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Bionomia

Parse people names from biodiversity occurrence data, apply basic regular expressions and heuristics to disambiguate them, and to make these occurrence records as entities that can be claimed by people via ORCID.
https://github.com/bionomia/bionomia

Last synced: about 11 hours ago
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Sinatra app to parse people names from biodiversity occurrence data, apply basic regular expressions and heuristics to disambiguate them, and to make these occurrence records as entities that can be claimed by people via ORCID.

README

        

# Bionomia
Sinatra app to parse people names from structured biodiversity occurrence data, apply basic regular expressions and heuristics to disambiguate them, and then allow them to be claimed by authenticated users via [ORCID](https://orcid.org). Authenticated users may also help other users that have either ORCID or Wikidata identifiers. The web application lives at [https://bionomia.net](https://bionomia.net).

[![Build Status](https://github.com/bionomia/bionomia/actions/workflows/ruby.yml/badge.svg)](https://github.com/bionomia/bionomia/actions)

## Translations

Strings of text in the user interface are translatable via [config/locales](config/locales). Large pages of text are fully translatable in the [views/static_i18n/](views/static_i18n/) directory.

[![Crowdin](https://badges.crowdin.net/bionomia/localized.svg)](https://crowdin.com/project/bionomia)

## Requirements

1. ruby 3.2.1+
2. Elasticsearch 8.10.2+
3. MySQL 8.0.34+
4. Redis 7.0.12+
5. Apache Spark 3+
6. Unix-based operating system to use GNU parallel to process GBIF downloads

## Installation

$ git clone https://github.com/bionomia/bionomia.git
$ cd bionomia
$ gem install bundler
$ bundle install
$ mysql -u root bionomia < db/bionomia.sql
$ cp config/settings/development.yml.sample config/settings/development.yml
# Adjust content of development.yml
# Copy and edit production.yml and test.yml as above
$ rackup -p 4567 config.ru

## License

The MIT License (MIT)

Copyright (c) David P. Shorthouse

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.


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GitHub Events

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Last Year

Committers metadata

Last synced: 27 days ago

Total Commits: 2,307
Total Committers: 5
Avg Commits per committer: 461.4
Development Distribution Score (DDS): 0.02

Commits in past year: 628
Committers in past year: 2
Avg Commits per committer in past year: 314.0
Development Distribution Score (DDS) in past year: 0.006

Name Email Commits
David Shorthouse d****e@g****m 2260
JCGiron e****e@g****m 26
dependabot[bot] 4****] 17
Marianna Simoes m****s@g****m 2
Matthew Blissett m****t@g****g 2

Committer domains:


Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 78
Total pull requests: 118
Average time to close issues: 5 months
Average time to close pull requests: about 16 hours
Total issue authors: 12
Total pull request authors: 3
Average comments per issue: 1.91
Average comments per pull request: 0.12
Merged pull request: 110
Bot issues: 0
Bot pull requests: 24

Past year issues: 56
Past year pull requests: 90
Past year average time to close issues: 6 days
Past year average time to close pull requests: about 14 hours
Past year issue authors: 9
Past year pull request authors: 2
Past year average comments per issue: 0.88
Past year average comments per pull request: 0.02
Past year merged pull request: 84
Past year bot issues: 0
Past year bot pull requests: 9

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/bionomia/bionomia

Top Issue Authors

  • dshorthouse (55)
  • abubelinha (4)
  • Archilegt (2)
  • DavidFichtmueller (2)
  • debpaul (2)
  • jhpoelen (2)
  • kcopas (2)
  • mjy (2)
  • mnhn-paul (2)
  • rdmpage (2)
  • tmcelrath (2)
  • michaelbravothomas (1)

Top Pull Request Authors

  • dshorthouse (92)
  • dependabot[bot] (24)
  • MichalTorma (2)

Top Issue Labels

  • enhancement (34)
  • bug (5)
  • high priority (3)
  • documentation (2)
  • help wanted (2)
  • dependencies (1)
  • new feature (1)

Top Pull Request Labels

  • dependencies (24)
  • ruby (24)

Dependencies

Gemfile rubygems
  • byebug >= 0 development
  • rake >= 0 development
  • rspec >= 0 development
  • actionview >= 0
  • active_record_union >= 0
  • activerecord >= 0
  • activerecord-import >= 0
  • activesupport >= 0
  • addressable >= 0
  • biodiversity >= 0
  • capitalize-names >= 0
  • charlock_holmes >= 0
  • chronic >= 0
  • colorize >= 0
  • composite_primary_keys >= 0
  • config >= 0
  • counter_culture >= 0
  • dwc-archive >= 0
  • dwc_agent >= 0
  • elasticsearch ~> 7.17
  • haml >= 0
  • htmlentities >= 0
  • i18n >= 0
  • i18n_data >= 0
  • iso_country_codes >= 0
  • mysql2 >= 0
  • namae >= 0
  • nokogiri >= 0
  • oauth2 >= 0
  • oj >= 0
  • omniauth-orcid >= 0
  • pagy >= 0
  • parallel >= 0
  • passenger >= 0
  • pluck_to_hash >= 0
  • pony >= 0
  • rack-contrib >= 0
  • rack-test >= 0
  • rack-tracker >= 0
  • redis >= 0
  • require_all >= 0
  • rest-client >= 0
  • rgl >= 0
  • rss >= 0
  • ruby-filemagic >= 0
  • ruby-progressbar >= 0
  • rubysl-securerandom >= 0
  • rubyzip >= 0
  • sanitize >= 0
  • sidekiq >= 0
  • sinatra >= 0
  • sinatra-cacher >= 0
  • sinatra-contrib >= 0
  • sinatra-flash >= 0
  • sinatra-outputbuffer >= 0
  • sinatra-support >= 0
  • sitemap_generator >= 0
  • sparql-client >= 0
  • sucker_punch >= 0
  • thin >= 0
  • twitter >= 0
  • typhoeus >= 0
  • wikidata-client >= 0
Gemfile.lock rubygems
  • 157 dependencies
.github/workflows/ruby.yml actions
  • actions/checkout v3 composite
  • ruby/setup-ruby v1 composite

Score: 5.703782474656201