def _submit_job(cls, job_script_name, env=None):
"""
:param job_script_name:
:return: the job manager job id
"""
# Create the qsub command for submitting the job
job_script_filename = "./{}.sh".format(job_script_name)
qsub_command = "qsub -N {} {} ".format(job_script_name,
job_script_filename)
output = run_command(qsub_command, env=env)
# get the job id
job_id = output.split()[2]
return job_id
def execute_executable(cls, name, task, input_values, execution_data):
""" Executes the Task as an executable for the given input values on the local machine
:param task: the task to execute
:type task: tigres.type.Task
:param input_values: the input values for the task
:type input_values: InputValues or list
:Example:
>>> from tigres.utils import Execution
>>> from tigres.core.execution import load_plugin
>>> engine = load_plugin(Execution.LOCAL_THREAD)
>>> from tigres import InputTypes, InputValues, Task, EXECUTABLE
>>> input_type_1 = InputTypes(None, [str])
>>> task1 = Task(None, EXECUTABLE, "/bin/echo", input_type_1)
>>> input_values_1 = InputValues(None, ['world'])
>>> engine.execute_executable("foo bar", task1, input_values_1,{'env':{}})
('world', 'DONE')
.. note::
The current implementation will coerce all arguments to strings when it builds the
command for command line execution
"""
output = None
if not execution_data or State.DONE not in list(execution_data.keys()):
cmd = create_executable_command(input_values, task)
# Get the current environment and pass it along to the executable
copy_os_env = copy(os.environ)
try:
copy_os_env.update(execution_data['env'])
output = run_command(cmd, env=copy_os_env)
if execution_data is not None:
execution_data[State.DONE] = State.DONE
except Exception as err:
raise TigresException(
"Exception caught for execution '{w}', Task '{t}'. Error: {e}".format(
w=name, t=task.name, e=err))
return output, State.DONE