def test_awsem_exception_no_space():
log = '[fputs] No space left on device' + \
'some text some text'
eh = AWSEMErrorHandler()
res = eh.parse_log(log)
assert res
with pytest.raises(AWSEMJobErrorException) as exec_info:
raise res
assert 'Not enough space' in str(exec_info.value)
assert '[fputs]' in str(exec_info.value)
def test_awsem_exception_no_space_for_docker():
log = "failed to register layer: Error processing tar file(exit status 1): " + \
"write /miniconda3/pkgs/python-3.7.6-h0371630_2.tar.bz2: no space left on device" + \
"some text some text"
eh = AWSEMErrorHandler()
res = eh.parse_log(log)
assert res
with pytest.raises(AWSEMJobErrorException) as exec_info:
raise res
assert 'No space for docker' in str(exec_info.value)
assert 'tar.bz2: no space left' in str(exec_info.value)
def test_awsem_exception_not_enough_space_for_input():
log = "sometext some text some other text " + \
"download failed: s3://somebucket/somefile to ../../data1/input/somefile " + \
"[Errno 28] No space left on device " + \
"some other text some other text"
eh = AWSEMErrorHandler()
res = eh.parse_log(log)
assert res
with pytest.raises(AWSEMJobErrorException) as exec_info:
raise res
assert 'Not enough space for input files' in str(exec_info.value)
def test_awsem_exception_cwl_missing_input():
log = "Workflow error, try again with --debug for more information:\n" + \
"Invalid job input record:\n" + \
"workflow_gatk-GenotypeGVCFs_plus_vcf-integrity-check.cwl:28:5: Missing required input parameter\n" + \
" 'chromosomes'\n" + \
"some text some text"
eh = AWSEMErrorHandler()
res = eh.parse_log(log)
assert res
with pytest.raises(AWSEMJobErrorException) as exec_info:
raise res
assert 'CWL missing input' in str(exec_info.value)
assert 'chromosomes' in str(exec_info.value)
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)
def test_general_awsem_error_msg():
eh = AWSEMErrorHandler()
res = eh.general_awsem_error_msg('somejobid')
assert res == 'Job encountered an error check log using tibanna log --job-id=somejobid [--sfn=stepfunction]'
def test_no_matching_error():
log = 'some text some text no error just some text'
eh = AWSEMErrorHandler()
res = eh.parse_log(log)
assert not res
def test_general_awsem_check_log_msg():
eh = AWSEMErrorHandler()
res = eh.general_awsem_check_log_msg('somejobid')
assert res == 'check log using tibanna log --job-id=somejobid [--sfn=stepfunction]'