dbolser/gist:edfd487f152048f5e34d Secret

## gistfile1.php
<?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.
#
# Further documentation for configuration settings may be found at:
# http://www.mediawiki.org/wiki/Manual:Configuration_settings

# 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 ) . PATH_SEPARATOR . get_include_path() );

require_once( "$IP/includes/DefaultSettings.php" );

if ( $wgCommandLineMode ) {
        if ( isset( $_SERVER ) && array_key_exists( 'REQUEST_METHOD', $_SERVER ) ) {
                die( "This script must be run from the command line\n" );
        }
}
## Uncomment this to disable output compression
# $wgDisableOutputCompression = true;

$wgSitename         = "Bioinformatics.Org Wiki";

## The URL base path to the directory containing the wiki;
## defaults for all runtime URL paths are based off of this.
## For more information on customizing the URLs please see:
## http://www.mediawiki.org/wiki/Manual:Short_URL
$wgScriptPath       = "/w";
$wgScriptExtension  = ".php";

## The relative URL path to the skins directory
$wgStylePath        = "$wgScriptPath/skins";

## The relative URL path to the logo.  Make sure you change this from the default,
## or else you'll overwrite your logo when you upgrade!
$wgLogo             = "$wgStylePath/common/images/wiki.png";

## UPO means: this is also a user preference option

$wgEnableEmail      = true;
$wgEnableUserEmail  = true; # UPO

$wgEmergencyContact = "webmaster@bioinformatics.org";
$wgPasswordSender = "webmaster@bioinformatics.org";

$wgEnotifUserTalk = true; # UPO
$wgEnotifWatchlist = true; # UPO
$wgEmailAuthentication = true;

## Database settings
$wgDBtype           = "mysql";
$wgDBserver         =
$wgDBname           =
$wgDBuser           =
$wgDBpassword       =

# MySQL specific settings
$wgDBprefix         = "mw_";

# MySQL table options to use during installation or update
$wgDBTableOptions   = "ENGINE=InnoDB, DEFAULT CHARSET=binary";

# Experimental charset support for MySQL 4.1/5.0.
$wgDBmysql5 = true;

## 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       = false;
$wgUseImageMagick = true;
$wgImageMagickConvertCommand = "/usr/bin/convert";

## If you use ImageMagick (or any other shell command) on a
## Linux server, this will need to be set to the name of an
## available UTF-8 locale
$wgShellLocale = "en_US.utf8";

## 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;

## Set $wgCacheDirectory to a writable directory on the web server
## to make your wiki go slightly faster. The directory should not
## be publically accessible from the web.
#$wgCacheDirectory = "$IP/cache";

$wgLocalInterwiki   = strtolower( $wgSitename );

$wgLanguageCode = "en";

$wgSecretKey =

## Default skin: you can change the default skin. Use the internal symbolic
## names, ie 'vector', '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 = "http://www.gnu.org/copyleft/fdl.html";
$wgRightsText = "GNU Free Documentation License 1.3";
$wgRightsIcon = "${wgScriptPath}/skins/common/images/gnu-fdl.png";
# $wgRightsCode = "gfdl1_3"; # Not yet used

$wgDiff3 = "/usr/bin/diff3";

# When you make changes to this configuration file, this will make
# sure that cached pages are cleared.
$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );


# All additional customization goes in this file:
require_once("../AdditionalSettings.php");


// Additional Settings.php

<?php

/*

A mixed bag of MediaWiki configuration and extensions.

*/

// Use this to make the whole site read-only
#$wgReadOnly = 'Testing!';


// Configure the 'short url'
// http://www.mediawiki.org/wiki/Manual:Short_URL
// The 'short url' settings must be used in the context of the
// correct Apache Alias ('Alias /wiki "/httpdroot/mediawiki/w/index.php")
$wgArticlePath = "/wiki/$1";
$wgUsePathInfo = true;


// Set the site logo
$wgLogo = 'http://www.bioinformatics.org/w/images/1/16/SiteLogo.png';


// Enable file uploads
$wgEnableUploads = true;


// Enable fancy search suggestions while typing
$wgEnableMWSuggest = true;


// Enable subpages in the main and 'project' namespace
$wgNamespacesWithSubpages[NS_MAIN] = true;
$wgNamespacesWithSubpages[NS_PROJECT] = true;


// Completely disable the cache!
$wgEnableParserCache = false;
$wgCachePages = false;


// ImageMagick version out? Fall back on GD
$wgUseImageMagick = false;


// Set the default skin!
$wgDefaultSkin  = 'vector';

// Don't ask
#$wgStyleVersion = 15;


// Extensions! Document these on the wiki! (You swine!)
// Did I miss any?

include_once('extensions/AdminLinks/AdminLinks.php');

include_once('extensions/ArrayExtension/ArrayExtension.php');

require_once('extensions/Asksql/Asksql.php');
$wgGroupPermissions['bureaucrat']['asksql'] = true;
$wgDBsqluser
$wgDBsqlpassword

require_once('extensions/CategoryTree/CategoryTree.php');

require_once('extensions/Cite/Cite.php');

include_once('extensions/DataTransfer/DataTransfer.php');

require_once('extensions/EmbedVideo/EmbedVideo.php');

require_once( 'extensions/ExternalData/ExternalData.php' );

#require_once("$IP/extensions/FCKeditor/FCKeditor.php");
#$wgDefaultUserOptions['riched_use_toggle'] = true;
#$wgDefaultUserOptions['riched_start_disabled'] = true;

require_once("$IP/extensions/HeaderTabs/HeaderTabs.php");

include_once('extensions/Interwiki/Interwiki.php');
$wgGroupPermissions['*']['interwiki'] = false;
$wgGroupPermissions['sysop']['interwiki'] = true;

#require_once("$IP/extensions/OpenID/OpenID.setup.php");
#$wgTrustRoot = '';

include_once('extensions/ParserFunctions/ParserFunctions.php');
$wgPFEnableStringFunctions = true;


## See
require_once('extensions/recaptcha/ReCaptcha.php');

// Sign up for these at http://recaptcha.net/api/getkey
$recaptcha_public_key
$recaptcha_private_key

// Fix the default captcha behaviour
$wgGroupPermissions['*'            ]['skipcaptcha'] = false;
$wgGroupPermissions['user'         ]['skipcaptcha'] = true;
$wgGroupPermissions['autoconfirmed']['skipcaptcha'] = true;
$wgGroupPermissions['bot'          ]['skipcaptcha'] = true; // registered bots
$wgGroupPermissions['sysop'        ]['skipcaptcha'] = true;

$wgCaptchaTriggers['edit']          = true;
$wgCaptchaTriggers['create']        = true;
$wgCaptchaTriggers['createaccount'] = true;


include_once('extensions/ReplaceText/ReplaceText.php');
$wgGroupPermissions['sysop']['replacetext'] = true;

include_once('extensions/SyntaxHighlight_GeSHi/SyntaxHighlight_GeSHi.php');

require_once('extensions/UserMerge/UserMerge.php');
$wgGroupPermissions['bureaucrat']['usermerge'] = true;

require_once( "$IP/extensions/Validator/Validator.php" );

require_once("$IP/extensions/Widgets/Widgets.php");
$wgGroupPermissions['sysop']['editwidgets'] = true;


include_once("$IP/extensions/SemanticMediaWiki/SemanticMediaWiki.php");
enableSemantics('bifx.org');

include_once('extensions/SemanticDrilldown/includes/SD_Settings.php');
$sdgFiltersSmallestFontSize=12;
$sdgFiltersLargestFontSize=20;

include_once('extensions/SemanticForms/includes/SF_Settings.php');

include_once("$IP/extensions/SemanticInternalObjects/SemanticInternalObjects.php");

include_once('extensions/SemanticResultFormats/SRF_Settings.php');
$srfgFormats[] = 'exhibit';
$srfgFormats[] = 'googlebar';
$srfgFormats[] = 'googlepie';
$srfgFormats[] = 'graph';

require_once('extensions/Maps/Maps.php');
$egGoogleMapsKey
#$egYahooMapsKey = ""; # https://developer.yahoo.com/wsregapp/

require_once('extensions/SemanticMaps/SemanticMaps.php');

require_once('extensions/Treeview/Treeview.php');


## See http://www.mediawiki.org/wiki/Extension:Selenium
include("$IP/extensions/Selenium/Selenium.php");


## See http://www.mediawiki.org/wiki/Extension:VariablesExtension
require_once( "$IP/extensions/Variables/Variables.php" );

## See http://www.mediawiki.org/wiki/Extension:StringFunctionsEscaped
## Note, this requires ParserFunctions (String Functions) above.
require_once("$IP/extensions/StringFunctionsEscaped/StringFunctionsEscaped.php");


require_once("$IP/extensions/GBrowse/gbrowse_img.php");


// I hope this can't hurt (copied from LocalSettings.php)

# When you make changes to this configuration file, this will make
# sure that cached pages are cleared.
$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
	<?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.
	#
	# Further documentation for configuration settings may be found at:
	# http://www.mediawiki.org/wiki/Manual:Configuration_settings

	# 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 ) . PATH_SEPARATOR . get_include_path() );

	require_once( "$IP/includes/DefaultSettings.php" );

	if ( $wgCommandLineMode ) {
	if ( isset( $_SERVER ) && array_key_exists( 'REQUEST_METHOD', $_SERVER ) ) {
	die( "This script must be run from the command line\n" );
	}
	}
	## Uncomment this to disable output compression
	# $wgDisableOutputCompression = true;

	$wgSitename = "Bioinformatics.Org Wiki";

	## The URL base path to the directory containing the wiki;
	## defaults for all runtime URL paths are based off of this.
	## For more information on customizing the URLs please see:
	## http://www.mediawiki.org/wiki/Manual:Short_URL
	$wgScriptPath = "/w";
	$wgScriptExtension = ".php";

	## The relative URL path to the skins directory
	$wgStylePath = "$wgScriptPath/skins";

	## The relative URL path to the logo. Make sure you change this from the default,
	## or else you'll overwrite your logo when you upgrade!
	$wgLogo = "$wgStylePath/common/images/wiki.png";

	## UPO means: this is also a user preference option

	$wgEnableEmail = true;
	$wgEnableUserEmail = true; # UPO

	$wgEmergencyContact = "webmaster@bioinformatics.org";
	$wgPasswordSender = "webmaster@bioinformatics.org";

	$wgEnotifUserTalk = true; # UPO
	$wgEnotifWatchlist = true; # UPO
	$wgEmailAuthentication = true;

	## Database settings
	$wgDBtype = "mysql";
	$wgDBserver =
	$wgDBname =
	$wgDBuser =
	$wgDBpassword =

	# MySQL specific settings
	$wgDBprefix = "mw_";

	# MySQL table options to use during installation or update
	$wgDBTableOptions = "ENGINE=InnoDB, DEFAULT CHARSET=binary";

	# Experimental charset support for MySQL 4.1/5.0.
	$wgDBmysql5 = true;

	## 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 = false;
	$wgUseImageMagick = true;
	$wgImageMagickConvertCommand = "/usr/bin/convert";

	## If you use ImageMagick (or any other shell command) on a
	## Linux server, this will need to be set to the name of an
	## available UTF-8 locale
	$wgShellLocale = "en_US.utf8";

	## 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;

	## Set $wgCacheDirectory to a writable directory on the web server
	## to make your wiki go slightly faster. The directory should not
	## be publically accessible from the web.
	#$wgCacheDirectory = "$IP/cache";

	$wgLocalInterwiki = strtolower( $wgSitename );

	$wgLanguageCode = "en";

	$wgSecretKey =

	## Default skin: you can change the default skin. Use the internal symbolic
	## names, ie 'vector', '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 = "http://www.gnu.org/copyleft/fdl.html";
	$wgRightsText = "GNU Free Documentation License 1.3";
	$wgRightsIcon = "${wgScriptPath}/skins/common/images/gnu-fdl.png";
	# $wgRightsCode = "gfdl1_3"; # Not yet used

	$wgDiff3 = "/usr/bin/diff3";

	# When you make changes to this configuration file, this will make
	# sure that cached pages are cleared.
	$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );


	# All additional customization goes in this file:
	require_once("../AdditionalSettings.php");





	// Additional Settings.php

	<?php

	/*

	A mixed bag of MediaWiki configuration and extensions.

	*/

	// Use this to make the whole site read-only
	#$wgReadOnly = 'Testing!';


	// Configure the 'short url'
	// http://www.mediawiki.org/wiki/Manual:Short_URL
	// The 'short url' settings must be used in the context of the
	// correct Apache Alias ('Alias /wiki "/httpdroot/mediawiki/w/index.php")
	$wgArticlePath = "/wiki/$1";
	$wgUsePathInfo = true;


	// Set the site logo
	$wgLogo = 'http://www.bioinformatics.org/w/images/1/16/SiteLogo.png';


	// Enable file uploads
	$wgEnableUploads = true;


	// Enable fancy search suggestions while typing
	$wgEnableMWSuggest = true;


	// Enable subpages in the main and 'project' namespace
	$wgNamespacesWithSubpages[NS_MAIN] = true;
	$wgNamespacesWithSubpages[NS_PROJECT] = true;


	// Completely disable the cache!
	$wgEnableParserCache = false;
	$wgCachePages = false;


	// ImageMagick version out? Fall back on GD
	$wgUseImageMagick = false;


	// Set the default skin!
	$wgDefaultSkin = 'vector';

	// Don't ask
	#$wgStyleVersion = 15;





	// Extensions! Document these on the wiki! (You swine!)
	// Did I miss any?

	include_once('extensions/AdminLinks/AdminLinks.php');

	include_once('extensions/ArrayExtension/ArrayExtension.php');

	require_once('extensions/Asksql/Asksql.php');
	$wgGroupPermissions['bureaucrat']['asksql'] = true;
	$wgDBsqluser
	$wgDBsqlpassword

	require_once('extensions/CategoryTree/CategoryTree.php');

	require_once('extensions/Cite/Cite.php');

	include_once('extensions/DataTransfer/DataTransfer.php');

	require_once('extensions/EmbedVideo/EmbedVideo.php');

	require_once( 'extensions/ExternalData/ExternalData.php' );

	#require_once("$IP/extensions/FCKeditor/FCKeditor.php");
	#$wgDefaultUserOptions['riched_use_toggle'] = true;
	#$wgDefaultUserOptions['riched_start_disabled'] = true;

	require_once("$IP/extensions/HeaderTabs/HeaderTabs.php");

	include_once('extensions/Interwiki/Interwiki.php');
	$wgGroupPermissions['*']['interwiki'] = false;
	$wgGroupPermissions['sysop']['interwiki'] = true;

	#require_once("$IP/extensions/OpenID/OpenID.setup.php");
	#$wgTrustRoot = '';

	include_once('extensions/ParserFunctions/ParserFunctions.php');
	$wgPFEnableStringFunctions = true;


	## See
	require_once('extensions/recaptcha/ReCaptcha.php');

	// Sign up for these at http://recaptcha.net/api/getkey
	$recaptcha_public_key
	$recaptcha_private_key

	// Fix the default captcha behaviour
	$wgGroupPermissions['*' ]['skipcaptcha'] = false;
	$wgGroupPermissions['user' ]['skipcaptcha'] = true;
	$wgGroupPermissions['autoconfirmed']['skipcaptcha'] = true;
	$wgGroupPermissions['bot' ]['skipcaptcha'] = true; // registered bots
	$wgGroupPermissions['sysop' ]['skipcaptcha'] = true;

	$wgCaptchaTriggers['edit'] = true;
	$wgCaptchaTriggers['create'] = true;
	$wgCaptchaTriggers['createaccount'] = true;


	include_once('extensions/ReplaceText/ReplaceText.php');
	$wgGroupPermissions['sysop']['replacetext'] = true;

	include_once('extensions/SyntaxHighlight_GeSHi/SyntaxHighlight_GeSHi.php');

	require_once('extensions/UserMerge/UserMerge.php');
	$wgGroupPermissions['bureaucrat']['usermerge'] = true;

	require_once( "$IP/extensions/Validator/Validator.php" );

	require_once("$IP/extensions/Widgets/Widgets.php");
	$wgGroupPermissions['sysop']['editwidgets'] = true;





	include_once("$IP/extensions/SemanticMediaWiki/SemanticMediaWiki.php");
	enableSemantics('bifx.org');

	include_once('extensions/SemanticDrilldown/includes/SD_Settings.php');
	$sdgFiltersSmallestFontSize=12;
	$sdgFiltersLargestFontSize=20;

	include_once('extensions/SemanticForms/includes/SF_Settings.php');

	include_once("$IP/extensions/SemanticInternalObjects/SemanticInternalObjects.php");

	include_once('extensions/SemanticResultFormats/SRF_Settings.php');
	$srfgFormats[] = 'exhibit';
	$srfgFormats[] = 'googlebar';
	$srfgFormats[] = 'googlepie';
	$srfgFormats[] = 'graph';

	require_once('extensions/Maps/Maps.php');
	$egGoogleMapsKey
	#$egYahooMapsKey = ""; # https://developer.yahoo.com/wsregapp/

	require_once('extensions/SemanticMaps/SemanticMaps.php');

	require_once('extensions/Treeview/Treeview.php');


	## See http://www.mediawiki.org/wiki/Extension:Selenium
	include("$IP/extensions/Selenium/Selenium.php");


	## See http://www.mediawiki.org/wiki/Extension:VariablesExtension
	require_once( "$IP/extensions/Variables/Variables.php" );

	## See http://www.mediawiki.org/wiki/Extension:StringFunctionsEscaped
	## Note, this requires ParserFunctions (String Functions) above.
	require_once("$IP/extensions/StringFunctionsEscaped/StringFunctionsEscaped.php");


	require_once("$IP/extensions/GBrowse/gbrowse_img.php");



	// I hope this can't hurt (copied from LocalSettings.php)

	# When you make changes to this configuration file, this will make
	# sure that cached pages are cleared.
	$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );