def test_molecule_get_structure(self):
name = 'water'
with App(argv=['molecule', 'get-structure', '--by-name', name]) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(
re.split(' +',
capturer.get_text().split('\n')[-1]),
['water', 'pubchem.compound', '962', 'InChI=1S/H2O/h1H2'])
namespace = 'chebi'
id = '15377'
with App(argv=[
'molecule', 'get-structure', '--by-id', '--namespace',
namespace, id
]) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(
re.split(' +',
capturer.get_text().split('\n')[-1]),
['', 'chebi', '15377', 'InChI=1S/H2O/h1H2'])
namespace = 'chebi'
id = '0'
with App(argv=[
'molecule', 'get-structure', '--by-id', '--namespace',
namespace, id
]) as app:
with CaptureOutput(merged=False) as capturer:
app.run()
self.assertEqual(capturer.stderr.get_text(),
'Unable to find structure')
def test_migrate(self):
with App(argv=['db', 'create']) as app:
app.run()
with App(argv=['db', 'migrate']) as app:
app.run()
self.assertTrue(os.path.isdir('migrations'))
self.assertNotEqual(os.listdir('migrations'), [])
def test_taxonomy_get_distance_to_root(self):
with App(argv=['taxonomy', 'get-distance-to-root', 'bacteria']) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(float(capturer.get_text()), 2.)
with App(argv=['taxonomy', 'get-distance-to-root', 'XXX']) as app:
self.assertRaises(SystemExit, lambda: app.run())
def test_drop(self):
with App(argv=['db', 'create']) as app:
app.run()
self.assertTrue(sqlalchemy_utils.functions.database_exists(self.url))
with App(argv=['db', 'drop']) as app:
app.run()
self.assertFalse(sqlalchemy_utils.functions.database_exists(self.url))
def test_taxonomy_get_parents(self):
with App(argv=['taxonomy', 'get-parents', 'bacteria']) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(capturer.get_text(),
"root\ncellular organisms")
with App(argv=['taxonomy', 'get-parents', 'XXX']) as app:
self.assertRaises(SystemExit, lambda: app.run())
def test_taxonomy_get_distance_to_common_ancestor(self):
with App(argv=[
'taxonomy', 'get-distance-to-common-ancestor',
'Mycoplasma genitalium', 'Mycoplasma pneumoniae'
]) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(float(capturer.get_text()), 1.)
with App(argv=[
'taxonomy', 'get-distance-to-common-ancestor',
'Mycoplasma genitalium', 'XXX'
]) as app:
self.assertRaises(SystemExit, lambda: app.run())
def test_get_version(self):
with CaptureOutput() as capture_output:
with App(argv=['-v']) as app:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(capture_output.get_text(),
datanator.__version__)
with CaptureOutput() as capture_output:
with App(argv=['--version']) as app:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(capture_output.get_text(),
datanator.__version__)
def test_taxonomy_get_rank(self):
with App(argv=['taxonomy', 'get-rank', '2097']) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(capturer.get_text(), "species")
with App(
argv=['taxonomy', 'get-rank', 'Mycoplasma genitalium']) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(capturer.get_text(), "species")
with App(argv=['taxonomy', 'get-rank', 'Mycoplasma genitalium XXX'
]) as app:
self.assertRaises(SystemExit, lambda: app.run())
def test_download_array_express(self):
with App(argv=['download', '--path=' +
self.dirname, 'array-express']) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertTrue(
os.path.exists(self.dirname + '/ArrayExpress.sqlite'))
def test_download_uniprot(self):
with App(argv=['download', '--path=' +
self.dirname, 'uniprot']) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertTrue(
os.path.exists(self.dirname + '/Uniprot.sqlite'))
def test_create_table_only(self):
sqlalchemy_utils.functions.create_database(self.url)
self.assertTrue(sqlalchemy_utils.functions.database_exists(self.url))
self.assertEqual(datanator.db.engine.table_names(), [])
with App(argv=['db', 'create']) as app:
app.run()
self.assertNotEqual(datanator.db.engine.table_names(), [])
def test_build_ecmdb(self):
with App(argv=[
'build', '--path=' +
self.dirname, '--max-entries=1', '--verbose=True', 'ecmdb'
]) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertTrue(os.path.exists(self.dirname + '/Ecmdb.sqlite'))
def test_upload_ref_seq(self):
with App(argv=[
'upload', 'reference-genome',
os.path.join(path.dirname(__file__), 'data_source',
'test_mpn_sequence.gb'), '--db-path', self.dirname
]) as app:
app.run()
self.assertTrue(
os.path.exists(os.path.join(self.dirname, 'Refseq.sqlite')))
def test_restore(self):
with App(argv=['db', 'create']) as app:
app.run()
self.assertTrue(sqlalchemy_utils.functions.database_exists(self.url))
session = sqlalchemy.orm.sessionmaker(bind=datanator.db.engine)()
query = session.query(datanator.core.models.Observation)
self.assertEqual(query.count(), 0)
session.close()
with App(argv=[
'db', 'restore', '--restore-schema', '--do-not-exit-on-error'
]) as app:
# todo: remove --restore-schema and --do-not-exit-on-error after fixing Alembic issue with migrations
app.run()
session = sqlalchemy.orm.sessionmaker(bind=datanator.db.engine)()
query = session.query(datanator.core.models.Observation)
self.assertGreater(query.count(), 0)
session.close()
def test_get_ec_number(self):
dr1p = 'OCC1OC(CC1O)OP([O-])([O-])=O'
dr5p = 'OC1CC(O)C(COP([O-])([O-])=O)O1'
reaction = 'Deoxyribose 1-phosphate --> Deoxyribose-5-P'
with App(argv=['reaction', 'get-ec-number', reaction]) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
print(re.split(' +', capturer.get_text().split('\n')))
self.assertEqual(
re.split(' +',
capturer.get_text().split('\n')[2]),
['5.4.2', '16.00'])
reaction = '{} --> {}'.format(dr1p, dr5p)
with App(argv=['reaction', 'get-ec-number', reaction]) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(
re.split(' +',
capturer.get_text().split('\n')[2]),
['5.4.2', '16.00'])
reaction = '{} > {}'.format(dr1p, dr5p)
with App(argv=['reaction', 'get-ec-number', reaction]) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(capturer.get_text(),
'The reaction is ill-formed')
reaction = 'xxxxxxxxx --> Deoxyribose-5-P'
with App(argv=['reaction', 'get-ec-number', reaction]) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertTrue(capturer.get_text().startswith(
'Unable to interpret participants:\n'))
def test(self):
with App(argv=[]) as app:
app.run()
with App(argv=['upload']) as app:
app.run()
with App(argv=['build']) as app:
app.run()
with App(argv=['download']) as app:
app.run()
with App(argv=['taxonomy']) as app:
app.run()
with App(argv=['molecule']) as app:
app.run()
with App(argv=['reaction']) as app:
app.run()
def test_GetDataController(self):
input_filename = os.path.join(os.path.dirname(__file__), 'fixtures',
'five_reactions.xlsx')
output_filename = os.path.join(self.dirname, 'output.xlsx')
argv = [
'get-data',
input_filename,
output_filename,
'--max-taxon-dist',
'8',
'--taxon-dist-scale',
'1.6',
'--include-variants',
'--temperature',
'37',
'--temperature-std',
'1',
'--ph',
'7.5',
'--ph-std',
'0.3',
]
with App(argv=argv) as app:
app.run()
def test_GenerateTemplateController(self):
filename = os.path.join(self.dirname, 'template.xlsx')
with App(argv=['generate-template', filename]) as app:
app.run()
self.assertTrue(os.path.isfile(filename))
def test_molecule_convert_structure(self):
with App(argv=['molecule', 'convert-structure', 'O', 'can']) as app:
with CaptureOutput(termination_delay=0.1) as capturer:
app.run()
self.assertEqual(capturer.get_text(), 'O')