commonmeta-ruby 3.0.0 → 3.0.2

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Files changed (14) hide show
  1. checksums.yaml +4 -4
  2. data/CHANGELOG.md +59 -59
  3. data/Gemfile.lock +10 -23
  4. data/README.md +307 -210
  5. data/commonmeta.gemspec +5 -12
  6. data/lib/commonmeta/author_utils.rb +1 -1
  7. data/lib/commonmeta/crossref_utils.rb +3 -1
  8. data/lib/commonmeta/readers/cff_reader.rb +1 -1
  9. data/lib/commonmeta/utils.rb +2 -2
  10. data/lib/commonmeta/version.rb +1 -1
  11. data/lib/commonmeta/writers/datacite_writer.rb +7 -14
  12. data/lib/commonmeta.rb +0 -4
  13. data/spec/writers/datacite_writer_spec.rb +1 -0
  14. metadata +17 -133
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data/CHANGELOG.md CHANGED
@@ -1,123 +1,123 @@
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  # Changelog
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- ## [Unreleased](https://github.com/front-matter/briard/tree/HEAD)
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+ ## [v3.0.1](https://github.com/front-matter/commonmeta-ruby/tree/v3.0.1) (2023-03-20)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.9.0...HEAD)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.9.0...v3.0.1)
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  **Merged pull requests:**
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- - Bump rack from 2.2.5 to 2.2.6.2 [\#21](https://github.com/front-matter/briard/pull/21) ([dependabot[bot]](https://github.com/apps/dependabot))
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- - Bump activesupport from 7.0.4 to 7.0.4.1 [\#20](https://github.com/front-matter/briard/pull/20) ([dependabot[bot]](https://github.com/apps/dependabot))
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+ - Bump rack from 2.2.5 to 2.2.6.2 [\#21](https://github.com/front-matter/commonmeta-ruby/pull/21) ([dependabot[bot]](https://github.com/apps/dependabot))
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+ - Bump activesupport from 7.0.4 to 7.0.4.1 [\#20](https://github.com/front-matter/commonmeta-ruby/pull/20) ([dependabot[bot]](https://github.com/apps/dependabot))
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- ## [v2.9.0](https://github.com/front-matter/briard/tree/v2.9.0) (2022-11-23)
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+ ## [v2.9.0](https://github.com/front-matter/commonmeta-ruby/tree/v2.9.0) (2022-11-23)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.8.2...v2.9.0)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.8.2...v2.9.0)
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- ## [v2.8.2](https://github.com/front-matter/briard/tree/v2.8.2) (2022-11-23)
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+ ## [v2.8.2](https://github.com/front-matter/commonmeta-ruby/tree/v2.8.2) (2022-11-23)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.8.0...v2.8.2)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.8.0...v2.8.2)
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- ## [v2.8.0](https://github.com/front-matter/briard/tree/v2.8.0) (2022-11-22)
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+ ## [v2.8.0](https://github.com/front-matter/commonmeta-ruby/tree/v2.8.0) (2022-11-22)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.6.5...v2.8.0)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.6.5...v2.8.0)
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- ## [v2.6.5](https://github.com/front-matter/briard/tree/v2.6.5) (2022-10-04)
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+ ## [v2.6.5](https://github.com/front-matter/commonmeta-ruby/tree/v2.6.5) (2022-10-04)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.6.4...v2.6.5)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.6.4...v2.6.5)
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- ## [v2.6.4](https://github.com/front-matter/briard/tree/v2.6.4) (2022-10-04)
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+ ## [v2.6.4](https://github.com/front-matter/commonmeta-ruby/tree/v2.6.4) (2022-10-04)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.6.3...v2.6.4)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.6.3...v2.6.4)
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- ## [v2.6.3](https://github.com/front-matter/briard/tree/v2.6.3) (2022-10-04)
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+ ## [v2.6.3](https://github.com/front-matter/commonmeta-ruby/tree/v2.6.3) (2022-10-04)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.5.1...v2.6.3)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.5.1...v2.6.3)
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- ## [v2.5.1](https://github.com/front-matter/briard/tree/v2.5.1) (2022-09-18)
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+ ## [v2.5.1](https://github.com/front-matter/commonmeta-ruby/tree/v2.5.1) (2022-09-18)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.5.0...v2.5.1)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.5.0...v2.5.1)
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- ## [v2.5.0](https://github.com/front-matter/briard/tree/v2.5.0) (2022-09-18)
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+ ## [v2.5.0](https://github.com/front-matter/commonmeta-ruby/tree/v2.5.0) (2022-09-18)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.4.2...v2.5.0)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.4.2...v2.5.0)
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  **Fixed bugs:**
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45
 
46
- - Incomplete URL substring sanitization [\#12](https://github.com/front-matter/briard/issues/12)
47
- - Incomplete URL substring sanitization [\#11](https://github.com/front-matter/briard/issues/11)
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- - Incomplete URL substring sanitization [\#10](https://github.com/front-matter/briard/issues/10)
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+ - Incomplete URL substring sanitization [\#12](https://github.com/front-matter/commonmeta-ruby/issues/12)
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+ - Incomplete URL substring sanitization [\#11](https://github.com/front-matter/commonmeta-ruby/issues/11)
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+ - Incomplete URL substring sanitization [\#10](https://github.com/front-matter/commonmeta-ruby/issues/10)
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- ## [v2.4.2](https://github.com/front-matter/briard/tree/v2.4.2) (2022-08-24)
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+ ## [v2.4.2](https://github.com/front-matter/commonmeta-ruby/tree/v2.4.2) (2022-08-24)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.4.1...v2.4.2)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.4.1...v2.4.2)
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- ## [v2.4.1](https://github.com/front-matter/briard/tree/v2.4.1) (2022-08-24)
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+ ## [v2.4.1](https://github.com/front-matter/commonmeta-ruby/tree/v2.4.1) (2022-08-24)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.4...v2.4.1)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.4...v2.4.1)
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- ## [v2.4](https://github.com/front-matter/briard/tree/v2.4) (2022-08-24)
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+ ## [v2.4](https://github.com/front-matter/commonmeta-ruby/tree/v2.4) (2022-08-24)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.3.1...v2.4)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.3.1...v2.4)
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- ## [v2.3.1](https://github.com/front-matter/briard/tree/v2.3.1) (2022-08-14)
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+ ## [v2.3.1](https://github.com/front-matter/commonmeta-ruby/tree/v2.3.1) (2022-08-14)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v.2.3...v2.3.1)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v.2.3...v2.3.1)
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- ## [v.2.3](https://github.com/front-matter/briard/tree/v.2.3) (2022-06-19)
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+ ## [v.2.3](https://github.com/front-matter/commonmeta-ruby/tree/v.2.3) (2022-06-19)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.2.9...v.2.3)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.2.9...v.2.3)
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- ## [v2.2.9](https://github.com/front-matter/briard/tree/v2.2.9) (2022-06-19)
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+ ## [v2.2.9](https://github.com/front-matter/commonmeta-ruby/tree/v2.2.9) (2022-06-19)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.2.7...v2.2.9)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.2.7...v2.2.9)
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- ## [v2.2.7](https://github.com/front-matter/briard/tree/v2.2.7) (2021-12-23)
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+ ## [v2.2.7](https://github.com/front-matter/commonmeta-ruby/tree/v2.2.7) (2021-12-23)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.2.6...v2.2.7)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.2.6...v2.2.7)
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- ## [v2.2.6](https://github.com/front-matter/briard/tree/v2.2.6) (2021-12-23)
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+ ## [v2.2.6](https://github.com/front-matter/commonmeta-ruby/tree/v2.2.6) (2021-12-23)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.2.5...v2.2.6)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.2.5...v2.2.6)
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- ## [v2.2.5](https://github.com/front-matter/briard/tree/v2.2.5) (2021-12-09)
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+ ## [v2.2.5](https://github.com/front-matter/commonmeta-ruby/tree/v2.2.5) (2021-12-09)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.2.4...v2.2.5)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.2.4...v2.2.5)
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- ## [v2.2.4](https://github.com/front-matter/briard/tree/v2.2.4) (2021-12-09)
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+ ## [v2.2.4](https://github.com/front-matter/commonmeta-ruby/tree/v2.2.4) (2021-12-09)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.2.3...v2.2.4)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.2.3...v2.2.4)
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- ## [v2.2.3](https://github.com/front-matter/briard/tree/v2.2.3) (2021-12-08)
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+ ## [v2.2.3](https://github.com/front-matter/commonmeta-ruby/tree/v2.2.3) (2021-12-08)
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- [Full Changelog](https://github.com/front-matter/briard/compare/v2.2.2...v2.2.3)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/v2.2.2...v2.2.3)
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- ## [v2.2.2](https://github.com/front-matter/briard/tree/v2.2.2) (2021-12-08)
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+ ## [v2.2.2](https://github.com/front-matter/commonmeta-ruby/tree/v2.2.2) (2021-12-08)
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- [Full Changelog](https://github.com/front-matter/briard/compare/2.2.1...v2.2.2)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/2.2.1...v2.2.2)
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- ## [2.2.1](https://github.com/front-matter/briard/tree/2.2.1) (2021-12-07)
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+ ## [2.2.1](https://github.com/front-matter/commonmeta-ruby/tree/2.2.1) (2021-12-07)
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- [Full Changelog](https://github.com/front-matter/briard/compare/2.2...2.2.1)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/2.2...2.2.1)
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- ## [2.2](https://github.com/front-matter/briard/tree/2.2) (2021-12-07)
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+ ## [2.2](https://github.com/front-matter/commonmeta-ruby/tree/2.2) (2021-12-07)
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- [Full Changelog](https://github.com/front-matter/briard/compare/2.1...2.2)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/2.1...2.2)
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- ## [2.1](https://github.com/front-matter/briard/tree/2.1) (2021-12-07)
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+ ## [2.1](https://github.com/front-matter/commonmeta-ruby/tree/2.1) (2021-12-07)
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- [Full Changelog](https://github.com/front-matter/briard/compare/2.0.2...2.1)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/2.0.2...2.1)
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- ## [2.0.2](https://github.com/front-matter/briard/tree/2.0.2) (2021-12-06)
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+ ## [2.0.2](https://github.com/front-matter/commonmeta-ruby/tree/2.0.2) (2021-12-06)
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- [Full Changelog](https://github.com/front-matter/briard/compare/2.0.1...2.0.2)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/2.0.1...2.0.2)
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- ## [2.0.1](https://github.com/front-matter/briard/tree/2.0.1) (2021-12-06)
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+ ## [2.0.1](https://github.com/front-matter/commonmeta-ruby/tree/2.0.1) (2021-12-06)
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- [Full Changelog](https://github.com/front-matter/briard/compare/2.0...2.0.1)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/2.0...2.0.1)
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- ## [2.0](https://github.com/front-matter/briard/tree/2.0) (2021-12-06)
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+ ## [2.0](https://github.com/front-matter/commonmeta-ruby/tree/2.0) (2021-12-06)
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- [Full Changelog](https://github.com/front-matter/briard/compare/d1adb0353c9b3abd0b8f64fed5e0970cf03b537c...2.0)
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+ [Full Changelog](https://github.com/front-matter/commonmeta-ruby/compare/d1adb0353c9b3abd0b8f64fed5e0970cf03b537c...2.0)
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data/Gemfile.lock CHANGED
@@ -1,31 +1,24 @@
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  PATH
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  remote: .
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  specs:
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- commonmeta-ruby (3.0.0)
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+ commonmeta-ruby (3.0.2)
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  activesupport (>= 4.2.5, < 8.0)
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  base32-url (>= 0.5.0, < 1)
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- benchmark_methods (~> 0.7)
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  bibtex-ruby (~> 6.0)
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- builder (~> 3.2, >= 3.2.2)
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+ builder (~> 3.2, >= 3.2.4)
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  citeproc-ruby (~> 2.0)
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- colorize (~> 0.8.1)
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- concurrent-ruby (~> 1.1, >= 1.1.5)
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  csl-styles (~> 2.0)
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  dotenv (~> 2.1, >= 2.1.1)
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  edtf (~> 3.0, >= 3.0.4)
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- gender_detector (~> 0.1.2)
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+ gender_detector (~> 2.0)
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  http (~> 5.1, >= 5.1.1)
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- iso8601 (~> 0.9.1)
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- json-ld-preloaded (~> 3.1, >= 3.1.3)
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+ json-ld-preloaded (~> 3.2, >= 3.2.2)
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  json_schemer (~> 0.2.23)
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  jsonlint (~> 0.3.0)
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  loofah (~> 2.19)
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  namae (~> 1.0)
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- nokogiri (~> 1.14, >= 1.14.2)
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- oj (~> 3.10)
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- oj_mimic_json (~> 1.0, >= 1.0.1)
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- postrank-uri (~> 1.0, >= 1.0.18)
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- public_suffix (= 2.0.5)
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+ postrank-uri (~> 1.1)
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+ public_suffix (~> 4.0, >= 4.0.7)
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  rdf-rdfxml (~> 3.2)
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  rdf-turtle (~> 3.2)
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  thor (~> 1.1, >= 1.1.0)
@@ -42,7 +35,6 @@ GEM
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  public_suffix (>= 2.0.2, < 6.0)
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  ast (2.4.2)
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  base32-url (0.6.0)
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- benchmark_methods (0.7)
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  bibtex-ruby (6.0.0)
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  latex-decode (~> 0.0)
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  builder (3.2.4)
@@ -53,7 +45,6 @@ GEM
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  csl (~> 2.0)
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  code-scanning-rubocop (0.6.1)
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  rubocop (~> 1.0)
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- colorize (0.8.1)
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  concurrent-ruby (1.2.2)
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  crack (0.4.5)
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  rexml
@@ -82,8 +73,7 @@ GEM
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  ffi-compiler (1.0.1)
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  ffi (>= 1.0.0)
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  rake
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- gender_detector (0.1.2)
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- unicode_utils (>= 1.3.0)
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+ gender_detector (2.0.0)
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  haml (5.2.2)
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  temple (>= 0.8.0)
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  tilt
@@ -100,7 +90,6 @@ GEM
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  http-form_data (2.3.0)
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  i18n (1.12.0)
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  concurrent-ruby (~> 1.0)
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- iso8601 (0.9.1)
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  json (2.6.3)
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  json-canonicalization (0.3.1)
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  json-ld (3.2.3)
@@ -136,16 +125,15 @@ GEM
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  nokogiri (1.14.2-arm64-darwin)
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  racc (~> 1.4)
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  oj (3.14.2)
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- oj_mimic_json (1.0.1)
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  optimist (3.0.1)
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  parallel (1.22.1)
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  parser (3.2.1.1)
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  ast (~> 2.4.1)
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- postrank-uri (1.0.24)
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+ postrank-uri (1.1)
145
133
  addressable (>= 2.4.0)
146
134
  nokogiri (>= 1.8.0)
147
- public_suffix (>= 2.0.0, < 2.1)
148
- public_suffix (2.0.5)
135
+ public_suffix (>= 4.0.0, < 5)
136
+ public_suffix (4.0.7)
149
137
  racc (1.6.2)
150
138
  rack (2.2.6.4)
151
139
  rack-test (2.1.0)
@@ -237,7 +225,6 @@ GEM
237
225
  unf_ext (0.0.8.2)
238
226
  unicode-display_width (2.4.2)
239
227
  unicode-types (1.8.0)
240
- unicode_utils (1.4.0)
241
228
  uri_template (0.7.0)
242
229
  vcr (6.1.0)
243
230
  webmock (3.18.1)
data/README.md CHANGED
@@ -84,128 +84,23 @@ All input is validated against the commonmeta JSON schema.
84
84
 
85
85
  ## Examples
86
86
 
87
- Read Crossref:
87
+ Read Crossref XML and write as BibTeX:
88
88
 
89
89
  ```
90
- commonmeta https://doi.org/10.7554/elife.01567 -t crossref
90
+ commonmeta https://doi.org/10.7554/elife.01567 -f crossref_xml -t bibtex
91
91
 
92
- <?xml version="1.0" encoding="UTF-8"?>
93
- <doi_records>
94
- <doi_record owner="10.7554" timestamp="2015-08-11 07:35:02">
95
- <crossref>
96
- <journal>
97
- <journal_metadata language="en">
98
- <full_title>eLife</full_title>
99
- <issn media_type="electronic">2050-084X</issn>
100
- </journal_metadata>
101
- <journal_issue>
102
- <publication_date media_type="online">
103
- <month>02</month>
104
- <day>11</day>
105
- <year>2014</year>
106
- </publication_date>
107
- <journal_volume>
108
- <volume>3</volume>
109
- </journal_volume>
110
- </journal_issue>
111
- <journal_article publication_type="full_text">
112
- <titles>
113
- <title>Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth</title>
114
- </titles>
115
- <contributors>
116
- <person_name contributor_role="author" sequence="first">
117
- <given_name>Martial</given_name>
118
- <surname>Sankar</surname>
119
- </person_name>
120
- <person_name contributor_role="author" sequence="additional">
121
- <given_name>Kaisa</given_name>
122
- <surname>Nieminen</surname>
123
- </person_name>
124
- <person_name contributor_role="author" sequence="additional">
125
- <given_name>Laura</given_name>
126
- <surname>Ragni</surname>
127
- </person_name>
128
- <person_name contributor_role="author" sequence="additional">
129
- <given_name>Ioannis</given_name>
130
- <surname>Xenarios</surname>
131
- </person_name>
132
- <person_name contributor_role="author" sequence="additional">
133
- <given_name>Christian S</given_name>
134
- <surname>Hardtke</surname>
135
- </person_name>
136
- </contributors>
137
- <publication_date media_type="online">
138
- <month>02</month>
139
- <day>11</day>
140
- <year>2014</year>
141
- </publication_date>
142
- <publisher_item>
143
- <identifier id_type="doi">10.7554/eLife.01567</identifier>
144
- </publisher_item>
145
- <crossmark>
146
- <crossmark_version>1</crossmark_version>
147
- <crossmark_policy>eLifesciences</crossmark_policy>
148
- <crossmark_domains>
149
- <crossmark_domain>
150
- <domain>www.elifesciences.org</domain>
151
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152
- </crossmark_domains>
153
- <crossmark_domain_exclusive>false</crossmark_domain_exclusive>
154
- <custom_metadata>
155
- <assertion name="received" label="Received" group_name="publication_history" group_label="Publication History" order="0">2013-09-20</assertion>
156
- <assertion name="accepted" label="Accepted" group_name="publication_history" group_label="Publication History" order="1">2013-12-24</assertion>
157
- <assertion name="published" label="Published" group_name="publication_history" group_label="Publication History" order="2">2014-02-11</assertion>
158
- <program name="fundref">
159
- <assertion name="fundgroup">
160
- <assertion name="funder_name">SystemsX</assertion>
161
- </assertion>
162
- <assertion name="fundgroup">
163
- <assertion name="funder_name">
164
- EMBO
165
- <assertion name="funder_identifier">http://dx.doi.org/10.13039/501100003043</assertion>
166
- </assertion>
167
- </assertion>
168
- <assertion name="fundgroup">
169
- <assertion name="funder_name">
170
- Swiss National Science Foundation
171
- <assertion name="funder_identifier">http://dx.doi.org/10.13039/501100001711</assertion>
172
- </assertion>
173
- </assertion>
174
- <assertion name="fundgroup">
175
- <assertion name="funder_name">
176
- University of Lausanne
177
- <assertion name="funder_identifier" provider="crossref">http://dx.doi.org/10.13039/501100006390</assertion>
178
- </assertion>
179
- </assertion>
180
- </program>
181
- <program name="AccessIndicators">
182
- <license_ref applies_to="vor">http://creativecommons.org/licenses/by/3.0/</license_ref>
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185
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186
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187
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188
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189
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190
- <resource>http://elifesciences.org/lookup/doi/10.7554/eLife.01567</resource>
191
- </doi_data>
192
- <citation_list>
193
- ...
194
- <citation key="22">
195
- <author>Sankar</author>
196
- <cYear>2014</cYear>
197
- <doi>10.5061/dryad.b835k</doi>
198
- </citation>
199
- ...
200
- </citation_list>
201
- <component_list>
202
- ...
203
- </component_list>
204
- </journal_article>
205
- </journal>
206
- </crossref>
207
- </doi_record>
208
- </doi_records>
92
+ @article{https://doi.org/10.7554/elife.01567,
93
+ doi = {10.7554/elife.01567},
94
+ url = {https://elifesciences.org/articles/01567},
95
+ author = {Sankar, Martial and Nieminen, Kaisa and Ragni, Laura and Xenarios, Ioannis and Hardtke, Christian S},
96
+ title = {Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth},
97
+ journal = {eLife},
98
+ volume = {3},
99
+ pages = {e01567},
100
+ publisher = {eLife Sciences Publications, Ltd},
101
+ year = {2014},
102
+ copyright = {CC-BY-3.0}
103
+ }
209
104
  ```
210
105
 
211
106
  Convert Crossref to schema.org/JSON-LD:
@@ -408,102 +303,304 @@ commonmeta https://doi.org/10.7554/elife.01567
408
303
 
409
304
  Convert Crossref to DataCite:
410
305
 
411
- ```
306
+ ```sh
412
307
  commonmeta https://doi.org/10.7554/elife.01567 -t datacite
413
308
 
414
- <?xml version="1.0" encoding="UTF-8"?>
415
- <resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
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- <creator>
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- <creatorName>Nieminen, Kaisa</creatorName>
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- <givenName>Kaisa</givenName>
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427
- </creator>
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- <creator>
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430
- <givenName>Laura</givenName>
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- <familyName>Ragni</familyName>
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- </creator>
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- <creator>
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- <creatorName>Xenarios, Ioannis</creatorName>
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- </creator>
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- <creator>
439
- <creatorName>Hardtke, Christian S</creatorName>
440
- <givenName>Christian S</givenName>
441
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442
- </creator>
443
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444
- <titles>
445
- <title>Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth</title>
446
- </titles>
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- <resourceType resourceTypeGeneral="Text">JournalArticle</resourceType>
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380
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419
+ {
420
+ "description": "Among various advantages, their small size makes model organisms preferred subjects of investigation. Yet, even in model systems detailed analysis of numerous developmental processes at cellular level is severely hampered by their scale. For instance, secondary growth of Arabidopsis hypocotyls creates a radial pattern of highly specialized tissues that comprises several thousand cells starting from a few dozen. This dynamic process is difficult to follow because of its scale and because it can only be investigated invasively, precluding comprehensive understanding of the cell proliferation, differentiation, and patterning events involved. To overcome such limitation, we established an automated quantitative histology approach. We acquired hypocotyl cross-sections from tiled high-resolution images and extracted their information content using custom high-throughput image processing and segmentation. Coupled with automated cell type recognition through machine learning, we could establish a cellular resolution atlas that reveals vascular morphodynamics during secondary growth, for example equidistant phloem pole formation.",
421
+ "descriptionType": "Abstract"
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+ {
540
+ "relatedIdentifier": "https://doi.org/10.1104/pp.104.040212",
541
+ "relatedIdentifierType": "DOI",
542
+ "relationType": "References"
543
+ },
544
+ {
545
+ "relatedIdentifier": "https://doi.org/10.1038/nbt1206-1565",
546
+ "relatedIdentifierType": "DOI",
547
+ "relationType": "References"
548
+ },
549
+ {
550
+ "relatedIdentifier": "https://doi.org/10.1073/pnas.77.3.1516",
551
+ "relatedIdentifierType": "DOI",
552
+ "relationType": "References"
553
+ },
554
+ {
555
+ "relatedIdentifier": "https://doi.org/10.1093/bioinformatics/btq046",
556
+ "relatedIdentifierType": "DOI",
557
+ "relationType": "References"
558
+ },
559
+ {
560
+ "relatedIdentifier": "https://doi.org/10.1105/tpc.111.084020",
561
+ "relatedIdentifierType": "DOI",
562
+ "relationType": "References"
563
+ },
564
+ {
565
+ "relatedIdentifier": "https://doi.org/10.5061/dryad.b835k",
566
+ "relatedIdentifierType": "DOI",
567
+ "relationType": "References"
568
+ },
569
+ {
570
+ "relatedIdentifier": "https://doi.org/10.1016/j.cub.2008.02.070",
571
+ "relatedIdentifierType": "DOI",
572
+ "relationType": "References"
573
+ },
574
+ {
575
+ "relatedIdentifier": "https://doi.org/10.1111/j.1469-8137.2010.03236.x",
576
+ "relatedIdentifierType": "DOI",
577
+ "relationType": "References"
578
+ },
579
+ {
580
+ "relatedIdentifier": "https://doi.org/10.1007/s00138-011-0345-9",
581
+ "relatedIdentifierType": "DOI",
582
+ "relationType": "References"
583
+ },
584
+ {
585
+ "relatedIdentifier": "https://doi.org/10.1016/j.cell.2012.02.048",
586
+ "relatedIdentifierType": "DOI",
587
+ "relationType": "References"
588
+ },
589
+ {
590
+ "relatedIdentifier": "https://doi.org/10.1038/ncb2764",
591
+ "relatedIdentifierType": "DOI",
592
+ "relationType": "References"
593
+ }
594
+ ],
595
+ "schemaVersion": "http://datacite.org/schema/kernel-4",
596
+ "agency": "Crossref",
597
+ "state": "findable"
598
+ }
502
599
  ```
503
600
 
504
601
  Convert Crossref to BibTeX:
505
602
 
506
- ```
603
+ ```sh
507
604
  commonmeta https://doi.org/10.7554/elife.01567 -t bibtex
508
605
 
509
606
  @article{https://doi.org/10.7554/elife.01567,
@@ -518,7 +615,7 @@ commonmeta https://doi.org/10.7554/elife.01567 -t bibtex
518
615
 
519
616
 
520
617
 
521
- Convert DataCite JSON to schema.org/JSON-LD:
618
+ Convert DataCite to schema.org/JSON-LD:
522
619
 
523
620
  ```sh
524
621
  commonmeta 10.5061/DRYAD.8515
data/commonmeta.gemspec CHANGED
@@ -20,28 +20,21 @@ Gem::Specification.new do |s|
20
20
  # Declare dependencies here, rather than in the Gemfile
21
21
  s.add_dependency 'activesupport', '>= 4.2.5', '< 8.0'
22
22
  s.add_dependency 'base32-url', '>= 0.5.0', '< 1'
23
- s.add_dependency 'benchmark_methods', '~> 0.7'
24
23
  s.add_dependency 'bibtex-ruby', '~> 6.0'
25
- s.add_dependency 'builder', '~> 3.2', '>= 3.2.2'
24
+ s.add_dependency 'builder', '~> 3.2', '>= 3.2.4'
26
25
  s.add_dependency 'citeproc-ruby', '~> 2.0'
27
- s.add_dependency 'colorize', '~> 0.8.1'
28
- s.add_dependency 'concurrent-ruby', '~> 1.1', '>= 1.1.5'
29
26
  s.add_dependency 'csl-styles', '~> 2.0'
30
27
  s.add_dependency 'dotenv', '~> 2.1', '>= 2.1.1'
31
28
  s.add_dependency 'edtf', '~> 3.0', '>= 3.0.4'
32
- s.add_dependency 'gender_detector', '~> 0.1.2'
29
+ s.add_dependency 'gender_detector', '~> 2.0'
33
30
  s.add_dependency 'http', '~> 5.1', '>= 5.1.1'
34
- s.add_dependency 'iso8601', '~> 0.9.1'
35
- s.add_dependency 'json-ld-preloaded', '~> 3.1', '>= 3.1.3'
31
+ s.add_dependency 'json-ld-preloaded', '~> 3.2', '>= 3.2.2'
36
32
  s.add_dependency 'jsonlint', '~> 0.3.0'
37
33
  s.add_dependency 'json_schemer', '~> 0.2.23'
38
34
  s.add_dependency 'loofah', '~> 2.19'
39
35
  s.add_dependency 'namae', '~> 1.0'
40
- s.add_dependency 'nokogiri', '~> 1.14', '>= 1.14.2'
41
- s.add_dependency 'oj', '~> 3.10'
42
- s.add_dependency 'oj_mimic_json', '~> 1.0', '>= 1.0.1'
43
- s.add_dependency 'postrank-uri', '~> 1.0', '>= 1.0.18'
44
- s.add_dependency 'public_suffix', '2.0.5'
36
+ s.add_dependency 'postrank-uri', '~> 1.1'
37
+ s.add_dependency 'public_suffix', '~> 4.0', '>= 4.0.7'
45
38
  s.add_dependency 'rdf-rdfxml', '~> 3.2'
46
39
  s.add_dependency 'rdf-turtle', '~> 3.2'
47
40
  s.add_dependency 'thor', '~> 1.1', '>= 1.1.0'
data/lib/commonmeta/author_utils.rb CHANGED
@@ -35,7 +35,7 @@ module Commonmeta
35
35
  ni['nameIdentifierScheme'] == 'ORCID'
36
36
  end
37
37
  id = id['nameIdentifier'] if id.present?
38
- # Crossref metadata
38
+ # Crossref metadata
39
39
  elsif id.nil? && author['ORCID'].present?
40
40
  id = author.fetch('ORCID')
41
41
  end
data/lib/commonmeta/crossref_utils.rb CHANGED
@@ -27,7 +27,9 @@ module Commonmeta
27
27
 
28
28
  def crossref_errors(xml: nil)
29
29
  filepath = File.expand_path('../../resources/crossref/crossref5.3.1.xsd', __dir__)
30
- schema = Nokogiri::XML::Schema(open(filepath))
30
+ File.open(filepath, 'r') do |f|
31
+ schema = Nokogiri::XML::Schema(f)
32
+ end
31
33
 
32
34
  schema.validate(Nokogiri::XML(xml, nil, 'UTF-8')).map(&:to_s).unwrap
33
35
  rescue Nokogiri::XML::SyntaxError => e
data/lib/commonmeta/readers/cff_reader.rb CHANGED
@@ -32,7 +32,7 @@ module Commonmeta
32
32
  id = normalize_id(options[:doi] || meta.fetch('doi',
33
33
  nil) || Array.wrap(meta.fetch('identifiers', nil)).find do |i|
34
34
  i['type'] == 'doi'
35
- end.fetch('value', nil))
35
+ end.to_h.fetch('value', nil))
36
36
  url = normalize_id(meta.fetch('repository-code', nil))
37
37
  creators = cff_creators(Array.wrap(meta.fetch('authors', nil)))
38
38
 
data/lib/commonmeta/utils.rb CHANGED
@@ -1053,10 +1053,10 @@ module Commonmeta
1053
1053
  end
1054
1054
 
1055
1055
  # parsing of incomplete iso8601 timestamps such as 2015-04 is broken
1056
- # in standard library
1056
+ # in standard library, so we use the edtf gem
1057
1057
  # return nil if invalid iso8601 timestamp
1058
1058
  def get_datetime_from_iso8601(iso8601_time)
1059
- ISO8601::DateTime.new(iso8601_time).to_time.utc
1059
+ Date.edtf(iso8601_time).to_time.utc
1060
1060
  rescue StandardError
1061
1061
  nil
1062
1062
  end
data/lib/commonmeta/version.rb CHANGED
@@ -1,5 +1,5 @@
1
1
  # frozen_string_literal: true
2
2
 
3
3
  module Commonmeta
4
- VERSION = '3.0.0'
4
+ VERSION = '3.0.2'
5
5
  end
data/lib/commonmeta/writers/datacite_writer.rb CHANGED
@@ -72,22 +72,15 @@ module Commonmeta
72
72
  def datacite_reference(reference)
73
73
  return nil unless reference.present? || !reference.is_a?(Hash)
74
74
 
75
- key = reference['relatedIdentifier']
76
- doi = nil
77
- url = nil
75
+ related_identifier = reference['doi'] || reference['url']
78
76
 
79
- if key.present?
80
- if key.start_with?('http')
81
- url = key
82
- else
83
- doi = key
84
- end
85
- end
77
+ return nil unless related_identifier.present?
78
+
79
+ related_identifier_type = reference['doi'] ? 'DOI' : 'URL'
86
80
 
87
- { 'relatedIdentifier' => doi,
88
- 'relatedIdentifierType' => 'DOI',
89
- 'relationType' => 'References',
90
- 'relatedMetadataScheme' => 'citeproc+json' }.compact
81
+ { 'relatedIdentifier' => related_identifier,
82
+ 'relatedIdentifierType' => related_identifier_type,
83
+ 'relationType' => 'References' }.compact
91
84
  end
92
85
  end
93
86
  end
data/lib/commonmeta.rb CHANGED
@@ -5,18 +5,14 @@ require 'active_support/all'
5
5
  require 'nokogiri'
6
6
  ActiveSupport::XmlMini.backend = 'Nokogiri'
7
7
  require 'http'
8
- require 'multi_json'
9
8
  require 'postrank-uri'
10
9
  require 'bibtex'
11
- require 'colorize'
12
10
  require 'loofah'
13
11
  require 'json/ld'
14
12
  require 'rdf/turtle'
15
13
  require 'rdf/rdfxml'
16
14
  require 'logger'
17
- require 'iso8601'
18
15
  require 'jsonlint'
19
- require 'benchmark_methods'
20
16
  require 'gender_detector'
21
17
  require 'citeproc/ruby'
22
18
  require 'citeproc'
data/spec/writers/datacite_writer_spec.rb CHANGED
@@ -13,6 +13,7 @@ describe Commonmeta::Metadata, vcr: true do
13
13
  'resourceTypeGeneral' => 'JournalArticle', 'ris' => 'JOUR', 'schemaOrg' => 'ScholarlyArticle')
14
14
  expect(datacite.fetch('titles')).to eq([{ 'title' => 'Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth' }])
15
15
  expect(datacite.fetch('relatedIdentifiers').length).to eq(27)
16
+ expect(datacite.fetch('relatedIdentifiers').first).to eq("relatedIdentifier"=>"https://doi.org/10.1038/nature02100", "relatedIdentifierType"=>"DOI", "relationType"=>"References")
16
17
  expect(datacite.fetch('rightsList')).to eq([{ 'rights' => 'Creative Commons Attribution 3.0 Unported',
17
18
  'rightsIdentifier' => 'cc-by-3.0',
18
19
  'rightsIdentifierScheme' => 'SPDX',
metadata CHANGED
@@ -1,7 +1,7 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: commonmeta-ruby
3
3
  version: !ruby/object:Gem::Version
4
- version: 3.0.0
4
+ version: 3.0.2
5
5
  platform: ruby
6
6
  authors:
7
7
  - Martin Fenner
@@ -50,20 +50,6 @@ dependencies:
50
50
  - - "<"
51
51
  - !ruby/object:Gem::Version
52
52
  version: '1'
53
- - !ruby/object:Gem::Dependency
54
- name: benchmark_methods
55
- requirement: !ruby/object:Gem::Requirement
56
- requirements:
57
- - - "~>"
58
- - !ruby/object:Gem::Version
59
- version: '0.7'
60
- type: :runtime
61
- prerelease: false
62
- version_requirements: !ruby/object:Gem::Requirement
63
- requirements:
64
- - - "~>"
65
- - !ruby/object:Gem::Version
66
- version: '0.7'
67
53
  - !ruby/object:Gem::Dependency
68
54
  name: bibtex-ruby
69
55
  requirement: !ruby/object:Gem::Requirement
@@ -87,7 +73,7 @@ dependencies:
87
73
  version: '3.2'
88
74
  - - ">="
89
75
  - !ruby/object:Gem::Version
90
- version: 3.2.2
76
+ version: 3.2.4
91
77
  type: :runtime
92
78
  prerelease: false
93
79
  version_requirements: !ruby/object:Gem::Requirement
@@ -97,7 +83,7 @@ dependencies:
97
83
  version: '3.2'
98
84
  - - ">="
99
85
  - !ruby/object:Gem::Version
100
- version: 3.2.2
86
+ version: 3.2.4
101
87
  - !ruby/object:Gem::Dependency
102
88
  name: citeproc-ruby
103
89
  requirement: !ruby/object:Gem::Requirement
@@ -112,40 +98,6 @@ dependencies:
112
98
  - - "~>"
113
99
  - !ruby/object:Gem::Version
114
100
  version: '2.0'
115
- - !ruby/object:Gem::Dependency
116
- name: colorize
117
- requirement: !ruby/object:Gem::Requirement
118
- requirements:
119
- - - "~>"
120
- - !ruby/object:Gem::Version
121
- version: 0.8.1
122
- type: :runtime
123
- prerelease: false
124
- version_requirements: !ruby/object:Gem::Requirement
125
- requirements:
126
- - - "~>"
127
- - !ruby/object:Gem::Version
128
- version: 0.8.1
129
- - !ruby/object:Gem::Dependency
130
- name: concurrent-ruby
131
- requirement: !ruby/object:Gem::Requirement
132
- requirements:
133
- - - "~>"
134
- - !ruby/object:Gem::Version
135
- version: '1.1'
136
- - - ">="
137
- - !ruby/object:Gem::Version
138
- version: 1.1.5
139
- type: :runtime
140
- prerelease: false
141
- version_requirements: !ruby/object:Gem::Requirement
142
- requirements:
143
- - - "~>"
144
- - !ruby/object:Gem::Version
145
- version: '1.1'
146
- - - ">="
147
- - !ruby/object:Gem::Version
148
- version: 1.1.5
149
101
  - !ruby/object:Gem::Dependency
150
102
  name: csl-styles
151
103
  requirement: !ruby/object:Gem::Requirement
@@ -206,14 +158,14 @@ dependencies:
206
158
  requirements:
207
159
  - - "~>"
208
160
  - !ruby/object:Gem::Version
209
- version: 0.1.2
161
+ version: '2.0'
210
162
  type: :runtime
211
163
  prerelease: false
212
164
  version_requirements: !ruby/object:Gem::Requirement
213
165
  requirements:
214
166
  - - "~>"
215
167
  - !ruby/object:Gem::Version
216
- version: 0.1.2
168
+ version: '2.0'
217
169
  - !ruby/object:Gem::Dependency
218
170
  name: http
219
171
  requirement: !ruby/object:Gem::Requirement
@@ -234,40 +186,26 @@ dependencies:
234
186
  - - ">="
235
187
  - !ruby/object:Gem::Version
236
188
  version: 5.1.1
237
- - !ruby/object:Gem::Dependency
238
- name: iso8601
239
- requirement: !ruby/object:Gem::Requirement
240
- requirements:
241
- - - "~>"
242
- - !ruby/object:Gem::Version
243
- version: 0.9.1
244
- type: :runtime
245
- prerelease: false
246
- version_requirements: !ruby/object:Gem::Requirement
247
- requirements:
248
- - - "~>"
249
- - !ruby/object:Gem::Version
250
- version: 0.9.1
251
189
  - !ruby/object:Gem::Dependency
252
190
  name: json-ld-preloaded
253
191
  requirement: !ruby/object:Gem::Requirement
254
192
  requirements:
255
193
  - - "~>"
256
194
  - !ruby/object:Gem::Version
257
- version: '3.1'
195
+ version: '3.2'
258
196
  - - ">="
259
197
  - !ruby/object:Gem::Version
260
- version: 3.1.3
198
+ version: 3.2.2
261
199
  type: :runtime
262
200
  prerelease: false
263
201
  version_requirements: !ruby/object:Gem::Requirement
264
202
  requirements:
265
203
  - - "~>"
266
204
  - !ruby/object:Gem::Version
267
- version: '3.1'
205
+ version: '3.2'
268
206
  - - ">="
269
207
  - !ruby/object:Gem::Version
270
- version: 3.1.3
208
+ version: 3.2.2
271
209
  - !ruby/object:Gem::Dependency
272
210
  name: jsonlint
273
211
  requirement: !ruby/object:Gem::Requirement
@@ -325,93 +263,39 @@ dependencies:
325
263
  - !ruby/object:Gem::Version
326
264
  version: '1.0'
327
265
  - !ruby/object:Gem::Dependency
328
- name: nokogiri
329
- requirement: !ruby/object:Gem::Requirement
330
- requirements:
331
- - - "~>"
332
- - !ruby/object:Gem::Version
333
- version: '1.14'
334
- - - ">="
335
- - !ruby/object:Gem::Version
336
- version: 1.14.2
337
- type: :runtime
338
- prerelease: false
339
- version_requirements: !ruby/object:Gem::Requirement
340
- requirements:
341
- - - "~>"
342
- - !ruby/object:Gem::Version
343
- version: '1.14'
344
- - - ">="
345
- - !ruby/object:Gem::Version
346
- version: 1.14.2
347
- - !ruby/object:Gem::Dependency
348
- name: oj
349
- requirement: !ruby/object:Gem::Requirement
350
- requirements:
351
- - - "~>"
352
- - !ruby/object:Gem::Version
353
- version: '3.10'
354
- type: :runtime
355
- prerelease: false
356
- version_requirements: !ruby/object:Gem::Requirement
357
- requirements:
358
- - - "~>"
359
- - !ruby/object:Gem::Version
360
- version: '3.10'
361
- - !ruby/object:Gem::Dependency
362
- name: oj_mimic_json
266
+ name: postrank-uri
363
267
  requirement: !ruby/object:Gem::Requirement
364
268
  requirements:
365
269
  - - "~>"
366
270
  - !ruby/object:Gem::Version
367
- version: '1.0'
368
- - - ">="
369
- - !ruby/object:Gem::Version
370
- version: 1.0.1
271
+ version: '1.1'
371
272
  type: :runtime
372
273
  prerelease: false
373
274
  version_requirements: !ruby/object:Gem::Requirement
374
275
  requirements:
375
276
  - - "~>"
376
277
  - !ruby/object:Gem::Version
377
- version: '1.0'
378
- - - ">="
379
- - !ruby/object:Gem::Version
380
- version: 1.0.1
278
+ version: '1.1'
381
279
  - !ruby/object:Gem::Dependency
382
- name: postrank-uri
280
+ name: public_suffix
383
281
  requirement: !ruby/object:Gem::Requirement
384
282
  requirements:
385
283
  - - "~>"
386
284
  - !ruby/object:Gem::Version
387
- version: '1.0'
285
+ version: '4.0'
388
286
  - - ">="
389
287
  - !ruby/object:Gem::Version
390
- version: 1.0.18
288
+ version: 4.0.7
391
289
  type: :runtime
392
290
  prerelease: false
393
291
  version_requirements: !ruby/object:Gem::Requirement
394
292
  requirements:
395
293
  - - "~>"
396
294
  - !ruby/object:Gem::Version
397
- version: '1.0'
295
+ version: '4.0'
398
296
  - - ">="
399
297
  - !ruby/object:Gem::Version
400
- version: 1.0.18
401
- - !ruby/object:Gem::Dependency
402
- name: public_suffix
403
- requirement: !ruby/object:Gem::Requirement
404
- requirements:
405
- - - '='
406
- - !ruby/object:Gem::Version
407
- version: 2.0.5
408
- type: :runtime
409
- prerelease: false
410
- version_requirements: !ruby/object:Gem::Requirement
411
- requirements:
412
- - - '='
413
- - !ruby/object:Gem::Version
414
- version: 2.0.5
298
+ version: 4.0.7
415
299
  - !ruby/object:Gem::Dependency
416
300
  name: rdf-rdfxml
417
301
  requirement: !ruby/object:Gem::Requirement