bolognese 1.0.1 → 1.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 14165d8b671c0f3e459bdf0c7ad0289f153a36de3265c692b3c80555d66130fe
-  data.tar.gz: 127ac92957eb3acf0e394ed89dbfb336812cb64f8010a3c57db13aa4f415c28e
+  metadata.gz: acbbf45161f598000d9ff25bb9377c5332eb1482830a2e2b4137aab2fcc33043
+  data.tar.gz: 3a6c992a04626c916ec2f579aad4f9ab303756071db6a8178499a996834416cd
 SHA512:
-  metadata.gz: 1361a1bd8634c0e43316341c07e6cc6f42f1ed4c996f9df1df9531d0068c1f79f6a3bdc735fdd5cac5969a367f8a066ba980ecf404658542d074a8bdea894667
-  data.tar.gz: f0d26f6bcd599374ad657caf732b79f75ed4d28d2460b5af1486f9d47a7e85ac3d5768a7c13eed7d90b2d864c4065ed9251108b89d477d4ff2023b6e73a4a6ee
+  metadata.gz: 65dba0019f3401ae22dbd8d05da1cda01900ab0f865a3b37c8b4d7983e7d8616779e0ad7b7a123815eef252db8c5734982321bcf5cc2cc599e75a70dec436417
+  data.tar.gz: d856dea89a299b900acd9462cf01b2cb1c88fe0d8619cd003b6f2fb4da4e54624e86bb580db50488c7d31a256c9fbede5802b185b126c253328c714bc3dd1191

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.0.1)
+    bolognese (1.0.2)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)

data/lib/bolognese/datacite_utils.rb

@@ -153,9 +153,9 @@ module Bolognese
     end
 
     def insert_version(xml)
-      return xml unless b_version.present?
+      return xml unless version.present?
 
-      xml.version(b_version)
+      xml.version(version)
     end
 
     def insert_related_identifiers(xml)

data/lib/bolognese/metadata.rb

@@ -6,7 +6,13 @@ module Bolognese
   class Metadata
     include Bolognese::MetadataUtils
 
-    attr_writer :id, :provider_id, :client_id, :doi
+    attr_writer :id, :provider_id, :client_id, :doi, :identifier, :creator, :title, :publisher, :rights, :dates, :date_published, :date_modified,
+                :date_updated, :journal, :volume, :first_page, :last_page, :url, :version, :resource_type_general,
+                :keywords, :editor, :description, :alternate_identifiers, :language, :size,
+                :formats, :schema_version, :resource_type_general, :meta, :periodical,
+                :format, :funding_references, :style, :locale, :state, :geo_location,
+                :type, :additional_type, :citeproc_type, :bibtex_type, :ris_type, :content_url, :related_identifiers
+
 
     def initialize(input: nil, from: nil, **options)
       id = normalize_id(input, options)
@@ -20,7 +26,7 @@ module Bolognese
       elsif input.present? && File.exist?(input)
         ext = File.extname(input)
         if %w(.bib .ris .xml .json).include?(ext)
-          hsh = { "b_url" => options[:b_url],
+          hsh = { "url" => options[:url],
             "state" => options[:state],
             "date_registered" => options[:date_registered],
             "date_updated" => options[:date_updated],
@@ -34,7 +40,7 @@ module Bolognese
           exit 1
         end
       else
-        hsh = { "b_url" => options[:b_url],
+        hsh = { "url" => options[:url],
                 "state" => options[:state],
                 "date_registered" => options[:date_registered],
                 "date_updated" => options[:date_updated],
@@ -57,7 +63,7 @@ module Bolognese
       @sandbox = options[:sandbox]
 
       # options that come from the datacite database
-      @b_url = hsh.to_h["b_url"].presence || options[:b_url].presence
+      @url = hsh.to_h["url"].presence || options[:url].presence
       @state = hsh.to_h["state"].presence
       @date_registered = hsh.to_h["date_registered"].presence
       @date_updated = hsh.to_h["date_updated"].presence
@@ -119,8 +125,8 @@ module Bolognese
       @size ||= meta.fetch("size", nil)
     end
 
-    def b_format
-      @b_format ||= meta.fetch("b_format", nil)
+    def formats
+      @formats ||= meta.fetch("formats", nil)
     end
 
     def schema_version
@@ -135,12 +141,12 @@ module Bolognese
       @related_identifiers ||= meta.fetch("related_identifiers", nil)
     end
 
-    def b_url
-      @b_url ||= meta.fetch("b_url", nil)
+    def url
+      @url ||= meta.fetch("url", nil)
     end
 
-    def b_version
-      @b_version ||= meta.fetch("b_version", nil)
+    def version
+      @version ||= meta.fetch("version", nil)
     end
 
     def publication_year

data/lib/bolognese/metadata_utils.rb

@@ -62,15 +62,7 @@ module Bolognese
     include Bolognese::Writers::TurtleWriter
 
     attr_accessor :string, :from, :sandbox, :meta, :regenerate, :issue, :contributor
-
-    attr_writer :identifier, :creator, :title, :publisher, :rights, :dates, :date_published, :date_modified,
-                :date_updated, :journal, :volume, :first_page, :last_page, :b_url, :b_version, :resource_type_general,
-                :keywords, :editor, :description, :alternate_identifiers, :language, :size,
-                :b_format, :schema_version, :resource_type_general, :meta, :periodical,
-                :format, :funding_references, :style, :locale, :state, :geo_location,
-                :type, :additional_type, :citeproc_type, :bibtex_type, :ris_type, :content_url, :related_identifiers
-
-    attr_reader :doc, :service_provider, :page_start, :page_end, :related_identifier, :reverse, :name_detector
+    attr_reader :doc, :service_provider, :page_start, :page_end, :reverse, :name_detector
 
     # replace DOI in XML if provided in options
     def raw
@@ -146,8 +138,8 @@ module Bolognese
         "page" => [first_page, last_page].compact.join("-").presence,
         "publisher" => publisher,
         "title" => parse_attributes(title, content: "text", first: true),
-        "URL" => b_url,
-        "version" => b_version,
+        "URL" => url,
+        "version" => version,
         "volume" => volume
       }.compact.symbolize_keys
     end

data/lib/bolognese/readers/bibtex_reader.rb

@@ -68,7 +68,7 @@ module Bolognese
           "resource_type_general" => Metadata::SO_TO_DC_TRANSLATIONS[type],
           "additional_type" => Bolognese::Utils::BIB_TO_CR_TRANSLATIONS[meta.try(:type).to_s] || meta.try(:type).to_s,
           "doi" => doi,
-          "b_url" => meta.try(:url).to_s,
+          "url" => meta.try(:url).to_s,
           "title" => meta.try(:title).to_s,
           "creator" => author,
           "periodical" => periodical,

data/lib/bolognese/readers/citeproc_reader.rb

@@ -66,7 +66,7 @@ module Bolognese
           "ris_type" => CP_TO_RIS_TRANSLATIONS[type] || "GEN",
           "resource_type_general" => Bolognese::Utils::SO_TO_DC_TRANSLATIONS[type],
           "doi" => doi_from_url(doi),
-          "b_url" => normalize_id(meta.fetch("URL", nil)),
+          "url" => normalize_id(meta.fetch("URL", nil)),
           "title" => meta.fetch("title", nil),
           "creator" => author,
           "periodical" => periodical,
@@ -77,7 +77,7 @@ module Bolognese
           #{}"pagination" => meta.pages.to_s.presence,
           "description" => meta.fetch("abstract", nil).present? ? { "text" => sanitize(meta.fetch("abstract")) } : nil,
           #{ }"rights" => { "id" => meta.field?(:copyright) && meta.copyright.to_s.presence },
-          "b_version" => meta.fetch("version", nil),
+          "version" => meta.fetch("version", nil),
           "keywords" => meta.fetch("categories", nil),
           "state" => state
         }

data/lib/bolognese/readers/codemeta_reader.rb

@@ -42,7 +42,7 @@ module Bolognese
           "resource_type_general" => Bolognese::Utils::SO_TO_DC_TRANSLATIONS[type],
           "identifier" => identifier,
           "doi" => validate_doi(id),
-          "b_url" => normalize_id(meta.fetch("codeRepository", nil)),
+          "url" => normalize_id(meta.fetch("codeRepository", nil)),
           "title" => meta.fetch("title", nil),
           "creator" => author,
           "editor" => editor,
@@ -53,7 +53,7 @@ module Bolognese
           "date_modified" => meta.fetch("dateModified", nil),
           "description" => meta.fetch("description", nil).present? ? { "text" => sanitize(meta.fetch("description")) } : nil,
           "rights" => { "id" => meta.fetch("license", nil) },
-          "b_version" => meta.fetch("version", nil),
+          "version" => meta.fetch("version", nil),
           "keywords" => meta.fetch("tags", nil),
           "state" => state
         }

data/lib/bolognese/readers/crossref_reader.rb

@@ -97,7 +97,7 @@ module Bolognese
           "ris_type" => Bolognese::Utils::CR_TO_RIS_TRANSLATIONS[additional_type] || "JOUR",
           "resource_type_general" => Bolognese::Utils::SO_TO_DC_TRANSLATIONS[type],
           "doi" => doi,
-          "b_url" => bibliographic_metadata.dig("doi_data", "resource"),
+          "url" => bibliographic_metadata.dig("doi_data", "resource"),
           "title" => parse_attributes(bibliographic_metadata.dig("titles", "title")),
           "alternate_identifiers" => crossref_alternate_identifiers(bibliographic_metadata),
           "creator" => crossref_people(bibliographic_metadata, "author"),
@@ -115,7 +115,7 @@ module Bolognese
           "last_page" => bibliographic_metadata.dig("pages", "last_page"),
           "description" => crossref_description(bibliographic_metadata),
           "rights" => crossref_license(program_metadata),
-          "b_version" => nil,
+          "version" => nil,
           "keywords" => nil,
           "language" => nil,
           "size" => nil,

data/lib/bolognese/readers/datacite_json_reader.rb

@@ -27,7 +27,7 @@ module Bolognese
           "ris_type" => Bolognese::Utils::SO_TO_RIS_TRANSLATIONS[resource_type_general.to_s.dasherize] || "GEN",
           "resource_type_general" => resource_type_general,
           "doi" => validate_doi(meta.fetch("doi", nil)),
-          "b_url" => normalize_id(meta.fetch("url", nil)),
+          "url" => normalize_id(meta.fetch("url", nil)),
           "title" => meta.fetch("title", nil),
           "alternate_identifiers" => meta.fetch("alternate-identifiers", nil),
           "creator" => meta.fetch("creator", nil),
@@ -42,11 +42,11 @@ module Bolognese
           "date_modified" => meta.fetch("date-modified", nil),
           "description" => meta.fetch("description", nil),
           "rights" => meta.fetch("rights", nil),
-          "b_version" => meta.fetch("version", nil),
+          "version" => meta.fetch("version", nil),
           "keywords" => meta.fetch("subject", nil),
           "language" => meta.fetch("language", nil),
           "size" => meta.fetch("size", nil),
-          "format" => meta.fetch("format", nil),
+          "formats" => meta.fetch("formats", nil),
           "geo_location" => meta.fetch("geo-location", nil),
           "schema_version" => meta.fetch("schema-version", nil),
           "state" => state

data/lib/bolognese/readers/datacite_reader.rb

@@ -39,7 +39,7 @@ module Bolognese
         end.compact
 
         { "string" => string,
-          "b_url" => attributes.fetch("url", nil),
+          "url" => attributes.fetch("url", nil),
           "state" => attributes.fetch("state", nil),
           "date_registered" => attributes.fetch("minted", nil),
           "date_updated" => attributes.fetch("updated", nil),
@@ -174,12 +174,12 @@ module Bolognese
           "date_modified" => datacite_date(dates, "Updated"),
           "description" => description,
           "rights" => rights,
-          "b_version" => meta.fetch("version", nil),
+          "version" => meta.fetch("version", nil),
           "keywords" => keywords,
           "language" => meta.fetch("language", nil),
           "geo_location" => geo_location,
           "related_identifiers" => related_identifiers,
-          "b_format" => formats,
+          "formats" => formats,
           "size" => sizes,
           "schema_version" => schema_version,
           "state" => state

data/lib/bolognese/readers/ris_reader.rb

@@ -67,7 +67,7 @@ module Bolognese
           "ris_type" => ris_type,
           "resource_type_general" => Metadata::SO_TO_DC_TRANSLATIONS[type],
           "doi" => doi,
-          "b_url" => meta.fetch("UR", nil),
+          "url" => meta.fetch("UR", nil),
           "title" => meta.fetch("T1", nil),
           "creator" => get_authors(author),
           "publisher" => meta.fetch("PB", "(:unav)"),

data/lib/bolognese/readers/schema_org_reader.rb

@@ -123,10 +123,10 @@ module Bolognese
           "doi" => validate_doi(id),
           "identifier" => identifier,
           "alternate_identifiers" => alternate_identifiers,
-          "b_url" => normalize_id(meta.fetch("url", nil)),
+          "url" => normalize_id(meta.fetch("url", nil)),
           "content_url" => Array.wrap(meta.fetch("contentUrl", nil)).unwrap,
           "size" => meta.fetch("contenSize", nil),
-          "format" => Array.wrap(meta.fetch("encodingFormat", nil) || meta.fetch("fileFormat", nil)).unwrap,
+          "formats" => Array.wrap(meta.fetch("encodingFormat", nil) || meta.fetch("fileFormat", nil)).unwrap,
           "title" => meta.fetch("name", nil),
           "creator" => author,
           "editor" => editor,
@@ -139,7 +139,7 @@ module Bolognese
           "date_modified" => meta.fetch("dateModified", nil),
           "description" => meta.fetch("description", nil).present? ? { "text" => sanitize(meta.fetch("description")) } : nil,
           "rights" => rights,
-          "b_version" => meta.fetch("version", nil),
+          "version" => meta.fetch("version", nil),
           "keywords" => meta.fetch("keywords", nil).to_s.split(", "),
           "state" => state,
           "schema_version" => meta.fetch("schemaVersion", nil),

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.0.1"
+  VERSION = "1.0.2"
 end

data/lib/bolognese/writers/bibtex_writer.rb

@@ -10,7 +10,7 @@ module Bolognese
           bibtex_type: bibtex_type.presence || "misc",
           bibtex_key: identifier,
           doi: doi,
-          url: b_url,
+          url: url,
           author: authors_as_string(creator),
           keywords: keywords.present? ? Array.wrap(keywords).map { |k| parse_attributes(k, content: "text", first: true) }.join(", ") : nil,
           language: language,

data/lib/bolognese/writers/codemeta_writer.rb

@@ -11,11 +11,11 @@ module Bolognese
           "@type" => type,
           "@id" => identifier,
           "identifier" => identifier,
-          "codeRepository" => b_url,
+          "codeRepository" => url,
           "title" => title,
           "agents" => creator,
           "description" => parse_attributes(description, content: "text", first: true),
-          "version" => b_version,
+          "version" => version,
           "tags" => keywords.to_s.split(", ").presence,
           "datePublished" => date_published,
           "dateModified" => date_modified,

data/lib/bolognese/writers/crosscite_writer.rb

@@ -7,7 +7,7 @@ module Bolognese
         hsh = {
           "id" => identifier,
           "doi" => doi,
-          "url" => b_url,
+          "url" => url,
           "type" => type,
           "additional_type" => additional_type,
           "citeproc_type" => citeproc_type,
@@ -27,8 +27,8 @@ module Bolognese
           "language" => language,
           "alternate_identifiers" => alternate_identifiers,
           "size" => size,
-          "format" => b_format,
-          "version" => b_version,
+          "formats" => formats,
+          "version" => version,
           "rights" => rights,
           "description" => description,
           "volume" => volume,

data/lib/bolognese/writers/datacite_json_writer.rb

@@ -7,7 +7,7 @@ module Bolognese
         hsh = {
           "id" => identifier,
           "doi" => doi,
-          "url" => b_url,
+          "url" => url,
           "creator" => creator,
           "title" => title,
           "publisher" => publisher,
@@ -24,8 +24,8 @@ module Bolognese
           "alternate-identifiers" => alternate_identifiers,
           "related-identifiers" => related_identifiers,
           "size" => size,
-          "format" => b_format,
-          "version" => b_version,
+          "formats" => formats,
+          "version" => version,
           "rights" => rights,
           "description" => description,
           "geo-location" => geo_location,

data/lib/bolognese/writers/jats_writer.rb

@@ -22,7 +22,7 @@ module Bolognese
         insert_issue(xml) if issue.present?
         insert_fpage(xml) if first_page.present?
         insert_lpage(xml) if last_page.present?
-        insert_version(xml) if b_version.present?
+        insert_version(xml) if version.present?
         insert_pub_id(xml)
       end
 
@@ -112,7 +112,7 @@ module Bolognese
       end
 
       def insert_version(xml)
-        xml.version(b_version)
+        xml.version(version)
       end
 
       def insert_pub_id(xml)

data/lib/bolognese/writers/ris_writer.rb

@@ -10,7 +10,7 @@ module Bolognese
           "T2" => periodical && periodical["title"],
           "AU" => to_ris(creator),
           "DO" => doi,
-          "UR" => b_url,
+          "UR" => url,
           "AB" => parse_attributes(description, content: "text", first: true),
           "KW" => Array.wrap(keywords).map { |k| parse_attributes(k, content: "text", first: true) }.presence,
           "PY" => publication_year,

data/lib/bolognese/writers/schema_org_writer.rb

@@ -8,18 +8,18 @@ module Bolognese
           "@type" => type,
           "@id" => identifier,
           "identifier" => to_schema_org_identifier(identifier, alternate_identifiers: alternate_identifiers),
-          "url" => b_url,
+          "url" => url,
           "additionalType" => additional_type,
           "name" => parse_attributes(title, content: "text", first: true),
           "author" => to_schema_org(creator),
           "editor" => to_schema_org(editor),
           "description" => parse_attributes(description, content: "text", first: true),
           "license" => Array.wrap(rights).map { |l| l["id"] }.compact.unwrap,
-          "version" => b_version,
+          "version" => version,
           "keywords" => keywords.present? ? Array.wrap(keywords).map { |k| parse_attributes(k, content: "text", first: true) }.join(", ") : nil,
           "inLanguage" => language,
           "contentSize" => size,
-          "encodingFormat" => b_format,
+          "encodingFormat" => formats,
           "dateCreated" => Array.wrap(dates).find { |d| d["type"] == "Created" }.to_h.fetch("__content__", nil),
           "datePublished" => date_published,
           "dateModified" => date_modified,

data/spec/readers/bibtex_reader_spec.rb

@@ -30,7 +30,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.7554/elife.01567")
       expect(subject.type).to eq("ScholarlyArticle")
-      expect(subject.b_url).to eq("http://elifesciences.org/lookup/doi/10.7554/eLife.01567")
+      expect(subject.url).to eq("http://elifesciences.org/lookup/doi/10.7554/eLife.01567")
       expect(subject.resource_type_general).to eq("Text")
       expect(subject.creator.length).to eq(5)
       expect(subject.creator.first).to eq("type"=>"Person", "name"=>"Martial Sankar", "givenName"=>"Martial", "familyName"=>"Sankar")

data/spec/readers/citeproc_reader_spec.rb

@@ -17,7 +17,7 @@ describe Bolognese::Metadata, vcr: true do
     it "BlogPosting" do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5438/4k3m-nyvg")
-      expect(subject.b_url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
+      expect(subject.url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
       expect(subject.type).to eq("BlogPosting")
       expect(subject.resource_type_general).to eq("Text")
       expect(subject.creator).to eq("type"=>"Person", "name"=>"Martin Fenner", "givenName"=>"Martin", "familyName"=>"Fenner")

data/spec/readers/codemeta_reader_spec.rb

@@ -19,7 +19,7 @@ describe Bolognese::Metadata, vcr: true do
     it "maremma" do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5438/qeg0-3gm3")
-      expect(subject.b_url).to eq("https://github.com/datacite/maremma")
+      expect(subject.url).to eq("https://github.com/datacite/maremma")
       expect(subject.type).to eq("SoftwareSourceCode")
       expect(subject.creator).to eq("type"=>"Person", "id"=>"http://orcid.org/0000-0003-0077-4738", "name"=>"Martin Fenner", "givenName"=>"Martin", "familyName"=>"Fenner")
       expect(subject.title).to eq("Maremma: a Ruby library for simplified network calls")
@@ -35,7 +35,7 @@ describe Bolognese::Metadata, vcr: true do
       input = fixture_path + 'codemeta.json'
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.identifier).to eq("https://doi.org/10.5063/f1m61h5x")
-      expect(subject.b_url).to eq("https://github.com/DataONEorg/rdataone")
+      expect(subject.url).to eq("https://github.com/DataONEorg/rdataone")
       expect(subject.type).to eq("SoftwareSourceCode")
       expect(subject.creator).to eq( [{"type"=>"Person",
                                       "id"=>"http://orcid.org/0000-0003-0077-4738",
@@ -51,7 +51,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.title).to eq("R Interface to the DataONE REST API")
       expect(subject.description["text"]).to start_with("Provides read and write access to data and metadata")
       expect(subject.keywords).to eq(["data sharing", "data repository", "DataONE"])
-      expect(subject.b_version).to eq("2.0.0")
+      expect(subject.version).to eq("2.0.0")
       expect(subject.dates).to eq("2016-05-27")
       expect(subject.date_published).to eq("2016-05-27")
       expect(subject.date_modified).to eq("2016-05-27")
@@ -63,7 +63,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5438/qeg0-3gm3")
-      expect(subject.b_url).to eq("https://github.com/datacite/maremma")
+      expect(subject.url).to eq("https://github.com/datacite/maremma")
       expect(subject.type).to eq("SoftwareSourceCode")
       expect(subject.creator).to eq("type"=>"Person", "id"=>"http://orcid.org/0000-0003-0077-4738", "name"=>"Martin Fenner", "givenName"=>"Martin", "familyName"=>"Fenner")
       expect(subject.title).to eq("Maremma: a Ruby library for simplified network calls")
@@ -80,7 +80,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5438/wr0x-e194")
-      expect(subject.b_url).to eq("https://github.com/datacite/metadata-reports")
+      expect(subject.url).to eq("https://github.com/datacite/metadata-reports")
       expect(subject.type).to eq("SoftwareSourceCode")
       expect(subject.creator.size).to eq(4)
       expect(subject.creator.last).to eq("type"=>"Person", "id"=>"https://orcid.org/0000-0001-8135-3489", "name"=>"Lars Holm Nielsen", "givenName"=>"Lars Holm", "familyName"=>"Nielsen")

data/spec/readers/crossref_reader_spec.rb

@@ -20,7 +20,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.7554/elife.01567")
       expect(subject.type).to eq("ScholarlyArticle")
-      expect(subject.b_url).to eq("https://elifesciences.org/articles/01567")
+      expect(subject.url).to eq("https://elifesciences.org/articles/01567")
       expect(subject.additional_type).to eq("JournalArticle")
       expect(subject.bibtex_type).to eq("article")
       expect(subject.ris_type).to eq("JOUR")
@@ -55,7 +55,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq(input)
-      expect(subject.b_url).to eq("http://dx.plos.org/10.1371/journal.pone.0000030")
+      expect(subject.url).to eq("http://dx.plos.org/10.1371/journal.pone.0000030")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("JournalArticle")
       expect(subject.bibtex_type).to eq("article")
@@ -83,7 +83,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq(input)
-      expect(subject.b_url).to eq("http://biorxiv.org/lookup/doi/10.1101/097196")
+      expect(subject.url).to eq("http://biorxiv.org/lookup/doi/10.1101/097196")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("PostedContent")
       expect(subject.bibtex_type).to eq("article")
@@ -106,7 +106,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.1890/0012-9658(2006)87%5B2832:tiopma%5D2.0.co;2")
-      expect(subject.b_url).to eq("http://doi.wiley.com/10.1890/0012-9658(2006)87[2832:TIOPMA]2.0.CO;2")
+      expect(subject.url).to eq("http://doi.wiley.com/10.1890/0012-9658(2006)87[2832:TIOPMA]2.0.CO;2")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("JournalArticle")
       expect(subject.resource_type_general).to eq("Text")
@@ -129,7 +129,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.1155/2012/291294")
-      expect(subject.b_url).to eq("http://www.hindawi.com/journals/pm/2012/291294/")
+      expect(subject.url).to eq("http://www.hindawi.com/journals/pm/2012/291294/")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("JournalArticle")
       expect(subject.resource_type_general).to eq("Text")
@@ -153,7 +153,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq(input)
-      expect(subject.b_url).to eq("http://linkinghub.elsevier.com/retrieve/pii/S0014299915002332")
+      expect(subject.url).to eq("http://linkinghub.elsevier.com/retrieve/pii/S0014299915002332")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("JournalArticle")
       expect(subject.resource_type_general).to eq("Text")
@@ -172,7 +172,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.2210/pdb4hhb/pdb")
-      expect(subject.b_url).to eq("ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz")
+      expect(subject.url).to eq("ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/hh/pdb4hhb.ent.gz")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("SaComponent")
       expect(subject.resource_type_general).to eq("Text")
@@ -195,7 +195,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.1007/978-3-662-46370-3_13")
-      expect(subject.b_url).to eq("http://link.springer.com/10.1007/978-3-662-46370-3_13")
+      expect(subject.url).to eq("http://link.springer.com/10.1007/978-3-662-46370-3_13")
       expect(subject.type).to eq("Chapter")
       expect(subject.additional_type).to eq("BookChapter")
       expect(subject.resource_type_general).to eq("Text")
@@ -216,7 +216,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq(input)
-      expect(subject.b_url).to eq("http://doi.wiley.com/10.1111/nph.14619")
+      expect(subject.url).to eq("http://doi.wiley.com/10.1111/nph.14619")
       expect(subject.type).to eq("ScholarlyArticle")
       expect(subject.additional_type).to eq("JournalArticle")
       expect(subject.resource_type_general).to eq("Text")

data/spec/readers/datacite_reader_spec.rb

@@ -19,7 +19,7 @@ describe Bolognese::Metadata, vcr: true do
     it "Dataset" do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5061/dryad.8515")
-      expect(subject.b_url).to eq("http://datadryad.org/resource/doi:10.5061/dryad.8515")
+      expect(subject.url).to eq("http://datadryad.org/resource/doi:10.5061/dryad.8515")
       expect(subject.type).to eq("Dataset")
       expect(subject.additional_type).to eq("DataPackage")
       expect(subject.resource_type_general).to eq("Dataset")
@@ -441,7 +441,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.alternate_identifiers).to eq("type"=>"ISBN", "name"=>"937-0-4523-12357-6")
       expect(subject.date_published).to eq("2010")
       expect(subject.size).to eq("256 pages")
-      expect(subject.b_format).to eq("pdf")
+      expect(subject.formats).to eq("pdf")
       expect(subject.content_url).to eq("https://example.org/report.pdf")
       expect(subject.publication_year).to eq(2010)
       expect(subject.related_identifiers.length).to eq(1)
@@ -568,7 +568,7 @@ describe Bolognese::Metadata, vcr: true do
                                      "givenName"=>"Henk",
                                      "familyName"=>"Eskes"}])
       expect(subject.title).to eq("Multi-Sensor Reanalysis (MSR) of total ozone, version 2")
-      expect(subject.b_version).to eq("2")
+      expect(subject.version).to eq("2")
       expect(subject.date_published).to eq("2015")
       expect(subject.publisher).to eq("Royal Netherlands Meteorological Institute (KNMI)")
       expect(subject.service_provider).to eq("DataCite")
@@ -682,7 +682,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5061/dryad.8515")
       expect(subject.doi).to eq("10.5061/dryad.8515")
-      expect(subject.b_url).to eq("http://datadryad.org/resource/doi:10.5061/dryad.8515")
+      expect(subject.url).to eq("http://datadryad.org/resource/doi:10.5061/dryad.8515")
       expect(subject.type).to eq("Dataset")
       expect(subject.title).to eq("A new malaria agent in African hominids.")
     end
@@ -692,7 +692,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5061/dryad.8515")
       expect(subject.doi).to eq("10.5061/dryad.8515")
-      expect(subject.b_url).to eq("http://datadryad.org/resource/doi:10.5061/dryad.8515")
+      expect(subject.url).to eq("http://datadryad.org/resource/doi:10.5061/dryad.8515")
       expect(subject.type).to eq("Dataset")
       expect(subject.title).to eq("Data from: A new malaria agent in African hominids.")
       expect(subject.state).to eq("registered")
@@ -716,13 +716,13 @@ describe Bolognese::Metadata, vcr: true do
 
   it "GTEx dataset" do
     input = fixture_path + 'gtex.xml'
-    b_url = "https://ors.datacite.org/doi:/10.25491/9hx8-ke93"
+    url = "https://ors.datacite.org/doi:/10.25491/9hx8-ke93"
     content_url = "https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz"
-    subject = Bolognese::Metadata.new(input: input, from: 'datacite', b_url: b_url, content_url: content_url)
+    subject = Bolognese::Metadata.new(input: input, from: 'datacite', url: url, content_url: content_url)
 
     expect(subject.valid?).to be true
     expect(subject.identifier).to eq("https://doi.org/10.25491/9hx8-ke93")
-    expect(subject.b_url).to eq("https://ors.datacite.org/doi:/10.25491/9hx8-ke93")
+    expect(subject.url).to eq("https://ors.datacite.org/doi:/10.25491/9hx8-ke93")
     expect(subject.content_url).to eq("https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz")
     expect(subject.type).to eq("Dataset")
     expect(subject.additional_type).to eq("DroNc-seq data")
@@ -732,7 +732,7 @@ describe Bolognese::Metadata, vcr: true do
     expect(subject.date_published).to eq("2017")
     expect(subject.related_identifiers.length).to eq(4)
     expect(subject.related_identifiers.last).to eq("id"=>"https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663", "related_identifier_type"=>"URL", "relation_type"=>"IsPartOf")
-    expect(subject.b_format).to eq("application/tar")
+    expect(subject.formats).to eq("application/tar")
     expect(subject.size).to eq("15.7M")
     expect(subject.periodical).to eq("id"=>"https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663", "title"=>"GTEx", "type"=>"DataCatalog")
     expect(subject.publisher).to eq("GTEx")

data/spec/readers/ris_reader_spec.rb

@@ -30,7 +30,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.7554/elife.01567")
       expect(subject.type).to eq("ScholarlyArticle")
-      expect(subject.b_url).to eq("http://elifesciences.org/lookup/doi/10.7554/eLife.01567")
+      expect(subject.url).to eq("http://elifesciences.org/lookup/doi/10.7554/eLife.01567")
       expect(subject.resource_type_general).to eq("Text")
       expect(subject.creator.length).to eq(5)
       expect(subject.creator.first).to eq("type"=>"Person",

data/spec/readers/schema_org_reader_spec.rb

@@ -20,7 +20,7 @@ describe Bolognese::Metadata, vcr: true do
     it "BlogPosting" do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5438/4k3m-nyvg")
-      expect(subject.b_url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
+      expect(subject.url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
       expect(subject.type).to eq("BlogPosting")
       expect(subject.creator).to eq("type"=>"Person", "id"=>"https://orcid.org/0000-0003-1419-2405", "name"=>"Martin Fenner", "givenName"=>"Martin", "familyName"=>"Fenner")
       expect(subject.title).to eq("Eating your own Dog Food")
@@ -38,7 +38,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5438/0000-00ss")
       expect(subject.doi).to eq("10.5438/0000-00ss")
-      expect(subject.b_url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
+      expect(subject.url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
       expect(subject.type).to eq("BlogPosting")
     end
 
@@ -49,7 +49,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.errors.first).to eq("43:0: ERROR: Element '{http://datacite.org/schema/kernel-4}publisher': [facet 'minLength'] The value has a length of '0'; this underruns the allowed minimum length of '1'.")
       expect(subject.identifier).to eq("https://doi.org/10.5281/zenodo.1196821")
       expect(subject.doi).to eq("10.5281/zenodo.1196821")
-      expect(subject.b_url).to eq("https://zenodo.org/record/1196821")
+      expect(subject.url).to eq("https://zenodo.org/record/1196821")
       expect(subject.type).to eq("Dataset")
       expect(subject.title).to eq("PsPM-SC4B: SCR, ECG, EMG, PSR and respiration measurements in a delay fear conditioning task with auditory CS and electrical US")
       expect(subject.creator.size).to eq(6)
@@ -62,7 +62,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.1594/pangaea.836178")
       expect(subject.doi).to eq("10.1594/pangaea.836178")
-      expect(subject.b_url).to eq("https://doi.pangaea.de/10.1594/PANGAEA.836178")
+      expect(subject.url).to eq("https://doi.pangaea.de/10.1594/PANGAEA.836178")
       expect(subject.type).to eq("Dataset")
       expect(subject.title).to eq("Hydrological and meteorological investigations in a lake near Kangerlussuaq, west Greenland")
       expect(subject.creator.size).to eq(8)
@@ -77,7 +77,7 @@ describe Bolognese::Metadata, vcr: true do
     #   #expect(subject.errors).to be true
     #   expect(subject.identifier).to eq("https://doi.org/10.3334/ornldaac/1418")
     #   expect(subject.doi).to eq("10.3334/ornldaac/1418")
-    #   expect(subject.b_url).to eq("https://doi.org/10.3334/ornldaac/1418")
+    #   expect(subject.url).to eq("https://doi.org/10.3334/ornldaac/1418")
     #   expect(subject.type).to eq("DataSet")
     #   expect(subject.title).to eq("AirMOSS: L2/3 Volumetric Soil Moisture Profiles Derived From Radar, 2012-2015")
     #   expect(subject.creator.size).to eq(8)
@@ -116,7 +116,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input)
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.5438/4k3m-nyvg")
-      expect(subject.b_url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
+      expect(subject.url).to eq("https://blog.datacite.org/eating-your-own-dog-food")
       expect(subject.type).to eq("BlogPosting")
       expect(subject.creator).to eq("type"=>"Person", "id"=>"http://orcid.org/0000-0003-1419-2405", "name"=>"Martin Fenner", "givenName"=>"Martin", "familyName"=>"Fenner")
       expect(subject.title).to eq("Eating your own Dog Food")
@@ -136,13 +136,13 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.25491/d50j-3083")
       expect(subject.alternate_identifiers).to eq("name"=>"687610993", "type"=>"md5")
-      expect(subject.b_url).to eq("https://ors.datacite.org/doi:/10.25491/d50j-3083")
+      expect(subject.url).to eq("https://ors.datacite.org/doi:/10.25491/d50j-3083")
       expect(subject.content_url).to eq("https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz")
       expect(subject.type).to eq("Dataset")
       expect(subject.additional_type).to eq("Gene expression matrices")
       expect(subject.creator).to eq("name"=>"The GTEx Consortium", "type"=>"Organization")
       expect(subject.title).to eq("Fully processed, filtered and normalized gene expression matrices (in BED format) for each tissue, which were used as input into FastQTL for eQTL discovery")
-      expect(subject.b_version).to eq("v7")
+      expect(subject.version).to eq("v7")
       expect(subject.keywords).to eq(["gtex", "annotation", "phenotype", "gene regulation", "transcriptomics"])
       expect(subject.date_published).to eq("2017")
       expect(subject.periodical).to eq("title"=>"GTEx", "type"=>"DataCatalog")
@@ -158,7 +158,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.23725/8na3-9s47")
       expect(subject.alternate_identifiers).to eq([{"name"=>"3b33f6b9338fccab0901b7d317577ea3", "type"=>"md5"}, {"name"=>"ark:/99999/fk41CrU4eszeLUDe", "type"=>"minid"}, {"name"=>"dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7", "type"=>"dataguid"}])
-      expect(subject.b_url).to eq("https://ors.datacite.org/doi:/10.23725/8na3-9s47")
+      expect(subject.url).to eq("https://ors.datacite.org/doi:/10.23725/8na3-9s47")
       expect(subject.content_url).to eq(["s3://cgp-commons-public/topmed_open_access/197bc047-e917-55ed-852d-d563cdbc50e4/NWD165827.recab.cram", "gs://topmed-irc-share/public/NWD165827.recab.cram"])
       expect(subject.type).to eq("Dataset")
       expect(subject.additional_type).to eq("CRAM file")
@@ -211,7 +211,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       expect(subject.identifier).to eq("https://doi.org/10.23725/7jg3-v803")
       expect(subject.alternate_identifiers).to eq([{"name"=>"ark:/99999/fk4E1n6n1YHKxPk", "type"=>"minid"}, {"name"=>"dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d", "type"=>"dataguid"}, {"name"=>"f9e72bdf25bf4b4f0e581d9218fec2eb", "type"=>"md5"}])
-      expect(subject.b_url).to eq("https://ors.datacite.org/doi:/10.23725/7jg3-v803")
+      expect(subject.url).to eq("https://ors.datacite.org/doi:/10.23725/7jg3-v803")
       expect(subject.content_url).to eq(["s3://cgp-commons-public/topmed_open_access/44a8837b-4456-5709-b56b-54e23000f13a/NWD100953.recab.cram","gs://topmed-irc-share/public/NWD100953.recab.cram","dos://dos.commons.ucsc-cgp.org/01b048d0-e128-4cb0-94e9-b2d2cab7563d?version=2018-05-26T133719.491772Z"])
       expect(subject.type).to eq("Dataset")
       expect(subject.additional_type).to eq("CRAM file")

data/spec/writers/schema_org_writer_spec.rb

@@ -119,9 +119,9 @@ describe Bolognese::Metadata, vcr: true do
 
     it "author is organization" do
       input = fixture_path + 'gtex.xml'
-      b_url = "https://ors.datacite.org/doi:/10.25491/9hx8-ke93"
+      url = "https://ors.datacite.org/doi:/10.25491/9hx8-ke93"
       content_url = "https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz"  
-      subject = Bolognese::Metadata.new(input: input, b_url: b_url, content_url: content_url, from: "datacite")
+      subject = Bolognese::Metadata.new(input: input, url: url, content_url: content_url, from: "datacite")
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.25491/9hx8-ke93")
       expect(json["author"]).to eq("@type"=>"Organization", "name"=>"The GTEx Consortium")

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.0.2
 platform: ruby
 authors:
 - Martin Fenner