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:
- Fetch User-Project-Experiment structure from openBIS: fetch_space_structure.py
- Fetch data from the Bode group (and other data storage) servers and upload the new data to openBIS: upload_data.py
- 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