briard 2.4.1 → 2.6.0

data/lib/briard/cli.rb

@@ -1,7 +1,6 @@
-# encoding: UTF-8
 # frozen_string_literal: true
 
-require "thor"
+require 'thor'
 
 require_relative 'doi_utils'
 require_relative 'utils'
@@ -18,18 +17,18 @@ module Briard
     # 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"
+    desc '--version, -v', 'print the version'
     def __print_version
       puts Briard::VERSION
     end
 
-    desc "", "convert metadata"
-    method_option :from, aliases: "-f"
-    method_option :to, aliases: "-t", default: "schema_org"
-    method_option :regenerate, :type => :boolean, :force => false
-    method_option :style, aliases: "-s", default: "apa"
-    method_option :locale, aliases: "-l", default: "en-US"
-    method_option :show_errors, :type => :boolean, :force => false
+    desc '', 'convert metadata'
+    method_option :from, aliases: '-f'
+    method_option :to, aliases: '-t', default: 'schema_org'
+    method_option :regenerate, type: :boolean, force: false
+    method_option :style, aliases: '-s', default: 'apa'
+    method_option :locale, aliases: '-l', default: 'en-US'
+    method_option :show_errors, type: :boolean, force: false
     method_option :depositor
     method_option :email
     method_option :registrant
@@ -44,16 +43,16 @@ module Briard
                               depositor: options[:depositor],
                               email: options[:email],
                               registrant: options[:registrant])
-      to = options[:to] || "schema_org"
+      to = options[:to] || 'schema_org'
 
       if options[:show_errors] && !metadata.valid?
-        $stderr.puts metadata.errors
+        warn metadata.errors
       else
         puts metadata.send(to)
       end
     end
 
-    desc "", "encode"
+    desc '', 'encode'
     def encode(prefix)
       puts encode_doi(prefix)
     end

data/lib/briard/crossref_utils.rb

@@ -6,17 +6,17 @@ module Briard
     # variables CROSSREF_DEPOSITOR_NAME, CROSSREF_DEPOSITOR_EMAIL and CROSSREF_REGISTRANT,
     # e.g. in a .env file
     def crossref_xml
-      @crossref_xml ||= Nokogiri::XML::Builder.new(:encoding => 'UTF-8') do |xml|
+      @crossref_xml ||= Nokogiri::XML::Builder.new(encoding: 'UTF-8') do |xml|
         xml.doi_batch(crossref_root_attributes) do
           xml.head do
             # we use a uuid as batch_id
             xml.doi_batch_id(SecureRandom.uuid)
             xml.timestamp(Time.now.utc.strftime('%Y%m%d%H%M%S'))
             xml.depositor do
-              xml.depositor_name(ENV['CROSSREF_DEPOSITOR_NAME'])
-              xml.email_address(ENV['CROSSREF_DEPOSITOR_EMAIL'])
+              xml.depositor_name(ENV.fetch('CROSSREF_DEPOSITOR_NAME', nil))
+              xml.email_address(ENV.fetch('CROSSREF_DEPOSITOR_EMAIL', nil))
             end
-            xml.registrant(ENV['CROSSREF_REGISTRANT'])
+            xml.registrant(ENV.fetch('CROSSREF_REGISTRANT', nil))
           end
           xml.body do
             insert_crossref_work(xml)
@@ -26,10 +26,10 @@ module Briard
     end
 
     def crossref_errors(xml: nil)
-      filepath = File.expand_path("../../../resources/crossref/crossref5.3.1.xsd", __FILE__)
+      filepath = File.expand_path('../../resources/crossref/crossref5.3.1.xsd', __dir__)
       schema = Nokogiri::XML::Schema(open(filepath))
 
-      schema.validate(Nokogiri::XML(xml, nil, 'UTF-8')).map { |error| error.to_s }.unwrap
+      schema.validate(Nokogiri::XML(xml, nil, 'UTF-8')).map(&:to_s).unwrap
     rescue Nokogiri::XML::SyntaxError => e
       e.message
     end
@@ -37,9 +37,10 @@ module Briard
     def insert_crossref_work(xml)
       return xml if doi.blank?
 
-      if types["resourceTypeGeneral"] == "JournalArticle"
+      case types['resourceTypeGeneral']
+      when 'JournalArticle'
         insert_journal(xml)
-      elsif types["resourceTypeGeneral"] == "Preprint"
+      when 'Preprint'
         insert_posted_content(xml)
       end
     end
@@ -47,15 +48,15 @@ module Briard
     def insert_journal(xml)
       xml.journal do
         if language.present?
-          xml.journal_metadata("language" => language) do
-            xml.full_title(container["title"])
+          xml.journal_metadata('language' => language) do
+            xml.full_title(container['title'])
           end
         else
           xml.journal_metadata do
-            xml.full_title(container["title"])
+            xml.full_title(container['title'])
           end
         end
-        xml.journal_article("publication_type" => "full_text") do
+        xml.journal_article('publication_type' => 'full_text') do
           insert_crossref_titles(xml)
           insert_crossref_creators(xml)
           insert_crossref_publication_date(xml)
@@ -70,7 +71,7 @@ module Briard
     end
 
     def insert_posted_content(xml)
-      posted_content = { "type" => "other", "language" => language }.compact
+      posted_content = { 'type' => 'other', 'language' => language }.compact
 
       xml.posted_content(posted_content) do
         insert_group_title(xml)
@@ -89,29 +90,35 @@ module Briard
     def insert_group_title(xml)
       return xml if subjects.blank?
 
-      xml.group_title(subjects.first["subject"].titleize)
+      xml.group_title(subjects.first['subject'].titleize)
     end
 
     def insert_crossref_creators(xml)
       xml.contributors do
         Array.wrap(creators).each_with_index do |au, index|
-          xml.person_name("contributor_role" => "author", "sequence" => index == 0 ? "first" : "additional") do
-            insert_crossref_person(xml, au, "author")
+          xml.person_name('contributor_role' => 'author',
+                          'sequence' => index.zero? ? 'first' : 'additional') do
+            insert_crossref_person(xml, au, 'author')
           end
         end
       end
     end
 
-    def insert_crossref_person(xml, person, type)
-      person_name = person["familyName"].present? ? [person["familyName"], person["givenName"]].compact.join(", ") : person["name"]
-      xml.given_name(person["givenName"]) if person["givenName"].present?
-      xml.surname(person["familyName"]) if person["familyName"].present?
-      if person.dig("nameIdentifiers", 0, "nameIdentifierScheme") == "ORCID"
-        xml.ORCID(person.dig("nameIdentifiers", 0, "nameIdentifier")) 
+    def insert_crossref_person(xml, person, _type)
+      person_name = if person['familyName'].present?
+                      [person['familyName'], person['givenName']].compact.join(', ')
+                    else
+                      person['name']
+                    end
+      xml.given_name(person['givenName']) if person['givenName'].present?
+      xml.surname(person['familyName']) if person['familyName'].present?
+      if person.dig('nameIdentifiers', 0, 'nameIdentifierScheme') == 'ORCID'
+        xml.ORCID(person.dig('nameIdentifiers', 0, 'nameIdentifier'))
       end
-      Array.wrap(person["affiliation"]).each do |affiliation|
-        attributes = { "affiliationIdentifier" => affiliation["affiliationIdentifier"], "affiliationIdentifierScheme" => affiliation["affiliationIdentifierScheme"], "schemeURI" => affiliation["schemeUri"] }.compact
-        xml.affiliation(affiliation["name"], attributes)
+      Array.wrap(person['affiliation']).each do |affiliation|
+        attributes = { 'affiliationIdentifier' => affiliation['affiliationIdentifier'],
+                       'affiliationIdentifierScheme' => affiliation['affiliationIdentifierScheme'], 'schemeURI' => affiliation['schemeUri'] }.compact
+        xml.affiliation(affiliation['name'], attributes)
       end
     end
 
@@ -119,7 +126,7 @@ module Briard
       xml.titles do
         Array.wrap(titles).each do |title|
           if title.is_a?(Hash)
-            xml.title(title["title"])
+            xml.title(title['title'])
           else
             xml.title(title)
           end
@@ -129,13 +136,13 @@ module Briard
 
     def insert_citation_list(xml)
       # filter out references
-      references = related_identifiers.find_all { |ri| ri["relationType"] == "References" }
+      references = related_identifiers.find_all { |ri| ri['relationType'] == 'References' }
       return xml if references.blank?
 
       xml.citation_list do
         references.each do |ref|
           xml.citation do
-            xml.doi(ref["relatedIdentifier"])
+            xml.doi(ref['relatedIdentifier'])
           end
         end
       end
@@ -157,20 +164,24 @@ module Briard
     # end
 
     def insert_crossref_alternate_identifiers(xml)
-      alternate_identifier = Array.wrap(identifiers).select { |r| r["identifierType"] != "DOI" }.first
+      alternate_identifier = Array.wrap(identifiers).reject do |r|
+        r['identifierType'] == 'DOI'
+      end.first
       return xml if alternate_identifier.blank?
 
-      xml.item_number(alternate_identifier["identifier"], "item_number_type" => alternate_identifier["identifierType"])
+      xml.item_number(alternate_identifier['identifier'],
+                      'item_number_type' => alternate_identifier['identifierType'])
     end
 
     def insert_crossref_access_indicators(xml)
       return xml if rights_list.blank?
 
-      rights_uri = Array.wrap(rights_list).map { |l| l["rightsUri"] }.first
+      rights_uri = Array.wrap(rights_list).map { |l| l['rightsUri'] }.first
 
-      xml.program("xmlns" => "http://www.crossref.org/AccessIndicators.xsd", "name" => "AccessIndicators") do
-        xml.license_ref(rights_uri, "applies_to" => "vor")
-        xml.license_ref(rights_uri, "applies_to" => "tdm")
+      xml.program('xmlns' => 'http://www.crossref.org/AccessIndicators.xsd',
+                  'name' => 'AccessIndicators') do
+        xml.license_ref(rights_uri, 'applies_to' => 'vor')
+        xml.license_ref(rights_uri, 'applies_to' => 'tdm')
       end
     end
 
@@ -206,7 +217,7 @@ module Briard
       xml.subjects do
         subjects.each do |subject|
           if subject.is_a?(Hash)
-            xml.subject(subject["subject"])
+            xml.subject(subject['subject'])
           else
             xml.subject(subject)
           end
@@ -220,7 +231,6 @@ module Briard
     #   xml.version(version_info)
     # end
 
-
     def insert_crossref_language(xml)
       return xml unless language.present?
 
@@ -231,8 +241,8 @@ module Briard
       return xml if date_registered.blank?
 
       date = get_datetime_from_iso8601(date_registered)
-      
-      xml.publication_date("media_type" => "online") do
+
+      xml.publication_date('media_type' => 'online') do
         xml.month(date.month) if date.month.present?
         xml.day(date.day) if date.day.present?
         xml.year(date.year) if date.year.present?
@@ -240,7 +250,7 @@ module Briard
     end
 
     def insert_posted_date(xml)
-      date_posted = get_date(dates, "Issued")
+      date_posted = get_date(dates, 'Issued')
       return xml if date_posted.blank?
 
       date = get_datetime_from_iso8601(date_posted)
@@ -266,9 +276,9 @@ module Briard
       xml.doi_data do
         xml.doi(doi)
         xml.resource(url)
-        xml.collection("property" => "text-mining") do
+        xml.collection('property' => 'text-mining') do
           xml.item do
-            xml.resource(url, "mime_type" => "text/html")
+            xml.resource(url, 'mime_type' => 'text/html')
           end
         end
       end
@@ -283,25 +293,27 @@ module Briard
             r = rights
           else
             r = {}
-            r["rights"] = rights
-            r["rightsUri"] = normalize_id(rights)
+            r['rights'] = rights
+            r['rightsUri'] = normalize_id(rights)
           end
 
           attributes = {
-            "rightsURI" => r["rightsUri"],
-            "rightsIdentifier" => r["rightsIdentifier"],
-            "rightsIdentifierScheme" => r["rightsIdentifierScheme"],
-            "schemeURI" => r["schemeUri"],
-            "xml:lang" => r["lang"]
+            'rightsURI' => r['rightsUri'],
+            'rightsIdentifier' => r['rightsIdentifier'],
+            'rightsIdentifierScheme' => r['rightsIdentifierScheme'],
+            'schemeURI' => r['schemeUri'],
+            'xml:lang' => r['lang']
           }.compact
 
-          xml.rights(r["rights"], attributes)
+          xml.rights(r['rights'], attributes)
         end
       end
     end
 
     def insert_crossref_issn(xml)
-      issn = container.to_h.fetch('identifierType', nil) == "ISSN" ? container.to_h.fetch('identifier', nil) : nil
+      issn = if container.to_h.fetch('identifierType', nil) == 'ISSN'
+               container.to_h.fetch('identifier', nil)
+             end
 
       return xml if issn.blank?
 
@@ -315,22 +327,22 @@ module Briard
         d = descriptions.first
       else
         d = {}
-        d["description"] = descriptions.first
+        d['description'] = descriptions.first
       end
 
-      xml.abstract("xmlns" => "http://www.ncbi.nlm.nih.gov/JATS1") do
-        xml.p(d["description"])
+      xml.abstract('xmlns' => 'http://www.ncbi.nlm.nih.gov/JATS1') do
+        xml.p(d['description'])
       end
     end
 
     def crossref_root_attributes
-      { :'xmlns:xsi' => 'http://www.w3.org/2001/XMLSchema-instance',
-        :'xsi:schemaLocation' => 'http://www.crossref.org/schema/5.3.1 https://www.crossref.org/schemas/crossref5.3.1.xsd',
-        :'xmlns' => 'http://www.crossref.org/schema/5.3.1',
-        :'xmlns:jats' => 'http://www.ncbi.nlm.nih.gov/JATS1',
-        :'xmlns:fr' => 'http://www.crossref.org/fundref.xsd',
-        :'xmlns:mml' => 'http://www.w3.org/1998/Math/MathML',
-        :'version' => '5.3.1' }
+      { 'xmlns:xsi': 'http://www.w3.org/2001/XMLSchema-instance',
+        'xsi:schemaLocation': 'http://www.crossref.org/schema/5.3.1 https://www.crossref.org/schemas/crossref5.3.1.xsd',
+        xmlns: 'http://www.crossref.org/schema/5.3.1',
+        'xmlns:jats': 'http://www.ncbi.nlm.nih.gov/JATS1',
+        'xmlns:fr': 'http://www.crossref.org/fundref.xsd',
+        'xmlns:mml': 'http://www.w3.org/1998/Math/MathML',
+        version: '5.3.1' }
     end
   end
-end 
+end