def test_create(self):
"""Creates a new PrepTemplate"""
pt = PrepTemplate.create(self.metadata, self.new_raw_data)
# The returned object has the correct id
self.assertEqual(pt.id, 3)
# The relevant rows to common_prep_info have been added.
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.common_prep_info WHERE raw_data_id=3")
# raw_data_id, sample_id, center_name, center_project_name,
# ebi_submission_accession, ebi_study_accession, emp_status_id,
# data_type_id
exp = [[3, 'SKB8.640193', 'ANL', 'Test Project', None, None, 1, 2],
[3, 'SKD8.640184', 'ANL', 'Test Project', None, None, 1, 2],
[3, 'SKB7.640196', 'ANL', 'Test Project', None, None, 1, 2]]
self.assertEqual(sorted(obs), sorted(exp))
# The relevant rows have been added to the raw_data_prep_columns
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.raw_data_prep_columns WHERE raw_data_id=3")
# raw_data_id, column_name, column_type
exp = [[3, "str_column", "varchar"]]
self.assertEqual(obs, exp)
# The new table exists
self.assertTrue(exists_table("prep_3", self.conn_handler))
# The new table hosts the correct values
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.prep_3")
# sample_id, str_column
exp = [['SKB8.640193', "Value for sample 1"],
['SKD8.640184', "Value for sample 2"],
['SKB7.640196', "Value for sample 3"]]
self.assertEqual(sorted(obs), sorted(exp))
def test_create(self):
"""Creates a new PrepTemplate"""
pt = PrepTemplate.create(self.metadata, self.new_raw_data)
# The returned object has the correct id
self.assertEqual(pt.id, 3)
# The relevant rows to common_prep_info have been added.
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.common_prep_info WHERE raw_data_id=3")
# raw_data_id, sample_id, center_name, center_project_name,
# ebi_submission_accession, ebi_study_accession, emp_status_id,
# data_type_id
exp = [[3, 'SKB8.640193', 'ANL', 'Test Project', 1, 2],
[3, 'SKD8.640184', 'ANL', 'Test Project', 1, 2],
[3, 'SKB7.640196', 'ANL', 'Test Project', 1, 2]]
self.assertEqual(sorted(obs), sorted(exp))
# The relevant rows have been added to the raw_data_prep_columns
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.raw_data_prep_columns WHERE raw_data_id=3")
# raw_data_id, column_name, column_type
exp = [[3, 'str_column', 'varchar'],
[3, 'ebi_submission_accession', 'varchar']]
self.assertEqual(obs, exp)
# The new table exists
self.assertTrue(exists_table("prep_3", self.conn_handler))
# The new table hosts the correct values
obs = self.conn_handler.execute_fetchall("SELECT * FROM qiita.prep_3")
# sample_id, str_column
exp = [['SKB8.640193', "Value for sample 1", None],
['SKD8.640184', "Value for sample 2", None],
['SKB7.640196', "Value for sample 3", None]]
self.assertEqual(sorted(obs), sorted(exp))
def test_exists_table(self):
"""Correctly checks if a table exists"""
# True cases
self.assertTrue(exists_table("filepath", self.conn_handler))
self.assertTrue(exists_table("qiita_user", self.conn_handler))
self.assertTrue(exists_table("analysis", self.conn_handler))
self.assertTrue(exists_table("prep_1", self.conn_handler))
self.assertTrue(exists_table("sample_1", self.conn_handler))
# False cases
self.assertFalse(exists_table("sample_2", self.conn_handler))
self.assertFalse(exists_table("prep_2", self.conn_handler))
self.assertFalse(exists_table("foo_table", self.conn_handler))
self.assertFalse(exists_table("bar_table", self.conn_handler))
def test_exists_table(self):
"""Correctly checks if a table exists"""
# True cases
self.assertTrue(exists_table("filepath", self.conn_handler))
self.assertTrue(exists_table("qiita_user", self.conn_handler))
self.assertTrue(exists_table("analysis", self.conn_handler))
self.assertTrue(exists_table("prep_1", self.conn_handler))
self.assertTrue(exists_table("sample_1", self.conn_handler))
# False cases
self.assertFalse(exists_table("sample_2", self.conn_handler))
self.assertFalse(exists_table("prep_2", self.conn_handler))
self.assertFalse(exists_table("foo_table", self.conn_handler))
self.assertFalse(exists_table("bar_table", self.conn_handler))
def exists(cls, obj_id):
r"""Checks if already exists a MetadataTemplate for the provided object
Parameters
----------
obj_id : int
The id to test if it exists on the database
Returns
-------
bool
True if already exists. False otherwise.
"""
cls._check_subclass()
return exists_table(cls._table_name(obj_id), SQLConnectionHandler())
def test_create(self):
"""Creates a new SampleTemplate"""
st = SampleTemplate.create(self.metadata, self.new_study)
# The returned object has the correct id
self.assertEqual(st.id, 2)
# The relevant rows to required_sample_info have been added.
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.required_sample_info WHERE study_id=2")
# study_id sample_id physical_location has_physical_specimen
# has_extracted_data sample_type required_sample_info_status_id
# collection_timestamp host_subject_id description
exp = [[
2, "Sample1", "location1", True, True, "type1", 1,
datetime(2014, 5, 29, 12, 24, 51), "NotIdentified",
"Test Sample 1", 42.42, 41.41
],
[
2, "Sample2", "location1", True, True, "type1", 1,
datetime(2014, 5, 29, 12, 24, 51), "NotIdentified",
"Test Sample 2", 4.2, 1.1
],
[
2, "Sample3", "location1", True, True, "type1", 1,
datetime(2014, 5, 29, 12, 24, 51), "NotIdentified",
"Test Sample 3", 4.8, 4.41
]]
self.assertEqual(obs, exp)
# The relevant rows have been added to the study_sample_columns
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study_sample_columns WHERE study_id=2")
# study_id, column_name, column_type
exp = [[2, "str_column", "varchar"]]
self.assertEqual(obs, exp)
# The new table exists
self.assertTrue(exists_table("sample_2", self.conn_handler))
# The new table hosts the correct values
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.sample_2")
# sample_id, str_column
exp = [['Sample1', "Value for sample 1"],
['Sample2', "Value for sample 2"],
['Sample3', "Value for sample 3"]]
self.assertEqual(obs, exp)
def test_create(self):
"""Creates a new SampleTemplate"""
st = SampleTemplate.create(self.metadata, self.new_study)
# The returned object has the correct id
self.assertEqual(st.id, 2)
# The relevant rows to required_sample_info have been added.
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.required_sample_info WHERE study_id=2")
# study_id sample_id physical_location has_physical_specimen
# has_extracted_data sample_type required_sample_info_status_id
# collection_timestamp host_subject_id description
exp = [[2, "Sample1", "location1", True, True, "type1", 1,
datetime(2014, 5, 29, 12, 24, 51), "NotIdentified",
"Test Sample 1"],
[2, "Sample2", "location1", True, True, "type1", 1,
datetime(2014, 5, 29, 12, 24, 51), "NotIdentified",
"Test Sample 2"],
[2, "Sample3", "location1", True, True, "type1", 1,
datetime(2014, 5, 29, 12, 24, 51), "NotIdentified",
"Test Sample 3"]]
self.assertEqual(obs, exp)
# The relevant rows have been added to the study_sample_columns
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.study_sample_columns WHERE study_id=2")
# study_id, column_name, column_type
exp = [[2, "str_column", "varchar"]]
self.assertEqual(obs, exp)
# The new table exists
self.assertTrue(exists_table("sample_2", self.conn_handler))
# The new table hosts the correct values
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.sample_2")
# sample_id, str_column
exp = [['Sample1', "Value for sample 1"],
['Sample2', "Value for sample 2"],
['Sample3', "Value for sample 3"]]
self.assertEqual(obs, exp)
