fix: - Integration tests.

SVN: 7547

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

@@ -39,6 +39,8 @@ public final class LogInvocationHandler implements InvocationHandler
 
     private final Class<?> classUsedToNameLogger;
 
+    private final boolean onlyIfAnnotated;
+
     /**
      * Creates a new instance.
      * 
@@ -49,11 +51,28 @@ public final class LogInvocationHandler implements InvocationHandler
      */
     public LogInvocationHandler(final Object object, final String name, final Level logLevel,
             final Class<?> classUsedToNameLogger)
+    {
+        this(object, name, logLevel, classUsedToNameLogger, false);
+    }
+
+    /**
+     * 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.
+     * @param classUsedToNameLogger Class used to specify the name of the logger.
+     * @param onlyIfAnnotated whether the log should be activated only if method is annotated with
+     *            {@link LogAnnotation}.
+     */
+    public LogInvocationHandler(final Object object, final String name, final Level logLevel,
+            final Class<?> classUsedToNameLogger, final boolean onlyIfAnnotated)
     {
         this.object = object;
         this.name = name;
         this.defaultLogLevel = logLevel;
         this.classUsedToNameLogger = classUsedToNameLogger;
+        this.onlyIfAnnotated = onlyIfAnnotated;
     }
 
     public Object invoke(final Object proxy, final Method method, final Object[] args)
@@ -78,57 +97,65 @@ public final class LogInvocationHandler implements InvocationHandler
             throw t;
         } finally
         {
-            final Level logLevel = getLogLevel(method);
-            final Logger logger = createLogger(method);
-            if (throwable != null || logger.isEnabledFor(logLevel))
+            final LogAnnotation logAnnotationOrNull = tryGetAnnotation(method);
+            if (onlyIfAnnotated == false || logAnnotationOrNull != null)
             {
-                final StringBuilder builder =
-                        new StringBuilder(throwable == null ? "Successful" : "Failed");
-                builder.append(" invocation of ");
-                builder.append(name).append('.').append(method.getName()).append('(');
-                if (args != null)
+                final Level logLevel = getLogLevel(method, logAnnotationOrNull);
+                final Logger logger = createLogger(method, logAnnotationOrNull);
+                if (throwable != null || logger.isEnabledFor(logLevel))
                 {
-                    for (int i = 0; i < args.length; i++)
+                    final StringBuilder builder =
+                            new StringBuilder(throwable == null ? "Successful" : "Failed");
+                    builder.append(" invocation of ");
+                    builder.append(name).append('.').append(method.getName()).append('(');
+                    if (args != null)
                     {
-                        builder.append(args[i]);
-                        if (i < args.length - 1)
+                        for (int i = 0; i < args.length; i++)
                         {
-                            builder.append(", ");
+                            builder.append(args[i]);
+                            if (i < args.length - 1)
+                            {
+                                builder.append(", ");
+                            }
                         }
                     }
-                }
-                builder.append(") took ").append(System.currentTimeMillis() - time).append(" msec");
-                if (throwable == null)
-                {
-                    logger.log(logLevel, builder.toString());
-                } else
-                {
-                    logger.error(builder.toString(), throwable);
+                    builder.append(") took ").append(System.currentTimeMillis() - time).append(
+                            " msec");
+                    if (throwable == null)
+                    {
+                        logger.log(logLevel, builder.toString());
+                    } else
+                    {
+                        logger.error(builder.toString(), throwable);
+                    }
                 }
             }
         }
     }
 
-    private final Level getLogLevel(final Method method)
+    private final LogAnnotation tryGetAnnotation(final Method method)
+    {
+        return method.getAnnotation(LogAnnotation.class);
+    }
+
+    private final Level getLogLevel(final Method method, final LogAnnotation annotationOrNull)
     {
-        final LogAnnotation annotation = method.getAnnotation(LogAnnotation.class);
-        if (annotation == null)
+        if (annotationOrNull == null)
         {
             return Level.DEBUG;
-        } else if (annotation.logLevel().equals(LogLevel.UNDEFINED))
+        } else if (annotationOrNull.logLevel().equals(LogLevel.UNDEFINED))
         {
             return defaultLogLevel;
         } else
         {
-            return Log4jSimpleLogger.toLog4jPriority(annotation.logLevel());
+            return Log4jSimpleLogger.toLog4jPriority(annotationOrNull.logLevel());
         }
     }
 
-    private final Logger createLogger(final Method method)
+    private final Logger createLogger(final Method method, final LogAnnotation annotationOrNull)
     {
-        final LogAnnotation annotation = method.getAnnotation(LogAnnotation.class);
         final LogCategory logCategory =
-                (annotation == null) ? LogCategory.OPERATION : annotation.logCategory();
+                (annotationOrNull == null) ? LogCategory.OPERATION : annotationOrNull.logCategory();
         return LogFactory.getLogger(logCategory, classUsedToNameLogger);
     }
 }
\ No newline at end of file

integration-tests/run.sh

@@ -597,7 +597,7 @@ function assert_correct_content_of_processing_dir {
     assert_same_content $TEST_DATA/3VCP1 $data_set
     assert_same_content $TEMPLATE/openBIS-client/testdata/register-experiments/processing-parameters.txt \
                         $DATA/processing-dir/processing-parameters-from-openbis
-    local bds_container=$DATA/main-store/Instance_integration-test/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE/Sample_3VCP1/
+    local bds_container=$DATA/main-store/Instance_CISD/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE/Sample_3VCP1/
     bds_container=$bds_container`ls -1 $bds_container | head -1`
     assert_dir_exists $bds_container
     local data_set2=$bds_container/data/original/microX_200801011213_3VCP1
@@ -609,7 +609,7 @@ function assert_correct_content_of_plate_3VCP1_in_store {
     local cell_plate=3VCP1
     echo ==== assert correct content of plate 3VCP1 in store ====
     
-    local main_dir=$DATA/main-store/Instance_integration-test/Group_CISD/Project_NEMO/Experiment_EXP1
+    local main_dir=$DATA/main-store/Instance_CISD/Group_CISD/Project_NEMO/Experiment_EXP1
     local raw_data_dir=$main_dir/ObservableType_HCS_IMAGE/Sample_3VCP1/
     assert_dir_exists $raw_data_dir
     # Picks up the first directory found
@@ -652,7 +652,7 @@ function assert_correct_content_of_plate_3VCP1_in_store {
     assert_equals_as_in_file microX $metadata_dir/data_set/producer_code
     assert_equals_as_in_file 3VCP1 $metadata_dir/sample/code
     assert_equals_as_in_file CELL_PLATE $metadata_dir/sample/type_code
-    assert_equals_as_in_file integration-test $metadata_dir/experiment_identifier/instance_code
+    assert_equals_as_in_file CISD $metadata_dir/experiment_identifier/instance_code
     assert_equals_as_in_file CISD $metadata_dir/experiment_identifier/group_code
     assert_equals_as_in_file NEMO $metadata_dir/experiment_identifier/project_code
     assert_equals_as_in_file EXP1 $metadata_dir/experiment_identifier/experiment_code
@@ -692,14 +692,14 @@ function assert_correct_content_of_invalid_plate_in_store {
     local data_set=$error_dir/microX_200801011213_$cell_plate
     assert_same_content $TEST_DATA/$cell_plate $data_set
     assert_file_exists $data_set.exception
-    assert_dir_empty $DATA/main-store/Instance_integration-test/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE/Sample_$cell_plate
+    assert_dir_empty $DATA/main-store/Instance_CISD/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE/Sample_$cell_plate
 }
     
 function assert_correct_content_of_image_analysis_data {
     local cell_plate=$1
     
     echo ====  check image analysis data for cell plate $cell_plate ====
-    local img_analysis=$DATA/main-store/Instance_integration-test/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE_ANALYSIS_DATA/Sample_$cell_plate/
+    local img_analysis=$DATA/main-store/Instance_CISD/Group_CISD/Project_NEMO/Experiment_EXP1/ObservableType_HCS_IMAGE_ANALYSIS_DATA/Sample_$cell_plate/
     assert_dir_exists $img_analysis
     # Picks up the first directory found
     img_analysis=$img_analysis`ls -1 $img_analysis | head -1`

integration-tests/templates/etlserver-all/etc/service.properties

 # Code of openBIS instance
-instance-code = integration-test
+instance-code = CISD
 
 # The root directory of the data store
 storeroot-dir = ../data/main-store
@@ -59,6 +59,7 @@ inputs=raw-data,image-analysis
 # ---------------------------------------------------------------------------
 # The directory to watch for incoming data.
 raw-data.incoming-dir = ../data/out-raw
+raw-data.group-code = CISD
 
 # The extractor plugin class to use for data set information extraction
 raw-data.data-set-info-extractor = ch.systemsx.cisd.etlserver.threev.DataSetInfoExtractorForDataAcquisition
@@ -94,6 +95,7 @@ raw-data.storage-processor.file-extractor = ch.systemsx.cisd.etlserver.imsb.HCSI
 # image-analysis thread
 # ---------------------------------------------------------------------------
 image-analysis.incoming-dir = ../data/out-analysis
+image-analysis.group-code = CISD
 
 image-analysis.data-set-info-extractor = ch.systemsx.cisd.etlserver.threev.DataSetInfoExtractorForImageAnalysis
 # Separator used to extract the barcode in the data set file name