Renku Workflow

Renku uses PROV-O and its own Renku ontology to represent workflows.

Run

Represents a workflow template.

class renku.core.models.workflow.run.OrderedSubprocess(*, id, index, process)

A subprocess with ordering.

Method generated by attrs for class OrderedSubprocess.

static generate_id(parent_id, index)

Generate an id for an OrderedSubprocess.

class renku.core.models.workflow.run.OrderedSubprocessSchema(*args, commit=None, client=None, **kwargs)

OrderedSubprocess schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.workflow.run.OrderedSubprocess

class renku.core.models.workflow.run.Run(*, commit=None, client=None, path=None, id=None, label=NOTHING, project=None, command=None, successcodes=NOTHING, subprocesses=NOTHING, arguments=NOTHING, inputs=NOTHING, outputs=NOTHING, run_parameters=NOTHING, name=None, description=None, keywords=NOTHING, activity=None)

Represents a renku run execution template.

Method generated by attrs for class Run.

property activity

Return the activity object.

add_subprocess(subprocess)

Adds a subprocess to this run.

as_jsonld()

Create JSON-LD.

classmethod from_factory(factory, client, commit, path, name, description, keywords)

Creates a Run from a CommandLineToolFactory.

classmethod from_jsonld(data)

Create an instance from JSON-LD data.

static generate_id(client, identifier=None)

Generate an id for an argument.

to_argv()

Convert run into argv list.

to_stream_repr()

Input/output stream representation.

update_id_and_label_from_commit_path(client, commit, path, is_subprocess=False)

Updates the _id and _label using supplied commit and path.

class renku.core.models.workflow.run.RunSchema(*args, commit=None, client=None, **kwargs)

Run schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.workflow.run.Run

Parameters

Represents a workflow template.

class renku.core.models.workflow.parameters.CommandArgument(*, id=None, label=None, default_value=None, description=None, name=None, position=None, prefix=None, value=None)

An argument to a command that is neither input nor output.

Method generated by attrs for class CommandArgument.

as_jsonld()

Create JSON-LD.

default_label()

Set default label.

default_name()

Create a default name.

classmethod from_jsonld(data)

Create an instance from JSON-LD data.

static generate_id(run_id, position=None)

Generate an id for an argument.

to_argv()

String representation (sames as cmd argument).

class renku.core.models.workflow.parameters.CommandArgumentSchema(*args, commit=None, client=None, **kwargs)

CommandArgument schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.workflow.parameters.CommandArgument

class renku.core.models.workflow.parameters.CommandInput(*, id=None, label=None, default_value=None, description=None, name=None, position=None, prefix=None, consumes, mapped_to=None)

An input to a command.

Method generated by attrs for class CommandInput.

as_jsonld()

Create JSON-LD.

default_label()

Set default label.

default_name()

Create a default name.

classmethod from_jsonld(data)

Create an instance from JSON-LD data.

static generate_id(run_id, position=None)

Generate an id for an argument.

to_argv()

String representation (sames as cmd argument).

to_stream_repr()

Input stream representation.

class renku.core.models.workflow.parameters.CommandInputSchema(*args, commit=None, client=None, **kwargs)

CommandArgument schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.workflow.parameters.CommandInput

class renku.core.models.workflow.parameters.CommandOutput(*, id=None, label=None, default_value=None, description=None, name=None, position=None, prefix=None, create_folder=False, produces, mapped_to=None)

An output of a command.

Method generated by attrs for class CommandOutput.

as_jsonld()

Create JSON-LD.

default_label()

Set default label.

default_name()

Create a default name.

classmethod from_jsonld(data)

Create an instance from JSON-LD data.

static generate_id(run_id, position=None)

Generate an id for an argument.

to_argv()

String representation (sames as cmd argument).

to_stream_repr()

Input stream representation.

class renku.core.models.workflow.parameters.CommandOutputSchema(*args, commit=None, client=None, **kwargs)

CommandArgument schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.workflow.parameters.CommandOutput

class renku.core.models.workflow.parameters.CommandParameter(*, id=None, label=None, default_value=None, description=None, name=None, position=None, prefix=None)

Represents a parameter for an execution template.

Method generated by attrs for class CommandParameter.

default_label()

Set default label.

default_name()

Create a default name.

property sanitized_id

Return _id sanitized for use in non-jsonld contexts.

class renku.core.models.workflow.parameters.CommandParameterSchema(*args, commit=None, client=None, **kwargs)

CommandParameter schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.workflow.parameters.CommandParameter

class renku.core.models.workflow.parameters.MappedIOStream(*, client=None, id=None, label=None, stream_type)

Represents an IO stream (stdin, stdout, stderr).

Method generated by attrs for class MappedIOStream.

as_jsonld()

Create JSON-LD.

default_id()

Generate an id for a mapped stream.

default_label()

Set default label.

classmethod from_jsonld(data)

Create an instance from JSON-LD data.

class renku.core.models.workflow.parameters.MappedIOStreamSchema(*args, commit=None, client=None, **kwargs)

MappedIOStream schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.workflow.parameters.MappedIOStream

class renku.core.models.workflow.parameters.RunParameter(*, id=None, label=None, name=None, value=None, type=None)

A run parameter that is set inside the script.

Method generated by attrs for class RunParameter.

as_jsonld()

Create JSON-LD.

default_label()

Set default label.

classmethod from_jsonld(data)

Create an instance from JSON-LD data.

static generate_id(run_id, name)

Generate an id.

class renku.core.models.workflow.parameters.RunParameterSchema(*args, commit=None, client=None, **kwargs)

RunParameter schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.workflow.parameters.RunParameter

Renku Workflow Conversion

Renku allows conversion of tracked workflows to runnable workflows in supported tools (Currently CWL)

CWL

Converter for workflows to cwl.

class renku.core.models.workflow.converters.cwl.CWLConverter

Converts a Run to cwl file(s).

static convert(run, basedir, path=None)

Convert the workflow to one ore more .cwl files.