WorkflowHub Knowledge Graph

A tool to generate a knowledge graph from a source of RO Crates. By default, this tool sources and generates an RDF graph of crates from WorkflowHub.

Getting Started

This tool is run as a Snakemake workflow. We recommend building a Docker container to run the workflow:

docker build -t knowledgegraph .

Then, you can run the workflow using the following command:

docker run --rm -v ./workflow-output:/app/output --user $(id -u):$(id -g) knowledgegraph

Where ./workflow-output is the directory where the output will be stored (already created for you in this repo) and the --user flag ensures that the output files are created with the correct permissions.

Structure

flowchart TD
    A[Source RO Crates] --> B[Check Outputs];
    B[Check Outputs] --> C[Report Downloaded RO Crates];
    B[Check Outputs]-->D[Merge RO Crates];
    D[Merge RO Crates]-->E[Create Merged Workflow Run RO Crate]

Loading

• source_ro_crates: This rule sources RO crates from the WorkflowHub API (source_crates.py) and then checks the output (check_outputs.py). This generates a list of expected file paths based on the workflow IDs and versions to facilitate the workflow.

• report_created_files: Optional. This rule reports the downloaded RO crates to the user.

• merge_files: This rule merges the downloaded RO crates into a single RDF graph (merge_ro_crates.py).

• create_ro_crate: This rule creates a merged workflow run RO crate from the merged RDF graph (create_ro_crate.py).

Contributing

Coding Style

• Code Formatting: We use Python Black for code formatting. Please format your code using Black before submitting a pull request (PR)
• Type Hinting: Please use type hints (PEP 484), and docstrings (PEP 257) in methods and classes.

Branching Strategy

• Branch Naming: When working on a new feature or bug fix, create a branch from develop. e.g. feature/description or bugfix/description.
• Development Branch: The develop branch is currently our main integration branch. Features and fixes should target develop through PRs.
• Feature Branches: These feature branches should be short-lived and focused. Once done, please create a pull request to merge it into develop.

License

BSD 2-Clause License