Merge branch 'main' of https://github.com/4Science/DSpace into CST-5249

.github/workflows/port_merged_pull_request.yml

@@ -39,6 +39,8 @@ jobs:
           # Copy all labels from original PR to (newly created) port PR
           # NOTE: The labels matching 'label_pattern' are automatically excluded
           copy_labels_pattern: '.*'
+          # Skip any merge commits in the ported PR. This means only non-merge commits are cherry-picked to the new PR
+          merge_commits: 'skip'
           # Use a personal access token (PAT) to create PR as 'dspace-bot' user.
           # A PAT is required in order for the new PR to trigger its own actions (for CI checks)
           github_token: ${{ secrets.PR_PORT_TOKEN }}

Dockerfile

@@ -51,7 +51,7 @@ RUN ant init_installation update_configs update_code update_webapps
 FROM tomcat:9-jdk${JDK_VERSION}
 # NOTE: DSPACE_INSTALL must align with the "dspace.dir" default configuration.
 ENV DSPACE_INSTALL=/dspace
-# Copy the /dspace directory from 'ant_build' containger to /dspace in this container
+# Copy the /dspace directory from 'ant_build' container to /dspace in this container
 COPY --from=ant_build /dspace $DSPACE_INSTALL
 # Expose Tomcat port and AJP port
 EXPOSE 8080 8009

docker-compose.yml

@@ -28,6 +28,7 @@ services:
       # proxies.trusted.ipranges: This setting is required for a REST API running in Docker to trust requests
       # from the host machine. This IP range MUST correspond to the 'dspacenet' subnet defined above.
       proxies__P__trusted__P__ipranges: '172.23.0'
+      LOGGING_CONFIG: /dspace/config/log4j2-container.xml
     image: "${DOCKER_OWNER:-dspace}/dspace:${DSPACE_VER:-latest-test}"
     build:
       context: .

dspace-api/pom.xml

@@ -102,7 +102,7 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>build-helper-maven-plugin</artifactId>
-                <version>3.0.0</version>
+                <version>3.4.0</version>
                 <executions>
                     <execution>
                         <phase>validate</phase>
@@ -116,7 +116,10 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>buildnumber-maven-plugin</artifactId>
-                <version>1.4</version>
+                <version>3.2.0</version>
+                <configuration>
+                    <revisionOnScmFailure>UNKNOWN_REVISION</revisionOnScmFailure>
+                </configuration>
                 <executions>
                     <execution>
                         <phase>validate</phase>
@@ -697,10 +700,6 @@
             <artifactId>annotations</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>joda-time</groupId>
-            <artifactId>joda-time</artifactId>
-        </dependency>
         <dependency>
             <groupId>javax.inject</groupId>
             <artifactId>javax.inject</artifactId>
@@ -770,7 +769,7 @@
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
-            <version>20230227</version>
+            <version>20231013</version>
         </dependency>
 
         <!-- Useful for testing command-line tools -->

dspace-api/src/main/java/org/dspace/access/status/AccessStatusHelper.java

@@ -22,9 +22,21 @@ public interface AccessStatusHelper {
      *
      * @param context the DSpace context
      * @param item    the item
+     * @param threshold the embargo threshold date
      * @return an access status value
      * @throws SQLException An exception that provides information on a database access error or other errors.
      */
     public String getAccessStatusFromItem(Context context, Item item, Date threshold)
         throws SQLException;
+
+    /**
+     * Retrieve embargo information for the item
+     *
+     * @param context the DSpace context
+     * @param item the item to check for embargo information
+     * @param threshold the embargo threshold date
+     * @return an embargo date
+     * @throws SQLException An exception that provides information on a database access error or other errors.
+     */
+    public String getEmbargoFromItem(Context context, Item item, Date threshold) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/access/status/AccessStatusServiceImpl.java

@@ -8,14 +8,15 @@
 package org.dspace.access.status;
 
 import java.sql.SQLException;
+import java.time.LocalDate;
+import java.time.ZoneId;
 import java.util.Date;
 
 import org.dspace.access.status.service.AccessStatusService;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 import org.dspace.core.service.PluginService;
 import org.dspace.services.ConfigurationService;
-import org.joda.time.LocalDate;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -55,12 +56,20 @@ public void init() throws Exception {
             int month = configurationService.getIntProperty("access.status.embargo.forever.month");
             int day = configurationService.getIntProperty("access.status.embargo.forever.day");
 
-            forever_date = new LocalDate(year, month, day).toDate();
+            forever_date = Date.from(LocalDate.of(year, month, day)
+                    .atStartOfDay()
+                    .atZone(ZoneId.systemDefault())
+                    .toInstant());
         }
     }
 
     @Override
     public String getAccessStatus(Context context, Item item) throws SQLException {
         return helper.getAccessStatusFromItem(context, item, forever_date);
     }
+
+    @Override
+    public String getEmbargoFromItem(Context context, Item item) throws SQLException {
+        return helper.getEmbargoFromItem(context, item, forever_date);
+    }
 }

dspace-api/src/main/java/org/dspace/access/status/DefaultAccessStatusHelper.java

@@ -26,13 +26,19 @@
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.eperson.Group;
+import org.joda.time.LocalDate;
 
 /**
  * Default plugin implementation of the access status helper.
  * The getAccessStatusFromItem method provides a simple logic to
  * calculate the access status of an item based on the policies of
  * the primary or the first bitstream in the original bundle.
  * Users can override this method for enhanced functionality.
+ *
+ * The getEmbargoInformationFromItem method provides a simple logic to
+ *  * retrieve embargo information of bitstreams from an item based on the policies of
+ *  * the primary or the first bitstream in the original bundle.
+ *  * Users can override this method for enhanced functionality.
  */
 public class DefaultAccessStatusHelper implements AccessStatusHelper {
     public static final String EMBARGO = "embargo";
@@ -54,12 +60,12 @@ public DefaultAccessStatusHelper() {
 
     /**
      * Look at the item's policies to determine an access status value.
-     * It is also considering a date threshold for embargos and restrictions.
+     * It is also considering a date threshold for embargoes and restrictions.
      *
      * If the item is null, simply returns the "unknown" value.
      *
      * @param context     the DSpace context
-     * @param item        the item to embargo
+     * @param item        the item to check for embargoes
      * @param threshold   the embargo threshold date
      * @return an access status value
      */
@@ -86,7 +92,7 @@ public String getAccessStatusFromItem(Context context, Item item, Date threshold
                 .findFirst()
                 .orElse(null);
         }
-        return caculateAccessStatusForDso(context, bitstream, threshold);
+        return calculateAccessStatusForDso(context, bitstream, threshold);
     }
 
     /**
@@ -104,7 +110,7 @@ public String getAccessStatusFromItem(Context context, Item item, Date threshold
      * @param threshold   the embargo threshold date
      * @return an access status value
      */
-    private String caculateAccessStatusForDso(Context context, DSpaceObject dso, Date threshold)
+    private String calculateAccessStatusForDso(Context context, DSpaceObject dso, Date threshold)
             throws SQLException {
         if (dso == null) {
             return METADATA_ONLY;
@@ -156,4 +162,87 @@ private String caculateAccessStatusForDso(Context context, DSpaceObject dso, Dat
         }
         return RESTRICTED;
     }
+
+    /**
+     * Look at the policies of the primary (or first) bitstream of the item to retrieve its embargo.
+     *
+     * If the item is null, simply returns an empty map with no embargo information.
+     *
+     * @param context     the DSpace context
+     * @param item        the item to embargo
+     * @return an access status value
+     */
+    @Override
+    public String getEmbargoFromItem(Context context, Item item, Date threshold)
+            throws SQLException {
+        Date embargoDate;
+
+        // If Item status is not "embargo" then return a null embargo date.
+        String accessStatus = getAccessStatusFromItem(context, item, threshold);
+
+        if (item == null || !accessStatus.equals(EMBARGO)) {
+            return null;
+        }
+        // Consider only the original bundles.
+        List<Bundle> bundles = item.getBundles(Constants.DEFAULT_BUNDLE_NAME);
+        // Check for primary bitstreams first.
+        Bitstream bitstream = bundles.stream()
+                .map(bundle -> bundle.getPrimaryBitstream())
+                .filter(Objects::nonNull)
+                .findFirst()
+                .orElse(null);
+        if (bitstream == null) {
+            // If there is no primary bitstream,
+            // take the first bitstream in the bundles.
+            bitstream = bundles.stream()
+                    .map(bundle -> bundle.getBitstreams())
+                    .flatMap(List::stream)
+                    .findFirst()
+                    .orElse(null);
+        }
+
+        if (bitstream == null) {
+            return null;
+        }
+
+        embargoDate = this.retrieveShortestEmbargo(context, bitstream);
+
+        return embargoDate != null ? embargoDate.toString() : null;
+    }
+
+    /**
+     *
+     */
+    private Date retrieveShortestEmbargo(Context context, Bitstream bitstream) throws SQLException {
+        Date embargoDate = null;
+        // Only consider read policies.
+        List<ResourcePolicy> policies = authorizeService
+                .getPoliciesActionFilter(context, bitstream, Constants.READ);
+
+        // Looks at all read policies.
+        for (ResourcePolicy policy : policies) {
+            boolean isValid = resourcePolicyService.isDateValid(policy);
+            Group group = policy.getGroup();
+
+            if (group != null && StringUtils.equals(group.getName(), Group.ANONYMOUS)) {
+                // Only calculate the status for the anonymous group.
+                if (!isValid) {
+                    // If the policy is not valid there is an active embargo
+                    Date startDate = policy.getStartDate();
+
+                    if (startDate != null && !startDate.before(LocalDate.now().toDate())) {
+                        // There is an active embargo: aim to take the shortest embargo (account for rare cases where
+                        // more than one resource policy exists)
+                        if (embargoDate == null) {
+                            embargoDate = startDate;
+                        } else {
+                            embargoDate = startDate.before(embargoDate) ? startDate : embargoDate;
+                        }
+                    }
+                }
+            }
+        }
+
+        return embargoDate;
+    }
 }

dspace-api/src/main/java/org/dspace/access/status/service/AccessStatusService.java

@@ -40,7 +40,18 @@ public interface AccessStatusService {
      *
      * @param context the DSpace context
      * @param item    the item
+     * @return an access status value
      * @throws SQLException An exception that provides information on a database access error or other errors.
      */
     public String getAccessStatus(Context context, Item item) throws SQLException;
+
+    /**
+     * Retrieve embargo information for the item
+     *
+     * @param context the DSpace context
+     * @param item the item to check for embargo information
+     * @return an embargo date
+     * @throws SQLException An exception that provides information on a database access error or other errors.
+     */
+    public String getEmbargoFromItem(Context context, Item item) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/app/bulkaccesscontrol/BulkAccessControl.java

@@ -464,7 +464,7 @@ private void setItemPolicies(Item item, BulkAccessControlInput accessControl)
             .forEach(accessCondition -> createResourcePolicy(item, accessCondition,
                 itemAccessConditions.get(accessCondition.getName())));
 
-        itemService.adjustItemPolicies(context, item, item.getOwningCollection());
+        itemService.adjustItemPolicies(context, item, item.getOwningCollection(), false);
     }
 
     /**

dspace-api/src/main/java/org/dspace/app/bulkedit/MetadataImport.java

@@ -578,6 +578,10 @@ public List<BulkEditChange> runImport(Context c, boolean change,
                             wfItem = workflowService.startWithoutNotify(c, wsItem);
                         }
                     } else {
+                        // Add provenance info
+                        String provenance = installItemService.getSubmittedByProvenanceMessage(c, wsItem.getItem());
+                        itemService.addMetadata(c, item, MetadataSchemaEnum.DC.getName(),
+                                "description", "provenance", "en", provenance);
                         // Install the item
                         installItemService.installItem(c, wsItem);
                     }
@@ -1363,7 +1367,7 @@ private int displayChanges(List<BulkEditChange> changes, boolean changed) {
      * is the field is defined as authority controlled
      */
     private static boolean isAuthorityControlledField(String md) {
-        String mdf = StringUtils.substringAfter(md, ":");
+        String mdf = md.contains(":") ? StringUtils.substringAfter(md, ":") : md;
         mdf = StringUtils.substringBefore(mdf, "[");
         return authorityControlled.contains(mdf);
     }

dspace-api/src/main/java/org/dspace/app/itemimport/ItemImportServiceImpl.java

@@ -774,6 +774,10 @@ protected Item addItem(Context c, List<Collection> mycollections, String path,
             // put item in system
             if (!isTest) {
                 try {
+                    // Add provenance info
+                    String provenance = installItemService.getSubmittedByProvenanceMessage(c, wi.getItem());
+                    itemService.addMetadata(c, wi.getItem(), MetadataSchemaEnum.DC.getName(),
+                        "description", "provenance", "en", provenance);
                     installItemService.installItem(c, wi, myhandle);
                 } catch (Exception e) {
                     workspaceItemService.deleteAll(c, wi);

dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java

@@ -21,6 +21,7 @@
 import org.apache.logging.log4j.Logger;
 import org.dspace.core.Context;
 import org.dspace.scripts.DSpaceRunnable;
+import org.dspace.scripts.DSpaceRunnable.StepResult;
 import org.dspace.scripts.configuration.ScriptConfiguration;
 import org.dspace.scripts.factory.ScriptServiceFactory;
 import org.dspace.scripts.handler.DSpaceRunnableHandler;
@@ -145,8 +146,13 @@ public static int handleScript(String[] args, Document commandConfigs,
     private static int executeScript(String[] args, DSpaceRunnableHandler dSpaceRunnableHandler,
                                      DSpaceRunnable script) {
         try {
-            script.initialize(args, dSpaceRunnableHandler, null);
-            script.run();
+            StepResult result = script.initialize(args, dSpaceRunnableHandler, null);
+            // check the StepResult, only run the script if the result is Continue;
+            // otherwise - for example the script is started with the help as argument, nothing is to do
+            if (StepResult.Continue.equals(result)) {
+                // runs the script, the normal initialization is successful
+                script.run();
+            }
             return 0;
         } catch (ParseException e) {
             script.printHelp();