def generate_inputs(
tool: Union[str, j.CommandTool, j.Workflow],
all=False,
name=None,
force=False,
additional_inputs=None,
with_resources=False,
quality_type: List[InputQualityType] = None,
recipes: List[str] = None,
hints: dict = None,
):
toolref = resolve_tool(tool, name, from_toolshed=True, force=force)
inputsdict = None
if additional_inputs:
inputsfile = get_file_from_searchname(additional_inputs, ".")
inputsdict = parse_dict(inputsfile)
values_to_ignore = set()
if recipes:
jc = JanisConfiguration.manager()
for k in jc.recipes.get_recipe_for_keys(recipes):
values_to_ignore.add(k)
if not toolref:
raise Exception("Couldn't find workflow with name: " + str(tool))
return toolref.generate_inputs_override(
additional_inputs=inputsdict,
with_resource_overrides=with_resources,
include_defaults=all,
values_to_ignore=values_to_ignore,
quality_type=quality_type,
hints=hints,
)
def cascade_inputs(
wf: Optional[Tool],
inputs: Optional[Union[Dict, List[Union[str, Dict]]]],
required_inputs: Optional[Dict],
batchrun_options: Optional[BatchRunRequirements] = None,
strict_inputs: bool = False,
):
list_of_input_dicts: List[Dict] = []
if inputs:
if not isinstance(inputs, list):
inputs = [inputs]
for inp in inputs:
if isinstance(inp, dict):
list_of_input_dicts.append(inp)
else:
inputsfile = get_file_from_searchname(inp, ".")
if inputsfile is None:
raise FileNotFoundError("Couldn't find inputs file: " +
str(inp))
list_of_input_dicts.append(parse_dict(inputsfile))
ins = None
if batchrun_options:
ins = cascade_batchrun_inputs(wf, list_of_input_dicts,
batchrun_options)
else:
ins = cascade_regular_inputs(list_of_input_dicts)
if strict_inputs:
# make all the inputs in "ins" required (make sure they don't override already required inputs)
required_inputs = {**ins, **(required_inputs or {})}
if required_inputs:
if wf is None:
raise Exception(
"cascade_inputs requires 'wf' parameter if required_inputs is present"
)
if isinstance(wf, DynamicWorkflow):
pass
else:
reqkeys = set(required_inputs.keys())
inkeys = set(wf.all_input_keys())
invalid_keys = reqkeys - inkeys
if len(invalid_keys) > 0:
raise Exception(
f"There were unrecognised inputs provided to the tool \"{wf.id()}\", keys: {', '.join(invalid_keys)}"
)
ins = {**ins, **(required_inputs or {})}
return ins
def translate(
tool: Union[str, j.CommandTool, Type[j.CommandTool], j.Workflow,
Type[j.Workflow]],
translation: str,
name: str = None,
hints: Optional[Dict[str, str]] = None,
output_dir: Optional[str] = None,
inputs: Union[str, dict] = None,
allow_empty_container=False,
container_override=None,
**kwargs,
):
toolref = resolve_tool(tool, name, from_toolshed=True)
if not toolref:
raise Exception(f"Couldn't find tool: '{tool}'")
inputsdict = None
if inputs:
inputsfile = get_file_from_searchname(inputs, ".")
inputsdict = parse_dict(inputsfile)
if isinstance(toolref, j.Workflow):
wfstr, _, _ = toolref.translate(
translation,
to_console=False,
to_disk=bool(output_dir),
export_path=output_dir or "./{language}",
hints=hints,
additional_inputs=inputsdict,
allow_empty_container=allow_empty_container,
container_override=container_override,
)
elif isinstance(toolref, (j.CommandTool, j.CodeTool)):
wfstr = toolref.translate(
translation=translation,
to_console=False,
to_disk=bool(output_dir),
export_path=output_dir or "./{language}",
allow_empty_container=allow_empty_container,
container_override=container_override,
)
else:
name = toolref.__name__ if isclass(
toolref) else toolref.__class__.__name__
raise Exception("Unsupported tool type: " + name)
print(wfstr, file=sys.stdout)
return wfstr
def generate_inputs(
jc: JanisConfiguration,
tool: Union[str, j.CommandTool, j.Workflow],
all=False,
name=None,
force=False,
additional_inputs=None,
with_resources=False,
quality_type: List[InputQualityType] = None,
recipes: List[str] = None,
hints: dict = None,
):
toolref, _ = resolve_tool(tool, name, from_toolshed=True, force=force)
inputsdict = None
if additional_inputs:
inputsfile = get_file_from_searchname(additional_inputs, ".")
inputsdict = parse_dict(inputsfile)
values_to_ignore = set()
if recipes:
if not jc:
Logger.warn(
"An internal error occurred when getting recipes from your config, please raise an issue on GitHub."
)
else:
for k in jc.recipes.get_recipe_for_keys(recipes):
values_to_ignore.add(k)
if not toolref:
raise Exception("Couldn't find workflow with name: " + str(tool))
d = toolref.generate_inputs_override(
additional_inputs=inputsdict,
with_resource_overrides=with_resources,
include_defaults=all,
values_to_ignore=values_to_ignore,
quality_type=quality_type,
hints=hints,
)
return d
def cascade_inputs(
wf: Workflow,
inputs: Optional[Union[Dict, List[Union[str, Dict]]]],
required_inputs: Optional[Dict],
batchrun_options: Optional[BatchRunRequirements],
):
list_of_input_dicts: List[Dict] = []
if inputs:
if not isinstance(inputs, list):
inputs = [inputs]
for inp in inputs:
if isinstance(inp, dict):
list_of_input_dicts.append(inp)
else:
inputsfile = get_file_from_searchname(inp, ".")
if inputsfile is None:
raise FileNotFoundError("Couldn't find inputs file: " + str(inp))
list_of_input_dicts.append(parse_dict(inputsfile))
if required_inputs:
reqkeys = set(required_inputs.keys())
inkeys = set(wf.all_input_keys())
invalid_keys = reqkeys - inkeys
if len(invalid_keys) > 0:
raise Exception(
f"There were unrecognised inputs provided to the tool \"{wf.id()}\", keys: {', '.join(invalid_keys)}"
)
list_of_input_dicts.append(parse_known_inputs(wf, required_inputs))
ins = None
if batchrun_options:
ins = cascade_batchrun_inputs(wf, list_of_input_dicts, batchrun_options)
else:
ins = cascade_regular_inputs(list_of_input_dicts)
return ins
def do_run(args):
if args.job:
from os import getcwd
workflow, workflow_ref = resolve_tool(
tool=args.workflow,
name=args.name,
from_toolshed=True,
only_toolbox=args.toolbox,
force=args.no_cache,
)
# parse and load the job file
Logger.info("Specified job file, ignoring all other parameters")
d = parse_dict(get_file_from_searchname(args.job, getcwd()))
job = PreparedJob(**d, workflow_reference=workflow_ref)
else:
job, workflow = prepare_from_args(args, run_prepare_processing=False)
jobfile = run_from_jobfile(workflow, jobfile=job, wait=args.wait)
Logger.info("Exiting")
raise SystemExit