def test_cli(self, ):
dirpath = tempfile.mkdtemp()
#dirpath = os.path.join(os.path.dirname(__file__), 'original_results')
infile = os.path.join(os.path.dirname(__file__), 'msp_files',
"massbank", "AC000001.txt")
call = "msp2db --msp_pth {} --source massbank -o {} -t sqlite " \
"--schema massbank".format(infile, os.path.join(dirpath,
'test_sqlite_cli.db'))
print(call)
os.system(call)
db_pth = os.path.join(dirpath, 'test_sqlite_cli.db')
# get original database info
conn = sqlite3.connect(
os.path.join(os.path.dirname(__file__), 'original_results',
'test_sqlite_cli.db'))
cursor = conn.cursor()
db_original = db_dict(cursor)
conn2 = sqlite3.connect(db_pth)
cursor2 = conn2.cursor()
db_new = db_dict(cursor2)
self.compare_db_d(db_new, db_original)
def test_cli_compound_lookup_false(self, ):
dirpath = tempfile.mkdtemp()
infile = os.path.join(os.path.dirname(__file__), 'msp_files',
"massbank", "AC000001.txt")
call = "msp2db --msp_pth {} --source massbank -o {} -t sqlite " \
"--ignore_compound_lookup " \
"--schema massbank".format(infile, os.path.join(dirpath,
'test_sqlite_cli_ignore_comp.db'))
print(call)
os.system(call)
db_pth = os.path.join(dirpath, 'test_sqlite_cli_ignore_comp.db')
conn2 = sqlite3.connect(db_pth)
cursor2 = conn2.cursor()
d_new = db_dict(cursor2)
match = re.search('.*(UNKNOWN).*', str(d_new['metab_compound'][0][0]))
if match:
comp = match.group(1)
else:
comp = ''
self.assertEqual(comp, 'UNKNOWN')
self.assertEqual(d_new['metab_compound'][0][1], "unknown name")
self.assertEqual(d_new['metab_compound'][0][2], None)
self.assertEqual(d_new['metab_compound'][0][3], None)
self.assertEqual(d_new['metab_compound'][0][4], None)
self.assertEqual(d_new['metab_compound'][0][5], None)
self.assertEqual(d_new['metab_compound'][0][6], None)
self.assertEqual(d_new['metab_compound'][0][7], None)
self.assertEqual(d_new['metab_compound'][0][8], None)
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_cli_compound_lookup_false(self, ):
dirpath = tempfile.mkdtemp()
infile = os.path.join(os.path.dirname(__file__), 'msp_files',
"massbank", "AC000001.txt")
call = "msp2db --msp_pth {} --source massbank -o {} -t sqlite " \
"--ignore_compound_lookup " \
"--schema massbank".format(infile, os.path.join(dirpath,
'test_sqlite_cli_ignore_comp.db'))
print(call)
os.system(call)
db_pth = os.path.join(dirpath, 'test_sqlite_cli_ignore_comp.db')
conn2 = sqlite3.connect(db_pth)
cursor2 = conn2.cursor()
d_new = db_dict(cursor2)
self.assertEqual(d_new['metab_compound'], [])
