adaptivemd.PythonTask

class adaptivemd.PythonTask(generator=None)

A special task that does a RPC python calls

Variables:

• then_func_name (str or None) – the name of the function of the TaskGenerator to be called with the resulting output
• store_output (bool) – if True then the result from the RPC called function will also be stored in the database. It can later be retrieved using the .output attribute on the task completed successfully

__init__(generator=None)

x.__init__(…) initializes x; see help(type(x)) for signature

Methods

__init__([generator])	x.__init__(…) initializes x; see help(type(x)) for signature
add_cb(event, cb)	Add a custom callback
add_conda_env(name)	Add loading a conda env to all tasks of this resource
add_files(files)	Add additional files to the task execution
add_path(path)	param path:a (list of) path(s) to be added to the $PATH variable before task execution
append(cmd)	Append a command to this task
args()	Return a list of args of the __init__ function of a class
backup_output_json(target)	Add an action that will copy the resulting JSON file to the given path
base()	Return the most parent class actually derived from StorableMixin
call(command, **kwargs)	Set the python function to be called with its arguments
cancel()	Mark a task as cancelled if it it not running or has been halted
descendants()	Return a list of all subclassed objects
fire(event, scheduler)	Fire an event like success or failed.
from_dict(dct)	Reconstruct an object from a dictionary representation
get(f[, name])	Get a file and make it available to the task in the main directory
get_uuid()	Create a new unique ID :returns: the unique number for an object in the project :rtype: long
has_failed()	Check if the task is done executing and has failed
idx(store)	Return the index which is used for the object in the given store.
is_done()	Check if the task is done executing.
link(f[, name])	Add an action to create a link to a file (under a new name)
named(name)	Attach a .name property to an object
objects()	Returns a dictionary of all storable objects
prepend(cmd)	Append a command to this task
put(f, target)	Put a file back and make it persistent
remove(f)	Add an action to remove a file or folder
restart()	Mark a task as being runnable if it was stopped or failed before
setenv(key, value)	Set an environment variable for the task
then(func_name)	Set the name of the function to be called from the generator after success
to_dict()	Convert object into a dictionary representation
touch(f)	Add an action to create an empty file or folder at a given location
was_successful()	Check if the task is done executing and was successful

Attributes

ACTIVE_LONG
CREATION_COUNT
FINAL_STATES
INSTANCE_UUID
RESTARTABLE_STATES
RUNNABLE_STATES
additional_files	list of Location return the list of files created other than taken care of by actions.
base_cls	Return the base class
base_cls_name	Return the name of the base class
cls	Return the class name as a string
dependency_okay	Check if all dependency tasks are successful
description	Return a lengthy description of the task for debugging and information
environment	dict str – str the dict of environment variables and their assigned value
main
modified_files	A set of all input files whose names match output names and hence will be overwritten
new_files	Return a set of all files the will be newly created by this task
output	Return the data contained in the output file
pre_add_paths	list of str the list of added paths to the $PATH variable by this task
pre_exec
ready	Check if this task is ready to be executed
script	list of str or Action the full script of this task.
source_locations	Return a set of all required file urls
sources	Return a set of all required input files
staged_files	Set of all staged files by the tasks generator
state
stderr
stdout
target_locations	Return a set of all new and overwritten file urls
targets	Return a set of all new and overwritten files
then_func
unstaged_input_files	Return a set of File objects that are used but are not part of the generator stage
worker

backup_output_json(target)

Add an action that will copy the resulting JSON file to the given path

Parameters:target (Location) – the place to copy the resulting output.json file to

output

Return the data contained in the output file

Returns: Return type:object

then(func_name)

Set the name of the function to be called from the generator after success

Parameters:func_name (str) – the function name to be called after success

call(command, **kwargs)

Set the python function to be called with its arguments

Parameters:

• command (function) – a python function defined inside a package or a function. If in a package then the package needs to be installed on the cluster to be called. A function defined in a local file can be called as long as dependencies are installed.
• kwargs (**kwargs) – named arguments to the function