Feature Request: Define Curation Workflow with Interlinked Config Files

[berntpopp]

Summary

Establish a structured curation workflow in the Gene Curator application, transitioning from gene data to pre-curation and then to the curation stage. This workflow should be outlined through config files, where each stage's config file references the relevant details from the previous stages' config files (e.g., gene, pre-curation, and curation configs).

Description

Currently, the curation process lacks a defined workflow that seamlessly integrates gene data, pre-curation, and curation stages. By implementing a series of interconnected config files, we can establish a clear and efficient workflow. Each config file will contain stage-specific parameters and settings, and will reference necessary details from the preceding stages' config files, ensuring continuity and consistency throughout the curation process.

Acceptance Criteria

• Develop config files for each stage of the curation process: gene, pre-curation, and curation.
• Ensure that each config file references relevant details from the previous stage's config file.
• Create a master config file that outlines the entire workflow, linking the individual stage configs.
• Implement logic in the application to read and follow the defined workflow based on these config files.
• Test the workflow thoroughly to ensure smooth transition and data integrity between stages.

User Stories

• As a data curator, I want a clear and defined workflow that guides me from gene data entry to the final curation.
• As a project manager, I need the curation process to be standardized and easily modifiable through configuration files.
• As a developer, I aim to implement a workflow that ensures consistency and minimizes the risk of data discrepancies between curation stages.

Implementation Details

• Define the structure and contents of each config file, ensuring they contain all necessary parameters for their respective curation stages.
• Link the configs so that each subsequent stage can access and utilize data from the previous stage.
• Develop functionality in the Gene Curator application to interpret and execute the workflow as defined by these config files.

Code Snippet Example for Config Files

// geneConfig.json
{
  "geneDataParameters": [...],
  "nextStage": "preCurationConfig.json"
}

// preCurationConfig.json
{
  "preCurationParameters": [...],
  "previousStage": "geneConfig.json",
  "nextStage": "curationConfig.json"
}

// curationConfig.json
{
  "curationParameters": [...],
  "previousStage": "preCurationConfig.json"
}
{
  "workflow": [
    "geneConfig.json",
    "preCurationConfig.json",
    "curationConfig.json"
  ]
}