https://github.com/ssciwr/mease-elabftw

A Python library for interacting with eLabFTW experiments
https://github.com/ssciwr/mease-elabftw

elabftw metadata

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A Python library for interacting with eLabFTW experiments

• Host: GitHub
• URL: https://github.com/ssciwr/mease-elabftw
• Owner: ssciwr
• License: mit
• Created: 2021-10-06T07:31:51.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2025-02-03T17:50:29.000Z (8 months ago)
• Last Synced: 2025-04-01T13:38:11.890Z (7 months ago)
• Topics: elabftw, metadata
• Language: Python
• Homepage:
• Size: 142 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 5
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# mease-elabftw

[![pypi](https://img.shields.io/pypi/v/mease-elabftw.svg)](https://pypi.org/project/mease-elabftw)

[![docs](https://readthedocs.org/projects/mease-elabftw/badge/?version=latest)](https://mease-elabftw.readthedocs.io/en/latest/?badge=latest)

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A Python library for interacting with [eLabFTW](https://www.elabftw.net/) experiments:

- Create [NWB](https://nwb-schema.readthedocs.io/en/latest/) metadata from an eLabFTW experiment

- Upload files (e.g. analysis result from HPC) to an eLabFTW experiment

- List eLabFTW experiments from the command line

## Setup

```bash

python -m pip install mease-elabftw

```

To authenticate requests to the eLabFTW server you also need to generate an API key in eLabFTW (User Panel -> API Keys -> GENERATE AN API KEY),

and then set the environment variable `ELABFTW_TOKEN` to this key, e.g.

```bash

export ELABFTW_TOKEN=abc123abc123abc123

```

## Use in Python

Get nwb metadata from an elabftw experiment to use in [mease-lab-to-nwb](https://github.com/ssciwr/mease-lab-to-nwb):

```pycon

>>> import mease_elabftw

>>> mease_elabftw.list_experiments("Liam")

['163: test fake experiment without json metadata (Liam Keegan, 2021-10-07)', '156: test fake experiment with json metadata (Liam Keegan, 2021-10-01)']

>>> metadata = mease_elabftw.get_nwb_metadata(156)

>>> metadata["NWBFile"]["session_description"]

test fake experiment with json metadata

>>> metadata["NWBFile"]["identifier"]

20211001-8b6f100d66f4312d539c52620f79d6a503c1e2d1

```

## Use from terminal

List all experiments on elabftw belonging to user "Liam":

```bash

$ elabftw-list Liam

163: test fake experiment without json metadata (Liam Keegan, 2021-10-07)

156: test fake experiment with json metadata (Liam Keegan, 2021-10-01)

```