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)[source]

Bases: ExternalBaseManager

Base class for Pulsar managers using DRMAA.

shutdown(timeout=None)[source]

Cleanup DRMAA session and call shutdown of parent.

pulsar.managers.base.directory module

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

Bases: BaseManager

job_stderr_contents(job_id)[source]

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

job_stdout_contents(job_id)[source]

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

read_command_line(job_id)[source]
return_code(job_id)[source]

Return integer indicating return code of specified execution or PULSAR_UNKNOWN_RETURN_CODE.

stderr_contents(job_id)[source]

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

stdout_contents(job_id)[source]

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

pulsar.managers.base.external module

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

Bases: DirectoryBaseManager

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

clean(job_id)[source]

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

get_status(job_id)[source]

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

kill(job_id)[source]

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)[source]

Bases: ManagerInterface

clean(job_id)[source]

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)[source]

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

system_properties()[source]
class pulsar.managers.base.DirectoryMaker(mode=None)[source]

Bases: object

make(path, recursive=False)[source]
class pulsar.managers.base.JobDirectory(staging_directory, job_id, lock_manager=None, directory_maker=None)[source]

Bases: RemoteJobDirectory

calculate_path(remote_path, input_type)[source]

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

contains_file(name)[source]
delete()[source]
exists()[source]
has_metadata(metadata_name)[source]
job_directory_contents()[source]
load_metadata(metadata_name, default=None)[source]
lock(name='.state')[source]
make_directory(name)[source]
metadata_directory_contents()[source]
open_file(name, mode='wb')[source]
outputs_directory_contents()[source]
read_file(name, size=-1, default=None)[source]
remove_file(name)[source]

Quietly remove a job file.

remove_metadata(metadata_name)[source]
setup()[source]
store_metadata(metadata_name, metadata_value)[source]
working_directory_contents()[source]
working_directory_file_contents(name)[source]
write_file(name, contents)[source]
pulsar.managers.base.get_id_assigner(assign_ids)[source]