def run_from_jobfile(
workflow: Union[str, j.Tool, Type[j.Tool]],
jobfile: PreparedJob,
engine: Union[str, Engine, None] = None,
wait: bool = False,
# specific engine args
cromwell_jar: Optional[str] = None,
cromwell_url: Optional[str] = None,
):
cm = ConfigManager(db_path=jobfile.db_path)
if not workflow:
raise Exception("Couldn't find workflow with name: " + str(workflow))
row = cm.create_task_base(
wf=workflow,
job=jobfile,
)
jobfile.execution_dir = row.execution_dir
jobfile.output_dir = row.output_dir
# set logger for submit
Logger.set_write_level(Logger.CONSOLE_LEVEL)
logpath = os.path.join(
WorkflowManager.get_path_for_component_and_dir(
row.execution_dir, WorkflowManager.WorkflowManagerPath.logs),
"janis-submit.log",
)
Logger.WRITE_LEVELS = {Logger.CONSOLE_LEVEL: (logpath, open(logpath, "a"))}
Logger.debug(f"Set submission logging to '{logpath}'")
print(row.submission_id, file=sys.stdout)
eng = get_engine_from_eng(
engine or jobfile.engine,
wid=row.submission_id,
execdir=WorkflowManager.get_path_for_component_and_dir(
row.execution_dir, WorkflowManager.WorkflowManagerPath.execution),
confdir=WorkflowManager.get_path_for_component_and_dir(
row.execution_dir,
WorkflowManager.WorkflowManagerPath.configuration),
logfile=os.path.join(
WorkflowManager.get_path_for_component_and_dir(
row.execution_dir, WorkflowManager.WorkflowManagerPath.logs),
"engine.log",
),
cromwell_jar=cromwell_jar,
cromwell_url=cromwell_url,
)
try:
wm = WorkflowManager.from_janis(
submission_id=row.submission_id,
tool=workflow,
engine=eng,
prepared_submission=jobfile,
wait=wait,
)
Logger.log("Finished starting task")
return wm
except KeyboardInterrupt:
Logger.info("Exiting...")
try:
wm.abort()
except:
pass
except Exception as e:
# Have to make sure we stop the engine if something happens when creating the task that causes
# janis to exit early
eng.stop_engine()
raise e
return wm
def fromjanis(
workflow: Union[str, j.Tool, Type[j.Tool]],
name: str = None,
engine: Union[str, Engine] = None,
filescheme: Union[str, FileScheme] = LocalFileScheme(),
validation_reqs=None,
batchrun_reqs=None,
hints: Optional[Dict[str, str]] = None,
output_dir: Optional[str] = None,
dryrun: bool = False,
inputs: Union[str, dict] = None,
required_inputs: dict = None,
watch=True,
max_cores=None,
max_memory=None,
force=False,
keep_intermediate_files=False,
recipes=None,
run_in_background=True,
run_in_foreground=None,
dbconfig=None,
only_toolbox=False,
no_store=False,
allow_empty_container=False,
check_files=True,
container_override: dict = None,
**kwargs,
):
cm = ConfigManager.manager()
jc = JanisConfiguration.manager()
wf: Optional[Tool] = resolve_tool(
tool=workflow,
name=name,
from_toolshed=True,
only_toolbox=only_toolbox,
force=force,
)
if not wf:
raise Exception("Couldn't find workflow with name: " + str(workflow))
# if isinstance(tool, j.CommandTool):
# tool = tool.wrapped_in_wf()
# elif isinstance(tool, j.CodeTool):
# tool = tool.wrapped_in_wf()
# organise inputs
inputsdict = {}
if recipes:
valuesfromrecipe = jc.recipes.get_recipe_for_keys(recipes)
inputsdict.update(valuesfromrecipe)
inputsdict.update(
cascade_inputs(
wf=wf,
inputs=inputs,
required_inputs=required_inputs,
batchrun_options=batchrun_reqs,
))
row = cm.create_task_base(wf,
outdir=output_dir,
store_in_centraldb=not no_store)
print(row.wid, file=sys.stdout)
engine = engine or jc.engine
eng = get_engine_from_eng(
engine,
wid=row.wid,
execdir=WorkflowManager.get_path_for_component_and_dir(
row.outputdir, WorkflowManager.WorkflowManagerPath.execution),
confdir=WorkflowManager.get_path_for_component_and_dir(
row.outputdir, WorkflowManager.WorkflowManagerPath.configuration),
logfile=os.path.join(
WorkflowManager.get_path_for_component_and_dir(
row.outputdir, WorkflowManager.WorkflowManagerPath.logs),
"engine.log",
),
watch=watch,
**kwargs,
)
fs = get_filescheme_from_fs(filescheme, **kwargs)
environment = Environment(f"custom_{wf.id()}", eng, fs)
try:
# Note: run_in_foreground can be None, so
# (not (run_in_foreground is True)) != (run_in_foreground is False)
should_run_in_background = (run_in_background is True
or jc.run_in_background is True
) and not (run_in_foreground is True)
tm = cm.start_task(
wid=row.wid,
tool=wf,
environment=environment,
validation_requirements=validation_reqs,
batchrun_requirements=batchrun_reqs,
task_path=row.outputdir,
hints=hints,
inputs_dict=inputsdict,
dryrun=dryrun,
watch=watch,
max_cores=max_cores,
max_memory=max_memory,
keep_intermediate_files=keep_intermediate_files,
run_in_background=should_run_in_background,
dbconfig=dbconfig,
allow_empty_container=allow_empty_container,
container_override=container_override,
check_files=check_files,
)
Logger.log("Finished starting task task")
return tm
except KeyboardInterrupt:
Logger.info("Exiting...")
except Exception as e:
# Have to make sure we stop the engine if something happens when creating the task that causes
# janis to exit early
environment.engine.stop_engine()
raise e