bolognese 1.8.3 → 1.8.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 8ef53004829fede6fdbcd4b5942a8e63950fe3b8bdcff770be69a66c34e6caa9
+  metadata.gz: 606a00508da9a9b0d3b64f2e2227ff37e97125f960a7f2aac3ea18ef25c9f077
+  data.tar.gz: b2f306899790dd5b18d0ab85deab2d6491c6da8e610f138585b0b0a8df93ad2e
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-  data.tar.gz: 2115e97733f06c4d67fdcf75eb8496758aa85a60b78888c296a6b25d1f7eb98ef5b9f82bff196b9c9e5544de75806c5787715b2aac2ea1848df027ec1d862eb8
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+  data.tar.gz: 81cb04f710c2822f7a4b255e184b492ee5ce642867a740cd0e75253d584458d9681c550e67bef069ec78a153d1accef16d1139439fafb095de71a9421249fe24

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.8.3)
+    bolognese (1.8.8)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)
@@ -25,7 +25,7 @@ PATH
       postrank-uri (~> 1.0, >= 1.0.18)
       rdf-rdfxml (~> 3.1)
       rdf-turtle (~> 3.1)
-      thor (~> 1.0, >= 1.0.1)
+      thor (>= 0.19)
 
 GEM
   remote: https://rubygems.org/
@@ -41,6 +41,7 @@ GEM
     benchmark_methods (0.7)
     bibtex-ruby (5.1.4)
       latex-decode (~> 0.0)
+    bigdecimal (2.0.0)
     builder (3.2.4)
     citeproc (1.0.10)
       namae (~> 1.0)
@@ -48,7 +49,7 @@ GEM
       citeproc (~> 1.0, >= 1.0.9)
       csl (~> 1.5)
     colorize (0.8.1)
-    concurrent-ruby (1.1.6)
+    concurrent-ruby (1.1.7)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
     crass (1.0.6)
@@ -121,7 +122,8 @@ GEM
     namae (1.0.1)
     nokogiri (1.10.10)
       mini_portile2 (~> 2.4.0)
-    oj (3.10.8)
+    oj (3.10.12)
+      bigdecimal (>= 1.0, < 3)
     oj_mimic_json (1.0.1)
     optimist (3.0.1)
     postrank-uri (1.0.24)
@@ -133,7 +135,7 @@ GEM
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
     rake (12.3.3)
-    rdf (3.1.4)
+    rdf (3.1.5)
       hamster (~> 3.0)
       link_header (~> 0.0, >= 0.0.8)
     rdf-aggregate-repo (3.1.0)
@@ -175,7 +177,7 @@ GEM
       rspec (~> 3)
     safe_yaml (1.0.5)
     scanf (1.0.0)
-    simplecov (0.18.5)
+    simplecov (0.19.0)
       docile (~> 1.1)
       simplecov-html (~> 0.11)
     simplecov-html (0.12.2)

data/bolognese.gemspec

@@ -23,7 +23,7 @@ Gem::Specification.new do |s|
   s.add_dependency 'builder', '~> 3.2', '>= 3.2.2'
   s.add_dependency 'activesupport', '>= 4.2.5'
   s.add_dependency 'bibtex-ruby', '>= 5.1.0'
-  s.add_dependency 'thor', '~> 1.0', '>= 1.0.1'
+  s.add_dependency 'thor', '>= 0.19'
   s.add_dependency 'colorize', '~> 0.8.1'
   s.add_dependency 'namae', '~> 1.0'
   s.add_dependency 'edtf', '~> 3.0', '>= 3.0.4'

data/lib/bolognese/readers/crossref_reader.rb

@@ -31,7 +31,7 @@ module Bolognese
         end
 
         # model should be one of book, conference, database, dissertation, journal, peer_review, posted_content,
-        # report-paper, sa_component, standard
+        # report_paper, sa_component, standard
         model = meta.dig("crossref").to_h.keys.last
 
         resource_type = nil
@@ -48,9 +48,13 @@ module Bolognese
           book_metadata = meta.dig("crossref", "book", "book_metadata")
           book_series_metadata = meta.dig("crossref", "book", "book_series_metadata")
           book_set_metadata = meta.dig("crossref", "book", "book_set_metadata")
-          bibliographic_metadata = meta.dig("crossref", "book", "content_item") || book_metadata || book_series_metadata
+          bibliographic_metadata = meta.dig("crossref", "book", "content_item") || book_metadata || book_series_metadata || book_set_metadata
           resource_type = bibliographic_metadata.fetch("component_type", nil) ? "book-" + bibliographic_metadata.fetch("component_type") : "book"
-          publisher = book_metadata.present? ? book_metadata.dig("publisher", "publisher_name") : book_series_metadata.dig("publisher", "publisher_name")
+          # publisher = if book_metadata.present?
+          #               book_metadata.dig("publisher", "publisher_name")
+          #             elsif book_series_metadata.present?
+          #               book_series_metadata.dig("publisher", "publisher_name")
+          #             end
         when "conference"
           event_metadata = meta.dig("crossref", "conference", "event_metadata") || {}
           bibliographic_metadata = meta.dig("crossref", "conference", "conference_paper").to_h
@@ -78,6 +82,11 @@ module Bolognese
         when "database"
           bibliographic_metadata = meta.dig("crossref", "database", "dataset").to_h
           resource_type = "dataset"
+        when "report_paper"
+          bibliographic_metadata = meta.dig("crossref", "report_paper", "report_paper_metadata").to_h
+          resource_type = "report"
+        when "peer_review"
+          bibliographic_metadata = meta.dig("crossref", "peer_review").to_h
         end
 
         resource_type = (resource_type || model).to_s.underscore.camelcase.presence
@@ -152,7 +161,7 @@ module Bolognese
                     end
 
         id = normalize_doi(options[:doi] || options[:id] || bibliographic_metadata.dig("doi_data", "doi"))
-        identifiers = [crossref_alternate_identifiers(bibliographic_metadata)].compact
+        identifiers = crossref_alternate_identifiers(bibliographic_metadata)
 
         { "id" => id,
           "types" => types,
@@ -165,7 +174,7 @@ module Bolognese
           "funding_references" => crossref_funding_reference(program_metadata),
           "publisher" => publisher,
           "container" => container,
-          "agency" => agency = options[:ra] || "Crossref",
+          "agency" => agency = options[:ra] || "crossref",
           "related_identifiers" => related_identifiers,
           "dates" => dates,
           "publication_year" => publication_year,
@@ -183,14 +192,23 @@ module Bolognese
 
       def crossref_alternate_identifiers(bibliographic_metadata)
         if bibliographic_metadata.dig("publisher_item", "item_number").present?
-          { "identifier" => parse_attributes(bibliographic_metadata.dig("publisher_item", "item_number")),
-            "identifierType" => "Publisher ID" }
+          Array.wrap(bibliographic_metadata.dig("publisher_item", "item_number")).map do |item|
+            if item.is_a?(String)
+              { "identifier" => item,
+                "identifierType" => "Publisher ID" }
+            else
+              { "identifier" => item.fetch("__content__", nil),
+                "identifierType" => item.fetch("item_number_type", nil) || "Publisher ID" }
+            end
+          end
         elsif parse_attributes(bibliographic_metadata.fetch("item_number", nil)).present?
-          { "identifier" => parse_attributes(bibliographic_metadata.fetch("item_number", nil)),
-            "identifierType" => "Publisher ID" }
+          [{ "identifier" => parse_attributes(bibliographic_metadata.fetch("item_number", nil)),
+            "identifierType" => "Publisher ID" }]
         elsif parse_attributes(bibliographic_metadata.fetch("isbn", nil)).present?
-          { "identifier" => parse_attributes(bibliographic_metadata.fetch("isbn", nil), first: true),
-            "identifierType" => "ISBN" }
+          [{ "identifier" => parse_attributes(bibliographic_metadata.fetch("isbn", nil), first: true),
+             "identifierType" => "ISBN" }]
+        else
+          []
         end
       end
 
@@ -239,7 +257,7 @@ module Bolognese
             { "nameType" => "Organizational",
               "name" => a["name"] || a["__content__"] }
           end
-        end.unwrap
+        end
       end
 
       def crossref_funding_reference(program_metadata)

data/lib/bolognese/readers/datacite_reader.rb

@@ -227,7 +227,7 @@ module Bolognese
           "contributors" => get_authors(Array.wrap(meta.dig("contributors", "contributor"))),
           "container" => set_container(meta),
           "publisher" => parse_attributes(meta.fetch("publisher", nil), first: true).to_s.strip.presence,
-          "agency" => "DataCite",
+          "agency" => "datacite",
           "funding_references" => funding_references,
           "dates" => dates,
           "publication_year" => parse_attributes(meta.fetch("publicationYear", nil), first: true).to_s.strip.presence,

data/lib/bolognese/utils.rb

@@ -7,6 +7,7 @@ module Bolognese
       "https://creativecommons.org/licenses/by/2.0" => "https://creativecommons.org/licenses/by/2.0/legalcode",
       "https://creativecommons.org/licenses/by/2.5" => "https://creativecommons.org/licenses/by/2.5/legalcode",
       "https://creativecommons.org/licenses/by/3.0" => "https://creativecommons.org/licenses/by/3.0/legalcode",
+      "https://creativecommons.org/licenses/by/3.0/us" => "https://creativecommons.org/licenses/by/3.0/legalcode",
       "https://creativecommons.org/licenses/by/4.0" => "https://creativecommons.org/licenses/by/4.0/legalcode",
       "https://creativecommons.org/licenses/by-nc/1.0" => "https://creativecommons.org/licenses/by-nc/1.0/legalcode",
       "https://creativecommons.org/licenses/by-nc/2.0" => "https://creativecommons.org/licenses/by-nc/2.0/legalcode",
@@ -117,7 +118,7 @@ module Bolognese
       "EditedBook" => "Book",
       "JournalArticle" => "ScholarlyArticle",
       "Journal" => nil,
-      "Report" => nil,
+      "Report" => "Report",
       "BookSeries" => nil,
       "ReportSeries" => nil,
       "BookTrack" => nil,
@@ -132,7 +133,8 @@ module Bolognese
       "ReferenceEntry" => nil,
       "JournalVolume" => "PublicationVolume",
       "BookSet" => nil,
-      "PostedContent" => "ScholarlyArticle"
+      "PostedContent" => "ScholarlyArticle",
+      "PeerReview" => "Review"
     }
 
     CR_TO_BIB_TRANSLATIONS = {
@@ -146,7 +148,7 @@ module Bolognese
       "EditedBook" => "book",
       "JournalArticle" => "article",
       "Journal" => nil,
-      "Report" => nil,
+      "Report" => "techreport",
       "BookSeries" => nil,
       "ReportSeries" => nil,
       "BookTrack" => nil,
@@ -205,6 +207,7 @@ module Bolognese
       "AudioObject" => "Sound",
       "Blog" => "Text",
       "BlogPosting" => "Text",
+      "Book" => "Text",
       "Chapter" => "Text",
       "Collection" => "Collection",
       "DataCatalog" => "Dataset",
@@ -213,9 +216,11 @@ module Bolognese
       "ImageObject" => "Image",
       "Movie" => "Audiovisual",
       "PublicationIssue" => "Text",
+      "Report" => "Text",
       "ScholarlyArticle" => "Text",
       "Thesis" => "Text",
       "Service" => "Service",
+      "Review" => "Text",
       "SoftwareSourceCode" => "Software",
       "VideoObject" => "Audiovisual",
       "WebPage" => "Text",
@@ -257,6 +262,7 @@ module Bolognese
       "ImageObject" => "graphic",
       "Movie" => "motion_picture",
       "PublicationIssue" => nil,
+      "Report" => "report",
       "ScholarlyArticle" => "article-journal",
       "Service" => nil,
       "Thesis" => "thesis",
@@ -277,6 +283,7 @@ module Bolognese
       "Event" => nil,
       "ImageObject" => "FIGURE",
       "Movie" => "MPCT",
+      "Report" => "RPRT",
       "PublicationIssue" => nil,
       "ScholarlyArticle" => "JOUR",
       "Service" => nil,
@@ -297,11 +304,11 @@ module Bolognese
       "EditedBook" => "BOOK",
       "JournalArticle" => "JOUR",
       "Journal" => nil,
-      "Report" => nil,
+      "Report" => "RPRT",
       "BookSeries" => nil,
       "ReportSeries" => nil,
       "BookTrack" => nil,
-      "Standard" => nil,
+      "Standard" => "STAND",
       "BookSection" => "CHAP",
       "BookPart" => "CHAP",
       "Book" => "BOOK",

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.8.3"
+  VERSION = "1.8.8"
 end

data/spec/fixtures/crosscite.json

@@ -58,6 +58,6 @@
         "description": "This tools are used to analyse the data produced by the Crosssover Experiment I designed to test Choice Architecture techniques as UI interventions in a SEEk4Science data catalogue. It contains:\n\n- Data structures for the experimental data.<br>\n- Visualisation functions<br>\n- Analysis functions\n\n## Installation\n\n- R<br>\n- python<br>\n- ipython 4\n\nClone and use.\n\n## Usage\n\n<br>\n```python<br>\nsource('parallel_plot.r')<br>\nwith(z, parallelset(trt,response, freq=count, alpha=0.2))<br>\n```\n\n<br>\n## Contributing\n\n1. Fork it!<br>\n2. Create your feature branch: `git checkout -b my-new-feature`<br>\n3. Commit your changes: `git commit -am 'Add some feature'`<br>\n4. Push to the branch: `git push origin my-new-feature`<br>\n5. Submit a pull request :D\n\n<br>\n## License\n\nThis work supports my PhD Thesis at University of Manchester."
     }],
     "schema_version": "http://datacite.org/schema/kernel-4",
-    "agency": "DataCite",
+    "agency": "datacite",
     "state": "findable"
 }

data/spec/fixtures/datacite.json

@@ -79,5 +79,5 @@
     "description": "Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for..."
   }],
   "schemaVersion": "http://datacite.org/schema/kernel-4",
-  "agency": "DataCite"
+  "agency": "datacite"
 }

data/spec/fixtures/datacite_software.json

@@ -17,5 +17,5 @@
   "publisher": "KNB Data Repository",
   "publication-year": "2016",
   "schema-version": "http://datacite.org/schema/kernel-3",
-  "agency": "DataCite"
+  "agency": "datacite"
 }

data/spec/fixtures/datacite_software_version.json

@@ -68,7 +68,7 @@
   "schemaVersion": "http://datacite.org/schema/kernel-4",
   "providerId": "cern",
   "clientId": "cern.zenodo",
-  "agency": "DataCite",
+  "agency": "datacite",
   "state": "findable"
 }
    

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_oup.yml

@@ -0,0 +1,91 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://doi.org/ra/10.1093
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Mozilla/5.0 (compatible; Maremma/4.7.1; mailto:info@datacite.org)
+      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:
+      Date:
+      - Wed, 29 Jul 2020 18:49:31 GMT
+      Content-Type:
+      - application/json;charset=UTF-8
+      Connection:
+      - keep-alive
+      Set-Cookie:
+      - __cfduid=d6614b5a2ad0605965c4795ee34c9c8951596048571; expires=Fri, 28-Aug-20
+        18:49:31 GMT; path=/; domain=.doi.org; HttpOnly; SameSite=Lax; Secure
+      Cf-Cache-Status:
+      - DYNAMIC
+      Cf-Request-Id:
+      - 043d8195850000c29fe4ae0200000001
+      Expect-Ct:
+      - max-age=604800, report-uri="https://report-uri.cloudflare.com/cdn-cgi/beacon/expect-ct"
+      Strict-Transport-Security:
+      - max-age=31536000; includeSubDomains; preload
+      Server:
+      - cloudflare
+      Cf-Ray:
+      - 5ba90535aee4c29f-FRA
+    body:
+      encoding: ASCII-8BIT
+      string: |-
+        [
+          {
+            "DOI": "10.1093",
+            "RA": "Crossref"
+          }
+        ]
+    http_version:
+  recorded_at: Wed, 29 Jul 2020 18:49:31 GMT
+- request:
+    method: get
+    uri: https://api.crossref.org/works/10.1093/oxfordhb/9780198746140.013.5/transform/application/vnd.crossref.unixsd+xml
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Mozilla/5.0 (compatible; Maremma/4.7.1; mailto:info@datacite.org)
+      Accept:
+      - text/xml
+  response:
+    status:
+      code: 200
+      message: OK
+    headers:
+      Link:
+      - <http://dx.doi.org/10.1093/oxfordhb/9780198746140.013.5>; rel="canonical"
+      Access-Control-Allow-Origin:
+      - "*"
+      Access-Control-Allow-Headers:
+      - X-Requested-With
+      Content-Length:
+      - '5031'
+      Server:
+      - http-kit
+      Date:
+      - Wed, 29 Jul 2020 18:49:32 GMT
+      X-Rate-Limit-Limit:
+      - '50'
+      X-Rate-Limit-Interval:
+      - 1s
+      Connection:
+      - close
+    body:
+      encoding: ASCII-8BIT
+      string: !binary |-
+        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data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/peer_review.yml

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+- request:
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+        rel="author", <http://orcid.org/0000-0002-4997-4063>; title="Alexander J Morley";
+        rel="author", <http://orcid.org/0000-0002-2023-1653>; title="Cole Lincoln
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+    http_version:
+  recorded_at: Sat, 22 Aug 2020 09:09:11 GMT
+recorded_with: VCR 3.0.3