Module zoo_calrissian_runner
Sub-modules
Variables
zoo
Classes
ResourceRequirement
class ResourceRequirement(
coresMin=None,
coresMax=None,
ramMin=None,
ramMax=None,
tmpdirMin=None,
tmpdirMax=None,
outdirMin=None,
outdirMax=None
)
Class variables
coresMax
coresMin
outdirMax
outdirMin
ramMax
ramMin
tmpdirMax
tmpdirMin
Static methods
from_dict
def from_dict(
env
)
Workflow
class Workflow(
cwl,
workflow_id
)
Static methods
get_resource_requirement
def get_resource_requirement(
elem
)
Gets the ResourceRequirement out of a CommandLineTool or Workflow
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
| elem | CommandLineTool or Workflow | CommandLineTool or Workflow | None |
Returns:
| Type | Description |
|---|---|
| None | cwl_utils.parser.cwl_v1_2.ResourceRequirement or ResourceRequirement |
has_scatter_requirement
def has_scatter_requirement(
workflow
)
Methods
eval_resource
def eval_resource(
self
)
get_object_by_id
def get_object_by_id(
self,
id
)
get_workflow
def get_workflow(
self
) -> cwl_utils.parser.cwl_v1_0.Workflow
get_workflow_inputs
def get_workflow_inputs(
self,
mandatory=False
)
ZooCalrissianRunner
class ZooCalrissianRunner(
cwl,
conf,
inputs,
outputs,
execution_handler: Optional[zoo_calrissian_runner.handlers.ExecutionHandler] = None
)
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
)
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
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
)
ZooConf
class ZooConf(
conf
)
ZooInputs
class ZooInputs(
inputs
)
Methods
get_input_value
def get_input_value(
self,
key
)
get_processing_parameters
def get_processing_parameters(
self
)
Returns a list with the input parameters keys
ZooOutputs
class ZooOutputs(
outputs
)
Methods
get_output_parameters
def get_output_parameters(
self
)
Returns a list with the output parameters keys
set_output
def set_output(
self,
value
)
set the output result value
ZooStub
class ZooStub(
)
Methods
update_status
def update_status(
self,
conf,
progress
)