def test_add_custom_errors2():
log = "sometext some text some other text " + \
"Exception: File is empty (1234567890abcdefg.regionPeak.gz) some other text"
eh = AWSEMErrorHandler()
eh.add_custom_errors([{
"error_type":
"No peak called",
"pattern":
"Exception: File is empty (.+.regionPeak.gz)"
}])
res = eh.parse_log(log)
assert res
with pytest.raises(AWSEMJobErrorException) as exec_info:
raise res
assert 'No peak called' in str(exec_info.value)
assert '1234567890abcdefg.regionPeak.gz' in str(exec_info.value)
def test_add_custom_errors():
log = "[M::mem_pestat] low and high boundaries for proper pairs: (1, 22)" + \
"[mem_sam_pe] paired reads have different names: " + \
"\"H3MVTCCXX:4:1101:1174861:0\", \"H3MVTCCXX:4:1101:743397:0\""
eh = AWSEMErrorHandler()
eh.add_custom_errors([{
"error_type": "Unmatching pairs in fastq",
"pattern": "paired reads have different names: .+",
"multiline": False
}])
assert len(eh.ErrorList) == len(eh._ErrorList) + 1
res = eh.parse_log(log)
assert res
with pytest.raises(AWSEMJobErrorException) as exec_info:
raise res
assert 'Unmatching pairs in fastq' in str(exec_info.value)
assert 'H3MVTCCXX:4:1101:1174861:0' in str(exec_info.value)