bolognese 0.13.1 → 0.13.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c5476704d65fca65c617a05bae7880bb8c55b750627679cdfe3ef576589097d5
-  data.tar.gz: 4a366ff9b493ff3e1b6503e02971f8d97fe077388687ff53f310cefcddf4edb3
+  metadata.gz: d80546e87d2832b4408b869a0b9dbe8cd6fd47b718fa96cb4680187e37266361
+  data.tar.gz: 5266faafe16fd6750af63857bc6029232e7a0ff45dba74114283bbdd45c536fc
 SHA512:
-  metadata.gz: e0e698a98ce8326a4a4a9a697e48dfd0b04cedd8cc5de1e2cd229c1d68fb66092db334ac891562fe4ab0b83e66d23dd40e888140d7286bc0aecc4cdb8376e764
-  data.tar.gz: ae6bf0a0518576936b55bd8984a72f495195af1f53cfc4cd020b94c90391419b10148fc605416c0eafbdb7e1da7aaaf24337fe1bc08eff63ac5814b04a878186
+  metadata.gz: 1f427e13c17577fbc48d309c1dfc37916cd4e8f8567c3b7da97074fad49631e88463e4e007c8c915db51de09e24359db7930a1e5d3604a550d2bfde5eb6d7715
+  data.tar.gz: bc0b392d86d63786ffd1e175440ad866b6ca1eb68cf313feb290f2f7b48721357fdf84c52929b0e3d544c93cce7f39c96954deeae140ad7ad4b7c71532425572

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (0.13.1)
+    bolognese (0.13.2)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)

data/lib/bolognese/readers/schema_org_reader.rb

@@ -92,6 +92,8 @@ module Bolognese
           "alternate_identifier" => alternate_identifier,
           "b_url" => normalize_id(meta.fetch("url", nil)),
           "content_url" => Array.wrap(meta.fetch("contentUrl", nil)).unwrap,
+          "content_size" => meta.fetch("contenSize", nil),
+          "content_format" => Array.wrap(meta.fetch("encodingFormat", nil) || meta.fetch("fileFormat", nil)).unwrap,
           "title" => meta.fetch("name", nil),
           "author" => author,
           "editor" => editor,

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "0.13.1"
+  VERSION = "0.13.2"
 end

data/lib/bolognese/writers/schema_org_writer.rb

@@ -19,6 +19,7 @@ module Bolognese
           "keywords" => keywords.present? ? Array.wrap(keywords).map { |k| parse_attributes(k, content: "text", first: true) }.join(", ") : nil,
           "inLanguage" => language,
           "contentSize" => content_size,
+          "encodingFormat" => content_format,
           "dateCreated" => date_created,
           "datePublished" => date_published,
           "dateModified" => date_modified,

data/spec/fixtures/gtex.xml

@@ -58,7 +58,10 @@
     <relatedIdentifier relationType="IsDocumentedBy" relatedIdentifierType="DOI">https://doi.org/10.1038/nature24277</relatedIdentifier>  
     <relatedIdentifier relationType="IsSupplementTo" relatedIdentifierType="DOI">https://doi.org/10.1038/nmeth.4407</relatedIdentifier> 
     <relatedIdentifier relationType="IsPartOf" relatedIdentifierType="URL">https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663</relatedIdentifier> 
-  </relatedIdentifiers>  
+  </relatedIdentifiers> 
+  <formats> 
+    <format>application/tar</format> 
+  </formats> 
   <sizes> 
     <size>15.7M</size> 
   </sizes>

data/spec/fixtures/schema_org_topmed.json

@@ -38,6 +38,10 @@
     "@type": "Organization",
     "name": "TOPMed"
   },
+  "citation": {
+    "@type": "Dataset",
+    "@id": "https://doi.org/10.23725/2g4s-qv04"
+  },
   "funding": {
     "@type": "Organization",
     "@id": "https://doi.org/10.13039/100000050",

data/spec/readers/datacite_reader_spec.rb

@@ -643,6 +643,7 @@ describe Bolognese::Metadata, vcr: true do
     expect(subject.keywords).to eq(["gtex", "annotation", "phenotype", "gene regulation", "transcriptomics"])
     expect(subject.date_published).to eq("2017")
     expect(subject.is_supplement_to).to eq("id"=>"https://doi.org/10.1038/nmeth.4407", "type"=>"CreativeWork")
+    expect(subject.content_format).to eq("application/tar")
     expect(subject.content_size).to eq("15.7M")
     expect(subject.container_title).to eq("GTEx")
     expect(subject.publisher).to eq("GTEx")

data/spec/readers/schema_org_reader_spec.rb

@@ -186,6 +186,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.keywords).to eq(["topmed", "whole genome sequencing"])
       expect(subject.date_published).to eq("2017-11-30")
       expect(subject.publisher).to eq("TOPMed")
+      expect(subject.references).to eq("id"=>"https://doi.org/10.23725/2g4s-qv04", "type"=>"Dataset")
       expect(subject.funding).to eq("id"=>"https://doi.org/10.13039/100000050", "name"=>"National Heart, Lung, and Blood Institute (NHLBI)", "type"=>"Organization")
     end
   end

data/spec/writers/schema_org_writer_spec.rb

@@ -133,6 +133,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@id"]).to eq("https://doi.org/10.25491/9hx8-ke93")
       expect(json["author"]).to eq("@type"=>"Organization", "name"=>"The GTEx Consortium")
       expect(json["url"]).to eq("https://ors.datacite.org/doi:/10.25491/9hx8-ke93")
+      expect(json["encodingFormat"]).to eq("application/tar")
       expect(json["contentSize"]).to eq("15.7M")
       expect(json["contentUrl"]).to eq("https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz")
       expect(json["includedInDataCatalog"]).to eq("@id"=>"https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663", "@type"=>"DataCatalog", "name"=>"GTEx")
@@ -253,6 +254,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["contentUrl"]).to eq(["s3://cgp-commons-public/topmed_open_access/197bc047-e917-55ed-852d-d563cdbc50e4/NWD165827.recab.cram", "gs://topmed-irc-share/public/NWD165827.recab.cram"])
       expect(json["schemaVersion"]).to eq("http://datacite.org/schema/kernel-4")
       expect(json["publisher"]).to eq("@type"=>"Organization", "name"=>"TOPMed")
+      expect(json["citation"]).to eq("@id"=>"https://doi.org/10.23725/2g4s-qv04", "@type"=>"Dataset")
       expect(json["funding"]).to eq("@id"=>"https://doi.org/10.13039/100000050", "@type"=>"Organization", "name"=>"National Heart, Lung, and Blood Institute (NHLBI)")
       expect(json["provider"]).to eq("@type"=>"Organization", "name"=>"DataCite")
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 0.13.1
+  version: 0.13.2
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-27 00:00:00.000000000 Z
+date: 2018-08-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma