heliport.cwl_execution.cwl_helpers package
Submodules
heliport.cwl_execution.cwl_helpers.cwl2rdf module
- heliport.cwl_execution.cwl_helpers.cwl2rdf.cwl_to_rdf(cwl_dict, uri)
- heliport.cwl_execution.cwl_helpers.cwl2rdf.main()
- heliport.cwl_execution.cwl_helpers.cwl2rdf.print_context(url_of_example_document_with_desired_version)
Only used to generate cwl_contexts dict.
heliport.cwl_execution.cwl_helpers.cwl_execution module
- class heliport.cwl_execution.cwl_helpers.cwl_execution.CWLExecutorManager(job_config, debug=False, auto_run=True, execution_id=None)
Bases:
object- property absolute_job_folder
- append_job_output_text(message)
- build_ssh_shell()
- config_invalid()
- configure_job_error(message='an undefined error occurred')
- configure_job_running()
- configure_job_stopped(status_code=0)
- classmethod data_source_filename(data_source: DataSource)
- static data_source_path(data_source: DataSource)
- static datasource_has_native_cwl_support(source: DataSource)
- download_data_with_curl(data_source: DataSource)
- execute(command: str)
- property execution_directory
- executor: CommandExecutor
- static extract_data_source_from_cwl_parameter(param)
- extract_inputs_from_tags(param, param_id)
- extract_pure_executable_cwl_and_token_inputs(exe)
- extract_pure_job_cwl_and_data_sources()
- static get_inputs_dict(exe)
- property job
- job_config: UserJobConfig
- property job_folder
- load_cwltool()
- load_node_js()
- load_venv()
- property login
- make_parameter_pure_and_extract_data_source_to_copy(param)
- prepare_job_folder()
- run()
- run_cwl_tool()
- save_connect(executor: CommandExecutor)
- save_metadata()
- save_profiling()
- set_tokens(job_cwl, token_inputs)
- property srun
- static strip_comments(option_string)
- test_directory_cwl_class(data_source)
- test_node_requirement()
- transfer_cwl(cwl, relative_location)
- transfer_data_source(data_source)
- transfer_ssh_data_source(data_source: DataSource)
- static update_renamed_workflow_steps(tool_cwl)
- property user
- heliport.cwl_execution.cwl_helpers.cwl_execution.save(commandline_argument: str) str
heliport.cwl_execution.cwl_helpers.cwl_generation module
- heliport.cwl_execution.cwl_helpers.cwl_generation.clean(s)
- heliport.cwl_execution.cwl_helpers.cwl_generation.filter_executables(executables, query_string)
- heliport.cwl_execution.cwl_helpers.cwl_generation.generate_cwl_filename(cwl, exe)
- heliport.cwl_execution.cwl_helpers.cwl_generation.parse_user_cwl(cwl, cwl_type)
- heliport.cwl_execution.cwl_helpers.cwl_generation.separate_prefix(underscore_dict, list_keys=None)
- heliport.cwl_execution.cwl_helpers.cwl_generation.set_attrs_job(job, attrs)
heliport.cwl_execution.cwl_helpers.cwl_job module
- class heliport.cwl_execution.cwl_helpers.cwl_job.CwlJob(parameters: List[CwlParameter], job_dict: Dict[str, Any | ParameterValue] | None = None, prefer_json=False, tag_class=None)
Bases:
object- static as_list(value, count)
- property cwl
- property cwl_str
- get_tag_list(name)
- get_value(name)
- property has_parameters
- property is_valid
- property json
- property parameter_details
- property unsupported_cwl_str
- property yaml
heliport.cwl_execution.cwl_helpers.cwl_parameter module
- class heliport.cwl_execution.cwl_helpers.cwl_parameter.AutoValue(value=None)
Bases:
ParameterValue- cwl = 'auto_value'
- is_valid = True
- value = 'auto_value'
- class heliport.cwl_execution.cwl_helpers.cwl_parameter.BooleanParameterValue(value=None)
Bases:
ParameterValue- property cwl
- property is_valid
- property value
- class heliport.cwl_execution.cwl_helpers.cwl_parameter.CwlParameter(name, value_type, description='')
Bases:
object- generate_parameter_value(value=None)
- property supported
- property type_count
- property type_type
- class heliport.cwl_execution.cwl_helpers.cwl_parameter.ParameterValue
Bases:
object- abstract property cwl
- abstract property is_valid
- property tag_list
- abstract property value
Value used in template.
- heliport.cwl_execution.cwl_helpers.cwl_parameter.cwl_split_type(type_str)
- heliport.cwl_execution.cwl_helpers.cwl_parameter.file_or_directory(type_str)
- heliport.cwl_execution.cwl_helpers.cwl_parameter.make_array(parameter_value_class)
- heliport.cwl_execution.cwl_helpers.cwl_parameter.make_optional(parameter_value_class)
- heliport.cwl_execution.cwl_helpers.cwl_parameter.simple_parameter_value(value_type)
- heliport.cwl_execution.cwl_helpers.cwl_parameter.try_int(s: str) int
- heliport.cwl_execution.cwl_helpers.cwl_parameter.value_class
alias of
FileParameterValue
heliport.cwl_execution.cwl_helpers.cwl_tool module
- heliport.cwl_execution.cwl_helpers.cwl_tool.base_command_decode_to_str(base_command)
- heliport.cwl_execution.cwl_helpers.cwl_tool.base_command_list_encode(base_command)
- heliport.cwl_execution.cwl_helpers.cwl_tool.cwl_to_tool_description(cwl_dict)
- heliport.cwl_execution.cwl_helpers.cwl_tool.tool_description_to_cwl(description_dict)
heliport.cwl_execution.cwl_helpers.cwl_workflow module
- heliport.cwl_execution.cwl_helpers.cwl_workflow.add_unique_labels(nodes)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.cwl_to_visualization_data(cwl)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.data_for_visualization_node(executable)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.default_str_to_type_dict(port)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.differentiate_nodes(nodes)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.generate_cwl_nonempty_id(cwl)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.generate_port_data(cwl_ports)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.get_edge_sources(edges, label_index)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.get_label_index(inputs, steps)
- heliport.cwl_execution.cwl_helpers.cwl_workflow.visualization_data_to_cwl(data, name, description)