briard 2.4.1 → 2.6.0

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Files changed (81) hide show
  1. checksums.yaml +4 -4
  2. data/.github/workflows/codeql-analysis.yml +72 -0
  3. data/.github/workflows/rubocop.yml +50 -0
  4. data/.rubocop.yml +144 -620
  5. data/.rubocop_todo.yml +76 -0
  6. data/CHANGELOG.md +22 -0
  7. data/Gemfile +2 -0
  8. data/Gemfile.lock +43 -6
  9. data/Rakefile +1 -1
  10. data/{bolognese.gemspec → briard.gemspec} +46 -38
  11. data/lib/briard/array.rb +2 -2
  12. data/lib/briard/author_utils.rb +79 -71
  13. data/lib/briard/cli.rb +12 -13
  14. data/lib/briard/crossref_utils.rb +73 -61
  15. data/lib/briard/datacite_utils.rb +132 -106
  16. data/lib/briard/doi_utils.rb +10 -10
  17. data/lib/briard/metadata.rb +96 -106
  18. data/lib/briard/metadata_utils.rb +87 -78
  19. data/lib/briard/readers/bibtex_reader.rb +65 -65
  20. data/lib/briard/readers/cff_reader.rb +88 -70
  21. data/lib/briard/readers/citeproc_reader.rb +90 -84
  22. data/lib/briard/readers/codemeta_reader.rb +68 -50
  23. data/lib/briard/readers/crosscite_reader.rb +2 -2
  24. data/lib/briard/readers/crossref_reader.rb +249 -210
  25. data/lib/briard/readers/datacite_json_reader.rb +3 -3
  26. data/lib/briard/readers/datacite_reader.rb +225 -189
  27. data/lib/briard/readers/npm_reader.rb +49 -42
  28. data/lib/briard/readers/ris_reader.rb +82 -80
  29. data/lib/briard/readers/schema_org_reader.rb +182 -159
  30. data/lib/briard/string.rb +1 -1
  31. data/lib/briard/utils.rb +4 -4
  32. data/lib/briard/version.rb +3 -1
  33. data/lib/briard/whitelist_scrubber.rb +11 -4
  34. data/lib/briard/writers/bibtex_writer.rb +14 -8
  35. data/lib/briard/writers/cff_writer.rb +33 -26
  36. data/lib/briard/writers/codemeta_writer.rb +19 -15
  37. data/lib/briard/writers/csv_writer.rb +6 -4
  38. data/lib/briard/writers/datacite_json_writer.rb +8 -2
  39. data/lib/briard/writers/jats_writer.rb +33 -28
  40. data/lib/briard/writers/rdf_xml_writer.rb +1 -1
  41. data/lib/briard/writers/ris_writer.rb +30 -18
  42. data/lib/briard/writers/turtle_writer.rb +1 -1
  43. data/lib/briard.rb +6 -6
  44. data/rubocop.sarif +0 -0
  45. data/spec/array_spec.rb +5 -5
  46. data/spec/author_utils_spec.rb +151 -132
  47. data/spec/datacite_utils_spec.rb +135 -83
  48. data/spec/doi_utils_spec.rb +168 -164
  49. data/spec/find_from_format_spec.rb +69 -69
  50. data/spec/fixtures/vcr_cassettes/Briard_Metadata/sanitize/onlies_keep_specific_tags.yml +65 -0
  51. data/spec/fixtures/vcr_cassettes/Briard_Metadata/sanitize/removes_a_tags.yml +65 -0
  52. data/spec/metadata_spec.rb +91 -90
  53. data/spec/readers/bibtex_reader_spec.rb +43 -38
  54. data/spec/readers/cff_reader_spec.rb +165 -153
  55. data/spec/readers/citeproc_reader_spec.rb +45 -40
  56. data/spec/readers/codemeta_reader_spec.rb +128 -115
  57. data/spec/readers/crosscite_reader_spec.rb +34 -24
  58. data/spec/readers/crossref_reader_spec.rb +1098 -939
  59. data/spec/readers/datacite_json_reader_spec.rb +53 -40
  60. data/spec/readers/datacite_reader_spec.rb +1541 -1337
  61. data/spec/readers/npm_reader_spec.rb +48 -43
  62. data/spec/readers/ris_reader_spec.rb +53 -47
  63. data/spec/readers/schema_org_reader_spec.rb +329 -267
  64. data/spec/spec_helper.rb +6 -5
  65. data/spec/utils_spec.rb +371 -347
  66. data/spec/writers/bibtex_writer_spec.rb +143 -143
  67. data/spec/writers/cff_writer_spec.rb +96 -90
  68. data/spec/writers/citation_writer_spec.rb +34 -33
  69. data/spec/writers/citeproc_writer_spec.rb +226 -224
  70. data/spec/writers/codemeta_writer_spec.rb +18 -16
  71. data/spec/writers/crosscite_writer_spec.rb +91 -73
  72. data/spec/writers/crossref_writer_spec.rb +99 -91
  73. data/spec/writers/csv_writer_spec.rb +70 -70
  74. data/spec/writers/datacite_json_writer_spec.rb +78 -68
  75. data/spec/writers/datacite_writer_spec.rb +417 -322
  76. data/spec/writers/jats_writer_spec.rb +177 -161
  77. data/spec/writers/rdf_xml_writer_spec.rb +68 -63
  78. data/spec/writers/ris_writer_spec.rb +162 -162
  79. data/spec/writers/turtle_writer_spec.rb +47 -47
  80. metadata +250 -160
  81. data/.github/workflows/release.yml +0 -47
checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA256:
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- metadata.gz: b7e24633fff358bc74c3a9feba1f4d13405ce3d1b3f7bf86e3abdc885fa9485d
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- data.tar.gz: 324d95ed0a15077a4a742544fd4f14b561775fc9f200a699078b3b64c456f12b
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+ metadata.gz: 3c0da06d466aa771b5721babd9f83515af15aabafe9ba4604622c727bb10ac24
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+ data.tar.gz: 7eb83dd15c81f11b31d412fd22a354cd2b39b454c40a3f48109233e49cc2c9ac
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  SHA512:
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- metadata.gz: 484ff5a7297b5971ab26a04fa3622f9da0e01a086a488d05cbc79a10beab1814d05f90a35a2d175d6b9e8d702bdb64c4ebd3a2940d4197842f0dd93887fbfda5
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- data.tar.gz: 3b137fdbb6c0c29114dd7279c5063b00f72b86a8945caadd8d6a436760227d56948a9b6802b41ae41e8b6018484880e6830999301da669bb80e8235fe0343da8
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+ metadata.gz: afedf2083bc3313858abd8d9b2e43d9be22ef242d44a26119748f4f03b5893642299a4d74e9b435c4dbdc0e039d6905ed3cbdb7f3eb33ff4e2a4630c99ff0714
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+ data.tar.gz: 4c74319d12d3ac671a68072d0e78f44f925055db0362117316d012fd1847b33131155298e28376dc0c5f3a7d4b6730e103df531b275072499959a201577c8e15
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+ # For most projects, this workflow file will not need changing; you simply need
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+ # to commit it to your repository.
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+ #
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+ # You may wish to alter this file to override the set of languages analyzed,
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+ # or to provide custom queries or build logic.
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+ #
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+ # ******** NOTE ********
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+ # We have attempted to detect the languages in your repository. Please check
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+ # the `language` matrix defined below to confirm you have the correct set of
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+ # supported CodeQL languages.
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+ #
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+ name: "CodeQL"
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+
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+ on:
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+ push:
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+ branches: [ "master" ]
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+ pull_request:
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+ # The branches below must be a subset of the branches above
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+ branches: [ "master" ]
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+ schedule:
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+ - cron: '42 21 * * 1'
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+
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+ jobs:
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+ analyze:
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+ name: Analyze
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+ runs-on: ubuntu-latest
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+ permissions:
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+ actions: read
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+ contents: read
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+ security-events: write
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+
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+ strategy:
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+ fail-fast: false
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+ matrix:
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+ language: [ 'ruby' ]
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+ # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ]
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+ # Learn more about CodeQL language support at https://aka.ms/codeql-docs/language-support
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+
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+ steps:
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+ - name: Checkout repository
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+ uses: actions/checkout@v3
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+
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+ # Initializes the CodeQL tools for scanning.
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+ - name: Initialize CodeQL
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+ uses: github/codeql-action/init@v2
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+ with:
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+ languages: ${{ matrix.language }}
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+ # If you wish to specify custom queries, you can do so here or in a config file.
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+ # By default, queries listed here will override any specified in a config file.
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+ # Prefix the list here with "+" to use these queries and those in the config file.
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+
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+ # Details on CodeQL's query packs refer to : https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
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+ # queries: security-extended,security-and-quality
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+
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+
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+ # Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
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+ # If this step fails, then you should remove it and run the build manually (see below)
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+ - name: Autobuild
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+ uses: github/codeql-action/autobuild@v2
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+
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+ # ℹ️ Command-line programs to run using the OS shell.
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+ # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
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+
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+ # If the Autobuild fails above, remove it and uncomment the following three lines.
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+ # modify them (or add more) to build your code if your project, please refer to the EXAMPLE below for guidance.
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+
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+ # - run: |
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+ # echo "Run, Build Application using script"
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+ # ./location_of_script_within_repo/buildscript.sh
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+
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+ - name: Perform CodeQL Analysis
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+ uses: github/codeql-action/analyze@v2
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+ # This workflow uses actions that are not certified by GitHub.
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+ # They are provided by a third-party and are governed by
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+ # separate terms of service, privacy policy, and support
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+ # documentation.
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+
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+ # pulled from repo
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+ name: "Rubocop"
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+
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+ on:
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+ push:
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+ branches: [ "master" ]
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+ pull_request:
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+ # The branches below must be a subset of the branches above
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+ branches: [ "master" ]
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+ schedule:
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+ - cron: '33 21 * * 2'
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+
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+ jobs:
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+ rubocop:
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+ runs-on: ubuntu-latest
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+ strategy:
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+ fail-fast: false
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+
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+ steps:
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+ - name: Checkout repository
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+ uses: actions/checkout@v3
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+
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+ # If running on a self-hosted runner, check it meets the requirements
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+ # listed at https://github.com/ruby/setup-ruby#using-self-hosted-runners
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+ - name: Set up Ruby
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+ uses: ruby/setup-ruby@v1
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+ with:
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+ ruby-version: 2.7
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+
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+ - name: Install dependencies
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+ run: bundle install
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+
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+ - name: RuboCop run
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+ run: |
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+ bash -c "
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+ bundle exec rubocop --require code_scanning --format CodeScanning::SarifFormatter -o rubocop.sarif
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+ [[ $? -ne 2 ]]
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+ "
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+
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+ # - name: Upload Sarif output
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+ # if: steps.check_files.outputs.files_exists == 'true'
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+ # uses: github/codeql-action/upload-sarif@v2
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+ # with:
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+ # # Path to SARIF file relative to the root of the repository
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+ # sarif_file: rubocop.sarif