diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogAnnotation.java b/common/source/java/ch/systemsx/cisd/common/logging/LogAnnotation.java
index 4e3b46f6c9d5813dc0066fab5801382fda94c027..203a32617df22238002fd2c8829e95e69b535ef0 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogAnnotation.java
+++ b/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;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogCategory.java b/common/source/java/ch/systemsx/cisd/common/logging/LogCategory.java
index e2377645bc7aaddc20fb00c9a8fd1600c5f9c012..23ef465420022f8784c114641b932a8c5185fc1c 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogCategory.java
+++ b/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;
+ }
}
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java b/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java
index 5bf4be148d38f594b97dd4a06d5d2e3c1d8d3225..ad2c37b98eaf440dfec184ec2ce009903427a238 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogFactory.java
+++ b/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));
+ }
+
}
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogInvocationHandler.java b/common/source/java/ch/systemsx/cisd/common/logging/LogInvocationHandler.java
index bae7d5c69d3b27699632d14bf085b523a247039a..d228981dc0262f91c895e89f5e3663043b1db4e5 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogInvocationHandler.java
+++ b/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
diff --git a/common/source/java/ch/systemsx/cisd/common/logging/LogLevel.java b/common/source/java/ch/systemsx/cisd/common/logging/LogLevel.java
index 4062e4ddd25aec4cef5458fd40d63e82e292af6f..efc86d649282c22ecca919851f5ec4d97c6cbdc4 100644
--- a/common/source/java/ch/systemsx/cisd/common/logging/LogLevel.java
+++ b/common/source/java/ch/systemsx/cisd/common/logging/LogLevel.java
@@ -1,11 +1,11 @@
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
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
index 65f2fd2c36f7762870974678d06ab23c14345f45..d0c99bbe4002eded519e2af9ce837d94cf2d6899 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
+++ b/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)
{
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
index c83eb104c156ff817f74cd2781a6dc5a329cbdb1..f3c5df833d39c58878710141d2348ed4b1e67788 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
+++ b/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>.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
index fcb988a22ff4a4e3d8450a7c543aa910197710ba..2622ce2162f360f17cd77cd1ead484805b3452be 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
+++ b/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();
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionParserTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionParserTest.java
index 5ae53f7963c0b1af4fcf28fcbed392d2a63a545a..721b5b75ce02209a732513e9a2a82e7cb7f880fc 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/db/DBRestrictionParserTest.java
+++ b/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()
{
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
index a8f0c1f8632232bcf75496faf03c9214bfd44f6c..ac0d353cc24cbe74c13092573652086e231df0b0 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
+++ b/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();