bolognese 0.9.56 → 0.9.58

data/spec/writers/schema_org_writer_spec.rb

@@ -7,8 +7,8 @@ describe Bolognese::Metadata, vcr: true do
       subject = Bolognese::Metadata.new(input: input, from: "crossref")
       json = JSON.parse(subject.schema_org)
       expect(json["@id"]).to eq("https://doi.org/10.7554/elife.01567")
-      expect(json["citation"].length).to eq(25)
-      expect(json["citation"].first).to eq("@id"=>"https://doi.org/10.1038/nature02100", "@type"=>"CreativeWork")
+      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"},
                                      {"name"=>"EMBO",
                                       "@type"=>"Organization",
@@ -36,7 +36,6 @@ 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.48440")
-      expect(json["url"]).to eq("https://zenodo.org/record/48440")
       expect(json["name"]).to eq("Analysis Tools For Crossover Experiment Of Ui Using Choice Architecture")
     end
 
@@ -45,7 +44,6 @@ 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["url"]).to eq( "http://datadryad.org/resource/doi: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"})
     end
 
@@ -54,7 +52,6 @@ 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["url"]).to eq("http://www.ccdc.cam.ac.uk/services/structure_request?id=doi:10.5517/cc8h01s&sid=DataCite")
       expect(json["@reverse"]).to eq("isBasedOn"=>{"@id"=>"https://doi.org/10.1107/s1600536804021154"})
     end
 
@@ -84,7 +81,6 @@ 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/10.5438/6423")
-      expect(json["url"]).to eq("https://project-thor.eu")
       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",

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 0.9.56
+  version: 0.9.58
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-10-21 00:00:00.000000000 Z
+date: 2017-10-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -166,6 +166,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: 0.11.3
+- !ruby/object:Gem::Dependency
+  name: iso8601
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.1
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 0.9.1
 - !ruby/object:Gem::Dependency
   name: postrank-uri
   requirement: !ruby/object:Gem::Requirement
@@ -485,6 +499,7 @@ files:
 - lib/bolognese/writers/crossref_writer.rb
 - lib/bolognese/writers/datacite_json_writer.rb
 - lib/bolognese/writers/datacite_writer.rb
+- lib/bolognese/writers/jats_writer.rb
 - lib/bolognese/writers/rdf_xml_writer.rb
 - lib/bolognese/writers/ris_writer.rb
 - lib/bolognese/writers/schema_org_writer.rb
@@ -557,11 +572,6 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/crossref/to_crossref.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/crossref/to_datacite.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/crossref/to_schema_org.yml
-- spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/default.yml
-- spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/to_bibtex.yml
-- spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/to_datacite.yml
-- spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/to_datacite_invalid.yml
-- spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/to_schema_org.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/default.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_bibtex.yml
 - spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_from_id/crossref/to_citation.yml
@@ -634,6 +644,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_ORCID_ID.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_SICI_DOI.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/DOI_with_data_citation.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/book_chapter.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/dataset.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/date_in_future.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/journal_article.yml
@@ -641,15 +652,12 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_metadata/posted_content.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_crossref_raw/journal_article.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/BlogPosting.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/BlogPosting_from_string.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/BlogPosting_in_test_system.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_in_test_system.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/DOI_not_found.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Dataset.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Funding.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Funding_schema_version_4.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Schema_4_1_from_string.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Schema_4_1_from_string_with_doi_in_options.yml
 - 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
@@ -659,10 +667,8 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/is_identical_to.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/keywords_with_attributes.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/leading_and_trailing_whitespace.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/missing_creator.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/multiple_author_names_in_one_creatorName.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/multiple_licenses.yml
-- spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_raw/BlogPosting.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_date_from_date_parts/date.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_date_from_date_parts/year-month.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_date_from_date_parts/year.yml
@@ -806,6 +812,14 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/with_data_citation.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/with_data_citation_schema_org.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_datacite_xml/with_editor.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/Dataset_in_schema_4_0.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/Text_pass-thru.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/book_chapter.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/maremma.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/with_ORCID_ID.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/with_data_citation.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/with_data_citation_schema_org.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_jats_xml/with_editor.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_ris/BlogPosting.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_ris/BlogPosting_schema_org.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_ris/Dataset.yml
@@ -847,6 +861,7 @@ files:
 - spec/writers/crossref_writer_spec.rb
 - spec/writers/datacite_json_writer_spec.rb
 - spec/writers/datacite_writer_spec.rb
+- spec/writers/jats_writer_spec.rb
 - spec/writers/rdf_xml_writer_spec.rb
 - spec/writers/ris_writer_spec.rb
 - spec/writers/schema_org_writer_spec.rb

data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/default.yml

@@ -1,38 +0,0 @@
----
-http_interactions:
-- request:
-    method: head
-    uri: https://doi.org/10.5438/4k3m-nyvg
-    body:
-      encoding: US-ASCII
-      string: ''
-    headers:
-      User-Agent:
-      - Maremma - https://github.com/datacite/maremma
-      Accept:
-      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
-  response:
-    status:
-      code: 303
-      message: See Other
-    headers:
-      Server:
-      - Apache-Coyote/1.1
-      Vary:
-      - Accept
-      Location:
-      - https://blog.datacite.org/eating-your-own-dog-food/
-      Expires:
-      - Mon, 25 Sep 2017 20:29:23 GMT
-      Content-Type:
-      - text/html;charset=utf-8
-      Content-Length:
-      - '187'
-      Date:
-      - Mon, 25 Sep 2017 19:30:24 GMT
-    body:
-      encoding: UTF-8
-      string: ''
-    http_version: 
-  recorded_at: Mon, 25 Sep 2017 19:30:25 GMT
-recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/to_bibtex.yml

@@ -1,38 +0,0 @@
----
-http_interactions:
-- request:
-    method: head
-    uri: https://doi.org/10.5438/4k3m-nyvg
-    body:
-      encoding: US-ASCII
-      string: ''
-    headers:
-      User-Agent:
-      - Maremma - https://github.com/datacite/maremma
-      Accept:
-      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
-  response:
-    status:
-      code: 303
-      message: See Other
-    headers:
-      Server:
-      - Apache-Coyote/1.1
-      Vary:
-      - Accept
-      Location:
-      - https://blog.datacite.org/eating-your-own-dog-food/
-      Expires:
-      - Mon, 25 Sep 2017 20:29:23 GMT
-      Content-Type:
-      - text/html;charset=utf-8
-      Content-Length:
-      - '187'
-      Date:
-      - Mon, 25 Sep 2017 19:30:22 GMT
-    body:
-      encoding: UTF-8
-      string: ''
-    http_version: 
-  recorded_at: Mon, 25 Sep 2017 19:30:23 GMT
-recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/to_datacite.yml

@@ -1,38 +0,0 @@
----
-http_interactions:
-- request:
-    method: head
-    uri: https://doi.org/10.5438/4k3m-nyvg
-    body:
-      encoding: US-ASCII
-      string: ''
-    headers:
-      User-Agent:
-      - Maremma - https://github.com/datacite/maremma
-      Accept:
-      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
-  response:
-    status:
-      code: 303
-      message: See Other
-    headers:
-      Server:
-      - Apache-Coyote/1.1
-      Vary:
-      - Accept
-      Location:
-      - https://blog.datacite.org/eating-your-own-dog-food/
-      Expires:
-      - Mon, 25 Sep 2017 20:29:23 GMT
-      Content-Type:
-      - text/html;charset=utf-8
-      Content-Length:
-      - '187'
-      Date:
-      - Mon, 25 Sep 2017 19:30:24 GMT
-    body:
-      encoding: UTF-8
-      string: ''
-    http_version: 
-  recorded_at: Mon, 25 Sep 2017 19:30:25 GMT
-recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/to_datacite_invalid.yml

@@ -1,38 +0,0 @@
----
-http_interactions:
-- request:
-    method: head
-    uri: https://doi.org/10.5438/4k3m-nyvg
-    body:
-      encoding: US-ASCII
-      string: ''
-    headers:
-      User-Agent:
-      - Maremma - https://github.com/datacite/maremma
-      Accept:
-      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
-  response:
-    status:
-      code: 303
-      message: See Other
-    headers:
-      Server:
-      - Apache-Coyote/1.1
-      Vary:
-      - Accept
-      Location:
-      - https://blog.datacite.org/eating-your-own-dog-food/
-      Expires:
-      - Mon, 25 Sep 2017 20:29:23 GMT
-      Content-Type:
-      - text/html;charset=utf-8
-      Content-Length:
-      - '187'
-      Date:
-      - Mon, 25 Sep 2017 19:30:21 GMT
-    body:
-      encoding: UTF-8
-      string: ''
-    http_version: 
-  recorded_at: Mon, 25 Sep 2017 19:30:22 GMT
-recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_CLI/convert_file/datacite/to_schema_org.yml

@@ -1,38 +0,0 @@
----
-http_interactions:
-- request:
-    method: head
-    uri: https://doi.org/10.5438/4k3m-nyvg
-    body:
-      encoding: US-ASCII
-      string: ''
-    headers:
-      User-Agent:
-      - Maremma - https://github.com/datacite/maremma
-      Accept:
-      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
-  response:
-    status:
-      code: 303
-      message: See Other
-    headers:
-      Server:
-      - Apache-Coyote/1.1
-      Vary:
-      - Accept
-      Location:
-      - https://blog.datacite.org/eating-your-own-dog-food/
-      Expires:
-      - Mon, 25 Sep 2017 20:29:23 GMT
-      Content-Type:
-      - text/html;charset=utf-8
-      Content-Length:
-      - '187'
-      Date:
-      - Mon, 25 Sep 2017 19:30:23 GMT
-    body:
-      encoding: UTF-8
-      string: ''
-    http_version: 
-  recorded_at: Mon, 25 Sep 2017 19:30:24 GMT
-recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/BlogPosting_from_string.yml

@@ -1,38 +0,0 @@
----
-http_interactions:
-- request:
-    method: head
-    uri: https://doi.org/10.5438/4k3m-nyvg
-    body:
-      encoding: US-ASCII
-      string: ''
-    headers:
-      User-Agent:
-      - Maremma - https://github.com/datacite/maremma
-      Accept:
-      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
-  response:
-    status:
-      code: 303
-      message: See Other
-    headers:
-      Server:
-      - Apache-Coyote/1.1
-      Vary:
-      - Accept
-      Location:
-      - https://blog.datacite.org/eating-your-own-dog-food/
-      Expires:
-      - Mon, 25 Sep 2017 19:29:21 GMT
-      Content-Type:
-      - text/html;charset=utf-8
-      Content-Length:
-      - '187'
-      Date:
-      - Mon, 25 Sep 2017 19:19:04 GMT
-    body:
-      encoding: UTF-8
-      string: ''
-    http_version: 
-  recorded_at: Mon, 25 Sep 2017 19:19:05 GMT
-recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Schema_4_1_from_string.yml

@@ -1,38 +0,0 @@
----
-http_interactions:
-- request:
-    method: head
-    uri: https://doi.org/10.5072/testpub
-    body:
-      encoding: US-ASCII
-      string: ''
-    headers:
-      User-Agent:
-      - Maremma - https://github.com/datacite/maremma
-      Accept:
-      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
-  response:
-    status:
-      code: 303
-      message: See Other
-    headers:
-      Server:
-      - Apache-Coyote/1.1
-      Vary:
-      - Accept
-      Location:
-      - http://www.inist.fr/
-      Expires:
-      - Mon, 25 Sep 2017 19:38:39 GMT
-      Content-Type:
-      - text/html;charset=utf-8
-      Content-Length:
-      - '125'
-      Date:
-      - Mon, 25 Sep 2017 19:18:55 GMT
-    body:
-      encoding: UTF-8
-      string: ''
-    http_version: 
-  recorded_at: Mon, 25 Sep 2017 19:18:55 GMT
-recorded_with: VCR 3.0.3

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/get_datacite_metadata/Schema_4_1_from_string_with_doi_in_options.yml

@@ -1,38 +0,0 @@
----
-http_interactions:
-- request:
-    method: head
-    uri: https://doi.org/10.5072/testpub2
-    body:
-      encoding: US-ASCII
-      string: ''
-    headers:
-      User-Agent:
-      - Maremma - https://github.com/datacite/maremma
-      Accept:
-      - text/html,application/json,application/xml;q=0.9, text/plain;q=0.8,image/png,*/*;q=0.5
-  response:
-    status:
-      code: 303
-      message: See Other
-    headers:
-      Server:
-      - Apache-Coyote/1.1
-      Vary:
-      - Accept
-      Location:
-      - http://www.datacite.org/testprefix
-      Expires:
-      - Mon, 09 Oct 2017 00:17:32 GMT
-      Content-Type:
-      - text/html;charset=utf-8
-      Content-Length:
-      - '153'
-      Date:
-      - Sun, 08 Oct 2017 23:20:48 GMT
-    body:
-      encoding: UTF-8
-      string: ''
-    http_version: 
-  recorded_at: Sun, 08 Oct 2017 23:20:48 GMT
-recorded_with: VCR 3.0.3