bolognese 1.5.21 → 1.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: '08a98e78c849527bb4f502522dfb758a856ec6454d4c9be58fbd43bd3d826695'
+  metadata.gz: 1a22da55003185429ddc212b5518e74cc414d94d5f87b8047f2ed07859bc8f0d
+  data.tar.gz: adcf4f5f25e7c820b2c23bf0f685f5af1e09c3ba3cd1ec4b850f180fe6919aa3
 SHA512:
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-  data.tar.gz: 0cc8738b5dda31898f84a735df09e5eb97c7242d9cc8091071d6b5ed1c718eee2f61b0e7977e051118a9e74b2b0169140cefc04f31aa7dd71ff4763af7d59c14
+  metadata.gz: 818dba03b12581b2345bf7da3728e99ed713bd16cf0367ccc61aeb072049564ad59f7e56b58d5e68a0c68d40eeafcb0402307721c5b42d8cfeb2c3f2a0fdc96a
+  data.tar.gz: 4dd76c4414a071860b76f108c5ef4145c188a1f909816c2d860c33dfc80b1dc55cffebd5060affabad5b79a6e2b88d61a0fe7107b3d133bfa0905cb866bc6199

data/.gitignore

@@ -55,3 +55,5 @@ coverage/
 .env.*
 !.env.example
 !.env.travis
+
+.vscode

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.5.21)
+    bolognese (1.6)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)
@@ -30,12 +30,12 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (6.0.2.2)
+    activesupport (6.0.3)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
       tzinfo (~> 1.1)
-      zeitwerk (~> 2.2)
+      zeitwerk (~> 2.2, >= 2.2.2)
     addressable (2.7.0)
       public_suffix (>= 2.0.2, < 5.0)
     benchmark_methods (0.7)
@@ -105,7 +105,7 @@ GEM
       oj (>= 2.8.3)
       oj_mimic_json (~> 1.0, >= 1.0.1)
     mini_portile2 (2.4.0)
-    minitest (5.14.0)
+    minitest (5.14.1)
     multi_json (1.14.1)
     multipart-post (2.1.1)
     namae (1.0.1)
@@ -150,7 +150,7 @@ GEM
       rspec-mocks (~> 3.9.0)
     rspec-core (3.9.2)
       rspec-support (~> 3.9.3)
-    rspec-expectations (3.9.1)
+    rspec-expectations (3.9.2)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.9.0)
     rspec-mocks (3.9.1)

data/lib/bolognese/datacite_utils.rb

@@ -172,9 +172,9 @@ module Bolognese
     end
 
     def insert_version(xml)
-      return xml unless version_info.present?
+      return xml unless version.present?
 
-      xml.version(version_info)
+      xml.version(version)
     end
 
 

data/lib/bolognese/metadata.rb

@@ -9,7 +9,7 @@ module Bolognese
     attr_accessor :string, :from, :sandbox, :meta, :regenerate, :issue, :show_errors
     attr_reader :doc, :page_start, :page_end
     attr_writer :id, :provider_id, :client_id, :doi, :identifiers, :creators, :contributors, :titles, :publisher, 
-                :rights_list, :dates, :publication_year, :volume, :url, :version_info,
+                :rights_list, :dates, :publication_year, :volume, :url, :version,
                 :subjects, :contributor, :descriptions, :language, :sizes,
                 :formats, :schema_version, :meta, :container, :agency,
                 :format, :funding_references, :state, :geo_locations,
@@ -106,7 +106,7 @@ module Bolognese
         :publication_year,
         :descriptions,
         :rights_list,
-        :version_info,
+        :version,
         :subjects,
         :language,
         :geo_locations,
@@ -189,10 +189,13 @@ module Bolognese
       @url ||= meta.fetch("url", nil)
     end
 
-    def version_info
-      @version_info ||= meta.fetch("version_info", nil) || meta.fetch("version", nil)
+    def version
+      @version ||= meta.fetch("version", nil)
     end
 
+    # for backwards compatibility
+    alias_attribute :version_info, :version
+
     def publication_year
       @publication_year ||= meta.fetch("publication_year", nil)
     end

data/lib/bolognese/metadata_utils.rb

@@ -158,7 +158,7 @@ module Bolognese
         "publisher" => publisher,
         "title" => parse_attributes(titles, content: "title", first: true),
         "URL" => url,
-        "version" => version_info
+        "version" => version
       }.compact.symbolize_keys
     end
 
@@ -180,7 +180,7 @@ module Bolognese
         "identifiers" => identifiers,
         "sizes" => sizes,
         "formats" => formats,
-        "version" => version_info,
+        "version" => version,
         "rights_list" => rights_list,
         "descriptions" => descriptions,
         "geo_locations" => geo_locations,

data/lib/bolognese/readers/citeproc_reader.rb

@@ -119,7 +119,7 @@ module Bolognese
           "publication_year" => publication_year,
           "descriptions" => meta.fetch("abstract", nil).present? ? [{ "description" => sanitize(meta.fetch("abstract")), "descriptionType" => "Abstract" }] : [],
           "rights_list" => rights_list,
-          "version_info" => meta.fetch("version", nil),
+          "version" => meta.fetch("version", nil),
           "subjects" => subjects,
           "state" => state
         }.merge(read_options)

data/lib/bolognese/readers/codemeta_reader.rb

@@ -79,7 +79,7 @@ module Bolognese
           "publication_year" => publication_year,
           "descriptions" => meta.fetch("description", nil).present? ? [{ "description" => sanitize(meta.fetch("description")), "descriptionType" => "Abstract" }] : nil,
           "rights_list" => [{ "rightsUri" => meta.fetch("license", nil) }.compact],
-          "version_info" => meta.fetch("version", nil),
+          "version" => meta.fetch("version", nil),
           "subjects" => subjects,
           "state" => state
         }.merge(read_options)

data/lib/bolognese/readers/crossref_reader.rb

@@ -172,7 +172,7 @@ module Bolognese
           "publication_year" => publication_year,
           "descriptions" => crossref_description(bibliographic_metadata),
           "rights_list" => crossref_license(program_metadata),
-          "version_info" => nil,
+          "version" => nil,
           "subjects" => nil,
           "language" => nil,
           "sizes" => nil,

data/lib/bolognese/readers/datacite_reader.rb

@@ -230,7 +230,7 @@ module Bolognese
           "publication_year" => parse_attributes(meta.fetch("publicationYear", nil), first: true).to_s.strip.presence,
           "descriptions" => descriptions,
           "rights_list" => Array.wrap(rights_list),
-          "version_info" => meta.fetch("version", nil).to_s.presence,
+          "version" => meta.fetch("version", nil).to_s.presence,
           "subjects" => subjects,
           "language" => parse_attributes(meta.fetch("language", nil), first: true).to_s.strip.presence,
           "geo_locations" => geo_locations,

data/lib/bolognese/readers/npm_reader.rb

@@ -105,7 +105,7 @@ module Bolognese
           #"publication_year" => publication_year,
           "descriptions" => meta.fetch("description", nil).present? ? [{ "description" => sanitize(meta.fetch("description")), "descriptionType" => "Abstract" }] : [],
           "rights_list" => rights_list,
-          "version_info" => meta.fetch("version", nil),
+          "version" => meta.fetch("version", nil),
           "subjects" => subjects
           #"state" => state
         }.merge(read_options)

data/lib/bolognese/readers/schema_org_reader.rb

@@ -173,7 +173,7 @@ module Bolognese
           "dates" => dates,
           "descriptions" => meta.fetch("description", nil).present? ? [{ "description" => sanitize(meta.fetch("description")), "descriptionType" => "Abstract" }] : nil,
           "rights_list" => rights_list,
-          "version_info" => meta.fetch("version", nil).to_s.presence,
+          "version" => meta.fetch("version", nil).to_s.presence,
           "subjects" => subjects,
           "state" => state,
           "schema_version" => meta.fetch("schemaVersion", nil).to_s.presence,

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.5.21"
+  VERSION = "1.6"
 end

data/lib/bolognese/writers/codemeta_writer.rb

@@ -15,7 +15,7 @@ module Bolognese
           "name" => parse_attributes(titles, content: "title", first: true),
           "authors" => creators,
           "description" => parse_attributes(descriptions, content: "description", first: true),
-          "version" => version_info,
+          "version" => version,
           "tags" => subjects.present? ? Array.wrap(subjects).map { |k| parse_attributes(k, content: "subject", first: true) } : nil,
           "datePublished" => get_date(dates, "Issued"),
           "dateModified" => get_date(dates, "Updated"),

data/lib/bolognese/writers/jats_writer.rb

@@ -22,7 +22,7 @@ module Bolognese
         insert_issue(xml) if container.to_h["issue"].present?
         insert_fpage(xml) if container.to_h["firstPage"].present?
         insert_lpage(xml) if container.to_h["lastPage"].present?
-        insert_version(xml) if version_info.present?
+        insert_version(xml) if version.present?
         insert_pub_id(xml)
       end
 
@@ -112,7 +112,7 @@ module Bolognese
       end
 
       def insert_version(xml)
-        xml.version(version_info)
+        xml.version(version)
       end
 
       def insert_pub_id(xml)

data/lib/bolognese/writers/schema_org_writer.rb

@@ -15,7 +15,7 @@ module Bolognese
           "editor" => to_schema_org_contributors(contributors),
           "description" => parse_attributes(descriptions, content: "description", first: true),
           "license" => Array.wrap(rights_list).map { |l| l["rightsUri"] }.compact.unwrap,
-          "version" => version_info,
+          "version" => version,
           "keywords" => subjects.present? ? Array.wrap(subjects).map { |k| parse_attributes(k, content: "subject", first: true) }.join(", ") : nil,
           "inLanguage" => language,
           "contentSize" => Array.wrap(sizes).unwrap,

data/spec/readers/codemeta_reader_spec.rb

@@ -68,7 +68,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.titles).to eq([{"title"=>"R Interface to the DataONE REST API"}])
       expect(subject.descriptions.first["description"]).to start_with("Provides read and write access to data and metadata")
       expect(subject.subjects).to eq([{"subject"=>"data sharing"}, {"subject"=>"data repository"}, {"subject"=>"DataONE"}])
-      expect(subject.version_info).to eq("2.0.0")
+      expect(subject.version).to eq("2.0.0")
       expect(subject.dates).to eq([{"date"=>"2016-05-27", "dateType"=>"Issued"}, {"date"=>"2016-05-27", "dateType"=>"Created"}, {"date"=>"2016-05-27", "dateType"=>"Updated"}])
       expect(subject.publication_year).to eq("2016")
       expect(subject.publisher).to eq("https://cran.r-project.org")

data/spec/readers/datacite_json_reader_spec.rb

@@ -69,7 +69,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.identifiers).to eq([{"identifier"=>"https://doi.org/10.5281/zenodo.28518", "identifierType"=>"DOI"}, {"identifier"=>"https://zenodo.org/record/28518", "identifierType"=>"URL"}])
       expect(subject.dates).to eq([{"date"=>"2015-08-19", "dateType"=>"Issued"}])
       expect(subject.publication_year).to eq("2015")
-      expect(subject.version_info).to eq("v0.3.2")
+      expect(subject.version).to eq("v0.3.2")
       expect(subject.datacite).to include("<version>v0.3.2</version>")
       expect(subject.related_identifiers.length).to eq(2)
       expect(subject.related_identifiers.first).to eq("relatedIdentifier"=>"https://github.com/jakevdp/supersmoother/tree/v0.3.2", "relatedIdentifierType"=>"URL", "relationType"=>"IsSupplementTo")

data/spec/readers/datacite_reader_spec.rb

@@ -867,7 +867,7 @@ describe Bolognese::Metadata, vcr: true do
                                      "nameIdentifiers"=> [{"nameIdentifier"=>"https://orcid.org/0000-0002-8743-4455", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}],
                                      "affiliation"=>[{"name"=>"Royal Netherlands Meteorological Institute (KNMI)"}]}])
       expect(subject.titles).to eq([{"title"=>"Multi-Sensor Reanalysis (MSR) of total ozone, version 2"}])
-      expect(subject.version_info).to eq("2")
+      expect(subject.version).to eq("2")
       expect(subject.dates).to eq([{"date"=>"2014-04-25", "dateType"=>"Available"}, {"date"=>"2015", "dateType"=>"Issued"}])
       expect(subject.publication_year).to eq("2015")
       expect(subject.publisher).to eq("Royal Netherlands Meteorological Institute (KNMI)")

data/spec/readers/npm_reader_spec.rb

@@ -24,7 +24,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.titles).to eq([{"title"=>"fullstack_app"}])
       expect(subject.descriptions).to be_empty
       expect(subject.rights_list).to eq([{"rights"=>"ISC"}])
-      expect(subject.version_info).to eq("1.0.0")
+      expect(subject.version).to eq("1.0.0")
       #expect(subject.dates).to eq([{"date"=>"2016-12-20", "dateType"=>"Issued"}])
       #expect(subject.publication_year).to eq("2016")
     end
@@ -40,7 +40,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.creators).to eq([{"name"=>":(unav)", "nameType"=>"Organizational"}])
       expect(subject.titles).to eq([{"title"=>"CITapp"}])
       expect(subject.descriptions).to eq([{"description"=>"Concealed Information Test app", "descriptionType"=>"Abstract"}])
-      expect(subject.version_info).to eq("1.1.0")
+      expect(subject.version).to eq("1.1.0")
       #expect(subject.dates).to eq([{"date"=>"2016-12-20", "dateType"=>"Issued"}])
       #expect(subject.publication_year).to eq("2016")
     end
@@ -58,7 +58,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.descriptions).to eq([{"description"=>
         +   "The EDAM Browser is a client-side web-based visualization javascript widget. Its goals are to help describing bio-related resources and service with EDAM, and to facilitate and foster community contributions to EDAM.",
            "descriptionType"=>"Abstract"}])
-      expect(subject.version_info).to eq("1.0.0")
+      expect(subject.version).to eq("1.0.0")
       #expect(subject.dates).to eq([{"date"=>"2016-12-20", "dateType"=>"Issued"}])
       #expect(subject.publication_year).to eq("2016")
     end

data/spec/readers/schema_org_reader_spec.rb

@@ -165,7 +165,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceType"=>"Gene expression matrices", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
       expect(subject.creators).to eq([{"name"=>"The GTEx Consortium", "nameType"=>"Organizational", "nameIdentifiers"=>[], "affiliation" => []}])
       expect(subject.titles).to eq([{"title"=>"Fully processed, filtered and normalized gene expression matrices (in BED format) for each tissue, which were used as input into FastQTL for eQTL discovery"}])
-      expect(subject.version_info).to eq("v7")
+      expect(subject.version).to eq("v7")
       expect(subject.subjects).to eq([{"subject"=>"gtex"}, {"subject"=>"annotation"}, {"subject"=>"phenotype"}, {"subject"=>"gene regulation"}, {"subject"=>"transcriptomics"}])
       expect(subject.dates).to eq([{"date"=>"2017", "dateType"=>"Issued"}])
       expect(subject.publication_year).to eq("2017")
@@ -275,7 +275,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
       # expect(subject.creators).to eq([{"familyName"=>"Lindman", "givenName"=>"Karin", "name"=>"Lindman, Karin", "nameIdentifiers"=>[{"nameIdentifier"=> "https://orcid.org/0000-0003-1298-517X", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}], "nameType"=>"Personal"}])
       expect(subject.titles).to eq([{"title"=>"Ovary data from the Visual Sweden project DROID"}])
-      expect(subject.version_info).to eq("1.0")
+      expect(subject.version).to eq("1.0")
       expect(subject.subjects).to eq([{"subject"=>"pathology"}, {"subject"=>"whole slide imaging"}, {"subject"=>"annotated"}])
       expect(subject.dates).to eq([{"date"=>"2019-01-09", "dateType"=>"Issued"}, {"date"=>"2019-01-09", "dateType"=>"Created"}, {"date"=>"2019-01-09", "dateType"=>"Updated"}])
       expect(subject.publication_year).to eq("2019")

data/spec/writers/datacite_writer_spec.rb

@@ -145,6 +145,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.dates).to eq([{"date"=>"2015-08-19", "dateType"=>"Issued"}])
       expect(subject.publication_year).to eq("2015")
       expect(subject.version_info).to eq("v0.3.2")
+      expect(subject.version).to eq("v0.3.2")
       expect(subject.publisher).to eq("Zenodo")
       expect(subject.agency).to eq("DataCite")
       expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-4")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.5.21
+  version: '1.6'
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-05-03 00:00:00.000000000 Z
+date: 2020-05-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma