bolognese 0.9.19 → 0.9.20

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8e774c4a8a3e9c8e2d6632ed0e6356bb9c54d611
-  data.tar.gz: 8230a49968ca28458cc71a55f57d90864db48b17
+  metadata.gz: a1304de5dc3d68ee4632cd83e521369960b14a34
+  data.tar.gz: 4347c44440c7a4e45425732b344f65680f67d28f
 SHA512:
-  metadata.gz: 55998c995185346c175798ee00517892aa0ac0bf5ed0059d751b38210421e501fd3b3dc7b51a20e2c43ae5803c04ff806e33b48acab134bc0966b28604937231
-  data.tar.gz: af2db0282a846b976d26f9c18e7e1e5561d28fcaa2949b0c43751c3ec3818058797fa34403de5411d24bfe93eead5d3d72bbb321bf45659e937b8a0f889be33a
+  metadata.gz: e96bf16236adef0b8b70358bc3c371050eff1e273643cdbf89ea1f33580dbaa7b307f8f7606943865a0152da1882397abfe64c52f2809c98fb2e264e45e87b7d
+  data.tar.gz: ea878cebd14beb3462474466c8d61ec0e4d17f245f415da5d38ed1b285506b4a77907e91be4517afdb911bc08d61d29e686e589fc2d22f97b8319f58d56965ee

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.9.19)
+    bolognese (0.9.20)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)

data/lib/bolognese/metadata.rb

@@ -79,7 +79,7 @@ module Bolognese
         @from = from || find_from_format(id: id)
 
         # generate name for method to call dynamically
-        string = send("get_" + @from, id: id)
+        string = @from.present? ? send("get_" + @from, id: id) : nil
       elsif File.exist?(input)
         ext = File.extname(input)
         if %w(.bib .ris .xml .json).include?(ext)
@@ -105,7 +105,7 @@ module Bolognese
     end
 
     def valid?
-      errors.nil?
+      exists? && errors.nil?
     end
 
     def errors

data/lib/bolognese/readers/crossref_reader.rb

@@ -228,8 +228,8 @@ module Bolognese
       def crossref_references(bibliographic_metadata)
          refs = bibliographic_metadata.dig("citation_list", "citation")
          Array.wrap(refs).select { |a| a["doi"].present? }.map do |c|
-           { "id" => normalize_id(c["doi"]),
-             "type" => "CreativeWork",
+           { "type" => "CreativeWork",
+             "id" => normalize_id(c["doi"]),
              "title" => c["article_title"] }.compact
          end.unwrap
       end

data/lib/bolognese/readers/datacite_reader.rb

@@ -8,6 +8,8 @@ module Bolognese
         url = "https://search.datacite.org/api?q=doi:#{doi}&fl=doi,xml,media,minted,updated&wt=json"
         response = Maremma.get url
         attributes = response.body.dig("data", "response", "docs").first
+        return nil unless attributes.present?
+
         string = attributes.fetch('xml', "PGhzaD48L2hzaD4=\n")
         string = Base64.decode64(string)
         if string.present?
@@ -144,7 +146,7 @@ module Bolognese
         arr = Array.wrap(meta.dig("relatedIdentifiers", "relatedIdentifier")).select { |r| %w(DOI URL).include?(r["relatedIdentifierType"]) }
         arr = arr.select { |r| relation_type.split(" ").include?(r["relationType"]) } if relation_type.present?
 
-        arr.map { |work| { "id" => normalize_id(work["__content__"]) } }.unwrap
+        arr.map { |work| { "type" => "CreativeWork", "id" => normalize_id(work["__content__"]) } }.unwrap
       end
 
       def datacite_is_identical_to(meta)

data/lib/bolognese/utils.rb

@@ -213,7 +213,7 @@ module Bolognese
 
       if /\A(?:(http|https):\/(\/)?(dx\.)?doi.org\/)?(doi:)?(10\.\d{4,5}\/.+)\z/.match(id)
         ra = get_doi_ra(id)
-        ra.present? ? ra.downcase : nil
+        %w(DataCite Crossref).include?(ra) ? ra.downcase : nil
       elsif /\A(?:(http|https):\/(\/)?orcid\.org\/)?(\d{4}-\d{4}-\d{4}-\d{3}[0-9X]+)\z/.match(id)
         "orcid"
       elsif /\A(http|https):\/(\/)?github\.com\/(.+)\z/.match(id)

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.9.19"
+  VERSION = "0.9.20"
 end

data/lib/bolognese/writers/bibtex_writer.rb

@@ -2,6 +2,8 @@ module Bolognese
   module Writers
     module BibtexWriter
       def bibtex
+        return nil unless valid?
+        
         bib = {
           bibtex_type: bibtex_type.presence || "misc",
           bibtex_key: id,

data/lib/bolognese/writers/citeproc_writer.rb

@@ -2,6 +2,8 @@ module Bolognese
   module Writers
     module CiteprocWriter
       def citeproc
+        return nil unless valid?
+        
         hsh = {
           "type" => citeproc_type,
           "id" => id,

data/lib/bolognese/writers/codemeta_writer.rb

@@ -2,6 +2,8 @@ module Bolognese
   module Writers
     module CodemetaWriter
       def codemeta
+        return nil unless valid?
+        
         hsh = {
           "@context" => id.present? ? "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld" : nil,
           "@type" => type,

data/lib/bolognese/writers/crosscite_writer.rb

@@ -2,6 +2,8 @@ module Bolognese
   module Writers
     module CrossciteWriter
       def crosscite
+        return nil unless valid?
+        
         hsh = {
           "id" => id,
           "doi" => doi,

data/lib/bolognese/writers/datacite_json_writer.rb

@@ -2,6 +2,8 @@ module Bolognese
   module Writers
     module DataciteJsonWriter
       def datacite_json
+        return nil unless valid?
+        
         hsh = {
           "id" => id,
           "doi" => doi,

data/lib/bolognese/writers/rdf_xml_writer.rb

@@ -2,6 +2,8 @@ module Bolognese
   module Writers
     module RdfXmlWriter
       def rdf_xml
+        return nil unless valid?
+        
         graph.dump(:rdfxml, prefixes: { schema: "http://schema.org/" })
       end
     end

data/lib/bolognese/writers/ris_writer.rb

@@ -2,6 +2,8 @@ module Bolognese
   module Writers
     module RisWriter
       def ris
+        return nil unless valid?
+        
         {
           "TY" => ris_type,
           "T1" => title,

data/lib/bolognese/writers/schema_org_writer.rb

@@ -2,8 +2,9 @@ module Bolognese
   module Writers
     module SchemaOrgWriter
       def schema_hsh
-        {
-          "@context" => id.present? ? "http://schema.org" : nil,
+        return nil unless valid?
+
+        { "@context" => id.present? ? "http://schema.org" : nil,
           "@type" => type,
           "@id" => id,
           "url" => url,
@@ -24,11 +25,11 @@ module Bolognese
           "pagination" => pagination,
           "spatialCoverage" => spatial_coverage,
           "sameAs" => same_as,
-          "isPartOf" => is_part_of.present? ? to_schema_org(is_part_of) : nil,
-          "hasPart" => has_part,
-          "predecessor_of" => is_previous_version_of,
-          "successor_of" => is_new_version_of,
-          "citation" => Array.wrap(references).map { |r| r.except("relationType").merge("@type" => "CreativeWork") }.unwrap,
+          "isPartOf" => to_schema_org(is_part_of),
+          "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,
           "schemaVersion" => schema_version,
           "publisher" => publisher.present? ? { "@type" => "Organization", "name" => publisher } : nil,

data/lib/bolognese/writers/turtle_writer.rb

@@ -2,6 +2,8 @@ module Bolognese
   module Writers
     module TurtleWriter
       def turtle
+        return nil unless valid?
+        
         graph.dump(:ttl, prefixes: { schema: "http://schema.org/" })
       end
     end

data/spec/datacite_utils_spec.rb

@@ -113,9 +113,8 @@ describe Bolognese::Metadata, vcr: true do
 
   context "insert_related_identifiers" do
     it "related_identifier" do
-      expect(subject.has_part).to eq([{"id"=>"https://doi.org/10.5061/dryad.8515/1"},
-                                      {"id"=>"https://doi.org/10.5061/dryad.8515/2"}])
-      expect(subject.is_referenced_by).to eq("id"=>"https://doi.org/10.1371/journal.ppat.1000446")
+      expect(subject.has_part).to eq([{"type"=>"CreativeWork", "id"=>"https://doi.org/10.5061/dryad.8515/1"}, {"type"=>"CreativeWork", "id"=>"https://doi.org/10.5061/dryad.8515/2"}])
+      expect(subject.is_referenced_by).to eq("type"=>"CreativeWork", "id"=>"https://doi.org/10.1371/journal.ppat.1000446")
     end
 
     it "insert" do

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml

@@ -0,0 +1,153 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://api.datacite.org/prefixes/10.5438
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - 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: ''
+    headers:
+      Access-Control-Allow-Headers:
+      - Content-Type,Accept,Accept-Encoding,Origin,User-Agent,Cache-Control,Keep-Alive
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+      Access-Control-Allow-Origin:
+      - "*"
+      Access-Control-Max-Age:
+      - '1728000'
+      Cache-Control:
+      - max-age=0, private, must-revalidate
+      Content-Type:
+      - application/vnd.api+json; charset=utf-8
+      Date:
+      - Sat, 13 May 2017 06:16:55 GMT
+      Etag:
+      - W/"b9f2d79281c542db437c42a5bac25ac8"
+      Server:
+      - openresty/1.11.2.2
+      Status:
+      - 200 OK
+      Vary:
+      - Accept-Encoding
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - SAMEORIGIN
+      X-Powered-By:
+      - Phusion Passenger 5.1.2
+      X-Request-Id:
+      - 3ff90a69-55b1-49a0-8d68-3b8989d6489c
+      X-Runtime:
+      - '0.760014'
+      X-Xss-Protection:
+      - 1; mode=block
+      Content-Length:
+      - '124'
+      Connection:
+      - keep-alive
+    body:
+      encoding: UTF-8
+      string: '{"data":{"id":"10.5438","type":"prefixes","attributes":{"registration-agency":"DataCite","updated":"2016-09-21T20:27:15Z"}}}'
+    http_version: 
+  recorded_at: Sat, 13 May 2017 06:16:56 GMT
+- request:
+    method: get
+    uri: https://search.datacite.org/api?fl=doi,xml,media,minted,updated&q=doi:10.5438/4k3m-nyvg&wt=json
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - 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: ''
+    headers:
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+      Access-Control-Allow-Origin:
+      - "*"
+      Content-Type:
+      - application/json;charset=UTF-8
+      Date:
+      - Sat, 13 May 2017 06:16:55 GMT
+      Server:
+      - openresty/1.11.2.2
+      Content-Length:
+      - '3025'
+      Connection:
+      - keep-alive
+    body:
+      encoding: UTF-8
+      string: '{"responseHeader":{"status":0,"QTime":1},"response":{"numFound":1,"start":0,"docs":[{"xml":"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","minted":"2016-12-19T20:49:21Z","updated":"2017-01-09T13:53:12Z","doi":"10.5438/4K3M-NYVG","media":["application/xml:https://blog.datacite.org/eating-your-own-dog-food/eating-your-own-dog-food.xml"]}]}}
+
+'
+    http_version: 
+  recorded_at: Sat, 13 May 2017 06:16:56 GMT
+- request:
+    method: get
+    uri: https://api.datacite.org/prefixes/10.0137
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - 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: 404
+      message: ''
+    headers:
+      Access-Control-Allow-Headers:
+      - Content-Type,Accept,Accept-Encoding,Origin,User-Agent,Cache-Control,Keep-Alive
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+      Access-Control-Allow-Origin:
+      - "*"
+      Cache-Control:
+      - no-cache
+      Content-Type:
+      - application/json; charset=utf-8
+      Date:
+      - Sat, 13 May 2017 06:16:56 GMT
+      Server:
+      - openresty/1.11.2.2
+      Status:
+      - 404 Not Found
+      Vary:
+      - Accept-Encoding
+      X-Content-Type-Options:
+      - nosniff
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+      - SAMEORIGIN
+      X-Powered-By:
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+      X-Runtime:
+      - '0.626899'
+      X-Xss-Protection:
+      - 1; mode=block
+      Connection:
+      - keep-alive
+    body:
+      encoding: UTF-8
+      string: '{"errors":[{"status":"404","title":"The resource you are looking for
+        doesn''t exist."}]}'
+    http_version: 
+  recorded_at: Sat, 13 May 2017 06:16:57 GMT
+recorded_with: VCR 3.0.3

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

@@ -0,0 +1,97 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://api.datacite.org/prefixes/10.4124
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - 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: ''
+    headers:
+      Access-Control-Allow-Headers:
+      - Content-Type,Accept,Accept-Encoding,Origin,User-Agent,Cache-Control,Keep-Alive
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+      Access-Control-Allow-Origin:
+      - "*"
+      Access-Control-Max-Age:
+      - '1728000'
+      Cache-Control:
+      - max-age=0, private, must-revalidate
+      Content-Type:
+      - application/vnd.api+json; charset=utf-8
+      Date:
+      - Sat, 13 May 2017 06:42:30 GMT
+      Etag:
+      - W/"fdee1bc1cd6b18e07cc52f94b7b59250"
+      Server:
+      - openresty/1.11.2.2
+      Status:
+      - 200 OK
+      Vary:
+      - Accept-Encoding
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - SAMEORIGIN
+      X-Powered-By:
+      - Phusion Passenger 5.1.2
+      X-Request-Id:
+      - c42d6b9f-c8c6-4aa2-a72b-fa37be5b4909
+      X-Runtime:
+      - '0.857722'
+      X-Xss-Protection:
+      - 1; mode=block
+      Connection:
+      - keep-alive
+    body:
+      encoding: UTF-8
+      string: '{"data":{"id":"10.4124","type":"prefixes","attributes":{"registration-agency":"DataCite","updated":"2016-09-21T20:27:04Z"}}}'
+    http_version: 
+  recorded_at: Sat, 13 May 2017 06:42:30 GMT
+- request:
+    method: get
+    uri: https://search.datacite.org/api?fl=doi,xml,media,minted,updated&q=doi:10.4124/05f6c379-dd68-4cdb-880d-33d3e9576d52/1&wt=json
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
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+      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: ''
+    headers:
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+      Access-Control-Allow-Origin:
+      - "*"
+      Content-Type:
+      - application/json;charset=UTF-8
+      Date:
+      - Sat, 13 May 2017 06:42:30 GMT
+      Server:
+      - openresty/1.11.2.2
+      Content-Length:
+      - '88'
+      Connection:
+      - keep-alive
+    body:
+      encoding: UTF-8
+      string: '{"responseHeader":{"status":0,"QTime":0},"response":{"numFound":0,"start":0,"docs":[]}}
+
+'
+    http_version: 
+  recorded_at: Sat, 13 May 2017 06:42:30 GMT
+recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/handle_input/DOI_RA_not_Crossref_or_DataCite.yml

@@ -0,0 +1,62 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://api.datacite.org/prefixes/10.3980
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - 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: ''
+    headers:
+      Access-Control-Allow-Headers:
+      - Content-Type,Accept,Accept-Encoding,Origin,User-Agent,Cache-Control,Keep-Alive
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+      Access-Control-Allow-Origin:
+      - "*"
+      Access-Control-Max-Age:
+      - '1728000'
+      Cache-Control:
+      - max-age=0, private, must-revalidate
+      Content-Type:
+      - application/vnd.api+json; charset=utf-8
+      Date:
+      - Sat, 13 May 2017 06:59:48 GMT
+      Etag:
+      - W/"622f4d07c90066bea8efc2105d2bf20c"
+      Server:
+      - openresty/1.11.2.2
+      Status:
+      - 200 OK
+      Vary:
+      - Accept-Encoding
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - SAMEORIGIN
+      X-Powered-By:
+      - Phusion Passenger 5.1.2
+      X-Request-Id:
+      - d9b2416d-a3f1-4316-85aa-ceede1128229
+      X-Runtime:
+      - '0.274890'
+      X-Xss-Protection:
+      - 1; mode=block
+      Content-Length:
+      - '129'
+      Connection:
+      - keep-alive
+    body:
+      encoding: UTF-8
+      string: '{"data":{"id":"10.3980","type":"prefixes","attributes":{"registration-agency":"10.SERV/ISTIC","updated":"2016-09-20T21:59:03Z"}}}'
+    http_version: 
+  recorded_at: Sat, 13 May 2017 06:59:48 GMT
+recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/handle_input/unknown_DOI_prefix.yml

@@ -0,0 +1,59 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://api.datacite.org/prefixes/10.0137
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma - 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: 404
+      message: ''
+    headers:
+      Access-Control-Allow-Headers:
+      - Content-Type,Accept,Accept-Encoding,Origin,User-Agent,Cache-Control,Keep-Alive
+      Access-Control-Allow-Methods:
+      - GET, POST, OPTIONS
+      Access-Control-Allow-Origin:
+      - "*"
+      Cache-Control:
+      - no-cache
+      Content-Type:
+      - application/json; charset=utf-8
+      Date:
+      - Sat, 13 May 2017 06:21:22 GMT
+      Server:
+      - openresty/1.11.2.2
+      Status:
+      - 404 Not Found
+      Vary:
+      - Accept-Encoding
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - SAMEORIGIN
+      X-Powered-By:
+      - Phusion Passenger 5.1.2
+      X-Request-Id:
+      - b40e59b7-5e41-4d32-b321-8178374af4c4
+      X-Runtime:
+      - '0.218928'
+      X-Xss-Protection:
+      - 1; mode=block
+      Content-Length:
+      - '87'
+      Connection:
+      - keep-alive
+    body:
+      encoding: UTF-8
+      string: '{"errors":[{"status":"404","title":"The resource you are looking for
+        doesn''t exist."}]}'
+    http_version: 
+  recorded_at: Sat, 13 May 2017 06:21:22 GMT
+recorded_with: VCR 3.0.3

data/spec/metadata_spec.rb

@@ -4,6 +4,22 @@ describe Bolognese::Metadata, vcr: true do
   let(:input) { "http://doi.org/10.5438/4K3M-NYVG" }
   subject { Bolognese::Metadata.new(input: input) }
 
+  context "handle input" do
+    it "unknown DOI prefix" do
+      input = "http://doi.org/10.0137/14802"
+      subject = Bolognese::Metadata.new(input: input)
+      expect(subject.valid?).to be false
+      expect(subject.bibtex).to be_nil
+    end
+
+    it "DOI RA not Crossref or DataCite" do
+      input = "http://doi.org/10.3980/j.issn.2222-3959.2015.03.07"
+      subject = Bolognese::Metadata.new(input: input)
+      expect(subject.valid?).to be false
+      expect(subject.bibtex).to be_nil
+    end
+  end
+
   context "find from format by ID" do
     it "crossref" do
       id = "https://doi.org/10.1371/journal.pone.0000030"
@@ -25,6 +41,11 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.find_from_format(id: id)).to eq("datacite")
     end
 
+    it "unknown DOI registration agency" do
+      id = "http://doi.org/10.0137/14802"
+      expect(subject.find_from_format(id: id)).to be_nil
+    end
+
     it "orcid" do
       id = "http://orcid.org/0000-0002-0159-2197"
       expect(subject.find_from_format(id: id)).to eq("orcid")

data/spec/readers/crossref_reader_spec.rb

@@ -138,8 +138,7 @@ describe Bolognese::Metadata, vcr: true do
     it "not found error" do
       input = "https://doi.org/10.7554/elife.01567x"
       subject = Bolognese::Metadata.new(input: input)
-      expect(subject.id).to be_nil
-      expect(subject.exists?).to be false
+      expect(subject.valid?).to be false
     end
   end
 end

data/spec/readers/datacite_json_reader_spec.rb

@@ -32,8 +32,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "datacite_json")
       expect(subject.valid?).to be false
       expect(subject.errors).to eq(["expected comma, not a string at line 4, column 11 [parse.c:381]"])
-      json = JSON.parse(subject.codemeta)
-      expect(json).to be_nil
+      expect(subject.codemeta).to be_nil
     end
 
     it "SoftwareSourceCode overlapping_keys" do
@@ -41,8 +40,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "datacite_json")
       expect(subject.valid?).to be false
       expect(subject.errors).to eq(["The same key is defined more than once: id"])
-      json = JSON.parse(subject.codemeta)
-      expect(json).to be_nil
+      expect(subject.codemeta).to be_nil
     end
   end
 end

data/spec/readers/datacite_reader_spec.rb

@@ -26,8 +26,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.alternate_name).to eq("type"=>"citation", "name"=>"Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.")
       expect(subject.license).to eq("id"=>"http://creativecommons.org/publicdomain/zero/1.0")
       expect(subject.date_published).to eq("2011")
-      expect(subject.has_part).to eq([{"id"=>"https://doi.org/10.5061/dryad.8515/1"}, {"id"=>"https://doi.org/10.5061/dryad.8515/2"}])
-      expect(subject.is_referenced_by).to eq("id"=>"https://doi.org/10.1371/journal.ppat.1000446")
+      expect(subject.has_part).to eq([{"type"=>"CreativeWork", "id"=>"https://doi.org/10.5061/dryad.8515/1"}, {"type"=>"CreativeWork", "id"=>"https://doi.org/10.5061/dryad.8515/2"}])
+      expect(subject.is_referenced_by).to eq("type"=>"CreativeWork", "id"=>"https://doi.org/10.1371/journal.ppat.1000446")
       expect(subject.publisher).to eq("Dryad Digital Repository")
       expect(subject.provider).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
@@ -47,8 +47,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.description["text"]).to start_with("Eating your own dog food")
       expect(subject.date_published).to eq("2016-12-20")
       expect(subject.date_modified).to eq("2016-12-20")
-      expect(subject.is_part_of).to eq("id"=>"https://doi.org/10.5438/0000-00ss")
-      expect(subject.references).to eq([{"id"=>"https://doi.org/10.5438/0012"}, {"id"=>"https://doi.org/10.5438/55e5-t5c0"}])
+      expect(subject.is_part_of).to eq("type"=>"CreativeWork", "id"=>"https://doi.org/10.5438/0000-00ss")
+      expect(subject.references).to eq([{"type"=>"CreativeWork", "id"=>"https://doi.org/10.5438/0012"}, {"type"=>"CreativeWork", "id"=>"https://doi.org/10.5438/55e5-t5c0"}])
       expect(subject.publisher).to eq("DataCite")
       expect(subject.provider).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-4")
@@ -84,7 +84,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.description["text"]).to start_with("This tools are used to analyse the data produced by the Crosssover Experiment")
       expect(subject.license).to eq([{"name"=>"Open Access"}, {"id"=>"https://creativecommons.org/licenses/by-nc-sa/4.0", "name"=>"Creative Commons Attribution-NonCommercial-ShareAlike"}])
       expect(subject.date_published).to eq("2016-03-27")
-      expect(subject.is_supplement_to).to eq("id"=>"https://github.com/kjgarza/frame_experiment_analysis/tree/v1.0")
+      expect(subject.is_supplement_to).to eq("type"=>"CreativeWork", "id"=>"https://github.com/kjgarza/frame_experiment_analysis/tree/v1.0")
       expect(subject.publisher).to eq("Zenodo")
       expect(subject.provider).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
@@ -104,7 +104,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.description["text"]).to start_with("<b>RAIN: RNA–protein Association and Interaction Networks")
       expect(subject.license).to eq("id"=>"https://creativecommons.org/licenses/by/4.0", "name"=>"CC-BY")
       expect(subject.date_published).to eq("2016")
-      expect(subject.is_identical_to).to eq("id"=>"https://doi.org/10.6084/m9.figshare.4234751")
+      expect(subject.is_identical_to).to eq("type"=>"CreativeWork", "id"=>"https://doi.org/10.6084/m9.figshare.4234751")
       expect(subject.publisher).to eq("Figshare")
       expect(subject.provider).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
@@ -202,8 +202,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.title).to eq("Eating your own Dog Food")
       expect(subject.alternate_name).to eq("type"=>"Local accession number", "name"=>"MS-49-3632-5083")
       expect(subject.date_published).to eq("2016-12-20")
-      expect(subject.is_part_of).to eq("id"=>"https://doi.org/10.5438/0000-00ss")
-      expect(subject.references).to eq([{"id"=>"https://doi.org/10.5438/0012"}, {"id"=>"https://doi.org/10.5438/55e5-t5c0"}])
+      expect(subject.is_part_of).to eq("type"=>"CreativeWork", "id"=>"https://doi.org/10.5438/0000-00ss")
+      expect(subject.references).to eq([{"type"=>"CreativeWork", "id"=>"https://doi.org/10.5438/0012"}, {"type"=>"CreativeWork", "id"=>"https://doi.org/10.5438/55e5-t5c0"}])
       expect(subject.provider).to eq("DataCite")
     end
 
@@ -223,6 +223,12 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")
     end
 
+    it "DOI not found" do
+      input = "https://doi.org/10.4124/05F6C379-DD68-4CDB-880D-33D3E9576D52/1"
+      subject = Bolognese::Metadata.new(input: input)
+      expect(subject.valid?).to be false
+    end
+
     # it "missing creator" do
     #   string = IO.read(fixture_path + "datacite_missing_creator.xml")
     #   subject = Bolognese::Metadata.new(string: string, regenerate: true)

data/spec/writers/datacite_writer_spec.rb

@@ -101,9 +101,9 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.alternate_name).to eq("type"=>"citation", "name"=>"Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.")
       expect(subject.license).to eq("id"=>"http://creativecommons.org/publicdomain/zero/1.0")
       expect(subject.date_published).to eq("2011")
-      expect(subject.has_part).to eq([{"id"=>"https://doi.org/10.5061/dryad.8515/1"},
-                                      {"id"=>"https://doi.org/10.5061/dryad.8515/2"}])
-      expect(subject.is_referenced_by).to eq("id"=>"https://doi.org/10.1371/journal.ppat.1000446")
+      expect(subject.has_part).to eq([{"type"=>"CreativeWork", "id"=>"https://doi.org/10.5061/dryad.8515/1"},
+                                      {"type"=>"CreativeWork", "id"=>"https://doi.org/10.5061/dryad.8515/2"}])
+      expect(subject.is_referenced_by).to eq("type"=>"CreativeWork", "id"=>"https://doi.org/10.1371/journal.ppat.1000446")
       expect(subject.publisher).to eq("Dryad Digital Repository")
       expect(subject.provider).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-3")

data/spec/writers/schema_org_writer_spec.rb

@@ -7,6 +7,8 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "crossref")
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.7554/elife.01567")
+      expect(json["citation"].length).to eq(25)
+      expect(json["citation"].first).to eq("@id"=>"https://doi.org/10.1038/nature02100", "@type"=>"CreativeWork")
       expect(json["funding"]).to eq([{"name"=>"SystemsX", "@type"=>"Organization"},
                                      {"name"=>"EMBO",
                                       "@type"=>"Organization",
@@ -80,6 +82,8 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.5438/6423")
+      expect(json["hasPart"].length).to eq(25)
+      expect(json["hasPart"].first).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5281/zenodo.30799")
       expect(json["funding"]).to eq("@type" => "Award",
                                     "funder" => {"@type"=>"Organization", "@id"=>"https://doi.org/10.13039/501100000780", "name"=>"European Commission"},
                                     "identifier" => "654039",

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 0.9.19
+  version: 0.9.20
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-05-12 00:00:00.000000000 Z
+date: 2017-05-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -567,6 +567,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/github.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/orcid.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/schema_org.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_by_ID/unknown_DOI_registration_agency.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/bibtex.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/citeproc.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/find_from_format_from_file/codemeta.yml
@@ -589,6 +590,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/not_found_error.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/posted_content.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/BlogPosting.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_not_found.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Dataset.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Funding_schema_version_4.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/author_only_full_name.yml
@@ -622,6 +624,8 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_one_author/name_with_role.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_schema_org_metadata/BlogPosting.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_schema_org_metadata/not_found_error.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/handle_input/DOI_RA_not_Crossref_or_DataCite.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/handle_input/unknown_DOI_prefix.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_alternate_identifiers/insert.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_contributors/none.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/insert_creators/insert.yml