Merge branch 'master' of https://github.com/datacite/cirneco

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)
@@ -36,41 +36,55 @@ 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)
       rdf-rdfxml (~> 2.0)
       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)

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:

lib/cirneco/api.rb

@@ -109,5 +109,27 @@ def get_media(doi, options={})
       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

lib/cirneco/doi.rb

@@ -138,5 +138,52 @@ def transfer(file)
 
       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

lib/cirneco/utils.rb

@@ -38,6 +38,18 @@ def generate_transfer_template(options={})
       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)

lib/cirneco/version.rb

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

spec/api_spec.rb

@@ -94,5 +94,13 @@
         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