bolognese 0.2.2

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Files changed (57) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +56 -0
  3. data/.travis.yml +23 -0
  4. data/Gemfile +3 -0
  5. data/Gemfile.lock +118 -0
  6. data/LICENSE +21 -0
  7. data/README.md +3 -0
  8. data/Rakefile +12 -0
  9. data/bin/bolognese +5 -0
  10. data/bolognese.gemspec +40 -0
  11. data/lib/bolognese.rb +12 -0
  12. data/lib/bolognese/author_utils.rb +61 -0
  13. data/lib/bolognese/cli.rb +38 -0
  14. data/lib/bolognese/crossref.rb +202 -0
  15. data/lib/bolognese/datacite.rb +157 -0
  16. data/lib/bolognese/date_utils.rb +48 -0
  17. data/lib/bolognese/doi_utils.rb +48 -0
  18. data/lib/bolognese/github.rb +106 -0
  19. data/lib/bolognese/metadata.rb +30 -0
  20. data/lib/bolognese/orcid.rb +24 -0
  21. data/lib/bolognese/pid_utils.rb +23 -0
  22. data/lib/bolognese/pubmed.rb +34 -0
  23. data/lib/bolognese/string.rb +5 -0
  24. data/lib/bolognese/utils.rb +27 -0
  25. data/lib/bolognese/version.rb +3 -0
  26. data/spec/cli_spec.rb +37 -0
  27. data/spec/crossref_spec.rb +113 -0
  28. data/spec/datacite_spec.rb +49 -0
  29. data/spec/doi_spec.rb +89 -0
  30. data/spec/fixtures/crossref.xml +742 -0
  31. data/spec/fixtures/datacite.xml +40 -0
  32. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/read/crossref/as_crossref.yml +760 -0
  33. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/read/crossref/as_schema_org.yml +1476 -0
  34. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/read/datacite/as_datacite.yml +214 -0
  35. data/spec/fixtures/vcr_cassettes/Bolognese_CLI/read/datacite/as_schema_org.yml +384 -0
  36. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/doi_registration_agency/crossref.yml +44 -0
  37. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/doi_registration_agency/datacite.yml +44 -0
  38. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/doi_registration_agency/medra.yml +44 -0
  39. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/doi_registration_agency/not_found.yml +44 -0
  40. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/get_metadata/DOI_test.yml +843 -0
  41. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/get_metadata/DOI_with_SICI_DOI.yml +277 -0
  42. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/get_metadata/DOI_with_data_citation.yml +15755 -0
  43. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/get_metadata/date_in_future.yml +2691 -0
  44. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/get_metadata/journal_article.yml +1857 -0
  45. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/get_metadata/not_found_error.yml +93 -0
  46. data/spec/fixtures/vcr_cassettes/Bolognese_Crossref/get_metadata/posted_content.yml +5715 -0
  47. data/spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/BlogPosting.yml +307 -0
  48. data/spec/fixtures/vcr_cassettes/Bolognese_Datacite/get_metadata/Dataset.yml +343 -0
  49. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_PID_provider/crossref.yml +44 -0
  50. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_PID_provider/crossref_doi_not_url.yml +44 -0
  51. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_PID_provider/datacite.yml +44 -0
  52. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_PID_provider/datacite_doi_http.yml +44 -0
  53. data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_PID_provider/orcid.yml +44 -0
  54. data/spec/metadata_spec.rb +35 -0
  55. data/spec/orcid_spec.rb +23 -0
  56. data/spec/spec_helper.rb +88 -0
  57. metadata +419 -0
@@ -0,0 +1,5 @@
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+ class String
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+ def my_titleize
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+ self.gsub(/(\b|_)(.)/) { "#{$1}#{$2.upcase}" }
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+ end
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+ end
@@ -0,0 +1,27 @@
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+ module Bolognese
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+ module Utils
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+ def parse_attributes(element)
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+ if element.is_a?(String)
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+ element
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+ elsif element.is_a?(Hash)
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+ element.fetch("text", nil)
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+ elsif element.is_a?(Array)
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+ element.map { |e| e.fetch("text", nil) }
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+ else
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+ nil
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+ end
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+ end
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+
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+ def parse_attribute(element)
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+ if element.is_a?(String)
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+ element
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+ elsif element.is_a?(Hash)
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+ element.fetch("text", nil)
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+ elsif element.is_a?(Array)
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+ element.first.fetch("text", nil)
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+ else
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+ nil
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+ end
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+ end
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+ end
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+ end
@@ -0,0 +1,3 @@
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+ module Bolognese
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+ VERSION = "0.2.2"
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+ end
@@ -0,0 +1,37 @@
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+ require 'spec_helper'
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+ require 'bolognese/cli'
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+
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+ describe Bolognese::CLI do
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+ let(:subject) do
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+ described_class.new
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+ end
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+
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+ describe "read", vcr: true do
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+ context "crossref" do
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+ let(:id) { "10.7554/eLife.01567" }
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+ it 'as schema_org' do
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+ subject.options = { as: "schema_org" }
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+ expect { subject.read id }.to output(/additionalType/).to_stdout
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+ end
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+
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+ it 'as crossref' do
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+ subject.options = { as: "crossref" }
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+ expect { subject.read id }.to output(/journal_metadata/).to_stdout
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+ end
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+ end
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+
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+ context "datacite" do
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+ let(:id) { "10.5061/dryad.8515" }
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+
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+ it 'as schema_org' do
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+ subject.options = { as: "schema_org" }
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+ expect { subject.read id }.to output(/Phylogeny, Malaria, Parasites, Taxonomy, Mitochondrial genome, Africa, Plasmodium/).to_stdout
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+ end
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+
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+ it 'as datacite' do
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+ subject.options = { as: "datacite" }
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+ expect { subject.read id }.to output(/http:\/\/datacite.org\/schema\/kernel-3/).to_stdout
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+ end
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+ end
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+ end
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+ end
@@ -0,0 +1,113 @@
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+ require 'spec_helper'
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+
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+ describe Bolognese::Crossref, vcr: true do
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+ context "get metadata" do
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+ let(:id) { "https://doi.org/10.1371/journal.pone.0000030" }
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+
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+ subject { Bolognese::Crossref.new(id) }
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+
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+ it "journal article" do
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+ expect(subject.id).to eq(id)
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+ expect(subject.type).to eq("ScholarlyArticle")
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+ expect(subject.additional_type).to eq("JournalArticle")
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+ expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Markus", "familyName"=>"Ralser"},
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+ {"@type"=>"Person", "givenName"=>"Gino", "familyName"=>"Heeren"},
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+ {"@type"=>"Person", "givenName"=>"Michael", "familyName"=>"Breitenbach"},
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+ {"@type"=>"Person", "givenName"=>"Hans", "familyName"=>"Lehrach"},
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+ {"@type"=>"Person", "givenName"=>"Sylvia", "familyName"=>"Krobitsch"}])
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+ expect(subject.editor).to eq([{"@type"=>"Person", "givenName"=>"Guilhem", "familyName"=>"Janbon"}])
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+ expect(subject.name).to eq("Triose Phosphate Isomerase Deficiency Is Caused by Altered Dimerization–Not Catalytic Inactivity–of the Mutant Enzymes")
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+ expect(subject.license).to eq("http://creativecommons.org/licenses/by/4.0/")
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+ expect(subject.date_published).to eq("2006-12-20")
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+ expect(subject.date_modified).to eq("2016-12-31T21:37:08Z")
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+ expect(subject.page_start).to eq("e30")
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+ expect(subject.is_part_of).to eq("@type"=>"Periodical", "name"=>"PLoS ONE", "issn"=>"1932-6203")
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+ expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
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+ end
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+
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+ it "posted_content" do
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+ id = "https://doi.org/10.1101/097196"
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+ subject = Bolognese::Crossref.new(id)
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+ expect(subject.id).to eq(id)
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+ expect(subject.type).to eq("CreativeWork")
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+ expect(subject.additional_type).to eq("PostedContent")
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+ expect(subject.author.count).to eq(10)
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+ expect(subject.author.last).to eq("@type"=>"Person", "@id"=>"http://orcid.org/0000-0003-4060-7360", "givenName"=>"Timothy", "familyName"=>"Clark")
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+ expect(subject.name).to eq("A Data Citation Roadmap for Scholarly Data Repositories")
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+ expect(subject.alternate_name).to eq("biorxiv;097196v1")
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+ expect(subject.description).to start_with("This article presents a practical roadmap")
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+ expect(subject.date_published).to eq("2016-12-28")
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+ expect(subject.date_modified).to eq("2016-12-29T00:10:20Z")
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+ expect(subject.is_part_of).to be_nil
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+ expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
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+ end
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+
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+ it "DOI with data citation" do
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+ id = "10.7554/eLife.01567"
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+ subject = Bolognese::Crossref.new(id)
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+ expect(subject.id).to eq("https://doi.org/10.7554/elife.01567")
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+ expect(subject.type).to eq("ScholarlyArticle")
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+ expect(subject.additional_type).to eq("JournalArticle")
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+ expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Martial", "familyName"=>"Sankar"},
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+ {"@type"=>"Person", "givenName"=>"Kaisa", "familyName"=>"Nieminen"},
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+ {"@type"=>"Person", "givenName"=>"Laura", "familyName"=>"Ragni"},
54
+ {"@type"=>"Person", "givenName"=>"Ioannis", "familyName"=>"Xenarios"},
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+ {"@type"=>"Person", "givenName"=>"Christian S", "familyName"=>"Hardtke"}])
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+ expect(subject.license).to eq("http://creativecommons.org/licenses/by/3.0/")
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+ expect(subject.name).to eq("Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth")
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+ expect(subject.date_published).to eq("2014-02-11")
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+ expect(subject.date_modified).to eq("2015-08-11T05:35:02Z")
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+ expect(subject.is_part_of).to eq("@type"=>"Periodical", "name"=>"eLife", "issn"=>"2050-084X")
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+ expect(subject.citation.count).to eq(27)
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+ expect(subject.citation[21]).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.b835k", "position"=>"22", "datePublished"=>"2014")
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+ expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
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+ end
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+
66
+ it "DOI with SICI DOI" do
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+ id = "https://doi.org/10.1890/0012-9658(2006)87[2832:tiopma]2.0.co;2"
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+ subject = Bolognese::Crossref.new(id)
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+ expect(subject.id).to eq("https://doi.org/10.1890/0012-9658(2006)87%5B2832:tiopma%5D2.0.co;2")
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+ expect(subject.type).to eq("ScholarlyArticle")
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+ expect(subject.additional_type).to eq("JournalArticle")
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+ expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"A.", "familyName"=>"Fenton"}, {"@type"=>"Person", "givenName"=>"S. A.", "familyName"=>"Rands"}])
73
+ expect(subject.license).to eq("http://doi.wiley.com/10.1002/tdm_license_1")
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+ expect(subject.name).to eq("THE IMPACT OF PARASITE MANIPULATION AND PREDATOR FORAGING BEHAVIOR ON PREDATOR–PREY COMMUNITIES")
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+ expect(subject.date_published).to eq("2006-11")
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+ expect(subject.date_modified).to eq("2016-10-04T17:20:17Z")
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+ expect(subject.page_start).to eq("2832")
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+ expect(subject.page_end).to eq("2841")
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+ expect(subject.is_part_of).to eq("@type"=>"Periodical", "name"=>"Ecology", "issn"=>"0012-9658")
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+ expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
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+ end
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+
83
+ it "date in future" do
84
+ id = "https://doi.org/10.1016/j.ejphar.2015.03.018"
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+ subject = Bolognese::Crossref.new(id)
86
+ expect(subject.id).to eq(id)
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+ expect(subject.type).to eq("ScholarlyArticle")
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+ expect(subject.additional_type).to eq("JournalArticle")
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+ expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Sarah E.", "familyName"=>"Beck"},
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+ {"@type"=>"Person", "givenName"=>"Suzanne E.", "familyName"=>"Queen"},
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+ {"@type"=>"Person", "givenName"=>"Kenneth W.", "familyName"=>"Witwer"},
92
+ {"@type"=>"Person", "givenName"=>"Kelly A.", "familyName"=>"Metcalf Pate"},
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+ {"@type"=>"Person", "givenName"=>"Lisa M.", "familyName"=>"Mangus"},
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+ {"@type"=>"Person", "givenName"=>"Lucio", "familyName"=>"Gama"},
95
+ {"@type"=>"Person", "givenName"=>"Robert J.", "familyName"=>"Adams"},
96
+ {"@type"=>"Person", "givenName"=>"Janice E.", "familyName"=>"Clements"},
97
+ {"@type"=>"Person", "givenName"=>"M.", "familyName"=>"Christine Zink"},
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+ {"@type"=>"Person", "givenName"=>"Joseph L.", "familyName"=>"Mankowski"}])
99
+ expect(subject.name).to eq("Paving the path to HIV neurotherapy: Predicting SIV CNS disease")
100
+ expect(subject.date_published).to eq("2015-07")
101
+ expect(subject.date_modified).to eq("2016-08-20T02:19:38Z")
102
+ expect(subject.is_part_of).to eq("@type"=>"Periodical", "name"=>"European Journal of Pharmacology", "issn"=>"00142999")
103
+ expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
104
+ end
105
+
106
+ it "not found error" do
107
+ id = "https://doi.org/10.1371/journal.pone.0000030x"
108
+ subject = Bolognese::Crossref.new(id)
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+ expect(subject.id).to eq(id)
110
+ expect(subject.exists?).to be false
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+ end
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+ end
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+ end
@@ -0,0 +1,49 @@
1
+ require 'spec_helper'
2
+
3
+ describe Bolognese::Datacite, vcr: true do
4
+ context "get metadata" do
5
+ let(:id) { "https://doi.org/10.5061/DRYAD.8515" }
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+
7
+ subject { Bolognese::Datacite.new(id) }
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+
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+ it "Dataset" do
10
+ expect(subject.id).to eq("https://doi.org/10.5061/dryad.8515")
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+ expect(subject.type).to eq("Dataset")
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+ expect(subject.additional_type).to eq("DataPackage")
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+ expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Benjamin", "familyName"=>"Ollomo"},
14
+ {"@type"=>"Person", "givenName"=>"Patrick", "familyName"=>"Durand"},
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+ {"@type"=>"Person", "givenName"=>"Franck", "familyName"=>"Prugnolle"},
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+ {"@type"=>"Person", "givenName"=>"Emmanuel J. P.", "familyName"=>"Douzery"},
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+ {"@type"=>"Person", "givenName"=>"Céline", "familyName"=>"Arnathau"},
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+ {"@type"=>"Person", "givenName"=>"Dieudonné", "familyName"=>"Nkoghe"},
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+ {"@type"=>"Person", "givenName"=>"Eric", "familyName"=>"Leroy"},
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+ {"@type"=>"Person", "givenName"=>"François", "familyName"=>"Renaud"}])
21
+ expect(subject.name).to eq("Data from: A new malaria agent in African hominids.")
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+ expect(subject.alternate_name).to eq("Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.")
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+ expect(subject.license).to eq("http://creativecommons.org/publicdomain/zero/1.0/")
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+ expect(subject.date_published).to eq("2011")
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+ expect(subject.has_part).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/1"},
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+ {"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/2"}])
27
+ expect(subject.citation).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.1371/journal.ppat.1000446"}])
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+ expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
29
+ end
30
+
31
+ it "BlogPosting" do
32
+ id = "https://doi.org/10.5438/4K3M-NYVG"
33
+ subject = Bolognese::Datacite.new(id)
34
+ expect(subject.id).to eq("https://doi.org/10.5438/4k3m-nyvg")
35
+ expect(subject.type).to eq("ScholarlyArticle")
36
+ expect(subject.additional_type).to eq("BlogPosting")
37
+ expect(subject.author).to eq([{"@type"=>"Person", "@id"=>"http://orcid.org/0000-0003-1419-2405", "givenName"=>"Martin", "familyName"=>"Fenner"}])
38
+ expect(subject.name).to eq("Eating your own Dog Food")
39
+ expect(subject.alternate_name).to eq("MS-49-3632-5083")
40
+ expect(subject.description).to start_with("Eating your own dog food")
41
+ expect(subject.date_published).to eq("2016-12-20")
42
+ expect(subject.date_modified).to eq("2016-12-20")
43
+ expect(subject.is_part_of).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5438/0000-00ss")
44
+ expect(subject.citation).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5438/0012"},
45
+ {"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5438/55e5-t5c0"}])
46
+ expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
47
+ end
48
+ end
49
+ end
@@ -0,0 +1,89 @@
1
+ require 'spec_helper'
2
+
3
+ describe Bolognese::Crossref, vcr: true do
4
+ let(:id) { "https://doi.org/10.1371/journal.pone.0000030" }
5
+
6
+ subject { Bolognese::Crossref.new(id) }
7
+
8
+ context "normalize doi" do
9
+ it "doi" do
10
+ doi = "10.5061/DRYAD.8515"
11
+ response = subject.normalize_doi(doi)
12
+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
13
+ end
14
+
15
+ it "doi with protocol" do
16
+ doi = "doi:10.5061/DRYAD.8515"
17
+ response = subject.normalize_doi(doi)
18
+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
19
+ end
20
+
21
+ it "SICI doi" do
22
+ doi = "10.1890/0012-9658(2006)87[2832:tiopma]2.0.co;2"
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+ response = subject.normalize_doi(doi)
24
+ expect(response).to eq("https://doi.org/10.1890/0012-9658(2006)87%5B2832:tiopma%5D2.0.co;2")
25
+ end
26
+
27
+ it "https url" do
28
+ doi = "https://doi.org/10.5061/dryad.8515"
29
+ response = subject.normalize_doi(doi)
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+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
31
+ end
32
+
33
+ it "dx.doi.org url" do
34
+ doi = "http://dx.doi.org/10.5061/dryad.8515"
35
+ response = subject.normalize_doi(doi)
36
+ expect(response).to eq("https://doi.org/10.5061/dryad.8515")
37
+ end
38
+
39
+ it "not valid doi prefix" do
40
+ doi = "https://doi.org/20.5061/dryad.8515"
41
+ response = subject.normalize_doi(doi)
42
+ expect(response).to be_nil
43
+ end
44
+
45
+ it "doi prefix with string" do
46
+ doi = "https://doi.org/10.506X/dryad.8515"
47
+ response = subject.normalize_doi(doi)
48
+ expect(response).to be_nil
49
+ end
50
+
51
+ it "doi prefix too long" do
52
+ doi = "https://doi.org/10.506123/dryad.8515"
53
+ response = subject.normalize_doi(doi)
54
+ expect(response).to be_nil
55
+ end
56
+
57
+ it "doi from url without doi proxy" do
58
+ doi = "https://handle.net/10.5061/dryad.8515"
59
+ response = subject.normalize_doi(doi)
60
+ expect(response).to be_nil
61
+ end
62
+ end
63
+
64
+ context "doi registration agency" do
65
+ it "datacite" do
66
+ doi = "https://doi.org/10.5061/dryad.8515"
67
+ response = subject.get_doi_ra(doi)
68
+ expect(response["name"]).to eq("DataCite")
69
+ end
70
+
71
+ it "crossref" do
72
+ doi = "https://doi.org/10.1371/journal.pone.0000030"
73
+ response = subject.get_doi_ra(doi)
74
+ expect(response["name"]).to eq("Crossref")
75
+ end
76
+
77
+ it "medra" do
78
+ doi = "https://doi.org/10.1392/roma081203"
79
+ response = subject.get_doi_ra(doi)
80
+ expect(response["name"]).to eq("mEDRA")
81
+ end
82
+
83
+ it "not found" do
84
+ doi = "https://doi.org/10.5061/dryad.8515x"
85
+ response = subject.get_doi_ra(doi)
86
+ expect(response["errors"]).to eq([{"DOI"=>"10.5061/DRYAD.8515X", "status"=>"Invalid DOI"}])
87
+ end
88
+ end
89
+ end
@@ -0,0 +1,742 @@
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+ <article_title>Human triose-phosphate isomerase deficiency: a single amino acid substitution results in a thermolabile enzyme.</article_title>
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+ <journal_title>Hum Genet</journal_title>
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+ <first_page>634</first_page>
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+ <cYear>1992</cYear>
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+ <article_title>Human triosephosphate isomerase: substitution of Arg for Gly at position 122 in a thermolabile electromorph variant, TPI-Manchester.</article_title>
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+ <journal_title>Blood</journal_title>
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+ <article_title>Human triosephosphate isomerase deficiency resulting from mutation of Phe-240.</article_title>
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+ <journal_title>C R Seances Soc Biol Fil</journal_title>
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+ <article_title>Search for the pathogenesis of the differing phenotype in two compound heterozygote Hungarian brothers with the same genotypic triosephosphate isomerase deficiency.</article_title>
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+ </citation>
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