commonmeta-ruby 3.5.2 → 3.5.3
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 +4 -4
- data/lib/commonmeta/metadata_utils.rb +2 -0
- data/lib/commonmeta/version.rb +1 -1
- data/lib/commonmeta/writers/commonmeta_writer.rb +11 -0
- data/spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_commonmeta/with_data_citation.yml +247 -0
- data/spec/writers/commonmeta_writer_spec.rb +43 -0
- metadata +5 -2
checksums.yaml
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metadata.gz:
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metadata.gz: 3c2acea093c17e097fef5234c724c32893b6df9bb8192fcd356bbee1321d5ad5
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data.tar.gz: 9a93f805c39e517b7659d91508918bb7ad84a9270700f9662f90910fcf081f21
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metadata.gz: 570d1f410f9dd9608967697c3f3f6476cf767877441d3626eccf9993d56d551588bf2b39d514f5cfcd96043ad44f379c325334802f015445d99e19438d05f5a7
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data.tar.gz: '0678f6e2adc93ac9d740654efc9b5583e525dc1496fc75d01d22be26939ac8f07fd0c00f58e635ce4a97e1344672ef162c95ddfae72f489b3db72e5a51eb028d'
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data/Gemfile.lock
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PATH
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remote: .
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specs:
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commonmeta-ruby (3.5.
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commonmeta-ruby (3.5.3)
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activesupport (>= 4.2.5, < 8.0)
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addressable (~> 2.8.1, < 2.8.2)
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base32-url (>= 0.7.0, < 1)
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feedparser (2.2.0)
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logutils (>= 0.6.1)
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textutils (>= 1.0.0)
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ffi (1.
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ffi (1.16.2)
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ffi-compiler (1.0.1)
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ffi (>= 1.0.0)
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rake
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rspec-xsd (0.1.0)
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nokogiri (~> 1.6)
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rspec (~> 3)
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rubocop (1.56.
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rubocop (1.56.4)
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base64 (~> 0.1.1)
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json (~> 2.3)
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language_server-protocol (>= 3.17.0)
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rubocop-rake (0.6.0)
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rubocop-rspec (2.24.
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rubocop-rspec (2.24.1)
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rubocop (~> 1.33)
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rubocop-capybara (~> 2.17)
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rubocop-factory_bot (~> 2.22)
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@@ -22,6 +22,7 @@ require_relative 'writers/bibtex_writer'
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require_relative 'writers/citation_writer'
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require_relative 'writers/cff_writer'
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require_relative 'writers/codemeta_writer'
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require_relative 'writers/commonmeta_writer'
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require_relative 'writers/crossref_xml_writer'
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require_relative 'writers/csl_writer'
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require_relative 'writers/csv_writer'
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@@ -56,6 +57,7 @@ module Commonmeta
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include Commonmeta::Writers::CitationWriter
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include Commonmeta::Writers::CffWriter
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include Commonmeta::Writers::CodemetaWriter
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include Commonmeta::Writers::CommonmetaWriter
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include Commonmeta::Writers::CrossrefXmlWriter
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include Commonmeta::Writers::CslWriter
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include Commonmeta::Writers::CsvWriter
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data/lib/commonmeta/version.rb
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message: OK
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headers:
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Date:
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- Sun, 01 Oct 2023 12:13:43 GMT
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- Jetty(9.4.40.v20210413)
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Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2014,2,11]],"date-time":"2014-02-11T00:00:00Z","timestamp":1392076800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"},{"start":{"date-parts":[[2014,2,11]],"date-time":"2014-02-11T00:00:00Z","timestamp":1392076800000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"},{"start":{"date-parts":[[2014,2,11]],"date-time":"2014-02-11T00:00:00Z","timestamp":1392076800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"},{"start":{"date-parts":[[2014,2,11]],"date-time":"2014-02-11T00:00:00Z","timestamp":1392076800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"},{"start":{"date-parts":[[2014,2,11]],"date-time":"2014-02-11T00:00:00Z","timestamp":1392076800000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"},{"start":{"date-parts":[[2014,2,11]],"date-time":"2014-02-11T00:00:00Z","timestamp":1392076800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"funder":[{"name":"SystemsX"},{"name":"EMBO
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longterm post-doctoral fellowships"},{"name":"Marie Heim-Voegtlin"},{"DOI":"10.13039\/501100006390","name":"University
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of Lausanne","doi-asserted-by":"crossref"},{"name":"SystemsX"},{"DOI":"10.13039\/501100003043","name":"EMBO","doi-asserted-by":"publisher"},{"DOI":"10.13039\/501100001711","name":"Swiss
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National Science Foundation","doi-asserted-by":"publisher"},{"DOI":"10.13039\/501100006390","name":"University
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of Lausanne","doi-asserted-by":"crossref"}],"content-domain":{"domain":["www.elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>Among
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various advantages, their small size makes model organisms preferred subjects
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of investigation. Yet, even in model systems detailed analysis of numerous
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developmental processes at cellular level is severely hampered by their scale.
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For instance, secondary growth of Arabidopsis hypocotyls creates a radial
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pattern of highly specialized tissues that comprises several thousand cells
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starting from a few dozen. This dynamic process is difficult to follow because
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of its scale and because it can only be investigated invasively, precluding
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comprehensive understanding of the cell proliferation, differentiation, and
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patterning events involved. To overcome such limitation, we established an
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automated quantitative histology approach. We acquired hypocotyl cross-sections
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from tiled high-resolution images and extracted their information content
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using custom high-throughput image processing and segmentation. Coupled with
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automated cell type recognition through machine learning, we could establish
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a cellular resolution atlas that reveals vascular morphodynamics during secondary
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growth, for example equidistant phloem pole formation.<\/jats:p>","DOI":"10.7554\/elife.01567","type":"journal-article","created":{"date-parts":[[2014,2,11]],"date-time":"2014-02-11T16:29:04Z","timestamp":1392136144000},"source":"Crossref","is-referenced-by-count":31,"title":["Automated
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quantitative histology reveals vascular morphodynamics during Arabidopsis
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hypocotyl secondary growth"],"prefix":"10.7554","volume":"3","author":[{"given":"Martial","family":"Sankar","sequence":"first","affiliation":[{"name":"Department
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of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland"}]},{"given":"Kaisa","family":"Nieminen","sequence":"additional","affiliation":[{"name":"Department
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of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland"}]},{"given":"Laura","family":"Ragni","sequence":"additional","affiliation":[{"name":"Department
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of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland"}]},{"given":"Ioannis","family":"Xenarios","sequence":"additional","affiliation":[{"name":"Vital-IT,
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Swiss Institute of Bioinformatics, Lausanne, Switzerland"}]},{"given":"Christian
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S","family":"Hardtke","sequence":"additional","affiliation":[{"name":"Department
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of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland"}]}],"member":"4374","published-online":{"date-parts":[[2014,2,11]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1038\/nature02100","article-title":"APL
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regulates vascular tissue identity in Arabidopsis","volume":"426","author":"Bonke","year":"2003","journal-title":"Nature"},{"key":"bib2","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1534\/genetics.109.104976","article-title":"In
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the beginning was the worm","volume":"182","author":"Brenner","year":"2009","journal-title":"Genetics"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1034\/j.1399-3054.2002.1140413.x","article-title":"Secondary
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xylem development in Arabidopsis: a model for wood formation","volume":"114","author":"Chaffey","year":"2002","journal-title":"Physiologia
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Plantarum"},{"key":"bib4","doi-asserted-by":"publisher","first-page":"2119","DOI":"10.1162\/089976601750399335","article-title":"Training
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nu-support vector classifiers: theory and algorithms","volume":"13","author":"Chang","year":"2001","journal-title":"Neural
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computation"},{"key":"bib5","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/BF00994018","article-title":"Support-vector
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Networks","volume":"20","author":"Cortes","year":"1995","journal-title":"Machine
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Learning"},{"key":"bib6","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1242\/dev.119.1.71","article-title":"Cellular
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organisation of the Arabidopsis thaliana root","volume":"119","author":"Dolan","year":"1993","journal-title":"Development"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.1016\/j.semcdb.2009.09.009","article-title":"Stem
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cell function during plant vascular development","volume":"20","author":"Elo","year":"2009","journal-title":"Seminars
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in Cell & Developmental Biology"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.1242\/dev.091314","article-title":"WOX4
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and WOX14 act downstream of the PXY receptor kinase to regulate plant vascular
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proliferation independently of any role in vascular organisation","volume":"140","author":"Etchells","year":"2013","journal-title":"Development"},{"key":"bib9","doi-asserted-by":"publisher","first-page":"e1002997","DOI":"10.1371\/journal.pgen.1002997","article-title":"Plant
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vascular cell division is maintained by an interaction between PXY and ethylene
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signalling","volume":"8","author":"Etchells","year":"2012","journal-title":"PLOS
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Genetics"},{"key":"bib10","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1038\/msb.2010.25","article-title":"Clustering
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phenotype populations by genome-wide RNAi and multiparametric imaging","volume":"6","author":"Fuchs","year":"2010","journal-title":"Molecular
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tool in R for frequency detection","volume":"110","author":"Granqvist","year":"2012","journal-title":"Bio
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Systems"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.pbi.2005.11.013","article-title":"Developmental
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mechanisms regulating secondary growth in woody plants","volume":"9","author":"Groover","year":"2006","journal-title":"Current
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Opinion in Plant Biology"},{"key":"bib13","doi-asserted-by":"publisher","first-page":"2618","DOI":"10.1105\/tpc.110.076083","article-title":"TDIF
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peptide signaling regulates vascular stem cell proliferation via the WOX4
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homeobox gene in Arabidopsis","volume":"22","author":"Hirakawa","year":"2010","journal-title":"Plant
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control of vascular stem cell fate by a CLE peptide\/receptor system","volume":"105","author":"Hirakawa","year":"2008","journal-title":"Proceedings
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compared to animals: the broadest comparative study of development","volume":"295","author":"Meyerowitz","year":"2002","journal-title":"Science"},{"key":"bib17","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1104\/pp.104.040212","article-title":"A
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weed for wood? Arabidopsis as a genetic model for xylem development","volume":"135","author":"Nieminen","year":"2004","journal-title":"Plant
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Physiol"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"1565","DOI":"10.1038\/nbt1206-1565","article-title":"What
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is a support vector machine?","volume":"24","author":"Noble","year":"2006","journal-title":"Nature
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of cultured mammalian cells by shape analysis and pattern recognition","volume":"77","author":"Olson","year":"1980","journal-title":"Proceedings
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R package for image processing with applications to cellular phenotypes","volume":"26","author":"Pau","year":"2010","journal-title":"Bioinformatics"},{"key":"bib21","doi-asserted-by":"publisher","first-page":"1322","DOI":"10.1105\/tpc.111.084020","article-title":"Mobile
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gibberellin directly stimulates Arabidopsis hypocotyl xylem expansion","volume":"23","author":"Ragni","year":"2011","journal-title":"Plant
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Cell"},{"key":"bib22","doi-asserted-by":"publisher","article-title":"Data
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from: Automated quantitative histology reveals vascular morphodynamics during
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Arabidopsis hypocotyl secondary growth","author":"Sankar","year":"2014","journal-title":"Dryad
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Digital Repository","DOI":"10.5061\/dryad.b835k"},{"key":"bib23","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1016\/j.cub.2008.02.070","article-title":"Flowering
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as a condition for xylem expansion in Arabidopsis hypocotyl and root","volume":"18","author":"Sibout","year":"2008","journal-title":"Current
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Biology"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1111\/j.1469-8137.2010.03236.x","article-title":"Evolution
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of development of vascular cambia and secondary growth","volume":"186","author":"Spicer","year":"2010","journal-title":"The
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New Phytologist"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"659","DOI":"10.1007\/s00138-011-0345-9","article-title":"Cell
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morphology classification and clutter mitigation in phase-contrast microscopy
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images using machine learning","volume":"23","author":"Theriault","year":"2012","journal-title":"Machine
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Vision and Applications"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"439","DOI":"10.1016\/j.cell.2012.02.048","article-title":"Mechanical
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stress acts via katanin to amplify differences in growth rate between adjacent
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cells in Arabidopsis","volume":"149","author":"Uyttewaal","year":"2012","journal-title":"Cell"},{"key":"bib27","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/ncb2764","article-title":"A
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screen for morphological complexity identifies regulators of switch-like transitions
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between discrete cell shapes","volume":"15","author":"Yin","year":"2013","journal-title":"Nature
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Immunology and Microbiology","General Biochemistry, Genetics and Molecular
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recorded_with: VCR 6.2.0
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+
# frozen_string_literal: true
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+
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require "spec_helper"
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+
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5
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+
describe Commonmeta::Metadata, vcr: true do
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+
context "write metadata as commonmeta" do
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7
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+
it "with data citation" do
|
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8
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+
input = "10.7554/eLife.01567"
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+
subject = described_class.new(input: input, from: "crossref")
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+
json = JSON.parse(subject.commonmeta)
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|
+
expect(json["id"]).to eq("https://doi.org/10.7554/elife.01567")
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+
expect(json["type"]).to eq("JournalArticle")
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+
expect(json["url"]).to eq("https://elifesciences.org/articles/01567")
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14
|
+
expect(json["titles"]).to eq([{ "title" => "Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth" }])
|
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15
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+
expect(json["contributors"].length).to eq(5)
|
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+
expect(json["contributors"].first).to eq("affiliation" => [{ "name" => "Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland" }],
|
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+
"contributorRoles" => ["Author"],
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+
"familyName" => "Sankar",
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+
"givenName" => "Martial",
|
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|
+
"type" => "Person")
|
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+
expect(json["container"]).to eq("identifier" => "2050-084X",
|
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|
+
"identifierType" => "ISSN",
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+
"title" => "eLife",
|
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+
"type" => "Journal",
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|
+
"volume" => "3")
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|
+
expect(json["publisher"]).to eq("id" => "https://api.crossref.org/members/4374", "name" => "eLife Sciences Publications, Ltd")
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|
+
expect(json["references"].length).to eq(27)
|
|
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|
+
expect(json["references"].first).to eq("key" => "bib1",
|
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|
+
"doi" => "https://doi.org/10.1038/nature02100",
|
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|
+
"contributor" => "Bonke",
|
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|
+
"title" => "APL regulates vascular tissue identity in Arabidopsis",
|
|
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|
+
"publicationYear" => "2003",
|
|
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|
+
"volume" => "426",
|
|
34
|
+
"firstPage" => "181",
|
|
35
|
+
"containerTitle" => "Nature")
|
|
36
|
+
expect(json["date"]).to eq("published"=>"2014-02-11", "updated"=>"2022-03-26")
|
|
37
|
+
expect(json["descriptions"].first["description"]).to start_with("Among various advantages,")
|
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|
+
expect(json["license"]).to eq("id"=>"CC-BY-3.0", "url"=>"https://creativecommons.org/licenses/by/3.0/legalcode")
|
|
39
|
+
expect(json["provider"]).to eq("Crossref")
|
|
40
|
+
expect(json["files"].first).to eq("mimeType"=>"application/pdf", "url"=>"https://cdn.elifesciences.org/articles/01567/elife-01567-v1.pdf")
|
|
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|
+
end
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|
+
end
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|
+
end
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: commonmeta-ruby
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 3.5.
|
|
4
|
+
version: 3.5.3
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Martin Fenner
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2023-
|
|
11
|
+
date: 2023-10-01 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: activesupport
|
|
@@ -644,6 +644,7 @@ files:
|
|
|
644
644
|
- lib/commonmeta/writers/cff_writer.rb
|
|
645
645
|
- lib/commonmeta/writers/citation_writer.rb
|
|
646
646
|
- lib/commonmeta/writers/codemeta_writer.rb
|
|
647
|
+
- lib/commonmeta/writers/commonmeta_writer.rb
|
|
647
648
|
- lib/commonmeta/writers/crossref_xml_writer.rb
|
|
648
649
|
- lib/commonmeta/writers/csl_writer.rb
|
|
649
650
|
- lib/commonmeta/writers/csv_writer.rb
|
|
@@ -928,6 +929,7 @@ files:
|
|
|
928
929
|
- spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_citation/software_w/version.yml
|
|
929
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|
- spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite.yml
|
|
930
931
|
- spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_codemeta/SoftwareSourceCode_DataCite_check_codemeta_v2.yml
|
|
932
|
+
- spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_commonmeta/with_data_citation.yml
|
|
931
933
|
- spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/another_schema_org_from_front-matter.yml
|
|
932
934
|
- spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/book_oup.yml
|
|
933
935
|
- spec/fixtures/vcr_cassettes/Commonmeta_Metadata/write_metadata_as_crossref/journal_article.yml
|
|
@@ -1026,6 +1028,7 @@ files:
|
|
|
1026
1028
|
- spec/writers/cff_writer_spec.rb
|
|
1027
1029
|
- spec/writers/citation_writer_spec.rb
|
|
1028
1030
|
- spec/writers/codemeta_writer_spec.rb
|
|
1031
|
+
- spec/writers/commonmeta_writer_spec.rb
|
|
1029
1032
|
- spec/writers/crossref_xml_writer_spec.rb
|
|
1030
1033
|
- spec/writers/csl_writer_spec.rb
|
|
1031
1034
|
- spec/writers/csv_writer_spec.rb
|