Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/SMART/Java/Python/mySql/MySqlConnection.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 #
2 # Copyright INRA-URGI 2009-2010
3 #
4 # This software is governed by the CeCILL license under French law and
5 # abiding by the rules of distribution of free software. You can use,
6 # modify and/ or redistribute the software under the terms of the CeCILL
7 # license as circulated by CEA, CNRS and INRIA at the following URL
8 # "http://www.cecill.info".
9 #
10 # As a counterpart to the access to the source code and rights to copy,
11 # modify and redistribute granted by the license, users are provided only
12 # with a limited warranty and the software's author, the holder of the
13 # economic rights, and the successive licensors have only limited
14 # liability.
15 #
16 # In this respect, the user's attention is drawn to the risks associated
17 # with loading, using, modifying and/or developing or reproducing the
18 # software by the user in light of its specific status of free software,
19 # that may mean that it is complicated to manipulate, and that also
20 # therefore means that it is reserved for developers and experienced
21 # professionals having in-depth computer knowledge. Users are therefore
22 # encouraged to load and test the software's suitability as regards their
23 # requirements in conditions enabling the security of their systems and/or
24 # data to be ensured and, more generally, to use and operate it in the
25 # same conditions as regards security.
26 #
27 # The fact that you are presently reading this means that you have had
28 # knowledge of the CeCILL license and that you accept its terms.
29 #
30 #! /usr/bin/env python
31 import os
32 import random
33 import sqlite3
34 from SMART.Java.Python.mySql.MySqlQuery import MySqlQuery
35
36
37 class MySqlConnection(object):
38 """Connection to a database"""
39
40 def __init__(self, verbosity = 0):
41 self.verbosity = verbosity
42 self.databaseName = "%s%ssmartdb%d" % (os.environ.get("SMARTTMPPATH", "."), os.sep, random.randint(0, 100000))
43 self.connection = sqlite3.connect(self.databaseName)
44 self.executeQuery("PRAGMA journal_mode = OFF")
45 self.executeQuery("PRAGMA synchronous = 0")
46 self.executeQuery("PRAGMA locking_mode = EXCLUSIVE")
47 self.executeQuery("PRAGMA count_change = OFF")
48 self.executeQuery("PRAGMA temp_store = 2")
49
50 def __del__(self):
51 self.connection.close()
52
53
54 def createDatabase(self):
55 pass
56
57
58 def deleteDatabase(self):
59 if os.path.exists(self.databaseName):
60 os.remove(self.databaseName)
61
62
63 def executeQuery(self, command, insertion = False):
64 cursor = self.connection.cursor()
65 query = MySqlQuery(cursor, self.verbosity)
66 try:
67 result = query.execute(command, insertion)
68 self.connection.commit()
69 except:
70 result = query.execute(command, insertion)
71 self.connection.commit()
72 if insertion:
73 return result
74 else:
75 return query
76
77
78 def executeManyQueries(self, commands):
79 cursor = self.connection.cursor()
80 query = MySqlQuery(cursor, self.verbosity)
81 try:
82 for cpt, command in enumerate(commands):
83 query.execute(command)
84 self.connection.commit()
85 except:
86 for cpt, command in enumerate(commands):
87 query.execute(command)
88 self.connection.commit()
89
90
91 def executeManyQueriesIterator(self, table):
92 cursor = self.connection.cursor()
93 query = MySqlQuery(cursor, self.verbosity)
94 try:
95 for command in table.getIterator():
96 query.execute(command)
97 self.connection.commit()
98 except:
99 for command in table.getIterator():
100 query.execute(command)
101 self.connection.commit()
102
103
104 def executeFormattedQuery(self, command, *parameters):
105 cursor = self.connection.cursor()
106 query = MySqlQuery(cursor, self.verbosity)
107 query.executeFormat(command, parameters)
108 self.connection.commit()
109 return query