bolognese 0.15.9 → 1.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: a1481cd48a439607449fea97c9034d7167cba73611c612dc9cd27c6e4b3c5e1d
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data/Gemfile.lock

@@ -1,13 +1,14 @@
 PATH
   remote: .
   specs:
-    bolognese (0.15.8)
+    bolognese (1.0)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)
       builder (~> 3.2, >= 3.2.2)
       citeproc-ruby (~> 1.1, >= 1.1.10)
       colorize (~> 0.8.1)
+      concurrent-ruby (~> 1.0.5)
       csl-styles (~> 1.0, >= 1.0.1.8)
       edtf (~> 3.0, >= 3.0.4)
       gender_detector (~> 0.1.2)
@@ -46,7 +47,7 @@ GEM
     codeclimate-test-reporter (1.0.9)
       simplecov (<= 0.13)
     colorize (0.8.1)
-    concurrent-ruby (1.1.3)
+    concurrent-ruby (1.0.5)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
     crass (1.0.4)
@@ -116,11 +117,11 @@ GEM
       nokogiri (>= 1.6.1, < 1.9)
       public_suffix (>= 2.0.0, < 2.1)
     public_suffix (2.0.5)
-    rack (2.0.6)
+    rack (2.0.5)
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
     rake (12.3.1)
-    rdf (3.0.6)
+    rdf (3.0.5)
       hamster (~> 3.0)
       link_header (~> 0.0, >= 0.0.8)
     rdf-aggregate-repo (2.2.1)
@@ -166,7 +167,7 @@ GEM
     sxp (1.0.1)
       rdf (>= 2.2, < 4.0)
     temple (0.8.0)
-    thor (0.20.3)
+    thor (0.20.0)
     thread_safe (0.3.6)
     tilt (2.0.8)
     trollop (2.9.9)
@@ -195,4 +196,4 @@ DEPENDENCIES
   webmock (~> 3.0, >= 3.0.1)
 
 BUNDLED WITH
-   1.16.2
+   1.16.1

data/bolognese.gemspec

@@ -37,6 +37,7 @@ Gem::Specification.new do |s|
   s.add_dependency 'rdf-rdfxml', '~> 2.0'
   s.add_dependency 'benchmark_methods', '~> 0.7'
   s.add_dependency 'gender_detector', '~> 0.1.2'
+  s.add_dependency 'concurrent-ruby', '~> 1.0.5'
   s.add_development_dependency 'bundler', '~> 1.0'
   s.add_development_dependency 'rspec', '~> 3.4'
   s.add_development_dependency 'rspec-xsd', '~> 0.1.0'

data/lib/bolognese/datacite_utils.rb

@@ -45,9 +45,9 @@ module Bolognese
 
     def insert_creators(xml)
       xml.creators do
-        Array.wrap(author).each do |creator|
+        Array.wrap(creator).each do |au|
           xml.creator do
-            insert_person(xml, creator, "creator")
+            insert_person(xml, au, "creator")
           end
         end
       end
@@ -85,7 +85,7 @@ module Bolognese
     end
 
     def insert_publisher(xml)
-      xml.publisher(publisher || container_title)
+      xml.publisher(publisher || periodical && periodical["title"])
     end
 
     def insert_publication_year(xml)
@@ -105,18 +105,17 @@ module Bolognese
     end
 
     def insert_alternate_identifiers(xml)
-      return xml unless alternate_identifier.present?
+      return xml unless alternate_identifiers.present?
 
       xml.alternateIdentifiers do
-        Array.wrap(alternate_identifier).each do |alt|
-          xml.alternateIdentifier(alt["name"], 'alternateIdentifierType' => alt["type"])
+        Array.wrap(alternate_identifiers).each do |alternate_identifier|
+          xml.alternateIdentifier(alternate_identifier["name"], 'alternateIdentifierType' => alternate_identifier["type"])
         end
       end
     end
 
     def insert_dates(xml)
       xml.dates do
-        insert_date(xml, date_created, 'Created') if date_created.present?
         insert_date(xml, date_published, 'Issued') if date_published.present?
         insert_date(xml, date_modified, 'Updated') if date_modified.present?
       end
@@ -127,10 +126,10 @@ module Bolognese
     end
 
     def insert_funding_references(xml)
-      return xml unless Array.wrap(funding).present?
+      return xml unless Array.wrap(funding_references).present?
 
       xml.fundingReferences do
-        Array.wrap(funding).each do |funding_reference|
+        Array.wrap(funding_references).each do |funding_reference|
           xml.fundingReference do
             insert_funding_reference(xml, funding_reference)
           end
@@ -139,8 +138,8 @@ module Bolognese
     end
 
     def insert_funding_reference(xml, funding_reference)
-      xml.funderName(funding_reference["name"]) if funding_reference["name"].present?
-      xml.funderIdentifier(funding_reference["id"], "funderIdentifierType" => "Crossref Funder ID") if funding_reference["id"].present?
+      xml.funderName(funding_reference["funder_name"]) if funding_reference["funder_name"].present?
+      xml.funderIdentifier(funding_reference["funder_identifier"], "funderIdentifierType" => "Crossref Funder ID") if funding_reference["funder_identifier"].present?
     end
 
     def insert_subjects(xml)
@@ -148,20 +147,7 @@ module Bolognese
 
       xml.subjects do
         keywords.each do |subject|
-          if subject.is_a?(String) then
-            # If we've been read from somewhere that it was just a string output that
-            xml.subject(subject)
-          else
-            # Otherwise we'll assume a hash and therefore find/add attributes as appropriate
-            subject_node = xml.subject(subject['text'])
-            if subject["subject_scheme"].present? then
-              subject_node['subjectScheme'] = subject["subject_scheme"]
-            end
-
-            if subject["scheme_uri"].present? then
-              subject_node['schemeURI'] = subject["scheme_uri"]
-            end
-          end
+          xml.subject(subject)
         end
       end
     end
@@ -172,43 +158,25 @@ module Bolognese
       xml.version(b_version)
     end
 
-    def rel_identifier
-      Array.wrap(related_identifier).map do |r|
-        related_identifier_type = r["issn"].present? ? "ISSN" : validate_url(r["id"])
-        if related_identifier_type == "ISSN"
-          content = r["issn"]
-        elsif related_identifier_type == "DOI"
-          content = doi_from_url(r["id"])
-        else
-          content = r["id"]
-        end
-
-        { "__content__" => content,
-          "related_identifier_type" => related_identifier_type,
-          "relation_type" => r["relationType"],
-          "resource_type_general" => r["resourceTypeGeneral"] }.compact
-      end
-    end
-
     def insert_related_identifiers(xml)
-      return xml unless rel_identifier.present?
+      return xml unless related_identifiers.present?
 
       xml.relatedIdentifiers do
-        rel_identifier.each do |related_identifier|
+        related_identifiers.each do |related_identifier|
           attributes = {
             'relatedIdentifierType' => related_identifier["related_identifier_type"],
             'relationType' => related_identifier["relation_type"],
             'resourceTypeGeneral' => related_identifier["resource_type_general"] }.compact
-          xml.relatedIdentifier(related_identifier["__content__"], attributes)
+          xml.relatedIdentifier(related_identifier["id"], attributes)
         end
       end
     end
 
     def insert_rights_list(xml)
-      return xml unless license.present?
+      return xml unless rights.present?
 
       xml.rightsList do
-        Array.wrap(license).each do |lic|
+        Array.wrap(rights).each do |lic|
           if lic.is_a?(Hash)
             l = lic
           else
@@ -223,11 +191,11 @@ module Bolognese
     end
 
     def insert_descriptions(xml)
-      return xml unless description.present? || container_title.present?
+      return xml unless description.present? || periodical && periodical["title"].present?
 
       xml.descriptions do
-        if container_title.present?
-          xml.description(container_title, 'descriptionType' => "SeriesInformation")
+        if periodical && periodical["title"].present?
+          xml.description(periodical["title"], 'descriptionType' => "SeriesInformation")
         end
 
         Array.wrap(description).each do |des|

data/lib/bolognese/doi_utils.rb

@@ -46,7 +46,7 @@ module Bolognese
       prefix = validate_prefix(doi)
       return nil if prefix.blank?
 
-      url = "https://api.datacite.org/prefixes/#{prefix}"
+      url = "https://app.datacite.org/prefixes/#{prefix}"
       result = Maremma.get(url)
 
       result.body.fetch("data", {}).fetch('attributes', {}).fetch('registration-agency', nil)

data/lib/bolognese/metadata_utils.rb

@@ -61,22 +61,14 @@ module Bolognese
     include Bolognese::Writers::SchemaOrgWriter
     include Bolognese::Writers::TurtleWriter
 
-    attr_accessor :string, :from, :sandbox, :meta, :regenerate, :issue, :contributor,
-                  :spatial_coverage
-
-    attr_writer :identifier, :author, :title, :publisher, :license,
-                :date_accepted, :date_available, :date_copyrighted, :date_collected, :date_published,
-                :date_submitted, :date_valid, :date_created, :date_modified, :date_updated, 
-                :journal, :volume, :first_page, :last_page, :b_url, :b_version, :resource_type_general,
-                :keywords, :editor, :description, :alternate_identifier, :language, :content_size,
-                :content_format, :schema_version, :has_part, :same_as, :resource_type_general,
-                :is_previous_version_of, :is_new_version_of, :is_cited_by, :cites,
-                :is_supplement_to, :is_supplemented_by, :is_continued_by, :continues,
-                :has_metadata, :is_metadata_for, :is_referenced_by, :references,
-                :is_documented_by, :documents, :is_compiled_by, :compiles,
-                :is_variant_form_of, :is_original_form_of, :is_reviewed_by, :reviews,
-                :is_derived_from, :is_source_of, :format, :funding, :style, :locale, :state,
-                :type, :additional_type, :citeproc_type, :bibtex_type, :ris_type, :content_url, :meta
+    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
 
@@ -123,8 +115,8 @@ module Bolognese
       @identifier ||= meta.fetch("id", nil)
     end
 
-    def alternate_identifier
-      @alternate_identifier ||= meta.fetch("alternate_identifier", nil)
+    def alternate_identifiers
+      @alternate_identifiers ||= meta.fetch("alternate_identifiers", nil)
     end
 
     def content_url
@@ -139,8 +131,8 @@ module Bolognese
       @title ||= meta.fetch("title", nil)
     end
 
-    def author
-      @author ||= meta.fetch("author", nil)
+    def creator
+      @creator ||= meta.fetch("creator", nil)
     end
 
     def editor
@@ -155,32 +147,8 @@ module Bolognese
       @service_provider ||= meta.fetch("service_provider", nil)
     end
 
-    def date_created
-      @date_created ||= meta.fetch("date_created", nil)
-    end
-
-    def date_accepted
-      @date_accepted ||= meta.fetch("date_accepted", nil)
-    end
-
-    def date_available
-      @date_available ||= meta.fetch("date_available", nil)
-    end
-
-    def date_copyrighted
-      @date_copyrighted ||= meta.fetch("date_copyrighted", nil)
-    end
-
-    def date_collected
-      @date_collected ||= meta.fetch("date_collected", nil)
-    end
-
-    def date_submitted
-      @date_submitted ||= meta.fetch("date_submitted", nil)
-    end
-
-    def date_valid
-      @date_valid ||= meta.fetch("date_valid", nil)
+    def dates
+      @dates ||= meta.fetch("dates", nil)
     end
 
     def date_published
@@ -191,14 +159,14 @@ module Bolognese
       @date_modified ||= meta.fetch("date_modified", nil)
     end
 
-    def date_registered
-      @date_registered ||= meta.fetch("date_registered", nil)
-    end
-
     def date_updated
       @date_updated ||= meta.fetch("date_updated", nil)
     end
 
+    def geo_location
+      @geo_location ||= meta.fetch("geo_location", nil)
+    end
+
     def volume
       @volume ||= meta.fetch("volume", nil)
     end
@@ -215,8 +183,8 @@ module Bolognese
       @description ||= meta.fetch("description", nil)
     end
 
-    def license
-      @license ||= meta.fetch("license", nil)
+    def rights
+      @rights ||= meta.fetch("rights", nil)
     end
 
     def keywords
@@ -227,82 +195,24 @@ module Bolognese
       @language ||= meta.fetch("language", nil)
     end
 
-    def content_size
-      @content_size ||= meta.fetch("content_size", nil)
+    def size
+      @size ||= meta.fetch("size", nil)
     end
 
-    def content_format
-      @content_format ||= meta.fetch("content_format", nil)
+    def b_format
+      @b_format ||= meta.fetch("b_format", nil)
     end
 
     def schema_version
       @schema_version ||= meta.fetch("schema_version", nil)
     end
 
-    def funding
-      @funding ||= meta.fetch("funding", nil)
-    end
-
-    def is_identical_to
-      meta.fetch("is_identical_to", nil)
-    end
-
-    def is_part_of
-      meta.fetch("is_part_of", nil)
-    end
-
-    def has_part
-      meta.fetch("has_part", nil)
-    end
-
-    def is_previous_version_of
-      meta.fetch("is_previous_of", nil)
-    end
-
-    def is_new_version_of
-      meta.fetch("is_new_version_of", nil)
-    end
-
-    def is_variant_form_of
-      meta.fetch("is_variant_form_of", nil)
-    end
-
-    def is_original_form_of
-      meta.fetch("is_original_form_of", nil)
-    end
-
-    def references
-      meta.fetch("references", nil)
-    end
-
-    def is_referenced_by
-      meta.fetch("is_referenced_by", nil)
-    end
-
-    def is_supplement_to
-      meta.fetch("is_supplement_to", nil)
-    end
-
-    def is_supplemented_by
-      meta.fetch("is_supplemented_by", nil)
-    end
-
-    def reviews
-      meta.fetch("reviews", nil)
-    end
-
-    def is_reviewed_by
-      meta.fetch("is_reviewed_by", nil)
-    end
-
-    def related_identifier_hsh(relation_type)
-      Array.wrap(send(relation_type)).select { |r| r["id"] || r["issn"] }
-        .map { |r| r.merge("relationType" => relation_type.camelize) }
+    def funding_references
+      @funding_references ||= meta.fetch("funding_references", nil)
     end
 
-    def related_identifier
-      relation_types = %w(is_part_of has_part references is_referenced_by is_supplement_to is_supplemented_by)
-      relation_types.reduce([]) { |sum, r| sum += related_identifier_hsh(r) }
+    def related_identifiers
+      @related_identifiers ||= meta.fetch("related_identifiers", nil)
     end
 
     def b_url
@@ -322,8 +232,8 @@ module Bolognese
       date_published.present? ? date_published[0..3].to_i.presence : nil
     end
 
-    def container_title
-      meta.fetch("container_title", nil) || Array.wrap(is_part_of).first.to_h.fetch("title", nil)
+    def periodical
+      @periodical ||= meta.fetch("periodical", nil)
     end
 
     def descriptions
@@ -331,8 +241,16 @@ module Bolognese
     end
 
     def reverse
-      { "citation" => Array.wrap(is_referenced_by).map { |r| { "@id" => r["id"] }}.unwrap,
-        "isBasedOn" => Array.wrap(is_supplement_to).map { |r| { "@id" => r["id"] }}.unwrap }.compact
+      { "citation" => Array.wrap(related_identifiers).select { |ri| ri["relation_type"] == "IsReferencedBy" }.map do |r| 
+        { "@id" => normalize_doi(r["id"]),
+          "@type" => r["resource_type_general"] || "CreativeWork",
+          "identifier" => r["related_identifier_type"] == "DOI" ? nil : to_identifier(r) }.compact
+        end.unwrap,
+        "isBasedOn" => Array.wrap(related_identifiers).select { |ri| ri["relation_type"] == "IsSupplementTo" }.map do |r| 
+          { "@id" => normalize_doi(r["id"]),
+            "@type" => r["resource_type_general"] || "CreativeWork",
+            "identifier" => r["related_identifier_type"] == "DOI" ? nil : to_identifier(r) }.compact
+        end.unwrap }.compact
     end
 
     def graph
@@ -345,12 +263,12 @@ module Bolognese
         "id" => identifier,
         "categories" => Array.wrap(keywords).map { |k| parse_attributes(k, content: "text", first: true) }.presence,
         "language" => language,
-        "author" => to_citeproc(author),
+        "author" => to_citeproc(creator),
         "editor" => to_citeproc(editor),
         "issued" => date_published ? get_date_parts(date_published) : nil,
-        "submitted" => date_submitted ? get_date_parts(date_submitted) : nil,
+        "submitted" => Array.wrap(dates).find { |d| d["type"] == "Submitted" }.to_h.fetch("__content__", nil),
         "abstract" => parse_attributes(description, content: "text", first: true),
-        "container-title" => container_title,
+        "container-title" => periodical && periodical["title"],
         "DOI" => doi,
         "issue" => issue,
         "page" => [first_page, last_page].compact.join("-").presence,