tests/sqltable_test.py

   1 import os, unittest
   2 from testlib import testutil, PygrTestProgram, SkipTest
   3 from pygr.sqlgraph import SQLTable, SQLTableNoCache,\
   4      MapView, GraphView, DBServerInfo, import_sqlite
   5 from pygr import logger
   6
   7 class SQLTable_Setup(unittest.TestCase):
   8     tableClass = SQLTable
   9     def __init__(self, *args, **kwargs):
  10         unittest.TestCase.__init__(self, *args, **kwargs)
  11         self.serverInfo = DBServerInfo() # share conn for all tests
  12     def setUp(self):
  13         try:
  14             self.load_data(writeable=self.writeable)
  15         except ImportError:
  16             raise SkipTest('missing MySQLdb module?')
  17     def load_data(self, tableName='test.sqltable_test', writeable=False):
  18         'create 3 tables and load 9 rows for our tests'
  19         self.tableName = tableName
  20         self.joinTable1 = joinTable1 = tableName + '1'
  21         self.joinTable2 = joinTable2 = tableName + '2'
  22         createTable = """\
  23         CREATE TABLE %s (primary_id INTEGER PRIMARY KEY %%(AUTO_INCREMENT)s, seq_id TEXT, start INTEGER, stop INTEGER)
  24         """ % tableName
  25         self.db = self.tableClass(tableName, dropIfExists=True,
  26                                   serverInfo=self.serverInfo,
  27                                   createTable=createTable,
  28                                   writeable=writeable)
  29         self.sourceDB = self.tableClass(joinTable1, serverInfo=self.serverInfo,
  30                                         dropIfExists=True, createTable="""\
  31         CREATE TABLE %s (my_id INTEGER PRIMARY KEY,
  32               other_id VARCHAR(16))
  33         """ % joinTable1)
  34         self.targetDB = self.tableClass(joinTable2, serverInfo=self.serverInfo,
  35                                         dropIfExists=True, createTable="""\
  36         CREATE TABLE %s (third_id INTEGER PRIMARY KEY,
  37               other_id VARCHAR(16))
  38         """ % joinTable2)
  39         sql = """
  40             INSERT INTO %s (seq_id, start, stop) VALUES ('seq1', 0, 10)
  41             INSERT INTO %s (seq_id, start, stop) VALUES ('seq2', 5, 15)
  42             INSERT INTO %s VALUES (2,'seq2')
  43             INSERT INTO %s VALUES (3,'seq3')
  44             INSERT INTO %s VALUES (4,'seq4')
  45             INSERT INTO %s VALUES (7, 'seq2')
  46             INSERT INTO %s VALUES (99, 'seq3')
  47             INSERT INTO %s VALUES (6, 'seq4')
  48             INSERT INTO %s VALUES (8, 'seq4')
  49         """ % tuple(([tableName]*2) + ([joinTable1]*3) + ([joinTable2]*4))
  50         for line in sql.strip().splitlines(): # insert our test data
  51             self.db.cursor.execute(line.strip())
  52     def tearDown(self):
  53         self.db.cursor.execute('drop table if exists %s' % self.tableName)
  54         self.db.cursor.execute('drop table if exists %s' % self.joinTable1)
  55         self.db.cursor.execute('drop table if exists %s' % self.joinTable2)
  56         self.serverInfo.close()
  57
  58 class SQLTable_Test(SQLTable_Setup):
  59     writeable = False # read-only database interface
  60     def test_keys(self):
  61         k = self.db.keys()
  62         k.sort()
  63         assert k == [1, 2]
  64     def test_len(self):
  65         assert len(self.db) == len(self.db.keys())
  66     def test_contains(self):
  67         assert 1 in self.db
  68         assert 2 in self.db
  69         assert 'foo' not in self.db
  70     def test_has_key(self):
  71         assert self.db.has_key(1)
  72         assert self.db.has_key(2)
  73         assert not self.db.has_key('foo')
  74     def test_get(self):
  75         assert self.db.get('foo') is None
  76         assert self.db.get(1) == self.db[1]
  77         assert self.db.get(2) == self.db[2]
  78     def test_items(self):
  79         i = [ k for (k,v) in self.db.items() ]
  80         i.sort()
  81         assert i == [1, 2]
  82     def test_iterkeys(self):
  83         kk = self.db.keys()
  84         kk.sort()
  85         ik = list(self.db.iterkeys())
  86         ik.sort()
  87         assert kk == ik
  88     def test_itervalues(self):
  89         kv = self.db.values()
  90         kv.sort()
  91         iv = list(self.db.itervalues())
  92         iv.sort()
  93         assert kv == iv
  94     def test_itervalues_long(self):
  95         """test iterator isolation from queries run inside iterator loop """
  96         sql = 'insert into %s (start) values (1)' % self.tableName
  97         for i in range(40000): # insert 40000 rows
  98             self.db.cursor.execute(sql)
  99         iv = []
 100         for o in self.db.itervalues():
 101             status = 99 in self.db # make it do a query inside iterator loop
 102             iv.append(o.id)
 103         kv = [o.id for o in self.db.values()]
 104         assert len(kv) == len(iv)
 105         assert kv == iv
 106     def test_iteritems(self):
 107         ki = self.db.items()
 108         ki.sort()
 109         ii = list(self.db.iteritems())
 110         ii.sort()
 111         assert ki == ii
 112     def test_readonly(self):
 113         'test error handling of write attempts to read-only DB'
 114         try:
 115             self.db.new(seq_id='freddy', start=3000, stop=4500)
 116             raise AssertionError('failed to trap attempt to write to db')
 117         except ValueError:
 118             pass
 119         o = self.db[1]
 120         try:
 121             self.db[33] = o
 122             raise AssertionError('failed to trap attempt to write to db')
 123         except ValueError:
 124             pass
 125         try:
 126             del self.db[2]
 127             raise AssertionError('failed to trap attempt to write to db')
 128         except ValueError:
 129             pass
 130
 131     ### @CTB need to test write access
 132     def test_mapview(self):
 133         'test MapView of SQL join'
 134         m = MapView(self.sourceDB, self.targetDB,"""\
 135         SELECT t2.third_id FROM %s t1, %s t2
 136            WHERE t1.my_id=%%s and t1.other_id=t2.other_id
 137         """ % (self.joinTable1,self.joinTable2), serverInfo=self.serverInfo)
 138         assert m[self.sourceDB[2]] == self.targetDB[7]
 139         assert m[self.sourceDB[3]] == self.targetDB[99]
 140         assert self.sourceDB[2] in m
 141         try:
 142             d = m[self.sourceDB[4]]
 143             raise AssertionError('failed to trap non-unique mapping')
 144         except KeyError:
 145             pass
 146         try:
 147             r = ~m
 148             raise AssertionError('failed to trap non-invertible mapping')
 149         except ValueError:
 150             pass
 151     def test_mapview_inverse(self):
 152         'test inverse MapView of SQL join'
 153         m = MapView(self.sourceDB, self.targetDB,"""\
 154         SELECT t2.third_id FROM %s t1, %s t2
 155            WHERE t1.my_id=%%s and t1.other_id=t2.other_id
 156         """ % (self.joinTable1,self.joinTable2), serverInfo=self.serverInfo,
 157                     inverseSQL="""\
 158         SELECT t1.my_id FROM %s t1, %s t2
 159            WHERE t2.third_id=%%s and t1.other_id=t2.other_id
 160         """ % (self.joinTable1,self.joinTable2))
 161         assert m[self.sourceDB[2]] == self.targetDB[7]
 162         assert m[self.sourceDB[3]] == self.targetDB[99]
 163         assert self.sourceDB[2] in m
 164         r = ~m # get the inverse
 165         assert self.sourceDB[2] == r[self.targetDB[7]]
 166         assert self.sourceDB[3] == r[self.targetDB[99]]
 167         assert self.targetDB[7] in r
 168
 169         try:
 170             d = m[self.sourceDB[4]]
 171             raise AssertionError('failed to trap non-unique mapping')
 172         except KeyError:
 173             pass
 174     def test_graphview(self):
 175         'test GraphView of SQL join'
 176         m = GraphView(self.sourceDB, self.targetDB,"""\
 177         SELECT t2.third_id FROM %s t1, %s t2
 178            WHERE t1.my_id=%%s and t1.other_id=t2.other_id
 179         """ % (self.joinTable1,self.joinTable2), serverInfo=self.serverInfo)
 180         d = m[self.sourceDB[4]]
 181         assert len(d) == 2
 182         assert self.targetDB[6] in d and self.targetDB[8] in d
 183         assert self.sourceDB[2] in m
 184
 185 class SQLiteBase(testutil.SQLite_Mixin):
 186     def sqlite_load(self):
 187         self.load_data('sqltable_test', writeable=self.writeable)
 188
 189 class SQLiteTable_Test(SQLiteBase, SQLTable_Test):
 190     pass
 191
 192 ## class SQLitePickle_Test(SQLiteTable_Test):
 193 ##     def setUp(self):
 194 ##         """Pickle / unpickle our serverInfo before trying to use it """
 195 ##         SQLiteTable_Test.setUp(self)
 196 ##         self.serverInfo.close()
 197 ##         import pickle
 198 ##         s = pickle.dumps(self.serverInfo)
 199 ##         del self.serverInfo
 200 ##         self.serverInfo = pickle.loads(s)
 201 ##         self.db = self.tableClass(self.tableName, serverInfo=self.serverInfo)
 202 ##         self.sourceDB = self.tableClass(self.joinTable1,
 203 ##                                         serverInfo=self.serverInfo)
 204 ##         self.targetDB = self.tableClass(self.joinTable2,
 205 ##                                         serverInfo=self.serverInfo)
 206
 207 class SQLTable_NoCache_Test(SQLTable_Test):
 208     tableClass = SQLTableNoCache
 209
 210 class SQLiteTable_NoCache_Test(SQLiteTable_Test):
 211     tableClass = SQLTableNoCache
 212
 213 class SQLTableRW_Test(SQLTable_Setup):
 214     'test write operations'
 215     writeable = True
 216     def test_new(self):
 217         'test row creation with auto inc ID'
 218         n = len(self.db)
 219         o = self.db.new(seq_id='freddy', start=3000, stop=4500)
 220         assert len(self.db) == n + 1
 221         t = self.tableClass(self.tableName,
 222                             serverInfo=self.serverInfo) # requery the db
 223         result = t[o.id]
 224         assert result.seq_id == 'freddy' and result.start==3000 \
 225                and result.stop==4500
 226     def test_new2(self):
 227         'check row creation with specified ID'
 228         n = len(self.db)
 229         o = self.db.new(id=99, seq_id='jeff', start=3000, stop=4500)
 230         assert len(self.db) == n + 1
 231         assert o.id == 99
 232         t = self.tableClass(self.tableName,
 233                             serverInfo=self.serverInfo) # requery the db
 234         result = t[99]
 235         assert result.seq_id == 'jeff' and result.start==3000 \
 236                and result.stop==4500
 237     def test_attr(self):
 238         'test changing an attr value'
 239         o = self.db[2]
 240         assert o.seq_id == 'seq2'
 241         o.seq_id = 'newval' # overwrite this attribute
 242         assert o.seq_id == 'newval' # check cached value
 243         t = self.tableClass(self.tableName,
 244                             serverInfo=self.serverInfo) # requery the db
 245         result = t[2]
 246         assert result.seq_id == 'newval'
 247     def test_delitem(self):
 248         'test deletion of a row'
 249         n = len(self.db)
 250         del self.db[1]
 251         assert len(self.db) == n - 1
 252         try:
 253             result = self.db[1]
 254             raise AssertionError('old ID still exists!')
 255         except KeyError:
 256             pass
 257     def test_setitem(self):
 258         'test assigning new ID to existing object'
 259         o = self.db.new(id=17, seq_id='bob', start=2000, stop=2500)
 260         self.db[13] = o
 261         assert o.id == 13
 262         try:
 263             result = self.db[17]
 264             raise AssertionError('old ID still exists!')
 265         except KeyError:
 266             pass
 267         t = self.tableClass(self.tableName,
 268                             serverInfo=self.serverInfo) # requery the db
 269         result = t[13]
 270         assert result.seq_id == 'bob' and result.start==2000 \
 271                and result.stop==2500
 272         try:
 273             result = t[17]
 274             raise AssertionError('old ID still exists!')
 275         except KeyError:
 276             pass
 277
 278
 279 class SQLiteTableRW_Test(SQLiteBase, SQLTableRW_Test):
 280     pass
 281
 282 class SQLTableRW_NoCache_Test(SQLTableRW_Test):
 283     tableClass = SQLTableNoCache
 284
 285 class SQLiteTableRW_NoCache_Test(SQLiteTableRW_Test):
 286     tableClass = SQLTableNoCache
 287
 288 class Ensembl_Test(unittest.TestCase):
 289
 290     def setUp(self):
 291         # test will be skipped if mysql module or ensembldb server unavailable
 292
 293         logger.debug('accessing ensembldb.ensembl.org')
 294         conn = DBServerInfo(host='ensembldb.ensembl.org', user='anonymous',
 295                             passwd='')
 296         try:
 297             translationDB = SQLTable('homo_sapiens_core_47_36i.translation',
 298                                      serverInfo=conn)
 299             exonDB = SQLTable('homo_sapiens_core_47_36i.exon', serverInfo=conn)
 300         except ImportError,e:
 301             raise SkipTest(e)
 302
 303         sql_statement = '''SELECT t3.exon_id FROM
 304 homo_sapiens_core_47_36i.translation AS tr,
 305 homo_sapiens_core_47_36i.exon_transcript AS t1,
 306 homo_sapiens_core_47_36i.exon_transcript AS t2,
 307 homo_sapiens_core_47_36i.exon_transcript AS t3 WHERE tr.translation_id = %s
 308 AND tr.transcript_id = t1.transcript_id AND t1.transcript_id =
 309 t2.transcript_id AND t2.transcript_id = t3.transcript_id AND t1.exon_id =
 310 tr.start_exon_id AND t2.exon_id = tr.end_exon_id AND t3.rank >= t1.rank AND
 311 t3.rank <= t2.rank ORDER BY t3.rank
 312             '''
 313         self.translationExons = GraphView(translationDB, exonDB,
 314                                           sql_statement, serverInfo=conn)
 315         self.translation = translationDB[15121]
 316
 317     def test_orderBy(self):
 318         "Ensemble access, test order by"
 319         'test issue 53: ensure that the ORDER BY results are correct'
 320         exons = self.translationExons[self.translation] # do the query
 321         result = [e.id for e in exons]
 322         correct = [95160,95020,95035,95050,95059,95069,95081,95088,95101,
 323                    95110,95172]
 324         self.assertEqual(result, correct) # make sure the exact order matches
 325
 326
 327 if __name__ == '__main__':
 328     PygrTestProgram(verbosity=2)