Merge pull request #1271 from datacite/schema-3-dep

Lupo Schema 3 Deprecation Tasks

app/validators/xml_schema_validator.rb

@@ -40,9 +40,15 @@ def validate_each(record, _attribute, value)
     kernel = get_valid_kernel(record.schema_version)
     return false if kernel.blank?
 
-    invalid_schemas = %w[http://datacite.org/schema/kernel-2.1 http://datacite.org/schema/kernel-2.2]
+    invalid_schemas = %w[
+      http://datacite.org/schema/kernel-2.1
+      http://datacite.org/schema/kernel-2.2
+      http://datacite.org/schema/kernel-3.0
+      http://datacite.org/schema/kernel-3.1
+      http://datacite.org/schema/kernel-3
+    ]
 
-    if record.new_record? && invalid_schemas.include?(record.schema_version)
+    if invalid_schemas.include?(record.schema_version)
       record.errors.add(:xml, "DOI #{record.uid}: Schema #{record.schema_version} is no longer supported")
       return false
     end

spec/fixtures/files/ns3.xml

@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ns0:resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xmlns:ns0="http://datacite.org/schema/kernel-3"
+  xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd">
+  <ns0:identifier identifierType="DOI">10.4231/D38G8FK8B</ns0:identifier>
+  <ns0:creators>
+    <ns0:creator>
+      <ns0:creatorName>Patiño, Carlos</ns0:creatorName>
+    </ns0:creator>
+    <ns0:creator>
+      <ns0:creatorName>Alzate-Vargas, Lorena</ns0:creatorName>
+    </ns0:creator>
+    <ns0:creator>
+      <ns0:creatorName>Li, Chunyu</ns0:creatorName>
+    </ns0:creator>
+    <ns0:creator>
+      <ns0:creatorName>Haley, Benjamin</ns0:creatorName>
+    </ns0:creator>
+    <ns0:creator>
+      <ns0:creatorName>Strachan, Alejandro</ns0:creatorName>
+    </ns0:creator>
+  </ns0:creators>
+  <ns0:titles>
+    <ns0:title>LAMMPS Data-File Generator</ns0:title>
+  </ns0:titles>
+  <ns0:publisher>nanoHUB</ns0:publisher>
+  <ns0:publicationYear>2018</ns0:publicationYear>
+  <ns0:dates>
+    <ns0:date dateType="Valid">2018-07-18</ns0:date>
+    <ns0:date dateType="Accepted">2018-07-18</ns0:date>
+  </ns0:dates>
+  <ns0:language>en</ns0:language>
+  <ns0:resourceType resourceTypeGeneral="Software">Simulation Tool</ns0:resourceType>
+  <ns0:version>1.5.2</ns0:version>
+  <ns0:descriptions>
+    <ns0:description descriptionType="Other">This tool generates all necessary input files for
+      LAMMPS simulations of molecular systems starting with an atomistic structure.</ns0:description>
+  </ns0:descriptions>
+</ns0:resource>

spec/fixtures/files/ns30.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ns0:resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ns0="http://datacite.org/schema/kernel-3.0" xsi:schemaLocation="http://datacite.org/schema/kernel-3.0 http://schema.datacite.org/meta/kernel-3.0/metadata.xsd"><ns0:identifier identifierType="DOI">10.4231/D38G8FK8B</ns0:identifier><ns0:creators><ns0:creator>	<ns0:creatorName>Patiño, Carlos</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Alzate-Vargas, Lorena</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Li, Chunyu</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Haley, Benjamin</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Strachan, Alejandro</ns0:creatorName></ns0:creator></ns0:creators><ns0:titles>	<ns0:title>LAMMPS Data-File Generator</ns0:title></ns0:titles><ns0:publisher>nanoHUB</ns0:publisher><ns0:publicationYear>2018</ns0:publicationYear><ns0:dates>	<ns0:date dateType="Valid">2018-07-18</ns0:date>	<ns0:date dateType="Accepted">2018-07-18</ns0:date></ns0:dates><ns0:language>en</ns0:language><ns0:resourceType resourceTypeGeneral="Software">Simulation Tool</ns0:resourceType><ns0:version>1.5.2</ns0:version><ns0:descriptions>	<ns0:description descriptionType="Other">This tool generates all necessary input files for LAMMPS simulations of molecular systems starting with an atomistic structure.</ns0:description></ns0:descriptions></ns0:resource>

spec/fixtures/files/ns31.xml

@@ -0,0 +1,2 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ns0:resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ns0="http://datacite.org/schema/kernel-3.1" xsi:schemaLocation="http://datacite.org/schema/kernel-3.1 http://schema.datacite.org/meta/kernel-3.1/metadata.xsd"><ns0:identifier identifierType="DOI">10.4231/D38G8FK8B</ns0:identifier><ns0:creators><ns0:creator>	<ns0:creatorName>Patiño, Carlos</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Alzate-Vargas, Lorena</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Li, Chunyu</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Haley, Benjamin</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Strachan, Alejandro</ns0:creatorName></ns0:creator></ns0:creators><ns0:titles>	<ns0:title>LAMMPS Data-File Generator</ns0:title></ns0:titles><ns0:publisher>nanoHUB</ns0:publisher><ns0:publicationYear>2018</ns0:publicationYear><ns0:dates>	<ns0:date dateType="Valid">2018-07-18</ns0:date>	<ns0:date dateType="Accepted">2018-07-18</ns0:date></ns0:dates><ns0:language>en</ns0:language><ns0:resourceType resourceTypeGeneral="Software">Simulation Tool</ns0:resourceType><ns0:version>1.5.2</ns0:version><ns0:descriptions>	<ns0:description descriptionType="Other">This tool generates all necessary input files for LAMMPS simulations of molecular systems starting with an atomistic structure.</ns0:description></ns0:descriptions></ns0:resource>

spec/requests/datacite_dois/post_spec.rb

@@ -888,62 +888,6 @@
       end
     end
 
-    context "when the request uses schema 3" do
-      let(:xml) { Base64.strict_encode64(file_fixture("datacite_schema_3.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 "creates a Doi" do
-        post "/dois", valid_attributes, headers
-
-        expect(last_response.status).to eq(201)
-        expect(json.dig("data", "attributes", "url")).to eq("http://www.bl.uk/pdf/patspec.pdf")
-        expect(json.dig("data", "attributes", "doi")).to eq("10.14454/10703")
-        expect(json.dig("data", "attributes", "titles")).to eq([{ "title" => "Data from: A new malaria agent in African hominids." }])
-        expect(json.dig("data", "attributes", "source")).to eq("test")
-        expect(json.dig("data", "attributes", "schemaVersion")).to eq("http://datacite.org/schema/kernel-3")
-        expect(json.dig("data", "attributes", "state")).to eq("findable")
-      end
-    end
-
-    context "when the request creates schema 3 with funder contributor type" do
-      let(:xml) { Base64.strict_encode64(file_fixture("datacite_schema_3.xml").read) }
-      let(:valid_attributes) do
-        {
-          "data" => {
-            "type" => "dois",
-            "attributes" => {
-              "doi" => "10.14454/10703",
-              "url" => "http://www.bl.uk/pdf/patspec.pdf",
-              "xml" => xml,
-              "contributors" => [{ "contributorType" => "Funder", "name" => "Wellcome Trust", "nameType" => "Organizational" }],
-              "source" => "test",
-              "event" => "publish",
-            },
-          },
-        }
-      end
-
-      it "creates a Doi" do
-        post "/dois", valid_attributes, headers
-
-        expect(last_response.status).to eq(422)
-        expect(json.fetch("errors", nil)).to eq([{ "source" => "xml", "title" => "DOI 10.14454/10703: No matching global declaration available for the validation root. at line 2, column 0", "uid" => "10.14454/10703" }])
-      end
-    end
-
     context "when the request has wrong object in nameIdentifiers" do
       let(:valid_attributes) { JSON.parse(file_fixture("datacite_wrong_nameIdentifiers.json").read) }
 
@@ -1024,6 +968,78 @@
       end
     end
 
+    context "when the xml request uses unsupported metadata version - kernel-3" do
+      let(:xml) { Base64.strict_encode64(file_fixture("ns3.xml").read) }
+      let(:valid_attributes) do
+        {
+          "data" => {
+            "type" => "dois",
+            "attributes" => {
+              "doi" => "10.14454/10703",
+              "url" => "http://www.bl.uk/pdf/patspec.pdf",
+              "xml" => xml,
+              "event" => "publish",
+            },
+          },
+        }
+      end
+
+      it "returns an error that schema is no longer supported" do
+        post "/dois", valid_attributes, headers
+
+        expect(last_response.status).to eq(422)
+        expect(json.fetch("errors", nil)).to eq([{ "source" => "xml", "title" => "DOI 10.14454/10703: Schema http://datacite.org/schema/kernel-3 is no longer supported", "uid" => "10.14454/10703" }])
+      end
+    end
+
+    context "when the xml request uses unsupported metadata version - kernel-3.0" do
+      let(:xml) { Base64.strict_encode64(file_fixture("ns30.xml").read) }
+      let(:valid_attributes) do
+        {
+          "data" => {
+            "type" => "dois",
+            "attributes" => {
+              "doi" => "10.14454/10703",
+              "url" => "http://www.bl.uk/pdf/patspec.pdf",
+              "xml" => xml,
+              "event" => "publish",
+            },
+          },
+        }
+      end
+
+      it "returns an error that schema is no longer supported" do
+        post "/dois", valid_attributes, headers
+
+        expect(last_response.status).to eq(422)
+        expect(json.fetch("errors", nil)).to eq([{ "source" => "xml", "title" => "DOI 10.14454/10703: Schema http://datacite.org/schema/kernel-3.0 is no longer supported", "uid" => "10.14454/10703" }])
+      end
+    end
+
+    context "when the xml request uses unsupported metadata version - kernel-3.1" do
+      let(:xml) { Base64.strict_encode64(file_fixture("ns31.xml").read) }
+      let(:valid_attributes) do
+        {
+          "data" => {
+            "type" => "dois",
+            "attributes" => {
+              "doi" => "10.14454/10703",
+              "url" => "http://www.bl.uk/pdf/patspec.pdf",
+              "xml" => xml,
+              "event" => "publish",
+            },
+          },
+        }
+      end
+
+      it "returns an error that schema is no longer supported" do
+        post "/dois", valid_attributes, headers
+
+        expect(last_response.status).to eq(422)
+        expect(json.fetch("errors", nil)).to eq([{ "source" => "xml", "title" => "DOI 10.14454/10703: Schema http://datacite.org/schema/kernel-3.1 is no longer supported", "uid" => "10.14454/10703" }])
+      end
+    end
+
     context "when the request uses schema 4.0" do
       let(:xml) { Base64.strict_encode64(file_fixture("schema_4.0.xml").read) }
       let(:valid_attributes) do
@@ -1593,30 +1609,6 @@
         end
       end
 
-      context "validates schema 3" do
-        let(:xml) { ::Base64.strict_encode64(File.read(file_fixture("datacite_schema_3.xml"))) }
-        let(:params) do
-          {
-            "data" => {
-              "type" => "dois",
-              "attributes" => {
-                "doi" => "10.14454/10703",
-                "xml" => xml,
-              },
-            },
-          }
-        end
-
-        it "validates a Doi" do
-          post "/dois/validate", params, headers
-
-          expect(last_response.status).to eq(200)
-          expect(json.dig("data", "attributes", "doi")).to eq("10.14454/10703")
-          expect(json.dig("data", "attributes", "titles")).to eq([{ "title" => "Data from: A new malaria agent in African hominids." }])
-          expect(json.dig("data", "attributes", "dates")).to eq([{ "date" => "2011", "dateType" => "Issued" }])
-        end
-      end
-
       context "validates schema 4.5 xml" do
         let(:xml) { ::Base64.strict_encode64(File.read(file_fixture("datacite-example-full-v4.5.xml"))) }
         let(:params) do
@@ -1878,91 +1870,6 @@
       end
     end
 
-    context "update individual attribute" do
-      let(:xml) { Base64.strict_encode64(file_fixture("datacite_schema_3.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
-      let(:update_attributes) do
-        {
-          "data" => {
-            "type" => "dois",
-            "attributes" => {
-              "schemaVersion" => "http://datacite.org/schema/kernel-4",
-              "regenerate" => true,
-            },
-          },
-        }
-      end
-
-      it "creates a Doi" do
-        post "/dois", valid_attributes, headers
-
-        expect(json.dig("data", "attributes", "doi")).to eq("10.14454/10703")
-        expect(json.dig("data", "attributes", "titles")).to eq([{ "title" => "Data from: A new malaria agent in African hominids." }])
-        expect(json.dig("data", "attributes", "schemaVersion")).to eq("http://datacite.org/schema/kernel-3")
-
-        doc = Nokogiri::XML(Base64.decode64(json.dig("data", "attributes", "xml")), nil, "UTF-8", &:noblanks)
-        expect(doc.collect_namespaces).to eq("xmlns" => "http://datacite.org/schema/kernel-3", "xmlns:dim" => "http://www.dspace.org/xmlns/dspace/dim", "xmlns:dryad" => "http://purl.org/dryad/terms/", "xmlns:dspace" => "http://www.dspace.org/xmlns/dspace/dim", "xmlns:mets" => "http://www.loc.gov/METS/", "xmlns:xsi" => "http://www.w3.org/2001/XMLSchema-instance")
-      end
-    end
-
-    context "mds doi" do
-      let(:xml) { Base64.strict_encode64(file_fixture("datacite_schema_3.xml").read) }
-      let(:valid_attributes) do
-        {
-          "data" => {
-            "type" => "dois",
-            "attributes" => {
-              "url" => "http://www.bl.uk/pdf/patspec.pdf",
-              "should_validate" => "true",
-              "source" => "mds",
-              "event" => "publish",
-            },
-          },
-        }
-      end
-
-      let(:update_attributes) do
-        {
-          "data" => {
-            "type" => "dois",
-            "attributes" => {
-              "doi" => "10.14454/10703",
-              "should_validate" => "true",
-              "xml" => xml,
-              "source" => "mds",
-              "event" => "show",
-            },
-          },
-        }
-      end
-
-      it "add metadata" do
-        put "/dois/10.14454/10703", update_attributes, headers
-
-        expect(json.dig("data", "attributes", "doi")).to eq("10.14454/10703")
-        expect(json.dig("data", "attributes", "schemaVersion")).to eq("http://datacite.org/schema/kernel-3")
-
-        put "/dois/10.14454/10703", valid_attributes, headers
-
-        expect(json.dig("data", "attributes", "doi")).to eq("10.14454/10703")
-        expect(json.dig("data", "attributes", "schemaVersion")).to eq("http://datacite.org/schema/kernel-3")
-        expect(json.dig("data", "attributes", "titles")).to eq([{ "title" => "Data from: A new malaria agent in African hominids." }])
-      end
-    end
-
     # Funder has been removed as valid contributor type in schema 4.0
     context "update contributor type with funder", elasticsearch: true do
       let(:update_attributes) do