Merge remote-tracking branch 'origin/main' into coar-notify-NotifySer…

…viceRestRepositoryIT-fix

.github/workflows/build.yml

@@ -49,7 +49,7 @@ jobs:
 
       # https://github.com/actions/setup-java
       - name: Install JDK ${{ matrix.java }}
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: ${{ matrix.java }}
           distribution: 'temurin'
@@ -65,14 +65,14 @@ jobs:
       # (This artifact is downloadable at the bottom of any job's summary page)
       - name: Upload Results of ${{ matrix.type }} to Artifact
         if: ${{ failure() }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.type }} results
           path: ${{ matrix.resultsdir }}
 
       # Upload code coverage report to artifact, so that it can be shared with the 'codecov' job (see below)
       - name: Upload code coverage report to Artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.type }} coverage report
           path: 'dspace/target/site/jacoco-aggregate/jacoco.xml'
@@ -91,7 +91,7 @@ jobs:
 
       # Download artifacts from previous 'tests' job
       - name: Download coverage artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
 
       # Now attempt upload to Codecov using its action.
       # NOTE: We use a retry action to retry the Codecov upload if it fails the first time.
@@ -101,10 +101,11 @@ jobs:
       - name: Upload coverage to Codecov.io
         uses: Wandalen/[email protected]
         with:
-          action: codecov/codecov-action@v3
+          action: codecov/codecov-action@v4
           # Ensure codecov-action throws an error when it fails to upload
           with: |
             fail_ci_if_error: true
+            token: ${{ secrets.CODECOV_TOKEN }}
           # Try re-running action 5 times max
           attempt_limit: 5
           # Run again in 30 seconds

.github/workflows/codescan.yml

@@ -39,7 +39,7 @@ jobs:
 
       # https://github.com/actions/setup-java
       - name: Install JDK
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'temurin'

.github/workflows/docker.yml

@@ -43,7 +43,7 @@ jobs:
     needs: dspace-dependencies
     uses: ./.github/workflows/reusable-docker-build.yml
     with:
-      build_id: dspace
+      build_id: dspace-prod
       image_name: dspace/dspace
       dockerfile_path: ./Dockerfile
     secrets:
@@ -120,7 +120,7 @@ jobs:
     if: github.repository == 'dspace/dspace'
     uses: ./.github/workflows/reusable-docker-build.yml
     with:
-      build_id: dspace-postgres-pgcrypto
+      build_id: dspace-postgres-pgcrypto-prod
       image_name: dspace/dspace-postgres-pgcrypto
       # Must build out of subdirectory to have access to install script for pgcrypto.
       # NOTE: this context will build the image based on the Dockerfile in the specified directory

.github/workflows/issue_opened.yml

@@ -16,7 +16,7 @@ jobs:
       # Only add to project board if issue is flagged as "needs triage" or has no labels
       # NOTE: By default we flag new issues as "needs triage" in our issue template
       if: (contains(github.event.issue.labels.*.name, 'needs triage') || join(github.event.issue.labels.*.name) == '')
-      uses: actions/add-to-project@v0.5.0
+      uses: actions/add-to-project@v1.0.0
       # Note, the authentication token below is an ORG level Secret. 
       # It must be created/recreated manually via a personal access token with admin:org, project, public_repo permissions
       # See: https://docs.github.com/en/actions/configuring-and-managing-workflows/authenticating-with-the-github_token#permissions-for-the-github_token

.github/workflows/pull_request_opened.yml

@@ -21,4 +21,4 @@ jobs:
     # Assign the PR to whomever created it. This is useful for visualizing assignments on project boards
     # See https://github.com/toshimaru/auto-author-assign
     - name: Assign PR to creator
-      uses: toshimaru/auto-author-assign@v2.0.1
+      uses: toshimaru/auto-author-assign@v2.1.0

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

@@ -68,9 +68,9 @@ env:
   # See "Redeploy" steps below for more details.
   REDEPLOY_SANDBOX_URL: ${{ secrets.REDEPLOY_SANDBOX_URL }}
   REDEPLOY_DEMO_URL: ${{ secrets.REDEPLOY_DEMO_URL }}
-  # Current DSpace maintenance branch (and architecture) which is deployed to demo.dspace.org / sandbox.dspace.org
-  # (NOTE: No deployment branch specified for sandbox.dspace.org as it uses the default_branch)
+  # Current DSpace branches (and architecture) which are deployed to demo.dspace.org & sandbox.dspace.org respectively
   DEPLOY_DEMO_BRANCH: 'dspace-7_x'
+  DEPLOY_SANDBOX_BRANCH: 'dspace-8.0-testathon'
   DEPLOY_ARCH: 'linux/amd64'
 
 jobs:
@@ -93,6 +93,14 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
+      # This step converts the slashes in the "arch" matrix values above into dashes & saves to env.ARCH_NAME
+      # E.g. "linux/amd64" becomes "linux-amd64"
+      # This is necessary because all upload artifacts CANNOT have special chars (like slashes)
+      - name: Prepare
+        run: |
+          platform=${{ matrix.arch }}
+          echo "ARCH_NAME=${platform//\//-}" >> $GITHUB_ENV
+
       # https://github.com/actions/checkout
       - name: Checkout codebase
         uses: actions/checkout@v4
@@ -152,9 +160,9 @@ jobs:
       # Upload digest to an artifact, so that it can be used in manifest below
       - name: Upload Docker build digest to artifact
         if: ${{ ! matrix.isPr }}
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: digests-${{ inputs.build_id }}
+          name: digests-${{ inputs.build_id }}-${{ env.ARCH_NAME }}
           path: /tmp/digests/*
           if-no-files-found: error
           retention-days: 1
@@ -166,13 +174,13 @@ jobs:
           !matrix.isPR &&
           env.REDEPLOY_SANDBOX_URL != '' &&
           matrix.arch == env.DEPLOY_ARCH &&
-          github.ref_name == github.event.repository.default_branch
+          github.ref_name == env.DEPLOY_SANDBOX_BRANCH
         run: |
           curl -X POST $REDEPLOY_SANDBOX_URL
 
       # If this build is NOT a PR and passed in a REDEPLOY_DEMO_URL secret,
       # Then redeploy https://demo.dspace.org if this build is for our deployment architecture and demo branch.
-      - name: Redeploy demo.dspace.org (based on maintenace branch)
+      - name: Redeploy demo.dspace.org (based on maintenance branch)
         if: |
           !matrix.isPR &&
           env.REDEPLOY_DEMO_URL != '' &&
@@ -192,10 +200,12 @@ jobs:
       - docker-build
     steps:
       - name: Download Docker build digests
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: digests-${{ inputs.build_id }}
           path: /tmp/digests
+          # Download digests for both AMD64 and ARM64 into same directory
+          pattern: digests-${{ inputs.build_id }}-*
+          merge-multiple: true
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3

dspace-api/pom.xml

@@ -458,7 +458,12 @@
             <artifactId>commons-validator</artifactId>
         </dependency>
         <dependency>
-            <groupId>com.sun.mail</groupId>
+            <groupId>jakarta.mail</groupId>
+            <artifactId>jakarta.mail-api</artifactId>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.angus</groupId>
             <artifactId>jakarta.mail</artifactId>
         </dependency>
         <dependency>

dspace-api/src/main/java/org/dspace/app/ldn/model/Citation.java

@@ -18,7 +18,7 @@ public class Citation extends Base {
     @JsonProperty("ietf:cite-as")
     private String ietfCiteAs;
 
-    @JsonProperty("url")
+    @JsonProperty("ietf:item")
     private Url url;
 
     /**

dspace-api/src/main/java/org/dspace/app/solrdatabaseresync/SolrDatabaseResyncCli.java

@@ -105,42 +105,56 @@ private void performStatusUpdate(Context context) throws SearchServiceException,
         solrQuery.addFilterQuery(dateRangeFilter);
         solrQuery.addField(SearchUtils.RESOURCE_ID_FIELD);
         solrQuery.addField(SearchUtils.RESOURCE_UNIQUE_ID);
+        solrQuery.setRows(0);
         QueryResponse response = solrSearchCore.getSolr().query(solrQuery, solrSearchCore.REQUEST_METHOD);
-
-        if (response != null) {
-            logInfoAndOut(response.getResults().size() + " items found to process");
-
-            for (SolrDocument doc : response.getResults()) {
-                String uuid = (String) doc.getFirstValue(SearchUtils.RESOURCE_ID_FIELD);
-                String uniqueId = (String) doc.getFirstValue(SearchUtils.RESOURCE_UNIQUE_ID);
-                logDebugAndOut("Processing item with UUID: " + uuid);
-
-                Optional<IndexableObject> indexableObject = Optional.empty();
-                try {
-                    indexableObject = indexObjectServiceFactory
-                            .getIndexableObjectFactory(uniqueId).findIndexableObject(context, uuid);
-                } catch (SQLException e) {
-                    log.warn("An exception occurred when attempting to retrieve item with UUID \"" + uuid +
-                            "\" from the database, removing related solr document", e);
-                }
-
-                try {
-                    if (indexableObject.isPresent()) {
-                        logDebugAndOut("Item exists in DB, updating solr document");
-                        updateItem(context, indexableObject.get());
-                    } else {
-                        logDebugAndOut("Item doesn't exist in DB, removing solr document");
-                        removeItem(context, uniqueId);
-                    }
-                } catch (SQLException | IOException e) {
-                    log.error(e.getMessage(), e);
+        if (response != null && response.getResults() != null) {
+            long nrOfPreDBResults = response.getResults().getNumFound();
+            if (nrOfPreDBResults > 0) {
+                logInfoAndOut(nrOfPreDBResults + " items found to process");
+                int batchSize = configurationService.getIntProperty("script.solr-database-resync.batch-size", 100);
+                for (int start = 0; start < nrOfPreDBResults; start += batchSize) {
+                    solrQuery.setStart(start);
+                    solrQuery.setRows(batchSize);
+                    performStatusUpdateOnNextBatch(context, solrQuery);
                 }
             }
         }
 
         indexingService.commit();
     }
 
+    private void performStatusUpdateOnNextBatch(Context context, SolrQuery solrQuery)
+            throws SolrServerException, IOException {
+        QueryResponse response = solrSearchCore.getSolr().query(solrQuery, solrSearchCore.REQUEST_METHOD);
+
+        for (SolrDocument doc : response.getResults()) {
+            String uuid = (String) doc.getFirstValue(SearchUtils.RESOURCE_ID_FIELD);
+            String uniqueId = (String) doc.getFirstValue(SearchUtils.RESOURCE_UNIQUE_ID);
+            logDebugAndOut("Processing item with UUID: " + uuid);
+
+            Optional<IndexableObject> indexableObject = Optional.empty();
+            try {
+                indexableObject = indexObjectServiceFactory
+                        .getIndexableObjectFactory(uniqueId).findIndexableObject(context, uuid);
+            } catch (SQLException e) {
+                log.warn("An exception occurred when attempting to retrieve item with UUID \"" + uuid +
+                        "\" from the database, removing related solr document", e);
+            }
+
+            try {
+                if (indexableObject.isPresent()) {
+                    logDebugAndOut("Item exists in DB, updating solr document");
+                    updateItem(context, indexableObject.get());
+                } else {
+                    logDebugAndOut("Item doesn't exist in DB, removing solr document");
+                    removeItem(context, uniqueId);
+                }
+            } catch (SQLException | IOException e) {
+                log.error(e.getMessage(), e);
+            }
+        }
+    }
+
     private void updateItem(Context context, IndexableObject indexableObject) throws SolrServerException, IOException {
         Map<String,Object> fieldModifier = new HashMap<>(1);
         fieldModifier.put("remove", STATUS_FIELD_PREDB);

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

@@ -629,6 +629,7 @@ public void update(Context context, T dso) throws SQLException, AuthorizeExcepti
                     // E.g. for an Author relationship,
                     //   the place should be updated using the same principle as dc.contributor.author.
                     StringUtils.startsWith(metadataValue.getAuthority(), Constants.VIRTUAL_AUTHORITY_PREFIX)
+                        && metadataValue instanceof RelationshipMetadataValue
                         && ((RelationshipMetadataValue) metadataValue).isUseForPlace()
                 ) {
                     int mvPlace = getMetadataValuePlace(fieldToLastPlace, metadataValue);

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

@@ -8,6 +8,7 @@
 package org.dspace.content;
 
 import java.sql.SQLException;
+import java.util.Collections;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.UUID;
@@ -51,12 +52,7 @@ public Entity findByItemId(Context context, UUID itemId, Integer limit, Integer
     @Override
     public EntityType getType(Context context, Entity entity) throws SQLException {
         Item item = entity.getItem();
-        List<MetadataValue> list = itemService.getMetadata(item, "dspace", "entity", "type", Item.ANY, false);
-        if (!list.isEmpty()) {
-            return entityTypeService.findByEntityType(context, list.get(0).getValue());
-        } else {
-            return null;
-        }
+        return itemService.getEntityType(context, item);
     }
 
     @Override
@@ -103,7 +99,12 @@ public List<RelationshipType> getAllRelationshipTypes(Context context, Entity en
     @Override
     public List<RelationshipType> getAllRelationshipTypes(Context context, Entity entity, Integer limit, Integer offset)
             throws SQLException {
-        return relationshipTypeService.findByEntityType(context, this.getType(context, entity), limit, offset);
+        EntityType entityType = this.getType(context, entity);
+        if (entityType != null) {
+            return relationshipTypeService.findByEntityType(context, entityType, limit, offset);
+        } else {
+            return Collections.emptyList();
+        }
     }
 
     @Override
@@ -115,7 +116,12 @@ public List<RelationshipType> getLeftRelationshipTypes(Context context, Entity e
     @Override
     public List<RelationshipType> getLeftRelationshipTypes(Context context, Entity entity, boolean isLeft,
                                                            Integer limit, Integer offset) throws SQLException {
-        return relationshipTypeService.findByEntityType(context, this.getType(context, entity), isLeft, limit, offset);
+        EntityType entityType = this.getType(context, entity);
+        if (entityType != null) {
+            return relationshipTypeService.findByEntityType(context, entityType, isLeft, limit, offset);
+        } else {
+            return Collections.emptyList();
+        }
     }
 
     @Override
@@ -128,7 +134,12 @@ public List<RelationshipType> getRightRelationshipTypes(Context context, Entity
     public List<RelationshipType> getRightRelationshipTypes(Context context, Entity entity, boolean isLeft,
                                                             Integer limit, Integer offset) throws SQLException {
 
-        return relationshipTypeService.findByEntityType(context, this.getType(context, entity), isLeft, limit, offset);
+        EntityType entityType = this.getType(context, entity);
+        if (entityType != null) {
+            return relationshipTypeService.findByEntityType(context, entityType, isLeft, limit, offset);
+        } else {
+            return Collections.emptyList();
+        }
     }
 
     @Override

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

@@ -96,11 +96,18 @@ public WorkspaceItem find(Context context, int id) throws SQLException {
     @Override
     public WorkspaceItem create(Context context, Collection collection, boolean template)
             throws AuthorizeException, SQLException {
-        return create(context, collection, null, template);
+        return create(context, collection, null, template, false);
     }
 
     @Override
-    public WorkspaceItem create(Context context, Collection collection, UUID uuid, boolean template)
+    public WorkspaceItem create(Context context, Collection collection, boolean template, boolean isNewVersion)
+            throws AuthorizeException, SQLException {
+        return create(context, collection, null, template, isNewVersion);
+    }
+
+    @Override
+    public WorkspaceItem create(Context context, Collection collection, UUID uuid, boolean template,
+                                boolean isNewVersion)
         throws AuthorizeException, SQLException {
         // Check the user has permission to ADD to the collection
         authorizeService.authorizeAction(context, collection, Constants.ADD);
@@ -174,8 +181,10 @@ public WorkspaceItem create(Context context, Collection collection, UUID uuid, b
 
         // If configured, register identifiers (eg handle, DOI) now. This is typically used with the Show Identifiers
         // submission step which previews minted handles and DOIs during the submission process. Default: false
+        // Additional check needed: if we are creating a new version of an existing item we skip the identifier
+        // generation here, as this will be performed when the new version is created in VersioningServiceImpl
         if (DSpaceServicesFactory.getInstance().getConfigurationService()
-                .getBooleanProperty("identifiers.submission.register", false)) {
+                .getBooleanProperty("identifiers.submission.register", false) && !isNewVersion) {
             try {
                 // Get map of filters to use for identifier types, while the item is in progress
                 Map<Class<? extends Identifier>, Filter> filters = FilterUtils.getIdentifierFilters(true);

dspace-api/src/main/java/org/dspace/content/packager/PackageUtils.java

@@ -503,7 +503,7 @@ public static DSpaceObject createDSpaceObject(Context context, DSpaceObject pare
                     wsi = workspaceItemService.create(context, (Collection)parent, params.useCollectionTemplate());
                 } else {
                     wsi = workspaceItemService.create(context, (Collection)parent,
-                            uuid, params.useCollectionTemplate());
+                            uuid, params.useCollectionTemplate(), false);
                 }
 
                 // Please note that we are returning an Item which is *NOT* yet in the Archive,