def test_manifest_write():
with tempfile.TemporaryDirectory() as tmpd:
manifest = Manifest(
os.path.join(test_data, 'file_set_good', 'files_good.tsv'))
manifest.validate()
(tsv_file, json_file) = manifest.write(
tmpd) # output new manifest in tsv and json.
def test_manifest_uuid_novalidate():
with tempfile.TemporaryDirectory() as tmpd:
manifest = Manifest(
os.path.join(test_data, 'file_set_good', 'files_good.tsv'))
assert manifest.get_uuid()
def test_manifest_existing_bad_uuid():
with tempfile.TemporaryDirectory() as tmpd:
manifest = Manifest(os.path.join(test_data, 'with_bad_uuid.tsv'))
manifest.validate()
def test_manifest_existing_uuid():
with tempfile.TemporaryDirectory() as tmpd:
manifest = Manifest(os.path.join(test_data, 'with_uuid.tsv'))
manifest.validate()
assert manifest.get_uuid() == '05218fd0-79e5-4214-92d5-e133cd16a798'
def test_manifest_bad_filetype():
infile = os.path.join(data_dir, 'SimplifiedManifest_v1.0.xls')
manifest = Manifest(infile)
manifest.validate()
def test_manifest_missing_required():
infile = os.path.join(data_dir, 'SimplifiedManifest_v1.0.tsv')
manifest = Manifest(infile)
manifest.validate()
def test_manifest_paired_extn_mismatch():
infile = os.path.join(test_data, 'pairedExtnMismatch.tsv')
manifest = Manifest(infile)
manifest.validate()
def test_manifest_file_set_good():
infile = os.path.join(test_data, 'file_set_good', 'files_good.tsv')
manifest = Manifest(infile)
manifest.validate(True)
as_json = json.dumps(manifest.for_json())
def test_manifest_body_head_order():
infile = os.path.join(test_data, 'bodyHeadOrder.tsv')
manifest = Manifest(infile)
manifest.validate()
def test_manifest_extn_file2():
infile = os.path.join(test_data, 'invalidExtnFile2.tsv')
manifest = Manifest(infile)
manifest.validate()
def test_manifest_dup_files_diff_row():
infile = os.path.join(test_data, 'dupFilesDiffRow.tsv')
manifest = Manifest(infile)
manifest.validate()
def test_manifest_dup_files_same_row():
infile = os.path.join(test_data, 'dupFilesSameRow.tsv')
manifest = Manifest(infile)
manifest.validate()
def test_manifest_period_body_val():
infile = os.path.join(test_data, 'periodBodyVal.tsv')
manifest = Manifest(infile)
manifest.validate()
def test_manifest_absent_body_val():
infile = os.path.join(test_data, 'absentBodyVal.tsv')
manifest = Manifest(infile)
manifest.validate()
'-i',
'--input',
dest='input',
metavar='FILE',
help='Input manifest in tsv formats',
required=True,
type=lambda s: cliutil.extn_check(parser, ('tsv'), s, readable=True))
parser.add_argument('-o',
'--output',
dest='output',
metavar='DIR',
help='Output manifest to this area, two files (tsv, json)',
required=True)
parser.add_argument('-c',
'--checkfiles',
dest='checkfiles',
action='store_true',
help='When present check file exist and are non-zero size')
args = parser.parse_args()
try:
manifest = Manifest(args.input)
manifest.validate()
(tsv_file, json_file) = manifest.write(
args.output) # output new manifest in tsv and json.
print("Created files:\n\t%s\n\t%s" % (tsv_file, json_file))
except ValidationError as ve:
print("ERROR: " + str(ve), file=sys.stderr)
exit(1)
