bolognese 1.9.5 → 1.9.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: b05a742623de63d8886a0537b8c967bddcec647de85d65897153bd1639524a78
-  data.tar.gz: adc7f82baf4a99cf8a4c3978a1b9b06278c1284127375d78fccba2c5d120dbb9
+  metadata.gz: ff3bcf60b444241f656e22e8b8af9c56596c76ac9962f1820e7a60325e03dc32
+  data.tar.gz: e4ed9204eeb068c97aadb672f74eb9605bb706f373b78c200e251a3e355f7296
 SHA512:
-  metadata.gz: 13fbe8970222b3de01236c11f5d0b7cb5c8fc639be3b39ece95e60a9eda1d21c25873acfece64b7805c73754a5b2e841306c1c59bda6244d98ce0b297e3b278c
-  data.tar.gz: 8a297ae52be86a370b4249f0be999696c70ab039e4d1f4303eb7d25a27541ab37c161864667d233223bbb3aefda967281a428ff6ce99de95e6b3789b445d126e
+  metadata.gz: 24a0093e1aa36d52a90b2e4db7ba125e3616f26c5f6420570d62ecc750d4a5b075bddc8d159a19e8a8305039066e9f1df27f3e68471a65261712044bcaaf4d1b
+  data.tar.gz: 82c64252ca5f03153aeecbac2d3f3d5f4dc29e50a2ef963fb80ae96271858f9e5e16856865eb0a43eb1686d0de7869f8089bea8395d74fa625e593cf6be0aee0

data/CHANGELOG.md

@@ -1,5 +1,27 @@
 # Changelog
 
+## [Unreleased](https://github.com/datacite/bolognese/tree/HEAD)
+
+[Full Changelog](https://github.com/datacite/bolognese/compare/1.9.5...HEAD)
+
+**Fixed bugs:**
+
+- Missing affiliationIdentiifer when used with schemaURI raises an error [\#116](https://github.com/datacite/bolognese/issues/116)
+- Optional numberType being treated as required generating error [\#112](https://github.com/datacite/bolognese/issues/112)
+
+**Closed issues:**
+
+- Book metadata seems to be ignored [\#113](https://github.com/datacite/bolognese/issues/113)
+- Namespaced XML Tags [\#109](https://github.com/datacite/bolognese/issues/109)
+
+**Merged pull requests:**
+
+- Fix missing affiliation identifier [\#117](https://github.com/datacite/bolognese/pull/117) ([richardhallett](https://github.com/richardhallett))
+
+## [1.9.5](https://github.com/datacite/bolognese/tree/1.9.5) (2021-04-20)
+
+[Full Changelog](https://github.com/datacite/bolognese/compare/1.9.4...1.9.5)
+
 ## [1.9.4](https://github.com/datacite/bolognese/tree/1.9.4) (2021-04-13)
 
 [Full Changelog](https://github.com/datacite/bolognese/compare/1.9.3...1.9.4)
@@ -997,14 +1019,14 @@
 
 [Full Changelog](https://github.com/datacite/bolognese/compare/v.0.11.15...v.0.11.16)
 
-## [v.0.11.15](https://github.com/datacite/bolognese/tree/v.0.11.15) (2018-08-01)
-
-[Full Changelog](https://github.com/datacite/bolognese/compare/v.0.11.14...v.0.11.15)
-
 **Fixed bugs:**
 
 - Handle xs:string attribute [\#32](https://github.com/datacite/bolognese/issues/32)
 
+## [v.0.11.15](https://github.com/datacite/bolognese/tree/v.0.11.15) (2018-08-01)
+
+[Full Changelog](https://github.com/datacite/bolognese/compare/v.0.11.14...v.0.11.15)
+
 ## [v.0.11.14](https://github.com/datacite/bolognese/tree/v.0.11.14) (2018-07-28)
 
 [Full Changelog](https://github.com/datacite/bolognese/compare/v.0.11.3...v.0.11.14)
@@ -1489,6 +1511,7 @@
 - Error displaying container-title [\#13](https://github.com/datacite/bolognese/issues/13)
 - Error parsing funding information [\#12](https://github.com/datacite/bolognese/issues/12)
 - crossref author id to orcid id?  [\#10](https://github.com/datacite/bolognese/issues/10)
+- Support funding information [\#7](https://github.com/datacite/bolognese/issues/7)
 - datacite: support subjectScheme and subjectURI [\#4](https://github.com/datacite/bolognese/issues/4)
 
 ## [v.0.9.21](https://github.com/datacite/bolognese/tree/v.0.9.21) (2017-06-03)
@@ -1499,7 +1522,6 @@
 
 - Abstract should be a string in Citeproc writer [\#11](https://github.com/datacite/bolognese/issues/11)
 - the Bolognese gem doesn't properly handle the optional language attribute. [\#8](https://github.com/datacite/bolognese/issues/8)
-- Support funding information [\#7](https://github.com/datacite/bolognese/issues/7)
 - datacite: support xml:lang in title [\#3](https://github.com/datacite/bolognese/issues/3)
 
 ## [v.0.9.20](https://github.com/datacite/bolognese/tree/v.0.9.20) (2017-05-13)

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.9.5)
+    bolognese (1.9.6)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)
@@ -30,7 +30,7 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (6.1.3.1)
+    activesupport (6.1.3.2)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 1.6, < 2)
       minitest (>= 5.1)
@@ -38,6 +38,7 @@ GEM
       zeitwerk (~> 2.3)
     addressable (2.7.0)
       public_suffix (>= 2.0.2, < 5.0)
+    amazing_print (1.3.0)
     benchmark_methods (0.7)
     bibtex-ruby (6.0.0)
       latex-decode (~> 0.0)
@@ -54,15 +55,17 @@ GEM
     crass (1.0.6)
     csl (1.5.2)
       namae (~> 1.0)
-    csl-styles (1.0.1.10)
+    csl-styles (1.0.1.11)
       csl (~> 1.0)
     diff-lcs (1.4.4)
     docile (1.3.5)
-    ebnf (2.1.2)
+    ebnf (2.1.3)
+      amazing_print (~> 1.2)
       htmlentities (~> 4.3)
       rdf (~> 3.1)
       scanf (~> 1.0)
       sxp (~> 1.1)
+      unicode-types (~> 1.6)
     edtf (3.0.6)
       activesupport (>= 3.0, < 7.0)
     excon (0.71.1)
@@ -191,6 +194,7 @@ GEM
     tilt (2.0.10)
     tzinfo (2.0.4)
       concurrent-ruby (~> 1.0)
+    unicode-types (1.6.0)
     unicode_utils (1.4.0)
     vcr (3.0.3)
     webmock (3.12.1)
@@ -215,4 +219,4 @@ DEPENDENCIES
   webmock (~> 3.0, >= 3.0.1)
 
 BUNDLED WITH
-   2.2.16
+   2.2.18

data/lib/bolognese/author_utils.rb

@@ -138,14 +138,19 @@ module Bolognese
 
     def get_affiliations(affiliations)
       Array.wrap(affiliations).map do |a|
+        affiliation_identifier = nil
         if a.is_a?(String)
           name = a.squish
-          affiliation_identifier = nil
           affiliation_identifier_scheme = nil
           scheme_uri = nil
         else
-          affiliation_identifier = a["affiliationIdentifier"]
-          affiliation_identifier = !affiliation_identifier.to_s.start_with?("https://") && a["schemeURI"].present? ? normalize_id(a["schemeURI"] + affiliation_identifier) : normalize_id(affiliation_identifier)
+          if a["affiliationIdentifier"].present?
+            affiliation_identifier = a["affiliationIdentifier"]
+            if a["schemeURI"].present?
+              schemeURI = a["schemeURI"].end_with?("/") ? a["schemeURI"] : a["schemeURI"] + "/"
+            end
+            affiliation_identifier = !affiliation_identifier.to_s.start_with?("https://") && schemeURI.present? ? normalize_id(schemeURI + affiliation_identifier) : normalize_id(affiliation_identifier)
+          end
           name = a["__content__"].to_s.squish.presence
           affiliation_identifier_scheme = a["affiliationIdentifierScheme"]
           scheme_uri = a["SchemeURI"]

data/lib/bolognese/doi_utils.rb

@@ -9,10 +9,11 @@ module Bolognese
     end
 
     def validate_funder_doi(doi)
-      doi = Array(/\A(?:(http|https):\/(\/)?(dx\.)?(doi.org|handle.test.datacite.org)\/)?(doi:)?(10\.13039\/)?(5.+)\z/.match(doi)).last
+      doi = Array(/\A(?:(http|https):\/(\/)?(dx\.)?(doi.org|handle.test.datacite.org)\/)?(doi:)?(10\.13039\/)?([1-9]\d+)\z/.match(doi)).last
+
       # remove non-printing whitespace and downcase
       if doi.present?
-        doi.delete("\u200B").downcase 
+        doi.delete("\u200B").downcase
         "https://doi.org/10.13039/#{doi}"
       end
     end

data/lib/bolognese/readers/crossref_reader.rb

@@ -56,10 +56,10 @@ module Bolognese
           #               book_series_metadata.dig("publisher", "publisher_name")
           #             end
         when "conference"
-          event_metadata = meta.dig("crossref", "conference", "event_metadata") || {}
+          event_metadata = meta.dig("crossref", "conference", "event_metadata") || {}
           bibliographic_metadata = meta.dig("crossref", "conference", "conference_paper").to_h
         when "journal"
-          journal_metadata = meta.dig("crossref", "journal", "journal_metadata") || {}
+          journal_metadata = meta.dig("crossref", "journal", "journal_metadata") || {}
           journal_issue = meta.dig("crossref", "journal", "journal_issue") || {}
           journal_article = meta.dig("crossref", "journal", "journal_article") || {}
           bibliographic_metadata = journal_article.presence || journal_issue.presence || journal_metadata
@@ -140,7 +140,8 @@ module Bolognese
         state = meta.present? || read_options.present? ? "findable" : "not_found"
 
         related_identifiers = Array.wrap(crossref_is_part_of(journal_metadata)) + Array.wrap(crossref_references(bibliographic_metadata))
-        container = if journal_metadata.present? || book_metadata.present?
+
+        container = if journal_metadata.present?
                       issn = normalize_issn(journal_metadata.to_h.fetch("issn", nil))
 
                       { "type" => "Journal",
@@ -151,6 +152,19 @@ module Bolognese
                         "issue" => parse_attributes(journal_issue.dig("issue")),
                         "firstPage" => bibliographic_metadata.dig("pages", "first_page") || parse_attributes(journal_article.to_h.dig("publisher_item", "item_number"), first: true),
                         "lastPage" => bibliographic_metadata.dig("pages", "last_page") }.compact
+
+                    # By using book_metadata, we can account for where resource_type is `BookChapter` and not assume its a whole book
+                    elsif book_metadata.present?
+                      identifiers = crossref_alternate_identifiers(book_metadata)
+
+                      {
+                        "type" => "Book",
+                        "title" => book_metadata.dig("titles", "title"),
+                        "firstPage" => bibliographic_metadata.dig("pages", "first_page"),
+                        "lastPage" => bibliographic_metadata.dig("pages", "last_page"),
+                        "identifiers" => identifiers,
+                      }.compact
+
                     elsif book_series_metadata.to_h.fetch("series_metadata", nil).present?
                       issn = normalize_issn(book_series_metadata.dig("series_metadata", "issn"))
 
@@ -162,7 +176,10 @@ module Bolognese
                     end
 
         id = normalize_doi(options[:doi] || options[:id] || bibliographic_metadata.dig("doi_data", "doi"))
-        identifiers = crossref_alternate_identifiers(bibliographic_metadata)
+
+        # Let sections override this in case of alternative metadata structures, such as book chapters, which
+        # have their meta inside `content_item`, but the main book indentifers inside of `book_metadata`
+        identifiers ||= crossref_alternate_identifiers(bibliographic_metadata)
 
         { "id" => id,
           "types" => types,

data/lib/bolognese/utils.rb

@@ -1306,8 +1306,8 @@ module Bolognese
         return [{
           "subject" => sanitize(hsh["__content__"] || hsh["subject"]),
           "subjectScheme" => hsh["subjectScheme"],
-          "schemeUri" => hsh["schemeURI"],
-          "valueUri" => hsh["valueURI"],
+          "schemeUri" => hsh["schemeURI"] || hsh["schemeURI"],
+          "valueUri" => hsh["valueURI"] || hsh["valueURI"],
           "classificationCode" => hsh["classificationCode"],
           "lang" => hsh["lang"] }.compact,
         {
@@ -1339,8 +1339,8 @@ module Bolognese
           "subject" => sanitize(hsh["__content__"] || hsh["subject"]),
           "subjectScheme" => hsh["subjectScheme"],
           "classificationCode" => hsh["classificationCode"],
-          "schemeUri" => hsh["schemeURI"],
-          "valueUri" => hsh["valueURI"],
+          "schemeUri" => hsh["schemeURI"] || hsh["schemeURI"],
+          "valueUri" => hsh["valueURI"] || hsh["valueURI"],
           "lang" => hsh["lang"] }.compact,
         {
           "subject" => "FOS: " + subject["fosLabel"],
@@ -1352,8 +1352,8 @@ module Bolognese
           "subject" => sanitize(hsh["__content__"] || hsh["subject"]),
           "subjectScheme" => hsh["subjectScheme"],
           "classificationCode" => hsh["classificationCode"],
-          "schemeUri" => hsh["schemeURI"],
-          "valueUri" => hsh["valueURI"],
+          "schemeUri" => hsh["schemeURI"] || hsh["schemeURI"],
+          "valueUri" => hsh["valueURI"] || hsh["valueURI"],
           "lang" => hsh["lang"] }.compact]
       end
     end

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.9.5"
+  VERSION = "1.9.6"
 end

data/lib/bolognese/writers/jats_writer.rb

@@ -76,7 +76,9 @@ module Bolognese
       end
 
       def insert_source(xml)
-        if is_article? || is_data? || is_chapter?
+        if is_chapter?
+          xml.source(publisher)
+        elsif is_article? || is_data?
           xml.source(container && container["title"] || publisher)
         else
           xml.source(parse_attributes(titles, content: "title", first: true))

data/spec/doi_utils_spec.rb

@@ -272,6 +272,18 @@ describe Bolognese::Metadata, vcr: true do
       response = subject.validate_funder_doi(doi)
       expect(response).to be_nil
     end
+
+    it { expect(subject.validate_funder_doi("10.13039/100000050")).to eq "https://doi.org/10.13039/100000050" }
+    it { expect(subject.validate_funder_doi("10.13039/100006492")).to eq "https://doi.org/10.13039/100006492" }
+    it { expect(subject.validate_funder_doi('http://handle.test.datacite.org/10.13039/100000080')).to eq "https://doi.org/10.13039/100000080" }
+    it { expect(subject.validate_funder_doi('https://doi.org/10.13039/100000001')).to eq "https://doi.org/10.13039/100000001" }
+    it { expect(subject.validate_funder_doi('http://doi.org/10.13039/501100001711')).to eq "https://doi.org/10.13039/501100001711" }
+    it { expect(subject.validate_funder_doi('https://dx.doi.org/10.13039/501100001711')).to eq "https://doi.org/10.13039/501100001711" }
+    it { expect(subject.validate_funder_doi('doi:10.13039/501100001711')).to eq "https://doi.org/10.13039/501100001711" }
+    it { expect(subject.validate_funder_doi('10.13039/501100001711')).to eq "https://doi.org/10.13039/501100001711" }
+    it { expect(subject.validate_funder_doi('501100001711')).to eq "https://doi.org/10.13039/501100001711" }
+    it { expect(subject.validate_funder_doi("https://doi.org/10.13039/5monkeymonkey")).to be_nil }
+    it { expect(subject.validate_funder_doi('10.13039/5monkeymonkey')).to be_nil }
   end
 
   context "validate prefix" do

data/spec/readers/crossref_reader_spec.rb

@@ -372,6 +372,11 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.publication_year).to eq("2015")
       expect(subject.publisher).to eq("Springer Science and Business Media LLC")
       expect(subject.agency).to eq("crossref")
+      expect(subject.container["type"]).to eq("Book")
+      expect(subject.container["title"]).to eq("Shoulder Stiffness")
+      expect(subject.container["firstPage"]).to eq("155")
+      expect(subject.container["lastPage"]).to eq("158")
+      expect(subject.container["identifiers"]).to eq([{"identifier"=>"978-3-662-46369-7", "identifierType"=>"ISBN"}])
     end
 
     it "another book chapter" do
@@ -387,6 +392,10 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.publication_year).to eq("2018")
       expect(subject.publisher).to eq("Springer Science and Business Media LLC")
       expect(subject.agency).to eq("crossref")
+      expect(subject.container["type"]).to eq("Book Series")
+      expect(subject.container["title"]).to eq("SpringerBriefs in Medical Earth Sciences")
+      expect(subject.container["identifier"]).to eq("2523-3629")
+      expect(subject.container["identifierType"]).to eq("ISSN")
     end
 
     it "yet another book chapter" do
@@ -402,6 +411,11 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.publication_year).to eq("2012")
       expect(subject.publisher).to eq("IGI Global")
       expect(subject.agency).to eq("crossref")
+      expect(subject.container["type"]).to eq("Book")
+      expect(subject.container["title"]).to eq("Graph-Based Methods in Computer Vision")
+      expect(subject.container["firstPage"]).to eq("72")
+      expect(subject.container["lastPage"]).to eq("94")
+      expect(subject.container["identifiers"]).to eq([{"identifier"=>"9781466618916", "identifierType"=>"ISBN"}])
     end
 
     it "missing creator" do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.9.5
+  version: 1.9.6
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2021-04-20 00:00:00.000000000 Z
+date: 2021-05-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma