A shared utility library for ZOO-Project CWL runners – centralizing reusable components across runners like Calrissian, Argo Workflows, and WES.
The zoo-runner-common repository provides core shared components used across multiple ZOO CWL runners. It avoids duplication by hosting:
- Common base classes (
BaseRunner) - Zoo-specific configuration handlers (
ZooConf,ZooInputs,ZooOutputs) - CWL workflow parsing and resource evaluation (
CWLWorkflow) - CWL wrapping utilities for stage-in, stage-out (
wrapper_utils) - Service stubs (
ZooStub) to update job status
zoo-runner-common
- base_runner.py # Abstract BaseRunner used by all CWL runners
- zoostub.py # ZooStub class to communicate with ZOO kernel
- zoo_conf.py # ZooConf, ZooInputs, ZooOutputs, CWLWorkflow, ResourceRequirement
- wrapper_utils.py # Utilities to wrap CWL workflow with stage-in/out
- init.py # Optional for Python package recognition
No external installation is needed. Just include the path in your PYTHONPATH or structure your runners to import directly:
export PYTHONPATH="$PYTHONPATH:/path/to/zoo-runner-common"Or structure your project such that imports like the following work:
from zoo_runner_common.base_runner import BaseRunner
from zoo_runner_common.zoo_conf import ZooConf, ZooInputs, ZooOutputs, CWLWorkflow| Module | Description |
|---|---|
| BaseRunner | Abstract runner blueprint all runners must extend |
| ZooConf | Parses conf.json, manages job ID, state |
| ZooInputs | Parses inputs.json, formats CWL-style parameters |
| ZooOutputs | Handles writing and setting output results |
| CWLWorkflow | Loads, parses, and analyzes CWL workflows |
| ResourceRequirement | Parses and evaluates CWL resource hints/requirements |
| wrapper_utils | Provides helper to build wrapped CWL pipeline |
| ZooStub | Interacts with ZOO's lenv for progress updates |
- zoo-wes-runner
- zoo-argowf-runner
- zoo-calrissian-runner