small refactorings

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/DvObject.java

@@ -208,6 +208,11 @@ public void setModificationTime(Timestamp modificationTime) {
     public Timestamp getIndexTime() {
         return indexTime;
     }
+
+    public boolean isIndexed() {
+
+        return this.indexTime != null;
+    }
 
     /**
      * indexTime is used for comparison with modificationTime so we know if the
@@ -329,6 +334,12 @@ public void setIdentifier(String identifier) {
     public boolean isIdentifierRegistered() {
         return identifierRegistered;
     }
+
+    public boolean isStale() {
+        return isIndexed()
+            ? this.indexTime.before(this.modificationTime)
+            : true;
+    }
 
     public void setIdentifierRegistered(boolean identifierRegistered) {
         this.identifierRegistered = identifierRegistered;

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/DvObjectContainer.java

@@ -18,7 +18,7 @@ public void setOwner(Dataverse owner) {
 
     @Override
     public Dataverse getOwner() {
-        return super.getOwner() != null ? (Dataverse) super.getOwner() : null;
+        return (Dataverse) super.getOwner();
     }
 
     public abstract boolean isPermissionRoot();

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/dataset/Dataset.java

@@ -9,6 +9,7 @@
 import edu.harvard.iq.dataverse.persistence.datafile.DataFileCategory;
 import edu.harvard.iq.dataverse.persistence.datafile.FileMetadata;
 import edu.harvard.iq.dataverse.persistence.datafile.license.FileTermsOfUse;
+import edu.harvard.iq.dataverse.persistence.dataverse.Dataverse;
 import edu.harvard.iq.dataverse.persistence.dataverse.link.DatasetLinkingDataverse;
 import edu.harvard.iq.dataverse.persistence.guestbook.Guestbook;
 import edu.harvard.iq.dataverse.persistence.harvest.HarvestStyle;
@@ -336,6 +337,10 @@ public DatasetVersion getLatestVersionForCopy() {
     public List<DatasetVersion> getVersions() {
         return versions;
     }
+
+    public Dataverse getRoot() {
+        return getOwner().getRoot();
+    }
 
     public void setVersions(List<DatasetVersion> versions) {
         this.versions = versions;
@@ -412,13 +417,12 @@ public boolean containsReleasedVersion() {
         return isReleased() && getReleasedVersion() != null;
     }
 
-    public DatasetVersion getReleasedVersion() {
-        for (DatasetVersion version : getVersions()) {
-            if (version.isReleased()) {
-                return version;
-            }
-        }
-        return null;
+    public DatasetVersion getReleasedVersion() { 
+        return getVersions()
+                .stream()
+                .filter(DatasetVersion::isReleased)
+                .findFirst()
+                .orElse(null);
     }
 
     public List<DataFileCategory> getCategories() {

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/dataset/DatasetVersion.java

@@ -61,6 +61,8 @@
 import java.util.stream.Stream;
 
 import static com.google.common.collect.Lists.newArrayList;
+import static org.apache.commons.lang3.StringUtils.EMPTY;
+import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 /**
  * @author skraffmiller
@@ -414,7 +416,7 @@ public VersionState getPriorVersionState() {
     public String getFriendlyVersionNumber() {
         return isDraft()
                 ? "DRAFT"
-                : versionNumber.toString() + "." + minorVersionNumber.toString();
+                : versionNumber + "." + minorVersionNumber;
     }
 
     public boolean isReleased() {
@@ -668,13 +670,8 @@ public String getDistributionDate() {
 
     // TODO: Consider renaming this method since it's also used for getting the "provider" for Schema.org JSON-LD.
     public String getRootDataverseNameForCitation() {
-        Dataverse root = dataset.getOwner();
-        while (root.getOwner() != null) {
-            root = root.getOwner();
-        }
-        String rootDataverseName = root.getName();
-        return StringUtils.isNotBlank(rootDataverseName)
-                ? rootDataverseName : StringUtils.EMPTY;
+        final String rootDataverseName = this.dataset.getRoot().getName();
+        return isNotBlank(rootDataverseName) ? rootDataverseName : EMPTY;
     }
 
     public String getAuthorsStr() {

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/dataverse/Dataverse.java

@@ -372,6 +372,10 @@ public boolean isHarvested() {
     public boolean isRoot() {
         return this.getOwner() == null;
     }
+
+    public boolean isNotRoot() {
+        return this.getOwner() != null;
+    }
 
     public List<Guestbook> getParentGuestbooks() {
         List<Guestbook> retList = new ArrayList<>();
@@ -759,6 +763,10 @@ public List<Dataverse> getOwners() {
         }
         return owners;
     }
+
+    public Dataverse getRoot() {
+        return isRoot() ? this : getOwner().getRoot();
+    }
 
     @Override
     public boolean equals(Object object) {

dataverse-persistence/src/test/java/edu/harvard/iq/dataverse/persistence/dataset/DatasetTest.java

@@ -1,22 +1,26 @@
 package edu.harvard.iq.dataverse.persistence.dataset;
 
-import com.google.common.collect.Lists;
-import edu.harvard.iq.dataverse.persistence.MocksFactory;
-import edu.harvard.iq.dataverse.persistence.dataset.DatasetVersion.VersionState;
-import org.junit.jupiter.api.Test;
-import org.junit.jupiter.params.ParameterizedTest;
-import org.junit.jupiter.params.provider.Arguments;
-import org.junit.jupiter.params.provider.MethodSource;
+import static org.assertj.core.api.Assertions.assertThat;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import java.sql.Timestamp;
 import java.time.Instant;
 import java.util.List;
 import java.util.stream.Stream;
 
-import static org.junit.jupiter.api.Assertions.assertNull;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertFalse;
-import static org.junit.jupiter.api.Assertions.assertTrue;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+
+import com.google.common.collect.Lists;
+
+import edu.harvard.iq.dataverse.persistence.MocksFactory;
+import edu.harvard.iq.dataverse.persistence.dataset.DatasetVersion.VersionState;
+import edu.harvard.iq.dataverse.persistence.dataverse.Dataverse;
 
 
 /**
@@ -115,6 +119,28 @@ public void testLocksManagement() {
         assertFalse(sut.isLocked());
 
     }
+
+    @Test
+    public void testGetRoot() {
+
+        Dataverse root = new Dataverse();
+        Dataverse child = new Dataverse();
+        child.setOwner(root);
+        Dataset grandChild = new Dataset();
+        grandChild.setOwner(child);
+
+        assertThat(root.getOwner()).isNull();
+        assertThat(root.isRoot()).isTrue();
+        assertThat(root.isNotRoot()).isFalse();
+
+        assertThat(child.getOwner()).isSameAs(root);
+        assertThat(child.isRoot()).isFalse();
+        assertThat(child.isNotRoot()).isTrue();       
+        assertThat(child.getRoot()).isSameAs(root);
+
+        assertThat(grandChild.getOwner()).isSameAs(child);
+        assertThat(grandChild.getRoot()).isSameAs(root);
+    }
 
     // -------------------- PRIVATE --------------------
 

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/DatasetDao.java

@@ -7,6 +7,7 @@
 import edu.harvard.iq.dataverse.engine.command.DataverseRequest;
 import edu.harvard.iq.dataverse.engine.command.impl.FinalizeDatasetPublicationCommand;
 import edu.harvard.iq.dataverse.globalid.GlobalIdServiceBean;
+import edu.harvard.iq.dataverse.persistence.DvObject;
 import edu.harvard.iq.dataverse.persistence.datafile.DataFile;
 import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
 import edu.harvard.iq.dataverse.persistence.dataset.DatasetField;
@@ -34,6 +35,10 @@
 import javax.persistence.StoredProcedureQuery;
 import javax.persistence.TemporalType;
 import javax.persistence.TypedQuery;
+
+import static java.lang.Math.max;
+import static java.util.stream.Collectors.toList;
+
 import java.io.InputStream;
 import java.sql.Timestamp;
 import java.time.Instant;
@@ -50,6 +55,7 @@
  */
 
 
+@SuppressWarnings("serial")
 @Stateless
 public class DatasetDao implements java.io.Serializable {
 
@@ -90,6 +96,10 @@ public List<Dataset> findByOwnerId(Long ownerId) {
     public List<Dataset> findAll() {
         return em.createQuery("select object(o) from Dataset as o order by o.id", Dataset.class).getResultList();
     }
+
+    public List<Dataset> findStaleOrMissingDatasets() {
+        return findAll().stream().filter(DvObject::isStale).collect(toList());
+    }
 
     public List<Dataset> findNotIndexedAfterEmbargo() {
         TypedQuery<Dataset> typedQuery = em.createQuery("select d from Dataset d, DvObject o where d.id = o.id and d.embargoDate < :actualTimestamp and d.embargoDate > o.indexTime", Dataset.class);
@@ -115,10 +125,7 @@ public List<Long> findAllUnindexed() {
      * @see DataverseDao#findAllOrSubset(long, long, boolean)
      */
     public List<Long> findAllOrSubset(long numPartitions, long partitionId, boolean skipIndexed) {
-        if (numPartitions < 1) {
-            long saneNumPartitions = 1;
-            numPartitions = saneNumPartitions;
-        }
+        numPartitions = max(numPartitions, 1);
         String skipClause = skipIndexed ? "AND o.indexTime is null " : "";
         TypedQuery<Long> typedQuery = em.createQuery("SELECT o.id FROM Dataset o WHERE MOD( o.id, :numPartitions) = :partitionId " +
                                                              skipClause +
@@ -216,9 +223,8 @@ public boolean isIdentifierUnique(String userIdentifier, Dataset dataset, Global
             return !persistentIdSvc.alreadyExists(dataset);
         } catch (Exception e) {
             //we can live with failure - means identifier not found remotely
+            return true;
         }
-
-        return true;
     }
 
     public boolean isIdentifierLocallyUnique(Dataset dataset) {

dataverse-webapp/src/main/java/edu/harvard/iq/dataverse/DataverseDao.java

@@ -27,6 +27,10 @@
 import javax.persistence.NonUniqueResultException;
 import javax.persistence.PersistenceContext;
 import javax.persistence.TypedQuery;
+
+import static java.lang.Math.max;
+import static java.util.stream.Collectors.toList;
+
 import java.io.File;
 import java.sql.Timestamp;
 import java.util.ArrayList;
@@ -37,6 +41,7 @@
 import java.util.Properties;
 import java.util.concurrent.Future;
 import java.util.logging.Logger;
+import java.util.stream.Collectors;
 
 /**
  * @author gdurand
@@ -95,6 +100,18 @@ public Dataverse find(Object pk) {
     public List<Dataverse> findAll() {
         return em.createNamedQuery("Dataverse.findAll").getResultList();
     }
+
+    /**
+     * @return Dataverses that should be reindexed either because they have
+     * never been indexed or their index time is before their modification time.
+     */
+    public List<Dataverse> findStaleOrMissingDataverses() {
+        return findAll()
+                .stream()
+                .filter(Dataverse::isNotRoot)
+                .filter(Dataverse::isStale)
+                .collect(toList());
+    }
 
     /**
      * @param numPartitions The number of partitions you intend to split the
@@ -109,10 +126,7 @@ public List<Dataverse> findAll() {
      * Otherwise, a subset of dataverses.
      */
     public List<Dataverse> findAllOrSubset(long numPartitions, long partitionId, boolean skipIndexed) {
-        if (numPartitions < 1) {
-            long saneNumPartitions = 1;
-            numPartitions = saneNumPartitions;
-        }
+        numPartitions = max(numPartitions, 1); 
         String skipClause = skipIndexed ? "AND o.indexTime is null " : "";
         TypedQuery<Dataverse> typedQuery = em.createQuery("SELECT OBJECT(o) FROM Dataverse AS o WHERE MOD( o.id, :numPartitions) = :partitionId " +
                                                                   skipClause +
@@ -123,15 +137,16 @@ public List<Dataverse> findAllOrSubset(long numPartitions, long partitionId, boo
     }
 
     public List<Long> findDataverseIdsForIndexing(boolean skipIndexed) {
-        if (skipIndexed) {
-            return em.createQuery("SELECT o.id FROM Dataverse o WHERE o.indexTime IS null ORDER BY o.id", Long.class).getResultList();
-        }
-        return em.createQuery("SELECT o.id FROM Dataverse o ORDER BY o.id", Long.class).getResultList();
+        final String query = skipIndexed 
+                ? "SELECT o.id FROM Dataverse o WHERE o.indexTime IS null ORDER BY o.id"
+                : "SELECT o.id FROM Dataverse o ORDER BY o.id";
+        return em.createQuery(query, Long.class).getResultList();
 
     }
 
     public List<Dataverse> findByOwnerId(Long ownerId) {
-        return em.createNamedQuery("Dataverse.findByOwnerId").setParameter("ownerId", ownerId).getResultList();
+        return em.createNamedQuery("Dataverse.findByOwnerId", Dataverse.class)
+                .setParameter("ownerId", ownerId).getResultList();
     }
 
     public List<Long> findIdsByOwnerId(Long ownerId) {
@@ -348,16 +363,12 @@ public List<Long> findAllDataverseDataverseChildren(Long dvId) {
         // get list of Dataverse children
         List<Long> dataverseChildren = findIdsByOwnerId(dvId);
 
-        if (dataverseChildren == null) {
-            return dataverseChildren;
-        } else {
-            List<Long> newChildren = new ArrayList<>();
-            for (Long childDvId : dataverseChildren) {
-                newChildren.addAll(findAllDataverseDataverseChildren(childDvId));
-            }
-            dataverseChildren.addAll(newChildren);
-            return dataverseChildren;
+        List<Long> newChildren = new ArrayList<>();
+        for (Long childDvId : dataverseChildren) {
+            newChildren.addAll(findAllDataverseDataverseChildren(childDvId));
         }
+        dataverseChildren.addAll(newChildren);
+        return dataverseChildren;
     }
 
     // function to recursively find ids of all children of a dataverse that are