cirneco 0.5.7 → 0.5.8

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 5848ad65bed8f39dfc0ca2cc41710494bb5951dd
-  data.tar.gz: bed67d95cb6a626863e75ba84cfd81ca6045fe3c
+  metadata.gz: bc53bd40a384ab3df63764308d8f6267f230975a
+  data.tar.gz: 8596911b41e4513f9c947c0cb0b2a345d57e2a8d
 SHA512:
-  metadata.gz: 30c52cd275ddea765d18c5ccc73ed4c14e9a5641fda8927e2af137023cf6a0af77e9291f5fb55f2c54fcf4ad2f47ea788b90c365eabce6fd55e631711f096fe5
-  data.tar.gz: 97e24c85ada43a7b00ede4a60db77b90a1a6d65a6514148ffbf0bd477d90835a690a76d1ddde5a518123be4ce495a138c49eaffd4d386d31245b7d06c0c7eeb0
+  metadata.gz: 508aeb634c7e6b5af2cb88ee30e6f9b031ca85456f02b237c497050b5ac34f608c04a0f694b9507c577f0859b802fe012f36e8939fd3037c7aee3c22e739b43b
+  data.tar.gz: bfccc96e67b81775f5747bf00d89d71537d4d1c3d4e73c27401ecb2bd48d330a0de047c03a0ce5b85d92a8d7f8058416ea707b6d7382da6548532d99ef9b0cd5

data/.gitignore

@@ -49,6 +49,9 @@ build-iPhoneSimulator/
 # unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
 .rvmrc
 
+# outputs
+*.xml
+
 coverage/
 spec/fixtures/doi.yml
 .env

data/.travis.yml

@@ -3,9 +3,12 @@ rvm:
 - 2.3.1
 
 before_install:
-  - sudo add-apt-repository ppa:kalakris/cmake -y
-  - sudo apt-get update -q
-  - sudo apt-get install cmake -y
+- wget https://github.com/jgm/pandoc/releases/download/1.15.2/pandoc-1.15.2-1-amd64.deb
+- sudo dpkg -i pandoc-1.15.2-1-amd64.deb
+- rm pandoc-1.15.2-1-amd64.deb
+- sudo add-apt-repository ppa:kalakris/cmake -y
+- sudo apt-get update -q
+- sudo apt-get install cmake -y
 
 install:
 - travis_retry bundle install

data/Gemfile.lock

@@ -1,10 +1,10 @@
 PATH
   remote: .
   specs:
-    cirneco (0.5.7)
+    cirneco (0.5.8)
       activesupport (~> 4.2, >= 4.2.5)
       base32-crockford-checksum (~> 0.2.2)
-      bergamasco (~> 0.1.1)
+      bergamasco (~> 0.2)
       builder (~> 3.2, >= 3.2.2)
       dotenv (~> 2.1, >= 2.1.1)
       maremma (~> 3.1)
@@ -20,11 +20,11 @@ GEM
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
-    addressable (2.5.0)
-      public_suffix (~> 2.0, >= 2.0.2)
+    addressable (2.3.8)
     base32-crockford-checksum (0.2.3)
-    bergamasco (0.1.4)
+    bergamasco (0.2.3)
       activesupport (~> 4.2, >= 4.2.5)
+      addressable (~> 2.3.8)
       builder (~> 3.2, >= 3.2.2)
       commonmarker (~> 0.14.0)
       loofah (~> 2.0, >= 2.0.3)
@@ -73,7 +73,6 @@ GEM
       mini_portile2 (~> 2.1.0)
     oj (2.13.1)
     pandoc-ruby (2.0.1)
-    public_suffix (2.0.4)
     rack (2.0.1)
     rack-test (0.6.3)
       rack (>= 1.0)

data/cirneco.gemspec

@@ -16,7 +16,7 @@ Gem::Specification.new do |s|
 
   # Declary dependencies here, rather than in the Gemfile
   s.add_dependency 'maremma', '~> 3.1'
-  s.add_dependency 'bergamasco', '~> 0.1.1'
+  s.add_dependency 'bergamasco', '~> 0.2'
   s.add_dependency 'base32-crockford-checksum', '~> 0.2.2'
   s.add_dependency 'nokogiri', '~> 1.6', '>= 1.6.8'
   s.add_dependency 'builder', '~> 3.2', '>= 3.2.2'

data/lib/cirneco/utils.rb

@@ -57,8 +57,6 @@ module Cirneco
         "DOI removed from #{filename}"
       elsif updated_file != file
         "DOI #{doi} added to #{filename}"
-      else
-        "DOI #{doi} found in #{filename}"
       end
     end
 
@@ -68,26 +66,78 @@ module Cirneco
       end.join("\n")
     end
 
-    def create_work_from_yaml(metadata:, **options)
-      return "Error" unless ["doi", "author", "title", "date", "summary"].all? { |k| metadata.key? k }
+    def generate_metadata_for_work(filepath, options={})
+      metadata = Bergamasco::Markdown.read_yaml_for_doi_metadata(filepath, options.except(:number))
+
+      return "Error: required metadata missing" unless ["author", "title", "date", "summary"].all? { |k| metadata.key? k }
+
+      # read in optional yaml configuration file for site
+      sitepath = options[:sitepath] || ENV['SITE_SITEPATH']
+      site_options = sitepath.present? ? Bergamasco::Markdown.read_yaml(sitepath) : {}
+
+      # read in optional yaml configuration file for authors
+      authorpath = options[:authorpath] || ENV['SITE_AUTHORPATH']
+      author_options = authorpath.present? ? Bergamasco::Markdown.read_yaml(authorpath) : {}
+
+      # required metadata
+      prefix = options[:prefix] || ENV['PREFIX']
+      metadata["doi"] ||= encode_doi(prefix, options)
+
+      site_url = site_options["site_url"] || ENV['SITE_URL']
+      metadata["url"] ||= url_from_path(site_url, filepath)
+
+      metadata["creators"] = Array(metadata["author"]).map do |a|
+        author = author_options.fetch(a, {})
+        if author.present?
+          { given_name: author["given"],
+            family_name: author["family"],
+            orcid: author["orcid"] }
+        else
+          { literal: a }
+        end
+      end
+
+      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"
+      resource_type_general = metadata["type"] == "Dataset" ? "Dataset" : "Text"
+
+      metadata["resource_type"] = { value: metadata["type"],
+                                    resource_type_general: resource_type_general }
+
+      # recommended metadata
+      metadata["descriptions"] = [{ value: metadata["summary"],
+                                    description_type: "Abstract" }]
 
-      creators = Array(metadata["author"])
+      # use default version 1.0
+      metadata["version"] ||= "1.0"
 
-      publisher = options[:publisher] || ENV['SITE_TITLE']
-      publication_year = metadata["date"][0..3].to_i
+      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 }]
 
-      resource_type = metadata["type"] || options[:type] || ENV['SITE_DEFAULT_TYPE'] || "BlogPosting"
-      resource_type_general = resource_type == "Dataset" ? "Dataset" : "Text"
+      metadata["subjects"] = Array(metadata["tags"]).select { |t| t != "featured" }
 
-      license_name = options[:license_name] || ENV['SITE_LICENCE_NAME'] || "Creative Commons Attribution"
-      license_url = options[:license_url] # || ENV['SITE_LICENCE_URL'] || "https://creativecommons.org/licenses/by/4.0/"
+      contributor = site_options["site_institution"] || ENV['SITE_INSTITUTION']
+      metadata["contributors"] = [{ literal: contributor, contributor_type: "HostingInstitution" }]
+
+      metadata = metadata.extract!(*%w(doi url creators title publisher
+        publication_year resource_type descriptions version rights_list subjects contributors
+        related_identifiers))
+    end
+
+    def url_from_path(site_url, filepath)
+      site_url.to_s.chomp("\\") + "/" + File.basename(filepath)[0..-9] + "/"
+    end
 
-      descriptions = [{ value: metadata["summary"], description_type: "Abstract" }]
+    def create_work_from_metadata(metadata, options={})
+      work = Cirneco::Work.new(metadata)
 
-      contributor = options[:hosting_institution] || ENV['SITE_HOSTING_INSTITUTION']
-      contributors = [{ literal: contrbutor }]
+      filename  = metadata["doi"].split("/", 2).last + ".xml"
+      IO.write(filename, work.data)
 
-      Cirneco::Work.new(doi: metadata["doi"], creators: creators, title: metadata["title"], publisher: publisher, publication_year: publication_year, resource_type: { value: resource_type, resource_type_general: resource_type_general }, rights: [{ value: license_name, rights_uri: license_url }], subjects: Array(metadata["tags"], descriptions: descriptions, contributors: contributors) )
+      work
     end
   end
 end

data/lib/cirneco/version.rb

@@ -1,3 +1,3 @@
 module Cirneco
-  VERSION = "0.5.7"
+  VERSION = "0.5.8"
 end

data/lib/cirneco/work.rb

@@ -11,26 +11,27 @@ module Cirneco
     include Cirneco::Api
     include Cirneco::Utils
 
-    attr_accessor :doi, :creators, :title, :publisher, :publication_year, :resource_type, :version, :related_identifiers, :rights_list, :descriptions, :subjects, :url, :media, :username, :password, :validation_errors
+    attr_accessor :doi, :url, :creators, :title, :publisher, :publication_year, :resource_type, :version, :related_identifiers, :rights_list, :descriptions, :contributors, :subjects, :media, :username, :password, :validation_errors
+
+    def initialize(metadata, **options)
+      @doi = metadata.fetch("doi", nil)
+      @url = metadata.fetch("url", nil)
+      @creators = metadata.fetch("creators", nil)
+      @title = metadata.fetch("title", nil)
+      @publisher = metadata.fetch("publisher", nil)
+      @publication_year = metadata.fetch("publication_year", nil)
+      @resource_type = metadata.fetch("resource_type", nil)
+      @version = metadata.fetch("version", nil)
+      @rights_list = metadata.fetch("rights_list", nil)
+      @subjects = metadata.fetch("subjects", nil)
+      @descriptions = metadata.fetch("descriptions", nil)
+      @contributors = metadata.fetch("contributors", nil)
+      @related_identifiers = metadata.fetch("related_identifiers", nil)
 
-    def initialize(doi:, creators:, title:, publisher:, publication_year:, resource_type:, **options)
-      @doi = doi
-      @creators = creators
-      @title = title
-      @publisher = publisher
-      @publication_year = publication_year
-      @resource_type = resource_type
-
-      @url = options.fetch(:url, nil)
       @media = options.fetch(:media, nil)
 
       @username = options.fetch(:username, nil)
       @password = options.fetch(:password, nil)
-
-      @version = options.fetch(:version, nil)
-      @rights_list = options.fetch(:rights_list, nil)
-      @descriptions = options.fetch(:descriptions, nil)
-      @related_identifiers = options.fetch(:related_identifiers, nil)
     end
 
     SCHEMA = File.expand_path("../../../resources/kernel-4.0/metadata.xsd", __FILE__)
@@ -55,8 +56,10 @@ module Cirneco
       insert_titles(xml)
       insert_publisher(xml)
       insert_publication_year(xml)
-      insert_subjects(xml)
       insert_resource_type(xml)
+      insert_subjects(xml)
+      insert_contributors(xml)
+      insert_related_identifiers(xml)
       insert_version(xml)
       insert_rights_list(xml)
       insert_descriptions(xml)
@@ -69,22 +72,35 @@ module Cirneco
     def insert_creators(xml)
       return nil unless creators.present?
 
-      xml.send(:'creators') do
+      xml.creators do
         creators.each do |creator|
           xml.creator do
-            insert_creator(xml, creator)
+            insert_person(xml, creator, "creator")
           end
         end
       end
     end
 
-    def insert_creator(xml, creator)
-      creator_name = [creator[:family_name], creator[:given_name], creator[:literal]].compact.join(", ")
+    def insert_contributors(xml)
+      return nil unless contributors.present?
 
-      xml.send(:'creatorName', creator_name)
-      xml.send(:'givenName', creator[:given_name]) if creator[:given_name].present?
-      xml.send(:'familyName', creator[:family_name]) if creator[:family_name].present?
-      xml.nameIdentifier(creator[:orcid], 'schemeURI' => 'http://orcid.org/', 'nameIdentifierScheme' => 'ORCID') if creator[:orcid].present?
+      xml.contributors do
+        contributors.each do |contributor|
+          xml.contributor("contributorType" => contributor[:contributor_type]) do
+            insert_person(xml, contributor, "contributor")
+          end
+        end
+      end
+    end
+
+    def insert_person(xml, person, type)
+      person_name = [person[:family_name], person[:given_name], person[:literal]].compact.join(", ")
+
+      xml.send(:'creatorName', person_name) if type == "creator"
+      xml.send(:'contributorName', person_name) if type == "contributor"
+      xml.send(:'givenName', person[:given_name]) if person[:given_name].present?
+      xml.send(:'familyName', person[:family_name]) if person[:family_name].present?
+      xml.nameIdentifier(person[:orcid], 'schemeURI' => 'http://orcid.org/', 'nameIdentifierScheme' => 'ORCID') if person[:orcid].present?
     end
 
     def insert_titles(xml)
@@ -125,6 +141,16 @@ module Cirneco
       xml.version(version)
     end
 
+    def insert_related_identifiers(xml)
+      return xml unless related_identifiers.present?
+
+      xml.relatedIdentifiers do
+        related_identifiers.each do |related_identifier|
+          xml.relatedIdentifier(related_identifier[:value], 'relatedIdentifierType' => related_identifier[:related_identifier_type], 'relationType' => related_identifier[:relation_type])
+        end
+      end
+    end
+
     def insert_rights_list(xml)
       return xml unless rights_list.present?
 
@@ -145,34 +171,6 @@ module Cirneco
       end
     end
 
-    def insert_contributors(xml)
-      return nil unless contributors.present?
-
-      xml.send(:'work:contributors') do
-        contributors.each do |contributor|
-          xml.contributor do
-            insert_contributor(xml, contributor)
-          end
-        end
-      end
-    end
-
-    def insert_contributor(xml, contributor)
-      if contributor[:orcid].present?
-        xml.send(:'common:contributor-orcid') do
-          xml.send(:'common:uri', contributor[:orcid])
-          xml.send(:'common:path', contributor[:orcid][17..-1])
-          xml.send(:'common:host', 'orcid.org')
-        end
-      end
-      xml.send(:'credit-name', contributor[:credit_name])
-      if contributor[:role]
-        xml.send(:'contributor-attributes') do
-          xml.send(:'contributor-role', contributor[:role])
-        end
-      end
-    end
-
     def without_control(s)
       r = ''
       s.each_codepoint do |c|

data/spec/api_spec.rb

@@ -2,12 +2,19 @@ require 'spec_helper'
 
 describe Cirneco::Work, vcr: true, :order => :defined do
   let(:doi) { "10.23725/0000-03VC" }
+  let(:url) { "http://www.datacite.org" }
   let(:creators) { [{ given_name: "Elizabeth", family_name: "Miller", orcid: "0000-0001-5000-0007", affiliation: "DataCite" }] }
   let(:title) { "Full DataCite XML Example" }
   let(:publisher) { "DataCite" }
   let(:publication_year) { 2014 }
   let(:resource_type) { { value: "XML", resource_type_general: "Software" } }
-  let(:url) { "http://www.datacite.org" }
+  let(:metadata) { { "doi" => doi,
+                     "url" => url,
+                     "creators" => creators,
+                     "title" => title,
+                     "publisher" => publisher,
+                     "publication_year" => publication_year,
+                     "resource_type" => resource_type } }
   let(:media) { [{ mime_type: "application/pdf", url:"http://www.datacite.org/cirneco-test.pdf" }]}
   let(:username) { ENV['MDS_USERNAME'] }
   let(:password) { ENV['MDS_PASSWORD'] }
@@ -15,16 +22,10 @@ describe Cirneco::Work, vcr: true, :order => :defined do
   let(:fixture_path) { "spec/fixtures/" }
   let(:samples_path) { "resources/kernel-4.0/samples/" }
 
-  subject { Cirneco::Work.new(doi: doi,
-                                    creators: creators,
-                                    title: title,
-                                    publisher: publisher,
-                                    publication_year: publication_year,
-                                    resource_type: resource_type,
-                                    url: url,
-                                    media: media,
-                                    username: username,
-                                    password: password) }
+ subject { Cirneco::Work.new(metadata,
+                             media: media,
+                             username: username,
+                             password: password) }
 
   describe "Metadata API" do
     describe "get" do