Tools and Workflows

Manage creation of tools and workflows for workflow tracking.

Command-line tool

Represent a CommandLineToolFactory for tracking workflows.

class renku.core.models.cwl.command_line_tool.CommandLineToolFactory(command_line, explicit_inputs=NOTHING, explicit_outputs=NOTHING, no_input_detection=False, no_output_detection=False, directory='.', working_dir='.', stdin=None, stderr=None, stdout=None, successCodes=NOTHING, annotations=None, messages=None, warnings=None)

Command Line Tool Factory.

Method generated by attrs for class CommandLineToolFactory.

add_indirect_inputs()

Read indirect inputs list and add them to explicit inputs.

add_indirect_outputs()

Read indirect outputs list and add them to explicit outputs.

find_explicit_inputs()

Yield explicit inputs and command line input bindings if any.

generate_process_run(commit, path, name=None, description=None, keywords=None)

Return an instance of ProcessRun.

guess_inputs(*arguments)

Yield command input parameters and command line bindings.

guess_outputs(candidates)

Yield detected output and changed command input parameter.

guess_type(value, ignore_filenames=None)

Return new value and CWL parameter type.

is_existing_path(candidate, ignore=None)

Return a path instance if it exists in current directory.

iter_input_files(basedir)

Yield tuples with input id and path.

split_command_and_args()

Return tuple with command and args from command line arguments.

validate_command_line(attribute, value)

Check the command line structure.

validate_path(attribute, value)

Path must exists.

watch(client, no_output=False)

Watch a Renku repository for changes to detect outputs.

renku.core.models.cwl.command_line_tool.add_indirect_parameter(working_dir, name, value)

Add a parameter to indirect parameters.

renku.core.models.cwl.command_line_tool.delete_indirect_files_list(working_dir)

Remove indirect inputs, outputs, and parameters list.

renku.core.models.cwl.command_line_tool.get_indirect_inputs_path(client_path)

Return path to file that contains indirect inputs list.

renku.core.models.cwl.command_line_tool.get_indirect_outputs_path(client_path)

Return path to file that contains indirect outputs list.

renku.core.models.cwl.command_line_tool.get_indirect_parameters_path(client_path)

Return path to file that contains indirect parameters list.

renku.core.models.cwl.command_line_tool.read_indirect_parameters(working_dir)

Read and return indirect parameters.

Annotation

Represent an annotation for a workflow.

class renku.core.models.cwl.annotation.Annotation(*, id, body=None, source=None)

Represents a custom annotation for a research object.

class renku.core.models.cwl.annotation.AnnotationSchema(*args, commit=None, client=None, **kwargs)

Annotation schema.

Create an instance.

class Meta

Meta class.

model

alias of renku.core.models.cwl.annotation.Annotation

Parameter

Represent parameters from the Common Workflow Language.

class renku.core.models.cwl.parameter.CommandInputParameter(id=None, streamable=None, type='string', description=None, default=None, inputBinding=None)

An input parameter for a CommandLineTool.

Method generated by attrs for class CommandInputParameter.

classmethod from_cwl(data)

Create instance from type definition.

to_argv(**kwargs)

Format command input parameter as shell argument.

class renku.core.models.cwl.parameter.CommandLineBinding(position=None, prefix=None, separate=True, itemSeparator=None, valueFrom=None, shellQuote=True)

Define the binding behavior when building the command line.

Method generated by attrs for class CommandLineBinding.

to_argv(default=None)

Format command line binding as shell argument.

class renku.core.models.cwl.parameter.CommandOutputBinding(glob=None)

Define the binding behavior for outputs.

Method generated by attrs for class CommandOutputBinding.

class renku.core.models.cwl.parameter.CommandOutputParameter(id=None, streamable=None, type='string', description=None, format=None, outputBinding=None)

Define an output parameter for a CommandLineTool.

Method generated by attrs for class CommandOutputParameter.

class renku.core.models.cwl.parameter.InputParameter(id=None, streamable=None, type='string', description=None, default=None, inputBinding=None)

An input parameter.

Method generated by attrs for class InputParameter.

class renku.core.models.cwl.parameter.OutputParameter(id=None, streamable=None, type='string', description=None, format=None, outputBinding=None)

An output parameter.

Method generated by attrs for class OutputParameter.

class renku.core.models.cwl.parameter.Parameter(streamable=None)

Define an input or output parameter to a process.

Method generated by attrs for class Parameter.

class renku.core.models.cwl.parameter.RunParameter(name=None, value=None)

Define a parameter for a Workflow that is not passed via command-line.

Method generated by attrs for class RunParameter.

class renku.core.models.cwl.parameter.WorkflowOutputParameter(id=None, streamable=None, type='string', description=None, format=None, outputBinding=None, outputSource=None)

Define an output parameter for a Workflow.

Method generated by attrs for class WorkflowOutputParameter.

renku.core.models.cwl.parameter.convert_default(value)

Convert a default value.

Types

Represent the Common Workflow Language types.

class renku.core.models.cwl.types.Directory(path=None, listing=NOTHING)

Represent a directory.

Method generated by attrs for class Directory.

class renku.core.models.cwl.types.Dirent(entryname=None, entry=None, writable=False)

Define a file or subdirectory.

Method generated by attrs for class Dirent.

class renku.core.models.cwl.types.File(path)

Represent a file.

Method generated by attrs for class File.

Workflow

Represent workflows from the Common Workflow Language.

class renku.core.models.cwl.workflow.Workflow(steps=NOTHING)

Define a workflow representation.

Method generated by attrs for class Workflow.

add_step(**kwargs)

Add a workflow step.

class renku.core.models.cwl.workflow.WorkflowStep(run, id=NOTHING, in_=None, out=None)

Define an executable element of a workflow.

Method generated by attrs for class WorkflowStep.

renku.core.models.cwl.workflow.convert_run(value)

Convert value to CWLClass if dict is given.