commonmeta-ruby 3.0.0 → 3.0.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: '00073489682d2a6d2d92def2bdabc4d0119fa4865a7e6eb52350d36c3162d642'
+  metadata.gz: e2856d9b6e5bf1a77fc44ce759aaec04be52527499e3174a78fe6810a55c115e
+  data.tar.gz: f359df0654a8763b0fe673a2fe25e70b624bbc0e7916227d363c10e8095f088d
 SHA512:
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-  data.tar.gz: 2171bf240f94f1c1d34e706ee578eac774f3484e9b70958e31ae1f6d5df2827d06fb42a6f91021cee5a6f5d839362558007d03e5727af8a12212a7859df0245b
+  metadata.gz: 2661a828b3483219293978916a7489c701d6122781983ea12671db189cea576b48ff8629242a0fee08b8df9a72b9a0a7747f2c7fd6631c6c87b2d485b7ffdc0b
+  data.tar.gz: 49cc2dac42c1c7d0bc92dbfca98f32d37fcd36f8278ba55ded256c7e7b488296665dc4bdb6eb3297827e09cd01a55d8d0dfc8e0692e45fed9bd11950ecba3e4c

data/Gemfile.lock

@@ -1,31 +1,25 @@
 PATH
   remote: .
   specs:
-    commonmeta-ruby (3.0.0)
+    commonmeta-ruby (3.0.1)
       activesupport (>= 4.2.5, < 8.0)
       base32-url (>= 0.5.0, < 1)
-      benchmark_methods (~> 0.7)
       bibtex-ruby (~> 6.0)
-      builder (~> 3.2, >= 3.2.2)
+      builder (~> 3.2, >= 3.2.4)
       citeproc-ruby (~> 2.0)
-      colorize (~> 0.8.1)
-      concurrent-ruby (~> 1.1, >= 1.1.5)
       csl-styles (~> 2.0)
       dotenv (~> 2.1, >= 2.1.1)
       edtf (~> 3.0, >= 3.0.4)
-      gender_detector (~> 0.1.2)
+      gender_detector (~> 2.0)
       http (~> 5.1, >= 5.1.1)
       iso8601 (~> 0.9.1)
-      json-ld-preloaded (~> 3.1, >= 3.1.3)
+      json-ld-preloaded (~> 3.2, >= 3.2.2)
       json_schemer (~> 0.2.23)
       jsonlint (~> 0.3.0)
       loofah (~> 2.19)
       namae (~> 1.0)
-      nokogiri (~> 1.14, >= 1.14.2)
-      oj (~> 3.10)
-      oj_mimic_json (~> 1.0, >= 1.0.1)
-      postrank-uri (~> 1.0, >= 1.0.18)
-      public_suffix (= 2.0.5)
+      postrank-uri (~> 1.1)
+      public_suffix (~> 4.0, >= 4.0.7)
       rdf-rdfxml (~> 3.2)
       rdf-turtle (~> 3.2)
       thor (~> 1.1, >= 1.1.0)
@@ -42,7 +36,6 @@ GEM
       public_suffix (>= 2.0.2, < 6.0)
     ast (2.4.2)
     base32-url (0.6.0)
-    benchmark_methods (0.7)
     bibtex-ruby (6.0.0)
       latex-decode (~> 0.0)
     builder (3.2.4)
@@ -53,7 +46,6 @@ GEM
       csl (~> 2.0)
     code-scanning-rubocop (0.6.1)
       rubocop (~> 1.0)
-    colorize (0.8.1)
     concurrent-ruby (1.2.2)
     crack (0.4.5)
       rexml
@@ -82,8 +74,7 @@ GEM
     ffi-compiler (1.0.1)
       ffi (>= 1.0.0)
       rake
-    gender_detector (0.1.2)
-      unicode_utils (>= 1.3.0)
+    gender_detector (2.0.0)
     haml (5.2.2)
       temple (>= 0.8.0)
       tilt
@@ -136,16 +127,15 @@ GEM
     nokogiri (1.14.2-arm64-darwin)
       racc (~> 1.4)
     oj (3.14.2)
-    oj_mimic_json (1.0.1)
     optimist (3.0.1)
     parallel (1.22.1)
     parser (3.2.1.1)
       ast (~> 2.4.1)
-    postrank-uri (1.0.24)
+    postrank-uri (1.1)
       addressable (>= 2.4.0)
       nokogiri (>= 1.8.0)
-      public_suffix (>= 2.0.0, < 2.1)
-    public_suffix (2.0.5)
+      public_suffix (>= 4.0.0, < 5)
+    public_suffix (4.0.7)
     racc (1.6.2)
     rack (2.2.6.4)
     rack-test (2.1.0)
@@ -237,7 +227,6 @@ GEM
     unf_ext (0.0.8.2)
     unicode-display_width (2.4.2)
     unicode-types (1.8.0)
-    unicode_utils (1.4.0)
     uri_template (0.7.0)
     vcr (6.1.0)
     webmock (3.18.1)

data/README.md

@@ -84,128 +84,23 @@ All input is validated against the commonmeta JSON schema.
 
 ## Examples
 
-Read Crossref:
+Read Crossref XML and write as BibTeX:
 
 ```
-commonmeta https://doi.org/10.7554/elife.01567 -t crossref
+commonmeta https://doi.org/10.7554/elife.01567 -f crossref_xml -t bibtex
 
-<?xml version="1.0" encoding="UTF-8"?>
-<doi_records>
-  <doi_record owner="10.7554" timestamp="2015-08-11 07:35:02">
-    <crossref>
-      <journal>
-        <journal_metadata language="en">
-          <full_title>eLife</full_title>
-          <issn media_type="electronic">2050-084X</issn>
-        </journal_metadata>
-        <journal_issue>
-          <publication_date media_type="online">
-            <month>02</month>
-            <day>11</day>
-            <year>2014</year>
-          </publication_date>
-          <journal_volume>
-            <volume>3</volume>
-          </journal_volume>
-        </journal_issue>
-        <journal_article publication_type="full_text">
-          <titles>
-            <title>Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth</title>
-          </titles>
-          <contributors>
-            <person_name contributor_role="author" sequence="first">
-              <given_name>Martial</given_name>
-              <surname>Sankar</surname>
-            </person_name>
-            <person_name contributor_role="author" sequence="additional">
-              <given_name>Kaisa</given_name>
-              <surname>Nieminen</surname>
-            </person_name>
-            <person_name contributor_role="author" sequence="additional">
-              <given_name>Laura</given_name>
-              <surname>Ragni</surname>
-            </person_name>
-            <person_name contributor_role="author" sequence="additional">
-              <given_name>Ioannis</given_name>
-              <surname>Xenarios</surname>
-            </person_name>
-            <person_name contributor_role="author" sequence="additional">
-              <given_name>Christian S</given_name>
-              <surname>Hardtke</surname>
-            </person_name>
-          </contributors>
-          <publication_date media_type="online">
-            <month>02</month>
-            <day>11</day>
-            <year>2014</year>
-          </publication_date>
-          <publisher_item>
-            <identifier id_type="doi">10.7554/eLife.01567</identifier>
-          </publisher_item>
-          <crossmark>
-            <crossmark_version>1</crossmark_version>
-            <crossmark_policy>eLifesciences</crossmark_policy>
-            <crossmark_domains>
-              <crossmark_domain>
-                <domain>www.elifesciences.org</domain>
-              </crossmark_domain>
-            </crossmark_domains>
-            <crossmark_domain_exclusive>false</crossmark_domain_exclusive>
-            <custom_metadata>
-              <assertion name="received" label="Received" group_name="publication_history" group_label="Publication History" order="0">2013-09-20</assertion>
-              <assertion name="accepted" label="Accepted" group_name="publication_history" group_label="Publication History" order="1">2013-12-24</assertion>
-              <assertion name="published" label="Published" group_name="publication_history" group_label="Publication History" order="2">2014-02-11</assertion>
-              <program name="fundref">
-                <assertion name="fundgroup">
-                  <assertion name="funder_name">SystemsX</assertion>
-                </assertion>
-                <assertion name="fundgroup">
-                  <assertion name="funder_name">
-                    EMBO
-                    <assertion name="funder_identifier">http://dx.doi.org/10.13039/501100003043</assertion>
-                  </assertion>
-                </assertion>
-                <assertion name="fundgroup">
-                  <assertion name="funder_name">
-                    Swiss National Science Foundation
-                    <assertion name="funder_identifier">http://dx.doi.org/10.13039/501100001711</assertion>
-                  </assertion>
-                </assertion>
-                <assertion name="fundgroup">
-                  <assertion name="funder_name">
-                    University of Lausanne
-                    <assertion name="funder_identifier" provider="crossref">http://dx.doi.org/10.13039/501100006390</assertion>
-                  </assertion>
-                </assertion>
-              </program>
-              <program name="AccessIndicators">
-                <license_ref applies_to="vor">http://creativecommons.org/licenses/by/3.0/</license_ref>
-                <license_ref applies_to="am">http://creativecommons.org/licenses/by/3.0/</license_ref>
-                <license_ref applies_to="tdm">http://creativecommons.org/licenses/by/3.0/</license_ref>
-              </program>
-            </custom_metadata>
-          </crossmark>
-          <doi_data>
-            <doi>10.7554/eLife.01567</doi>
-            <resource>http://elifesciences.org/lookup/doi/10.7554/eLife.01567</resource>
-          </doi_data>
-          <citation_list>
-            ...
-            <citation key="22">
-              <author>Sankar</author>
-              <cYear>2014</cYear>
-              <doi>10.5061/dryad.b835k</doi>
-            </citation>
-            ...
-          </citation_list>
-          <component_list>
-           ...
-          </component_list>
-        </journal_article>
-      </journal>
-    </crossref>
-  </doi_record>
-</doi_records>
+@article{https://doi.org/10.7554/elife.01567,
+  doi = {10.7554/elife.01567},
+  url = {https://elifesciences.org/articles/01567},
+  author = {Sankar, Martial and Nieminen, Kaisa and Ragni, Laura and Xenarios, Ioannis and Hardtke, Christian S},
+  title = {Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth},
+  journal = {eLife},
+  volume = {3},
+  pages = {e01567},
+  publisher = {eLife Sciences Publications, Ltd},
+  year = {2014},
+  copyright = {CC-BY-3.0}
+}
 ```
 
 Convert Crossref to schema.org/JSON-LD:

data/commonmeta.gemspec

@@ -20,28 +20,22 @@ Gem::Specification.new do |s|
   # Declare dependencies here, rather than in the Gemfile
   s.add_dependency 'activesupport', '>= 4.2.5', '< 8.0'
   s.add_dependency 'base32-url', '>= 0.5.0', '< 1'
-  s.add_dependency 'benchmark_methods', '~> 0.7'
   s.add_dependency 'bibtex-ruby', '~> 6.0'
-  s.add_dependency 'builder', '~> 3.2', '>= 3.2.2'
+  s.add_dependency 'builder', '~> 3.2', '>= 3.2.4'
   s.add_dependency 'citeproc-ruby', '~> 2.0'
-  s.add_dependency 'colorize', '~> 0.8.1'
-  s.add_dependency 'concurrent-ruby', '~> 1.1', '>= 1.1.5'
   s.add_dependency 'csl-styles', '~> 2.0'
   s.add_dependency 'dotenv', '~> 2.1', '>= 2.1.1'
   s.add_dependency 'edtf', '~> 3.0', '>= 3.0.4'
-  s.add_dependency 'gender_detector', '~> 0.1.2'
+  s.add_dependency 'gender_detector', '~> 2.0'
   s.add_dependency 'http', '~> 5.1', '>= 5.1.1'
   s.add_dependency 'iso8601', '~> 0.9.1'
-  s.add_dependency 'json-ld-preloaded', '~> 3.1', '>= 3.1.3'
+  s.add_dependency 'json-ld-preloaded', '~> 3.2', '>= 3.2.2'
   s.add_dependency 'jsonlint', '~> 0.3.0'
   s.add_dependency 'json_schemer', '~> 0.2.23'
   s.add_dependency 'loofah', '~> 2.19'
   s.add_dependency 'namae', '~> 1.0'
-  s.add_dependency 'nokogiri', '~> 1.14', '>= 1.14.2'
-  s.add_dependency 'oj', '~> 3.10'
-  s.add_dependency 'oj_mimic_json', '~> 1.0', '>= 1.0.1'
-  s.add_dependency 'postrank-uri', '~> 1.0', '>= 1.0.18'
-  s.add_dependency 'public_suffix', '2.0.5'
+  s.add_dependency 'postrank-uri', '~> 1.1'
+  s.add_dependency 'public_suffix', '~> 4.0', '>= 4.0.7'
   s.add_dependency 'rdf-rdfxml', '~> 3.2'
   s.add_dependency 'rdf-turtle', '~> 3.2'
   s.add_dependency 'thor', '~> 1.1', '>= 1.1.0'

data/lib/commonmeta/crossref_utils.rb

@@ -27,7 +27,9 @@ module Commonmeta
 
     def crossref_errors(xml: nil)
       filepath = File.expand_path('../../resources/crossref/crossref5.3.1.xsd', __dir__)
-      schema = Nokogiri::XML::Schema(open(filepath))
+      File.open(filepath, 'r') do |f|
+        schema = Nokogiri::XML::Schema(f)
+      end
 
       schema.validate(Nokogiri::XML(xml, nil, 'UTF-8')).map(&:to_s).unwrap
     rescue Nokogiri::XML::SyntaxError => e

data/lib/commonmeta/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Commonmeta
-  VERSION = '3.0.0'
+  VERSION = '3.0.1'
 end

data/lib/commonmeta/writers/datacite_writer.rb

@@ -72,22 +72,15 @@ module Commonmeta
       def datacite_reference(reference)
         return nil unless reference.present? || !reference.is_a?(Hash)
 
-        key = reference['relatedIdentifier']
-        doi = nil
-        url = nil
+        related_identifier = reference['doi'] || reference['url']
 
-        if key.present?
-          if key.start_with?('http')
-            url = key
-          else
-            doi = key
-          end
-        end
+        return nil unless related_identifier.present?
+
+        related_identifier_type = reference['doi'] ? 'DOI' : 'URL'
 
-        { 'relatedIdentifier' => doi,
-          'relatedIdentifierType' => 'DOI',
-          'relationType' => 'References',
-          'relatedMetadataScheme' => 'citeproc+json' }.compact
+        { 'relatedIdentifier' => related_identifier,
+          'relatedIdentifierType' => related_identifier_type,
+          'relationType' => 'References' }.compact
       end
     end
   end

data/lib/commonmeta.rb

@@ -5,10 +5,8 @@ require 'active_support/all'
 require 'nokogiri'
 ActiveSupport::XmlMini.backend = 'Nokogiri'
 require 'http'
-require 'multi_json'
 require 'postrank-uri'
 require 'bibtex'
-require 'colorize'
 require 'loofah'
 require 'json/ld'
 require 'rdf/turtle'
@@ -16,7 +14,6 @@ require 'rdf/rdfxml'
 require 'logger'
 require 'iso8601'
 require 'jsonlint'
-require 'benchmark_methods'
 require 'gender_detector'
 require 'citeproc/ruby'
 require 'citeproc'

data/spec/writers/datacite_writer_spec.rb

@@ -13,6 +13,7 @@ describe Commonmeta::Metadata, vcr: true do
                                             'resourceTypeGeneral' => 'JournalArticle', 'ris' => 'JOUR', 'schemaOrg' => 'ScholarlyArticle')
       expect(datacite.fetch('titles')).to eq([{ 'title' => 'Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth' }])
       expect(datacite.fetch('relatedIdentifiers').length).to eq(27)
+      expect(datacite.fetch('relatedIdentifiers').first).to eq("relatedIdentifier"=>"https://doi.org/10.1038/nature02100", "relatedIdentifierType"=>"DOI", "relationType"=>"References")
       expect(datacite.fetch('rightsList')).to eq([{ 'rights' => 'Creative Commons Attribution 3.0 Unported',
                                                     'rightsIdentifier' => 'cc-by-3.0',
                                                     'rightsIdentifierScheme' => 'SPDX',

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: commonmeta-ruby
 version: !ruby/object:Gem::Version
-  version: 3.0.0
+  version: 3.0.1
 platform: ruby
 authors:
 - Martin Fenner
@@ -50,20 +50,6 @@ dependencies:
     - - "<"
       - !ruby/object:Gem::Version
         version: '1'
-- !ruby/object:Gem::Dependency
-  name: benchmark_methods
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.7'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '0.7'
 - !ruby/object:Gem::Dependency
   name: bibtex-ruby
   requirement: !ruby/object:Gem::Requirement
@@ -87,7 +73,7 @@ dependencies:
         version: '3.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.2.2
+        version: 3.2.4
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
@@ -97,7 +83,7 @@ dependencies:
         version: '3.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.2.2
+        version: 3.2.4
 - !ruby/object:Gem::Dependency
   name: citeproc-ruby
   requirement: !ruby/object:Gem::Requirement
@@ -112,40 +98,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '2.0'
-- !ruby/object:Gem::Dependency
-  name: colorize
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.8.1
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: 0.8.1
-- !ruby/object:Gem::Dependency
-  name: concurrent-ruby
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.1'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.1.5
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.1'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.1.5
 - !ruby/object:Gem::Dependency
   name: csl-styles
   requirement: !ruby/object:Gem::Requirement
@@ -206,14 +158,14 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.1.2
+        version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: 0.1.2
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: http
   requirement: !ruby/object:Gem::Requirement
@@ -254,20 +206,20 @@ dependencies:
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.1'
+        version: '3.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.1.3
+        version: 3.2.2
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '3.1'
+        version: '3.2'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 3.1.3
+        version: 3.2.2
 - !ruby/object:Gem::Dependency
   name: jsonlint
   requirement: !ruby/object:Gem::Requirement
@@ -325,93 +277,39 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '1.0'
 - !ruby/object:Gem::Dependency
-  name: nokogiri
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.14'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.14.2
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.14'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.14.2
-- !ruby/object:Gem::Dependency
-  name: oj
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.10'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '3.10'
-- !ruby/object:Gem::Dependency
-  name: oj_mimic_json
+  name: postrank-uri
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: '1.1'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
-    - - ">="
-      - !ruby/object:Gem::Version
-        version: 1.0.1
+        version: '1.1'
 - !ruby/object:Gem::Dependency
-  name: postrank-uri
+  name: public_suffix
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '4.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.18
+        version: 4.0.7
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '4.0'
     - - ">="
       - !ruby/object:Gem::Version
-        version: 1.0.18
-- !ruby/object:Gem::Dependency
-  name: public_suffix
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 2.0.5
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - '='
-      - !ruby/object:Gem::Version
-        version: 2.0.5
+        version: 4.0.7
 - !ruby/object:Gem::Dependency
   name: rdf-rdfxml
   requirement: !ruby/object:Gem::Requirement