tests/sqlsequence_test.py

   1 # test will be skipped if MySqlDB is unavailable
   2
   3 import unittest, string
   4 from testlib import testutil, SkipTest, PygrTestProgram
   5 from pygr import sqlgraph, seqdb, classutil, logger
   6
   7 class SQLSequence_Test(unittest.TestCase):
   8     '''Basic SQL sequence class tests
   9
  10     This test setup uses the common (?) method of having the
  11     SQLSequence objects created by a SQLTable object rather than
  12     instantiating the SQLSequence objects directly.
  13     '''
  14     def setUp(self, serverInfo=None, dbname='test.sqlsequence_test'):
  15         if not testutil.mysql_enabled():
  16             raise SkipTest, "no MySQL installed"
  17
  18         createTable = """\
  19         CREATE TABLE %s
  20              (primary_id INTEGER PRIMARY KEY %%(AUTO_INCREMENT)s, sequence TEXT)
  21         """ % dbname
  22
  23         self.db = sqlgraph.SQLTable(dbname, serverInfo=serverInfo,
  24                                     dropIfExists=True,
  25                                     createTable=createTable,
  26                                     attrAlias=dict(seq='sequence'))
  27
  28         self.db.cursor.execute("""\
  29         INSERT INTO %s (sequence)
  30               VALUES ('CACCCTGCCCCATCTCCCCAGCCTGGCCCCTCGTGTCTCAGAACCCTCGGGGGGAGGCACAGAAGCCTTCGGGG')
  31         """ % dbname)
  32
  33         self.db.cursor.execute("""\
  34         INSERT INTO %s (sequence)
  35               VALUES ('GAAAGAAAGAAAGAAAGAAAGAAAGAGAGAGAGAGAGACAGAAG')
  36         """ % dbname)
  37
  38         class DNASeqRow(seqdb.DNASQLSequence):
  39             def __len__(self): # just speed optimization
  40                 return self._select('length(sequence)') # SQL SELECT expression
  41
  42         # force the table object to return DNASeqRow objects
  43         self.db.objclass(DNASeqRow)
  44
  45         self.row1 = self.db[1]
  46         self.row2 = self.db[2]
  47         self.EQ = self.assertEqual
  48
  49     def tearDown(self):
  50         self.db.cursor.execute('drop table if exists test.sqlsequence_test')
  51
  52     def test_print(self):
  53         "Testing identities"
  54         self.EQ(str(self.row2), 'GAAAGAAAGAAAGAAAGAAAGAAAGAGAGAGAGAGAGACAGAAG')
  55         self.EQ(repr(self.row2), '2[0:44]')
  56
  57     def test_len(self):
  58         "Testing lengths"
  59         self.EQ(len(self.row2), 44)
  60
  61     def test_strslice(self):
  62         "Testing slices"
  63         self.EQ(self.row2.strslice(3,10), 'AGAAAGA')
  64
  65     def init_subclass_test(self):
  66         "Testing subclassing"
  67         self.row2._init_subclass(self.db)
  68
  69 class SQLiteSequence_Test(testutil.SQLite_Mixin, SQLSequence_Test):
  70     def sqlite_load(self):
  71         SQLSequence_Test.setUp(self, self.serverInfo, 'sqlsequence_test')
  72
  73 def get_suite():
  74     "Returns the testsuite"
  75     tests = []
  76
  77     # detect mysql
  78     if testutil.mysql_enabled():
  79         tests.append(SQLSequence_Test)
  80     else:
  81         testutil.info('*** skipping SQLSequence_Test')
  82     if testutil.sqlite_enabled():
  83         tests.append(SQLiteSequence_Test)
  84     else:
  85         testutil.info('*** skipping SQLSequence_Test')
  86
  87     return testutil.make_suite(tests)
  88
  89 if __name__ == '__main__':
  90     PygrTestProgram(verbosity=2)