diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
index 745e96e1ea76891bceda3894230d4bc0bc3b5a38..d626cd91230e4cb5e52f0f2905d1dd34ff67a652 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransaction.java
@@ -80,12 +80,10 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchSubCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
- * Imaging-specific transaction. Handles image datasets in a special way, other datasets are
- * registered using a standard procedure.
+ * Imaging-specific transaction. Handles image datasets in a special way, other datasets are registered using a standard procedure.
* <p>
- * Note that this transaction is not parametrized by a concrete {@link DataSetInformation} subclass.
- * It has to deal with {@link ImageDataSetInformation}, {@link FeatureVectorDataSetInformation} and
- * {@link DataSetInformation} at the same time.
+ * Note that this transaction is not parametrized by a concrete {@link DataSetInformation} subclass. It has to deal with
+ * {@link ImageDataSetInformation}, {@link FeatureVectorDataSetInformation} and {@link DataSetInformation} at the same time.
*/
@SuppressWarnings("rawtypes")
public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTransaction
@@ -143,7 +141,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
incomingFolderWithImages, imageDatasetFactory, imageCache);
return createNewImageDataSet(details);
}
-
+
@SuppressWarnings("unchecked")
public IImageDataSet createNewImageDataSetFromDataSet(SimpleImageDataConfig imageDataSet, IImageDataSet dataSet)
{
@@ -160,7 +158,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
originalDataSet.getRegistrationDetails().getDataSetInformation().addSecondaryDataSetInformation(secondaryDataSet);
return createImageDataSet(details, originalDataSet);
}
-
+
public IDataSet createNewOverviewImageDataSet(SimpleImageDataConfig imageDataSet,
File incomingFolderWithImages)
{
@@ -302,12 +300,10 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
}
/**
- * Creates container dataset which contains dataset with original images (created on the fly).
- * If thumbnails are required they are generated and moved to a thumbnail dataset which becomes
- * a part of the container as well.
+ * Creates container dataset which contains dataset with original images (created on the fly). If thumbnails are required they are generated and
+ * moved to a thumbnail dataset which becomes a part of the container as well.
* <p>
- * The original images dataset is special - it contains description of what should be saved in
- * imaging database by the storage processor.
+ * The original images dataset is special - it contains description of what should be saved in imaging database by the storage processor.
*
* @return container dataset.
*/
@@ -361,8 +357,8 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
}
containedDataSetCodes.add(mainDataset.getDataSetCode());
-
- createRepresentativeThumbnailByImageGenerationAlgorithm(imageDataSetInformation, containedDataSetCodes,
+
+ createRepresentativeThumbnailByImageGenerationAlgorithm(imageDataSetInformation, containedDataSetCodes,
thumbnailDatasets);
for (IDataSet thumbnailDataset : thumbnailDatasets)
@@ -376,7 +372,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
containerDataset.setThumbnailDatasets(thumbnailDatasets);
String containerDataSetCode = containerDataset.getDataSetCode();
imageDataSetInformation.setContainerDatasetPermId(containerDataSetCode);
-
+
return containerDataset;
}
@@ -389,7 +385,8 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
return;
}
List<BufferedImage> images = algorithm.generateImages(imageDataSetInformation, imageCache);
- if (images.size() > 0) {
+ if (images.size() > 0)
+ {
IDataSet representative = createNewDataSet(algorithm.getDataSetTypeCode());
for (int i = 0; i < images.size(); i++)
{
@@ -398,10 +395,10 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
File f = new File(imageFile);
try
{
- ImageIO.write(imageData, "png", f);
+ ImageIO.write(imageData, "png", f);
} catch (IOException e)
{
- throw new EnvironmentFailureException("Can not save representative thumbnail to file '"
+ throw new EnvironmentFailureException("Can not save representative thumbnail to file '"
+ f + "': " + e, e);
}
}
@@ -781,7 +778,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
}
@SuppressWarnings(
- { "cast", "unchecked" })
+ { "cast", "unchecked" })
@Override
public IDataSet createNewDataSet(DataSetRegistrationDetails registrationDetails)
{
@@ -802,8 +799,8 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
}
/**
- * If we are dealing with the image dataset container then the move operation is delegated to
- * the original dataset. Otherwise a default implementation is used.
+ * If we are dealing with the image dataset container then the move operation is delegated to the original dataset. Otherwise a default
+ * implementation is used.
*/
@Override
public String moveFile(String src, IDataSet dst)
@@ -812,8 +809,8 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
}
/**
- * If we are dealing with the image dataset container then the move operation is delegated to
- * the original dataset. Otherwise a default implementation is used.
+ * If we are dealing with the image dataset container then the move operation is delegated to the original dataset. Otherwise a default
+ * implementation is used.
*/
@Override
public String moveFile(String src, IDataSet dst, String dstInDataset)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
index 032a0ee9e378608e9bb4c8d046747cfb0b5edd45..0d1d3208de8d135c8758928fed250cc5e2840bd4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
@@ -24,6 +24,7 @@ import net.lemnik.eodsql.DynamicTransactionQuery;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationContext;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDSSRegistrationLogger;
import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetUpdatable;
import ch.systemsx.cisd.etlserver.registrator.api.v2.IExperiment;
@@ -69,7 +70,7 @@ public class ImagingDataSetRegistrationTransactionV2Delegate implements
private final ImagingDataSetRegistrationTransaction transaction;
@Override
- public IImageDataSet createNewImageDataSetFromDataSet(SimpleImageDataConfig imageDataSet,IImageDataSet dataSet)
+ public IImageDataSet createNewImageDataSetFromDataSet(SimpleImageDataConfig imageDataSet, IImageDataSet dataSet)
{
return transaction.createNewImageDataSetFromDataSet(imageDataSet, dataSet);
}
@@ -474,4 +475,10 @@ public class ImagingDataSetRegistrationTransactionV2Delegate implements
return transaction.createNewLink(dst, dstInDataset, linkName, linkTarget);
}
+ @Override
+ public IDSSRegistrationLogger getLogger()
+ {
+ return transaction.getLogger();
+ }
+
}