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yoda

A system for reliable, long-term storing and archiving large amounts of research data during all stages of a study.

https://github.com/utrechtuniversity/yoda

Science Score: 44.0%

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
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.5%) to scientific vocabulary

Keywords

ansible automated-deployment data irods research utrecht-university yoda

Keywords from Contributors

interactive mesh interpretability profiles sequences generic projection standardization optim embedded
Last synced: 6 months ago · JSON representation ·

Repository

A system for reliable, long-term storing and archiving large amounts of research data during all stages of a study.

Basic Info
Statistics
  • Stars: 51
  • Watchers: 8
  • Forks: 24
  • Open Issues: 55
  • Releases: 9
Topics
ansible automated-deployment data irods research utrecht-university yoda
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation Security

README.md


Yoda logo

A system for reliable, long-term storing and archiving large amounts of research data during all stages of a study.

Explore the docs

Report Bug . Request Feature . Share an idea . Ask a question

Release License

About the project

Yoda is a research data management solution developed by Utrecht University and used by multiple institutes around the world. It enables researchers and their partners to securely deposit, share, publish and preserve large amounts of research data during all stages of a research project.

This is the main repository of Yoda. It contains the Ansible playbook for automated deployment, as well as the documentation.

Requirements

Control machine requirements

Managed node requirements

Documentation

Documentation is hosted on: https://utrechtuniversity.github.io/yoda/

Contributing

Code

Instructions on how to setup your development environment and other useful instructions for development can be found in the documentation.

Bug reports

We use GitHub for bug tracking. Please search existing issues and create a new one if the issue is not yet tracked.

Questions and ideas

The best place to reach us about questions and ideas regarding Yoda is on our GitHub Discussions page.

License

This project is licensed under the GPL-v3 license. The full license can be found in LICENSE.

Owner

  • Name: Utrecht University
  • Login: UtrechtUniversity
  • Kind: organization
  • Email: info.rdm@uu.nl
  • Location: Utrecht, The Netherlands

The central place for managing code and software for Utrecht University researchers and employees

Citation (CITATION.cff) 

# CFF: https://citation-file-format.github.io/
cff-version: 1.2.0
title: Yoda
message: >-
  If you use this software, please consider citing the
  following works.
type: software
authors:
  - family-names: Smeele
    given-names: Ton
  - family-names: Westerhof
    given-names: Lazlo
  - family-names: Smeele
    given-names: Chris
  - family-names: van Schip
    given-names: Rob
  - family-names: Croes
    given-names: Felix A.
  - family-names: Hoogerwerf
    given-names: Maarten
  - family-names: Kleinloog
    given-names: Hans
  - family-names: Alebregtse
    given-names: Jurgen
  - family-names: van de Hoef
    given-names: Rick
  - family-names: de Mooij
    given-names: Jan
  - family-names: de Raaff
    given-names: Harm
  - family-names: van Elk
    given-names: Roy
  - family-names: Frederiks
    given-names: Paul
  - family-names: de Ruiter
    given-names: Joris
  - family-names: Snel
    given-names: Sietse
  - family-names: Zondergeld
    given-names: Jelmer
  - family-names: Kaur
    given-names: Sirjan
  - family-names: Saliers
    given-names: Claire
  - family-names: Fu
    given-names: Dylan
  - family-names: Triantafyllou
    given-names: Leonidas
  - family-names: Laudisa
    given-names: Costanza

repository-code: 'https://github.com/utrechtuniversity/yoda'
abstract: >-
  Yoda is a research data management service that enables
  researchers to securely deposit, share, publish and
  preserve large amounts of research data.
keywords:
  - rdm
license: GPL-3.0-only
version: 1.9.0
date-released: '2024-02-15'

contact:
  - name: Utrecht University Yoda Team
    email: yoda@uu.nl

references:
  - title: 'Using iRODS to manage, share and publish research data: Yoda'
    type: conference-paper
    authors:
      - family-names: Smeele
        given-names: Ton
      - family-names: Westerhof
        given-names: Lazlo
    collection-title: iRODS User Group Meeting 2018 Proceedings
    year: 2018
    url: 'https://irods.org/uploads/2018/Smeele-UtrechtUni-Yoda-paper.pdf'

GitHub Events

Total
  • Issues event: 15
  • Watch event: 7
  • Delete event: 93
  • Issue comment event: 36
  • Push event: 450
  • Pull request review comment event: 32
  • Pull request review event: 80
  • Pull request event: 154
  • Fork event: 2
  • Create event: 93
Last Year
  • Issues event: 15
  • Watch event: 7
  • Delete event: 93
  • Issue comment event: 36
  • Push event: 450
  • Pull request review comment event: 32
  • Pull request review event: 80
  • Pull request event: 154
  • Fork event: 2
  • Create event: 93

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 2,942
  • Total Committers: 31
  • Avg Commits per committer: 94.903
  • Development Distribution Score (DDS): 0.402
Past Year
  • Commits: 238
  • Committers: 8
  • Avg Commits per committer: 29.75
  • Development Distribution Score (DDS): 0.609
Top Committers
Name Email Commits
Lazlo Westerhof l****f@u****l 1,758
Sietse Snel s****l@u****l 545
Felix A. Croes f****x@d****l 155
Hans j****g@u****l 101
Paul Frederiks p****s@d****l 58
dependabot[bot] 4****] 45
claravox c****x 44
aucuparia a****a 37
aucuparia a****a 31
Harm de Raaff h****e@g****m 28
Rick van de Hoef r****f@u****l 20
hanskleinloog 3****g 20
alebr001 3****1 16
kaur16 s****r@u****l 14
alebr001 j****e@u****l 12
Dylan Hsin x****1@u****l 10
Leonidas Triantafyllou l****i 8
Chris Smeele c****e@x****l 8
Roy r****k@g****m 7
Paul Frederiks p****s@e****m 5
Maarten Hoogerwerf m****f@g****m 4
reavdhoef 4****f 3
Roy van Elk g****b@r****l 2
Marco Roeland m****d@u****l 2
Ton Smeele a****e@u****l 2
claudisa-uu c****a@u****l 2
RobvanSchip r****p@u****l 1
R.E.A. van de Hoef R****f@u****l 1
Terrell Russell t****l@g****m 1
ccacciari c****i 1
and 1 more...
Committer Domains (Top 20 + Academic)
uu.nl: 12 royvanelk.nl: 1 ebay.com: 1 xs4all.nl: 1 developers.nl: 1 dworkin.nl: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 69
  • Total pull requests: 313
  • Average time to close issues: 6 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 24
  • Total pull request authors: 16
  • Average comments per issue: 1.06
  • Average comments per pull request: 0.12
  • Merged pull requests: 249
  • Bot issues: 0
  • Bot pull requests: 57
Past Year
  • Issues: 14
  • Pull requests: 151
  • Average time to close issues: about 10 hours
  • Average time to close pull requests: 8 days
  • Issue authors: 8
  • Pull request authors: 8
  • Average comments per issue: 0.14
  • Average comments per pull request: 0.13
  • Merged pull requests: 106
  • Bot issues: 0
  • Bot pull requests: 34
View more stats
Top Authors
Issue Authors
  • Danny-dK (16)
  • peer35 (7)
  • ccacciari (7)
  • erikvdbergh (4)
  • NikaVK (4)
  • DorienHuijser (4)
  • Jos-London (3)
  • JKK19 (3)
  • mkorthof (2)
  • stelpstraATeur (2)
  • yoda-eur (2)
  • trbKnl (2)
  • chStaiger (2)
  • kalylian (1)
  • acnewton (1)
Pull Request Authors
  • stsnel (74)
  • dependabot[bot] (57)
  • claravox (41)
  • lwesterhof (40)
  • aucuparia (26)
  • FuHsinyu (19)
  • leonidastri (19)
  • reavdhoef (11)
  • claudisa-uu (8)
  • kaur16 (6)
  • HarmdR (4)
  • stefan-wolfsheimer (2)
  • maartenhoog (2)
  • mkorthof (2)
  • RobvanSchip (1)
Top Labels
Issue Labels
enhancement (42) bug (19) consortium (15)
Pull Request Labels
dependencies (57) github_actions (28) ruby (12) python (7) consortium (2)

Dependencies

.github/workflows/ansible-lint.yml actions
  • actions/checkout v3 composite
  • ansible-community/ansible-lint-action main composite
.github/workflows/documentation.yml actions
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  • actions/cache v1 composite
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roles/dms_archive_mock/files/dms-archive-mock/requirements.txt pypi
  • Flask ==2.0.3
  • numpy ==1.19.5
  • requests ==2.27.1
roles/dms_archive_mock/files/dms-archive-mock/setup.py pypi
  • Flask ==2.0.3
  • numpy ==1.19.5
  • requests ==2.27.1
docs/Gemfile rubygems
  • github-pages >= 0 development
docs/Gemfile.lock rubygems
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  • minima 2.5.1
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  • octokit 4.25.1
  • pathutil 0.16.2
  • public_suffix 4.0.7
  • racc 1.6.2
  • rb-fsevent 0.11.2
  • rb-inotify 0.10.1
  • rexml 3.2.5
  • rouge 3.26.0
  • ruby2_keywords 0.0.5
  • rubyzip 2.3.2
  • safe_yaml 1.0.5
  • sass 3.7.4
  • sass-listen 4.0.0
  • sawyer 0.9.2
  • simpleidn 0.2.1
  • terminal-table 1.8.0
  • thread_safe 0.3.6
  • typhoeus 1.4.0
  • tzinfo 1.2.10
  • unf 0.1.4
  • unf_ext 0.0.8.2
  • unicode-display_width 1.8.0
  • zeitwerk 2.6.6
.github/workflows/build-push-image-davrods.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
.github/workflows/build-push-image-eus.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
.github/workflows/build-push-image-mailpit.yml actions
  • actions/checkout v3 composite
  • docker/login-action v2 composite
.github/workflows/build-push-image-portal.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
.github/workflows/build-push-image-provider.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v4 composite
  • docker/login-action v2 composite
.github/workflows/build-push-image-public.yml actions
  • actions/checkout v3 composite
  • docker/build-push-action v4 composite
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.github/workflows/build-push-image-web-mock.yml actions
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.github/workflows/docker-lint.yml actions
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  • jbergstroem/hadolint-gh-action v1 composite
docker/compose/docker-compose.yml docker
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  • ghcr.io/utrechtuniversity/yoda-mailpit dev-1.9
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  • ghcr.io/utrechtuniversity/yoda-provider dev-1.9
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  • postgres 15
docker/compose-with-bind-mounts/docker-compose.yml docker
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  • postgres 15
docker/images/davrods/Dockerfile docker
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docker/images/yoda_eus/Dockerfile docker
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docker/images/yoda_irods_icat/Dockerfile docker
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docker/images/yoda_portal/Dockerfile docker
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docker/images/yoda_public/Dockerfile docker
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docker/images/yoda_web_mock/Dockerfile docker
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