LMS-192 + LMS-147

SVN: 4545

common/source/java/ch/systemsx/cisd/common/logging/LogAnnotation.java

@@ -24,7 +24,7 @@ import java.lang.annotation.Target;
 
 /**
  * Log annotation for methods invoked by {@link LogInvocationHandler}.
- *
+ * 
  * @author Franz-Josef Elmer
  */
 @Retention(RetentionPolicy.RUNTIME)
@@ -32,6 +32,7 @@ import java.lang.annotation.Target;
 @Inherited
 public @interface LogAnnotation
 {
-    public LogCategory logCategory() default LogCategory.ACCESS;
+    public LogCategory logCategory() default LogCategory.OPERATION;
+
     public LogLevel logLevel() default LogLevel.UNDEFINED;
 }

common/source/java/ch/systemsx/cisd/common/logging/LogCategory.java

@@ -25,9 +25,9 @@ public enum LogCategory
 {
 
     /** Log category for data (read) access events. */
-    ACCESS,
+    ACCESS(true),
     /** Log category for authentication and authorization events. */
-    AUTH,
+    AUTH(true),
     /** Log category for log events related to the machine's state (low-level). */
     MACHINE,
     /**
@@ -41,6 +41,23 @@ public enum LogCategory
     /** Log category for (normal) operational events. */
     OPERATION,
     /** Log category for data manipulation events (write access). */
-    TRACKING
+    TRACKING(true);
+
+    final boolean adminLog;
+
+    private LogCategory(boolean adminLog)
+    {
+        this.adminLog = adminLog;
+    }
+
+    private LogCategory()
+    {
+        this(false);
+    }
+
+    public boolean isAdminLog()
+    {
+        return adminLog;
+    }
 
 }

common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java

@@ -40,6 +40,20 @@ public final class LogFactory
         return category.name() + "." + clazz.getCanonicalName();
     }
 
+    /**
+     * @return The logger name for the given {@link LogCategory}. Needs to be used for admin logs (i.e.
+     *         {@link LogCategory#isAdminLog()} needs to return <code>true</code>). It will contain the name of the
+     *         <var>category</var>.
+     */
+    public static String getLoggerName(LogCategory category)
+    {
+        if (category.isAdminLog() == false)
+        {
+            throw new IllegalArgumentException("Only admin logs are allowed here, but we got " + category + ".");
+        }
+        return category.name() ;
+    }
+
     /**
      * @return The logger for the given {@link LogCategory} and {@link Class}. The name of the logger will contain the
      *         name of the <var>category</var>, followed by the canonical name of <var>clazz</var>.
@@ -48,4 +62,15 @@ public final class LogFactory
     {
         return Logger.getLogger(getLoggerName(category, clazz));
     }
+
+    /**
+     * @return The logger for the given {@link LogCategory}. Needs to be an admin log (i.e.
+     *         {@link LogCategory#isAdminLog()} needs to return <code>true</code>). The name of the logger will
+     *         contain the name of the <var>category</var>.
+     */
+    public static Logger getLogger(LogCategory category)
+    {
+        return Logger.getLogger(getLoggerName(category));
+    }
+
 }

common/source/java/ch/systemsx/cisd/common/logging/LogInvocationHandler.java

@@ -26,19 +26,22 @@ import org.apache.log4j.Logger;
 
 /**
  * Invocation handler used to log invocations.
- *
+ * 
  * @author Franz-Josef Elmer
  */
 public final class LogInvocationHandler implements InvocationHandler
 {
     private final Object object;
+
     private final String name;
+
     private final Level defaultLogLevel;
+
     private final Class<?> classUsedToNameLogger;
 
     /**
      * Creates a new instance.
-     *
+     * 
      * @param object Object whose invocations should be logged.
      * @param name Meaningful name of <code>object</code>. Will be used in the log message.
      * @param logLevel The log level to use for normal (successful) events.
@@ -102,13 +105,13 @@ public final class LogInvocationHandler implements InvocationHandler
             }
         }
     }
-    
+
     private Level getLogLevel(Method method)
     {
         final LogAnnotation annotation = method.getAnnotation(LogAnnotation.class);
         if (annotation == null)
         {
-            return Level.DEBUG; 
+            return Level.DEBUG;
         } else if (annotation.logLevel().equals(LogLevel.UNDEFINED))
         {
             return defaultLogLevel;
@@ -117,11 +120,11 @@ public final class LogInvocationHandler implements InvocationHandler
             return Log4jSimpleLogger.toLog4jPriority(annotation.logLevel());
         }
     }
-    
-     private Logger createLogger(Method method)
+
+    private Logger createLogger(Method method)
     {
         final LogAnnotation annotation = method.getAnnotation(LogAnnotation.class);
-        final LogCategory logCategory = (annotation == null) ? LogCategory.ACCESS : annotation.logCategory();
+        final LogCategory logCategory = (annotation == null) ? LogCategory.OPERATION : annotation.logCategory();
         return LogFactory.getLogger(logCategory, classUsedToNameLogger);
     }
 }
\ No newline at end of file

common/source/java/ch/systemsx/cisd/common/logging/LogLevel.java

 package ch.systemsx.cisd.common.logging;
 
-/** 
+/**
  * A simple form of log levels.
  * 
- *  @author Bernd RInn
+ * @author Bernd Rinn
  */
 public enum LogLevel
 {
-    UNDEFINED, OFF, TRACE, DEBUG, INFO, WARN, ERROR
+    UNDEFINED, OFF, TRACE, DEBUG, INFO, WARN, ERROR;
 }
\ No newline at end of file

common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java

@@ -73,7 +73,8 @@ public class DefaultParser<E> implements IParser<E>
     // Parser
     //
 
-    public final List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter) throws ParsingException
+    public final List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter, final long headerLength)
+            throws ParsingException
     {
         final List<E> elements = new ArrayList<E>();
         synchronized (lineTokenizer)
@@ -90,6 +91,12 @@ public class DefaultParser<E> implements IParser<E>
                     E object = null;
                     try
                     {
+                        if (tokens.length > headerLength)
+                        {
+                            throw new RuntimeException(String.format(
+                                    "Line <%s> has more columns (%s) than the header (%s)", number, String
+                                            .valueOf(tokens.length), String.valueOf(headerLength)));
+                        }
                         object = createObject(tokens);
                     } catch (final ParserException parserException)
                     {

common/source/java/ch/systemsx/cisd/common/parser/IParser.java

@@ -32,9 +32,11 @@ public interface IParser<E>
      * Parses the lines delivered by the specified iterator and creating elements of type <code>E</code>.
      * 
      * @param lineFilter A filter lines have to pass in order to be parsed.
+     * @param headerLength number of columns in the header
      * @return a <code>List</code> of elements.
      */
-    public List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter) throws ParsingException;
+    public List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter, final long headerLength)
+            throws ParsingException;
 
     /**
      * Sets the <code>IParserObjectFactory</code>.

common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java

@@ -35,28 +35,34 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
 
 /**
- * Convenient class to load a tab file and deliver a list of beans of type <code>T</code>. The following
- * formats for the column headers are recognized.
- * <ol><li>Column headers in first line:
- *     <pre>
+ * Convenient class to load a tab file and deliver a list of beans of type <code>T</code>. The following formats for
+ * the column headers are recognized.
+ * <ol>
+ * <li>Column headers in first line:
+ * 
+ * <pre>
  *     column1  column2 column2
- *     </pre>
- *     <li>Comment section:
- *     <pre>
+ * </pre>
+ * 
+ * <li>Comment section:
+ * 
+ * <pre>
  *     # 1. line of comment
  *     # 2. line of comment
  *     # ...
  *     column1  column2 column2
- *     </pre>
- *     <li>Column headers at the end of the comment section:
- *     <pre>
+ * </pre>
+ * 
+ * <li>Column headers at the end of the comment section:
+ * 
+ * <pre>
  *     # 1. line of comment
  *     # 2. line of comment
  *     # ...
  *     #
  *     #column1  column2 column2
- *     </pre>
- *     
+ * </pre>
+ * 
  * </ol>
  * 
  * @author Franz-Josef Elmer
@@ -103,8 +109,7 @@ public class TabFileLoader<T>
             IOUtils.closeQuietly(reader);
         }
     }
-    
-    
+
     List<T> load(Reader reader)
     {
         List<T> result = new ArrayList<T>();
@@ -128,18 +133,19 @@ public class TabFileLoader<T>
         }
         @SuppressWarnings("null")
         final String headerLine = previousLineHasColumnHeaders ? previousLine.getText().substring(1) : line.getText();
-        
+
         final DefaultParser<T> parser = new DefaultParser<T>();
         final String[] tokens = StringUtils.split(headerLine, "\t");
+        final long headerLength = tokens.length;
         notUnique(tokens);
         final IAliasPropertyMapper propertyMapper = new HeaderFilePropertyMapper(tokens);
         parser.setObjectFactory(factory.createFactory(propertyMapper));
         ILineFilter filter = AlwaysAcceptLineFilter.INSTANCE;
         if (previousLineHasColumnHeaders)
         {
-            result.addAll(parser.parse(Arrays.asList(line).iterator(), filter));
+            result.addAll(parser.parse(Arrays.asList(line).iterator(), filter, headerLength));
         }
-        result.addAll(parser.parse(lineIterator, filter));
+        result.addAll(parser.parse(lineIterator, filter, headerLength));
         return result;
     }
 
@@ -149,6 +155,7 @@ public class TabFileLoader<T>
         Iterator<Line> iterator = new Iterator<Line>()
             {
                 private int lineNumber;
+
                 public void remove()
                 {
                     lineIterator.remove();

common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionParserTest.java

@@ -16,7 +16,9 @@
 
 package ch.systemsx.cisd.common.db;
 
-import static org.testng.AssertJUnit.*;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
 
 import java.io.File;
 import java.util.Arrays;
@@ -34,8 +36,9 @@ import ch.systemsx.cisd.common.logging.LogMonitoringAppender;
 import ch.systemsx.cisd.common.utilities.FileUtilities;
 
 /**
- * Test cases for the @{link DBREstrictionParser}.
+ * Test cases for the
  * 
+ * @{link DBREstrictionParser}.
  * @author Bernd Rinn
  */
 public class DBRestrictionParserTest
@@ -65,9 +68,8 @@ public class DBRestrictionParserTest
     {
         String invalidDomainStatement = "create domain bla for varchar(0)";
         final List<String> domainScript =
-                Arrays.asList("create table sometable", "create domain user_id as varchar(15)",
-                        invalidDomainStatement, "create domain code as varchar(8)",
-                        "create domain description_80 as varchar(81)");
+                Arrays.asList("create table sometable", "create domain user_id as varchar(15)", invalidDomainStatement,
+                        "create domain code as varchar(8)", "create domain description_80 as varchar(81)");
         final LogMonitoringAppender appender =
                 LogMonitoringAppender.addAppender(LogCategory.OPERATION, "line \"" + invalidDomainStatement
                         + "\" starts like a domain definition, but key word 'AS' is missing.");
@@ -89,9 +91,8 @@ public class DBRestrictionParserTest
     @Test
     public void testDefaultKeywordInDomain()
     {
-        final List<String> domainScript =
-            Arrays.asList("create domain vc22 as varchar(22) default 'nothing special'");
-        
+        final List<String> domainScript = Arrays.asList("create domain vc22 as varchar(22) default 'nothing special'");
+
         final LogMonitoringAppender appender = LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
         try
         {
@@ -104,13 +105,12 @@ public class DBRestrictionParserTest
             LogMonitoringAppender.removeAppender(appender);
         }
     }
-    
+
     @Test
     public void testDoublePrecisionInDomain()
     {
-        final List<String> domainScript =
-            Arrays.asList("create domain dp as double precision");
-        
+        final List<String> domainScript = Arrays.asList("create domain dp as double precision");
+
         final LogMonitoringAppender appender = LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
         try
         {
@@ -122,13 +122,12 @@ public class DBRestrictionParserTest
             LogMonitoringAppender.removeAppender(appender);
         }
     }
-    
+
     @Test
     public void testDoublePrecisionAndDefaultInDomain()
     {
-        final List<String> domainScript =
-            Arrays.asList("create domain dp as double precision default 3.14159");
-        
+        final List<String> domainScript = Arrays.asList("create domain dp as double precision default 3.14159");
+
         final LogMonitoringAppender appender = LogMonitoringAppender.addAppender(LogCategory.OPERATION, "ill-formed");
         try
         {
@@ -140,7 +139,7 @@ public class DBRestrictionParserTest
             LogMonitoringAppender.removeAppender(appender);
         }
     }
-    
+
     @Test
     public void testColumnLengths()
     {

common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java

@@ -31,17 +31,19 @@ import org.testng.annotations.Test;
  */
 public final class DefaultParserTest
 {
-    private final static List<String> text 
-            = Arrays.asList("", "# This is a comment", "firstName\tlastName\taddress\tcity",
-                            "Charles\tDarwin\tHumboldt Ave. 1865\t4242 Somewhere",
-                            "Albert\tEinstein\tNewton Road 1905\t4711 Princton");
+    private final static List<String> text =
+            Arrays.asList("", "# This is a comment", "firstName\tlastName\taddress\tcity",
+                    "Charles\tDarwin\tHumboldt Ave. 1865\t4242 Somewhere",
+                    "Albert\tEinstein\tNewton Road 1905\t4711 Princton");
+
+    private final static long HEADER_LENGTH = 4;
 
     @Test
     public final void testParseWithoutFactoryAndHeader()
     {
         final IParser<String[]> parser = new DefaultParser<String[]>();
         parser.setObjectFactory(IParserObjectFactory.STRING_ARRAY_OBJECT_FACTORY);
-        final List<String[]> result = parser.parse(createLineIterator(), new HeaderLineFilter());
+        final List<String[]> result = parser.parse(createLineIterator(), new HeaderLineFilter(), HEADER_LENGTH);
         assertEquals(3, result.size());
         assertEquals(result.get(0)[0], "firstName");
         assertEquals(result.get(1)[1], "Darwin");
@@ -54,7 +56,7 @@ public final class DefaultParserTest
     {
         final IParser<String[]> parser = new DefaultParser<String[]>();
         parser.setObjectFactory(IParserObjectFactory.STRING_ARRAY_OBJECT_FACTORY);
-        final List<String[]> result = parser.parse(createLineIterator(), new HeaderLineFilter(3));
+        final List<String[]> result = parser.parse(createLineIterator(), new HeaderLineFilter(3), HEADER_LENGTH);
         assertEquals(2, result.size());
         assertEquals(result.get(0)[0], "Charles");
         assertEquals(result.get(1)[1], "Einstein");
@@ -77,31 +79,33 @@ public final class DefaultParserTest
         parser.setObjectFactory(IParserObjectFactory.STRING_ARRAY_OBJECT_FACTORY);
         try
         {
-            parser.parse(createLineIterator(), new HeaderLineFilter(2));
+            parser.parse(createLineIterator(), new HeaderLineFilter(2), HEADER_LENGTH);
         } catch (ParsingException ex)
         {
-            assertEquals(
-                    "Creating an object with following tokens '[firstName, lastName, address, city]' failed.",
-                    ex.getMessage());
+            assertEquals("Creating an object with following tokens '[firstName, lastName, address, city]' failed.", ex
+                    .getMessage());
             assertEquals(3, ex.getLineNumber());
         }
     }
-    
+
     private Iterator<Line> createLineIterator()
     {
         return new Iterator<Line>()
             {
                 private Iterator<String> iterator = text.iterator();
+
                 private int lineNumber;
+
                 public void remove()
                 {
                     throw new UnsupportedOperationException();
                 }
+
                 public Line next()
                 {
                     return new Line(++lineNumber, iterator.next());
                 }
-        
+
                 public boolean hasNext()
                 {
                     return iterator.hasNext();