def test_validate(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=['validate', 'dna', 'ACGT']) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'validate', 'dna',
'ACG[id: "ala" | structure: {}]T'.format(ala_inchi)
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=['validate', 'dna', 'ACGT[']) as app:
# run app
app.run()
def test_help(self):
with self.assertRaises(SystemExit):
with __main__.App(argv=[]) as app:
app.run()
with self.assertRaises(SystemExit):
with __main__.App(argv=['--help']) as app:
app.run()
def test_version(self):
with __main__.App(argv=['-v']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(captured.stdout.get_text(),
bpforms.__version__)
self.assertEqual(captured.stderr.get_text(), '')
with __main__.App(argv=['--version']) as app:
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with self.assertRaises(SystemExit):
app.run()
self.assertEqual(captured.stdout.get_text(),
bpforms.__version__)
self.assertEqual(captured.stderr.get_text(), '')
def verify_large_polymers(self, form_type, alphabet):
# test Python API
form = form_type()
for i_trial in range(6):
self.verify_large_polymer(form, alphabet, i_trial)
# test CLI
with __main__.App(argv=['get-properties', form.alphabet.id, alphabet * pow(2, 5)]) as app:
app.run()
with __main__.App(argv=['get-properties', form.alphabet.id, alphabet * pow(2, 5), '--ph', '7.4']) as app:
app.run()
# test REST API
client = rest.app.test_client()
rv = client.post('/api/bpform/', json=dict(alphabet=form.alphabet.id, seq=alphabet * pow(2, 5),
ph=7.4, major_tautomer=True))
self.assertEqual(rv.status_code, 200)
def test_validate(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(
argv=['validate', 'canonical_dna', 'ACGT']) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'validate', 'canonical_dna',
('ACG'
'[id: "dI" | structure: "{}"'
' | l-bond-atom: P30'
' | l-displaced-atom: O33-1'
' | r-bond-atom: O34'
' | r-displaced-atom: H34'
' ]'
'T').format(dIMP_smiles)
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(), 'Form is valid')
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(
argv=['validate', 'canonical_dna', 'ACGT[']) as app:
# run app
app.run()
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=[
'validate', 'canonical_dna',
('ACGT'
'[id: "dI" | structure: "{}" | l-displaced-atom: O33-1 ]'
).format(dIMP_smiles)
]) as app:
# run app
app.run()
def test_get_major_micro_species(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'get-major-micro-species', 'canonical_dna',
('[id: "dI" | structure: "{0}"'
' | l-bond-atom: P30'
' | l-displaced-atom: O33-1'
' | r-bond-atom: O34'
' | r-displaced-atom: H34'
' ]'
'[id: "dI" | structure: "{0}"'
' | l-bond-atom: P30'
' | l-displaced-atom: O33-1'
' | r-bond-atom: O34'
' | r-displaced-atom: H34'
' ]').format(dIMP_smiles), '14.'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
smiles = captured.stdout.get_text()
self.assertEqual(
captured.stdout.get_text(),
('OC[C@H]1O[C@H](C[C@@H]1O)[N+]1(C=Nc2c1nc[n-]'
'c2=O)C1CC([O-])C(COP(=O)([O-])OC2CC(OC2COP(=O)'
'([O-])[O-])[N+]2(C=Nc3c2nc[n-]c3=O)[C@H]2C[C@H]'
'(O)[C@@H](CO)O2)O1'))
with self.assertRaises(SystemExit):
with __main__.App(argv=[
'get-major-micro-species', 'canonical_dna', 'ACGT[', '7.'
]) as app:
# run app
app.run()
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=[
'get-major-micro-species', 'canonical_dna',
('ACGT'
'[id: "dI" | structure: "{}" | l-displaced-atom: O33-1 ]'
).format(dI_smiles), '7.'
]) as app:
# run app
app.run()
def test_get_properties(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=['get-properties', 'dna', 'ACGT']) as app:
# run app
app.run()
# test that the CLI produced the correct output
text = captured.stdout.get_text()
self.assertIn('Length: 4', text)
self.assertIn('Formula: C39H46N15O28P4', text)
self.assertIn('Molecular weight: 1296.769047992', text)
self.assertIn('Charge: -5', text)
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
base_seq = ''.join([
'[structure: {}]'.format(
bpforms.dna.dna_alphabet.A.get_inchi()),
'[structure: {}]'.format(
bpforms.dna.dna_alphabet.C.get_inchi()),
'[structure: {}]'.format(
bpforms.dna.dna_alphabet.G.get_inchi()),
'[structure: {}]'.format(
bpforms.dna.dna_alphabet.T.get_inchi()),
])
with __main__.App(
argv=['get-properties', 'dna', base_seq, '--ph', '7.0'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
text = captured.stdout.get_text()
self.assertIn('Length: 4', text)
self.assertIn('Formula: C39H43N15O28P4', text)
self.assertIn('Molecular weight: 1293.745047992', text)
self.assertIn('Charge: -8', text)
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaises(SystemExit):
with __main__.App(argv=['get-properties', 'dna', 'ACGT[']) as app:
# run app
app.run()
def test_protonate(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'protonate', 'dna',
'[id: "ala" | structure: {0}][id: "ala" | structure: {0}]'.
format(ala_inchi), '14.'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(
captured.stdout.get_text(),
'[id: "ala" | structure: {0}][id: "ala" | structure: {0}]'.
format(ala_inchi_ph_14))
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaises(SystemExit):
with __main__.App(argv=['protonate', 'dna', 'ACGT[', '7.']) as app:
# run app
app.run()
def test_viz_alphabet(self):
path = os.path.join(self.tempdir, 'alphabet.html')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(
argv=['viz-alphabet', 'canonical_dna', path]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(),
'Visualization saved to {}'.format(path))
self.assertTrue(os.path.isfile(path))
def test_export_ontos(self):
path = os.path.join(self.tempdir, 'onto.obo')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'export-ontos', path, '--alphabet', 'protein',
'--max-monomers', '10', '--max-xlinks', '10'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertEqual(captured.stdout.get_text(),
'Ontology saved to {}'.format(path))
self.assertTrue(os.path.isfile(path))
def test_build_alphabets(self):
self.assertFalse(os.path.isfile(bpforms.alphabet.dna.filename))
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'build-alphabets', '--alphabet', 'dna', '--max-monomers',
'3'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
self.assertIn('Alphabets successfully built',
captured.stdout.get_text())
self.assertTrue(os.path.isfile(bpforms.alphabet.dna.filename))
def test_get_properties(self):
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(
argv=['get-properties', 'canonical_dna', 'ACGT']) as app:
# run app
app.run()
# test that the CLI produced the correct output
text = captured.stdout.get_text()
self.assertIn('Length: 4', text)
self.assertNotIn('Structure: None', text)
self.assertIn('Formula: C39', text)
self.assertIn('Molecular weight: ', text)
self.assertIn('Charge: -', text)
self.assertEqual(captured.stderr.get_text(), '')
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'get-properties', 'canonical_dna', 'ACGT', '--ph', '7.0'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
text = captured.stdout.get_text()
self.assertIn('Length: 4', text)
self.assertIn(
'Structure: ' +
('Cc1cn(C2CC(O)C(COP(=O)([O-])OC3CC(OC3COP(=O)([O-])OC3CC(OC3COP(=O)([O-])'
'OC3CC(OC3COP(=O)([O-])[O-])n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c3nc(N)[nH]'
'c4=O)O2)c(=O)[nH]c1=O'), text)
self.assertIn('Formula: C39', text)
self.assertIn('Molecular weight: 1248.772047992', text)
self.assertIn('Charge: -5', text)
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'get-properties', 'canonical_dna', 'ACGT', '--ph', '7.0'
]) as app:
# run app
with mock.patch.object(bpforms.BpForm,
'export',
side_effect=Exception('error')):
app.run()
# test that the CLI produced the correct output
text = captured.stdout.get_text()
self.assertIn('Length: 4', text)
self.assertIn('Structure: None', text)
self.assertIn('Formula: None', text)
self.assertIn('Molecular weight: None', text)
self.assertIn('Charge: None', text)
with capturer.CaptureOutput(merged=False, relay=False) as captured:
with __main__.App(argv=[
'get-properties', 'canonical_dna', 'ACGT', '--circular'
]) as app:
# run app
app.run()
# test that the CLI produced the correct output
text = captured.stdout.get_text()
self.assertIn('Length: 4', text)
self.assertNotIn('Structure: None', text)
self.assertIn('Formula: C39', text)
self.assertIn('Molecular weight: ', text)
self.assertIn('Charge: -', text)
self.assertEqual(captured.stderr.get_text(), '')
with self.assertRaises(SystemExit):
with __main__.App(
argv=['get-properties', 'canonical_dna', 'ACGT[']) as app:
# run app
app.run()
with self.assertRaisesRegex(SystemExit, '^Form is invalid'):
with __main__.App(argv=[
'get-properties', 'canonical_dna',
('ACGT'
'[id: "dI" | structure: "{}" | backbone-displaced-atom: H10 ]'
).format(dI_smiles)
]) as app:
# run app
app.run()