# 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)