zoo-template-common¶

Welcome to the documentation for zoo-template-common, a Python package providing common execution handlers and utilities for ZOO-Project CWL workflow templates.

Overview¶

This package provides a simple, extensible base class (CommonExecutionHandler) for handling CWL workflow execution in ZOO-Project templates. It includes basic functionality for STAC catalog processing, pod configuration, and output management.

Key Features¶

CommonExecutionHandler: Base class for CWL workflow execution handlers
- Pre/post execution hooks
- STAC catalog output processing
- Pod environment variable and node selector management
- Secrets handling
- Tool log management
CustomStacIO: STAC I/O class for S3 operations using boto3
- Read/write STAC catalogs from/to S3
- Support for both S3 and local file systems

Quick Example¶

from zoo_template_common import CommonExecutionHandler
from zoo_calrissian_runner import ZooCalrissianRunner

def my_workflow(conf, inputs, outputs):
    execution_handler = CommonExecutionHandler(conf=conf, outputs=outputs)

    runner = ZooCalrissianRunner(
        cwl=cwl,
        conf=conf,
        inputs=inputs,
        outputs=outputs,
        execution_handler=execution_handler,
    )

    exit_status = runner.execute()
    return exit_status

Templates Using This Package¶

eoepca-proc-service-template: Extends CommonExecutionHandler with EOEPCA Workspace API integration
zoo-service-template (EOAP): Uses CommonExecutionHandler as-is or extends it

Installation¶

pip install zoo-template-common

Or from Git:

pip install git+https://github.com/EOEPCA/zoo-template-common.git@main