pulsar.managers.base package

Submodules

pulsar.managers.base.base_drmaa module

Module defines a base class for Pulsar managers using DRMAA.

class pulsar.managers.base.base_drmaa.BaseDrmaaManager(name, app, **kwds)

Bases: ExternalBaseManager

Base class for Pulsar managers using DRMAA.

shutdown(timeout=None)

Cleanup DRMAA session and call shutdown of parent.

pulsar.managers.base.directory module

class pulsar.managers.base.directory.DirectoryBaseManager(name, app, **kwds)

Bases: BaseManager

job_stderr_contents(job_id)

After completion, return contents of stderr of the job as produced by the job runner.

job_stdout_contents(job_id)

After completion, return contents of stdout of the job as produced by the job runner.

read_command_line(job_id)

return_code(job_id)

Return integer indicating return code of specified execution or PULSAR_UNKNOWN_RETURN_CODE.

stderr_contents(job_id)

After completion, return contents of stderr of the tool script.

stdout_contents(job_id)

After completion, return contents of stdout of the tool script.

pulsar.managers.base.external module

class pulsar.managers.base.external.ExternalBaseManager(name, app, **kwds)

Bases: DirectoryBaseManager

Base class for managers that interact with external distributed resource managers.

clean(job_id)

Delete job directory and clean up resources associated with job with id job_id.

get_status(job_id)

Return status of job as string, currently supported statuses include ‘cancelled’, ‘running’, ‘queued’, and ‘complete’.

kill(job_id)

End or cancel execution of the specified job.

Module contents

Base Classes and Infrastructure Supporting Concret Manager Implementations.

class pulsar.managers.base.BaseManager(name, app, **kwds)

Bases: ManagerInterface

clean(job_id)

Delete job directory and clean up resources associated with job with id job_id.

job_directory(job_id)

Return a JobDirectory abstraction describing the state of the job working directory.

setup_job(input_job_id, tool_id, tool_version)

Setup a job directory for specified input (galaxy) job id, tool id, and tool version.

system_properties()

class pulsar.managers.base.DirectoryMaker(mode=None)

Bases: object

make(path, recursive=False)

class pulsar.managers.base.JobDirectory(staging_directory, job_id, lock_manager=None, directory_maker=None)

Bases: RemoteJobDirectory

calculate_path(remote_path, input_type)

Verify remote_path is in directory for input_type inputs and create directory if needed.

contains_file(name)

delete()

exists()

has_metadata(metadata_name)

job_directory_contents()

load_metadata(metadata_name, default=None)

lock(name='.state')

make_directory(name)

metadata_directory_contents()

open_file(name, mode='wb')

outputs_directory_contents()

read_file(name, size=-1, default=None)

remove_file(name)

Quietly remove a job file.

remove_metadata(metadata_name)

setup()

store_metadata(metadata_name, metadata_value)

working_directory_contents()

working_directory_file_contents(name)

write_file(name, contents)

pulsar.managers.base.get_id_assigner(assign_ids)