cwltool.job

Module Contents

Classes

JobBase	Base class for get_requirement().
CommandLineJob	Base class for get_requirement().
ContainerCommandLineJob	Commandline job using containers.

Functions

relink_initialworkdir(pathmapper, host_outdir, container_outdir, inplace_update = False)
neverquote(string, pos = 0, endpos = 0)

Attributes

needs_shell_quoting_re
FORCE_SHELLED_POPEN
SHELL_COMMAND_TEMPLATE
CollectOutputsType
CONTROL_CODE_RE

cwltool.job.needs_shell_quoting_re

cwltool.job.FORCE_SHELLED_POPEN

cwltool.job.SHELL_COMMAND_TEMPLATE = Multiline-String

Show Value

#!/bin/bash
python3 "run_job.py" "job.json"

cwltool.job.relink_initialworkdir(pathmapper, host_outdir, container_outdir, inplace_update=False)

Parameters

• pathmapper (cwltool.pathmapper.PathMapper) –

• host_outdir (str) –

• container_outdir (str) –

• inplace_update (bool) –

Return type

None

cwltool.job.neverquote(string, pos=0, endpos=0)

Parameters

• string (str) –

• pos (int) –

• endpos (int) –

Return type

Optional[Match[str]]

cwltool.job.CollectOutputsType

class cwltool.job.JobBase(builder, joborder, make_path_mapper, requirements, hints, name)

Bases: cwltool.utils.HasReqsHints

Base class for get_requirement().

Parameters

• builder (cwltool.builder.Builder) –

• joborder (cwltool.utils.CWLObjectType) –

• make_path_mapper (Callable[Ellipsis, cwltool.pathmapper.PathMapper]) –

• requirements (List[cwltool.utils.CWLObjectType]) –

• hints (List[cwltool.utils.CWLObjectType]) –

• name (str) –

__repr__(self)

Represent this Job object.

Return type

str

abstract run(self, runtimeContext, tmpdir_lock=None)

Parameters

• runtimeContext (cwltool.context.RuntimeContext) –

• tmpdir_lock (Optional[threading.Lock]) –

Return type

None

prepare_environment(self, runtimeContext, envVarReq)

Set up environment variables.

Here we prepare the environment for the job, based on any preserved variables and EnvVarRequirement. Later, changes due to MPIRequirement, Secrets, or SoftwareRequirement are applied (in that order).

Parameters

• runtimeContext (cwltool.context.RuntimeContext) –

• envVarReq (Mapping[str, str]) –

Return type

None

process_monitor(self, sproc)

Parameters

self (subprocess.Popen[str]) –

Return type

None

class cwltool.job.CommandLineJob(builder, joborder, make_path_mapper, requirements, hints, name)

Bases: JobBase

Base class for get_requirement().

Parameters

• builder (cwltool.builder.Builder) –

• joborder (cwltool.utils.CWLObjectType) –

• make_path_mapper (Callable[Ellipsis, cwltool.pathmapper.PathMapper]) –

• requirements (List[cwltool.utils.CWLObjectType]) –

• hints (List[cwltool.utils.CWLObjectType]) –

• name (str) –

run(self, runtimeContext, tmpdir_lock=None)

Parameters

• runtimeContext (cwltool.context.RuntimeContext) –

• tmpdir_lock (Optional[threading.Lock]) –

Return type

None

cwltool.job.CONTROL_CODE_RE = \x1b\[[0-9;]*[a-zA-Z]

class cwltool.job.ContainerCommandLineJob(builder, joborder, make_path_mapper, requirements, hints, name)

Bases: JobBase

Commandline job using containers.

Parameters

• builder (cwltool.builder.Builder) –

• joborder (cwltool.utils.CWLObjectType) –

• make_path_mapper (Callable[Ellipsis, cwltool.pathmapper.PathMapper]) –

• requirements (List[cwltool.utils.CWLObjectType]) –

• hints (List[cwltool.utils.CWLObjectType]) –

• name (str) –

CONTAINER_TMPDIR :str = /tmp

abstract get_from_requirements(self, r, pull_image, force_pull, tmp_outdir_prefix)

Parameters

• r (cwltool.utils.CWLObjectType) –

• pull_image (bool) –

• force_pull (bool) –

• tmp_outdir_prefix (str) –

Return type

Optional[str]

abstract create_runtime(self, env, runtime_context)

Return the list of commands to run the selected container engine.

Parameters

• env (MutableMapping[str, str]) –

• runtime_context (cwltool.context.RuntimeContext) –

Return type

Tuple[List[str], Optional[str]]

abstract static append_volume(runtime, source, target, writable=False)

Add binding arguments to the runtime list.

Parameters

• runtime (List[str]) –

• source (str) –

• target (str) –

• writable (bool) –

Return type

None

abstract add_file_or_directory_volume(self, runtime, volume, host_outdir_tgt)

Append volume a file/dir mapping to the runtime option list.

Parameters

• runtime (List[str]) –

• volume (cwltool.pathmapper.MapperEnt) –

• host_outdir_tgt (Optional[str]) –

Return type

None

abstract add_writable_file_volume(self, runtime, volume, host_outdir_tgt, tmpdir_prefix)

Append a writable file mapping to the runtime option list.

Parameters

• runtime (List[str]) –

• volume (cwltool.pathmapper.MapperEnt) –

• host_outdir_tgt (Optional[str]) –

• tmpdir_prefix (str) –

Return type

None

abstract add_writable_directory_volume(self, runtime, volume, host_outdir_tgt, tmpdir_prefix)

Append a writable directory mapping to the runtime option list.

Parameters

• runtime (List[str]) –

• volume (cwltool.pathmapper.MapperEnt) –

• host_outdir_tgt (Optional[str]) –

• tmpdir_prefix (str) –

Return type

None

create_file_and_add_volume(self, runtime, volume, host_outdir_tgt, secret_store, tmpdir_prefix)

Create the file and add a mapping.

Parameters

• runtime (List[str]) –

• volume (cwltool.pathmapper.MapperEnt) –

• host_outdir_tgt (Optional[str]) –

• secret_store (Optional[cwltool.secrets.SecretStore]) –

• tmpdir_prefix (str) –

Return type

str

add_volumes(self, pathmapper, runtime, tmpdir_prefix, secret_store=None, any_path_okay=False)

Append volume mappings to the runtime option list.

Parameters

• pathmapper (cwltool.pathmapper.PathMapper) –

• runtime (List[str]) –

• tmpdir_prefix (str) –

• secret_store (Optional[cwltool.secrets.SecretStore]) –

• any_path_okay (bool) –

Return type

None

run(self, runtimeContext, tmpdir_lock=None)

Parameters

• runtimeContext (cwltool.context.RuntimeContext) –

• tmpdir_lock (Optional[threading.Lock]) –

Return type

None

docker_monitor(self, cidfile, tmpdir_prefix, cleanup_cidfile, process)

Record memory usage of the running Docker container.

Parameters

• cidfile (str) –

• tmpdir_prefix (str) –

• cleanup_cidfile (bool) –

• process (subprocess.Popen[str]) –

Return type

None