From 65a6ac97631d6f3043ea8becc6384a6a85e633b4 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 15 Mar 2011 20:43:38 +0000
Subject: [PATCH] LMS-2069, LMS-2085 better error logging, small hcs dropbox
API improvement
SVN: 20346
---
.../dss/etl/AbstractImageStorageProcessor.java | 4 +++-
.../dss/etl/dto/api/v1/SimpleImageDataConfig.java | 12 ++++++++++++
.../dss/etl/jython/JythonPlateDataSetHandler.java | 4 ++--
.../etl/jython/SimpleImageDataSetRegistrator.java | 9 +++++++++
4 files changed, 26 insertions(+), 3 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
index 6a4e1f677ca..61124ba7b4c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java
@@ -252,6 +252,7 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
AbstractStorageProcessorTransaction
{
private IImagingQueryDAO dbTransaction;
+
// used when HDF5 is used to store original data
private boolean shouldDeleteOriginalDataOnCommit;
@@ -618,7 +619,8 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
if (imageDataSetInfo.isValid() == false)
{
throw ConfigurationFailureException
- .fromTemplate("Invalid image dataset info object, check if your jython script fills all the fields: "
+ .fromTemplate("Invalid image dataset info object, check if your jython script fills all the required fields. "
+ + "Or maybe the recognized files extensions is set incorrectly? Dataset: "
+ imageDataSetInfo);
}
Geometry tileGeometry =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
index dd4e9816b75..221dd019ded 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
@@ -101,6 +101,8 @@ abstract public class SimpleImageDataConfig
private boolean generateThumbnailsWithImageMagic = false;
+ private boolean generateThumbnailsInHighQuality = false;
+
private double allowedMachineLoadDuringThumbnailsGeneration = 1.0;
private boolean storeChannelsOnExperimentLevel = false;
@@ -125,6 +127,7 @@ abstract public class SimpleImageDataConfig
thumbnailsStorageFormat.setMaxWidth(getMaxThumbnailWidthAndHeight());
thumbnailsStorageFormat.setMaxHeight(getMaxThumbnailWidthAndHeight());
thumbnailsStorageFormat.setGenerateWithImageMagic(generateThumbnailsWithImageMagic);
+ thumbnailsStorageFormat.setHighQuality(generateThumbnailsInHighQuality);
imageStorageConfiguraton.setThumbnailsStorageFormat(thumbnailsStorageFormat);
}
return imageStorageConfiguraton;
@@ -225,6 +228,15 @@ abstract public class SimpleImageDataConfig
this.generateThumbnailsWithImageMagic = generateWithImageMagic;
}
+ /**
+ * if true and thumbnails generation is switched on, thumbnails will be generated with high
+ * quality.
+ */
+ public void setGenerateHighQualityThumbnails(boolean highQualityThumbnails)
+ {
+ this.generateThumbnailsInHighQuality = highQualityThumbnails;
+ }
+
/** Should all dataset in one experiment use the same channels? By default set to false. */
public void setStoreChannelsOnExperimentLevel(boolean storeChannelsOnExperimentLevel)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
index 3f70572ad39..9caf65bc9e3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
@@ -86,7 +86,7 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
}
/** a simple method to register the described image dataset in a separate transaction */
- public void registerImageDataset(SimpleImageDataConfig imageDataSet,
+ public boolean registerImageDataset(SimpleImageDataConfig imageDataSet,
File incomingDatasetFolder,
DataSetRegistrationService<ImageDataSetInformation> service)
{
@@ -96,7 +96,7 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
service.transaction(incomingDatasetFolder, imageDatasetFactory);
IDataSet newDataset = transaction.createNewDataSet(imageDatasetDetails);
transaction.moveFile(incomingDatasetFolder.getPath(), newDataset);
- transaction.commit();
+ return transaction.commit();
}
// ----
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
index 1fb9d628ff5..ca07053cf93 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
@@ -22,6 +22,8 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileOperations;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
@@ -117,6 +119,13 @@ public class SimpleImageDataSetRegistrator
imageTokens.ensureValid();
imageTokensList.add(new ImageTokensWithPath(imageTokens, imageRelativePath));
}
+ if (imageTokensList.size() == 0)
+ {
+ throw UserFailureException.fromTemplate(
+ "Incoming directory '%s' contains no images with extensions %s!",
+ incomingDirectory.getPath(),
+ CollectionUtils.abbreviate(imageDataSet.getRecognizedImageExtensions(), -1));
+ }
return imageTokensList;
}
--
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