Merge remote-tracking branch 'refs/remotes/upstream/main' into async_…

…indexing

# Conflicts:
#	services/src/main/java/org/fao/geonet/api/processing/DatabaseProcessUtils.java

CONTRIBUTING.md

@@ -2,7 +2,8 @@
 
 Thank you for contributing to GeoNetwork!
 
-* Free-software: GeoNetwork is free-software, using the [GNU GENERAL PUBLIC LICENSE](LICENSE.md). Contributions provided by you, or your employer, are required to be compatible with this free-software license.
+* Free-software: GeoNetwork is free-software, using the [GNU GENERAL PUBLIC LICENSE](LICENSE.md).
+* Contributions provided by you, or your employer, are required to be compatible with this free-software license. You will therefor be asked to sign the [Contributor License Agreement](https://cla-assistant.io/geonetwork/) when you are contributing to the repositories. This process is automatically enabled when you create your first pull request via https://cla-assistant.io/.
 * Pull-request: GeoNetwork uses a pull-request workflow to review and accept changes. Pull-requests must be submitted against the *main* branch first, and may be back ported as required.
 
 # Pull requests

README.md

@@ -31,5 +31,8 @@ Developer documentation located in ``README.md`` files in the code-base:
 * [Software Development Documentation](/software_development/) provides instructions for setting up a development environment, building GeoNetwork, compiling user documentation, and making a releases.
 * Module specific documentation can be found in each module:
 
+## Individual Contributor Licenses signed using the CLS Assistant
+[![CLA assistant](https://cla-assistant.io/readme/badge/geonetwork/geonetwork)](https://cla-assistant.io/geonetwork/geonetwork)
+
 ## Open Source Security Foundation (OpenSSF) best practices status
-[![OpenSSF Best Practices](https://www.bestpractices.dev/projects/8626/badge)](https://www.bestpractices.dev/projects/8626)
+[![OpenSSF Best Practices](https://www.bestpractices.dev/projects/8626/badge)](https://www.bestpractices.dev/projects/8626) 

cachingxslt/pom.xml

@@ -31,7 +31,7 @@
   <parent>
     <groupId>org.geonetwork-opensource</groupId>
     <artifactId>geonetwork</artifactId>
-    <version>4.4.6-SNAPSHOT</version>
+    <version>4.4.7-SNAPSHOT</version>
   </parent>
 
 

common/pom.xml

@@ -31,7 +31,7 @@
   <parent>
     <groupId>org.geonetwork-opensource</groupId>
     <artifactId>geonetwork</artifactId>
-    <version>4.4.6-SNAPSHOT</version>
+    <version>4.4.7-SNAPSHOT</version>
   </parent>
 
 

core/pom.xml

@@ -27,7 +27,7 @@
   <parent>
     <artifactId>geonetwork</artifactId>
     <groupId>org.geonetwork-opensource</groupId>
-    <version>4.4.6-SNAPSHOT</version>
+    <version>4.4.7-SNAPSHOT</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
 

core/src/main/java/org/fao/geonet/api/exception/GeonetMaxUploadSizeExceededException.java

@@ -0,0 +1,81 @@
+/*
+ * Copyright (C) 2001-2024 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.api.exception;
+
+import java.util.Locale;
+
+import org.fao.geonet.exceptions.LocalizedException;
+
+public class GeonetMaxUploadSizeExceededException extends LocalizedException {
+
+    public GeonetMaxUploadSizeExceededException() {
+        super();
+    }
+
+    public GeonetMaxUploadSizeExceededException(String message) {
+        super(message);
+    }
+
+    public GeonetMaxUploadSizeExceededException(String message, Throwable cause) {
+        super(message, cause);
+    }
+
+    public GeonetMaxUploadSizeExceededException(Throwable cause) {
+        super(cause);
+    }
+
+    protected String getResourceBundleBeanQualifier() {
+        return "apiMessages";
+    }
+
+    @Override
+    public GeonetMaxUploadSizeExceededException withMessageKey(String messageKey) {
+        super.withMessageKey(messageKey);
+        return this;
+    }
+
+    @Override
+    public GeonetMaxUploadSizeExceededException withMessageKey(String messageKey, Object[] messageKeyArgs) {
+        super.withMessageKey(messageKey, messageKeyArgs);
+        return this;
+    }
+
+    @Override
+    public GeonetMaxUploadSizeExceededException withDescriptionKey(String descriptionKey) {
+        super.withDescriptionKey(descriptionKey);
+        return this;
+    }
+
+    @Override
+    public GeonetMaxUploadSizeExceededException withDescriptionKey(String descriptionKey, Object[] descriptionKeyArgs) {
+        super.withDescriptionKey(descriptionKey, descriptionKeyArgs);
+        return this;
+    }
+
+    @Override
+    public GeonetMaxUploadSizeExceededException withLocale(Locale locale) {
+        super.withLocale(locale);
+        return this;
+    }
+}

core/src/main/java/org/fao/geonet/api/records/attachments/AbstractStore.java

@@ -286,7 +286,7 @@ public String toString() {
 
     private String escapeResourceManagementExternalProperties(String value) {
         return value.replace(RESOURCE_MANAGEMENT_EXTERNAL_PROPERTIES_SEPARATOR, RESOURCE_MANAGEMENT_EXTERNAL_PROPERTIES_ESCAPED_SEPARATOR);
-}
+    }
 
     /**
      * Create an encoded base 64 object id contains the following fields to uniquely identify the resource

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

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2001-2016 Food and Agriculture Organization of the
+ * Copyright (C) 2001-2024 Food and Agriculture Organization of the
  * United Nations (FAO-UN), United Nations World Food Programme (WFP)
  * and United Nations Environment Programme (UNEP)
  *
@@ -51,30 +51,30 @@
  * Manage objects selection for a user session.
  */
 public class SelectionManager {
-
     public static final String SELECTION_METADATA = "metadata";
-    public static final String SELECTION_BUCKET = "bucket";
+    // Bucket name used in the search UI to store the selected the metadata
+    public static final String SELECTION_BUCKET = "s101";
     // used to limit select all if get system setting maxrecords fails or contains value we can't parse
     public static final int DEFAULT_MAXHITS = 1000;
     public static final String ADD_ALL_SELECTED = "add-all";
     public static final String REMOVE_ALL_SELECTED = "remove-all";
     public static final String ADD_SELECTED = "add";
     public static final String REMOVE_SELECTED = "remove";
     public static final String CLEAR_ADD_SELECTED = "clear-add";
-    private Hashtable<String, Set<String>> selections = null;
+    private Hashtable<String, Set<String>> selections;
 
     private SelectionManager() {
-        selections = new Hashtable<String, Set<String>>(0);
+        selections = new Hashtable<>(0);
 
         Set<String> MDSelection = Collections
-            .synchronizedSet(new HashSet<String>(0));
+            .synchronizedSet(new HashSet<>(0));
         selections.put(SELECTION_METADATA, MDSelection);
     }
 
 
     public Map<String, Integer> getSelectionsAndSize() {
         return selections.entrySet().stream().collect(Collectors.toMap(
-            e -> e.getKey(),
+            Map.Entry::getKey,
             e -> e.getValue().size()
         ));
     }
@@ -183,7 +183,7 @@ public int updateSelection(String type,
         // Get the selection manager or create it
         Set<String> selection = this.getSelection(type);
         if (selection == null) {
-            selection = Collections.synchronizedSet(new HashSet<String>());
+            selection = Collections.synchronizedSet(new HashSet<>());
             this.selections.put(type, selection);
         }
 
@@ -192,30 +192,21 @@ public int updateSelection(String type,
                 this.selectAll(type, context, session);
             else if (selected.equals(REMOVE_ALL_SELECTED))
                 this.close(type);
-            else if (selected.equals(ADD_SELECTED) && listOfIdentifiers.size() > 0) {
+            else if (selected.equals(ADD_SELECTED) && !listOfIdentifiers.isEmpty()) {
                 // TODO ? Should we check that the element exist first ?
-                for (String paramid : listOfIdentifiers) {
-                    selection.add(paramid);
-                }
-            } else if (selected.equals(REMOVE_SELECTED) && listOfIdentifiers.size() > 0) {
+                selection.addAll(listOfIdentifiers);
+            } else if (selected.equals(REMOVE_SELECTED) && !listOfIdentifiers.isEmpty()) {
                 for (String paramid : listOfIdentifiers) {
                     selection.remove(paramid);
                 }
-            } else if (selected.equals(CLEAR_ADD_SELECTED) && listOfIdentifiers.size() > 0) {
+            } else if (selected.equals(CLEAR_ADD_SELECTED) && !listOfIdentifiers.isEmpty()) {
                 this.close(type);
-                for (String paramid : listOfIdentifiers) {
-                    selection.add(paramid);
-                }
+                selection.addAll(listOfIdentifiers);
             }
         }
 
         // Remove empty/null element from the selection
-        Iterator<String> iter = selection.iterator();
-        while (iter.hasNext()) {
-            Object element = iter.next();
-            if (element == null)
-                iter.remove();
-        }
+        selection.removeIf(Objects::isNull);
 
         return selection.size();
     }
@@ -241,14 +232,12 @@ public void selectAll(String type, ServiceContext context, UserSession session)
 
         if (StringUtils.isNotEmpty(type)) {
             JsonNode request = (JsonNode) session.getProperty(Geonet.Session.SEARCH_REQUEST + type);
-            if (request == null) {
-                return;
-            } else {
+            if (request != null) {
                 final SearchResponse searchResponse;
                 try {
                     EsSearchManager searchManager = context.getBean(EsSearchManager.class);
                     searchResponse = searchManager.query(request.get("query"), FIELDLIST_UUID, 0, maxhits);
-                    List<String> uuidList = new ArrayList();
+                    List<String> uuidList = new ArrayList<>();
                     ObjectMapper objectMapper = new ObjectMapper();
                     for (Hit h : (List<Hit>) searchResponse.hits().hits()) {
                         uuidList.add((String) objectMapper.convertValue(h.source(), Map.class).get(Geonet.IndexFieldNames.UUID));
@@ -293,7 +282,7 @@ public Set<String> getSelection(String type) {
         Set<String> sel = selections.get(type);
         if (sel == null) {
             Set<String> MDSelection = Collections
-                .synchronizedSet(new HashSet<String>(0));
+                .synchronizedSet(new HashSet<>(0));
             selections.put(type, MDSelection);
         }
         return selections.get(type);

core/src/main/java/org/fao/geonet/kernel/datamanager/IMetadataUtils.java

@@ -549,4 +549,31 @@ void setCreativeCommons(ServiceContext context, String id, String licenseurl, St
      * @param dest
      */
     void replaceFiles(AbstractMetadata original, AbstractMetadata dest);
+
+    /**
+     * Get the metadata after preforming a search and replace on it.
+     * @param uuid    The UUID of the metadata to search for.
+     * @param search  The string to search for.
+     * @param replace The string to replace the search string with.
+     * @return The metadata with the search and replace applied.
+     */
+    String selectOneWithSearchAndReplace(String uuid, String search, String replace);
+
+    /**
+     * Get the metadata after preforming a regex search and replace on it.
+     * @param uuid    The UUID of the metadata to search for.
+     * @param search  The string to search for.
+     * @param replace The string to replace the search string with.
+     * @return The metadata with the search and replace applied.
+     */
+    String selectOneWithRegexSearchAndReplaceWithFlags(String uuid, String search, String replace, String flags);
+
+    /**
+     * Get the metadata after preforming a regex search and replace on it.
+     * @param uuid    The UUID of the metadata to search for.
+     * @param search  The string to search for.
+     * @param replace The string to replace the search string with.
+     * @return The metadata with the search and replace applied.
+     */
+    String selectOneWithRegexSearchAndReplace(String uuid, String search, String replace);
 }

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

@@ -1029,4 +1029,19 @@ public void cloneFiles(AbstractMetadata original, AbstractMetadata dest) {
     public void replaceFiles(AbstractMetadata original, AbstractMetadata dest) {
         // Empty implementation for non-draft mode as not used
     }
+
+    @Override
+    public String selectOneWithSearchAndReplace(String uuid, String search, String replace) {
+        return metadataRepository.selectOneWithSearchAndReplace(uuid, search, replace);
+    }
+
+    @Override
+    public String selectOneWithRegexSearchAndReplaceWithFlags(String uuid, String search, String replace, String flags) {
+        return metadataRepository.selectOneWithRegexSearchAndReplaceWithFlags(uuid, search, replace, flags);
+    }
+
+    @Override
+    public String selectOneWithRegexSearchAndReplace(String uuid, String search, String replace) {
+        return metadataRepository.selectOneWithRegexSearchAndReplace(uuid, search, replace);
+    }
 }

core/src/main/java/org/fao/geonet/kernel/datamanager/draft/DraftMetadataUtils.java

@@ -679,6 +679,7 @@ private void cloneStoreFileUploadRequests(AbstractMetadata original, AbstractMet
             metadataFileUpload.setFileSize(mfu.getFileSize());
             metadataFileUpload.setUploadDate(mfu.getUploadDate());
             metadataFileUpload.setUserName(mfu.getUserName());
+            metadataFileUpload.setDeletedDate(mfu.getDeletedDate());
 
             repo.save(metadataFileUpload);
         }
@@ -691,4 +692,31 @@ public void setListOfStatusCreatingDraft(Set<String> listOfStatusCreatingDraft)
     public Set<String> getListOfStatusCreatingDraft() {
         return listOfStatusToTriggerDraftCreation;
     }
+
+    @Override
+    public String selectOneWithSearchAndReplace(String uuid, String search, String replace) {
+        String updatedXml = metadataDraftRepository.selectOneWithSearchAndReplace(uuid, search, replace);
+        if (updatedXml == null) {
+            updatedXml = super.selectOneWithSearchAndReplace(uuid, search, replace);
+        }
+        return updatedXml;
+    }
+
+    @Override
+    public String selectOneWithRegexSearchAndReplaceWithFlags(String uuid, String search, String replace, String flags) {
+        String updatedXml = metadataDraftRepository.selectOneWithRegexSearchAndReplaceWithFlags(uuid, search, replace, flags);
+        if (updatedXml == null) {
+            updatedXml = super.selectOneWithRegexSearchAndReplaceWithFlags(uuid, search, replace, flags);
+        }
+        return updatedXml;
+    }
+
+    @Override
+    public String selectOneWithRegexSearchAndReplace(String uuid, String search, String replace) {
+        String updatedXml = metadataDraftRepository.selectOneWithRegexSearchAndReplace(uuid, search, replace);
+        if (updatedXml == null) {
+            updatedXml = super.selectOneWithRegexSearchAndReplace(uuid, search, replace);
+        }
+        return updatedXml;
+    }
 }

core/src/main/java/org/fao/geonet/kernel/metadata/DefaultStatusActions.java

@@ -48,6 +48,8 @@
 import org.springframework.context.ApplicationContext;
 
 import java.util.*;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import static org.fao.geonet.kernel.setting.Settings.SYSTEM_FEEDBACK_EMAIL;
 import static org.fao.geonet.util.LocalizedEmailComponent.ComponentType.*;
@@ -330,22 +332,24 @@ protected void notify(List<User> userToNotify, MetadataStatus status) throws Exc
             );
         }
 
-        LocalizedEmail localizedEmail = new LocalizedEmail(false);
-        localizedEmail.addComponents(emailSubjectComponent, emailMessageComponent, emailSalutationComponent);
-
-        String subject = localizedEmail.getParsedSubject(feedbackLocales);
-
         for (User user : userToNotify) {
+            LocalizedEmail localizedEmail = new LocalizedEmail(false);
+
             String userName = Joiner.on(" ").skipNulls().join(user.getName(), user.getSurname());
             //If we have a userName add the salutation
             String message;
             if (StringUtils.isEmpty(userName)) {
+                localizedEmail.addComponents(emailSubjectComponent, emailMessageComponent);
+
                 message = localizedEmail.getParsedMessage(feedbackLocales);
             } else {
+                localizedEmail.addComponents(emailSubjectComponent, emailMessageComponent, emailSalutationComponent);
+
                 Map<String, String> replacements = new HashMap<>();
                 replacements.put("{{userName}}", userName);
                 message = localizedEmail.getParsedMessage(feedbackLocales, replacements);
             }
+            String subject = localizedEmail.getParsedSubject(feedbackLocales);
             sendEmail(user.getEmail(), subject, message);
         }
     }
@@ -449,7 +453,9 @@ public static List<User> getUserToNotify(StatusValueNotificationLevel notificati
                 }
             }
         }
-        return users;
+
+        // Filter out users without email
+        return users.stream().filter(u -> StringUtils.isNotEmpty(u.getEmail())).collect(Collectors.toList());
     }
 
     public static List<Group> getGroupToNotify(StatusValueNotificationLevel notificationLevel, List<String> groupNames) {