def test_create(self):
"""Correctly creates the rows in the DB for the reference"""
# Check that the returned object has the correct id
obs = Reference.create(self.name, self.version, self.seqs_fp,
self.tax_fp, self.tree_fp)
self.assertEqual(obs.id, 2)
# Check that the information on the database is correct
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.reference WHERE reference_id=2")
exp = [[2, self.name, self.version, 15, 16, 17]]
self.assertEqual(obs, exp)
# Check that the filepaths have been correctly added to the DB
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.filepath WHERE filepath_id=15 or "
"filepath_id=16 or filepath_id=17")
exp_seq = join(
self.db_dir,
"%s_%s_%s" % (self.name, self.version, basename(self.seqs_fp)))
exp_tax = join(
self.db_dir,
"%s_%s_%s" % (self.name, self.version, basename(self.tax_fp)))
exp_tree = join(
self.db_dir,
"%s_%s_%s" % (self.name, self.version, basename(self.tree_fp)))
exp = [[15, exp_seq, 9, '0', 1], [16, exp_tax, 10, '0', 1],
[17, exp_tree, 11, '0', 1]]
self.assertEqual(obs, exp)
def test_create(self):
"""Correctly creates the rows in the DB for the reference"""
# Check that the returned object has the correct id
obs = Reference.create(self.name, self.version, self.seqs_fp,
self.tax_fp, self.tree_fp)
self.assertEqual(obs.id, 2)
# Check that the information on the database is correct
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.reference WHERE reference_id=2")
exp = [[2, self.name, self.version, 19, 20, 21]]
self.assertEqual(obs, exp)
# Check that the filepaths have been correctly added to the DB
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.filepath WHERE filepath_id=19 or "
"filepath_id=20 or filepath_id=21")
exp_seq = "%s_%s_%s" % (self.name, self.version,
basename(self.seqs_fp))
exp_tax = "%s_%s_%s" % (self.name, self.version,
basename(self.tax_fp))
exp_tree = "%s_%s_%s" % (self.name, self.version,
basename(self.tree_fp))
exp = [[19, exp_seq, 10, '0', 1, 6],
[20, exp_tax, 11, '0', 1, 6],
[21, exp_tree, 12, '0', 1, 6]]
self.assertEqual(obs, exp)
def test_purge_filepaths_null_cols(self):
# For more details about the source of the issue that motivates this
# test: http://www.depesz.com/2008/08/13/nulls-vs-not-in/
# In the current set up, the only place where we can actually have a
# null value in a filepath id is in the reference table. Add a new
# reference without tree and taxonomy:
fd, seqs_fp = mkstemp(suffix="_seqs.fna")
close(fd)
ref = Reference.create("null_db", "13_2", seqs_fp)
self.files_to_remove.append(ref.sequence_fp)
self._common_purge_filpeaths_test()
def test_purge_filepaths_null_cols(self):
# For more details about the source of the issue that motivates this
# test: http://www.depesz.com/2008/08/13/nulls-vs-not-in/
# In the current set up, the only place where we can actually have a
# null value in a filepath id is in the reference table. Add a new
# reference without tree and taxonomy:
fd, seqs_fp = mkstemp(suffix="_seqs.fna")
close(fd)
ref = Reference.create("null_db", "13_2", seqs_fp)
self.files_to_remove.append(ref.sequence_fp)
self._common_purge_filpeaths_test()