bolognese 0.3 → 0.4.1

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@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.3)
+    bolognese (0.4.1)
       activesupport (~> 4.2, >= 4.2.5)
       builder (~> 3.2, >= 3.2.2)
       dotenv (~> 2.1, >= 2.1.1)

data/README.md

@@ -1,3 +1,83 @@
 # bolognese
 
-Command-line utility for conversion of DOI metadata.
+Command-line utility for conversion of DOI metadata from and to [schema.org](https://schema.org) in JSON-LD.
+
+## Features
+
+* convert [Crossref XML](https://support.crossref.org/hc/en-us/articles/214936283-UNIXREF-query-output-format) to schema.org/JSON-LD
+* convert [DataCite XML](http://schema.datacite.org/) to schema.org/JSON-LD
+* fetch schema.org/JSON-LD from a URL
+* convert schema.org/JSON-LD to [DataCite XML](http://schema.datacite.org/)
+* convert Crossref XML to [DataCite XML](http://schema.datacite.org/)
+
+Conversion to Crossref XML is not yet supported.
+
+## Installation
+
+The usual way with Bundler: add the following to your `Gemfile` to install the
+current version of the gem:
+
+```ruby
+gem 'bolognese'
+```
+
+Then run `bundle install` to install into your environment.
+
+You can also install the gem system-wide in the usual way:
+
+```bash
+gem install bolognese
+```
+
+## Commands
+
+The bolognese commands understand URLs and DOIs as arguments. The `--as` command
+line flag sets the format, either `crossref`, `datacite`, or `schema_org` (default).
+
+## Examples
+
+Convert Crossref XML to schema.org/JSON-LD:
+```
+bolognese read https://doi.org/10.7554/elife.01567
+```
+
+Read Crossref XML:
+```
+bolognese read https://doi.org/10.7554/elife.01567 --as crossref
+```
+
+Convert Crossref XML to DataCite XML:
+```
+bolognese read https://doi.org/10.7554/elife.01567 --as datacite
+```
+
+Convert DataCite XML to schema.org/JSON-LD:
+```
+bolognese read 10.5061/DRYAD.8515
+```
+
+Read DataCite XML:
+```
+bolognese read 10.5061/DRYAD.8515 --as datacite
+```
+
+## Development
+
+We use rspec for unit testing:
+
+```
+bundle exec rspec
+```
+
+Follow along via [Github Issues](https://github.com/datacite/bolognese/issues).
+
+### Note on Patches/Pull Requests
+
+* Fork the project
+* Write tests for your new feature or a test that reproduces a bug
+* Implement your feature or make a bug fix
+* Do not mess with Rakefile, version or history
+* Commit, push and make a pull request. Bonus points for topical branches.
+
+## License
+**bolognese** is released under the [MIT License](https://github.com/datacite/bolognese/blob/master/LICENSE.md).

data/lib/bolognese.rb

@@ -7,6 +7,7 @@ require "bolognese/version"
 require "bolognese/metadata"
 require "bolognese/crossref"
 require "bolognese/datacite"
+require "bolognese/schema_org"
 require "bolognese/orcid"
 require "bolognese/cli"
 require "bolognese/string"

data/lib/bolognese/author_utils.rb

@@ -48,6 +48,7 @@ module Bolognese
       Array(authors).map { |author| get_one_author(author, options) }
     end
 
+    # pase nameIdentifier from DataCite
     def get_name_identifier(author)
       name_identifier = author.dig("nameIdentifier", "text")
       name_identifier_scheme = author.dig("nameIdentifier", "nameIdentifierScheme") || "ORCID"

data/lib/bolognese/cli.rb

@@ -19,19 +19,19 @@ module Bolognese
     desc "read pid", "read metadata for PID"
     method_option :as, default: "schema_org"
     def read(pid)
-      provider = Metadata.new(pid).provider
+      provider = Metadata.new(id: pid).provider
 
       case
       when provider == "crossref" && options[:as] == "crossref"
-        puts Crossref.new(pid).raw
+        puts Crossref.new(id: pid).raw
       when provider == "crossref" && options[:as] == "datacite"
-        puts Crossref.new(pid).as_datacite
+        puts Crossref.new(id: pid).as_datacite
       when provider == "crossref"
-        puts Crossref.new(pid).as_schema_org
+        puts Crossref.new(id: pid).as_schema_org
       when provider == "datacite" && options[:as] == "datacite"
-        puts Datacite.new(pid).raw
+        puts Datacite.new(id: pid).raw
       when "datacite"
-        puts Datacite.new(pid).as_schema_org
+        puts Datacite.new(id: pid).as_schema_org
       else
         puts "not implemented"
       end

data/lib/bolognese/crossref.rb

@@ -1,12 +1,5 @@
-require_relative 'doi_utils'
-require_relative 'datacite_utils'
-require_relative 'utils'
-
 module Bolognese
   class Crossref < Metadata
-    include Bolognese::DoiUtils
-    include Bolognese::Utils
-    include Bolognese::DataciteUtils
 
     # CrossRef types from https://api.crossref.org/types
     CR_TO_SO_TRANSLATIONS = {
@@ -38,15 +31,17 @@ module Bolognese
       "PostedContent" => nil
     }
 
-    attr_reader = :id, :metadata, :schema_org
+    attr_reader = :id, :raw, :metadata, :schema_org
 
-    def initialize(doi)
-      @id = normalize_doi(doi)
-    end
+    def initialize(id: nil, string: nil)
+      id = normalize_doi(id) if id.present?
 
-    def raw
-      response = Maremma.get(@id, accept: "application/vnd.crossref.unixref+xml", host: true, raw: true)
-      @raw ||= response.body.fetch("data", nil)
+      if string.present?
+        @raw = string
+      elsif id.present?
+        response = Maremma.get(id, accept: "application/vnd.crossref.unixref+xml", host: true, raw: true)
+        @raw = response.body.fetch("data", nil)
+      end
     end
 
     def metadata
@@ -58,7 +53,11 @@ module Bolognese
     end
 
     def doi
-      doi_from_url(id)
+      bibliographic_metadata.dig("doi_data", "doi")
+    end
+
+    def id
+      normalize_doi(doi)
     end
 
     def journal_metadata
@@ -69,7 +68,7 @@ module Bolognese
       if metadata.dig("crossref", "journal", "journal_article").present?
         metadata.dig("crossref", "journal", "journal_article")
       else
-        k = metadata.dig("crossref").keys.last
+        k = metadata.fetch("crossref", {}).keys.last
         metadata.dig("crossref", k).presence || {}
       end
     end
@@ -104,7 +103,12 @@ module Bolognese
     end
 
     def description
-      bibliographic_metadata.fetch("abstract", {}).values.first
+      des = bibliographic_metadata.fetch("abstract", {}).values.first
+      if des.is_a?(Hash)
+        des.to_xml
+      elsif des.is_a?(String)
+        des
+      end
     end
 
     def license
@@ -124,7 +128,7 @@ module Bolognese
       person = bibliographic_metadata.dig("contributors", "person_name")
       Array(person).select { |a| a["contributor_role"] == "author" }.map do |a|
         { "@type" => "Person",
-          "@id" => a["ORCID"],
+          "@id" => parse_attribute(a["ORCID"]),
           "givenName" => a["given_name"],
           "familyName" => a["surname"] }.compact
       end
@@ -134,7 +138,7 @@ module Bolognese
       person = bibliographic_metadata.dig("contributors", "person_name")
       Array(person).select { |a| a["contributor_role"] == "editor" }.map do |a|
         { "@type" => "Person",
-          "@id" => a["ORCID"],
+          "@id" => parse_attribute(a["ORCID"]),
           "givenName" => a["given_name"],
           "familyName" => a["surname"] }.compact
       end.presence

data/lib/bolognese/datacite.rb

@@ -1,12 +1,5 @@
-require_relative 'doi_utils'
-require_relative 'datacite_utils'
-require_relative 'utils'
-
 module Bolognese
   class Datacite < Metadata
-    include Bolognese::DoiUtils
-    include Bolognese::DataciteUtils
-    include Bolognese::Utils
 
     DC_TO_SO_TRANSLATIONS = {
       "Audiovisual" => "VideoObject",
@@ -25,15 +18,17 @@ module Bolognese
       "Other" => "CreativeWork"
     }
 
-    attr_reader = :id, :metadata, :schema_org
+    attr_reader = :id, :raw, :metadata, :schema_org
 
-    def initialize(doi)
-      @id = normalize_doi(doi)
-    end
+    def initialize(id: nil, string: nil)
+      id = normalize_doi(id) if id.present?
 
-    def raw
-      response = Maremma.get(id, accept: "application/vnd.datacite.datacite+xml", raw: true)
-      @raw = response.body.fetch("data", nil)
+      if string.present?
+        @raw = string
+      elsif id.present?
+        response = Maremma.get(id, accept: "application/vnd.datacite.datacite+xml", raw: true)
+        @raw = response.body.fetch("data", nil)
+      end
     end
 
     def metadata
@@ -45,7 +40,11 @@ module Bolognese
     end
 
     def doi
-      doi_from_url(id)
+      metadata.fetch("identifier", {}).fetch("text", nil)
+    end
+
+    def id
+      normalize_doi(doi)
     end
 
     def type
@@ -67,7 +66,12 @@ module Bolognese
     end
 
     def description
-      metadata.dig("descriptions", "description", "text")
+      des = metadata.dig("descriptions", "description", "text")
+      if des.is_a?(Hash)
+        des.to_xml
+      elsif des.is_a?(String)
+        des.strip
+      end
     end
 
     def license
@@ -89,7 +93,7 @@ module Bolognese
     end
 
     def dates
-      Array(metadata.dig("dates", "date"))
+      Array.wrap(metadata.dig("dates", "date"))
     end
 
     def date_created

data/lib/bolognese/datacite_utils.rb

@@ -22,6 +22,7 @@ module Bolognese
 
     LICENSE_NAMES = {
       "http://creativecommons.org/publicdomain/zero/1.0/" => "Public Domain (CC0 1.0)",
+      "http://creativecommons.org/licenses/by/3.0/" => "Creative Commons Attribution 3.0 (CC-BY 3.0)",
       "https://creativecommons.org/licenses/by/4.0/" => "Creative Commons Attribution 4.0 (CC-BY 4.0)",
       "https://creativecommons.org/licenses/by-nc/4.0/" => "Creative Commons Attribution Noncommercial 4.0 (CC-BY-NC 4.0)",
       "https://creativecommons.org/licenses/by-sa/4.0/" => "Creative Commons Attribution Share Alike 4.0 (CC-BY-SA 4.0)",
@@ -88,7 +89,7 @@ module Bolognese
 
       xml.contributors do
         Array(editor).each do |contributor|
-          xml.contributor("contributorType" => contributor[:contributor_type]) do
+          xml.contributor("contributorType" => "Editor") do
             insert_person(xml, contributor, "contributor")
           end
         end
@@ -96,12 +97,12 @@ module Bolognese
     end
 
     def insert_person(xml, person, type)
-      person_name = [person["familyName"], person["givenName"], person["name"]].compact.join(", ")
+      person_name = [person["familyName"], person["givenName"]].compact.join(", ").presence || person["name"]
 
       xml.send(:'creatorName', person_name) if type == "creator"
       xml.send(:'contributorName', person_name) if type == "contributor"
-      xml.send(:'givenName', person[:given_name]) if person["givenName"].present?
-      xml.send(:'familyName', person[:family_name]) if person["familyName"].present?
+      xml.send(:'givenName', person["givenName"]) if person["givenName"].present?
+      xml.send(:'familyName', person["familyName"]) if person["familyName"].present?
       xml.nameIdentifier(person["@id"], 'schemeURI' => 'http://orcid.org/', 'nameIdentifierScheme' => 'ORCID') if person["@id"].present?
     end
 
@@ -165,6 +166,14 @@ module Bolognese
       xml.version(version)
     end
 
+        def is_part_of
+      related_identifiers("IsPartOf").first
+    end
+
+    def related_identifiers
+      Array.wrap(is_part_of) + Array(has_part) + Array(citation)
+    end
+
     def insert_related_identifiers(xml)
       return xml unless related_identifiers.present?
 
@@ -187,7 +196,7 @@ module Bolognese
       return xml unless description.present?
 
       xml.descriptions do
-        xml.description(description)
+        xml.description(description, 'descriptionType' => "Abstract")
       end
     end
 

data/lib/bolognese/doi_utils.rb

@@ -18,9 +18,9 @@ module Bolognese
     def doi_from_url(url)
       if /(http|https):\/\/(dx\.)?doi\.org\/(\w+)/.match(url)
         uri = Addressable::URI.parse(url)
-        uri.path[1..-1].upcase
+        uri.path[1..-1].downcase
       elsif url.is_a?(String) && url.starts_with?("doi:")
-        url[4..-1].upcase
+        url[4..-1].downcase
       end
     end
 
@@ -43,6 +43,5 @@ module Bolognese
         { "errors" => response.body.fetch("errors", nil) || response.body.fetch("data", nil) }
       end
     end
-
   end
 end

data/lib/bolognese/metadata.rb

@@ -1,7 +1,7 @@
 require_relative 'doi_utils'
 require_relative 'author_utils'
 require_relative 'date_utils'
-require_relative 'pid_utils'
+require_relative 'datacite_utils'
 require_relative 'utils'
 
 module Bolognese
@@ -9,12 +9,12 @@ module Bolognese
     include Bolognese::DoiUtils
     include Bolognese::AuthorUtils
     include Bolognese::DateUtils
-    include Bolognese::PidUtils
+    include Bolognese::DataciteUtils
     include Bolognese::Utils
 
-    attr_reader :id, :provider
+    attr_reader :id, :raw, :provider
 
-    def initialize(id)
+    def initialize(id: nil)
       @id = normalize_id(id)
       @provider = find_provider(@id)
     end
@@ -24,7 +24,13 @@ module Bolognese
     end
 
     def find_provider(id)
-      get_doi_ra(id).fetch("id", nil) || "orcid"
+      if /(http|https):\/\/(dx\.)?doi\.org\/(\w+)/.match(id)
+        get_doi_ra(id).fetch("id", nil)
+      elsif /\A(?:http:\/\/orcid\.org\/)?(\d{4}-\d{4}-\d{4}-\d{3}[0-9X]+)\z/.match(id)
+        "orcid"
+      else
+        "schema_org"
+      end
     end
   end
 end

data/lib/bolognese/orcid.rb

@@ -1,6 +1,6 @@
 module Bolognese
   class Orcid < Metadata
-    include Bolognese::PidUtils
+    include Bolognese::Utils
     # def get_orcid_metadata(orcid, options = {})
     #   return {} if orcid.blank?
 

data/lib/bolognese/schema_org.rb

@@ -0,0 +1,157 @@
+module Bolognese
+  class SchemaOrg < Metadata
+
+    DC_TO_SO_TRANSLATIONS = {
+      "Audiovisual" => "VideoObject",
+      "Collection" => "Collection",
+      "Dataset" => "Dataset",
+      "Event" => "Event",
+      "Image" => "ImageObject",
+      "InteractiveResource" => nil,
+      "Model" => nil,
+      "PhysicalObject" => nil,
+      "Service" => "Service",
+      "Software" => "SoftwareSourceCode",
+      "Sound" => "AudioObject",
+      "Text" => "ScholarlyArticle",
+      "Workflow" => nil,
+      "Other" => "CreativeWork"
+    }
+
+    attr_reader = :id, :raw, :metadata, :schema_org
+
+    def initialize(id: nil, string: nil)
+      id = normalize_url(id) if id.present?
+
+      if string.present?
+        @raw = string
+      elsif id.present?
+        response = Maremma.get(id)
+        @raw = response.body.fetch("data", nil)
+      end
+    end
+
+    def metadata
+      @metadata ||= begin
+        if raw.present?
+          doc = Nokogiri::XML(raw)
+          tag = doc.at_xpath('//script[@type="application/ld+json"]')
+          Maremma.from_json(tag)
+        else
+          {}
+        end
+      end
+    end
+
+    def exists?
+      metadata.present?
+    end
+
+    def doi
+      doi_from_url(id)
+    end
+
+    def id
+      normalize_url(metadata.fetch("@id", nil))
+    end
+
+    def url
+      normalize_url(metadata.fetch("url", nil))
+    end
+
+    def type
+      metadata.fetch("@type", nil)
+    end
+
+    def additional_type
+      metadata.fetch("additionalType", nil)
+    end
+
+    def name
+      metadata.fetch("name", nil)
+    end
+
+    def alternate_name
+      metadata.fetch("alternateName", nil)
+    end
+
+    def author
+      Array(metadata.fetch("author", nil)).map { |a| a.except("name") }
+    end
+
+    def description
+      metadata.fetch("description", nil)
+    end
+
+    def license
+      metadata.fetch("license", nil)
+    end
+
+    def version
+      metadata.fetch("version", nil)
+    end
+
+    def keywords
+      metadata.fetch("keywords", nil)
+    end
+
+    def date_created
+      metadata.fetch("dateCreated", nil)
+    end
+
+    def date_published
+      metadata.fetch("datePublished", nil)
+    end
+
+    def date_modified
+      metadata.fetch("dateModified", nil)
+    end
+
+    def related_identifiers(relation_type)
+      normalize_ids(metadata.fetch(relation_type, nil))
+    end
+
+    def is_part_of
+      related_identifiers("isPartOf").first
+    end
+
+    def has_part
+      related_identifiers("hasPart")
+    end
+
+    def citation
+      related_identifiers("citation")
+    end
+
+    def publisher
+      metadata.fetch("publisher", nil)
+    end
+
+    def provider
+      metadata.fetch("provider", nil)
+    end
+
+    def as_schema_org
+      { "@context" => "http://schema.org",
+        "@type" => type,
+        "@id" => id,
+        "url" => url,
+        "name" => name,
+        "alternateName" => alternate_name,
+        "author" => author,
+        "description" => description,
+        "license" => license,
+        "version" => version,
+        "keywords" => keywords,
+        "dateCreated" => date_created,
+        "datePublished" => date_published,
+        "dateModified" => date_modified,
+        "isPartOf" => is_part_of,
+        "hasPart" => has_part,
+        "citation" => citation,
+        "publisher" => publisher,
+        "provider" => provider
+      }.compact
+    end
+  end
+end