orcestra-downloader

Simplified access to download data from orcestra.ca

Table of Contents

• Installation
  • 1. Recommended CLI access
  • 2. Install into pixi project
  • 3. Install with pip
• Usage
  • Available Dataset Types
  • Basic Commands
  • Examples
  • Refreshing Cache
  • Downloading Datasets
  • Command Reference
• Troubleshooting
• Contributing

Installation

1. Recommended CLI access

The recommended way to use orcestra-downloader is through its CLI tool, which can be easily done without ever installing it on your system. You can run the CLI directly using pixi or uvx commands.

pixi exec via conda

pixi exec orcestra-downloader --help Output

uvx via pypi

uvx orcestra-downloader --help Output

2. Install into pixi project

If you wish to use orcestra-downloader in a pixi project, you can install orcestra-downloader into your project.

conda-forge:

pixi add orcestra-downloader         # from conda-forge

pixi add --pypi orcestra-downloader  # from pypi

3. Install with pip

If you have a python virtual environment set up, you can install orcestra-downloader directly using pip or python -m pip.

To install the package, use pip:

pip install orcestra-downloader

Usage

The orcestra-downloader provides a convenient command-line interface to interact with the orcestra.ca API. The CLI allows you to list, view, and download various datasets easily.

Available Dataset Types

🔬 Seven different dataset types are available through orcestra.ca:

Dataset Type Description pharmacosets Pharmacological screening datasets icbsets Immune checkpoint blockade datasets radiosets Radiotherapy response datasets xevasets Xenograft-derived datasets toxicosets Toxicological screening datasets radiomicsets Radiomics datasets clinicalgenomics Clinical genomics datasets

Basic Commands

🧑‍💻 Each dataset type supports these common commands:

# List all items in a dataset orcestra-downloader [dataset_type] list # Print a table of items in a dataset orcestra-downloader [dataset_type] table [DATASET_NAME] # Download a file for a dataset orcestra-downloader [dataset_type] download [DATASET_NAME] # Download all files for a dataset orcestra-downloader [dataset_type] download-all

Examples

📋 Basic listing and table commands

# List all radiosets orcestra-downloader radiosets list # Print a table of all xevasets after refreshing the cache orcestra-downloader xevasets table --force # Print a table of a specific dataset with more details orcestra-downloader pharmacosets table GDSC_2020(v2-8.2)

👀 Command Demo

Refreshing Cache

💡 orcestra-downloader uses a cache to store dataset metadata from the Orcestra API. This should be located at ~/.cache/orcestra-downloader.

By default, the tool will only update cache when used 7 days after the last update. To refresh the cache, use the --refresh flag. orcestra-downloader --refresh

Downloading Datasets

⬇️ Download specific datasets or entire collections:

# Download a specific pharmacoset orcestra-downloader pharmacosets download 'GDSC_2020(v2-8.2)' # Download multiple datasets at once orcestra-downloader radiomicsets download HNSCC_Features RADCURE_Features # Specify a custom download directory orcestra-downloader toxicosets download 'DrugMatrix Rat' --directory ./my-data-folder # Download all datasets of a specific type (with progress bar) orcestra-downloader xevasets download-all # Force overwrite of existing files orcestra-downloader icbsets download-all --overwrite

Command Reference

⚙️ Global options available for all commands:

Options: -r, --refresh Fetch all datasets and hydrate the cache. -h, --help Show this message and exit. -q, --quiet Suppress all logging except errors. -v, --verbose Increase verbosity of logging (0-3: ERROR, WARNING, INFO, DEBUG).

⌨️ Dataset-specific command options For the list command: Options: --force Force fetch new data. --no-pretty Disable pretty printing. For the table command: Arguments: [NAME OF DATASET] Optional dataset name for detailed information. Options: --force Force fetch new data. For the download command: Arguments: [ORCESTRA DATASET NAME] Required dataset name(s) to download. Options: -o, --overwrite Overwrite existing file if it exists. -d, --directory PATH Directory to save the file to. --force Force fetch new data from the API. For the download-all command: Options: -o, --overwrite Overwrite existing files if they exist. -d, --directory PATH Directory to save the files to. --force Force fetch new data from the API.

Troubleshooting

❓ Common issues and solutions:

Cache issues: If you're getting outdated information, try using the --refresh flag or --force option. Download errors: Check your internet connection and make sure the orcestra.ca API is accessible. Permission errors: Ensure you have write permissions to the download directory. Dataset not found: Make sure the dataset name is correct and exists on orcestra.ca.

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

If you encounter any issues or have questions, please open an issue on the GitHub repository: https://github.com/bhklab/orcestra-downloader/issues