Merge branch 'DSpace:main' into synced

.dockerignore

@@ -6,6 +6,5 @@ dspace/modules/*/target/
 Dockerfile.*
 dspace/src/main/docker/dspace-postgres-pgcrypto
 dspace/src/main/docker/dspace-postgres-pgcrypto-curl
-dspace/src/main/docker/solr
 dspace/src/main/docker/README.md
 dspace/src/main/docker-compose/

.github/workflows/build.yml

@@ -79,6 +79,39 @@ jobs:
           name: ${{ matrix.type }} results
           path: ${{ matrix.resultsdir }}
 
-      # https://github.com/codecov/codecov-action
+      # 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
+        with:
+          name: ${{ matrix.type }} coverage report
+          path: 'dspace/target/site/jacoco-aggregate/jacoco.xml'
+          retention-days: 14
+
+  # Codecov upload is a separate job in order to allow us to restart this separate from the entire build/test
+  # job above. This is necessary because Codecov uploads seem to randomly fail at times.
+  # See https://community.codecov.com/t/upload-issues-unable-to-locate-build-via-github-actions-api/3954
+  codecov:
+    # Must run after 'tests' job above
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      # Download artifacts from previous 'tests' job
+      - name: Download coverage artifacts
+        uses: actions/download-artifact@v3
+
+      # 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.
+      #
+      # Retry action: https://github.com/marketplace/actions/retry-action
+      # Codecov action: https://github.com/codecov/codecov-action
       - name: Upload coverage to Codecov.io
-        uses: codecov/codecov-action@v3
+        uses: Wandalen/wretry.action@v1.0.36
+        with:
+          action: codecov/codecov-action@v3
+          # Try upload 5 times max
+          attempt_limit: 5
+          # Run again in 30 seconds
+          attempt_delay: 30000

.github/workflows/docker.yml

@@ -170,3 +170,86 @@ jobs:
           # Use tags / labels provided by 'docker/metadata-action' above
           tags: ${{ steps.meta_build_cli.outputs.tags }}
           labels: ${{ steps.meta_build_cli.outputs.labels }}
+
+      ###########################################
+      # Build/Push the 'dspace/dspace-solr' image
+      ###########################################
+      # Get Metadata for docker_build_solr step below
+      - name: Sync metadata (tags, labels) from GitHub to Docker for 'dspace-solr' image
+        id: meta_build_solr
+        uses: docker/metadata-action@v4
+        with:
+          images: dspace/dspace-solr
+          tags: ${{ env.IMAGE_TAGS }}
+          flavor: ${{ env.TAGS_FLAVOR }}
+
+      - name: Build and push 'dspace-solr' image
+        id: docker_build_solr
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          file: ./dspace/src/main/docker/dspace-solr/Dockerfile
+          platforms: ${{ env.PLATFORMS }}
+          # For pull requests, we run the Docker build (to ensure no PR changes break the build),
+          # but we ONLY do an image push to DockerHub if it's NOT a PR
+          push: ${{ github.event_name != 'pull_request' }}
+          # Use tags / labels provided by 'docker/metadata-action' above
+          tags: ${{ steps.meta_build_solr.outputs.tags }}
+          labels: ${{ steps.meta_build_solr.outputs.labels }}
+
+      ###########################################################
+      # Build/Push the 'dspace/dspace-postgres-pgcrypto' image
+      ###########################################################
+      # Get Metadata for docker_build_postgres step below
+      - name: Sync metadata (tags, labels) from GitHub to Docker for 'dspace-postgres-pgcrypto' image
+        id: meta_build_postgres
+        uses: docker/metadata-action@v4
+        with:
+          images: dspace/dspace-postgres-pgcrypto
+          tags: ${{ env.IMAGE_TAGS }}
+          flavor: ${{ env.TAGS_FLAVOR }}
+
+      - name: Build and push 'dspace-postgres-pgcrypto' image
+        id: docker_build_postgres
+        uses: docker/build-push-action@v3
+        with:
+          # Must build out of subdirectory to have access to install script for pgcrypto
+          context: ./dspace/src/main/docker/dspace-postgres-pgcrypto/
+          dockerfile: Dockerfile
+          platforms: ${{ env.PLATFORMS }}
+          # For pull requests, we run the Docker build (to ensure no PR changes break the build),
+          # but we ONLY do an image push to DockerHub if it's NOT a PR
+          push: ${{ github.event_name != 'pull_request' }}
+          # Use tags / labels provided by 'docker/metadata-action' above
+          tags: ${{ steps.meta_build_postgres.outputs.tags }}
+          labels: ${{ steps.meta_build_postgres.outputs.labels }}
+
+      ###########################################################
+      # Build/Push the 'dspace/dspace-postgres-pgcrypto' image ('-loadsql' tag)
+      ###########################################################
+      # Get Metadata for docker_build_postgres_loadsql step below
+      - name: Sync metadata (tags, labels) from GitHub to Docker for 'dspace-postgres-pgcrypto-loadsql' image
+        id: meta_build_postgres_loadsql
+        uses: docker/metadata-action@v4
+        with:
+          images: dspace/dspace-postgres-pgcrypto
+          tags: ${{ env.IMAGE_TAGS }}
+          # Suffix all tags with "-loadsql". Otherwise, it uses the same
+          # tagging logic as the primary 'dspace/dspace-postgres-pgcrypto' image above.
+          flavor: ${{ env.TAGS_FLAVOR }}
+            suffix=-loadsql
+
+      - name: Build and push 'dspace-postgres-pgcrypto-loadsql' image
+        id: docker_build_postgres_loadsql
+        uses: docker/build-push-action@v3
+        with:
+          # Must build out of subdirectory to have access to install script for pgcrypto
+          context: ./dspace/src/main/docker/dspace-postgres-pgcrypto-curl/
+          dockerfile: Dockerfile
+          platforms: ${{ env.PLATFORMS }}
+          # For pull requests, we run the Docker build (to ensure no PR changes break the build),
+          # but we ONLY do an image push to DockerHub if it's NOT a PR
+          push: ${{ github.event_name != 'pull_request' }}
+          # Use tags / labels provided by 'docker/metadata-action' above
+          tags: ${{ steps.meta_build_postgres_loadsql.outputs.tags }}
+          labels: ${{ steps.meta_build_postgres_loadsql.outputs.labels }}

.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@v0.3.0
+      uses: actions/add-to-project@v0.5.0
       # 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/label_merge_conflicts.yml

@@ -23,7 +23,7 @@ jobs:
     steps:
       # See: https://github.com/prince-chrismc/label-merge-conflicts-action
       - name: Auto-label PRs with merge conflicts
-        uses: prince-chrismc/label-merge-conflicts-action@v2
+        uses: prince-chrismc/label-merge-conflicts-action@v3
         # Add "merge conflict" label if a merge conflict is detected. Remove it when resolved.
         # Note, the authentication token is created automatically
         # See: https://docs.github.com/en/actions/configuring-and-managing-workflows/authenticating-with-the-github_token

Dockerfile

@@ -31,7 +31,7 @@ ARG TARGET_DIR=dspace-installer
 COPY --from=build /install /dspace-src
 WORKDIR /dspace-src
 # Create the initial install deployment using ANT
-ENV ANT_VERSION 1.10.12
+ENV ANT_VERSION 1.10.13
 ENV ANT_HOME /tmp/ant-$ANT_VERSION
 ENV PATH $ANT_HOME/bin:$PATH
 # Need wget to install ant

Dockerfile.cli

@@ -30,7 +30,7 @@ ARG TARGET_DIR=dspace-installer
 COPY --from=build /install /dspace-src
 WORKDIR /dspace-src
 # Create the initial install deployment using ANT
-ENV ANT_VERSION 1.10.12
+ENV ANT_VERSION 1.10.13
 ENV ANT_HOME /tmp/ant-$ANT_VERSION
 ENV PATH $ANT_HOME/bin:$PATH
 # Need wget to install ant

docker-compose.yml

@@ -62,13 +62,17 @@ services:
       while (!</dev/tcp/dspacedb/5432) > /dev/null 2>&1; do sleep 1; done;
       /dspace/bin/dspace database migrate
       catalina.sh run
-  # DSpace database container
+  # DSpace PostgreSQL database container
   dspacedb:
     container_name: dspacedb
+    # Uses a custom Postgres image with pgcrypto installed
+    image: "${DOCKER_OWNER:-dspace}/dspace-postgres-pgcrypto:${DSPACE_VER:-dspace-7_x}"
+    build:
+      # Must build out of subdirectory to have access to install script for pgcrypto
+      context: ./dspace/src/main/docker/dspace-postgres-pgcrypto/
     environment:
       PGDATA: /pgdata
-    # Uses a custom Postgres image with pgcrypto installed
-    image: dspace/dspace-postgres-pgcrypto
+      POSTGRES_PASSWORD: dspace
     networks:
       dspacenet:
     ports:
@@ -77,12 +81,17 @@ services:
     stdin_open: true
     tty: true
     volumes:
+    # Keep Postgres data directory between reboots
     - pgdata:/pgdata
   # DSpace Solr container
   dspacesolr:
     container_name: dspacesolr
-    # Uses official Solr image at https://hub.docker.com/_/solr/
-    image: solr:8.11-slim
+    image: "${DOCKER_OWNER:-dspace}/dspace-solr:${DSPACE_VER:-dspace-7_x}"
+    build:
+      context: .
+      dockerfile: ./dspace/src/main/docker/dspace-solr/Dockerfile
+      args:
+        SOLR_VERSION: "${SOLR_VER:-8.11}"
     networks:
       dspacenet:
     ports:
@@ -92,30 +101,25 @@ services:
     tty: true
     working_dir: /var/solr/data
     volumes:
-    # Mount our local Solr core configs so that they are available as Solr configsets on container
-    - ./dspace/solr/authority:/opt/solr/server/solr/configsets/authority
-    - ./dspace/solr/oai:/opt/solr/server/solr/configsets/oai
-    - ./dspace/solr/search:/opt/solr/server/solr/configsets/search
-    - ./dspace/solr/statistics:/opt/solr/server/solr/configsets/statistics
     # Keep Solr data directory between reboots
     - solr_data:/var/solr/data
-    # Initialize all DSpace Solr cores using the mounted local configsets (see above), then start Solr
+    # Initialize all DSpace Solr cores then start Solr:
     # * First, run precreate-core to create the core (if it doesn't yet exist). If exists already, this is a no-op
-    # * Second, copy updated configs from mounted configsets to this core. If it already existed, this updates core
-    #   to the latest configs. If it's a newly created core, this is a no-op.
+    # * Second, copy configsets to this core:
+    #   Updates to Solr configs require the container to be rebuilt/restarted: `docker compose -p d7 up -d --build dspacesolr`
     entrypoint:
     - /bin/bash
     - '-c'
     - |
       init-var-solr
       precreate-core authority /opt/solr/server/solr/configsets/authority
-      cp -r -u /opt/solr/server/solr/configsets/authority/* authority
+      cp -r /opt/solr/server/solr/configsets/authority/* authority
       precreate-core oai /opt/solr/server/solr/configsets/oai
-      cp -r -u /opt/solr/server/solr/configsets/oai/* oai
+      cp -r /opt/solr/server/solr/configsets/oai/* oai
       precreate-core search /opt/solr/server/solr/configsets/search
-      cp -r -u /opt/solr/server/solr/configsets/search/* search
+      cp -r /opt/solr/server/solr/configsets/search/* search
       precreate-core statistics /opt/solr/server/solr/configsets/statistics
-      cp -r -u /opt/solr/server/solr/configsets/statistics/* statistics
+      cp -r /opt/solr/server/solr/configsets/statistics/* statistics
       exec solr -f
 volumes:
   assetstore:

dspace-api/pom.xml

@@ -776,7 +776,7 @@
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
-            <version>20180130</version>
+            <version>20230227</version>
         </dependency>
 
         <!-- Useful for testing command-line tools -->

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

@@ -51,6 +51,7 @@
 import org.dspace.content.service.CommunityService;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
+import org.dspace.core.I18nUtil;
 import org.dspace.discovery.IndexableObject;
 import org.dspace.discovery.indexobject.IndexableCollection;
 import org.dspace.discovery.indexobject.IndexableCommunity;
@@ -91,6 +92,7 @@ public class SyndicationFeed {
 
     // default DC fields for entry
     protected String defaultTitleField = "dc.title";
+    protected String defaultDescriptionField = "dc.description";
     protected String defaultAuthorField = "dc.contributor.author";
     protected String defaultDateField = "dc.date.issued";
     private static final String[] defaultDescriptionFields =
@@ -196,15 +198,15 @@ public void populate(HttpServletRequest request, Context context, IndexableObjec
         // dso is null for the whole site, or a search without scope
         if (dso == null) {
             defaultTitle = configurationService.getProperty("dspace.name");
-            feed.setDescription(localize(labels, MSG_FEED_DESCRIPTION));
+            defaultDescriptionField = localize(labels, MSG_FEED_DESCRIPTION);
             objectURL = resolveURL(request, null);
         } else {
             Bitstream logo = null;
             if (dso instanceof IndexableCollection) {
                 Collection col = ((IndexableCollection) dso).getIndexedObject();
                 defaultTitle = col.getName();
-                feed.setDescription(collectionService.getMetadataFirstValue(col,
-                        CollectionService.MD_SHORT_DESCRIPTION, Item.ANY));
+                defaultDescriptionField = collectionService.getMetadataFirstValue(col,
+                        CollectionService.MD_SHORT_DESCRIPTION, Item.ANY);
                 logo = col.getLogo();
                 String cols = configurationService.getProperty("webui.feed.podcast.collections");
                 if (cols != null && cols.length() > 1 && cols.contains(col.getHandle())) {
@@ -214,8 +216,8 @@ public void populate(HttpServletRequest request, Context context, IndexableObjec
             } else if (dso instanceof IndexableCommunity) {
                 Community comm = ((IndexableCommunity) dso).getIndexedObject();
                 defaultTitle = comm.getName();
-                feed.setDescription(communityService.getMetadataFirstValue(comm,
-                        CommunityService.MD_SHORT_DESCRIPTION, Item.ANY));
+                defaultDescriptionField = communityService.getMetadataFirstValue(comm,
+                        CommunityService.MD_SHORT_DESCRIPTION, Item.ANY);
                 logo = comm.getLogo();
                 String comms = configurationService.getProperty("webui.feed.podcast.communities");
                 if (comms != null && comms.length() > 1 && comms.contains(comm.getHandle())) {
@@ -230,6 +232,12 @@ public void populate(HttpServletRequest request, Context context, IndexableObjec
         }
         feed.setTitle(labels.containsKey(MSG_FEED_TITLE) ?
                           localize(labels, MSG_FEED_TITLE) : defaultTitle);
+
+        if (defaultDescriptionField == null || defaultDescriptionField == "") {
+            defaultDescriptionField = I18nUtil.getMessage("org.dspace.app.util.SyndicationFeed.no-description");
+        }
+
+        feed.setDescription(defaultDescriptionField);
         feed.setLink(objectURL);
         feed.setPublishedDate(new Date());
         feed.setUri(objectURL);

dspace-api/src/main/java/org/dspace/authenticate/IPAuthentication.java

@@ -52,11 +52,6 @@ public class IPAuthentication implements AuthenticationMethod {
      */
     private static Logger log = org.apache.logging.log4j.LogManager.getLogger(IPAuthentication.class);
 
-    /**
-     * Whether to look for x-forwarded headers for logging IP addresses
-     */
-    protected static Boolean useProxies;
-
     /**
      * All the IP matchers
      */
@@ -250,7 +245,7 @@ public List<Group> getSpecialGroups(Context context, HttpServletRequest request)
 
             log.debug(LogHelper.getHeader(context, "authenticated",
                                            "special_groups=" + gsb.toString()
-                                           + " (by IP=" + addr + ", useProxies=" + useProxies.toString() + ")"
+                                           + " (by IP=" + addr + ")"
                                           ));
         }
 

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

@@ -332,8 +332,8 @@ public void updateLastModified(Context context, Bitstream bitstream) {
     }
 
     @Override
-    public List<Bitstream> findDeletedBitstreams(Context context) throws SQLException {
-        return bitstreamDAO.findDeletedBitstreams(context);
+    public List<Bitstream> findDeletedBitstreams(Context context, int limit, int offset) throws SQLException {
+        return bitstreamDAO.findDeletedBitstreams(context, limit, offset);
     }
 
     @Override

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

@@ -48,6 +48,12 @@ public abstract class DSpaceObject implements Serializable, ReloadableEntity<jav
     @Transient
     private StringBuffer eventDetails = null;
 
+    /**
+     * The same order should be applied inside this comparator
+     * {@link MetadataValueComparators#defaultComparator} to preserve
+     * ordering while the list has been modified and not yet persisted
+     * and reloaded.
+     */
     @OneToMany(fetch = FetchType.LAZY, mappedBy = "dSpaceObject", cascade = CascadeType.ALL, orphanRemoval = true)
     @OrderBy("metadataField, place")
     private List<MetadataValue> metadata = new ArrayList<>();
@@ -116,7 +122,7 @@ protected void addDetails(String d) {
      * @return summary of event details, or null if there are none.
      */
     public String getDetails() {
-        return (eventDetails == null ? null : eventDetails.toString());
+        return eventDetails == null ? null : eventDetails.toString();
     }
 
     /**
@@ -145,7 +151,7 @@ public UUID getID() {
      * one
      */
     public String getHandle() {
-        return (CollectionUtils.isNotEmpty(handles) ? handles.get(0).getHandle() : null);
+        return CollectionUtils.isNotEmpty(handles) ? handles.get(0).getHandle() : null;
     }
 
     void setHandle(List<Handle> handle) {