galaxy.jobs.runners.util.cli.job package

Abstract base class for cli job plugins.

class galaxy.jobs.runners.util.cli.job.BaseJobExec(**params)[source]

Bases: object

__init__(**params)[source]: Constructor for CLI job executor.

job_script_kwargs(ofile, efile, job_name)[source]: Return extra keyword argument for consumption by job script module.

abstract submit(script_file)[source]: Given specified script_file path, yield command to submit it to external job manager.

abstract delete(job_id)[source]: Given job id, return command to stop execution or dequeue specified job.

abstract get_status(job_ids=None)[source]: Return command to get statuses of specified job ids.

abstract get_single_status(job_id)[source]: Return command to get the status of a single, specified job.

abstract parse_status(status: str, job_ids: list[str]) → dict[str, JobState][source]: Parse the statuses of output from get_status command.

abstract parse_single_status(status: str, job_id: str, shell) → JobState[source]: Parse the status of output from get_single_status command.

get_failure_reason(job_id)[source]: Return the failure reason for the given job_id.

parse_failure_reason(reason, job_id)[source]: Parses the failure reason, assigning it against a

galaxy.jobs.runners.util.cli.job.job_states: alias of JobState

Submodules

galaxy.jobs.runners.util.cli.job.lsf module

class galaxy.jobs.runners.util.cli.job.lsf.LSF(**params)[source]

Bases: BaseJobExec

job_script_kwargs(ofile, efile, job_name)[source]: Return extra keyword argument for consumption by job script module.

submit(script_file)[source]: Given specified script_file path, yield command to submit it to external job manager.

delete(job_id)[source]: Given job id, return command to stop execution or dequeue specified job.

get_status(job_ids=None)[source]: Return command to get statuses of specified job ids.

get_single_status(job_id)[source]: Return command to get the status of a single, specified job.

parse_status(status, job_ids)[source]: Parse the statuses of output from get_status command.

parse_single_status(status, job_id, shell_interfance)[source]: Parse the status of output from get_single_status command.

get_failure_reason(job_id)[source]: Return the failure reason for the given job_id.

parse_failure_reason(reason, job_id)[source]: Parses the failure reason, assigning it against a

galaxy.jobs.runners.util.cli.job.pbs module

class galaxy.jobs.runners.util.cli.job.pbs.OpenPBS(**params)[source]

Bases: Torque

ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to OpenPBS CLI plugin: %s'

get_status(job_ids=None)[source]: Return command to get statuses of specified job ids.

get_single_status(job_id)[source]: Return command to get the status of a single, specified job.

parse_status(status, job_ids)[source]: Parse the statuses of output from get_status command.

galaxy.jobs.runners.util.cli.job.slurm module

class galaxy.jobs.runners.util.cli.job.slurm.Slurm(**kwargs)[source]

Bases: BaseJobExec

slurm_longjobstate_to_shortjobstate = {'BOOT_FAIL': 'BF', 'CANCELLED': 'CA', 'COMPLETED': 'CD', 'DEADLINE': 'DL', 'FAILED': 'F', 'NODE_FAIL': 'NF', 'OUT_OF_MEMORY': 'OOM', 'PENDING': 'PD', 'PREEMPTED': 'PR', 'REQUEUED': 'RQ', 'RESIZING': 'RS', 'REVOKED': 'RV', 'RUNNING': 'R', 'SUSPENDED': 'S', 'TIMEOUT': 'TO', 'UNKNOWN': 'UN'}

slurmstate_runnerstate_map = {'OOM': 'memory_limit_reached', 'TO': 'walltime_reached', 'UN': 'unknown_error'}

__init__(**kwargs)[source]: Constructor for CLI job executor.

job_script_kwargs(ofile, efile, job_name)[source]: Return extra keyword argument for consumption by job script module.

submit(script_file)[source]: Given specified script_file path, yield command to submit it to external job manager.

delete(job_id)[source]: Given job id, return command to stop execution or dequeue specified job.

get_status(job_ids=None)[source]: Return command to get statuses of specified job ids.

get_single_status(job_id)[source]: Return command to get the status of a single, specified job.

parse_status(status, job_ids)[source]: Parse the statuses of output from get_status command.

parse_single_status(status, job_id, shell)[source]: Parse the status of output from get_single_status command.

get_failure_reason(job_id)[source]: Return the failure reason for the given job_id.

parse_failure_reason(reason, job_id)[source]: Parses the failure reason, assigning it against a

galaxy.jobs.runners.util.cli.job.slurm_torque module

class galaxy.jobs.runners.util.cli.job.slurm_torque.SlurmTorque(**params)[source]

Bases: Torque

A CLI job executor for Slurm’s Torque compatibility mode. This differs from real torque CLI in that -x command line is not available so job status needs to be parsed from qstat table instead of XML.

get_status(job_ids=None)[source]: Return command to get statuses of specified job ids.

parse_status(status, job_ids)[source]: Parse the statuses of output from get_status command.

galaxy.jobs.runners.util.cli.job.torque module

class galaxy.jobs.runners.util.cli.job.torque.Torque(**params)[source]

Bases: BaseJobExec

ERROR_MESSAGE_UNRECOGNIZED_ARG = 'Unrecognized long argument passed to Torque CLI plugin: %s'

job_script_kwargs(ofile, efile, job_name)[source]: Return extra keyword argument for consumption by job script module.

submit(script_file)[source]: Given specified script_file path, yield command to submit it to external job manager.

delete(job_id)[source]: Given job id, return command to stop execution or dequeue specified job.

get_status(job_ids=None)[source]: Return command to get statuses of specified job ids.

get_single_status(job_id)[source]: Return command to get the status of a single, specified job.

parse_status(status, job_ids)[source]: Parse the statuses of output from get_status command.

parse_single_status(status, job_id, shell)[source]: Parse the status of output from get_single_status command.