Refactorings 27

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

@@ -1,26 +1,5 @@
 package edu.harvard.iq.dataverse.persistence;
 
-import edu.harvard.iq.dataverse.persistence.datafile.DataFile;
-import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
-import edu.harvard.iq.dataverse.persistence.dataverse.Dataverse;
-import edu.harvard.iq.dataverse.persistence.user.AuthenticatedUser;
-import edu.harvard.iq.dataverse.persistence.user.RoleAssignment;
-
-import javax.persistence.Column;
-import javax.persistence.DiscriminatorColumn;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.Id;
-import javax.persistence.Index;
-import javax.persistence.Inheritance;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.UniqueConstraint;
-
 import static javax.persistence.CascadeType.ALL;
 import static javax.persistence.CascadeType.MERGE;
 import static javax.persistence.CascadeType.PERSIST;
@@ -32,41 +11,35 @@
 import static org.apache.commons.lang3.StringUtils.SPACE;
 import static org.apache.commons.lang3.StringUtils.isNotEmpty;
 
+import java.io.Serializable;
 import java.sql.Timestamp;
 import java.text.SimpleDateFormat;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.List;
 import java.util.Objects;
 import java.util.Set;
-import java.io.Serializable;
 
-/**
- * Base of the object hierarchy for "anything that can be inside a dataverse".
- *
- * @author michael
- */
+import javax.persistence.Column;
+import javax.persistence.DiscriminatorColumn;
+import javax.persistence.Entity;
+import javax.persistence.GeneratedValue;
+import javax.persistence.Id;
+import javax.persistence.Index;
+import javax.persistence.Inheritance;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.Table;
+import javax.persistence.Temporal;
+import javax.persistence.UniqueConstraint;
+
+import edu.harvard.iq.dataverse.persistence.datafile.DataFile;
+import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
+import edu.harvard.iq.dataverse.persistence.dataverse.Dataverse;
+import edu.harvard.iq.dataverse.persistence.user.AuthenticatedUser;
+import edu.harvard.iq.dataverse.persistence.user.RoleAssignment;
+
 @SuppressWarnings("serial")
-@NamedQueries({
-        @NamedQuery(name = "DvObject.findAll",
-                query = "SELECT o FROM DvObject o ORDER BY o.id"),
-        @NamedQuery(name = "DvObject.findById",
-                query = "SELECT o FROM DvObject o WHERE o.id=:id"),
-        @NamedQuery(name = "DvObject.ownedObjectsById",
-                query = "SELECT COUNT(obj) FROM DvObject obj WHERE obj.owner.id=:id"),
-        @NamedQuery(name = "DvObject.findByGlobalId",
-                query = "SELECT o FROM DvObject o WHERE o.identifier=:identifier and o.authority=:authority and o.protocol=:protocol and o.dtype=:dtype"),
-
-        @NamedQuery(name = "DvObject.findByAlternativeGlobalId",
-                query = "SELECT o FROM DvObject o, AlternativePersistentIdentifier a  WHERE o.id = a.dvObject.id and a.identifier=:identifier and a.authority=:authority and a.protocol=:protocol and o.dtype=:dtype"),
-
-        @NamedQuery(name = "DvObject.findByProtocolIdentifierAuthority",
-                query = "SELECT o FROM DvObject o WHERE o.identifier=:identifier and o.authority=:authority and o.protocol=:protocol"),
-        @NamedQuery(name = "DvObject.findByOwnerId",
-                query = "SELECT o FROM DvObject o WHERE o.owner.id=:ownerId"),
-        @NamedQuery(name = "DvObject.findByAuthenticatedUserId",
-                query = "SELECT o FROM DvObject o WHERE o.creator.id=:ownerId or o.releaseUser.id=:releaseUserId")
-})
 @Entity
 // Inheritance strategy "JOINED" will create 4 db tables - 
 // the top-level dvobject, with the common columns, and the 3 child classes - 

fairchive-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/DvObjectRepository.java

@@ -0,0 +1,70 @@
+package edu.harvard.iq.dataverse.persistence;
+
+import java.util.List;
+import java.util.Optional;
+
+import javax.ejb.Stateless;
+
+@Stateless
+public class DvObjectRepository extends JpaRepository<Long, DvObject> {
+
+    public DvObjectRepository() {
+        super(DvObject.class);
+    }
+
+    public List<DvObject> findByOwnerId(final Long id) {
+        return createQuery("SELECT o FROM DvObject o WHERE o.owner.id=:id")
+                .setParameter("id", id)
+                .getResultList();
+    }
+
+    public boolean hasData(final Long id) {
+        return this.em.createQuery(
+        		"SELECT COUNT(obj) FROM DvObject obj WHERE obj.owner.id=:id", 
+        		Long.class)
+                .setParameter("id", id)
+                .getSingleResult() > 0;
+    }
+
+    public List<DvObject> findByAuthenticatedUserId(final Long id) {
+        return createQuery(
+        		"SELECT o FROM DvObject o WHERE o.creator.id=:id or o.releaseUser.id=:id")
+                .setParameter("id", id)
+                .getResultList();
+    }
+
+    public Optional<DvObject> findByGlobalId(final String protocol, 
+    		final String authority, final String identifier) {
+        return getSingleResult(createQuery(
+        		"SELECT o FROM DvObject o " + 
+        		"WHERE o.identifier=:identifier and o.authority=:authority and o.protocol=:protocol")
+                .setParameter("protocol", protocol)
+                .setParameter("authority", authority)
+                .setParameter("identifier", identifier));
+    }
+
+    public Optional<DvObject> findByGlobalId(final String protocol, 
+    		final String authority, final String identifier, final String type) {
+        return getSingleResult(createQuery(
+        		"SELECT o FROM DvObject o " + 
+        		"WHERE o.identifier=:identifier and o.authority=:authority " + 
+        				"and o.protocol=:protocol and o.dtype=:type")
+                .setParameter("protocol", protocol)
+                .setParameter("authority", authority)
+                .setParameter("identifier", identifier)
+                .setParameter("type", type));
+    }
+
+    public Optional<DvObject> findByAlternativeGlobalId(final String protocol, 
+    		final String authority, final String identifier, final String type) {
+        return getSingleResult(createQuery(
+        		"SELECT o FROM DvObject o, AlternativePersistentIdentifier a " +
+        		" WHERE o.id = a.dvObject.id and a.identifier=:identifier " +
+        				" and a.authority=:authority and a.protocol=:protocol " +
+        				" and o.dtype=:type")
+                .setParameter("protocol", protocol)
+                .setParameter("authority", authority)
+                .setParameter("identifier", identifier)
+                .setParameter("type", type));
+    }
+}

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

@@ -1,15 +1,15 @@
 package edu.harvard.iq.dataverse.persistence.dataset;
 
-import org.apache.commons.lang3.StringUtils;
-
+import static java.util.stream.Collectors.toList;
 import static java.util.stream.Collectors.toMap;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
-import java.util.stream.Collectors;
+
+import org.apache.commons.lang3.StringUtils;
 
 public class FieldValueDivider {
     private static final FieldValueDivider EMPTY = new FieldValueDivider();
@@ -24,57 +24,57 @@ private FieldValueDivider() { }
     // -------------------- LOGIC --------------------
 
     @SuppressWarnings("unchecked")
-    public static FieldValueDivider create(DatasetFieldType fieldType) {
-        boolean hasDivider = fieldType.hasMetadata("divider");
-        if (!hasDivider) {
-            return EMPTY;
-        }
-        Map<String, Object> dividerData = (Map<String, Object>) fieldType.getMetadata("divider");
-        FieldValueDivider divider = new FieldValueDivider();
-        divider.sourceFieldName = (String) dividerData.get("source");
-        divider.fieldsToCopyNames.addAll((List<String>) dividerData.get("copy"));
-        return divider;
-    }
+	public static FieldValueDivider create(final DatasetFieldType fieldType) {
+		if (fieldType.hasMetadata("divider")) {
+			final Map<String, Object> dividerData = (Map<String, Object>) fieldType.getMetadata("divider");
+			final FieldValueDivider divider = new FieldValueDivider();
+			divider.sourceFieldName = (String) dividerData.get("source");
+			divider.fieldsToCopyNames.addAll((List<String>) dividerData.get("copy"));
+			return divider;
+		} else {
+			return EMPTY;
+		}
+	}
 
     public List<DatasetField> divide(DatasetField sourceCompound, String delimiter) {
-        List<DatasetField> fields = new ArrayList<>();
-        DatasetField sourceField = sourceCompound.getDatasetFieldsChildren().stream()
-                .filter(f -> sourceFieldName.equals(f.getTypeName()))
-                .findFirst().orElse(null);
-        if (sourceField == null) {
-            return fields;
-        }
-        List<String> values = splitValue(sourceField, delimiter);
-        Map<String, String> valuesToCopy = prepareValuesToCopy(sourceCompound);
-        for (int i = 0; i < values.size(); i++) {
-            fields.add(i == 0
-                    ? sourceCompound
-                    : DatasetField.createNewEmptyDatasetField(sourceCompound.getDatasetFieldType(), null));
-            for (DatasetField subfield : fields.get(i).getDatasetFieldsChildren()) {
-                String name = subfield.getTypeName();
-                if (sourceFieldName.equals(name)) {
-                    subfield.setFieldValue(values.get(i));
-                } else if (valuesToCopy.containsKey(name)) {
-                    subfield.setFieldValue(valuesToCopy.get(name));
-                }
-            }
-        }
-        return fields;
+        final List<DatasetField> result = new ArrayList<>();
+        sourceCompound.getDatasetFieldsChildren().stream()
+                .filter(f -> this.sourceFieldName.equals(f.getTypeName()))
+                .findFirst()
+                .map(sourceField -> splitValue(sourceField, delimiter))
+                .ifPresent(values -> {
+                    final Map<String, String> valuesToCopy = prepareValuesToCopy(sourceCompound);
+                    for (int i = 0; i < values.size(); i++) {
+                        result.add(i == 0
+                                ? sourceCompound
+                                : DatasetField.createNewEmptyDatasetField(sourceCompound.getDatasetFieldType(), null));
+                        
+                        for (DatasetField subfield : result.get(i).getDatasetFieldsChildren()) {
+                            String name = subfield.getTypeName();
+                            if (this.sourceFieldName.equals(name)) {
+                                subfield.setFieldValue(values.get(i));
+                            } else if (valuesToCopy.containsKey(name)) {
+                                subfield.setFieldValue(valuesToCopy.get(name));
+                            }
+                        }
+                    }
+                });
+        return result;
     }
 
     // -------------------- PRIVATE --------------------
 
-    private List<String> splitValue(DatasetField sourceField, String delimiter) {
-        String value = sourceField.getFieldValue().getOrElse(StringUtils.EMPTY);
+    private List<String> splitValue(final DatasetField sourceField, final String delimiter) {
+        final String value = sourceField.getFieldValue().getOrElse(StringUtils.EMPTY);
         return Arrays.stream(value.split(delimiter))
                 .filter(StringUtils::isNotBlank)
                 .map(String::trim)
-                .collect(Collectors.toList());
+                .collect(toList());
     }
 
-    private Map<String, String> prepareValuesToCopy(DatasetField sourceCompound) {
+    private Map<String, String> prepareValuesToCopy(final DatasetField sourceCompound) {
         return sourceCompound.getDatasetFieldsChildren().stream()
-                .filter(f -> fieldsToCopyNames.contains(f.getTypeName())
+                .filter(f -> this.fieldsToCopyNames.contains(f.getTypeName())
                         && isNotBlank(f.getFieldValue().getOrElse(StringUtils.EMPTY)))
                 .collect(toMap(DatasetField::getTypeName, f -> f.getFieldValue().get(), (prev, next) -> next));
     }

fairchive-webapp/src/main/java/edu/harvard/iq/dataverse/DataFileServiceBean.java

@@ -37,6 +37,7 @@
 import edu.harvard.iq.dataverse.dataaccess.ImageThumbConverter;
 import edu.harvard.iq.dataverse.dataaccess.StorageIO;
 import edu.harvard.iq.dataverse.globalid.GlobalIdServiceBean;
+import edu.harvard.iq.dataverse.persistence.DvObjectRepository;
 import edu.harvard.iq.dataverse.persistence.GlobalId;
 import edu.harvard.iq.dataverse.persistence.datafile.DataFile;
 import edu.harvard.iq.dataverse.persistence.datafile.DataFileRepository;
@@ -73,6 +74,8 @@ public class DataFileServiceBean implements Serializable {
     private DataFileRepository fileRepo;
     @Inject
     private FileMetadataRepository fileMetadataRepo;
+    @Inject
+    private DvObjectRepository dvObjectRepository;
 
     @PersistenceContext(unitName = "VDCNet-ejbPU")
     private EntityManager em;
@@ -87,7 +90,7 @@ public Optional<DataFile> find(final Long id) {
 
     public DataFile findByGlobalId(final String globalId) {
         return (DataFile) this.dvObjectService.findByGlobalId(globalId, 
-        		DataFile.DATAFILE_DTYPE_STRING);
+        		DataFile.DATAFILE_DTYPE_STRING).orElse(null);
     }
 
     public Optional<DataFile> findReplacementFile(final Long previousFileId) {
@@ -432,20 +435,17 @@ public String generateDataFileIdentifier(DataFile datafile, GlobalIdServiceBean
      *
      * @return {@code true} iff the global identifier is unique.
      */
-    public boolean isGlobalIdUnique(String userIdentifier, DataFile datafile, GlobalIdServiceBean idServiceBean) {
+    public boolean isGlobalIdUnique(String userIdentifier, DataFile datafile, 
+    		GlobalIdServiceBean idServiceBean) {
         String testAuthority = datafile.getAuthority() != null
                 ? datafile.getAuthority()
                 : settingsService.getValueForKey(Authority);
         String testProtocol = datafile.getProtocol() != null
                 ? datafile.getProtocol()
                 : settingsService.getValueForKey(Protocol);
 
-        boolean unique = em.createNamedQuery("DvObject.findByProtocolIdentifierAuthority")
-                      .setParameter("protocol", testProtocol)
-                      .setParameter("authority", testAuthority)
-                      .setParameter("identifier", userIdentifier)
-                      .getResultList().isEmpty();
-
+        boolean unique = ! this.dvObjectRepository.
+        		findByGlobalId(testProtocol, testAuthority, userIdentifier).isPresent();
         try {
             if (idServiceBean.alreadyExists(new GlobalId(testProtocol,
                     testAuthority, userIdentifier))) {

fairchive-webapp/src/main/java/edu/harvard/iq/dataverse/DvObjectDao.java

@@ -9,6 +9,7 @@
 
 import edu.harvard.iq.dataverse.dataset.DatasetService;
 import edu.harvard.iq.dataverse.persistence.DvObject;
+import edu.harvard.iq.dataverse.persistence.DvObjectRepository;
 import edu.harvard.iq.dataverse.persistence.dataset.Dataset;
 import edu.harvard.iq.dataverse.persistence.dataverse.Dataverse;
 
@@ -17,11 +18,15 @@ public class DvObjectDao {
 
     private DataverseDao dataverseDao;
     private DatasetService datasetService;
+    private DvObjectRepository dvObjectRepository;
 
     @Inject
-    public DvObjectDao(DataverseDao dataverseDao, DatasetService datasetService) {
+    public DvObjectDao(final DataverseDao dataverseDao, 
+    		final DatasetService datasetService, 
+    		final DvObjectRepository dvObjectRepository) {
         this.dataverseDao = dataverseDao;
         this.datasetService = datasetService;
+        this.dvObjectRepository = dvObjectRepository;
     }
 
     public DvObjectDao() {
@@ -40,16 +45,10 @@ public DvObjectDao() {
      */
     public DvObject findDvo(String id) {
         if (isNumeric(id)) {
-            return this.findDvo(Long.valueOf(id));
+            return this.dvObjectRepository.getById(Long.valueOf(id));
         } else {
-            Dataverse d = dataverseDao.findByAlias(id);
+            final Dataverse d = dataverseDao.findByAlias(id);
             return (d != null) ? d : datasetService.findByGlobalId(id);
         }
     }
-
-    private DvObject findDvo(Long id) {
-        return em.createNamedQuery("DvObject.findById", DvObject.class)
-                 .setParameter("id", id)
-                 .getSingleResult();
-    }
 }