def test_update_preprocessed_data_from_cmd(self):
exp_ppd = PreprocessedData(Study(1).preprocessed_data()[0])
exp_fps = exp_ppd.get_filepaths()
# The original paths mush exist, but they're not included in the test
# so create them here
for _, fp, _ in exp_fps:
with open(fp, 'w') as f:
f.write("")
next_fp_id = get_count('qiita.filepath') + 1
exp_fps.append(
(next_fp_id,
join(self.db_ppd_dir, "%s_split_library_log.txt" % exp_ppd.id),
'log'))
ppd = update_preprocessed_data_from_cmd(self.test_slo, 1)
# Check that the modified preprocessed data is the correct one
self.assertEqual(ppd.id, exp_ppd.id)
# Check that the filepaths returned are correct
# We need to sort the list returned from the db because the ordering
# on that list is based on db modification time, rather than id
obs_fps = sorted(ppd.get_filepaths())
self.assertEqual(obs_fps, sorted(exp_fps))
# Check that the checksums have been updated
sql = "SELECT checksum FROM qiita.filepath WHERE filepath_id=%s"
# Checksum of the fasta file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[0][0],))[0]
self.assertEqual(obs_checksum, '3532748626')
# Checksum of the fastq file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[1][0],))[0]
self.assertEqual(obs_checksum, '2958832064')
# Checksum of the demux file
# The checksum is generated dynamically, so the checksum changes
# We are going to test that the checksum is not the one that was
# before, which corresponds to an empty file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[2][0],))[0]
self.assertTrue(isinstance(obs_checksum, str))
self.assertNotEqual(obs_checksum, '852952723')
self.assertTrue(len(obs_checksum) > 0)
# Checksum of the log file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[3][0],))[0]
self.assertEqual(obs_checksum, '626839734')
def test_update_preprocessed_data_from_cmd_ppd(self):
exp_ppd = PreprocessedData(2)
next_fp_id = get_count('qiita.filepath') + 1
exp_fps = []
path_builder = partial(join, self.db_ppd_dir)
suffix_types = [("seqs.fna", "preprocessed_fasta"),
("seqs.fastq", "preprocessed_fastq"),
("seqs.demux", "preprocessed_demux"),
("split_library_log.txt", "log")]
for id_, vals in enumerate(suffix_types, start=next_fp_id):
suffix, fp_type = vals
exp_fps.append(
(id_, path_builder("%s_%s" % (exp_ppd.id, suffix)), fp_type))
ppd = update_preprocessed_data_from_cmd(self.test_slo, 1, 2)
# Check that the modified preprocessed data is the correct one
self.assertEqual(ppd.id, exp_ppd.id)
# Check that the filepaths returned are correct
# We need to sort the list returned from the db because the ordering
# on that list is based on db modification time, rather than id
obs_fps = sorted(ppd.get_filepaths())
self.assertEqual(obs_fps, exp_fps)
# Check that the checksums have been updated
sql = "SELECT checksum FROM qiita.filepath WHERE filepath_id=%s"
# Checksum of the fasta file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[0][0],))[0]
self.assertEqual(obs_checksum, '3532748626')
# Checksum of the fastq file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[1][0],))[0]
self.assertEqual(obs_checksum, '2958832064')
# Checksum of the demux file
# The checksum is generated dynamically, so the checksum changes
# We are going to test that the checksum is not the one that was
# before, which corresponds to an empty file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[2][0],))[0]
self.assertTrue(isinstance(obs_checksum, str))
self.assertNotEqual(obs_checksum, '852952723')
self.assertTrue(len(obs_checksum) > 0)
# Checksum of the log file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[3][0],))[0]
self.assertEqual(obs_checksum, '626839734')
def test_update_preprocessed_data_from_cmd_ppd(self):
exp_ppd = PreprocessedData(2)
next_fp_id = get_count('qiita.filepath') + 1
exp_fps = []
path_builder = partial(join, self.db_ppd_dir)
suffix_types = [("seqs.fna", "preprocessed_fasta"),
("seqs.fastq", "preprocessed_fastq"),
("seqs.demux", "preprocessed_demux"),
("split_library_log.txt", "log")]
for id_, vals in enumerate(suffix_types, start=next_fp_id):
suffix, fp_type = vals
exp_fps.append(
(id_, path_builder("%s_%s" % (exp_ppd.id, suffix)), fp_type))
ppd = update_preprocessed_data_from_cmd(self.test_slo, 1, 2)
# Check that the modified preprocessed data is the correct one
self.assertEqual(ppd.id, exp_ppd.id)
# Check that the filepaths returned are correct
# We need to sort the list returned from the db because the ordering
# on that list is based on db modification time, rather than id
obs_fps = sorted(ppd.get_filepaths())
self.assertEqual(obs_fps, exp_fps)
# Check that the checksums have been updated
sql = "SELECT checksum FROM qiita.filepath WHERE filepath_id=%s"
# Checksum of the fasta file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[0][0], ))[0]
self.assertEqual(obs_checksum, '3532748626')
# Checksum of the fastq file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[1][0], ))[0]
self.assertEqual(obs_checksum, '2958832064')
# Checksum of the demux file
# The checksum is generated dynamically, so the checksum changes
# We are going to test that the checksum is not the one that was
# before, which corresponds to an empty file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[2][0], ))[0]
self.assertTrue(isinstance(obs_checksum, str))
self.assertNotEqual(obs_checksum, '852952723')
self.assertTrue(len(obs_checksum) > 0)
# Checksum of the log file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[3][0], ))[0]
self.assertEqual(obs_checksum, '626839734')
def test_update_preprocessed_data_from_cmd(self):
exp_ppd = PreprocessedData(Study(1).preprocessed_data()[0])
exp_fps = exp_ppd.get_filepaths()
# The original paths mush exist, but they're not included in the test
# so create them here
for _, fp, _ in exp_fps:
with open(fp, 'w') as f:
f.write("")
next_fp_id = get_count('qiita.filepath') + 1
exp_fps.append((next_fp_id,
join(self.db_ppd_dir,
"%s_split_library_log.txt" % exp_ppd.id), 'log'))
ppd = update_preprocessed_data_from_cmd(self.test_slo, 1)
# Check that the modified preprocessed data is the correct one
self.assertEqual(ppd.id, exp_ppd.id)
# Check that the filepaths returned are correct
# We need to sort the list returned from the db because the ordering
# on that list is based on db modification time, rather than id
obs_fps = sorted(ppd.get_filepaths())
self.assertEqual(obs_fps, exp_fps)
# Check that the checksums have been updated
sql = "SELECT checksum FROM qiita.filepath WHERE filepath_id=%s"
# Checksum of the fasta file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[0][0], ))[0]
self.assertEqual(obs_checksum, '3532748626')
# Checksum of the fastq file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[1][0], ))[0]
self.assertEqual(obs_checksum, '2958832064')
# Checksum of the demux file
# The checksum is generated dynamically, so the checksum changes
# We are going to test that the checksum is not the one that was
# before, which corresponds to an empty file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[2][0], ))[0]
self.assertTrue(isinstance(obs_checksum, str))
self.assertNotEqual(obs_checksum, '852952723')
self.assertTrue(len(obs_checksum) > 0)
# Checksum of the log file
obs_checksum = self.conn_handler.execute_fetchone(
sql, (obs_fps[3][0], ))[0]
self.assertEqual(obs_checksum, '626839734')
def test_update_preprocessed_data_from_cmd_error_wrong_ppd(self):
with self.assertRaises(ValueError):
update_preprocessed_data_from_cmd(self.test_slo, 1, 100)
def test_update_preprocessed_data_from_cmd_error_missing_files(self):
with self.assertRaises(IOError):
update_preprocessed_data_from_cmd(self.missing_slo, 1)
def test_update_preprocessed_data_from_cmd_error_no_ppd(self):
with self.assertRaises(ValueError):
update_preprocessed_data_from_cmd(self.test_slo,
self.no_ppd_study.id)
def test_update_preprocessed_data_from_cmd_error_wrong_ppd(self):
with self.assertRaises(ValueError):
update_preprocessed_data_from_cmd(self.test_slo, 1, 100)
def test_update_preprocessed_data_from_cmd_error_missing_files(self):
with self.assertRaises(IOError):
update_preprocessed_data_from_cmd(self.missing_slo, 1)
def test_update_preprocessed_data_from_cmd_error_no_ppd(self):
with self.assertRaises(ValueError):
update_preprocessed_data_from_cmd(self.test_slo,
self.no_ppd_study.id)
