bolognese 0.11.7 → 0.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: ab8d985c2807f050a4d6e3b65c8da6aee333552e67cdf1f5ea1256bd8ae87635
-  data.tar.gz: 9acaf0de81a4c2dc307f7bd8314b7bb2cf5117b7ab3a1750aea10838ecbc8453
+  metadata.gz: b569e2bb9f0bf75501740c1f43c0c916c7a85f55a0ec7efa27c9c04b685ed3a5
+  data.tar.gz: 95d0e9485923922ac0a078c071bd644c1628b05d8a01888c2e81989c7be534ff
 SHA512:
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-  data.tar.gz: 07b2aa98887c6d9a3e648e1d0d1709d0906c6e67bffc69594342be2772fbad1b2356a7a08ae8daf63a6ef090718b2ac4990fe5656a9eece06e9a2f5da67d9350
+  metadata.gz: e72f93fde195b2659c28c529efc2d856c9df955ff0c56b8aa2a4f91bf0a3943af178a3d133f29d042aab3711764a3eb287e7702a9c6c970fd740d6bdd3bad810
+  data.tar.gz: 4988a36ff5526f7402a13aee011f48ede46b5e4087917a0410190e2f8f35ca6ce5a28c74ea92dea7734d89212d7caae588f869445d55112338920f3b09e8be5b

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.11.7)
+    bolognese (0.12)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)
@@ -24,7 +24,7 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (5.2.0)
+    activesupport (5.2.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
@@ -63,7 +63,7 @@ GEM
       concurrent-ruby (~> 1.0)
     hashdiff (0.3.7)
     htmlentities (4.3.4)
-    i18n (1.0.1)
+    i18n (1.1.0)
       concurrent-ruby (~> 1.0)
     iso8601 (0.9.1)
     json (2.1.0)
@@ -78,7 +78,7 @@ GEM
     loofah (2.2.2)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
-    maremma (4.1)
+    maremma (4.1.1)
       activesupport (>= 4.2.5, < 6)
       addressable (>= 2.3.6)
       builder (~> 3.2, >= 3.2.2)
@@ -127,19 +127,19 @@ GEM
       rdf (>= 2.2, < 4.0)
     rdf-xsd (3.0.0)
       rdf (~> 3.0)
-    rspec (3.7.0)
-      rspec-core (~> 3.7.0)
-      rspec-expectations (~> 3.7.0)
-      rspec-mocks (~> 3.7.0)
-    rspec-core (3.7.1)
-      rspec-support (~> 3.7.0)
-    rspec-expectations (3.7.0)
+    rspec (3.8.0)
+      rspec-core (~> 3.8.0)
+      rspec-expectations (~> 3.8.0)
+      rspec-mocks (~> 3.8.0)
+    rspec-core (3.8.0)
+      rspec-support (~> 3.8.0)
+    rspec-expectations (3.8.1)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.7.0)
-    rspec-mocks (3.7.0)
+      rspec-support (~> 3.8.0)
+    rspec-mocks (3.8.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.7.0)
-    rspec-support (3.7.1)
+      rspec-support (~> 3.8.0)
+    rspec-support (3.8.0)
     rspec-xsd (0.1.0)
       nokogiri (~> 1.6)
       rspec (~> 3)

data/lib/bolognese/datacite_utils.rb

@@ -105,10 +105,10 @@ module Bolognese
     end
 
     def insert_alternate_identifiers(xml)
-      return xml unless alternate_name.present?
+      return xml unless alternate_identifier.present?
 
       xml.alternateIdentifiers do
-        Array.wrap(alternate_name).each do |alt|
+        Array.wrap(alternate_identifier).each do |alt|
           xml.alternateIdentifier(alt["name"], 'alternateIdentifierType' => alt["type"])
         end
       end

data/lib/bolognese/metadata.rb

@@ -32,7 +32,8 @@ module Bolognese
                 "date_registered" => options[:date_registered],
                 "date_updated" => options[:date_updated],
                 "provider_id" => options[:provider_id],
-                "client_id" => options[:client_id] }
+                "client_id" => options[:client_id],
+                "content_url" => options[:content_url] }
         string = input
         @from = from || find_from_format(string: string)
       end
@@ -55,6 +56,7 @@ module Bolognese
       @date_updated = hsh.to_h["date_updated"].presence
       @provider_id = hsh.to_h["provider_id"].presence
       @client_id = hsh.to_h["client_id"].presence
+      @content_url = hsh.to_h["content_url"].presence
 
       # generate name for method to call dynamically
       @meta = @from.present? ? send("read_" + @from, string: string, sandbox: options[:sandbox]) : {}

data/lib/bolognese/metadata_utils.rb

@@ -68,7 +68,7 @@ module Bolognese
                 :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_name, :language, :content_size,
+                :keywords, :editor, :description, :alternate_identifier, :language, :content_size,
                 :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,
@@ -76,7 +76,7 @@ module Bolognese
                 :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, :meta
+                :type, :additional_type, :citeproc_type, :bibtex_type, :ris_type, :content_url, :meta
 
     attr_reader :doc, :service_provider, :page_start, :page_end, :related_identifier, :reverse, :name_detector
 
@@ -123,6 +123,14 @@ module Bolognese
       @identifier ||= meta.fetch("id", nil)
     end
 
+    def alternate_identifier
+      @alternate_identifier ||= meta.fetch("alternate_identifier", nil)
+    end
+
+    def content_url
+      @content_url ||= meta.fetch("content_url", nil)
+    end
+
     def state
       @state ||= meta.fetch("state", nil)
     end
@@ -131,10 +139,6 @@ module Bolognese
       @title ||= meta.fetch("title", nil)
     end
 
-    def alternate_name
-      @alternate_name ||= meta.fetch("alternate_name", nil)
-    end
-
     def author
       @author ||= meta.fetch("author", nil)
     end

data/lib/bolognese/readers/codemeta_reader.rb

@@ -39,7 +39,6 @@ module Bolognese
           "doi" => validate_doi(id),
           "b_url" => normalize_id(meta.fetch("codeRepository", nil)),
           "title" => meta.fetch("title", nil),
-          "alternate_name" => meta.fetch("alternateName", nil),
           "author" => author,
           "editor" => editor,
           "publisher" => publisher,

data/lib/bolognese/readers/crossref_reader.rb

@@ -91,7 +91,7 @@ module Bolognese
           "doi" => doi,
           "b_url" => bibliographic_metadata.dig("doi_data", "resource"),
           "title" => parse_attributes(bibliographic_metadata.dig("titles", "title")),
-          "alternate_name" => crossref_alternate_name(bibliographic_metadata),
+          "alternate_identifier" => crossref_alternate_identifier(bibliographic_metadata),
           "author" => crossref_people(bibliographic_metadata, "author"),
           "editor" => crossref_people(bibliographic_metadata, "editor"),
           "funding" => crossref_funding_reference(program_metadata),
@@ -116,7 +116,7 @@ module Bolognese
         }
       end
 
-      def crossref_alternate_name(bibliographic_metadata)
+      def crossref_alternate_identifier(bibliographic_metadata)
         if bibliographic_metadata.fetch("publisher_item", nil).present?
           parse_attributes(bibliographic_metadata.dig("publisher_item", "item_number"))
         else

data/lib/bolognese/readers/datacite_json_reader.rb

@@ -23,7 +23,7 @@ module Bolognese
           "doi" => validate_doi(meta.fetch("doi", nil)),
           "b_url" => normalize_id(meta.fetch("url", nil)),
           "title" => meta.fetch("title", nil),
-          "alternate_name" => meta.fetch("alternate-identifier", nil),
+          "alternate_identifier" => meta.fetch("alternate-identifier", nil),
           "author" => meta.fetch("creator", nil),
           "editor" => meta.fetch("contributor", nil),
           "publisher" => meta.fetch("publisher", nil),

data/lib/bolognese/readers/datacite_reader.rb

@@ -35,13 +35,18 @@ module Bolognese
           string = doc.to_xml(:indent => 2)
         end
 
+        content_url = Array.wrap(attributes.fetch("media", nil)).map do |media|
+          media.split(":", 2).last
+        end.compact
+
         { "string" => string,
           "b_url" => attributes.fetch("url", nil),
           "state" => attributes.fetch("state", nil),
           "date_registered" => attributes.fetch("minted", nil),
           "date_updated" => attributes.fetch("updated", nil),
           "provider_id" => attributes.fetch("allocator_symbol", nil),
-          "client_id" => attributes.fetch("datacentre_symbol", nil) }
+          "client_id" => attributes.fetch("datacentre_symbol", nil),
+          "content_url" => content_url }
       end
 
       def read_datacite(string: nil, **options)
@@ -80,8 +85,8 @@ module Bolognese
 
         container_title = Array.wrap(meta.dig("descriptions", "description")).find { |r| r["descriptionType"] == "SeriesInformation" }.to_h.fetch("__content__", nil)
 
-        alternate_name = Array.wrap(meta.dig("alternateIdentifiers", "alternateIdentifier")).map do |r|
-          { "type" => r["alternateIdentifierType"], "name" => r["__content__"] }.compact
+        alternate_identifier = Array.wrap(meta.dig("alternateIdentifiers", "alternateIdentifier")).map do |r|
+          { "type" => r["alternateIdentifierType"], "name" => r["__content__"] }
         end.unwrap
         description = Array.wrap(meta.dig("descriptions", "description")).select { |r| r["descriptionType"] != "SeriesInformation" }.map do |r|
           { "type" => r["descriptionType"], "text" => sanitize(r["__content__"]) }.compact
@@ -113,9 +118,9 @@ module Bolognese
           "ris_type" => Bolognese::Utils::CR_TO_RIS_TRANSLATIONS[additional_type.to_s.underscore.camelcase] || Bolognese::Utils::DC_TO_RIS_TRANSLATIONS[resource_type_general.to_s.dasherize] || "GEN",
           "resource_type_general" => resource_type_general,
           "doi" => doi,
+          "alternate_identifier" => alternate_identifier,
           "url" => options.fetch(:url, nil),
           "title" => title,
-          "alternate_name" => alternate_name,
           "author" => get_authors(Array.wrap(meta.dig("creators", "creator"))),
           "editor" => get_authors(Array.wrap(meta.dig("contributors", "contributor")).select { |r| r["contributorType"] == "Editor" }),
           "container_title" => container_title,
@@ -132,7 +137,7 @@ module Bolognese
           "date_created" => datacite_date(dates, "Created"),
           "date_accepted" => datacite_date(dates, "Accepted"),
           "date_available" => datacite_date(dates, "Available"),
-          "date_copyrighted" => datacite_date(dates, "Copyrightes"),
+          "date_copyrighted" => datacite_date(dates, "Copyrights"),
           "date_collected" => datacite_date(dates, "Collected"),
           "date_submitted" => datacite_date(dates, "Submitted"),
           "date_valid" => datacite_date(dates, "Valid"),

data/lib/bolognese/readers/ris_reader.rb

@@ -61,7 +61,6 @@ module Bolognese
           "doi" => doi,
           "b_url" => meta.fetch("UR", nil),
           "title" => meta.fetch("T1", nil),
-          "alternate_name" => meta.fetch("AN", nil),
           "author" => get_authors(author),
           "publisher" => meta.fetch("PB", nil),
           "is_part_of" => is_part_of,

data/lib/bolognese/readers/schema_org_reader.rb

@@ -67,10 +67,9 @@ module Bolognese
           "ris_type" => Bolognese::Utils::SO_TO_RIS_TRANSLATIONS[resource_type_general.to_s.dasherize] || "GEN",
           "resource_type_general" => resource_type_general,
           "doi" => validate_doi(id),
-          "identifier" => id,
+          "identifier" => meta.fetch("identifier", nil),
           "b_url" => normalize_id(meta.fetch("url", nil)),
           "title" => meta.fetch("name", nil),
-          "alternate_name" => meta.fetch("alternateName", nil),
           "author" => author,
           "editor" => editor,
           "publisher" => publisher,

data/lib/bolognese/utils.rb

@@ -523,15 +523,34 @@ module Bolognese
     end
 
     def to_schema_org_container(element, options={})
+      return nil unless options[:container_title].present?
+
       mapping = { "type" => "@type", "id" => "@id", "title" => "name" }
 
       element ||= {}
       element["type"] ||= (type == "Dataset") ? "DataCatalog" : "Periodical"
-      element["title"] = options[:container_title] if options[:container_title].present?
+      element["title"] = options[:container_title]
 
       map_hash_keys(element: element, mapping: mapping)
     end
 
+    def to_schema_org_identifier(element, options={})
+      if options[:alternate_identifier].present?
+        [identifier] + Array.wrap(options[:alternate_identifier]).map do |ai|
+                         if ai["type"].to_s.downcase == "url"
+                           ai["name"]
+                         else
+                           { 
+                             "@type" => "PropertyValue",
+                             "propertyID" => ai["type"],
+                             "value" => ai["name"] }
+                         end
+                       end
+      else
+        identifier
+      end
+    end
+
     def from_schema_org(element)
       mapping = { "@type" => "type", "@id" => "id" }
 

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.11.7"
+  VERSION = "0.12"
 end

data/lib/bolognese/writers/crosscite_writer.rb

@@ -33,7 +33,7 @@ module Bolognese
           "date_updated" => date_updated,
           "date_valid" => date_valid,
           "language" => language,
-          "alternate_name" => alternate_name,
+          "alternate_identifier" => alternate_identifier,
           "content_size" => content_size,
           "version" => b_version,
           "license" => license,

data/lib/bolognese/writers/datacite_json_writer.rb

@@ -29,7 +29,7 @@ module Bolognese
           "date_valid" => date_valid,
           "publication_year" => publication_year,
           "language" => language,
-          "alternate_identifier" => alternate_name,
+          "alternate_identifier" => alternate_identifier,
           "references" => references,
           "is_referenced_by" => is_referenced_by,
           "is_part_of" => is_part_of,

data/lib/bolognese/writers/ris_writer.rb

@@ -15,7 +15,6 @@ module Bolognese
           "KW" => Array.wrap(keywords).map { |k| parse_attributes(k, content: "text", first: true) }.presence,
           "PY" => publication_year,
           "PB" => publisher,
-          "AN" => parse_attributes(alternate_name, content: "name").presence,
           "LA" => language,
           "VL" => volume,
           "IS" => issue,

data/lib/bolognese/writers/schema_org_writer.rb

@@ -7,11 +7,10 @@ module Bolognese
         { "@context" => identifier.present? ? "http://schema.org" : nil,
           "@type" => type,
           "@id" => identifier,
-          "identifier" => identifier,
+          "identifier" => to_schema_org_identifier(identifier, alternate_identifier: alternate_identifier),
           "url" => b_url,
           "additionalType" => additional_type,
           "name" => parse_attributes(title, content: "text", first: true),
-          "alternateName" => parse_attributes(alternate_name, content: "name", first: true),
           "author" => to_schema_org(author),
           "editor" => to_schema_org(editor),
           "description" => parse_attributes(description, content: "text", first: true),
@@ -27,13 +26,15 @@ module Bolognese
           "pageEnd" => last_page,
           "spatialCoverage" => spatial_coverage,
           "sameAs" => to_schema_org(is_identical_to),
-          "isPartOf" => to_schema_org_container(is_part_of, container_title: container_title),
+          "isPartOf" => type == "Dataset" ? nil : to_schema_org_container(is_part_of, container_title: container_title),
           "hasPart" => to_schema_org(has_part),
           "predecessor_of" => to_schema_org(is_previous_version_of),
           "successor_of" => to_schema_org(is_new_version_of),
           "citation" => to_schema_org(references),
           "@reverse" => reverse.presence,
+          "contentUrl" => content_url,
           "schemaVersion" => schema_version,
+          "includedInDataCatalog" => type == "Dataset" ? to_schema_org_container(is_part_of, container_title: container_title) : nil,
           "publisher" => publisher.present? ? { "@type" => "Organization", "name" => publisher } : nil,
           "funding" => to_schema_org(funding),
           "provider" => service_provider.present? ? { "@type" => "Organization", "name" => service_provider } : nil

data/spec/fixtures/crosscite.json

@@ -18,7 +18,7 @@
     "publisher": "Zenodo",
     "keywords": ["choice architecture", "crossover experiment", "hci"],
     "date_published": "2016-03-27",
-    "alternate_name": {
+    "alternate_identifier": {
         "type": "URL",
         "name": "http://zenodo.org/record/48440"
     },

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/content_url.yml

@@ -0,0 +1,89 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://app.datacite.org/prefixes/10.23725
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Mozilla/5.0 (compatible; Maremma/4.1.1; +https://github.com/datacite/maremma)
+      Accept:
+      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
+  response:
+    status:
+      code: 200
+      message: OK
+    headers:
+      Date:
+      - Wed, 22 Aug 2018 06:38:30 GMT
+      Content-Type:
+      - application/vnd.api+json; charset=utf-8
+      Connection:
+      - keep-alive
+      Status:
+      - 200 OK
+      X-Anonymous-Consumer:
+      - 'true'
+      Cache-Control:
+      - max-age=0, private, must-revalidate
+      Vary:
+      - Accept-Encoding, Origin
+      X-Request-Id:
+      - 3d4d8c6a-a2bd-4060-875f-07725945597f
+      Etag:
+      - W/"56c426765344bcbbece7b2dea9a07f50"
+      X-Runtime:
+      - '0.013853'
+      X-Powered-By:
+      - Phusion Passenger 5.3.4
+      Server:
+      - nginx/1.14.0 + Phusion Passenger 5.3.4
+    body:
+      encoding: ASCII-8BIT
+      string: '{"data":{"id":"10.23725","type":"prefixes","attributes":{"registration-agency":"DataCite","created":"2016-09-26T14:06:03.000Z","updated":null},"relationships":{"clients":{"data":[{"id":"datacite.topmed","type":"clients"}]},"providers":{"data":[{"id":"datacite","type":"providers"}]}}},"included":[{"id":"datacite.topmed","type":"clients","attributes":{"name":"TOPMed","symbol":"DATACITE.TOPMED","year":2018,"contact-name":"Martin
+        Fenner","contact-email":"mfenner@datacite.org","domains":"*","url":null,"is-active":true,"has-password":false,"created":"2018-08-06T12:46:43Z","updated":"2018-08-22T02:36:18Z"},"relationships":{"prefixes":{"meta":{}},"provider":{"meta":{}},"repository":{"meta":{}}}},{"id":"datacite","type":"providers","attributes":{"name":"DataCite","symbol":"DATACITE","website":null,"contact-name":"DataCite
+        Support","contact-email":"info@datacite.org","phone":null,"description":null,"country":"DE","logo-url":null,"institution-type":null,"is-active":true,"has-password":true,"joined":null,"created":"2011-12-07T13:41:07.000Z","updated":"2018-08-22T02:25:51.000Z"},"relationships":{"clients":{"meta":{}},"prefixes":{"meta":{}}}}]}'
+    http_version: 
+  recorded_at: Wed, 22 Aug 2018 06:38:30 GMT
+- request:
+    method: get
+    uri: https://search.datacite.org/api?defType=edismax&fl=doi,url,xml,state,allocator_symbol,datacentre_symbol,media,minted,updated&q=10.23725/8na3-9s47&wt=json
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Mozilla/5.0 (compatible; Maremma/4.1.1; +https://github.com/datacite/maremma)
+      Accept:
+      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
+  response:
+    status:
+      code: 200
+      message: OK
+    headers:
+      Date:
+      - Wed, 22 Aug 2018 06:38:30 GMT
+      Content-Type:
+      - application/json;charset=UTF-8
+      Connection:
+      - keep-alive
+      Server:
+      - nginx/1.10.3 (Ubuntu)
+      Access-Control-Allow-Origin:
+      - "*"
+      Access-Control-Allow-Methods:
+      - GET, POST, PUT, DELETE, OPTIONS
+      Access-Control-Allow-Headers:
+      - DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization
+      Access-Control-Expose-Headers:
+      - DNT,X-CustomHeader,Keep-Alive,User-Agent,X-Requested-With,If-Modified-Since,Cache-Control,Content-Type,Content-Range,Range,Authorization
+    body:
+      encoding: ASCII-8BIT
+      string: 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+  recorded_at: Wed, 22 Aug 2018 06:38:30 GMT
+recorded_with: VCR 3.0.3