OpenBIS Bode group data registration

This repository contains the code to register & synchronize data in openBIS by connecting to the raw data in the Bode group & external ETH servers.

Main functionalities:

1. Fetch User-Project-Experiment structure from openBIS: fetch_space_structure.py
2. Fetch data from the Bode group (and other data storage) servers and upload the new data to openBIS: upload_data.py
3. Transform NMR data to a format that can be uploaded to openBIS: NMR_to_openBIS.py

For the regular registration of the data, the scripts, upload_data.sh and crontab_helper_NMR.sh, are used and are run as cron jobs on the server.

The main documentation is here: https://openbis.readthedocs.io/en/latest/software-developer-documentation/apis/python-v3-api.html

Setup

setup environment with make

make env
conda activate ./env

Important notes

• Data name should follow the convention:
  • Please no not use '-' and '.' in any of the names, as this is used as a separator
  • Bode - {USER_ETH_ID_UPPER_CASE}-{PROJECT_CODE_UPPER_CASE}-{EXPERIMENT_CODE_UPPER_CASE}-{DESCRIPTION}
  • USER_ETH_ID: ETH ID of the user, upper case
  • PROJECT_CODE: code of the project that the user made in openbis, upper case
  • EXPERIMENT_CODE: code of the experiment that the user made in openbis, upper case
  • DESCRIPTION: description of the data, does not need to be upper case