bolognese 0.7.1 → 0.7.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 588daf5d103c64b25e4c06709dc6815c32f67587
+  metadata.gz: bc292f3921b5634ec479a7e392fd8f9c476b5739
+  data.tar.gz: 33a44a56720c036829596fad78a38674dc1bcdef
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-  data.tar.gz: 2772cbe1d11e52aa3835279161e826552dc3ddda889109d460d8a79996f94202784b689ce65172a9ee0af08c2e65f51d8dbd99a3e01a152f86231e400e65f9f4
+  metadata.gz: 14e2ba1b16d38ffdf5bb839596b7c1b73e62fa2d2a35cca89d3c615801334f26c36dc302f87080a112ea5be6165614a49816a218242c86632422c4b937c7612b
+  data.tar.gz: 5415c8c7283392900c4558d3b732099dc47216774207ce47d369221df3c2bf096abfdb0ca79e4a955b67135288c2d2ee80375b684c43a205bf163bb68b142785

data/Gemfile.lock

@@ -1,10 +1,11 @@
 PATH
   remote: .
   specs:
-    bolognese (0.7.1)
+    bolognese (0.7.2)
       activesupport (~> 4.2, >= 4.2.5)
       bibtex-ruby (~> 4.1)
       builder (~> 3.2, >= 3.2.2)
+      colorize (~> 0.8.1)
       maremma (~> 3.5)
       namae (~> 0.10.2)
       nokogiri (~> 1.6, >= 1.6.8)
@@ -23,8 +24,9 @@ GEM
     bibtex-ruby (4.4.3)
       latex-decode (~> 0.0)
     builder (3.2.3)
-    codeclimate-test-reporter (1.0.5)
+    codeclimate-test-reporter (1.0.6)
       simplecov
+    colorize (0.8.1)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
     diff-lcs (1.3)
@@ -92,7 +94,7 @@ GEM
       simplecov-html (~> 0.10.0)
     simplecov-html (0.10.0)
     thor (0.19.4)
-    thread_safe (0.3.5)
+    thread_safe (0.3.6)
     tzinfo (1.2.2)
       thread_safe (~> 0.1)
     unicode (0.4.4.2)

data/README.md

@@ -105,6 +105,11 @@ Commands:
   bolognese --version, -v   # print the version
   bolognese help [COMMAND]  # Describe available commands or one specific command
 ```
+## Errors
+
+Errors are returned to STDOUT.
+
+All DataCite XML input is validated against the corresponding schema version (kernel 2.1, 2.2, 3, or 4).
 
 ## Examples
 

data/bolognese.gemspec

@@ -21,6 +21,7 @@ Gem::Specification.new do |s|
   s.add_dependency 'activesupport', '~> 4.2', '>= 4.2.5'
   s.add_dependency 'bibtex-ruby', '~> 4.1'
   s.add_dependency 'thor', '~> 0.19'
+  s.add_dependency 'colorize', '~> 0.8.1'
   s.add_dependency 'namae', '~> 0.10.2'
   s.add_dependency 'postrank-uri', '~> 1.0', '>= 1.0.18'
   s.add_development_dependency 'bundler', '~> 1.0'

data/lib/bolognese.rb

@@ -3,6 +3,7 @@ require 'nokogiri'
 require 'maremma'
 require 'postrank-uri'
 require 'bibtex'
+require 'colorize'
 
 require "bolognese/version"
 require "bolognese/metadata"

data/lib/bolognese/bibtex.rb

@@ -30,8 +30,6 @@ module Bolognese
       @raw = string
     end
 
-    alias_method :schema_org, :as_schema_org
-
     def metadata
       @metadata ||= raw.present? ? BibTeX.parse(raw).first : {}
     end
@@ -40,6 +38,10 @@ module Bolognese
       metadata.present?
     end
 
+    def valid?
+      true
+    end
+
     def type
       BIB_TO_SO_TRANSLATIONS[metadata.type.to_s] || "ScholarlyArticle"
     end

data/lib/bolognese/cli.rb

@@ -11,7 +11,7 @@ module Bolognese
     include Bolognese::Utils
 
     def self.exit_on_failure?
-      false
+      true
     end
 
     # from http://stackoverflow.com/questions/22809972/adding-a-version-option-to-a-ruby-thor-cli
@@ -25,7 +25,7 @@ module Bolognese
     desc "", "convert metadata"
     method_option :from, aliases: "-f"
     method_option :to, aliases: "-t", default: "schema_org"
-    method_option :schema_version
+    method_option :regenerate, :type => :boolean, :force => false
     def convert(input)
       id = normalize_id(input)
 
@@ -45,7 +45,7 @@ module Bolognese
 
       to = options[:to] || "schema_org"
 
-      write(id: id, string: string, from: from, to: to, schema_version: options[:schema_version])
+      write(id: id, string: string, from: from, to: to, regenerate: options[:regenerate])
     end
 
     default_task :convert

data/lib/bolognese/codemeta.rb

@@ -12,9 +12,6 @@ module Bolognese
       end
     end
 
-    alias_method :schema_org, :as_schema_org
-    alias_method :bibtex, :as_bibtex
-
     def metadata
       @metadata ||= raw.present? ? Maremma.from_json(raw) : {}
     end
@@ -23,6 +20,10 @@ module Bolognese
       metadata.present?
     end
 
+    def valid?
+      true
+    end
+
     def doi
       doi_from_url(id)
     end

data/lib/bolognese/crossref.rb

@@ -72,10 +72,6 @@ module Bolognese
     end
 
     alias_method :crossref, :raw
-    alias_method :as_crossref, :raw
-    alias_method :schema_org, :as_schema_org
-    alias_method :codemeta, :as_codemeta
-    alias_method :bibtex, :as_bibtex
 
     def metadata
       @metadata ||= raw.present? ? Maremma.from_xml(raw).fetch("doi_records", {}).fetch("doi_record", {}) : {}
@@ -85,6 +81,10 @@ module Bolognese
       metadata.present?
     end
 
+    def valid?
+      true
+    end
+
     def doi
       bibliographic_metadata.dig("doi_data", "doi")
     end

data/lib/bolognese/datacite.rb

@@ -18,7 +18,9 @@ module Bolognese
       "Other" => "CreativeWork"
     }
 
-    def initialize(id: nil, string: nil, schema_version: nil)
+    SCHEMA = File.expand_path("../../../resources/kernel-4.0/metadata.xsd", __FILE__)
+
+    def initialize(id: nil, string: nil, regenerate: false)
       id = normalize_doi(id) if id.present?
 
       if string.present?
@@ -28,25 +30,12 @@ module Bolognese
         @raw = response.body.fetch("data", nil)
       end
 
-      @schema_version = schema_version
-    end
-
-    alias_method :schema_org, :as_schema_org
-    alias_method :codemeta, :as_codemeta
-    alias_method :bibtex, :as_bibtex
-
-    def schema_version
-      @schema_version ||= metadata.fetch("xsi:schemaLocation", "").split(" ").first
+      @should_passthru = !regenerate
     end
 
-    # show DataCite XML in different version if schema_version option is provided
-    # currently only supports 4.0
+    # generate new DataCite XML version 4.0 if regenerate (!should_passthru) option is provided
     def datacite
-      if schema_version != metadata.fetch("xsi:schemaLocation", "").split(" ").first
-        as_datacite
-      else
-        raw
-      end
+      should_passthru ? raw : datacite_xml
     end
 
     def metadata
@@ -57,6 +46,25 @@ module Bolognese
       metadata.present?
     end
 
+    def valid?
+      errors.blank?
+    end
+
+    def errors
+      arr = schema.validate(Nokogiri::XML(raw)).map { |error| error.to_s }
+      array_unwrap(arr)
+    end
+
+    def schema_version
+      metadata.fetch("xmlns", nil)
+    end
+
+    def schema
+      kernel = schema_version.split("/").last
+      filepath = File.expand_path("../../../resources/#{kernel}/metadata.xsd", __FILE__)
+      Nokogiri::XML::Schema(open(filepath))
+    end
+
     def doi
       metadata.fetch("identifier", {}).fetch("__content__", nil)
     end
@@ -90,13 +98,12 @@ module Bolognese
       parse_attributes(metadata.dig("alternateIdentifiers", "alternateIdentifier"))
     end
 
+    def descriptions
+      Array.wrap(metadata.dig("descriptions", "description"))
+    end
+
     def description
-      des = metadata.dig("descriptions", "description", "__content__")
-      if des.is_a?(Hash)
-        des.to_xml
-      elsif des.is_a?(String)
-        des.strip
-      end
+      parse_attributes(descriptions)
     end
 
     def license

data/lib/bolognese/datacite_utils.rb

@@ -38,22 +38,19 @@ module Bolognese
     end
 
     def datacite_xml
-      Nokogiri::XML::Builder.new(:encoding => 'UTF-8') do |xml|
+      @datacite_xml ||= Nokogiri::XML::Builder.new(:encoding => 'UTF-8') do |xml|
         xml.resource(root_attributes) do
           insert_work(xml)
         end
       end.to_xml
     end
 
-    def as_datacite
-      if validation_errors.blank?
-        datacite_xml
-      end
+    def datacite
+      datacite_xml
     end
 
-    def validation_errors
-      @validation_errors ||= schema.validate(Nokogiri::XML(datacite_xml))
-                                   .map { |error| error.to_s }
+    def datacite_errors
+      @datacite_errors ||= schema.validate(Nokogiri::XML(datacite)).map { |error| error.to_s }
     end
 
     def insert_work(xml)
@@ -227,10 +224,20 @@ module Bolognese
     end
 
     def insert_descriptions(xml)
-      return xml unless description.present?
+      return xml unless descriptions.present?
 
       xml.descriptions do
-        xml.description(description, 'descriptionType' => "Abstract")
+        Array.wrap(description).each do |des|
+          insert_description(xml, des)
+        end
+      end
+    end
+
+    def insert_description(xml, des)
+      if des.is_a?(String)
+        xml.description(des.strip, 'descriptionType' => "Abstract")
+      elsif des.is_a?(Hash)
+        xml.description(des["__content__"].strip, 'descriptionType' => des["descriptionType"],)
       end
     end
 

data/lib/bolognese/metadata.rb

@@ -16,14 +16,17 @@ module Bolognese
       :additional_type, :alternate_name, :url, :version, :keywords, :editor,
       :page_start, :page_end, :date_modified, :language, :spatial_coverage,
       :content_size, :funder, :journal, :bibtex_type, :date_created, :has_part,
-      :publisher, :contributor, :schema_version, :same_as, :predecessor_of, :successor_of
-
-    alias_method :datacite, :as_datacite
+      :publisher, :contributor, :same_as, :predecessor_of,
+      :successor_of, :should_passthru, :datacite_errors
 
     def publication_year
       date_published && date_published[0..3]
     end
 
+    def descriptions
+      Array.wrap(description)
+    end
+
     def pagination
       [page_start, page_end].compact.join("-").presence
     end
@@ -32,7 +35,7 @@ module Bolognese
       publisher.to_h.fetch("name", nil)
     end
 
-    def as_schema_org
+    def schema_org
       { "@context" => id.present? ? "http://schema.org" : nil,
         "@type" => type,
         "@id" => id,
@@ -67,7 +70,7 @@ module Bolognese
       }.compact.to_json
     end
 
-    def as_codemeta
+    def codemeta
       { "@context" => id.present? ? "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld" : nil,
         "@type" => type,
         "@id" => id,
@@ -85,7 +88,7 @@ module Bolognese
       }.compact.to_json
     end
 
-    def as_bibtex
+    def bibtex
       bib = {
         bibtex_type: bibtex_type.to_sym,
         bibtex_key: id,
@@ -100,7 +103,6 @@ module Bolognese
         publisher: publisher_string,
         year: publication_year
       }.compact
-
       BibTeX::Entry.new(bib).to_s
     end
   end

data/lib/bolognese/schema_org.rb

@@ -13,10 +13,6 @@ module Bolognese
       end
     end
 
-    alias_method :schema_org, :as_schema_org
-    alias_method :codemeta, :as_codemeta
-    alias_method :bibtex, :as_bibtex
-
     def metadata
       @metadata ||= raw.present? ? Maremma.from_json(raw) : {}
     end
@@ -25,6 +21,10 @@ module Bolognese
       metadata.present?
     end
 
+    def valid?
+      true
+    end
+
     def doi
       doi_from_url(id)
     end

data/lib/bolognese/utils.rb

@@ -28,7 +28,7 @@ module Bolognese
         "bibtex"
       elsif options[:ext] == ".xml" && Maremma.from_xml(string).dig("doi_records", "doi_record", "crossref")
         "crossref"
-      elsif options[:ext] == ".xml" && Maremma.from_xml(string).dig("resource", "xmlns") == "http://datacite.org/schema/kernel-4"
+      elsif options[:ext] == ".xml" && Maremma.from_xml(string).dig("resource", "xmlns").start_with?("http://datacite.org/schema/kernel")
         "datacite"
       elsif options[:filename] == "codemeta.json"
         "codemeta"
@@ -39,13 +39,17 @@ module Bolognese
       if from.present?
         p = case from
             when "crossref" then Crossref.new(id: id, string: string)
-            when "datacite" then Datacite.new(id: id, string: string, schema_version: options[:schema_version])
+            when "datacite" then Datacite.new(id: id, string: string, regenerate: options[:regenerate])
             when "codemeta" then Codemeta.new(id: id, string: string)
             when "bibtex" then Bibtex.new(string: string)
             else SchemaOrg.new(id: id)
             end
 
-        puts p.send(to)
+        if p.valid?
+          puts p.send(to)
+        else
+          $stderr.puts p.errors.colorize(:red)
+        end
       else
         puts "not implemented"
       end

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.7.1"
+  VERSION = "0.7.2"
 end

data/resources/kernel-2.1/include/datacite-contributorType-v1.1.xsd

@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!-- Version 1.0 - Created 2011-01-13 - FZ, TIB, Germany -->
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" targetNamespace="http://datacite.org/schema/kernel-2.1" elementFormDefault="qualified">
+	<xs:simpleType name="contributorType">
+		<xs:annotation>
+			<xs:documentation>The type of contributor of the resource.</xs:documentation>
+		</xs:annotation>
+		<xs:restriction base="xs:string">
+			<xs:enumeration value="ContactPerson"/>
+			<xs:enumeration value="DataCollector"/>
+			<xs:enumeration value="DataManager"/>
+			<xs:enumeration value="Editor"/>
+			<xs:enumeration value="HostingInstitution"/>
+			<xs:enumeration value="ProjectLeader"/>
+			<xs:enumeration value="ProjectMember"/>
+			<xs:enumeration value="RegistrationAgency"/>
+			<xs:enumeration value="RegistrationAuthority"/>
+			<xs:enumeration value="Researcher"/>
+			<xs:enumeration value="WorkPackageLeader"/>
+		</xs:restriction>
+	</xs:simpleType>
+</xs:schema>

data/resources/kernel-2.1/include/datacite-contributorType-v2.xsd

@@ -0,0 +1,3 @@
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns="http://datacite.org/schema/kernel-2.1" targetNamespace="http://datacite.org/schema/kernel-2.1" elementFormDefault="qualified">
+	<xs:include schemaLocation="datacite-contributorType-v1.1.xsd"/>
+</xs:schema>