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https://github.com/iBridges-for-iRODS/iBridges
A wrapper around the python-irodsclient to allow for easy interaction with iRODS servers.
https://github.com/iBridges-for-iRODS/iBridges
data-analysis data-engineering data-science datascience irods-client
Last synced: about 2 months ago
JSON representation
A wrapper around the python-irodsclient to allow for easy interaction with iRODS servers.
- Host: GitHub
- URL: https://github.com/iBridges-for-iRODS/iBridges
- Owner: iBridges-for-iRODS
- License: mit
- Created: 2023-11-27T12:26:57.000Z (about 1 year ago)
- Default Branch: develop
- Last Pushed: 2024-10-29T09:29:06.000Z (3 months ago)
- Last Synced: 2024-10-29T11:43:18.287Z (3 months ago)
- Topics: data-analysis, data-engineering, data-science, datascience, irods-client
- Language: Python
- Homepage: https://ibridges.readthedocs.io/en/
- Size: 3.53 MB
- Stars: 15
- Watchers: 5
- Forks: 8
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-utrecht-university - iBridges - Python API and commandline interface to easily interact with Yoda and iRODS servers (Projects / Research software)
- awesome-utrecht-university - iBridges - Python API and commandline interface to easily interact with Yoda and iRODS servers (Projects / Research software)
README
# iBridges 
iBridges is a library for scientific programmers who are working with data in iRODS. We provide a wrapper around the [python-irodsclient](https://pypi.org/project/python-irodsclient/) to facilitate easy interaction with the iRODS server. iBridges is currently still in very active development.
[](https://badge.fury.io/py/ibridges)
[](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/integration-tests-irods.yml)
[](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/integration-tests-yoda.yml)
[](https://github.com/iBridges-for-iRods/iBridges/actions/workflows/main.yml)
[](https://doi.org/10.5281/zenodo.12583187)
## Highlights
- Works on Windows, Mac OS and Linux
- Runs on Python 3.8 or higher.
- Supported iRODS server versions: 4.2.11 or higher and 4.3.0 or higher.
- **Interactive connection** to your iRODS server.
- **Upload** and **Download** your data.
- Manipulate the **metadata** on the iRODS server.
- **Synchronise** your data between your local computer and the iRODS server.
- Create and manipulate **Tickets** to temporarily grant access to outside users.
- **Search** through all metadata for your dataset or collection.
- Small number of dependencies (`python-irodsclient` and `tqdm`)
- Safe default options when working with your data.
**iBridges** also has a graphical user interface, which you can install [here](https://github.com/iBridges-for-iRods/iBridges-GUI).
Report Bug
.
Request Feature
.
Share an idea
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Leave some feedback
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Ask a question
## Installation
There are two main ways to install iBridges. The recommended way is to use the stable version that is available on PyPi:
```bash
pip install ibridges
```
If you want to install the unstable version to test out new features, you can install the development branch:
```bash
pip install git+https://github.com/iBridges-for-iRods/iBridges.git@develop
```
## Configuration
You will need to have a so-called `irods_environment.json`. Please follow the [documentation](https://ibridges.readthedocs.io/en/latest/cli.html) how to set it up.
## Usage
Below are some basic examples of the features in iBridges.
```py
# Create an iRODS session
from ibridges.interactive import interactive_auth
session = interactive_auth()
# Upload data
from ibridges import upload
upload(session, "/your/local/path", "/irods/path")
# Download data
from ibridges import download
download(session, "/irods/path", "/other/local/path")
```
## Command line interface
To simply upload or download data you do not need to write full python program, we offer a command line interface (see also [the documentation](https://ibridges.readthedocs.io/en/latest/)).
- Establish a connection
```bash
ibridges init
```
- List a collection
```bash
# list your home collection
ibridges list
# list a different collection in your home
ibridges list "irods:~/"
# list a collection on a different path than your home
ibridges list "irods:/full/irods/path"
```
- Upload data
```bash
ibridges upload my_file.json "irods:~/some_collection"
```
- Download data
```bash
ibridges download "irods:~/some_collection/some_object" download_dir
```
- Synchronise data
```bash
ibridges sync some_local_directory "irods:~/some_collection"
## Tutorials
### Documentation
- **[ReadTheDocs](https://ibridges.readthedocs.io/en/latest/)**
### Guides
- [Manual with examples](tutorials/00-FirstSteps.ipynb)
### Beginners tutorials
- [Setup client configuration](tutorials/01-Setup-and-connect.ipynb)
- [iRODS Paths](tutorials/02-iRODS-paths.ipynb)
- [Working with data](tutorials/03-Working-with-data.ipynb)
- [Metadata](tutorials/04-Metadata.ipynb)
- [Sharing data](tutorials/05-Data-Sharing.ipynb)
- [Synchronising data](tutorials/06-Data-sync.ipynb)
## Do I have to choose between the *python-irodsclient* and *iBridges*?
No. *iBridges* itself is based on the *python-irodsclient*. When you connect to iRODS a *python-irodsclient* `irods.iRODSSession` is automatically created with which you can access all functionality of the *python-irodsclient*.
## Authors
**Christine Staiger (Maintainer) [ORCID](https://orcid.org/0000-0002-6754-7647)**
- *Wageningen University & Research* 2021 - 2022
- *Utrecht University* 2022
**Tim van Daalen**, *Wageningen University & Research* 2021
**Maarten Schermer (Maintainer) [ORCID](https://orcid.org/my-orcid?orcid=0000-0001-6770-3155)**, *Utrecht University* 2023
**Raoul Schram (Maintainer) [ORCID](https://orcid.org/my-orcid?orcid=0000-0001-6616-230X)**.
*Utrecht University* 2023
## Contributors
**J.P. Mc Farland**,
*University of Groningen, Center for Information Technology*, 2022
## License
This project is licensed under the MIT license.
The full license can be found in [LICENSE](LICENSE).