zoo-runner-common 0.1.0

Shared utilities for ZOO-Project CWL runners

zoo-runner-common

A shared utility library for ZOO-Project CWL runners – centralizing reusable components across runners like Calrissian, Argo Workflows, and WES.

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Overview

The zoo-runner-common repository provides core shared components used across multiple ZOO CWL runners. It eliminates code duplication by hosting:

• Common base class (BaseRunner) with 8+ shared methods
• Zoo-specific configuration handlers (ZooConf, ZooInputs, ZooOutputs)
• CWL workflow parsing and resource evaluation (CWLWorkflow)
• Execution handler interface (ExecutionHandler) for hooks
• Service stubs (ZooStub) to communicate with ZOO kernel

Key Benefits

• ✅ ~437 lines of code duplication eliminated across 3 runners
• ✅ Single source of truth for common functionality
• ✅ Easier maintenance - fix once, benefit everywhere
• ✅ Consistent behavior across all runners

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Directory Structure

zoo-runner-common/
├── base_runner.py      # Abstract BaseRunner with common methods
├── zoo_conf.py         # ZooConf, ZooInputs, ZooOutputs, CWLWorkflow
├── handlers.py         # ExecutionHandler abstract base class
├── zoostub.py          # ZooStub for ZOO kernel communication
└── __init__.py         # Package initialization

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Installation

As a dependency (recommended)

Add to your runner's pyproject.toml:

[project]
dependencies = [
    "zoo-runner-common @ git+https://github.com/ZOO-Project/zoo-runner-common.git@main",
]

Local development

export PYTHONPATH="$PYTHONPATH:/path/to/zoo-runner-common"

Or use relative imports:

import sys
sys.path.insert(0, os.path.abspath('../zoo-runner-common'))
from base_runner import BaseRunner
from zoo_conf import ZooConf, ZooInputs, ZooOutputs, CWLWorkflow
from handlers import ExecutionHandler

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Components

BaseRunner (base_runner.py)

Abstract base class providing common functionality for all CWL runners:

Methods provided:

• get_workflow_id() - Get workflow identifier
• get_workflow_inputs(mandatory=False) - Get workflow input parameters
• get_max_cores() - Get maximum CPU cores from CWL
• get_max_ram() - Get maximum RAM from CWL
• get_volume_size(unit='Gi') - Calculate volume size (supports Mi/Gi)
• assert_parameters(mandatory=True) - Validate required inputs
• get_processing_parameters() - Get execution parameters
• get_namespace_name() - Generate unique namespace name
• update_status(progress, message) - Update execution status
• prepare() - Pre-execution preparation with hooks
• finalize(log, output, usage_report, tool_logs) - Post-execution finalization

Abstract methods (to implement):

• wrap() - Wrap CWL with stage-in/stage-out
• execute() - Execute the workflow

Zoo Configuration Classes (zoo_conf.py)

Class	Description
ZooConf	Wraps ZOO configuration dictionary
ZooInputs	Handles input parameter conversion and validation
ZooOutputs	Manages output parameters
CWLWorkflow	Parses CWL, evaluates resources, handles scatter
ResourceRequirement	CWL resource hints dataclass

Key Features:

• Advanced type conversion (int, float, bool, arrays)
• File handling with format metadata
• OGC bounding box support
• NULL value handling
• Array inputs with isArray

ExecutionHandler (handlers.py)

Abstract base class for execution customization:

class ExecutionHandler(ABC):
    @abstractmethod
    def pre_execution_hook(self): pass
    
    @abstractmethod
    def post_execution_hook(self, log, output, usage_report, tool_logs): pass
    
    @abstractmethod
    def get_secrets(self): pass
    
    @abstractmethod
    def get_pod_env_vars(self): pass
    
    @abstractmethod
    def get_pod_node_selector(self): pass
    
    @abstractmethod
    def handle_outputs(self, log, output, usage_report, tool_logs): pass
    
    @abstractmethod
    def get_additional_parameters(self): pass

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Usage Example

from zoo_runner_common.base_runner import BaseRunner
from zoo_runner_common.handlers import ExecutionHandler

class MyCustomRunner(BaseRunner):
    def wrap(self):
        # Implement CWL wrapping logic
        return wrapped_cwl
    
    def execute(self):
        # Prepare execution
        cwljob = self.prepare()
        
        # Execute workflow (custom logic)
        result = my_executor.run(cwljob.cwl, cwljob.params)
        
        # Finalize
        self.finalize(log, output, usage_report, tool_logs)
        return result

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Runners Using zoo-runner-common

Runner	Backend	Repository
zoo-calrissian-runner	Calrissian/Kubernetes	EOEPCA/zoo-calrissian-runner
zoo-argowf-runner	Argo Workflows	ZOO-Project/zoo-argowf-runner
zoo-wes-runner	WES/TOIL	ZOO-Project/zoo-wes-runner

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Module Reference

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

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Used By

• zoo-wes-runner
• zoo-argowf-runner
• zoo-calrissian-runner