1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
|
# 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)
|
