Merge backend dspace8.3 into UoEMainLibrary-dspace-8_x

.github/workflows/codescan.yml

@@ -47,7 +47,7 @@ jobs:
       # Initializes the CodeQL tools for scanning.
       # https://github.com/github/codeql-action
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v2
+        uses: github/codeql-action/init@v3
         with:
           # Codescan Javascript as well since a few JS files exist in REST API's interface
           languages: java, javascript
@@ -56,8 +56,8 @@ jobs:
       # NOTE: Based on testing, this autobuild process works well for DSpace. A custom
       # DSpace build w/caching (like in build.yml) was about the same speed as autobuild.
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v2
+        uses: github/codeql-action/autobuild@v3
 
       # Perform GitHub Code Scanning.
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3

.github/workflows/docker.yml

@@ -220,6 +220,19 @@ jobs:
           result=$(wget -O- -q http://127.0.0.1:8080/server/api/core/collections)
           echo "$result"
           echo "$result" |  grep -oE "\"Dog in Yard\","
+      # Verify basic backend logging is working.
+      # 1. Access the top communities list. Verify that the "Before request" INFO statement is logged
+      # 2. Access an invalid endpoint (and ignore 404 response). Verify that a "status:404" WARN statement is logged
+      - name: Verify backend is logging properly
+        run: |
+          wget -O/dev/null -q http://127.0.0.1:8080/server/api/core/communities/search/top
+          logs=$(docker compose -f docker-compose.yml logs -n 5 dspace)
+          echo "$logs"
+          echo "$logs" | grep -o "Before request \[GET /server/api/core/communities/search/top\]"
+          wget -O/dev/null -q http://127.0.0.1:8080/server/api/does/not/exist || true
+          logs=$(docker compose -f docker-compose.yml logs -n 5 dspace)
+          echo "$logs"
+          echo "$logs" | grep -o "status:404 exception: The repository type does.not was not found"
       # Verify Handle Server can be stared and is working properly
       # 1. First generate the "[dspace]/handle-server" folder with the sitebndl.zip
       # 2. Start the Handle Server (and wait 20 seconds to let it start up)

.github/workflows/reusable-docker-build.yml

@@ -164,7 +164,7 @@ jobs:
           # Use GitHub cache to load cached Docker images and cache the results of this build
           # This decreases the number of images we need to fetch from DockerHub
           cache-from: type=gha,scope=${{ inputs.build_id }}
-          cache-to: type=gha,scope=${{ inputs.build_id }},mode=max
+          cache-to: type=gha,scope=${{ inputs.build_id }},mode=min
 
       # Export the digest of Docker build locally
       - name: Export Docker build digest
@@ -216,7 +216,7 @@ jobs:
           # Use GitHub cache to load cached Docker images and cache the results of this build
           # This decreases the number of images we need to fetch from DockerHub
           cache-from: type=gha,scope=${{ inputs.build_id }}
-          cache-to: type=gha,scope=${{ inputs.build_id }},mode=max
+          cache-to: type=gha,scope=${{ inputs.build_id }},mode=min
           # Export image to a local TAR file
           outputs: type=docker,dest=/tmp/${{ inputs.build_id }}.tar
 
@@ -298,9 +298,12 @@ jobs:
       # 'regctl' is used to more easily copy the image to DockerHub and obtain the digest from DockerHub
       # See https://github.com/regclient/regclient/blob/main/docs/regctl.md
       - name: Install regctl for Docker registry tools
-        uses: regclient/actions/regctl-installer@main
-        with:
-          release: 'v0.8.0'
+        run: |
+          export REGCTL_VERSION=v0.9.2
+          mkdir -p bin
+          curl -sSLo bin/regctl https://github.com/regclient/regclient/releases/download/${REGCTL_VERSION}/regctl-linux-amd64
+          chmod a+x bin/regctl
+          echo "$(pwd)/bin" >> $GITHUB_PATH
 
       # This recreates Docker tags for DockerHub
       - name: Add Docker metadata for image

dspace-api/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>8.2</version>
+        <version>8.3</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -99,20 +99,6 @@
                 </executions>
             </plugin>
 
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>build-helper-maven-plugin</artifactId>
-                <version>3.6.1</version>
-                <executions>
-                    <execution>
-                        <phase>validate</phase>
-                        <goals>
-                            <goal>maven-version</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>buildnumber-maven-plugin</artifactId>
@@ -653,6 +639,7 @@
             <version>1.1.1</version>
         </dependency>
 
+        <!-- guava is needed by OAuth, Guice, Mockserver, ORCID, Solr, JClouds -->
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
@@ -729,9 +716,25 @@
 
         <!-- S3 -->
         <dependency>
-            <groupId>com.amazonaws</groupId>
-            <artifactId>aws-java-sdk-s3</artifactId>
-            <version>1.12.785</version>
+            <groupId>software.amazon.awssdk</groupId>
+            <artifactId>s3</artifactId>
+            <version>2.38.8</version>
+            <exclusions>
+              <exclusion>
+                <groupId>software.amazon.awssdk</groupId>
+                <artifactId>netty-nio-client</artifactId>
+              </exclusion>
+              <exclusion>
+                <groupId>software.amazon.awssdk</groupId>
+                <artifactId>apache-client</artifactId>
+              </exclusion>
+            </exclusions>
+        </dependency>
+
+        <dependency>
+            <groupId>software.amazon.awssdk.crt</groupId>
+            <artifactId>aws-crt</artifactId>
+            <version>0.39.4</version>
         </dependency>
 
         <!-- TODO: This may need to be replaced with the "orcid-model" artifact once this ticket is resolved:
@@ -772,7 +775,7 @@
         <dependency>
             <groupId>com.opencsv</groupId>
             <artifactId>opencsv</artifactId>
-            <version>5.11.1</version>
+            <version>5.12.0</version>
         </dependency>
 
         <!-- Email templating -->
@@ -785,14 +788,14 @@
         <dependency>
             <groupId>org.xmlunit</groupId>
             <artifactId>xmlunit-core</artifactId>
-            <version>2.10.2</version>
+            <version>2.11.0</version>
             <scope>test</scope>
         </dependency>
 
         <dependency>
             <groupId>org.apache.bcel</groupId>
             <artifactId>bcel</artifactId>
-            <version>6.10.0</version>
+            <version>6.11.0</version>
             <scope>test</scope>
         </dependency>
 
@@ -843,22 +846,12 @@
                 </exclusion>
             </exclusions>
         </dependency>
-        
+
         <dependency>
-            <groupId>io.findify</groupId>
-            <artifactId>s3mock_2.13</artifactId>
-            <version>0.2.6</version>
-            <scope>test</scope>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.amazonawsl</groupId>
-                    <artifactId>aws-java-sdk-s3</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>com.amazonaws</groupId>
-                    <artifactId>aws-java-sdk-s3</artifactId>
-                </exclusion>
-            </exclusions>
+          <groupId>com.adobe.testing</groupId>
+          <artifactId>s3mock-testcontainers</artifactId>
+          <version>4.10.0</version>
+          <scope>test</scope>
         </dependency>
 
         <dependency>

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

@@ -18,6 +18,7 @@
 import java.sql.SQLException;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
+import java.time.ZoneOffset;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.Iterator;
@@ -154,7 +155,7 @@ public void internalRun() throws Exception {
         }
 
         ObjectMapper mapper = new ObjectMapper();
-        mapper.setTimeZone(TimeZone.getTimeZone("UTC"));
+        mapper.setTimeZone(TimeZone.getTimeZone(ZoneOffset.UTC));
         BulkAccessControlInput accessControl;
         context = new Context(Context.Mode.BATCH_EDIT);
         setEPerson(context);

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

@@ -14,6 +14,8 @@
 import java.util.List;
 import java.util.UUID;
 
+import org.apache.commons.cli.DefaultParser;
+import org.apache.commons.cli.DefaultParser.Builder;
 import org.apache.commons.cli.ParseException;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataDSpaceCsvExportServiceImpl;
@@ -167,4 +169,14 @@ public IndexableObject resolveScope(Context context, String id) throws SQLExcept
         }
         return scopeObj;
     }
+
+    @Override
+    protected StepResult parse(String[] args) throws ParseException {
+        commandLine = new DefaultParser().parse(getScriptConfiguration().getOptions(), args);
+        Builder builder = new DefaultParser().builder();
+        builder.setStripLeadingAndTrailingQuotes(false);
+        commandLine = builder.build().parse(getScriptConfiguration().getOptions(), args);
+        setup();
+        return StepResult.Continue;
+    }
 }

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

@@ -494,7 +494,7 @@ public List<BulkEditChange> runImport(Context c, boolean change,
 
                 // Check it has an owning collection
                 List<String> collections = line.get("collection");
-                if (collections == null) {
+                if (collections == null || collections.isEmpty()) {
                     throw new MetadataImportException(
                         "New items must have a 'collection' assigned in the form of a handle");
                 }

dspace-api/src/main/java/org/dspace/app/checker/ChecksumChecker.java

@@ -98,15 +98,15 @@ public static void main(String[] args) throws SQLException {
         options.addOption("h", "help", false, "Help");
         options.addOption("d", "duration", true, "Checking duration");
         options.addOption("c", "count", true, "Check count");
-        options.addOption("a", "handle", true, "Specify a handle to check");
+        options.addOption("i", "handle", true, "Specify a handle to check");
         options.addOption("v", "verbose", false, "Report all processing");
 
         Option option;
 
         option = Option.builder("b")
                 .longOpt("bitstream-ids")
                 .hasArgs()
-                .desc("Space separated list of bitstream ids")
+                .desc("Space separated list of bitstream UUIDs")
                 .build();
         options.addOption(option);
 
@@ -132,6 +132,17 @@ public static void main(String[] args) throws SQLException {
         try {
             context = new Context();
 
+            int mutuallyExclusiveOpts = 0;
+            for (char c : new char[]{'l', 'L', 'd', 'b', 'i','c'}) {
+                if (line.hasOption(c)) {
+                    mutuallyExclusiveOpts++;
+                }
+            }
+            if (mutuallyExclusiveOpts > 1) {
+                System.err.println("Please use only one option of -l, -L, -d, -b, -i, or -c");
+                LOG.error("Please use only one option of -l, -L, -d, -b, -i, or -c");
+                System.exit(1);
+            }
 
             // Prune stage
             if (line.hasOption('p')) {
@@ -169,13 +180,13 @@ public static void main(String[] args) throws SQLException {
                         bitstreams.add(bitstreamService.find(context, UUID.fromString(ids[i])));
                     } catch (NumberFormatException nfe) {
                         System.err.println("The following argument: " + ids[i]
-                                               + " is not an integer");
+                                               + " is not an UUID");
                         System.exit(0);
                     }
                 }
                 dispatcher = new IteratorDispatcher(bitstreams.iterator());
-            } else if (line.hasOption('a')) {
-                dispatcher = new HandleDispatcher(context, line.getOptionValue('a'));
+            } else if (line.hasOption('i')) {
+                dispatcher = new HandleDispatcher(context, line.getOptionValue('i'));
             } else if (line.hasOption('d')) {
                 // run checker process for specified duration
                 try {
@@ -185,6 +196,8 @@ public static void main(String[] args) throws SQLException {
                             + Utils.parseDuration(line
                                                       .getOptionValue('d'))));
                 } catch (Exception e) {
+                    System.err.println("Couldn't parse " + line.getOptionValue('d')
+                                  + " as a duration");
                     LOG.fatal("Couldn't parse " + line.getOptionValue('d')
                                   + " as a duration: ", e);
                     System.exit(0);
@@ -228,18 +241,24 @@ public static void main(String[] args) throws SQLException {
     private static void printHelp(Options options) {
         HelpFormatter myhelp = new HelpFormatter();
 
-        myhelp.printHelp("Checksum Checker\n", options);
-        System.out.println("\nSpecify a duration for checker process, using s(seconds),"
-                               + "m(minutes), or h(hours): ChecksumChecker -d 30s"
-                               + " OR ChecksumChecker -d 30m"
-                               + " OR ChecksumChecker -d 2h");
-        System.out.println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
-        System.out.println("\nLoop once through all bitstreams: "
-                               + "ChecksumChecker -l");
-        System.out.println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
-        System.out.println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
-        System.out.println("\nReport all processing (verbose)(default reports only errors): ChecksumChecker -v");
-        System.out.println("\nDefault (no arguments) is equivalent to '-c 1'");
+        myhelp.printHelp("checker\n", options);
+        System.out.println("\nChecksum Checker usage examples:");
+        System.out.println("\nThe following options are mutually exclusive:");
+        System.out.println(" - Specify a duration for checker process, using s(seconds),"
+                               + "m(minutes), or h(hours): checker -d 30s"
+                               + " OR checker -d 30m"
+                               + " OR checker -d 2h");
+        System.out.println(" - Specify bitstream UUIDs: checker -b 550e8400-e29b-41d4-a716-446655440000"
+                               + " f3f2e850-b5d4-11ef-ac7e-96584d5248b2");
+        System.out.println(" - Specify handle: checker -i 12345/100");
+        System.out.println(" - Loop once through all bitstreams: "
+                               + "checker -l");
+        System.out.println(" - Loop continuously through all bitstreams: checker -L");
+        System.out.println(" - Check a defined number of bitstreams: checker -c 10");
+        System.out.println("\nThe following options can be used in combination with others above:");
+        System.out.println(" - Report all processing to checker.log (by default logs only errors): checker -v");
+        System.out.println(" - Prune old results from the database: checker -p");
+        System.out.println("\nDefault (no arguments) is equivalent to 'checker -c 1'\n");
         System.exit(0);
     }
 

dspace-api/src/main/java/org/dspace/app/itemexport/ItemExportServiceImpl.java

@@ -352,7 +352,7 @@ protected void writeHandle(Context c, Item i, File destDir)
 
     /**
      * Create the 'collections' file.  List handles of all Collections which
-     * contain this Item.  The "owning" Collection is listed first.
+     * contain this Item. The "owning" Collection is listed first.
      *
      * @param item list collections holding this Item.
      * @param destDir write the file here.
@@ -363,12 +363,14 @@ protected void writeCollections(Item item, File destDir)
         File outFile = new File(destDir, "collections");
         if (outFile.createNewFile()) {
             try (PrintWriter out = new PrintWriter(new FileWriter(outFile))) {
-                String ownerHandle = item.getOwningCollection().getHandle();
-                out.println(ownerHandle);
+                Collection owningCollection = item.getOwningCollection();
+                // The owning collection is null for workspace and workflow items
+                if (owningCollection != null) {
+                    out.println(owningCollection.getHandle());
+                }
                 for (Collection collection : item.getCollections()) {
-                    String collectionHandle = collection.getHandle();
-                    if (!collectionHandle.equals(ownerHandle)) {
-                        out.println(collectionHandle);
+                    if (!collection.equals(owningCollection)) {
+                        out.println(collection.getHandle());
                     }
                 }
             }