bolognese 1.0.6 → 1.0.7
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/lib/bolognese/author_utils.rb +1 -1
- data/lib/bolognese/datacite_utils.rb +51 -55
- data/lib/bolognese/metadata.rb +16 -16
- data/lib/bolognese/metadata_utils.rb +5 -5
- data/lib/bolognese/readers/bibtex_reader.rb +4 -4
- data/lib/bolognese/readers/citeproc_reader.rb +9 -6
- data/lib/bolognese/readers/codemeta_reader.rb +7 -4
- data/lib/bolognese/readers/crossref_reader.rb +23 -17
- data/lib/bolognese/readers/datacite_json_reader.rb +21 -19
- data/lib/bolognese/readers/datacite_reader.rb +30 -66
- data/lib/bolognese/readers/ris_reader.rb +6 -3
- data/lib/bolognese/readers/schema_org_reader.rb +12 -9
- data/lib/bolognese/utils.rb +15 -14
- data/lib/bolognese/version.rb +1 -1
- data/lib/bolognese/writers/bibtex_writer.rb +2 -2
- data/lib/bolognese/writers/codemeta_writer.rb +3 -3
- data/lib/bolognese/writers/crosscite_writer.rb +6 -6
- data/lib/bolognese/writers/datacite_json_writer.rb +9 -9
- data/lib/bolognese/writers/jats_writer.rb +4 -4
- data/lib/bolognese/writers/ris_writer.rb +4 -4
- data/lib/bolognese/writers/schema_org_writer.rb +6 -6
- data/spec/author_utils_spec.rb +1 -1
- data/spec/datacite_utils_spec.rb +2 -2
- data/spec/fixtures/crosscite.json +26 -16
- data/spec/fixtures/datacite.json +20 -14
- data/spec/fixtures/datacite_software.json +10 -6
- data/spec/readers/bibtex_reader_spec.rb +6 -6
- data/spec/readers/citeproc_reader_spec.rb +3 -3
- data/spec/readers/codemeta_reader_spec.rb +14 -14
- data/spec/readers/crosscite_reader_spec.rb +8 -9
- data/spec/readers/crossref_reader_spec.rb +31 -28
- data/spec/readers/datacite_json_reader_spec.rb +20 -6
- data/spec/readers/datacite_reader_spec.rb +94 -93
- data/spec/readers/ris_reader_spec.rb +5 -5
- data/spec/readers/schema_org_reader_spec.rb +41 -34
- data/spec/utils_spec.rb +3 -3
- data/spec/writers/bibtex_writer_spec.rb +1 -1
- data/spec/writers/citeproc_writer_spec.rb +1 -1
- data/spec/writers/codemeta_writer_spec.rb +15 -15
- data/spec/writers/crosscite_writer_spec.rb +16 -16
- data/spec/writers/datacite_json_writer_spec.rb +17 -17
- data/spec/writers/datacite_writer_spec.rb +26 -26
- data/spec/writers/ris_writer_spec.rb +2 -1
- metadata +2 -2
@@ -26,7 +26,7 @@ describe Bolognese::Metadata, vcr: true do
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("resourceType", "resourceTypeGeneral")).to eq("Text")
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expect(datacite.dig("creators", "creator").count).to eq(7)
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expect(datacite.dig("creators", "creator")[2]).to eq("creatorName" => "Hernandez, Beatriz",
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expect(datacite.dig("creators", "creator")[2]).to eq("creatorName" => {"__content__"=>"Hernandez, Beatriz", "nameType"=>"Personal"},
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"familyName" => "Hernandez",
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"givenName" => "Beatriz",
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"nameIdentifier" => {"schemeURI"=>"http://orcid.org/", "nameIdentifierScheme"=>"ORCID", "__content__"=>"http://orcid.org/0000-0003-2043-4925"})
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@@ -37,7 +37,7 @@ describe Bolognese::Metadata, vcr: true do
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subject = Bolognese::Metadata.new(input: input, from: "crossref")
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expect(subject.valid?).to be true
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("contributors", "contributor")).to eq("
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expect(datacite.dig("contributors", "contributor")).to eq("contributorName"=>{"__content__"=>"Janbon, Guilhem", "nameType"=>"Personal"}, "contributorType"=>"Other", "familyName"=>"Janbon", "givenName"=>"Guilhem")
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end
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it "Crossref DOI" do
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@@ -50,7 +50,7 @@ describe Bolognese::Metadata, vcr: true do
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expect(datacite.dig("descriptions", "description").first).to eq("__content__"=>"eLife", "descriptionType"=>"SeriesInformation")
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expect(datacite.dig("descriptions", "description", 1, "__content__")).to start_with("Among various advantages, their small size makes model organisms preferred subjects of investigation.")
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expect(datacite.dig("creators", "creator").count).to eq(5)
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expect(datacite.dig("creators", "creator").first).to eq("creatorName"=>"Sankar, Martial", "
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expect(datacite.dig("creators", "creator").first).to eq("creatorName"=>{"__content__"=>"Sankar, Martial", "nameType"=>"Personal"}, "familyName"=>"Sankar", "givenName"=>"Martial")
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end
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it "BlogPosting Citeproc JSON" do
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@@ -62,7 +62,7 @@ describe Bolognese::Metadata, vcr: true do
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expect(datacite.dig("titles", "title")).to eq("Eating your own Dog Food")
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expect(datacite.dig("descriptions", "description").first).to eq("__content__"=>"DataCite Blog", "descriptionType"=>"SeriesInformation")
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expect(datacite.dig("descriptions", "description", 1, "__content__")).to start_with("Eating your own dog food")
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expect(datacite.dig("creators", "creator")).to eq("creatorName"=>"Fenner, Martin", "
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expect(datacite.dig("creators", "creator")).to eq("creatorName"=>{"__content__"=>"Fenner, Martin", "nameType"=>"Personal"}, "familyName"=>"Fenner", "givenName"=>"Martin")
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end
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it "rdataone" do
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expect(subject.valid?).to be true
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("titles", "title")).to eq("R Interface to the DataONE REST API")
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expect(datacite.dig("creators", "creator")).to eq([{"creatorName"=>"Jones, Matt",
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expect(datacite.dig("creators", "creator")).to eq([{"creatorName"=>{"__content__"=>"Jones, Matt", "nameType"=>"Personal"},
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"givenName"=>"Matt",
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"familyName"=>"Jones",
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"nameIdentifier"=>
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{"schemeURI"=>"http://orcid.org/",
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"nameIdentifierScheme"=>"ORCID",
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"__content__"=>"http://orcid.org/0000-0003-0077-4738"}},
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{"creatorName"=>"Slaughter, Peter",
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{"creatorName"=>{"__content__"=>"Slaughter, Peter", "nameType"=>"Personal"},
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"givenName"=>"Peter",
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"familyName"=>"Slaughter",
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"nameIdentifier"=>
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{"schemeURI"=>"http://orcid.org/",
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"nameIdentifierScheme"=>"ORCID",
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"__content__"=>"http://orcid.org/0000-0002-2192-403X"}},
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{"creatorName"=>"University Of California, Santa Barbara"}])
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{"creatorName"=>{"__content__"=>"University Of California, Santa Barbara", "nameType"=>"Organizational"}}])
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expect(datacite.fetch("version")).to eq("2.0.0")
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end
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@@ -95,7 +95,7 @@ describe Bolognese::Metadata, vcr: true do
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expect(subject.valid?).to be true
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("titles", "title")).to eq("Maremma: a Ruby library for simplified network calls")
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expect(datacite.dig("creators", "creator")).to eq("creatorName"=>"Fenner, Martin", "givenName"=>"Martin", "familyName"=>"Fenner", "nameIdentifier"=>{"schemeURI"=>"http://orcid.org/", "nameIdentifierScheme"=>"ORCID", "__content__"=>"http://orcid.org/0000-0003-0077-4738"})
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expect(datacite.dig("creators", "creator")).to eq("creatorName"=> {"__content__"=>"Fenner, Martin", "nameType"=>"Personal"}, "givenName"=>"Martin", "familyName"=>"Fenner", "nameIdentifier"=>{"schemeURI"=>"http://orcid.org/", "nameIdentifierScheme"=>"ORCID", "__content__"=>"http://orcid.org/0000-0003-0077-4738"})
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end
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it "Text pass-thru" do
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expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"article-journal", "resource_type"=>"Paper", "resource_type_general"=>"Text", "ris"=>"RPRT", "type"=>"ScholarlyArticle")
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expect(subject.creator.length).to eq(20)
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expect(subject.creator.first).to eq("type"=>"Person", "familyName" => "Paglione", "givenName" => "Laura", "id" => "https://orcid.org/0000-0003-3188-6273", "name" => "Laura Paglione")
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expect(subject.
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expect(subject.
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expect(subject.titles).to eq([{"title"=>"Recommendation of: ORCID Works Metadata Working Group"}])
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expect(subject.rights_list).to eq([{"rights_uri"=>"https://creativecommons.org/publicdomain/zero/1.0", "rights"=>"CC-0"}])
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expect(subject.dates).to eq([{"date"=>"2017-06-28", "date_type"=>"Created"}, {"date"=>"2017-06-28", "date_type"=>"Updated"}, {"date"=>"2017", "date_type"=>"Issued"}])
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expect(subject.publication_year).to eq("2017")
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expect(subject.publisher).to eq("Figshare")
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expect(subject.types).to eq("bibtex"=>"article", "citeproc"=>"article-journal", "resource_type"=>"Paper", "resource_type_general"=>"Text", "ris"=>"RPRT", "type"=>"ScholarlyArticle")
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expect(subject.creator.length).to eq(20)
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expect(subject.creator.first).to eq("type"=>"Person", "familyName" => "Paglione", "givenName" => "Laura", "id" => "https://orcid.org/0000-0003-3188-6273", "name" => "Laura Paglione")
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expect(subject.
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expect(subject.
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expect(subject.titles).to eq([{"title"=>"Recommendation of: ORCID Works Metadata Working Group"}])
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expect(subject.rights_list).to eq([{"rights_uri"=>"https://creativecommons.org/publicdomain/zero/1.0", "rights"=>"CC-0"}])
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expect(subject.dates).to eq([{"date"=>"2017-06-28", "date_type"=>"Created"}, {"date"=>"2017-06-28", "date_type"=>"Updated"}, {"date"=>"2017", "date_type"=>"Issued"}])
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expect(subject.publication_year).to eq("2017")
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expect(subject.publisher).to eq("Figshare")
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expect(subject.types).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resource_type"=>"DataPackage", "resource_type_general"=>"Dataset", "ris"=>"DATA", "type"=>"Dataset")
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expect(subject.creator.length).to eq(8)
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expect(subject.creator.first).to eq("type"=>"Person", "name"=>"Benjamin Ollomo", "givenName"=>"Benjamin", "familyName"=>"Ollomo")
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expect(subject.
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expect(subject.alternate_identifiers).to eq("
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expect(subject.
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expect(subject.titles).to eq([{"title"=>"Data from: A new malaria agent in African hominids."}])
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expect(subject.alternate_identifiers).to eq([{"alternate_identifier"=> "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.", "alternate_identifier_type"=>"citation"}])
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expect(subject.rights_list).to eq([{"rights_uri"=>"http://creativecommons.org/publicdomain/zero/1.0"}])
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expect(subject.dates).to eq([{"date"=>"2011", "date_type"=>"Issued"}])
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expect(subject.publication_year).to eq("2011")
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expect(subject.related_identifiers.length).to eq(6)
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expect(subject.related_identifiers.last).to eq("
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expect(subject.related_identifiers.last).to eq("related_identifier"=>"19478877", "related_identifier_type"=>"PMID", "relation_type"=>"IsSupplementTo")
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expect(subject.publisher).to eq("Dryad Digital Repository")
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expect(subject.service_provider).to eq("DataCite")
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expect(subject.schema_version).to eq("http://datacite.org/schema/kernel-4")
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input = "10.7554/eLife.01567"
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subject = Bolognese::Metadata.new(input: input, from: "crossref")
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subject.doi = "10.5061/DRYAD.8515"
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subject.
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subject.titles = "Data from: Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth"
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subject.types = { "type" => "Dataset", "resource_type_general" => "Dataset" }
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expect(subject.valid?).to be true
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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it "change description" do
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input = "10.7554/eLife.01567"
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subject = Bolognese::Metadata.new(input: input, from: "crossref")
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subject.
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subject.descriptions = { "description" => "This is an abstract." }
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expect(subject.valid?).to be true
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("descriptions", "description")).to eq([{"__content__"=>"eLife", "descriptionType"=>"SeriesInformation"}, {"__content__"=>"This is an abstract.", "descriptionType"=>"Abstract"}])
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it "change description no input" do
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input = nil
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subject = Bolognese::Metadata.new(input: input, from: "datacite", doi: "10.4124/05f6c379-dd68-4cdb-880d-33d3e9576d52/1")
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subject.
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subject.descriptions = "This is an abstract."
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expect(subject.valid?).to be false
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("descriptions", "description")).to eq("descriptionType"=>"Abstract", "__content__"=>"This is an abstract.")
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input = nil
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subject = Bolognese::Metadata.new(input: input, doi: "10.4124/05f6c379-dd68-4cdb-880d-33d3e9576d52/1")
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subject.creator = [{"creatorName"=>"Fenner, Martin", "givenName"=>"Martin", "familyName"=>"Fenner"}]
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subject.
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subject.titles = [ "Data from: Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth" ]
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subject.publisher = "Dryad"
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subject.types = "Dataset"
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subject.publication_year = "2011"
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it "change license" do
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input = "10.7554/eLife.01567"
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subject = Bolognese::Metadata.new(input: input, from: "crossref")
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subject.
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subject.rights_list = [{ "rights_uri" => "https://creativecommons.org/licenses/by-nc-sa/4.0", "rights" => "Creative Commons Attribution-NonCommercial-ShareAlike" }]
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expect(subject.valid?).to be true
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("rightsList", "rights")).to eq("rightsURI"=>"https://creativecommons.org/licenses/by-nc-sa/4.0", "__content__"=>"Creative Commons Attribution-NonCommercial-ShareAlike")
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it "change license url" do
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input = "10.7554/eLife.01567"
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subject = Bolognese::Metadata.new(input: input, from: "crossref")
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subject.
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subject.rights_list = [{ "rights_uri" => "https://creativecommons.org/licenses/by-nc-sa/4.0" }]
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expect(subject.valid?).to be true
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("rightsList", "rights")).to eq("rightsURI"=>"https://creativecommons.org/licenses/by-nc-sa/4.0"
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expect(datacite.dig("rightsList", "rights")).to eq("rightsURI"=>"https://creativecommons.org/licenses/by-nc-sa/4.0")
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end
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it "change license name" do
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input = "10.7554/eLife.01567"
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subject = Bolognese::Metadata.new(input: input, from: "crossref")
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subject.
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subject.rights_list = [{ "rights" => "Creative Commons Attribution-NonCommercial-ShareAlike" }]
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expect(subject.valid?).to be true
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("rightsList", "rights")).to eq("Creative Commons Attribution-NonCommercial-ShareAlike")
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input = "10.7554/eLife.01567"
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subject = Bolognese::Metadata.new(input: input, from: "crossref")
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subject.doi = "123"
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subject.
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subject.titles = "Data from: Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth"
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subject.types = "Dataset"
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expect(subject.doi).to eq("123")
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expect(subject.valid?).to be false
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datacite = Maremma.from_xml(subject.datacite).fetch("resource", {})
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expect(datacite.dig("identifier", "__content__")).to eq("10.25491/d50j-3083")
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expect(datacite.dig("creators", "creator").count).to eq(1)
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expect(datacite.dig("creators", "creator")).to eq("creatorName"=>"The GTEx Consortium")
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expect(datacite.dig("creators", "creator")).to eq("creatorName"=>{"__content__"=>"The GTEx Consortium", "nameType"=>"Organizational"})
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expect(datacite.dig("resourceType", "resourceTypeGeneral")).to eq("Dataset")
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expect(datacite.dig("resourceType", "__content__")).to eq("Gene expression matrices")
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expect(datacite.dig("titles", "title")).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")
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it "Crossref DOI" do
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67
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input = fixture_path + "crossref.bib"
|
68
68
|
subject = Bolognese::Metadata.new(input: input, from: "bibtex")
|
69
|
+
|
69
70
|
ris = subject.ris.split("\r\n")
|
70
71
|
expect(ris[0]).to eq("TY - JOUR")
|
71
72
|
expect(ris[1]).to eq("T1 - Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth")
|
@@ -119,7 +120,7 @@ describe Bolognese::Metadata, vcr: true do
|
|
119
120
|
input = fixture_path + "datacite.json"
|
120
121
|
subject = Bolognese::Metadata.new(input: input, from: "datacite_json")
|
121
122
|
ris = subject.ris.split("\r\n")
|
122
|
-
expect(ris[0]).to eq("TY -
|
123
|
+
expect(ris[0]).to eq("TY - RPRT")
|
123
124
|
expect(ris[1]).to eq("T1 - Eating your own Dog Food")
|
124
125
|
expect(ris[2]).to eq("AU - Fenner, Martin")
|
125
126
|
expect(ris[3]).to eq("DO - 10.5438/4k3m-nyvg")
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bolognese
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 1.0.
|
4
|
+
version: 1.0.7
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Martin Fenner
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2018-11-
|
11
|
+
date: 2018-11-12 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: maremma
|