+++ /dev/null
-<?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 = "Planteome Annotation Wiki - Development";
-
-## 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
-$wgScriptPath = "/w";
-$wgArticlePath = "/wiki/$1";
-$wgUsePathInfo = true;
-$wgScriptExtension = ".php5";
-
-## The relative URL path to the skins directory
-$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 = "$wgStylePath/common/images/wiki_logo_with_text.png";
-
-## UPO means: this is also a user preference option
-
-$wgEnableEmail = true;
-$wgEnableUserEmail = true; # UPO
-
-$wgEmergencyContact = "preecej@science.oregonstate.edu";
-$wgPasswordSender = "preecej@science.oregonstate.edu";
-
-$wgEnotifUserTalk = true; # UPO
-$wgEnotifWatchlist = true; # UPO
-$wgEmailAuthentication = true;
-
-## Database settings
-$wgDBtype = "mysql";
-$wgDBserver = $_SERVER['dev_wgDBServer'];
-$wgDBname = $_SERVER['dev_wgDBName'];
-$wgDBuser = $_SERVER['dev_wgDBUser'];
-$wgDBpassword = $_SERVER['dev_wgDBPassword'];
-$JobRunRate = 1;
-
-# MySQL specific settings
-$wgDBprefix = "";
-
-# MySQL table options to use during installation or update
-$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";
-
-$wgSecretKey = "c7f2e0aee38b819689a65337257ed2d6c4eb7157e44563781da69bbfd3e2e45b";
-
-## Default skin: you can change the default skin. Use the internal symbolic
-## names, ie 'vector', 'monobook':
-$wgDefaultSkin = 'planteome';
-
-## 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
-$wgRightsUrl = "http://creativecommons.org/licenses/by-nc-sa/3.0/";
-$wgRightsText = "Attribution-NonCommercial-ShareAlike 3.0 Unported";
-$wgRightsIcon = "http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png";
-# $wgRightsCode = "[license_code]"; # Not yet used
-
-$wgDiff3 = "/usr/bin/diff3";
-
-# BEGIN: Justin Preece - Config changes and Semantic Bundle (SMW and other extensions)
-# (moved from top of file to address premature reference to $wgScriptPath)
-
-$wgHiddenPrefs[] = 'skin';
-$wgUseAjax = true;
-
-#include_once("$IP/extensions/DataTransfer_PS/DataTransfer.php");
-
-require_once( "$IP/extensions/semantic-bundle/SemanticBundleSettings.php" );
-require_once( "$IP/extensions/semantic-bundle/SemanticBundle.php" );
-
-include("$IP/extensions/SimpleForms/SimpleForms.php");
-
-$sfgAutocompletionURLs['remote_PO_terms'] = 'http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&qval=<substr>&format=json&max=20';
-$sfgAutocompleteOnAllChars = false;
-
-# END: Justin Preece - Semantic Bundle (SMW and other extensions)
-
-/** Allow client-side caching of pages */
-$wgCachePages = false;
-
-/**
- * * Set this to current time to invalidate all prior cached pages. Affects both
- * * client- and server-side caching.
- * * You can get the current date on your server by using the command:
- * * date +%Y%m%d%H%M%S
- * */
-$wgCacheEpoch = 'date +%Y%m%d%H%M%S';
-
-
-# When you make changes to this configuration file, this will make
-# sure that cached pages are cleared.
-$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
+++ /dev/null
-<?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 = "Planteome Annotation Wiki - Prototype";
-
-## 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
-$wgScriptPath = "/w";
-$wgArticlePath = "/wiki/$1";
-$wgUsePathInfo = true;
-$wgScriptExtension = ".php5";
-
-## The relative URL path to the skins directory
-$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 = "$wgStylePath/common/images/wiki_logo_proto.png";
-
-## UPO means: this is also a user preference option
-
-$wgEnableEmail = true;
-$wgEnableUserEmail = true; # UPO
-
-$wgEmergencyContact = "preecej@science.oregonstate.edu";
-$wgPasswordSender = "preecej@science.oregonstate.edu";
-
-$wgEnotifUserTalk = true; # UPO
-$wgEnotifWatchlist = true; # UPO
-$wgEmailAuthentication = true;
-
-## Database settings
-$wgDBtype = "mysql";
-$wgDBserver = $_SERVER['proto_wgDBServer'];
-$wgDBname = $_SERVER['proto_wgDBName'];
-$wgDBuser = $_SERVER['proto_wgDBUser'];
-$wgDBpassword = $_SERVER['proto_wgDBPassword'];
-$wgJobRunRate = 1;
-
-# MySQL specific settings
-$wgDBprefix = "";
-
-# MySQL table options to use during installation or update
-$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";
-
-$wgSecretKey = "2030c0cc408640a1809ec82a9fb16e660d9988a63aeb77871a94c94a5f2d2c56";
-
-## Default skin: you can change the default skin. Use the internal symbolic
-## names, ie 'vector', 'monobook':
-$wgDefaultSkin = 'planteome';
-
-## 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
-$wgRightsUrl = "http://creativecommons.org/licenses/by-nc-sa/3.0/";
-$wgRightsText = "Attribution-NonCommercial-ShareAlike 3.0 Unported";
-$wgRightsIcon = "http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png";
-# $wgRightsCode = "[license_code]"; # Not yet used
-
-$wgDiff3 = "/usr/bin/diff3";
-
-
-# BEGIN 04/04/11: Justin Preece - Add'l Extensions
-$wgHiddenPrefs[] = 'skin';
-$wgUseAjax = true;
-include("$IP/extensions/SimpleForms/SimpleForms.php");
-
-require_once( "$IP/extensions/ParserFunctions/ParserFunctions.php" );
-$wgPFEnableStringFunctions = true;
-
-require_once( "$IP/extensions/Variables/Variables.php" );
-require_once( "$IP/extensions/Loops/Loops.php" );
-
-# END 04/04/11: Justin Preece - Add'l Extensions
-
-# BEGIN 02/22/11: Justin Preece - Semantic Bundle (SMW and other extensions)
-# (moved from top of file to address premature reference to $wgScriptPath)
-
-#include_once("$IP/extensions/DataTransfer_PS/DataTransfer.php");
-
-require_once( "$IP/extensions/semantic-bundle/SemanticBundleSettings.php" );
-require_once( "$IP/extensions/semantic-bundle/SemanticBundle.php" );
-
-$sfgAutocompletionURLs['remote_PO_terms'] = 'http://proto.planteome.org/w/prototyping/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&qval=<substr>&format=json&max=20';
-$sfgAutocompleteOnAllChars = false;
-
-# END 02/22/11: Justin Preece - Semantic Bundle (SMW and other extensions)
-
-/** Allow client-side caching of pages */
-$wgCachePages = false;
-
-/**
- * * Set this to current time to invalidate all prior cached pages. Affects both
- * * client- and server-side caching.
- * * You can get the current date on your server by using the command:
- * * date +%Y%m%d%H%M%S
- * */
-$wgCacheEpoch = 'date +%Y%m%d%H%M%S';
-
-
-# When you make changes to this configuration file, this will make
-# sure that cached pages are cleared.
-$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
+++ /dev/null
-<?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 = "Planteome Annotation Wiki - Test";
-
-## 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
-$wgScriptPath = "/paw";
-$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_logo_with_text.png";
-
-## UPO means: this is also a user preference option
-
-$wgEnableEmail = true;
-$wgEnableUserEmail = true; # UPO
-
-$wgEmergencyContact = "preecej@science.oregonstate.edu";
-$wgPasswordSender = "preecej@science.oregonstate.edu";
-
-$wgEnotifUserTalk = true; # UPO
-$wgEnotifWatchlist = true; # UPO
-$wgEmailAuthentication = true;
-
-## Database settings
-$wgDBtype = "mysql";
-$wgDBserver = "floret.cgrb.oregonstate.local";
-$wgDBname = "test_planteome_annotate";
-$wgDBuser = "p_a_wiki_db";
-$wgDBpassword = "1yCoP3r5icuM";
-$JobRunRate = 1;
-
-# MySQL specific settings
-$wgDBprefix = "";
-
-# 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";
-
-$wgSecretKey = "9fbf4140fef09d215376947e74fef8cd873b79b5f97cdf4baf6cf5226db8b706";
-
-## Default skin: you can change the default skin. Use the internal symbolic
-## names, ie 'vector', 'monobook':
-$wgDefaultSkin = 'planteome';
-
-## 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
-$wgRightsUrl = "http://creativecommons.org/licenses/by-nc-sa/3.0/";
-$wgRightsText = "Attribution-NonCommercial-ShareAlike 3.0 Unported";
-$wgRightsIcon = "http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png";
-# $wgRightsCode = "[license_code]"; # Not yet used
-
-$wgDiff3 = "/usr/bin/diff3";
-
-# BEGIN: Justin Preece - Config changes and Semantic Bundle (SMW and other extensions)
-# (moved from top of file to address premature reference to $wgScriptPath)
-
-#$wgHiddenPrefs[] = 'skin';
-#$wgUseAjax = true;
-
-#include_once("$IP/extensions/DataTransfer_PS/DataTransfer.php");
-
-require_once( "$IP/extensions/semantic-bundle/SemanticBundleSettings.php" );
-require_once( "$IP/extensions/semantic-bundle/SemanticBundle.php" );
-
-#include("$IP/extensions/SimpleForms/SimpleForms.php");
-
-$sfgAutocompletionURLs['remote_PO_terms'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&qval=<substr>&format=json&max=20';
-$sfgAutocompleteOnAllChars = false;
-
-# END: Justin Preece - Semantic Bundle (SMW and other extensions)
-
-/** Allow client-side caching of pages */
-$wgCachePages = false;
-
-/**
- * * Set this to current time to invalidate all prior cached pages. Affects both
- * * client- and server-side caching.
- * * You can get the current date on your server by using the command:
- * * date +%Y%m%d%H%M%S
- * */
-$wgCacheEpoch = 'date +%Y%m%d%H%M%S';
-
-# When you make changes to this configuration file, this will make
-# sure that cached pages are cleared.
-$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
+++ /dev/null
-<?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 = "Planteome Annotation Wiki - Test";
-
-## 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
-$wgScriptPath = "/paw";
-$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_logo_with_text.png";
-
-## UPO means: this is also a user preference option
-
-$wgEnableEmail = true;
-$wgEnableUserEmail = true; # UPO
-
-$wgEmergencyContact = "preecej@science.oregonstate.edu";
-$wgPasswordSender = "preecej@science.oregonstate.edu";
-
-$wgEnotifUserTalk = true; # UPO
-$wgEnotifWatchlist = true; # UPO
-$wgEmailAuthentication = true;
-
-## Database settings
-$wgDBtype = "mysql";
-$wgDBserver = $_SERVER['test_wgDBServer'];
-$wgDBname = $_SERVER['test_wgDBName'];;
-$wgDBuser = $_SERVER['test_wgDBUser'];
-$wgDBpassword = $_SERVER['test_wgDBPassword'];
-$JobRunRate = 1;
-
-# MySQL specific settings
-$wgDBprefix = "";
-
-# MySQL table options to use during installation or update
-$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";
-
-$wgSecretKey = "9fbf4140fef09d215376947e74fef8cd873b79b5f97cdf4baf6cf5226db8b706";
-
-## Default skin: you can change the default skin. Use the internal symbolic
-## names, ie 'vector', 'monobook':
-$wgDefaultSkin = 'planteome';
-
-## 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
-$wgRightsUrl = "http://creativecommons.org/licenses/by-nc-sa/3.0/";
-$wgRightsText = "Attribution-NonCommercial-ShareAlike 3.0 Unported";
-$wgRightsIcon = "http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png";
-# $wgRightsCode = "[license_code]"; # Not yet used
-
-$wgDiff3 = "/usr/bin/diff3";
-
-# BEGIN: Justin Preece - Config changes and Semantic Bundle (SMW and other extensions)
-# (moved from top of file to address premature reference to $wgScriptPath)
-
-#$wgHiddenPrefs[] = 'skin';
-#$wgUseAjax = true;
-
-#include_once("$IP/extensions/DataTransfer_PS/DataTransfer.php");
-
-require_once( "$IP/extensions/semantic-bundle/SemanticBundleSettings.php" );
-require_once( "$IP/extensions/semantic-bundle/SemanticBundle.php" );
-
-#include("$IP/extensions/SimpleForms/SimpleForms.php");
-
-$sfgAutocompletionURLs['remote_PO_terms'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&qval=<substr>&format=json&max=20';
-$sfgAutocompleteOnAllChars = false;
-
-# END: Justin Preece - Semantic Bundle (SMW and other extensions)
-
-/** Allow client-side caching of pages */
-$wgCachePages = false;
-
-/**
- * * Set this to current time to invalidate all prior cached pages. Affects both
- * * client- and server-side caching.
- * * You can get the current date on your server by using the command:
- * * date +%Y%m%d%H%M%S
- * */
-$wgCacheEpoch = 'date +%Y%m%d%H%M%S';
-
-# When you make changes to this configuration file, this will make
-# sure that cached pages are cleared.
-$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
+++ /dev/null
-<?php
-if ( !defined( 'MEDIAWIKI' ) ) {
- echo "This file is not a valid entry point.";
- exit( 1 );
-}
-
-# Semantic MediaWiki basic installation.
-# More info: http://semantic-mediawiki.org/wiki/Help:Installation
-$wgServerName = "palea.cgrb.oregonstate.edu";
-
-include_once( "$IP/extensions/SemanticMediaWiki/SemanticMediaWiki.php" );
-enableSemantics($wgServerName);
-
-# Semantic Result Formats
-# More info: http://semantic-mediawiki.org/wiki/Help:Semantic_Result_Formats#Installation
-#include_once( "$IP/extensions/SemanticResultFormats/SemanticResultFormats.php" );
-
-# Semantic Forms
-# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Forms
-include_once( "$IP/extensions/SemanticForms/SemanticForms.php" );
-
-# Semantic Forms Inputs
-# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Forms_Inputs
-#include_once( "$IP/extensions/SemanticFormsInputs/SemanticFormsInputs.php" );
-
-# Semantic Compound Queries
-# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Compound_Queries
-#include_once( "$IP/extensions/SemanticCompoundQueries/SemanticCompoundQueries.php" );
-
-# Semantic Drilldown
-# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Drilldown#Installation
-#include_once( "$IP/extensions/SemanticDrilldown/SemanticDrilldown.php" );
-
-# Validator, Maps and Semantic Maps
-# If you're planning to use Google Maps or Yahoo! Maps, you should also set
-# $egGoogleMapsKey and $egYahooMapsKey.
-# More info:
-# http://www.mediawiki.org/wiki/Extension:Maps#Download_and_installation
-# http://www.mediawiki.org/wiki/Extension:Semantic_Maps#Download_and_installation
-#include_once( "$IP/extensions/Validator/Validator.php" );
-#include_once( "$IP/extensions/Maps/Maps.php" );
-#include_once( "$IP/extensions/SemanticMaps/SemanticMaps.php" );
-
-# Semantic Tasks
-# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Tasks#Installation
-#include_once( "$IP/extensions/SemanticTasks/SemanticTasks.php" );
-
-# Semantic Internal Objects
-# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Internal_Objects
-include_once( "$IP/extensions/SemanticInternalObjects/SemanticInternalObjects.php" );
-
-# Admin Links
-# More info: http://www.mediawiki.org/wiki/Extension:Admin_Links#Installation
-#include_once( "$IP/extensions/AdminLinks/AdminLinks.php" );
-
-# Approved Revs
-# More info: http://www.mediawiki.org/wiki/Extension:Approved_Revs#Installation
-#include_once( "$IP/extensions/ApprovedRevs/ApprovedRevs.php" );
-
-# ArrayExtension
-# More info: http://www.mediawiki.org/wiki/Extension:ArrayExtension#Installation
-#include_once( "$IP/extensions/ArrayExtension/ArrayExtension.php" );
-
-# Data Transfer
-# More info: http://www.mediawiki.org/wiki/Extension:Data_Transfer#Installation
-include_once( "$IP/extensions/DataTransfer/DataTransfer.php" );
-
-# External Data
-# More info: http://www.mediawiki.org/wiki/Extension:External_Data#Installation
-include_once( "$IP/extensions/ExternalData/ExternalData.php" );
-
-# Header Tabs
-# More info: http://www.mediawiki.org/wiki/Extension:Header_Tabs#Installation
-include_once( "$IP/extensions/HeaderTabs/HeaderTabs.php" );
-
-# Page Object Model (POM)
-# More info: http://www.mediawiki.org/wiki/Extension:Page_Object_Model#Installation
-#include_once( "$IP/extensions/PageObjectModel/PageObjectModel.php" );
-
-# ParserFunctions
-# More info: http://www.mediawiki.org/wiki/Extension:ParserFunctions
-require_once( "$IP/extensions/ParserFunctions/ParserFunctions.php" );
-$wgPFEnableStringFunctions = true;
-
-# Replace Text
-# More info: http://www.mediawiki.org/wiki/Extension:Replace_Text#Installation
-#require_once( "$IP/extensions/ReplaceText/ReplaceText.php" );
-
-# Widgets
-# Also need to do some permission setup: http://www.mediawiki.org/wiki/Extension:Widgets#Folder_permissions
-# More info: http://www.mediawiki.org/wiki/Extension:Widgets#Installation
-#require_once( "$IP/extensions/Widgets/Widgets.php" );
-#$wgGroupPermissions['sysop']['editwidgets'] = true;
--- /dev/null
+<?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 = "Planteome Annotation Wiki - Development";
+
+## 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
+$wgScriptPath = "/w";
+$wgArticlePath = "/wiki/$1";
+$wgUsePathInfo = true;
+$wgScriptExtension = ".php5";
+
+## The relative URL path to the skins directory
+$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 = "$wgStylePath/common/images/wiki_logo_with_text.png";
+
+## UPO means: this is also a user preference option
+
+$wgEnableEmail = true;
+$wgEnableUserEmail = true; # UPO
+
+$wgEmergencyContact = "preecej@science.oregonstate.edu";
+$wgPasswordSender = "preecej@science.oregonstate.edu";
+
+$wgEnotifUserTalk = true; # UPO
+$wgEnotifWatchlist = true; # UPO
+$wgEmailAuthentication = true;
+
+## Database settings
+$wgDBtype = "mysql";
+$wgDBserver = $_SERVER['dev_wgDBServer'];
+$wgDBname = $_SERVER['dev_wgDBName'];
+$wgDBuser = $_SERVER['dev_wgDBUser'];
+$wgDBpassword = $_SERVER['dev_wgDBPassword'];
+$JobRunRate = 1;
+
+# MySQL specific settings
+$wgDBprefix = "";
+
+# MySQL table options to use during installation or update
+$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";
+
+$wgSecretKey = "c7f2e0aee38b819689a65337257ed2d6c4eb7157e44563781da69bbfd3e2e45b";
+
+## Default skin: you can change the default skin. Use the internal symbolic
+## names, ie 'vector', 'monobook':
+$wgDefaultSkin = 'planteome';
+
+## 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
+$wgRightsUrl = "http://creativecommons.org/licenses/by-nc-sa/3.0/";
+$wgRightsText = "Attribution-NonCommercial-ShareAlike 3.0 Unported";
+$wgRightsIcon = "http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png";
+# $wgRightsCode = "[license_code]"; # Not yet used
+
+$wgDiff3 = "/usr/bin/diff3";
+
+# BEGIN: Justin Preece - Config changes and Semantic Bundle (SMW and other extensions)
+# (moved from top of file to address premature reference to $wgScriptPath)
+
+$wgHiddenPrefs[] = 'skin';
+$wgUseAjax = true;
+
+#include_once("$IP/extensions/DataTransfer_PS/DataTransfer.php");
+
+require_once( "$IP/extensions/semantic-bundle/SemanticBundleSettings.php" );
+require_once( "$IP/extensions/semantic-bundle/SemanticBundle.php" );
+
+include("$IP/extensions/SimpleForms/SimpleForms.php");
+
+$sfgAutocompletionURLs['remote_PO_terms'] = 'http://dev.planteome.org/w/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&qval=<substr>&format=json&max=20';
+$sfgAutocompleteOnAllChars = false;
+
+# END: Justin Preece - Semantic Bundle (SMW and other extensions)
+
+/** Allow client-side caching of pages */
+$wgCachePages = false;
+
+/**
+ * * Set this to current time to invalidate all prior cached pages. Affects both
+ * * client- and server-side caching.
+ * * You can get the current date on your server by using the command:
+ * * date +%Y%m%d%H%M%S
+ * */
+$wgCacheEpoch = 'date +%Y%m%d%H%M%S';
+
+
+# When you make changes to this configuration file, this will make
+# sure that cached pages are cleared.
+$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
--- /dev/null
+<?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 = "Planteome Annotation Wiki - Prototype";
+
+## 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
+$wgScriptPath = "/w";
+$wgArticlePath = "/wiki/$1";
+$wgUsePathInfo = true;
+$wgScriptExtension = ".php5";
+
+## The relative URL path to the skins directory
+$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 = "$wgStylePath/common/images/wiki_logo_proto.png";
+
+## UPO means: this is also a user preference option
+
+$wgEnableEmail = true;
+$wgEnableUserEmail = true; # UPO
+
+$wgEmergencyContact = "preecej@science.oregonstate.edu";
+$wgPasswordSender = "preecej@science.oregonstate.edu";
+
+$wgEnotifUserTalk = true; # UPO
+$wgEnotifWatchlist = true; # UPO
+$wgEmailAuthentication = true;
+
+## Database settings
+$wgDBtype = "mysql";
+$wgDBserver = $_SERVER['proto_wgDBServer'];
+$wgDBname = $_SERVER['proto_wgDBName'];
+$wgDBuser = $_SERVER['proto_wgDBUser'];
+$wgDBpassword = $_SERVER['proto_wgDBPassword'];
+$wgJobRunRate = 1;
+
+# MySQL specific settings
+$wgDBprefix = "";
+
+# MySQL table options to use during installation or update
+$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";
+
+$wgSecretKey = "2030c0cc408640a1809ec82a9fb16e660d9988a63aeb77871a94c94a5f2d2c56";
+
+## Default skin: you can change the default skin. Use the internal symbolic
+## names, ie 'vector', 'monobook':
+$wgDefaultSkin = 'planteome';
+
+## 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
+$wgRightsUrl = "http://creativecommons.org/licenses/by-nc-sa/3.0/";
+$wgRightsText = "Attribution-NonCommercial-ShareAlike 3.0 Unported";
+$wgRightsIcon = "http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png";
+# $wgRightsCode = "[license_code]"; # Not yet used
+
+$wgDiff3 = "/usr/bin/diff3";
+
+
+# BEGIN 04/04/11: Justin Preece - Add'l Extensions
+$wgHiddenPrefs[] = 'skin';
+$wgUseAjax = true;
+include("$IP/extensions/SimpleForms/SimpleForms.php");
+
+require_once( "$IP/extensions/ParserFunctions/ParserFunctions.php" );
+$wgPFEnableStringFunctions = true;
+
+require_once( "$IP/extensions/Variables/Variables.php" );
+require_once( "$IP/extensions/Loops/Loops.php" );
+
+# END 04/04/11: Justin Preece - Add'l Extensions
+
+# BEGIN 02/22/11: Justin Preece - Semantic Bundle (SMW and other extensions)
+# (moved from top of file to address premature reference to $wgScriptPath)
+
+#include_once("$IP/extensions/DataTransfer_PS/DataTransfer.php");
+
+require_once( "$IP/extensions/semantic-bundle/SemanticBundleSettings.php" );
+require_once( "$IP/extensions/semantic-bundle/SemanticBundle.php" );
+
+$sfgAutocompletionURLs['remote_PO_terms'] = 'http://proto.planteome.org/w/prototyping/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&qval=<substr>&format=json&max=20';
+$sfgAutocompleteOnAllChars = false;
+
+# END 02/22/11: Justin Preece - Semantic Bundle (SMW and other extensions)
+
+/** Allow client-side caching of pages */
+$wgCachePages = false;
+
+/**
+ * * Set this to current time to invalidate all prior cached pages. Affects both
+ * * client- and server-side caching.
+ * * You can get the current date on your server by using the command:
+ * * date +%Y%m%d%H%M%S
+ * */
+$wgCacheEpoch = 'date +%Y%m%d%H%M%S';
+
+
+# When you make changes to this configuration file, this will make
+# sure that cached pages are cleared.
+$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
--- /dev/null
+<?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 = "Planteome Annotation Wiki - Test";
+
+## 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
+$wgScriptPath = "/paw";
+$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_logo_with_text.png";
+
+## UPO means: this is also a user preference option
+
+$wgEnableEmail = true;
+$wgEnableUserEmail = true; # UPO
+
+$wgEmergencyContact = "preecej@science.oregonstate.edu";
+$wgPasswordSender = "preecej@science.oregonstate.edu";
+
+$wgEnotifUserTalk = true; # UPO
+$wgEnotifWatchlist = true; # UPO
+$wgEmailAuthentication = true;
+
+## Database settings
+$wgDBtype = "mysql";
+$wgDBserver = "floret.cgrb.oregonstate.local";
+$wgDBname = "test_planteome_annotate";
+$wgDBuser = "p_a_wiki_db";
+$wgDBpassword = "1yCoP3r5icuM";
+$JobRunRate = 1;
+
+# MySQL specific settings
+$wgDBprefix = "";
+
+# 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";
+
+$wgSecretKey = "9fbf4140fef09d215376947e74fef8cd873b79b5f97cdf4baf6cf5226db8b706";
+
+## Default skin: you can change the default skin. Use the internal symbolic
+## names, ie 'vector', 'monobook':
+$wgDefaultSkin = 'planteome';
+
+## 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
+$wgRightsUrl = "http://creativecommons.org/licenses/by-nc-sa/3.0/";
+$wgRightsText = "Attribution-NonCommercial-ShareAlike 3.0 Unported";
+$wgRightsIcon = "http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png";
+# $wgRightsCode = "[license_code]"; # Not yet used
+
+$wgDiff3 = "/usr/bin/diff3";
+
+# BEGIN: Justin Preece - Config changes and Semantic Bundle (SMW and other extensions)
+# (moved from top of file to address premature reference to $wgScriptPath)
+
+#$wgHiddenPrefs[] = 'skin';
+#$wgUseAjax = true;
+
+#include_once("$IP/extensions/DataTransfer_PS/DataTransfer.php");
+
+require_once( "$IP/extensions/semantic-bundle/SemanticBundleSettings.php" );
+require_once( "$IP/extensions/semantic-bundle/SemanticBundle.php" );
+
+#include("$IP/extensions/SimpleForms/SimpleForms.php");
+
+$sfgAutocompletionURLs['remote_PO_terms'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&qval=<substr>&format=json&max=20';
+$sfgAutocompleteOnAllChars = false;
+
+# END: Justin Preece - Semantic Bundle (SMW and other extensions)
+
+/** Allow client-side caching of pages */
+$wgCachePages = false;
+
+/**
+ * * Set this to current time to invalidate all prior cached pages. Affects both
+ * * client- and server-side caching.
+ * * You can get the current date on your server by using the command:
+ * * date +%Y%m%d%H%M%S
+ * */
+$wgCacheEpoch = 'date +%Y%m%d%H%M%S';
+
+# When you make changes to this configuration file, this will make
+# sure that cached pages are cleared.
+$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
--- /dev/null
+<?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 = "Planteome Annotation Wiki - Test";
+
+## 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
+$wgScriptPath = "/paw";
+$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_logo_with_text.png";
+
+## UPO means: this is also a user preference option
+
+$wgEnableEmail = true;
+$wgEnableUserEmail = true; # UPO
+
+$wgEmergencyContact = "preecej@science.oregonstate.edu";
+$wgPasswordSender = "preecej@science.oregonstate.edu";
+
+$wgEnotifUserTalk = true; # UPO
+$wgEnotifWatchlist = true; # UPO
+$wgEmailAuthentication = true;
+
+## Database settings
+$wgDBtype = "mysql";
+$wgDBserver = $_SERVER['test_wgDBServer'];
+$wgDBname = $_SERVER['test_wgDBName'];;
+$wgDBuser = $_SERVER['test_wgDBUser'];
+$wgDBpassword = $_SERVER['test_wgDBPassword'];
+$JobRunRate = 1;
+
+# MySQL specific settings
+$wgDBprefix = "";
+
+# MySQL table options to use during installation or update
+$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";
+
+$wgSecretKey = "9fbf4140fef09d215376947e74fef8cd873b79b5f97cdf4baf6cf5226db8b706";
+
+## Default skin: you can change the default skin. Use the internal symbolic
+## names, ie 'vector', 'monobook':
+$wgDefaultSkin = 'planteome';
+
+## 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
+$wgRightsUrl = "http://creativecommons.org/licenses/by-nc-sa/3.0/";
+$wgRightsText = "Attribution-NonCommercial-ShareAlike 3.0 Unported";
+$wgRightsIcon = "http://i.creativecommons.org/l/by-nc-sa/3.0/88x31.png";
+# $wgRightsCode = "[license_code]"; # Not yet used
+
+$wgDiff3 = "/usr/bin/diff3";
+
+# BEGIN: Justin Preece - Config changes and Semantic Bundle (SMW and other extensions)
+# (moved from top of file to address premature reference to $wgScriptPath)
+
+#$wgHiddenPrefs[] = 'skin';
+#$wgUseAjax = true;
+
+#include_once("$IP/extensions/DataTransfer_PS/DataTransfer.php");
+
+require_once( "$IP/extensions/semantic-bundle/SemanticBundleSettings.php" );
+require_once( "$IP/extensions/semantic-bundle/SemanticBundle.php" );
+
+#include("$IP/extensions/SimpleForms/SimpleForms.php");
+
+$sfgAutocompletionURLs['remote_PO_terms'] = 'http://palea.cgrb.oregonstate.edu/paw/services/TermSearch_JSON.php?user=paw&type=autocomplete&field=name&qval=<substr>&format=json&max=20';
+$sfgAutocompleteOnAllChars = false;
+
+# END: Justin Preece - Semantic Bundle (SMW and other extensions)
+
+/** Allow client-side caching of pages */
+$wgCachePages = false;
+
+/**
+ * * Set this to current time to invalidate all prior cached pages. Affects both
+ * * client- and server-side caching.
+ * * You can get the current date on your server by using the command:
+ * * date +%Y%m%d%H%M%S
+ * */
+$wgCacheEpoch = 'date +%Y%m%d%H%M%S';
+
+# When you make changes to this configuration file, this will make
+# sure that cached pages are cleared.
+$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) );
--- /dev/null
+<?php
+if ( !defined( 'MEDIAWIKI' ) ) {
+ echo "This file is not a valid entry point.";
+ exit( 1 );
+}
+
+# Semantic MediaWiki basic installation.
+# More info: http://semantic-mediawiki.org/wiki/Help:Installation
+$wgServerName = "palea.cgrb.oregonstate.edu";
+
+include_once( "$IP/extensions/SemanticMediaWiki/SemanticMediaWiki.php" );
+enableSemantics($wgServerName);
+
+# Semantic Result Formats
+# More info: http://semantic-mediawiki.org/wiki/Help:Semantic_Result_Formats#Installation
+#include_once( "$IP/extensions/SemanticResultFormats/SemanticResultFormats.php" );
+
+# Semantic Forms
+# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Forms
+include_once( "$IP/extensions/SemanticForms/SemanticForms.php" );
+
+# Semantic Forms Inputs
+# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Forms_Inputs
+#include_once( "$IP/extensions/SemanticFormsInputs/SemanticFormsInputs.php" );
+
+# Semantic Compound Queries
+# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Compound_Queries
+#include_once( "$IP/extensions/SemanticCompoundQueries/SemanticCompoundQueries.php" );
+
+# Semantic Drilldown
+# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Drilldown#Installation
+#include_once( "$IP/extensions/SemanticDrilldown/SemanticDrilldown.php" );
+
+# Validator, Maps and Semantic Maps
+# If you're planning to use Google Maps or Yahoo! Maps, you should also set
+# $egGoogleMapsKey and $egYahooMapsKey.
+# More info:
+# http://www.mediawiki.org/wiki/Extension:Maps#Download_and_installation
+# http://www.mediawiki.org/wiki/Extension:Semantic_Maps#Download_and_installation
+#include_once( "$IP/extensions/Validator/Validator.php" );
+#include_once( "$IP/extensions/Maps/Maps.php" );
+#include_once( "$IP/extensions/SemanticMaps/SemanticMaps.php" );
+
+# Semantic Tasks
+# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Tasks#Installation
+#include_once( "$IP/extensions/SemanticTasks/SemanticTasks.php" );
+
+# Semantic Internal Objects
+# More info: http://www.mediawiki.org/wiki/Extension:Semantic_Internal_Objects
+include_once( "$IP/extensions/SemanticInternalObjects/SemanticInternalObjects.php" );
+
+# Admin Links
+# More info: http://www.mediawiki.org/wiki/Extension:Admin_Links#Installation
+#include_once( "$IP/extensions/AdminLinks/AdminLinks.php" );
+
+# Approved Revs
+# More info: http://www.mediawiki.org/wiki/Extension:Approved_Revs#Installation
+#include_once( "$IP/extensions/ApprovedRevs/ApprovedRevs.php" );
+
+# ArrayExtension
+# More info: http://www.mediawiki.org/wiki/Extension:ArrayExtension#Installation
+#include_once( "$IP/extensions/ArrayExtension/ArrayExtension.php" );
+
+# Data Transfer
+# More info: http://www.mediawiki.org/wiki/Extension:Data_Transfer#Installation
+include_once( "$IP/extensions/DataTransfer/DataTransfer.php" );
+
+# External Data
+# More info: http://www.mediawiki.org/wiki/Extension:External_Data#Installation
+include_once( "$IP/extensions/ExternalData/ExternalData.php" );
+
+# Header Tabs
+# More info: http://www.mediawiki.org/wiki/Extension:Header_Tabs#Installation
+include_once( "$IP/extensions/HeaderTabs/HeaderTabs.php" );
+
+# Page Object Model (POM)
+# More info: http://www.mediawiki.org/wiki/Extension:Page_Object_Model#Installation
+#include_once( "$IP/extensions/PageObjectModel/PageObjectModel.php" );
+
+# ParserFunctions
+# More info: http://www.mediawiki.org/wiki/Extension:ParserFunctions
+require_once( "$IP/extensions/ParserFunctions/ParserFunctions.php" );
+$wgPFEnableStringFunctions = true;
+
+# Replace Text
+# More info: http://www.mediawiki.org/wiki/Extension:Replace_Text#Installation
+#require_once( "$IP/extensions/ReplaceText/ReplaceText.php" );
+
+# Widgets
+# Also need to do some permission setup: http://www.mediawiki.org/wiki/Extension:Widgets#Folder_permissions
+# More info: http://www.mediawiki.org/wiki/Extension:Widgets#Installation
+#require_once( "$IP/extensions/Widgets/Widgets.php" );
+#$wgGroupPermissions['sysop']['editwidgets'] = true;
projects / old-jaiswallab-svn / .git / commitdiff