diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
index 33e1a0d7624bfe9779ad0144fdaf6034cfd22ad3..ca719c975129b06163f8c384ccf1ae8470c400a0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
@@ -39,6 +39,7 @@ public class HCSImageDatasetLoaderFactory
return factories;
}
+ /** the loader has to be closed when it is not used any more to free database resources! */
public static final IHCSImageDatasetLoader create(File datasetRootDir, String datasetCode)
{
return createImageDBLoader(datasetRootDir, datasetCode);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index 41330166b7f07a28f3882895467332ca01b1e303..9cff9157c5c85e6ed6297a5665de6b33c69197c4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -162,6 +162,12 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
return imagingDbDao;
}
+ @Override
+ protected void finalize()
+ {
+ DssScreeningUtils.closeQuietly(imagingDbDao);
+ }
+
private IEncapsulatedOpenBISService getService()
{
synchronized (this)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
index e23282d2e1b8ba738177f1fc18fe4b4542c1d41f..2f9d7a6a1fa8476ecda60e64a43163f6336c0338 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java
@@ -52,28 +52,32 @@ public class ImageChannelsUtils
{
IHCSImageDatasetLoader imageAccessor =
HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
- List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
-
- Size thumbnailSizeOrNull = params.tryGetThumbnailSize();
- if (params.isMergeAllChannels())
+ try
{
- for (String chosenChannel : imageAccessor.getImageParameters().getChannelsCodes())
+ List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
+
+ Size thumbnailSizeOrNull = params.tryGetThumbnailSize();
+ if (params.isMergeAllChannels())
+ {
+ for (String chosenChannel : imageAccessor.getImageParameters().getChannelsCodes())
+ {
+ AbsoluteImageReference image =
+ getImage(imageAccessor, params.getChannelStack(), chosenChannel,
+ thumbnailSizeOrNull);
+ images.add(image);
+ }
+ } else
{
AbsoluteImageReference image =
- getImage(imageAccessor, params.getChannelStack(), chosenChannel,
+ getImage(imageAccessor, params.getChannelStack(), params.getChannel(),
thumbnailSizeOrNull);
images.add(image);
}
- } else
+ return images;
+ } finally
{
- AbsoluteImageReference image =
- getImage(imageAccessor, params.getChannelStack(), params.getChannel(),
- thumbnailSizeOrNull);
- images.add(image);
+ imageAccessor.close();
}
- imageAccessor.close();
-
- return images;
}
/**
@@ -251,8 +255,8 @@ public class ImageChannelsUtils
Size thumbnailSizeOrNull)
{
AbsoluteImageReference image =
- imageAccessor
- .tryGetImage(chosenChannelCode, channelStackReference, thumbnailSizeOrNull);
+ imageAccessor.tryGetImage(chosenChannelCode, channelStackReference,
+ thumbnailSizeOrNull);
if (image != null)
{
return image;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
index cb9dc5c0e3de0087d6b01a3fac5acba3d7ff2725..07030a7805832ab8ee1629d948ba617cf82baf3a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
@@ -123,13 +123,22 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
private IImagingQueryDAO getDAO()
{
- if (dao == null)
+ synchronized (this)
{
- dao = DssScreeningUtils.createQuery();
+ if (dao == null)
+ {
+ dao = DssScreeningUtils.createQuery();
+ }
}
return dao;
}
+ @Override
+ protected void finalize()
+ {
+ DssScreeningUtils.closeQuietly(dao);
+ }
+
private IEncapsulatedOpenBISService getService()
{
if (service == null)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index df09fe0eb62a55113564d52d1c75df039679e42c..774415062c0f593c47fd89c22a14f5eadc02c48f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -81,6 +81,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
*/
public static final int MINOR_VERSION = 2;
+ // this dao will hold one connection to the database
private IImagingQueryDAO dao;
public DssServiceRpcScreening(String storeRootDir)
@@ -168,13 +169,18 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
{
IHCSImageDatasetLoader imageAccessor =
HCSImageDatasetLoaderFactory.create(datasetRoot, dataset.getDatasetCode());
- IContent imageFile = getAnyImagePath(imageAccessor, dataset);
- PlateImageParameters params = imageAccessor.getImageParameters();
- imageAccessor.close();
- int tilesNumber = params.getTileColsNum() * params.getTileRowsNum();
- BufferedImage image = ImageUtil.loadImage(imageFile.getInputStream());
- return new ImageDatasetMetadata(dataset, params.getChannelsCodes(), params
- .getChannelsLabels(), tilesNumber, image.getWidth(), image.getHeight());
+ try
+ {
+ IContent imageFile = getAnyImagePath(imageAccessor, dataset);
+ PlateImageParameters params = imageAccessor.getImageParameters();
+ int tilesNumber = params.getTileColsNum() * params.getTileRowsNum();
+ BufferedImage image = ImageUtil.loadImage(imageFile.getInputStream());
+ return new ImageDatasetMetadata(dataset, params.getChannelsCodes(), params
+ .getChannelsLabels(), tilesNumber, image.getWidth(), image.getHeight());
+ } finally
+ {
+ imageAccessor.close();
+ }
}
private static IContent getAnyImagePath(IHCSImageDatasetLoader imageAccessor,
@@ -468,13 +474,22 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private IImagingQueryDAO getDAO()
{
- if (dao == null)
+ synchronized (this)
{
- dao = DssScreeningUtils.createQuery();
+ if (dao == null)
+ {
+ dao = DssScreeningUtils.createQuery();
+ }
}
return dao;
}
+ @Override
+ protected void finalize()
+ {
+ DssScreeningUtils.closeQuietly(dao);
+ }
+
public int getMajorVersion()
{
return MAJOR_VERSION;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
index bfdd0ed0fc561f37f8ab0a832332891343a06ae1..16790a0860e352da4d3643ed546bdf198632358a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/shared/DssScreeningUtils.java
@@ -26,7 +26,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImag
/**
* Utility methods for DSS.
- *
+ *
* @author Franz-Josef Elmer
*/
public class DssScreeningUtils
@@ -34,6 +34,10 @@ public class DssScreeningUtils
/**
* Creates a DAO based on imaging database specified in DSS service.properties by data source
* {@link ScreeningConstants#IMAGING_DATA_SOURCE}.
+ * <p>
+ * Query has to be closed as soon as it is not used, otherwise we will run out of available
+ * connections quickly!
+ * </p>
*/
public static IImagingQueryDAO createQuery()
{
@@ -43,4 +47,18 @@ public class DssScreeningUtils
return QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
}
+ /** Closes the query if it is not null, ignores the exceptions */
+ public static void closeQuietly(IImagingQueryDAO queryOrNull)
+ {
+ if (queryOrNull != null)
+ {
+ try
+ {
+ queryOrNull.close();
+ } catch (RuntimeException ex)
+ {
+ }
+ }
+ }
+
}