def main():
"""
iodp_samples_magic.py
OPTIONS:
-f FILE, input csv file
-Fsa FILE, output er_samples.txt file for updating, default is to overwrite er_samples.txt
"""
if "-h" in sys.argv:
print main.__doc__
sys.exit()
dataframe = extractor.command_line_dataframe([['WD', False, '.'], ['ID', False, '.'], ['f', True, ''], ['Fsa', False, None]])
args = sys.argv
checked_args = extractor.extract_and_check_args(args, dataframe)
samp_file, output_samp_file, output_dir_path, input_dir_path = extractor.get_vars(['f', 'Fsa', 'WD', 'ID'], checked_args)
ipmag.iodp_samples_magic(samp_file, output_samp_file, output_dir_path, input_dir_path)
def test_content_with_right_format(self):
reference_file = os.path.join(WD, 'data_files', 'testing', 'odp_magic',
'odp_magic_er_samples.txt')
infile = os.path.join(self.input_dir, 'samples_318_U1359_B.csv')
program_ran, outfile = ipmag.iodp_samples_magic(infile)
self.assertEqual(
open(reference_file).readlines(),
open(outfile).readlines())
def test_with_right_format(self):
reference_file = os.path.join(WD, 'testing', 'odp_magic',
'odp_magic_er_samples.txt')
infile = os.path.join(self.input_dir, 'samples_318_U1359_B.csv')
program_ran, outfile = ipmag.iodp_samples_magic(infile)
self.assertTrue(program_ran)
expected_file = os.path.join('.', 'er_samples.txt')
self.assertEqual(outfile, expected_file)
self.assertTrue(os.path.isfile(outfile))
def test_with_right_format(self):
reference_file = os.path.join(WD, 'testing', 'odp_magic',
'odp_magic_er_samples.txt')
infile = os.path.join(self.input_dir, 'samples_318_U1359_B.csv')
program_ran, outfile = ipmag.iodp_samples_magic(infile)
self.assertTrue(program_ran)
expected_file = os.path.join('.', 'er_samples.txt')
self.assertEqual(outfile, expected_file)
self.assertTrue(os.path.isfile(outfile))
def test_content_with_right_format(self):
reference_file = os.path.join(WD, 'data_files', 'testing',
'odp_magic', 'odp_magic_er_samples.txt')
infile = os.path.join(self.input_dir, 'samples_318_U1359_B.csv')
program_ran, outfile = ipmag.iodp_samples_magic(infile)
with open(reference_file) as ref_file:
ref_lines = ref_file.readlines()
with open(outfile) as out_file:
out_lines = out_file.readlines()
self.assertTrue(program_ran)
self.assertEqual(ref_lines, out_lines)
def test_with_wrong_format(self):
infile = os.path.join(self.input_dir, 'GCR_U1359_B_coresummary.csv')
program_ran, error_message = ipmag.iodp_samples_magic(infile)
self.assertFalse(program_ran)
expected_error = 'Could not extract the necessary data from your input file.\nPlease make sure you are providing a correctly formated IODP samples csv file.'
self.assertEqual(error_message, expected_error)
def test_with_wrong_format(self):
infile = os.path.join(self.input_dir, 'GCR_U1359_B_coresummary.csv')
program_ran, error_message = ipmag.iodp_samples_magic(infile)
self.assertFalse(program_ran)
expected_error = 'Could not extract the necessary data from your input file.\nPlease make sure you are providing a correctly formated IODP samples csv file.'
self.assertEqual(error_message, expected_error)
def test_content_with_right_format(self):
reference_file = os.path.join(WD, 'pmagpy_data_files', 'testing',
'odp_magic', 'odp_magic_er_samples.txt')
infile = os.path.join(self.input_dir, 'samples_318_U1359_B.csv')
program_ran, outfile = ipmag.iodp_samples_magic(infile)
self.assertEqual(open(reference_file).readlines(), open(outfile).readlines())
