Bump commons-net:commons-net from 3.9.0 to 3.11.1

.github/workflows/sonarcloud.yml

@@ -2,9 +2,7 @@ name: SonarCloud QA
 on:
   push:
     branches:
-      - main
-      - 4.0.x
-      - 3.12.x
+      - geocat_v4.2.3_report_custom
   pull_request:
     types: [opened, synchronize, reopened]
 jobs:
@@ -19,12 +17,9 @@ jobs:
         with:
           fetch-depth: 0  # Shallow clones should be disabled for a better relevancy of analysis
           submodules: 'recursive'
-      # For building GeoNetwork, JDK8 is necessary, but for running
-      # the SonarQube plugin, JDK11 is necessary.
-      # So, first install JDK 8, build GeoNetwork, then install JDK11
-      # and run SonarQube:
-      - name: Set up JDK 8
-        uses: actions/[email protected]
+          show-progress: 'false'
+      - name: Set up JDK 11
+        uses: actions/[email protected]
         with:
           java-version: 8
           distribution: 'temurin'
@@ -37,11 +32,13 @@ jobs:
           restore-keys: ${{ runner.os }}-sonar
       - name: Build GN
         run: mvn -B package -DskipTests
-      - name: Set up JDK 11
-        uses: actions/[email protected]
+
+      - name: Set up JDK 21 # Sonarcloud analyzer needs at least JDK 17
+        uses: actions/[email protected]
         with:
           distribution: 'temurin'
-          java-version: '11'
+          java-version: '21'
+          cache: 'maven'
       - name: Analyze with Sonar
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}  # Needed to get PR information, if any

common/src/main/java/org/fao/geonet/exceptions/GNException.java

@@ -0,0 +1,34 @@
+//=============================================================================
+//===	Copyright (C) 2001-2023 Food and Agriculture Organization of the
+//===	United Nations (FAO-UN), United Nations World Food Programme (WFP)
+//===	and United Nations Environment Programme (UNEP)
+//===
+//===	This program is free software; you can redistribute it and/or modify
+//===	it under the terms of the GNU General Public License as published by
+//===	the Free Software Foundation; either version 2 of the License, or (at
+//===	your option) any later version.
+//===
+//===	This program is distributed in the hope that it will be useful, but
+//===	WITHOUT ANY WARRANTY; without even the implied warranty of
+//===	MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+//===	General Public License for more details.
+//===
+//===	You should have received a copy of the GNU General Public License
+//===	along with this program; if not, write to the Free Software
+//===	Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA
+//===
+//===	Contact: Jeroen Ticheler - FAO - Viale delle Terme di Caracalla 2,
+//===	Rome - Italy. email: [email protected]
+//==============================================================================
+package org.fao.geonet.exceptions;
+
+public class GNException extends RuntimeException {
+
+    public GNException(String msg) {
+        super(msg);
+    }
+
+    public GNException(String msg, Throwable cause) {
+        super(msg, cause);
+    }
+}

core/src/main/java/org/fao/geonet/kernel/SpringLocalServiceInvoker.java

@@ -22,8 +22,6 @@
  */
 package org.fao.geonet.kernel;
 
-import org.fao.geonet.NodeInfo;
-import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.mock.web.MockHttpServletRequest;
 import org.springframework.mock.web.MockHttpServletResponse;
 import org.springframework.mock.web.MockHttpSession;
@@ -43,16 +41,19 @@
 
 public class SpringLocalServiceInvoker {
 
-    @Autowired
-    public RequestMappingHandlerMapping requestMappingHandlerMapping;
+    public final RequestMappingHandlerMapping requestMappingHandlerMapping;
 
-    @Autowired
-    public RequestMappingHandlerAdapter requestMappingHandlerAdapter;
+    public final RequestMappingHandlerAdapter requestMappingHandlerAdapter;
 
     private HandlerMethodArgumentResolverComposite argumentResolvers;
     private HandlerMethodReturnValueHandlerComposite returnValueHandlers;
     private DefaultDataBinderFactory webDataBinderFactory;
 
+    public SpringLocalServiceInvoker(RequestMappingHandlerMapping requestMappingHandlerMapping, RequestMappingHandlerAdapter requestMappingHandlerAdapter) {
+        this.requestMappingHandlerMapping = requestMappingHandlerMapping;
+        this.requestMappingHandlerAdapter = requestMappingHandlerAdapter;
+    }
+
     public void init() {
         argumentResolvers = new HandlerMethodArgumentResolverComposite().addResolvers(requestMappingHandlerAdapter.getArgumentResolvers());
         returnValueHandlers = new HandlerMethodReturnValueHandlerComposite().addHandlers(requestMappingHandlerAdapter.getReturnValueHandlers());

core/src/main/java/org/fao/geonet/kernel/Thesaurus.java

@@ -1100,7 +1100,7 @@ public KeywordBean getKeyword(String uri, String... languages) {
         String cacheKey = "getKeyword" + uri + Arrays.stream(languages).collect(Collectors.joining(""));
         Object cacheValue = THESAURUS_SEARCH_CACHE.getIfPresent(cacheKey);
         if (cacheValue != null) {
-            return (KeywordBean) cacheValue;
+            //return (KeywordBean) cacheValue;
         }
 
         List<KeywordBean> keywords;

core/src/main/java/org/fao/geonet/kernel/datamanager/base/BaseMetadataManager.java

@@ -23,6 +23,7 @@
 
 package org.fao.geonet.kernel.datamanager.base;
 
+import com.google.common.annotations.VisibleForTesting;
 import com.google.common.base.Function;
 import com.google.common.base.Optional;
 import com.google.common.base.Predicate;
@@ -33,19 +34,20 @@
 import jeeves.transaction.TransactionTask;
 import jeeves.xlink.Processor;
 import org.apache.commons.lang.StringUtils;
+import org.elasticsearch.action.search.SearchResponse;
 import org.fao.geonet.ApplicationContextHolder;
 import org.fao.geonet.constants.Edit;
 import org.fao.geonet.constants.Geonet;
 import org.fao.geonet.constants.Params;
 import org.fao.geonet.domain.*;
+import org.fao.geonet.exceptions.GNException;
 import org.fao.geonet.exceptions.UnAuthorizedException;
 import org.fao.geonet.kernel.*;
 import org.fao.geonet.kernel.datamanager.*;
 import org.fao.geonet.kernel.schema.MetadataSchema;
 import org.fao.geonet.kernel.schema.SchemaPlugin;
 import org.fao.geonet.kernel.search.EsSearchManager;
 import org.fao.geonet.kernel.search.IndexingMode;
-import org.fao.geonet.kernel.search.MetaSearcher;
 import org.fao.geonet.kernel.search.index.BatchOpsMetadataReindexer;
 import org.fao.geonet.kernel.setting.SettingManager;
 import org.fao.geonet.kernel.setting.Settings;
@@ -104,8 +106,6 @@ public class BaseMetadataManager implements IMetadataManager {
     @Autowired
     private GroupRepository groupRepository;
     @Autowired
-    private MetadataStatusRepository metadataStatusRepository;
-    @Autowired
     private MetadataValidationRepository metadataValidationRepository;
     @Autowired
     private MetadataRepository metadataRepository;
@@ -141,6 +141,10 @@ public class BaseMetadataManager implements IMetadataManager {
 
     @Autowired
     private ApplicationContext _applicationContext;
+
+    @VisibleForTesting
+    public int maxMdsReferencingSubTemplate = 10000;
+
     @PersistenceContext
     private EntityManager _entityManager;
 
@@ -747,6 +751,9 @@ public synchronized AbstractMetadata updateMetadata(final ServiceContext context
                     getSearchManager().delete(String.format("+uuid:\"%s\"", uuidBeforeUfo));
                 }
                 metadataIndexer.indexMetadata(metadataId, true, indexingMode);
+                if (metadata.getDataInfo().getType() == MetadataType.SUB_TEMPLATE) {
+                    indexMdsReferencingSubTemplate(context, metadata);
+                }
             }
         }
 
@@ -1314,4 +1321,26 @@ boolean hasReferencingMetadata(ServiceContext context, AbstractMetadata metadata
         return this.searchManager.query(query.toString(), null, 0, 0).getHits().getTotalHits().value > 0;
     }
 
+    private void indexMdsReferencingSubTemplate(ServiceContext context, AbstractMetadata subTemplate) throws Exception {
+        StringBuilder query = new StringBuilder(String.format("xlink:*%s*", subTemplate.getUuid()));
+        SearchResponse response = this.searchManager.query(query.toString(), null, 0, maxMdsReferencingSubTemplate);
+        if (response.getHits().getTotalHits().value > maxMdsReferencingSubTemplate) {
+            throw new GNException("Not implemented");
+        }
+        ArrayList<String> toIndex = new ArrayList<>();
+        response.getHits().forEach(consumer -> {
+            String consumerUuid = consumer.getId();
+            try {
+                String consumerId = this.metadataUtils.getMetadataId(consumerUuid);
+                if (consumerId != null) {
+                    toIndex.add(consumerId);
+                }
+            } catch (RuntimeException e) {
+                throw e;
+            } catch (Exception e) {
+                throw new RuntimeException(e);
+            }
+        });
+        metadataIndexer.batchIndexInThreadPool(context, toIndex);
+    }
 }

core/src/main/java/org/fao/geonet/kernel/mef/Importer.java

@@ -519,6 +519,8 @@ public static void importRecord(String uuid, MEFLib.UuidAction uuidAction, List<
                     if (Log.isDebugEnabled(Geonet.MEF)) {
                         Log.debug(Geonet.MEF, "Deleting existing metadata with UUID : " + uuid);
                     }
+                    Store store = context.getBean("resourceStore", Store.class);
+                    store.delResources(context, uuid, true);
                     metadataManager.deleteMetadata(context, dm.getMetadataId(uuid));
                     metadataManager.flush();
                 }

core/src/main/java/org/fao/geonet/util/XslUtil.java

@@ -459,6 +459,17 @@ public static String getNodeLogo(String key) {
         return source.isPresent() ? source.get().getLogo() : "";
     }
 
+    public static String getDiscoveryServiceUuid(String key) {
+        Optional<Source> source = getSource(key);
+        if (source.isPresent() && source.get().getType() == SourceType.subportal) {
+            return source.get().getServiceRecord();
+        } else {
+            SettingManager settingsMan = ApplicationContextHolder.get().getBean(SettingManager.class);
+            String uuid = settingsMan.getValue(SYSTEM_CSW_CAPABILITY_RECORD_UUID);
+            return "-1".equals(uuid) ? "" : uuid;
+        }
+    }
+
     private static Optional<Source> getSource(String idOrUuid) {
         SettingManager settingsMan = ApplicationContextHolder.get().getBean(SettingManager.class);
         if (StringUtils.isEmpty(idOrUuid)) {

core/src/main/java/org/fao/geonet/web/XFrameOptionsFilter.java

@@ -79,16 +79,7 @@ public void init(FilterConfig filterConfig) throws ServletException {
                     "XFrameOptions filter url parameter is missing for mode ALLOW-FROM. Setting mode to DENY.");
                 mode = MODE_DENY;
             } else {
-                try {
-                    URL urlValue = new URL(url);
-                    domain = urlValue.getHost() +
-                            ((urlValue.getPort() == -1) ? "" : ":" + urlValue.getPort());
-
-                } catch (MalformedURLException ex) {
-                    Log.info(Geonet.GEONETWORK, String.format(
-                            "XFrameOptions filter url parameter (%s) is not valid for mode ALLOW-FROM. Setting mode to DENY.", url));
-                    mode = MODE_DENY;
-                }
+                domain = url;
             }
         }
 

core/src/test/java/org/fao/geonet/GeonetTestFixture.java

@@ -40,7 +40,6 @@
 import org.fao.geonet.utils.IO;
 import org.fao.geonet.utils.TransformerFactoryFactory;
 import org.fao.geonet.utils.Xml;
-import org.geotools.data.DataStore;
 import org.jdom.Element;
 import org.springframework.beans.factory.NoSuchBeanDefinitionException;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -68,14 +67,21 @@ public class GeonetTestFixture {
     private volatile static FileSystemPool.CreatedFs templateFs;
     private volatile static SchemaManager templateSchemaManager;
     @Autowired
-    private EsSearchManager templateSearchManager;
-    @Autowired
-    protected DataStore dataStore;
+    private EsSearchManager esSearchManager;
     @Autowired
     private ConfigurableApplicationContext _applicationContext;
     @Autowired
     private IsoLanguagesMapper isoLanguagesMapper;
-
+    @Autowired
+    private GeonetworkDataDirectory geonetworkDataDirectory;
+    @Autowired
+    private ThesaurusManager thesaurusManager;
+    @Autowired
+    private DataManager dataManager;
+    @Autowired
+    private DataSource dataSource;
+    @Autowired
+    private SettingManager settingManager;
     private FileSystemPool.CreatedFs currentFs;
 
 
@@ -111,17 +117,15 @@ public boolean accept(Path entry) throws IOException {
                     }
                 });
 
-
                 Path schemaPluginsDir = templateDataDirectory.resolve("config/schema_plugins");
                 deploySchema(webappDir, schemaPluginsDir);
 
-                final GeonetworkDataDirectory geonetworkDataDirectory = _applicationContext.getBean(GeonetworkDataDirectory.class);
-                final ServiceConfig serviceConfig = new ServiceConfig(Lists.<Element>newArrayList());
+                final ServiceConfig serviceConfig = new ServiceConfig(Lists.newArrayList());
                 geonetworkDataDirectory.init("geonetwork", webappDir, templateDataDirectory, serviceConfig, null);
                 test.addTestSpecificData(geonetworkDataDirectory);
 
                 // Create ES index
-               _applicationContext.getBean(EsSearchManager.class).init(false, Optional.empty());
+                esSearchManager.init(true, Optional.empty());
 
                 templateSchemaManager = initSchemaManager(webappDir, geonetworkDataDirectory);
 
@@ -130,7 +134,7 @@ public boolean accept(Path entry) throws IOException {
             isoLanguagesMapper.reinit();
         }
 
-        final String fsName = test.getClass().getSimpleName().replaceAll("[^a-z0-9A-Z]", "") + UUID.randomUUID().toString();
+        final String fsName = test.getClass().getSimpleName().replaceAll("[^a-z0-9A-Z]", "") + UUID.randomUUID();
         currentFs = FILE_SYSTEM_POOL.get(fsName);
 
         assertTrue(Files.isDirectory(currentFs.dataDir.resolve("config")));
@@ -142,35 +146,21 @@ public boolean accept(Path entry) throws IOException {
         final GeonetworkDataDirectory dataDir = configureDataDir(test, webappDir, currentFs.dataDir);
         configureNewSchemaManager(dataDir, webappDir);
 
-        // TODO: I don't know why but this corrupts other tests that will fail depending on the run order:
-        //  assertCorrectDataDir();
-        // for example, running GeonetworkDataDirectoryMultiNodeServiceConfigOnlySystemDataDirSetTest, then
-        // GeonetworkDataDirectoryMultiNodeSystemPropertyOnlySystemDataDirSetTest with that line enabled, the second fails.
-
-//        if (test.resetLuceneIndex()) {
-//            _directoryFactory.resetIndex();
-//        }
-
         ServiceContext serviceContext = test.createServiceContext();
 
         ApplicationContextHolder.set(_applicationContext);
         serviceContext.setAsThreadLocal();
-//      TODOES
-//        _applicationContext.getBean(EsSearchManager.class).initNonStaticData(100);
-        _applicationContext.getBean(DataManager.class).init(serviceContext, false);
-        _applicationContext.getBean(ThesaurusManager.class).init(true, serviceContext, "WEB-INF/data/config/codelist");
 
+        dataManager.init(serviceContext, false);
+        thesaurusManager.init(true, serviceContext, "WEB-INF/data/config/codelist");
 
         addSourceUUID(dataDir);
 
-        final DataSource dataSource = _applicationContext.getBean(DataSource.class);
         try (Connection conn = dataSource.getConnection()) {
-            ThreadUtils.init(conn.getMetaData().getURL(), _applicationContext.getBean(SettingManager.class));
+            ThreadUtils.init(conn.getMetaData().getURL(), settingManager);
         }
-
     }
 
-
     protected void configureNewSchemaManager(GeonetworkDataDirectory dataDir, Path webappDir) throws Exception {
         final SchemaManager schemaManager = _applicationContext.getBean(SchemaManager.class);
         schemaManager.configureFrom(templateSchemaManager, webappDir, dataDir);
@@ -179,7 +169,7 @@ protected void configureNewSchemaManager(GeonetworkDataDirectory dataDir, Path w
 
     protected void addSourceUUID(GeonetworkDataDirectory dataDirectory) {
         String siteUuid = dataDirectory.getSystemDataDir().getFileName().toString();
-        _applicationContext.getBean(SettingManager.class).setSiteUuid(siteUuid);
+        settingManager.setSiteUuid(siteUuid);
         final SourceRepository sourceRepository = _applicationContext.getBean(SourceRepository.class);
         List<Source> sources = sourceRepository.findAll();
         if (sources.isEmpty()) {