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WRROC <> GA4GH API Conversion Tool Project

Introduction

The purpose of this document is to explore the mapping between the WRROC (Workflow Run RO-Crate) profiles and the GA4GH Cloud API schemas, focusing specifically on the Task Execution Service (TES) and Workflow Execution Service (WES) APIs. This document aims to address the following questions:

  1. How could an RO-Crate be packaged from a TES run, such that the RO-Crate contains all necessary info to restart that TES run?
  2. Which additional information is required to package a valid Process Run Crate from the TES run?
  3. How could an RO-Crate be packaged from a WES run, such that the RO-Crate contains all necessary info to restart that WES run?
  4. Which additional information is required to package a valid Workflow Run Crate from the WES run?

Mapping of TES to RO-Crate

Required Information for TES Run

The following table maps the properties of the TES schema to the RO-Crate schema. This mapping ensures that all necessary information from a TES run is captured in the RO-Crate to enable the restart of the TES run.

TES Property RO-Crate Property Mapping Status Notes
id identifier 1-to-1 match  
name name 1-to-1 match  
description description 1-to-1 match  
state status Vague match Requires additional context
inputs input 1-to-many match Needs further breakdown
outputs output 1-to-many match Needs further breakdown
resources resources 1-to-1 match  
creation_time dateCreated 1-to-1 match  
start_time startTime 1-to-1 match  
end_time endTime 1-to-1 match  
… … … …

Additional Information for Process Run Crate

To create a valid Process Run Crate from a TES run, the following additional properties are required:

Additional Property Required for Process Run Crate Notes
software Yes Details of the software used
environment variables Yes Environment setup details
provenance Yes Provenance information
… … …

Mapping of WES to RO-Crate

Required Information for WES Run

The following table maps the properties of the WES schema to the RO-Crate schema. This mapping ensures that all necessary information from a WES run is captured in the RO-Crate to enable the restart of the WES run.

WES Property RO-Crate Property Mapping Status Notes
id identifier 1-to-1 match  
workflow_name name 1-to-1 match  
workflow_params parameters 1-to-1 match  
workflow_engine_name engine 1-to-1 match  
state status Vague match Requires additional context
inputs input 1-to-many match Needs further breakdown
outputs output 1-to-many match Needs further breakdown
creation_time dateCreated 1-to-1 match  
start_time startTime 1-to-1 match  
end_time endTime 1-to-1 match  
… … … …

Additional Information for Workflow Run Crate

To create a valid Workflow Run Crate from a WES run, the following additional properties are required:

Additional Property Required for Workflow Run Crate Notes
software Yes Details of the software used
environment variables Yes Environment setup details
provenance Yes Provenance information
… … …

Summary of Gaps and Recommendations

This section summarizes the gaps identified in the mappings and provides recommendations for addressing these gaps to improve the general applicability of the conversion tool.

Recommendations

Appendices