def test_read_mzxml_ramped(self):
mde = magma.MsDataEngine(self.db_session, 1, 1000, 5, 0.001, 0.005, 3)
mzxml_file = pkg_resources.resource_filename(
'magma', "tests/ramped_collision_data.mzXML")
mde.store_mzxml_file(mzxml_file)
scandata = self.db_session.query(Scan).count()
self.assertEqual(scandata, 2)
def test_read_mzxml(self):
mde = magma.MsDataEngine(self.db_session, -1, 10000, 5, 0.001, 0.005, 3)
mzxml_file=pkg_resources.resource_filename('magma', "tests/theogallin.mzXML")
mde.store_mzxml_file(mzxml_file)
with self.assertRaises(DataProcessingError) as cm:
mde.store_mzxml_file(mzxml_file)
self.assertEqual(str(cm.exception), 'Attempt to read MS data twice')
scandata = self.db_session.query(Scan).count()
self.assertEqual(scandata,4)
ae = magma.AnnotateEngine(self.db_session,0,3,1,0,5,0)
ae.build_spectra()
def test_store_manual_tree_unallowed_element(self):
mde = magma.MsDataEngine(self.db_session, -1, 1000, 5, 0.001, 0.005, 3)
# create corrupt manual tree file
import tempfile, os
treefile = tempfile.NamedTemporaryFile(delete=False)
treefile.write('C6H5At: 999 (C6H5: 1000, At: 100)')
treefile.close()
with self.assertRaises(FileFormatError) as cm:
mde.store_manual_tree(treefile.name,-1)
self.assertEqual(str(cm.exception), 'Element not allowed in formula tree: At')
os.remove(treefile.name)
def test_generate_ions(self):
mde = magma.MsDataEngine(self.db_session, 1, 1000, 5, 0.001, 0.005, 3)
ae = magma.AnnotateEngine(self.db_session,
False,
3,
1,
0,
5,
True,
adducts='Na,K')
self.assertIsInstance(ae, magma.AnnotateEngine)
self.assertEqual(ae.ions, [{
0: '[M]+'
}, {
1.0078250321: '[M+H]+',
22.9897692809: '[M+Na]+',
38.96370668: '[M+K]+'
}])
def test_it(self):
molblock = """Theogallin
Mrv0541 05061310592D
24 25 0 0 0 0 999 V2000
5.0013 2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5724 2.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0013 6.1875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7158 4.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2868 2.4750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0013 1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5724 1.2375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2868 5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0013 4.5375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2868 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2868 4.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.2868 3.3000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1530 6.4746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7158 5.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7158 0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.8579 0.8250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.5724 6.1875 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.2868 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.5724 4.5375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.5724 3.7125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.7656 7.2031 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.9774 6.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.5403 5.8038 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.0013 3.7125 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5 1 2 0 0 0 0
5 2 1 0 0 0 0
6 1 1 0 0 0 0
7 2 2 0 0 0 0
8 3 1 0 0 0 0
9 4 1 0 0 0 0
10 6 2 0 0 0 0
10 7 1 0 0 0 0
11 8 1 0 0 0 0
11 9 1 0 0 0 0
12 5 1 0 0 0 0
14 3 1 0 0 0 0
14 4 1 0 0 0 0
14 13 1 0 0 0 0
15 6 1 0 0 0 0
16 7 1 0 0 0 0
17 8 1 0 0 0 0
18 10 1 0 0 0 0
19 11 1 0 0 0 0
20 12 2 0 0 0 0
21 13 2 0 0 0 0
22 13 1 0 0 0 0
23 14 1 0 0 0 0
24 9 1 0 0 0 0
24 12 1 0 0 0 0
M END
"""
class Stub(object):
pass
# search_structure gets called by pp.Server.submit
# submit will import modules, during test we have do the same
import magma.pars as pars
import magma.types as types
import magma.fragmentation_cy as fragcy
import magma.fragmentation_py as fragpy
magma.magma = Stub()
magma.magma.pars = pars
magma.magma.types = types
magma.magma.fragmentation_cy = fragcy
magma.magma.fragmentation_py = fragpy
magma.MsDataEngine(self.db_session, 1, 10000, 5, 0.001, 0.005, 5)
ae = magma.AnnotateEngine(self.db_session,
False,
3,
1,
0,
5,
True,
adducts='Na,K')
mol = Chem.MolFromMolBlock(molblock)
mim = 344.07434673460006
molcharge = 1
# TODO fill peaks
peaks = []
fast = False
result = magma.search_structure(mol, mim, molcharge, peaks,
ae.max_broken_bonds,
ae.max_water_losses, ae.precision,
ae.mz_precision_abs, ae.use_all_peaks,
ae.ionisation_mode,
ae.skip_fragmentation, fast, ae.ions)
self.assertEqual(result, ([], 0))
def test_store_manual_subtree_corrupt_endlessloop(self):
mde = magma.MsDataEngine(self.db_session, 1, 1000, 5, 0.001, 0.005, 3)
# create corrupt manual tree file
import tempfile, os
treefile = tempfile.NamedTemporaryFile(mode='w', delete=False)
treefile.write("""320.2: 999 (
123.12 1
135.2 3
139.2 3
145.18 2
147.04 1
149.136 39
149.92 1
150.32 2
150.56 1
150.88 1
151.28 1
153.36 1
155.04 2
155.296 2
159.1 1
161.28 5
162.64 1
163.155 43
167.145 230
167.808 4
168.4 5
169.06 7
169.68 1
175.177 8
175.52 1
177.12 4
179.114 92
179.509 5
179.74 1
179.92 2
180.168 5
181.04 1
181.44 1
189.28 2
191.12 1
195.04 3
195.28 2
203.235 23
203.44 3
205.2 1
205.68 1
206.96 4
207.2 4
207.36 1
208.088 13
219.232 14
220.88 1
221.12 4
223.28 1
229.12 5
257.283 254
257.92 4
258.32 2
258.733 3
259.32 1
273.12 3
275.268 97
282.88 1
283.23 4
291.251 9
291.52 3
301.242 254
302 3
302.4 2
319.155 999
319.8 2
)
""")
treefile.close()
with self.assertRaises(FileFormatError) as cm:
mde.store_manual_tree(treefile.name, 0)
self.assertEqual(str(cm.exception), 'Corrupt Tree format ...')
os.remove(treefile.name)
