toil.utils.toilClean

Delete a job store used by a previous Toil workflow invocation.

Attributes

logger

Exceptions

NoSuchJobStoreException

Indicates that the specified job store does not exist.

Classes

Toil

A context manager that represents a Toil workflow.

Functions

parser_with_common_options([provisioner_options, ...])

set_logging_from_options(options)

main()

Module Contents

class toil.utils.toilClean.Toil(options)[source]

Bases: ContextManager[Toil]

A context manager that represents a Toil workflow.

Specifically the batch system, job store, and its configuration.

Parameters:

options (argparse.Namespace)

config: Config
__enter__()[source]

Derive configuration from the command line options.

Then load the job store and, on restart, consolidate the derived configuration with the one from the previous invocation of the workflow.

Return type:

Toil

__exit__(exc_type, exc_val, exc_tb)[source]

Clean up after a workflow invocation.

Depending on the configuration, delete the job store.

Parameters:
Return type:

Literal[False]

start(rootJob)[source]

Invoke a Toil workflow with the given job as the root for an initial run.

This method must be called in the body of a with Toil(...) as toil: statement. This method should not be called more than once for a workflow that has not finished.

Parameters:

rootJob (toil.job.Job) – The root job of the workflow

Returns:

The root job’s return value

Return type:

Any

restart()[source]

Restarts a workflow that has been interrupted.

Returns:

The root job’s return value

Return type:

Any

classmethod getJobStore(locator)[source]

Create an instance of the concrete job store implementation that matches the given locator.

Parameters:

locator (str) – The location of the job store to be represent by the instance

Returns:

an instance of a concrete subclass of AbstractJobStore

Return type:

toil.jobStores.abstractJobStore.AbstractJobStore

static parseLocator(locator)[source]
Parameters:

locator (str)

Return type:

Tuple[str, str]

static buildLocator(name, rest)[source]
Parameters:
Return type:

str

classmethod resumeJobStore(locator)[source]
Parameters:

locator (str)

Return type:

toil.jobStores.abstractJobStore.AbstractJobStore

static createBatchSystem(config)[source]

Create an instance of the batch system specified in the given config.

Parameters:

config (Config) – the current configuration

Returns:

an instance of a concrete subclass of AbstractBatchSystem

Return type:

toil.batchSystems.abstractBatchSystem.AbstractBatchSystem

importFile(srcUrl: str, sharedFileName: str, symlink: bool = True) → None[source]
importFile(srcUrl: str, sharedFileName: None = None, symlink: bool = True) → toil.fileStores.FileID
import_file(src_uri: str, shared_file_name: str, symlink: bool = True, check_existence: bool = True) → None[source]
import_file(src_uri: str, shared_file_name: None = None, symlink: bool = True, check_existence: bool = True) → toil.fileStores.FileID

Import the file at the given URL into the job store.

By default, returns None if the file does not exist.

Parameters:

check_existence – If true, raise FileNotFoundError if the file does not exist. If false, return None when the file does not exist.

See toil.jobStores.abstractJobStore.AbstractJobStore.importFile() for a full description

exportFile(jobStoreFileID, dstUrl)[source]
Parameters:
Return type:

None

export_file(file_id, dst_uri)[source]

Export file to destination pointed at by the destination URL.

See toil.jobStores.abstractJobStore.AbstractJobStore.exportFile() for a full description

Parameters:
Return type:

None

static normalize_uri(uri, check_existence=False)[source]

Given a URI, if it has no scheme, prepend “file:”.

Parameters:

  • check_existence (bool) – If set, raise FileNotFoundError if a URI points to a local file that does not exist.

  • uri (str)

Return type:

str

static getToilWorkDir(configWorkDir=None)[source]

Return a path to a writable directory under which per-workflow directories exist.

This directory is always required to exist on a machine, even if the Toil worker has not run yet. If your workers and leader have different temp directories, you may need to set TOIL_WORKDIR.

Parameters:

configWorkDir (Optional[str]) – Value passed to the program using the –workDir flag

Returns:

Path to the Toil work directory, constant across all machines

Return type:

str

classmethod get_toil_coordination_dir(config_work_dir, config_coordination_dir)[source]

Return a path to a writable directory, which will be in memory if convenient. Ought to be used for file locking and coordination.

Parameters:

  • config_work_dir (Optional[str]) – Value passed to the program using the –workDir flag

  • config_coordination_dir (Optional[str]) – Value passed to the program using the –coordinationDir flag

  • workflow_id – Used if a tmpdir_prefix exists to create full directory paths unique per workflow

Returns:

Path to the Toil coordination directory. Ought to be on a POSIX filesystem that allows directories containing open files to be deleted.

Return type:

str

static get_workflow_path_component(workflow_id)[source]

Get a safe filesystem path component for a workflow.

Will be consistent for all processes on a given machine, and different for all processes on different machines.

Parameters:

workflow_id (str) – The ID of the current Toil workflow.

Return type:

str

classmethod getLocalWorkflowDir(workflowID, configWorkDir=None)[source]

Return the directory where worker directories and the cache will be located for this workflow on this machine.

Parameters:

  • configWorkDir (Optional[str]) – Value passed to the program using the –workDir flag

  • workflowID (str)

Returns:

Path to the local workflow directory on this machine

Return type:

str

classmethod get_local_workflow_coordination_dir(workflow_id, config_work_dir, config_coordination_dir)[source]

Return the directory where coordination files should be located for this workflow on this machine. These include internal Toil databases and lock files for the machine.

If an in-memory filesystem is available, it is used. Otherwise, the local workflow directory, which may be on a shared network filesystem, is used.

Parameters:

  • workflow_id (str) – Unique ID of the current workflow.

  • config_work_dir (Optional[str]) – Value used for the work directory in the current Toil Config.

  • config_coordination_dir (Optional[str]) – Value used for the coordination directory in the current Toil Config.

Returns:

Path to the local workflow coordination directory on this machine.

Return type:

str

toil.utils.toilClean.parser_with_common_options(provisioner_options=False, jobstore_option=True, prog=None, default_log_level=None)[source]
Parameters:

  • provisioner_options (bool)

  • jobstore_option (bool)

  • prog (Optional[str])

  • default_log_level (Optional[int])

Return type:

configargparse.ArgParser

exception toil.utils.toilClean.NoSuchJobStoreException(locator, prefix)[source]

Bases: LocatorException

Indicates that the specified job store does not exist.

Parameters:
toil.utils.toilClean.set_logging_from_options(options)[source]
Parameters:

options (Union[toil.common.Config, argparse.Namespace])

Return type:

None

toil.utils.toilClean.logger
toil.utils.toilClean.main()[source]
Return type:

None