{"id":25541053,"url":"https://github.com/kit-data-manager/nmr_fair-dos","last_synced_at":"2026-05-05T04:06:46.543Z","repository":{"id":275809131,"uuid":"883024510","full_name":"kit-data-manager/nmr_FAIR-DOs","owner":"kit-data-manager","description":"This tool extracts metadata regarding NMR data from multiple repositories and creates FAIR-DOs for them.","archived":false,"fork":false,"pushed_at":"2025-02-07T15:45:53.000Z","size":1758,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-02-14T15:41:57.788Z","etag":null,"topics":["chemotion","cli","elasticsearch","extraction-tool","fair-dos","kit-data-manager","nmrxiv"],"latest_commit_sha":null,"homepage":"https://kit-data-manager.github.io/nmr_FAIR-DOs/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kit-data-manager.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS.md","dei":null,"publiccode":null,"codemeta":"codemeta.json"}},"created_at":"2024-11-04T08:46:59.000Z","updated_at":"2025-02-12T17:41:39.000Z","dependencies_parsed_at":"2025-02-04T18:33:50.177Z","dependency_job_id":null,"html_url":"https://github.com/kit-data-manager/nmr_FAIR-DOs","commit_stats":null,"previous_names":["maximiliani/nmr_fair-dos","kit-data-manager/nmr_fair-dos"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kit-data-manager%2Fnmr_FAIR-DOs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kit-data-manager%2Fnmr_FAIR-DOs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kit-data-manager%2Fnmr_FAIR-DOs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kit-data-manager%2Fnmr_FAIR-DOs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kit-data-manager","download_url":"https://codeload.github.com/kit-data-manager/nmr_FAIR-DOs/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239790319,"owners_count":19697541,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["chemotion","cli","elasticsearch","extraction-tool","fair-dos","kit-data-manager","nmrxiv"],"created_at":"2025-02-20T06:28:56.532Z","updated_at":"2026-05-05T04:06:46.538Z","avatar_url":"https://github.com/kit-data-manager.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[\n![Docs](https://img.shields.io/badge/read-docs-success)\n](https://kit-data-manager.github.io/nmr_FAIR-DOs)\n[\n![CI](https://img.shields.io/github/actions/workflow/status/kit-data-manager/nmr_FAIR-DOs/ci.yml?branch=main\u0026label=ci)\n](https://github.com/kit-data-manager/nmr_FAIR-DOs/actions/workflows/ci.yml)\n\n\n\u003c!-- --8\u003c-- [start:abstract] --\u003e\n# nmr_FAIR-DOs\n\nThis project creates FAIR Digital Objects (FAIR-DOs) for multiple repositories, registers them with the [Typed PID-Maker](https://github.com/kit-data-manager/pit-service) and indexes them in an Elasticsearch instance.\n\nCurrently, these repositories are supported:\n\n- [NMRXiv](https://nmrxiv.org)\n- [Chemotion](https://chemotion-repository.net)\n\nSee the [created FAIR-DOs](https://bwsyncandshare.kit.edu/s/P6qt5ecGsDa2yan) of the project.\n\nIf you want to explore these FAIR-DOs in a user-friendly manner, please visit the [search interface](https://metarepo.nffa.eu/nep-search).\nFor more information, see the [documentation](https://kit-data-manager.github.io/nmr_FAIR-DOs/main).\n\n\n\u003c!-- --8\u003c-- [end:abstract] --\u003e\n\u003c!-- --8\u003c-- [start:quickstart] --\u003e\n\n## Installation\n\nClone this project and use [Poetry](https://python-poetry.org/) to install the dependencies.\n\n```bash\ngit clone https://github.com/kit-data-manager/nmr_FAIR-DOs.git\ncd nmr_FAIR-DOs\npoetry install\n```\n\nThis project works with Python \u003e 3.8.\n\n## Getting Started\n\nGet 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.\n```bash\npoetry run nmr_FAIR-DOs-cli --help\n```\n\nTo create FAIR-DOs for all NMR data in the repositories and log the output, run the following command:\n```bash\npoetry run nmr_FAIR-DOs-cli createallavailable 2\u003e\u00261 | tee full.log\n```\n\n\u003c!-- --8\u003c-- [end:quickstart] --\u003e\n\n## Troubleshooting\n\n### When I try installing the package, I get an `IndexError: list index out of range`\n\nMake sure you have `pip` \u003e 21.2 (see `pip --version`), older versions have a bug causing\nthis problem. If the installed version is older, you can upgrade it with\n`pip install --upgrade pip` and then try again to install the package.\n\n**You can find more information in the\n[documentation](https://kit-data-manager.github.io/nmr_FAIR-DOs/).**\n\n\u003c!-- --8\u003c-- [start:citation] --\u003e\n\n## How to Cite\n\nIf you want to cite this project in your scientific work,\nplease use the [citation file](https://citation-file-format.github.io/)\nin the [repository](https://github.com/kit-data-manager/nmr_FAIR-DOs/blob/main/CITATION.cff).\n\n\u003c!-- --8\u003c-- [end:citation] --\u003e\n\u003c!-- --8\u003c-- [start:acknowledgements] --\u003e\n\n## Acknowledgements\nThis is a Python project generated from the [fair-python-cookiecutter](https://github.com/Materials-Data-Science-and-Informatics/fair-python-cookiecutter) template.\n\nWe kindly thank all\n[authors and contributors](https://kit-data-manager.github.io/nmr_FAIR-DOs/latest/credits).\n\nThis tool was created at [Karlsruhe Institute of Technology (KIT)](https://kit.edu) at the [Scientific Computing Center (SCC)](https://scc.kit.edu) in the department [Data Exploitation Methods (DEM)](https://www.scc.kit.edu/ueberuns/dem.php).\n\nThis 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.\n**TODO: relevant organizational acknowledgements (employers, funders)**\n\n\u003c!-- --8\u003c-- [end:acknowledgements] --\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkit-data-manager%2Fnmr_fair-dos","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkit-data-manager%2Fnmr_fair-dos","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkit-data-manager%2Fnmr_fair-dos/lists"}