bolognese 1.0.29 → 1.0.30

data/spec/writers/schema_org_writer_spec.rb

@@ -10,7 +10,7 @@ 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", "issn"=>"2050-084X")
-      expect(json["periodical"]).to eq("@type"=>"Periodical", "name"=>"eLife", "issn"=>"2050-084X")
+      expect(json["periodical"]).to eq("@type"=>"Journal", "identifier"=>"2050-084X", "identifierType"=>"ISSN", "name"=>"eLife", "volume"=>"3")
       expect(json["citation"].length).to eq(26)
       expect(json["citation"].first).to eq("@id"=>"https://doi.org/10.1038/nature02100", "@type"=>"CreativeWork")
       expect(json["funder"]).to eq([{"name"=>"SystemsX", "@type"=>"Organization"},
@@ -32,7 +32,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@id"]).to eq("https://doi.org/10.5438/qeg0-3gm3")
       expect(json["@type"]).to eq("SoftwareSourceCode")
       expect(json["name"]).to eq("Maremma: a Ruby library for simplified network calls")
-      expect(json["author"]).to eq("name"=>"Martin Fenner", "givenName"=>"Martin", "familyName"=>"Fenner", "@type"=>"Person", "@id"=>"http://orcid.org/0000-0003-0077-4738")
+      expect(json["author"]).to eq("name"=>"Martin Fenner", "givenName"=>"Martin", "familyName"=>"Fenner", "@type"=>"Person", "@id"=>"https://orcid.org/0000-0003-0077-4738", "affiliation" => {"@type"=>"Organization", "name"=>"DataCite"})
     end
 
     it "Schema.org JSON" do
@@ -71,12 +71,14 @@ describe Bolognese::Metadata, vcr: true do
                                      "givenName"=>"Matt",
                                      "familyName"=>"Jones",
                                      "@type"=>"Person",
-                                     "@id"=>"http://orcid.org/0000-0003-0077-4738"},
+                                     "@id"=>"https://orcid.org/0000-0003-0077-4738",
+                                     "affiliation"=>{"@type"=>"Organization", "name"=>"NCEAS"}},
                                     {"name"=>"Peter Slaughter",
                                      "givenName"=>"Peter",
                                      "familyName"=>"Slaughter",
                                      "@type"=>"Person",
-                                     "@id"=>"http://orcid.org/0000-0002-2192-403X"},
+                                     "@id"=>"https://orcid.org/0000-0002-2192-403X",
+                                     "affiliation"=>{"@type"=>"Organization", "name"=>"NCEAS"}},
                                     {"name"=>"University Of California, Santa Barbara", "@type"=>"Organization"}])
       expect(json["version"]).to eq("2.0.0")
     end
@@ -142,7 +144,7 @@ describe Bolognese::Metadata, vcr: true do
       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")
+      expect(json["periodical"]).to eq("@type"=>"Series", "firstPage"=>"Spain; 3353", "lastPage"=>"3356", "name"=>"23rd European Photovoltaic Solar Energy Conference and Exhibition", "volume"=>"1-5 September 2008")
     end
 
     it "data catalog" do
@@ -154,7 +156,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["name"]).to eq("Covariates used in eQTL analysis. Includes genotyping principal components and PEER factors")
       expect(json["author"]).to eq("@type"=>"Organization", "name"=>"The GTEx Consortium")
       expect(json["includedInDataCatalog"]).to eq("@type"=>"DataCatalog", "name"=>"GTEx")
-      expect(json["identifier"]).to eq([{"@type"=>"PropertyValue", "propertyID"=>"doi", "value"=>"https://doi.org/10.25491/8kmc-g314"},{"@type"=>"PropertyValue", "propertyID"=>"md5", "value"=>"c7c89fe7366d50cd75448aa603c9de58"}])
+      expect(json["identifier"]).to eq([{"@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.25491/8kmc-g314"},{"@type"=>"PropertyValue", "propertyID"=>"md5", "value"=>"c7c89fe7366d50cd75448aa603c9de58"}])
       expect(json["contentUrl"]).to eq("https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_covariates.tar.gz")
     end
 
@@ -169,7 +171,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["includedInDataCatalog"]).to be_nil
       expect(json["identifier"]).to eq(
         [{"@type"=>"PropertyValue",
-          "propertyID"=>"doi",
+          "propertyID"=>"DOI",
           "value"=>"https://doi.org/10.23725/8na3-9s47"},
          {"@type"=>"PropertyValue",
           "propertyID"=>"minid",
@@ -193,9 +195,19 @@ describe Bolognese::Metadata, vcr: true do
       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["author"][2]).to eq("@id"=>"https://orcid.org/0000-0002-8862-1404", "@type"=>"Person", "familyName"=>"Stacy", "givenName"=>"Erin", "name"=>"Erin Stacy", "affiliation" => {"@type"=>"Organization", "name"=>"UC Merced"})
       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"})
+      expect(json["spatialCoverage"]).to eq([{"@type"=>"Place",
+        "geo"=>
+        {"@type"=>"GeoCoordinates",
+         "address"=>"Providence Creek (Lower, Upper and P301)",
+         "latitude"=>"37.047756",
+         "longitude"=>"-119.221094"}},
+        {"@type"=>"Place",
+         "geo"=>
+        {"@type"=>"GeoShape",
+         "address"=>"Providence Creek (Lower, Upper and P301)",
+         "box"=>"37.046 -119.211 37.075 -119.182"}}])
     end
 
     it "geo_location_box" do
@@ -208,23 +220,37 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["author"]).to eq([{"@type"=>"Person",
         "familyName"=>"Tara Oceans Consortium",
         "givenName"=>"Coordinators",
-        "name"=>"Tara Oceans Consortium, Coordinators"},
+        "name"=>"Coordinators Tara Oceans Consortium"},
        {"@type"=>"Person",
         "familyName"=>"Tara Oceans Expedition",
         "givenName"=>"Participants",
-        "name"=>"Tara Oceans Expedition, Participants"}])
+        "name"=>"Participants Tara Oceans Expedition"}])
       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["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 "geo_location_polygon" do
+      input = fixture_path + 'datacite-example-polygon-v4.1.xml'
+      subject = Bolognese::Metadata.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json["@id"]).to eq("https://doi.org/10.5072/example-polygon")
+      expect(json["@type"]).to eq("Dataset")
+      expect(json["name"]).to eq("Meteo measurements at the Sand Motor")
+      expect(json["author"]).to eq("@type"=>"Person", "familyName"=>"Den Heijer", "givenName"=>"C", "name"=>"C Den Heijer")
+      expect(json["includedInDataCatalog"]).to be_nil
+      expect(json["identifier"]).to eq("@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.5072/example-polygon")
+      expect(json["spatialCoverage"].dig("geo", "polygon").length).to eq(34)
+      expect(json["spatialCoverage"].dig("geo", "polygon").first).to eq(["4.1738852605822", "52.03913926329928"])
+    end
+
     it "from schema_org gtex" do
       input = fixture_path + 'schema_org_gtex.json'
       subject = Bolognese::Metadata.new(input: input, from: "schema_org")
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.25491/d50j-3083")
       expect(json["@type"]).to eq("Dataset")
-      expect(json["identifier"]).to eq([{"@type"=>"PropertyValue", "propertyID"=>"doi", "value"=>"https://doi.org/10.25491/d50j-3083"}, {"@type"=>"PropertyValue", "propertyID"=>"md5", "value"=>"687610993"}])
+      expect(json["identifier"]).to eq([{"@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.25491/d50j-3083"}, {"@type"=>"PropertyValue", "propertyID"=>"md5", "value"=>"687610993"}])
       expect(json["url"]).to eq("https://ors.datacite.org/doi:/10.25491/d50j-3083")
       expect(json["additionalType"]).to eq("Gene expression matrices")
       expect(json["name"]).to eq("Fully processed, filtered and normalized gene expression matrices (in BED format) for each tissue, which were used as input into FastQTL for eQTL discovery")
@@ -268,7 +294,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@type"]).to eq("Dataset")
       expect(json["identifier"]).to eq(
         [{"@type"=>"PropertyValue",
-          "propertyID"=>"doi",
+          "propertyID"=>"DOI",
           "value"=>"https://doi.org/10.23725/8na3-9s47"},
          {"@type"=>"PropertyValue",
           "propertyID"=>"md5",

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.0.29
+  version: 1.0.30
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-05 00:00:00.000000000 Z
+date: 2018-12-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -672,10 +672,12 @@ files:
 - spec/fixtures/datacite-example-complicated-v4.1.xml
 - spec/fixtures/datacite-example-geolocation-2.xml
 - spec/fixtures/datacite-example-geolocation.xml
+- spec/fixtures/datacite-example-polygon-v4.1.xml
 - spec/fixtures/datacite-geolocation-empty.xml
 - spec/fixtures/datacite-metadata-sample-complicated-v2.2.xml
 - spec/fixtures/datacite-multiple-language.xml
 - spec/fixtures/datacite-multiple-rights.xml
+- spec/fixtures/datacite-seriesinformation.xml
 - spec/fixtures/datacite-xml-lang.xml
 - spec/fixtures/datacite.json
 - spec/fixtures/datacite.xml
@@ -847,6 +849,10 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_schema_org_metadata/harvard_dataverse_via_identifiers_org.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_schema_org_metadata/pangaea.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_schema_org_metadata/zenodo.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_series_information/only_title.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_series_information/title_and_pages.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_series_information/title_volume_and_pages.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_series_information/title_volume_issue_and_pages.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/github/github_as_codemeta_url.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/github/github_from_url.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/github/github_from_url_file.yml
@@ -873,6 +879,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/is_personal_name_/has_id.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/is_personal_name_/has_known_given_name.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/is_personal_name_/has_no_info.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/is_personal_name_/has_orcid_id.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/is_personal_name_/has_type_organization.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/jsonlint/missing_comma.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/jsonlint/nil.yml
@@ -913,6 +920,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/sanitize/should_remove_a_tags.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/to_schema_org/with_id.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/to_schema_org_identifier/with_alternate_identifier.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/to_schema_org_identifiers/with_identifiers.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid/validate_orcid.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid/validate_orcid_https.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/validate_orcid/validate_orcid_id.yml