nmr_fair-dos
This tool extracts metadata regarding NMR data from multiple repositories and creates FAIR-DOs for them.
Science Score: 62.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
2 of 2 committers (100.0%) from academic institutions -
✓Institutional organization owner
Organization kit-data-manager has institutional domain (www.scc.kit.edu) -
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (15.7%) to scientific vocabulary
Keywords
Repository
This tool extracts metadata regarding NMR data from multiple repositories and creates FAIR-DOs for them.
Basic Info
- Host: GitHub
- Owner: kit-data-manager
- License: apache-2.0
- Language: Python
- Default Branch: main
- Homepage: https://kit-data-manager.github.io/nmr_FAIR-DOs/
- Size: 1.68 MB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Topics
Metadata Files
README.md
nmr_FAIR-DOs
This project creates FAIR Digital Objects (FAIR-DOs) for multiple repositories, registers them with the Typed PID-Maker and indexes them in an Elasticsearch instance.
Currently, these repositories are supported:
See the created FAIR-DOs of the project.
If you want to explore these FAIR-DOs in a user-friendly manner, please visit the search interface. For more information, see the documentation.
Installation
Clone this project and use Poetry to install the dependencies.
bash
git clone https://github.com/kit-data-manager/nmr_FAIR-DOs.git
cd nmr_FAIR-DOs
poetry install
This project works with Python > 3.8.
Getting Started
Get started by running the command line interface (CLI) with the nmr_FAIR-DOs command. You can use the --help flag to see the available options.
bash
poetry run nmr_FAIR-DOs-cli --help
To create FAIR-DOs for all NMR data in the repositories and log the output, run the following command:
bash
poetry run nmr_FAIR-DOs-cli createallavailable 2>&1 | tee full.log
Troubleshooting
When I try installing the package, I get an IndexError: list index out of range
Make sure you have pip > 21.2 (see pip --version), older versions have a bug causing
this problem. If the installed version is older, you can upgrade it with
pip install --upgrade pip and then try again to install the package.
You can find more information in the documentation.
How to Cite
If you want to cite this project in your scientific work, please use the citation file in the repository.
Acknowledgements
This is a Python project generated from the fair-python-cookiecutter template.
We kindly thank all authors and contributors.
This tool was created at Karlsruhe Institute of Technology (KIT) at the Scientific Computing Center (SCC) in the department Data Exploitation Methods (DEM).
This work is supported by the consortium NFDI-MatWerk, funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI 38/1 – project number 460247524. TODO: relevant organizational acknowledgements (employers, funders)
Owner
- Name: KIT Data Manager
- Login: kit-data-manager
- Kind: organization
- Email: webmaster@datamanger.kit.edu
- Location: Karlsruhe, Germany
- Website: https://www.scc.kit.edu/ueberuns/dem.php
- Repositories: 56
- Profile: https://github.com/kit-data-manager
Generic software and recommendations for FAIR research data management by DEM.
Citation (CITATION.cff)
cff-version: 1.2.0 type: software message: If you use this software, please cite it using this metadata. title: "nmr_FAIR-DOs" version: "0.1.0" abstract: "This tool extracts metadata regarding NMR data from multiple repositories and creates FAIR-DOs for them." repository-code: "https://github.com/kit-data-manager/nmr_FAIR-DOs" license: "Apache-2.0" keywords: - FAIR-DOs - metadata - repositories - NMR - Chemotion - NMRXiv - Elasticsearch - KIT-Data-Manager authors: - family-names: Inckmann given-names: Maximilian email: maximilian.inckmann@kit.edu orcid: https://orcid.org/0009-0005-2800-4833 affiliation: Karlsruhe Institute of Technology (KIT) contact: - orcid: https://orcid.org/0009-0005-2800-4833 family-names: Inckmann email: maximilian.inckmann@kit.edu given-names: Maximilian url: https://kit-data-manager.github.io/nmr_FAIR-DOs
CodeMeta (codemeta.json)
{
"@context": [
"https://doi.org/10.5063/schema/codemeta-2.0",
"https://w3id.org/software-iodata",
"https://raw.githubusercontent.com/jantman/repostatus.org/master/badges/latest/ontology.jsonld",
"https://schema.org",
"https://w3id.org/software-types"
],
"@type": "SoftwareSourceCode",
"author": [
{
"@type": "Person",
"givenName": "Maximilian",
"familyName": "Inckmann",
"email": "maximilian.inckmann@kit.edu",
"@id": "https://orcid.org/0009-0005-2800-4833"
}
],
"name": "nmr_FAIR-DOs",
"description": "This tool extracts metadata regarding NMR data from multiple repositories and creates FAIR-DOs for them.",
"version": "0.1.0",
"keywords": [
"FAIR-DOs",
"metadata",
"repositories",
"NMR",
"Chemotion",
"NMRXiv",
"Elasticsearch",
"KIT-Data-Manager"
],
"maintainer": [
{
"@type": "Person",
"givenName": "Maximilian",
"familyName": "Inckmann",
"email": "maximilian.inckmann@kit.edu",
"@id": "https://orcid.org/0009-0005-2800-4833"
}
],
"license": [
"https://spdx.org/licenses/Apache-2.0"
],
"softwareHelp": "https://kit-data-manager.github.io/nmr_FAIR-DOs",
"codeRepository": "https://github.com/kit-data-manager/nmr_FAIR-DOs",
"buildInstructions": "https://kit-data-manager.github.io/nmr_FAIR-DOs",
"url": "https://kit-data-manager.github.io/nmr_FAIR-DOs"
}GitHub Events
Total
- Release event: 3
- Watch event: 1
- Delete event: 3
- Push event: 11
- Pull request event: 2
- Create event: 5
Last Year
- Release event: 3
- Watch event: 1
- Delete event: 3
- Push event: 11
- Pull request event: 2
- Create event: 5
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Maximilian Inckmann | m****n@k****u | 35 |
| Andreas Pfeil | a****l@k****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 16
- Total pull requests: 2
- Average time to close issues: 6 days
- Average time to close pull requests: 5 days
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 0.19
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 16
- Pull requests: 2
- Average time to close issues: 6 days
- Average time to close pull requests: 5 days
- Issue authors: 2
- Pull request authors: 1
- Average comments per issue: 0.19
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- craquet (6)
- maximiliani (4)
Pull Request Authors
- Pfeil (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/cache v4 composite
- actions/checkout v4 composite
- actions/setup-python v5 composite
- actions/checkout v3 composite
- actions/setup-python v4 composite
- pypa/gh-action-pypi-publish release/v1 composite
- softprops/action-gh-release v1 composite
- 116 dependencies
- httpx ^0.27.0 develop
- hypothesis ^6.108.5 develop
- licensecheck ^2024.2 develop
- poethepoet ^0.27.0 develop
- pre-commit ^3.5.0 develop
- pytest ^8.3.2 develop
- pytest-cov ^5.0.0 develop
- anybadge ^1.14.0 docs
- black ^24.4.2 docs
- interrogate ^1.7.0 docs
- markdown-exec ^1.9.3 docs
- markdown-include ^0.8.1 docs
- mike ^2.1.2 docs
- mkdocs ^1.6.0 docs
- mkdocs-coverage ^1.1.0 docs
- mkdocs-gen-files ^0.5.0 docs
- mkdocs-literate-nav ^0.6.1 docs
- mkdocs-macros-plugin ^1.0.5 docs
- mkdocs-material ^9.5.30 docs
- mkdocs-section-index ^0.3.9 docs
- mkdocstrings ^0.25.2 docs
- pymdown-extensions ^10.9 docs
- aiohttp ^3.11.11
- basemodel ^20190604.1625
- elasticsearch ^8.17.0
- fastapi ^0.115.6
- python ^3.12
- python-dotenv ^1.0.1
- requests ^2.32.3
- typer ^0.15.1
- types-requests ^2.32.0.20241016
- uvicorn ^0.34.0