def test_no_read_files_in_list(self):
"""
The file list in the sample sheet is invalid
:return:
"""
directory = path.join(path_to_module, "fake_dir_data")
file_path = path.join(directory, "no_read_files.csv")
with self.assertRaises(SampleSheetError):
res = sample_parser._parse_samples(file_path)
def test_no_forward_read(self):
"""
No Valid files were found with names given in sample sheet
:return:
"""
directory = path.join(path_to_module, "fake_dir_data")
file_path = path.join(directory, "no_forward.csv")
with self.assertRaises(SampleSheetError):
res = sample_parser._parse_samples(file_path)
def test_no_reverse_read_with_comma(self):
"""
The file list in the sample sheet is invalid
:return:
"""
directory = path.join(path_to_module, "fake_dir_data")
file_path = path.join(directory, "no_reverse_with_comma.csv")
res = sample_parser._parse_samples(file_path)
# This should have an empty file reverse
self.assertEqual(res[0]["File_Reverse"], "")
def test_valid(self):
"""
Given a valid sample sheet, parse correctly
:return:
"""
sheet_file = path.join(path_to_module, "fake_dir_data",
"SampleList_simple.csv")
file_name_1 = "file_1.fastq.gz"
file_name_2 = "file_2.fastq.gz"
res = sample_parser._parse_samples(sheet_file)
# Check we have 1 sample
self.assertEqual(len(res), 1)
# Check if data is correct
self.assertEqual(res[0].sample_name, "my-sample-1")
self.assertEqual(res[0].get_uploadable_dict()["sample_project"], "75")
self.assertEqual(res[0].get_uploadable_dict()["File_Forward"], file_name_1)
self.assertEqual(res[0].get_uploadable_dict()["File_Reverse"], file_name_2)