def test_two_flags(self):
self.assertDictEqual(
{
"flag1": True,
"flag2": True
},
parse_additional_arguments(["--flag1", "--flag2"]),
)
def test_parse_two_prefixes_and_value(self):
self.assertDictEqual(
{
"myprefix1": "value1",
"myprefix2": "value2"
},
parse_additional_arguments(
["--myprefix1", "value1", "--myprefix2", "value2"]),
)
def test_specified_multiple_nargs(self):
self.assertDictEqual(
{"t": [[1, 2], ["a", "b"]]},
parse_additional_arguments(["-t", "1", "2", "-t", "a", "b"]),
)
def test_specified_multiple(self):
self.assertDictEqual({"t": [1, 2]},
parse_additional_arguments(["-t", "1", "-t",
"2"]))
def test_parse_multiple_mixed_values(self):
self.assertDictEqual(
{"my_mixed_bag": [4.7, True, "valueish", 0]},
parse_additional_arguments(
["--my-mixed-bag", "4.7", "true", "valueish", "0"]),
)
def test_parse_three_values(self):
self.assertDictEqual(
{"myprefix": ["val1", "val2", "val3"]},
parse_additional_arguments(["--myprefix", "val1", "val2", "val3"]),
)
def test_parse_prefix_and_value(self):
self.assertDictEqual({"myprefix": "value"},
parse_additional_arguments(
["--myprefix", "value"]))
def test_one_flag(self):
self.assertDictEqual({"sampleflag": True},
parse_additional_arguments(["--sampleflag"]))
def do_run(args):
jc = JanisConfiguration.initial_configuration(args.config)
validation_reqs, batchrun_reqs = None, None
if args.validation_fields:
Logger.info("Will prepare validation")
validation_reqs = ValidationRequirements(
truthVCF=args.validation_truth_vcf,
reference=args.validation_reference,
fields=args.validation_fields,
intervals=args.validation_intervals,
)
if args.batchrun:
Logger.info("Will prepare batch run")
batchrun_reqs = BatchRunRequirements(fields=args.batchrun_fields,
groupby=args.batchrun_groupby)
hints = {
k[5:]: v
for k, v in vars(args).items()
if k.startswith("hint_") and v is not None
}
# the args.extra_inputs parameter are inputs that we MUST match
# we'll need to parse them manually and then pass them to fromjanis as requiring a match
required_inputs = parse_additional_arguments(args.extra_inputs)
inputs = args.inputs or []
# we'll manually suck "inputs" out of the extra parms, otherwise it's actually really
# annoying if you forget to put the inputs before the workflow positional argument.
# TBH, we could automatically do this for all params, but it's a little trickier
if "inputs" in required_inputs:
ins = required_inputs.pop("inputs")
inputs.extend(ins if isinstance(ins, list) else [ins])
if "i" in required_inputs:
ins = required_inputs.pop("i")
inputs.extend(ins if isinstance(ins, list) else [ins])
keep_intermediate_files = args.keep_intermediate_files is True
db_config = jc.cromwell.get_database_config_helper()
if args.mysql:
db_config.should_manage_mysql = True
if args.no_database:
db_config.skip_database = True
if args.development:
# no change for using mysql, as a database is the default
keep_intermediate_files = True
JanisConfiguration.manager().cromwell.call_caching_enabled = True
wid = fromjanis(
args.workflow,
name=args.name,
validation_reqs=validation_reqs,
batchrun_reqs=batchrun_reqs,
engine=args.engine,
filescheme=args.filescheme,
hints=hints,
output_dir=args.output_dir,
inputs=inputs,
required_inputs=required_inputs,
filescheme_ssh_binding=args.filescheme_ssh_binding,
cromwell_url=args.cromwell_url,
watch=args.progress,
max_cores=args.max_cores,
max_mem=args.max_memory,
force=args.no_cache,
recipes=args.recipe,
keep_intermediate_files=keep_intermediate_files,
run_in_background=(args.background is True),
run_in_foreground=(args.foreground is True),
dbconfig=db_config,
only_toolbox=args.toolbox,
no_store=args.no_store,
allow_empty_container=args.allow_empty_container,
check_files=not args.skip_file_check,
container_override=parse_container_override_format(
args.container_override),
)
Logger.info("Exiting")
raise SystemExit
def prepare_from_args(
args, run_prepare_processing: bool) -> Tuple[PreparedJob, Tool]:
jc = JanisConfiguration.initial_configuration(path=args.config)
# the args.extra_inputs parameter are inputs that we MUST match
# we'll need to parse them manually and then pass them to fromjanis as requiring a match
required_inputs = parse_additional_arguments(args.extra_inputs)
inputs = args.inputs or []
# we'll manually suck "inputs" out of the extra parms, otherwise it's actually really
# annoying if you forget to put the inputs before the workflow positional argument.
# TBH, we could automatically do this for all params, but it's a little trickier
if "inputs" in required_inputs:
ins = required_inputs.pop("inputs")
inputs.extend(ins if isinstance(ins, list) else [ins])
if "i" in required_inputs:
ins = required_inputs.pop("i")
inputs.extend(ins if isinstance(ins, list) else [ins])
validation, batchrun = None, None
if args.validation_fields:
Logger.info("Will prepare validation")
validation = ValidationRequirements(
truthVCF=args.validation_truth_vcf,
reference=args.validation_reference,
fields=args.validation_fields,
intervals=args.validation_intervals,
)
if args.batchrun:
Logger.info("Will prepare batch run")
batchrun = BatchRunRequirements(fields=args.batchrun_fields,
groupby=args.batchrun_groupby)
db_type: Optional[DatabaseTypeToUse] = None
if args.no_database:
db_type = DatabaseTypeToUse.none
elif args.mysql:
db_type = DatabaseTypeToUse.managed
try:
source_hints = args.source_hint
except:
source_hints = []
wf, wf_reference = resolve_tool(
tool=args.workflow,
name=args.name,
from_toolshed=True,
only_toolbox=args.toolbox,
force=args.no_cache,
)
job = prepare_job(
run_prepare_processing=run_prepare_processing,
tool=wf,
workflow_reference=wf_reference,
jc=jc,
engine=args.engine,
output_dir=args.output_dir,
execution_dir=args.execution_dir,
max_cores=args.max_cores,
max_memory=args.max_memory,
max_duration=args.max_duration,
run_in_foreground=args.foreground is True,
run_in_background=args.background is True,
check_files=not args.skip_file_check,
container_override=parse_container_override_format(
args.container_override),
skip_digest_lookup=args.skip_digest_lookup,
skip_digest_cache=args.skip_digest_cache,
hints={
k[5:]: v
for k, v in vars(args).items()
if k.startswith("hint_") and v is not None
},
validation_reqs=validation,
batchrun_reqs=batchrun,
# inputs
inputs=inputs,
required_inputs=required_inputs,
watch=args.progress,
recipes=args.recipe,
keep_intermediate_files=args.keep_intermediate_files is True,
no_store=args.no_store,
allow_empty_container=args.allow_empty_container,
strict_inputs=args.strict_inputs,
db_type=db_type,
source_hints=source_hints,
post_run_script=args.post_run_script,
localise_all_files=args.localise_all_files,
)
return job, wf