cirneco 0.9.26 → 0.9.27

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 1cc8643645d23b3d2995639c6ee153e006547918e4fffa0cd64063a9628722b0
-  data.tar.gz: f66ce1ea88a7b0f3b80fa3625d50bcc1f48e5a97761baab5f7b36f9e1a2bbfac
+  metadata.gz: ec85888aef2b21ee69038033d3621ea95e54f09a11dc02104394746a8d0e1d32
+  data.tar.gz: dcc0d3ea2fca7104ee5c5931e893932a6c9b1d477fe8a12b826f77af73521321
 SHA512:
-  metadata.gz: 902fdaeccbd4f869e97ed44fbbd91fa77d7430e25ab9612a8e446c278f0402db241cc54a07772490a8a80d2227dda5f299837a83621f25796c528ad6bfba146d
-  data.tar.gz: 636c9bf5ea8b5f9049241ded6fc0d7a16ab08372b4b2d5a2d46d3de440ce62512d4effe5a10f7ac0d275749ec1b9a8e338fcb71fd35a00371123c6e57d1d79e0
+  metadata.gz: d81746148cb2aa4f6ccf0c0c6260616cdb361dc0352ae75625bfc5c1ca708b4f491cf10ad4b89d8ff0e33d4b6a8d5f936f925cb56be7f0eacb8992fe92026be4
+  data.tar.gz: 4bf3bbd0d6be50310e2a64ec5d2cd4862ddbef80b54354ed841de9d8c98cb4a4c9d849695136769ac59d9cc8c6f29aa27b9f06796e3232b9a84d50f0a1f8be7c

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    cirneco (0.9.26)
+    cirneco (0.9.27)
       activesupport (>= 4.2.5, < 6)
       base32-url (~> 0.5)
       bergamasco (~> 0.3)
@@ -15,7 +15,7 @@ PATH
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (5.2.1)
+    activesupport (5.2.2)
       concurrent-ruby (~> 1.0, >= 1.0.2)
       i18n (>= 0.7, < 2)
       minitest (~> 5.1)
@@ -36,19 +36,22 @@ GEM
       safe_yaml (~> 1.0, >= 1.0.4)
     bibtex-ruby (4.4.7)
       latex-decode (~> 0.0)
-    bolognese (0.14.1)
+    bolognese (0.15.9)
       activesupport (>= 4.2.5, < 6)
       benchmark_methods (~> 0.7)
       bibtex-ruby (~> 4.1)
       builder (~> 3.2, >= 3.2.2)
+      citeproc-ruby (~> 1.1, >= 1.1.10)
       colorize (~> 0.8.1)
+      csl-styles (~> 1.0, >= 1.0.1.8)
+      edtf (~> 3.0, >= 3.0.4)
       gender_detector (~> 0.1.2)
       iso8601 (~> 0.9.1)
       json-ld (~> 2.1, >= 2.1.2)
       jsonlint (~> 0.2.0)
       loofah (~> 2.0, >= 2.0.3)
       maremma (>= 3.5.7, < 5)
-      namae (~> 0.11.3)
+      namae (~> 1.0)
       nokogiri (~> 1.8.1)
       oj (>= 2.8.3)
       postrank-uri (~> 1.0, >= 1.0.18)
@@ -56,21 +59,32 @@ GEM
       rdf-turtle (~> 2.2)
       thor (~> 0.19)
     builder (3.2.3)
+    citeproc (1.0.9)
+      namae (~> 1.0)
+    citeproc-ruby (1.1.10)
+      citeproc (~> 1.0, >= 1.0.9)
+      csl (~> 1.5)
     codeclimate-test-reporter (1.0.7)
       simplecov
     colorize (0.8.1)
-    concurrent-ruby (1.0.5)
+    concurrent-ruby (1.1.3)
     crack (0.4.3)
       safe_yaml (~> 1.0.0)
     crass (1.0.4)
+    csl (1.5.0)
+      namae (~> 1.0)
+    csl-styles (1.0.1.9)
+      csl (~> 1.0)
     diff-lcs (1.3)
     docile (1.1.5)
     dotenv (2.5.0)
     ebnf (1.1.3)
       rdf (~> 3.0)
       sxp (~> 1.0)
+    edtf (3.0.4)
+      activesupport (>= 3.0, < 6.0)
     excon (0.62.0)
-    faraday (0.15.2)
+    faraday (0.15.4)
       multipart-post (>= 1.2, < 3)
     faraday-encoding (0.0.5)
       faraday
@@ -85,7 +99,7 @@ GEM
       concurrent-ruby (~> 1.0)
     hashdiff (0.3.7)
     htmlentities (4.3.4)
-    i18n (1.1.0)
+    i18n (1.2.0)
       concurrent-ruby (~> 1.0)
     iso8601 (0.9.1)
     json (2.1.0)
@@ -97,7 +111,7 @@ GEM
       trollop (~> 2)
     latex-decode (0.3.1)
     link_header (0.0.8)
-    loofah (2.2.2)
+    loofah (2.2.3)
       crass (~> 1.0.2)
       nokogiri (>= 1.5.9)
     maremma (4.1.1)
@@ -115,7 +129,7 @@ GEM
     minitest (5.11.3)
     multi_json (1.13.1)
     multipart-post (2.0.0)
-    namae (0.11.3)
+    namae (1.0.1)
     nokogiri (1.8.4)
       mini_portile2 (~> 2.3.0)
     oj (2.18.5)
@@ -129,7 +143,7 @@ GEM
     rack-test (0.8.3)
       rack (>= 1.0, < 3)
     rake (12.3.1)
-    rdf (3.0.3)
+    rdf (3.0.7)
       hamster (~> 3.0)
       link_header (~> 0.0, >= 0.0.8)
     rdf-aggregate-repo (2.2.1)
@@ -175,9 +189,9 @@ GEM
     sxp (1.0.1)
       rdf (>= 2.2, < 4.0)
     temple (0.8.0)
-    thor (0.20.0)
+    thor (0.20.3)
     thread_safe (0.3.6)
-    tilt (2.0.8)
+    tilt (2.0.9)
     trollop (2.9.9)
     tzinfo (1.2.5)
       thread_safe (~> 0.1)

data/README.md

@@ -140,6 +140,20 @@ Transfer a list of DOIs. A list of DOIs must be provided in a file
 cirneco doi transfer --target DATACITE.DATACITE --jwt {YOUR-JSON-WEB-TOKEN} ./doi_transfer.txt
 ```
 
+Change the state of a list of DOIs. Note that all DOIS in the list must be in the ![previous state](https://support.datacite.org/docs/doi-states). A list of DOIs must be provided in a file
+
+```
+10.5438/5aep-2n86
+10.5438/cd2b-xj80
+```
+
+In this example, we change alist of `registered` DOI to `findable` DOIS.
+
+```shell
+cirneco doi bulk_state_change --target_state findable ./test_doi_status_change.csv
+```
+
+
 ## Development
 
 We use rspec for unit testing:

data/lib/cirneco/api.rb

@@ -109,5 +109,27 @@ module Cirneco
       end
       response
     end
+  
+    def update_rest_doi(doi, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "JWT or Username or password missing" }] }) unless options[:jwt].present? || (options[:username].present? && options[:password].present?)
+
+      api_url = options[:sandbox] ? 'https://api.test.datacite.org' : 'https://api.datacite.org'
+
+      url = URI.encode("#{api_url}/dois/#{doi}")
+      if options[:jwt].present?
+        Maremma.patch(url, content_type: 'application/vnd.api+json;charset=UTF-8', data: options[:data], bearer: options[:jwt]) 
+      else
+        Maremma.patch(url, content_type: 'application/vnd.api+json;charset=UTF-8', data: options[:data], username: options[:username], password: options[:password])
+      end
+    end
+
+    def get_rest_doi(doi, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      api_url = options[:sandbox] ? 'https://api.test.datacite.org' : 'https://api.datacite.org'
+
+      url = "#{api_url}/dois/#{doi}"
+      Maremma.get(url, accept: 'application/vnd.api+json;charset=UTF-8', username: options[:username], password: options[:password], raw: true)
+    end
   end
 end

data/lib/cirneco/doi.rb

@@ -97,7 +97,7 @@ module Cirneco
     def decode(doi)
       number = decode_doi(doi)
 
-      if number > 0
+      unless number.nil?
         puts "DOI #{doi} was encoded with #{number}"
       else
         puts "DOI #{doi} could not be decoded"
@@ -106,7 +106,7 @@ module Cirneco
 
     desc "check DOI", "check DOI using base32-url checksum"
     def check(doi)
-      if decode_doi(doi) > 0
+      unless decode_doi(doi).nil?
         puts "Checksum for #{doi} is valid"
       else
         puts "Checksum for #{doi} is not valid"
@@ -138,5 +138,52 @@ module Cirneco
 
       puts "#{count} DOIs transfered."
     end
+
+    desc "change DOIs state", "modify states of list of DOIs"
+    method_option :target_state,  :type => :string
+    method_option :username, :default => ENV['MDS_USERNAME']
+    method_option :password, :default => ENV['MDS_PASSWORD']
+    method_option :sandbox, :type => :boolean, :force => false
+    method_option :jwt, :default => ENV['JWT']
+    def bulk_state_change(file)
+      count = 0
+      File.foreach(file) do |line|
+        doi = line.rstrip
+        next unless doi.present?
+
+        previous_state, operation = case options[:target_state]
+        when "findable"
+          ["registered", "publish"]
+        when "registered"
+          ["draft", "register"]
+        end
+
+        meta = generate_state_change_template({operation: operation})
+
+        metadata_reponse = get_rest_doi(doi, options)
+
+        unless [200].include?(metadata_reponse.status)
+          puts "#{doi} was not found #{metadata_reponse.status}"
+          next
+        end
+        
+        metadata = JSON.parse(metadata_reponse.body.fetch("data", []))
+        if metadata.dig("data","attributes","state") == previous_state
+          response = update_rest_doi(doi, options.merge(data: meta.to_json))
+        else
+          puts "#{doi} is in the wrong state for change. #{doi} was not changed"
+          next
+        end
+
+        if [200, 201].include?(response.status)
+          puts "#{doi} Updated to #{options[:target_state]}."
+          count += 1
+        else
+          puts "Error: #{doi} " + response.body["errors"].first.fetch("title", "An error occured")
+        end
+      end
+
+      puts "#{count} DOIs updated."
+    end
   end
 end

data/lib/cirneco/utils.rb

@@ -38,9 +38,21 @@ module Cirneco
       response
     end
 
+    def generate_state_change_template(options={})
+      response = {
+        "data" => {
+          "type" => "dois",
+          "attributes" => {
+            "event" => options[:operation]
+          }
+        }
+      }
+      response
+    end
+
     def decode_doi(doi)
       prefix, string = doi.split('/', 2)
-      Base32::URL.decode(string, checksum: true).to_i
+      Base32::URL.decode(string, checksum: true)
     end
 
     def encode_doi(prefix, options={})

data/lib/cirneco/version.rb

@@ -1,3 +1,3 @@
 module Cirneco
-  VERSION = "0.9.26"
+  VERSION = "0.9.27"
 end

data/spec/api_spec.rb

@@ -94,5 +94,13 @@ describe Cirneco::Work, vcr: true, :order => :defined do
         expect(media).to eq([{:mime_type=>"application/pdf", :url=>"http://www.datacite.org/cirneco-test.pdf"}])
       end
     end
+
+    describe "get_rest_doi" do
+      it 'should get doi' do
+        r = subject.get_rest_doi(subject.doi, options)
+        response = JSON.parse(r.body.fetch("data", []))
+        expect(response.dig("data","id")).to eq("10.5438/6brg-2m37")
+      end
+    end
   end
 end

data/spec/doi_spec.rb

@@ -70,5 +70,9 @@ describe Cirneco::Doi do
       doi = "5072/0000-03VA"
       expect { subject.check doi }.to output("Checksum for #{doi} is not valid\n").to_stdout
     end
+    it 'checks a doi usercase' do
+      doi = "5072/0000-0098"
+      expect { subject.check doi }.to output("Checksum for #{doi} is valid\n").to_stdout
+    end
   end
 end

data/spec/fixtures/vcr_cassettes/Cirneco_Work/Media_API/get_rest_doi/should_get_doi.yml

@@ -0,0 +1,225 @@
+---
+http_interactions:
+- request:
+    method: get
+    uri: https://api.test.datacite.org/dois/10.5438/6brg-2m37
+    body:
+      encoding: US-ASCII
+      string: ''
+    headers:
+      User-Agent:
+      - Mozilla/5.0 (compatible; Maremma/4.1.1; +https://github.com/datacite/maremma)
+      Accept:
+      - application/vnd.api+json;charset=UTF-8
+      Authorization:
+      - Basic <MDS_TOKEN>
+  response:
+    status:
+      code: 200
+      message: OK
+    headers:
+      Date:
+      - Mon, 07 Jan 2019 14:53:06 GMT
+      Content-Type:
+      - application/json; charset=utf-8
+      Connection:
+      - keep-alive
+      Status:
+      - 200 OK
+      Cache-Control:
+      - max-age=0, private, must-revalidate
+      Vary:
+      - Accept-Encoding, Origin
+      X-Credential-Username:
+      - datacite
+      X-Request-Id:
+      - 79fa6e0e-6114-465a-9fcf-96600f8d626f
+      Etag:
+      - W/"ccea8f9dded875fa76a16e0d98602eb5"
+      X-Runtime:
+      - '0.029013'
+      X-Powered-By:
+      - Phusion Passenger 6.0.0
+      Server:
+      - nginx/1.15.7 + Phusion Passenger 6.0.0
+    body:
+      encoding: ASCII-8BIT
+      string: !binary |-
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+    http_version: 
+  recorded_at: Mon, 07 Jan 2019 14:53:06 GMT
+recorded_with: VCR 3.0.3

data/spec/utils_spec.rb

@@ -32,7 +32,7 @@ describe Cirneco::DataCenter, vcr: true, :order => :defined do
 
     it 'should decode doi not encoded' do
       doi = "10.23725/mds-client-ruby-test"
-      expect(subject.decode_doi(doi)).to eq(0)
+      expect(subject.decode_doi(doi)).to be_nil
     end
 
     it 'should encode doi' do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cirneco
 version: !ruby/object:Gem::Version
-  version: 0.9.26
+  version: 0.9.27
 platform: ruby
 authors:
 - Martin Fenner
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-09-20 00:00:00.000000000 Z
+date: 2019-01-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: maremma
@@ -274,22 +274,22 @@ dependencies:
   name: codeclimate-test-reporter
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
     - - ">="
       - !ruby/object:Gem::Version
         version: 1.0.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: simplecov
   requirement: !ruby/object:Gem::Requirement
@@ -371,6 +371,7 @@ files:
 - spec/fixtures/vcr_cassettes/Cirneco_Work/DOI_API/get/should_get_doi_not_found.yml
 - spec/fixtures/vcr_cassettes/Cirneco_Work/DOI_API/put/should_put_doi.yml
 - spec/fixtures/vcr_cassettes/Cirneco_Work/Media_API/get/should_get_media.yml
+- spec/fixtures/vcr_cassettes/Cirneco_Work/Media_API/get_rest_doi/should_get_doi.yml
 - spec/fixtures/vcr_cassettes/Cirneco_Work/Media_API/post/should_post_media.yml
 - spec/fixtures/vcr_cassettes/Cirneco_Work/Metadata_API/delete/should_delete_metadata.yml
 - spec/fixtures/vcr_cassettes/Cirneco_Work/Metadata_API/get/should_get_metadata.yml
@@ -399,8 +400,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.7.7
+rubygems_version: 3.0.2
 signing_key: 
 specification_version: 4
 summary: Ruby client library for the DataCite MDS