylePath/common/images/wiki.png";
$wgLogo = "/wiki/kudoslogo.jpg";
$wgUploadPath = "$wgScriptPath/images";
$wgUploadDirectory = "$IP/images";
$wgEnableEmail = true;
$wgEnableUserEmail = true;
$wgEmergencyContact = "[EMAIL PROTECTED]";
$wgPasswordSender = "[EMAIL PROTECTED]";
## For a detailed description of the following switches see
## http://meta.wikimedia.org/Enotif and http://meta.wikimedia.org/Eauthent
## There are many more options for fine tuning available see
## /includes/DefaultSettings.php
## UPO means: this is also a user preference option
$wgEnotifUserTalk = true; # UPO
$wgEnotifWatchlist = true; # UPO
$wgEmailAuthentication = true;
$wgDBserver = "localhost";
$wgDBname = "wikidb";
$wgDBuser = "wikiuser";
$wgDBpassword = "wikius3r";
$wgDBprefix = "";
$wgDBtype = "mysql";
# Experimental charset support for MySQL 4.1/5.0.
$wgDBmysql5 = false;
## Shared memory settings
$wgMainCacheType = CACHE_NONE;
$wgMemCachedServers = array();
## To enable image uploads, make sure the 'images' directory
## is writable, then set this to true:
$wgEnableUploads = true;
$wgUseImageResize = true;
$wgUseImageMagick = true;
$wgImageMagickConvertCommand = "/usr/bin/convert";
## If you want to use image uploads under safe mode,
## create the directories images/archive, images/thumb and
## images/temp, and make them all writable. Then uncomment
## this, if it's not already uncommented:
# $wgHashedUploadDirectory = false;
## If you have the appropriate support software installed
## you can enable inline LaTeX equations:
$wgUseTeX = false;
$wgMathPath = "{$wgUploadPath}/math";
$wgMathDirectory = "{$wgUploadDirectory}/math";
$wgTmpDirectory = "{$wgUploadDirectory}/tmp";
$wgLocalInterwiki = $wgSitename;
$wgLanguageCode = "en";
$wgProxyKey =
"92f522cd48ab6238ea573a26be39dff0c4c8515fb3f9d2968dd54f4e7f13fa7a";
## Default skin: you can change the default skin. Use the internal symbolic
## names, ie 'standard', 'nostalgia', 'cologneblue', 'monobook':
$wgDefaultSkin = 'monobook';
## For attaching licensing metadata to pages, and displaying an
## appropriate copyright notice / icon. GNU Free Documentation
## License and Creative Commons licenses are supported so far.
# $wgEnableCreativeCommonsRdf = true;
$wgRightsPage = ""; # Set to the title of a wiki page that describes your
license/copyright
$wgRightsUrl = "";
$wgRightsText = "";
$wgRightsIcon = "";
# $wgRightsCode = ""; # Not yet used
$wgDiff3 = "/usr/bin/diff3";
# When you make changes to this configuration file, this will make
# sure that cached pages are cleared.
$configdate = gmdate( 'YmdHis', @filemtime( __FILE__ ) );
$wgCacheEpoch = max( $wgCacheEpoch, $configdate );
# Customised Groups and permission settings
# APS 20070920
$wgGroupPermissions['*']['edit'] = false;
$wgGroupPermissions['user']['edit'] = true;
$wgPutIPinRC = true;
$wgSkipSkins = array("myskin","chick","nostalgia","simple","standard");
# JMol configuration settings
# APS 20070920
$wgStrictFileExtensions = false;
$wgCheckFileExtensions = false;
$wgVerifyMimeTypes = false;
$wgMimeDetectorCommand = "file --brief --mime";
$wgFileExtensions += array ( 'mol', 'pdf', 'xls', 'doc', 'ppt', 'zip', 'Z',
'tar', 'gz', 'cml', 'sdf', 'msv', 'mol2', 'pdb' );
require_once( "extensions/Jmol/JmolExtension.php" );
# MOE settings
# APS 20091106
require_once( "extensions/SMILESMoleculeImage/SMILESMoleculeImage.php" );
$wgDebugLogFile = "$wgScriptPath/wiki.1.11.debug.log";
?>
------------------------------------
Cheers,
A.
==========================================
Dr Adrian Stevens
Head Computational Chemistry
KuDOS Pharmaceuticals Ltd
26 Foundry Lane
Horsham
RH13 5PX
England
t: +44 1403 248844
f: +44 1403 248855
410 Cambridge Science Park
Milton Road
Cambridge
CB4 0PE
England
t: +44 1223 719719
f: +44 1223 719720
www.kudospharma.co.uk
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