def test_sql_file_not_exists(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -k'+
' -digits 3 -sql /tmp/scipion.sql -filename DMY_ABC_0001.mrc')
if os.path.isfile('/tmp/scipion.sql'):
os.remove('/tmp/scipion.sql')
with self.assertRaises(IOError):
with patch('sys.stdout', new=MagicMock()):
obj = s.starfleet_master(sys.argv)
def test_nonexist_microg_folder_and_force(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -k'+
' -digits 3 -files_list 1 2 3 -filename DMY_ABC_0001.mrc '+
'-image_folder nonexisting/ -f')
with open('/tmp/in.star', 'w+b'):
pass
obj = s.starfleet_master(sys.argv)
self.assertEqual(1, obj.check)
def setUp(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -k '+
' -digits 4 -filename a_0001.mrc -image_folder /tmp'+
' -sql /tmp/scipion.sql')
with open('/tmp/in.star', 'w') as f:
f.write(normal_starfile)
with open('/tmp/scipion.sql', 'w') as f:
f.write(sql_file)
self.obj = s.starfleet_master(sys.argv)
def setUp(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -make_ctf '+
' -digits 4 -filename 20160126_BRCA1_GO_0001.mrc')
self.epa_list = ['20160126_BRCA1_GO_0092_ctffind.log', '20160126_BRCA1_GO_0002_ctffind.log',
'20160126_BRCA1_GO_0091_ctffind.log', '20160126_BRCA1_GO_0001_ctffind.log']
with open('/tmp/in.star', 'w') as f:
f.write(normal_starfile)
self.obj = s.starfleet_master(sys.argv)
self.obj.read_star()
self.obj.create_epa_list()
def test_remove_mode_ctf_starfile(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -r -files_list 91 92'+
' -digits 4 -filename 20160126_BRCA1_GO_0001.mrc')
with open('/tmp/in.star', 'w') as f:
f.write(ctf_starfile)
obj = s.starfleet_master(sys.argv)
obj.read_star()
obj.write_star()
with open(obj.o, 'r') as f:
self.assertMultiLineEqual(f.read(), self.exp_ctf_starfile)
def test_ctf_starfile_in(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -k -files_list 1 2 3'+
' -digits 4 -filename 20160126_BRCA1_GO_0001.mrc')
with open('/tmp/in.star', 'w') as f:
f.write(ctf_starfile)
obj = s.starfleet_master(sys.argv)
h,f = obj.read_star()
self.assertEqual(self.ctf_header, ''.join(obj.header))
self.assertEqual(self.ctf_header, ''.join(h))
self.assertEqual(self.ctf_files, obj.files_in)
self.assertEqual(self.ctf_files, f)
def setUp(self):
for i in ['20160126_BRCA1_GO_0001.mrc',
'20160126_BRCA1_GO_0002.mrc',
'20160126_BRCA1_GO_0091.mrc',
'20160126_BRCA1_GO_0092.mrc']:
with open(('/tmp/'+i), 'w+b'):
pass
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -k -files_list 1 2 92 93'+
' -digits 4 -filename 20160126_BRCA1_GO_0001.mrc -image_folder /tmp')
with open('/tmp/in.star', 'w') as f:
f.write(normal_starfile)
self.obj = s.starfleet_master(sys.argv)
h,f = self.obj.read_star()
def test_nonexist_microg_folder_and_not_force(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -k'+
' -digits 3 -files_list 1 2 3 -filename DMY_ABC_0001.mrc '+
' -image_folder nonexisting/')
with self.assertRaises(IOError):
s.starfleet_master(sys.argv)
def test_list_in_parsed_arguments(self):
os.remove('/tmp/out.star')
self.assertEqual(['001','002'],
s.starfleet_master(sys.argv).lst)
def test_input_file_not_exists(self):
if os.path.isfile('/tmp/in.star'):
os.remove('/tmp/in.star')
with self.assertRaises(IOError):
s.starfleet_master(sys.argv)
def test_no_sql_no_files_list_make_ctf(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star '+
' -digits 3 -filename DMY_ABC_0001.mrc -make_ctf')
with open('/tmp/in.star','w'):
pass
self.assertTrue(s.starfleet_master(sys.argv).check)
def test_no_sql_no_files_list(self):
sys.argv = shlex.split('test.py -i /tmp/in.star -o /tmp/out.star -k'+
' -digits 3 -filename DMY_ABC_0001.mrc')
with self.assertRaises(ValueError):
with patch('sys.stdout', new=MagicMock()):
obj = s.starfleet_master(sys.argv)