Merge branch 'master' of https://github.com/DSpace/DSpace into mydspace_clean

.travis.yml

@@ -26,19 +26,20 @@ before_install:
 # Skip install stage, as we'll do it below
 install: "echo 'Skipping install stage, dependencies will be downloaded during build and test stages.'"
 
-# Two stage Build and Test
+# Build DSpace and run both Unit and Integration Tests
-# 1. Install & Unit Test APIs
-# 2. Assemble DSpace
 script:
-  # 1. [Install & Unit Test] Check source code licenses and run source code Unit Tests
+  # Summary of flags used (below):
   #     license:check           => Validate all source code license headers
   #     -Dmaven.test.skip=false => Enable DSpace Unit Tests
   #     -DskipITs=false         => Enable DSpace Integration Tests
-  #        -P !assembly            => Skip normal assembly (as it can be memory intensive)
+  #     -P !assembly            => Skip assembly of "dspace-installer" directory (as it can be memory intensive)
   #     -B                      => Maven batch/non-interactive mode (recommended for CI)
   #     -V                      => Display Maven version info before build
   #     -Dsurefire.rerunFailingTestsCount=2 => try again for flakey tests, and keep track of/report on number of retries
   - "mvn clean install license:check -Dmaven.test.skip=false -DskipITs=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
-  # 2. [Assemble DSpace] Ensure overlay & assembly process works (from [src]/dspace/)
+
-  #        -P !assembly => SKIP the actual building of [src]/dspace/dspace-installer (as it can be memory intensive)
+# After a successful build and test (see 'script'), send code coverage reports to coveralls.io
-  - "cd dspace && mvn package -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
+# These code coverage reports are generated by jacoco-maven-plugin (during test process above).
+after_success:
+  # Run "verify", enabling the "coveralls" profile. This sends our reports to coveralls.io (see coveralls-maven-plugin)
+  - "cd dspace && mvn verify -P coveralls"

Dockerfile.jdk8

@@ -15,7 +15,8 @@ WORKDIR /app
 
 # The dspace-install directory will be written to /install
 RUN mkdir /install \
-    && chown -Rv dspace: /install
+    && chown -Rv dspace: /install \
+    && chown -Rv dspace: /app
 
 USER dspace
 

Dockerfile.jdk8-test

@@ -15,7 +15,8 @@ WORKDIR /app
 
 # The dspace-install directory will be written to /install
 RUN mkdir /install \
-    && chown -Rv dspace: /install
+    && chown -Rv dspace: /install \
+    && chown -Rv dspace: /app
 
 USER dspace
 

dspace-api/pom.xml

@@ -587,7 +587,7 @@
         <dependency>
             <groupId>org.apache.solr</groupId>
             <artifactId>solr-solrj</artifactId>
-            <version>${solr.version}</version>
+            <version>${solr.client.version}</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -622,7 +622,7 @@
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-core</artifactId>
-            <version>4.10.4</version>
+            <version>${solr.client.version}</version>
         </dependency>
 
         <dependency>

dspace-api/src/main/java/org/dspace/app/util/IndexVersion.java

@@ -121,20 +121,24 @@ public class IndexVersion {
             }
 
             // Open this index directory in Lucene
-            Directory indexDir = FSDirectory.open(dir);
+            Directory indexDir = FSDirectory.open(dir.toPath());
 
             // Get info on the Lucene segment file(s) in index directory
-            SegmentInfos sis = new SegmentInfos();
+            SegmentInfos sis;
             try {
-                sis.read(indexDir);
+                sis = SegmentInfos.readLatestCommit(indexDir);
             } catch (IOException ie) {
                 // Wrap default IOException, providing more info about which directory cannot be read
                 throw new IOException("Could not read Lucene segments files in " + dir.getAbsolutePath(), ie);
             }
 
+            if (null == sis) {
+                throw new IOException("Could not read Lucene segments files in " + dir.getAbsolutePath());
+            }
+
             // If we have a valid Solr index dir, but it has no existing segments
             // then just return an empty string. It's a valid but empty index.
-            if (sis != null && sis.size() == 0) {
+            if (sis.size() == 0) {
                 return "";
             }
 

dspace-api/src/main/java/org/dspace/authority/AuthoritySearchService.java

@@ -7,6 +7,7 @@
  */
 package org.dspace.authority;
 
+import java.io.IOException;
 import java.net.MalformedURLException;
 import java.util.List;
 
@@ -22,7 +23,8 @@ import org.apache.solr.client.solrj.response.QueryResponse;
  */
 public interface AuthoritySearchService {
 
-    public QueryResponse search(SolrQuery query) throws SolrServerException, MalformedURLException;
+    public QueryResponse search(SolrQuery query)
+            throws SolrServerException, MalformedURLException, IOException;
 
     public List<String> getAllIndexedMetadataFields() throws Exception;
 

dspace-api/src/main/java/org/dspace/authority/AuthoritySolrServiceImpl.java

@@ -15,7 +15,7 @@ import java.util.List;
 import org.apache.logging.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.apache.solr.client.solrj.response.FacetField;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrInputDocument;
@@ -39,16 +39,17 @@ public class AuthoritySolrServiceImpl implements AuthorityIndexingService, Autho
     /**
      * Non-Static CommonsHttpSolrServer for processing indexing events.
      */
-    protected HttpSolrServer solr = null;
+    protected HttpSolrClient solr = null;
 
-    protected HttpSolrServer getSolr() throws MalformedURLException, SolrServerException {
+    protected HttpSolrClient getSolr()
+            throws MalformedURLException, SolrServerException, IOException {
         if (solr == null) {
 
             String solrService = ConfigurationManager.getProperty("solr.authority.server");
 
             log.debug("Solr authority URL: " + solrService);
 
-            solr = new HttpSolrServer(solrService);
+            solr = new HttpSolrClient.Builder(solrService).build();
             solr.setBaseURL(solrService);
 
             SolrQuery solrQuery = new SolrQuery().setQuery("*:*");
@@ -129,7 +130,8 @@ public class AuthoritySolrServiceImpl implements AuthorityIndexingService, Autho
     }
 
     @Override
-    public QueryResponse search(SolrQuery query) throws SolrServerException, MalformedURLException {
+    public QueryResponse search(SolrQuery query)
+            throws SolrServerException, MalformedURLException, IOException {
         return getSolr().query(query);
     }
 

dspace-api/src/main/java/org/dspace/content/BitstreamServiceImpl.java

@@ -462,13 +462,6 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
         return bitstreamDAO.getNotReferencedBitstreams(context);
     }
 
-    @Override
-    public void addMetadata(Context context, Bitstream dso, MetadataField metadataField, String lang,
-                            List<String> values, List<String> authorities, List<Integer> confidences)
-        throws SQLException {
-        addMetadata(context, dso, metadataField, lang, values, authorities, confidences, null);
-    }
-
     public Long getLastModified(Bitstream bitstream) {
         return bitstreamStorageService.getLastModified(bitstream);
     }

dspace-api/src/main/java/org/dspace/content/CollectionServiceImpl.java

@@ -372,7 +372,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
             log.error(LogManager.getHeader(context, "setWorkflowGroup",
                     "collection_id=" + collection.getID() + " " + e.getMessage()), e);
         }
-        if (!StringUtils.equals("default", workflow.getID())) {
+        if (!StringUtils.equals(XmlWorkflowFactory.LEGACY_WORKFLOW_NAME, workflow.getID())) {
             throw new IllegalArgumentException(
                     "setWorkflowGroup can be used only on collection with the default basic dspace workflow. "
                     + "Instead, the collection: "

dspace-api/src/main/java/org/dspace/content/DSpaceObjectServiceImpl.java

@@ -231,7 +231,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
 
     @Override
     public void addMetadata(Context context, T dso, MetadataField metadataField, String lang, List<String> values,
-                            List<String> authorities, List<Integer> confidences, List<Integer> places)
+                            List<String> authorities, List<Integer> confidences)
         throws SQLException {
         boolean authorityControlled = metadataAuthorityService.isAuthorityControlled(metadataField);
         boolean authorityRequired = metadataAuthorityService.isAuthorityRequired(metadataField);
@@ -703,15 +703,4 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
         }
     }
 
-    @Override
-    public void addMetadata(Context context, T dso, MetadataField metadataField, String lang, List<String> values,
-            List<String> authorities, List<Integer> confidences) throws SQLException {
-        addMetadata(context, dso, metadataField, lang, values, authorities, confidences, null);
-    }
-
-    @Override
-    public void addMetadata(Context context, T dso, MetadataField metadataField, String language, String value,
-            String authority, int confidence, int place) throws SQLException {
-        addMetadata(context, dso, metadataField, language, value, authority, confidence);
-    }
 }

dspace-api/src/main/java/org/dspace/content/InProgressSubmission.java

@@ -10,7 +10,6 @@ package org.dspace.content;
 import java.io.Serializable;
 import java.sql.SQLException;
 
-import org.dspace.authorize.AuthorizeException;
 import org.dspace.browse.IndexableObject;
 import org.dspace.eperson.EPerson;
 
@@ -29,11 +28,6 @@ public interface InProgressSubmission<ID extends Serializable> extends Indexable
      */
     ID getID();
 
-    /**
-     * Update the submission, including the unarchived item.
-     */
-    void update() throws SQLException, AuthorizeException;
-
     /**
      * Get the incomplete item object
      *

dspace-api/src/main/java/org/dspace/content/WorkspaceItem.java

@@ -27,9 +27,7 @@ import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
 import org.apache.commons.lang3.builder.HashCodeBuilder;
-import org.dspace.authorize.AuthorizeException;
 import org.dspace.browse.IndexableObject;
-import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.ReloadableEntity;
@@ -245,20 +243,6 @@ public class WorkspaceItem
         supervisorGroups.add(group);
     }
 
-    @Override
-    public void update() throws SQLException, AuthorizeException {
-
-        Context context = null;
-        try {
-            context = new Context();
-            ContentServiceFactory.getInstance().getWorkspaceItemService().update(context, this);
-        } finally {
-            if (context != null && context.isValid()) {
-                context.abort();
-            }
-        }
-    }
-
     @Override
     public int getType() {
         return Constants.WORKSPACEITEM;

dspace-api/src/main/java/org/dspace/content/authority/SolrAuthority.java

@@ -89,9 +89,9 @@ public class SolrAuthority implements ChoiceAuthority {
         String localSortField = "";
         if (StringUtils.isNotBlank(locale)) {
             localSortField = sortField + "_" + locale;
-            queryArgs.setSortField(localSortField, SolrQuery.ORDER.asc);
+            queryArgs.addSort(localSortField, SolrQuery.ORDER.asc);
         } else {
-            queryArgs.setSortField(sortField, SolrQuery.ORDER.asc);
+            queryArgs.addSort(sortField, SolrQuery.ORDER.asc);
         }
 
         Choices result;
@@ -100,14 +100,14 @@ public class SolrAuthority implements ChoiceAuthority {
             boolean hasMore = false;
             QueryResponse searchResponse = getSearchService().search(queryArgs);
             SolrDocumentList authDocs = searchResponse.getResults();
-            ArrayList<Choice> choices = new ArrayList<Choice>();
+            ArrayList<Choice> choices = new ArrayList<>();
             if (authDocs != null) {
                 max = (int) searchResponse.getResults().getNumFound();
                 int maxDocs = authDocs.size();
                 if (limit < maxDocs) {
                     maxDocs = limit;
                 }
-                List<AuthorityValue> alreadyPresent = new ArrayList<AuthorityValue>();
+                List<AuthorityValue> alreadyPresent = new ArrayList<>();
                 for (int i = 0; i < maxDocs; i++) {
                     SolrDocument solrDocument = authDocs.get(i);
                     if (solrDocument != null) {

dspace-api/src/main/java/org/dspace/content/service/DSpaceObjectService.java

@@ -239,26 +239,6 @@ public interface DSpaceObjectService<T extends DSpaceObject> extends FindableObj
     public void addMetadata(Context context, T dso, MetadataField metadataField, String lang, List<String> values,
             List<String> authorities, List<Integer> confidences) throws SQLException;
 
-    /**
-     * Add metadata fields. These are appended to existing values.
-     * Use <code>clearDC</code> to remove values. The values are insert in the
-     * positions passed in the places argument.
-     *
-     * @param context       DSpace context
-     * @param dso           DSpaceObject
-     * @param metadataField the metadata field to which the value is to be set
-     * @param lang          the ISO639 language code, optionally followed by an underscore
-     *                      and the ISO3166 country code. <code>null</code> means the
-     *                      value has no language (for example, a date).
-     * @param values        the values to add.
-     * @param authorities   the external authority key for this value (or null)
-     * @param confidences   the authority confidence (default 0)
-     * @param places        the places to use for the supplied values
-     * @throws SQLException if database error
-     */
-    public void addMetadata(Context context, T dso, MetadataField metadataField, String lang, List<String> values,
-            List<String> authorities, List<Integer> confidences, List<Integer> places) throws SQLException;
-
     /**
      * Shortcut for {@link #addMetadata(Context, DSpaceObject, MetadataField, String, List, List, List)} when a single
      * value need to be added
@@ -275,23 +255,6 @@ public interface DSpaceObjectService<T extends DSpaceObject> extends FindableObj
     public void addMetadata(Context context, T dso, MetadataField metadataField, String language, String value,
             String authority, int confidence) throws SQLException;
 
-    /**
-     * Shortcut for {@link #addMetadata(Context, DSpaceObject, MetadataField, String, List, List, List, List)} when a
-     * single value need to be added
-     * 
-     * @param context
-     * @param dso
-     * @param metadataField
-     * @param language
-     * @param value
-     * @param authority
-     * @param confidence
-     * @param place
-     * @throws SQLException
-     */
-    public void addMetadata(Context context, T dso, MetadataField metadataField, String language, String value,
-            String authority, int confidence, int place) throws SQLException;
-
     public void addMetadata(Context context, T dso, MetadataField metadataField, String language, String value)
         throws SQLException;
 

dspace-api/src/main/java/org/dspace/core/Constants.java

@@ -66,20 +66,20 @@ public class Constants {
     public static final int WORKFLOWITEM = 9;
 
     /**
-     * Type of pool task workflow objects
+     * Type of pool task objects
      */
-    public static final int WORKFLOW_POOL = 10;
+    public static final int POOLTASK = 10;
 
     /**
-     * Type of pool task workflow objects
+     * Type of claimed task objects
      */
-    public static final int WORKFLOW_CLAIMED = 11;
+    public static final int CLAIMEDTASK = 11;
 
     /**
      * lets you look up type names from the type IDs
      */
     public static final String[] typeText = { "BITSTREAM", "BUNDLE", "ITEM", "COLLECTION", "COMMUNITY", "SITE", "GROUP",
-        "EPERSON", "WORKSPACEITEM", "WORKFLOWITEM", "WORKFLOW POOL", "WORKFLOW CLAIMED" };
+        "EPERSON", "WORKSPACEITEM", "WORKFLOWITEM", "POOLTASK", "CLAIMEDTASK" };
 
     /**
      * Special Bundle and Bitstream Names:

dspace-api/src/main/java/org/dspace/ctask/test/WorkflowReportTest.java

@@ -0,0 +1,39 @@
+/**
+ * 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.ctask.test;
+
+import java.io.IOException;
+
+import org.dspace.content.DSpaceObject;
+import org.dspace.curate.AbstractCurationTask;
+import org.dspace.curate.Curator;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Curation task which simply reports its invocation without changing anything.
+ * Meant for testing.
+ *
+ * @author mhwood
+ */
+public class WorkflowReportTest
+        extends AbstractCurationTask {
+    private static final Logger LOG = LoggerFactory.getLogger(WorkflowReportTest.class);
+
+    @Override
+    public int perform(DSpaceObject dso)
+            throws IOException {
+        LOG.info("Class {} as task {} received 'perform' for object {}",
+                WorkflowReportTest.class.getSimpleName(), taskId, dso);
+        curator.report(String.format(
+                "Class %s as task %s received 'perform' for object %s%n",
+                WorkflowReportTest.class.getSimpleName(), taskId, dso));
+        return Curator.CURATE_SUCCESS;
+    }
+}

dspace-api/src/main/java/org/dspace/curate/CurationCli.java

@@ -9,6 +9,10 @@ package org.dspace.curate;
 
 import java.io.BufferedReader;
 import java.io.FileReader;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.PrintStream;
+import java.io.Writer;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.Map;
@@ -18,6 +22,7 @@ import org.apache.commons.cli.CommandLineParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.PosixParser;
+import org.apache.commons.io.output.NullOutputStream;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.core.Context;
 import org.dspace.core.factory.CoreServiceFactory;
@@ -57,7 +62,9 @@ public class CurationCli {
         options.addOption("e", "eperson", true,
                           "email address of curating eperson");
         options.addOption("r", "reporter", true,
-                          "reporter to manage results - use '-' to report to console. If absent, no reporting");
+                "relative or absolute path to the desired report file.  "
+                        + "Use '-' to report to console.  "
+                        + "If absent, no reporting");
         options.addOption("s", "scope", true,
                           "transaction scope to impose: use 'object', 'curation', or 'open'. If absent, 'open' " +
                               "applies");
@@ -165,9 +172,17 @@ public class CurationCli {
         }
 
         Curator curator = new Curator();
-        if (reporterName != null) {
+        OutputStream reporter;
-            curator.setReporter(reporterName);
+        if (null == reporterName) {
+            reporter = new NullOutputStream();
+        } else if ("-".equals(reporterName)) {
+            reporter = System.out;
+        } else {
+            reporter = new PrintStream(reporterName);
         }
+        Writer reportWriter = new OutputStreamWriter(reporter);
+        curator.setReporter(reportWriter);
+
         if (scope != null) {
             Curator.TxScope txScope = Curator.TxScope.valueOf(scope.toUpperCase());
             curator.setTransactionScope(txScope);

dspace-api/src/main/java/org/dspace/curate/Curator.java

@@ -15,6 +15,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
@@ -69,16 +70,12 @@ public class Curator {
         INTERACTIVE, BATCH, ANY
     }
 
-    ;
-
     // transaction scopes
     public static enum TxScope {
         OBJECT, CURATION, OPEN
     }
 
-    ;
+    private static final Logger log = LogManager.getLogger();
-
-    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(Curator.class);
 
     protected static final ThreadLocal<Context> curationCtx = new ThreadLocal<>();
 
@@ -86,7 +83,7 @@ public class Curator {
     protected Map<String, TaskRunner> trMap = new HashMap<>();
     protected List<String> perfList = new ArrayList<>();
     protected TaskQueue taskQ = null;
-    protected String reporter = null;
+    protected Appendable reporter = null;
     protected Invoked iMode = null;
     protected TaskResolver resolver = new TaskResolver();
     protected TxScope txScope = TxScope.OPEN;
@@ -193,7 +190,7 @@ public class Curator {
      *                 causes reporting to standard out.
      * @return return self (Curator instance) with reporter set
      */
-    public Curator setReporter(String reporter) {
+    public Curator setReporter(Appendable reporter) {
         this.reporter = reporter;
         return this;
     }
@@ -346,9 +343,10 @@ public class Curator {
      * @param message the message to output to the reporting stream.
      */
     public void report(String message) {
-        // Stub for now
+        try {
-        if ("-".equals(reporter)) {
+            reporter.append(message);
-            System.out.println(message);
+        } catch (IOException ex) {
+            log.error("Task reporting failure", ex);
         }
     }
 

dspace-api/src/main/java/org/dspace/curate/FileReporter.java

@@ -0,0 +1,88 @@
+/**
+ * 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.curate;
+
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.GregorianCalendar;
+
+import org.dspace.services.ConfigurationService;
+import org.dspace.utils.DSpace;
+
+/**
+ * Save a curation report to a unique file in the reports directory.
+ * Reports are named by the date and time of day, for example:
+ * "curation-20180916T113903045.report".
+ *
+ * @author mhwood
+ */
+public class FileReporter
+        implements Reporter {
+    private final Writer writer;
+
+    /**
+     * Open a writer to a file in a directory named by the configuration
+     * property {@code report.dir}, or in {@code [DSpace]/reports} if not
+     * configured.
+     *
+     * @throws IOException if there is a problem with the file path.
+     */
+    public FileReporter()
+            throws IOException {
+        // Calculate a unique(?) file name.
+        Date now = GregorianCalendar.getInstance().getTime();
+        SimpleDateFormat sdf = new SimpleDateFormat("yyyyMMdd'T'hhmmssSSS");
+        String filename = String.format("curation-%s.report", sdf.format(now));
+
+        // Build a path to the directory which is to receive the file.
+        ConfigurationService cfg = new DSpace().getConfigurationService();
+        String reportDir = cfg.getProperty("report.dir");
+        Path reportPath;
+        if (null == reportDir) {
+            reportPath = Paths.get(cfg.getProperty("dspace.dir"),
+                    "reports",
+                    filename);
+        } else {
+            reportPath = Paths.get(reportDir, filename);
+        }
+
+        // Open the file.
+        writer = new FileWriter(reportPath.toFile());
+    }
+
+    @Override
+    public Appendable append(CharSequence cs)
+            throws IOException {
+        writer.append(cs);
+        return this;
+    }
+
+    @Override
+    public Appendable append(CharSequence cs, int i, int i1)
+            throws IOException {
+        writer.append(cs, i, i1);
+        return this;
+    }
+
+    @Override
+    public Appendable append(char c) throws IOException {
+        writer.append(c);
+        return this;
+    }
+
+    @Override
+    public void close() throws Exception {
+        writer.close();
+    }
+}

dspace-api/src/main/java/org/dspace/curate/LogReporter.java

@@ -0,0 +1,62 @@
+/**
+ * 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.curate;
+
+import java.io.IOException;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Write curation report records through the logging framework.
+ * Whole lines (strings ending in '\n') are written to the log category "curation".
+ * Any partial line is flushed when the reporter is {@code close()}d.
+ *
+ * @author mhwood
+ */
+public class LogReporter
+        implements Reporter {
+    private static final Logger LOG = LoggerFactory.getLogger("curation");
+    private final StringBuilder buffer = new StringBuilder();
+
+    @Override
+    public Appendable append(CharSequence cs)
+            throws IOException {
+        for (int pos = 0; pos < cs.length(); pos++) {
+            char c = cs.charAt(pos);
+            if (c == '\n') {
+                LOG.info(buffer.toString());
+                buffer.delete(0, buffer.length()); // Clear the buffer
+            } else {
+                buffer.append(c);
+            }
+        }
+        return this;
+    }
+
+    @Override
+    public Appendable append(CharSequence cs, int i, int i1)
+            throws IOException {
+        return append(cs.subSequence(i, i1));
+    }
+
+    @Override
+    public Appendable append(char c)
+            throws IOException {
+        return append(String.valueOf(c));
+    }
+
+    @Override
+    public void close()
+            throws Exception {
+        if (buffer.length() > 0) {
+            LOG.info(buffer.toString());
+        }
+    }
+}

dspace-api/src/main/java/org/dspace/curate/Reporter.java

@@ -0,0 +1,18 @@
+/**
+ * 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.curate;
+
+/**
+ * A marker interface needed to make curation reporter classes into plugins.
+ *
+ * @author mhwood
+ */
+public interface Reporter
+        extends Appendable, AutoCloseable {
+}

dspace-api/src/main/java/org/dspace/curate/WorkflowCuratorServiceImpl.java

@@ -30,6 +30,8 @@ import org.dspace.content.Item;
 import org.dspace.content.service.CollectionService;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
+import org.dspace.core.factory.CoreServiceFactory;
+import org.dspace.core.service.PluginService;
 import org.dspace.curate.service.WorkflowCuratorService;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
@@ -56,9 +58,10 @@ import org.springframework.beans.factory.annotation.Autowired;
 public class WorkflowCuratorServiceImpl implements WorkflowCuratorService {
 
     /**
-     * log4j logger
+     * Logging category
      */
-    private Logger log = org.apache.logging.log4j.LogManager.getLogger(WorkflowCuratorServiceImpl.class);
+    private static final Logger log
+        = org.apache.logging.log4j.LogManager.getLogger();
 
     protected Map<String, TaskSet> tsMap = new HashMap<String, TaskSet>();
 
@@ -118,6 +121,7 @@ public class WorkflowCuratorServiceImpl implements WorkflowCuratorService {
             Curator curator = new Curator();
             // are we going to perform, or just put on queue?
             if (step.queue != null) {
+                // The queue runner will call setReporter
                 for (Task task : step.tasks) {
                     curator.addTask(task.name);
                 }
@@ -125,7 +129,18 @@ public class WorkflowCuratorServiceImpl implements WorkflowCuratorService {
                 basicWorkflowItemService.update(c, wfi);
                 return false;
             } else {
-                return curate(curator, c, wfi);
+                PluginService plugins = CoreServiceFactory.getInstance()
+                        .getPluginService();
+                try (Reporter reporter
+                        = (Reporter) plugins
+                        .getSinglePlugin(Reporter.class);) {
+                    curator.setReporter(reporter);
+                    boolean status = curate(curator, c, wfi);
+                    reporter.close();
+                    return status;
+                } catch (Exception e) {
+                    log.error("Failed to close report", e);
+                }
             }
         }
         return true;

dspace-api/src/main/java/org/dspace/discovery/IndexClient.java

@@ -262,9 +262,10 @@ public class IndexClient {
      * @param line    the command line options
      * @param indexer the solr indexer
      * @throws SearchServiceException in case of a solr exception
+     * @throws java.io.IOException passed through
      */
     protected static void checkRebuildSpellCheck(CommandLine line, IndexingService indexer)
-        throws SearchServiceException {
+        throws SearchServiceException, IOException {
         if (line.hasOption("s")) {
             log.info("Rebuilding spell checker.");
             indexer.buildSpellCheck();

dspace-api/src/main/java/org/dspace/discovery/IndexingService.java

@@ -64,5 +64,5 @@ public interface IndexingService {
 
     void optimize() throws SearchServiceException;
 
-    void buildSpellCheck() throws SearchServiceException;
+    void buildSpellCheck() throws SearchServiceException, IOException;
 }

dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java

@@ -46,11 +46,11 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.DateFormatUtils;
 import org.apache.commons.validator.routines.UrlValidator;
 import org.apache.logging.log4j.Logger;
+import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrRequest;
-import org.apache.solr.client.solrj.SolrServer;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.apache.solr.client.solrj.request.AbstractUpdateRequest;
 import org.apache.solr.client.solrj.request.ContentStreamUpdateRequest;
 import org.apache.solr.client.solrj.response.FacetField;
@@ -203,14 +203,14 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     /**
      * Non-Static SolrServer for processing indexing events.
      */
-    protected SolrServer solr = null;
+    protected SolrClient solr = null;
 
 
     protected SolrServiceImpl() {
 
     }
 
-    protected SolrServer getSolr() {
+    protected SolrClient getSolr() {
         if (solr == null) {
             String solrService = DSpaceServicesFactory.getInstance().getConfigurationService()
                                                       .getProperty("discovery.search.server");
@@ -220,7 +220,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 .getBooleanProperty("discovery", "solr.url.validation.enabled", true)) {
                 try {
                     log.debug("Solr URL: " + solrService);
-                    HttpSolrServer solrServer = new HttpSolrServer(solrService);
+                    HttpSolrClient solrServer = new HttpSolrClient.Builder(solrService).build();
 
                     solrServer.setBaseURL(solrService);
                     solrServer.setUseMultiPartPost(true);
@@ -236,7 +236,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     DatabaseUtils.checkReindexDiscovery(this);
 
                     solr = solrServer;
-                } catch (SolrServerException e) {
+                } catch (SolrServerException | IOException e) {
                     log.error("Error while initializing solr server", e);
                 }
             } else {
@@ -526,7 +526,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         if (force) {
             try {
                 getSolr().deleteByQuery(
-                    "search.resourcetype:[" + Constants.ITEM + " TO " + Constants.WORKFLOW_CLAIMED + "]");
+                    "search.resourcetype:[" + Constants.ITEM + " TO " + Constants.CLAIMEDTASK + "]");
             } catch (Exception e) {
                 throw new SearchServiceException(e.getMessage(), e);
             }
@@ -535,8 +535,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             cleanIndex(false, Constants.COLLECTION);
             cleanIndex(false, Constants.COMMUNITY);
             cleanIndex(false, Constants.WORKSPACEITEM);
-            cleanIndex(false, Constants.WORKFLOW_POOL);
+            cleanIndex(false, Constants.POOLTASK);
-            cleanIndex(false, Constants.WORKFLOW_CLAIMED);
+            cleanIndex(false, Constants.CLAIMEDTASK);
             cleanIndex(false, Constants.WORKFLOWITEM);
         }
     }
@@ -613,7 +613,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     }
 
     @Override
-    public void buildSpellCheck() throws SearchServiceException {
+    public void buildSpellCheck()
+            throws SearchServiceException, IOException {
         try {
             if (getSolr() == null) {
                 return;
@@ -1636,7 +1637,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             if (claimedTasks != null) {
                 for (ClaimedTask claimedTask : claimedTasks) {
                     SolrInputDocument claimDoc = doc.deepCopy();
-                    addBasicInfoToDocument(claimDoc, Constants.WORKFLOW_CLAIMED, claimedTask.getID(), null, locations);
+                    addBasicInfoToDocument(claimDoc, Constants.CLAIMEDTASK, claimedTask.getID(), null, locations);
                     addFacetIndex(claimDoc, "action", claimedTask.getActionID(), claimedTask.getActionID());
                     addFacetIndex(claimDoc, "step", claimedTask.getStepID(), claimedTask.getStepID());
 
@@ -1657,7 +1658,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             if (pools != null) {
                 for (PoolTask poolTask : pools) {
                     SolrInputDocument claimDoc = doc.deepCopy();
-                    addBasicInfoToDocument(claimDoc, Constants.WORKFLOW_POOL, poolTask.getID(), null, locations);
+                    addBasicInfoToDocument(claimDoc, Constants.POOLTASK, poolTask.getID(), null, locations);
                     addFacetIndex(claimDoc, "action", poolTask.getActionID(), poolTask.getActionID());
                     addFacetIndex(claimDoc, "step", poolTask.getStepID(), poolTask.getStepID());
 
@@ -1939,7 +1940,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 order = SolrQuery.ORDER.desc;
             }
 
-            solrQuery.addSortField(discoveryQuery.getSortField(), order);
+            solrQuery.addSort(discoveryQuery.getSortField(), order);
         }
 
         for (String property : discoveryQuery.getProperties().keySet()) {
@@ -2219,8 +2220,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             switch (type) {
                 case Constants.WORKSPACEITEM:
                 case Constants.WORKFLOWITEM:
-                case Constants.WORKFLOW_POOL:
+                case Constants.POOLTASK:
-                case Constants.WORKFLOW_CLAIMED:
+                case Constants.CLAIMEDTASK:
                     uid = Integer.parseInt((String) id);
                     break;
                 default:
@@ -2261,7 +2262,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             solrQuery.setStart(offset);
             solrQuery.setRows(max);
             if (orderfield != null) {
-                solrQuery.setSortField(orderfield, ascending ? SolrQuery.ORDER.asc : SolrQuery.ORDER.desc);
+                solrQuery.addSort(orderfield, ascending ? SolrQuery.ORDER.asc : SolrQuery.ORDER.desc);
             }
             if (filterquery != null) {
                 solrQuery.addFilterQuery(filterquery);

dspace-api/src/main/java/org/dspace/statistics/SolrLoggerServiceImpl.java

@@ -45,10 +45,10 @@ import org.apache.commons.lang3.time.DateFormatUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.DefaultHttpClient;
+import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrQuery;
-import org.apache.solr.client.solrj.SolrServer;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.apache.solr.client.solrj.request.AbstractUpdateRequest;
 import org.apache.solr.client.solrj.request.ContentStreamUpdateRequest;
 import org.apache.solr.client.solrj.request.CoreAdminRequest;
@@ -107,7 +107,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             org.apache.logging.log4j.LogManager.getLogger(SolrLoggerServiceImpl.class);
 
     private static final String MULTIPLE_VALUES_SPLITTER = "|";
-    protected SolrServer solr;
+    protected SolrClient solr;
 
     public static final String DATE_FORMAT_8601 = "yyyy-MM-dd'T'HH:mm:ss.SSS'Z'";
 
@@ -115,7 +115,9 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
     protected DatabaseReader locationService;
 
-    private static List<String> statisticYearCores = new ArrayList<String>();
+    protected boolean useProxies;
+
+    private static final List<String> statisticYearCores = new ArrayList<>();
     private static boolean statisticYearCoresInit = false;
 
     @Autowired(required = true)
@@ -154,11 +156,11 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
         log.info("solr-statistics.server:" + configurationService.getProperty("solr-statistics.server"));
         log.info("usage-statistics.dbfile:" + configurationService.getProperty("usage-statistics.dbfile"));
 
-        HttpSolrServer server = null;
+        HttpSolrClient server = null;
 
         if (configurationService.getProperty("solr-statistics.server") != null) {
             try {
-                server = new HttpSolrServer(configurationService.getProperty("solr-statistics.server"));
+                server = new HttpSolrClient.Builder(configurationService.getProperty("solr-statistics.server")).build();
             } catch (Exception e) {
                 log.error("Error accessing Solr server configured in 'solr-statistics.server'", e);
             }
@@ -346,14 +348,14 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
         }
 
         if (dspaceObject != null) {
-            doc1.addField("id", dspaceObject.getID());
+            doc1.addField("id", dspaceObject.getID().toString());
             doc1.addField("type", dspaceObject.getType());
             storeParents(doc1, dspaceObject);
         }
         // Save the current time
         doc1.addField("time", DateFormatUtils.format(new Date(), DATE_FORMAT_8601));
         if (currentUser != null) {
-            doc1.addField("epersonid", currentUser.getID());
+            doc1.addField("epersonid", currentUser.getID().toString());
         }
 
         return doc1;
@@ -416,14 +418,14 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
         }
 
         if (dspaceObject != null) {
-            doc1.addField("id", dspaceObject.getID());
+            doc1.addField("id", dspaceObject.getID().toString());
             doc1.addField("type", dspaceObject.getType());
             storeParents(doc1, dspaceObject);
         }
         // Save the current time
         doc1.addField("time", DateFormatUtils.format(new Date(), DATE_FORMAT_8601));
         if (currentUser != null) {
-            doc1.addField("epersonid", currentUser.getID());
+            doc1.addField("epersonid", currentUser.getID().toString());
         }
 
         return doc1;
@@ -452,7 +454,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             }
             //Store the scope
             if (scope != null) {
-                solrDoc.addField("scopeId", scope.getID());
+                solrDoc.addField("scopeId", scope.getID().toString());
                 solrDoc.addField("scopeType", scope.getType());
             }
 
@@ -487,7 +489,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             SolrInputDocument solrDoc = getCommonSolrDoc(usageWorkflowEvent.getObject(), null, null);
 
             //Log the current collection & the scope !
-            solrDoc.addField("owningColl", usageWorkflowEvent.getScope().getID());
+            solrDoc.addField("owningColl", usageWorkflowEvent.getScope().getID().toString());
             storeParents(solrDoc, usageWorkflowEvent.getScope());
 
             if (usageWorkflowEvent.getWorkflowStep() != null) {
@@ -499,25 +501,25 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             if (usageWorkflowEvent.getGroupOwners() != null) {
                 for (int i = 0; i < usageWorkflowEvent.getGroupOwners().length; i++) {
                     Group group = usageWorkflowEvent.getGroupOwners()[i];
-                    solrDoc.addField("owner", "g" + group.getID());
+                    solrDoc.addField("owner", "g" + group.getID().toString());
                 }
             }
             if (usageWorkflowEvent.getEpersonOwners() != null) {
                 for (int i = 0; i < usageWorkflowEvent.getEpersonOwners().length; i++) {
                     EPerson ePerson = usageWorkflowEvent.getEpersonOwners()[i];
-                    solrDoc.addField("owner", "e" + ePerson.getID());
+                    solrDoc.addField("owner", "e" + ePerson.getID().toString());
                 }
             }
 
-            solrDoc.addField("workflowItemId", usageWorkflowEvent.getWorkflowItem().getID());
+            solrDoc.addField("workflowItemId", usageWorkflowEvent.getWorkflowItem().getID().toString());
 
             EPerson submitter = ((Item) usageWorkflowEvent.getObject()).getSubmitter();
             if (submitter != null) {
-                solrDoc.addField("submitter", submitter.getID());
+                solrDoc.addField("submitter", submitter.getID().toString());
             }
             solrDoc.addField("statistics_type", StatisticsType.WORKFLOW.text());
             if (usageWorkflowEvent.getActor() != null) {
-                solrDoc.addField("actor", usageWorkflowEvent.getActor().getID());
+                solrDoc.addField("actor", usageWorkflowEvent.getActor().getID().toString());
             }
 
             solr.add(solrDoc);
@@ -535,21 +537,21 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             Community comm = (Community) dso;
             List<Community> parentCommunities = comm.getParentCommunities();
             for (Community parent : parentCommunities) {
-                doc1.addField("owningComm", parent.getID());
+                doc1.addField("owningComm", parent.getID().toString());
                 storeParents(doc1, parent);
             }
         } else if (dso instanceof Collection) {
             Collection coll = (Collection) dso;
             List<Community> communities = coll.getCommunities();
             for (Community community : communities) {
-                doc1.addField("owningComm", community.getID());
+                doc1.addField("owningComm", community.getID().toString());
                 storeParents(doc1, community);
             }
         } else if (dso instanceof Item) {
             Item item = (Item) dso;
             List<Collection> collections = item.getCollections();
             for (Collection collection : collections) {
-                doc1.addField("owningColl", collection.getID());
+                doc1.addField("owningColl", collection.getID().toString());
                 storeParents(doc1, collection);
             }
         } else if (dso instanceof Bitstream) {
@@ -558,7 +560,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             for (Bundle bundle : bundles) {
                 List<Item> items = bundle.getItems();
                 for (Item item : items) {
-                    doc1.addField("owningItem", item.getID());
+                    doc1.addField("owningItem", item.getID().toString());
                     storeParents(doc1, item);
                 }
             }
@@ -579,12 +581,13 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
     @Override
     public Map<String, List<String>> queryField(String query,
-                                                List oldFieldVals, String field) {
+                                                List oldFieldVals, String field)
-        Map<String, List<String>> currentValsStored = new HashMap<String, List<String>>();
+            throws IOException {
+        Map<String, List<String>> currentValsStored = new HashMap<>();
         try {
             // Get one document (since all the metadata for all the values
             // should be the same just get the first one we find
-            Map<String, String> params = new HashMap<String, String>();
+            Map<String, String> params = new HashMap<>();
             params.put("q", query);
             params.put("rows", "1");
             MapSolrParams solrParams = new MapSolrParams(params);
@@ -602,8 +605,18 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
     public class ResultProcessor {
 
+        private SolrInputDocument toSolrInputDocument(SolrDocument d) {
+            SolrInputDocument doc = new SolrInputDocument();
+
+            for (String name : d.getFieldNames()) {
+                doc.addField(name, d.getFieldValue(name));
+            }
+
+            return doc;
+        }
+
         public void execute(String query) throws SolrServerException, IOException {
-            Map<String, String> params = new HashMap<String, String>();
+            Map<String, String> params = new HashMap<>();
             params.put("q", query);
             params.put("rows", "10");
             if (0 < statisticYearCores.size()) {
@@ -612,17 +625,23 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             MapSolrParams solrParams = new MapSolrParams(params);
             QueryResponse response = solr.query(solrParams);
 
-            long numbFound = response.getResults().getNumFound();
+            SolrDocumentList results = response.getResults();
+            long numbFound = results.getNumFound();
 
             // process the first batch
-            process(response.getResults());
+            for (SolrDocument result : results) {
+                process(toSolrInputDocument(result));
+            }
 
             // Run over the rest
             for (int i = 10; i < numbFound; i += 10) {
                 params.put("start", String.valueOf(i));
                 solrParams = new MapSolrParams(params);
                 response = solr.query(solrParams);
-                process(response.getResults());
+                results = response.getResults();
+                for (SolrDocument result : results) {
+                    process(toSolrInputDocument(result));
+                }
             }
 
         }
@@ -638,8 +657,8 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
          * @throws IOException         A general class of exceptions produced by failed or interrupted I/O operations.
          * @throws SolrServerException Exception from the Solr server to the solrj Java client.
          */
-        public void process(List<SolrDocument> docs) throws IOException, SolrServerException {
+        public void process(List<SolrInputDocument> docs) throws IOException, SolrServerException {
-            for (SolrDocument doc : docs) {
+            for (SolrInputDocument doc : docs) {
                 process(doc);
             }
         }
@@ -651,7 +670,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
          * @throws IOException         A general class of exceptions produced by failed or interrupted I/O operations.
          * @throws SolrServerException Exception from the Solr server to the solrj Java client.
          */
-        public void process(SolrDocument doc) throws IOException, SolrServerException {
+        public void process(SolrInputDocument doc) throws IOException, SolrServerException {
 
 
         }
@@ -667,11 +686,10 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
                 /* Result Process to alter record to be identified as a bot */
                 ResultProcessor processor = new ResultProcessor() {
                     @Override
-                    public void process(SolrDocument doc) throws IOException, SolrServerException {
+                    public void process(SolrInputDocument doc) throws IOException, SolrServerException {
-                        doc.removeFields("isBot");
+                        doc.removeField("isBot");
                         doc.addField("isBot", true);
-                        SolrInputDocument newInput = ClientUtils.toSolrInputDocument(doc);
+                        solr.add(doc);
-                        solr.add(newInput);
                         log.info("Marked " + doc.getFieldValue("ip") + " as bot");
                     }
                 };
@@ -697,11 +715,10 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             /* Result Process to alter record to be identified as a bot */
             ResultProcessor processor = new ResultProcessor() {
                 @Override
-                public void process(SolrDocument doc) throws IOException, SolrServerException {
+                public void process(SolrInputDocument doc) throws IOException, SolrServerException {
-                    doc.removeFields("isBot");
+                    doc.removeField("isBot");
                     doc.addField("isBot", true);
-                    SolrInputDocument newInput = ClientUtils.toSolrInputDocument(doc);
+                    solr.add(doc);
-                    solr.add(newInput);
                 }
             };
 
@@ -748,11 +765,12 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
         // QueryResponse queryResponse = solr.query()//query(query, null, -1,
         // null, null, null);
 
-        final List<SolrDocument> docsToUpdate = new ArrayList<SolrDocument>();
+        final List<SolrInputDocument> docsToUpdate = new ArrayList<>();
 
         ResultProcessor processor = new ResultProcessor() {
             @Override
-            public void process(List<SolrDocument> docs) throws IOException, SolrServerException {
+            public void process(List<SolrInputDocument> docs)
+                    throws IOException, SolrServerException {
                 docsToUpdate.addAll(docs);
             }
         };
@@ -764,7 +782,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
         // Add the new (updated onces
         for (int i = 0; i < docsToUpdate.size(); i++) {
-            SolrDocument solrDocument = docsToUpdate.get(i);
+            SolrInputDocument solrDocument = docsToUpdate.get(i);
             // Now loop over our fieldname actions
             for (int j = 0; j < fieldNames.size(); j++) {
                 String fieldName = fieldNames.get(j);
@@ -772,7 +790,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
                 if (action.equals("addOne") || action.equals("replace")) {
                     if (action.equals("replace")) {
-                        solrDocument.removeFields(fieldName);
+                        solrDocument.removeField(fieldName);
                     }
 
                     for (Object fieldValue : fieldValues) {
@@ -782,7 +800,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
                     // Remove the field
                     java.util.Collection<Object> values = solrDocument
                         .getFieldValues(fieldName);
-                    solrDocument.removeFields(fieldName);
+                    solrDocument.removeField(fieldName);
                     for (Object value : values) {
                         // Keep all the values besides the one we need to remove
                         if (!fieldValues.contains((value))) {
@@ -791,9 +809,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
                     }
                 }
             }
-            SolrInputDocument newInput = ClientUtils
+            solr.add(solrDocument);
-                .toSolrInputDocument(solrDocument);
-            solr.add(newInput);
         }
         solr.commit();
         // System.out.println("SolrLogger.update(\""+query+"\"):"+(new
@@ -801,14 +817,16 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
     }
 
     @Override
-    public void query(String query, int max) throws SolrServerException {
+    public void query(String query, int max)
+            throws SolrServerException, IOException {
         query(query, null, null, 0, max, null, null, null, null, null, false);
     }
 
     @Override
     public ObjectCount[] queryFacetField(String query,
                                          String filterQuery, String facetField, int max, boolean showTotal,
-                                         List<String> facetQueries) throws SolrServerException {
+                                         List<String> facetQueries)
+            throws SolrServerException, IOException {
         QueryResponse queryResponse = query(query, filterQuery, facetField,
                                             0, max, null, null, null, facetQueries, null, false);
         if (queryResponse == null) {
@@ -844,7 +862,8 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
     @Override
     public ObjectCount[] queryFacetDate(String query,
                                         String filterQuery, int max, String dateType, String dateStart,
-                                        String dateEnd, boolean showTotal, Context context) throws SolrServerException {
+                                        String dateEnd, boolean showTotal, Context context)
+            throws SolrServerException, IOException {
         QueryResponse queryResponse = query(query, filterQuery, null, 0, max,
                                             dateType, dateStart, dateEnd, null, null, false);
         if (queryResponse == null) {
@@ -876,7 +895,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
     @Override
     public Map<String, Integer> queryFacetQuery(String query,
                                                 String filterQuery, List<String> facetQueries)
-        throws SolrServerException {
+        throws SolrServerException, IOException {
         QueryResponse response = query(query, filterQuery, null, 0, 1, null, null,
                                        null, facetQueries, null, false);
         return response.getFacetQuery();
@@ -884,7 +903,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
     @Override
     public ObjectCount queryTotal(String query, String filterQuery)
-        throws SolrServerException {
+        throws SolrServerException, IOException {
         QueryResponse queryResponse = query(query, filterQuery, null, 0, -1, null,
                                             null, null, null, null, false);
         ObjectCount objCount = new ObjectCount();
@@ -942,7 +961,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
     public QueryResponse query(String query, String filterQuery,
                                String facetField, int rows, int max, String dateType, String dateStart,
                                String dateEnd, List<String> facetQueries, String sort, boolean ascending)
-        throws SolrServerException {
+        throws SolrServerException, IOException {
         if (solr == null) {
             return null;
         }
@@ -1001,7 +1020,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
         }
 
         if (sort != null) {
-            solrQuery.setSortField(sort, (ascending ? SolrQuery.ORDER.asc : SolrQuery.ORDER.desc));
+            solrQuery.addSort(sort, (ascending ? SolrQuery.ORDER.asc : SolrQuery.ORDER.desc));
         }
 
         String[] bundles = configurationService.getArrayProperty("solr-statistics.query.filter.bundles");
@@ -1035,7 +1054,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
         try {
             // solr.set
             response = solr.query(solrQuery);
-        } catch (SolrServerException e) {
+        } catch (SolrServerException | IOException e) {
             log.error("Error searching Solr usage events using query {}", query, e);
             throw e;
         }
@@ -1086,7 +1105,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
     @Override
     public void shardSolrIndex() throws IOException, SolrServerException {
-        if (!(solr instanceof HttpSolrServer)) {
+        if (!(solr instanceof HttpSolrClient)) {
             return;
         }
 
@@ -1152,14 +1171,14 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
             //Start by creating a new core
             String coreName = "statistics-" + dcStart.getYearUTC();
-            HttpSolrServer statisticsYearServer = createCore((HttpSolrServer) solr, coreName);
+            HttpSolrClient statisticsYearServer = createCore((HttpSolrClient) solr, coreName);
 
             System.out.println("Moving: " + totalRecords + " into core " + coreName);
             log.info("Moving: " + totalRecords + " records into core " + coreName);
 
-            List<File> filesToUpload = new ArrayList<File>();
+            List<File> filesToUpload = new ArrayList<>();
             for (int i = 0; i < totalRecords; i += 10000) {
-                String solrRequestUrl = ((HttpSolrServer) solr).getBaseURL() + "/select";
+                String solrRequestUrl = ((HttpSolrClient) solr).getBaseURL() + "/select";
                 solrRequestUrl = generateURL(solrRequestUrl, yearQueryParams);
 
                 HttpGet get = new HttpGet(solrRequestUrl);
@@ -1210,13 +1229,13 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
         FileUtils.deleteDirectory(tempDirectory);
     }
 
-    protected HttpSolrServer createCore(HttpSolrServer solr, String coreName) throws IOException, SolrServerException {
+    protected HttpSolrClient createCore(HttpSolrClient solr, String coreName) throws IOException, SolrServerException {
         String solrDir = configurationService.getProperty("dspace.dir") + File.separator + "solr" + File.separator;
         String baseSolrUrl = solr.getBaseURL().replace("statistics", "");
 
         //DS-3458: Test to see if a solr core already exists.  If it exists, return that server.  Otherwise create a
         // new one.
-        HttpSolrServer returnServer = new HttpSolrServer(baseSolrUrl + "/" + coreName);
+        HttpSolrClient returnServer = new HttpSolrClient.Builder(baseSolrUrl + "/" + coreName).build();
         try {
             SolrPingResponse ping = returnServer.ping();
             log.debug(String.format("Ping of Solr Core [%s] Returned with Status [%d]", coreName, ping.getStatus()));
@@ -1234,7 +1253,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
         //The config files for a statistics shard reside wihtin the statistics repository
         create.setInstanceDir("statistics");
         create.setDataDir(solrDir + coreName + File.separator + "data");
-        HttpSolrServer solrServer = new HttpSolrServer(baseSolrUrl);
+        HttpSolrClient solrServer = new HttpSolrClient.Builder(baseSolrUrl).build();
         create.process(solrServer);
         log.info("Created core with name: " + coreName);
         return returnServer;
@@ -1268,7 +1287,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
     @Override
     public void reindexBitstreamHits(boolean removeDeletedBitstreams) throws Exception {
-        if (!(solr instanceof HttpSolrServer)) {
+        if (!(solr instanceof HttpSolrClient)) {
             return;
         }
 
@@ -1288,16 +1307,16 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             File tempDirectory = new File(
                 configurationService.getProperty("dspace.dir") + File.separator + "temp" + File.separator);
             tempDirectory.mkdirs();
-            List<File> tempCsvFiles = new ArrayList<File>();
+            List<File> tempCsvFiles = new ArrayList<>();
             for (int i = 0; i < totalRecords; i += 10000) {
-                Map<String, String> params = new HashMap<String, String>();
+                Map<String, String> params = new HashMap<>();
                 params.put(CommonParams.Q, "*:*");
                 params.put(CommonParams.FQ, "-bundleName:[* TO *] AND type:" + Constants.BITSTREAM);
                 params.put(CommonParams.WT, "csv");
                 params.put(CommonParams.ROWS, String.valueOf(10000));
                 params.put(CommonParams.START, String.valueOf(i));
 
-                String solrRequestUrl = ((HttpSolrServer) solr).getBaseURL() + "/select";
+                String solrRequestUrl = ((HttpSolrClient) solr).getBaseURL() + "/select";
                 solrRequestUrl = generateURL(solrRequestUrl, params);
 
                 HttpGet get = new HttpGet(solrRequestUrl);
@@ -1507,7 +1526,7 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
      * This code is synchonized in the event that 2 threads trigger the initialization at the same time.
      */
     protected synchronized void initSolrYearCores() {
-        if (statisticYearCoresInit || !(solr instanceof HttpSolrServer)) {
+        if (statisticYearCoresInit || !(solr instanceof HttpSolrClient)) {
             return;
         }
         try {
@@ -1523,17 +1542,20 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
                 }
             });
             //Base url should like : http://localhost:{port.number}/solr
-            String baseSolrUrl = ((HttpSolrServer) solr).getBaseURL().replace("statistics", "");
+            String baseSolrUrl = ((HttpSolrClient) solr).getBaseURL().replace("statistics", "");
             for (File solrCoreFile : solrCoreFiles) {
                 log.info("Loading core with name: " + solrCoreFile.getName());
 
-                createCore((HttpSolrServer) solr, solrCoreFile.getName());
+                createCore((HttpSolrClient) solr, solrCoreFile.getName());
                 //Add it to our cores list so we can query it !
                 statisticYearCores
                     .add(baseSolrUrl.replace("http://", "").replace("https://", "") + solrCoreFile.getName());
             }
             //Also add the core containing the current year !
-            statisticYearCores.add(((HttpSolrServer) solr).getBaseURL().replace("http://", "").replace("https://", ""));
+            statisticYearCores.add(((HttpSolrClient) solr)
+                    .getBaseURL()
+                    .replace("http://", "")
+                    .replace("https://", ""));
         } catch (Exception e) {
             log.error(e.getMessage(), e);
         }

dspace-api/src/main/java/org/dspace/statistics/content/StatisticsBSAdapter.java

@@ -7,6 +7,7 @@
  */
 package org.dspace.statistics.content;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -48,7 +49,7 @@ public class StatisticsBSAdapter {
     public StatisticsBSAdapter() {
         displayItemViews = false;
         displayBitstreamViews = false;
-        filters = new ArrayList<StatisticsFilter>();
+        filters = new ArrayList<>();
         solrLoggerService = StatisticsServiceFactory.getInstance().getSolrLoggerService();
     }
 
@@ -60,8 +61,10 @@ public class StatisticsBSAdapter {
      * @param item      the item from which we need our visits
      * @return the number of visits
      * @throws SolrServerException Exception from the Solr server to the solrj Java client.
+     * @throws java.io.IOException passed through.
      */
-    public long getNumberOfVisits(int visitType, Item item) throws SolrServerException {
+    public long getNumberOfVisits(int visitType, Item item)
+            throws SolrServerException, IOException {
         switch (visitType) {
             case ITEM_VISITS:
                 return solrLoggerService

dspace-api/src/main/java/org/dspace/statistics/content/StatisticsDataSearches.java

@@ -59,7 +59,7 @@ public class StatisticsDataSearches extends StatisticsData {
         }
 
         List<StatisticsFilter> filters = getFilters();
-        List<String> defaultFilters = new ArrayList<String>();
+        List<String> defaultFilters = new ArrayList<>();
         for (StatisticsFilter statisticsFilter : filters) {
             defaultFilters.add(statisticsFilter.toQuery());
         }
@@ -221,7 +221,8 @@ public class StatisticsDataSearches extends StatisticsData {
         return query;
     }
 
-    protected ObjectCount getTotalPageViews(String query, String defaultFilterQuery) throws SolrServerException {
+    protected ObjectCount getTotalPageViews(String query, String defaultFilterQuery)
+            throws SolrServerException, IOException {
         StringBuilder fqBuffer;
         fqBuffer = new StringBuilder(defaultFilterQuery);
         if (0 < fqBuffer.length()) {

dspace-api/src/main/java/org/dspace/statistics/content/StatisticsDataVisits.java

@@ -7,6 +7,7 @@
  */
 package org.dspace.statistics.content;
 
+import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.sql.SQLException;
 import java.text.ParseException;
@@ -117,7 +118,7 @@ public class StatisticsDataVisits extends StatisticsData {
 
     @Override
     public Dataset createDataset(Context context) throws SQLException,
-        SolrServerException, ParseException {
+        SolrServerException, ParseException, IOException {
         // Check if we already have one.
         // If we do then give it back.
         if (getDataset() != null) {
@@ -127,7 +128,7 @@ public class StatisticsDataVisits extends StatisticsData {
         ///////////////////////////
         // 1. DETERMINE OUR AXIS //
         ///////////////////////////
-        ArrayList<DatasetQuery> datasetQueries = new ArrayList<DatasetQuery>();
+        ArrayList<DatasetQuery> datasetQueries = new ArrayList<>();
         for (int i = 0; i < getDatasetGenerators().size(); i++) {
             DatasetGenerator dataSet = getDatasetGenerators().get(i);
             processAxis(context, dataSet, datasetQueries);
@@ -703,7 +704,8 @@ public class StatisticsDataVisits extends StatisticsData {
 
 
     protected ObjectCount[] queryFacetField(DatasetQuery dataset, String query,
-                                            String filterQuery) throws SolrServerException {
+                                            String filterQuery)
+            throws SolrServerException, IOException {
         String facetType = dataset.getFacetField() == null ? "id" : dataset
             .getFacetField();
         return solrLoggerService.queryFacetField(query, filterQuery, facetType,

dspace-api/src/main/java/org/dspace/statistics/content/StatisticsDataWorkflow.java

@@ -38,7 +38,7 @@ import org.dspace.statistics.SolrLoggerServiceImpl;
 import org.dspace.statistics.content.filter.StatisticsFilter;
 
 /**
- * A workflow data implementation that will query the statistics backend for workflow information
+ * A workflow data implementation that will query the statistics backend for workflow information.
  *
  * @author Kevin Van de Velde (kevin at atmire dot com)
  * @author Ben Bosman (ben at atmire dot com)
@@ -166,19 +166,21 @@ public class StatisticsDataWorkflow extends StatisticsData {
      * @param typeGenerator the type generator
      * @return counts for each facet by name.
      * @throws org.apache.solr.client.solrj.SolrServerException passed through.
+     * @throws java.io.IOException passed through.
      */
-    protected Map<String, Long> getTotalFacetCounts(DatasetTypeGenerator typeGenerator) throws SolrServerException {
+    protected Map<String, Long> getTotalFacetCounts(DatasetTypeGenerator typeGenerator)
+            throws SolrServerException, IOException {
         ObjectCount[] objectCounts = solrLoggerService
             .queryFacetField(getQuery(), null, typeGenerator.getType(), -1, false, null);
-        Map<String, Long> result = new HashMap<String, Long>();
+        Map<String, Long> result = new HashMap<>();
         for (ObjectCount objectCount : objectCounts) {
             result.put(objectCount.getValue(), objectCount.getCount());
         }
         return result;
     }
 
-
+    protected Date getOldestWorkflowItemDate()
-    protected Date getOldestWorkflowItemDate() throws SolrServerException {
+            throws SolrServerException, IOException {
         ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
         String workflowStartDate = configurationService.getProperty("usage-statistics.workflow-start-date");
         if (workflowStartDate == null) {

dspace-api/src/main/java/org/dspace/statistics/service/SolrLoggerService.java

@@ -88,11 +88,12 @@ public interface SolrLoggerService {
      * @throws IOException         A general class of exceptions produced by failed or interrupted I/O operations.
      * @throws SolrServerException Exception from the Solr server to the solrj Java client.
      */
-    public void removeIndex(String query) throws IOException,
+    public void removeIndex(String query)
-        SolrServerException;
+            throws IOException, SolrServerException;
 
     public Map<String, List<String>> queryField(String query,
-                                                List oldFieldVals, String field);
+                                                List oldFieldVals, String field)
+            throws IOException;
 
     public void markRobotsByIP();
 
@@ -115,7 +116,8 @@ public interface SolrLoggerService {
                        List<String> fieldNames, List<List<Object>> fieldValuesList)
         throws SolrServerException, IOException;
 
-    public void query(String query, int max) throws SolrServerException;
+    public void query(String query, int max)
+            throws SolrServerException, IOException;
 
     /**
      * Query used to get values grouped by the given facet field.
@@ -130,10 +132,12 @@ public interface SolrLoggerService {
      * @param facetQueries list of facet queries
      * @return an array containing our results
      * @throws SolrServerException Exception from the Solr server to the solrj Java client.
+     * @throws java.io.IOException passed through.
      */
     public ObjectCount[] queryFacetField(String query,
                                          String filterQuery, String facetField, int max, boolean showTotal,
-                                         List<String> facetQueries) throws SolrServerException;
+                                         List<String> facetQueries)
+            throws SolrServerException, IOException;
 
     /**
      * Query used to get values grouped by the date.
@@ -152,22 +156,24 @@ public interface SolrLoggerService {
      * @param context     The relevant DSpace Context.
      * @return and array containing our results
      * @throws SolrServerException Exception from the Solr server to the solrj Java client.
+     * @throws java.io.IOException passed through.
      */
     public ObjectCount[] queryFacetDate(String query,
                                         String filterQuery, int max, String dateType, String dateStart,
-                                        String dateEnd, boolean showTotal, Context context) throws SolrServerException;
+                                        String dateEnd, boolean showTotal, Context context)
+            throws SolrServerException, IOException;
 
     public Map<String, Integer> queryFacetQuery(String query,
                                                 String filterQuery, List<String> facetQueries)
-        throws SolrServerException;
+            throws SolrServerException, IOException;
 
     public ObjectCount queryTotal(String query, String filterQuery)
-        throws SolrServerException;
+            throws SolrServerException, IOException;
 
     public QueryResponse query(String query, String filterQuery,
                                String facetField, int rows, int max, String dateType, String dateStart,
                                String dateEnd, List<String> facetQueries, String sort, boolean ascending)
-        throws SolrServerException;
+            throws SolrServerException, IOException;
 
     /**
      * Returns in a filterQuery string all the ip addresses that should be ignored

dspace-api/src/main/java/org/dspace/statistics/util/StatisticsImporter.java

@@ -36,7 +36,7 @@ import org.apache.commons.cli.PosixParser;
 import org.apache.commons.lang3.time.DateFormatUtils;
 import org.apache.logging.log4j.Logger;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.apache.solr.common.SolrInputDocument;
 import org.dspace.content.Bitstream;
 import org.dspace.content.Collection;
@@ -80,7 +80,7 @@ public class StatisticsImporter {
     /**
      * Solr server connection
      */
-    private static HttpSolrServer solr;
+    private static HttpSolrClient solr;
 
     /**
      * GEOIP lookup service
@@ -468,7 +468,7 @@ public class StatisticsImporter {
         if (verbose) {
             System.out.println("Writing to solr server at: " + sserver);
         }
-        solr = new HttpSolrServer(sserver);
+        solr = new HttpSolrClient.Builder(sserver).build();
 
         String dbPath = ConfigurationManager.getProperty("usage-statistics", "dbfile");
         try {

dspace-api/src/main/java/org/dspace/storage/rdbms/DatabaseUtils.java

@@ -10,6 +10,7 @@ package org.dspace.storage.rdbms;
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.IOException;
+import java.io.InputStream;
 import java.io.InputStreamReader;
 import java.sql.Connection;
 import java.sql.DatabaseMetaData;
@@ -23,6 +24,7 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import javax.sql.DataSource;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.dspace.core.Context;
@@ -88,7 +90,8 @@ public class DatabaseUtils {
         // Usage checks
         if (argv.length < 1) {
             System.out.println("\nDatabase action argument is missing.");
-            System.out.println("Valid actions: 'test', 'info', 'migrate', 'repair', 'validate' or 'clean'");
+            System.out.println("Valid actions: 'test', 'info', 'migrate', 'repair', 'validate', " +
+                    "'update-sequences' or 'clean'");
             System.out.println("\nOr, type 'database help' for more information.\n");
             System.exit(1);
         }
@@ -328,23 +331,48 @@ public class DatabaseUtils {
                     e.printStackTrace();
                     System.exit(1);
                 }
+            } else if (argv[0].equalsIgnoreCase("update-sequences")) {
+                try (Connection connection = dataSource.getConnection()) {
+                    String dbType = getDbType(connection);
+                    String sqlfile = "org/dspace/storage/rdbms/sqlmigration/" + dbType +
+                            "/update-sequences.sql";
+                    InputStream sqlstream = DatabaseUtils.class.getClassLoader().getResourceAsStream(sqlfile);
+                    if (sqlstream != null) {
+                        String s = IOUtils.toString(sqlstream, "UTF-8");
+                        if (!s.isEmpty()) {
+                            System.out.println("Running " + sqlfile);
+                            connection.createStatement().execute(s);
+                            System.out.println("update-sequences complete");
+                        } else {
+                            System.err.println(sqlfile + " contains no SQL to execute");
+                        }
+                    } else {
+                        System.err.println(sqlfile + " not found");
+                    }
+                }
             } else {
                 System.out.println("\nUsage: database [action]");
-                System.out.println("Valid actions: 'test', 'info', 'migrate', 'repair' or 'clean'");
+                System.out.println("Valid actions: 'test', 'info', 'migrate', 'repair', " +
+                    "'update-sequences' or 'clean'");
                 System.out.println(
-                    " - test          = Performs a test connection to database to validate connection settings");
+                    " - test             = Performs a test connection to database to " +
+                    "validate connection settings");
                 System.out.println(
                     " - info / status    = Describe basic info/status about database, including validating the " +
                     "compatibility of this database");
-                System.out.println(" - migrate       = Migrate the database to the latest version");
                 System.out.println(
-                    " - repair        = Attempt to repair any previously failed database migrations or checksum " +
+                    " - migrate          = Migrate the database to the latest version");
-                        "mismatches (via Flyway repair)");
+                System.out.println(
+                    " - repair           = Attempt to repair any previously failed database " +
+                    "migrations or checksum mismatches (via Flyway repair)");
                 System.out.println(
                     " - validate         = Validate current database's migration status (via Flyway validate), " +
                     "validating all migration checksums.");
                 System.out.println(
-                    " - clean         = DESTROY all data and tables in database (WARNING there is no going back!). " +
+                    " - update-sequences = Update database sequences after running AIP ingest.");
+                System.out.println(
+                    " - clean            = DESTROY all data and tables in database " +
+                    "(WARNING there is no going back!). " +
                     "Requires 'db.cleanDisabled=false' setting in config.");
                 System.out.println("");
                 System.exit(0);

dspace-api/src/main/java/org/dspace/util/SolrImportExport.java

@@ -31,7 +31,7 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.apache.solr.client.solrj.request.AbstractUpdateRequest;
 import org.apache.solr.client.solrj.request.ContentStreamUpdateRequest;
 import org.apache.solr.client.solrj.request.CoreAdminRequest;
@@ -275,7 +275,7 @@ public class SolrImportExport {
         }
 
         try {
-            HttpSolrServer adminSolr = new HttpSolrServer(baseSolrUrl);
+            HttpSolrClient adminSolr = new HttpSolrClient.Builder(baseSolrUrl).build();
 
             // try to find out size of core and compare with free space in export directory
             CoreAdminResponse status = CoreAdminRequest.getStatus(indexName, adminSolr);
@@ -342,7 +342,7 @@ public class SolrImportExport {
             }
 
             // commit changes
-            HttpSolrServer origSolr = new HttpSolrServer(origSolrUrl);
+            HttpSolrClient origSolr = new HttpSolrClient.Builder(origSolrUrl).build();
             origSolr.commit();
 
             // swap back (statistics now going to actual core name in actual data dir)
@@ -424,7 +424,7 @@ public class SolrImportExport {
                                                     + indexName);
         }
 
-        HttpSolrServer solr = new HttpSolrServer(solrUrl);
+        HttpSolrClient solr = new HttpSolrClient.Builder(solrUrl).build();
 
         // must get multivalue fields before clearing
         List<String> multivaluedFields = getMultiValuedFields(solr);
@@ -471,7 +471,7 @@ public class SolrImportExport {
      * @param solr the solr server to query.
      * @return A list containing all multi-valued fields, or an empty list if none are found / there aren't any.
      */
-    private static List<String> getMultiValuedFields(HttpSolrServer solr) {
+    private static List<String> getMultiValuedFields(HttpSolrClient solr) {
         List<String> result = new ArrayList<>();
         try {
             LukeRequest request = new LukeRequest();
@@ -497,7 +497,7 @@ public class SolrImportExport {
      * @throws SolrServerException if there is a problem in communicating with Solr.
      */
     public static void clearIndex(String solrUrl) throws IOException, SolrServerException {
-        HttpSolrServer solr = new HttpSolrServer(solrUrl);
+        HttpSolrClient solr = new HttpSolrClient.Builder(solrUrl).build();
         solr.deleteByQuery("*:*");
         solr.commit();
         solr.optimize();
@@ -536,7 +536,7 @@ public class SolrImportExport {
                                                     + indexName);
         }
 
-        HttpSolrServer solr = new HttpSolrServer(solrUrl);
+        HttpSolrClient solr = new HttpSolrClient.Builder(solrUrl).build();
 
         SolrQuery query = new SolrQuery("*:*");
         if (StringUtils.isNotBlank(fromWhen)) {

dspace-api/src/main/java/org/dspace/util/SolrUpgradePre6xStatistics.java

@@ -24,10 +24,9 @@ import org.apache.commons.cli.PosixParser;
 import org.apache.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.apache.solr.client.solrj.response.FacetField;
 import org.apache.solr.client.solrj.response.QueryResponse;
-import org.apache.solr.client.solrj.util.ClientUtils;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrDocumentList;
 import org.apache.solr.common.SolrInputDocument;
@@ -92,7 +91,7 @@ public class SolrUpgradePre6xStatistics {
     private int numProcessed = 0;
     private long totalCache = 0;
     private long numUncache = 0;
-    private List<SolrInputDocument> docs = new ArrayList<SolrInputDocument>();
+    private final List<SolrInputDocument> docs = new ArrayList<>();
     private Context context;
 
     //Enum to identify the named SOLR statistics fields to update
@@ -122,7 +121,7 @@ public class SolrUpgradePre6xStatistics {
 
     // This code will operate on one shard at a time, therefore the SOLR web service will be accessed directly rather
     // than make use of the DSpace Solr Logger which only writes to the current shard
-    private HttpSolrServer server;
+    private final HttpSolrClient server;
 
     //Allows for smart use of hibernate cache
     private Item lastItem = null;
@@ -137,6 +136,7 @@ public class SolrUpgradePre6xStatistics {
      * Construct the utility class from the command line options
      * @param indexName name of the statistics shard to update
      * @param numRec    maximum number of records to process
+     * @param batchSize batch this many documents before updating.
      * @throws IOException
      * @throws SolrServerException
      */
@@ -145,8 +145,8 @@ public class SolrUpgradePre6xStatistics {
         String serverPath = configurationService.getProperty("solr-statistics.server");
         serverPath = serverPath.replaceAll("statistics$", indexName);
         System.out.println("Connecting to " + serverPath);
-        server = new HttpSolrServer(serverPath);
+        server = new HttpSolrClient.Builder(serverPath)
-        server.setMaxTotalConnections(1);
+                .build();
         this.numRec = numRec;
         this.batchSize = batchSize;
         refreshContext();
@@ -374,7 +374,7 @@ public class SolrUpgradePre6xStatistics {
     /*
      * Report on the existence of legacy id records within a shard
      */
-    private void runReport() throws SolrServerException {
+    private void runReport() throws SolrServerException, IOException {
         System.out.println();
         System.out.println("=================================================================");
         System.out.println("\t*** Statistics Records with Legacy Id ***\n");
@@ -388,10 +388,9 @@ public class SolrUpgradePre6xStatistics {
     /*
      * Report on the existence of specific legacy id records within a shard
      */
-    private long runReportQuery() throws SolrServerException {
+    private long runReportQuery() throws SolrServerException, IOException {
-        StringBuilder sb = new StringBuilder(MIGQUERY);
         SolrQuery sQ = new SolrQuery();
-        sQ.setQuery(sb.toString());
+        sQ.setQuery(MIGQUERY);
         sQ.setFacet(true);
         sQ.addFacetField("type");
         sQ.addFacetField("scopeType");
@@ -495,7 +494,10 @@ public class SolrUpgradePre6xStatistics {
 
         for (int i = 0; i < sdl.size() && (numProcessed < numRec); i++) {
             SolrDocument sd = sdl.get(i);
-            SolrInputDocument input = ClientUtils.toSolrInputDocument(sd);
+            SolrInputDocument input = new SolrInputDocument(); //ClientUtils.toSolrInputDocument(sd);
+            for (String name : sd.getFieldNames()) { // https://stackoverflow.com/a/38536843/2916377
+                input.addField(name, sd.getFieldValue(name));
+            }
             input.remove("_version_");
             for (FIELD col : FIELD.values()) {
                 mapField(input, col);

dspace-api/src/main/java/org/dspace/workflowbasic/BasicWorkflowItem.java

@@ -21,14 +21,12 @@ import javax.persistence.OneToOne;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
-import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
 import org.dspace.content.Item;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
 import org.dspace.workflow.WorkflowItem;
-import org.dspace.workflow.factory.WorkflowServiceFactory;
 
 /**
  * Class representing an item going through the workflow process in DSpace
@@ -188,20 +186,6 @@ public class BasicWorkflowItem implements WorkflowItem {
         this.publishedBefore = b;
     }
 
-    @Override
-    public void update() throws SQLException, AuthorizeException {
-
-        Context context = null;
-        try {
-            context = new Context();
-            WorkflowServiceFactory.getInstance().getWorkflowItemService().update(context, this);
-        } finally {
-            if (context != null && context.isValid()) {
-                context.abort();
-            }
-        }
-    }
-
     @Override
     public int getType() {
         return Constants.WORKFLOWITEM;

dspace-api/src/main/java/org/dspace/xmlworkflow/XmlWorkflowServiceImpl.java

@@ -315,6 +315,11 @@ public class XmlWorkflowServiceImpl implements XmlWorkflowService {
             Step currentStep = currentActionConfig.getStep();
             if (currentActionConfig.getProcessingAction().isAuthorized(c, request, wi)) {
                 ActionResult outcome = currentActionConfig.getProcessingAction().execute(c, wi, currentStep, request);
+                // the cancel action is the default when the request is not understood or a "back to mydspace" was
+                // pressed in the old UI
+                if (outcome.getType() == ActionResult.TYPE.TYPE_CANCEL) {
+                    throw new WorkflowException("Unprocessable request for the action " + currentStep.getId());
+                }
                 c.addEvent(new Event(Event.MODIFY, Constants.ITEM, wi.getItem().getID(), null,
                         itemService.getIdentifiers(c, wi.getItem())));
                 return processOutcome(c, user, workflow, currentStep, currentActionConfig, outcome, wi, false);
@@ -668,6 +673,8 @@ public class XmlWorkflowServiceImpl implements XmlWorkflowService {
             removeUserItemPolicies(c, wi.getItem(), task.getOwner());
             claimedTaskService.delete(c, task);
         }
+        c.addEvent(new Event(Event.MODIFY, Constants.ITEM, wi.getItem().getID(), null,
+                itemService.getIdentifiers(c, wi.getItem())));
     }
 
     /*
@@ -1058,17 +1065,10 @@ public class XmlWorkflowServiceImpl implements XmlWorkflowService {
     }
 
     protected void revokeReviewerPolicies(Context context, Item item) throws SQLException, AuthorizeException {
-        // get bundle "ORIGINAL"
+        List<Bundle> bundles = item.getBundles();
-        Bundle originalBundle;
-        try {
-            originalBundle = itemService.getBundles(item, "ORIGINAL").get(0);
-        } catch (IndexOutOfBoundsException ex) {
-            originalBundle = null;
-        }
 
+        for (Bundle originalBundle : bundles) {
             // remove bitstream and bundle level policies
-        if (originalBundle != null) {
-            // We added policies for Bitstreams of the bundle "original" only
             for (Bitstream bitstream : originalBundle.getBitstreams()) {
                 authorizeService.removeAllPoliciesByDSOAndType(context, bitstream, ResourcePolicy.TYPE_WORKFLOW);
             }

dspace-api/src/main/java/org/dspace/xmlworkflow/factory/XmlWorkflowFactory.java

@@ -28,6 +28,8 @@ import org.dspace.xmlworkflow.state.actions.WorkflowActionConfig;
  */
 public interface XmlWorkflowFactory {
 
+    public final String LEGACY_WORKFLOW_NAME = "default";
+
     public Workflow getWorkflow(Collection collection) throws IOException, WorkflowConfigurationException, SQLException;
 
     public Step createStep(Workflow workflow, String stepID) throws WorkflowConfigurationException, IOException;

dspace-api/src/main/java/org/dspace/xmlworkflow/storedcomponents/ClaimedTask.java

@@ -7,9 +7,6 @@
  */
 package org.dspace.xmlworkflow.storedcomponents;
 
-import java.util.HashMap;
-import java.util.Map;
-
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
@@ -20,7 +17,6 @@ import javax.persistence.JoinColumn;
 import javax.persistence.ManyToOne;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
-import javax.persistence.Transient;
 
 import org.dspace.browse.IndexableObject;
 import org.dspace.core.Constants;
@@ -40,9 +36,6 @@ import org.dspace.eperson.EPerson;
 @Table(name = "cwf_claimtask")
 public class ClaimedTask implements ReloadableEntity<Integer>, IndexableObject<Integer> {
 
-    @Transient
-    public transient Map<String, Object> extraInfo = new HashMap<String, Object>();
-
     @Id
     @Column(name = "claimtask_id")
     @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "cwf_claimtask_seq")
@@ -126,7 +119,7 @@ public class ClaimedTask implements ReloadableEntity<Integer>, IndexableObject<I
 
     @Override
     public int getType() {
-        return Constants.WORKFLOW_CLAIMED;
+        return Constants.CLAIMEDTASK;
     }
 
 }

dspace-api/src/main/java/org/dspace/xmlworkflow/storedcomponents/ClaimedTaskServiceImpl.java

@@ -39,7 +39,7 @@ public class ClaimedTaskServiceImpl implements ClaimedTaskService {
 
     @Override
     public int getSupportsTypeConstant() {
-        return Constants.WORKFLOW_CLAIMED;
+        return Constants.CLAIMEDTASK;
     }
 
     @Override

dspace-api/src/main/java/org/dspace/xmlworkflow/storedcomponents/PoolTask.java

@@ -7,9 +7,6 @@
  */
 package org.dspace.xmlworkflow.storedcomponents;
 
-import java.util.HashMap;
-import java.util.Map;
-
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
@@ -21,7 +18,6 @@ import javax.persistence.ManyToOne;
 import javax.persistence.OneToOne;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
-import javax.persistence.Transient;
 
 import org.dspace.browse.IndexableObject;
 import org.dspace.core.Constants;
@@ -42,9 +38,6 @@ import org.dspace.eperson.Group;
 @Table(name = "cwf_pooltask")
 public class PoolTask implements ReloadableEntity<Integer>, IndexableObject<Integer> {
 
-    @Transient
-    public transient Map<String, Object> extraInfo = new HashMap<String, Object>();
-
     @Id
     @Column(name = "pooltask_id")
     @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "cwf_pooltask_seq")
@@ -141,7 +134,7 @@ public class PoolTask implements ReloadableEntity<Integer>, IndexableObject<Inte
 
     @Override
     public int getType() {
-        return Constants.WORKFLOW_POOL;
+        return Constants.POOLTASK;
     }
 
 }

dspace-api/src/main/java/org/dspace/xmlworkflow/storedcomponents/PoolTaskServiceImpl.java

@@ -50,7 +50,7 @@ public class PoolTaskServiceImpl implements PoolTaskService {
 
     @Override
     public int getSupportsTypeConstant() {
-        return Constants.WORKFLOW_POOL;
+        return Constants.POOLTASK;
     }
 
     @Override

dspace-api/src/main/java/org/dspace/xmlworkflow/storedcomponents/XmlWorkflowItem.java

@@ -21,7 +21,6 @@ import javax.persistence.OneToOne;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
-import org.dspace.authorize.AuthorizeException;
 import org.dspace.browse.IndexableObject;
 import org.dspace.content.Collection;
 import org.dspace.content.Item;
@@ -30,7 +29,6 @@ import org.dspace.core.Context;
 import org.dspace.core.ReloadableEntity;
 import org.dspace.eperson.EPerson;
 import org.dspace.workflow.WorkflowItem;
-import org.dspace.workflow.factory.WorkflowServiceFactory;
 
 /**
  * Class representing an item going through the workflow process in DSpace
@@ -139,20 +137,6 @@ public class XmlWorkflowItem implements WorkflowItem, ReloadableEntity<Integer>,
         this.publishedBefore = b;
     }
 
-    @Override
-    public void update() throws SQLException, AuthorizeException {
-
-        Context context = null;
-        try {
-            context = new Context();
-            WorkflowServiceFactory.getInstance().getWorkflowItemService().update(context, this);
-        } finally {
-            if (context != null && context.isValid()) {
-                context.abort();
-            }
-        }
-    }
-
     @Override
     public int getState() {
         // FIXME not used by the xml workflow, should be removed when the basic workflow is removed and the interfaces

dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/oracle/update-sequences.sql

@@ -0,0 +1,79 @@
+--
+-- 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/
+--
+
+-- SQL code to update the ID (primary key) generating sequences, if some
+-- import operation has set explicit IDs.
+--
+-- Sequences are used to generate IDs for new rows in the database.  If a
+-- bulk import operation, such as an SQL dump, specifies primary keys for
+-- imported data explicitly, the sequences are out of sync and need updating.
+-- This SQL code does just that.
+--
+-- This should rarely be needed; any bulk import should be performed using the
+-- org.dspace.content API which is safe to use concurrently and in multiple
+-- JVMs.  The SQL code below will typically only be required after a direct
+-- SQL data dump from a backup or somesuch.
+
+-- The 'updateseq' procedure was derived from incseq.sql found at:
+-- http://www.akadia.com/services/scripts/incseq.sql
+
+DECLARE
+ PROCEDURE updateseq ( seq IN VARCHAR,
+                       tbl IN VARCHAR,
+                       attr IN VARCHAR,
+                       cond IN VARCHAR DEFAULT '' ) IS
+   curr NUMBER := 0;
+   BEGIN
+     EXECUTE IMMEDIATE 'SELECT max(' || attr
+             || ') FROM ' || tbl
+             || ' ' || cond
+             INTO curr;
+     curr := curr + 1;
+     EXECUTE IMMEDIATE 'DROP SEQUENCE ' || seq;
+     EXECUTE IMMEDIATE 'CREATE SEQUENCE '
+             || seq
+             || ' START WITH '
+             || NVL(curr, 1);
+   END updateseq;
+
+BEGIN
+  updateseq('bitstreamformatregistry_seq', 'bitstreamformatregistry',
+            'bitstream_format_id');
+  updateseq('fileextension_seq', 'fileextension', 'file_extension_id');
+  updateseq('resourcepolicy_seq', 'resourcepolicy', 'policy_id');
+  updateseq('workspaceitem_seq', 'workspaceitem', 'workspace_item_id');
+  updateseq('workflowitem_seq', 'workflowitem', 'workflow_id');
+  updateseq('tasklistitem_seq', 'tasklistitem', 'tasklist_id');
+  updateseq('registrationdata_seq', 'registrationdata',
+            'registrationdata_id');
+  updateseq('subscription_seq', 'subscription', 'subscription_id');
+  updateseq('metadatafieldregistry_seq', 'metadatafieldregistry',
+            'metadata_field_id');
+  updateseq('metadatavalue_seq', 'metadatavalue', 'metadata_value_id');
+  updateseq('metadataschemaregistry_seq', 'metadataschemaregistry',
+            'metadata_schema_id');
+  updateseq('harvested_collection_seq', 'harvested_collection', 'id');
+  updateseq('harvested_item_seq', 'harvested_item', 'id');
+  updateseq('webapp_seq', 'webapp', 'webapp_id');
+  updateseq('requestitem_seq', 'requestitem', 'requestitem_id');
+  updateseq('handle_id_seq', 'handle', 'handle_id');
+
+  -- Handle Sequence is a special case.  Since Handles minted by DSpace
+  -- use the 'handle_seq', we need to ensure the next assigned handle
+  -- will *always* be unique.  So, 'handle_seq' always needs to be set
+  -- to the value of the *largest* handle suffix.  That way when the
+  -- next handle is assigned, it will use the next largest number. This
+  -- query does the following:
+  --   For all 'handle' values which have a number in their suffix
+  --   (after '/'), find the maximum suffix value, convert it to a
+  --   number, and set the 'handle_seq' to start at the next value (see
+  --   updateseq above for more).
+  updateseq('handle_seq', 'handle',
+            q'{to_number(regexp_replace(handle, '.*/', ''), '999999999999')}',
+            q'{WHERE REGEXP_LIKE(handle, '^.*/[0123456789]*$')}');
+END;

dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres/README.md

@@ -17,4 +17,16 @@ not realize you manually ran one or more scripts.
 
 Please see the Flyway Documentation for more information: http://flywaydb.org/
 
+## Using the update-sequences.sql script
+
+The `update-sequences.sql` script in this directory may still be used to update
+your internal database counts if you feel they have gotten out of "sync". This
+may sometimes occur after large restores of content (e.g. when using the DSpace
+[AIP Backup and Restore](https://wiki.duraspace.org/display/DSDOC5x/AIP+Backup+and+Restore) 
+feature).
+
+This `update-sequences.sql` script can be executed by running 
+"dspace database update-sequences". It will not harm your 
+database (or its contents) in any way. It just ensures all database counts (i.e.
+sequences) are properly set to the next available value.
 

dspace-api/src/main/resources/org/dspace/storage/rdbms/sqlmigration/postgres/update-sequences.sql

@@ -1,35 +1,10 @@
 --
--- update-sequences.sql
+-- 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
 --
--- Copyright (c) 2002-2016, The DSpace Foundation.  All rights reserved.
+-- http://www.dspace.org/license/
 --
--- Redistribution and use in source and binary forms, with or without
--- modification, are permitted provided that the following conditions are
--- met:
--- 
--- - Redistributions of source code must retain the above copyright
--- notice, this list of conditions and the following disclaimer.
--- 
--- - Redistributions in binary form must reproduce the above copyright
--- notice, this list of conditions and the following disclaimer in the
--- documentation and/or other materials provided with the distribution.
--- 
--- Neither the name of the DSpace Foundation nor the names of its
--- contributors may be used to endorse or promote products derived from
--- this software without specific prior written permission.
--- 
--- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
--- ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
--- LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
--- A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
--- HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
--- INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
--- BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
--- OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
--- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
--- TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
--- USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
--- DAMAGE.
 
 -- SQL code to update the ID (primary key) generating sequences, if some
 -- import operation has set explicit IDs.

dspace-api/src/test/data/dspaceFolder/solr/solr.xml

@@ -0,0 +1,2 @@
+<?xml version='1.0'?>
+<solr/>

dspace-api/src/test/java/org/dspace/curate/CuratorTest.java

@@ -58,7 +58,7 @@ public class CuratorTest
 
         // Get and configure a Curator.
         Curator instance = new Curator();
-        instance.setReporter("-"); // Send any report to standard out. FIXME when DS-3989 is merged
+        instance.setReporter(System.out); // Send any report to standard out.
         instance.addTask(TASK_NAME);
 
         // Configure the run.

dspace-api/src/test/java/org/dspace/curate/ITCurator.java

@@ -0,0 +1,202 @@
+/**
+ * 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.curate;
+
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.regex.Pattern;
+
+import org.dspace.AbstractUnitTest;
+import org.dspace.authorize.AuthorizeException;
+import org.dspace.content.Community;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Site;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.services.ConfigurationService;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Assert;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Drive the Curator and check results.
+ *
+ * @author mhwood
+ */
+public class ITCurator
+        extends AbstractUnitTest {
+    Logger LOG = LoggerFactory.getLogger(ITCurator.class);
+
+    public ITCurator() {
+    }
+
+    @BeforeClass
+    public static void setUpClass() {
+    }
+
+    @AfterClass
+    public static void tearDownClass() {
+    }
+
+    @Before
+    public void setUp() {
+    }
+
+    @After
+    public void tearDown() {
+    }
+
+    /**
+     * The report should contain contributions from all tasks and all curated objects.
+     *
+     * @throws SQLException passed through.
+     * @throws IOException passed through.
+     * @throws AuthorizeException passed through.
+     */
+    @Test
+    public void testCurate_Reporting()
+            throws SQLException, IOException, AuthorizeException {
+        // Configure for testing.
+        ConfigurationService cfg = kernelImpl.getConfigurationService();
+        cfg.setProperty("plugin.named.org.dspace.curate.CurationTask",
+                Task1.class.getName() + " = task1");
+        cfg.addPropertyValue("plugin.named.org.dspace.curate.CurationTask",
+                Task2.class.getName() + " = task2");
+
+        // Create some structure.
+        context.turnOffAuthorisationSystem();
+        Site site = ContentServiceFactory.getInstance()
+                .getSiteService()
+                .findSite(context);
+        Community community = ContentServiceFactory.getInstance()
+                .getCommunityService()
+                .create(null, context);
+
+        // Run some tasks.
+        ListReporter reporter = new ListReporter();
+        Curator curator = new Curator();
+        curator.setReporter(reporter);
+        curator.addTask("task1");
+        curator.addTask("task2");
+        curator.curate(context, site);
+
+        // Validate the results.
+        List<String> report = reporter.getReport();
+        for (String aReport : report) {
+            LOG.info("Report:  {}", aReport);
+        }
+        Pattern pattern;
+        pattern = Pattern.compile(String.format("task1.*%s", site.getHandle()));
+        Assert.assertTrue("A report should mention 'task1' and site's handle",
+                reportMatcher(report, pattern));
+        pattern = Pattern.compile(String.format("task1.*%s", community.getHandle()));
+        Assert.assertTrue("A report should mention 'task1' and the community's handle",
+                reportMatcher(report, pattern));
+        pattern = Pattern.compile(String.format("task2.*%s", site.getHandle()));
+        Assert.assertTrue("A report should mention 'task2' and the Site's handle",
+                reportMatcher(report, pattern));
+        pattern = Pattern.compile(String.format("task2.*%s", community.getHandle()));
+        Assert.assertTrue("A report should mention 'task2' and the community's handle",
+                reportMatcher(report, pattern));
+    }
+
+    /**
+     * Match a collection of strings against a regular expression.\
+     *
+     * @param reports strings to be searched.
+     * @param pattern expression to be matched.
+     * @return true if at least one string matches the expression.
+     */
+    private boolean reportMatcher(List<String> reports, Pattern pattern) {
+        for (String aReport : reports) {
+            if (pattern.matcher(aReport).find()) {
+                return true;
+            }
+        }
+        return false;
+    }
+
+    /**
+     * Dummy curation task for testing.  Reports how it was invoked.
+     *
+     * @author mhwood
+     */
+    public static class Task1 extends AbstractCurationTask {
+        public Task1() {
+        }
+
+        @Override
+        public int perform(DSpaceObject dso)
+                throws IOException {
+            curator.report(String.format(
+                    "Task1 received 'perform' on taskId '%s' for object '%s'%n",
+                    taskId, dso.getHandle()));
+            return Curator.CURATE_SUCCESS;
+        }
+    }
+
+    /**
+     * Dummy curation task for testing.  Reports how it was invoked.
+     *
+     * @author mhwood
+     */
+    public static class Task2 extends AbstractCurationTask {
+        public Task2() {
+        }
+
+        @Override
+        public int perform(DSpaceObject dso) throws IOException {
+            curator.report(String.format(
+                    "Task2 received 'perform' on taskId '%s' for object '%s'%n",
+                    taskId, dso.getHandle()));
+            return Curator.CURATE_SUCCESS;
+        }
+    }
+
+    /**
+     * Absorb report strings into a sequential collection.
+     */
+    class ListReporter
+            implements Appendable {
+        private final List<String> report = new ArrayList<>();
+
+        /**
+         * Get the content of the report accumulator.
+         * @return accumulated reports.
+         */
+        List<String> getReport() {
+            return report;
+        }
+
+        @Override
+        public Appendable append(CharSequence cs)
+                throws IOException {
+            report.add(cs.toString());
+            return this;
+        }
+
+        @Override
+        public Appendable append(CharSequence cs, int i, int i1)
+                throws IOException {
+            throw new UnsupportedOperationException("Not supported yet.");
+        }
+
+        @Override
+        public Appendable append(char c)
+                throws IOException {
+            throw new UnsupportedOperationException("Not supported yet.");
+        }
+    }
+}

dspace-oai/pom.xml

@@ -188,7 +188,7 @@
         <dependency>
             <groupId>org.apache.solr</groupId>
             <artifactId>solr-solrj</artifactId>
-            <version>${solr.version}</version>
+            <version>${solr.client.version}</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.codehaus.woodstox</groupId>

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

@@ -14,7 +14,6 @@ import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.net.ConnectException;
 import java.sql.SQLException;
-import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -27,7 +26,6 @@ import java.util.UUID;
 import javax.xml.stream.XMLStreamException;
 
 import com.lyncode.xoai.dataprovider.exceptions.ConfigurationException;
-import com.lyncode.xoai.dataprovider.exceptions.MetadataBindException;
 import com.lyncode.xoai.dataprovider.exceptions.WritingXmlException;
 import com.lyncode.xoai.dataprovider.xml.XmlOutputContext;
 import org.apache.commons.cli.CommandLine;
@@ -36,9 +34,9 @@ import org.apache.commons.cli.Options;
 import org.apache.commons.cli.PosixParser;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrQuery.ORDER;
-import org.apache.solr.client.solrj.SolrServer;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.common.SolrDocumentList;
 import org.apache.solr.common.SolrInputDocument;
@@ -148,7 +146,7 @@ public class XOAI {
             } else {
                 SolrQuery solrParams = new SolrQuery("*:*")
                     .addField("item.lastmodified")
-                    .addSortField("item.lastmodified", ORDER.desc).setRows(1);
+                    .addSort("item.lastmodified", ORDER.desc).setRows(1);
 
                 SolrDocumentList results = DSpaceSolrSearch.query(solrServerResolver.getServer(), solrParams);
                 if (results.getNumFound() == 0) {
@@ -176,7 +174,7 @@ public class XOAI {
         }
     }
 
-    private int index(Date last) throws DSpaceSolrIndexerException {
+    private int index(Date last) throws DSpaceSolrIndexerException, IOException {
         System.out
             .println("Incremental import. Searching for documents modified after: "
                          + last.toString());
@@ -209,7 +207,7 @@ public class XOAI {
      *         visibility since the last update.
      * @throws DSpaceSolrIndexerException
      */
-    private Iterator<Item> getItemsWithPossibleChangesBefore(Date last) throws DSpaceSolrIndexerException {
+    private Iterator<Item> getItemsWithPossibleChangesBefore(Date last) throws DSpaceSolrIndexerException, IOException {
         try {
             SolrQuery params = new SolrQuery("item.willChangeStatus:true").addField("item.id");
             SolrDocumentList documents = DSpaceSolrSearch.query(solrServerResolver.getServer(), params);
@@ -251,7 +249,7 @@ public class XOAI {
      *            Item that should be checked for its presence in the index.
      * @return has it been indexed?
      */
-    private boolean checkIfIndexed(Item item) {
+    private boolean checkIfIndexed(Item item) throws IOException {
         SolrQuery params = new SolrQuery("item.id:" + item.getID().toString()).addField("item.id");
         try {
             SolrDocumentList documents = DSpaceSolrSearch.query(solrServerResolver.getServer(), params);
@@ -267,7 +265,7 @@ public class XOAI {
      *            Item that should be checked for its presence in the index.
      * @return has it been indexed?
      */
-    private boolean checkIfVisibleInOAI(Item item) {
+    private boolean checkIfVisibleInOAI(Item item) throws IOException {
         SolrQuery params = new SolrQuery("item.id:" + item.getID().toString()).addField("item.public");
         try {
             SolrDocumentList documents = DSpaceSolrSearch.query(solrServerResolver.getServer(), params);
@@ -286,7 +284,7 @@ public class XOAI {
         try {
             int i = 0;
             int batchSize = configurationService.getIntProperty("oai.import.batch.size", 1000);
-            SolrServer server = solrServerResolver.getServer();
+            SolrClient server = solrServerResolver.getServer();
             ArrayList<SolrInputDocument> list = new ArrayList<>();
             while (iterator.hasNext()) {
                 try {
@@ -299,8 +297,7 @@ public class XOAI {
                     //Uncache the item to keep memory consumption low
                     context.uncacheEntity(item);
 
-                } catch (SQLException | MetadataBindException | ParseException
+                } catch (SQLException | IOException | XMLStreamException | WritingXmlException ex) {
-                    | XMLStreamException | WritingXmlException ex) {
                     log.error(ex.getMessage(), ex);
                 }
                 i++;
@@ -363,9 +360,9 @@ public class XOAI {
     }
 
     private SolrInputDocument index(Item item)
-            throws SQLException, MetadataBindException, ParseException, XMLStreamException, WritingXmlException {
+            throws SQLException, IOException, XMLStreamException, WritingXmlException {
         SolrInputDocument doc = new SolrInputDocument();
-        doc.addField("item.id", item.getID());
+        doc.addField("item.id", item.getID().toString());
 
         String handle = item.getHandle();
         doc.addField("item.handle", handle);

dspace-oai/src/main/java/org/dspace/xoai/services/api/solr/SolrServerResolver.java

@@ -7,9 +7,9 @@
  */
 package org.dspace.xoai.services.api.solr;
 
-import org.apache.solr.client.solrj.SolrServer;
+import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrServerException;
 
 public interface SolrServerResolver {
-    SolrServer getServer() throws SolrServerException;
+    SolrClient getServer() throws SolrServerException;
 }

dspace-oai/src/main/java/org/dspace/xoai/services/impl/solr/DSpaceSolrServerResolver.java

@@ -9,25 +9,25 @@ package org.dspace.xoai.services.impl.solr;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.apache.solr.client.solrj.SolrServer;
+import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.dspace.xoai.services.api.config.ConfigurationService;
 import org.dspace.xoai.services.api.solr.SolrServerResolver;
 import org.springframework.beans.factory.annotation.Autowired;
 
 public class DSpaceSolrServerResolver implements SolrServerResolver {
-    private static Logger log = LogManager.getLogger(DSpaceSolrServerResolver.class);
+    private static final Logger log = LogManager.getLogger(DSpaceSolrServerResolver.class);
-    private static SolrServer server = null;
+    private static SolrClient server = null;
 
     @Autowired
     private ConfigurationService configurationService;
 
     @Override
-    public SolrServer getServer() throws SolrServerException {
+    public SolrClient getServer() throws SolrServerException {
         if (server == null) {
             try {
-                server = new HttpSolrServer(configurationService.getProperty("oai", "solr.url"));
+                server = new HttpSolrClient.Builder(configurationService.getProperty("oai", "solr.url")).build();
                 log.debug("Solr Server Initialized");
             } catch (Exception e) {
                 log.error(e.getMessage(), e);

dspace-oai/src/main/java/org/dspace/xoai/services/impl/xoai/DSpaceItemSolrRepository.java

@@ -7,6 +7,7 @@
  */
 package org.dspace.xoai.services.impl.xoai;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.regex.Pattern;
@@ -21,8 +22,8 @@ import com.lyncode.xoai.dataprovider.exceptions.IdDoesNotExistException;
 import com.lyncode.xoai.dataprovider.filter.ScopedFilter;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrQuery;
-import org.apache.solr.client.solrj.SolrServer;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrDocumentList;
 import org.dspace.xoai.data.DSpaceSolrItem;
@@ -37,11 +38,11 @@ import org.dspace.xoai.solr.exceptions.SolrSearchEmptyException;
  * @author Lyncode Development Team (dspace at lyncode dot com)
  */
 public class DSpaceItemSolrRepository extends DSpaceItemRepository {
-    private static Logger log = LogManager.getLogger(DSpaceItemSolrRepository.class);
+    private static final Logger log = LogManager.getLogger(DSpaceItemSolrRepository.class);
-    private SolrServer server;
+    private final SolrClient server;
-    private SolrQueryResolver solrQueryResolver;
+    private final SolrQueryResolver solrQueryResolver;
 
-    public DSpaceItemSolrRepository(SolrServer server, CollectionsService collectionsService,
+    public DSpaceItemSolrRepository(SolrClient server, CollectionsService collectionsService,
                                     HandleResolver handleResolver, SolrQueryResolver solrQueryResolver) {
         super(collectionsService, handleResolver);
         this.server = server;
@@ -58,7 +59,7 @@ public class DSpaceItemSolrRepository extends DSpaceItemRepository {
             try {
                 SolrQuery params = new SolrQuery("item.handle:" + parts[2]);
                 return new DSpaceSolrItem(DSpaceSolrSearch.querySingle(server, params));
-            } catch (SolrSearchEmptyException ex) {
+            } catch (SolrSearchEmptyException | IOException ex) {
                 throw new IdDoesNotExistException(ex);
             }
         }
@@ -79,9 +80,9 @@ public class DSpaceItemSolrRepository extends DSpaceItemRepository {
                     }
                 });
             return new ListItemIdentifiersResult(queryResult.hasMore(), identifierList, queryResult.getTotal());
-        } catch (DSpaceSolrException ex) {
+        } catch (DSpaceSolrException | IOException ex) {
             log.error(ex.getMessage(), ex);
-            return new ListItemIdentifiersResult(false, new ArrayList<ItemIdentifier>());
+            return new ListItemIdentifiersResult(false, new ArrayList<>());
         }
     }
 
@@ -91,14 +92,15 @@ public class DSpaceItemSolrRepository extends DSpaceItemRepository {
         try {
             QueryResult queryResult = retrieveItems(filters, offset, length);
             return new ListItemsResults(queryResult.hasMore(), queryResult.getResults(), queryResult.getTotal());
-        } catch (DSpaceSolrException ex) {
+        } catch (DSpaceSolrException | IOException ex) {
             log.error(ex.getMessage(), ex);
-            return new ListItemsResults(false, new ArrayList<Item>());
+            return new ListItemsResults(false, new ArrayList<>());
         }
     }
 
-    private QueryResult retrieveItems(List<ScopedFilter> filters, int offset, int length) throws DSpaceSolrException {
+    private QueryResult retrieveItems(List<ScopedFilter> filters, int offset, int length)
-        List<Item> list = new ArrayList<Item>();
+            throws DSpaceSolrException, IOException {
+        List<Item> list = new ArrayList<>();
         SolrQuery params = new SolrQuery(solrQueryResolver.buildQuery(filters))
             .setRows(length)
             .setStart(offset);

dspace-oai/src/main/java/org/dspace/xoai/solr/DSpaceSolrSearch.java

@@ -8,9 +8,11 @@
 
 package org.dspace.xoai.solr;
 
+import java.io.IOException;
+
+import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrQuery.ORDER;
-import org.apache.solr.client.solrj.SolrServer;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrDocument;
@@ -28,10 +30,10 @@ public class DSpaceSolrSearch {
      */
     private DSpaceSolrSearch() { }
 
-    public static SolrDocumentList query(SolrServer server, SolrQuery solrParams)
+    public static SolrDocumentList query(SolrClient server, SolrQuery solrParams)
-        throws DSpaceSolrException {
+        throws DSpaceSolrException, IOException {
         try {
-            solrParams.addSortField("item.id", ORDER.asc);
+            solrParams.addSort("item.id", ORDER.asc);
             QueryResponse response = server.query(solrParams);
             return response.getResults();
         } catch (SolrServerException ex) {
@@ -39,10 +41,10 @@ public class DSpaceSolrSearch {
         }
     }
 
-    public static SolrDocument querySingle(SolrServer server, SolrQuery solrParams)
+    public static SolrDocument querySingle(SolrClient server, SolrQuery solrParams)
-        throws SolrSearchEmptyException {
+        throws SolrSearchEmptyException, IOException {
         try {
-            solrParams.addSortField("item.id", ORDER.asc);
+            solrParams.addSort("item.id", ORDER.asc);
             QueryResponse response = server.query(solrParams);
             if (response.getResults().getNumFound() > 0) {
                 return response.getResults().get(0);

dspace-oai/src/main/java/org/dspace/xoai/solr/DSpaceSolrServer.java

@@ -10,29 +10,29 @@ package org.dspace.xoai.solr;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.apache.solr.client.solrj.SolrServer;
+import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrServerException;
-import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.impl.HttpSolrClient;
 import org.dspace.core.ConfigurationManager;
 
 /**
  * @author Lyncode Development Team (dspace at lyncode dot com)
  */
 public class DSpaceSolrServer {
-    private static Logger log = LogManager.getLogger(DSpaceSolrServer.class);
+    private static final Logger log = LogManager.getLogger(DSpaceSolrServer.class);
 
-    private static SolrServer _server = null;
+    private static SolrClient _server = null;
 
     /**
      * Default constructor
      */
     private DSpaceSolrServer() { }
 
-    public static SolrServer getServer() throws SolrServerException {
+    public static SolrClient getServer() throws SolrServerException {
         if (_server == null) {
             try {
-                _server = new HttpSolrServer(
+                _server = new HttpSolrClient.Builder(
-                    ConfigurationManager.getProperty("oai", "solr.url"));
+                    ConfigurationManager.getProperty("oai", "solr.url")).build();
                 log.debug("Solr Server Initialized");
             } catch (Exception e) {
                 log.error(e.getMessage(), e);

dspace-oai/src/test/java/org/dspace/xoai/tests/helpers/stubs/ItemRepositoryBuilder.java

@@ -10,6 +10,7 @@ package org.dspace.xoai.tests.helpers.stubs;
 import static com.lyncode.xoai.dataprovider.core.Granularity.Second;
 
 import java.io.ByteArrayOutputStream;
+import java.io.IOException;
 import java.sql.SQLException;
 import java.text.ParseException;
 import java.util.ArrayList;
@@ -23,13 +24,14 @@ import com.lyncode.xoai.dataprovider.exceptions.MetadataBindException;
 import com.lyncode.xoai.dataprovider.exceptions.WritingXmlException;
 import com.lyncode.xoai.dataprovider.xml.XmlOutputContext;
 import com.lyncode.xoai.dataprovider.xml.xoai.Metadata;
-import org.apache.solr.client.solrj.SolrServer;
+import org.apache.solr.client.solrj.SolrClient;
+import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.common.SolrInputDocument;
 
 public class ItemRepositoryBuilder {
-    private SolrServer solrServer;
+    private final SolrClient solrServer;
 
-    public ItemRepositoryBuilder(SolrServer solrServer) {
+    public ItemRepositoryBuilder(SolrClient solrServer) {
         this.solrServer = solrServer;
     }
 
@@ -37,7 +39,9 @@ public class ItemRepositoryBuilder {
         try {
             solrServer.add(index(builder));
             solrServer.commit();
-        } catch (Exception e) {
+        } catch (MetadataBindException | WritingXmlException | IOException
+                | SQLException | ParseException | XMLStreamException
+                | SolrServerException e) {
             throw new RuntimeException(e);
         }
         return this;
@@ -74,9 +78,9 @@ public class ItemRepositoryBuilder {
     }
 
     public static class DSpaceItemBuilder {
-        private List<String> collections = new ArrayList<String>();
+        private final List<String> collections = new ArrayList<>();
-        private List<String> communities = new ArrayList<String>();
+        private final List<String> communities = new ArrayList<>();
-        private MetadataBuilder metadataBuilder = new MetadataBuilder();
+        private final MetadataBuilder metadataBuilder = new MetadataBuilder();
         private String handle;
         private int id;
         private String submitter;

dspace-oai/src/test/java/org/dspace/xoai/tests/integration/xoai/AbstractDSpaceTest.java

@@ -19,7 +19,7 @@ import com.lyncode.xoai.dataprovider.services.api.ResourceResolver;
 import com.lyncode.xoai.dataprovider.services.impl.BaseDateProvider;
 import com.lyncode.xoai.dataprovider.xml.xoaiconfig.Configuration;
 import com.lyncode.xoai.dataprovider.xml.xoaiconfig.FormatConfiguration;
-import org.apache.solr.client.solrj.SolrServer;
+import org.apache.solr.client.solrj.SolrClient;
 import org.dspace.xoai.controller.DSpaceOAIDataProvider;
 import org.dspace.xoai.services.api.EarliestDateResolver;
 import org.dspace.xoai.services.api.FieldResolver;
@@ -51,7 +51,7 @@ import org.springframework.web.context.WebApplicationContext;
 @WebAppConfiguration
 @ContextConfiguration(classes = {DSpaceTestConfiguration.class, DSpaceOAIDataProvider.class})
 public abstract class AbstractDSpaceTest {
-    private static BaseDateProvider baseDateProvider = new BaseDateProvider();
+    private static final BaseDateProvider baseDateProvider = new BaseDateProvider();
     @Autowired
     WebApplicationContext wac;
     private MockMvc mockMvc;
@@ -62,7 +62,7 @@ public abstract class AbstractDSpaceTest {
     private StubbedEarliestDateResolver earliestDateResolver;
     private StubbedSetRepository setRepository;
     private StubbedResourceResolver resourceResolver;
-    private SolrServer solrServer;
+    private SolrClient solrServer;
 
     @Before
     public void setup() {

dspace-services/src/main/java/org/dspace/servicemanager/config/DSpaceConfigurationService.java

@@ -346,6 +346,26 @@ public final class DSpaceConfigurationService implements ConfigurationService {
         }
     }
 
+    @Override
+    public synchronized boolean addPropertyValue(String name, Object value) {
+        if (name == null) {
+            throw new IllegalArgumentException("name cannot be null for setting configuration");
+        }
+        if (value == null) {
+            throw new IllegalArgumentException("configuration value may not be null");
+        }
+
+        // If the value is a type of String, trim any leading/trailing spaces before saving it.
+        if (String.class.isInstance(value)) {
+            value = ((String) value).trim();
+        }
+
+        Configuration configuration = getConfiguration();
+        boolean isNew = !configuration.containsKey(name);
+        configuration.addProperty(name, value);
+        return isNew;
+    }
+
     /* (non-Javadoc)
      * @see org.dspace.services.ConfigurationService#setProperty(java.lang.String, java.lang.Object)
      */

dspace-services/src/main/java/org/dspace/servicemanager/config/DSpaceEnvironmentConfiguration.java

@@ -0,0 +1,98 @@
+/**
+ * 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.servicemanager.config;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.commons.configuration2.MapConfiguration;
+import org.apache.commons.lang3.StringUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Bash does not allow environment variables that contain dots in their name.
+ * This Configuration loads environment variables that contains two underlines
+ * and replaces "__P__" -> "." and "__D__" -> "-"
+ * E.g.: dspace__P__baseUrl will be read as dspace.baseUrl.
+ * E.g.: my__D__dspace__P__prop will be read as my-dspace.prop.
+ *
+ * Most of this file was copied from org.apache.commons.configuration2.EnvironmentConfiguration.
+ *
+ * @author Pascal-Nicolas Becker -- dspace at pascal dash becker dot de
+ */
+public class DSpaceEnvironmentConfiguration extends MapConfiguration {
+
+    private static Logger log = LoggerFactory.getLogger(DSpaceEnvironmentConfiguration.class);
+
+    /**
+     * Create a Configuration based on the environment variables.
+     *
+     * @see System#getenv()
+     */
+    public DSpaceEnvironmentConfiguration() {
+        super(getModifiedEnvMap());
+    }
+
+    public static Map<String, Object> getModifiedEnvMap() {
+        HashMap<String, Object> env = new HashMap<>(System.getenv().size());
+        for (String key : System.getenv().keySet()) {
+            // ignore all properties that do not contain __ as those will be loaded
+            // by apache commons config environment lookup.
+            if (!StringUtils.contains(key, "__")) {
+                continue;
+            }
+
+            // replace "__P__" with a single dot.
+            // replace "__D__" with a single dash.
+            String lookup = StringUtils.replace(key, "__P__", ".");
+            lookup = StringUtils.replace(lookup, "__D__", "-");
+            if (System.getenv(key) != null) {
+                // store the new key with the old value in our new properties map.
+                env.put(lookup, System.getenv(key));
+                log.debug("Found env " + lookup + " = " + System.getenv(key) + ".");
+            } else {
+                log.debug("Didn't found env " + lookup + ".");
+            }
+        }
+        return env;
+    }
+
+    /**
+     * Adds a property to this configuration. Because this configuration is
+     * read-only, this operation is not allowed and will cause an exception.
+     *
+     * @param key   the key of the property to be added
+     * @param value the property value
+     */
+    @Override
+    protected void addPropertyDirect(String key, Object value) {
+        throw new UnsupportedOperationException("EnvironmentConfiguration is read-only!");
+    }
+
+    /**
+     * Removes a property from this configuration. Because this configuration is
+     * read-only, this operation is not allowed and will cause an exception.
+     *
+     * @param key the key of the property to be removed
+     */
+    @Override
+    protected void clearPropertyDirect(String key) {
+        throw new UnsupportedOperationException("EnvironmentConfiguration is read-only!");
+    }
+
+    /**
+     * Removes all properties from this configuration. Because this
+     * configuration is read-only, this operation is not allowed and will cause
+     * an exception.
+     */
+    @Override
+    protected void clearInternal() {
+        throw new UnsupportedOperationException("EnvironmentConfiguration is read-only!");
+    }
+}

dspace-services/src/main/java/org/dspace/servicemanager/config/DSpaceEnvironmentConfigurationBuilderProvider.java

@@ -0,0 +1,33 @@
+/**
+ * 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.servicemanager.config;
+
+import java.util.Collections;
+
+import org.apache.commons.configuration2.builder.BasicBuilderParameters;
+import org.apache.commons.configuration2.builder.combined.BaseConfigurationBuilderProvider;
+
+/**
+ * Configures DSpaceEnvironmentConfiguration. Reuses BasicConfigurationBuilder and its parameters.
+ *
+ * @author Pascal-Nicolas Becker -- dspace at pascal dash becker dot de
+ */
+public class DSpaceEnvironmentConfigurationBuilderProvider extends BaseConfigurationBuilderProvider {
+
+    /**
+     * Creates a new instance of {@code BaseConfigurationBuilderProvider} and
+     * initializes all its properties.
+     */
+    public DSpaceEnvironmentConfigurationBuilderProvider() {
+        super("org.apache.commons.configuration2.builder.BasicConfigurationBuilder",
+                null,
+                "org.dspace.servicemanager.config.DSpaceEnvironmentConfiguration",
+                // this probably contains much more than we need, nevertheless reusing it is easier than rewriting
+                Collections.singleton(BasicBuilderParameters.class.getName()));
+    }
+}

dspace-services/src/main/java/org/dspace/services/ConfigurationService.java

@@ -237,6 +237,16 @@ public interface ConfigurationService {
      */
     public boolean hasProperty(String name);
 
+    /**
+     * Add a value to a configuration property.
+     *
+     * @param name the property name.  May not be null.
+     * @param value the property value.  May not be null.
+     * @return true if a new property was created.
+     * @throws IllegalArgumentException if the name or value is null.
+     */
+    public boolean addPropertyValue(String name, Object value);
+
     /**
      * Set a configuration property (setting) in the system.
      * Type is not important here since conversion happens automatically

dspace-solr/pom.xml

@@ -1,297 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-
-    <!--
-       Licensed to the Apache Software Foundation (ASF) under one or more
-       contributor license agreements. See the NOTICE file distributed
-       with this work for additional information regarding copyright
-       ownership. The ASF licenses this file to you under the Apache
-       License, Version 2.0 (the "License"); you may not use this file
-       except in compliance with the License. You may obtain a copy of
-       the License at http://www.apache.org/licenses/LICENSE-2.0 Unless
-       required by applicable law or agreed to in writing, software
-       distributed under the License is distributed on an "AS IS" BASIS,
-       WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
-       implied. See the License for the specific language governing
-       permissions and limitations under the License.
-    -->
-
-    <modelVersion>4.0.0</modelVersion>
-
-    <parent>
-        <groupId>org.dspace</groupId>
-        <artifactId>dspace-parent</artifactId>
-        <version>7.0-SNAPSHOT</version>
-        <relativePath>..</relativePath>
-    </parent>
-
-    <groupId>org.dspace</groupId>
-    <artifactId>dspace-solr</artifactId>
-    <name>Apache Solr Webapp</name>
-    <description>Apache Solr Server</description>
-    <packaging>war</packaging>
-
-    <properties>
-        <!-- WARNING: When updating this dependency be sure to check the "zookeeper" pinned version !-->
-        <solr.version>4.10.4</solr.version>
-        <!-- 'root.basedir' is the path to the root [dspace-src] dir. It must be redefined by each child POM,
-             as it is used to reference the LICENSE_HEADER and *.properties file(s) in that directory. -->
-        <root.basedir>${basedir}/..</root.basedir>
-    </properties>
-
-    <build>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-war-plugin</artifactId>
-                <configuration>
-                    <!-- This 'dspace-solr' WAR overlays the Apache Solr Web Application
-                         available in Maven Central -->
-                    <overlays>
-                        <overlay>
-                            <groupId>org.apache.solr</groupId>
-                            <artifactId>solr</artifactId>
-                            <!--
-                            Exclude the solr core named apache-solr-core, this is needed because the dspace-solr changes
-                            need to take precendence over the solr-core, the solr-core will still be loaded in the solr-core.jar
-                            -->
-                            <excludes>
-                                <exclude>WEB-INF/lib/apache-solr-core-${solr.version}.jar</exclude>
-                            </excludes>
-                        </overlay>
-                    </overlays>
-                    <!-- Filter the web.xml (needed for IDE compatibility/debugging) -->
-                    <filteringDeploymentDescriptors>true</filteringDeploymentDescriptors>
-                </configuration>
-                <executions>
-                    <execution>
-                        <!-- This execution creates a normal WAR (with all JARs, etc)-->
-                        <id>webapp</id>
-                        <configuration>
-                            <primaryArtifact>true</primaryArtifact>
-                            <archiveClasses>true</archiveClasses>
-                            <attachClasses>true</attachClasses>
-                            <classesClassifier>classes</classesClassifier>
-                            <warSourceExcludes>WEB-INF/classes/**</warSourceExcludes>
-                            <packagingExcludes>
-                                WEB-INF/classes/**,
-                                WEB-INF/lib/slf4j-jdk14-*.jar,
-                                WEB-INF/lib/log4j-over-slf4j-*.jar
-                            </packagingExcludes>
-                        </configuration>
-                        <goals>
-                            <goal>war</goal>
-                        </goals>
-                        <phase>package</phase>
-                    </execution>
-                    <execution>
-                        <!-- This execution creates a "skinny" WAR (without any JARs included)-->
-                        <id>skinny</id>
-                        <configuration>
-                            <primaryArtifact>false</primaryArtifact>
-                            <classifier>skinny</classifier>
-                            <warSourceExcludes>WEB-INF/lib/**,WEB-INF/classes/**</warSourceExcludes>
-                            <packagingExcludes>WEB-INF/lib/**,WEB-INF/classes/**</packagingExcludes>
-                        </configuration>
-                        <goals>
-                            <goal>war</goal>
-                        </goals>
-                        <phase>package</phase>
-                    </execution>
-                </executions>
-            </plugin>
-        </plugins>
-    </build>
-
-    <dependencies>
-        <!-- Depends on the Apache 'solr' web application (see Overlay settings above)-->
-        <dependency>
-            <groupId>org.apache.solr</groupId>
-            <artifactId>solr</artifactId>
-            <version>${solr.version}</version>
-            <type>war</type>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.solr</groupId>
-            <artifactId>solr-core</artifactId>
-            <version>${solr.version}</version>
-            <type>jar</type>
-            <exclusions>
-                <exclusion>
-                    <groupId>jdk.tools</groupId>
-                    <artifactId>jdk.tools</artifactId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>javax.servlet</artifactId>
-                    <groupId>org.eclipse.jetty.orbit</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-continuation</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-deploy</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-http</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-io</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-jmx</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-security</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-server</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-servlet</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-util</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-webapp</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-xml</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.zookeeper</groupId>
-		    <artifactId>zookeeper</artifactId>
-                </exclusion>
-		<exclusion>
-                    <groupId>log4j</groupId>
-                    <artifactId>log4j</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.solr</groupId>
-            <artifactId>solr-cell</artifactId>
-            <version>${solr.version}</version>
-            <exclusions>
-                <exclusion>
-                    <artifactId>javax.servlet</artifactId>
-                    <groupId>org.eclipse.jetty.orbit</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-continuation</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-deploy</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-http</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-io</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-jmx</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-security</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-server</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-servlet</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-util</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-webapp</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <artifactId>jetty-xml</artifactId>
-                    <groupId>org.eclipse.jetty</groupId>
-                </exclusion>
-                <exclusion>
-                    <groupId>log4j</groupId>
-                    <artifactId>log4j</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.zookeeper</groupId>
-                    <artifactId>zookeeper</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
-        <!--This version is pinned on this one, since solr introduces both 3.4.5 & 3.4.6-->
-        <dependency>
-            <groupId>org.apache.zookeeper</groupId>
-            <artifactId>zookeeper</artifactId>
-	    <version>3.4.6</version>
-	    <exclusions>
-                <exclusion>
-                    <groupId>log4j</groupId>
-                    <artifactId>log4j</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>slf4j-log4j12</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
-        <!-- Replace J.U.L. logging with log4j -->
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-jul</artifactId>
-            <version>${log4j.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-core</artifactId>
-        </dependency>
-	<dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-web</artifactId>
-	</dependency>
-	<dependency>
-            <groupId>org.apache.logging.log4j</groupId>
-            <artifactId>log4j-slf4j-impl</artifactId>
-	</dependency>
-        <dependency>
-            <groupId>commons-logging</groupId>
-            <artifactId>commons-logging</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>javax.servlet</groupId>
-            <artifactId>javax.servlet-api</artifactId>
-            <scope>provided</scope>
-        </dependency>
-    </dependencies>
-
-</project>

dspace-solr/src/main/java/org/dspace/solr/filters/LocalHostRestrictionFilter.java

@@ -1,65 +0,0 @@
-/**
- * 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.solr.filters;
-
-import java.io.IOException;
-import java.net.InetAddress;
-import javax.servlet.Filter;
-import javax.servlet.FilterChain;
-import javax.servlet.FilterConfig;
-import javax.servlet.ServletException;
-import javax.servlet.ServletRequest;
-import javax.servlet.ServletResponse;
-import javax.servlet.http.HttpServletResponse;
-
-public class LocalHostRestrictionFilter implements Filter {
-
-    private boolean enabled = true;
-
-    public LocalHostRestrictionFilter() {
-        // TODO Auto-generated constructor stub
-    }
-
-    public void destroy() {
-        // TODO Auto-generated method stub
-
-    }
-
-    public void doFilter(ServletRequest request, ServletResponse response,
-                         FilterChain chain)
-        throws IOException, ServletException {
-
-        if (enabled) {
-            InetAddress ia = InetAddress.getLocalHost();
-            String localAddr = ia.getHostAddress();
-            String remoteAddr = request.getRemoteAddr();
-
-            if (!(localAddr.equals(remoteAddr) ||
-                remoteAddr.equals("127.0.0.1") ||
-                remoteAddr.startsWith("0:0:0:0:0:0:0:1"))) {
-                ((HttpServletResponse) response).sendError(403);
-                return;
-            }
-
-        }
-
-        chain.doFilter(request, response);
-    }
-
-    /**
-     *
-     */
-    public void init(FilterConfig arg0)
-        throws ServletException {
-        String restrict = arg0.getServletContext().getInitParameter(
-            "LocalHostRestrictionFilter.localhost");
-        if ("false".equalsIgnoreCase(restrict)) {
-            enabled = false;
-        }
-    }
-}

dspace-solr/src/main/webapp/WEB-INF/web.xml

@@ -1,213 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!--
-
-    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/
-
--->
-
-<web-app version='2.5'
-         xmlns='http://java.sun.com/xml/ns/javaee'
-         xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance'
-         xsi:schemaLocation='http://java.sun.com/xml/ns/javaee
-	      http://java.sun.com/xml/ns/javaee/web-app_2_5.xsd'>
-
-    <!-- Uncomment if you are trying to use a Resin version before 3.0.19.
-      Their XML implementation isn't entirely compatible with Xerces.
-      Below are the implementations to use with Sun's JVM.
-    <system-property javax.xml.xpath.XPathFactory=
-               "com.sun.org.apache.xpath.internal.jaxp.XPathFactoryImpl"/>
-    <system-property javax.xml.parsers.DocumentBuilderFactory=
-               "com.sun.org.apache.xerces.internal.jaxp.DocumentBuilderFactoryImpl"/>
-    <system-property javax.xml.parsers.SAXParserFactory=
-               "com.sun.org.apache.xerces.internal.jaxp.SAXParserFactoryImpl"/>
-     -->
-
-    <env-entry>
-        <description>Solr home:  configuration, cores etc.</description>
-        <env-entry-name>solr/home</env-entry-name>
-        <env-entry-value>${dspace.dir}/solr</env-entry-value>
-        <env-entry-type>java.lang.String</env-entry-type>
-    </env-entry>
-
-    <!-- Tell Solr where its log4j configuration is located -->
-    <!-- NOTE: Solr cannot use the default DSpace log4j configuration as it
-         isn't initialized until the DSpace Kernel starts up, and we don't want
-         Solr to depend on the DSpace Kernel/API -->
-    <context-param>
-        <description>
-	    URL locating a Log4J configuration file (properties or XML).
-	</description>
-        <param-name>log4jConfiguration</param-name>
-        <param-value>${dspace.dir}/config/log4j-solr.xml</param-value>
-    </context-param>
-
-    <listener>
-        <listener-class>org.apache.logging.log4j.web.Log4jServletContextListener</listener-class>
-    </listener>
-
-    <filter>
-        <description>Activate logging</description>
-        <filter-name>log4jServletFilter</filter-name>
-        <filter-class>org.apache.logging.log4j.web.Log4jServletFilter</filter-class>
-    </filter>
-
-    <!-- Any path (name) registered in solrconfig.xml will be sent to that filter -->
-    <filter>
-        <filter-name>LocalHostRestrictionFilter</filter-name>
-        <filter-class>org.dspace.solr.filters.LocalHostRestrictionFilter</filter-class>
-    </filter>
-
-    <!-- Any path (name) registered in solrconfig.xml will be sent to that filter -->
-    <filter>
-        <filter-name>SolrRequestFilter</filter-name>
-        <filter-class>org.apache.solr.servlet.SolrDispatchFilter</filter-class>
-        <!-- If you are wiring Solr into a larger web application which controls
-             the web context root, you will probably want to mount Solr under
-             a path prefix (app.war with /app/solr mounted into it, for example).
-             You will need to put this prefix in front of the SolrDispatchFilter
-             url-pattern mapping too (/solr/*), and also on any paths for
-             legacy Solr servlet mappings you may be using.
-             For the Admin UI to work properly in a path-prefixed configuration,
-             the admin folder containing the resources needs to be under the app context root
-             named to match the path-prefix.  For example:
-
-                .war
-                   xxx
-                     js
-                       main.js
-        -->
-        <!--
-        <init-param>
-          <param-name>path-prefix</param-name>
-          <param-value>/xxx</param-value>
-        </init-param>
-        -->
-    </filter>
-
-    <filter-mapping>
-        <filter-name>log4jServletFilter</filter-name>
-        <url-pattern>/*</url-pattern>
-        <dispatcher>REQUEST</dispatcher>
-        <dispatcher>FORWARD</dispatcher>
-        <dispatcher>INCLUDE</dispatcher>
-        <dispatcher>ERROR</dispatcher>
-    </filter-mapping>
-
-    <filter-mapping>
-        <filter-name>LocalHostRestrictionFilter</filter-name>
-        <url-pattern>/*</url-pattern>
-    </filter-mapping>
-
-    <filter-mapping>
-        <!--
-          NOTE: When using multicore, /admin JSP URLs with a core specified
-          such as /solr/coreName/admin/stats.jsp get forwarded by a
-          RequestDispatcher to /solr/admin/stats.jsp with the specified core
-          put into request scope keyed as "org.apache.solr.SolrCore".
-
-          It is unnecessary, and potentially problematic, to have the SolrDispatchFilter
-          configured to also filter on forwards.  Do not configure
-          this dispatcher as <dispatcher>FORWARD</dispatcher>.
-        -->
-        <filter-name>SolrRequestFilter</filter-name>
-        <url-pattern>/*</url-pattern>
-    </filter-mapping>
-
-    <!-- Otherwise it will continue to the old servlets -->
-
-    <servlet>
-        <servlet-name>Zookeeper</servlet-name>
-        <servlet-class>org.apache.solr.servlet.ZookeeperInfoServlet</servlet-class>
-    </servlet>
-
-    <servlet>
-        <servlet-name>LoadAdminUI</servlet-name>
-        <servlet-class>org.apache.solr.servlet.LoadAdminUiServlet</servlet-class>
-    </servlet>
-
-    <!-- Remove in Solr 5.0 -->
-    <!-- This sends SC_MOVED_PERMANENTLY (301) for resources that changed in 4.0 -->
-    <servlet>
-        <servlet-name>RedirectOldAdminUI</servlet-name>
-        <servlet-class>org.apache.solr.servlet.RedirectServlet</servlet-class>
-        <init-param>
-            <param-name>destination</param-name>
-            <param-value>${context}/#/</param-value>
-        </init-param>
-    </servlet>
-
-    <servlet>
-        <servlet-name>RedirectOldZookeeper</servlet-name>
-        <servlet-class>org.apache.solr.servlet.RedirectServlet</servlet-class>
-        <init-param>
-            <param-name>destination</param-name>
-            <param-value>${context}/zookeeper</param-value>
-        </init-param>
-    </servlet>
-
-    <servlet>
-        <servlet-name>RedirectLogging</servlet-name>
-        <servlet-class>org.apache.solr.servlet.RedirectServlet</servlet-class>
-        <init-param>
-            <param-name>destination</param-name>
-            <param-value>${context}/#/~logging</param-value>
-        </init-param>
-    </servlet>
-
-    <servlet>
-        <servlet-name>SolrRestApi</servlet-name>
-        <servlet-class>org.restlet.ext.servlet.ServerServlet</servlet-class>
-        <init-param>
-            <param-name>org.restlet.application</param-name>
-            <param-value>org.apache.solr.rest.SolrRestApi</param-value>
-        </init-param>
-    </servlet>
-
-    <servlet-mapping>
-        <servlet-name>RedirectOldAdminUI</servlet-name>
-        <url-pattern>/admin/</url-pattern>
-    </servlet-mapping>
-    <servlet-mapping>
-        <servlet-name>RedirectOldAdminUI</servlet-name>
-        <url-pattern>/admin</url-pattern>
-    </servlet-mapping>
-    <servlet-mapping>
-        <servlet-name>RedirectOldZookeeper</servlet-name>
-        <url-pattern>/zookeeper.jsp</url-pattern>
-    </servlet-mapping>
-    <servlet-mapping>
-        <servlet-name>RedirectLogging</servlet-name>
-        <url-pattern>/logging</url-pattern>
-    </servlet-mapping>
-
-    <!-- Servlet Mapping -->
-    <servlet-mapping>
-        <servlet-name>Zookeeper</servlet-name>
-        <url-pattern>/zookeeper</url-pattern>
-    </servlet-mapping>
-
-    <servlet-mapping>
-        <servlet-name>LoadAdminUI</servlet-name>
-        <url-pattern>/admin.html</url-pattern>
-    </servlet-mapping>
-
-    <servlet-mapping>
-        <servlet-name>SolrRestApi</servlet-name>
-        <url-pattern>/schema/*</url-pattern>
-    </servlet-mapping>
-
-    <mime-mapping>
-        <extension>.xsl</extension>
-        <!-- per http://www.w3.org/TR/2006/PR-xslt20-20061121/ -->
-        <mime-type>application/xslt+xml</mime-type>
-    </mime-mapping>
-
-    <welcome-file-list>
-        <welcome-file>admin.html</welcome-file>
-    </welcome-file-list>
-
-</web-app>

dspace-spring-rest/pom.xml

@@ -126,6 +126,7 @@
                                 <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
                                 <!-- Turn off any DSpace logging -->
                                 <dspace.log.init.disable>true</dspace.log.init.disable>
+                                <solr.install.dir>${agnostic.build.dir}/testing/dspace/solr/</solr.install.dir>
                             </systemPropertyVariables>
                         </configuration>
                     </plugin>
@@ -139,6 +140,7 @@
                                 <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
                                 <!-- Turn off any DSpace logging -->
                                 <dspace.log.init.disable>true</dspace.log.init.disable>
+                                <solr.install.dir>${agnostic.build.dir}/testing/dspace/solr/</solr.install.dir>
                             </systemPropertyVariables>
                         </configuration>
                     </plugin>
@@ -198,32 +200,11 @@
             <artifactId>spring-boot-starter-aop</artifactId>
             <version>${spring-boot.version}</version>
         </dependency>
+
         <dependency>
-            <groupId>org.springframework.boot</groupId>
+            <groupId>com.flipkart.zjsonpatch</groupId>
-            <artifactId>spring-boot-starter-test</artifactId>
+            <artifactId>zjsonpatch</artifactId>
-            <version>${spring-boot.version}</version>
+            <version>0.4.6</version>
-            <scope>test</scope>
-            <exclusions>
-                <!-- Temporary exclusion to avoid dependency conflict with version of org.json:json used by dspace-api.
-                     NOTE: THIS CAN BE REMOVED ONCE WE UPGRADE TO SPRING-BOOT v1.5 (or above), see DS-3802
-                     As of Spring-Boot 1.5, org.json:json is no longer used by spring-boot-starter-test -->
-                <exclusion>
-                    <groupId>org.json</groupId>
-                    <artifactId>json</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>com.jayway.jsonpath</groupId>
-            <artifactId>json-path</artifactId>
-            <scope>test</scope>
-            <version>${json-path.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>com.jayway.jsonpath</groupId>
-            <artifactId>json-path-assert</artifactId>
-            <version>${json-path.version}</version>
-            <scope>test</scope>
         </dependency>
 
         <!-- The HAL Browser -->
@@ -235,7 +216,6 @@
                  header (bad signature) during the tomcat startup
                  force the use of the previous version as the jar file
                  looks corrupted in the maven repository -->
-            <!-- <version>2.5.5.RELEASE</version> -->
         </dependency>
 
         <!-- Add in Spring Security for AuthN and AuthZ -->
@@ -276,13 +256,9 @@
             <groupId>org.dspace</groupId>
             <artifactId>dspace-services</artifactId>
         </dependency>
-
-        <!-- Apache Commons Collections 4.1 (used for MultiValuedMap to store metadata values for views) -->
-        <!-- NOTE: Currently DSpace API / Services still used 3.2 and may need upgrading at some point -->
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-collections4</artifactId>
-            <version>4.1</version>
         </dependency>
         <dependency>
             <groupId>joda-time</groupId>
@@ -291,10 +267,42 @@
         <dependency>
             <groupId>com.nimbusds</groupId>
             <artifactId>nimbus-jose-jwt</artifactId>
-            <version>4.23</version>
+            <version>6.2</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.solr</groupId>
+            <artifactId>solr-solrj</artifactId>
+            <version>${solr.client.version}</version>
         </dependency>
 
         <!-- TEST DEPENDENCIES -->
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-test</artifactId>
+            <version>${spring-boot.version}</version>
+            <scope>test</scope>
+            <exclusions>
+                <!-- Temporary exclusion to avoid dependency conflict with version of org.json:json used by dspace-api.
+                     NOTE: THIS CAN BE REMOVED ONCE WE UPGRADE TO SPRING-BOOT v1.5 (or above), see DS-3802
+                     As of Spring-Boot 1.5, org.json:json is no longer used by spring-boot-starter-test -->
+                <exclusion>
+                    <groupId>org.json</groupId>
+                    <artifactId>json</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>com.jayway.jsonpath</groupId>
+            <artifactId>json-path</artifactId>
+            <scope>test</scope>
+            <version>${json-path.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>com.jayway.jsonpath</groupId>
+            <artifactId>json-path-assert</artifactId>
+            <version>${json-path.version}</version>
+            <scope>test</scope>
+        </dependency>
         <dependency> <!-- Keep jmockit before junit -->
             <groupId>org.jmockit</groupId>
             <artifactId>jmockit</artifactId>
@@ -320,28 +328,146 @@
             <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
+        <!-- Solr Core is needed for Integration Tests (to run a MockSolrServer)     -->
+        <!-- The following Solr / Lucene dependencies also support integration tests -->
         <dependency>
-            <groupId>org.dspace</groupId>
+            <groupId>org.apache.solr</groupId>
-            <artifactId>dspace-solr</artifactId>
+            <artifactId>solr-core</artifactId>
-            <classifier>classes</classifier>
+            <version>${solr.client.version}</version>
             <scope>test</scope>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-continuation</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-deploy</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-http</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-io</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-jmx</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-rewrite</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-security</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-server</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-servlet</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-servlets</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-util</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-webapp</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-xml</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
+        <dependency>
+            <groupId>org.apache.solr</groupId>
+            <artifactId>solr-cell</artifactId>
+            <version>${solr.client.version}</version>
+            <scope>test</scope>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-continuation</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-deploy</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-http</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-io</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-jmx</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-rewrite</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-security</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-server</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-servlet</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-servlets</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-util</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-webapp</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-xml</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <!-- Reminder: Keep icu4j (in Parent POM) synced with version used by lucene-analyzers-icu below,
+             otherwise ICUFoldingFilterFactory may throw errors in tests.  -->
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-analyzers-icu</artifactId>
-            <version>${solr.version}</version>
+            <version>${solr.client.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-analyzers-smartcn</artifactId>
-            <version>${solr.version}</version>
+            <version>${solr.client.version}</version>
             <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-analyzers-stempel</artifactId>
-            <version>${solr.version}</version>
+            <version>${solr.client.version}</version>
             <scope>test</scope>
         </dependency>
 

dspace-spring-rest/src/main/java/org/dspace/app/rest/converter/AInprogressItemConverter.java

@@ -0,0 +1,153 @@
+/**
+ * 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.app.rest.converter;
+
+import java.io.Serializable;
+import java.sql.SQLException;
+import java.util.List;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
+import org.dspace.app.rest.model.AInprogressSubmissionRest;
+import org.dspace.app.rest.model.ErrorRest;
+import org.dspace.app.rest.model.SubmissionDefinitionRest;
+import org.dspace.app.rest.model.SubmissionSectionRest;
+import org.dspace.app.rest.submit.AbstractRestProcessingStep;
+import org.dspace.app.rest.submit.SubmissionService;
+import org.dspace.app.util.SubmissionConfigReader;
+import org.dspace.app.util.SubmissionConfigReaderException;
+import org.dspace.app.util.SubmissionStepConfig;
+import org.dspace.content.Collection;
+import org.dspace.content.InProgressSubmission;
+import org.dspace.content.Item;
+import org.dspace.eperson.EPerson;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * Abstract implementation providing the common functionalities for all the inprogressSubmission Converter
+ * 
+ * @author Andrea Bollini (andrea.bollini at 4science.it)
+ *
+ * @param <T>
+ *            the DSpace API inprogressSubmission object
+ * @param <R>
+ *            the DSpace REST inprogressSubmission representation
+ * @param <ID>
+ *            the Serializable class used as primary key
+ */
+public abstract class AInprogressItemConverter<T extends InProgressSubmission<ID>,
+                            R extends AInprogressSubmissionRest<ID>, ID extends Serializable>
+        implements IndexableDSpaceObjectConverter<T, R> {
+
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(AInprogressItemConverter.class);
+
+    @Autowired
+    private EPersonConverter epersonConverter;
+
+    @Autowired
+    private ItemConverter itemConverter;
+
+    @Autowired
+    private CollectionConverter collectionConverter;
+
+    protected SubmissionConfigReader submissionConfigReader;
+
+    @Autowired
+    private SubmissionDefinitionConverter submissionDefinitionConverter;
+
+    @Autowired
+    private SubmissionSectionConverter submissionSectionConverter;
+
+    @Autowired
+    SubmissionService submissionService;
+
+    public AInprogressItemConverter() throws SubmissionConfigReaderException {
+        submissionConfigReader = new SubmissionConfigReader();
+    }
+
+    protected void fillFromModel(T obj, R witem) {
+        Collection collection = obj.getCollection();
+        Item item = obj.getItem();
+        EPerson submitter = null;
+        try {
+            submitter = obj.getSubmitter();
+        } catch (SQLException e) {
+            throw new RuntimeException(e.getMessage(), e);
+        }
+
+        witem.setId(obj.getID());
+        witem.setCollection(collection != null ? collectionConverter.convert(collection) : null);
+        witem.setItem(itemConverter.convert(item));
+        witem.setSubmitter(epersonConverter.convert(submitter));
+
+        // 1. retrieve the submission definition
+        // 2. iterate over the submission section to allow to plugin additional
+        // info
+
+        if (collection != null) {
+            SubmissionDefinitionRest def = submissionDefinitionConverter
+                .convert(submissionConfigReader.getSubmissionConfigByCollection(collection.getHandle()));
+            witem.setSubmissionDefinition(def);
+            for (SubmissionSectionRest sections : def.getPanels()) {
+                SubmissionStepConfig stepConfig = submissionSectionConverter.toModel(sections);
+
+                /*
+                 * First, load the step processing class (using the current
+                 * class loader)
+                 */
+                ClassLoader loader = this.getClass().getClassLoader();
+                Class stepClass;
+                try {
+                    stepClass = loader.loadClass(stepConfig.getProcessingClassName());
+
+                    Object stepInstance = stepClass.newInstance();
+
+                    if (stepInstance instanceof AbstractRestProcessingStep) {
+                        // load the interface for this step
+                        AbstractRestProcessingStep stepProcessing =
+                            (AbstractRestProcessingStep) stepClass.newInstance();
+                        for (ErrorRest error : stepProcessing.validate(submissionService, obj, stepConfig)) {
+                            addError(witem.getErrors(), error);
+                        }
+                        witem.getSections()
+                            .put(sections.getId(), stepProcessing.getData(submissionService, obj, stepConfig));
+                    } else {
+                        log.warn("The submission step class specified by '" + stepConfig.getProcessingClassName() +
+                                 "' does not extend the class org.dspace.app.rest.submit.AbstractRestProcessingStep!" +
+                                 " Therefore it cannot be used by the Configurable Submission as the " +
+                                 "<processing-class>!");
+                    }
+
+                } catch (Exception e) {
+                    log.error("An error occurred during the unmarshal of the data for the section " + sections.getId()
+                            + " - reported error: " + e.getMessage(), e);
+                }
+
+            }
+        }
+    }
+
+    private void addError(List<ErrorRest> errors, ErrorRest toAdd) {
+
+        boolean found = false;
+        String i18nKey = toAdd.getMessage();
+        if (StringUtils.isNotBlank(i18nKey)) {
+            for (ErrorRest error : errors) {
+                if (i18nKey.equals(error.getMessage())) {
+                    error.getPaths().addAll(toAdd.getPaths());
+                    found = true;
+                    break;
+                }
+            }
+        }
+        if (!found) {
+            errors.add(toAdd);
+        }
+    }
+
+}

dspace-spring-rest/src/main/java/org/dspace/app/rest/converter/ClaimedTaskConverter.java

@@ -7,7 +7,6 @@
  */
 package org.dspace.app.rest.converter;
 
-import org.apache.log4j.Logger;
 import org.dspace.app.rest.model.ClaimedTaskRest;
 import org.dspace.browse.IndexableObject;
 import org.dspace.xmlworkflow.storedcomponents.ClaimedTask;
@@ -25,11 +24,12 @@ import org.springframework.stereotype.Component;
 public class ClaimedTaskConverter
     implements IndexableDSpaceObjectConverter<ClaimedTask, org.dspace.app.rest.model.ClaimedTaskRest> {
 
-    private static final Logger log = Logger.getLogger(ClaimedTaskConverter.class);
-
     @Autowired
     private WorkflowItemConverter workflowItemConverter;
 
+    @Autowired
+    private EPersonConverter epersonConverter;
+
     @Override
     public ClaimedTaskRest fromModel(ClaimedTask obj) {
         ClaimedTaskRest taskRest = new ClaimedTaskRest();
@@ -39,6 +39,7 @@ public class ClaimedTaskConverter
         taskRest.setWorkflowitem(workflowItemConverter.convert(witem));
         taskRest.setAction(obj.getActionID());
         taskRest.setStep(obj.getStepID());
+        taskRest.setOwner(epersonConverter.convert(obj.getOwner()));
         return taskRest;
     }
 

dspace-spring-rest/src/main/java/org/dspace/app/rest/converter/JsonPatchConverter.java

@@ -116,7 +116,8 @@ public class JsonPatchConverter implements PatchConverter<JsonNode> {
             Object value = operation.getValue();
 
             if (value != null) {
-                opNode.set("value", mapper.valueToTree(value));
+                opNode.set("value", value instanceof JsonValueEvaluator ? ((JsonValueEvaluator) value).getValueNode()
+                        : mapper.valueToTree(value));
             }
 
             patchNode.add(opNode);

dspace-spring-rest/src/main/java/org/dspace/app/rest/converter/PoolTaskConverter.java

@@ -7,7 +7,6 @@
  */
 package org.dspace.app.rest.converter;
 
-import org.apache.log4j.Logger;
 import org.dspace.app.rest.model.PoolTaskRest;
 import org.dspace.browse.IndexableObject;
 import org.dspace.xmlworkflow.storedcomponents.PoolTask;
@@ -25,8 +24,6 @@ import org.springframework.stereotype.Component;
 public class PoolTaskConverter
     implements IndexableDSpaceObjectConverter<PoolTask, org.dspace.app.rest.model.PoolTaskRest> {
 
-    private static final Logger log = Logger.getLogger(PoolTaskConverter.class);
-
     @Autowired
     private WorkflowItemConverter workflowItemConverter;
 

dspace-spring-rest/src/main/java/org/dspace/app/rest/converter/WorkflowItemConverter.java

@@ -7,26 +7,10 @@
  */
 package org.dspace.app.rest.converter;
 
-import java.sql.SQLException;
-import java.util.List;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.log4j.Logger;
-import org.dspace.app.rest.model.ErrorRest;
-import org.dspace.app.rest.model.SubmissionDefinitionRest;
-import org.dspace.app.rest.model.SubmissionSectionRest;
 import org.dspace.app.rest.model.WorkflowItemRest;
-import org.dspace.app.rest.submit.AbstractRestProcessingStep;
-import org.dspace.app.rest.submit.SubmissionService;
-import org.dspace.app.util.SubmissionConfigReader;
 import org.dspace.app.util.SubmissionConfigReaderException;
-import org.dspace.app.util.SubmissionStepConfig;
 import org.dspace.browse.IndexableObject;
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
-import org.dspace.eperson.EPerson;
 import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 /**
@@ -38,95 +22,16 @@ import org.springframework.stereotype.Component;
  */
 @Component
 public class WorkflowItemConverter
-    implements IndexableDSpaceObjectConverter<XmlWorkflowItem, org.dspace.app.rest.model.WorkflowItemRest> {
+    extends AInprogressItemConverter<XmlWorkflowItem, org.dspace.app.rest.model.WorkflowItemRest, Integer> {
-
-    private static final Logger log = Logger.getLogger(WorkflowItemConverter.class);
-
-    @Autowired
-    private EPersonConverter epersonConverter;
-
-    @Autowired
-    private ItemConverter itemConverter;
-
-    @Autowired
-    private CollectionConverter collectionConverter;
-
-    private SubmissionConfigReader submissionConfigReader;
-
-    @Autowired
-    private SubmissionDefinitionConverter submissionDefinitionConverter;
-    @Autowired
-    private SubmissionSectionConverter submissionSectionConverter;
-
-    @Autowired
-    SubmissionService submissionService;
 
     public WorkflowItemConverter() throws SubmissionConfigReaderException {
-        submissionConfigReader = new SubmissionConfigReader();
+        super();
     }
 
     @Override
     public WorkflowItemRest fromModel(XmlWorkflowItem obj) {
         WorkflowItemRest witem = new WorkflowItemRest();
-
+        fillFromModel(obj, witem);
-        Collection collection = obj.getCollection();
-        Item item = obj.getItem();
-        EPerson submitter = null;
-        try {
-            submitter = obj.getSubmitter();
-        } catch (SQLException e) {
-            throw new RuntimeException(e.getMessage(), e);
-        }
-
-        witem.setId(obj.getID());
-        witem.setCollection(collection != null ? collectionConverter.convert(collection) : null);
-        witem.setItem(itemConverter.convert(item));
-        witem.setSubmitter(epersonConverter.convert(submitter));
-
-        // 1. retrieve the submission definition
-        // 2. iterate over the submission section to allow to plugin additional
-        // info
-
-        if (collection != null) {
-            SubmissionDefinitionRest def = submissionDefinitionConverter
-                .convert(submissionConfigReader.getSubmissionConfigByCollection(collection.getHandle()));
-            witem.setSubmissionDefinition(def);
-            for (SubmissionSectionRest sections : def.getPanels()) {
-                SubmissionStepConfig stepConfig = submissionSectionConverter.toModel(sections);
-
-                /*
-                 * First, load the step processing class (using the current
-                 * class loader)
-                 */
-                ClassLoader loader = this.getClass().getClassLoader();
-                Class stepClass;
-                try {
-                    stepClass = loader.loadClass(stepConfig.getProcessingClassName());
-
-                    Object stepInstance = stepClass.newInstance();
-
-                    if (stepInstance instanceof AbstractRestProcessingStep) {
-                        // load the interface for this step
-                        AbstractRestProcessingStep stepProcessing =
-                            (AbstractRestProcessingStep) stepClass.newInstance();
-                        for (ErrorRest error : stepProcessing.validate(submissionService, obj, stepConfig)) {
-                            addError(witem.getErrors(), error);
-                        }
-                        witem.getSections()
-                            .put(sections.getId(), stepProcessing.getData(submissionService, obj, stepConfig));
-                    } else {
-                        log.warn("The submission step class specified by '" + stepConfig.getProcessingClassName() +
-                                 "' does not extend the class org.dspace.app.rest.submit.AbstractRestProcessingStep!" +
-                                 " Therefore it cannot be used by the Configurable Submission as the " +
-                                 "<processing-class>!");
-                    }
-
-                } catch (Exception e) {
-                    log.error(e.getMessage(), e);
-                }
-
-            }
-        }
         return witem;
     }
 
@@ -135,25 +40,6 @@ public class WorkflowItemConverter
         return null;
     }
 
-
-    private void addError(List<ErrorRest> errors, ErrorRest toAdd) {
-
-        boolean found = false;
-        String i18nKey = toAdd.getMessage();
-        if (StringUtils.isNotBlank(i18nKey)) {
-            for (ErrorRest error : errors) {
-                if (i18nKey.equals(error.getMessage())) {
-                    error.getPaths().addAll(toAdd.getPaths());
-                    found = true;
-                    break;
-                }
-            }
-        }
-        if (!found) {
-            errors.add(toAdd);
-        }
-    }
-
     @Override
     public boolean supportsModel(IndexableObject object) {
         return object instanceof XmlWorkflowItem;

dspace-spring-rest/src/main/java/org/dspace/app/rest/converter/WorkspaceItemConverter.java

@@ -7,26 +7,10 @@
  */
 package org.dspace.app.rest.converter;
 
-import java.sql.SQLException;
-import java.util.List;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
-import org.dspace.app.rest.model.ErrorRest;
-import org.dspace.app.rest.model.SubmissionDefinitionRest;
-import org.dspace.app.rest.model.SubmissionSectionRest;
 import org.dspace.app.rest.model.WorkspaceItemRest;
-import org.dspace.app.rest.submit.AbstractRestProcessingStep;
-import org.dspace.app.rest.submit.SubmissionService;
-import org.dspace.app.util.SubmissionConfigReader;
 import org.dspace.app.util.SubmissionConfigReaderException;
-import org.dspace.app.util.SubmissionStepConfig;
 import org.dspace.browse.IndexableObject;
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
 import org.dspace.content.WorkspaceItem;
-import org.dspace.eperson.EPerson;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
 /**
@@ -37,96 +21,17 @@ import org.springframework.stereotype.Component;
  */
 @Component
 public class WorkspaceItemConverter
-        implements
+    extends AInprogressItemConverter<WorkspaceItem, WorkspaceItemRest, Integer> {
-        IndexableDSpaceObjectConverter<org.dspace.content.WorkspaceItem, org.dspace.app.rest.model.WorkspaceItemRest> {
-
-    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(WorkspaceItemConverter.class);
-
-    @Autowired
-    private EPersonConverter epersonConverter;
-
-    @Autowired
-    private ItemConverter itemConverter;
-
-    @Autowired
-    private CollectionConverter collectionConverter;
-
-    private SubmissionConfigReader submissionConfigReader;
-
-    @Autowired
-    private SubmissionDefinitionConverter submissionDefinitionConverter;
-    @Autowired
-    private SubmissionSectionConverter submissionSectionConverter;
-
-    @Autowired
-    SubmissionService submissionService;
 
     public WorkspaceItemConverter() throws SubmissionConfigReaderException {
-        submissionConfigReader = new SubmissionConfigReader();
+        super();
     }
 
     @Override
     public WorkspaceItemRest fromModel(org.dspace.content.WorkspaceItem obj) {
         WorkspaceItemRest witem = new WorkspaceItemRest();
 
-        Collection collection = obj.getCollection();
+        fillFromModel(obj, witem);
-        Item item = obj.getItem();
-        EPerson submitter = null;
-        try {
-            submitter = obj.getSubmitter();
-        } catch (SQLException e) {
-            throw new RuntimeException(e.getMessage(), e);
-        }
-
-        witem.setId(obj.getID());
-        witem.setCollection(collection != null ? collectionConverter.convert(collection) : null);
-        witem.setItem(itemConverter.convert(item));
-        witem.setSubmitter(epersonConverter.convert(submitter));
-
-        // 1. retrieve the submission definition
-        // 2. iterate over the submission section to allow to plugin additional
-        // info
-
-        if (collection != null) {
-            SubmissionDefinitionRest def = submissionDefinitionConverter
-                .convert(submissionConfigReader.getSubmissionConfigByCollection(collection.getHandle()));
-            witem.setSubmissionDefinition(def);
-            for (SubmissionSectionRest sections : def.getPanels()) {
-                SubmissionStepConfig stepConfig = submissionSectionConverter.toModel(sections);
-
-                /*
-                 * First, load the step processing class (using the current
-                 * class loader)
-                 */
-                ClassLoader loader = this.getClass().getClassLoader();
-                Class stepClass;
-                try {
-                    stepClass = loader.loadClass(stepConfig.getProcessingClassName());
-
-                    Object stepInstance = stepClass.newInstance();
-
-                    if (stepInstance instanceof AbstractRestProcessingStep) {
-                        // load the interface for this step
-                        AbstractRestProcessingStep stepProcessing =
-                            (AbstractRestProcessingStep) stepClass.newInstance();
-                        for (ErrorRest error : stepProcessing.validate(submissionService, obj, stepConfig)) {
-                            addError(witem.getErrors(), error);
-                        }
-                        witem.getSections()
-                            .put(sections.getId(), stepProcessing.getData(submissionService, obj, stepConfig));
-                    } else {
-                        log.warn("The submission step class specified by '" + stepConfig.getProcessingClassName() +
-                                 "' does not extend the class org.dspace.app.rest.submit.AbstractRestProcessingStep!" +
-                                 " Therefore it cannot be used by the Configurable Submission as the " +
-                                 "<processing-class>!");
-                    }
-
-                } catch (Exception e) {
-                    log.error(e.getMessage(), e);
-                }
-
-            }
-        }
         return witem;
     }
 
@@ -135,25 +40,6 @@ public class WorkspaceItemConverter
         return null;
     }
 
-
-    private void addError(List<ErrorRest> errors, ErrorRest toAdd) {
-
-        boolean found = false;
-        String i18nKey = toAdd.getMessage();
-        if (StringUtils.isNotBlank(i18nKey)) {
-            for (ErrorRest error : errors) {
-                if (i18nKey.equals(error.getMessage())) {
-                    error.getPaths().addAll(toAdd.getPaths());
-                    found = true;
-                    break;
-                }
-            }
-        }
-        if (!found) {
-            errors.add(toAdd);
-        }
-    }
-
     @Override
     public boolean supportsModel(IndexableObject object) {
         return object instanceof WorkspaceItem;

dspace-spring-rest/src/main/java/org/dspace/app/rest/exception/DSpaceApiExceptionControllerAdvice.java

@@ -11,7 +11,6 @@ import static org.springframework.web.servlet.DispatcherServlet.EXCEPTION_ATTRIB
 
 import java.io.IOException;
 import java.sql.SQLException;
-
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
@@ -19,13 +18,16 @@ import org.dspace.app.rest.security.RestAuthenticationService;
 import org.dspace.authorize.AuthorizeException;
 import org.springframework.beans.TypeMismatchException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.annotation.AnnotationUtils;
 import org.springframework.data.repository.support.QueryMethodParameterConversionException;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.AccessDeniedException;
 import org.springframework.web.bind.MissingServletRequestParameterException;
 import org.springframework.web.bind.annotation.ControllerAdvice;
 import org.springframework.web.bind.annotation.ExceptionHandler;
+import org.springframework.web.bind.annotation.ResponseStatus;
 import org.springframework.web.context.request.WebRequest;
 import org.springframework.web.servlet.mvc.method.annotation.ResponseEntityExceptionHandler;
 
@@ -42,7 +44,7 @@ public class DSpaceApiExceptionControllerAdvice extends ResponseEntityExceptionH
     @Autowired
     private RestAuthenticationService restAuthenticationService;
 
-    @ExceptionHandler({AuthorizeException.class, RESTAuthorizationException.class})
+    @ExceptionHandler({AuthorizeException.class, RESTAuthorizationException.class, AccessDeniedException.class})
     protected void handleAuthorizeException(HttpServletRequest request, HttpServletResponse response, Exception ex)
         throws IOException {
         if (restAuthenticationService.hasAuthenticationData(request)) {
@@ -73,7 +75,7 @@ public class DSpaceApiExceptionControllerAdvice extends ResponseEntityExceptionH
                           HttpServletResponse.SC_INTERNAL_SERVER_ERROR);
     }
 
-    @ExceptionHandler({MissingParameterException.class, QueryMethodParameterConversionException.class})
+    @ExceptionHandler( {MissingParameterException.class, QueryMethodParameterConversionException.class})
     protected void ParameterConversionException(HttpServletRequest request, HttpServletResponse response, Exception ex)
         throws IOException {
 
@@ -87,7 +89,8 @@ public class DSpaceApiExceptionControllerAdvice extends ResponseEntityExceptionH
 
     @Override
     protected ResponseEntity<Object> handleMissingServletRequestParameter(MissingServletRequestParameterException ex,
-            HttpHeaders headers, HttpStatus status, WebRequest request) {
+                                                                          HttpHeaders headers, HttpStatus status,
+                                                                          WebRequest request) {
         // we want the 422 status for missing parameter as it seems to be the common behavior for REST application, see
         // https://stackoverflow.com/questions/3050518/what-http-status-response-code-should-i-use-if-the-request-is-missing-a-required
         return super.handleMissingServletRequestParameter(ex, headers, HttpStatus.UNPROCESSABLE_ENTITY, request);
@@ -102,6 +105,22 @@ public class DSpaceApiExceptionControllerAdvice extends ResponseEntityExceptionH
         return super.handleTypeMismatch(ex, headers, HttpStatus.UNPROCESSABLE_ENTITY, request);
     }
 
+    @ExceptionHandler(Exception.class)
+    protected void handleGenericException(HttpServletRequest request, HttpServletResponse response, Exception ex)
+        throws IOException {
+        ResponseStatus responseStatusAnnotation = AnnotationUtils.findAnnotation(ex.getClass(), ResponseStatus.class);
+
+        int returnCode = 0;
+        if (responseStatusAnnotation != null) {
+            returnCode = responseStatusAnnotation.code().value();
+        } else {
+            returnCode = HttpServletResponse.SC_INTERNAL_SERVER_ERROR;
+        }
+        sendErrorResponse(request, response, ex, "An Exception has occured", returnCode);
+
+    }
+
+
     private void sendErrorResponse(final HttpServletRequest request, final HttpServletResponse response,
                                    final Exception ex, final String message, final int statusCode) throws IOException {
         //Make sure Spring picks up this exception

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/AInprogressSubmissionRest.java

@@ -0,0 +1,93 @@
+/**
+ * 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.app.rest.model;
+
+import java.io.Serializable;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.Map;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+
+/**
+ * Abstract class to share common aspects between the REST representation of inprogressSubmission
+ * 
+ * @author Andrea Bollini (andrea.bollini at 4science.it)
+ *
+ * @param <T>
+ *            the serializable class used as primary key
+ */
+public abstract class AInprogressSubmissionRest<T extends Serializable> extends BaseObjectRest<T> {
+
+    private Date lastModified = new Date();
+    private Map<String, Serializable> sections;
+    @JsonIgnore
+    private CollectionRest collection;
+    @JsonIgnore
+    private ItemRest item;
+    @JsonIgnore
+    private SubmissionDefinitionRest submissionDefinition;
+    @JsonIgnore
+    private EPersonRest submitter;
+
+    public AInprogressSubmissionRest() {
+        super();
+    }
+
+    public Date getLastModified() {
+        return lastModified;
+    }
+
+    public void setLastModified(Date lastModified) {
+        this.lastModified = lastModified;
+    }
+
+    public ItemRest getItem() {
+        return item;
+    }
+
+    public void setItem(ItemRest item) {
+        this.item = item;
+    }
+
+    public SubmissionDefinitionRest getSubmissionDefinition() {
+        return submissionDefinition;
+    }
+
+    public void setSubmissionDefinition(SubmissionDefinitionRest submissionDefinition) {
+        this.submissionDefinition = submissionDefinition;
+    }
+
+    public EPersonRest getSubmitter() {
+        return submitter;
+    }
+
+    public void setSubmitter(EPersonRest submitter) {
+        this.submitter = submitter;
+    }
+
+    public Map<String, Serializable> getSections() {
+        if (sections == null) {
+            sections = new HashMap<String, Serializable>();
+        }
+        return sections;
+    }
+
+    public void setSections(Map<String, Serializable> sections) {
+        this.sections = sections;
+    }
+
+    public CollectionRest getCollection() {
+        return collection;
+    }
+
+    public void setCollection(CollectionRest collection) {
+        this.collection = collection;
+    }
+
+}

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/ClaimedTaskRest.java

@@ -24,6 +24,9 @@ public class ClaimedTaskRest extends BaseObjectRest<Integer> {
 
     private String action;
 
+    @JsonIgnore
+    private EPersonRest owner;
+
     @JsonIgnore
     private WorkflowItemRest workflowitem;
 
@@ -66,6 +69,18 @@ public class ClaimedTaskRest extends BaseObjectRest<Integer> {
         this.action = action;
     }
 
+    /**
+     * @see ClaimedTaskRest#getOwner()
+     * @return the owner of the task
+     */
+    public EPersonRest getOwner() {
+        return owner;
+    }
+
+    public void setOwner(EPersonRest owner) {
+        this.owner = owner;
+    }
+
     /**
      * 
      * @return the WorkflowItemRest that belong to this claimed task

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/MetadataRest.java

@@ -61,4 +61,9 @@ public class MetadataRest {
         map.put(key, Arrays.asList(values));
         return this;
     }
+
+    @Override
+    public boolean equals(Object object) {
+        return object instanceof MetadataRest && ((MetadataRest) object).getMap().equals(map);
+    }
 }

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/WorkflowItemRest.java

@@ -7,12 +7,6 @@
  */
 package org.dspace.app.rest.model;
 
-import java.io.Serializable;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.Map;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.dspace.app.rest.RestResourceController;
 
 /**
@@ -20,26 +14,10 @@ import org.dspace.app.rest.RestResourceController;
  *
  * @author Andrea Bollini (andrea.bollini at 4science.it)
  */
-public class WorkflowItemRest extends BaseObjectRest<Integer> {
+public class WorkflowItemRest extends AInprogressSubmissionRest<Integer> {
     public static final String NAME = "workflowitem";
     public static final String CATEGORY = RestAddressableModel.WORKFLOW;
 
-    private Date lastModified = new Date();
-
-    private Map<String, Serializable> sections;
-
-    @JsonIgnore
-    private CollectionRest collection;
-
-    @JsonIgnore
-    private ItemRest item;
-
-    @JsonIgnore
-    private SubmissionDefinitionRest submissionDefinition;
-
-    @JsonIgnore
-    private EPersonRest submitter;
-
     @Override
     public String getCategory() {
         return CATEGORY;
@@ -50,83 +28,8 @@ public class WorkflowItemRest extends BaseObjectRest<Integer> {
         return NAME;
     }
 
-    /**
-     * 
-     * @return the timestamp of the last modification done to the workflowitem
-     */
-    public Date getLastModified() {
-        return lastModified;
-    }
-
-    public void setLastModified(Date lastModified) {
-        this.lastModified = lastModified;
-    }
-
-    /**
-     * 
-     * @return the item wrapped by the workflowitem
-     */
-    public ItemRest getItem() {
-        return item;
-    }
-
-    public void setItem(ItemRest item) {
-        this.item = item;
-    }
-
-    /**
-     * 
-     * @return the SubmissionDefinition used by the workflowitem
-     */
-    public SubmissionDefinitionRest getSubmissionDefinition() {
-        return submissionDefinition;
-    }
-
-    public void setSubmissionDefinition(SubmissionDefinitionRest submissionDefinition) {
-        this.submissionDefinition = submissionDefinition;
-    }
-
-    /**
-     * 
-     * @return the submitter
-     */
-    public EPersonRest getSubmitter() {
-        return submitter;
-    }
-
-    public void setSubmitter(EPersonRest submitter) {
-        this.submitter = submitter;
-    }
-
     @Override
     public Class getController() {
         return RestResourceController.class;
     }
-
-    /**
-     * 
-     * @return the data of the workflowitem organized according to the submission definition
-     */
-    public Map<String, Serializable> getSections() {
-        if (sections == null) {
-            sections = new HashMap<String, Serializable>();
-        }
-        return sections;
-    }
-
-    public void setSections(Map<String, Serializable> sections) {
-        this.sections = sections;
-    }
-
-    /**
-     * 
-     * @return the collection where the workflow is in progress
-     */
-    public CollectionRest getCollection() {
-        return collection;
-    }
-
-    public void setCollection(CollectionRest collection) {
-        this.collection = collection;
-    }
 }

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/WorkspaceItemRest.java

@@ -7,12 +7,6 @@
  */
 package org.dspace.app.rest.model;
 
-import java.io.Serializable;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.Map;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.dspace.app.rest.RestResourceController;
 
 /**
@@ -20,26 +14,10 @@ import org.dspace.app.rest.RestResourceController;
  *
  * @author Andrea Bollini (andrea.bollini at 4science.it)
  */
-public class WorkspaceItemRest extends BaseObjectRest<Integer> {
+public class WorkspaceItemRest extends AInprogressSubmissionRest<Integer> {
     public static final String NAME = "workspaceitem";
     public static final String CATEGORY = RestAddressableModel.SUBMISSION;
 
-    private Date lastModified = new Date();
-
-    private Map<String, Serializable> sections;
-
-    @JsonIgnore
-    private CollectionRest collection;
-
-    @JsonIgnore
-    private ItemRest item;
-
-    @JsonIgnore
-    private SubmissionDefinitionRest submissionDefinition;
-
-    @JsonIgnore
-    private EPersonRest submitter;
-
     @Override
     public String getCategory() {
         return CATEGORY;
@@ -50,59 +28,8 @@ public class WorkspaceItemRest extends BaseObjectRest<Integer> {
         return NAME;
     }
 
-    public Date getLastModified() {
-        return lastModified;
-    }
-
-    public void setLastModified(Date lastModified) {
-        this.lastModified = lastModified;
-    }
-
-    public ItemRest getItem() {
-        return item;
-    }
-
-    public void setItem(ItemRest item) {
-        this.item = item;
-    }
-
-    public SubmissionDefinitionRest getSubmissionDefinition() {
-        return submissionDefinition;
-    }
-
-    public void setSubmissionDefinition(SubmissionDefinitionRest submissionDefinition) {
-        this.submissionDefinition = submissionDefinition;
-    }
-
-    public EPersonRest getSubmitter() {
-        return submitter;
-    }
-
-    public void setSubmitter(EPersonRest submitter) {
-        this.submitter = submitter;
-    }
-
     @Override
     public Class getController() {
         return RestResourceController.class;
     }
-
-    public Map<String, Serializable> getSections() {
-        if (sections == null) {
-            sections = new HashMap<String, Serializable>();
-        }
-        return sections;
-    }
-
-    public void setSections(Map<String, Serializable> sections) {
-        this.sections = sections;
-    }
-
-    public CollectionRest getCollection() {
-        return collection;
-    }
-
-    public void setCollection(CollectionRest collection) {
-        this.collection = collection;
-    }
 }

dspace-spring-rest/src/main/java/org/dspace/app/rest/model/patch/JsonValueEvaluator.java

@@ -44,4 +44,7 @@ public class JsonValueEvaluator implements LateObjectEvaluator {
         }
     }
 
+    public JsonNode getValueNode() {
+        return this.valueNode;
+    }
 }

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/BitstreamRestRepository.java

@@ -14,11 +14,14 @@ import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
 import java.util.UUID;
+import javax.servlet.http.HttpServletRequest;
 
 import org.dspace.app.rest.converter.BitstreamConverter;
 import org.dspace.app.rest.exception.UnprocessableEntityException;
 import org.dspace.app.rest.model.BitstreamRest;
 import org.dspace.app.rest.model.hateoas.BitstreamResource;
+import org.dspace.app.rest.model.patch.Patch;
+import org.dspace.app.rest.repository.patch.DSpaceObjectPatch;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Bitstream;
 import org.dspace.content.service.BitstreamService;
@@ -39,16 +42,15 @@ import org.springframework.stereotype.Component;
  */
 
 @Component(BitstreamRest.CATEGORY + "." + BitstreamRest.NAME)
-public class BitstreamRestRepository extends DSpaceRestRepository<BitstreamRest, UUID> {
+public class BitstreamRestRepository extends DSpaceObjectRestRepository<Bitstream, BitstreamRest> {
+
+    private final BitstreamService bs;
 
     @Autowired
-    BitstreamService bs;
+    public BitstreamRestRepository(BitstreamService dsoService,
-
+                                   BitstreamConverter dsoConverter) {
-    @Autowired
+        super(dsoService, dsoConverter, new DSpaceObjectPatch<BitstreamRest>() { });
-    BitstreamConverter converter;
+        this.bs = dsoService;
-
-    public BitstreamRestRepository() {
-        System.out.println("Repository initialized by Spring");
     }
 
     @Override
@@ -70,7 +72,7 @@ public class BitstreamRestRepository extends DSpaceRestRepository<BitstreamRest,
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        return converter.fromModel(bit);
+        return dsoConverter.fromModel(bit);
     }
 
     @Override
@@ -88,10 +90,17 @@ public class BitstreamRestRepository extends DSpaceRestRepository<BitstreamRest,
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<BitstreamRest> page = new PageImpl<Bitstream>(bit, pageable, total).map(converter);
+        Page<BitstreamRest> page = new PageImpl<Bitstream>(bit, pageable, total).map(dsoConverter);
         return page;
     }
 
+    @Override
+    @PreAuthorize("hasPermission(#id, 'BITSTREAM', 'WRITE')")
+    protected void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID id,
+                         Patch patch) throws AuthorizeException, SQLException {
+        patchDSpaceObject(apiCategory, model, id, patch);
+    }
+
     @Override
     public Class<BitstreamRest> getDomainClass() {
         return BitstreamRest.class;

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/ClaimedTaskRestRepository.java

@@ -27,12 +27,11 @@ import org.dspace.app.rest.model.ClaimedTaskRest;
 import org.dspace.app.rest.model.PoolTaskRest;
 import org.dspace.app.rest.model.hateoas.ClaimedTaskResource;
 import org.dspace.authorize.AuthorizeException;
+import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.service.EPersonService;
-import org.dspace.event.Event;
 import org.dspace.workflow.WorkflowException;
 import org.dspace.xmlworkflow.WorkflowConfigurationException;
 import org.dspace.xmlworkflow.factory.XmlWorkflowServiceFactory;
@@ -48,6 +47,8 @@ import org.dspace.xmlworkflow.storedcomponents.service.ClaimedTaskService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.rest.webmvc.ResourceNotFoundException;
+import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Component;
 
 /**
@@ -79,7 +80,11 @@ public class ClaimedTaskRestRepository extends DSpaceRestRepository<ClaimedTaskR
     @Autowired
     WorkflowRequirementsService workflowRequirementsService;
 
+    @Autowired
+    AuthorizeService authorizeService;
+
     @Override
+    @PreAuthorize("hasPermission(#id, 'CLAIMEDTASK', 'READ')")
     public ClaimedTaskRest findOne(Context context, Integer id) {
         ClaimedTask task = null;
         try {
@@ -94,12 +99,24 @@ public class ClaimedTaskRestRepository extends DSpaceRestRepository<ClaimedTaskR
     }
 
     @SearchRestMethod(name = "findByUser")
-    public Page<ClaimedTaskRest> findByUser(@Parameter(value = "uuid") UUID userID, Pageable pageable) {
+    public Page<ClaimedTaskRest> findByUser(@Parameter(value = "uuid", required = true) UUID userID,
+            Pageable pageable) {
+        //FIXME this should be secured with annotation but they are currently ignored by search methods
         List<ClaimedTask> tasks = null;
         try {
             Context context = obtainContext();
+            EPerson currentUser = context.getCurrentUser();
+            if (currentUser == null) {
+                throw new RESTAuthorizationException(
+                    "This endpoint is available only to logged-in user to search for their"
+                    + " own claimed tasks or the admins");
+            }
+            if (authorizeService.isAdmin(context) || userID.equals(currentUser.getID())) {
                 EPerson ep = epersonService.find(context, userID);
                 tasks = claimedTaskService.findByEperson(context, ep);
+            } else {
+                throw new RESTAuthorizationException("Only administrators can search for claimed tasks of other users");
+            }
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
@@ -118,10 +135,14 @@ public class ClaimedTaskRestRepository extends DSpaceRestRepository<ClaimedTaskR
     }
 
     @Override
+    @PreAuthorize("hasPermission(#id, 'CLAIMEDTASK', 'WRITE')")
     protected ClaimedTaskRest action(Context context, HttpServletRequest request, Integer id)
         throws SQLException, IOException {
         ClaimedTask task = null;
         task = claimedTaskService.find(context, id);
+        if (task == null) {
+            throw new ResourceNotFoundException("ClaimedTask ID " + id + " not found");
+        }
         XmlWorkflowServiceFactory factory = (XmlWorkflowServiceFactory) XmlWorkflowServiceFactory.getInstance();
         Workflow workflow;
         try {
@@ -136,10 +157,6 @@ public class ClaimedTaskRestRepository extends DSpaceRestRepository<ClaimedTaskR
                 throw new UnprocessableEntityException(
                         "Missing required fields: " + StringUtils.join(Action.getErrorFields(request), ","));
             }
-            // workflowRequirementsService.removeClaimedUser(context, task.getWorkflowItem(), task.getOwner(), task
-            // .getStepID());
-            context.addEvent(new Event(Event.MODIFY, Constants.ITEM, task.getWorkflowItem().getItem().getID(), null,
-                itemService.getIdentifiers(context, task.getWorkflowItem().getItem())));
         } catch (AuthorizeException e) {
             throw new RESTAuthorizationException(e);
         } catch (WorkflowException e) {
@@ -157,15 +174,17 @@ public class ClaimedTaskRestRepository extends DSpaceRestRepository<ClaimedTaskR
      * enough other claimed tasks for the same workflowitem.
      * 
      */
+    @PreAuthorize("hasPermission(#id, 'CLAIMEDTASK', 'DELETE')")
     protected void delete(Context context, Integer id) {
         ClaimedTask task = null;
         try {
             task = claimedTaskService.find(context, id);
+            if (task == null) {
+                throw new ResourceNotFoundException("ClaimedTask ID " + id + " not found");
+            }
             XmlWorkflowItem workflowItem = task.getWorkflowItem();
             workflowService.deleteClaimedTask(context, workflowItem, task);
             workflowRequirementsService.removeClaimedUser(context, workflowItem, task.getOwner(), task.getStepID());
-            context.addEvent(new Event(Event.MODIFY, Constants.ITEM, workflowItem.getItem().getID(), null,
-                itemService.getIdentifiers(context, workflowItem.getItem())));
         } catch (AuthorizeException e) {
             throw new RESTAuthorizationException(e);
         } catch (SQLException | IOException | WorkflowConfigurationException e) {

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/CollectionRestRepository.java

@@ -12,7 +12,6 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
-
 import javax.servlet.ServletInputStream;
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.BadRequestException;
@@ -29,6 +28,8 @@ import org.dspace.app.rest.exception.UnprocessableEntityException;
 import org.dspace.app.rest.model.CollectionRest;
 import org.dspace.app.rest.model.CommunityRest;
 import org.dspace.app.rest.model.hateoas.CollectionResource;
+import org.dspace.app.rest.model.patch.Patch;
+import org.dspace.app.rest.repository.patch.DSpaceObjectPatch;
 import org.dspace.app.rest.utils.CollectionRestEqualityUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
@@ -53,14 +54,13 @@ import org.springframework.stereotype.Component;
  */
 
 @Component(CollectionRest.CATEGORY + "." + CollectionRest.NAME)
-public class CollectionRestRepository extends DSpaceRestRepository<CollectionRest, UUID> {
+public class CollectionRestRepository extends DSpaceObjectRestRepository<Collection, CollectionRest> {
+
+    private final CollectionService cs;
 
     @Autowired
     CommunityService communityService;
 
-    @Autowired
-    CollectionService cs;
-
     @Autowired
     CollectionConverter converter;
 
@@ -71,8 +71,10 @@ public class CollectionRestRepository extends DSpaceRestRepository<CollectionRes
     CollectionRestEqualityUtils collectionRestEqualityUtils;
 
 
-    public CollectionRestRepository() {
+    public CollectionRestRepository(CollectionService dsoService,
-        System.out.println("Repository initialized by Spring");
+                                    CollectionConverter dsoConverter) {
+        super(dsoService, dsoConverter, new DSpaceObjectPatch<CollectionRest>() {});
+        this.cs = dsoService;
     }
 
     @Override
@@ -87,7 +89,7 @@ public class CollectionRestRepository extends DSpaceRestRepository<CollectionRes
         if (collection == null) {
             return null;
         }
-        return converter.fromModel(collection);
+        return dsoConverter.fromModel(collection);
     }
 
     @Override
@@ -104,7 +106,7 @@ public class CollectionRestRepository extends DSpaceRestRepository<CollectionRes
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<CollectionRest> page = new PageImpl<Collection>(collections, pageable, total).map(converter);
+        Page<CollectionRest> page = new PageImpl<Collection>(collections, pageable, total).map(dsoConverter);
         return page;
     }
 
@@ -128,7 +130,7 @@ public class CollectionRestRepository extends DSpaceRestRepository<CollectionRes
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<CollectionRest> page = utils.getPage(collections, pageable).map(converter);
+        Page<CollectionRest> page = utils.getPage(collections, pageable).map(dsoConverter);
         return page;
     }
 
@@ -145,10 +147,17 @@ public class CollectionRestRepository extends DSpaceRestRepository<CollectionRes
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<CollectionRest> page = utils.getPage(collections, pageable).map(converter);
+        Page<CollectionRest> page = utils.getPage(collections, pageable).map(dsoConverter);
         return page;
     }
 
+    @Override
+    @PreAuthorize("hasPermission(#id, 'COLLECTION', 'WRITE')")
+    protected void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID id,
+                         Patch patch) throws AuthorizeException, SQLException {
+        patchDSpaceObject(apiCategory, model, id, patch);
+    }
+
     @Override
     public Class<CollectionRest> getDomainClass() {
         return CollectionRest.class;
@@ -252,5 +261,4 @@ public class CollectionRestRepository extends DSpaceRestRepository<CollectionRes
             throw new RuntimeException("Unable to delete collection because the logo couldn't be deleted", e);
         }
     }
-
 }

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/CommunityRestRepository.java

@@ -12,7 +12,6 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
-
 import javax.servlet.ServletInputStream;
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.BadRequestException;
@@ -28,6 +27,8 @@ import org.dspace.app.rest.exception.RepositoryMethodNotImplementedException;
 import org.dspace.app.rest.exception.UnprocessableEntityException;
 import org.dspace.app.rest.model.CommunityRest;
 import org.dspace.app.rest.model.hateoas.CommunityResource;
+import org.dspace.app.rest.model.patch.Patch;
+import org.dspace.app.rest.repository.patch.DSpaceObjectPatch;
 import org.dspace.app.rest.utils.CommunityRestEqualityUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Community;
@@ -49,10 +50,9 @@ import org.springframework.stereotype.Component;
  */
 
 @Component(CommunityRest.CATEGORY + "." + CommunityRest.NAME)
-public class CommunityRestRepository extends DSpaceRestRepository<CommunityRest, UUID> {
+public class CommunityRestRepository extends DSpaceObjectRestRepository<Community, CommunityRest> {
 
-    @Autowired
+    private final CommunityService cs;
-    CommunityService cs;
 
     @Autowired
     CommunityConverter converter;
@@ -63,8 +63,10 @@ public class CommunityRestRepository extends DSpaceRestRepository<CommunityRest,
     @Autowired
     CommunityRestEqualityUtils communityRestEqualityUtils;
 
-    public CommunityRestRepository() {
+    public CommunityRestRepository(CommunityService dsoService,
-        System.out.println("Repository initialized by Spring");
+                                   CommunityConverter dsoConverter) {
+        super(dsoService, dsoConverter, new DSpaceObjectPatch<CommunityRest>() {});
+        this.cs = dsoService;
     }
 
     @Override
@@ -107,7 +109,7 @@ public class CommunityRestRepository extends DSpaceRestRepository<CommunityRest,
             throw new RuntimeException(e.getMessage(), e);
         }
 
-        return converter.convert(community);
+        return dsoConverter.convert(community);
     }
 
     @Override
@@ -122,7 +124,7 @@ public class CommunityRestRepository extends DSpaceRestRepository<CommunityRest,
         if (community == null) {
             return null;
         }
-        return converter.fromModel(community);
+        return dsoConverter.fromModel(community);
     }
 
     @Override
@@ -139,7 +141,7 @@ public class CommunityRestRepository extends DSpaceRestRepository<CommunityRest,
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<CommunityRest> page = new PageImpl<Community>(communities, pageable, total).map(converter);
+        Page<CommunityRest> page = new PageImpl<Community>(communities, pageable, total).map(dsoConverter);
         return page;
     }
 
@@ -153,7 +155,7 @@ public class CommunityRestRepository extends DSpaceRestRepository<CommunityRest,
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<CommunityRest> page = utils.getPage(topCommunities, pageable).map(converter);
+        Page<CommunityRest> page = utils.getPage(topCommunities, pageable).map(dsoConverter);
         return page;
     }
 
@@ -174,10 +176,17 @@ public class CommunityRestRepository extends DSpaceRestRepository<CommunityRest,
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<CommunityRest> page = utils.getPage(subCommunities, pageable).map(converter);
+        Page<CommunityRest> page = utils.getPage(subCommunities, pageable).map(dsoConverter);
         return page;
     }
 
+    @Override
+    @PreAuthorize("hasPermission(#id, 'COMMUNITY', 'WRITE')")
+    protected void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID id,
+                         Patch patch) throws AuthorizeException, SQLException {
+        patchDSpaceObject(apiCategory, model, id, patch);
+    }
+
     @Override
     public Class<CommunityRest> getDomainClass() {
         return CommunityRest.class;
@@ -233,5 +242,4 @@ public class CommunityRestRepository extends DSpaceRestRepository<CommunityRest,
             throw new RuntimeException("Unable to delete community because the logo couldn't be deleted", e);
         }
     }
-
 }

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/DSpaceObjectRestRepository.java

@@ -0,0 +1,86 @@
+/**
+ * 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.app.rest.repository;
+
+import java.sql.SQLException;
+import java.util.UUID;
+
+import org.dspace.app.rest.converter.DSpaceObjectConverter;
+import org.dspace.app.rest.converter.MetadataConverter;
+import org.dspace.app.rest.exception.UnprocessableEntityException;
+import org.dspace.app.rest.model.DSpaceObjectRest;
+import org.dspace.app.rest.model.patch.Patch;
+import org.dspace.app.rest.repository.patch.DSpaceObjectPatch;
+import org.dspace.authorize.AuthorizeException;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.service.DSpaceObjectService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.rest.webmvc.ResourceNotFoundException;
+
+/**
+ * Base class for DSpaceObject-based Rest Repositories, providing common functionality.
+ *
+ * @param <M> the specific type of DSpaceObject.
+ * @param <R> the corresponding DSpaceObjectRest.
+ */
+public abstract class DSpaceObjectRestRepository<M extends DSpaceObject, R extends DSpaceObjectRest>
+        extends DSpaceRestRepository<R, UUID> {
+
+    final DSpaceObjectService<M> dsoService;
+    final DSpaceObjectPatch<R> dsoPatch;
+    final DSpaceObjectConverter<M, R> dsoConverter;
+
+    @Autowired
+    MetadataConverter metadataConverter;
+
+    DSpaceObjectRestRepository(DSpaceObjectService<M> dsoService,
+                               DSpaceObjectConverter<M, R> dsoConverter,
+                               DSpaceObjectPatch<R> dsoPatch) {
+        this.dsoService = dsoService;
+        this.dsoPatch = dsoPatch;
+        this.dsoConverter = dsoConverter;
+    }
+
+    /**
+     * Updates the DSpaceObject according to the given Patch.
+     *
+     * @param apiCategory the api category.
+     * @param model the api model.
+     * @param id the id of the DSpaceObject.
+     * @param patch the patch to apply.
+     * @throws AuthorizeException if the action is unauthorized.
+     * @throws ResourceNotFoundException if the DSpace object was not found.
+     * @throws SQLException if a database error occurs.
+     * @throws UnprocessableEntityException if the patch attempts to modify an unmodifiable attribute of the object.
+     */
+    protected void patchDSpaceObject(String apiCategory, String model, UUID id, Patch patch)
+            throws AuthorizeException, ResourceNotFoundException, SQLException, UnprocessableEntityException {
+        M dso = dsoService.find(obtainContext(), id);
+        if (dso == null) {
+            throw new ResourceNotFoundException(apiCategory + "." + model + " with id: " + id + " not found");
+        }
+        R dsoRest = dsoPatch.patch(findOne(id), patch.getOperations());
+        updateDSpaceObject(dso, dsoRest);
+    }
+
+    /**
+     * Applies the changes in the given rest DSpace object to the model DSpace object.
+     * The default implementation updates metadata if needed. Subclasses should extend
+     * to support updates of additional properties.
+     *
+     * @param dso the dso to apply changes to.
+     * @param dsoRest the rest representation of the new desired state.
+     */
+    protected void updateDSpaceObject(M dso, R dsoRest)
+            throws AuthorizeException, SQLException {
+        R origDsoRest = dsoConverter.fromModel(dso);
+        if (!origDsoRest.getMetadata().equals(dsoRest.getMetadata())) {
+            metadataConverter.setMetadata(obtainContext(), dso, dsoRest.getMetadata());
+        }
+    }
+}

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/EPersonRestRepository.java

@@ -12,7 +12,6 @@ import java.sql.SQLException;
 import java.util.List;
 import java.util.Objects;
 import java.util.UUID;
-
 import javax.servlet.http.HttpServletRequest;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -21,25 +20,21 @@ import org.dspace.app.rest.Parameter;
 import org.dspace.app.rest.SearchRestMethod;
 import org.dspace.app.rest.converter.EPersonConverter;
 import org.dspace.app.rest.converter.MetadataConverter;
-import org.dspace.app.rest.exception.PatchBadRequestException;
 import org.dspace.app.rest.exception.RESTAuthorizationException;
 import org.dspace.app.rest.exception.UnprocessableEntityException;
 import org.dspace.app.rest.model.EPersonRest;
 import org.dspace.app.rest.model.hateoas.EPersonResource;
-import org.dspace.app.rest.model.patch.Operation;
 import org.dspace.app.rest.model.patch.Patch;
 import org.dspace.app.rest.repository.patch.EPersonPatch;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
-import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
-import org.springframework.data.rest.webmvc.ResourceNotFoundException;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Component;
 
@@ -51,14 +46,12 @@ import org.springframework.stereotype.Component;
  */
 
 @Component(EPersonRest.CATEGORY + "." + EPersonRest.NAME)
-public class EPersonRestRepository extends DSpaceRestRepository<EPersonRest, UUID> {
+public class EPersonRestRepository extends DSpaceObjectRestRepository<EPerson, EPersonRest> {
-    EPersonService es = EPersonServiceFactory.getInstance().getEPersonService();
 
     @Autowired
     AuthorizeService authorizeService;
 
-    @Autowired
+    private final EPersonService es;
-    EPersonConverter converter;
 
     @Autowired
     MetadataConverter metadataConverter;
@@ -66,6 +59,13 @@ public class EPersonRestRepository extends DSpaceRestRepository<EPersonRest, UUI
     @Autowired
     EPersonPatch epersonPatch;
 
+    public EPersonRestRepository(EPersonService dsoService,
+                                 EPersonConverter dsoConverter,
+                                 EPersonPatch dsoPatch) {
+        super(dsoService, dsoConverter, dsoPatch);
+        this.es = dsoService;
+    }
+
     @Override
     protected EPersonRest createAndReturn(Context context)
             throws AuthorizeException {
@@ -97,7 +97,7 @@ public class EPersonRestRepository extends DSpaceRestRepository<EPersonRest, UUI
             throw new RuntimeException(e.getMessage(), e);
         }
 
-        return converter.convert(eperson);
+        return dsoConverter.convert(eperson);
     }
 
     @Override
@@ -112,7 +112,7 @@ public class EPersonRestRepository extends DSpaceRestRepository<EPersonRest, UUI
         if (eperson == null) {
             return null;
         }
-        return converter.fromModel(eperson);
+        return dsoConverter.fromModel(eperson);
     }
 
     @Override
@@ -130,7 +130,7 @@ public class EPersonRestRepository extends DSpaceRestRepository<EPersonRest, UUI
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<EPersonRest> page = new PageImpl<EPerson>(epersons, pageable, total).map(converter);
+        Page<EPersonRest> page = new PageImpl<EPerson>(epersons, pageable, total).map(dsoConverter);
         return page;
     }
 
@@ -156,7 +156,7 @@ public class EPersonRestRepository extends DSpaceRestRepository<EPersonRest, UUI
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<EPersonRest> page = new PageImpl<EPerson>(epersons, pageable, total).map(converter);
+        Page<EPersonRest> page = new PageImpl<EPerson>(epersons, pageable, total).map(dsoConverter);
         return page;
     }
 
@@ -182,42 +182,22 @@ public class EPersonRestRepository extends DSpaceRestRepository<EPersonRest, UUI
         if (eperson == null) {
             return null;
         }
-        return converter.fromModel(eperson);
+        return dsoConverter.fromModel(eperson);
     }
 
     @Override
     @PreAuthorize("hasAuthority('ADMIN')")
-    public void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID uuid,
+    protected void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID uuid,
-                      Patch patch)
+                         Patch patch) throws AuthorizeException, SQLException {
-            throws UnprocessableEntityException, PatchBadRequestException, AuthorizeException,
+        patchDSpaceObject(apiCategory, model, uuid, patch);
-            ResourceNotFoundException {
-
-        try {
-            EPerson eperson = es.find(context, uuid);
-            if (eperson == null) {
-                throw new ResourceNotFoundException(apiCategory + "." + model + " with id: " + uuid + " not found");
-            }
-            List<Operation> operations = patch.getOperations();
-            EPersonRest ePersonRest = findOne(context, uuid);
-            EPersonRest patchedModel = (EPersonRest) epersonPatch.patch(ePersonRest, operations);
-            updatePatchedValues(context, patchedModel, eperson);
-
-        } catch (SQLException e) {
-            throw new RuntimeException(e.getMessage(), e);
-        }
     }
 
-    /**
+    @Override
-     * Applies changes in the rest model.
+    protected void updateDSpaceObject(EPerson ePerson, EPersonRest ePersonRest)
-     * @param context
+            throws AuthorizeException, SQLException {
-     * @param ePersonRest the updated eperson rest
+        super.updateDSpaceObject(ePerson, ePersonRest);
-     * @param ePerson the eperson content object
-     * @throws SQLException
-     * @throws AuthorizeException
-     */
-    private void updatePatchedValues(Context context, EPersonRest ePersonRest, EPerson ePerson)
-            throws SQLException, AuthorizeException {
 
+        Context context = obtainContext();
         if (ePersonRest.getPassword() != null) {
             es.setPassword(ePerson, ePersonRest.getPassword());
         }
@@ -232,7 +212,6 @@ public class EPersonRestRepository extends DSpaceRestRepository<EPersonRest, UUI
         }
 
         es.update(context, ePerson);
-
     }
 
     @Override

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/GroupRestRepository.java

@@ -21,6 +21,8 @@ import org.dspace.app.rest.exception.RepositoryMethodNotImplementedException;
 import org.dspace.app.rest.exception.UnprocessableEntityException;
 import org.dspace.app.rest.model.GroupRest;
 import org.dspace.app.rest.model.hateoas.GroupResource;
+import org.dspace.app.rest.model.patch.Patch;
+import org.dspace.app.rest.repository.patch.DSpaceObjectPatch;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.core.Context;
 import org.dspace.eperson.Group;
@@ -39,12 +41,16 @@ import org.springframework.stereotype.Component;
  */
 
 @Component(GroupRest.CATEGORY + "." + GroupRest.NAME)
-public class GroupRestRepository extends DSpaceRestRepository<GroupRest, UUID> {
+public class GroupRestRepository extends DSpaceObjectRestRepository<Group, GroupRest> {
     @Autowired
     GroupService gs;
 
     @Autowired
-    GroupConverter converter;
+    GroupRestRepository(GroupService dsoService,
+                        GroupConverter dsoConverter) {
+        super(dsoService, dsoConverter, new DSpaceObjectPatch<GroupRest>() {});
+        this.gs = dsoService;
+    }
 
     @Autowired
     MetadataConverter metadataConverter;
@@ -73,7 +79,7 @@ public class GroupRestRepository extends DSpaceRestRepository<GroupRest, UUID> {
             throw new RuntimeException(excSQL.getMessage(), excSQL);
         }
 
-        return converter.convert(group);
+        return dsoConverter.convert(group);
     }
 
     @Override
@@ -88,7 +94,7 @@ public class GroupRestRepository extends DSpaceRestRepository<GroupRest, UUID> {
         if (group == null) {
             return null;
         }
-        return converter.fromModel(group);
+        return dsoConverter.fromModel(group);
     }
 
     @PreAuthorize("hasAuthority('ADMIN')")
@@ -102,10 +108,17 @@ public class GroupRestRepository extends DSpaceRestRepository<GroupRest, UUID> {
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<GroupRest> page = new PageImpl<Group>(groups, pageable, total).map(converter);
+        Page<GroupRest> page = new PageImpl<Group>(groups, pageable, total).map(dsoConverter);
         return page;
     }
 
+    @Override
+    @PreAuthorize("hasPermission(#id, 'GROUP', 'WRITE')")
+    protected void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID id,
+                         Patch patch) throws AuthorizeException, SQLException {
+        patchDSpaceObject(apiCategory, model, id, patch);
+    }
+
     @Override
     public Class<GroupRest> getDomainClass() {
         return GroupRest.class;

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/ItemRestRepository.java

@@ -23,12 +23,10 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Logger;
 import org.dspace.app.rest.converter.ItemConverter;
 import org.dspace.app.rest.converter.MetadataConverter;
-import org.dspace.app.rest.exception.PatchBadRequestException;
 import org.dspace.app.rest.exception.RepositoryMethodNotImplementedException;
 import org.dspace.app.rest.exception.UnprocessableEntityException;
 import org.dspace.app.rest.model.ItemRest;
 import org.dspace.app.rest.model.hateoas.ItemResource;
-import org.dspace.app.rest.model.patch.Operation;
 import org.dspace.app.rest.model.patch.Patch;
 import org.dspace.app.rest.repository.patch.ItemPatch;
 import org.dspace.authorize.AuthorizeException;
@@ -56,15 +54,11 @@ import org.springframework.stereotype.Component;
  */
 
 @Component(ItemRest.CATEGORY + "." + ItemRest.NAME)
-public class ItemRestRepository extends DSpaceRestRepository<ItemRest, UUID> {
+public class ItemRestRepository extends DSpaceObjectRestRepository<Item, ItemRest> {
 
     private static final Logger log = Logger.getLogger(ItemRestRepository.class);
 
-    @Autowired
+    private final ItemService is;
-    ItemService is;
-
-    @Autowired
-    ItemConverter converter;
 
     @Autowired
     MetadataConverter metadataConverter;
@@ -84,8 +78,11 @@ public class ItemRestRepository extends DSpaceRestRepository<ItemRest, UUID> {
     @Autowired
     InstallItemService installItemService;
 
-    public ItemRestRepository() {
+    public ItemRestRepository(ItemService dsoService,
-        System.out.println("Repository initialized by Spring");
+                              ItemConverter dsoConverter,
+                              ItemPatch dsoPatch) {
+        super(dsoService, dsoConverter, dsoPatch);
+        this.is = dsoService;
     }
 
     @Override
@@ -100,7 +97,7 @@ public class ItemRestRepository extends DSpaceRestRepository<ItemRest, UUID> {
         if (item == null) {
             return null;
         }
-        return converter.fromModel(item);
+        return dsoConverter.fromModel(item);
     }
 
     @Override
@@ -119,41 +116,23 @@ public class ItemRestRepository extends DSpaceRestRepository<ItemRest, UUID> {
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<ItemRest> page = new PageImpl<Item>(items, pageable, total).map(converter);
+        Page<ItemRest> page = new PageImpl<Item>(items, pageable, total).map(dsoConverter);
         return page;
     }
 
     @Override
-    public void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID uuid,
+    @PreAuthorize("hasPermission(#id, 'ITEM', 'WRITE')")
-                      Patch patch)
+    protected void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID id,
-            throws UnprocessableEntityException, PatchBadRequestException, SQLException, AuthorizeException,
+                         Patch patch) throws AuthorizeException, SQLException {
-            ResourceNotFoundException {
+        patchDSpaceObject(apiCategory, model, id, patch);
-
-        Item item = is.find(context, uuid);
-
-        if (item == null) {
-            throw new ResourceNotFoundException(apiCategory + "." + model + " with id: " + uuid + " not found");
     }
 
-        List<Operation> operations = patch.getOperations();
+    @Override
-        ItemRest itemRest = findOne(uuid);
+    protected void updateDSpaceObject(Item item, ItemRest itemRest)
+            throws AuthorizeException, SQLException  {
+        super.updateDSpaceObject(item, itemRest);
 
-        ItemRest patchedModel = (ItemRest) itemPatch.patch(itemRest, operations);
+        Context context = obtainContext();
-        updatePatchedValues(context, patchedModel, item);
-    }
-
-    /**
-     * Persists changes to the rest model.
-     * @param context
-     * @param itemRest the updated item rest resource
-     * @param item the item content object
-     * @throws SQLException
-     * @throws AuthorizeException
-     */
-    private void updatePatchedValues(Context context, ItemRest itemRest, Item item)
-            throws SQLException, AuthorizeException {
-
-        try {
         if (itemRest.getWithdrawn() != item.isWithdrawn()) {
             if (itemRest.getWithdrawn()) {
                 is.withdraw(context, item);
@@ -165,10 +144,6 @@ public class ItemRestRepository extends DSpaceRestRepository<ItemRest, UUID> {
             item.setDiscoverable(itemRest.getDiscoverable());
             is.update(context, item);
         }
-        } catch (SQLException | AuthorizeException e) {
-            e.printStackTrace();
-            throw e;
-        }
     }
 
     @Override
@@ -242,7 +217,7 @@ public class ItemRestRepository extends DSpaceRestRepository<ItemRest, UUID> {
 
         Item itemToReturn = installItemService.installItem(context, workspaceItem);
 
-        return converter.fromModel(itemToReturn);
+        return dsoConverter.fromModel(itemToReturn);
     }
 
     @Override
@@ -271,6 +246,6 @@ public class ItemRestRepository extends DSpaceRestRepository<ItemRest, UUID> {
                                                    + uuid + ", "
                                                    + itemRest.getId());
         }
-        return converter.fromModel(item);
+        return dsoConverter.fromModel(item);
     }
 }

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/PoolTaskRestRepository.java

@@ -24,6 +24,7 @@ import org.dspace.app.rest.exception.UnprocessableEntityException;
 import org.dspace.app.rest.model.PoolTaskRest;
 import org.dspace.app.rest.model.hateoas.PoolTaskResource;
 import org.dspace.authorize.AuthorizeException;
+import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
@@ -41,6 +42,7 @@ import org.dspace.xmlworkflow.storedcomponents.service.PoolTaskService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
+import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Component;
 
 /**
@@ -72,7 +74,11 @@ public class PoolTaskRestRepository extends DSpaceRestRepository<PoolTaskRest, I
     @Autowired
     WorkflowRequirementsService workflowRequirementsService;
 
+    @Autowired
+    AuthorizeService authorizeService;
+
     @Override
+    @PreAuthorize("hasPermission(#id, 'POOLTASK', 'READ')")
     public PoolTaskRest findOne(Context context, Integer id) {
         PoolTask task = null;
         try {
@@ -91,8 +97,19 @@ public class PoolTaskRestRepository extends DSpaceRestRepository<PoolTaskRest, I
         List<PoolTask> tasks = null;
         try {
             Context context = obtainContext();
+            //FIXME this should be secured with annotation but they are currently ignored by search methods
+            EPerson currentUser = context.getCurrentUser();
+            if (currentUser == null) {
+                throw new RESTAuthorizationException(
+                    "This endpoint is available only to logged-in user"
+                    + " to search for their own pool tasks or the admins");
+            }
+            if (authorizeService.isAdmin(context) || userID.equals(currentUser.getID())) {
                 EPerson ep = epersonService.find(context, userID);
                 tasks = poolTaskService.findByEperson(context, ep);
+            } else {
+                throw new RESTAuthorizationException("Only administrators can search for pool tasks of other users");
+            }
         } catch (AuthorizeException e) {
             throw new RESTAuthorizationException(e);
         } catch (SQLException | IOException e) {
@@ -113,6 +130,7 @@ public class PoolTaskRestRepository extends DSpaceRestRepository<PoolTaskRest, I
     }
 
     @Override
+    @PreAuthorize("hasPermission(#id, 'POOLTASK', 'WRITE')")
     protected PoolTaskRest action(Context context, HttpServletRequest request, Integer id)
         throws SQLException, IOException {
         PoolTask task = null;

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/SiteRestRepository.java

@@ -11,10 +11,14 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
+import javax.servlet.http.HttpServletRequest;
 
 import org.dspace.app.rest.converter.SiteConverter;
 import org.dspace.app.rest.model.SiteRest;
 import org.dspace.app.rest.model.hateoas.SiteResource;
+import org.dspace.app.rest.model.patch.Patch;
+import org.dspace.app.rest.repository.patch.DSpaceObjectPatch;
+import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Site;
 import org.dspace.content.service.SiteService;
 import org.dspace.core.Context;
@@ -22,6 +26,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
+import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Component;
 
 /**
@@ -31,16 +36,15 @@ import org.springframework.stereotype.Component;
  */
 
 @Component(SiteRest.CATEGORY + "." + SiteRest.NAME)
-public class SiteRestRepository extends DSpaceRestRepository<SiteRest, UUID> {
+public class SiteRestRepository extends DSpaceObjectRestRepository<Site, SiteRest> {
+
+    private final SiteService sitesv;
 
     @Autowired
-    SiteService sitesv;
+    public SiteRestRepository(SiteService dsoService,
-
+                              SiteConverter dsoConverter) {
-    @Autowired
+        super(dsoService, dsoConverter, new DSpaceObjectPatch<SiteRest>() {});
-    SiteConverter converter;
+        this.sitesv = dsoService;
-
-
-    public SiteRestRepository() {
     }
 
     @Override
@@ -54,7 +58,7 @@ public class SiteRestRepository extends DSpaceRestRepository<SiteRest, UUID> {
         if (site == null) {
             return null;
         }
-        return converter.fromModel(site);
+        return dsoConverter.fromModel(site);
     }
 
     @Override
@@ -66,10 +70,17 @@ public class SiteRestRepository extends DSpaceRestRepository<SiteRest, UUID> {
         } catch (SQLException e) {
             throw new RuntimeException(e.getMessage(), e);
         }
-        Page<SiteRest> page = new PageImpl<Site>(sites, pageable, total).map(converter);
+        Page<SiteRest> page = new PageImpl<Site>(sites, pageable, total).map(dsoConverter);
         return page;
     }
 
+    @Override
+    @PreAuthorize("hasAuthority('ADMIN')")
+    protected void patch(Context context, HttpServletRequest request, String apiCategory, String model, UUID id,
+                         Patch patch) throws AuthorizeException, SQLException {
+        patchDSpaceObject(apiCategory, model, id, patch);
+    }
+
     @Override
     public Class<SiteRest> getDomainClass() {
         return SiteRest.class;

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/patch/AbstractResourcePatch.java

@@ -30,7 +30,7 @@ public abstract class AbstractResourcePatch<R extends RestModel> {
      * @throws UnprocessableEntityException
      * @throws PatchBadRequestException
      */
-    public RestModel patch(R restModel, List<Operation> operations) {
+    public R patch(R restModel, List<Operation> operations) {
 
         // Note: the list of possible operations is taken from JsonPatchConverter class. Does not implement
         // test https://tools.ietf.org/html/rfc6902#section-4.6

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/patch/DSpaceObjectPatch.java

@@ -0,0 +1,81 @@
+/**
+ * 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.app.rest.repository.patch;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+import com.flipkart.zjsonpatch.JsonPatch;
+import org.dspace.app.rest.converter.JsonPatchConverter;
+import org.dspace.app.rest.model.DSpaceObjectRest;
+import org.dspace.app.rest.model.MetadataRest;
+import org.dspace.app.rest.model.patch.Operation;
+import org.dspace.app.rest.model.patch.Patch;
+
+/**
+ * Base class for DSpaceObject-based PATCH operations, providing common functionality.
+ *
+ * @param <R> the type of DSpaceObjectRest object the class is applicable to.
+ */
+public abstract class DSpaceObjectPatch<R extends DSpaceObjectRest> extends AbstractResourcePatch<R> {
+
+    private static final String METADATA_PATH = "/metadata";
+
+    private ObjectMapper objectMapper = new ObjectMapper();
+
+    private JsonPatchConverter jsonPatchConverter = new JsonPatchConverter(objectMapper);
+
+    /**
+     * Applies the given patch operations to the given DSpaceObjectRest instance.
+     *
+     * This extends the default implementation by first applying metadata-based patch operations,
+     * then applying any others.
+     *
+     * @param dsoRest the instance to apply the changes to.
+     * @param operations the list of patch operations.
+     * @return the modified DSpaceObectRest instance.
+     */
+    @Override
+    public R patch(R dsoRest, List<Operation> operations) {
+        List<Operation> metadataOperations = new ArrayList<>();
+        List<Operation> otherOperations = new ArrayList<>();
+
+        for (Operation operation : operations) {
+            String path = operation.getPath();
+            if (path.equals(METADATA_PATH) || path.startsWith(METADATA_PATH + "/")) {
+                metadataOperations.add(operation);
+            } else {
+                otherOperations.add(operation);
+            }
+        }
+
+        if (!metadataOperations.isEmpty()) {
+            dsoRest.setMetadata(applyMetadataPatch(
+                    jsonPatchConverter.convert(new Patch(metadataOperations)),
+                    dsoRest.getMetadata()));
+        }
+
+        return super.patch(dsoRest, otherOperations);
+    }
+
+    private MetadataRest applyMetadataPatch(JsonNode patch, MetadataRest metadataRest) {
+        try {
+            ObjectNode objectNode = objectMapper.createObjectNode();
+            JsonNode metadataNode = objectMapper.valueToTree(metadataRest);
+            objectNode.replace("metadata", metadataNode);
+            JsonPatch.applyInPlace(patch, objectNode);
+            return objectMapper.treeToValue(objectNode.get("metadata"), MetadataRest.class);
+        } catch (IOException e) {
+            throw new IllegalArgumentException(e);
+        }
+    }
+}

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/patch/EPersonPatch.java

@@ -20,7 +20,7 @@ import org.springframework.stereotype.Component;
  * Provides patch operations for eperson updates.
  */
 @Component
-public class EPersonPatch extends AbstractResourcePatch<EPersonRest> {
+public class EPersonPatch extends DSpaceObjectPatch<EPersonRest> {
 
     @Autowired
     EPersonOperationFactory patchFactory;

dspace-spring-rest/src/main/java/org/dspace/app/rest/repository/patch/ItemPatch.java

@@ -20,7 +20,7 @@ import org.springframework.stereotype.Component;
  * Provides PATCH operations for item updates.
  */
 @Component
-public class ItemPatch extends AbstractResourcePatch<ItemRest> {
+public class ItemPatch extends DSpaceObjectPatch<ItemRest> {
 
     @Autowired
     ItemOperationFactory patchFactory;

dspace-spring-rest/src/main/java/org/dspace/app/rest/security/ClaimedTaskRestPermissionEvaluatorPlugin.java

@@ -0,0 +1,80 @@
+/**
+ * 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.app.rest.security;
+
+import java.io.Serializable;
+import java.sql.SQLException;
+
+import org.dspace.app.rest.utils.ContextUtil;
+import org.dspace.core.Constants;
+import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
+import org.dspace.eperson.service.EPersonService;
+import org.dspace.services.RequestService;
+import org.dspace.services.model.Request;
+import org.dspace.xmlworkflow.storedcomponents.ClaimedTask;
+import org.dspace.xmlworkflow.storedcomponents.service.ClaimedTaskService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.core.Authentication;
+import org.springframework.stereotype.Component;
+
+/**
+ * An authenticated user is allowed to interact with a claimed task only if he own it
+ * claim.
+ * 
+ * @author Andrea Bollini (andrea.bollini at 4science.it)
+ */
+@Component
+public class ClaimedTaskRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
+
+    private static final Logger log = LoggerFactory.getLogger(ClaimedTaskRestPermissionEvaluatorPlugin.class);
+
+    @Autowired
+    private RequestService requestService;
+
+    @Autowired
+    private ClaimedTaskService claimedTaskService;
+
+    @Autowired
+    private EPersonService ePersonService;
+
+    @Override
+    public boolean hasPermission(Authentication authentication, Serializable targetId,
+                                 String targetType, Object permission) {
+
+        if (Constants.getTypeID(targetType) != Constants.CLAIMEDTASK) {
+            return false;
+        }
+
+        Request request = requestService.getCurrentRequest();
+        Context context = ContextUtil.obtainContext(request.getServletRequest());
+        EPerson ePerson = null;
+        try {
+            ePerson = ePersonService.findByEmail(context, (String) authentication.getPrincipal());
+            if (ePerson == null) {
+                return false;
+            }
+            Integer dsoId = Integer.parseInt(targetId.toString());
+            ClaimedTask claimedTask = claimedTaskService.find(context, dsoId);
+            // If the claimed task is null then we give permission so we can throw another status code instead
+            if (claimedTask == null) {
+                return true;
+            }
+            // task's owner can interact with it
+            if (claimedTask != null && ePerson.equals(claimedTask.getOwner())) {
+                return true;
+            }
+
+        } catch (SQLException e) {
+            log.error(e.getMessage(), e);
+        }
+        return false;
+    }
+}

dspace-spring-rest/src/main/java/org/dspace/app/rest/security/PoolTaskRestPermissionEvaluatorPlugin.java

@@ -0,0 +1,85 @@
+/**
+ * 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.app.rest.security;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.sql.SQLException;
+
+import org.dspace.app.rest.utils.ContextUtil;
+import org.dspace.authorize.AuthorizeException;
+import org.dspace.core.Constants;
+import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
+import org.dspace.eperson.service.EPersonService;
+import org.dspace.services.RequestService;
+import org.dspace.services.model.Request;
+import org.dspace.xmlworkflow.storedcomponents.PoolTask;
+import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
+import org.dspace.xmlworkflow.storedcomponents.service.PoolTaskService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.core.Authentication;
+import org.springframework.stereotype.Component;
+
+/**
+ * An authenticated user is allowed to interact with a pool task only if it is in his list.
+ * 
+ * @author Andrea Bollini (andrea.bollini at 4science.it)
+ */
+@Component
+public class PoolTaskRestPermissionEvaluatorPlugin extends RestObjectPermissionEvaluatorPlugin {
+
+    private static final Logger log = LoggerFactory.getLogger(PoolTaskRestPermissionEvaluatorPlugin.class);
+
+    @Autowired
+    private RequestService requestService;
+
+    @Autowired
+    private PoolTaskService poolTaskService;
+
+    @Autowired
+    private EPersonService ePersonService;
+
+    @Override
+    public boolean hasPermission(Authentication authentication, Serializable targetId,
+                                 String targetType, Object permission) {
+
+        if (Constants.getTypeID(targetType) != Constants.POOLTASK) {
+            return false;
+        }
+
+        Request request = requestService.getCurrentRequest();
+        Context context = ContextUtil.obtainContext(request.getServletRequest());
+        EPerson ePerson = null;
+        try {
+            ePerson = ePersonService.findByEmail(context, (String) authentication.getPrincipal());
+            if (ePerson == null) {
+                return false;
+            }
+            Integer dsoId = Integer.parseInt(targetId.toString());
+
+            PoolTask poolTask = poolTaskService.find(context, dsoId);
+            // If the pool task is null then we give permission so we can throw another status code instead
+            if (poolTask == null) {
+                return true;
+            }
+
+            XmlWorkflowItem workflowItem = poolTask.getWorkflowItem();
+
+            PoolTask poolTask2 = poolTaskService.findByWorkflowIdAndEPerson(context, workflowItem, ePerson);
+            if (poolTask2 != null && poolTask2.getID() == poolTask.getID()) {
+                return true;
+            }
+        } catch (SQLException | AuthorizeException | IOException e) {
+            log.error(e.getMessage(), e);
+        }
+        return false;
+    }
+}

dspace-spring-rest/src/main/java/org/dspace/app/rest/submit/SubmissionService.java

@@ -213,19 +213,28 @@ public class SubmissionService {
             char[] arr = new char[1024];
             StringBuilder buffer = new StringBuilder();
             int numCharsRead = reader.read(arr, 0, arr.length);
+            if (numCharsRead > 0) {
                 buffer.append(arr, 0, numCharsRead);
+            }
             if (numCharsRead == arr.length) {
-                throw new RuntimeException("Malformed body... too long");
+                throw new UnprocessableEntityException("Malformed body... too long");
             }
             String regex = "\\/api\\/" + WorkspaceItemRest.CATEGORY + "\\/" + English.plural(WorkspaceItemRest.NAME)
                     + "\\/";
             String[] split = buffer.toString().split(regex, 2);
             if (split.length != 2) {
-                throw new RuntimeException("Malformed body..." + buffer);
+                throw new UnprocessableEntityException("Malformed body..." + buffer);
             }
             // END FIXME
-            WorkspaceItem wsi = workspaceItemService.find(context, Integer.parseInt(split[1]));
+            WorkspaceItem wsi = null;
-
+            try {
+                wsi = workspaceItemService.find(context, Integer.parseInt(split[1]));
+            } catch (NumberFormatException e) {
+                throw new UnprocessableEntityException("The provided workspaceitem URI is not valid");
+            }
+            if (wsi == null) {
+                throw new UnprocessableEntityException("Workspace item is not found");
+            }
             if (!workspaceItemConverter.convert(wsi).getErrors().isEmpty()) {
                 throw new UnprocessableEntityException(
                         "Start workflow failed due to validation error on workspaceitem");

dspace-spring-rest/src/main/resources/application.properties

@@ -86,26 +86,23 @@ server.context-parameters.dspace.dir=${dspace.dir}
 
 # Error handling settings
 # Always include the fullstacktrace in error pages
-# (Our Error page hides this stacktrace so it only is visible in HTML source)
 # Can be set to "never" if you don't want it.
 server.error.include-stacktrace = always
 
 ######################
 # Spring Boot Autoconfigure
 #
-# DISABLE a few autoconfiguration scripts, as DSpace configures these already
+# DISABLE a few autoconfiguration scripts, as DSpace initializes/configures these already
 # * DataSourceAutoConfiguration (DB connection / datasource)
 # * FlywayAutoConfiguration (Flyway migrations)
+# * HibernateJpaAutoConfiguration (Hibernate)
+# * SolrAutoConfiguration (Solr)
 #
-# TODO: If we go with Spring boot, we should investigate whether it's worth
+# TODO: At some point we may want to investigate whether we can re-enable these and remove the custom DSpace init code
-# re-enabling these and removing the custom DSpace initialization code
-#spring.autoconfigure.exclude=org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration, \
-#                             org.springframework.boot.autoconfigure.orm.jpa.HibernateJpaAutoConfiguration, \
-#                             org.springframework.boot.autoconfigure.flyway.FlywayAutoConfiguration
-
 spring.autoconfigure.exclude=org.springframework.boot.autoconfigure.jdbc.DataSourceAutoConfiguration, \
                              org.springframework.boot.autoconfigure.orm.jpa.HibernateJpaAutoConfiguration, \
-                             org.springframework.boot.autoconfigure.flyway.FlywayAutoConfiguration
+                             org.springframework.boot.autoconfigure.flyway.FlywayAutoConfiguration, \
+                             org.springframework.boot.autoconfigure.solr.SolrAutoConfiguration
 
 #########################
 # Spring Boot Logging levels

dspace-spring-rest/src/test/java/org/dspace/app/rest/BitstreamRestRepositoryIT.java

@@ -27,11 +27,13 @@ import org.dspace.app.rest.builder.ItemBuilder;
 import org.dspace.app.rest.matcher.BitstreamFormatMatcher;
 import org.dspace.app.rest.matcher.BitstreamMatcher;
 import org.dspace.app.rest.test.AbstractControllerIntegrationTest;
+import org.dspace.app.rest.test.MetadataPatchSuite;
 import org.dspace.content.Bitstream;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.Item;
 import org.dspace.content.service.BitstreamService;
+import org.dspace.eperson.EPerson;
 import org.hamcrest.Matchers;
 import org.junit.Ignore;
 import org.junit.Test;
@@ -587,4 +589,25 @@ public class BitstreamRestRepositoryIT extends AbstractControllerIntegrationTest
         getClient(token).perform(delete("/api/core/bitstreams/" + col.getLogo().getID()))
                    .andExpect(status().is(422));
     }
+
+    @Test
+    public void patchBitstreamMetadataAuthorized() throws Exception {
+        runPatchMetadataTests(admin, 200);
+    }
+
+    @Test
+    public void patchBitstreamMetadataUnauthorized() throws Exception {
+        runPatchMetadataTests(eperson, 403);
+    }
+
+    private void runPatchMetadataTests(EPerson asUser, int expectedStatus) throws Exception {
+        context.turnOffAuthorisationSystem();
+        parentCommunity = CommunityBuilder.createCommunity(context).withName("Community").withLogo("logo_community")
+                .build();
+        context.restoreAuthSystemState();
+        String token = getAuthToken(asUser.getEmail(), password);
+
+        new MetadataPatchSuite().runWith(getClient(token), "/api/core/bitstreams/"
+                + parentCommunity.getLogo().getID(), expectedStatus);
+    }
 }

dspace-spring-rest/src/test/java/org/dspace/app/rest/CollectionRestRepositoryIT.java

@@ -31,10 +31,12 @@ import org.dspace.app.rest.model.CollectionRest;
 import org.dspace.app.rest.model.MetadataRest;
 import org.dspace.app.rest.model.MetadataValueRest;
 import org.dspace.app.rest.test.AbstractControllerIntegrationTest;
+import org.dspace.app.rest.test.MetadataPatchSuite;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.core.Constants;
+import org.dspace.eperson.EPerson;
 import org.hamcrest.Matchers;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -624,6 +626,24 @@ public class CollectionRestRepositoryIT extends AbstractControllerIntegrationTes
         ;
 
         authorizeService.removePoliciesActionFilter(context, eperson, Constants.WRITE);
+    }
 
+    public void patchCollectionMetadataAuthorized() throws Exception {
+        runPatchMetadataTests(admin, 200);
+    }
+
+    @Test
+    public void patchCollectionMetadataUnauthorized() throws Exception {
+        runPatchMetadataTests(eperson, 403);
+    }
+
+    private void runPatchMetadataTests(EPerson asUser, int expectedStatus) throws Exception {
+        context.turnOffAuthorisationSystem();
+        parentCommunity = CommunityBuilder.createCommunity(context).withName("Community").build();
+        Collection col = CollectionBuilder.createCollection(context, parentCommunity).withName("Collection").build();
+        context.restoreAuthSystemState();
+        String token = getAuthToken(asUser.getEmail(), password);
+
+        new MetadataPatchSuite().runWith(getClient(token), "/api/core/collections/" + col.getID(), expectedStatus);
     }
 }

dspace-spring-rest/src/test/java/org/dspace/app/rest/CommunityRestRepositoryIT.java

@@ -33,10 +33,12 @@ import org.dspace.app.rest.model.CommunityRest;
 import org.dspace.app.rest.model.MetadataRest;
 import org.dspace.app.rest.model.MetadataValueRest;
 import org.dspace.app.rest.test.AbstractControllerIntegrationTest;
+import org.dspace.app.rest.test.MetadataPatchSuite;
 import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.core.Constants;
+import org.dspace.eperson.EPerson;
 import org.hamcrest.Matchers;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -852,4 +854,22 @@ public class CommunityRestRepositoryIT extends AbstractControllerIntegrationTest
 
     }
 
+    public void patchCommunityMetadataAuthorized() throws Exception {
+        runPatchMetadataTests(admin, 200);
+    }
+
+    @Test
+    public void patchCommunityMetadataUnauthorized() throws Exception {
+        runPatchMetadataTests(eperson, 403);
+    }
+
+    private void runPatchMetadataTests(EPerson asUser, int expectedStatus) throws Exception {
+        context.turnOffAuthorisationSystem();
+        parentCommunity = CommunityBuilder.createCommunity(context).withName("Community").build();
+        context.restoreAuthSystemState();
+        String token = getAuthToken(asUser.getEmail(), password);
+
+        new MetadataPatchSuite().runWith(getClient(token), "/api/core/communities/"
+                + parentCommunity.getID(), expectedStatus);
+    }
 }