Module zoo_wes_runner.base

Bases classes for Zoo runners.

These are derived here from the zoo-calrissian-runner because no generic abstract classes exist.

Variables

logger

Classes

BaseZooRunner

class BaseZooRunner(
    cwl,
    conf,
    inputs,
    outputs,
    execution_handler: Optional[zoo_calrissian_runner.handlers.ExecutionHandler] = None
)

Mangle the ZooCalrissianRunner to be a base class to inherit from.

Ancestors (in MRO)

• zoo_calrissian_runner.ZooCalrissianRunner

Descendants

• zoo_wes_runner.wes_runner.ZooWESRunner

Static methods

shorten_namespace

def shorten_namespace(
    value: str
) -> str

shortens the namespace to 63 characters

Methods

assert_parameters

def assert_parameters(
    self
)

checks all mandatory processing parameters were provided

execute

def execute(
    self
)

This function should be implmented to provide job exection logic.

get_max_cores

def get_max_cores(
    self
) -> int

returns the maximum number of cores that pods can use

get_max_ram

def get_max_ram(
    self
) -> str

returns the maximum RAM that pods can use

get_namespace_name

def get_namespace_name(
    self
)

creates or returns the namespace

get_processing_parameters

def get_processing_parameters(
    self
)

Gets the processing parameters from the zoo inputs

get_volume_size

def get_volume_size(
    self
) -> str

returns volume size that the pods share

get_workflow_id

def get_workflow_id(
    self
)

returns the workflow id (CWL entry point)

get_workflow_inputs

def get_workflow_inputs(
    self,
    mandatory=False
)

Returns the CWL workflow inputs

prepare

def prepare(
    self
)

Generic pre-execution which applies to all handlers.

update_status

def update_status(
    self,
    progress: int,
    message: str = None
) -> None

updates the execution progress (%) and provides an optional message

wrap

def wrap(
    self
)