Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/sql/DbSQLite.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import sqlite3 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import os |
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3 import sys |
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4 |
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5 #TODO: update...compare with DbMySql.py |
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6 class DbSQLite(object): |
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7 |
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8 ## Constructor |
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9 # |
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10 # @param host string db file path |
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11 # @param cfgFileName string configuration file name |
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12 # |
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13 # @note when a parameter is left blank, the constructor is able |
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14 # to set attribute values from environment variable: REPET_HOST, |
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15 # |
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16 def __init__(self, host = ""): |
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17 if host != "": |
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18 self.host = host |
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19 else: |
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20 msg = "ERROR: no host specified" |
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21 sys.stderr.write( "%s\n" % msg ) |
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22 sys.exit(1) |
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23 # remove open() and cursor from init() use directly outside this class ... |
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24 self.open() |
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25 self.cursor = self.db.cursor() |
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26 |
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27 ## Connect to the DbSQLite database |
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28 # |
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29 # @param verbose integer (default = 0) |
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30 # |
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31 def open( self, verbose = 0, nb = 0 ): |
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32 try: |
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33 #sqlite.connect(":memory:", check_same_thread = False) |
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34 self.db = sqlite3.connect(self.host, check_same_thread= False, isolation_level=None, detect_types=sqlite3.PARSE_DECLTYPES) |
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35 except sqlite3.Error, e: |
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36 if verbose > 0: |
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37 print "ERROR %s" % e |
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38 sys.stdout.flush() |
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39 return False |
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40 return True |
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41 |
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42 ## Execute a SQL query |
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43 # |
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44 # @param qry string SQL query to execute |
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45 # @param params parameters of SQL query |
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46 # |
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47 def execute( self, qry, params=None ): |
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48 try : |
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49 if params == None: |
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50 self.cursor.execute( qry ) |
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51 else: |
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52 self.cursor.execute( qry, params ) |
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53 except Exception, e: |
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54 #TODO Must be test |
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55 try : |
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56 if params == None: |
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57 self.cursor.execute( qry ) |
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58 else: |
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59 self.cursor.execute( qry, params ) |
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60 except Exception, e: |
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61 print "Erreur : %s" % e |
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62 |
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63 ## Retrieve the results of a SQL query |
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64 # |
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65 def fetchall(self): |
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66 return self.cursor.fetchall() |
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67 |
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68 ## Record a new table in the 'info_table' table |
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69 # |
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70 # @param tableName string table name |
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71 # @param info string information on the table origin |
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72 # |
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73 def updateInfoTable( self, tableName, info ): |
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74 if not self.doesTableExist( "info_tables" ): |
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75 sqlCmd = "CREATE TABLE info_tables ( name varchar(255), file varchar(255) )" |
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76 self.execute( sqlCmd ) |
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77 sqlCmd = 'INSERT INTO info_tables VALUES ("%s","%s")' % (tableName, info) |
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78 self.execute( sqlCmd ) |
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79 |
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80 def createTable(self, tableName, dataType, overwrite=False, verbose=0): |
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81 if verbose > 0: |
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82 print "creating table '%s' from file '%s' of type '%s'..." % (tableName, dataType) |
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83 sys.stdout.flush() |
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84 if overwrite: |
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85 self.dropTable(tableName) |
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86 if dataType.lower() in ["job", "jobs"]: |
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87 self.createJobTable(tableName) |
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88 else: |
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89 print "ERROR: unknown type %s" % (dataType) |
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90 self.close() |
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91 sys.exit(1) |
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92 if verbose > 0: |
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93 print "done!"; sys.stdout.flush() |
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94 |
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95 ## Create a job table |
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96 # |
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97 # @param tablename new table name |
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98 # |
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99 def createJobTable( self, tablename ): |
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100 sqlCmd = "CREATE TABLE %s" % ( tablename ) |
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101 sqlCmd += " ( jobid INT UNSIGNED" |
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102 sqlCmd += ", jobname VARCHAR(255)" |
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103 sqlCmd += ", groupid VARCHAR(255)" |
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104 sqlCmd += ", command TEXT" |
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105 sqlCmd += ", launcher VARCHAR(1024)" |
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106 sqlCmd += ", queue VARCHAR(255)" |
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107 sqlCmd += ", status VARCHAR(255)" |
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108 sqlCmd += ", time timestamp" |
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109 sqlCmd += ", node VARCHAR(255) )" |
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110 self.execute( sqlCmd ) |
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111 |
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112 self.updateInfoTable( tablename, "job table" ) |
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113 sqlCmd = "CREATE INDEX igroupid ON " + tablename + " ( groupid )" |
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114 self.execute( sqlCmd ) |
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115 |
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116 ## Test if a table exists |
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117 # |
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118 # @param table string table name |
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119 # @return boolean True if the table exists, False otherwise |
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120 # |
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121 def doesTableExist( self, table ): |
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122 qry = "PRAGMA table_info(%s)" % (table) |
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123 self.execute( qry ) |
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124 results = self.cursor.fetchall() |
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125 if results: |
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126 return True |
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127 return False |
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128 |
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129 def isEmpty( self, tableName ): |
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130 return self.getSize( tableName ) == 0 |
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131 |
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132 ## Give the rows number of the table |
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133 # |
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134 # @param tableName string table name |
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135 # |
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136 def getSize( self, tableName ): |
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137 qry = "SELECT count(*) FROM %s;" % ( tableName ) |
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138 self.execute( qry ) |
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139 res = self.fetchall() |
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140 return int( res[0][0] ) |
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141 |
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142 ## Remove a table if it exists |
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143 # |
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144 # @param table string table name |
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145 # @param verbose integer (default = 0) |
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146 # |
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147 def dropTable( self, table, verbose = 0 ): |
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148 if self.doesTableExist( table ): |
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149 sqlCmd = "DROP TABLE %s" % ( table ) |
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150 self.execute( sqlCmd ) |
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151 sqlCmd = 'DELETE FROM info_tables WHERE name = "%s"' % ( table ) |
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152 self.execute( sqlCmd ) |
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153 |
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154 ## Get a list with the fields |
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155 # |
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156 def getFieldList( self, table ): |
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157 lFields = [] |
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158 sqlCmd = "PRAGMA table_info(%s)" % ( table ) |
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159 self.execute( sqlCmd ) |
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160 lResults = self.fetchall() |
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161 for res in lResults: |
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162 lFields.append( res[1] ) |
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163 return lFields |
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164 |
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165 ## delete this SQLite database session |
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166 # |
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167 def delete(self): |
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168 os.remove(self.host) |
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169 |
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170 ## Close the connection |
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171 # |
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172 def close( self ): |
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173 self.db.close() |