bolognese 0.11.7 → 0.12

data/spec/utils_spec.rb

@@ -235,6 +235,24 @@ describe Bolognese::Metadata, vcr: true do
     end
   end
 
+  context "to_schema_org_identifier" do
+    it "with alternate_identifier" do
+      identifier = "https://doi.org/10.23725/8na3-9s47"
+      alternate_identifier = [{"type"=>"md5", "name"=>"3b33f6b9338fccab0901b7d317577ea3"}, {"type"=>"minid", "name"=>"ark:/99999/fk41CrU4eszeLUDe"}, {"type"=>"dataguid", "name"=>"dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7"}]
+      response = subject.to_schema_org_identifier(identifier, alternate_identifier: alternate_identifier)
+      expect(response).to eq(["https://doi.org/10.1101/097196",
+        {"@type"=>"PropertyValue",
+         "propertyID"=>"md5",
+         "value"=>"3b33f6b9338fccab0901b7d317577ea3"},
+        {"@type"=>"PropertyValue",
+         "propertyID"=>"minid",
+         "value"=>"ark:/99999/fk41CrU4eszeLUDe"},
+        {"@type"=>"PropertyValue",
+         "propertyID"=>"dataguid",
+         "value"=>"dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7"}])
+    end
+  end
+
   context "sanitize" do
     it 'should remove a tags' do
       text = "In 1998 <strong>Tim Berners-Lee</strong> coined the term <a href=\"https://www.w3.org/Provider/Style/URI\">cool URIs</a>"

data/spec/writers/datacite_writer_spec.rb

@@ -145,7 +145,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(subject.author.length).to eq(8)
       expect(subject.author.first).to eq("type"=>"Person", "name"=>"Benjamin Ollomo", "givenName"=>"Benjamin", "familyName"=>"Ollomo")
       expect(subject.title).to eq("Data from: A new malaria agent in African hominids.")
-      expect(subject.alternate_name).to eq("type"=>"citation", "name"=>"Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.")
+      expect(subject.alternate_identifier).to eq("type"=>"citation", "name"=>"Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.")
       expect(subject.license).to eq("id"=>"http://creativecommons.org/publicdomain/zero/1.0")
       expect(subject.date_published).to eq("2011")
       expect(subject.has_part).to eq([{"type"=>"CreativeWork", "id"=>"https://doi.org/10.5061/dryad.8515/1"},

data/spec/writers/ris_writer_spec.rb

@@ -54,9 +54,8 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[11]).to eq("KW  - medical competence")
       expect(ris[21]).to eq("PY  - 2017")
       expect(ris[22]).to eq("PB  - German Medical Science GMS Publishing House")
-      expect(ris[23]).to eq("AN  - urn:nbn:de:0183-zma0011024")
-      expect(ris[25]).to eq("LA  - en")
-      expect(ris[26]).to eq("ER  - ")
+      expect(ris[23]).to eq("LA  - en")
+      expect(ris[24]).to eq("ER  - ")
     end
 
     it "Crossref DOI" do
@@ -89,8 +88,7 @@ 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("AN  - MS-49-3632-5083")
-      expect(ris[11]).to eq("ER  - ")
+      expect(ris[10]).to eq("ER  - ")
     end
 
     it "BlogPosting Citeproc JSON" do
@@ -122,8 +120,7 @@ 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("AN  - MS-49-3632-5083")
-      expect(ris[11]).to eq("ER  - ")
+      expect(ris[10]).to eq("ER  - ")
     end
 
     it "BlogPosting schema.org" do
@@ -140,8 +137,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[7]).to eq("KW  - datacite")
       expect(ris[11]).to eq("PY  - 2016")
       expect(ris[12]).to eq("PB  - DataCite")
-      expect(ris[13]).to eq("AN  - MS-49-3632-5083")
-      expect(ris[14]).to eq("ER  - ")
+      expect(ris[13]).to eq("ER  - ")
     end
 
     it "Dataset" do
@@ -157,8 +153,7 @@ describe Bolognese::Metadata, vcr: true do
       expect(ris[13]).to eq("KW  - Malaria")
       expect(ris[19]).to eq("PY  - 2011")
       expect(ris[20]).to eq("PB  - Dryad Digital Repository")
-      expect(ris[21]).to eq("AN  - Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.")
-      expect(ris[22]).to eq("ER  - ")
+      expect(ris[21]).to eq("ER  - ")
     end
 
     it "maremma" do

data/spec/writers/schema_org_writer_spec.rb

@@ -142,5 +142,40 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["author"].count).to eq(3)
       expect(json["author"].first).to eq("@type"=>"Person", "name"=>"P. Llamas", "givenName"=>"P.", "familyName"=>"Llamas")
     end
+
+    it "data catalog" do
+      input = "10.25491/8KMC-G314"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      json = JSON.parse(subject.schema_org)
+      expect(json["@id"]).to eq("https://doi.org/10.25491/8kmc-g314")
+      expect(json["@type"]).to eq("Dataset")
+      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(["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
+
+    it "alternate identifiers" do
+      input = "10.23725/8na3-9s47"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      json = JSON.parse(subject.schema_org)
+      expect(json["@id"]).to eq("https://doi.org/10.23725/8na3-9s47")
+      expect(json["@type"]).to eq("Dataset")
+      expect(json["name"]).to eq("NWD165827.recab.cram")
+      expect(json["author"]).to eq("@type"=>"Organization", "name"=>"TOPMed IRC")
+      expect(json["includedInDataCatalog"]).to be_nil
+      expect(json["identifier"]).to eq(["https://doi.org/10.23725/8na3-9s47",
+        {"@type"=>"PropertyValue",
+         "propertyID"=>"md5",
+         "value"=>"3b33f6b9338fccab0901b7d317577ea3"},
+        {"@type"=>"PropertyValue",
+         "propertyID"=>"minid",
+         "value"=>"ark:/99999/fk41CrU4eszeLUDe"},
+        {"@type"=>"PropertyValue",
+          "propertyID"=>"dataguid",
+          "value"=>"dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7"}])
+      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"])
+    end
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 0.11.7
+  version: '0.12'
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-01 00:00:00.000000000 Z
+date: 2018-08-22 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -708,6 +708,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/author_only_full_name.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/author_with_scheme.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/author_with_wrong_orcid_scheme.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/content_url.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/date.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/dissertation.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/doi_with_sign.yml
@@ -751,6 +752,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_schema_org_metadata/BlogPosting.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_schema_org_metadata/BlogPosting_with_new_DOI.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_schema_org_metadata/harvard_dataverse.yml
+- 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/github/github_as_codemeta_url.yml
@@ -818,6 +820,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/sanitize/should_only_keep_specific_tags.yml
 - 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/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
@@ -900,6 +903,8 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Schema_org_JSON.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_schema_org/Schema_org_JSON_IsSupplementTo.yml
 - 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/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
@@ -908,6 +913,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_turtle/BlogPosting_Citeproc_JSON.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_turtle/Crossref_DOI.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_turtle/Dataset.yml
+- spec/fixtures/vivli.xml
 - spec/metadata_spec.rb
 - spec/readers/bibtex_reader_spec.rb
 - spec/readers/citeproc_reader_spec.rb