def setUp(self):
self.table_basename = 'biomdb_tests'
self.biomdb = BiomDB(table_basename=self.table_basename)
class BiomDBTests(TestCase):
def setUp(self):
self.table_basename = 'biomdb_tests'
self.biomdb = BiomDB(table_basename=self.table_basename)
def tearDown(self):
self.biomdb.dropTable()
def test_tmp_table_count(self):
"""Count the number of tmp tables in the db"""
exp = 0
obs = self.biomdb._tmp_table_count()
self.assertEqual(obs, exp)
self.assertEqual(len(self.biomdb._tmp_tables), 0)
newtable = self.biomdb.createTempTable()
exp = 1
obs = self.biomdb._tmp_table_count()
self.assertEqual(obs,exp)
self.assertEqual(len(self.biomdb._tmp_tables), 1)
def test_get_new_tableid(self):
"""Get a new table id"""
exp = '_'.join([self.table_basename, '1'])
obs = self.biomdb._get_new_tableid()
self.assertEqual(obs,exp)
def test_createTempTable_empty(self):
"""Create a new temporary table"""
exp_name = '_'.join([self.table_basename, '1'])
obs_name = self.biomdb.createTempTable()
cursor = self.biomdb.con.cursor()
cursor.execute("SELECT COUNT(*) FROM %s" % exp_name)
exp = ((0,),)
obs = cursor.fetchall()
self.assertEqual(obs,exp)
def test_createTempTable_fromexisting(self):
"""Creates a new temporary table from another table"""
# create tmp table and put stuff in it
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, '1','a',10)
self.biomdb.setItem(table, '10','c',20)
new_table = self.biomdb.createTempTable(from_table=table)
cursor = self.biomdb.con.cursor()
cursor.execute("select * from %s" % new_table)
obs = sorted(cursor.fetchall())
exp = [('1','a',10), ('10','c',20)]
self.assertEqual(obs,exp)
def test_createTempTable_fromsamples(self):
"""Creates a new temporary table from another table samples"""
# create tmp table and put stuff in it
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, '1','a',10)
self.biomdb.setItem(table, '10','a',20)
self.biomdb.setItem(table, '10','e',30)
new_table = self.biomdb.createTempTable(from_table=table,
from_samples=['a'])
cursor = self.biomdb.con.cursor()
cursor.execute("select * from %s" % new_table)
obs = sorted(cursor.fetchall())
exp = [('1','a',10),('10','a',20)]
self.assertEqual(obs,exp)
new_table = self.biomdb.createTempTable(table, ['x'])
cursor = self.biomdb.con.cursor()
cursor.execute("select * from %s" % new_table)
obs = sorted(cursor.fetchall())
exp = []
self.assertEqual(obs,exp)
def test_createTempTable_fromobs(self):
"""Creates a new temporary table from another table obs"""
# create tmp table and put stuff in it
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, '1','a',10)
self.biomdb.setItem(table, '10','a',20)
self.biomdb.setItem(table, '10','e',30)
new_table = self.biomdb.createTempTable(from_table=table,
from_obs=['10'])
cursor = self.biomdb.con.cursor()
cursor.execute("select * from %s" % new_table)
obs = sorted(cursor.fetchall())
exp = [('10','a',20),('10','e',30)]
self.assertEqual(obs,exp)
new_table = self.biomdb.createTempTable(table, None, from_obs=['x'])
cursor = self.biomdb.con.cursor()
cursor.execute("select * from %s" % new_table)
obs = sorted(cursor.fetchall())
exp = []
self.assertEqual(obs,exp)
def test_createTempTable_bothaxes(self):
"""Bail if both axes are specified"""
# create tmp table and put stuff in it
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, '1','a',10)
self.biomdb.setItem(table, '10','a',20)
self.biomdb.setItem(table, '10','e',30)
self.assertRaises(ValueError, self.biomdb.createTempTable, table, ['a'],
['10'])
def test_dropTable(self):
"""Drop temporary table or tables"""
table = self.biomdb.createTempTable()
self.biomdb.dropTable(table)
self.assertRaises(ProgrammingError,self.biomdb.setItem,table,'a','b',10)
self.assertRaises(OperationalError, self.biomdb.dropTable, table)
def test_getItem(self):
"""gets an item"""
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, 'a','b',10)
self.assertEqual(self.biomdb.getItem(table, 'a','b'), 10)
self.assertEqual(self.biomdb.getItem(table, 'x','y'), 0)
def test_setItem(self):
"""sets an item"""
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, 'a','b',10)
self.assertEqual(self.biomdb.getItem(table, 'a','b'), 10)
self.biomdb.setItem(table, 'a','b', 100)
self.assertEqual(self.biomdb.getItem(table, 'a','b'), 100)
cursor = self.biomdb.con.cursor()
cursor.execute("select count(*) from %s" % table)
exp = ((1L,),)
obs = cursor.fetchall()
self.assertEqual(obs,exp)
def getSampleByObs(self):
"""Gets all samples associated to an observation"""
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, 'a','1',10)
self.biomdb.setItem(table, 'a','2',20)
self.biomdb.setItem(table, 'x','3',30)
self.biomdb.setItem(table, 'x','4',40)
exp = (('a','1',10), ('a','2',20))
obs = sorted(self.biomdb.getSampleByObs(table, 'a'))
self.assertEqual(obs,exp)
exp = ()
obs = self.biomdb.getSampleByObs(table,'asasd')
self.assertEqual(obs,exp)
def getObsBySample(self):
"""Gets all observations associated to a sample"""
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, 'a','1',10)
self.biomdb.setItem(table, 'a','2',20)
self.biomdb.setItem(table, 'x','2',30)
self.biomdb.setItem(table, 'x','4',40)
exp = (('a','2',20), ('x','2',30))
obs = sorted(self.biomdb.getObsBySample(table, '2'))
self.assertEqual(obs,exp)
exp = ()
obs = self.biomdb.getObsBySample(table,'asasd')
self.assertEqual(obs,exp)
def test_deleteItem(self):
"""deletes an item"""
table = self.biomdb.createTempTable()
self.biomdb.setItem(table, 'a','b',10)
self.biomdb.deleteItem(table, 'a','b')
self.assertEqual(self.biomdb.getItem(table,'a','b'), 0)
# do it once more... dont complain if nothing to delete
self.biomdb.deleteItem(table, 'a','b')
self.assertEqual(self.biomdb.getItem(table,'a','b'), 0)
def test_tableEquality_eq(self):
"""checks if tables are equal"""
table1 = self.biomdb.createTempTable()
self.biomdb.setItem(table1, '1','b',10)
self.biomdb.setItem(table1, '2','b',20)
self.biomdb.setItem(table1, '3','b',30)
table2 = self.biomdb.createTempTable()
self.biomdb.setItem(table2, '1','b',10)
self.biomdb.setItem(table2, '2','b',20)
self.biomdb.setItem(table2, '3','b',30)
self.assertTrue(self.biomdb.tableEquality(table1, table2))
def test_tableEquality_eq_value(self):
"""checks if tables are equal"""
table1 = self.biomdb.createTempTable()
self.biomdb.setItem(table1, '1','b',10)
self.biomdb.setItem(table1, '2','b',20)
self.biomdb.setItem(table1, '3','b',30)
table2 = self.biomdb.createTempTable()
self.biomdb.setItem(table2, '1','b',10)
self.biomdb.setItem(table2, '2','b',20)
self.biomdb.setItem(table2, '3','b',-30)
self.assertFalse(self.biomdb.tableEquality(table1, table2))
def test_tableEquality_eq_label(self):
"""checks if tables are equal"""
table1 = self.biomdb.createTempTable()
self.biomdb.setItem(table1, '1','b',10)
self.biomdb.setItem(table1, '2','b',20)
self.biomdb.setItem(table1, '3','b',30)
table2 = self.biomdb.createTempTable()
self.biomdb.setItem(table2, '1','b',10)
self.biomdb.setItem(table2, '2','b',20)
self.biomdb.setItem(table2, 'x','b',30)
self.assertFalse(self.biomdb.tableEquality(table1, table2))