inm_rspace.workflow module

Examples

A fully automated workflow that takes RSpace documents with attached CSV files and plots them:

The Input fields in the RSpace document look like this:

The automatically generated Output field looks like this:

The code for this example can be found here.

API documentation

class inm_rspace.workflow.Workflow(document: dict, path='/home/runner')

Bases: object

Parent class defining an API for Python workflows that are executed on

RSpace documents.

In order to define a new workflow,

• declare a new Python class as subclass of this Workflow class

• in that class, redefine functions define(self) and workflow(self, …). (see documentation of those functions below and this example workflow.

check_args(fun)

Check if the keyword arguments provided to the workflow actually match the valid keyword arguments of a given Python function

Parameters:

fun (function) – The Python functions whose kwargs to check

check_completed()

Check if the requested workflow has already been completed.

check_workflow()

Check if the requested workflow matches this one. This returns immediately if field_name[‘workflow’] is None.

define()

Define the properties of the Workflow.

This function should be redefined for every newly created subclass of Workflow.

To request a Workflow, an RSpace document must contain at least the following categories fields, whose field names you specify here:

• self.field_name[‘completed’]: a ‘yes’/’no’ tick box specifying whether the workflow was already completed. The workflow will only run if this field says ‘no’ and automatically update it to ‘yes’ upon successful completion.

• self.field_name[‘input’]: a ‘Text’ field to which you attach the input files to the workflow

• self.field_name[‘output’]: a ‘Text’ field to which the workflow attaches its output files

  In addition to the mandatory fields, you can also define the following:

• self.field_name[‘kwargs’]: a ‘String’ field that contains valid keyword arguments (defined by self.expected[‘kwargs’]) to the member function self.workflow.

• self.field_name[‘workflow’]: a ‘String’ field which lets you specify the workflow you want to execute. If used, the workflow will only execute if its Python class name matches the content of this field. Otherwise, it will always execute if all the necessary fields are present. This option lets you create RSpace Forms eligible for more than one workflow.

download_files(files)

Download files from the Rspace Gallery into this workflow’s working directory.

Parameters:

files (list<dict>) – List of Rspace file objects

get_args()

Read the keyword arguments from the kwargs field of the Rspace document.

get_input_files()

Check if all expected input files have been provided in the request. If yes, download them.

init_members()

Initialize all internal variables.

prepare()

Prepare for workflow execution:

• check if request has already been completed

• check if the requested workflow matches this one

• create a working directory for the workflow

• try to download files from the request

reset_document()

Reset the request document to an empty ‘output’ field and ‘completed’ field ‘no’.

run()

Run the entire Workflow.

This function is typically the same for every subclass of this Workflow class. It calls self.workflow(…), which is where you put the actual backend of the workflow.

summary()

Summarize the success of the workflow based on generated error codes.

update_document()

Update the request document with the results of the workflow.

workflow(**kwargs)

The actual workflow to be executed.

This function should be redefined for every subclass of this Workflow class.

inm_rspace.workflow.get_file_paths(field)

Not yet working!