Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/bhklab/orcestra-downloader

Seamless CLI access to orcestra datasets

https://github.com/bhklab/orcestra-downloader

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (13.1%) to scientific vocabulary

Keywords from Contributors

data-profiling actions integrations interpretability standardization animal hack autograder report
Last synced: 11 months ago · JSON representation

Repository

Seamless CLI access to orcestra datasets

Basic Info
Statistics
  • Stars: 0
  • Watchers: 3
  • Forks: 1
  • Open Issues: 4
  • Releases: 18
Created over 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

# orcestra-downloader Simplified access to download data from orcestra.ca [![pixi-badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json&style=flat-square)](https://github.com/prefix-dev/pixi) [![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json&style=flat-square)](https://github.com/astral-sh/ruff) [![Built with Material for MkDocs](https://img.shields.io/badge/mkdocs--material-gray?logo=materialformkdocs&style=flat-square)](https://github.com/squidfunk/mkdocs-material) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/orcestra-downloader)](https://pypi.org/project/orcestra-downloader/) ![GitHub release (latest by date)](https://img.shields.io/github/v/release/bhklab/orcestra-downloader?label=GitHub%20Release&style=flat-square) [![PyPI - Version](https://img.shields.io/pypi/v/orcestra-downloader)](https://pypi.org/project/orcestra-downloader/) [![Downloads](https://static.pepy.tech/badge/orcestra-downloader)](https://pepy.tech/project/orcestra-downloader) ![GitHub last commit](https://img.shields.io/github/last-commit/bhklab/orcestra-downloader?style=flat-square) ![GitHub issues](https://img.shields.io/github/issues/bhklab/orcestra-downloader?style=flat-square) ![GitHub pull requests](https://img.shields.io/github/issues-pr/bhklab/orcestra-downloader?style=flat-square) ![GitHub contributors](https://img.shields.io/github/contributors/bhklab/orcestra-downloader?style=flat-square) ![GitHub stars](https://img.shields.io/github/stars/bhklab/orcestra-downloader?style=flat-square) ![GitHub forks](https://img.shields.io/github/forks/bhklab/orcestra-downloader?style=flat-square)

Table of Contents

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

```console pixi exec orcestra-downloader --help ```
Output ![pixi-exec-help](assets/pixi-exec-help.png)

uvx via pypi

```console uvx orcestra-downloader --help ```
Output ![uvx-help](assets/uvx-help.png)

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:

```console 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:

console 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

:microscope: 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

:technologist: Each dataset type supports these common commands:
```bash # 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

:clipboard: Basic listing and table commands
```console # 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) ```
:eyes: Command Demo ![orcestra-gif](./tapes/orcestra.gif)

Refreshing Cache

:bulb: `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. ```console orcestra-downloader --refresh ```

Downloading Datasets

:arrow_down: Download specific datasets or entire collections:
```console # 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

:gear: Global options available for all commands:
```console 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). ```
:keyboard: Dataset-specific command options For the `list` command: ```console Options: --force Force fetch new data. --no-pretty Disable pretty printing. ``` For the `table` command: ```console Arguments: [NAME OF DATASET] Optional dataset name for detailed information. Options: --force Force fetch new data. ``` For the `download` command: ```console 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: ```console 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

:question: 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

Owner

  • Name: BHKLAB
  • Login: bhklab
  • Kind: organization
  • Location: Toronto, Ontario, Canada

The Haibe-Kains Laboratory @ Princess Margaret Cancer Centre

GitHub Events

Total
  • Create event: 24
  • Issues event: 5
  • Release event: 18
  • Watch event: 1
  • Issue comment event: 4
  • Push event: 77
  • Pull request event: 8
  • Fork event: 1
Last Year
  • Create event: 24
  • Issues event: 5
  • Release event: 18
  • Watch event: 1
  • Issue comment event: 4
  • Push event: 77
  • Pull request event: 8
  • Fork event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 79
  • Total Committers: 3
  • Avg Commits per committer: 26.333
  • Development Distribution Score (DDS): 0.241
Past Year
  • Commits: 79
  • Committers: 3
  • Avg Commits per committer: 26.333
  • Development Distribution Score (DDS): 0.241
Top Committers
Name Email Commits
Jermiah Joseph j****8@g****m 60
semantic-release s****e 18
github-actions[bot] 4****] 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 4
  • Total pull requests: 9
  • Average time to close issues: about 16 hours
  • Average time to close pull requests: 11 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 0.25
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 4
Past Year
  • Issues: 4
  • Pull requests: 9
  • Average time to close issues: about 16 hours
  • Average time to close pull requests: 11 days
  • Issue authors: 3
  • Pull request authors: 2
  • Average comments per issue: 0.25
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 4
View more stats
Top Authors
Issue Authors
  • jjjermiah (2)
  • strixy16 (1)
  • mugpeng (1)
Pull Request Authors
  • jjjermiah (6)
  • github-actions[bot] (4)
Top Labels
Issue Labels
Pull Request Labels
pixi (4)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 46 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 16
  • Total maintainers: 1
pypi.org: orcestra-downloader

Simplified access to download data from orcestra.ca

  • Versions: 16
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 46 Last month
Rankings
Dependent packages count: 9.9%
Average: 32.8%
Dependent repos count: 55.8%
Maintainers (1)
bhaibeka
Last synced: 11 months ago