nomad-polymerization-reactions 0.2.0

A NOMAD plugin for polymerization reactions.

A NOMAD plugin providing schemas, search apps, and data transformation utilities for polymerization data extracted from publications.

Availability

This plugin is hosted on NOMAD's example Oasis. You can use the built-in schemas Monomer and PolymerizationReaction to create entries. You can also use a dedicated search app to look up polymerization-specific entries here.

Installation

Install the package in your local environment with pip:

pip install git+https://github.com/FAIRmat-NFDI/nomad-polymerization-reactions.git

Adding this plugin to NOMAD Oasis

The plugin can be added to a NOMAD Oasis instance in a few steps, provided that you have access to the repository hosting the Oasis.

Read the NOMAD plugin documentation for all details on how to deploy the plugin on your NOMAD instance. If you wanna get started with a new Oasis, start here.

Using the CLI for data transformation

The package provides utility functions for transforming JSON files into NOMAD entry archives. These archives have archive.json ending and are processed by NOMAD once uploaded. The m_def key in the archives helps NOMAD to identify which data schema to use.

Here's how you can convert a JSON file into an NOMAD entry archive that uses nomad_polymerization_reactions.schema_packages.polymerization.Monomer schema:

nomad-polymerization archive monomer.json

If you want to create an archive that uses nomad_polymerization_reactions.schema_packages.polymerization.PolymerizationReaction schema, use the polymerization mode:

nomad-polymerization archive polymerization_reaction.json --mode polymerization

You can specify multiple filepaths in the same command or even use directory paths. All the .json files in the directory will be transformed into archives:

nomad-polymerization archive /folder/polymerization/ --mode polymerization

By default, the command will create the archives in the same directory where it runs. If you want to create them in the same directory as the JSON file, use the flag --same-dir:

nomad-polymerization archive /folder/sub-folder/monomer.json --same-dir
# creates `monomer.archive.json` file in `/folder/sub-folder/`

The JSON files used for transformation should have a fixed format. You can find the data models for JSON files here.

License

Distributed under the terms of the Apache Software License 2.0 license, "nomad-polymerization-reactions" is free and open source software.