def test_to_soft(self): gsm = GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns1) soft = ("^SAMPLE = name\n" "!Sample_name = SAMPLE\n" "#a = first column\n" "#b = second column\n" "#c = third column\n" "!sample_table_begin\n" "a\tb\tc\n" "1\t2\t3\n" "4\t5\t6\n" "!sample_table_end") self.assertEqual(gsm._get_object_as_soft(), soft)
def setUp(self): self.header1 = ['a', 'b', 'c'] self.header2 = ['a', 'b', 'd'] self.columns_desc = [['first column'], ['second column'], ['third column']] self.data = [[1, 2, 3], [4, 5, 6]] self.table1 = DataFrame(self.data, columns=self.header1) self.table2 = DataFrame(self.data, columns=self.header2) self.columns1 = DataFrame(self.columns_desc, self.header1, columns=['description']) self.columns2 = DataFrame(self.columns_desc, self.header2, columns=['description']) self.metadata = {'name': 'PLATFORM'} self.gpl = GPL(name='name', table=self.table1, metadata=self.metadata, columns=self.columns1) self.gsm1 = GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns1) self.gsm2 = GSM(name='name', table=self.table2, metadata=self.metadata, columns=self.columns2) self.gsms = {'a': self.gsm1, 'b': self.gsm2} self.gpls = {'a': self.gpl}
def test_get_table_as_string(self): gsm = GSM( name="name", table=self.table1, metadata=self.metadata, columns=self.columns1, ) table = ("!sample_table_begin\n" "a\tb\tc\n" "1\t2\t3\n" "4\t5\t6\n" "!sample_table_end") self.assertEqual(gsm._get_table_as_string(), table)
def test_creation_of_object(self): with self.assertRaises(ValueError): GSM(name='name', table=['a'], metadata=self.metadata, columns=self.columns1) with self.assertRaises(ValueError): GSM(name='name', table=self.table1, metadata=[], columns=self.columns1) with self.assertRaises(ValueError): GSM(name='name', table=self.table1, metadata=self.metadata, columns=[]) with self.assertRaises(DataIncompatibilityException): GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns2) with self.assertRaises(ValueError): GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns_no_desc) GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns1)
def test_metadata_as_string(self): metadata = {'name': ['SAMPLE1'], 'data': ["Normal"]} metadata_soft = ("!Sample_data = Normal\n" "!Sample_name = SAMPLE1") gsm = GSM(name='name', table=self.table1, metadata=metadata, columns=self.columns1) self.assertEqual(gsm._get_metadata_as_string(), metadata_soft)
def test_get_type(self): gsm = GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns1) self.assertEqual(gsm.get_type(), None)
def test_simple_data(self): gsm = GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns1) self.assertEqual(gsm.table.ix[0, 'a'], 1) self.assertEqual(gsm.table.ix[1, 'b'], 5)
def test_get_columns_as_string(self): gsm = GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns1) columns = ("#a = first column\n" "#b = second column\n" "#c = third column") self.assertEqual(gsm._get_columns_as_string(), columns)
def test_metadata_as_string(self): metadata = {'name': ['SAMPLE1'], 'data': ["Normal"]} gsm = GSM(name='name', table=self.table1, metadata=metadata, columns=self.columns1) self.assertIn("!Sample_data = Normal", gsm._get_metadata_as_string()) self.assertIn("!Sample_name = SAMPLE1", gsm._get_metadata_as_string())