def test_example_multi_file(self):
dirpath = tempfile.mkdtemp()
#dirpath = os.path.join(os.path.dirname(__file__), 'original_results')
db_pth = os.path.join(dirpath, 'test_msp_dir.db')
create_db(file_pth=db_pth)
dir_pth = os.path.join(os.path.dirname(__file__), "msp_files",
"massbank")
libdata = LibraryData(msp_pth=dir_pth,
db_pth=db_pth,
db_type='sqlite',
schema='massbank',
source='test',
mslevel=None,
chunk=200)
db_new = libdata.get_db_dict()
# get original database info
conn = sqlite3.connect(
os.path.join(os.path.dirname(__file__), 'original_results',
'test_msp_dir.db'))
cursor = conn.cursor()
db_original = db_dict(cursor)
self.compare_db_d(db_new, db_original)
def test_mona_files(self):
self.maxDiff = None
dirpath = tempfile.mkdtemp()
#dirpath = os.path.join(os.path.dirname(__file__), 'original_results')
db_pth = os.path.join(dirpath, 'test_msp_mona.db')
create_db(file_pth=db_pth)
libdata = LibraryData(msp_pth=os.path.join(
os.path.dirname(__file__), 'msp_files', 'mona',
'MoNA-export-Pathogen_Box-small.msp'),
db_pth=db_pth,
db_type='sqlite',
schema='mona',
source='pathogen',
mslevel=None,
chunk=2)
libdata = LibraryData(msp_pth=os.path.join(
os.path.dirname(__file__), 'msp_files', 'mona',
'MoNA-export-MetaboBASE-small.msp'),
db_pth=db_pth,
db_type='sqlite',
schema='mona',
source='massbank',
mslevel=None,
chunk=2)
libdata = LibraryData(msp_pth=os.path.join(
os.path.dirname(__file__), 'msp_files', 'mona',
'MoNA-export-MassBank-small.msp'),
db_pth=db_pth,
db_type='sqlite',
schema='mona',
source='metabobase',
mslevel=None,
chunk=2)
db_new = libdata.get_db_dict()
# get original database info
conn = sqlite3.connect(
os.path.join(os.path.dirname(__file__), 'original_results',
'test_msp_mona.db'))
cursor = conn.cursor()
db_original = db_dict(cursor)
self.compare_db_d(db_new, db_original)
def _test_example_single_file(self, example_file_pth, name):
# Parse all example files
dirpath = tempfile.mkdtemp()
db_pth = os.path.join(dirpath, name + '.db')
create_db(file_pth=db_pth)
libdata = LibraryData(msp_pth=example_file_pth,
db_pth=db_pth,
db_type="sqlite",
schema='massbank',
source='test',
mslevel=None,
chunk=200)
return libdata, db_pth
def test_create_db(self, ):
dirpath = tempfile.mkdtemp()
# Parse all example files
db_pth = os.path.join(os.path.dirname(__file__), dirpath,
'test_sqlite_db_create.db')
create_db(file_pth=db_pth)
print(db_pth)
conn = sqlite3.connect(db_pth)
cursor = conn.cursor()
# test tables exist
self.assertTrue(check_table_exists_sqlite(cursor, 'library_spectra'))
self.assertTrue(
check_table_exists_sqlite(cursor, 'library_spectra_meta'))
self.assertTrue(
check_table_exists_sqlite(cursor, 'library_spectra_source'))
self.assertTrue(check_table_exists_sqlite(cursor, 'metab_compound'))
import os
from msp2db.parse import LibraryData
from msp2db.db import create_db
ts = time.time()
st = datetime.datetime.fromtimestamp(ts).strftime('%Y_%m_%d_%H_%M_%S')
db_pth = os.path.join(
sys.argv[1],
'spectral_library_massbank_gnps_lipidblast_hmdb_{}.db'.format(st))
#############################################################
# Create database
#############################################################
create_db(file_pth=db_pth)
print("#############################################################")
print('# GNPS')
print("#############################################################")
libdata = LibraryData(msp_pth='/media/sf_DATA/mona/MoNA-export-GNPS.msp',
db_pth=db_pth,
db_type='sqlite',
schema='mona',
source='gnps',
mslevel=None,
chunk=200)
print("#############################################################")
print('# HMDB')
print("#############################################################")