Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/mySql/MySqlQuery.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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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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1 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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12 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 #
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30
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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31 class MySqlQuery(object):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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32 """Query to a database"""
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33
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34 def __init__(self, cursor, verbosity = 0):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 self.verbosity = verbosity
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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36 self.cursor = cursor
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 self.insertedId = None
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39
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40 def __del__(self):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 self.cursor.close()
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42
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43
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44 def execute(self, query, insertion = False):
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45 if self.verbosity > 99:
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46 print "Querying %s" % (query)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 try:
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48 results = self.cursor.execute(query)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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49 except Exception:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 raise Exception("Error! Command \"%s\" failed!" % (query))
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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51 if insertion:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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52 return self.cursor.lastrowid
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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53 return results
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54
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55
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56 def executeFormat(self, query, parameters):
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57 if self.verbosity > 99:
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58 print "Querying %s |" % (query),
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59 for parameter in parameters:
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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60 print parameter,
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61 print
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62 results = self.cursor.execute(query, parameters)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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63 return results
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64
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65
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66 def getLine(self):
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67 return self.cursor.fetchone()
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68
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69
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70 def getLines(self, lines = None):
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71 if lines == None:
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72 return self.cursor.fetchall()
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73 return self.cursor.fetchmany(lines)
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74
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75
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76 def isEmpty(self):
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77 self.getLines()
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78 return self.cursor.rowcount == None or self.cursor.rowcount == 0
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79
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80
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81 def getInsertedId(self):
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82 return self.insertedId
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83
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84
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85 def getIterator(self):
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86 line = self.getLine()
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87 while line != None:
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88 yield line
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89 line = self.getLine()
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90
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91
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92 def show(self):
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93 for line in self.getIterator():
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94 print line