Datacite xml improvements

src/main/java/edu/harvard/iq/dataverse/DataFile.java

@@ -1123,4 +1123,23 @@ private boolean tagExists(String tagLabel) {
         }
         return false;
     }
+
+    public boolean isDeaccessioned() {
+        // return true, if all published versions were deaccessioned
+        boolean inDeaccessionedVersions = false;
+        for (FileMetadata fmd : getFileMetadatas()) {
+            DatasetVersion testDsv = fmd.getDatasetVersion();
+            if (testDsv.isReleased()) {
+                return false;
+            }
+            // Also check for draft version
+            if (testDsv.isDraft()) {
+                return false;
+            }
+            if (testDsv.isDeaccessioned()) {
+                inDeaccessionedVersions = true;
+            }
+        }
+        return inDeaccessionedVersions; // since any published version would have already returned
+    }
 } // end of class

src/main/java/edu/harvard/iq/dataverse/DatasetFieldConstant.java

@@ -157,6 +157,8 @@ public class DatasetFieldConstant implements java.io.Serializable  {
     public final static String confidentialityDeclaration="confidentialityDeclaration";
     public final static String specialPermissions="specialPermissions";
     public final static String restrictions="restrictions";
+    @Deprecated
+    //Doesn't appear to be used and is not datasetContact
     public final static String contact="contact";
     public final static String citationRequirements="citationRequirements";
     public final static String depositorRequirements="depositorRequirements";

src/main/java/edu/harvard/iq/dataverse/DatasetServiceBean.java

@@ -947,7 +947,7 @@ public void callFinalizePublishCommandAsynchronously(Long datasetId, CommandCont
         try {
             Thread.sleep(1000);
         } catch (Exception ex) {
-            logger.warning("Failed to sleep for a second.");
+            logger.warning("Failed to sleep for one second.");
         }
         logger.fine("Running FinalizeDatasetPublicationCommand, asynchronously");
         Dataset theDataset = find(datasetId);

src/main/java/edu/harvard/iq/dataverse/DatasetVersion.java

@@ -1342,7 +1342,7 @@ public List<String[]> getGeographicCoverage() {
                     }
                     geoCoverages.add(coverageItem);
                 }
-
+                break;
             }
         }
         return geoCoverages;

src/main/java/edu/harvard/iq/dataverse/ExternalIdentifier.java

@@ -12,7 +12,9 @@ public enum ExternalIdentifier {
     GND("GND", "https://d-nb.info/gnd/%s", "^1[01]?\\d{7}[0-9X]|[47]\\d{6}-\\d|[1-9]\\d{0,7}-[0-9X]|3\\d{7}[0-9X]$"),
     // note: DAI is missing from this list, because it doesn't have resolvable URL
     ResearcherID("ResearcherID", "https://publons.com/researcher/%s/", "^[A-Z\\d][A-Z\\d-]+[A-Z\\d]$"),
-    ScopusID("ScopusID", "https://www.scopus.com/authid/detail.uri?authorId=%s", "^\\d*$");
+    ScopusID("ScopusID", "https://www.scopus.com/authid/detail.uri?authorId=%s", "^\\d*$"),
+    //Requiring ROR to be URL form as we use it where there is no id type field and matching any 9 digit number starting with 0 seems a bit aggressive
+    ROR("ROR", "https://ror.org/%s", "^(https:\\/\\/ror.org\\/)0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}$");
 
     private String name;
     private String template;

src/main/java/edu/harvard/iq/dataverse/GlobalId.java

@@ -100,6 +100,13 @@ public String asURL() {
         }
         return null;
     }
+
+    public String asRawIdentifier() {
+        if (protocol == null || authority == null || identifier == null) {
+            return "";
+        }
+        return authority + separator + identifier;
+    }
 
 
 

src/main/java/edu/harvard/iq/dataverse/engine/command/impl/FinalizeDatasetPublicationCommand.java

@@ -211,7 +211,7 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
 
 	if (theDataset.getLatestVersion().getVersionState() != RELEASED) {
             // some imported datasets may already be released.
-
+	        theDataset.getLatestVersion().setVersionState(RELEASED);
             if (!datasetExternallyReleased) {
                 publicizeExternalIdentifier(theDataset, ctxt);
                 // Will throw a CommandException, unless successful.
@@ -220,7 +220,6 @@ public Dataset execute(CommandContext ctxt) throws CommandException {
                 // a failure - it will remove any locks, and it will send a
                 // proper notification to the user(s). 
             }
-            theDataset.getLatestVersion().setVersionState(RELEASED);
         }
 
         final Dataset ds = ctxt.em().merge(theDataset);

src/main/java/edu/harvard/iq/dataverse/export/DataCiteExporter.java

@@ -7,6 +7,7 @@
 import io.gdcc.spi.export.ExportException;
 import io.gdcc.spi.export.Exporter;
 import io.gdcc.spi.export.XMLExporter;
+import edu.harvard.iq.dataverse.pidproviders.doi.XmlMetadataTemplate;
 import edu.harvard.iq.dataverse.util.BundleUtil;
 import java.io.IOException;
 import java.io.OutputStream;
@@ -20,11 +21,7 @@
  */
 @AutoService(Exporter.class)
 public class DataCiteExporter implements XMLExporter {
-
-    private static String DEFAULT_XML_NAMESPACE = "http://datacite.org/schema/kernel-3";
-    private static String DEFAULT_XML_SCHEMALOCATION = "http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd";
-    private static String DEFAULT_XML_VERSION = "3.0";
-
+
     public static final String NAME = "Datacite";
 
     @Override
@@ -60,17 +57,17 @@ public Boolean isAvailableToUsers() {
 
     @Override
     public String getXMLNameSpace() {
-        return DataCiteExporter.DEFAULT_XML_NAMESPACE;
+        return XmlMetadataTemplate.XML_NAMESPACE;
     }
 
     @Override
     public String getXMLSchemaLocation() {
-        return DataCiteExporter.DEFAULT_XML_SCHEMALOCATION;
+        return XmlMetadataTemplate.XML_SCHEMA_LOCATION;
     }
 
     @Override
     public String getXMLSchemaVersion() {
-        return DataCiteExporter.DEFAULT_XML_VERSION;
+        return XmlMetadataTemplate.XML_SCHEMA_VERSION;
     }
 
 }