Add all the source codes into the github.

1 files changed, 127 insertions, 0 deletions

diff --git a/web/webqtl/maintainance/updateMenuJS.py b/web/webqtl/maintainance/updateMenuJS.py
new file mode 100755
index 00000000..8b6e25d3
--- /dev/null
+++ b/web/webqtl/maintainance/updateMenuJS.py
@@ -0,0 +1,127 @@
+# 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()