OpenBIS Upload Helper

A simple upload tool for OpenBIS that parses metadata from the specified files, creates a preview of the data, and uploads the files and preview images along with the metadata to OpenBIS.

The structure of the metadata and some upload settings are specific to the OpenBIS instance used at BAM and the BAM Data Store.

Folder Structure

• Main Folder: The Python Code for the Graphical User Interface, files specifying the requirements and license, and this readme file
• Parser: Collection of classes for parsing metadata from different files (a list of currently implemented parsers can be found here)
• Documentation: Additional resources used in this documentation

Installation:

Clone (or download) the repository, set up and activate a virtual environment, and install the packages from requirements.txt. For Windows:

git clone https://github.com/BAMresearch/openbis-upload-helper
cd openbis-upload-helper
python -m venv .\venv
venv\Scripts\activate
pip install -r requirements.txt

How to run:

After installation, the program can be run by simply double-clicking the OpenBISUploadHelper.bat file (on Windows), or by activating the virtual environment and running the script from the command line. For Windows:

cd OpenBIS_Upload_Helper
venv\Scripts\activate
python OpenBISUploadHelper.py

How to use:

• Select the file(s) you want to upload by clicking on the three dots ... next to the text field for Files
• You can select whether you want to create a Preview Image (selected by default), create a Metadata File (disabled by default), and upload everything to OpenBIS (selected by default). If you select the second option, the parsed metadata will be written to a file (you can use this option and disable the upload if you are only interested in extracting metadata with the parsers).
• Enter your User Name. The script can be configured to automatically select the default Space Name and Project Name for this user (see source code for an example)
• Enter your Password (will be hidden with * characters)
• Select the Space Name from the dropdown list (or type it into the field)
• Select the Project Name from the dropdown list (or type it into the field)
• Give the Experiment Name to which these files belong
• Click on Export

This will automatically create a new Experimental Step matching the type of characterization data you selected in the specified Experiment of the Prject in the Space selected above. If the Experiment does not exist, it will be created automatically. The program will then attempt to find the right parser to use with these data, extract the metadata, create a preview image and/or metadata file (if the corresponding options were selected above), and upload everything to OpenBIS, filling the metadata fields of the Experimental Step accordingly. The program can also be configured to automatically set the parents for this Experimental Step to the corresponding Instrument from the OpenBIS Inventory (see source code for an example)

Parsers that are currently implemented:

• Infrared Spectroscopy Data, exported as csv from ThermoFischer Scientific OMNIC Software
• Nuclear Magnetic Resonance Spectroscopy Data, saved as JCAMP-DX files by Oxford Instruments SpinFlow Software for the XPulse instrument
• Scanning Electron Microscopy Image Data, saved as tif files by the Software of the Zeiss Supra 40 SEM
• Transmission Electron Microscopy Image Data:
  • Saved as tif files by the Software of the ThermoFisher Scientific Talos F200S
  • Saved as emd files by the Software of the ThermoFisher Scientific Talos F200S
  • Saved as dm3 files by the Software of the JEOL JEM-2200FS TEM
• Optical Spectroscopy Data, exported as txt from the SoftMax Pro Software of the MolecularDevices Spectramax Platereader
• Dynamic Light Scattering data, exported as csv from Malvern Zetasizer Instruments (Legacy) - For export from SQL Databases of the current Software, see here

License:

• The code for the Upload Helper Tool and the parsers are published under the MIT license.
• The code for parsing DM3 files is a slightly modified version of the code from Pierre-Ivan Raynal, published on Github under the MIT license.
• The meta- and master-data schemata the parsers produce after extracting the metadata are Copyright (C) by the authors, all rights reserved.