This project implements the new nomad@FAIRDI infrastructure. It is currently used to enable users to upload data, process the data, maintain a version of the NOMAD archive and meta-info, provide search, inspection, and download to all NOMAD raw and archive data. As a long term strategy, this project will integrate, refactor, and re-write more and more of the existing NOMAD CoE components.

The overall goal of nomad@FAIRDI is to provide common interfaces to the main services of NOMAD: Repository, Archive, and Encyclopedia. These interfaces comprise a graphical web-based UI that allows users to upload data, supervise data processing, inspect and download metadata, raw-files, and archive data, provide visual tools to explore the data, and to learn more about advanced use modes, like API and Analytics Toolkit. The second interface is a unified REST API with various endpoints that represent the core NOMAD services. This will allow users the automated use of NOMAD for managing their data, and using data on NOMAD for analytics. A specific way of using the API is through the NOMAD Analytics Toolkit, which is revamped as a separate project.

Furthermore, this projects aims at establishing NOMAD as a distributed platform for material science data sharing and management. This includes the on-site deployment of NOMAD as a standalone service (oasis), the federated use of NOMAD through a serious of full and partial mirrors, the integration of 3rd party material science databases (i.e. Aflow, OQMD, Materials Project), and support for open APIs and standards like the Optimade API.

Getting started

Read the docs. The documentation is part of the source code. It covers aspects like introduction, architecture, development setup/deployment, contributing, and API reference.

Read the docs on the latest deployed version

You can access the running system and its documentation here:

https://repository.nomad-coe.eu/uploads/api/docs

Generate the docs from the source

First, clone this repo and init its submodules:

git clone git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-FAIR.git
cd nomad-FAIR
git submodule init --depth 1

Second, create and source your own virtual python environment:

pip install virtualenv
virtualenv -p `which python3` .pyenv
source .pyenv/bin/activate

Third, install the development dependencies, including the documentation system sphinx:

pip install --upgrade pip
pip install --upgrade setuptools
pip install -r requirements.txt

Forth, generate the documentation:

cd docs
make html

Conintue with reading the documentation for further setup and contribution guidelines:

cd .build/html
python -m http.server 8888

Open http://localhost:8888/html/setup.html in your browser.

Change log

Omitted versions are plain bugfix releases with only minor changes and fixes.

v0.6.0

• GUI URL, and API endpoint that resolves NOMAD CoE legary PIDs
• Support for datasets in the GUI
• more flexible search python module and repo API
• minor bugfixes

v0.5.2

• allows to download large files over longer time period
• streamlined deployment without API+GUI proxy
• minor bugfixes

v0.5.1

• integrated parsers Dmol3, qbox, molcas, fleur, and onetep
• API endpoint for query based raw file download
• improvements to admin cli: e.g. clean staging files, reprocess uploads based on codes
• improved error handling in the GUI
• lots of parser bugfixes
• lots of minor bugfixes

v0.5.0

The first production version of nomad@fairdi as the upload API and gui for NOMAD

• Production ready software and deployments (term agreements, better GUI docs)
• Raw file API with support to list directories. This replaces the files calculation metadata key. It was necessary due to arbitrary large lists of auxfiles in some calculations.
• Search interface that contains all features of the CoE Repository GUI.
• Refactored search API that allows to search for entries (paginated + scroll), metrics based on quantity aggregations (+ paginated entries), quantity aggregations with all values via after key (+ paginated entries).
• reprocessing of published results (e.g. after parser/normalizer improvements)
• mirror functionality
• refactored command line interface (CLI)
• potential GUI user tracking capabilities
• many minor bugfixes

v0.4.7

• more migration scripts
• minor bugfixes

v0.4.6

• admin commands to directly manipulate upload data
• additional migration scripts
• fixed system normalizer to understand indexed atom labels correctly
• many minor bugfixes

v0.4.5

• improved uploads view with published uploads
• support for publishing to the existing nomad CoE repository
• many minor bugfixes

v0.4.4

• improved GUI navigation
• support for multiple domains
• info API endpoint
• metainfo browser
• support for latest exciting version
• bugfixes in system normalization
• many minor bugfixes

v0.4.3

• more flexible celery routing
• config via nomad.yml
• repo_db can be disabled
• publishing of calculations with failed processing
• cli for managing running processing tasks

v0.4.2

• bugfixes regarding the migration
• better migration configurability and reproducibility
• scales to multi node kubernetes deployment