def test_get_structure_engine_default(self):
ms = magma.MagmaSession(':memory:', 'My description')
se = ms.get_structure_engine()
self.assertIsInstance(se, magma.StructureEngine)
self.assertFalse(hasattr(se, 'pubchem_engine'))
def test_get_structure_engine_custom(self):
ms = magma.MagmaSession(':memory:', 'My description')
args = {
'pubchem_names': True,
}
se = ms.get_structure_engine(**args)
self.assertIsInstance(se, magma.StructureEngine)
self.assertIsInstance(se.pubchem_engine, magma.PubChemEngine)
def test_get_ms_data_engine_default(self):
ms = magma.MagmaSession(':memory:', u'My description')
se = ms.get_ms_data_engine()
self.assertIsInstance(se, magma.MsDataEngine)
rundata = ms.db_session.query(Run).one()
self.assertDictContainsSubset({
'ionisation_mode': 1,
'abs_peak_cutoff': 1000,
'max_ms_level': 10,
'mz_precision':5.0,
'precursor_mz_precision':0.005
}, rundata.__dict__)
def test_get_ms_data_engine_custom(self):
ms = magma.MagmaSession(':memory:', 'My description')
args = {
'ionisation_mode': -1,
'abs_peak_cutoff': 10001,
'max_ms_level': 101,
'mz_precision': 0.01,
'precursor_mz_precision': 0.05
}
se = ms.get_ms_data_engine(**args)
self.assertIsInstance(se, magma.MsDataEngine)
rundata = ms.db_session.query(Run).one()
self.assertDictContainsSubset(args, rundata.__dict__)
def test_get_annotate_engine_default(self):
ms = magma.MagmaSession(':memory:', u'My description')
ms.get_ms_data_engine()
se = ms.get_annotate_engine()
self.assertIsInstance(se, magma.AnnotateEngine)
rundata = ms.db_session.query(Run).one()
self.assertDictContainsSubset({
'skip_fragmentation':False,
'max_broken_bonds':3,
'ms_intensity_cutoff':1e6,
'msms_intensity_cutoff':5,
'use_all_peaks':False
}, rundata.__dict__)
def test_construct_with_existing_db(self):
# create db with run description
import tempfile, os
dbfile = tempfile.NamedTemporaryFile(delete=False)
engine = create_engine('sqlite:///' + dbfile.name)
Base.metadata.create_all(engine)
session = sessionmaker(bind=engine)()
session.add(Run(description='My first description'))
session.commit()
dbfile.close()
ms = magma.MagmaSession(dbfile.name, 'My second description')
rundata = ms.db_session.query(Run).one()
# first description is not overwritten
self.assertEqual(rundata.description, 'My first description')
os.remove(dbfile.name)
choices=['GNPS', 'MSP'])
ap.add_argument('experiment_id', help="Experiment ID", type=int)
ap.add_argument('magma_db', help="(Non-)existing magma database", type=str)
ap.add_argument('spectra_path', help="path to spectra", type=str)
return ap
# MAIN
import glob
args = arg_parser().parse_args(sys.argv[1:])
# if magma_db exists it is reused, skipping the parts that create and run the magma job
db_exists = os.path.isfile(args.magma_db)
if not db_exists:
magma_session = magma.MagmaSession(args.magma_db, 'ms2lda_dataset',
'debug')
ms_data_engine = magma_session.get_ms_data_engine(
ionisation_mode=args.mode,
abs_peak_cutoff=0,
mz_precision=20,
mz_precision_abs=0.005)
struct_engine = magma_session.get_structure_engine(pubchem_names=False)
annotate_engine = magma_session.get_annotate_engine(
ms_intensity_cutoff=0, msms_intensity_cutoff=0)
if os.path.isdir(args.spectra_path):
files = glob.glob(args.spectra_path + '/*')
else:
files = [args.spectra_path]
loader = loaders[args.loader]()
with stdout2stderr():
def get_magma_session(self, db, description="", log='warn'):
return magma.MagmaSession(db, description, log)
def test_construct_with_new_db(self):
ms = magma.MagmaSession(':memory:', 'My description')
self.assertIsInstance(ms, magma.MagmaSession)
rundata = ms.db_session.query(Run).one()
self.assertEqual(rundata.description, 'My description')
