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comparison SMART/Java/Python/mySql/MySqlTable.py @ 36:44d5973c188c

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date Tue, 30 Apr 2013 15:02:29 -0400
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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 import re
31 import sys
32
33 class MySqlTable(object):
34 """
35 Store a table of a mySQL database, used for transcripts or exons
36 Record a a name and a type (int, float, double) for each column
37 @ivar name: name of the table
38 @type name: string
39 @ivar variables: name of the columns
40 @type variables: list of string
41 @ivar types: type of the columns
42 @type types: dict of string
43 @ivar mySqlConnection: connection to a database
44 @type mySqlConnection: class L{MySqlConnection<MySqlConnection>}
45 @ivar nbLines: number of rows
46 @type nbLines: int
47 @ivar verbosity: verbosity
48 @type verbosity: int
49 """
50
51 def __init__(self, connection, name, verbosity = 0):
52 """
53 Constructor
54 Possibly retrieve column names and types if table exists
55 @param mySqlConnection: connection to a databas
56 @type mySqlConnection: class L{MySqlConnection<MySqlConnection>}
57 @param name: name of the table
58 @type name: string
59 @param verbosity: verbosity
60 @type verbosity: int
61 """
62 self.name = name
63 self.variables = []
64 self.types = {}
65 self.sizes = {}
66 self.nbLines = None
67 self.verbosity = verbosity
68 self.mySqlConnection = connection
69 queryTables = self.mySqlConnection.executeQuery("SELECT name FROM sqlite_master WHERE type LIKE 'table' AND name LIKE '%s'" % (self.name))
70 self.created = not queryTables.isEmpty()
71 if self.created:
72 queryFields = self.mySqlConnection.executeQuery("PRAGMA table_info('%s')" % (name))
73 for field in queryFields.getIterator():
74 if field[1] != "id":
75 self.variables.append(field[1])
76 self.types[field[1]] = field[2]
77 self.sizes[field[1]] = field[3]
78
79
80 def getName(self):
81 return self.name
82
83
84 def create(self, variables, types, sizes):
85 """
86 Create a table using give column names and types
87 @param variables: names of the columns
88 @type variables: list of string
89 @param types: types of the columns
90 @type types: dict of string
91 @param sizes: sizes of the types
92 @type sizes: dict of int
93 """
94 self.variables = variables
95 self.types = types
96 self.sizes = sizes
97 if self.created:
98 self.remove()
99 query = "CREATE TABLE '%s' (id INTEGER PRIMARY KEY" % (self.name)
100 for variable in variables:
101 query = "%s, %s %s(%d)" % (query, variable, types[variable], sizes[variable])
102 query += ")"
103 self.mySqlConnection.executeQuery(query)
104 self.created = True
105
106
107 def insertMany(self, lines):
108 """
109 Insert many lines
110 @param lines: the list of values
111 @type lines: list of lists
112 """
113 commands = []
114 for values in lines:
115 commands.append("INSERT INTO '%s' (%s) VALUES (%s)" % (self.name, ", ".join(self.variables), ", ".join([MySqlTable.formatSql(values[variable], self.types[variable], self.sizes[variable]) for variable in self.variables])))
116 self.mySqlConnection.executeManyQueries(commands)
117
118
119 def insertManyFormatted(self, lines):
120 """
121 Insert many lines
122 @param lines: the list of values
123 @type lines: list of lists
124 """
125 replacer = ["?"] * len(self.variables)
126 command = "INSERT INTO '%s' (%s) VALUES (%s)" % (self.name, ", ".join(self.variables), ", ".join(replacer))
127 values = [[line[variable] for variable in self.variables] for line in lines]
128 self.mySqlConnection.executeManyFormattedQueries(command, values)
129
130
131 def rename(self, name):
132 """
133 Rename the table
134 @param name: the new name
135 @type name: string
136 """
137 self.mySqlConnection.executeQuery("RENAME TABLE '%s' TO '%s'" % (self.name, name))
138 self.name = name
139
140
141 def copy(self, table):
142 """
143 Copy the given table this one
144 @param table: the table to be copied
145 @type table: class L{MySqlTable<MySqlTable>}
146 """
147 variables = []
148 types = {}
149 sizes = {}
150 fields = self.mySqlConnection.executeQuery("PRAGMA table_info(%s)" % (table.name))
151 for field in fields.getIterator():
152 if field[1] != "id":
153 variables.append(field[1])
154 m = re.search(r"(\w+)\((\d+)\)", field[2])
155 if m == None:
156 raise Exception("\nFormat %s in table %s is strange." % (field[2], table.name))
157 types[field[1]] = m.group(1)
158 sizes[field[1]] = int(m.group(2))
159 self.create(variables, types, sizes)
160 self.mySqlConnection.executeQuery("INSERT INTO '%s' SELECT * FROM %s" % (self.name, table.name))
161
162
163 def add(self, table):
164 """
165 Add the content of a table to this one
166 @param table: the table to be added
167 @type table: class L{MySqlTable<MySqlTable>}
168 """
169 self.mySqlConnection.executeQuery("INSERT INTO '%s' SELECT * FROM %s" % (self.name, table.name))
170 self.created = True
171
172
173 def exists(self):
174 """
175 Check if the table exists in mySQL
176 @return: true if it exits
177 """
178 return self.created
179
180
181 def remove(self):
182 """
183 Remove this table
184 """
185 if self.exists():
186 query = "DROP TABLE IF EXISTS '%s'" % (self.name)
187 self.mySqlConnection.executeQuery(query)
188 self.created = False
189
190
191 def clear(self):
192 """
193 Clear the content of this table
194 """
195 self.mySqlConnection.executeQuery("DELETE FROM '%s'" % (self.name))
196
197
198 def getNbElements(self):
199 """
200 Count the number of rows in the table
201 """
202 command = "SELECT COUNT(id) FROM '%s'" % (self.name)
203 query = self.mySqlConnection.executeQuery(command)
204 return int(query.getLine()[0])
205
206
207 def formatSql(self, value, type, size):
208 """
209 Format a value using MySQL encapsulation
210 """
211 if type.find("int") != -1:
212 return "%d" % value
213 if type.find("float") != -1:
214 return "%.10f" % value
215 if type.find("double") != -1:
216 return "%.20f" % value
217 if type.find("varchar") != -1:
218 if len(value) > size:
219 return "'%s'" % value[0:size]
220 return "'%s'" % value
221 raise Exception("Do not understand type %s" % (type))
222 formatSql = classmethod(formatSql)
223
224
225 def addLine(self, values):
226 """
227 Add a row to this table
228 @param values: the values of the row
229 @type values: dict
230 @return: the id of the added row
231 """
232 sqlValues = [values[variable] for variable in self.variables]
233 command = "INSERT INTO '%s' (%%s) VALUES (%s)" % (self.name, ", ".join(self.variables))
234 id = self.mySqlConnection.executeFormattedQueryQuery(command, sqlValues, True)
235 return id
236 sqlValues = []
237 for variable in self.variables:
238 sqlValues.append(self.formatSql(values[variable], self.types[variable], self.sizes[variable]))
239 command = "INSERT INTO '%s' (%s) VALUES (%s)" % (self.name, ", ".join(self.variables), ", ".join(sqlValues))
240 id = self.mySqlConnection.executeQuery(command, True)
241 return id
242
243
244 def retrieveFromId(self, id):
245 """
246 Retrieve a row from its id
247 @param id: the id of the row
248 @type id: int
249 @return: the row
250 """
251 query = self.mySqlConnection.executeQuery("SELECT * FROM '%s' WHERE id = %d" % (self.name, id))
252 result = query.getLine()
253 if result == None:
254 raise Exception("Error! Id %d is not in the table %s!" % (id, self.name))
255 return result
256
257
258 def retrieveBulkFromId(self, ids):
259 """
260 Retrieve a row from its id
261 @param id: the ids of the row
262 @type id: list of int
263 @return: the row
264 """
265 if not ids:
266 return []
267 MAXSIZE = 1000
268 results = []
269 for batch in range(len(ids) / MAXSIZE + 1):
270 theseIds = ids[batch * MAXSIZE : (batch+1) * MAXSIZE]
271 if theseIds:
272 query = self.mySqlConnection.executeQuery("SELECT * FROM '%s' WHERE id IN (%s)" % (self.name, ", ".join(["%d" % (id) for id in theseIds])))
273 lines = query.getLines()
274 if len(lines) != len(theseIds):
275 raise Exception("Error! Some Ids of (%s) is are missing in the table '%s' (got %d instead of %d)!" % (", ".join(["%d" % (id) for id in theseIds]), self.name, len(lines)), len(theseIds))
276 results.extend(lines)
277 return results
278
279
280 def removeFromId(self, id):
281 """
282 Remove a row from its id
283 @param id: the id of the row
284 @type id: int
285 """
286 self.mySqlConnection.executeQuery("DELETE FROM '%s' WHERE id = %d" % (self.name, id))
287
288
289 def getIterator(self):
290 """
291 Iterate on the content of table
292 @return: iterator to the rows of the table
293 """
294 if not self.created:
295 return
296 MAXSIZE = 1000
297 query = self.mySqlConnection.executeQuery("SELECT count(id) FROM '%s'" % (self.name))
298 nbRows = int(query.getLine()[0])
299 for chunk in range((nbRows / MAXSIZE) + 1):
300 query = self.mySqlConnection.executeQuery("SELECT * FROM '%s' LIMIT %d, %d" % (self.name, chunk * MAXSIZE, MAXSIZE))
301 for line in query.getIterator():
302 yield line
303
304
305 def createIndex(self, indexName, values, unique = False, fullText = False):
306 """
307 Add an index on the table
308 @param indexName: name of the index
309 @type indexName: string
310 @param values: values to be indexed
311 @type values: string
312 @param unique: if the index is unique
313 @type unique: boolean
314 @param fullText: whether full text should be indexed
315 @type fullText: boolean
316 """
317 self.mySqlConnection.executeQuery("CREATE %s%sINDEX '%s' ON '%s' (%s)" % ("UNIQUE " if unique else "", "FULLTEXT " if fullText else "", indexName, self.name, ", ".join(values)))
318
319
320 def setDefaultTagValue(self, field, name, value):
321 """
322 Add a tag value
323 @param name: name of the tag
324 @type name: string
325 @param value: value of the tag
326 @type value: string or int
327 """
328 newData = {}
329 for line in MySqlTable.getIterator(self):
330 id = line[0]
331 tags = line[field]
332 if tags == '':
333 newTag = "%s=%s" % (name, value)
334 else:
335 newTag = "%s;%s=%s" % (tags, name, value)
336 if name not in [tag.split("=")[0] for tag in tags.split(";")]:
337 newData[id] = newTag
338 for id, tag in newData.iteritems():
339 query = self.mySqlConnection.executeQuery("UPDATE '%s' SET tags = '%s' WHERE id = %i" % (self.name, tag, id))
340
341
342
343 def show(self):
344 """
345 Drop the content of the current table
346 """
347 query = self.mySqlConnection.executeQuery("SELECT * FROM '%s'" % (self.name))
348 print query.getLines()
349