Item 7490: Fix custom pipeline logger

api/resources/credits/jars.txt

@@ -42,6 +42,7 @@ jxl-2.6.3.jar|API|2.6.3|{link:jexcelapi|http://www.jexcelapi.org/}|{link:LGPL|ht
 kaptcha-2.3.jar|Captcha generator|2.3|{link:kaptcha|http://code.google.com/p/kaptcha/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|nicka|User signup forms
 log4j-api-2.13.3.jar|Log4j|2.13.3|{link:Apache|https://logging.apache.org/log4j/2.x/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|ankurj|Logging
 log4j-core-2.13.3.jar|Log4j|2.13.3|{link:Apache|https://logging.apache.org/log4j/2.x/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|ankurj|Logging
+log4j-1.2-api-2.13.3.jar|Log4j|2.13.3|{link:Apache|https://logging.apache.org/log4j/2.x/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|ankurj|Logging
 objenesis-1.0.jar|Objenesis|1.0|{link:Objenesis|http://code.google.com/p/objenesis/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jeckels|Library for instantiating Java objects, dependency of jMock
 opencsv-2.3.jar|OpenCSV|2.3|{link:OpenCSV|http://opencsv.sourceforge.net/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|adam|Parsing CSV Files
 patricia-trie-0.6.jar|PATRICIA Trie|0.6|{link:PATRICIA Trie|http://code.google.com/p/patricia-trie/}|{link:Apache 2.0|http://www.apache.org/licenses/LICENSE-2.0}|jeckels|PATRICIA Trie data structure implementation

api/src/org/labkey/api/data/Table.java

@@ -443,7 +443,7 @@ static void logException(@Nullable SQLFragment sql, @Nullable Connection conn, S
             if (RuntimeSQLException.isConstraintException(e) && (StringUtils.startsWithIgnoreCase(trim, "INSERT") || StringUtils.startsWithIgnoreCase(trim, "UPDATE")))
             {
                 // Log this ConstraintException if log Level is WARN (the default) or lower. Skip logging for callers that request just ERRORs.
-                if (Level.WARN.intLevel() >= logLevel.intLevel())
+                if (Level.WARN.isMoreSpecificThan(logLevel))
                 {
                     _log.warn("SQL Exception", e);
                     _logQuery(Level.WARN, sql, conn);
@@ -452,7 +452,7 @@ static void logException(@Nullable SQLFragment sql, @Nullable Connection conn, S
             else
             {
                 // Log this SQLException if log level is ERROR or lower.
-                if (Level.ERROR.intLevel() >= logLevel.intLevel())
+                if (Level.ERROR.isMoreSpecificThan(logLevel))
                 {
                     _log.error("SQL Exception", e);
                     _logQuery(Level.ERROR, sql, conn);

api/src/org/labkey/api/pipeline/PipelineJob.java

@@ -1436,6 +1436,7 @@ public void error(String message)
         {
             _job.getClassLogger().error(getSystemLogMessage(message));
             write(message, null, Level.ERROR.toString());
+            setErrorStatus(message);
         }
 
         @Override
@@ -1451,6 +1452,7 @@ public void fatal(String message)
         {
             _job.getClassLogger().fatal(getSystemLogMessage(message));
             write(message, null, Level.FATAL.toString());
+            setErrorStatus(message);
         }
 
         @Override
@@ -1461,6 +1463,14 @@ public void fatal(String message, Throwable t)
             setErrorStatus(message);
         }
 
+        // called from LogOutputStream.flush()
+        @Override
+        public void log(Level level, String message)
+        {
+           _job.getClassLogger().log(level, message);
+           write(message, null, level.toString());
+        }
+
         private String getSystemLogMessage(Object message)
         {
             StringBuilder sb = new StringBuilder();
@@ -1506,7 +1516,7 @@ public void write(String message, @Nullable Throwable t, String level)
             {
                 var line = formattedDate + " " +
                         String.format("%-5s", level) +
-                        " : " +
+                        ": " +
                         message;
                 writer.write(line);
                 writer.write(LINE_SEP);

api/src/org/labkey/api/query/MetadataParseWarning.java

@@ -33,7 +33,7 @@ public MetadataParseWarning(String message)
     public MetadataParseWarning(String message, Throwable cause, int line, int column)
     {
         super(message, cause, line, column);
-        _level = Level.WARN.intLevel();
+        _level = Level.WARN;
     }
 
     public MetadataParseWarning(String queryName, QueryParseException other)

api/src/org/labkey/api/query/QueryParseException.java

@@ -29,7 +29,7 @@ public class QueryParseException extends QueryException
 {
     protected int _line;
     protected int _column;
-    protected int _level = Level.ERROR.intLevel();
+    protected Level _level = Level.ERROR;
 
     public QueryParseException(String message, Throwable cause, int line, int column)
     {
@@ -47,12 +47,12 @@ public QueryParseException(String queryName, QueryParseException other)
 
     public boolean isError()
     {
-        return _level >= Level.ERROR.intLevel();
+        return _level.isMoreSpecificThan(Level.ERROR);
     }
 
     public boolean isWarning()
     {
-        return _level < Level.ERROR.intLevel();
+        return _level.isLessSpecificThan(Level.ERROR);
     }
 
 
@@ -62,7 +62,7 @@ public String getMessage()
         String ret = super.getMessage();
         if (_line != 0)
         {
-            if (_level == Level.WARN.intLevel())
+            if (_level.intLevel() == Level.WARN.intLevel())
                 ret = "Warning on line " + _line + ": " + ret;
             else
                 ret = "Error on line " + _line + ": " + ret;

api/src/org/labkey/api/query/QueryParseWarning.java

@@ -28,6 +28,6 @@ public class QueryParseWarning extends QueryParseException
     public QueryParseWarning(String message, Throwable cause, int line, int column)
     {
         super(message, cause, line, column);
-        _level = Level.WARN.intLevel();
+        _level = Level.WARN;
     }
 }

study/src/org/labkey/study/importer/SpecimenImporter.java

@@ -3514,7 +3514,7 @@ protected void checkForConflictingSpecimens(DbSchema schema, String tempTable, L
                     }
                 }
 
-                _logger.error(sb);
+                _logger.error(sb.toString());
 
                 // If conflicts are found, stop the import.
                 throw new IllegalStateException(sb.toString());