Merged in DSC-1243 (pull request DSpace#1139)

[DSC-1243] added virtualField generator for primary and alt dois

dspace-api/src/main/java/org/dspace/content/integration/crosswalks/virtualfields/ItemDOIService.java

@@ -0,0 +1,59 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.integration.crosswalks.virtualfields;
+
+import java.util.Comparator;
+import java.util.List;
+
+import org.dspace.content.Item;
+import org.dspace.content.MetadataValue;
+import org.dspace.content.service.ItemService;
+import org.dspace.services.ConfigurationService;
+import org.springframework.beans.factory.annotation.Autowired;
+
+
+public class ItemDOIService {
+    static final String CFG_PREFIX = "identifier.doi.prefix";
+
+    static final String DOI_METADATA = "dc.identifier.doi";
+
+    @Autowired
+    protected ItemService itemService;
+    @Autowired
+    private ConfigurationService configurationService;
+
+    public String[] getAlternativeDOIFromItem(Item item) {
+        List<MetadataValue> metadataValueList = itemService.getMetadataByMetadataString(item, DOI_METADATA);
+        return getAlternativeDOI(metadataValueList, getPrimaryDOI(metadataValueList));
+    }
+    private String[] getAlternativeDOI(List<MetadataValue> metadataValueList, String primaryValue) {
+        return metadataValueList.stream().map(MetadataValue::getValue)
+                .filter(value -> !value.equals(primaryValue)).toArray(String[]::new);
+    }
+
+    public String getPrimaryDOIFromItem(Item item) {
+        return getPrimaryDOI(itemService.getMetadataByMetadataString(item, DOI_METADATA));
+    }
+
+    private String getPrimaryDOI(List<MetadataValue> metadataValueList) {
+        return metadataValueList.stream().filter(metadata -> metadata.getValue().contains(getPrefix()))
+                .min(Comparator.comparingInt(MetadataValue::getPlace)).map(MetadataValue::getValue)
+                .orElse(!metadataValueList.isEmpty() ? metadataValueList.get(0).getValue() : null);
+    }
+
+    protected String getPrefix() {
+        String prefix;
+        prefix = this.configurationService.getProperty(CFG_PREFIX);
+        if (null == prefix) {
+            throw new RuntimeException("Unable to load DOI prefix from "
+                    + "configuration. Cannot find property " +
+                    CFG_PREFIX + ".");
+        }
+        return prefix;
+    }
+}

dspace-api/src/main/java/org/dspace/content/integration/crosswalks/virtualfields/VirtualFieldAlternativeDOI.java

@@ -0,0 +1,30 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.integration.crosswalks.virtualfields;
+
+import org.apache.commons.lang3.StringUtils;
+import org.dspace.content.Item;
+import org.dspace.core.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+
+
+public class VirtualFieldAlternativeDOI implements VirtualField {
+
+    @Autowired
+    private ItemDOIService itemDOIService;
+
+    @Override
+    public String[] getMetadata(Context context, Item item, String fieldName) {
+        String[] qualifiers = StringUtils.split(fieldName, ".");
+        if (qualifiers.length != 3) {
+            throw new IllegalArgumentException("Invalid field name " + fieldName);
+        }
+
+        return itemDOIService.getAlternativeDOIFromItem(item);
+    }
+}

dspace-api/src/main/java/org/dspace/content/integration/crosswalks/virtualfields/VirtualFieldPrimaryDOI.java

@@ -0,0 +1,30 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.integration.crosswalks.virtualfields;
+
+import org.apache.commons.lang3.StringUtils;
+import org.dspace.content.Item;
+import org.dspace.core.Context;
+import org.springframework.beans.factory.annotation.Autowired;
+
+
+public class VirtualFieldPrimaryDOI implements VirtualField {
+
+    @Autowired
+    private ItemDOIService itemDOIService;
+
+    @Override
+    public String[] getMetadata(Context context, Item item, String fieldName) {
+        String[] qualifiers = StringUtils.split(fieldName, ".");
+        if (qualifiers.length != 3) {
+            throw new IllegalArgumentException("Invalid field name " + fieldName);
+        }
+
+        return new String[] {itemDOIService.getPrimaryDOIFromItem(item)};
+    }
+}

dspace-api/src/test/data/dspaceFolder/config/crosswalks/template/virtual-field-doi-json.template

@@ -0,0 +1,4 @@
+{
+	"primary-doi": "@virtual.primary-doi.dc-identifier-doi@",
+	"alternative-doi": "@virtual.alternative-doi.dc-identifier-doi@",
+}

dspace-api/src/test/data/dspaceFolder/config/spring/api/test-beans.xml

@@ -22,6 +22,16 @@
 		<property name="linesPostProcessor" ref="jsonPostProcessor" />
 	</bean>
 
+    <bean class="org.dspace.content.integration.crosswalks.ReferCrosswalk" id="referCrosswalkVirtualFieldDOI">
+        <property name="templateFileName" value="crosswalks/template/virtual-field-doi-json.template"/>
+        <property name="mimeType" value="application/json; charset=UTF-8"/>
+        <property name="fileName" value="test.json"/>
+        <property name="entityType" value="Publication"/>
+        <property name="crosswalkMode" value="#{T(org.dspace.content.crosswalk.CrosswalkMode).SINGLE}"/>
+        <property name="converter" ref="jsonValueConverter" />
+        <property name="linesPostProcessor" ref="jsonPostProcessor" />
+    </bean>
+
     <bean class="org.dspace.content.integration.crosswalks.ReferCrosswalk" id="referCrosswalkVirtualFieldVocabulary">
 		<property name="templateFileName" value="crosswalks/template/virtual-field-vocabulary-json.template"/>
 		<property name="mimeType" value="application/json; charset=UTF-8"/>

dspace-api/src/test/java/org/dspace/content/integration/crosswalks/ReferCrosswalkIT.java

@@ -69,6 +69,7 @@
 import org.dspace.eperson.EPerson;
 import org.dspace.layout.CrisLayoutBox;
 import org.dspace.layout.LayoutSecurity;
+import org.dspace.services.ConfigurationService;
 import org.dspace.utils.DSpace;
 import org.json.JSONObject;
 import org.junit.After;
@@ -82,6 +83,7 @@
  *
  */
 public class ReferCrosswalkIT extends AbstractIntegrationTestWithDatabase {
+    static final String CFG_PREFIX = "identifier.doi.prefix";
 
     private static final String BASE_OUTPUT_DIR_PATH = "./target/testing/dspace/assetstore/crosswalk/";
 
@@ -99,6 +101,8 @@ public class ReferCrosswalkIT extends AbstractIntegrationTestWithDatabase {
 
     private VirtualField virtualFieldId;
 
+    private ConfigurationService configurationService;
+
     @Before
     public void setup() throws SQLException, AuthorizeException {
 
@@ -117,6 +121,8 @@ public void setup() throws SQLException, AuthorizeException {
         when(mockedVirtualFieldId.getMetadata(any(), any(), any())).thenReturn(new String[] { "mock-id" });
         this.virtualFieldMapper.setVirtualField("id", mockedVirtualFieldId);
 
+        this.configurationService = new DSpace().getSingletonService(ConfigurationService.class);
+
         context.turnOffAuthorisationSystem();
         community = createCommunity(context).build();
         collection = createCollection(context, community).withAdminGroup(eperson).build();
@@ -2530,6 +2536,82 @@ public void testVirtualBitstreamFieldWithProject() throws Exception {
         assertThat(resultLines[54].trim(), equalTo("</project>"));
     }
 
+    @Test
+    public void testExportToDataciteFormatItemWithThreeDOI() throws Exception {
+        String prefix;
+        prefix = this.configurationService.getProperty(CFG_PREFIX);
+        if (null == prefix) {
+            throw new RuntimeException("Unable to load DOI prefix from "
+                    + "configuration. Cannot find property " +
+                    CFG_PREFIX + ".");
+        }
+
+        context.turnOffAuthorisationSystem();
+
+        Item publication = createItem(context, collection)
+                .withEntityType("Publication")
+                .withTitle("publication title")
+                .withDoiIdentifier("test doi")
+                .withDoiIdentifier("test doi2")
+                .withDoiIdentifier("test" + prefix + "test")
+                .build();
+
+        context.restoreAuthSystemState();
+
+        ReferCrosswalk referCrosswalk = new DSpace().getServiceManager()
+                .getServiceByName("referCrosswalkVirtualFieldDOI", ReferCrosswalk.class);
+        assertThat(referCrosswalk, notNullValue());
+
+        ByteArrayOutputStream out = new ByteArrayOutputStream();
+        referCrosswalk.disseminate(context, publication, out);
+
+        String[] resultLines = out.toString().split("\n");
+
+        assertThat(resultLines.length, is(5));
+        assertThat(resultLines[0].trim(), is("{"));
+        assertThat(resultLines[1].trim(), is("\"primary-doi\": \"test" + prefix + "test\","));
+        assertThat(resultLines[2].trim(), is("\"alternative-doi\": \"test doi\","));
+        assertThat(resultLines[3].trim(), is("\"alternative-doi\": \"test doi2\""));
+        assertThat(resultLines[4].trim(), is("}"));
+    }
+
+    @Test
+    public void testExportToDataciteFormatItemWithSingleDOINotMatchingPrefix() throws Exception {
+        String prefix;
+        prefix = this.configurationService.getProperty(CFG_PREFIX);
+        if (null == prefix) {
+            throw new RuntimeException("Unable to load DOI prefix from "
+                    + "configuration. Cannot find property " +
+                    CFG_PREFIX + ".");
+        }
+
+        context.turnOffAuthorisationSystem();
+
+        Item publication = createItem(context, collection)
+                .withEntityType("Publication")
+                .withTitle("publication title")
+                .withDoiIdentifier("test doi")
+                .build();
+
+        context.restoreAuthSystemState();
+
+        ReferCrosswalk referCrosswalk = new DSpace().getServiceManager()
+                .getServiceByName("referCrosswalkVirtualFieldDOI", ReferCrosswalk.class);
+        assertThat(referCrosswalk, notNullValue());
+
+        ByteArrayOutputStream out = new ByteArrayOutputStream();
+        referCrosswalk.disseminate(context, publication, out);
+
+        String[] resultLines = out.toString().split("\n");
+
+        assertThat(resultLines.length, is(3));
+        assertThat(resultLines[0].trim(), is("{"));
+        assertThat(resultLines[1].trim(), is("\"primary-doi\": \"test doi\""));
+        assertThat(resultLines[2].trim(), is("}"));
+    }
+
+
+
 
     private void createSelectedRelationship(Item author, Item publication, RelationshipType selectedRelationshipType) {
         createRelationshipBuilder(context, publication, author, selectedRelationshipType, -1, -1).build();

dspace-oai/src/main/java/org/dspace/xoai/app/DataciteDOIItemCompilePlugin.java

@@ -0,0 +1,75 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.xoai.app;
+
+import java.util.Arrays;
+import java.util.List;
+
+import com.lyncode.xoai.dataprovider.xml.xoai.Element;
+import com.lyncode.xoai.dataprovider.xml.xoai.Metadata;
+import org.apache.commons.lang.StringUtils;
+import org.dspace.content.Item;
+import org.dspace.content.integration.crosswalks.virtualfields.ItemDOIService;
+import org.dspace.core.Context;
+import org.dspace.xoai.util.ItemUtils;
+import org.springframework.beans.factory.annotation.Autowired;
+
+
+/**
+ * XOAIExtensionItemCompilePlugin aims to add structured information about the
+ * DOIs of the item (if any).
+ * The xoai document will be enriched with a structure like that
+ * <code>
+ *   <element name="other">
+ *       <element name="datacite">
+ *          <element name="primary">
+ *              <field name="doi"></field>
+ *          </element>
+ *          <element name="alternative">
+ *              <field name="doi"></field>
+ *               ...
+ *              <field name="doi"></field>
+ *          </element>
+ *       </element>
+ *   </element>
+ * </code>
+ *
+ */
+public class DataciteDOIItemCompilePlugin implements XOAIExtensionItemCompilePlugin {
+
+    @Autowired
+    private ItemDOIService itemDOIService;
+
+    @Override
+    public Metadata additionalMetadata(Context context, Metadata metadata, Item item) {
+        String primaryDoiValue = itemDOIService.getPrimaryDOIFromItem(item);
+        String[] alternativeDoiValue = itemDOIService.getAlternativeDOIFromItem(item);
+        Element datacite = ItemUtils.create("datacite");
+        if (StringUtils.isNotBlank(primaryDoiValue)) {
+            Element primary = ItemUtils.create("primary");
+            datacite.getElement().add(primary);
+            primary.getField().add(ItemUtils.createValue("doi", primaryDoiValue));
+            if (alternativeDoiValue != null && alternativeDoiValue.length != 0) {
+                Element alternative = ItemUtils.create("alternative");
+                datacite.getElement().add(alternative);
+                Arrays.stream(alternativeDoiValue)
+                        .forEach(value -> alternative.getField().add(ItemUtils.createValue("doi", value)));
+            }
+            Element other;
+            List<Element> elements = metadata.getElement();
+            if (ItemUtils.getElement(elements, "others") != null) {
+                other = ItemUtils.getElement(elements, "others");
+            } else {
+                other = ItemUtils.create("others");
+            }
+            other.getElement().add(datacite);
+        }
+        return metadata;
+    }
+
+}

dspace/config/crosswalks/oai/metadataFormats/oai_openaire.xsl

@@ -93,6 +93,14 @@
             <!-- CREATIVE COMMON LICENSE -->
             <xsl:apply-templates
                 select="doc:metadata/doc:element[@name='others']/doc:element[@name='cc']" mode="oaire" />
+            <!-- primary doi identifier -->
+            <xsl:apply-templates
+                    select="doc:metadata/doc:element[@name='others']/doc:element[@name='datacite']/doc:element[@name='primary']"
+                    mode="datacite" />
+<!--            alternative doi identifiers-->
+            <xsl:apply-templates
+                    select="doc:metadata/doc:element[@name='others']/doc:element[@name='datacite']/doc:element[@name='alternative']"
+                    mode="datacite_altid" />
         </oaire:resource>
     </xsl:template>
 
@@ -1668,6 +1676,26 @@
         </oaire:licenseCondition>
     </xsl:template>
 
+    <xsl:template match="doc:element[@name='others']/doc:element[@name='datacite']/doc:element[@name='primary']"
+                  mode="datacite">
+        <!-- only process the first element -->
+        <datacite:identifier>
+            <xsl:attribute name="identifierType">doi</xsl:attribute>
+            <xsl:value-of select="./doc:field[@name='doi']/text()"/>
+        </datacite:identifier>
+    </xsl:template>
+
+    <!-- for each alternative doi -->
+    <xsl:template match="doc:element[@name='others']/doc:element[@name='datacite']/doc:element[@name='alternative']" mode="datacite_altid">
+        <xsl:for-each select="./doc:field[@name='doi']">
+
+                <datacite:alternateIdentifier>
+                    <xsl:attribute name="alternateIdentifierType">doi</xsl:attribute>
+                    <xsl:value-of select="./text()"/>
+                </datacite:alternateIdentifier>
+        </xsl:for-each>
+    </xsl:template>
+
     <!-- ignore all non specified text values or attributes -->
     <xsl:template match="text()|@*"/>
     <xsl:template match="text()|@*" mode="oaire"/>

dspace/config/crosswalks/template/patent-datacite-xml.template

@@ -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-4.4/metadata.xsd">
-  <identifier identifierType="DOI">@dc.identifier.doi@</identifier>
+  <identifier identifierType="DOI">@virtual.primary-doi.dc-identifier-doi@</identifier>
   <creators>
       @group.dc-contributor-author.start@
       <creator>
@@ -28,6 +28,7 @@
   <resourceType resourceTypeGeneral="@virtual.mapConverter.type2datacite.dc-type@" />
   <alternateIdentifiers>
     <alternateIdentifier alternateIdentifierType="url">@dc.identifier.uri@</alternateIdentifier>
+    <alternateIdentifier alternateIdentifierType="doi">@virtual.alternative-doi.dc-identifier-doi@</alternateIdentifier>
   </alternateIdentifiers>
   <version>@dc.description.version@</version>
   <rightsList>