Module zoo_wes_runner.wes_runner

Variables

logger

class ZooWESRunner(
    *args,
    **kwargs
)

We wrap the base zoo runner but add our own execution step.

def shorten_namespace(
    value: str
) -> str

shortens the namespace to 63 characters

def assert_parameters(
    self
)

checks all mandatory processing parameters were provided

def dismiss(
    self
)

Cancel the job.

def execute(
    self
)

Execute some CWL on a WES Server.

def get_max_cores(
    self
) -> int

returns the maximum number of cores that pods can use

def get_max_ram(
    self
) -> str

returns the maximum RAM that pods can use

def get_namespace_name(
    self
)

creates or returns the namespace

def get_processing_parameters(
    self
)

Gets the processing parameters from the zoo inputs

def get_volume_size(
    self
) -> str

returns volume size that the pods share

def get_workflow_id(
    self
)

returns the workflow id (CWL entry point)

def get_workflow_inputs(
    self,
    mandatory=False
)

Returns the CWL workflow inputs

def prepare(
    self
)

Generic pre-execution which applies to all handlers.

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

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

def wrap(
    self
)