cirneco 0.5.8 → 0.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: bc53bd40a384ab3df63764308d8f6267f230975a
-  data.tar.gz: 8596911b41e4513f9c947c0cb0b2a345d57e2a8d
+  metadata.gz: c681eb9e780bbbe04eda5adbef5a576d122e7c08
+  data.tar.gz: 0317daa84b9387a623d3a2683f01d5a95128f6cf
 SHA512:
-  metadata.gz: 508aeb634c7e6b5af2cb88ee30e6f9b031ca85456f02b237c497050b5ac34f608c04a0f694b9507c577f0859b802fe012f36e8939fd3037c7aee3c22e739b43b
-  data.tar.gz: bfccc96e67b81775f5747bf00d89d71537d4d1c3d4e73c27401ecb2bd48d330a0de047c03a0ce5b85d92a8d7f8058416ea707b6d7382da6548532d99ef9b0cd5
+  metadata.gz: 2fd2af304e416f63f1bdd02363b3a0ca121842bf3a84c8e3ce66b670f7334d07963b5125ec60d29eb8f766ff928e7fe25ccfeae85a73744e3fcf5b5a5981e22d
+  data.tar.gz: 49b4707a22657ddd0660f635dcbac7e618a03dfa0f659a998419a1daf28f6af8f10b3e5b5ae21764e9687134ac03162f3b7242c63f5795b9f5159aec3994529d

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    cirneco (0.5.8)
+    cirneco (0.6)
       activesupport (~> 4.2, >= 4.2.5)
       base32-crockford-checksum (~> 0.2.2)
       bergamasco (~> 0.2)
@@ -22,7 +22,7 @@ GEM
       tzinfo (~> 1.1)
     addressable (2.3.8)
     base32-crockford-checksum (0.2.3)
-    bergamasco (0.2.3)
+    bergamasco (0.2.11)
       activesupport (~> 4.2, >= 4.2.5)
       addressable (~> 2.3.8)
       builder (~> 3.2, >= 3.2.2)

data/lib/cirneco/utils.rb

@@ -32,32 +32,41 @@ module Cirneco
       filename = File.basename(filepath)
       return "File #{filename} ignored: not a markdown file" unless File.extname(filepath) == ".md"
 
-      file = IO.read(filepath)
+      old_metadata = Bergamasco::Markdown.read_yaml_for_doi_metadata(filepath)
+      return nil if old_metadata["doi"]
 
-      if options[:unregister]
-        doi = nil
-      else
-        prefix = options[:prefix] || ENV['PREFIX']
-        doi = encode_doi(prefix, options)
-      end
+      metadata = generate_metadata_for_work(filepath, options)
+      work = register_work_for_metadata(metadata)
 
-      updated_file = Bergamasco::Markdown.update_file(file, { "doi" => doi })
+      # datapath = options[:datapath] || ENV['DATAPATH'] || "data/doi.yml"
+      # data = Bergamasco::Markdown.read_yaml(datapath) || []
+      # data = [data] if data.is_a?(Hash)
+      # new_data = [{ "filename" => filename, "doi" => doi, "date" => Time.now.utc.iso8601 }]
+      # Bergamasco::Markdown.write_yaml(datapath, data + new_data)
 
-      if updated_file != file
-        IO.write(filepath, updated_file)
+      new_metadata = Bergamasco::Markdown.update_file(filepath, { "doi" => metadata["doi"] })
+      "DOI #{new_metadata["doi"]} added for #{filename}"
+    end
 
-        datapath = options[:datapath] || ENV['DATAPATH'] || "data/doi.yml"
-        data = Bergamasco::Markdown.read_yaml(datapath) || []
-        data = [data] if data.is_a?(Hash)
-        new_data = [{ "filename" => filename, "doi" => doi, "date" => Time.now.utc.iso8601 }]
-        Bergamasco::Markdown.write_yaml(datapath, data + new_data)
-      end
+    # currently only supports markdown files with YAML header
+    def unregister_file(filepath, options={})
+      filename = File.basename(filepath)
+      return "File #{filename} ignored: not a markdown file" unless File.extname(filepath) == ".md"
 
-      if doi.nil?
-        "DOI removed from #{filename}"
-      elsif updated_file != file
-        "DOI #{doi} added to #{filename}"
-      end
+      old_metadata = Bergamasco::Markdown.read_yaml_for_doi_metadata(filepath)
+      return nil unless old_metadata["doi"]
+
+      metadata = generate_metadata_for_work(filepath, options)
+      work = unregister_work_for_metadata(metadata)
+
+      # datapath = options[:datapath] || ENV['DATAPATH'] || "data/doi.yml"
+      # data = Bergamasco::Markdown.read_yaml(datapath) || []
+      # data = [data] if data.is_a?(Hash)
+      # new_data = [{ "filename" => filename, "doi" => doi, "date" => Time.now.utc.iso8601 }]
+      # Bergamasco::Markdown.write_yaml(datapath, data + new_data)
+
+      new_metadata = Bergamasco::Markdown.update_file(filepath, { "doi" => nil })
+      "DOI #{old_metadata["doi"]} removed for #{filename}"
     end
 
     def register_all_files(folderpath, options={})
@@ -66,6 +75,12 @@ module Cirneco
       end.join("\n")
     end
 
+    def unregister_all_files(folderpath, options={})
+      Dir.glob("#{folderpath}/*.md").map do |filepath|
+        unregister_file(filepath, options)
+      end.join("\n")
+    end
+
     def generate_metadata_for_work(filepath, options={})
       metadata = Bergamasco::Markdown.read_yaml_for_doi_metadata(filepath, options.except(:number))
 
@@ -79,8 +94,12 @@ module Cirneco
       authorpath = options[:authorpath] || ENV['SITE_AUTHORPATH']
       author_options = authorpath.present? ? Bergamasco::Markdown.read_yaml(authorpath) : {}
 
+      # read in optional yaml configuration file for references
+      referencespath = options[:referencespath] || ENV['SITE_REFERENCESPATH']
+      references = referencespath.present? ? Bergamasco::Markdown.read_yaml(referencespath) : {}
+
       # required metadata
-      prefix = options[:prefix] || ENV['PREFIX']
+      prefix = options[:prefix] || site_options["prefix"] || ENV['SITE_PREFIX']
       metadata["doi"] ||= encode_doi(prefix, options)
 
       site_url = site_options["site_url"] || ENV['SITE_URL']
@@ -100,7 +119,7 @@ module Cirneco
       metadata["publisher"] = site_options["site_title"] || ENV['SITE_TITLE']
       metadata["publication_year"] = metadata["date"][0..3].to_i
 
-      metadata["type"] ||= site_options["site_default_type"] || ENV['SITE_DEFAULT_TYPE'] || "BlogPosting"
+      metadata["type"] ||= site_options["default_type"] || ENV['SITE_DEFAULT_TYPE'] || "BlogPosting"
       resource_type_general = metadata["type"] == "Dataset" ? "Dataset" : "Text"
 
       metadata["resource_type"] = { value: metadata["type"],
@@ -113,13 +132,51 @@ module Cirneco
       # use default version 1.0
       metadata["version"] ||= "1.0"
 
+      # fetch reference metadata if available
+      metadata["related_identifiers"] = Array(metadata["references"]).map do |r|
+        reference = references.fetch(r, {})
+        if reference.present?
+          if reference["DOI"].present?
+            value = reference["DOI"].upcase
+            type = "DOI"
+          elsif /(http|https):\/\/(dx\.)?doi\.org\/(\w+)/.match(reference["URL"])
+            uri = Addressable::URI.parse(reference["URL"])
+            value = uri.path[1..-1].upcase
+            type = "DOI"
+          elsif reference["URL"].present?
+            value = reference["URL"]
+            type = "URL"
+          else
+            type = nil
+          end
+        else
+          if /(http|https):\/\/(dx\.)?doi\.org\/(\w+)/.match(r)
+            uri = Addressable::URI.parse(r)
+            value = uri.path[1..-1].upcase
+            type = "DOI"
+          elsif /(http|https):\/\//.match(r)
+            uri = Addressable::URI.parse(r)
+            value = uri.normalize.to_s
+            type = "URL"
+          else
+            type = nil
+          end
+        end
+
+        {
+          value: value,
+          related_identifier_type: type,
+          relation_type: "References"
+        }
+      end.select { |t| t[:related_identifier_type].present? }
+
       license_name = site_options.fetch("license", {}).fetch("name", nil) || ENV['SITE_LICENCE_NAME'] || "Creative Commons Attribution"
       license_url = site_options.fetch("license", {}).fetch("url", nil) || ENV['SITE_LICENCE_URL'] || "https://creativecommons.org/licenses/by/4.0/"
       metadata["rights_list"] = [{ value: license_name, rights_uri: license_url }]
 
       metadata["subjects"] = Array(metadata["tags"]).select { |t| t != "featured" }
 
-      contributor = site_options["site_institution"] || ENV['SITE_INSTITUTION']
+      contributor = site_options["institution"] || ENV['SITE_INSTITUTION']
       metadata["contributors"] = [{ literal: contributor, contributor_type: "HostingInstitution" }]
 
       metadata = metadata.extract!(*%w(doi url creators title publisher
@@ -131,7 +188,7 @@ module Cirneco
       site_url.to_s.chomp("\\") + "/" + File.basename(filepath)[0..-9] + "/"
     end
 
-    def create_work_from_metadata(metadata, options={})
+    def register_work_for_metadata(metadata)
       work = Cirneco::Work.new(metadata)
 
       filename  = metadata["doi"].split("/", 2).last + ".xml"
@@ -139,5 +196,14 @@ module Cirneco
 
       work
     end
+
+    def unregister_work_for_metadata(metadata)
+      work = Cirneco::Work.new(metadata)
+
+      filename  = metadata["doi"].split("/", 2).last + ".xml"
+      File.delete(filename)
+
+      work
+    end
   end
 end

data/lib/cirneco/version.rb

@@ -1,3 +1,3 @@
 module Cirneco
-  VERSION = "0.5.8"
+  VERSION = "0.6"
 end

data/spec/fixtures/references.yaml

@@ -0,0 +1,1060 @@
+---
+references:
+- id: http://doi.org/10.5281/zenodo.32412
+  type: article-journal
+  author:
+  - family: Mayo
+    given: Christine
+  - family: Hull
+    given: Elizabeth A.
+  - family: Vision
+    given: Todd J.
+  issued:
+  - year: '2015'
+  title: 'The location of the citation: changing practices in how publications cite
+    original data in the Dryad Digital Repository'
+  publisher: Zenodo
+  URL: http://zenodo.org/record/32412
+  DOI: 10.5281/zenodo.32412
+
+- id: Kratz:2015cr
+  type: article-journal
+  author:
+  - family: Kratz
+    given: John E
+  - family: Strasser
+    given: Carly
+  issued:
+  - year: '2015'
+    month: '8'
+  title: Making data count
+  container-title: Scientific Data
+  page: '150039'
+  volume: '2'
+  URL: http://www.nature.com/articles/sdata201539
+  DOI: 10.1038/sdata.2015.39
+
+- id: Eysenbach:2006jo
+  type: article-journal
+  author:
+  - family: Eysenbach
+    given: Gunther
+  issued:
+  - year: '2006'
+    month: '5'
+  title: Citation advantage of open access articles.
+  container-title: PLoS biology
+  page: 'e157'
+  volume: '4'
+  issue: '5'
+  URL: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=16683865&retmode=ref&cmd=prlinks
+  DOI: 10.1371/journal.pbio.0040157
+  PMCID: PMC1459247
+  PMID: '16683865'
+
+- id: Piwowar:2013cc
+  type: article-journal
+  author:
+  - family: Piwowar
+    given: Heather A
+  - family: Vision
+    given: Todd J
+  issued:
+  - year: '2013'
+  title: Data reuse and the open data citation advantage
+  container-title: PeerJ
+  page: 'e175'
+  volume: '1'
+  DOI: 10.7717/peerj.175
+
+- id: Irisarri:2013
+  type: dataset
+  author:
+  - family: Irisarri
+    given: Iker
+  - family: San Mauro
+    given: Diego
+  - family: Abascal
+    given: Federico
+  - family: Ohler
+    given: Annemarie
+  - family: Vences
+    given: Miguel
+  - family: Zardoya
+    given: Rafael
+  issued:
+  - year: '2013'
+  title: 'Data from: The origin of modern frogs (Neobatrachia) was accompanied by
+    acceleration in mitochondrial and nuclear substitution rates'
+  publisher: Dryad Digital Repository
+  URL: http://doi.org/10.5061/DRYAD.3QD54
+  DOI: 10.5061/DRYAD.3QD54
+
+- id: Irisarri:2012gv
+  type: article-journal
+  author:
+  - family: Irisarri
+    given: Iker
+  - family: San Mauro
+    given: Diego
+  - family: Abascal
+    given: Federico
+  - family: Ohler
+    given: Annemarie
+  - family: Vences
+    given: Miguel
+  - family: Zardoya
+    given: Rafael
+  issued:
+  - year: '2012'
+  title: The origin of modern frogs (Neobatrachia) was accompanied by acceleration
+    in mitochondrial and nuclear substitution rates.
+  container-title: BMC genomics
+  page: '626'
+  volume: '13'
+  URL: http://www.biomedcentral.com/1471-2164/13/626/
+  DOI: 10.1186/1471-2164-13-626
+  PMCID: PMC3551647
+  PMID: '23153022'
+
+- id: https://doi.org/10.5281/ZENODO.20046
+  type: dataset
+  author:
+  - family: Fenner
+    given: Martin
+  - family: Jen Song
+    given: Jen
+  - family: Dennis
+    given: Zach
+  - family: Whitwell
+    given: Martyn
+  - family: Osowski
+    given: Joe
+  - family: Ivimey-Cook
+    given: Ruth
+  - family: Cave
+    given: Richard
+  - family: Lin
+    given: Jennifer
+  - family: Chodacki
+    given: John
+  issued:
+  - year: '2015'
+  title: Lagotto 4.2.1
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/ZENODO.20046
+
+- id: Barlow:1818
+  type: dataset
+  author:
+  - family: Barlow
+    given: Chester
+  issued:
+  - year: '1818'
+  title: Pilot Boat \#3, on the bar
+  publisher: Museum of Vertebrate Zoology
+  URL: http://doi.org/10.7299/X7MK6BM6
+  DOI: 10.7299/X7MK6BM6
+
+- id: Oshu:1955
+  type: dataset
+  author:
+  - family: Oregon Medical School
+    given: University
+    dropping-particle: of
+  issued:
+  - year: '1955'
+  title: Unidentified man reading a book in the Old Library
+  publisher: Oregon Health & Science University
+  URL: http://doi.org/10.6083/M4MP51XQ
+  DOI: 10.6083/M4MP51XQ
+
+- id: Unknown:1926
+  type: dataset
+  author:
+  - family: Unknown
+  issued:
+  - year: '1926'
+  title: Workmen digging up the road at the corner of Belmont Avenue and Burhans Street
+    in Paterson, New Jersey
+  URL: http://doi.org/10.7282/T38C9WT9
+  DOI: 10.7282/T38C9WT9
+
+- id: https://orcid.org/about/what-is-orcid/principles
+  type: no-type
+  issued:
+  - year: '2011'
+  title: Our Principles
+  publisher: ORCID
+  URL: https://orcid.org/about/what-is-orcid/principles
+
+- id: https://doi.org/10.3932/ETHZ-A-000159123
+  type: no-type
+  author:
+  - family: Unknown
+  issued:
+  - year: '1931'
+  title: Hannover, Blick auf Hannover
+  publisher: ETH-Bibliothek Zürich, Bildarchiv
+  URL: https://doi.org/10.3932/ETHZ-A-000159123
+  DOI: 10.3932/ETHZ-A-000159123
+
+- id: https://doi.org/10.5281/ZENODO.30799
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  - family: Demeranville
+    given: Tom
+  - family: Kotarski
+    given: Rachael
+  - family: Vision
+    given: Todd
+  - family: Rueda
+    given: Laura
+  - family: Dasler
+    given: Robin
+  - family: Haak
+    given: Laure
+  - family: Cruse
+    given: Patricia
+  - literal: THOR Consortium
+  issued:
+  - year: '2015'
+  title: 'D2.1: Artefact, Contributor, and Organisation Relationship Data Schema'
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/ZENODO.30799
+  DOI: 10.5281/ZENODO.30799
+
+- id: https://doi.org/10.6084/M9.FIGSHARE.1314859
+  type: no-type
+  author:
+  - family: Bilder
+    given: Geoffrey
+  - family: Lin
+    given: Jennifer
+  - family: Neylon
+    given: Cameron
+  issued:
+  - year: '2015'
+  title: Principles for Open Scholarly Infrastructures-v1
+  publisher: Figshare
+  URL: https://doi.org/10.6084/M9.FIGSHARE.1314859
+
+- id: https://doi.org/10.5281/zenodo.34671
+  type: no-type
+  author:
+  - family: Rueda
+    given: Laura
+  issued:
+  - year: '2015'
+  title: DataCite Profiles and ORCID Auto-Update, an Introduction to DataCite
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.34671
+
+- id: https://doi.org/10.5281/zenodo.34670
+  type: no-type
+  author:
+  - family: Brown
+    given: Josh
+  issued:
+  - year: '2015'
+  title: DataCite/ORCID auto-update and inbox, all you need to know
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.34670
+
+- id: https://doi.org/10.5281/zenodo.34673
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2015'
+  title: DataCite/ORCID Integration
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.34673
+
+- id: https://doi.org/10.5334/jors.be
+  type: article-journal
+  author:
+  - family: Katz
+    given: Daniel
+  issued:
+  - year: '2014'
+    month: '9'
+  title: Transitive Credit as a Means to Address Social and Technological Concerns
+    Stemming from Citation and Attribution of Digital Products
+  container-title: Journal of Open Research Software
+  publisher: Ubiquity Press, Ltd.
+  page: 'e20'
+  volume: '2'
+  issue: '1'
+  URL: https://doi.org/10.5334/jors.be
+
+- id: https://doi.org/10.5281/zenodo.31780
+  type: no-type
+  author:
+  - family: Bilder
+    given: Geoffrey
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2015'
+  title: DOI Myths... busted
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31780
+
+- id: https://doi.org/10.5281/zenodo.31782
+  type: no-type
+  author:
+  - family: Angjeli
+    given: Anila
+  issued:
+  - year: '2015'
+  title: 'Managing identities: Interconnecting research and other domains'
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31782
+
+- id: https://doi.org/10.5281/zenodo.31783
+  type: no-type
+  author:
+  - family: Kunze
+    given: John
+  issued:
+  - year: '2015'
+  title: 'Names, Things, and Open Identifier Infrastructure: N2T and ARKs'
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31783
+
+- id: https://doi.org/10.5281/zenodo.31784
+  type: no-type
+  author:
+  - family: Lannom
+    given: Larry
+  issued:
+  - year: '2015'
+  title: DONA Foundation, Administering the Global Handle Registry (GHR)
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31784
+
+- id: https://doi.org/10.5281/zenodo.31785
+  type: no-type
+  author:
+  - family: Schwardmann
+    given: Ulrich
+  issued:
+  - year: '2015'
+  title: ePIC - Persistent Identifiers for eResearch
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31785
+
+- id: https://doi.org/10.5281/zenodo.31786
+  type: no-type
+  author:
+  - family: Cambon-Thomsen
+    given: Anne
+  issued:
+  - year: '2015'
+  title: 'BRIF: Bioresource research impact factor (framework)'
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31786
+
+- id: https://doi.org/10.5281/zenodo.31787
+  type: no-type
+  author:
+  - family: Dallmeier-Thiessen
+    given: Sünje
+  issued:
+  - year: '2015'
+  title: Enabling services for data intensive research with THOR
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31787
+
+- id: https://doi.org/10.5281/zenodo.31788
+  type: no-type
+  author:
+  - family: Lehnert
+    given: Kerstin
+  issued:
+  - year: '2015'
+  title: 'IGSN: International Geo Sample Number. Unambiguous Citation of Physical
+    Samples'
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31788
+
+- id: https://doi.org/10.5281/zenodo.31789
+  type: no-type
+  author:
+  - family: Lin
+    given: Jennifer
+  issued:
+  - year: '2015'
+  title: Making Data Count
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31789
+
+- id: https://doi.org/10.5281/zenodo.31790
+  type: no-type
+  author:
+  - family: Weigel
+    given: Tobias
+  issued:
+  - year: '2015'
+  title: PID usage at DKRZ, the role of RDA and ePIC policies
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31790
+
+- id: https://doi.org/10.5281/zenodo.31792
+  type: no-type
+  author:
+  - family: Paglione
+    given: Laura
+  issued:
+  - year: '2015'
+  title: Connecting people to their scholarly activity and outputs
+  publisher: Zenodo
+  URL: https://doi.org/10.5281/zenodo.31792
+
+- id: https://vimeo.com/147743305
+  type: no-type
+  author:
+  - family: Rueda
+    given: Laura
+  - family: Brown
+    given: Josh
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2015'
+  title: DataCite Profiles and ORCID Auto-Update
+  publisher: DataCite
+  URL: https://vimeo.com/147743305
+
+- id: https://blog.datacite.org/data-driven-development
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2015'
+  title: Data-Driven Development
+  publisher: DataCite Blog
+  URL: https://blog.datacite.org/data-driven-development
+
+- id: https://blog.datacite.org/explaining-the-datacite-orcid-auto-update
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2015'
+  title: Explaining the DataCite/ORCID Auto-update
+  publisher: DataCite Blog
+  URL: https://blog.datacite.org/explaining-the-datacite-orcid-auto-update
+
+- id: https://blog.datacite.org/adding-references-to-the-datacite-blog
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2015'
+  title: Adding References to the DataCite Blog
+  publisher: DataCite Blog
+  URL: https://blog.datacite.org/adding-references-to-the-datacite-blog
+
+- id: https://blog.datacite.org/recap
+  type: no-type
+  author:
+  - family: Cruse
+    given: Trisha
+  issued:
+  - year: '2015'
+  title: 'Recap: Persistent Identifiers in Paris'
+  publisher: DataCite Blog
+  URL: https://blog.datacite.org/recap
+
+- id: http://doi.org/10.2312/RE3.008
+  type: article-journal
+  author:
+  - family: Rücknagel
+    given: Jessika
+  - family: Vierkant
+    given: Paul
+  - family: Ulrich
+    given: Robert
+  - family: Kloska
+    given: Gabriele
+  - family: Schnepf
+    given: Edeltraud
+  - family: Fichtmüller
+    given: David
+  - family: Reuter
+    given: Evelyn
+  - family: Semrau
+    given: Angelika
+  - family: Kindling
+    given: Maxi
+  - family: Pampel
+    given: H.
+  - family: Witt
+    given: Michael
+  - family: Fritze
+    given: Florian
+  - family: Sandt
+    given: Stephanie
+    dropping-particle: van de
+  - family: Klump
+    given: Jens
+  - family: Goebelbecker
+    given: Hans-Jürgen
+  - family: Skarupianski
+    given: Michael
+  - family: Bertelmann
+    given: Roland
+  - family: Schirmbacher
+    given: Peter
+  - family: Scholze
+    given: Frank
+  - family: Kramer
+    given: Claudia
+  - family: Fuchs
+    given: Claudio
+  - family: Spier
+    given: Shaked
+  - family: Kirchhoff
+    given: Agnes
+  issued:
+  - year: '2015'
+  title: Metadata Schema for the Description of Research Data Repositories
+  publisher: GFZ Germans Research Center for Geosciences
+  URL: http://doi.org/10.2312/RE3.008
+
+- id: http://doi.org/10.1103/physrevlett.116.061102
+  type: article-journal
+  author:
+  - family: Abbott
+    given: B.P.
+  - family: Abbott
+    given: R.
+  - family: Abbott
+    given: T.D.
+  - family: Abernathy
+    given: M. R.
+  - family: Acernese
+    given: F.
+  - family: Ackley
+    given: K.
+  - family: Adams
+    given: C.
+  - family: Adams
+    given: T.
+  - family: Addesso
+    given: P.
+  - family: Zweizig
+    given: J.
+  issued:
+  - year: '2016'
+    month: '2'
+  title: Observation of Gravitational Waves from a Binary Black Hole Merger
+  container-title: Phys. Rev. Lett.
+  publisher: American Physical Society (APS)
+  volume: '116'
+  issue: '6'
+  URL: http://doi.org/10.1103/physrevlett.116.061102
+
+- id: http://doi.org/10.7935/K5MW2F23
+  type: dataset
+  author:
+  - literal: LIGO Scientific Collaboration
+  issued:
+  - year: '2016'
+  title: Data release for event GW150914
+  publisher: LIGO Scientific Collaboration
+  URL: http://doi.org/10.7935/K5MW2F23
+
+- id: http://doi.org/10.7484/INSPIREHEP.DATA.26B4.TY5F
+  type: dataset
+  author:
+  - family: Aad
+    given: Georges
+  - family: Abajyan
+    given: Tatevik
+  - family: Abbott
+    given: Brad
+  - family: Abdallah
+    given: Jalal
+  - family: Abdel Khalek
+    given: Samah
+  - family: Abdinov
+    given: Ovsat
+  - family: Aben
+    given: Rosemarie
+  - family: Abi
+    given: Babak
+  - family: Abolins
+    given: Maris
+  - family: Zwalinski
+    given: Lukasz
+  issued:
+  - year: '2013'
+  title: 'Data from Figure 7 from: Measurements of Higgs boson production and couplings
+    in diboson final states with the ATLAS detector at the LHC'
+  publisher: HEPDATA
+  URL: http://doi.org/10.7484/INSPIREHEP.DATA.26B4.TY5F
+
+- id: http://doi.org/10.7484/INSPIREHEP.DATA.RF5P.6M3K
+  type: dataset
+  author:
+  - family: Aad
+    given: Georges
+  - family: Abajyan
+    given: Tatevik
+  - family: Abbott
+    given: Brad
+  - family: Abdallah
+    given: Jalal
+  - family: Abdel Khalek
+    given: Samah
+  - family: Abdinov
+    given: Ovsat
+  - family: Aben
+    given: Rosemarie
+  - family: Abi
+    given: Babak
+  - family: Abolins
+    given: Maris
+  - family: Zwalinski
+    given: Lukasz
+  issued:
+  - year: '2013'
+  title: 'Data from Figure 7 from: Measurements of Higgs boson production and couplings
+    in diboson final states with the ATLAS detector at the LHC'
+  publisher: HEPDATA
+  URL: http://doi.org/10.7484/INSPIREHEP.DATA.RF5P.6M3K
+
+- id: http://doi.org/10.7484/INSPIREHEP.DATA.A78C.HK44
+  type: dataset
+  author:
+  - family: Aad
+    given: Georges
+  - family: Abajyan
+    given: Tatevik
+  - family: Abbott
+    given: Brad
+  - family: Abdallah
+    given: Jalal
+  - family: Abdel Khalek
+    given: Samah
+  - family: Abdinov
+    given: Ovsat
+  - family: Aben
+    given: Rosemarie
+  - family: Abi
+    given: Babak
+  - family: Abolins
+    given: Maris
+  - family: Zwalinski
+    given: Lukasz
+  issued:
+  - year: '2013'
+  title: 'Data from Figure 7 from: Measurements of Higgs boson production and couplings
+    in diboson final states with the ATLAS detector at the LHC'
+  publisher: HEPDATA
+  URL: http://doi.org/10.7484/INSPIREHEP.DATA.A78C.HK44
+
+- id: http://doi.org/10.5438/0010
+  type: article-journal
+  author:
+  - literal: DataCite Metadata Working Group
+  issued:
+  - year: '2014'
+  title: DataCite Metadata Schema for the Publication and Citation of Research Data
+    v3.1
+  publisher: DataCite e.V.
+  URL: http://doi.org/10.5438/0010
+
+- id: http://doi.org/10.5281/ZENODO.49516
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  - family: Wass
+    given: Joe
+  - family: Song
+    given: Jen
+  - family: Dennis
+    given: Zach
+  - family: Whitwell
+    given: Martyn
+  - family: Osowski
+    given: Joe
+  - family: Ivimey-Cook
+    given: Ruth
+  - family: Cave
+    given: Richard
+  - family: Lin
+    given: Jennifer
+  - family: Chodacki
+    given: John
+  issued:
+  - year: '2016'
+  title: Lagotto 5.0.1
+  publisher: Zenodo
+  URL: http://doi.org/10.5281/ZENODO.49516
+
+- id: http://doi.org/10.3334/CDIAC/00001
+  type: dataset
+  author:
+  - literal: Environmental Sciences Division, Oak Ridge National Laboratory
+  issued:
+  - year: '2009'
+  title: Global, Regional, and National Fossil-Fuel CO2 Emissions
+  publisher: Carbon Dioxide Information Analysis Center (CDIAC)
+  URL: http://doi.org/10.3334/CDIAC/00001
+
+- id: https://blog.datacite.org/to-better-understand-research-communication-we-need-a-groid-group-object-identifier
+  type: no-type
+  author:
+  - family: Katz
+    given: Dan S.
+  issued:
+  - year: '2016'
+  title: To better understand research communication, we need a GROID (group object
+    identifier)
+  publisher: DataCite Blog
+  URL: https://blog.datacite.org/to-better-understand-research-communication-we-need-a-groid-group-object-identifier
+
+- id: https://blog.datacite.org/reference-lists-and-tables-of-content
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2015'
+  title: Reference Lists and Tables of Content
+  publisher: DataCite Blog
+  URL: https://blog.datacite.org/reference-lists-and-tables-of-content
+
+- id: https://figshare.com/blog/Unveiling_figshare_Collections_a_new_way_to_group_content/202
+  type: no-type
+  author:
+  - family: Hyndman
+    given: Alan
+  issued:
+  - year: '2016'
+  title: Unveiling figshare ’Collections’ - a new way to group content
+  publisher: Figshare Blog
+  URL: https://figshare.com/blog/Unveiling_figshare_Collections_a_new_way_to_group_content/202
+
+- id: http://doi.org/10.15252/msb.20156658
+  type: article-journal
+  author:
+  - family: McEntyre
+    given: J.
+  - family: Sarkans
+    given: U.
+  - family: Brazma
+    given: A.
+  issued:
+  - year: '2015'
+    month: '12'
+  title: The BioStudies database
+  container-title: Molecular Systems Biology
+  publisher: EMBO
+  page: '847-847'
+  volume: '11'
+  issue: '12'
+  URL: http://doi.org/10.15252/msb.20156658
+  DOI: 10.15252/msb.20156658
+
+- id: http://doi.org/10.7717/peerj-cs.1
+  type: article-journal
+  author:
+  - family: Starr
+    given: Joan
+  - family: Castro
+    given: Eleni
+  - family: Crosas
+    given: Mercè
+  - family: Dumontier
+    given: Michel
+  - family: Downs
+    given: Robert R.
+  - family: Duerr
+    given: Ruth
+  - family: Haak
+    given: Laurel L.
+  - family: Haendel
+    given: Melissa
+  - family: Herman
+    given: Ivan
+  - family: Hodson
+    given: Simon
+  - family: Hourclé
+    given: Joe
+  - family: Kratz
+    given: John Ernest
+  - family: Lin
+    given: Jennifer
+  - family: Nielsen
+    given: Lars Holm
+  - family: Nurnberger
+    given: Amy
+  - family: Proell
+    given: Stefan
+  - family: Rauber
+    given: Andreas
+  - family: Sacchi
+    given: Simone
+  - family: Smith
+    given: Arthur
+  - family: Taylor
+    given: Mike
+  - family: Clark
+    given: Tim
+  issued:
+  - year: '2015'
+    month: '5'
+  title: Achieving human and machine accessibility of cited data in scholarly publications
+  container-title: PeerJ Computer Science
+  publisher: PeerJ
+  page: 'e1'
+  volume: '1'
+  URL: http://doi.org/10.7717/peerj-cs.1
+  DOI: 10.7717/peerj-cs.1
+
+- id: https://blog.datacite.org/thinking-about-csv
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2016'
+  title: Thinking about CSV
+  publisher: DataCite Blog
+  URL: https://blog.datacite.org/thinking-about-csv
+
+- id: https://github.com/datacite/jekyll-csvy
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  issued:
+  - year: '2016'
+  title: 'jekyll-csvy: Jekyll converter for CSVY files'
+  title-short: jekyll-csvy
+  publisher: GitHub
+  URL: https://github.com/datacite/jekyll-csvy
+
+- id: https://cran.r-project.org/web/packages/rio/index.html
+  type: no-type
+  author:
+  - family: Becker
+    given: Jason
+  - family: Chan
+    given: Chung-hong
+  - family: Chan
+    given: Geoffrey CH
+  - family: Leeper
+    given: Thomas J.
+  - family: Gandrud
+    given: Christopher
+  - family: MacDonald
+    given: Andrew
+  - family: Zahn
+    given: Ista
+  issued:
+  - year: '2016'
+  title: 'rio: A Swiss-Army Knife for Data I/O'
+  publisher: CRAN
+  URL: https://cran.r-project.org/web/packages/rio/index.html
+
+- id: http://doi.org/10.6084/M9.FIGSHARE.3364708.V1
+  type: no-type
+  author:
+  - family: Karcher
+    given: Sebastian
+  issued:
+  - year: '2016'
+  title: Zotero for Data Repositories
+  publisher: Figshare
+  URL: http://doi.org/10.6084/M9.FIGSHARE.3364708.V1
+  DOI: 10.6084/M9.FIGSHARE.3364708.V1
+
+- id: http://doi.org/10.1145/2783446.2783605
+  type: paper-conference
+  author:
+  - family: Garza
+    given: Kristian
+  - family: Goble
+    given: Carole
+  - family: Brooke
+    given: John
+  - family: Jay
+    given: Caroline
+  issued:
+  - year: '2015'
+  title: Framing the community data system interface
+  container-title: Proceedings of the 2015 British HCI Conference on - British HCI
+    15
+  publisher: Association for Computing Machinery (ACM)
+  URL: http://doi.org/10.1145/2783446.2783605
+  DOI: 10.1145/2783446.2783605
+
+- id: http://doi.org/10.7717/peerj-cs.86
+  type: article-journal
+  author:
+  - family: Smith
+    given: AM
+  - family: Katz
+    given: DS
+  - family: Niemeyer
+    given: KE
+  - family: FORCE11-Software-Citation-Working-Group
+  issued:
+  - year: '2016'
+    month: september
+  title: Software citation principles
+  container-title: PeerJ Computer Science
+  publisher: PeerJ
+  URL: https://peerj.com/articles/cs-86/
+  DOI: 10.7717/peerj-cs.86
+
+- id: http://doi.org/10.5438/0012
+  type: article-journal
+  author:
+  - literal: DataCite Metadata Working Group
+  issued:
+  - year: '2016'
+  title: DataCite Metadata Schema for the Publication and Citation of Research Data
+    v4.0
+  publisher: DataCite e.V.
+  URL: http://doi.org/10.5438/0012
+
+- id: https://doi.org/10.5438/2906
+  type: no-type
+  author:
+  - family: Cruse
+    given: Patricia
+  - family: Haak
+    given: Laure
+  - family: Pentz
+    given: Ed
+  issued:
+  - year: '2016'
+  title: 'Organization Identifier Project: A Way Forward'
+  publisher: ORCID
+  URL: https://doi.org/10.5438/2906
+  DOI: 10.5438/2906
+
+- id: https://doi.org/10.5438/7885
+  type: no-type
+  author:
+  - family: Fenner
+    given: Martin
+  - family: Paglione
+    given: Laura
+  - family: Demeranville
+    given: Tom
+  - family: Bilder
+    given: Geoff
+  issued:
+  - year: '2016'
+  title: Technical Considerations for an Organization Identifier Registry
+  publisher: ORCID
+  URL: https://doi.org/10.5438/7885
+  DOI: 10.5438/7885
+
+- id: https://doi.org/10.5438/4716
+  type: no-type
+  author:
+  - family: Bilder
+    given: Geoffrey
+  - family: Brown
+    given: Josh
+  - family: Demeranville
+    given: Tom
+  issued:
+  - year: '2016'
+  title: 'Organisation identifiers: current provider survey'
+  publisher: ORCID
+  URL: https://doi.org/10.5438/4716
+  DOI: 10.5438/4716
+
+- id: https://doi.org/10.6084/M9.FIGSHARE.3479141
+  type: no-type
+  author:
+  - family: Demeranville
+    given: Tom
+  - family: Brown
+    given: Josh
+  - family: Fenner
+    given: Martin
+  - family: Cruse
+    given: Patricia
+  - family: Haak
+    given: Laure
+  - family: Paglione
+    given: Laura
+  - family: Bilder
+    given: Geoffrey
+  - family: Lin
+    given: Jennifer
+  - family: Pentz
+    given: Ed
+  issued:
+  - year: '2016'
+  title: Organisation Identifiers - Minimum viable product requirements
+  publisher: Figshare
+  URL: https://doi.org/10.6084/M9.FIGSHARE.3479141
+  DOI: 10.6084/M9.FIGSHARE.3479141
+
+- id: https://doi.org/10.1371/journal.pone.0115253
+  type: article-journal
+  author:
+  - family: Klein
+    given: Martin
+  - family: Sompel
+    given: Herbert Van de
+  - family: Sanderson
+    given: Robert
+  - family: Shankar
+    given: Harihar
+  - family: Balakireva
+    given: Lyudmila
+  - family: Zhou
+    given: Ke
+  - family: Tobin
+    given: Richard
+  issued:
+  - year: '2014'
+    month: '12'
+  title: 'Scholarly Context Not Found: One in Five Articles Suffers from Reference
+    Rot'
+  title-short: Scholarly Context Not Found
+  container-title: PLOS ONE
+  page: 'e115253'
+  volume: '9'
+  issue: '12'
+  keyword: Archives, Communications, Computer and information sciences, Evolutionary
+    immunology, Extrapolation, Internet, Publication ethics, Species interactions
+  URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115253
+  DOI: 10.1371/journal.pone.0115253
+  ISSN: '1932-6203'
+
+- id: https://www.w3.org/Provider/Style/URI
+  type: no-type
+  author:
+  - family: Berners-Lee
+    given: Tim
+  issued:
+  - year: '1998'
+  accessed:
+  - year: '2016'
+    month: '12'
+    day: '14'
+  title: 'Hypertext Style: Cool URIs don’t change.'
+  title-short: Hypertext Style
+  URL: https://www.w3.org/Provider/Style/URI
+...

data/spec/fixtures/site.yml

@@ -1,7 +1,8 @@
 site_url: https://blog.datacite.org
 site_title: DataCite Blog
-site_default_type: BlogPosting
-site_institution: DataCite
+default_type: BlogPosting
+institution: DataCite
+prefix: 10.23725
 license:
   name: Creative Commons Attribution
   url: "https://creativecommons.org/licenses/by/4.0/"

data/spec/utils_spec.rb

@@ -45,19 +45,25 @@ describe Cirneco::DataCenter, vcr: true, :order => :defined do
       filepath = fixture_path + 'cool-dois.html.md'
       number = 123
       response = subject.register_file(filepath, number: number)
-      expect(response).to eq("DOI 10.23725/0000-03VC added to cool-dois.html.md")
+      expect(response).to eq("DOI 10.23725/0000-03VC added for cool-dois.html.md")
     end
 
-    it 'should register_file unregister' do
+    it 'should unregister_file' do
       filepath = fixture_path + 'cool-dois.html.md'
-      response = subject.register_file(filepath, unregister: true)
-      expect(response).to eq("DOI removed from cool-dois.html.md")
+      response = subject.unregister_file(filepath)
+      expect(response).to eq("DOI 10.23725/0000-03VC removed for cool-dois.html.md")
     end
 
-    it 'should register_all_files unregister' do
+    it 'should register_all_files' do
       number = 123
-      response = subject.register_all_files(fixture_path, number: number, unregister: true)
-      expect(response).to eq("DOI removed from cool-dois.html.md")
+      response = subject.register_all_files(fixture_path, number: number)
+      expect(response).to eq("DOI 10.23725/0000-03VC added for cool-dois.html.md")
+    end
+
+    it 'should unregister_all_files' do
+      number = 123
+      response = subject.unregister_all_files(fixture_path)
+      expect(response).to eq("DOI 10.23725/0000-03VC removed for cool-dois.html.md")
     end
 
     it 'should ignore non-markdown file for register_file' do
@@ -72,7 +78,7 @@ describe Cirneco::DataCenter, vcr: true, :order => :defined do
       metadata = subject.generate_metadata_for_work(filepath, number: number, csl: 'spec/fixtures/apa.csl', bibliography: 'spec/fixtures/references.bib')
       expect(metadata["url"]).to eq("https://blog.datacite.org/cool-dois/")
       expect(metadata["creators"]).to eq([{:given_name=>"Martin", :family_name=>"Fenner", :orcid=>"0000-0003-1419-2405"}])
-      expect(metadata["descriptions"]).to eq([{:value=>"In 1998 Tim Berners-Lee coined the term cool URIs (1998), that is URIs that don’t change. We know that URLs referenced in the scholarly literature are often not cool, leading to link rot (Klein et al., 2014) and making it hard or impossible to find...",:description_type=>"Abstract"}])
+      expect(metadata["descriptions"]).to eq([{:value=>"In 1998 Tim Berners-Lee coined the term cool URIs (1998), that is URIs that don’t change. We know that URLs referenced in the scholarly literature are often not cool, leading to link rot (Klein et al., 2014) and making it hard or impossible to find the referenced resource.",:description_type=>"Abstract"}])
       expect(metadata["related_identifiers"]).to eq([{:value=>"https://www.w3.org/Provider/Style/URI",
           :related_identifier_type=>"URL",
           :relation_type=>"References"},
@@ -81,11 +87,11 @@ describe Cirneco::DataCenter, vcr: true, :order => :defined do
           :relation_type=>"References" }])
     end
 
-    it 'should create_work_from_yaml' do
+    it 'should register_work_for_metadata' do
       filepath = fixture_path + 'cool-dois.html.md'
       number = 123
       metadata = subject.generate_metadata_for_work(filepath, number: number, csl: 'spec/fixtures/apa.csl', bibliography: 'spec/fixtures/references.bib')
-      work = subject.create_work_from_metadata(metadata)
+      work = subject.register_work_for_metadata(metadata)
       expect(work.validation_errors).to be_empty
     end
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: cirneco
 version: !ruby/object:Gem::Version
-  version: 0.5.8
+  version: '0.6'
 platform: ruby
 authors:
 - Martin Fenner
@@ -346,6 +346,7 @@ files:
 - spec/fixtures/cool-dois.html.md
 - spec/fixtures/cool-dois.yml
 - spec/fixtures/references.bib
+- spec/fixtures/references.yaml
 - spec/fixtures/site.yml
 - spec/fixtures/vcr_cassettes/Cirneco_DataCenter/get/should_get_all_dois_by_prefix.yml
 - spec/fixtures/vcr_cassettes/Cirneco_DataCenter/get/should_get_next_doi.yml