bolognese 0.2.2

data/lib/bolognese/string.rb

@@ -0,0 +1,5 @@
+class String
+  def my_titleize
+    self.gsub(/(\b|_)(.)/) { "#{$1}#{$2.upcase}" }
+  end
+end

data/lib/bolognese/utils.rb

@@ -0,0 +1,27 @@
+module Bolognese
+  module Utils
+    def parse_attributes(element)
+      if element.is_a?(String)
+        element
+      elsif element.is_a?(Hash)
+        element.fetch("text", nil)
+      elsif element.is_a?(Array)
+        element.map { |e| e.fetch("text", nil) }
+      else
+        nil
+      end
+    end
+
+    def parse_attribute(element)
+      if element.is_a?(String)
+        element
+      elsif element.is_a?(Hash)
+        element.fetch("text", nil)
+      elsif element.is_a?(Array)
+        element.first.fetch("text", nil)
+      else
+        nil
+      end
+    end
+  end
+end

data/lib/bolognese/version.rb

@@ -0,0 +1,3 @@
+module Bolognese
+  VERSION = "0.2.2"
+end

data/spec/cli_spec.rb

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+require 'spec_helper'
+require 'bolognese/cli'
+
+describe Bolognese::CLI do
+  let(:subject) do
+    described_class.new
+  end
+
+  describe "read", vcr: true do
+    context "crossref" do
+      let(:id) { "10.7554/eLife.01567" }
+      it 'as schema_org' do
+        subject.options = { as: "schema_org" }
+        expect { subject.read id }.to output(/additionalType/).to_stdout
+      end
+
+      it 'as crossref' do
+        subject.options = { as: "crossref" }
+        expect { subject.read id }.to output(/journal_metadata/).to_stdout
+      end
+    end
+
+    context "datacite" do
+      let(:id) { "10.5061/dryad.8515" }
+
+      it 'as schema_org' do
+        subject.options = { as: "schema_org" }
+        expect { subject.read id }.to output(/Phylogeny, Malaria, Parasites, Taxonomy, Mitochondrial genome, Africa, Plasmodium/).to_stdout
+      end
+
+      it 'as datacite' do
+        subject.options = { as: "datacite" }
+        expect { subject.read id }.to output(/http:\/\/datacite.org\/schema\/kernel-3/).to_stdout
+      end
+    end
+  end
+end

data/spec/crossref_spec.rb

@@ -0,0 +1,113 @@
+require 'spec_helper'
+
+describe Bolognese::Crossref, vcr: true do
+  context "get metadata" do
+    let(:id) { "https://doi.org/10.1371/journal.pone.0000030" }
+
+    subject { Bolognese::Crossref.new(id) }
+
+    it "journal article" do
+      expect(subject.id).to eq(id)
+      expect(subject.type).to eq("ScholarlyArticle")
+      expect(subject.additional_type).to eq("JournalArticle")
+      expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Markus", "familyName"=>"Ralser"},
+                                    {"@type"=>"Person", "givenName"=>"Gino", "familyName"=>"Heeren"},
+                                    {"@type"=>"Person", "givenName"=>"Michael", "familyName"=>"Breitenbach"},
+                                    {"@type"=>"Person", "givenName"=>"Hans", "familyName"=>"Lehrach"},
+                                    {"@type"=>"Person", "givenName"=>"Sylvia", "familyName"=>"Krobitsch"}])
+      expect(subject.editor).to eq([{"@type"=>"Person", "givenName"=>"Guilhem", "familyName"=>"Janbon"}])
+      expect(subject.name).to eq("Triose Phosphate Isomerase Deficiency Is Caused by Altered Dimerization–Not Catalytic Inactivity–of the Mutant Enzymes")
+      expect(subject.license).to eq("http://creativecommons.org/licenses/by/4.0/")
+      expect(subject.date_published).to eq("2006-12-20")
+      expect(subject.date_modified).to eq("2016-12-31T21:37:08Z")
+      expect(subject.page_start).to eq("e30")
+      expect(subject.is_part_of).to eq("@type"=>"Periodical", "name"=>"PLoS ONE", "issn"=>"1932-6203")
+      expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
+    end
+
+    it "posted_content" do
+      id = "https://doi.org/10.1101/097196"
+      subject = Bolognese::Crossref.new(id)
+      expect(subject.id).to eq(id)
+      expect(subject.type).to eq("CreativeWork")
+      expect(subject.additional_type).to eq("PostedContent")
+      expect(subject.author.count).to eq(10)
+      expect(subject.author.last).to eq("@type"=>"Person", "@id"=>"http://orcid.org/0000-0003-4060-7360", "givenName"=>"Timothy", "familyName"=>"Clark")
+      expect(subject.name).to eq("A Data Citation Roadmap for Scholarly Data Repositories")
+      expect(subject.alternate_name).to eq("biorxiv;097196v1")
+      expect(subject.description).to start_with("This article presents a practical roadmap")
+      expect(subject.date_published).to eq("2016-12-28")
+      expect(subject.date_modified).to eq("2016-12-29T00:10:20Z")
+      expect(subject.is_part_of).to be_nil
+      expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
+    end
+
+    it "DOI with data citation" do
+      id = "10.7554/eLife.01567"
+      subject = Bolognese::Crossref.new(id)
+      expect(subject.id).to eq("https://doi.org/10.7554/elife.01567")
+      expect(subject.type).to eq("ScholarlyArticle")
+      expect(subject.additional_type).to eq("JournalArticle")
+      expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Martial", "familyName"=>"Sankar"},
+                                    {"@type"=>"Person", "givenName"=>"Kaisa", "familyName"=>"Nieminen"},
+                                    {"@type"=>"Person", "givenName"=>"Laura", "familyName"=>"Ragni"},
+                                    {"@type"=>"Person", "givenName"=>"Ioannis", "familyName"=>"Xenarios"},
+                                    {"@type"=>"Person", "givenName"=>"Christian S", "familyName"=>"Hardtke"}])
+      expect(subject.license).to eq("http://creativecommons.org/licenses/by/3.0/")
+      expect(subject.name).to eq("Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth")
+      expect(subject.date_published).to eq("2014-02-11")
+      expect(subject.date_modified).to eq("2015-08-11T05:35:02Z")
+      expect(subject.is_part_of).to eq("@type"=>"Periodical", "name"=>"eLife", "issn"=>"2050-084X")
+      expect(subject.citation.count).to eq(27)
+      expect(subject.citation[21]).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.b835k", "position"=>"22", "datePublished"=>"2014")
+      expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
+    end
+
+    it "DOI with SICI DOI" do
+      id = "https://doi.org/10.1890/0012-9658(2006)87[2832:tiopma]2.0.co;2"
+      subject = Bolognese::Crossref.new(id)
+      expect(subject.id).to eq("https://doi.org/10.1890/0012-9658(2006)87%5B2832:tiopma%5D2.0.co;2")
+      expect(subject.type).to eq("ScholarlyArticle")
+      expect(subject.additional_type).to eq("JournalArticle")
+      expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"A.", "familyName"=>"Fenton"}, {"@type"=>"Person", "givenName"=>"S. A.", "familyName"=>"Rands"}])
+      expect(subject.license).to eq("http://doi.wiley.com/10.1002/tdm_license_1")
+      expect(subject.name).to eq("THE IMPACT OF PARASITE MANIPULATION AND PREDATOR FORAGING BEHAVIOR ON PREDATOR–PREY COMMUNITIES")
+      expect(subject.date_published).to eq("2006-11")
+      expect(subject.date_modified).to eq("2016-10-04T17:20:17Z")
+      expect(subject.page_start).to eq("2832")
+      expect(subject.page_end).to eq("2841")
+      expect(subject.is_part_of).to eq("@type"=>"Periodical", "name"=>"Ecology", "issn"=>"0012-9658")
+      expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
+    end
+
+    it "date in future" do
+      id = "https://doi.org/10.1016/j.ejphar.2015.03.018"
+      subject = Bolognese::Crossref.new(id)
+      expect(subject.id).to eq(id)
+      expect(subject.type).to eq("ScholarlyArticle")
+      expect(subject.additional_type).to eq("JournalArticle")
+      expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Sarah E.", "familyName"=>"Beck"},
+                                    {"@type"=>"Person", "givenName"=>"Suzanne E.", "familyName"=>"Queen"},
+                                    {"@type"=>"Person", "givenName"=>"Kenneth W.", "familyName"=>"Witwer"},
+                                    {"@type"=>"Person", "givenName"=>"Kelly A.", "familyName"=>"Metcalf Pate"},
+                                    {"@type"=>"Person", "givenName"=>"Lisa M.", "familyName"=>"Mangus"},
+                                    {"@type"=>"Person", "givenName"=>"Lucio", "familyName"=>"Gama"},
+                                    {"@type"=>"Person", "givenName"=>"Robert J.", "familyName"=>"Adams"},
+                                    {"@type"=>"Person", "givenName"=>"Janice E.", "familyName"=>"Clements"},
+                                    {"@type"=>"Person", "givenName"=>"M.", "familyName"=>"Christine Zink"},
+                                    {"@type"=>"Person", "givenName"=>"Joseph L.", "familyName"=>"Mankowski"}])
+      expect(subject.name).to eq("Paving the path to HIV neurotherapy: Predicting SIV CNS disease")
+      expect(subject.date_published).to eq("2015-07")
+      expect(subject.date_modified).to eq("2016-08-20T02:19:38Z")
+      expect(subject.is_part_of).to eq("@type"=>"Periodical", "name"=>"European Journal of Pharmacology", "issn"=>"00142999")
+      expect(subject.provider).to eq("@type"=>"Organization", "name"=>"Crossref")
+    end
+
+    it "not found error" do
+      id = "https://doi.org/10.1371/journal.pone.0000030x"
+      subject = Bolognese::Crossref.new(id)
+      expect(subject.id).to eq(id)
+      expect(subject.exists?).to be false
+    end
+  end
+end

data/spec/datacite_spec.rb

@@ -0,0 +1,49 @@
+require 'spec_helper'
+
+describe Bolognese::Datacite, vcr: true do
+  context "get metadata" do
+    let(:id) { "https://doi.org/10.5061/DRYAD.8515" }
+
+    subject { Bolognese::Datacite.new(id) }
+
+    it "Dataset" do
+      expect(subject.id).to eq("https://doi.org/10.5061/dryad.8515")
+      expect(subject.type).to eq("Dataset")
+      expect(subject.additional_type).to eq("DataPackage")
+      expect(subject.author).to eq([{"@type"=>"Person", "givenName"=>"Benjamin", "familyName"=>"Ollomo"},
+                                    {"@type"=>"Person", "givenName"=>"Patrick", "familyName"=>"Durand"},
+                                    {"@type"=>"Person", "givenName"=>"Franck", "familyName"=>"Prugnolle"},
+                                    {"@type"=>"Person", "givenName"=>"Emmanuel J. P.", "familyName"=>"Douzery"},
+                                    {"@type"=>"Person", "givenName"=>"Céline", "familyName"=>"Arnathau"},
+                                    {"@type"=>"Person", "givenName"=>"Dieudonné", "familyName"=>"Nkoghe"},
+                                    {"@type"=>"Person", "givenName"=>"Eric", "familyName"=>"Leroy"},
+                                    {"@type"=>"Person", "givenName"=>"François", "familyName"=>"Renaud"}])
+      expect(subject.name).to eq("Data from: A new malaria agent in African hominids.")
+      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.")
+      expect(subject.license).to eq("http://creativecommons.org/publicdomain/zero/1.0/")
+      expect(subject.date_published).to eq("2011")
+      expect(subject.has_part).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/1"},
+                                      {"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5061/dryad.8515/2"}])
+      expect(subject.citation).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.1371/journal.ppat.1000446"}])
+      expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
+    end
+
+    it "BlogPosting" do
+      id = "https://doi.org/10.5438/4K3M-NYVG"
+      subject = Bolognese::Datacite.new(id)
+      expect(subject.id).to eq("https://doi.org/10.5438/4k3m-nyvg")
+      expect(subject.type).to eq("ScholarlyArticle")
+      expect(subject.additional_type).to eq("BlogPosting")
+      expect(subject.author).to eq([{"@type"=>"Person", "@id"=>"http://orcid.org/0000-0003-1419-2405", "givenName"=>"Martin", "familyName"=>"Fenner"}])
+      expect(subject.name).to eq("Eating your own Dog Food")
+      expect(subject.alternate_name).to eq("MS-49-3632-5083")
+      expect(subject.description).to start_with("Eating your own dog food")
+      expect(subject.date_published).to eq("2016-12-20")
+      expect(subject.date_modified).to eq("2016-12-20")
+      expect(subject.is_part_of).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5438/0000-00ss")
+      expect(subject.citation).to eq([{"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5438/0012"},
+                                      {"@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5438/55e5-t5c0"}])
+      expect(subject.provider).to eq("@type"=>"Organization", "name"=>"DataCite")
+    end
+  end
+end

data/spec/doi_spec.rb

@@ -0,0 +1,89 @@
+require 'spec_helper'
+
+describe Bolognese::Crossref, vcr: true do
+  let(:id) { "https://doi.org/10.1371/journal.pone.0000030" }
+
+  subject { Bolognese::Crossref.new(id) }
+
+  context "normalize doi" do
+    it "doi" do
+      doi = "10.5061/DRYAD.8515"
+      response = subject.normalize_doi(doi)
+      expect(response).to eq("https://doi.org/10.5061/dryad.8515")
+    end
+
+    it "doi with protocol" do
+      doi = "doi:10.5061/DRYAD.8515"
+      response = subject.normalize_doi(doi)
+      expect(response).to eq("https://doi.org/10.5061/dryad.8515")
+    end
+
+    it "SICI doi" do
+      doi = "10.1890/0012-9658(2006)87[2832:tiopma]2.0.co;2"
+      response = subject.normalize_doi(doi)
+      expect(response).to eq("https://doi.org/10.1890/0012-9658(2006)87%5B2832:tiopma%5D2.0.co;2")
+    end
+
+    it "https url" do
+      doi = "https://doi.org/10.5061/dryad.8515"
+      response = subject.normalize_doi(doi)
+      expect(response).to eq("https://doi.org/10.5061/dryad.8515")
+    end
+
+    it "dx.doi.org url" do
+      doi = "http://dx.doi.org/10.5061/dryad.8515"
+      response = subject.normalize_doi(doi)
+      expect(response).to eq("https://doi.org/10.5061/dryad.8515")
+    end
+
+    it "not valid doi prefix" do
+      doi = "https://doi.org/20.5061/dryad.8515"
+      response = subject.normalize_doi(doi)
+      expect(response).to be_nil
+    end
+
+    it "doi prefix with string" do
+      doi = "https://doi.org/10.506X/dryad.8515"
+      response = subject.normalize_doi(doi)
+      expect(response).to be_nil
+    end
+
+    it "doi prefix too long" do
+      doi = "https://doi.org/10.506123/dryad.8515"
+      response = subject.normalize_doi(doi)
+      expect(response).to be_nil
+    end
+
+    it "doi from url without doi proxy" do
+      doi = "https://handle.net/10.5061/dryad.8515"
+      response = subject.normalize_doi(doi)
+      expect(response).to be_nil
+    end
+  end
+
+  context "doi registration agency" do
+    it "datacite" do
+      doi = "https://doi.org/10.5061/dryad.8515"
+      response = subject.get_doi_ra(doi)
+      expect(response["name"]).to eq("DataCite")
+    end
+
+    it "crossref" do
+      doi = "https://doi.org/10.1371/journal.pone.0000030"
+      response = subject.get_doi_ra(doi)
+      expect(response["name"]).to eq("Crossref")
+    end
+
+    it "medra" do
+      doi = "https://doi.org/10.1392/roma081203"
+      response = subject.get_doi_ra(doi)
+      expect(response["name"]).to eq("mEDRA")
+    end
+
+    it "not found" do
+      doi = "https://doi.org/10.5061/dryad.8515x"
+      response = subject.get_doi_ra(doi)
+      expect(response["errors"]).to eq([{"DOI"=>"10.5061/DRYAD.8515X", "status"=>"Invalid DOI"}])
+    end
+  end
+end

data/spec/fixtures/crossref.xml

@@ -0,0 +1,742 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<doi_records>
+  <doi_record owner="10.1371" timestamp="2016-12-31 22:37:08">
+    <crossref>
+      <journal>
+        <journal_metadata language="en">
+          <full_title>PLoS ONE</full_title>
+          <abbrev_title>PLoS ONE</abbrev_title>
+          <issn media_type="electronic">1932-6203</issn>
+        </journal_metadata>
+        <journal_issue>
+          <publication_date media_type="online">
+            <month>12</month>
+            <day>20</day>
+            <year>2006</year>
+          </publication_date>
+          <journal_volume>
+            <volume>1</volume>
+          </journal_volume>
+          <issue>1</issue>
+        </journal_issue>
+        <journal_article publication_type="full_text">
+          <titles>
+            <title>Triose Phosphate Isomerase Deficiency Is Caused by Altered Dimerization–Not Catalytic Inactivity–of the Mutant Enzymes</title>
+          </titles>
+          <contributors>
+            <person_name contributor_role="author" sequence="first">
+              <given_name>Markus</given_name>
+              <surname>Ralser</surname>
+            </person_name>
+            <person_name contributor_role="author" sequence="additional">
+              <given_name>Gino</given_name>
+              <surname>Heeren</surname>
+            </person_name>
+            <person_name contributor_role="author" sequence="additional">
+              <given_name>Michael</given_name>
+              <surname>Breitenbach</surname>
+            </person_name>
+            <person_name contributor_role="author" sequence="additional">
+              <given_name>Hans</given_name>
+              <surname>Lehrach</surname>
+            </person_name>
+            <person_name contributor_role="author" sequence="additional">
+              <given_name>Sylvia</given_name>
+              <surname>Krobitsch</surname>
+            </person_name>
+            <person_name contributor_role="editor" sequence="first">
+              <given_name>Guilhem</given_name>
+              <surname>Janbon</surname>
+            </person_name>
+          </contributors>
+          <publication_date media_type="online">
+            <month>12</month>
+            <day>20</day>
+            <year>2006</year>
+          </publication_date>
+          <pages>
+            <first_page>e30</first_page>
+          </pages>
+          <publisher_item>
+            <item_number>10.1371/journal.pone.0000030</item_number>
+          </publisher_item>
+          <crossmark>
+            <crossmark_version>1</crossmark_version>
+            <crossmark_policy>10.1371/journal.pone.corrections_policy</crossmark_policy>
+            <crossmark_domains>
+              <crossmark_domain>
+                <domain>www.plosone.org</domain>
+              </crossmark_domain>
+            </crossmark_domains>
+            <crossmark_domain_exclusive>false</crossmark_domain_exclusive>
+            <custom_metadata>
+              <program name="AccessIndicators">
+                <license_ref>http://creativecommons.org/licenses/by/4.0/</license_ref>
+              </program>
+            </custom_metadata>
+          </crossmark>
+          <doi_data>
+            <doi>10.1371/journal.pone.0000030</doi>
+            <timestamp>20161231025645</timestamp>
+            <resource>http://dx.plos.org/10.1371/journal.pone.0000030</resource>
+            <collection property="crawler-based">
+              <item crawler="iParadigms">
+                <resource>http://dx.plos.org/10.1371/journal.pone.0000030</resource>
+              </item>
+            </collection>
+          </doi_data>
+          <citation_list>
+            <citation key="ref1">
+              <journal_title>N Engl J Med</journal_title>
+              <author>AS Schneider</author>
+              <volume>272</volume>
+              <first_page>229</first_page>
+              <cYear>1965</cYear>
+              <article_title>Hereditary Hemolytic Anemia with Triosephosphate Isomerase Deficiency.</article_title>
+            </citation>
+            <citation key="ref2">
+              <journal_title>Baillieres Best Pract Res Clin Haematol</journal_title>
+              <author>AS Schneider</author>
+              <volume>13</volume>
+              <first_page>119</first_page>
+              <cYear>2000</cYear>
+              <article_title>Triosephosphate isomerase deficiency: historical perspectives and molecular aspects.</article_title>
+            </citation>
+            <citation key="ref3">
+              <journal_title>Blood Cells Mol Dis</journal_title>
+              <author>A Schneider</author>
+              <volume>22</volume>
+              <first_page>82</first_page>
+              <cYear>1996</cYear>
+              <article_title>Hematologically important mutations: triosephosphate isomerase.</article_title>
+            </citation>
+            <citation key="ref4">
+              <journal_title>Biochem Soc Trans</journal_title>
+              <author>J Olah</author>
+              <volume>30</volume>
+              <first_page>30</first_page>
+              <cYear>2002</cYear>
+              <article_title>Triosephosphate isomerase deficiency: a neurodegenerative misfolding disease.</article_title>
+            </citation>
+            <citation key="ref5">
+              <journal_title>Am J Hum Genet</journal_title>
+              <author>M Watanabe</author>
+              <volume>58</volume>
+              <first_page>308</first_page>
+              <cYear>1996</cYear>
+              <article_title>Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus.</article_title>
+            </citation>
+            <citation key="ref6">
+              <journal_title>Ann Hum Genet</journal_title>
+              <author>HW Mohrenweiser</author>
+              <volume>51 ( Pt 4)</volume>
+              <first_page>303</first_page>
+              <cYear>1987</cYear>
+              <article_title>Frequency and distribution of rare electrophoretic mobility variants in a population of human newborns in Ann Arbor, Michigan.</article_title>
+            </citation>
+            <citation key="ref7">
+              <journal_title>Pediatr Res</journal_title>
+              <author>HW Mohrenweiser</author>
+              <volume>16</volume>
+              <first_page>960</first_page>
+              <cYear>1982</cYear>
+              <article_title>Elevated frequency of carriers for triosephosphate isomerase deficiency in newborn infants.</article_title>
+            </citation>
+            <citation key="ref8">
+              <journal_title>Hum Genet</journal_title>
+              <author>SW Eber</author>
+              <volume>67</volume>
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