bolognese 1.6.2 → 1.6.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: ebc11d65b789fb08e97dafa25c2e9e0b2ddfb6085011478498f2e619ebdd605c
+  metadata.gz: e096d175d7f9184274a6a18584aeb10a15f24c88c5e34f42916ec0cf6fc5e052
+  data.tar.gz: b5b2034bb8cf6c902faa88eecc3866a112b8520e12bacb375dcc3b24ba3ead89
 SHA512:
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-  data.tar.gz: e30113a9e7ceddb8772a8e26310c7bc9ecdb349c93a33596c4d2ff0167c12650631e7dee7860c32a2e4dd8323453ed6acd7315c292060aef5a03954fbca61682
+  metadata.gz: e0263214c5bb855eed1a018ade0b94709683cb9fcbf14f692909ef727aebf51a71098fed2946e100cf212b6de0ee6c76390fdc4612e00003859ce8bd56784a8d
+  data.tar.gz: '081329825dec027a324fdd71784554242a416e80f55e3957e63439be1ca906d28b8c28a937f397e2bfcfd1442369ba48cdf3b2f94a4a33b3ece13b770db65871'

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.6.2)
+    bolognese (1.6.3)
       activesupport (>= 4.2.5)
       benchmark_methods (~> 0.7)
       bibtex-ruby (>= 5.1.0)

data/lib/bolognese/datacite_utils.rb

@@ -172,9 +172,9 @@ module Bolognese
     end
 
     def insert_version(xml)
-      return xml unless version.present?
+      return xml unless version_info.present?
 
-      xml.version(version)
+      xml.version(version_info)
     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,
+                :rights_list, :dates, :publication_year, :volume, :url, :version_info,
                 :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,
+        :version_info,
         :subjects,
         :language,
         :geo_locations,
@@ -189,13 +189,10 @@ module Bolognese
       @url ||= meta.fetch("url", nil)
     end
 
-    def version
-      @version ||= meta.fetch("version", nil)
+    def version_info
+      @version_info ||= meta.fetch("version_info", nil) || 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
+        "version" => version_info
       }.compact.symbolize_keys
     end
 
@@ -180,7 +180,7 @@ module Bolognese
         "identifiers" => identifiers,
         "sizes" => sizes,
         "formats" => formats,
-        "version" => version,
+        "version" => version_info,
         "rights_list" => rights_list,
         "descriptions" => descriptions,
         "geo_locations" => geo_locations,

data/lib/bolognese/readers/citeproc_reader.rb

@@ -121,7 +121,7 @@ module Bolognese
           "publication_year" => publication_year,
           "descriptions" => meta.fetch("abstract", nil).present? ? [{ "description" => sanitize(meta.fetch("abstract")), "descriptionType" => "Abstract" }] : [],
           "rights_list" => rights_list,
-          "version" => meta.fetch("version", nil),
+          "version_info" => meta.fetch("version", nil),
           "subjects" => subjects,
           "state" => state
         }.merge(read_options)

data/lib/bolognese/readers/codemeta_reader.rb

@@ -81,7 +81,7 @@ 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" => meta.fetch("version", nil),
+          "version_info" => 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" => nil,
+          "version_info" => nil,
           "subjects" => nil,
           "language" => nil,
           "sizes" => nil,

data/lib/bolognese/readers/datacite_reader.rb

@@ -235,7 +235,7 @@ 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" => meta.fetch("version", nil).to_s.presence,
+          "version_info" => 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" => meta.fetch("version", nil),
+          "version_info" => meta.fetch("version", nil),
           "subjects" => subjects
           #"state" => state
         }.merge(read_options)

data/lib/bolognese/readers/schema_org_reader.rb

@@ -178,7 +178,7 @@ module Bolognese
           "dates" => dates,
           "descriptions" => meta.fetch("description", nil).present? ? [{ "description" => sanitize(meta.fetch("description")), "descriptionType" => "Abstract" }] : nil,
           "rights_list" => rights_list,
-          "version" => meta.fetch("version", nil).to_s.presence,
+          "version_info" => 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 = "1.6.2"
+  VERSION = "1.6.3"
 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,
+          "version" => version_info,
           "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.present?
+        insert_version(xml) if version_info.present?
         insert_pub_id(xml)
       end
 
@@ -112,7 +112,7 @@ module Bolognese
       end
 
       def insert_version(xml)
-        xml.version(version)
+        xml.version(version_info)
       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,
+          "version" => version_info,
           "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).to eq("2.0.0")
+      expect(subject.version_info).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).to eq("v0.3.2")
+      expect(subject.version_info).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

@@ -967,7 +967,7 @@ 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).to eq("2")
+      expect(subject.version_info).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).to eq("1.0.0")
+      expect(subject.version_info).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).to eq("1.1.0")
+      expect(subject.version_info).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).to eq("1.0.0")
+      expect(subject.version_info).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

@@ -180,7 +180,7 @@ 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).to eq("v7")
+      expect(subject.version_info).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")
@@ -290,7 +290,7 @@ 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).to eq("1.0")
+      expect(subject.version_info).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

@@ -145,7 +145,6 @@ 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

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.6.2
+  version: 1.6.3
 platform: ruby
 authors:
 - Martin Fenner