Updates for compatibility with DSpace 9.3

pom.xml

@@ -331,8 +331,8 @@
                     <artifactId>jaxb-api</artifactId>
                 </exclusion>
                 <exclusion>
-                    <groupId>log4j</groupId>
-                    <artifactId>log4j</artifactId>
+                    <groupId>org.apache.logging.log4j</groupId>
+                    <artifactId>log4j-core</artifactId>
                 </exclusion>
                 <exclusion>
                     <groupId>org.glassfish.jaxb</groupId>

src/main/java/org/dspace/ctask/replicate/AbstractPackagerTask.java

@@ -25,6 +25,8 @@
  * @see org.dspace.content.packager.PackageIngester
  */
 public abstract class AbstractPackagerTask extends AbstractCurationTask {
+    private static final Logger log = LogManager.getLogger();
+
     // Name of recursive mode option configurable in curation task configuration file
     private final String recursiveMode = "recursiveMode";
 
@@ -34,8 +36,6 @@ public abstract class AbstractPackagerTask extends AbstractCurationTask {
     // Name of useCollectionTemplate option configurable in curation task configuration file
     private final String useCollectionTemplate = "useCollectionTemplate";
 
-    private static Logger log = LogManager.getLogger();
-
     /**
      * Loads pre-configured PackageParameters settings from a given Module
      * configuration file (specified by 'moduleName').
@@ -47,7 +47,7 @@ public abstract class AbstractPackagerTask extends AbstractCurationTask {
      * <p>
      * Valid 'options' include all packager options supported by the
      * Packager class, e.g. AIP packagers minimally support these options:
-     * https://wiki.lyrasis.org/display/DSDOC6x/AIP+Backup+and+Restore#AIPBackupandRestore-AdditionalPackagerOptions
+     * https://wiki.lyrasis.org/display/DSDOC9x/AIP+Backup+and+Restore#AIPBackupandRestore-AdditionalPackagerOptions
      * <p>
      * Please note that different Packager classes will support different options.
      * You should determine which options are valid for your Packager class
@@ -100,7 +100,7 @@ protected PackageParameters loadPackagerParameters(String moduleName) {
                         pkgParams.addProperty(option, value);
                     }
 
-                    log.debug("Set package parameter property <" + option + "> to value <" + value + ">");
+                    log.debug("Set package parameter property <{}> to value <{}>", option, value);
                 }
             }
 

src/main/java/org/dspace/ctask/replicate/BagItReplaceWithAIP.java

@@ -40,17 +40,16 @@
  */
 @Mutative
 public class BagItReplaceWithAIP extends AbstractCurationTask {
+    private final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
+    private final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
+    private final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    private final SiteService siteService = ContentServiceFactory.getInstance().getSiteService();
 
     private String archFmt;
 
     // Group where all AIPs are stored
     private String storeGroupName;
 
-    private CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
-    private CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
-    private ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-    private SiteService siteService = ContentServiceFactory.getInstance().getSiteService();
-
     @Override
     public void init(Curator curator, String taskId) throws IOException {
         super.init(curator, taskId);

src/main/java/org/dspace/ctask/replicate/BagItReplicateConsumer.java

@@ -62,13 +62,13 @@
  * @author richardrodgers
  */
 public class BagItReplicateConsumer implements Consumer {
-    private Logger log = LogManager.getLogger();
+    private final Logger log = LogManager.getLogger();
 
-    private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
-    private PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
-    private CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
-    private CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
-    private ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    private final ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
+    private final PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
+    private final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
+    private final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
+    private final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
     private ReplicaManager repMan = null;
     private TaskQueue taskQueue = null;

src/main/java/org/dspace/ctask/replicate/BagItRestoreFromAIP.java

@@ -57,8 +57,13 @@
 @Distributive
 @Mutative
 public class BagItRestoreFromAIP extends AbstractCurationTask {
+    private static final Logger log = LogManager.getLogger();
+
+    private final EmbargoService embargoService = EmbargoServiceFactory.getInstance().getEmbargoService();
+    private final WorkspaceItemService workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService();
+    private final InstallItemService installItemService = ContentServiceFactory.getInstance().getInstallItemService();
+    private final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
 
-    private static Logger log = LogManager.getLogger();
     private String archFmt;
 
     // Group where all AIPs are stored
@@ -67,11 +72,6 @@ public class BagItRestoreFromAIP extends AbstractCurationTask {
     // Group where object deletion catalog/records are stored
     private String deleteGroupName;
 
-    private EmbargoService embargoService = EmbargoServiceFactory.getInstance().getEmbargoService();
-    private WorkspaceItemService workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService();
-    private InstallItemService installItemService = ContentServiceFactory.getInstance().getInstallItemService();
-    private CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
-
     @Override
     public void init(Curator curator, String taskId) throws IOException {
         super.init(curator, taskId);
@@ -224,10 +224,10 @@ private void recoverItem(Context ctx, File archive, String objId, Properties pro
             packer.unpack(archive);
             // Install item
             Item item = installItemService.restoreItem(ctx, wi, objId);
-            String colls = props.getProperty(OTHER_IDS);
-            if (colls != null) {
+            String collections = props.getProperty(OTHER_IDS);
+            if (collections != null) {
                 // reset linked collections
-                for (String link : colls.split(",")) {
+                for (String link : collections.split(",")) {
                     Collection linkC = (Collection) handleService.resolveToObject(ctx, link);
                     collectionService.addItem(ctx, linkC, item);
                 }
@@ -251,17 +251,21 @@ private void recoverItem(Context ctx, File archive, String objId, Properties pro
      * @throws IOException if IO error
      */
     private void recoverCollection(Context ctx, File archive, String collId, String commId) throws IOException {
-        Collection coll = null;
         try {
             if (commId != null) {
-                Community pcomm = (Community) handleService.resolveToObject(ctx, commId);
-                coll = collectionService.create(ctx, pcomm, collId);
+                Community parentCommunity = (Community) handleService.resolveToObject(ctx, commId);
+                Collection collection = collectionService.create(ctx, parentCommunity, collId);
+
+                if (collection != null) {
+                    // update with AIP data
+                    Packer packer = PackerFactory.instance(ctx, collection);
+                    packer.unpack(archive);
+                } else {
+                    log.error("Unable to restore collection {} because it could not be found.", collId);
+                }
             } else {
-                log.error("Collection '" + collId + "' lacks parent community");
+                log.error("Collection '{}' lacks parent community", collId);
             }
-            // update with AIP data
-            Packer packer = PackerFactory.instance(ctx, coll);
-            packer.unpack(archive);
         } catch (AuthorizeException | SQLException authE) {
             throw new IOException(authE);
         }
@@ -277,16 +281,17 @@ private void recoverCollection(Context ctx, File archive, String collId, String
      */
     private void recoverCommunity(Context ctx, File archive, String commId, String parentId) throws IOException {
         // if not top-level, have parent create it
-        Community comm = null;
+        Community community = null;
         try {
             if (parentId != null) {
-                Community pcomm = (Community) handleService.resolveToObject(ctx, parentId);
-                comm = communityService.createSubcommunity(ctx, pcomm, commId);
+                Community parentCommunity = (Community) handleService.resolveToObject(ctx, parentId);
+                community = communityService.createSubcommunity(ctx, parentCommunity, commId);
             } else {
-                comm = communityService.create(null, ctx, commId);
+                community = communityService.create(null, ctx, commId);
             }
+
             // update with AIP data
-            Packer packer = PackerFactory.instance(ctx, comm);
+            Packer packer = PackerFactory.instance(ctx, community);
             packer.unpack(archive);
         } catch (AuthorizeException | SQLException authE) {
             throw new IOException(authE);

src/main/java/org/dspace/ctask/replicate/METSReplicateConsumer.java

@@ -82,14 +82,14 @@
  * @author richardrodgers
  */
 public class METSReplicateConsumer implements Consumer {
-    private Logger log = LogManager.getLogger();
-
-    private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
-    private PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
-    private SiteService siteService = ContentServiceFactory.getInstance().getSiteService();
-    private CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
-    private CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
-    private ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    private final Logger log = LogManager.getLogger();
+
+    private final ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
+    private final PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
+    private final SiteService siteService = ContentServiceFactory.getInstance().getSiteService();
+    private final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
+    private final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
+    private final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
     private ReplicaManager repMan = null;
     private TaskQueue taskQueue = null;

src/main/java/org/dspace/ctask/replicate/METSRestoreFromAIP.java

@@ -33,7 +33,7 @@
 @Distributive
 @Mutative
 public class METSRestoreFromAIP extends AbstractPackagerTask {
-    private Logger log = LogManager.getLogger();
+    private final Logger log = LogManager.getLogger();
 
     private String archFmt;
 

src/main/java/org/dspace/ctask/replicate/MoveToTrashSingleAIP.java

@@ -21,7 +21,7 @@
 
 /**
  * MoveToTrashSingleAIP task moves a single AIP from one group (folder) in external
- * storage to another group (folder). Currently it always moves content
+ * storage to another group (folder). Currently, it always moves content
  * from the 'group.aip.name' store to the 'group.delete.name' store, essentially
  * moving the content into a "trash" folder.
  * <P>
@@ -37,8 +37,6 @@
  */
 @Distributive
 public class MoveToTrashSingleAIP extends AbstractCurationTask {
-    private static Logger log = LogManager.getLogger();
-
     // Source and destination group where AIP will be moved to
     private String srcGroupName;
     private String destGroupName;

src/main/java/org/dspace/ctask/replicate/RemoveAIP.java

@@ -41,6 +41,9 @@
 public class RemoveAIP extends AbstractCurationTask {
     private static final Logger log = LogManager.getLogger();
 
+    private final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
+    private final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+
     private String archFmt;
 
     // Group where all AIPs are stored
@@ -49,9 +52,6 @@ public class RemoveAIP extends AbstractCurationTask {
     // Group where object deletion catalog/records are stored
     private String deleteGroupName;
 
-    private CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
-    private ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-
     @Override
     public void init(Curator curator, String taskId) throws IOException {
         super.init(curator, taskId);

src/main/java/org/dspace/ctask/replicate/ReplicaManager.java

@@ -40,11 +40,11 @@
  * @author richardrodgers
  */
 public class ReplicaManager {
-    private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
-    private PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
-    private HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
+    private final ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
+    private final PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
+    private final HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
 
-    private Logger log = LogManager.getLogger();
+    private final Logger log = LogManager.getLogger();
     // singleton instance
     private static ReplicaManager instance = null;
     // the replica provider

src/main/java/org/dspace/ctask/replicate/checkm/RemoveManifest.java

@@ -42,13 +42,12 @@
  */
 @Distributive
 public class RemoveManifest extends AbstractCurationTask {
+    private final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
+    private final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
     // Group where all Manifests are stored
     private String manifestGroupName;
 
-    private CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
-    private ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-
     @Override
     public void init(Curator curator, String taskId) throws IOException {
         super.init(curator, taskId);
@@ -98,27 +97,27 @@ private void remove(Context context, ReplicaManager repMan, DSpaceObject dso) th
         repMan.removeObject(manifestGroupName, objId);
         report("Removing manifest for: " + objId);
         if (dso instanceof Collection) {
-            Collection coll = (Collection)dso;
+            Collection collection = (Collection)dso;
             try {
-                Iterator<Item> iter = itemService.findByCollection(context, coll);
+                Iterator<Item> iter = itemService.findByCollection(context, collection);
                 while (iter.hasNext()) {
                     remove(context, repMan, iter.next());
                 }
             } catch (SQLException sqlE) {
                 throw new IOException(sqlE);
             }
         } else if (dso instanceof Community) {
-            Community comm = (Community)dso;
-            for (Community subcomm : comm.getSubcommunities()) {
-                remove(context, repMan, subcomm);
+            Community community = (Community)dso;
+            for (Community subCommunity : community.getSubcommunities()) {
+                remove(context, repMan, subCommunity);
             }
-            for (Collection coll : comm.getCollections()) {
+            for (Collection coll : community.getCollections()) {
                 remove(context, repMan, coll);
             }
         } else if (dso instanceof Site) {
             List<Community> topCommunities = communityService.findAllTop(context);
-            for (Community subcomm : topCommunities) {
-                remove(context, repMan, subcomm);
+            for (Community subCommunity : topCommunities) {
+                remove(context, repMan, subCommunity);
             }
         }
     }

src/main/java/org/dspace/ctask/replicate/checkm/TransmitManifest.java

@@ -50,6 +50,10 @@
  */
 @Distributive
 public class TransmitManifest extends AbstractCurationTask {
+    private static final Logger log = LogManager.getLogger();
+
+    private final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
+    private final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
     // Version of CDL Checkm spec that this manifest conforms to
     private static final String CKM_VSN = "0.7";
@@ -62,11 +66,6 @@ public class TransmitManifest extends AbstractCurationTask {
     // Group where all Manifests will be stored
     private String manifestGroupName;
 
-    private static Logger log = LogManager.getLogger();
-
-    private CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
-    private ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-
     @Override
     public void init(Curator curator, String taskId) throws IOException {
         super.init(curator, taskId);

src/main/java/org/dspace/ctask/replicate/store/LocalObjectStore.java

@@ -103,12 +103,18 @@ public long transferObject(String group, File file) throws IOException {
 
         File archDir = new File(storeDir, group);
         if (!archDir.isDirectory()) {
-            archDir.mkdirs();
+            boolean successful = archDir.mkdirs();
+            if (!successful) {
+                log.warn("Cannot create directory: '{}'.", archDir);
+            }
         }
 
         File archFile = new File(archDir, file.getName());
         if (archFile.exists()) {
-            archFile.delete();
+            boolean successful = archFile.delete();
+            if (!successful) {
+                log.warn("Cannot delete archive file: '{}'.", archFile);
+            }
         }
 
         if (!file.renameTo(archFile)) {

src/main/java/org/dspace/pack/bagit/BagItAipReader.java

@@ -58,7 +58,6 @@
  * @since 2020-03-19
  */
 public class BagItAipReader {
-
     private final Logger logger = LoggerFactory.getLogger(BagItAipReader.class);
 
     private final String dataDirectory = "data";