IRIDA Uploader Script

This Python script (irida.py) is rather a wrapper of iridauploader to provide functionality to interact with IRIDA ("legacy"), allowing users to create projects, prepare sample lists, and upload data.

Features

• Create projects in IRIDA
• Prepare sample lists for uploading
• Upload run folders to IRIDA
• Support for both single and batch uploads
• Flexible configuration options (file, environment variables, or interactive prompt)

Prerequisites

• Python 3.x
• Required Python packages are listed in requirements.txt

Installation

1. Clone this repository or download the irida.py script.
2. Install the required packages using the requirements.txt file:

pip install -r requirements.txt

Usage

The script provides two main commands: prepare and upload.

Prepare Command

Prepares a folder of fastq files for uploading to IRIDA by creating a project (if needed) and generating a sample list.

python irida.py prepare [OPTIONS] [PATH]

Options:

• --pid: Project ID (optional)
• --name: Project Name (optional), if not provided, the script will use the provided folder name
• --pe/--se: Are the fastq files Paired-End? (default: False)
• --sort/--no-sort: Sort samples by name (default: False)
• --pattern: Scan fastq files with a pattern (default: "*_R1_001.fastq.gz")
• --config: Path to IRIDA config file

Upload Command

Uploads a run folder to IRIDA.

python irida.py upload [OPTIONS] DIRECTORY

Options:

• --force-upload: Force upload (flag)
• --continue-upload: Start uploading from where the last upload left off (flag)
• --upload_mode: Upload mode (choices: default, assemblies, fast5; default: default)
• --config: Path to IRIDA config file

Configuration

The script can be configured using a configuration file, environment variables, or interactive prompts. The configuration includes:

• IRIDA base URL
• Client ID
• Client Secret
• Username
• Password
• API timeout

You can provide configuration in one of the following formats:

Config file

[Settings]
client_id = CHANGE-ME
client_secret = CHANGE-ME
username = CHANGE-ME
password = CHANGE-ME
base_url = CHANGE-ME
parser = directory
timeout = 1500

Environment variables

You can export a list of environment variables like below before running the script.

export IRIDA_BASE_URL=CHANGE-ME
export IRIDA_CLIENT_ID=CHANGE-ME
export IRIDA_CLIENT_SECRET=CHANGE-ME
export IRIDA_USERNAME=CHANGE-ME
export IRIDA_PASSWORD=CHANGE-ME
export IRIDA_TIMEOUT=CHANGE-ME

Prompting

If neither the config file nor environment variables provide all the necessary configuration parameters, the script will prompt you for any missing information. For example, if your config file only contains base_url, you will be asked to provide the remaining 5 parameters interactively.

Examples

1. Prepare a folder for upload:

python irida.py prepare --pe --sort /path/to/fastq/folder

2. Upload a prepared folder to IRIDA:

python irida.py upload --force-upload /path/to/prepared/folder

Notes

• Ensure you have the necessary permissions to access IRIDA and the local directories.
• The script creates temporary configuration files that are automatically deleted upon script exit.
• For security, avoid storing sensitive information like passwords in plain text configuration files.

Dependencies

All required dependencies are listed in the requirements.txt file. To view the specific versions and packages required, please refer to this file.

Contributing

Contributions to improve the script are welcome. Please ensure to follow the existing code style and add unit tests for any new functionality.

License

MIT License

Copyright (c) [2024] [Thanh Le Viet]