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_head(self):
gsm = GSM(name='name', table=self.table1, metadata=self.metadata,
columns=self.columns1)
try:
gsm.head()
except Exception:
self.fail("GSM.head() raised error!")
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_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"]}
metadata_soft = ("!Sample_data = Normal\n"
"!Sample_name = SAMPLE1")
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())
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())
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_get_type(self):
gsm = GSM(
name="name",
table=self.table1,
metadata=self.metadata,
columns=self.columns1,
)
self.assertEqual(gsm.get_type(), None)
def test_get_metadata_attribute(self):
metadata = {'name': 'SAMPLE', 'samples': ["sam1", "sam2"]}
gsm = GSM(name='name', table=self.table1, metadata=self.metadata, columns=self.columns1)
gsm2 = GSM(name='name', table=self.table1, metadata=metadata, columns=self.columns1)
with self.assertRaises(TypeError):
gsm2.get_metadata_attribute('name')
self.assertEqual(gsm.get_metadata_attribute('name'), "SAMPLE")
self.assertEqual(gsm2.get_metadata_attribute('samples'), ["sam1", "sam2"])
with self.assertRaises(NoMetadataException):
gsm.get_metadata_attribute('dupa')
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 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_simple_data(self):
gsm = GSM(
name="name",
table=self.table1,
metadata=self.metadata,
columns=self.columns1,
)
self.assertEqual(gsm.table.loc[0, "a"], 1)
self.assertEqual(gsm.table.loc[1, "b"], 5)
def test_get_metadata_attribute(self):
metadata = {"name": "SAMPLE", "samples": ["sam1", "sam2"]}
gsm = GSM(
name="name",
table=self.table1,
metadata=self.metadata,
columns=self.columns1,
)
gsm2 = GSM(name="name",
table=self.table1,
metadata=metadata,
columns=self.columns1)
with self.assertRaises(TypeError):
gsm2.get_metadata_attribute("name")
self.assertEqual(gsm.get_metadata_attribute("name"), "SAMPLE")
self.assertEqual(gsm2.get_metadata_attribute("samples"),
["sam1", "sam2"])
with self.assertRaises(NoMetadataException):
gsm.get_metadata_attribute("dupa")
def test_creation_of_object(self):
with self.assertRaises(ValueError):
GSM(name='name',
table=['a'],
metadata=self.metadata,
columns=self.columns1)
with self.assertRaises(TypeError):
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_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())