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: pulsar.managers.base.external.ExternalBaseManager
Base class for Pulsar managers using DRMAA.
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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: pulsar.managers.base.BaseManager
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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.
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read_command_line
(job_id)[source]
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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: pulsar.managers.base.directory.DirectoryBaseManager
Base class for managers that interact with external distributed
resource managers.
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clean
(job_id)[source]
Delete job directory and clean up resources associated with job with
id job_id.
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get_status
(job_id)[source]
Return status of job as string, currently supported statuses include
‘cancelled’, ‘running’, ‘queued’, and ‘complete’.
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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: pulsar.managers.ManagerInterface
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clean
(job_id)[source]
Delete job directory and clean up resources associated with job with
id job_id.
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job_directory
(job_id)
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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.
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system_properties
()[source]
-
class
pulsar.managers.base.
DirectoryMaker
(mode=None)[source]
Bases: object
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make
(path, recursive=False)[source]
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class
pulsar.managers.base.
JobDirectory
(staging_directory, job_id, lock_manager=None, directory_maker=None)[source]
Bases: pulsar.client.job_directory.RemoteJobDirectory
-
calculate_path
(remote_path, input_type)[source]
Verify remote_path is in directory for input_type inputs
and create directory if needed.
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contains_file
(name)[source]
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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]
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read_file
(name, size=-1, default=None)[source]
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remove_file
(name)[source]
Quietly remove a job file.
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remove_metadata
(metadata_name)[source]
-
setup
()[source]
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store_metadata
(metadata_name, metadata_value)[source]
-
working_directory_contents
()[source]
-
working_directory_file_contents
(name)[source]
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write_file
(name, contents)[source]
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pulsar.managers.base.
get_id_assigner
(assign_ids)[source]