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

app/controllers/concerns/error_serializable.rb

@@ -9,7 +9,7 @@ def serialize_errors(errors)
         source = err.keys.first
 
         Array.wrap(err.values.first).each do |title|
-          sum << { source: source, title: title.is_a?(String) ? title.capitalize : title.to_s }
+          sum << { source: source, title: title.is_a?(String) ? title.sub(/^./, &:upcase) : title.to_s }
         end
 
         sum

app/controllers/dois_controller.rb

@@ -291,6 +291,7 @@ def validate
   def create
     logger = Logger.new(STDOUT)
     # logger.info safe_params.inspect
+    fail CanCan::AuthorizationNotPerformed unless current_user.present?
 
     @doi = Doi.new(safe_params)
 

app/controllers/export_controller.rb

@@ -141,7 +141,7 @@ def organizations
             page_num = 2
             while page_num <= total_pages
                 page = { size: 1000, number: page_num }
-                response = Client.query(nil, page: page)
+                response = Client.query(nil, page: page, include_deleted: true)
                 clients = clients + response.records.to_a
                 page_num += 1
             end

app/validators/xml_schema_validator.rb

@@ -39,16 +39,16 @@ def validate_each(record, attribute, value)
       record.errors[:xml] << "Schema #{record.schema_version} is no longer supported"
       return false
     end
-    
+
     filepath = Bundler.rubygems.find_name('bolognese').first.full_gem_path + "/resources/#{kernel}/metadata.xsd"
     schema = Nokogiri::XML::Schema(open(filepath))
-  
+
     schema.validate(Nokogiri::XML(value, nil, 'UTF-8')).reduce({}) do |sum, error|
       location, level, source, text = error.message.split(": ", 4)
       line, column = location.split(":", 2)
       title = text.to_s.strip + " at line #{line}, column #{column}" if line.present?
       source = source.split("}").last[0..-2] if line.present?
-      source = schema_attributes(source) if source.present?  
+      source = schema_attributes(source) if source.present?
       record.errors[source.to_sym] << title
     end
   rescue Nokogiri::XML::SyntaxError => e

db/schema.rb

@@ -12,7 +12,7 @@
 
 ActiveRecord::Schema.define(version: 2019_08_07_002912) do
 
-  create_table "active_storage_attachments", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin ROW_FORMAT=DYNAMIC", force: :cascade do |t|
+  create_table "active_storage_attachments", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin", force: :cascade do |t|
     t.string "name", limit: 191, null: false
     t.string "record_type", null: false
     t.bigint "record_id", null: false
@@ -22,7 +22,7 @@
     t.index ["record_type", "record_id", "name", "blob_id"], name: "index_active_storage_attachments_uniqueness", unique: true
   end
 
-  create_table "active_storage_blobs", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin ROW_FORMAT=DYNAMIC", force: :cascade do |t|
+  create_table "active_storage_blobs", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin", force: :cascade do |t|
     t.string "key", limit: 191, null: false
     t.string "filename", limit: 191, null: false
     t.string "content_type", limit: 191
@@ -85,7 +85,7 @@
     t.index ["prefixes"], name: "FKE7FBD674AF86A1C7"
   end
 
-  create_table "audits", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin ROW_FORMAT=DYNAMIC", force: :cascade do |t|
+  create_table "audits", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin", force: :cascade do |t|
     t.integer "auditable_id"
     t.string "auditable_type"
     t.integer "associated_id"
@@ -107,6 +107,17 @@
     t.index ["user_id", "user_type"], name: "user_index"
   end
 
+  create_table "contacts", options: "ENGINE=InnoDB DEFAULT CHARSET=latin1", force: :cascade do |t|
+    t.bigint "allocator"
+    t.string "email"
+    t.string "given_name"
+    t.string "family_name"
+    t.string "role"
+    t.datetime "created_at", null: false
+    t.datetime "updated_at", null: false
+    t.index ["allocator"], name: "fk_rails_5c598567a8"
+  end
+
   create_table "datacentre", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT", force: :cascade do |t|
     t.text "comments", limit: 4294967295
     t.string "system_email", null: false
@@ -128,8 +139,7 @@
     t.text "url"
     t.string "software", limit: 191
     t.text "description"
-    t.string "client_type", limit: 191, default: "repository"
-    t.string "doaj_journal_id", limit: 191
+    t.string "client_type", limit: 191
     t.json "issn"
     t.json "certificate"
     t.json "repository_type"
@@ -211,7 +221,7 @@
     t.index ["url"], name: "index_dataset_on_url", length: 100
   end
 
-  create_table "events", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_bin ROW_FORMAT=DYNAMIC", force: :cascade do |t|
+  create_table "events", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8mb4", force: :cascade do |t|
     t.text "uuid", null: false
     t.text "subj_id", null: false
     t.text "obj_id"
@@ -238,7 +248,7 @@
     t.index ["uuid"], name: "index_events_on_uuid", unique: true, length: 36
   end
 
-  create_table "media", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8", force: :cascade do |t|
+  create_table "media", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT", force: :cascade do |t|
     t.datetime "created"
     t.string "media_type", limit: 80
     t.datetime "updated"
@@ -250,7 +260,7 @@
     t.index ["url"], name: "index_media_on_url", length: 100
   end
 
-  create_table "metadata", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8", force: :cascade do |t|
+  create_table "metadata", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT", force: :cascade do |t|
     t.datetime "created"
     t.integer "metadata_version"
     t.integer "version"
@@ -262,7 +272,7 @@
     t.index ["dataset"], name: "FKE52D7B2F4D3D6B1B"
   end
 
-  create_table "prefix", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8", force: :cascade do |t|
+  create_table "prefix", options: "ENGINE=InnoDB DEFAULT CHARSET=utf8 ROW_FORMAT=COMPACT", force: :cascade do |t|
     t.datetime "created"
     t.string "prefix", limit: 80, null: false
     t.integer "version"
@@ -301,6 +311,7 @@
 
   add_foreign_key "allocator_prefixes", "allocator", column: "allocator", name: "FKE7FBD67446EBD781"
   add_foreign_key "allocator_prefixes", "prefix", column: "prefixes", name: "FKE7FBD674AF86A1C7"
+  add_foreign_key "contacts", "allocator", column: "allocator"
   add_foreign_key "datacentre", "allocator", column: "allocator", name: "FK6695D60546EBD781"
   add_foreign_key "datacentre_prefixes", "datacentre", column: "datacentre", name: "FK13A1B3BA47B5F5FF"
   add_foreign_key "datacentre_prefixes", "prefix", column: "prefixes", name: "FK13A1B3BAAF86A1C7"

spec/fixtures/files/datacite_malformed_creator_name_type.xml

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<resource xmlns="http://datacite.org/schema/kernel-4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
+  <identifier identifierType="DOI">10.25670/oi2018-001on</identifier>
+  <titles>
+    <title xml:lang="sl">Učinkovitost kanabinoidov pri zdravljenju raka</title>
+    <title xml:lang="sl" titleType="Subtitle">mit ali resnica</title>
+    <title xml:lang="en" titleType="TranslatedTitle">Therapeutic Efficacy of Cannabinoids in Cancer Treatment</title>
+    <title xml:lang="en" titleType="Subtitle">Myth or Fact</title>
+  </titles>
+  <creators>
+    <creator>
+      <creatorName nameType="personal">Grošelj, Blaž</creatorName>
+      <givenName>Blaž</givenName>
+      <familyName>Grošelj</familyName>
+      <affiliation>Onkološki inštitut Ljubljana</affiliation>
+    </creator>
+  </creators>
+  <publisher>Onkološki inštitut Ljubljana</publisher>
+  <publicationYear>2018</publicationYear>
+  <resourceType resourceTypeGeneral="Text">Journal Article</resourceType>
+  <subjects>
+    <subject subjectScheme="DDC">610 Medical sciences; Medicine</subject>
+    <subject xml:lang="en">cancer</subject>
+    <subject xml:lang="en">cannabinoids</subject>
+  </subjects>
+  <dates>
+    <date dateType="Issued">2018-06-20</date>
+  </dates>
+  <relatedIdentifiers>
+    <relatedIdentifier relatedIdentifierType="ISSN" relationType="IsPartOf">1581-3215</relatedIdentifier>
+  </relatedIdentifiers>
+  <descriptions>
+    <description xml:lang="en" descriptionType="Other">The use of cannabis derivatives (cannabinoids) in oncology is sometimes indicated in the symptomatic treatment of nausea and vomiting, in pain management and in some neuropsychiatric disorders. In the recent years, there has been a growing interest in determining the anticancer effects of cannabinoids. Based on our clinical experience, we know that many patients use cannabinoids, among them also those with the aim of curing their disease. But despite the extensive and convincing data on the anticancer properties of cannabinoids from in vitro studies on cell cultures and studies on animal models, these properties have not (yet) been confirmed in a clinical trial. This paper summarises the currently available data on the potential of cannabinoid use in the clinical practice of oncology.</description>
+    <description descriptionType="SeriesInformation" xml:lang="sl">Onkologija, leto XXII, št. 1, junij 2018</description>
+    <description descriptionType="SeriesInformation" xml:lang="en">Onkologija, Volume XXII, No. 1, June 2018</description>
+  </descriptions>
+  <language>sl</language>
+  <formats>
+    <format>pdf</format>
+  </formats>
+  <rightsList>
+    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International license (CC BY 4.0)</rights>
+  </rightsList>
+</resource>

spec/requests/dois_spec.rb

@@ -338,7 +338,7 @@
 
       it 'updates the doi' do
         put "/dois/#{doi.doi}", valid_attributes, admin_headers
-        
+
         expect(last_response.status).to eq(200)
         expect(json.dig('data', 'attributes', 'sizes')).to eq(sizes)
       end
@@ -386,7 +386,7 @@
         put "/dois/#{doi.doi}", valid_attributes, headers
 
         expect(last_response.status).to eq(422)
-        expect(json["errors"]).to eq([{"source"=>"creators", "title"=>"Missing child element(s). expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0"}])
+        expect(json["errors"]).to eq([{"source"=>"creators", "title"=>"Missing child element(s). Expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0"}])
       end
     end
 
@@ -502,7 +502,7 @@
         put "/dois/#{doi_id}", valid_attributes, headers
 
         expect(last_response.status).to eq(422)
-        expect(json["errors"]).to eq([{"source"=>"creators", "title"=>"Missing child element(s). expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0"}])
+        expect(json["errors"]).to eq([{"source"=>"creators", "title"=>"Missing child element(s). Expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0"}])
       end
     end
 
@@ -528,7 +528,7 @@
         put "/dois/#{doi_id}", valid_attributes, headers
 
         expect(last_response.status).to eq(422)
-        expect(json["errors"]).to eq([{"source"=>"creators", "title"=>"Missing child element(s). expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0"}])
+        expect(json["errors"]).to eq([{"source"=>"creators", "title"=>"Missing child element(s). Expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0"}])
       end
     end
 
@@ -616,7 +616,7 @@
         patch "/dois/#{doi.doi}", valid_attributes, headers
 
         expect(last_response.status).to eq(422)
-        expect(json['errors']).to eq([{"source"=>"titles", "title"=>"Title 'submitted chemical data for inchikey=yapqbxqyljrxsa-uhfffaoysa-n' should be an object instead of a string."}])
+        expect(json['errors']).to eq([{"source"=>"titles", "title"=>"Title 'Submitted chemical data for InChIKey=YAPQBXQYLJRXSA-UHFFFAOYSA-N' should be an object instead of a string."}])
       end
     end
 
@@ -966,6 +966,30 @@
       end
     end
 
+    context 'when the request is valid no password' do
+      let(:xml) { Base64.strict_encode64(file_fixture('datacite.xml').read) }
+      let(:valid_attributes) do
+        {
+          "data" => {
+            "type" => "dois",
+            "attributes" => {
+              "doi" => "10.14454/10703",
+              "url" => "http://www.bl.uk/pdf/patspec.pdf",
+              "xml" => xml,
+              "source" => "test",
+              "event" => "publish"
+            }
+          }
+        }
+      end
+
+      it 'fails to create a Doi' do
+        post '/dois', valid_attributes
+
+        expect(last_response.status).to eq(401)
+      end
+    end
+
     context 'when the request is valid random doi' do
       let(:xml) { Base64.strict_encode64(file_fixture('datacite.xml').read) }
       let(:valid_attributes) do
@@ -1216,7 +1240,7 @@
         }
       HEREDOC
       ) }
-        
+
       let(:valid_attributes) do
         {
           "data" => {
@@ -1975,7 +1999,7 @@
         post '/dois', not_valid_attributes, headers
 
         expect(last_response.status).to eq(422)
-        expect(json["errors"]).to eq([{"source"=>"creators", "title"=>"Missing child element(s). expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0"}])
+        expect(json["errors"]).to eq([{"source"=>"creators", "title"=>"Missing child element(s). Expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0"}])
       end
     end
 
@@ -2068,7 +2092,7 @@
 
           expect(last_response.status).to eq(200)
           expect(json['errors'].size).to eq(1)
-          expect(json['errors'].first).to eq("source"=>"creators", "title"=>"Missing child element(s). expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0")
+          expect(json['errors'].first).to eq("source"=>"creators", "title"=>"Missing child element(s). Expected is ( {http://datacite.org/schema/kernel-4}creator ). at line 4, column 0")
         end
       end
 
@@ -2091,7 +2115,29 @@
 
           expect(last_response.status).to eq(200)
           expect(json['errors'].size).to eq(1)
-          expect(json['errors'].first).to eq("source"=>"creatorName", "title"=>"This element is not expected. expected is ( {http://datacite.org/schema/kernel-4}affiliation ). at line 16, column 0")
+          expect(json['errors'].first).to eq("source"=>"creatorName", "title"=>"This element is not expected. Expected is ( {http://datacite.org/schema/kernel-4}affiliation ). at line 16, column 0")
+        end
+      end
+
+      context 'when attribute type names are wrong' do
+        let(:xml) { ::Base64.strict_encode64(File.read(file_fixture('datacite_malformed_creator_name_type.xml'))) }
+        let(:params) do
+          {
+            "data" => {
+              "type" => "dois",
+              "attributes" => {
+                "doi" => "10.14454/10703",
+                "xml" => xml,
+              }
+            }
+          }
+        end
+
+        it 'validates types are in right format' do
+          post '/dois/validate', params, headers
+
+          expect(last_response.status).to eq(200)
+          expect(json['errors'].first).to eq("source"=>"creatorName', attribute 'nameType","title"=>"[facet 'enumeration'] The value 'personal' is not an element of the set {'Organizational', 'Personal'}. at line 12, column 0")
         end
       end