Workflow

class openmsimodel.workflow.workflow.Workflow(*args, **kwargs)

Bases: Runnable

Class to model a workflow, typically a set of processing steps, experiments, and characterizations, into GEMD, a data model. the definition of a workflow is meant to be flexible to the needs of the user. Workflows can be composed to construct even larger GEMD graphs. It offers utilities functions to build the model flexibly, break it down into smaller, easier to manage blocks, or complete operations such as dumping and loading models into/from JSONs.

ARGUMENT_PARSER_TYPE

alias of OpenMSIModelParser

build()

This function builds the entire GEMD model that represents a certain Workflow. to be overwritten by child objects of Workflow that correspond to a specific workflow / user case.

thin_dumps()

dumps the entire model into a JSON per object, each representing the ‘thin’ version’ of the object in which pointers (i.e., true value) are replaced by links (e.g., uuid).

dumps()

dumps the entire model into a single JSON, which contains all the model objects with data pointers (!= links).

thin_loads()

loads the entire model from a list of JSONs, each representing the ‘thin’ version’ of the model object in which pointers (i.e., true value) are replaced by links (e.g., uuid).

loads()

loads the entire model from a single JSON, which contains all the model objects with data pointers (!= links)

local_out(item)

function object to run on individual item during recursion :param item: json item to write its destination se

classmethod get_command_line_arguments()

Get the list of argument names and the dictionary of argument names/default values to add to the argument parser

Returns:

args, a list of argument names recognized by the argument parser

Return type:

list(str)

Returns:

kwargs, a dictionary of default argument values keyed by argument names recognized by the argument parser

Return type:

dict

classmethod run_from_command_line(args=None)

Child classes should implement this function to do whatever it is they do when they run from the command line

Parameters:

args (list) – the list of arguments to send to the parser instead of getting them from sys.argv