Harvester / Localfilesystem / Log properly to harvester log file. (ge…

…onetwork#7660)

* Harvester / Localfilesystem / Log properly to harvester log file.

Follow up of geonetwork#2765
and fix harvester logger which was not reporting any error anymore into the harvester logfile that user can download after harvest.

![image](https://github.com/geonetwork/core-geonetwork/assets/1701393/d84e643f-6713-4821-9d04-bde2e9c1c911)

It only reports:
```
2024-01-25T11:06:22,547 WARN  [geonetwork.harvester] - Start of alignment for : SEANOE
2024-01-25T11:08:25,135 INFO  [geonetwork.harvester] - Ended harvesting from node : SEANOE (LocalFilesystemHarvester)
```

If using the harvester logger as before, then the log file properly contains errors
```
2024-01-25T11:06:22,547 WARN  [geonetwork.harvester] - Start of alignment for : SEANOE
2024-01-25T11:06:55,675 ERROR [geonetwork.harvester] - Error transforming JSON into XML from file /data/75639.json, ignoring
2024-01-25T11:07:33,893 ERROR [geonetwork.harvester] - Error transforming JSON into XML from file /data/59178.json, ignoring
2024-01-25T11:08:25,135 INFO  [geonetwork.harvester] - Ended harvesting from node : SEANOE (LocalFilesystemHarvester)
```

To test, try to import a file which whill trigger error like invalid
XML.

* Harvester / Localfilesystem / Remove duplicated privileges deletion and add option to append privileges (in case user wants to also manage locally privileges).

* Update LocalFilesystemHarvester.java

common/src/main/java/org/fao/geonet/Logger.java

@@ -23,8 +23,6 @@
 
 package org.fao.geonet;
 
-//=============================================================================
-
 import org.apache.logging.log4j.core.appender.FileAppender;
 
 /**
@@ -37,87 +35,102 @@ public interface Logger {
      *
      * @return check if debug logging is enabled
      */
-    public boolean isDebugEnabled();
+    boolean isDebugEnabled();
 
     /**
      * Log debug message used indicate module troubleshoot module activity.
      *
      * @param message debug message used to provide in
      */
-    public void debug(String message);
+    void debug(String message);
+
+    void debug(String message, Throwable throwable);
+
+    void debug(String message, Object... object);
 
     /**
      * Log information message indicating module progress.
      *
      * @param message information message indicating progress
      */
-    public void info(String message);
+    void info(String message);
+
+    void info(String message, Throwable throwable);
 
-    /** Log warning message indicating potentially harmful situation, module
+    void info(String message, Object... object);
+
+    /**
+     * Log warning message indicating potentially harmful situation, module
      * will continue to try and complete current activity.
      *
      * @param message Warning message indicating potentially harmful situation
      */
-    public void warning(String message);
+    void warning(String message);
+
+    void warning(String message, Throwable throwable);
+
+    void warning(String message, Object... object);
 
     /**
      * Log error message indicating module cannot continue current activity.
      *
      * @param message Error message
      */
-    public void error(String message);
+    void error(String message);
+
+    void error(String message, Throwable throwable);
+
+    void error(String message, Object... object);
 
     /**
      * Log error message using provided throwable, indicating module cannot continue
      * current activity.
      *
      * @param ex Cause of error condition.
      */
-    public void error(Throwable ex);
+    void error(Throwable ex);
 
     /**
      * Log severe message, indicating application cannot continue to operate.
      *
      * @param message severe message
      */
-    public void fatal(String message);
+    void fatal(String message);
 
     /**
      * Functional module used for logging messages (for example {@code jeeves.engine}).
      *
      * @return functional module used for logging messages.
      */
-    public String getModule();
+    String getModule();
 
     /**
      * Configure logger with log4j {@link FileAppender}, used for output.
-     *
+     * <p>
      * The file appender is also responsible for log file location provided by {@link #getFileAppender()}.
      *
      * @param fileAppender Log4j FileAppender
      */
-    public void setAppender(FileAppender fileAppender);
+    void setAppender(FileAppender fileAppender);
 
     /**
      * The log file name from the file appender for this module.
-     *
+     * <p>
      * Note both module and fallback module are provided allowing providing a better opportunity
      * to learn the log file location. Harvesters use the log file name parent directory as a good
      * location to create {@code /harvester_logs/} folder.
-     *
+     * <p>
      * Built-in configuration uses log file location {@code logs/geonetwork.log} relative to the current directory, or relative to system property {@code log_file}.
      *
      * @return logfile location of {@code logs/geonetwork.log} file
      */
-    public String getFileAppender();
+    String getFileAppender();
 
     /**
      * Access to omodule logging level, providing
+     *
      * @return
      */
-    public org.apache.logging.log4j.Level getThreshold();
+    org.apache.logging.log4j.Level getThreshold();
 
 }
-
-//=============================================================================
-

common/src/main/java/org/fao/geonet/utils/Log.java

@@ -24,22 +24,18 @@
 package org.fao.geonet.utils;
 
 
-import org.apache.log4j.Priority;
 import org.apache.log4j.bridge.AppenderWrapper;
 import org.apache.logging.log4j.Level;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.logging.log4j.core.Appender;
+import org.apache.logging.log4j.core.LoggerContext;
 import org.apache.logging.log4j.core.appender.FileAppender;
 import org.apache.logging.log4j.core.appender.RollingFileAppender;
-import org.apache.logging.log4j.core.LoggerContext;
 import org.apache.logging.log4j.core.config.Configuration;
 import org.apache.logging.log4j.core.config.LoggerConfig;
 
 import java.io.File;
-import java.util.Enumeration;
-
-//=============================================================================
 
 /**
  * Jeeves logging integration, defining functional logger categories by module
@@ -125,8 +121,12 @@ public static void debug(String module, Object message) {
         LogManager.getLogger(module).debug(message);
     }
 
-    public static void debug(String module, Object message, Exception e) {
-        LogManager.getLogger(module).debug(message, e);
+    public static void debug(String module, String message, Object... objects) {
+        LogManager.getLogger(module).debug(message, objects);
+    }
+
+    public static void debug(String module, String message, Throwable throwable) {
+        LogManager.getLogger(module).debug(message, throwable);
     }
 
     public static boolean isDebugEnabled(String module) {
@@ -157,10 +157,15 @@ public static void info(String module, Object message) {
         LogManager.getLogger(module).info(message);
     }
 
-    public static void info(String module, Object message, Throwable t) {
-        LogManager.getLogger(module).info(message, t);
+    public static void info(String module, String message, Object... objects) {
+        LogManager.getLogger(module).info(message, objects);
+    }
+
+    public static void info(String module, String message, Throwable throwable) {
+        LogManager.getLogger(module).info(message, throwable);
     }
 
+
     //---------------------------------------------------------------------------
 
     public static void warning(String module, Object message) {
@@ -182,6 +187,14 @@ public static void error(String module, Object message, Throwable t) {
         LogManager.getLogger(module).error(message, t);
     }
 
+    public static void error(String module, String message, Object... objects) {
+        LogManager.getLogger(module).error(message, objects);
+    }
+
+    public static void error(String module, String message, Throwable throwable) {
+        LogManager.getLogger(module).error(message, throwable);
+    }
+
     //---------------------------------------------------------------------------
 
     public static void fatal(String module, Object message) {
@@ -225,18 +238,58 @@ public void debug(String message) {
                 Log.debug(module, message);
             }
 
+            @Override
+            public void debug(String message, Throwable throwable) {
+                Log.debug(module, message, throwable);
+            }
+
+            @Override
+            public void debug(String message, Object... object) {
+                Log.debug(module, message, object);
+            }
+
             public void info(String message) {
                 Log.info(module, message);
             }
 
+            @Override
+            public void info(String message, Throwable throwable) {
+                Log.info(module, message, throwable);
+            }
+
+            @Override
+            public void info(String message, Object... object) {
+                Log.info(module, message, object);
+            }
+
             public void warning(String message) {
                 Log.warning(module, message);
             }
 
+            @Override
+            public void warning(String message, Throwable throwable) {
+                Log.warning(module, message, throwable);
+            }
+
+            @Override
+            public void warning(String message, Object... object) {
+
+            }
+
             public void error(String message) {
                 Log.error(module, message);
             }
 
+            @Override
+            public void error(String message, Throwable throwable) {
+                Log.error(module, message, throwable);
+            }
+
+            @Override
+            public void error(String message, Object... object) {
+                Log.error(module, message, object);
+            }
+
             public void fatal(String message) {
                 Log.fatal(module, message);
             }
@@ -279,7 +332,7 @@ public String getFileAppender() {
                     }
                 }
                 LoggerConfig fallbackConfig = configuration.getLoggers().get(fallbackModule);
-                if( fallbackConfig != null) {
+                if (fallbackConfig != null) {
                     for (Appender appender : fallbackConfig.getAppenders().values()) {
                         File file = toLogFile(appender);
                         if (file != null && file.exists()) {

core/src/main/java/jeeves/server/context/BasicContext.java

@@ -143,21 +143,61 @@ public void debug(final String message) {
         logger.debug(message);
     }
 
+    @Override
+    public void debug(String message, Throwable throwable) {
+        logger.debug(message, throwable);
+    }
+
+    @Override
+    public void debug(String message, Object... object) {
+        logger.debug(message, object);
+    }
+
     @Override
     public void info(final String message) {
         logger.info(message);
     }
 
+    @Override
+    public void info(String message, Throwable throwable) {
+        logger.info(message, throwable);
+    }
+
+    @Override
+    public void info(String message, Object... object) {
+        logger.info(message, object);
+    }
+
     @Override
     public void warning(final String message) {
         logger.warning(message);
     }
 
+    @Override
+    public void warning(String message, Throwable throwable) {
+        logger.warning(message, throwable);
+    }
+
+    @Override
+    public void warning(String message, Object... object) {
+        logger.warning(message, object);
+    }
+
     @Override
     public void error(final String message) {
         logger.error(message);
     }
 
+    @Override
+    public void error(String message, Throwable throwable) {
+        logger.error(message, throwable);
+    }
+
+    @Override
+    public void error(String message, Object... object) {
+        logger.error(message, object);
+    }
+
     @Override
     public void error(Throwable ex) {
         logger.error(ex);
@@ -200,6 +240,3 @@ public String getNodeId() {
         return NodeInfo.DEFAULT_NODE;
     }
 }
-
-//=============================================================================
-

harvesters/src/main/java/org/fao/geonet/kernel/harvest/BaseAligner.java

@@ -119,9 +119,9 @@ public void addPrivileges(String id, Iterable<Privileges> privilegesIterable, Gr
             String name = localGroups.getName(priv.getGroupId());
 
             if (name == null) {
-                LOGGER.debug("    - Skipping removed group with id:{}", priv.getGroupId());
+                LOGGER.debug("    - Skipping removed group with id: {}", priv.getGroupId());
             } else {
-                LOGGER.debug("    - Setting privileges for group : {}", name);
+                LOGGER.debug("    - Setting privileges for group: {}", name);
                 for (int opId : priv.getOperations()) {
                     name = dataManager.getAccessManager().getPrivilegeName(opId);
                     //--- all existing operation

harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/AbstractHarvester.java

@@ -140,8 +140,12 @@ public abstract class AbstractHarvester<T extends HarvestResult, P extends Abstr
     protected P params;
     protected T result;
 
+
     protected Logger log = Log.createLogger(Geonet.HARVESTER);
 
+    public Logger getLogger() {
+        return log;
+    }
     private Element loadedInfo;
     private String id;
     private volatile Status status;

harvesters/src/main/java/org/fao/geonet/kernel/harvest/harvester/localfilesystem/LocalFilesystemHarvester.java

@@ -45,7 +45,6 @@
 import org.fao.geonet.kernel.harvest.harvester.HarvestResult;
 import org.fao.geonet.kernel.search.IndexingMode;
 import org.fao.geonet.repository.MetadataRepository;
-import org.fao.geonet.repository.OperationAllowedRepository;
 import org.fao.geonet.repository.specification.MetadataSpecs;
 import org.fao.geonet.utils.IO;
 import org.jdom.Element;
@@ -158,8 +157,6 @@ void updateMetadata(Element xml, final String id, GroupMapper localGroups, final
             metadataManager.save(metadata);
         }
 
-        OperationAllowedRepository repository = context.getBean(OperationAllowedRepository.class);
-        repository.deleteAllByMetadataId(Integer.parseInt(id));
         aligner.addPrivileges(id, params.getPrivileges(), localGroups, context);
 
         metadata.getCategories().clear();