bolognese 1.1.2 → 1.1.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 27940cced27604c5cf349c682939611611daf7acc5cd786672483f7f99cffa2d
-  data.tar.gz: bdb4a1dc2100975979a63ed70800fd8593c17f24b7c4a347aed4e7c647a8d42e
+  metadata.gz: 224da431c7712a8499b7c00b00c5704ccf111ecdbd228d6554bfa613c5909713
+  data.tar.gz: caf8827bdef8f4a427825d8ea5575c65427962f9cd94e8a92d8e404e4b23e56a
 SHA512:
-  metadata.gz: a5a082bd917f785cc61555de341bebe47adb241cc913be30fe39d596e4c6c03457ca472dceca6367e7a7d9235348a26fdbff579b95a8db55d56a5fcb3f98df4f
-  data.tar.gz: 6fb9777ed5f5435a59aec51aa63135b80f735378dfa8c065191d01e70f51c05694eb3ee9798c2c3982d5f9416c04c8948331129ed98025dcdd5c96036f08a1d1
+  metadata.gz: 14595a1ce26d31dba01ef9abde8d85d04e4f65de6adc8a10c34287b5ad5dfc2916a3f03016e7700899d9f49aeb725348dcbc3dd10c720f5e2ae8e38f3a2cf86c
+  data.tar.gz: 6f2a0c9d428bf2b280871253f5449ee89b365996e2f8c46d12f6abd346fdd40653ec26846f524693fcdbd67098b4859477f0202de3ceb09339d40f420b3c9d4c

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    bolognese (1.1.2)
+    bolognese (1.1.3)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)

data/lib/bolognese/readers/codemeta_reader.rb

@@ -36,7 +36,10 @@ module Bolognese
         id = Array.wrap(identifiers).first.to_h.fetch("identifier", nil)
         doi = Array.wrap(identifiers).find { |r| r["identifierType"] == "DOI" }.to_h.fetch("identifier", nil)
 
-        creators = get_authors(from_schema_org_creators(Array.wrap(meta.fetch("agents", nil))))
+        has_agents = meta.fetch("agents", nil)
+        authors =  has_agents.nil? ? meta.fetch("authors", nil) : has_agents
+        creators = get_authors(from_schema_org_creators(Array.wrap(authors)))
+
         contributors = get_authors(from_schema_org_contributors(Array.wrap(meta.fetch("editor", nil))))
         dates = []
         dates << { "date" => meta.fetch("datePublished"), "dateType" => "Issued" } if meta.fetch("datePublished", nil).present?
@@ -58,12 +61,16 @@ module Bolognese
           { "subject" => s }
         end
 
+        has_title = meta.fetch("title", nil)
+
+        titles =  has_title.nil? ?  [{ "title" => meta.fetch("name", nil) }] : [{ "title" => has_title }]  
+
         { "id" => id,
           "types" => types,
           "identifiers" => identifiers,
           "doi" => doi_from_url(doi),
           "url" => normalize_id(meta.fetch("codeRepository", nil)),
-          "titles" => [{ "title" => meta.fetch("title", nil) }],
+          "titles" => titles,
           "creators" => creators,
           "contributors" => contributors,
           "publisher" => publisher,

data/lib/bolognese/version.rb

@@ -1,3 +1,3 @@
 module Bolognese
-  VERSION = "1.1.2"
+  VERSION = "1.1.3"
 end

data/lib/bolognese/writers/codemeta_writer.rb

@@ -12,8 +12,8 @@ module Bolognese
           "@id" => normalize_doi(doi),
           "identifier" => to_schema_org_identifiers(identifiers),
           "codeRepository" => url,
-          "title" => parse_attributes(titles, content: "title", first: true),
-          "agents" => creators,
+          "name" => parse_attributes(titles, content: "title", first: true),
+          "authors" => creators,
           "description" => parse_attributes(descriptions, content: "description", first: true),
           "version" => version_info,
           "tags" => subjects.present? ? Array.wrap(subjects).map { |k| parse_attributes(k, content: "subject", first: true) } : nil,

data/spec/fixtures/codemeta_v2.json

@@ -0,0 +1,86 @@
+{
+	"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
+	"@type": "SoftwareSourceCode",
+	"authors": [{
+		"@id": "http://orcid.org/0000-0003-0077-4738",
+		"@type": "person",
+		"email": "jones@nceas.ucsb.edu",
+		"name": "Matt Jones",
+		"affiliation": "NCEAS",
+		"mustBeCited": true,
+		"isMaintainer": true,
+		"isRightsHolder": true,
+		"role": {
+			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
+			"roleCode": [
+				"originator",
+				"resourceProvider"
+			]
+		}
+	}, {
+		"@id": "http://orcid.org/0000-0002-2192-403X",
+		"@type": "person",
+		"email": "slaughter@nceas.ucsb.edu",
+		"name": "Peter Slaughter",
+		"affiliation": "NCEAS",
+		"mustBeCited": true,
+		"isMaintainer": false,
+		"isRightsHolder": false,
+		"role": {
+			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
+			"roleCode": "contributor"
+		}
+	}, {
+		"@type": "organization",
+		"email": "info@ucop.edu",
+		"name": "University of California, Santa Barbara",
+		"role": {
+			"namespace": "http://www.ngdc.noaa.gov/metadata/published/xsd/schema/resources/Codelist/gmxCodelists.xml#CI_RoleCode",
+			"roleCode": "copyrightHolder"
+		}
+	}],
+	"depends": {
+		"@type": "URL",
+		"@value": "https://github.com/ropensci/datapack"
+	},
+	"identifier": "http://dx.doi.org/10.5063/F1M61H5X",
+	"codeRepository": "https://github.com/DataONEorg/rdataone",
+	"controlledTem": "software",
+	"datePublished": "2016-05-27",
+	"dateModified": "2016-05-27",
+	"dateCreated": "2016-05-27",
+	"description": "Provides read and write access to data and metadata from the DataONE network of data repositories.Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository.Users can also insert and update data objects on repositories that support these methods.",
+	"downloadLink": "https://cran.r-project.org/src/contrib/dataone_2.0.0.tar.gz",
+	"funding": "National Science Foundation grant #012345678",
+	"isAutomatedBuild": false,
+	"issueTracker": "https://github.com/DataONEorg/rdataone/issues",
+	"licenseId": "Apache-2.0",
+	"publisher": "https://cran.r-project.org",
+	"tags": [
+		"data sharing",
+		"data repository",
+		"DataONE"
+	],
+	"name": "R Interface to the DataONE REST API",
+	"version": "2.0.0",
+	"uploadedBy": {
+		"@id": "http://orcid.org/0000-0003-0077-4738",
+		"@type": "person",
+		"email": "mbjones@nceas.ucsb.edu",
+		"name": "Matt Jones"
+	},
+	"programmingLanguage": {
+		"name": "R",
+		"version": "> 3.1.1",
+		"URL": "https://www.r-project.org"
+	},
+	"readme": "https://github.com/DataONEorg/rdataone/README.md",
+	"relatedPublications": "ISBN:0201703726",
+	"relationship": {
+		"relationshipType": "isPartOf",
+		"relatedIdentifier": "urn:uuid:F1A0A7AF-ECF3-4C7D-B675-7C6949963995",
+		"relatedIdentifierType": "UUID"
+	},
+	"softwarePaperCitationIdentifiers": "http://doi.org/0000/0000",
+	"zippedCode": "https://cran.r-project.org/src/contrib/dataone_2.0.0.tar.gz"
+}

data/spec/fixtures/maremma/codemeta.json

@@ -2,7 +2,7 @@
 	"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
 	"@type": "SoftwareSourceCode",
 	"@id": "https://doi.org/10.5438/QEG0-3GM3",
-	"agents": {
+	"authors": {
 		"@id": "http://orcid.org/0000-0003-0077-4738",
 		"@type": "person",
 		"name": "Martin Fenner",

data/spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml

@@ -0,0 +1,60 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://api.datacite.org/dois/10.5063/f1m61h5x
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Mozilla/5.0 (compatible; Maremma/4.2.1; +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: 200
+      message: OK
+    headers:
+      Date:
+      - Tue, 22 Jan 2019 10:40:18 GMT
+      Content-Type:
+      - application/json; charset=utf-8
+      Connection:
+      - keep-alive
+      Status:
+      - 200 OK
+      X-Anonymous-Consumer:
+      - 'true'
+      Cache-Control:
+      - max-age=0, private, must-revalidate
+      Vary:
+      - Accept-Encoding, Origin
+      X-Request-Id:
+      - 48c91bca-5323-4337-8889-6fda12bb6952
+      Etag:
+      - W/"cd7a4f850597028d5190ad0be9c79b23"
+      X-Runtime:
+      - '0.026371'
+      X-Powered-By:
+      - Phusion Passenger 6.0.1
+      Server:
+      - nginx/1.15.8 + Phusion Passenger 6.0.1
+    body:
+      encoding: ASCII-8BIT
+      string: '{"data":{"id":"10.5063/f1m61h5x","type":"dois","attributes":{"doi":"10.5063/f1m61h5x","prefix":"10.5063","suffix":"f1m61h5x","identifiers":[{"identifier":"https://doi.org/10.5063/f1m61h5x","identifierType":"DOI"}],"creators":[{"name":"Jones,
+        Matthew B.; Slaughter, Peter; Nahf, Rob; Boettiger, Carl ; Jones, Chris; Read,
+        Jordan; Walker, Lauren; Hart, Edmund; Chamberlain, Scott"}],"titles":[{"title":"dataone:
+        R interface to the DataONE network of data repositories"}],"publisher":"KNB
+        Data Repository","container":{},"publicationYear":2016,"subjects":[],"contributors":[],"dates":[{"date":"2016","dateType":"Issued"}],"language":null,"types":{"ris":"COMP","bibtex":"misc","citeproc":"article","schemaOrg":"SoftwareSourceCode","resourceTypeGeneral":"Software"},"relatedIdentifiers":[],"sizes":[],"formats":[],"version":null,"rightsList":[],"descriptions":[],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://github.com/DataONEorg/rdataone","contentUrl":null,"metadataVersion":1,"schemaVersion":"http://datacite.org/schema/kernel-3","source":null,"isActive":true,"state":"findable","reason":null,"created":"2016-03-12T03:15:03.000Z","registered":"2016-03-12T03:15:04.000Z","updated":"2018-10-07T13:22:40.000Z"},"relationships":{"client":{"data":{"id":"cdl.nceas","type":"clients"}},"media":{"data":[]}}},"included":[{"id":"cdl.nceas","type":"clients","attributes":{"name":"National
+        Center for Ecological Analysis and Synthesis (NCEAS)","symbol":"CDL.NCEAS","year":2011,"contactName":"EZID
+        Support Desk","contactEmail":"ezid@ucop.edu","description":"The NCEAS Data
+        Repository contains information about the research data sets collected and
+        collated as part of NCEAS'' funded activities. Information in the NCEAS Data
+        Repository is concurrently available through the Knowledge Network for Biocomplexity
+        (KNB), an international data repository. A number of the data sets were synthesized
+        from multiple data sources that originated from the efforts of many contributors,
+        while others originated from a single","domains":"*","url":"https://data.nceas.ucsb.edu/","created":"2011-12-13T04:27:25.000Z","updated":"2018-12-20T23:09:38.000Z","isActive":true,"hasPassword":true},"relationships":{"provider":{"data":{"id":"cdl","type":"providers"}},"repository":{"data":{"id":"10.17616/R3FW2J","type":"repositories"}},"prefixes":{"data":[{"id":"10.5063","type":"prefixes"},{"id":"10.5072","type":"prefixes"}]}}}]}'
+    http_version: 
+  recorded_at: Tue, 22 Jan 2019 10:40:18 GMT
+recorded_with: VCR 3.0.3

data/spec/writers/codemeta_writer_spec.rb

@@ -28,10 +28,19 @@ describe Bolognese::Metadata, vcr: true do
       expect(json["@id"]).to eq("https://doi.org/10.5063/f1m61h5x")
       expect(json["@type"]).to eq("SoftwareSourceCode")
       expect(json["identifier"]).to eq("@type"=>"PropertyValue", "propertyID"=>"DOI", "value"=>"https://doi.org/10.5063/f1m61h5x")
-      expect(json["agents"]).to eq([{"name"=>"Jones, Matthew B.; Slaughter, Peter; Nahf, Rob; Boettiger, Carl ; Jones, Chris; Read, Jordan; Walker, Lauren; Hart, Edmund; Chamberlain, Scott"}])
-      expect(json["title"]).to eq("dataone: R interface to the DataONE network of data repositories")
+      expect(json["authors"]).to eq([{"name"=>"Jones, Matthew B.; Slaughter, Peter; Nahf, Rob; Boettiger, Carl ; Jones, Chris; Read, Jordan; Walker, Lauren; Hart, Edmund; Chamberlain, Scott"}])
+      expect(json["name"]).to eq("dataone: R interface to the DataONE network of data repositories")
       expect(json["datePublished"]).to eq("2016")
       expect(json["publisher"]).to eq("KNB Data Repository")
     end
+
+    it "SoftwareSourceCode DataCite check codemeta v2" do
+      input = "https://doi.org/10.5063/f1m61h5x"
+      subject = Bolognese::Metadata.new(input: input, from: "datacite")
+      expect(subject.valid?).to be true
+      json = JSON.parse(subject.codemeta)
+      expect(json["agents"]).to  be_nil
+      expect(json["title"]).to  be_nil
+    end
   end
 end

data/spec/writers/crosscite_writer_spec.rb

@@ -65,6 +65,16 @@ describe Bolognese::Metadata, vcr: true do
       expect(crosscite["version"]).to eq("2.0.0")
     end
 
+    it "rdataone codemeta v2" do
+      input = fixture_path + 'codemeta_v2.json'
+      subject = Bolognese::Metadata.new(input: input, from: "codemeta")
+      crosscite = JSON.parse(subject.crosscite)
+      expect(crosscite["titles"]).to eq([{"title"=>"R Interface to the DataONE REST API"}])
+      expect(crosscite["creators"].length).to eq(3)
+      expect(crosscite["creators"].last).to eq("nameType" => "Organizational", "name"=>"University Of California, Santa Barbara")
+      expect(crosscite["version"]).to eq("2.0.0")
+    end
+
     it "datacite database attributes" do
       input = "https://doi.org/10.5061/DRYAD.8515"
       subject = Bolognese::Metadata.new(input: input, from: "datacite")

data/spec/writers/datacite_writer_spec.rb

@@ -87,6 +87,28 @@ describe Bolognese::Metadata, vcr: true do
       expect(datacite.fetch("version")).to eq("2.0.0")
     end
 
+    it "rdataone and codemeta_v2" do
+      input = fixture_path + 'codemeta_v2.json'
+      subject = Bolognese::Metadata.new(input: input, from: "codemeta")
+      expect(subject.valid?).to be true
+      datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
+      expect(datacite.dig("titles", "title")).to eq("R Interface to the DataONE REST API")
+      expect(datacite.dig("creators", "creator")).to eq([{"creatorName"=>{"__content__"=>"Jones, Matt", "nameType"=>"Personal"},
+                                                          "givenName"=>"Matt",
+                                                          "familyName"=>"Jones",
+                                                          "nameIdentifier"=>
+                                                         {"nameIdentifierScheme"=>"ORCID",
+                                                          "__content__"=>"https://orcid.org/0000-0003-0077-4738"}},
+                                                         {"creatorName"=>{"__content__"=>"Slaughter, Peter", "nameType"=>"Personal"},
+                                                           "givenName"=>"Peter",
+                                                           "familyName"=>"Slaughter",
+                                                          "nameIdentifier"=>
+                                                         {"nameIdentifierScheme"=>"ORCID",
+                                                          "__content__"=>"https://orcid.org/0000-0002-2192-403X"}},
+                                                         {"creatorName"=>{"__content__"=>"University Of California, Santa Barbara", "nameType"=>"Organizational"}}])
+      expect(datacite.fetch("version")).to eq("2.0.0")
+    end
+
     it "maremma" do
       input = "https://github.com/datacite/maremma"
       subject = Bolognese::Metadata.new(input: input, from: "codemeta")

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bolognese
 version: !ruby/object:Gem::Version
-  version: 1.1.2
+  version: 1.1.3
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2019-01-12 00:00:00.000000000 Z
+date: 2019-02-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -664,6 +664,7 @@ files:
 - spec/fixtures/citeproc-no-categories.json
 - spec/fixtures/citeproc.json
 - spec/fixtures/codemeta.json
+- spec/fixtures/codemeta_v2.json
 - spec/fixtures/crosscite.json
 - spec/fixtures/crossref.bib
 - spec/fixtures/crossref.ris
@@ -958,6 +959,7 @@ files:
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/software.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_citeproc/with_pages.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml
+- spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crosscite/datacite_database_attributes.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crosscite/maremma.yml
 - spec/fixtures/vcr_cassettes/Bolognese_Metadata/write_metadata_as_crosscite/with_ORCID_ID.yml