def test_get_qiime_minimal_mapping_single_reverse_primer(self):
conn_handler = SQLConnectionHandler()
conn_handler
sql = """INSERT INTO qiita.prep_columns
(prep_template_id, column_name, column_type)
VALUES (1, 'reverselinkerprimer', 'varchar');
ALTER TABLE qiita.prep_1
ADD COLUMN reverselinkerprimer varchar;
DELETE FROM qiita.prep_columns
WHERE prep_template_id = 1 AND column_name = 'run_prefix';
ALTER TABLE qiita.prep_1 DROP COLUMN run_prefix;
UPDATE qiita.prep_1 SET reverselinkerprimer = %s
"""
conn_handler.execute(sql, ('GTGCCAGCM',))
prep_template = PrepTemplate(1)
prep_template.generate_files()
out_dir = mkdtemp()
obs_fps = _get_qiime_minimal_mapping(prep_template, out_dir)
exp_fps = [join(out_dir, 'prep_1_MMF.txt')]
# Check that the returned list is as expected
self.assertEqual(obs_fps, exp_fps)
# Check that the file exists
self.assertTrue(exists(exp_fps[0]))
# Check the contents of the file
with open(exp_fps[0], "U") as f:
self.assertEqual(f.read(), EXP_PREP_RLP)
def test_get_qiime_minimal_mapping_single_no_run_prefix(self):
conn_handler = SQLConnectionHandler()
sql = """DELETE FROM qiita.prep_columns
WHERE prep_template_id = 1 AND column_name = 'run_prefix';
ALTER TABLE qiita.prep_1 DROP COLUMN run_prefix"""
conn_handler.execute(sql)
prep_template = PrepTemplate(1)
prep_template.generate_files()
out_dir = mkdtemp()
obs_fps = _get_qiime_minimal_mapping(prep_template, out_dir)
exp_fps = [join(out_dir, 'prep_1_MMF.txt')]
# Check that the returned list is as expected
self.assertEqual(obs_fps, exp_fps)
# Check that the file exists
self.assertTrue(exists(exp_fps[0]))
# Check the contents of the file
with open(exp_fps[0], "U") as f:
self.assertEqual(f.read(), EXP_PREP)