# frozen_string_literal: true
require 'spec_helper'
describe Commonmeta::Metadata, vcr: true do
let(:fixture_path) { 'spec/fixtures/' }
context 'get schema_org raw' do
it 'BlogPosting' do
input = "#{fixture_path}schema_org.json"
subject = described_class.new(input: input)
expect(subject.raw).to eq(File.read(input).strip)
end
end
context 'get schema_org metadata' do
it 'BlogPosting' do
input = 'https://blog.front-matter.io/posts/eating-your-own-dog-food'
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.53731/r79vxn1-97aq74v-ag58n')
expect(subject.url).to eq('https://blog.front-matter.io/posts/eating-your-own-dog-food')
expect(subject.type).to eq('Article')
expect(subject.creators).to eq([{ 'familyName' => 'Fenner',
'givenName' => 'Martin',
'id' => 'https://orcid.org/0000-0003-1419-2405',
'type' => 'Person' }])
expect(subject.titles).to eq([{ 'title' => 'Eating your own Dog Food' }])
expect(subject.descriptions.first['description']).to start_with('Eating your own dog food')
expect(subject.subjects).to eq([{ 'subject' => 'Feature' }])
expect(subject.date).to eq('published' => '2016-12-20T00:00:00Z',
'updated' => '2022-08-15T09:06:22Z')
expect(subject.references.length).to eq(0)
expect(subject.publisher).to eq('name' => 'Front Matter')
end
it 'BlogPosting with new DOI' do
input = 'https://blog.front-matter.io/posts/eating-your-own-dog-food'
subject = described_class.new(input: input, doi: '10.5438/0000-00ss')
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.5438/0000-00ss')
expect(subject.url).to eq('https://blog.front-matter.io/posts/eating-your-own-dog-food')
expect(subject.type).to eq('Article')
end
it 'BlogPosting with type as array' do
input = "#{fixture_path}schema_org_type_as_array.json"
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.5438/4k3m-nyvg')
expect(subject.url).to eq('https://blog.datacite.org/eating-your-own-dog-food')
expect(subject.type).to eq('Article')
expect(subject.creators).to eq([{ 'affiliation' => [{ 'name' => 'DataCite' }],
'familyName' => 'Fenner', 'givenName' => 'Martin',
'id' => 'https://orcid.org/0000-0003-1419-2405',
'type' => 'Person' }])
expect(subject.titles).to eq([{ 'title' => 'Eating your own Dog Food' }])
expect(subject.descriptions.first['description']).to start_with('Eating your own dog food')
expect(subject.subjects).to eq([{ 'subject' => 'Datacite' }, { 'subject' => 'Doi' },
{ 'subject' => 'Metadata' }, { 'subject' => 'Featured' }])
expect(subject.date).to eq('created' => '2016-12-20',
'published' => '2016-12-20',
'updated' => '2016-12-20')
expect(subject.references.length).to eq(2)
expect(subject.references.last).to eq('doi' => '10.5438/55e5-t5c0',
'key' => 'https://doi.org/10.5438/55e5-t5c0')
expect(subject.publisher).to eq('name' => 'DataCite')
end
context 'get schema_org metadata front matter' do
it 'BlogPosting' do
input = 'https://blog.front-matter.io/posts/step-forward-for-software-citation'
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.53731/r9531p1-97aq74v-ag78v')
expect(subject.url).to eq('https://blog.front-matter.io/posts/step-forward-for-software-citation')
expect(subject.type).to eq('Article')
expect(subject.creators).to eq([{ 'familyName' => 'Fenner',
'givenName' => 'Martin',
'id' => 'https://orcid.org/0000-0003-1419-2405',
'type' => 'Person' }])
expect(subject.titles).to eq([{ 'title' => 'A step forward for software citation: GitHub's enhanced software citation support' }])
expect(subject.descriptions.first['description']).to start_with('On August 19, GitHub announced software citation')
expect(subject.subjects).to eq([{ 'subject' => 'News' }])
expect(subject.date).to eq('published' => '2021-08-24T16:57:24Z',
'updated' => '2022-08-15T19:05:14Z')
expect(subject.references.length).to eq(0)
expect(subject.container).to eq("identifier"=>"https://blog.front-matter.io/", "identifierType"=>"URL", "title"=>"Front Matter", "type"=>"Periodical")
expect(subject.publisher).to eq('name' => 'Front Matter')
end
end
it 'zenodo' do
input = 'https://www.zenodo.org/record/1196821'
subject = described_class.new(input: input, from: 'schema_org')
# expect(subject.valid?).to be true
expect(subject.language).to eq('eng')
expect(subject.id).to eq('https://doi.org/10.5281/zenodo.1196821')
expect(subject.url).to eq('https://zenodo.org/record/1196821')
expect(subject.type).to eq('Dataset')
expect(subject.titles).to eq([{ 'title' => 'PsPM-SC4B: SCR, ECG, EMG, PSR and respiration measurements in a delay fear conditioning task with auditory CS and electrical US' }])
expect(subject.creators.size).to eq(6)
expect(subject.creators.first).to eq('type' => 'Person', 'givenName' => 'Matthias',
'familyName' => 'Staib', 'id' => 'https://orcid.org/0000-0001-9688-838X', 'affiliation' => [{ 'name' => 'University of Zurich, Zurich, Switzerland' }])
expect(subject.publisher).to eq('name' => 'Zenodo')
expect(subject.subjects).to eq([{ 'subject' => 'Pupil size response' },
{ 'subject' => 'Skin conductance response' },
{ 'subject' => 'Electrocardiogram' },
{ 'subject' => 'Electromyogram' },
{ 'subject' => 'Electrodermal activity' },
{ 'subject' => 'Galvanic skin response' },
{ 'subject' => 'Psr' },
{ 'subject' => 'Scr' },
{ 'subject' => 'Ecg' },
{ 'subject' => 'Emg' },
{ 'subject' => 'Eda' },
{ 'subject' => 'Gsr' }])
end
it 'pangaea' do
input = 'https://doi.pangaea.de/10.1594/PANGAEA.836178'
subject = described_class.new(input: input, from: 'schema_org')
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.1594/pangaea.836178')
expect(subject.url).to eq('https://doi.pangaea.de/10.1594/PANGAEA.836178')
expect(subject.type).to eq('Dataset')
expect(subject.titles).to eq([{ 'title' => 'Hydrological and meteorological investigations in a lake near Kangerlussuaq, west Greenland' }])
expect(subject.creators.size).to eq(8)
expect(subject.creators.first).to eq('type' => 'Person',
'givenName' => 'Emma', 'familyName' => 'Johansson')
expect(subject.publisher).to eq('name' => 'PANGAEA')
end
# TODO: check redirections
# it "ornl" do
# input = "https://doi.org/10.3334/ornldaac/1339"
# subject = Commonmeta::Metadata.new(input: input, from: "schema_org")
# # expect(subject.valid?).to be true
# expect(subject.id).to eq("https://doi.org/10.3334/ornldaac/1339")
# expect(subject.url).to eq("https://doi.org/10.3334/ornldaac/1339")
# expect(subject.type).to eq("bibtex"=>"misc", "citeproc"=>"article-journal", "ris"=>"GEN", "schemaOrg"=>"DataSet")
# expect(subject.titles).to eq([{"title"=>"Soil Moisture Profiles and Temperature Data from SoilSCAPE Sites, USA"}])
# expect(subject.creators.size).to eq(12)
# expect(subject.creators.first).to eq("familyName"=>"MOGHADDAM", "givenName"=>"M.", "name"=>"MOGHADDAM, M.", "type"=>"Person", "nameIdentifiers"=>[], "affiliation" => [])
# end
it 'harvard dataverse' do
input = 'https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/NJ7XSO'
subject = described_class.new(input: input, from: 'schema_org')
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.7910/dvn/nj7xso')
expect(subject.type).to eq('Dataset')
expect(subject.titles).to eq([{ 'title' => 'Summary data ankylosing spondylitis GWAS' }])
expect(subject.container).to eq('identifier' => 'https://dataverse.harvard.edu',
'identifierType' => 'URL', 'title' => 'Harvard Dataverse', 'type' => 'DataRepository')
expect(subject.creators).to eq([{
'name' => 'International Genetics of Ankylosing Spondylitis Consortium (IGAS)'
}])
expect(subject.subjects).to eq([{ 'subject' => 'Medicine, health and life sciences' },
{ 'subject' => 'genome-wide association studies' },
{ 'subject' => 'Ankylosing spondylitis' }])
end
it 'upstream blog' do
input = 'https://upstream.force11.org/elife-reviewed-preprints-interview-with-fiona-hutton'
subject = described_class.new(input: input, from: 'schema_org')
expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.54900/8d7emer-rm2pg72')
expect(subject.type).to eq('Article')
expect(subject.titles).to eq([{ 'title' => 'eLife Reviewed Preprints: Interview with Fiona Hutton' }])
expect(subject.container).to eq('identifier' => 'https://upstream.force11.org/',
'identifierType' => 'URL', 'title' => 'Upstream', 'type' => 'Periodical')
expect(subject.creators.size).to eq(2)
expect(subject.creators.first).to eq('familyName' => 'Hutton',
'givenName' => 'Fiona',
'type' => 'Person')
expect(subject.subjects).to eq([{ 'subject' => 'Interviews' }])
expect(subject.publisher).to eq('name' => 'Upstream')
expect(subject.date).to eq('published' => '2022-11-15T10:29:38Z',
'updated' => '2023-06-17T20:18:54Z')
expect(subject.license).to eq('id' => 'CC-BY-4.0',
'url' => 'https://creativecommons.org/licenses/by/4.0/legalcode')
end
# TODO: check 403 status in DOI resolver
# it "harvard dataverse via identifiers.org" do
# input = "https://identifiers.org/doi/10.7910/DVN/NJ7XSO"
# subject = Commonmeta::Metadata.new(input: input, from: "schema_org")
# # expect(subject.valid?).to be true
# expect(subject.id).to eq("https://doi.org/10.7910/dvn/nj7xso")
# expect(subject.type).to eq("bibtex"=>"misc", "citeproc"=>"dataset", "resourceTypeGeneral"=>"Dataset", "ris"=>"DATA", "schemaOrg"=>"Dataset")
# expect(subject.titles).to eq([{"title"=>"Summary data ankylosing spondylitis GWAS"}])
# expect(subject.container).to eq("identifier"=>"https://dataverse.harvard.edu", "identifierType"=>"URL", "title"=>"Harvard Dataverse", "type"=>"DataRepository")
# expect(subject.creators).to eq([{"name" => "International Genetics Of Ankylosing Spondylitis Consortium (IGAS)", "nameIdentifiers"=>[], "affiliation" => []}])
# end
end
context 'get schema_org metadata as string' do
it 'BlogPosting' do
input = "#{fixture_path}schema_org.json"
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.language).to eq('en')
expect(subject.id).to eq('https://doi.org/10.5438/4k3m-nyvg')
expect(subject.url).to eq('https://blog.datacite.org/eating-your-own-dog-food')
expect(subject.type).to eq('Article')
expect(subject.creators).to eq([{ 'familyName' => 'Fenner', 'givenName' => 'Martin',
'id' => 'https://orcid.org/0000-0003-1419-2405',
'type' => 'Person' }])
expect(subject.titles).to eq([{ 'title' => 'Eating your own Dog Food' }])
expect(subject.descriptions.first['description']).to start_with('Eating your own dog food')
expect(subject.subjects).to eq([{ 'subject' => 'Datacite' }, { 'subject' => 'Doi' },
{ 'subject' => 'Metadata' }, { 'subject' => 'Featured' }])
expect(subject.date).to eq('created' => '2016-12-20',
'published' => '2016-12-20',
'updated' => '2016-12-20')
expect(subject.references.length).to eq(2)
expect(subject.references.last).to eq('doi' => '10.5438/55e5-t5c0',
'key' => 'https://doi.org/10.5438/55e5-t5c0')
expect(subject.publisher).to eq('name' => 'DataCite')
end
it 'GTEx dataset' do
input = "#{fixture_path}schema_org_gtex.json"
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.25491/d50j-3083')
expect(subject.alternate_identifiers).to eq([{ 'alternateIdentifier' => '687610993',
'alternateIdentifierType' => 'md5' }])
expect(subject.url).to eq('https://ors.datacite.org/doi:/10.25491/d50j-3083')
expect(subject.content_url).to eq(['https://storage.googleapis.com/gtex_analysis_v7/single_tissue_eqtl_data/GTEx_Analysis_v7_eQTL_expression_matrices.tar.gz'])
expect(subject.type).to eq('Dataset')
expect(subject.creators).to eq([{ 'name' => 'The GTEx Consortium',
'type' => 'Organization' }])
expect(subject.titles).to eq([{ 'title' => '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(subject.version).to eq('v7')
expect(subject.subjects).to eq([{ 'subject' => 'Gtex' }, { 'subject' => 'Annotation' },
{ 'subject' => 'Phenotype' }, { 'subject' => 'Gene regulation' }, { 'subject' => 'Transcriptomics' }])
expect(subject.date).to eq('published' => '2017')
expect(subject.container).to eq('title' => 'GTEx', 'type' => 'DataRepository')
expect(subject.publisher).to eq('name' => 'GTEx')
expect(subject.funding_references.length).to eq(7)
expect(subject.funding_references.first).to eq(
'funderIdentifier' => 'https://doi.org/10.13039/100000052', 'funderIdentifierType' => 'Crossref Funder ID', 'funderName' => 'Common Fund of the Office of the Director of the NIH'
)
end
it 'TOPMed dataset' do
input = "#{fixture_path}schema_org_topmed.json"
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.alternate_identifiers).to eq([{ 'alternateIdentifier' => '3b33f6b9338fccab0901b7d317577ea3',
'alternateIdentifierType' => 'md5' },
{ 'alternateIdentifier' => 'ark:/99999/fk41CrU4eszeLUDe',
'alternateIdentifierType' => 'minid' },
{ 'alternateIdentifier' => 'dg.4503/c3d66dc9-58da-411c-83c4-dd656aa3c4b7',
'alternateIdentifierType' => 'dataguid' }])
expect(subject.url).to eq('https://ors.datacite.org/doi:/10.23725/8na3-9s47')
expect(subject.content_url).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(subject.type).to eq('Dataset')
expect(subject.creators).to eq([{ 'name' => 'TOPMed IRC', 'type' => 'Organization' }])
expect(subject.titles).to eq([{ 'title' => 'NWD165827.recab.cram' }])
expect(subject.subjects).to eq([{ 'subject' => 'Topmed' },
{ 'subject' => 'Whole genome sequencing' }])
expect(subject.date).to eq('published' => '2017-11-30')
expect(subject.publisher).to eq('name' => 'TOPMed')
expect(subject.references).to eq([{ 'doi' => '10.23725/2g4s-qv04',
'key' => 'https://doi.org/10.23725/2g4s-qv04' }])
expect(subject.funding_references).to eq([{
'funderIdentifier' => 'https://doi.org/10.13039/100000050', 'funderIdentifierType' => 'Crossref Funder ID', 'funderName' => 'National Heart, Lung, and Blood Institute (NHLBI)'
}])
end
it 'tdl_iodp dataset' do
input = "#{fixture_path}schema_org_tdl_iodp_invalid_authors.json"
subject = described_class.new(input: input)
expect(subject.valid?).to be false
end
it 'geolocation' do
input = "#{fixture_path}schema_org_geolocation.json"
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.6071/z7wc73')
expect(subject.alternate_identifiers).to be_nil
expect(subject.type).to eq('Dataset')
expect(subject.creators.length).to eq(6)
expect(subject.creators.first).to eq('familyName' => 'Bales', 'givenName' => 'Roger',
'type' => 'Person')
expect(subject.titles).to eq([{ 'title' => 'Southern Sierra Critical Zone Observatory (SSCZO), Providence Creek meteorological data, soil moisture and temperature, snow depth and air temperature' }])
expect(subject.subjects).to eq([{ 'subject' => 'Earth sciences' },
{ 'subject' => 'Soil moisture' },
{ 'subject' => 'Soil temperature' },
{ 'subject' => 'Snow depth' },
{ 'subject' => 'Air temperature' },
{ 'subject' => 'Water balance' },
{ 'subject' => 'Nevada' },
{ 'subject' => 'Sierra (mountain range)' }])
expect(subject.date).to eq('published' => '2013', 'updated' => '2014-10-17')
expect(subject.publisher).to eq('name' => 'UC Merced')
expect(subject.funding_references).to eq([{ 'funderName' => 'National Science Foundation, Division of Earth Sciences, Critical Zone Observatories' }])
expect(subject.geo_locations).to eq([{
'geoLocationPlace' => 'Providence Creek (Lower, Upper and P301)', 'geoLocationPoint' => {
'pointLatitude' => '37.047756', 'pointLongitude' => '-119.221094'
}
}])
end
it 'geolocation geoshape' do
input = "#{fixture_path}schema_org_geoshape.json"
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.language).to eq('en')
expect(subject.id).to eq('https://doi.org/10.1594/pangaea.842237')
expect(subject.type).to eq('Dataset')
expect(subject.creators.length).to eq(2)
expect(subject.creators.first).to eq('name' => 'Tara Oceans Consortium, Coordinators',
'type' => 'Organization')
expect(subject.titles).to eq([{ 'title' => 'Registry of all stations from the Tara Oceans Expedition (2009-2013)' }])
expect(subject.date).to eq('published' => '2015-02-03')
expect(subject.publisher).to eq('name' => 'PANGAEA')
expect(subject.geo_locations).to eq([{ 'geoLocationBox' => { 'eastBoundLongitude' => '174.9006',
'northBoundLatitude' => '79.6753', 'southBoundLatitude' => '-64.3088', 'westBoundLongitude' => '-168.5182' } }])
end
it 'schema_org list' do
data = File.read("#{fixture_path}schema_org_list.json").strip
input = JSON.parse(data).first.to_json
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.23725/7jg3-v803')
expect(subject.alternate_identifiers).to eq([{ 'alternateIdentifier' => 'ark:/99999/fk4E1n6n1YHKxPk',
'alternateIdentifierType' => 'minid' },
{ 'alternateIdentifier' => 'dg.4503/01b048d0-e128-4cb0-94e9-b2d2cab7563d',
'alternateIdentifierType' => 'dataguid' },
{ 'alternateIdentifier' => 'f9e72bdf25bf4b4f0e581d9218fec2eb',
'alternateIdentifierType' => 'md5' }])
expect(subject.url).to eq('https://ors.datacite.org/doi:/10.23725/7jg3-v803')
expect(subject.content_url).to eq([
's3://cgp-commons-public/topmed_open_access/44a8837b-4456-5709-b56b-54e23000f13a/NWD100953.recab.cram', 'gs://topmed-irc-share/public/NWD100953.recab.cram', 'dos://dos.commons.ucsc-cgp.org/01b048d0-e128-4cb0-94e9-b2d2cab7563d?version=2018-05-26T133719.491772Z'
])
expect(subject.type).to eq('Dataset')
expect(subject.creators).to eq([{ 'name' => 'TOPMed', 'type' => 'Organization' }])
expect(subject.titles).to eq([{ 'title' => 'NWD100953.recab.cram' }])
expect(subject.subjects).to eq([{ 'subject' => 'Topmed' },
{ 'subject' => 'Whole genome sequencing' }])
expect(subject.date).to eq('published' => '2017-11-30')
expect(subject.publisher).to eq('name' => 'TOPMed')
expect(subject.funding_references).to eq([{
'funderIdentifier' => 'https://doi.org/10.13039/100000050', 'funderIdentifierType' => 'Crossref Funder ID', 'funderName' => 'National Heart, Lung, and Blood Institute (NHLBI)'
}])
end
it 'aida dataset' do
input = "#{fixture_path}aida.json"
subject = described_class.new(input: input)
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.23698/aida/drov')
expect(subject.url).to eq('https://doi.aida.medtech4health.se/10.23698/aida/drov')
expect(subject.type).to eq('Dataset')
# expect(subject.creators).to eq([{"familyName"=>"Lindman", "givenName"=>"Karin", "name"=>"Lindman, Karin", "nameIdentifiers"=>[{"nameIdentifier"=> "https://orcid.org/0000-0003-1298-517X", "nameIdentifierScheme"=>"ORCID", "schemeUri"=>"https://orcid.org"}], "type"=>"Person"}])
expect(subject.titles).to eq([{ 'title' => 'Ovary data from the Visual Sweden project DROID' }])
expect(subject.version).to eq('1.0')
expect(subject.subjects).to eq([{ 'subject' => 'Pathology' }, { 'subject' => 'Whole slide imaging' },
{ 'subject' => 'Annotated' }])
expect(subject.date).to eq('created' => '2019-01-09',
'published' => '2019-01-09',
'updated' => '2019-01-09')
expect(subject.id).to eq('https://doi.org/10.23698/aida/drov')
expect(subject.publisher).to eq('name' => 'AIDA')
expect(subject.license).to eq('url' => 'https://datasets.aida.medtech4health.se/10.23698/aida/drov#license')
end
it 'from attributes' do
subject = described_class.new(input: nil,
from: 'schema_org',
doi: '10.5281/zenodo.1239',
creators: [{ 'type' => 'Person', 'name' => 'Jahn, Najko', 'givenName' => 'Najko',
'familyName' => 'Jahn' }],
titles: [{ 'title' => 'Publication Fp7 Funding Acknowledgment - Plos Openaire' }],
descriptions: [{
'description' => 'The dataset contains a sample of metadata describing papers', 'descriptionType' => 'Abstract'
}],
publisher: { 'name' => 'Zenodo' },
date: { 'published' => '2013-04-03' },
funding_references: [{ 'awardNumber' => '246686',
'awardTitle' => 'Open Access Infrastructure for Research in Europe',
'awardUri' => 'info:eu-repo/grantAgreement/EC/FP7/246686/',
'funderIdentifier' => 'https://doi.org/10.13039/501100000780',
'funderIdentifierType' => 'Crossref Funder ID',
'funderName' => 'European Commission' }],
type: 'Dataset')
# expect(subject.valid?).to be true
expect(subject.id).to eq('https://doi.org/10.5281/zenodo.1239')
expect(subject.type).to eq('Dataset')
expect(subject.creators).to eq([{ 'familyName' => 'Jahn', 'givenName' => 'Najko',
'name' => 'Jahn, Najko', 'type' => 'Person' }])
expect(subject.titles).to eq([{ 'title' => 'Publication Fp7 Funding Acknowledgment - Plos Openaire' }])
expect(subject.descriptions.first['description']).to start_with('The dataset contains a sample of metadata describing papers')
expect(subject.date).to eq('published' => '2013-04-03')
expect(subject.publisher).to eq('name' => 'Zenodo')
expect(subject.funding_references).to eq([{ 'awardNumber' => '246686',
'awardTitle' => 'Open Access Infrastructure for Research in Europe',
'awardUri' => 'info:eu-repo/grantAgreement/EC/FP7/246686/',
'funderIdentifier' => 'https://doi.org/10.13039/501100000780',
'funderIdentifierType' => 'Crossref Funder ID',
'funderName' => 'European Commission' }])
end
end
end