def test_normalise_tsv():
'''
No conversion, just copies the file
'''
with tempfile.TemporaryDirectory() as tmpd:
normalise(setup_args(data_dir, 'tsv', tmpd))
pass
def test_normalise_no_output():
infile = os.path.join(data_dir, 'SimplifiedManifest_v1.0.xlsx')
with tempfile.TemporaryDirectory() as tmpd:
shutil.copy(infile, tmpd)
infile = os.path.join(tmpd, os.path.basename(infile))
args = Namespace(input=infile, output=None)
normalise(args)
pass
def test_normalise_same_in_out_tsv():
'''
In and out are the same so no action taken (warning produced)
'''
infile = os.path.join(data_dir, 'SimplifiedManifest_v1.0.tsv')
args = Namespace(input=infile, output=infile)
normalise(args)
pass
#!/usr/bin/env python3
"""Converts manifests from various types to TSV"""
# python builtin
import argparse
import pkg_resources # part of setuptools
# this project
from cgp_seq_input_val import constants, cliutil
from cgp_seq_input_val.manifest import normalise
version = pkg_resources.require("cgp_seq_input_val")[0].version
## read variables, auto help text
parser = argparse.ArgumentParser(description='Convert manifest files to common denominator (tsv)',
epilog='Input can be [xls|xlsx|csv|tsv]. "tsv" is just copied to maintain tool-chain')
parser.add_argument('-v', '--version', action='version', version='%(prog)s ' + version)
parser.add_argument('-i', '--input', dest='input', metavar='FILE',
help='Input manifest in friendly formats', required=True,
type=lambda s: cliutil.extn_check(parser, constants.MANIFEST_EXTNS, s, readable=True))
parser.add_argument('-o', '--output', dest='output', metavar='FILE',
help='Output file *.tsv [default: sub. extension]', required=False,
type=lambda s: cliutil.extn_check(parser, ('tsv'), s))
args = parser.parse_args()
normalise(args)
def test_normalise_tsv_no_output():
infile = os.path.join(data_dir, 'SimplifiedManifest_v1.0.tsv')
args = Namespace(input=infile, output=None)
normalise(args)
pass
def test_normalise_csv():
with tempfile.TemporaryDirectory() as tmpd:
normalise(setup_args(data_dir, 'csv', tmpd))
pass