Add all the source codes into the github.

1 files changed, 102 insertions, 0 deletions

diff --git a/web/webqtl/maintainance/checkInfoFile.py b/web/webqtl/maintainance/checkInfoFile.py
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+# 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
+#
+# Last updated by NL 2011/01/28
+
+# created by Ning Liu 2011/01/27
+# This script is to check whether dataset related Info file exist or not; if not, the tempate Info file will be generated
+# This script should be only run at GeneNetwork production server
+
+import sys, os
+import MySQLdb
+
+current_file_name = __file__
+pathname = os.path.dirname( current_file_name )
+abs_path = os.path.abspath(pathname)
+sys.path.insert(0, abs_path + '/..')
+
+from base import template
+from base import webqtlConfig
+from base import header
+from base import footer
+
+# 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()
+
+InfoFilePath =webqtlConfig.HTMLPATH+'dbdoc/'
+		
+# create template for Info file
+def createTemplateForInfoFile(datasetId=None,datasetFullName=None,InfoFileURL=None):
+	#template.py has been changed with dynamic header and footer
+	userInfo=""
+	headerInfo=header.header_string % userInfo
+	serverInfo=""
+	footerInfo=footer.footer_string % serverInfo
+	
+	title =datasetFullName
+	contentTitle = '''
+	<P class="title">%s<A HREF="/webqtl/main.py?FormID=editHtml"><img src="/images/modify.gif" alt="modify this page" border= 0 valign="middle"></A><BR><BR>
+	''' % datasetFullName	
+	content ='''
+	Accession number: <A HREF="/webqtl/main.py?FormID=sharinginfo&GN_AccessionId=%s">GN%s</A></P>
+	<br><br>
+	This page will be updated soon. 
+	<br><br>
+	''' % (datasetId,datasetId)	
+	
+	body=contentTitle+content
+	# Note: 'templateParameters' includes parameters required for template.py
+	# templateParameters = ['title','basehref','js1','js2','layer','header','body', 'footer']
+	templateParameters =[title,'','','','',headerInfo,body,footerInfo]
+	
+	# build template file
+	templateFile=template.template % tuple(templateParameters)		
+	InfoFileHandler = open(InfoFileURL, 'w')
+	# write template file into Info .html file
+	InfoFileHandler.write(templateFile)
+	InfoFileHandler.close()
+	
+	
+# select all ProbeSet names from datatable 'ProbeSetFreeze'
+cursor.execute("select Id, Name, FullName from  ProbeSetFreeze ")		
+results = cursor.fetchall()
+for item in results:
+	datasetId = item[0]
+	datasetName =item[1]
+	datasetFullName =item[2]
+	InfoFileURL = InfoFilePath+datasetName+".html"
+	# check Info html file exist or not
+	if not os.path.exists(InfoFileURL):
+		createTemplateForInfoFile(datasetId=datasetId,datasetFullName=datasetFullName,InfoFileURL=InfoFileURL)
+
+		
+
+
+
+
+
+
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+