diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
index e97c29ad8d6c704567d47a25d6c8e19d927a5d3f..dabeb5ad7a955faaf1b76fd766a2834f15ed65bb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
@@ -57,7 +57,6 @@ import ch.systemsx.cisd.etlserver.AbstractStorageProcessor;
import ch.systemsx.cisd.etlserver.IHCSImageFileAccepter;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.PlateDimension;
-import ch.systemsx.cisd.etlserver.PlateDimensionParser;
import ch.systemsx.cisd.hdf5.HDF5FactoryProvider;
import ch.systemsx.cisd.hdf5.IHDF5Writer;
import ch.systemsx.cisd.openbis.dss.Constants;
@@ -67,7 +66,6 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
/**
@@ -78,7 +76,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
public final class PlateStorageProcessor extends AbstractStorageProcessor
{
-
/** The directory where <i>original</i> data could be found. */
private static final String DIR_ORIGINAL = "original";
@@ -90,13 +87,15 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
// tiles geometry, e.g. 3x4 if the well is divided into 12 tiles (3 rows, 4 columns)
private static final String SPOT_GEOMETRY_PROPERTY = "well_geometry";
-
+
private static final String THUMBNAIL_MAX_WIDTH_PROPERTY = "thumbnail-max-width";
+
private static final int DEFAULT_THUMBNAIL_MAX_WIDTH = 200;
private static final String THUMBNAIL_MAX_HEIGHT_PROPERTY = "thumbnail-max-height";
+
private static final int DEFAULT_THUMBNAIL_MAX_HEIGHT = 160;
-
+
private static final String FILE_EXTRACTOR_PROPERTY = "file-extractor";
// a class of the old-style image extractor
@@ -114,9 +113,9 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private final List<String> channelNames;
private final int thumbnailMaxWidth;
-
+
private final int thumbnailMaxHeight;
-
+
// one of the extractors is always null and one not null
private final IHCSImageFileExtractor imageFileExtractor;
@@ -185,19 +184,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private ScreeningContainerDatasetInfo createScreeningDatasetInfo(Experiment experiment,
DataSetInformation dataSetInformation)
{
- ScreeningContainerDatasetInfo info = new ScreeningContainerDatasetInfo();
- info.setExperimentPermId(experiment.getPermId());
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
- dataSetInformation.tryToGetSample();
- assert sample != null : "no sample connected to a dataset";
- info.setContainerPermId(sample.getPermId());
- info.setDatasetPermId(dataSetInformation.getDataSetCode());
-
- PlateDimension plateGeometry = getPlateGeometry(dataSetInformation);
- int plateRows = plateGeometry.getRowsNum();
- int plateCols = plateGeometry.getColsNum();
- info.setContainerRows(plateRows);
- info.setContainerColumns(plateCols);
+ ScreeningContainerDatasetInfo info =
+ ScreeningContainerDatasetInfo.createScreeningDatasetInfo(dataSetInformation);
info.setTileRows(spotGeometry.getRows());
info.setTileColumns(spotGeometry.getColumns());
@@ -207,16 +195,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private PlateDimension getPlateGeometry(final DataSetInformation dataSetInformation)
{
- final IEntityProperty[] sampleProperties = dataSetInformation.getProperties();
- final PlateDimension plateDimension =
- PlateDimensionParser.tryToGetPlateDimension(sampleProperties);
- if (plateDimension == null)
- {
- throw new EnvironmentFailureException(
- "Missing plate geometry for the plate registered for sample identifier '"
- + dataSetInformation.getSampleIdentifier() + "'.");
- }
- return plateDimension;
+ return ScreeningContainerDatasetInfo.getPlateGeometry(dataSetInformation);
}
// ---------------------------------
@@ -291,9 +270,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
List<AcquiredPlateImage> plateImages = extractionResult.getImages();
File imagesInStoreFolder = moveFileToDirectory(incomingDataSetDirectory, originalFolder);
-
+
createThumbnails(rootDirectory, imagesInStoreFolder, plateImages);
-
storeInDatabase(experiment, dataSetInformation, extractionResult);
return rootDirectory;
@@ -305,9 +283,10 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
File thumbnailsFile = new File(rootDirectory, Constants.HDF5_CONTAINER_FILE_NAME);
IHDF5Writer writer = HDF5FactoryProvider.get().open(thumbnailsFile);
String relativeImagesDirectory =
- getRelativeImagesDirectory(rootDirectory, imagesInStoreFolder);
- String relativeThumbnailFilePath = getRelativeImagesDirectory(rootDirectory, thumbnailsFile);
-
+ getRelativeImagesDirectory(rootDirectory, imagesInStoreFolder);
+ String relativeThumbnailFilePath =
+ getRelativeImagesDirectory(rootDirectory, thumbnailsFile);
+
for (AcquiredPlateImage plateImage : plateImages)
{
RelativeImageReference imageReference = plateImage.getImageReference();
@@ -315,7 +294,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
imageReference.setRelativeImageFolder(relativeImagesDirectory);
File img = new File(imagesInStoreFolder, imagePath);
BufferedImage image = ImageUtil.loadImage(img);
- BufferedImage thumbnail = ImageUtil.createThumbnail(image, thumbnailMaxWidth, thumbnailMaxHeight);
+ BufferedImage thumbnail =
+ ImageUtil.createThumbnail(image, thumbnailMaxWidth, thumbnailMaxHeight);
ByteArrayOutputStream output = new ByteArrayOutputStream();
try
{
@@ -337,7 +317,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
}
writer.close();
}
-
+
private String getRelativeImagesDirectory(File rootDirectory, File imagesInStoreFolder)
{
String root = rootDirectory.getAbsolutePath();
@@ -399,7 +379,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
}
final HCSImageFileExtractionResult result =
extractor.extract(incomingDataSetDirectory, dataSetInformation);
-
+
if (operationLog.isInfoEnabled())
{
long duration = System.currentTimeMillis() - extractionStart;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
index 5c160ddc3a3668dccf8928f5c2ef5b55d925e0f2..5ce42fcdf786b6ce8bfe8849b22711be6ddd81cf 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
@@ -16,6 +16,13 @@
package ch.systemsx.cisd.openbis.dss.etl;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.etlserver.PlateDimension;
+import ch.systemsx.cisd.etlserver.PlateDimensionParser;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+
/**
* Describes one dataset container (e.g. plate) with images.
*
@@ -103,4 +110,39 @@ public class ScreeningContainerDatasetInfo
this.tileColumns = tileColumns;
}
+ public static ScreeningContainerDatasetInfo createScreeningDatasetInfo(
+ DataSetInformation dataSetInformation)
+ {
+ Experiment experiment = dataSetInformation.tryToGetExperiment();
+ ScreeningContainerDatasetInfo info = new ScreeningContainerDatasetInfo();
+ info.setExperimentPermId(experiment.getPermId());
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
+ dataSetInformation.tryToGetSample();
+ assert sample != null : "no sample connected to a dataset";
+ info.setContainerPermId(sample.getPermId());
+ info.setDatasetPermId(dataSetInformation.getDataSetCode());
+
+ PlateDimension plateGeometry = getPlateGeometry(dataSetInformation);
+ int plateRows = plateGeometry.getRowsNum();
+ int plateCols = plateGeometry.getColsNum();
+ info.setContainerRows(plateRows);
+ info.setContainerColumns(plateCols);
+
+ return info;
+ }
+
+ static PlateDimension getPlateGeometry(final DataSetInformation dataSetInformation)
+ {
+ final IEntityProperty[] sampleProperties = dataSetInformation.getProperties();
+ final PlateDimension plateDimension =
+ PlateDimensionParser.tryToGetPlateDimension(sampleProperties);
+ if (plateDimension == null)
+ {
+ throw new EnvironmentFailureException(
+ "Missing plate geometry for the plate registered for sample identifier '"
+ + dataSetInformation.getSampleIdentifier() + "'.");
+ }
+ return plateDimension;
+ }
+
}
\ No newline at end of file