cwltool.context

Shared context objects that replace use of kwargs.

Attributes

default_make_tool

Classes

ContextBase	Shared kwargs based initializer for RuntimeContext and LoadingContext.
LoadingContext	Shared kwargs based initializer for RuntimeContext and LoadingContext.
RuntimeContext	Shared kwargs based initializer for RuntimeContext and LoadingContext.

Functions

make_tool_notimpl(toolpath_object, loadingContext)	Fake implementation of the make tool function.
log_handler(outdir, base_path_logs, stdout_path, ...)	Move logs from log location to final output.
set_log_dir(outdir, log_dir, subdir_name)	Set the log directory.
getdefault(val, default)	Return the val using the default as backup in case the val is None.

Module Contents

class cwltool.context.ContextBase(kwargs=None)

Shared kwargs based initializer for RuntimeContext and LoadingContext.

Parameters:

kwargs (dict[str, Any] | None)

cwltool.context.make_tool_notimpl(toolpath_object, loadingContext)

Fake implementation of the make tool function.

Parameters:

• toolpath_object (ruamel.yaml.comments.CommentedMap)

• loadingContext (LoadingContext)

Return type:

cwltool.process.Process

cwltool.context.default_make_tool

cwltool.context.log_handler(outdir, base_path_logs, stdout_path, stderr_path)

Move logs from log location to final output.

Parameters:

• outdir (str)

• base_path_logs (str)

• stdout_path (str | None)

• stderr_path (str | None)

Return type:

None

cwltool.context.set_log_dir(outdir, log_dir, subdir_name)

Set the log directory.

Parameters:

• outdir (str)

• log_dir (str)

• subdir_name (str)

Return type:

str

class cwltool.context.LoadingContext(kwargs=None)

Bases: ContextBase

Shared kwargs based initializer for RuntimeContext and LoadingContext.

Parameters:

kwargs (dict[str, Any] | None)

debug: bool = False

metadata: cwl_utils.types.CWLObjectType

requirements: list[cwl_utils.types.CWLObjectType] | None = None

hints: list[cwl_utils.types.CWLObjectType] | None = None

overrides_list: list[cwl_utils.types.CWLObjectType] = []

loader: schema_salad.ref_resolver.Loader | None = None

avsc_names: schema_salad.avro.schema.Names | None = None

disable_js_validation: bool = False

js_hint_options_file: str | None = None

do_validate: bool = True

enable_dev: bool = False

strict: bool = True

resolver: cwltool.utils.ResolverType | None = None

fetcher_constructor: schema_salad.utils.FetcherCallableType | None = None

construct_tool_object

orcid: str = ''

cwl_full_name: str = ''

host_provenance: bool = False

user_provenance: bool = False

do_update: bool | None = None

jobdefaults: ruamel.yaml.comments.CommentedMap | None = None

doc_cache: bool = True

relax_path_checks: bool = False

singularity: bool = False

podman: bool = False

eval_timeout: float = 60

codegen_idx: dict[str, tuple[Any, cwl_utils.parser.cwl_v1_2.LoadingOptions]]

fast_parser = False

skip_resolve_all = False

skip_schemas = False

copy()

Return a copy of this LoadingContext.

Return type:

LoadingContext

class cwltool.context.RuntimeContext(kwargs=None)

Bases: ContextBase

Shared kwargs based initializer for RuntimeContext and LoadingContext.

Parameters:

kwargs (dict[str, Any] | None)

outdir: str | None = None

tmpdir: str = ''

tmpdir_prefix: str

tmp_outdir_prefix: str = ''

stagedir: str = ''

user_space_docker_cmd: str | None = None

secret_store: cwltool.secrets.SecretStore | None = None

no_read_only: bool = False

custom_net: str | None = None

no_match_user: bool = False

preserve_environment: collections.abc.Iterable[str] | None = None

preserve_entire_environment: bool = False

use_container: bool = True

force_docker_pull: bool = False

rm_tmpdir: bool = True

pull_image: bool = True

rm_container: bool = True

move_outputs: Literal['move'] | Literal['leave'] | Literal['copy'] = 'move'

log_dir: str = ''

set_log_dir

log_dir_handler

streaming_allowed: bool = False

singularity: bool = False

image_base_path: str | None = None

podman: bool = False

debug: bool = False

compute_checksum: bool = True

name: str = ''

default_container: str | None = ''

find_default_container: collections.abc.Callable[[cwltool.utils.HasReqsHints], str | None] | None = None

cachedir: str | None = None

part_of: str = ''

basedir: str = ''

toplevel: bool = False

mutation_manager: cwltool.mutation.MutationManager | None = None

make_fs_access

path_mapper

builder: cwltool.builder.Builder | None = None

docker_outdir: str = ''

docker_tmpdir: str = ''

docker_stagedir: str = ''

js_console: bool = False

job_script_provider: cwltool.software_requirements.DependenciesConfiguration | None = None

select_resources: RuntimeContext.__init__.select_resources_callable | None = None

eval_timeout: float = 60

postScatterEval: collections.abc.Callable[[cwl_utils.types.CWLObjectType], cwl_utils.types.CWLObjectType | None] | None = None

on_error: Literal['stop'] | Literal['continue'] = 'stop'

strict_memory_limit: bool = False

strict_cpu_limit: bool = False

cidfile_dir: str | None = None

cidfile_prefix: str | None = None

workflow_eval_lock: threading.Condition | None = None

orcid: str = ''

cwl_full_name: str = ''

process_run_id: str | None = None

prov_host: bool = False

prov_user: bool = False

mpi_config: cwltool.mpi.MpiConfig

default_stdout: IO[bytes] | TextIO | None = None

default_stderr: IO[bytes] | TextIO | None = None

validate_only: bool = False

validate_stdout: SupportsWrite[str] | None = None

workflow_job_step_name_callback: None | collections.abc.Callable[[cwltool.workflow_job.WorkflowJobStep, cwl_utils.types.CWLObjectType], str] = None

get_outdir()

Return outdir or create one with tmp_outdir_prefix.

Return type:

str

get_tmpdir()

Return tmpdir or create one with tmpdir_prefix.

Return type:

str

get_stagedir()

Return stagedir or create one with tmpdir_prefix.

Return type:

str

create_tmpdir()

Create a temporary directory that respects tmpdir_prefix.

Return type:

str

create_outdir()

Create a temporary directory that respects tmp_outdir_prefix.

Return type:

str

copy()

Return a copy of this RuntimeContext.

Return type:

RuntimeContext

cwltool.context.getdefault(val, default)

Return the val using the default as backup in case the val is None.

Parameters:

• val (Any)

• default (Any)

Return type:

Any