From 1d6ff15b32e476eb8323fc2a90b95d26e5af5e24 Mon Sep 17 00:00:00 2001 From: preecej Date: Wed, 27 Oct 2010 02:13:40 +0000 Subject: [PATCH] renamed www to mac_www and added folder for semantic wiki code, esp versioned php but also test scripts svn path=/; revision=78 --- preecej/{www => mac_www}/index.html | 0 preecej/{www => mac_www}/index.php | 0 preecej/{www => mac_www}/index.pl | 0 .../reactome_chebi_mapping.pl | 16 +- preecej/semantic_wiki/LocalSettings.php | 159 ++++++++++++++++++ 5 files changed, 168 insertions(+), 7 deletions(-) rename preecej/{www => mac_www}/index.html (100%) rename preecej/{www => mac_www}/index.php (100%) rename preecej/{www => mac_www}/index.pl (100%) create mode 100644 preecej/semantic_wiki/LocalSettings.php diff --git a/preecej/www/index.html b/preecej/mac_www/index.html similarity index 100% rename from preecej/www/index.html rename to preecej/mac_www/index.html diff --git a/preecej/www/index.php b/preecej/mac_www/index.php similarity index 100% rename from preecej/www/index.php rename to preecej/mac_www/index.php diff --git a/preecej/www/index.pl b/preecej/mac_www/index.pl similarity index 100% rename from preecej/www/index.pl rename to preecej/mac_www/index.pl diff --git a/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl b/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl index 6159dd5..899134a 100755 --- a/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl +++ b/preecej/perl_singletons/reactome_chebi_mapping/reactome_chebi_mapping.pl @@ -4,9 +4,10 @@ use strict; # --------------------------------------------------------------------------- # Rice Reactome - CHEBI Ontology Mapping Script # -# Justin Preece, 10/06/10 +# Justin Preece, 10/06q/10 # v1.0: 10/13/10 (svn rev. 66) # v1.1: 10/20/10 (svn rev. 70) +# v2.0: 10/21/10 (svn rev. ?) # # Purpose: Map CHEBI ontology terms onto Rice Reactome database. # @@ -18,7 +19,7 @@ use strict; # (Header) [ReactomeID] [Compound_Name] [CAS] [LIGAND] [RiceCyc] # (Row) 923893 S-adenosyl-L-methionine 29908-03-0 C00019 S-ADENOSYLMETHIONINE ** the '-' (dash) symbol will be applied to any empty columns # -# Outputs: tab-del mapping file (reactome_chebi_mapping.txt) +# Outputs: tab-del mapping file (reactome_chebi_mapping_results_sorted.txt) # # [ReactomeID] [CHEBI] [XREF_Type] [XREF_ID] # 923893 15414 CAS 29908-03-0 @@ -41,13 +42,14 @@ use GO::Parser; # --------------------------------------------------------------------------- # set paths to data files -my $data_path = "/home/preecej/Documents/projects/reactome/"; +my $data_path = "/Users/cindypreece/Desktop/work/Documents/projects/reactome/"; +#my $data_path = "/home/preecej/Documents/projects/reactome/"; my $chebi_obo_file = "chebi.obo"; my $reactome_file = "RiceReferenceMolecules.txt"; -my $mapped_output_file = "1.1_reactome_chebi_mapping_complete.txt"; -my $sorted_output_file = "1.1_reactome_chebi_mapping_complete_sorted.txt"; -my $unique_mappings = "1.1_reactome_unique_mappings.txt"; -my $sorted_no_match_file = "1.1_reactome_entries_with_no_chebi_match.txt"; +my $mapped_output_file = "2.0_reactome_chebi_mapping_complete.txt"; +my $sorted_output_file = "2.0_reactome_chebi_mapping_complete_sorted.txt"; +my $unique_mappings = "2.0_reactome_unique_mappings.txt"; +my $sorted_no_match_file = "2.0_reactome_entries_with_no_chebi_match.txt"; # options my $allow_obsolete_terms = 1; diff --git a/preecej/semantic_wiki/LocalSettings.php b/preecej/semantic_wiki/LocalSettings.php new file mode 100644 index 0000000..9659acb --- /dev/null +++ b/preecej/semantic_wiki/LocalSettings.php @@ -0,0 +1,159 @@ +'; + +# Data Transfer extension +include_once("$IP/extensions/DataTransfer/DataTransfer.php"); + +# External Data extension +include_once("$IP/extensions/ExternalData/ExternalData.php"); + +# END 09/30/10: Justin Preece - added for Semantic MediaWiki and related extensions + + + +## Uncomment this to disable output compression +# $wgDisableOutputCompression = true; + +$wgSitename = "AnnoWiki"; + +## 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 +$wgScriptPath = "/AnnoWiki"; +$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/A1_sterileflowers_wiki_icon.jpg"; + +## 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 = "annowiki"; +$wgDBuser = "annowikiuser"; +$wgDBpassword = "annowikiuser-pw"; + +# 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"; + +$wgSecretKey = "469aad58c7cc5ab0ec223dbf1316d16a6ded21cfa01f9e23d6ef22dee92a3224"; + +## Default skin: you can change the default skin. Use the internal symbolic +## names, ie 'vector', 'monobook': +$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 +$wgRightsUrl = ""; +$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. +$wgCacheEpoch = max( $wgCacheEpoch, gmdate( 'YmdHis', @filemtime( __FILE__ ) ) ); -- 2.34.1