bolognese 0.7.2 → 0.8

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: d9c8e7a4955f749653d35917dae9f3a459c0f2da
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data/Gemfile.lock

@@ -1,11 +1,12 @@
 PATH
   remote: .
   specs:
-    bolognese (0.7.2)
+    bolognese (0.8)
       activesupport (~> 4.2, >= 4.2.5)
       bibtex-ruby (~> 4.1)
       builder (~> 3.2, >= 3.2.2)
       colorize (~> 0.8.1)
+      loofah (~> 2.0, >= 2.0.3)
       maremma (~> 3.5)
       namae (~> 0.10.2)
       nokogiri (~> 1.6, >= 1.6.8)
@@ -43,6 +44,8 @@ GEM
     json (2.0.3)
     latex-decode (0.2.2)
       unicode (~> 0.4)
+    loofah (2.0.3)
+      nokogiri (>= 1.5.9)
     maremma (3.5.1)
       activesupport (~> 4.2, >= 4.2.5)
       addressable (>= 2.3.6)

data/README.md

@@ -1,8 +1,10 @@
+[![Identifier](https://img.shields.io/badge/doi-10.5438%2Fn138--z3mk-fca709.svg)](https://doi.org/10.5438/n138-z3mk)
+[![Gem Version](https://badge.fury.io/rb/bolognese.svg)](https://badge.fury.io/rb/bolognese)
 [![Build Status](https://travis-ci.org/datacite/bolognese.svg?branch=master)](https://travis-ci.org/datacite/bolognese)
 [![Code Climate](https://codeclimate.com/github/datacite/bolognese/badges/gpa.svg)](https://codeclimate.com/github/datacite/bolognese)
 [![Test Coverage](https://codeclimate.com/github/datacite/bolognese/badges/coverage.svg)](https://codeclimate.com/github/datacite/bolognese/coverage)
 
-# Bolognese
+# Bolognese: a Ruby library for conversion of DOI Metadata
 
 Ruby gem and command-line utility for conversion of DOI metadata from and to different metadata formats, including [schema.org](https://schema.org).
 
@@ -36,25 +38,32 @@ Bolognese reads and/or writes these metadata formats:
       <td>Yes</td>
     </tr>
     <tr>
-        <td><a href='http://schema.org/'>Schema.org in JSON-LD</a></td>
-        <td>schema_org</td>
-        <td>application/vnd.schemaorg.ld+json</td>
-        <td>Yes</td>
-        <td>Yes</td>
+      <td><a href='https://api.datacite.org/'>DataCite JSON</a></td>
+      <td>datacite</td>
+      <td>application/vnd.datacite+json</td>
+      <td>Yes</td>
+      <td>Yes</td>
     </tr>
     <tr>
-        <td><a href='https://codemeta.github.io/'>Codemeta</a></td>
-        <td>codemeta</td>
-        <td>application/ld+json</td>
-        <td>Yes</td>
-        <td>Yes</td>
+      <td><a href='http://schema.org/'>Schema.org in JSON-LD</a></td>
+      <td>schema_org</td>
+      <td>application/vnd.schemaorg.ld+json</td>
+      <td>Yes</td>
+      <td>Yes</td>
     </tr>
     <tr>
-        <td><a href='http://en.wikipedia.org/wiki/BibTeX'>BibTeX</a></td>
-        <td>bibtex</td>
-        <td>application/x-bibtex</td>
-        <td>Yes</td>
-        <td>Yes</td>
+      <td><a href='https://codemeta.github.io/'>Codemeta</a></td>
+      <td>codemeta</td>
+      <td>application/ld+json</td>
+      <td>Yes</td>
+      <td>Yes</td>
+    </tr>
+    <tr>
+      <td><a href='http://en.wikipedia.org/wiki/BibTeX'>BibTeX</a></td>
+      <td>bibtex</td>
+      <td>application/x-bibtex</td>
+      <td>Yes</td>
+      <td>Yes</td>
     </tr>
   </tbody>
 </table>

data/bolognese.gemspec

@@ -8,7 +8,7 @@ Gem::Specification.new do |s|
   s.homepage      = "https://github.com/datacite/bolognese"
   s.summary       = "Ruby client library for conversion of DOI Metadata"
   s.date          = Date.today
-  s.description   = "Convert DOI metadata to and from Crossref and DataCite XML, as well as schema.org/JSON-LD"
+  s.description   = "Ruby gem and command-line utility for conversion of DOI metadata from and to different metadata formats, including schema.org."
   s.require_paths = ["lib"]
   s.version       = Bolognese::VERSION
   s.extra_rdoc_files = ["README.md"]
@@ -17,6 +17,7 @@ Gem::Specification.new do |s|
   # Declary dependencies here, rather than in the Gemfile
   s.add_dependency 'maremma', '~> 3.5'
   s.add_dependency 'nokogiri', '~> 1.6', '>= 1.6.8'
+  s.add_dependency 'loofah', '~> 2.0', '>= 2.0.3'
   s.add_dependency 'builder', '~> 3.2', '>= 3.2.2'
   s.add_dependency 'activesupport', '~> 4.2', '>= 4.2.5'
   s.add_dependency 'bibtex-ruby', '~> 4.1'

data/codemeta.json

@@ -0,0 +1,39 @@
+{
+	"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
+	"@type": "SoftwareSourceCode",
+	"@id": "https://doi.org/10.5438/N138-Z3MK",
+	"agents": {
+		"@id": "http://orcid.org/0000-0003-0077-4738",
+		"@type": "person",
+		"name": "Martin Fenner",
+		"affiliation": "DataCite",
+		"mustBeCited": true,
+		"isMaintainer": true,
+		"isRightsHolder": true
+	},
+	"identifier": "https://doi.org/10.5438/N138-Z3MK",
+	"codeRepository": "https://github.com/datacite/bolognese",
+	"dateCreated": "2017-02-13",
+	"datePublished": "2017-02-25",
+	"dateModified": "2017-02-25",
+	"description": "Ruby gem and command-line utility for conversion of DOI metadata from and to different metadata formats, including schema.org.",
+	"isAutomatedBuild": true,
+	"licenseId": "MIT",
+	"publisher": "DataCite",
+	"tags": [
+		"doi",
+		"metadata",
+		"crossref",
+		"datacite",
+		"schema.org",
+		"bibtex",
+		"codemeta"
+	],
+	"title": "Bolognese: a Ruby library for conversion of DOI Metadata",
+	"programmingLanguage": {
+		"name": "Ruby",
+		"version": "≥ 2.3.3",
+		"URL": "https://www.ruby-lang.org"
+	},
+	"readme": "https://github.com/datacite/bolognese/blob/master/README.md"
+}

data/lib/bolognese.rb

@@ -4,14 +4,18 @@ require 'maremma'
 require 'postrank-uri'
 require 'bibtex'
 require 'colorize'
+require 'loofah'
 
 require "bolognese/version"
 require "bolognese/metadata"
 require "bolognese/crossref"
 require "bolognese/datacite"
+require "bolognese/datacite_json"
 require "bolognese/schema_org"
 require "bolognese/codemeta"
 require "bolognese/bibtex"
 require "bolognese/orcid"
 require "bolognese/cli"
 require "bolognese/string"
+require "bolognese/array"
+require "bolognese/whitelist_scrubber"

data/lib/bolognese/array.rb

@@ -0,0 +1,11 @@
+# turn array into hash or nil, depending on array size. Reverses Array.wrap,
+# but uses self to allow chaining with Array.wrap
+class Array
+  def unwrap
+    case self.length
+    when 0 then nil
+    when 1 then self.first
+    else self
+    end
+  end
+end

data/lib/bolognese/author_utils.rb

@@ -4,25 +4,34 @@ module Bolognese
   module AuthorUtils
     # only assume personal name when using sort-order: "Turing, Alan"
     def get_one_author(author)
-      orcid = get_name_identifier(author)
-      author = author.fetch("creatorName", nil)
+      type = author.fetch("type", nil) && author.fetch("type").titleize
+      id = author.fetch("id", nil).presence || get_name_identifier(author)
+      name = author.fetch("creatorName", nil) ||
+             author.fetch("contributorName", nil) ||
+             author.fetch("name", nil)
+      name = cleanup_author(name)
+      given_name = author.fetch("givenName", nil)
+      family_name = author.fetch("familyName", nil)
 
-      return { "name" => "" } if author.to_s.strip.blank?
+      author = { "type" => type || "Person",
+                 "id" => id,
+                 "name" => name,
+                 "givenName" => given_name,
+                 "familyName" => family_name }.compact
 
-      author = cleanup_author(author)
-      names = Namae.parse(author)
+      return author if family_name.present?
 
-      if names.blank? || !is_personal_name?(author)
-        { "@type" => "Agent",
-          "@id" => orcid,
-          "name" => author }.compact
-      else
-        name = names.first
+      if is_personal_name?(author)
+        names = Namae.parse(name)
+        parsed_name = names.first
 
-        { "@type" => "Person",
-          "@id" => orcid,
-          "givenName" => name.given,
-          "familyName" => name.family }.compact
+        { "type" => "Person",
+          "id" => id,
+          "name" => [parsed_name.given, parsed_name.family].join(" "),
+          "givenName" => parsed_name.given,
+          "familyName" => parsed_name.family }.compact
+      else
+        { "type" => type, "name" => name }.compact
       end
     end
 
@@ -37,15 +46,20 @@ module Bolognese
     end
 
     def is_personal_name?(author)
-      return true if author.include?(",")
+      return false if author.fetch("type", "").downcase == "organization"
+      return true if author.fetch("type", "").downcase == "person" ||
+                     author.fetch("id", "").start_with?("http://orcid.org") ||
+                     author.fetch("familyName", "").present? ||
+                     author.fetch("name", "").include?(",")
 
       # lookup given name
       #::NameDetector.name_exists?(author.split.first)
+      false
     end
 
     # parse array of author strings into CSL format
     def get_authors(authors)
-      Array(authors).map { |author| get_one_author(author) }
+      Array.wrap(authors).map { |author| get_one_author(author) }.unwrap
     end
 
     # parse nameIdentifier from DataCite
@@ -61,12 +75,12 @@ module Bolognese
 
     def authors_as_string(authors)
       Array.wrap(authors).map do |a|
-        if a["@type"] == "organization"
-          "{" + a["name"] + "}"
-        elsif a["familyName"].present?
+        if a["familyName"].present?
           [a["familyName"], a["givenName"]].join(", ")
-        else
+        elsif a["type"] == "Person"
           a["name"]
+        elsif a["name"].present?
+          "{" + a["name"] + "}"
         end
       end.join(" and ").presence
     end

data/lib/bolognese/bibtex.rb

@@ -70,7 +70,7 @@ module Bolognese
       end
     end
 
-    def name
+    def title
       metadata.title
     end
 
@@ -88,7 +88,7 @@ module Bolognese
 
     def is_part_of
       if metadata.journal.present?
-        { "@type" => "Periodical",
+        { "type" => "Periodical",
           "name" => metadata.journal.to_s,
           "issn" => metadata.issn.to_s.presence }.compact
       else
@@ -97,11 +97,11 @@ module Bolognese
     end
 
     def description
-      metadata.field?(:abstract) && metadata.abstract.to_s.presence
+      { "text" => metadata.field?(:abstract) && metadata.abstract.to_s.presence }
     end
 
     def license
-      metadata.field?(:copyright) && metadata.copyright.to_s.presence
+      { "id" => metadata.field?(:copyright) && metadata.copyright.to_s.presence }
     end
   end
 end

data/lib/bolognese/codemeta.rb

@@ -56,7 +56,7 @@ module Bolognese
       Bolognese::Bibtex::SO_TO_BIB_TRANSLATIONS[type] || "misc"
     end
 
-    def name
+    def title
       metadata.fetch("title", nil)
     end
 
@@ -65,20 +65,21 @@ module Bolognese
     end
 
     def author
-      arr = Array.wrap(metadata.fetch("agents", nil)).map { |a| a.slice("@type", "@id", "name") }
-      array_unwrap(arr)
+      authors = from_schema_org(Array.wrap(metadata.fetch("agents", nil)))
+      get_authors(authors)
     end
 
     def editor
-      Array(metadata.fetch("editor", nil)).map { |a| a.except("name") }.presence
+      editors = from_schema_org(Array.wrap(metadata.fetch("editor", nil)))
+      get_authors(editors)
     end
 
     def description
-      metadata.fetch("description", nil)
+      { "text" => metadata.fetch("description", nil) }
     end
 
     def license
-      metadata.fetch("license", nil)
+      { "id" => metadata.fetch("license", nil) }
     end
 
     def version
@@ -122,13 +123,7 @@ module Bolognese
     end
 
     def publisher
-      p = metadata.fetch("publisher", nil)
-      if p.is_a?(Hash)
-        p
-      elsif p.is_a?(String)
-        { "@type" => "Organization",
-          "name" => p }
-      end
+      metadata.fetch("publisher", nil)
     end
 
     def container_title

data/lib/bolognese/crossref.rb

@@ -68,6 +68,7 @@ module Bolognese
       elsif id.present?
         response = Maremma.get(id, accept: "application/vnd.crossref.unixref+xml", host: true, raw: true)
         @raw = response.body.fetch("data", nil)
+        @raw = Nokogiri::XML(@raw, &:noblanks).to_s if @raw.present?
       end
     end
 
@@ -132,7 +133,7 @@ module Bolognese
       CR_TO_BIB_TRANSLATIONS[additional_type] || "misc"
     end
 
-    def name
+    def title
       parse_attributes(bibliographic_metadata.dig("titles", "title"))
     end
 
@@ -172,23 +173,21 @@ module Bolognese
 
     def people(contributor_role)
       person = bibliographic_metadata.dig("contributors", "person_name")
-      arr = Array.wrap(person).select { |a| a["contributor_role"] == contributor_role }.map do |a|
-        { "@type" => "Person",
-          "@id" => parse_attributes(a["ORCID"]),
+      Array.wrap(person).select { |a| a["contributor_role"] == contributor_role }.map do |a|
+        { "type" => "Person",
+          "id" => parse_attributes(a["ORCID"]),
+          "name" => [a["given_name"], a["surname"]].join(" "),
           "givenName" => a["given_name"],
           "familyName" => a["surname"] }.compact
-      end
-      array_unwrap(arr)
+      end.unwrap
     end
 
     def funder
       fundref = Array.wrap(program_metadata).find { |a| a["name"] == "fundref" } || {}
-      arr = Array.wrap(fundref.fetch("assertion", [])).select { |a| a["name"] == "fundgroup" }.map do |f|
-        { "@type" => "Organization",
-          "@id" => normalize_id(f.dig("assertion", "assertion", "__content__")),
+      Array.wrap(fundref.fetch("assertion", [])).select { |a| a["name"] == "fundgroup" }.map do |f|
+        { "id" => normalize_id(f.dig("assertion", "assertion", "__content__")),
           "name" => f.dig("assertion", "__content__").strip }.compact
-      end
-      array_unwrap(arr)
+      end.unwrap
     end
 
     def date_published
@@ -215,7 +214,7 @@ module Bolognese
 
     def is_part_of
       if journal_metadata.present?
-        { "@type" => "Periodical",
+        { "type" => "Periodical",
           "name" => journal_metadata["full_title"],
           "issn" => parse_attributes(journal_metadata.fetch("issn", nil)) }.compact
       else
@@ -229,20 +228,23 @@ module Bolognese
 
     alias_method :journal, :container_title
 
-    def citation
-       citations = bibliographic_metadata.dig("citation_list", "citation")
-       Array.wrap(citations).map do |c|
-         { "@type" => "CreativeWork",
-           "@id" => normalize_id(c["doi"]),
+    def related_identifier(relation_type: nil)
+      references
+    end
+
+    def references
+       refs = bibliographic_metadata.dig("citation_list", "citation")
+       Array.wrap(refs).map do |c|
+         { "id" => normalize_id(c["doi"]),
+           "relationType" => "Cites",
            "position" => c["key"],
            "name" => c["article_title"],
            "datePublished" => c["cYear"] }.compact
-       end.presence
+       end.unwrap
     end
 
     def provider
-      { "@type" => "Organization",
-        "name" => "Crossref" }
+      "Crossref"
     end
   end
 end