Bio.DocSQL

1 #!/usr/bin/env python 2 # 3 # Copyright 2002-2003 by Michael Hoffman. All rights reserved. 4 # This code is part of the Biopython distribution and governed by its 5 # license. Please see the LICENSE file that should have been included 6 # as part of this package. 7 8 """ 9 Bio.DocSQL: easy access to DB API databases. 10 11 >>> import os 12 >>> import MySQLdb 13 >>> from Bio import DocSQL 14 >>> db=MySQLdb.connect(passwd='', db='test') 15 >>> class CreatePeople(DocSQL.Create): 16 ... ''' 17 ... CREATE TEMPORARY TABLE people 18 ... (id INT UNSIGNED NOT NULL PRIMARY KEY AUTO_INCREMENT, 19 ... last_name TINYTEXT, 20 ... first_name TINYTEXT) 21 ... ''' 22 ... 23 >>> CreatePeople(connection=db) 24 CreatePeople(message=Success) 25 """ 26 27 __version__ = "$Revision: 1.13 $" 28 # $Source: /home/bartek/cvs2bzr/biopython_fastimport/cvs_repo/biopython/Bio/DocSQL.py,v $ 29 30 import sys 31 32 from Bio import MissingPythonDependencyError 33 34 try: 35 import MySQLdb 36 except: 37 raise MissingPythonDependencyError("Install MySQLdb if you want to use " 38 "Bio.DocSQL.") 39 40 connection = None 41

42 -class NoInsertionError(Exception):

43 pass

44

45 -def _check_is_public(name):

46 if name[:6] == "_names": 47 raise AttributeError

48

49 -class QueryRow(list):

50 - def __init__(self, cursor):

51 try: 52 row = cursor.fetchone() 53 super(QueryRow, self).__init__(row) 54 except TypeError: 55 raise StopIteration 56 57 object.__setattr__(self, "_names", [x[0] for x in cursor.description]) # FIXME: legacy 58 object.__setattr__(self, "_names_hash", {}) 59 60 for i, name in enumerate(self._names): 61 self._names_hash[name] = i

62

63 - def __getattr__(self, name):

64 _check_is_public(name) 65 try: 66 return self[self._names_hash[name]] 67 except (KeyError, AttributeError): 68 raise AttributeError("'%s' object has no attribute '%s'" \ 69 % (self.__class__.__name__, name))

70

71 - def __setattr__(self, name, value):

72 try: 73 self._names_hash 74 except AttributeError: 75 return object.__setattr__(self, name, value) 76 77 _check_is_public(name) 78 try: 79 index = self._names_hash[name] 80 self[index] = value 81 except KeyError: 82 return object.__setattr__(self, name, value)

83

84 -class Query(object):

85 """ 86 SHOW TABLES 87 """ 88 MSG_FAILURE = "Failure" 89 MSG_SUCCESS = "Success" 90 message = "not executed" 91 error_message = "" 92 prefix = "" 93 suffix = "" 94 row_class = QueryRow 95

96 - def __init__(self, *args, **keywds):

97 try: 98 self.connection = keywds['connection'] 99 except KeyError: 100 self.connection = connection 101 try: 102 self.diagnostics = keywds['diagnostics'] 103 except KeyError: 104 self.diagnostics = 0 105 106 self.statement = self.prefix + self.__doc__ + self.suffix 107 self.params = args

108

109 - def __iter__(self):

110 return IterationCursor(self, self.connection)

111

112 - def __repr__(self):

113 return "%s(message=%s)" % (self.__class__.__name__, self.message)

114

115 - def cursor(self):

116 return iter(self).cursor

117

118 - def dump(self):

119 for item in self: 120 print item

121

122 -class QueryGeneric(Query):

123 - def __init__(self, statement, *args, **keywds):

124 Query.__init__(self, *args, **keywds) 125 self.statement = statement,

126

127 -class IterationCursor(object):

128 - def __init__(self, query, connection=connection):

129 if connection is None: 130 raise TypeError("database connection is None") 131 self.cursor = connection.cursor() 132 self.row_class = query.row_class 133 if query.diagnostics: 134 print >>sys.stderr, query.statement 135 print >>sys.stderr, query.params 136 self.cursor.execute(query.statement, query.params)

137

138 - def next(self):

139 return self.row_class(self.cursor)

140

141 -class QuerySingle(Query, QueryRow):

142 ignore_warnings = 0

143 - def __init__(self, *args, **keywds):

144 message = self.MSG_FAILURE 145 Query.__init__(self, *args, **keywds) 146 try: 147 self.single_cursor = Query.cursor(self) 148 except MySQLdb.Warning: 149 if not self.ignore_warnings: 150 raise 151 self.row_class.__init__(self, self.cursor()) 152 object.__setattr__(self, "message", self.MSG_SUCCESS)

153

154 - def cursor(self):

155 return self.single_cursor

156

157 -class QueryAll(list, Query):

158 - def __init__(self, *args, **keywds):

159 Query.__init__(self, *args, **keywds) 160 list.__init__(self, map(self.process_row, self.cursor().fetchall()))

161

162 - def process_row(self, row):

163 return row

164

165 -class QueryAllFirstItem(QueryAll):

166 - def process_row(self, row):

167 return row[0]

168

169 -class Create(QuerySingle):

170 - def __init__(self, *args, **keywds):

171 try: 172 QuerySingle.__init__(self, *args, **keywds) 173 except StopIteration: 174 self.message = self.MSG_SUCCESS

175

176 -class Update(Create):

177 pass

178

179 -class Insert(Create):

180 MSG_INTEGRITY_ERROR = "Couldn't insert: %s. " 181

182 - def __init__(self, *args, **keywds):

183 try: 184 Create.__init__(self, *args, **keywds) 185 except MySQLdb.IntegrityError, error_data: 186 self.error_message += self.MSG_INTEGRITY_ERROR % error_data[1] 187 try: 188 self.total_count 189 except AttributeError: 190 self.total_count = 0 191 192 raise MySQLdb.IntegrityError(self.error_message) 193 194 self.id = self.cursor().insert_id() 195 try: 196 self.total_count += self.cursor().rowcount 197 except AttributeError: 198 self.total_count = self.cursor().rowcount 199 200 if self.cursor().rowcount == 0: 201 raise NoInsertionError

202

203 -def _test(*args, **keywds):

204 import doctest, sys 205 doctest.testmod(sys.modules[__name__], *args, **keywds)

206 207 if __name__ == "__main__": 208 if __debug__: 209 _test() 210

Source Code for Module Bio.DocSQL