cirneco 0.9.20 → 0.9.21

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 3fb078ecfae4e617adca6f7aaf9b857afe63381868c2d0a4826eb8481838c1af
-  data.tar.gz: d3b31bb507169a3979df77ba6f8f8a7add95316b08e25f013a73dcd4a50581ca
+  metadata.gz: a244cdbbb1fca3cc527a2f1114afa1646d82100ac8fbcabfb765e4029ecca712
+  data.tar.gz: f862c16828d3809da5633aa6ba094d45b1228cdf23760da86d72be738c1f5179
 SHA512:
-  metadata.gz: 6834e6c25f262d966538020ff0f5db221dcad6797bff1bab9f494adac257d4f8044b58055a70804a8cd5f710c7f9212614d8c11fd65672cc2d76c9b523d37837
-  data.tar.gz: 2454097fa4fe48e6236f3564b0a5f6a191ea4909a2787b15c14f7aa2ee8b32bc98e76ffc346c2fd8637a3e1bef9e87e8e2a1b607436d8404d7ce89328ca5d888
+  metadata.gz: f0ff8fa02880535859594d56313720d0620c6e298fae37785c26c5d7e96191a613b88cc5cb0c6daceb742249f5857cad5caf15fb4e113987712ff145454a535c
+  data.tar.gz: 10ed272c36c2f079c6dff35e1b7826c1c322127248a6856f091f065ef5a58edfc1c3befce53620a55cfc378baaad788d3da50acc5e1fb4d9688977058f8de0ed

data/Gemfile.lock

@@ -1,23 +1,23 @@
 PATH
   remote: .
   specs:
-    cirneco (0.9.20)
+    cirneco (0.9.21)
       activesupport (>= 4.2.5, < 6)
       base32-url (~> 0.5)
       bergamasco (~> 0.3)
       bolognese (~> 0.9)
       builder (~> 3.2, >= 3.2.2)
       dotenv (~> 2.1, >= 2.1.1)
-      maremma (~> 3.5, >= 3.5.7)
+      maremma (>= 4.1, < 5)
       nokogiri (~> 1.8.1)
       thor (~> 0.19)
 
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (5.1.4)
+    activesupport (5.2.1)
       concurrent-ruby (~> 1.0, >= 1.0.2)
-      i18n (~> 0.7)
+      i18n (>= 0.7, < 2)
       minitest (~> 5.1)
       tzinfo (~> 1.1)
     addressable (2.5.2)
@@ -34,9 +34,9 @@ GEM
       oj (>= 2.8.3)
       pandoc-ruby (~> 2.0, >= 2.0.0)
       safe_yaml (~> 1.0, >= 1.0.4)
-    bibtex-ruby (4.4.5)
+    bibtex-ruby (4.4.7)
       latex-decode (~> 0.0)
-    bolognese (0.9.73)
+    bolognese (0.13.3)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)
@@ -47,7 +47,7 @@ GEM
       json-ld (~> 2.1, >= 2.1.2)
       jsonlint (~> 0.2.0)
       loofah (~> 2.0, >= 2.0.3)
-      maremma (~> 3.5, >= 3.5.7)
+      maremma (>= 3.5.7, < 5)
       namae (~> 0.11.3)
       nokogiri (~> 1.8.1)
       oj (>= 2.8.3)
@@ -62,19 +62,19 @@ GEM
     concurrent-ruby (1.0.5)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
-    crass (1.0.3)
+    crass (1.0.4)
     diff-lcs (1.3)
     docile (1.1.5)
-    dotenv (2.2.1)
+    dotenv (2.5.0)
     ebnf (1.1.2)
       rdf (>= 2.2, < 4.0)
       sxp (~> 1.0)
-    excon (0.45.4)
-    faraday (0.9.2)
+    excon (0.62.0)
+    faraday (0.15.2)
       multipart-post (>= 1.2, < 3)
     faraday-encoding (0.0.4)
       faraday
-    faraday_middleware (0.10.1)
+    faraday_middleware (0.12.2)
       faraday (>= 0.7.4, < 1.0)
     gender_detector (0.1.2)
       unicode_utils (>= 1.3.0)
@@ -85,7 +85,7 @@ GEM
       concurrent-ruby (~> 1.0)
     hashdiff (0.3.7)
     htmlentities (4.3.4)
-    i18n (0.9.3)
+    i18n (1.1.0)
       concurrent-ruby (~> 1.0)
     iso8601 (0.9.1)
     json (2.1.0)
@@ -97,17 +97,17 @@ GEM
       trollop (~> 2)
     latex-decode (0.3.1)
     link_header (0.0.8)
-    loofah (2.1.1)
+    loofah (2.2.2)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
-    maremma (3.6.2)
+    maremma (4.1.1)
       activesupport (>= 4.2.5, < 6)
       addressable (>= 2.3.6)
       builder (~> 3.2, >= 3.2.2)
-      excon (~> 0.45.0)
-      faraday (~> 0.9.2)
-      faraday-encoding (~> 0.0.1)
-      faraday_middleware (~> 0.10.0)
+      excon (~> 0.60)
+      faraday (~> 0.14)
+      faraday-encoding (~> 0.0.4)
+      faraday_middleware (~> 0.12.0)
       multi_json (~> 1.12)
       nokogiri (~> 1.8.1)
       oj (>= 2.8.3)
@@ -116,7 +116,7 @@ GEM
     multi_json (1.13.1)
     multipart-post (2.0.0)
     namae (0.11.3)
-    nokogiri (1.8.2)
+    nokogiri (1.8.4)
       mini_portile2 (~> 2.3.0)
     oj (2.18.5)
     pandoc-ruby (2.0.2)
@@ -125,21 +125,21 @@ GEM
       nokogiri (>= 1.6.1, < 1.9)
       public_suffix (>= 2.0.0, < 2.1)
     public_suffix (2.0.5)
-    rack (2.0.4)
-    rack-test (0.8.2)
+    rack (2.0.5)
+    rack-test (0.8.3)
       rack (>= 1.0, < 3)
-    rake (12.3.0)
-    rdf (3.0.1)
+    rake (12.3.1)
+    rdf (3.0.2)
       hamster (~> 3.0)
       link_header (~> 0.0, >= 0.0.8)
     rdf-aggregate-repo (2.2.1)
       rdf (>= 2.2, < 4.0)
-    rdf-rdfa (2.2.4)
+    rdf-rdfa (3.0.1)
       haml (~> 5.0)
       htmlentities (~> 4.3)
-      rdf (>= 2.2, < 4.0)
+      rdf (~> 3.0)
       rdf-aggregate-repo (>= 2.2, < 4.0)
-      rdf-xsd (>= 2.2, < 4.0)
+      rdf-xsd (~> 3.0)
     rdf-rdfxml (2.2.1)
       htmlentities (~> 4.3)
       rdf (>= 2.2, < 4.0)
@@ -150,19 +150,19 @@ GEM
       rdf (>= 2.2, < 4.0)
     rdf-xsd (3.0.0)
       rdf (~> 3.0)
-    rspec (3.7.0)
-      rspec-core (~> 3.7.0)
-      rspec-expectations (~> 3.7.0)
-      rspec-mocks (~> 3.7.0)
-    rspec-core (3.7.1)
-      rspec-support (~> 3.7.0)
-    rspec-expectations (3.7.0)
+    rspec (3.8.0)
+      rspec-core (~> 3.8.0)
+      rspec-expectations (~> 3.8.0)
+      rspec-mocks (~> 3.8.0)
+    rspec-core (3.8.0)
+      rspec-support (~> 3.8.0)
+    rspec-expectations (3.8.1)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.7.0)
-    rspec-mocks (3.7.0)
+      rspec-support (~> 3.8.0)
+    rspec-mocks (3.8.0)
       diff-lcs (>= 1.2.0, < 2.0)
-      rspec-support (~> 3.7.0)
-    rspec-support (3.7.1)
+      rspec-support (~> 3.8.0)
+    rspec-support (3.8.0)
     rspec-xsd (0.1.0)
       nokogiri (~> 1.6)
       rspec (~> 3)
@@ -178,12 +178,12 @@ GEM
     thor (0.20.0)
     thread_safe (0.3.6)
     tilt (2.0.8)
-    trollop (2.1.2)
-    tzinfo (1.2.4)
+    trollop (2.9.9)
+    tzinfo (1.2.5)
       thread_safe (~> 0.1)
     unicode_utils (1.4.0)
     vcr (3.0.3)
-    webmock (3.3.0)
+    webmock (3.4.2)
       addressable (>= 2.3.6)
       crack (>= 0.3.2)
       hashdiff
@@ -204,4 +204,4 @@ DEPENDENCIES
   webmock (~> 3.0, >= 3.0.1)
 
 BUNDLED WITH
-   1.16.0
+   1.16.1

data/cirneco.gemspec

@@ -15,7 +15,7 @@ Gem::Specification.new do |s|
   s.license       = 'MIT'
 
   # Declary dependencies here, rather than in the Gemfile
-  s.add_dependency 'maremma', '~> 3.5', '>= 3.5.7'
+  s.add_dependency 'maremma', '>= 4.1', '< 5'
   s.add_dependency 'bergamasco', '~> 0.3'
   s.add_dependency 'bolognese', '~> 0.9'
   s.add_dependency 'base32-url', '~> 0.5'

data/lib/cirneco/api.rb

@@ -12,6 +12,15 @@ module Cirneco
       Maremma.post(url, content_type: 'application/xml;charset=UTF-8', data: data, username: options[:username], password: options[:password])
     end
 
+    def put_metadata(doi, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/metadata/#{doi}"
+      Maremma.put(url, content_type: 'application/xml;charset=UTF-8', data: options[:data], username: options[:username], password: options[:password])
+    end
+
     def get_metadata(doi, options={})
       return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
 

data/lib/cirneco/media.rb

@@ -44,7 +44,5 @@ module Cirneco
         puts response.body["data"]
       end
     end
-
-
   end
 end

data/lib/cirneco/metadata.rb

@@ -43,6 +43,30 @@ module Cirneco
       end
     end
 
+    desc "put DOIs", "put metadata for multiple DOIs"
+    method_option :username, :default => ENV['MDS_USERNAME']
+    method_option :password, :default => ENV['MDS_PASSWORD']
+    method_option :sandbox, :type => :boolean, :force => false
+    def put(file)
+      data = JSON.parse(IO.read(file))
+      count = 0
+      data.each do |json|
+        doi = doi_from_url(json["@id"])
+        next unless doi.present?
+
+        response = put_metadata(doi, options.merge(data: json.to_json))
+
+        if response.body["errors"]
+          puts "Error: " + response.body["errors"].first.fetch("title", "An error occured")
+        else
+          puts response.headers["Location"]
+          count += 1
+        end
+      end
+
+      puts "#{count} DOIs registered/updated."
+    end
+
     desc "delete DOI", "hide metadata for DOI"
     method_option :username, :default => ENV['MDS_USERNAME']
     method_option :password, :default => ENV['MDS_PASSWORD']

data/lib/cirneco/version.rb

@@ -1,3 +1,3 @@
 module Cirneco
-  VERSION = "0.9.20"
+  VERSION = "0.9.21"
 end

data/resources/kernel-4.0/samples/datacite-example-complicated-v4.1.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
-  <identifier identifierType="DOI">10.5072/079j-xh42</identifier>
+  <identifier identifierType="DOI">10.5438/6brg-2m37</identifier>
   <creators>
     <creator>
       <creatorName nameType="Personal">Smith, John</creatorName>

data/spec/api_spec.rb

@@ -19,9 +19,9 @@ describe Cirneco::Work, vcr: true, :order => :defined do
     context "post" do
       it 'should post metadata' do
         response = subject.post_metadata(subject.datacite, options)
-        expect(response.body["data"]).to eq("OK (10.5072/079j-xh42)")
+        expect(response.body["data"]).to eq("OK (10.5438/6BRG-2M37)")
         expect(response.status).to eq(201)
-        expect(response.headers["Location"]).to eq("http://mds.test.datacite.org/metadata/10.5072/079j-xh42")
+        expect(response.headers["Location"]).to eq("https://mds.test.datacite.org/metadata/10.5438/6brg-2m37")
       end
     end
 
@@ -55,8 +55,8 @@ describe Cirneco::Work, vcr: true, :order => :defined do
       it 'should get all dois' do
         response = subject.get_dois(options)
         dois = response.body["data"]
-        expect(dois.length).to eq(9)
-        expect(dois.first).to eq("10.5072/0007-NW90")
+        expect(dois.length).to eq(438)
+        expect(dois.first).to eq("10.5438/0000-00SS")
       end
 
       it 'should get doi' do
@@ -91,7 +91,7 @@ describe Cirneco::Work, vcr: true, :order => :defined do
         response = subject.get_media(subject.doi, options)
         media = response.body["data"]
         expect(media.length).to eq(1)
-        expect(media.first).to eq(:mime_type=>"application/pdf", :url=>"http://www.datacite.org/cirneco-test.pdf")
+        expect(media).to eq([{:mime_type=>"application/pdf", :url=>"http://www.datacite.org/cirneco-test.pdf"}])
       end
     end
   end

data/spec/doi_spec.rb

@@ -8,7 +8,7 @@ describe Cirneco::Doi do
 
   let(:number) { 123 }
   let(:prefix) { ENV['PREFIX'] }
-  let(:doi) { "10.5072/079j-xh42" }
+  let(:doi) { "10.5072/nmr3-xm61" }
   let(:url) { "http://www.datacite.org" }
   let(:username) { ENV['MDS_USERNAME'] }
   let(:password) { ENV['MDS_PASSWORD'] }
@@ -25,7 +25,7 @@ describe Cirneco::Doi do
     context "get" do
       it 'should get all dois' do
         subject.options = api_options.merge(limit: 3)
-        expect { subject.get "all" }.to output("10.5072/0007-NW90\n10.5072/079J-XH42\n10.5072/1-4CWY-2C14\n").to_stdout
+        expect { subject.get "all" }.to output("10.5438/0000-00SS\n10.5438/0000-01HC\n10.5438/0000-03VC\n").to_stdout
       end
 
       it 'should get doi' do
@@ -50,7 +50,7 @@ describe Cirneco::Doi do
   context "base32" do
     it 'generates a doi' do
       subject.options = { number: number, prefix: prefix }
-      expect { subject.generate }.to output("10.5072/0000-3v20\n").to_stdout
+      expect { subject.generate }.to output("10.5438/0000-3v20\n").to_stdout
     end
 
     it 'requires a prefix' do
@@ -59,7 +59,7 @@ describe Cirneco::Doi do
     end
 
     it 'decodes a doi' do
-      expect { subject.decode doi }.to output("DOI #{doi} was encoded with 7654321\n").to_stdout
+      expect { subject.decode doi }.to output("DOI #{doi} was encoded with 726405044\n").to_stdout
     end
 
     it 'checks a doi' do