Removed everything from 'web' directory except genofiles and renamed the directory to 'genotype_files'

1 files changed, 0 insertions, 127 deletions

diff --git a/web/webqtl/maintainance/updateMenuJS.py b/web/webqtl/maintainance/updateMenuJS.py
deleted file mode 100755
index 8b6e25d3..00000000
--- a/web/webqtl/maintainance/updateMenuJS.py
+++ /dev/null
@@ -1,127 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# created by Lei Yan 02/08/2011
-import sys, os
-import MySQLdb
-import string
-
-
-
-abs_path = os.path.abspath(os.path.dirname(__file__))
-path1 = abs_path + "/.."
-path2 = abs_path + "/../../javascript"
-sys.path.insert(0, path1)
-
-#must import GN python files after add path
-from base import webqtlConfig
-
-# build MySql database connection
-con = MySQLdb.Connect(db=webqtlConfig.DB_NAME, host=webqtlConfig.MYSQL_SERVER, user=webqtlConfig.DB_USER, passwd=webqtlConfig.DB_PASSWD)
-cursor = con.cursor()
-cursor.execute("SELECT id,menuname FROM Species ORDER BY OrderId")
-results = list(cursor.fetchall())
-collectionsText = ""
-for result in results:
-	specieid = result[0]
-	speciename = result[1]
-	collectionsText += ("['" + speciename + "', ")
-	collectionsText += ("null, ")
-	collectionsText += ("null, ")
-	collectionsText += "\n"
-	cursor.execute("select name from InbredSet where speciesid=" + str(specieid))
-	results2 = list(cursor.fetchall())
-	for result2 in results2:
-		inbredsetName = result2[0]
-		if not cmp(inbredsetName, "BXD300"):
-			continue
-		collectionsText += "\t"
-		collectionsText += ("['" + inbredsetName + "', ")
-		collectionsText += ("'/webqtl/main.py?FormID=dispSelection&RISet=" + inbredsetName + "'], ")
-		collectionsText += "\n"
-	collectionsText += "],"
-	collectionsText += "\n"
-collectionsText = collectionsText.strip()
-
-jstext = """/*
-  --- menu items --- 
-  note that this structure has changed its format since previous version.
-  additional third parameter is added for item scope settings.
-  Now this structure is compatible with Tigra Menu GOLD.
-  Format description can be found in product documentation.
-*/
-var MENU_ITEMS = [
-	['menu_grp1', null, null,
-		['GeneNetwork Intro', '/home.html'],
-		['Enter Trait Data', '/webqtl/main.py?FormID=submitSingleTrait'],
-		['Batch Submission', '/webqtl/main.py?FormID=batSubmit'],
-	],
-	['menu_grp2', null, null,
-		['Search Databases', '/'],
-		['Tissue Correlation', '/webqtl/main.py?FormID=tissueCorrelation'],
-		['SNP Browser', '/webqtl/main.py?FormID=snpBrowser'],
-		['Gene Wiki', '/webqtl/main.py?FormID=geneWiki'],
-		['Interval Analyst', '/webqtl/main.py?FormID=intervalAnalyst'],
-		['QTLminer', '/webqtl/main.py?FormID=qtlminer'],
-		['GenomeGraph', '/dbResults.html'],
-		['Trait Collections',null,null,
-%s
-		],
-		['Scriptable Interface', '/CGIDoc.html'],
-		/* ['Simple Query Interface', '/GUI.html'], */
-		['Database Information',null,null,
-			['Database Schema', '/webqtl/main.py?FormID=schemaShowPage'],
-		],
-		['Data Sharing', '/webqtl/main.py?FormID=sharing'],
-		['Microarray Annotations', '/webqtl/main.py?FormID=annotation'],
-	],
-	['menu_grp3', null, null,
-		['Movies','http://www.genenetwork.org/tutorial/movies'],
-		['Tutorials', null, null, 
-                ['GN Barley Tutorial','/tutorial/pdf/GN_Barley_Tutorial.pdf'],
-                ['GN Powerpoint', '/tutorial/ppt/index.html']],
-		['HTML Tour','/tutorial/WebQTLTour/'],
-		['FAQ','/faq.html'],
-		['Glossary of Terms','/glossary.html'],
-		['GN MediaWiki','http://wiki.genenetwork.org/'],
-	],
-	['menu_grp4', '/whats_new.html'
-	],
-	['menu_grp5', '/reference.html'
-	],
-	['menu_grp6', null, null,
-		['Conditions and Limitation', '/conditionsofUse.html'],
-		['Data Sharing Policy', '/dataSharing.html'],
-		['Status and Contacts', '/statusandContact.html'],
-		['Privacy Policy', '/privacy.html'],
-	],
-	['menu_grp8', '/links.html'
-	],
-];
-"""
-
-# create menu_items.js file
-fileHandler = open(path2 + '/menu_items.js', 'w')
-fileHandler.write(jstext % collectionsText)
-fileHandler.close()