bolognese 0.2.2

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 3a6b175047cc9fe1cae1eba94b41164dd0c9e406
+  data.tar.gz: f78c9e066599d1a2b6db5c66cc1a19e8024dd73b
+SHA512:
+  metadata.gz: fede61f6811145761b605513ae01345508e8f60a7e2d807d22ac17fd80096326d7ab4af1a8b3ca117c1856adb2f31012a23ed3392023d8f9213b424d32c2e459
+  data.tar.gz: 4ddc0ca66cda0fbb1ea3d10021d97b1f532f733dd221c39509d1994a4c51da09f27da515fdb0536d086d425d3d0075a00fb6f498e9813802e19b0bcde70cbb87

data/.gitignore

@@ -0,0 +1,56 @@
+*.gem
+*.rbc
+/.config
+/coverage/
+/InstalledFiles
+/pkg/
+/spec/reports/
+/spec/examples.txt
+/test/tmp/
+/test/version_tmp/
+/tmp/
+
+# Used by dotenv library to load environment variables.
+# .env
+
+## Specific to RubyMotion:
+.dat*
+.repl_history
+build/
+*.bridgesupport
+build-iPhoneOS/
+build-iPhoneSimulator/
+
+## Specific to RubyMotion (use of CocoaPods):
+#
+# We recommend against adding the Pods directory to your .gitignore. However
+# you should judge for yourself, the pros and cons are mentioned at:
+# https://guides.cocoapods.org/using/using-cocoapods.html#should-i-check-the-pods-directory-into-source-control
+#
+# vendor/Pods/
+
+## Documentation cache and generated files:
+/.yardoc/
+/_yardoc/
+/doc/
+/rdoc/
+
+## Environment normalization:
+/.bundle/
+/vendor/bundle
+/lib/bundler/man/
+
+# for a library or gem, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# Gemfile.lock
+# .ruby-version
+# .ruby-gemset
+
+# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
+.rvmrc
+
+coverage/
+.env
+.env.*
+!.env.example
+!.env.travis

data/.travis.yml

@@ -0,0 +1,23 @@
+language: ruby
+rvm:
+- 2.3.3
+
+before_install:
+- export TZ=Europe/Berlin
+
+install:
+- travis_retry bundle install
+
+script: bundle exec rspec
+
+notifications:
+  email: false
+
+deploy:
+  provider: rubygems
+  api_key:
+    secure: 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
+  gem: bolognese
+  on:
+    tags: true
+    repo: datacite/bolognese

data/Gemfile

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+source 'https://rubygems.org'
+
+gemspec

data/Gemfile.lock

@@ -0,0 +1,118 @@
+PATH
+  remote: .
+  specs:
+    Bolognese (0.2)
+      activesupport (~> 4.2, >= 4.2.5)
+      builder (~> 3.2, >= 3.2.2)
+      dotenv (~> 2.1, >= 2.1.1)
+      maremma (~> 3.5)
+      namae (~> 0.10.2)
+      nokogiri (~> 1.6, >= 1.6.8)
+      postrank-uri (~> 1.0, >= 1.0.18)
+      thor (~> 0.19)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    activesupport (4.2.7.1)
+      i18n (~> 0.7)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.3, >= 0.3.4)
+      tzinfo (~> 1.1)
+    addressable (2.3.8)
+    builder (3.2.3)
+    codeclimate-test-reporter (1.0.5)
+      simplecov
+    crack (0.4.3)
+      safe_yaml (~> 1.0.0)
+    diff-lcs (1.3)
+    docile (1.1.5)
+    dotenv (2.2.0)
+    excon (0.45.4)
+    faraday (0.9.2)
+      multipart-post (>= 1.2, < 3)
+    faraday-encoding (0.0.4)
+      faraday
+    faraday_middleware (0.10.1)
+      faraday (>= 0.7.4, < 1.0)
+    hashdiff (0.3.2)
+    i18n (0.8.0)
+    json (1.8.6)
+    maremma (3.5)
+      activesupport (~> 4.2, >= 4.2.5)
+      addressable (>= 2.3.6)
+      builder (~> 3.2, >= 3.2.2)
+      excon (~> 0.45.0)
+      faraday (~> 0.9.2)
+      faraday-encoding (~> 0.0.1)
+      faraday_middleware (~> 0.10.0)
+      multi_json (~> 1.11.2)
+      nokogiri (~> 1.6.7)
+      oj (~> 2.18, >= 2.18.1)
+    mini_portile2 (2.1.0)
+    minitest (5.10.1)
+    multi_json (1.11.3)
+    multipart-post (2.0.0)
+    namae (0.10.2)
+    nokogiri (1.6.8.1)
+      mini_portile2 (~> 2.1.0)
+    oj (2.18.1)
+    postrank-uri (1.0.18)
+      addressable (~> 2.3.0)
+      nokogiri (~> 1.6.1)
+      public_suffix (~> 1.1.3)
+    public_suffix (1.1.3)
+    rack (2.0.1)
+    rack-test (0.6.3)
+      rack (>= 1.0)
+    rake (12.0.0)
+    rspec (3.5.0)
+      rspec-core (~> 3.5.0)
+      rspec-expectations (~> 3.5.0)
+      rspec-mocks (~> 3.5.0)
+    rspec-core (3.5.4)
+      rspec-support (~> 3.5.0)
+    rspec-expectations (3.5.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.5.0)
+    rspec-mocks (3.5.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.5.0)
+    rspec-support (3.5.0)
+    rspec-xsd (0.1.0)
+      nokogiri (~> 1.6)
+      rspec (~> 3)
+    safe_yaml (1.0.4)
+    simplecov (0.12.0)
+      docile (~> 1.1.0)
+      json (>= 1.8, < 3)
+      simplecov-html (~> 0.10.0)
+    simplecov-html (0.10.0)
+    thor (0.19.4)
+    thread_safe (0.3.5)
+    tzinfo (1.2.2)
+      thread_safe (~> 0.1)
+    vcr (3.0.3)
+    webmock (1.24.6)
+      addressable (>= 2.3.6)
+      crack (>= 0.3.2)
+      hashdiff
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  Bolognese!
+  bundler (~> 1.0)
+  codeclimate-test-reporter (~> 1.0, >= 1.0.0)
+  rack-test (~> 0)
+  rake (~> 12.0)
+  rspec (~> 3.4)
+  rspec-xsd (~> 0.1.0)
+  simplecov (~> 0.12.0)
+  vcr (~> 3.0, >= 3.0.3)
+  webmock (~> 1.22, >= 1.22.3)
+
+BUNDLED WITH
+   1.12.5

data/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 DataCite
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

@@ -0,0 +1,3 @@
+# bolognese
+
+Command-line utility for conversion of DOI metadata.

data/Rakefile

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+#!/usr/bin/env rake
+
+require 'bundler'
+require 'rake'
+require 'yaml'
+require 'rspec/core/rake_task'
+
+Bundler::GemHelper.install_tasks
+RSpec::Core::RakeTask.new('spec')
+
+# default task is running rspec tests
+task :default => :spec

data/bin/bolognese

@@ -0,0 +1,5 @@
+#!/usr/bin/env ruby
+
+require File.expand_path("../../lib/bolognese", __FILE__)
+
+Bolognese::CLI.start

data/bolognese.gemspec

@@ -0,0 +1,40 @@
+require "date"
+require File.expand_path("../lib/bolognese/version", __FILE__)
+
+Gem::Specification.new do |s|
+  s.authors       = "Martin Fenner"
+  s.email         = "mfenner@datacite.org"
+  s.name          = "bolognese"
+  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.require_paths = ["lib"]
+  s.version       = Bolognese::VERSION
+  s.extra_rdoc_files = ["README.md"]
+  s.license       = 'MIT'
+
+  # 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 'builder', '~> 3.2', '>= 3.2.2'
+  s.add_dependency 'activesupport', '~> 4.2', '>= 4.2.5'
+  s.add_dependency 'dotenv', '~> 2.1', '>= 2.1.1'
+  s.add_dependency 'thor', '~> 0.19'
+  s.add_dependency 'namae', '~> 0.10.2'
+  s.add_dependency 'postrank-uri', '~> 1.0', '>= 1.0.18'
+  s.add_development_dependency 'bundler', '~> 1.0'
+  s.add_development_dependency 'rspec', '~> 3.4'
+  s.add_development_dependency 'rspec-xsd', '~> 0.1.0'
+  s.add_development_dependency 'rake', '~> 12.0'
+  s.add_development_dependency 'rack-test', '~> 0'
+  s.add_development_dependency 'vcr', '~> 3.0', '>= 3.0.3'
+  s.add_development_dependency 'webmock', '~> 1.22', '>= 1.22.3'
+  s.add_development_dependency 'codeclimate-test-reporter', '~> 1.0', '>= 1.0.0'
+  s.add_development_dependency 'simplecov', '~> 0.12.0'
+
+  s.require_paths = ["lib"]
+  s.files       = `git ls-files`.split($/)
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.executables = ["bolognese"]
+end

data/lib/bolognese.rb

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+require 'active_support/all'
+require 'nokogiri'
+require 'maremma'
+require 'postrank-uri'
+
+require "bolognese/version"
+require "bolognese/metadata"
+require "bolognese/crossref"
+require "bolognese/datacite"
+require "bolognese/orcid"
+require "bolognese/cli"
+require "bolognese/string"

data/lib/bolognese/author_utils.rb

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+require 'namae'
+
+module Bolognese
+  module AuthorUtils
+    # only assume personal name when using sort-order: "Turing, Alan"
+    def get_one_author(author, options = {})
+      orcid = get_name_identifier(author)
+      author = author.fetch("creatorName", nil)
+
+      return { "Name" => "" } if author.strip.blank?
+
+      author = cleanup_author(author)
+      names = Namae.parse(author)
+
+      if names.blank? || is_personal_name?(author).blank?
+        { "@type" => "Agent",
+          "@id" => orcid,
+          "Name" => author }.compact
+      else
+        name = names.first
+
+        { "@type" => "Person",
+          "@id" => orcid,
+          "givenName" => name.given,
+          "familyName" => name.family }.compact
+      end
+    end
+
+    def cleanup_author(author)
+      # detect pattern "Smith J.", but not "Smith, John K."
+      author = author.gsub(/[[:space:]]([A-Z]\.)?(-?[A-Z]\.)$/, ', \1\2') unless author.include?(",")
+
+      # titleize strings
+      # remove non-standard space characters
+      author.my_titleize
+            .gsub(/[[:space:]]/, ' ')
+    end
+
+    def is_personal_name?(author)
+      return true if author.include?(",")
+
+      # lookup given name
+      #::NameDetector.name_exists?(author.split.first)
+    end
+
+    # parse array of author strings into CSL format
+    def get_authors(authors, options={})
+      Array(authors).map { |author| get_one_author(author, options) }
+    end
+
+    def get_name_identifier(author)
+      name_identifier = author.dig("nameIdentifier", "text")
+      name_identifier_scheme = author.dig("nameIdentifier", "nameIdentifierScheme") || "ORCID"
+      if name_identifier_scheme.downcase == "orcid" && name_identifier = validate_orcid(name_identifier)
+        "http://orcid.org/#{name_identifier}"
+      else
+        nil
+      end
+    end
+  end
+end

data/lib/bolognese/cli.rb

@@ -0,0 +1,38 @@
+# encoding: UTF-8
+
+require "thor"
+
+module Bolognese
+  class CLI < Thor
+    def self.exit_on_failure?
+      true
+    end
+
+    # from http://stackoverflow.com/questions/22809972/adding-a-version-option-to-a-ruby-thor-cli
+    map %w[--version -v] => :__print_version
+
+    desc "--version, -v", "print the version"
+    def __print_version
+      puts Bolognese::VERSION
+    end
+
+    desc "read pid", "read metadata for PID"
+    method_option :as, :default => "schema_org"
+    def read(pid)
+      provider = Metadata.new(pid).provider
+
+      case
+      when provider == "crossref" && options[:as] == "crossref"
+        puts Crossref.new(pid).raw
+      when provider == "crossref"
+        puts Crossref.new(pid).as_schema_org
+      when provider == "datacite" && options[:as] == "datacite"
+        puts Datacite.new(pid).raw
+      when "datacite"
+        puts Datacite.new(pid).as_schema_org
+      else
+        puts "not implemented"
+      end
+    end
+  end
+end

data/lib/bolognese/crossref.rb

@@ -0,0 +1,202 @@
+require_relative 'doi_utils'
+require_relative 'utils'
+
+module Bolognese
+  class Crossref < Metadata
+    include Bolognese::DoiUtils
+    include Bolognese::Utils
+
+    # CrossRef types from https://api.crossref.org/types
+    CROSSREF_TYPE_TRANSLATIONS = {
+      "Proceedings" => nil,
+      "ReferenceBook" => nil,
+      "JournalIssue" => nil,
+      "ProceedingsArticle" => nil,
+      "Other" => nil,
+      "Dissertation" => "Thesis",
+      "Dataset" => "Dataset",
+      "EditedBook" => "Book",
+      "JournalArticle" => "ScholarlyArticle",
+      "Journal" => nil,
+      "Report" => nil,
+      "BookSeries" => nil,
+      "ReportSeries" => nil,
+      "BookTrack" => nil,
+      "Standard" => nil,
+      "BookSection" => nil,
+      "BookPart" => nil,
+      "Book" => "Book",
+      "BookChapter" => "Chapter",
+      "StandardSeries" => nil,
+      "Monograph" => "Book",
+      "Component" => nil,
+      "ReferenceEntry" => nil,
+      "JournalVolume" => nil,
+      "BookSet" => nil,
+      "PostedContent" => nil
+    }
+
+    attr_reader = :id, :metadata, :schema_org
+
+    def initialize(doi)
+      @id = normalize_doi(doi)
+    end
+
+    def raw
+      response = Maremma.get(@id, accept: "application/vnd.crossref.unixref+xml", host: true, raw: true)
+      @raw ||= response.body.fetch("data", nil)
+    end
+
+    def metadata
+      @metadata ||= raw.present? ? Maremma.from_xml(raw).fetch("doi_records", {}).fetch("doi_record", {}) : {}
+    end
+
+    def exists?
+      metadata.present?
+    end
+
+    def journal_metadata
+      metadata.dig("crossref", "journal", "journal_metadata").presence || {}
+    end
+
+    def bibliographic_metadata
+      if metadata.dig("crossref", "journal", "journal_article").present?
+        metadata.dig("crossref", "journal", "journal_article")
+      else
+        k = metadata.dig("crossref").keys.last
+        metadata.dig("crossref", k).presence || {}
+      end
+    end
+
+    def program_metadata
+      bibliographic_metadata.dig("program") ||
+      bibliographic_metadata.dig("crossmark", "custom_metadata", "program") || {}
+    end
+
+    def additional_type
+      if metadata.dig("crossref", "journal").present?
+        metadata.dig("crossref", "journal").keys.last.camelize
+      else
+        metadata.dig("crossref").keys.last.camelize
+      end
+    end
+
+    def type
+      CROSSREF_TYPE_TRANSLATIONS[additional_type] || "CreativeWork"
+    end
+
+    def name
+      parse_attribute(bibliographic_metadata.dig("titles", "title"))
+    end
+
+    def alternate_name
+      if bibliographic_metadata.fetch("publisher_item", nil).present?
+        parse_attribute(bibliographic_metadata.dig("publisher_item", "item_number"))
+      else
+        parse_attribute(bibliographic_metadata.fetch("item_number", nil))
+      end
+    end
+
+    def description
+      bibliographic_metadata.fetch("abstract", {}).values.first
+    end
+
+    def license
+      access_indicator = Array.wrap(program_metadata).find { |m| m["name"] == "AccessIndicators" }
+      if access_indicator.present?
+        parse_attribute(access_indicator["license_ref"])
+      else
+        nil
+      end
+    end
+
+    def author
+      person = bibliographic_metadata.dig("contributors", "person_name")
+      Array(person).select { |a| a["contributor_role"] == "author" }.map do |a|
+        { "@type" => "Person",
+          "@id" => a["ORCID"],
+          "givenName" => a["given_name"],
+          "familyName" => a["surname"] }.compact
+      end
+    end
+
+    def editor
+      person = bibliographic_metadata.dig("contributors", "person_name")
+      Array(person).select { |a| a["contributor_role"] == "editor" }.map do |a|
+        { "@type" => "Person",
+          "@id" => a["ORCID"],
+          "givenName" => a["given_name"],
+          "familyName" => a["surname"] }.compact
+      end.presence
+    end
+
+    def date_published
+      pub_date = bibliographic_metadata.fetch("publication_date", nil) ||
+        bibliographic_metadata.fetch("acceptance_date", nil)
+      if pub_date.present?
+        get_date_from_parts(pub_date["year"], pub_date["month"], pub_date["day"])
+      else
+        nil
+      end
+    end
+
+    def date_modified
+      Time.parse(metadata.fetch("timestamp", "")).utc.iso8601
+    end
+
+    def page_start
+      bibliographic_metadata.dig("pages", "first_page")
+    end
+
+    def page_end
+      bibliographic_metadata.dig("pages", "last_page")
+    end
+
+    def is_part_of
+      if journal_metadata.present?
+        { "@type" => "Periodical",
+          "name" => journal_metadata["full_title"],
+          "issn" => parse_attribute(journal_metadata.fetch("issn", nil)) }.compact
+      else
+        nil
+      end
+    end
+
+    def citation
+       citations = bibliographic_metadata.dig("citation_list", "citation")
+       Array(citations).map do |c|
+         { "@type" => "CreativeWork",
+           "@id" => normalize_doi(c["doi"]),
+           "position" => c["key"],
+           "name" => c["article_title"],
+           "datePublished" => c["cYear"] }.compact
+       end.presence
+    end
+
+    def provider
+      { "@type" => "Organization",
+        "name" => "Crossref" }
+    end
+
+    def as_schema_org
+      { "@context" => "http://schema.org",
+        "@type" => type,
+        "@id" => id,
+        "additionalType" => additional_type,
+        "name" => name,
+        "alternateName" => alternate_name,
+        "author" => author,
+        "editor" => editor,
+        "description" => description,
+        "license" => license,
+        "datePublished" => date_published,
+        "dateModified" => date_modified,
+        "pageStart" => page_start,
+        "pageEnd" => page_end,
+        "isPartOf" => is_part_of,
+        "citation" => citation,
+        "provider" => provider
+      }.compact
+    end
+  end
+end