cerise.job_store package

Submodules

cerise.job_store.job_state module

class cerise.job_store.job_state.JobState

Bases: enum.Enum

Enum JobState

CANCELLED = 'Cancelled'

FINISHED = 'Finished'

PERMANENT_FAILURE = 'PermanentFailure'

RUNNING = 'Running'

RUNNING_CR = 'RunningCR'

STAGING_IN = 'StagingIn'

STAGING_IN_CR = 'StagingCR'

STAGING_OUT = 'Destaging'

STAGING_OUT_CR = 'DestagingCR'

SUBMITTED = 'Submitted'

SUCCESS = 'Success'

SYSTEM_ERROR = 'SystemError'

TEMPORARY_FAILURE = 'TemporaryFailure'

WAITING = 'Waiting'

WAITING_CR = 'WaitingCR'

cancellation_active = <function JobState.cancellation_active>

is_final = <function JobState.is_final>

is_remote = <function JobState.is_remote>

to_cwl_state_string = <function JobState.to_cwl_state_string>

cerise.job_store.sqlite_job module

class cerise.job_store.sqlite_job.SQLiteJob(store: Any, job_id: str)

Bases: object

This class provides the internal representation of a job. These are stored inside the service. Note that there is also a JobDescription, which is defined in the Swagger definition and part of the REST API, and a Cerulean JobDescription class, which describes a job to start on a remote compute resource.

Creates a new SQLiteJob object.

This contains only a job id and a reference to the store; the data about the job are in the database.

Parameters:

• store (SQLiteJobStore) – The store this job is stored by
• id – The id of the job, a string containing a GUID

add_log(level: int, message: Union[str, List[str]]) → None

Add a message to the job’s log.

Parameters:

• level – Level of importance
• message – The log message.

critical(message: Union[str, List[str]]) → None

Add a message to the job’s log at level CRITICAL.

Parameters:message – The log message.

debug(message: Union[str, List[str]]) → None

Add a message to the job’s log at level DEBUG.

Parameters:message – The log message.

error(message: Union[str, List[str]]) → None

Add a message to the job’s log at level ERROR.

Parameters:message – The log message.

id = None

Job id, a string containing a UUID.

Type:str

info(message: Union[str, List[str]]) → None

Add a message to the job’s log at level INFO.

Parameters:message – The log message.

local_input

Input JSON string, as specified by the submitter.

local_output

The serialised JSON output object describing the destaged outputs.

log

Log output as of last update.

name

Name, as specified by the submitter.

please_delete

Whether the job should be deleted.

remote_error

cwl-runner stderr output as of last update.

remote_input_path

The absolute remote path of the input description file.

remote_job_id

The id the remote scheduler gave to this job.

remote_output

cwl-runner output as of last update.

remote_stderr_path

The absolute remote path of the standard error dump.

remote_stdout_path

The absolute remote path of the standard output dump.

remote_system_err_path

The absolute remote path of the system error dump.

remote_system_out_path

The absolute remote path of the system out dump.

remote_workdir_path

The absolute remote path of the working directory.

remote_workflow_path

The absolute remote path of the CWL workflow file.

required_num_cores

The number of cores to reserve for this workflow.

resolve_retry_count

How many times we’ve tried to resolve.

state

Current state of the job.

time_limit

The time to reserve, in seconds. If 0, use cluster default.

try_transition(from_state: cerise.job_store.job_state.JobState, to_state: cerise.job_store.job_state.JobState) → bool

Attempts to transition the job’s state to a new one.

If the current state equals from_state, it is set to to_state, and True is returned, otherwise False is returned and the current state remains what it was.

Parameters:

• from_state – The expected current state
• to_state – The desired next state

Returns:

True iff the transition was successful.

warning(message: Union[str, List[str]]) → None

Add a message to the job’s log at level WARNING.

Parameters:message – The log message.

workflow

Workflow file URI, as specified by the submitter.

workflow_content

The content of the workflow description file, or None if it has not been resolved yet.

cerise.job_store.sqlite_job_store module

exception cerise.job_store.sqlite_job_store.JobNotFound

Bases: RuntimeError

class cerise.job_store.sqlite_job_store.SQLiteJobStore(dbfile: str)

Bases: object

A JobStore that stores jobs in a SQLite database. You must acquire the store to do anything with it or the jobs stored in it. It’s a context manager, so use a with statement:

with self._store:

job = self._store.get_job(id) # go ahead and modify job

# don’t touch self._store or keep any references to jobs

Having multiple nested with statements is okay, so you can call other functions that use the store and acquire it themselves without incident.

Parameters:dbfile (str) – The path to the file storing the database.

create_job(name: str, workflow: str, job_input: str) → str

Create a job.

Parameters:

• name – The user-assigned name of the job
• workflow – A string containing a URL pointing to the workflow
• job_input – A string containing a json description of a json string.

Returns:

A string containing the job id.

delete_job(job_id: str) → None

Delete the job with the given id.

Parameters:job_id – A string containing the id of the job to be deleted.

get_job(job_id: str) → cerise.job_store.sqlite_job.SQLiteJob

Return the job with the given id.

Parameters:job_id – A string containing a job id, as obtained from create_job() or list_jobs(). Returns:The job object corresponding to the given id.

list_jobs() → List[cerise.job_store.sqlite_job.SQLiteJob]

Return a list of all currently known jobs.

Returns:A list of SQLiteJob objects.

Module contents