bolognese 0.15.9 → 1.0

data/spec/writers/ris_writer_spec.rb

@@ -17,8 +17,10 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[9]).to eq("UR  - https://elifesciences.org/articles/01567")
       expect(ris[10]).to  start_with("AB  - Among various advantages")
       expect(ris[11]).to eq("PY  - 2014")
-      expect(ris[12]).to eq("VL  - 3")
-      expect(ris[13]).to eq("ER  - ")
+      expect(ris[12]).to eq("PB  - (:unav)")
+      expect(ris[13]).to eq("VL  - 3")
+      expect(ris[14]).to eq("SN  - 2050-084X")
+      expect(ris[15]).to eq("ER  - ")
     end
 
     it "with pages" do
@@ -34,10 +36,12 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[11]).to eq("UR  - http://www.hindawi.com/journals/pm/2012/291294/")
       expect(ris[12]).to start_with("AB  - . To find a statistically significant separation point for the QuantiFERON")
       expect(ris[13]).to eq("PY  - 2012")
-      expect(ris[14]).to eq("VL  - 2012")
-      expect(ris[15]).to eq("SP  - 1")
-      expect(ris[16]).to eq("EP  - 7")
-      expect(ris[17]).to eq("ER  - ")
+      expect(ris[14]).to eq("PB  - (:unav)")
+      expect(ris[15]).to eq("VL  - 2012")
+      expect(ris[16]).to eq("SP  - 1")
+      expect(ris[17]).to eq("EP  - 7")
+      expect(ris[18]).to eq("SN  - 2090-1836")
+      expect(ris[19]).to eq("ER  - ")
     end
 
     it "alternate name" do
@@ -55,7 +59,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[21]).to eq("PY  - 2017")
       expect(ris[22]).to eq("PB  - German Medical Science GMS Publishing House")
       expect(ris[23]).to eq("LA  - en")
-      expect(ris[24]).to eq("ER  - ")
+      expect(ris[24]).to eq("SN  - 2366-5017")
+      expect(ris[25]).to eq("ER  - ")
     end
 
     it "Crossref DOI" do
@@ -72,7 +77,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[11]).to eq("PY  - 2014")
       expect(ris[12]).to eq("PB  - {eLife} Sciences Organisation, Ltd.")
       expect(ris[13]).to eq("VL  - 3")
-      expect(ris[14]).to eq("ER  - ")
+      expect(ris[14]).to eq("SN  - 2050-084X")
+      expect(ris[15]).to eq("ER  - ")
     end
 
     it "BlogPosting" do
@@ -88,7 +94,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[5]).to eq("KW  - datacite")
       expect(ris[8]).to eq("PY  - 2016")
       expect(ris[9]).to eq("PB  - DataCite")
-      expect(ris[10]).to eq("ER  - ")
+      expect(ris[10]).to eq("SN  - 10.5438/0000-00ss")
+      expect(ris[11]).to eq("ER  - ")
     end
 
     it "BlogPosting Citeproc JSON" do
@@ -120,7 +127,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[5]).to eq("KW  - datacite")
       expect(ris[8]).to eq("PY  - 2016")
       expect(ris[9]).to eq("PB  - DataCite")
-      expect(ris[10]).to eq("ER  - ")
+      expect(ris[10]).to eq("SN  - 10.5438/0000-00ss")
+      expect(ris[11]).to eq("ER  - ")
     end
 
     it "BlogPosting schema.org" do
@@ -129,14 +137,14 @@ describe Bolognese::Metadata, vcr: true do
       ris = subject.ris.split("\r\n")
       expect(ris[0]).to eq("TY  - GEN")
       expect(ris[1]).to eq("T1  - Eating your own Dog Food")
-      expect(ris[2]).to eq("T2  - DataCite Blog")
-      expect(ris[3]).to eq("AU  - Fenner, Martin")
-      expect(ris[4]).to eq("DO  - 10.5438/4k3m-nyvg")
-      expect(ris[5]).to eq("UR  - https://blog.datacite.org/eating-your-own-dog-food")
-      expect(ris[6]).to eq("AB  - Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...")
-      expect(ris[7]).to eq("KW  - datacite")
-      expect(ris[11]).to eq("PY  - 2016")
-      expect(ris[12]).to eq("PB  - DataCite")
+      expect(ris[2]).to eq("AU  - Fenner, Martin")
+      expect(ris[3]).to eq("DO  - 10.5438/4k3m-nyvg")
+      expect(ris[4]).to eq("UR  - https://blog.datacite.org/eating-your-own-dog-food")
+      expect(ris[5]).to eq("AB  - Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...")
+      expect(ris[6]).to eq("KW  - datacite")
+      expect(ris[10]).to eq("PY  - 2016")
+      expect(ris[11]).to eq("PB  - DataCite")
+      expect(ris[12]).to eq("SN  - 10.5438/0000-00ss")
       expect(ris[13]).to eq("ER  - ")
     end
 

data/spec/writers/schema_org_writer_spec.rb

@@ -10,9 +10,10 @@ describe Bolognese::Metadata, vcr: true do
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.7554/elife.01567")
       expect(json["isPartOf"]).to eq("@type"=>"Periodical", "name"=>"eLife", "issn"=>"2050-084X")
+      expect(json["periodical"]).to eq("@type"=>"Periodical", "name"=>"eLife", "issn"=>"2050-084X")
       expect(json["citation"].length).to eq(26)
       expect(json["citation"].first).to eq("@id"=>"https://doi.org/10.1038/nature02100", "@type"=>"CreativeWork", "name" => "APL regulates vascular tissue identity in Arabidopsis")
-      expect(json["funding"]).to eq([{"name"=>"SystemsX", "@type"=>"Organization"},
+      expect(json["funder"]).to eq([{"name"=>"SystemsX", "@type"=>"Organization"},
                                      {"name"=>"EMBO",
                                       "@type"=>"Organization",
                                       "@id"=>"https://doi.org/10.13039/501100003043"},
@@ -47,7 +48,8 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.5061/dryad.8515")
-      expect(json["@reverse"]).to eq("citation"=>{"@id"=>"https://doi.org/10.1371/journal.ppat.1000446"}, "isBasedOn"=>{"@id"=>"https://doi.org/10.1371/journal.ppat.1000446"})
+      expect(json["@reverse"]).to eq("citation" => [{"@id"=>"https://doi.org/10.1371/journal.ppat.1000446", "@type"=>"CreativeWork"}, {"@type"=>"CreativeWork", "identifier"=>{"@type"=>"PropertyValue", "propertyID"=>"PMID", "value"=>"19478877"}}],
+        "isBasedOn" => [{"@id"=>"https://doi.org/10.1371/journal.ppat.1000446", "@type"=>"CreativeWork"}, {"@type"=>"CreativeWork", "identifier"=>{"@type"=>"PropertyValue", "propertyID"=>"PMID", "value"=>"19478877"}}])
     end
 
     it "Schema.org JSON IsSupplementTo" do
@@ -55,7 +57,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.5517/cc8h01s")
-      expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1107/s1600536804021154"})
+      expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1107/s1600536804021154", "@type"=>"CreativeWork"})
     end
 
     it "rdataone" do
@@ -86,11 +88,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@id"]).to eq("https://doi.org/10.5438/6423")
       expect(json["hasPart"].length).to eq(25)
       expect(json["hasPart"].first).to eq("@type"=>"CreativeWork", "@id"=>"https://doi.org/10.5281/zenodo.30799")
-      expect(json["funding"]).to eq("@type" => "Award",
-                                    "funder" => {"@type"=>"Organization", "@id"=>"https://doi.org/10.13039/501100000780", "name"=>"European Commission"},
-                                    "identifier" => "654039",
-                                    "name" => "THOR – Technical and Human Infrastructure for Open Research",
-                                    "url" => "http://cordis.europa.eu/project/rcn/194927_en.html")
+      expect(json["funder"]).to eq("@id"=>"https://doi.org/10.13039/501100000780", "@type"=>"Organization", "name"=>"European Commission")
     end
 
     it "Funding OpenAIRE" do
@@ -98,11 +96,7 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.5281/zenodo.1239")
-      expect(json["funding"]).to eq("@type" => "Award",
-                                    "funder" => {"@type"=>"Organization", "@id"=>"https://doi.org/10.13039/501100000780", "name"=>"European Commission"},
-                                    "identifier" => "246686",
-                                    "name" => "Open Access Infrastructure for Research in Europe",
-                                    "url" => "info:eu-repo/grantAgreement/EC/FP7/246686/")
+      expect(json["funder"]).to eq("@id"=>"https://doi.org/10.13039/501100000780", "@type"=>"Organization", "name"=>"European Commission")
     end
 
     it "subject scheme" do
@@ -129,7 +123,6 @@ describe Bolognese::Metadata, vcr: true do
       content_url = "https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz"  
       subject = Bolognese::Metadata.new(input: input, b_url: b_url, content_url: content_url, from: "datacite")
       json = JSON.parse(subject.schema_org)
-      puts json
       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")
@@ -137,19 +130,19 @@ describe Bolognese::Metadata, vcr: true do
       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")
-      expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1038/nmeth.4407"})
+      expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1038/nmeth.4407", "@type"=>"CreativeWork"})
     end
 
     it "series information" do
       input = "10.4229/23RDEUPVSEC2008-5CO.8.3"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")
       json = JSON.parse(subject.schema_org)
-      expect(json["isPartOf"]).to eq("@type"=>"Periodical", "name"=>"23rd European Photovoltaic Solar Energy Conference and Exhibition, 1-5 September 2008, Valencia, Spain; 3353-3356")
       expect(json["@id"]).to eq("https://doi.org/10.4229/23rdeupvsec2008-5co.8.3")
       expect(json["@type"]).to eq("ScholarlyArticle")
       expect(json["name"]).to eq("Rural Electrification With Hybrid Power Systems Based on Renewables - Technical System Configurations From the Point of View of the European Industry")
       expect(json["author"].count).to eq(3)
       expect(json["author"].first).to eq("@type"=>"Person", "name"=>"P. Llamas", "givenName"=>"P.", "familyName"=>"Llamas")
+      expect(json["periodical"]).to eq("@type"=>"Periodical", "name"=>"23rd European Photovoltaic Solar Energy Conference and Exhibition, 1-5 September 2008, Valencia, Spain; 3353-3356")
     end
 
     it "data catalog" do
@@ -191,6 +184,40 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["contentUrl"]).to include("s3://cgp-commons-public/topmed_open_access/197bc047-e917-55ed-852d-d563cdbc50e4/NWD165827.recab.cram", "gs://topmed-irc-share/public/NWD165827.recab.cram")
     end
 
+    it "geo_location_point" do
+      input = fixture_path + 'datacite-example-geolocation-2.xml'
+      doi = "10.6071/Z7WC73"
+      subject = Bolognese::Metadata.new(input: input, doi: doi)
+      json = JSON.parse(subject.schema_org)
+      expect(json["@id"]).to eq("https://doi.org/10.6071/z7wc73")
+      expect(json["@type"]).to eq("Dataset")
+      expect(json["name"]).to eq("Southern Sierra Critical Zone Observatory (SSCZO), Providence Creek\n      meteorological data, soil moisture and temperature, snow depth and air\n      temperature")
+      expect(json["author"].length).to eq(6)
+      expect(json["author"][2]).to eq("@id"=>"https://orcid.org/0000-0002-8862-1404", "@type"=>"Person", "familyName"=>"Stacy", "givenName"=>"Erin", "name"=>"Erin Stacy")
+      expect(json["includedInDataCatalog"]).to be_nil
+      expect(json["spatialCoverage"]).to eq("@type"=>"Place", "geo"=>{"@type"=>"GeoCoordinates", "address"=>"Providence Creek (Lower, Upper and P301)", "latitude"=>"37.047756", "longitude"=>"-119.221094"})
+    end
+
+    it "geo_location_box" do
+      input = "10.1594/PANGAEA.842237"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      json = JSON.parse(subject.schema_org)
+      expect(json["@id"]).to eq("https://doi.org/10.1594/pangaea.842237")
+      expect(json["@type"]).to eq("Dataset")
+      expect(json["name"]).to eq("Registry of all stations from the Tara Oceans Expedition (2009-2013)")
+      expect(json["author"]).to eq([{"@type"=>"Person",
+        "familyName"=>"Tara Oceans Consortium",
+        "givenName"=>"Coordinators",
+        "name"=>"Tara Oceans Consortium, Coordinators"},
+       {"@type"=>"Person",
+        "familyName"=>"Tara Oceans Expedition",
+        "givenName"=>"Participants",
+        "name"=>"Tara Oceans Expedition, Participants"}])
+      expect(json["includedInDataCatalog"]).to be_nil
+      expect(json["identifier"]).to eq("@type"=>"PropertyValue", "propertyID"=>"doi", "value"=>"https://doi.org/10.1594/pangaea.842237")
+      expect(json["spatialCoverage"]).to eq("@type"=>"Place", "geo"=>{"@type"=>"GeoShape", "box"=>"-64.3088 -168.5182 79.6753 174.9006"})
+    end
+
     it "from schema_org gtex" do
       input = fixture_path + 'schema_org_gtex.json'
       subject = Bolognese::Metadata.new(input: input, from: "schema_org")
@@ -209,7 +236,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["schemaVersion"]).to eq("http://datacite.org/schema/kernel-4")
       expect(json["includedInDataCatalog"]).to eq("@type"=>"DataCatalog", "name"=>"GTEx")
       expect(json["publisher"]).to eq("@type"=>"Organization", "name"=>"GTEx")
-      expect(json["funding"]).to eq([{"@id"=>"https://doi.org/10.13039/100000052",
+      expect(json["funder"]).to eq([{"@id"=>"https://doi.org/10.13039/100000052",
         "name"=>"Common Fund of the Office of the Director of the NIH",
         "@type"=>"Organization"},
        {"@id"=>"https://doi.org/10.13039/100000054",
@@ -262,7 +289,7 @@ describe Bolognese::Metadata, vcr: true do
       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["funder"]).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
   end

data/spec/writers/turtle_writer_spec.rb

@@ -18,7 +18,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.valid?).to be true
       ttl = subject.turtle.split("\n")
       expect(ttl[0]).to eq("@prefix schema: <http://schema.org/> .")
-      expect(ttl[2]).to eq("<https://doi.org/10.1371/journal.ppat.1000446> schema:citation <https://doi.org/10.5061/dryad.8515>;")
+      expect(ttl[2]).to eq("<https://doi.org/10.1371/journal.ppat.1000446> a schema:CreativeWork;")
     end
 
     # it "BlogPosting" do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 0.15.9
+  version: '1.0'
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-23 00:00:00.000000000 Z
+date: 2018-11-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -358,6 +358,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.1.2
+- !ruby/object:Gem::Dependency
+  name: concurrent-ruby
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.0.5
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.0.5
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -655,6 +669,8 @@ files:
 - spec/fixtures/datacite-example-complicated-v3.0.xml
 - spec/fixtures/datacite-example-complicated-v4.0.xml
 - spec/fixtures/datacite-example-complicated-v4.1.xml
+- spec/fixtures/datacite-example-geolocation-2.xml
+- spec/fixtures/datacite-example-geolocation.xml
 - spec/fixtures/datacite-metadata-sample-complicated-v2.2.xml
 - spec/fixtures/datacite.json
 - spec/fixtures/datacite.xml
@@ -672,6 +688,8 @@ files:
 - spec/fixtures/pure.ris
 - spec/fixtures/schema_4.0.xml
 - spec/fixtures/schema_org.json
+- spec/fixtures/schema_org_geolocation.json
+- spec/fixtures/schema_org_geoshape.json
 - spec/fixtures/schema_org_gtex.json
 - spec/fixtures/schema_org_list.json
 - spec/fixtures/schema_org_topmed.json
@@ -970,6 +988,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Schema_org_JSON_isReferencedBy.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/alternate_identifiers.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/data_catalog.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/geo_location_box.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/journal_article.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/maremma_schema_org_JSON.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/series_information.yml
@@ -1024,7 +1043,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.7.8
+rubygems_version: 2.7.7
 signing_key: 
 specification_version: 4
 summary: Ruby client library for conversion of DOI Metadata