lcsb-icommands 1.1.0

iRODS client for automatic data ingestion via OAuth2/Keycloak

lcsb-icommands - iRODS Client for Automatic Ingestion

OAuth2-based data ingestion system for iRODS, using the same Keycloak authentication as Mango.

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Overview

User Laptop → Keycloak (OAuth2) → lcsb-icommands Client
                      ↓
         lcsb-icommands Server (validates token) → iRODS HTTP API

• Browser-based OAuth2 login (SSO on VPN)
• Direct file upload from laptop or staging from server landing zone
• 1-hour sessions with auto-refresh
• iRODS password never exposed to users

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Quick Start

Install

pip install lcsb-icommands

Note: On Linux/macOS, pip install --user puts scripts in ~/.local/bin. If commands like lcsb-icommands or ils are not found, add this to your ~/.bashrc:

export PATH="$HOME/.local/bin:$PATH"
source ~/.bashrc

Usage

lcsb-icommands login                                              # Authenticate (once per session)
lcsb-icommands upload My_project/dataset_01 ./my_files/          # Upload files from laptop
lcsb-icommands staging /server/landing/dir --project P --dataset D  # Stage from server landing zone
lcsb-icommands ls                                                 # List projects
lcsb-icommands ls My_project                                      # List datasets in a project
lcsb-icommands download My_project/dataset_01 ./output/           # Download files

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Documentation

See SETUP.md for full installation and configuration guide.

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Repository Structure

lcsb-icommands/
├── client/
│   └── lcsb_icommands.py      # CLI client (single-file, distribute to users)
├── server/
│   └── main.py             # FastAPI server
├── http_api.py             # iRODS HTTP API client
├── INSTALL.sh              # Server installation script
└── SETUP.md                # Full setup guide

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Version: 2.0.0 Author: Sandesh Patil ([e-mail])