bolognese 0.9.91 → 0.9.92

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 42571f806fa0ddb4fa5e9fc9bd69acd8ad632cf935e4632521b4a42bc0151a93
-  data.tar.gz: f79d228d759b0b9f0ae68755311490e8f80bddcc9b0ad00333317496ae5ef029
+  metadata.gz: 1fc93bdfbb7b18ae1bcc2dea7fac1315bbded2528ce63b994f0344dfb6921e59
+  data.tar.gz: f3058ac14a37d485479ec15fcc60169bd51da84d37fa3c5e4a09e58719bb3f60
 SHA512:
-  metadata.gz: 44eea3f6e8013da74b50dd291c74d8a9add5450f5759adab0ed0e057a007515a36fd4a34f091f4fbb75c105b5103f6deb150a46857d65b74074b1c9fe9024541
-  data.tar.gz: 89cc85c5a62e5ad783b805b312b4574ce2aa55c0a41b22d3070130b213a20914105e8e3992cdc202287b4d47028b603f2b77336f27f67ba10505996d0f435072
+  metadata.gz: bd335df02add3896831a38a04cb4276a58ea63ef6b9b8561d560e028e61574b5ee0c8468bcd2f048f8812f5f681c552a07d98468a277460957b6565ff0a67ff4
+  data.tar.gz: aa1ef7bb3dd3bbe3c1faaaa98117f24728a5d868fb09d7fa98776475223cb270ae93ca84571301c2b02afb129e7d46809c5468dff23dd58e24c38e84c0141a8c

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.9.91)
+    bolognese (0.9.92)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)

data/lib/bolognese/author_utils.rb

@@ -19,10 +19,10 @@ module Bolognese
              parse_attributes(author.fetch("contributorName", nil)) ||
              author.fetch("name", nil)
 
-
-      name = cleanup_author(name)
       given_name = author.fetch("givenName", nil)
       family_name = author.fetch("familyName", nil)
+      name = cleanup_author(name)
+      name = [family_name, given_name].join(", ") if name.blank? && family_name.present?
 
       author = { "type" => type || "Person",
                  "id" => id,
@@ -58,6 +58,8 @@ module Bolognese
     end
 
     def cleanup_author(author)
+      return nil unless author.present?
+
       # detect pattern "Smith J.", but not "Smith, John K."
       author = author.gsub(/[[:space:]]([A-Z]\.)?(-?[A-Z]\.)$/, ', \1\2') unless author.include?(",")
 

data/lib/bolognese/metadata.rb

@@ -401,7 +401,7 @@ module Bolognese
     end
 
     def container_title
-      Array.wrap(is_part_of).length == 1 ? is_part_of.to_h.fetch("title", nil) : nil
+      Array.wrap(is_part_of).first.to_h.fetch("title", nil)
     end
 
     def descriptions

data/lib/bolognese/readers/schema_org_reader.rb

@@ -16,7 +16,10 @@ module Bolognese
         id = normalize_id(id)
         response = Maremma.get(id)
         doc = Nokogiri::XML(response.body.fetch("data", nil), nil, 'UTF-8')
-        string = doc.at_xpath('//script[@type="application/ld+json"]')
+        #string = doc.at_xpath('//script[@type="application/ld+json"]')
+        # workaround for xhtml documents
+        nodeset = doc.css("script")
+        string = nodeset.find { |element| element["type"] == "application/ld+json" }
         string = string.text if string.present?
 
         { "string" => string }
@@ -31,15 +34,26 @@ module Bolognese
         meta = string.present? ? Maremma.from_json(string) : {}
 
         id = normalize_id(meta.fetch("@id", nil) || options[:id])
-        type = meta.fetch("@type", nil)
+        type = meta.fetch("@type", nil) && meta.fetch("@type").camelcase
         resource_type_general = Bolognese::Utils::SO_TO_DC_TRANSLATIONS[type]
-        author = get_authors(from_schema_org(Array.wrap(meta.fetch("author", nil))))
+        authors = meta.fetch("author", nil) || meta.fetch("creator", nil)
+        author = get_authors(from_schema_org(Array.wrap(authors)))
         editor = get_authors(from_schema_org(Array.wrap(meta.fetch("editor", nil))))
         publisher = if meta.dig("publisher").is_a?(Hash)
                       meta.dig("publisher", "name")
                     elsif publisher.is_a?(String)
                       meta.dig("publisher")
                     end
+
+        included_in_data_catalog = from_schema_org(Array.wrap(meta.fetch("includedInDataCatalog", nil)))
+        included_in_data_catalog = Array.wrap(included_in_data_catalog).map { |dc| { "title" => dc["name"], "url" => dc["url"] } }
+        is_part_of = schema_org_is_part_of(meta) || included_in_data_catalog
+
+        license = {
+          "id" => parse_attributes(meta.fetch("license", nil), content: "id", first: true),
+          "name" => parse_attributes(meta.fetch("license", nil), content: "name", first: true)
+        }
+
         date_published = meta.fetch("datePublished", nil)
         state = meta.present? ? "findable" : "not_found"
 
@@ -58,7 +72,7 @@ module Bolognese
           "publisher" => meta.dig("publisher", "name"),
           "service_provider" => meta.fetch("provider", nil),
           "is_identical_to" => schema_org_is_identical_to(meta),
-          "is_part_of" => schema_org_is_part_of(meta),
+          "is_part_of" => is_part_of,
           "has_part" => schema_org_has_part(meta),
           "references" => schema_org_references(meta),
           "is_referenced_by" => schema_org_is_referenced_by(meta),
@@ -68,7 +82,7 @@ module Bolognese
           "date_published" => date_published,
           "date_modified" => meta.fetch("dateModified", nil),
           "description" => meta.fetch("description", nil).present? ? { "text" => sanitize(meta.fetch("description")) } : nil,
-          "license" => { "id" => meta.fetch("license", nil) },
+          "license" => license,
           "b_version" => meta.fetch("version", nil),
           "keywords" => meta.fetch("keywords", nil).to_s.split(", "),
           "state" => state

data/lib/bolognese/utils.rb

@@ -289,7 +289,7 @@ module Bolognese
         "datacite_json"
       elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("issued", "date-parts").present?
         "citeproc"
-      elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("@context").to_s.start_with?("http://schema.org")
+      elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("@context").to_s.start_with?("http://schema.org", "https://schema.org")
         "schema_org"
       elsif options[:ext] == ".json" && Maremma.from_json(string).to_h.dig("@context") == ("https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld")
         "codemeta"
@@ -307,7 +307,7 @@ module Bolognese
         "datacite_json"
       elsif Maremma.from_json(string).to_h.dig("issued", "date-parts").present?
         "citeproc"
-      elsif Maremma.from_json(string).to_h.dig("@context").to_s.start_with?("http://schema.org")
+      elsif Maremma.from_json(string).to_h.dig("@context").to_s.start_with?("http://schema.org", "https://schema.org")
         "schema_org"
       elsif Maremma.from_json(string).to_h.dig("@context") == ("https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld")
         "codemeta"

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.9.91"
+  VERSION = "0.9.92"
 end

data/spec/author_utils_spec.rb

@@ -141,6 +141,12 @@ describe Bolognese::Metadata, vcr: true do
       response = subject.get_one_author(meta.dig("creators", "creator"))
       expect(response).to eq("type"=>"Person", "id"=>"https://orcid.org/0000-0003-4514-4211", "name"=>"Thomas Dubos", "givenName"=>"Thomas", "familyName"=>"Dubos", "identifier"=>["https://orcid.org/0000-0003-4514-4211", "http://isni.org/isni/0000-0003-5752-6882"])
     end
+
+    it "only familyName and givenName" do
+      input = "https://doi.pangaea.de/10.1594/PANGAEA.836178"
+      subject = Bolognese::Metadata.new(input: input, from: "schema_org")
+      expect(subject.author.first).to eq("type"=>"Person", "name"=>"Johansson, Emma", "givenName"=>"Emma", "familyName"=>"Johansson")
+    end
   end
 
   context "get_name_identifiers" do

data/spec/find_from_format_spec.rb

@@ -0,0 +1,30 @@
+require 'spec_helper'
+require 'bolognese/cli'
+
+describe Bolognese::CLI do
+  context "find_from_format_by_id", vcr: true do
+    let(:subject) do
+      described_class.new
+    end
+
+    it "crossref" do
+      id = "https://doi.org/10.7554/eLife.01567"
+      expect(subject.find_from_format_by_id(id)).to eq("crossref")
+    end
+
+    it "datacite" do
+      id = "https://doi.org/10.5061/DRYAD.8515"
+      expect(subject.find_from_format_by_id(id)).to eq("datacite")
+    end
+
+    it "codemeta" do
+      id = "https://github.com/datacite/maremma"
+      expect(subject.find_from_format_by_id(id)).to eq("codemeta")
+    end
+
+    it "schema_org" do
+      id = "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/GAOC03"
+      expect(subject.find_from_format_by_id(id)).to eq("schema_org")
+    end
+  end
+end

data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/crossref.yml

@@ -0,0 +1,48 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://app.datacite.org/prefixes/10.7554
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma 4.0.5 - 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:
+      - Sun, 18 Mar 2018 06:54:15 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
+      Etag:
+      - W/"258c3a49bbc303b1229efe2fae9cc9e2"
+      X-Runtime:
+      - '0.774787'
+      X-Request-Id:
+      - 0cfc9b22-6085-479a-869d-2b70024f3423
+      X-Powered-By:
+      - Phusion Passenger 5.2.1
+      Server:
+      - nginx/1.12.2 + Phusion Passenger 5.2.1
+    body:
+      encoding: ASCII-8BIT
+      string: '{"data":{"id":"10.7554","type":"handles","attributes":{"registration-agency":"Crossref","created":null,"updated":"2016-09-21T21:07:27Z"},"relationships":{"clients":{"data":[]},"providers":{"data":[]}}}}'
+    http_version: 
+  recorded_at: Sun, 18 Mar 2018 06:54:15 GMT
+recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_CLI/find_from_format_by_id/datacite.yml

@@ -0,0 +1,50 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://app.datacite.org/prefixes/10.5061
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Maremma 4.0.5 - 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:
+      - Sun, 18 Mar 2018 06:54:43 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:
+      - 744df000-0eec-4750-a9a5-92e8552c01eb
+      Etag:
+      - W/"b88da514519eb2584bb29d491bf684df"
+      X-Runtime:
+      - '0.015930'
+      X-Powered-By:
+      - Phusion Passenger 5.2.1
+      Server:
+      - nginx/1.12.2 + Phusion Passenger 5.2.1
+    body:
+      encoding: ASCII-8BIT
+      string: '{"data":{"id":"10.5061","type":"prefixes","attributes":{"registration-agency":"DataCite","created":"2010-01-01T00:00:00.000Z","updated":null},"relationships":{"clients":{"data":[{"id":"cdl.dryad","type":"clients"}]},"providers":{"data":[{"id":"cdl","type":"providers"}]}}},"included":[{"id":"cdl.dryad","type":"clients","attributes":{"name":"Dryad","symbol":"CDL.DRYAD","year":2013,"contact-name":"Greg
+        Janee","contact-email":"gjanee@ucop.edu","domains":"*","url":null,"is-active":true,"has-password":false,"created":"2013-02-19T17:42:03Z","updated":"2018-03-18T02:30:16Z"},"relationships":{"prefixes":{"meta":{}},"provider":{"meta":{}},"repository":{"meta":{}}}},{"id":"cdl","type":"providers","attributes":{"name":"California
+        Digital Library","symbol":"CDL","year":2010,"contact-name":"Greg Janee","contact-email":"gjanee@ucop.edu","logo-url":"https://assets.datacite.org/images/members/cdl.png","is-active":true,"has-password":true,"created":"2010-01-01T00:00:00.000Z","updated":"2018-03-18T02:25:51.000Z"},"relationships":{"clients":{"meta":{}},"prefixes":{"meta":{}}}}]}'
+    http_version: 
+  recorded_at: Sun, 18 Mar 2018 06:54:43 GMT
+recorded_with: VCR 3.0.3

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

@@ -8,7 +8,7 @@ http_interactions:
       string: ''
     headers:
       User-Agent:
-      - Maremma - https://github.com/datacite/maremma
+      - Maremma 4.0.5 - 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:
@@ -17,7 +17,7 @@ http_interactions:
       message: OK
     headers:
       Date:
-      - Sun, 25 Feb 2018 14:11:37 GMT
+      - Sun, 18 Mar 2018 08:52:36 GMT
       Content-Type:
       - application/vnd.api+json; charset=utf-8
       Connection:
@@ -30,21 +30,24 @@ http_interactions:
       - max-age=0, private, must-revalidate
       Vary:
       - Accept-Encoding, Origin
+      X-Request-Id:
+      - a8b85e9e-93bb-4d46-8960-8d0125dfa5dd
       Etag:
-      - W/"93b8b1f570105aa6606601deb773685a"
+      - W/"1e26530619c2dc28abc777879a8d98da"
       X-Runtime:
-      - '0.020383'
-      X-Request-Id:
-      - 6129e642-4bc8-42ff-8b73-6068eecc6577
+      - '0.017074'
       X-Powered-By:
-      - Phusion Passenger 5.2.0
+      - Phusion Passenger 5.2.1
       Server:
-      - nginx/1.12.2 + Phusion Passenger 5.2.0
+      - nginx/1.12.2 + Phusion Passenger 5.2.1
     body:
       encoding: ASCII-8BIT
-      string: '{"data":{"id":"10.5438","type":"prefixes","attributes":{"registration-agency":"DataCite","created":"2011-03-30T08:56:21.000Z","updated":null},"relationships":{"clients":{"data":[{"id":"datacite.datacite","type":"clients"}]},"providers":{"data":[{"id":"datacite","type":"providers"}]}}},"included":[{"id":"datacite.datacite","type":"clients","attributes":{"name":"DataCite","symbol":"DATACITE.DATACITE","year":2011,"contact-name":"DataCite","contact-email":"support@datacite.org","domains":"*","url":null,"is-active":true,"has-password":true,"created":"2011-12-07T13:43:39Z","updated":"2018-02-25T02:30:09Z"},"relationships":{"prefixes":{"meta":{}},"provider":{"meta":{}},"repository":{"meta":{}}}},{"id":"datacite","type":"providers","attributes":{"name":"DataCite","symbol":"DATACITE","year":2011,"contact-name":"DataCite","contact-email":"support@datacite.org","logo-url":"https://assets.datacite.org/images/members/datacite.png","is-active":true,"has-password":true,"created":"2011-12-07T13:41:07.000Z","updated":"2018-02-25T02:25:51.000Z"},"relationships":{"clients":{"meta":{}},"prefixes":{"meta":{}}}}]}'
+      string: '{"data":{"id":"10.5438","type":"prefixes","attributes":{"registration-agency":"DataCite","created":"2011-03-30T08:56:21.000Z","updated":null},"relationships":{"clients":{"data":[{"id":"datacite.datacite","type":"clients"},{"id":"test.datacite","type":"clients"}]},"providers":{"data":[{"id":"datacite","type":"providers"},{"id":"test","type":"providers"}]}}},"included":[{"id":"datacite.datacite","type":"clients","attributes":{"name":"DataCite","symbol":"DATACITE.DATACITE","year":2011,"contact-name":"DataCite","contact-email":"support@datacite.org","domains":"*","url":null,"is-active":true,"has-password":true,"created":"2011-12-07T13:43:39Z","updated":"2018-03-18T02:30:10Z"},"relationships":{"prefixes":{"meta":{}},"provider":{"meta":{}},"repository":{"meta":{}}}},{"id":"test.datacite","type":"clients","attributes":{"name":"DataCite
+        Staff Test Client","symbol":"TEST.DATACITE","year":2018,"contact-name":"DataCite
+        Support","contact-email":"support@datacite.org","domains":"*","url":null,"is-active":true,"has-password":true,"created":"2018-03-15T12:19:33Z","updated":"2018-03-18T02:31:01Z"},"relationships":{"prefixes":{"meta":{}},"provider":{"meta":{}},"repository":{"meta":{}}}},{"id":"datacite","type":"providers","attributes":{"name":"DataCite","symbol":"DATACITE","year":2011,"contact-name":"DataCite","contact-email":"support@datacite.org","logo-url":"https://assets.datacite.org/images/members/datacite.png","is-active":true,"has-password":true,"created":"2011-12-07T13:41:07.000Z","updated":"2018-03-18T02:25:52.000Z"},"relationships":{"clients":{"meta":{}},"prefixes":{"meta":{}}}},{"id":"test","type":"providers","attributes":{"name":"DataCite
+        Test Provider","symbol":"TEST","year":2010,"contact-name":"DataCite Support","contact-email":"tech@datacite.org","logo-url":"https://assets.datacite.org/images/members/test.png","is-active":true,"has-password":true,"created":"2010-01-01T00:00:00.000Z","updated":"2018-03-18T02:25:51.000Z"},"relationships":{"clients":{"meta":{}},"prefixes":{"meta":{}}}}]}'
     http_version: 
-  recorded_at: Sun, 25 Feb 2018 14:11:37 GMT
+  recorded_at: Sun, 18 Mar 2018 08:52:36 GMT
 - request:
     method: get
     uri: https://app.datacite.org/dois/10.5438/4k3m-nyvg?include=client,provider
@@ -53,7 +56,7 @@ http_interactions:
       string: ''
     headers:
       User-Agent:
-      - Maremma - https://github.com/datacite/maremma
+      - Maremma 4.0.5 - 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:
@@ -62,7 +65,7 @@ http_interactions:
       message: OK
     headers:
       Date:
-      - Sun, 25 Feb 2018 14:11:37 GMT
+      - Sun, 18 Mar 2018 08:52:36 GMT
       Content-Type:
       - application/vnd.api+json; charset=utf-8
       Connection:
@@ -75,27 +78,27 @@ http_interactions:
       - max-age=0, private, must-revalidate
       Vary:
       - Accept-Encoding, Origin
+      X-Request-Id:
+      - 83e6efd1-575c-4142-ad24-012b224d88a3
       Etag:
-      - W/"b2312843e7cf55dbec405967f26f4052"
+      - W/"4b5a70bd53bbdcef89ee5152a2a4506c"
       X-Runtime:
-      - '0.013110'
-      X-Request-Id:
-      - d009e0e7-50ab-4d29-9228-70f5b1e3faab
+      - '0.018967'
       X-Powered-By:
-      - Phusion Passenger 5.2.0
+      - Phusion Passenger 5.2.1
       Server:
-      - nginx/1.12.2 + Phusion Passenger 5.2.0
+      - nginx/1.12.2 + Phusion Passenger 5.2.1
     body:
       encoding: ASCII-8BIT
-      string: '{"data":{"id":"10.5438/4k3m-nyvg","type":"dois","attributes":{"doi":"10.5438/4k3m-nyvg","identifier":"https://doi.org/10.5438/4k3m-nyvg","url":null,"author":{"type":"Person","id":"https://orcid.org/0000-0003-1419-2405","name":"Fenner,
-        Martin","given-name":"Martin","family-name":"Fenner"},"title":"Eating your
-        own Dog Food","container-title":"DataCite","description":{"type":"Abstract","text":"Eating
+      string: '{"data":{"id":"10.5438/4k3m-nyvg","type":"dois","attributes":{"doi":"10.5438/4k3m-nyvg","prefix":"10.5438","suffix":"4k3m-nyvg","identifier":"https://doi.org/10.5438/4k3m-nyvg","url":null,"creator":[{"type":"Person","id":"https://orcid.org/0000-0003-1419-2405","name":"Fenner,
+        Martin","given-name":"Martin","family-name":"Fenner"}],"title":"Eating your
+        own Dog Food","publisher":"DataCite","resource-type-subtype":"BlogPosting","description":"Eating
         your own dog food is a slang term to describe that an organization should
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