def test_run_add_columns_no_new_columns2(self):
in_metadata = "%s/simple_metadata.csv" % data_dir
in_data = "%s/new_metadata.csv" % data_dir
index_column = "header"
join_on = "taxon"
new_columns = []
out_metadata = "%s/tmp.add_columns2.csv" % data_dir
where_column = None
log_file = "%s/tmp.add_columns.log" % data_dir
expected = "%s/expected_add_columns2.csv" % data_dir
add_columns(in_metadata, in_data, index_column, join_on, new_columns,
out_metadata, where_column, log_file)
self.assertTrue(filecmp.cmp(out_metadata, expected, shallow=False))
os.unlink(out_metadata)
os.unlink(log_file)
def test_run_add_columns_force_overwrite(self):
in_metadata = "%s/simple_metadata.csv" % data_dir
in_data = "%s/new_metadata.csv" % data_dir
index_column = "header"
join_on = "taxon"
new_columns = ["mut1", "parrot"]
out_metadata = "%s/tmp.add_columns.csv" % data_dir
where_column = None
log_file = "%s/tmp.add_columns.log" % data_dir
force_overwrite = True
expected = "%s/expected_add_columns3.csv" % data_dir
add_columns(in_metadata, in_data, index_column, join_on, new_columns,
out_metadata, where_column, log_file, force_overwrite)
self.assertTrue(filecmp.cmp(out_metadata, expected, shallow=False))
os.unlink(out_metadata)
os.unlink(log_file)
def run(options):
add_columns(options.in_metadata, options.in_data, options.index_column,
options.join_on, options.new_columns, options.out_metadata,
options.where_column, options.log_file,
options.force_overwrite)