def test_expanding_convert_inputs(self):
overlay = os.path.abspath(
package_path('src/mavis_config/overlay.json'))
main = os.path.abspath(package_path('src/mavis_config/config.json'))
conf = {
'reference.annotations': [EXISTING_FILE],
'skip_stage.validate': True,
'reference.reference_genome': [EXISTING_FILE],
'libraries': {
'AAAA': {
'disease_status': 'diseased',
'protocol': 'genome',
'assign': ['dlly'],
}
},
'convert': {
'dlly': {
'file_type': 'delly',
'inputs': [package_path('src/mavis_config/*.json')],
}
},
'output_dir': '.',
}
validate_config(
conf,
stage='setup',
)
assert conf['libraries']['AAAA']['assign'] == ['dlly']
assert conf['convert']['dlly']['inputs'] == [main, overlay]
def test_missing_output_dir_for_convert(self):
with pytest.raises(WorkflowError) as err:
conf = {
'reference.annotations': [EXISTING_FILE],
'skip_stage.validate': True,
'reference.reference_genome': [EXISTING_FILE],
'libraries': {
'AAAA': {
'disease_status': 'diseased',
'protocol': 'genome',
'assign': ['dlly'],
}
},
'convert': {
'dlly': {
'file_type': 'delly',
'inputs': [package_path('src/mavis_config/*.json')],
}
},
}
validate_config(
conf,
stage='setup',
)
assert 'missing required property: output_dir' in str(err)
def test_error_on_missing_libraries(self):
with pytest.raises(WorkflowError) as err:
validate_config(
{
'reference.annotations': [EXISTING_FILE],
'reference.aligner_reference': [EXISTING_FILE],
'reference.reference_genome': [EXISTING_FILE],
},
stage='setup',
)
assert 'missing required property: libraries' in str(err)
def test_library_missing_assign(self):
with pytest.raises(WorkflowError) as err:
conf = validate_config(
{
'reference.annotations': [EXISTING_FILE],
'skip_stage.validate': True,
'reference.reference_genome': [EXISTING_FILE],
'libraries': {
'AAAA': {
'disease_status': 'diseased',
'protocol': 'genome'
}
},
},
stage='setup',
)
assert 'ValidationError: \'assign\' is a required property' in str(err)
def main(argv: Optional[List[str]] = None):
"""
sets up the parser and checks the validity of command line args
loads reference files and redirects into subcommand main functions
Args:
argv: List of arguments, defaults to command line arguments
"""
if argv is None: # need to do at run time or patching will not behave as expected
argv = sys.argv[1:]
start_time = int(time.time())
parser, args = create_parser(argv)
if args.command == SUBCOMMAND.OVERLAY:
args = check_overlay_args(args, parser)
log_conf = {
'format': '{asctime} [{levelname}] {message}',
'style': '{',
'level': args.log_level,
}
original_logging_handlers = logging.root.handlers[:]
for handler in logging.root.handlers:
logging.root.removeHandler(handler)
if args.log: # redirect stdout AND stderr to a log file
log_conf['filename'] = args.log
logging.basicConfig(**log_conf)
_util.logger.info(f'MAVIS: {__version__}')
_util.logger.info(f'hostname: {platform.node()}')
_util.log_arguments(args)
config: Dict = dict()
try:
if args.command != SUBCOMMAND.CONVERT:
with open(args.config, 'r') as fh:
config = json.load(fh)
validate_config(
config,
args.command,
)
except AttributeError as err:
raise err
if args.command == SUBCOMMAND.VALIDATE:
args.aligner_version = get_aligner_version(config['validate.aligner'])
# try checking the input files exist
try:
args.inputs = _util.bash_expands(*args.inputs)
except AttributeError:
pass
except FileNotFoundError:
parser.error('--inputs file(s) for {} {} do not exist'.format(
args.command, args.inputs))
# decide which main function to execute
command = args.command
try:
if command == SUBCOMMAND.CLUSTER:
cluster_main.main(
inputs=args.inputs,
output=args.output,
start_time=start_time,
config=config,
library=args.library,
)
elif command == SUBCOMMAND.VALIDATE:
validate_main.main(
inputs=args.inputs,
output=args.output,
start_time=start_time,
config=config,
library=args.library,
)
elif command == SUBCOMMAND.ANNOTATE:
annotate_main.main(
inputs=args.inputs,
output=args.output,
start_time=start_time,
config=config,
library=args.library,
)
elif command == SUBCOMMAND.PAIR:
pairing_main.main(
inputs=args.inputs,
output=args.output,
start_time=start_time,
config=config,
)
elif command == SUBCOMMAND.SUMMARY:
summary_main.main(
inputs=args.inputs,
output=args.output,
start_time=start_time,
config=config,
)
elif command == SUBCOMMAND.CONVERT:
convert_main(
args.inputs,
args.outputfile,
args.file_type,
args.strand_specific,
args.assume_no_untemplated,
)
elif command == SUBCOMMAND.SETUP:
# add bam stats to the config if missing
if not config.get('skip_stage.validate'):
_config.add_bamstats_to_config(config)
_util.logger.info(f'writing: {args.outputfile}')
with open(args.outputfile, 'w') as fh:
fh.write(json.dumps(config, sort_keys=True, indent=' '))
else:
overlay_main(
buffer_length=args.buffer_length,
gene_name=args.gene_name,
markers=args.markers,
read_depth_plots=args.read_depth_plots,
config=config,
output=args.output,
)
duration = int(time.time()) - start_time
hours = duration - duration % 3600
minutes = duration - hours - (duration - hours) % 60
seconds = duration - hours - minutes
_util.logger.info('run time (hh/mm/ss): {}:{:02d}:{:02d}'.format(
hours // 3600, minutes // 60, seconds))
_util.logger.info(f'run time (s): {duration}')
except Exception as err:
raise err
finally:
try:
for handler in logging.root.handlers:
logging.root.removeHandler(handler)
for handler in original_logging_handlers:
logging.root.addHandler(handler)
except Exception as err:
print(err)
def test_error_on_missing_aligner_reference(self):
with pytest.raises(WorkflowError) as err:
validate_config({'reference.annotations': [EXISTING_FILE]},
stage='setup')
assert 'missing required property: reference.aligner_reference' in str(
err)
def test_ok_with_required(self):
with not_raises(WorkflowError):
validate_config(
{'reference.annotations': [EXISTING_FILE]},
stage='overlay',
)
def test_error_on_missing_required(self):
with pytest.raises(WorkflowError):
validate_config({}, stage='overlay')