commonmeta-ruby 3.0.0

data/spec/writers/schema_org_writer_spec.rb

@@ -0,0 +1,301 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+
+describe Commonmeta::Metadata, vcr: true do
+  context 'write metadata as schema_org' do
+    it 'journal article' do
+      input = '10.7554/eLife.01567'
+      subject = described_class.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['@type']).to eq('ScholarlyArticle')
+      expect(json['periodical']).to eq('@type' => 'Periodical', 'issn' => '2050-084X',
+                                       'name' => 'eLife')
+      expect(json['citation'].length).to eq(27)
+      expect(json['citation'].first).to eq('@id' => 'https://doi.org/10.1038/nature02100',
+                                           '@type' => 'CreativeWork', 'datePublished' => '2003', 'name' => 'APL regulates vascular tissue identity in Arabidopsis')
+      expect(json['funder']).to eq([{ '@type' => 'Organization', 'name' => 'SystemsX' },
+                                    { '@type' => 'Organization',
+                                      'name' => 'EMBO longterm post-doctoral fellowships' },
+                                    { '@type' => 'Organization', 'name' => 'Marie Heim-Voegtlin' },
+                                    { '@id' => 'https://doi.org/10.13039/501100006390',
+                                      '@type' => 'Organization',
+                                      'name' => 'University of Lausanne' },
+                                    { '@type' => 'Organization', 'name' => 'SystemsX' },
+                                    { '@id' => 'https://doi.org/10.13039/501100003043',
+                                      '@type' => 'Organization',
+                                      'name' => 'EMBO' },
+                                    { '@id' => 'https://doi.org/10.13039/501100001711',
+                                      '@type' => 'Organization',
+                                      'name' => 'Swiss National Science Foundation' },
+                                    { '@id' => 'https://doi.org/10.13039/501100006390',
+                                      '@type' => 'Organization',
+                                      'name' => 'University of Lausanne' }])
+      expect(json['license']).to eq('https://creativecommons.org/licenses/by/3.0/legalcode')
+    end
+
+    it 'maremma schema.org JSON' do
+      input = 'https://github.com/datacite/maremma'
+      subject = described_class.new(input: input, from: 'codemeta')
+      json = JSON.parse(subject.schema_org)
+      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('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
+      input = 'https://doi.org/10.5281/ZENODO.48440'
+      subject = described_class.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['@type']).to eq('SoftwareSourceCode')
+      expect(json['name']).to eq('Analysis Tools For Crossover Experiment Of Ui Using Choice Architecture')
+      expect(json['license']).to eq('https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode')
+    end
+
+    it 'Another Schema.org JSON' do
+      input = 'https://doi.org/10.5061/DRYAD.8515'
+      subject = described_class.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['@type']).to eq('Dataset')
+      expect(json['license']).to eq('https://creativecommons.org/publicdomain/zero/1.0/legalcode')
+      expect(json['keywords']).to eq('Plasmodium, malaria, mitochondrial genome, Parasites')
+    end
+
+    it 'Schema.org JSON Cyark' do
+      input = 'https://doi.org/10.26301/jgf3-jm06'
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.26301/jgf3-jm06')
+      expect(json['@type']).to eq('Dataset')
+    end
+
+    it 'rdataone' do
+      input = "#{fixture_path}codemeta.json"
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.5063/f1m61h5x')
+      expect(json['@type']).to eq('SoftwareSourceCode')
+      expect(json['name']).to eq('R Interface to the DataONE REST API')
+      expect(json['author']).to eq([{ 'givenName' => 'Matt',
+                                      'familyName' => 'Jones',
+                                      '@type' => 'Person',
+                                      '@id' => 'https://orcid.org/0000-0003-0077-4738',
+                                      'affiliation' => [{ '@type' => 'Organization',
+                                                          'name' => 'NCEAS' }] },
+                                    { 'givenName' => 'Peter',
+                                      'familyName' => 'Slaughter',
+                                      '@type' => 'Person',
+                                      '@id' => 'https://orcid.org/0000-0002-2192-403X',
+                                      'affiliation' => [{ '@type' => 'Organization',
+                                                          'name' => 'NCEAS' }] },
+                                    { '@type' => 'Organization',
+                                      'name' => 'University of California, Santa Barbara' }])
+      expect(json['version']).to eq('2.0.0')
+      expect(json['keywords']).to eq('data sharing, data repository, dataone')
+    end
+
+    it 'Funding' do
+      input = 'https://doi.org/10.5438/6423'
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.5438/6423')
+      expect(json['@type']).to eq('CreativeWork')
+      expect(json['funder']).to eq('@id' => 'https://doi.org/10.13039/501100000780',
+                                   '@type' => 'Organization', 'name' => 'European Commission')
+      expect(json['license']).to eq('https://creativecommons.org/licenses/by/4.0/legalcode')
+    end
+
+    it 'Funding OpenAIRE' do
+      input = 'https://doi.org/10.5281/ZENODO.1239'
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.5281/zenodo.1239')
+      expect(json['@type']).to eq('Dataset')
+      expect(json['funder']).to eq('@id' => 'https://doi.org/10.13039/501100000780',
+                                   '@type' => 'Organization', 'name' => 'European Commission')
+      expect(json['license']).to eq('https://creativecommons.org/publicdomain/zero/1.0/legalcode')
+    end
+
+    it 'subject scheme' do
+      input = 'https://doi.org/10.4232/1.2745'
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.4232/1.2745')
+      expect(json['@type']).to eq('Dataset')
+      expect(json['name']).to eq('Flash Eurobarometer 54 (Madrid Summit)')
+      expect(json['keywords']).to eq('KAT12 International Institutions, Relations, Conditions, Internationale Politik und Internationale Organisationen, Wirtschaftssysteme und wirtschaftliche Entwicklung, International politics and organisations, Economic systems and development')
+    end
+
+    it 'subject scheme multiple keywords' do
+      input = 'https://doi.org/10.1594/pangaea.721193'
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.1594/pangaea.721193')
+      expect(json['@type']).to eq('Dataset')
+      expect(json['name']).to eq('Seawater carbonate chemistry and processes during experiments with Crassostrea gigas, 2007')
+      expect(json['keywords']).to include('Animalia, Bottles or small containers/Aquaria (<20 L)')
+      expect(json['license']).to eq('https://creativecommons.org/licenses/by/3.0/legalcode')
+    end
+
+    it 'series information' do
+      input = '10.4229/23RDEUPVSEC2008-5CO.8.3'
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.4229/23rdeupvsec2008-5co.8.3')
+      expect(json['@type']).to eq('CreativeWork')
+      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', 'familyName' => 'Llamas',
+                                         'givenName' => 'P.')
+      expect(json['periodical']).to eq('@type' => 'Periodical',
+                                       'name' => '23rd European Photovoltaic Solar Energy Conference and Exhibition')
+    end
+
+    it 'data catalog' do
+      input = '10.25491/8KMC-G314'
+      subject = described_class.new(input: input)
+      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('@type' => 'PropertyValue', 'propertyID' => 'md5',
+                                       'value' => 'c7c89fe7366d50cd75448aa603c9de58')
+    end
+
+    it 'alternate identifiers' do
+      input = '10.23725/8na3-9s47'
+      subject = described_class.new(input: input)
+      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('name' => 'TOPMed')
+      expect(json['includedInDataCatalog']).to be_empty
+      expect(json['identifier']).to eq(
+        [{ '@type' => 'PropertyValue',
+           'propertyID' => 'minid',
+           'value' => 'ark:/99999/fk41CrU4eszeLUDe' },
+         { '@type' => 'PropertyValue',
+           'propertyID' => 'dataguid',
+           'value' => 'dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7' },
+         { '@type' => 'PropertyValue',
+           'propertyID' => 'md5',
+           'value' => '3b33f6b9338fccab0901b7d317577ea3' }]
+      )
+    end
+
+    it 'geo_location_box' do
+      input = '10.1594/PANGAEA.842237'
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.1594/pangaea.842237')
+      expect(json['@type']).to eq('Dataset')
+      expect(json['name']).to eq('Registry of all stations from the Tara Oceans Expedition (2009-2013)')
+      expect(json['author']).to eq([{ '@type' => 'Person', 'familyName' => 'Tara Oceans Consortium',
+                                      'givenName' => 'Coordinators' },
+                                    { '@type' => 'Person', 'familyName' => 'Tara Oceans Expedition',
+                                      'givenName' => 'Participants' }])
+      expect(json['includedInDataCatalog']).to be_empty
+      expect(json['spatialCoverage']).to eq('@type' => 'Place',
+                                            'geo' => {
+                                              '@type' => 'GeoShape', 'box' => '-64.3088 -168.5182 79.6753 174.9006'
+                                            })
+      expect(json['license']).to eq('https://creativecommons.org/licenses/by/3.0/legalcode')
+    end
+
+    it 'from schema_org gtex' do
+      input = "#{fixture_path}schema_org_gtex.json"
+      subject = described_class.new(input: input)
+      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' => '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')
+      expect(json['version']).to eq('v7')
+      expect(json['author']).to eq('@type' => 'Organization', 'name' => 'The GTEx Consortium')
+      expect(json['keywords']).to eq('gtex, annotation, phenotype, gene regulation, transcriptomics')
+      expect(json['datePublished']).to eq('2017')
+      expect(json['contentUrl']).to eq('https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz')
+      expect(json['schemaVersion']).to eq('http://datacite.org/schema/kernel-4')
+      expect(json['includedInDataCatalog']).to eq('@type' => 'DataCatalog', 'name' => 'GTEx')
+      expect(json['publisher']).to eq('@type' => 'Organization', 'name' => 'GTEx')
+      expect(json['funder']).to eq([{ '@id' => 'https://doi.org/10.13039/100000052',
+                                      'name' => 'Common Fund of the Office of the Director of the NIH',
+                                      '@type' => 'Organization' },
+                                    { '@id' => 'https://doi.org/10.13039/100000054',
+                                      'name' => 'National Cancer Institute (NCI)',
+                                      '@type' => 'Organization' },
+                                    { '@id' => 'https://doi.org/10.13039/100000051',
+                                      'name' => 'National Human Genome Research Institute (NHGRI)',
+                                      '@type' => 'Organization' },
+                                    { '@id' => 'https://doi.org/10.13039/100000050',
+                                      'name' => 'National Heart, Lung, and Blood Institute (NHLBI)',
+                                      '@type' => 'Organization' },
+                                    { '@id' => 'https://doi.org/10.13039/100000026',
+                                      'name' => 'National Institute on Drug Abuse (NIDA)',
+                                      '@type' => 'Organization' },
+                                    { '@id' => 'https://doi.org/10.13039/100000025',
+                                      'name' => 'National Institute of Mental Health (NIMH)',
+                                      '@type' => 'Organization' },
+                                    { '@id' => 'https://doi.org/10.13039/100000065',
+                                      'name' => 'National Institute of Neurological Disorders and Stroke (NINDS)',
+                                      '@type' => 'Organization' }])
+      expect(json['provider']).to eq('@type' => 'Organization', 'name' => 'DataCite')
+    end
+
+    it 'from schema_org topmed' do
+      input = "#{fixture_path}schema_org_topmed.json"
+      subject = described_class.new(input: input)
+      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['identifier']).to eq(
+        [{ '@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['url']).to eq('https://ors.datacite.org/doi:/10.23725/8na3-9s47')
+      expect(json['additionalType']).to eq('CRAM file')
+      expect(json['name']).to eq('NWD165827.recab.cram')
+      expect(json['author']).to eq('@type' => 'Organization', 'name' => 'TOPMed IRC')
+      expect(json['keywords']).to eq('topmed, whole genome sequencing')
+      expect(json['datePublished']).to eq('2017-11-30')
+      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'
+                                       ])
+      expect(json['schemaVersion']).to eq('http://datacite.org/schema/kernel-4')
+      expect(json['publisher']).to eq('@type' => 'Organization', 'name' => 'TOPMed')
+      expect(json['citation']).to eq([{ '@id' => 'https://doi.org/10.23725/2g4s-qv04',
+                                        '@type' => 'CreativeWork' }])
+      expect(json['funder']).to eq('@id' => 'https://doi.org/10.13039/100000050',
+                                   '@type' => 'Organization', 'name' => 'National Heart, Lung, and Blood Institute (NHLBI)')
+      expect(json['provider']).to eq('@type' => 'Organization', 'name' => 'DataCite')
+    end
+
+    it 'interactive resource without dates' do
+      input = 'https://doi.org/10.34747/g6yb-3412'
+      subject = described_class.new(input: input)
+      json = JSON.parse(subject.schema_org)
+      expect(json['@id']).to eq('https://doi.org/10.34747/g6yb-3412')
+      expect(json['@type']).to eq('CreativeWork')
+      expect(json['datePublished']).to eq('2019')
+    end
+  end
+end

data/spec/writers/turtle_writer_spec.rb

@@ -0,0 +1,85 @@
+# frozen_string_literal: true
+
+require 'spec_helper'
+
+describe Commonmeta::Metadata, vcr: true do
+  context 'write metadata as turtle' do
+    it 'Crossref DOI' do
+      input = "#{fixture_path}crossref.bib"
+      subject = described_class.new(input: input, from: 'bibtex')
+      ttl = subject.turtle.split("\n")
+      expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+      expect(ttl[2]).to eq('<https://doi.org/10.7554/elife.01567> a schema:ScholarlyArticle;')
+    end
+
+    it 'Dataset' do
+      input = 'https://doi.org/10.5061/DRYAD.8515'
+      subject = described_class.new(input: input, from: 'datacite')
+      expect(subject.valid?).to be true
+      ttl = subject.turtle.split("\n")
+      expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+      expect(ttl[2]).to eq('<https://doi.org/10.5061/dryad.8515> a schema:Dataset;')
+    end
+
+    it 'BlogPosting' do
+      input = 'https://doi.org/10.5438/4K3M-NYVG'
+      subject = described_class.new(input: input, from: 'datacite')
+      expect(subject.valid?).to be true
+      ttl = subject.turtle.split("\n")
+      expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+      expect(ttl[2]).to eq('<https://doi.org/10.5438/4k3m-nyvg> a schema:Article;')
+    end
+
+    it 'BlogPosting Citeproc JSON' do
+      input = "#{fixture_path}citeproc.json"
+      subject = described_class.new(input: input, from: 'csl')
+      ttl = subject.turtle.split("\n")
+      expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+      expect(ttl[2]).to eq('<https://doi.org/10.5438/4k3m-nyvg> a schema:Article;')
+    end
+
+    it 'BlogPosting DataCite JSON' do
+      input = "#{fixture_path}datacite.json"
+      subject = described_class.new(input: input, from: 'datacite')
+      ttl = subject.turtle.split("\n")
+      expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+      expect(ttl[2]).to eq('<https://doi.org/10.5438/4k3m-nyvg> a schema:Article;')
+    end
+
+    # it 'BlogPosting schema.org' do
+    #   input = 'https://blog.front-matter.io/posts/eating-your-own-dog-food//'
+    #   subject = described_class.new(input: input, from: 'schema_org')
+    #   expect(subject.valid?).to be true
+    #   ttl = subject.turtle.split("\n")
+    #   expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+    #   expect(ttl[2]).to eq('<https://doi.org/10.53731/r79vxn1-97aq74v-ag58n> a schema:Article;')
+    #   expect(ttl[3]).to eq('  schema:author <https://orcid.org/0000-0003-1419-2405>;')
+    # end
+
+    it 'DataONE' do
+      input = "#{fixture_path}codemeta.json"
+      subject = described_class.new(input: input, from: 'codemeta')
+      ttl = subject.turtle.split("\n")
+      expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+      expect(ttl[2]).to eq('<https://doi.org/10.5063/f1m61h5x> a schema:SoftwareSourceCode;')
+    end
+
+    it 'journal article' do
+      input = '10.7554/eLife.01567'
+      subject = described_class.new(input: input, from: 'crossref')
+      expect(subject.valid?).to be true
+      ttl = subject.turtle.split("\n")
+      expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+      expect(ttl[2]).to eq('<https://doi.org/10.7554/elife.01567> a schema:ScholarlyArticle;')
+    end
+
+    it 'with pages' do
+      input = 'https://doi.org/10.1155/2012/291294'
+      subject = described_class.new(input: input, from: 'crossref')
+      expect(subject.valid?).to be true
+      ttl = subject.turtle.split("\n")
+      expect(ttl[0]).to eq('@prefix schema: <http://schema.org/> .')
+      expect(ttl[2]).to eq('<https://doi.org/10.1155/2012/291294> a schema:ScholarlyArticle;')
+    end
+  end
+end