KBDatalakeApps

KBase Datalake Applications - A collection of apps for interacting with the KBase data lake, including data retrieval, processing, and analysis utilities.

This is a KBase module generated by the KBase Software Development Kit (SDK).

Setup

This project was created with the create-new-project Claude command and includes:

• Virtual environment management via venvman
• Claude Code integration via claude-commands
• Cursor workspace configuration

Prerequisites

• Python 3.11+
• KBase SDK installed (Learn more)
• venvman for virtual environment management
• claude-commands for Claude Code integration

Installation

1. Open the Cursor workspace:

   code !KBDatalakeApps.code-workspace

2. Activate the virtual environment:

   source activate.sh
   # or
   venvman activate KBDatalakeApps

3. Install dependencies:

   pip install -r requirements.txt

KBase SDK Setup

Add your KBase developer token to test_local/test.cfg and run:

make
kb-sdk test

After making any additional changes to this repo, run kb-sdk test again to verify that everything still works.

Project Structure

KBDatalakeApps/
├── agent-io/              # Claude command execution tracking
├── lib/
│   └── KBDatalakeApps/
│       └── KBDatalakeAppsImpl.py  # Implementation code
├── ui/
│   └── narrative/
│       └── methods/       # Narrative UI definitions
├── test/                  # Unit tests
├── data/                  # Reference data (<100MB)
├── scripts/               # Utility scripts
├── .claude/               # Claude Code configuration
│   ├── CLAUDE.md          # System prompt
│   └── commands/          # Claude commands (managed by claude-commands)
├── KBDatalakeApps.spec    # KIDL specification
├── kbase.yml              # Module metadata
├── Dockerfile             # Container definition
└── !KBDatalakeApps.code-workspace  # Cursor workspace

Apps

run_datalake_query

Query the KBase datalake for various data types including:

• Genomes
• Metabolic Models
• Media definitions
• Assemblies

Development

Adding New Apps

1. Define the function in KBDatalakeApps.spec
2. Run make to compile the spec
3. Implement the function in lib/KBDatalakeApps/KBDatalakeAppsImpl.py
4. Create UI files in ui/narrative/methods/<app_name>/
5. Write tests in test/

KBUtilLib Integration

This module uses KBUtilLib for common functionality:

• KBWSUtils - Workspace operations
• KBCallbackUtils - Callback server handling
• SharedEnvUtils - Configuration and token management

Claude Code Integration

This project includes Claude Code integration:

• Command tracking stored in agent-io/ for project history
• Commands automatically installed to .claude/commands/ (managed by claude-commands)
• Update commands: claude-commands update

Installation from Another Module

To use this code in another SDK module:

kb-sdk install KBDatalakeApps

Help

• KBase SDK Documentation
• FAQ
• Troubleshooting Guide

Author

• chenry - Owner and primary author

License

See LICENSE file.