def test_complete_with_controls_to_biowdl_new_json():
result_json = """
{"samples": [
{"readgroups": [
{"lib_id": "lib1",
"id": "rg1",
"R1": "r1.fq",
"R1_md5": "hello",
"R2": "r2.fq",
"R2_md5": "hey"
}
],
"id": "s1"},
{"readgroups": [
{"lib_id": "lib1",
"id": "rg1",
"R1": "r1.fq",
"R1_md5": "aa",
"R2": "r2.fq",
"R2_md5": "bb"
}
],
"id": "s2",
"control": "s1"}]
}
"""
result_json_loaded = json.loads(result_json)
assert result_json_loaded == json.loads(
samplegroup_to_biowdl_new_json(COMPLETE_WITH_CONTROL_SAMPLEGROUP))
def test_main(correct_md5sum_samplesheet, capsys):
sys.argv = [
"biowdl-input-converter", "--check-file-md5sums",
str(correct_md5sum_samplesheet)
]
biowdl_input_converter.main()
stdout = capsys.readouterr().out
correct_output = output_conversions.samplegroup_to_biowdl_new_json(
input_conversions.samplesheet_csv_to_samplegroup(
correct_md5sum_samplesheet)) + '\n'
assert stdout == correct_output
def test_main_output_file(correct_md5sum_samplesheet):
output_file = Path(tempfile.mkstemp()[1])
sys.argv = [
"biowdl-input-converter", "--check-file-md5sums", "-o",
str(output_file),
str(correct_md5sum_samplesheet)
]
biowdl_input_converter.main()
output_contents = output_file.read_text()
correct_output = output_conversions.samplegroup_to_biowdl_new_json(
input_conversions.samplesheet_csv_to_samplegroup(
correct_md5sum_samplesheet)) + '\n'
assert output_contents == correct_output
os.remove(str(output_file))
def test_without_md5sum_to_biowdl_new_json():
result_json = """
{"samples": [
{"readgroups": [
{"lib_id": "lib1",
"id": "rg1",
"R1": "r1.fq",
"R2": "r2.fq"
}
],
"id": "s1"},
{"readgroups": [
{"lib_id": "lib1",
"id": "rg1",
"R1": "r1.fq",
"R2": "r2.fq"
}
],
"id": "s2"}]
}
"""
result_json_loaded = json.loads(result_json)
assert result_json_loaded == json.loads(
samplegroup_to_biowdl_new_json(WITHOUT_MD5_SAMPLEGROUP))
def test_nosuffix():
samplesheet = FILESDIR / Path("804935870934875")
output = samplesheet_to_json(samplesheet, fileformat='yaml')
correct_output = output_conversions.samplegroup_to_biowdl_new_json(
input_conversions.biowdl_yaml_to_samplegroup(samplesheet))
assert output == correct_output
def test_yaml_samplesheet_to_json():
samplesheet = FILESDIR / Path("complete.yml")
output = samplesheet_to_json(samplesheet, file_presence_check=False)
correct_output = output_conversions.samplegroup_to_biowdl_new_json(
input_conversions.biowdl_yaml_to_samplegroup(samplesheet))
assert output == correct_output
def test_samplesheet_to_json_no_checks():
output = samplesheet_to_json(COMPLETE_CSV, file_presence_check=False)
correct_output = output_conversions.samplegroup_to_biowdl_new_json(
input_conversions.samplesheet_csv_to_samplegroup(COMPLETE_CSV))
assert output == correct_output