def test_ec20_xlsx_unit(capsys):
"""If the input worklist file doesn't even exist..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'foo.xlsx'))
assert error_code == 20
check_run_qc(capsys, 1, 'Input file is missing:',
RESOURCE_BASE / 'empty_file')
def test_ec18_unit(capsys):
"""If the input worklist file has the wrong extension..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'foo.foo'))
assert error_code == 18
check_run_qc(capsys, 1, 'Input file has bad extension:',
RESOURCE_BASE / 'empty_file')
def test_ec19_unit(capsys):
"""If the input worklist file isn't a file..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE))
assert error_code == 19
check_run_qc(capsys, 1, 'Input is not a file:',
RESOURCE_BASE / 'empty_file')
def test_ec15_unit(capsys):
"""If a CRAM is missing or not a file..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_15.tsv'))
assert error_code == 15
check_run_qc(capsys, 1, 'CRAM is missing:',
RESOURCE_BASE / 'tsv_main/ec_15_expect.tsv')
def test_ec17_xlsx_unit(capsys):
"""If the input worklist file has bad contents..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'bad.xlsx'))
assert error_code == 17
check_run_qc(capsys, 1, 'Input file has bad contents:',
RESOURCE_BASE / 'empty_file')
def test_ec13_unit(capsys):
"""If a CRAM file is too bad to read..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_13.tsv'))
assert error_code == 13
check_run_qc(capsys, 1, 'CRAM is bad:',
RESOURCE_BASE / 'tsv_main/ec_13_expect.tsv')
def test_ec14_unit(capsys):
"""If a JSON is missing or not a file..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_14.tsv'))
assert error_code == 14
check_run_qc(capsys, 1, 'JSON is missing:',
RESOURCE_BASE / 'tsv_main/ec_14_expect.tsv')
def test_ec10_unit(capsys):
"""If an RG in a CRAM file is missing an SM..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_10.tsv'))
assert error_code == 10
check_run_qc(capsys, 1, 'An RG in the CRAM is missing its SM:',
RESOURCE_BASE / 'tsv_main/ec_10_expect.tsv')
def test_ec12_unit(capsys):
"""If a JSON file is too bad to read..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_12.tsv'))
assert error_code == 12
check_run_qc(capsys, 1, 'JSON is bad:',
RESOURCE_BASE / 'tsv_main/ec_12_expect.tsv')
def test_ec7_unit(capsys):
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_7.xlsx.tsv'))
assert error_code == 7
check_run_qc(capsys, 1, 'CRAM contains multiple values for sample.',
RESOURCE_BASE / 'tsv_main/ec_7_expect.tsv')
def test_ec9_unit(capsys):
"""If an RG in a CRAM file is missing a PU..."""
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_9.tsv'))
assert error_code == 9
check_run_qc(capsys, 1, 'An RG in the CRAM is missing its PU:',
RESOURCE_BASE / 'tsv_main/ec_9_expect.tsv')
def test_ec6_unit(capsys):
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_6.xlsx.tsv'))
assert error_code == 6
check_run_qc(capsys, 1, 'CRAM has wrong sample name.',
RESOURCE_BASE / 'tsv_main/ec_6_expect.tsv')
def test_ec5_unit(capsys):
error_code = mplx_qc.run_qc(
str(RESOURCE_BASE / 'tsv_jwatt/ec_5_b.xlsx.tsv'))
assert error_code == 5
check_run_qc(capsys, 3, 'CRAM and JSON have different sample names.',
RESOURCE_BASE / 'tsv_jwatt/ec_5_expect.tsv')
def test_ec4_unit(capsys):
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_4.xlsx.tsv'))
assert error_code == 4
check_run_qc(capsys, 1, 'Duplicate barcodes in CRAM.',
RESOURCE_BASE / 'tsv_main/ec_4_expect.tsv')
def test_ec2_unit(capsys):
error_code = mplx_qc.run_qc(
str(RESOURCE_BASE / 'tsv_jwatt/ec_2_b.xlsx.tsv'))
assert error_code == 2
check_run_qc(capsys, 3, 'CRAM and JSON have mismatching sets of barcodes.',
RESOURCE_BASE / 'tsv_jwatt/ec_2_expect.tsv')
def test_ec0_unit(capsys):
error_code = mplx_qc.run_qc(str(RESOURCE_BASE / 'tsv_main/ec_0.xlsx.tsv'))
out, err = capsys.readouterr()
print(out)
print(err, file=sys.stderr)
assert error_code == 0