From 9fbb74965edc20f2768cce827333994d057c502c Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 28 Jul 2010 09:01:25 +0000
Subject: [PATCH] SE-281 DynamiX plugin fixes, screening bugfixes: show correct
plate size even when datasets are not loaded, magnify the well image if there
is only one tile
SVN: 17252
---
.../cisd/etlserver/BDSStorageProcessor.java | 2 +
.../cisd/etlserver/PlateDimension.java | 2 +
.../cisd/etlserver/PlateDimensionParser.java | 2 +
.../etlserver/BDSStorageProcessorTest.java | 2 +
.../generic/server/business/bo/ISampleBO.java | 5 +
.../generic/server/business/bo/SampleBO.java | 8 ++
.../openbis/dss/etl/HCSImageCheckList.java | 18 ++-
.../dss/etl/PlateStorageProcessor.java | 2 +-
.../etl/ScreeningContainerDatasetInfo.java | 4 +-
.../etl/dynamix/HCSImageFileExtractor.java | 12 +-
.../detailviewers/WellContentDialog.java | 67 +++-------
.../server/logic/PlateContentLoader.java | 23 +++-
.../shared/basic/dto/PlateContent.java | 4 +-
.../shared/basic/dto/PlateImages.java | 25 ++--
.../screening/shared/dto/PlateDimension.java | 79 +++++++++++
.../shared/dto/PlateDimensionParser.java | 126 ++++++++++++++++++
.../imaging/dataaccess/IImagingQueryDAO.java | 6 +-
.../genedata/FeatureStorageProcessorTest.java | 2 +-
18 files changed, 302 insertions(+), 87 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimension.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimensionParser.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
index c30d02a09b3..7a4e03f5159 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
@@ -85,6 +85,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
*
* @author Christian Ribeaud
*/
+// TODO 2010-07-28, Tomasz Pylak: remove this class
+@Deprecated
public final class BDSStorageProcessor extends AbstractStorageProcessor implements
IHCSImageFileAccepter
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimension.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimension.java
index b7ee40deb35..5cd56019c4c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimension.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimension.java
@@ -24,6 +24,8 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
/**
* @author Tomasz Pylak
*/
+// TODO 2010-07-28, Tomasz Pylak: remove this class together with BDS
+@Deprecated
public class PlateDimension extends AbstractHashable implements Serializable
{
private static final long serialVersionUID = IServer.VERSION;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimensionParser.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimensionParser.java
index 6e334a7b791..9a02274cd00 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimensionParser.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/PlateDimensionParser.java
@@ -24,6 +24,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
*
* @author Tomasz Pylak
*/
+// TODO 2010-07-28, Tomasz Pylak: remove this class together with BDS
+@Deprecated
public class PlateDimensionParser
{
public static final String PLATE_GEOMETRY_PROPERTY_NAME = "$PLATE_GEOMETRY";
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
index dd60be44203..02522823955 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
@@ -78,6 +78,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
*
* @author Christian Ribeaud
*/
+// TODO 2010-07-28, Tomasz Pylak: remove this class
+@Deprecated
@Friend(toClasses = DssPropertyParametersUtil.class)
public final class BDSStorageProcessorTest extends AbstractFileSystemTestCase
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleBO.java
index 95601d34d4b..5caf7a2bad1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ISampleBO.java
@@ -52,6 +52,11 @@ public interface ISampleBO extends IEntityBusinessObject
*/
public void enrichWithPropertyTypes();
+ /**
+ * Enrich with properties.
+ */
+ public void enrichWithProperties();
+
/**
* Returns the loaded or defined sample or <code>null</code>.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
index 86d33b575e8..2448908f521 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
@@ -319,4 +319,12 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
HibernateUtils.initialize(sample.getSampleType().getSampleTypePropertyTypes());
}
}
+
+ public void enrichWithProperties()
+ {
+ if (sample != null)
+ {
+ HibernateUtils.initialize(sample.getProperties());
+ }
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
index 95827467dc2..73fa86b240c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
@@ -23,7 +23,7 @@ import java.util.Map;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
-import ch.systemsx.cisd.etlserver.PlateDimension;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimension;
/**
* Helper class to set the <code>is_complete</code> flag in the <i>BDS</i> library.
@@ -84,11 +84,12 @@ public final class HCSImageCheckList
{
throw new IllegalArgumentException("Invalid channel/well/tile: " + image);
}
- if (check.isCheckedOff())
+ Float timepointOrNull = image.tryGetTimePoint();
+ if (check.isCheckedOff(timepointOrNull))
{
throw new IllegalArgumentException("Image already handled: " + image);
}
- check.checkOff();
+ check.checkOff(timepointOrNull);
}
private static FullLocation createLocation(AcquiredPlateImage image)
@@ -102,7 +103,7 @@ public final class HCSImageCheckList
final List<FullLocation> fullLocations = new ArrayList<FullLocation>();
for (final Map.Entry<FullLocation, Check> entry : imageMap.entrySet())
{
- if (entry.getValue().isCheckedOff() == false)
+ if (entry.getValue().isCheckedOff(null) == false)
{
fullLocations.add(entry.getKey());
}
@@ -118,14 +119,17 @@ public final class HCSImageCheckList
{
private boolean checkedOff;
- final void checkOff()
+ private List<Float> timepoints = new ArrayList<Float>();
+
+ final void checkOff(Float timepointOrNull)
{
+ timepoints.add(timepointOrNull);
checkedOff = true;
}
- final boolean isCheckedOff()
+ final boolean isCheckedOff(Float timepointOrNull)
{
- return checkedOff;
+ return checkedOff && (timepointOrNull == null || timepoints.contains(timepointOrNull));
}
}
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 76a6cfb7bd8..f4be0d65f92 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
@@ -56,7 +56,6 @@ import ch.systemsx.cisd.common.utilities.PropertyUtils;
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.hdf5.HDF5FactoryProvider;
import ch.systemsx.cisd.hdf5.IHDF5Writer;
import ch.systemsx.cisd.openbis.dss.Constants;
@@ -67,6 +66,7 @@ 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.dto.StorageFormat;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimension;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
/**
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 e44701a7fb8..e2665aa68bb 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
@@ -17,12 +17,12 @@
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;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimension;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimensionParser;
/**
* Describes one dataset container (e.g. plate) with images.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
index e3b4b51cbe5..88320361ef9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.dss.etl.dynamix;
import java.io.File;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
import java.util.Properties;
import java.util.Set;
@@ -81,7 +82,7 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
{
final String[] tokens = StringUtils.split(plateLocation, "_");
boolean isLeft = (tokens[0].equalsIgnoreCase("left"));
- Integer pos = Integer.parseInt(plateLocation.substring(3));
+ Integer pos = Integer.parseInt(tokens[1].substring(3));
assert pos > 0 && pos <= 576 : "wrong position: " + pos;
int sideShift = isLeft ? 1 : 0;
@@ -93,10 +94,9 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
}
@Override
- /* @param timepointToken - format 20100227152439 */
protected final Float tryGetTimepoint(final String timepointToken)
{
- return Float.parseFloat(timepointToken);
+ return new Float(timepointToken);
}
@Override
@@ -120,8 +120,10 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
info.setPlateLocationToken(tokens[0] + "_" + tokens[2]);
info.setWellLocationToken(null);
info.setChannelToken(tokens[1]);
- // 20100227152439
- info.setTimepointToken(tokens[3].substring(1) + tokens[4]);
+
+ File[] images = imageFile.getParentFile().listFiles();
+ Arrays.sort(images);
+ info.setTimepointToken("" + Arrays.asList(images).indexOf(imageFile));
return info;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
index b09b816c529..caf19ad69da 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
-import java.util.ArrayList;
import java.util.List;
import com.extjs.gxt.ui.client.Style.Scroll;
@@ -47,7 +46,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.S
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ChannelChooser.DefaultChannelState;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ChannelChooser.IChanneledViewerFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImageParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
@@ -61,6 +59,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
public class WellContentDialog extends Dialog
{
+ private static final int SINGLE_IMG_SIZE_MULTIPLY_FACTOR = 3;
+
public static void showContentDialog(final WellData wellData, DefaultChannelState channelState,
final ScreeningViewContext viewContext)
{
@@ -86,8 +86,9 @@ public class WellContentDialog extends Dialog
createImageViewer(images, channelState, viewContext, imgW, imgH);
container.add(imageViewer);
- dialogWidth = imgW * Math.max(2, images.getTileColsNum()) + 100;
- dialogHeight = imgH * images.getTileRowsNum() + 300;
+ int imageSizeMultiplyFactor = getImageSizeMultiplyFactor(images);
+ dialogWidth = imgW * imageSizeMultiplyFactor * images.getTileColsNum() + 100;
+ dialogHeight = imgH * imageSizeMultiplyFactor * images.getTileRowsNum() + 300;
} else
{
dialogWidth = 300;
@@ -97,6 +98,17 @@ public class WellContentDialog extends Dialog
setupContentAndShow(contentDialog, container, dialogWidth, dialogHeight, title);
}
+ private static int getImageSizeMultiplyFactor(WellImages images)
+ {
+ if (images.getTileColsNum() == 1 && images.getTileRowsNum() == 1)
+ {
+ return SINGLE_IMG_SIZE_MULTIPLY_FACTOR;
+ } else
+ {
+ return 1;
+ }
+ }
+
// ----------------
private final WellMetadata metadataOrNull;
@@ -213,61 +225,20 @@ public class WellContentDialog extends Dialog
DefaultChannelState channelState, final IViewContext<?> viewContext,
final int imageWidth, final int imageHeight)
{
+ final int imageSizeMultiplyFactor = getImageSizeMultiplyFactor(images);
final IChanneledViewerFactory viewerFactory = new IChanneledViewerFactory()
{
public LayoutContainer create(String channel)
{
String sessionId = getSessionId(viewContext);
- return createTilesGrid(images, channel, sessionId, imageWidth, imageHeight);
+ return createTilesGrid(images, channel, sessionId, imageWidth
+ * imageSizeMultiplyFactor, imageHeight * imageSizeMultiplyFactor);
}
};
return ChannelChooser.createViewerWithChannelChooser(viewerFactory, channelState, images
.getChannelsNames());
}
- /** view with channel chooser, no metadata are displayed */
- public static void showContentDialog(final WellContent wellContent,
- DefaultChannelState channelState, final IViewContext<?> viewContext,
- final int imageWidthPx, final int imageHeightPx)
- {
- final IChanneledViewerFactory viewerFactory = new IChanneledViewerFactory()
- {
- public Widget create(String channel)
- {
- return createImageViewerForChannel(viewContext, wellContent, imageWidthPx,
- imageHeightPx, channel);
- }
- };
- DatasetImagesReference imageDataset = wellContent.tryGetImages();
-
- int dialogWidth;
- int dialogHeight;
- List<String> channelsNames = new ArrayList<String>();
- if (imageDataset != null)
- {
- PlateImageParameters imageParameters = imageDataset.getImageParameters();
- channelsNames = imageParameters.getChannelsNames();
- dialogWidth = imageWidthPx * Math.max(2, imageParameters.getTileColsNum()) + 100;
- dialogHeight = imageHeightPx * imageParameters.getTileRowsNum() + 300;
- } else
- {
- dialogWidth = 300;
- dialogHeight = 160;
- }
- Widget content =
- ChannelChooser.createViewerWithChannelChooser(viewerFactory, channelState,
- channelsNames);
- setupContentAndShow(new Dialog(), content, dialogWidth, dialogHeight,
- createDialogTitle(wellContent));
- }
-
- private static String createDialogTitle(WellContent wellContent)
- {
- String content = wellContent.getMaterialContent().getCode();
- return "Plate: " + wellContent.getPlate().getCode() + ", well: "
- + wellContent.getWell().getCode() + ", content: " + content;
- }
-
/**
* Creates a view for the specified channel.
*
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index 6f0ec5ad69d..150adfba1f4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -25,15 +25,18 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.translator.EntityPropertyTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
@@ -41,6 +44,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImagePara
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimensionParser;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
/**
@@ -108,7 +112,16 @@ public class PlateContentLoader
List<WellMetadata> wells = loadWells(new TechId(HibernateUtils.getId(plate)));
DatasetImagesReference datasetImagesReference =
loadImages(createExternalDataTable(), externalData);
- return new PlateImages(translate(plate), wells, datasetImagesReference);
+ Geometry plateGeometry = getPlateGeometry(plate);
+ return new PlateImages(translate(plate), wells, datasetImagesReference, plateGeometry
+ .getNumberOfRows(), plateGeometry.getNumberOfColumns());
+ }
+
+ private Geometry getPlateGeometry(SamplePE plate)
+ {
+ List<IEntityProperty> properties =
+ EntityPropertyTranslator.translate(plate.getProperties(), null);
+ return PlateDimensionParser.getPlateGeometry(properties);
}
private ExternalDataPE loadDataset(TechId datasetId)
@@ -205,8 +218,11 @@ public class PlateContentLoader
analysisDataset = ScreeningUtils.createDatasetReference(analysisDatasets.get(0));
}
- return new PlateContent(plate, wells, imageDataset, imageDatasets.size(), analysisDataset,
- analysisDatasets.size());
+ Geometry plateGeometry = PlateDimensionParser.getPlateGeometry(plate.getProperties());
+ int rows = plateGeometry.getNumberOfRows();
+ int cols = plateGeometry.getNumberOfColumns();
+ return new PlateContent(plate, wells, rows, cols, imageDataset, imageDatasets.size(),
+ analysisDataset, analysisDatasets.size());
}
private IExternalDataTable createExternalDataTable()
@@ -218,6 +234,7 @@ public class PlateContentLoader
{
ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
sampleBO.loadDataByTechId(plateId);
+ sampleBO.enrichWithProperties();
SamplePE sample = sampleBO.getSample();
return translate(sample);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateContent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateContent.java
index ceaec98477a..94d50bd44dd 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateContent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateContent.java
@@ -46,7 +46,7 @@ public class PlateContent implements IsSerializable
{
}
- public PlateContent(Sample plate, List<WellMetadata> wells,
+ public PlateContent(Sample plate, List<WellMetadata> wells, int plateRowsNum, int plateColsNum,
DatasetImagesReference imagesOrNull, int imageDatasetsNumber,
DatasetReference imageAnalysisDatasetOrNull, int imageAnalysisDatasetsNumber)
{
@@ -54,7 +54,7 @@ public class PlateContent implements IsSerializable
|| (imagesOrNull == null && imageDatasetsNumber != 1);
assert (imageAnalysisDatasetOrNull != null && imageAnalysisDatasetsNumber == 1)
|| (imageAnalysisDatasetOrNull == null && imageAnalysisDatasetsNumber != 1);
- this.plateImages = new PlateImages(plate, wells, imagesOrNull);
+ this.plateImages = new PlateImages(plate, wells, imagesOrNull, plateRowsNum, plateColsNum);
this.imageDatasetsNumber = imageDatasetsNumber;
this.imageAnalysisDatasetOrNull = imageAnalysisDatasetOrNull;
this.imageAnalysisDatasetsNumber = imageAnalysisDatasetsNumber;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java
index af4061dc5b1..8ebdaf5887b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImages.java
@@ -42,6 +42,9 @@ public class PlateImages implements IsSerializable
// null if dataset with images does not exist
private DatasetImagesReference imagesOrNull;
+ // plate dimension
+ private int plateRowsNum, plateColsNum;
+
// GWT only
@SuppressWarnings("unused")
private PlateImages()
@@ -49,11 +52,13 @@ public class PlateImages implements IsSerializable
}
public PlateImages(Sample plate, List<WellMetadata> wellsMetadata,
- DatasetImagesReference imagesOrNull)
+ DatasetImagesReference imagesOrNull, int plateRowsNum, int plateColsNum)
{
this.plate = plate;
this.wellsMetadata = wellsMetadata;
this.imagesOrNull = imagesOrNull;
+ this.plateRowsNum = plateRowsNum;
+ this.plateColsNum = plateColsNum;
}
public List<WellMetadata> getWells()
@@ -74,25 +79,11 @@ public class PlateImages implements IsSerializable
public int getRowsNum()
{
- if (imagesOrNull != null)
- {
- return imagesOrNull.getImageParameters().getRowsNum();
- } else
- {
- // TODO 2009-12-09, Tomasz Pylak: calculate rows number on the basis of metadata
- return 16;
- }
+ return plateRowsNum;
}
public int getColsNum()
{
- if (imagesOrNull != null)
- {
- return imagesOrNull.getImageParameters().getColsNum();
- } else
- {
- // TODO 2009-12-09, Tomasz Pylak: calculate rows number on the basis of metadata
- return 24;
- }
+ return plateColsNum;
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimension.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimension.java
new file mode 100644
index 00000000000..4f5f0c06b67
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimension.java
@@ -0,0 +1,79 @@
+/*
+ * Copyright 2007 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.shared.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class PlateDimension extends AbstractHashable implements Serializable
+{
+ private static final long serialVersionUID = IServer.VERSION;
+
+ private int rowsNum;
+
+ private int colsNum;
+
+ // for internal use only
+ public PlateDimension()
+ {
+ this(0, 0);
+ }
+
+ public PlateDimension(int rowsNum, int colsNum)
+ {
+ super();
+ this.rowsNum = rowsNum;
+ this.colsNum = colsNum;
+ }
+
+ public int getRowsNum()
+ {
+ return rowsNum;
+ }
+
+ public void setRowsNum(int rowsNum)
+ {
+ this.rowsNum = rowsNum;
+ }
+
+ public int getColsNum()
+ {
+ return colsNum;
+ }
+
+ public void setColsNum(int colsNum)
+ {
+ this.colsNum = colsNum;
+ }
+
+ public Geometry getPlateGeometry()
+ {
+ return Geometry.createFromRowColDimensions(rowsNum, colsNum);
+ }
+
+ @Override
+ public String toString()
+ {
+ return "(" + rowsNum + ", " + colsNum + ")";
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimensionParser.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimensionParser.java
new file mode 100644
index 00000000000..48a2171d205
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/PlateDimensionParser.java
@@ -0,0 +1,126 @@
+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.shared.dto;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+
+/**
+ * Extractor and parser of the plate geometry from an array of properties.
+ *
+ * @author Tomasz Pylak
+ */
+public class PlateDimensionParser
+{
+ public static final String PLATE_GEOMETRY_PROPERTY_NAME = "$PLATE_GEOMETRY";
+
+ /**
+ * Returns the plate geometry from the specified properties.
+ *
+ * @throws IllegalArgumentException if either their isn't such a property or it has an invalid
+ * value.
+ */
+ public static PlateDimension getPlateDimension(final IEntityProperty[] properties)
+ {
+ final PlateDimension plateDimension = tryToGetPlateDimension(properties);
+ if (plateDimension == null)
+ {
+ throw new IllegalArgumentException("Cannot find property "
+ + PLATE_GEOMETRY_PROPERTY_NAME);
+ }
+ return plateDimension;
+ }
+
+ /**
+ * Tries to get the plate geometry from the specified properties.
+ *
+ * @return <code>null</code> if their isn't such a property.
+ * @throws IllegalArgumentException if the property for the plate geometry has an invalid value.
+ */
+ public static PlateDimension tryToGetPlateDimension(final IEntityProperty[] properties)
+ {
+ assert properties != null : "Unspecified properties";
+ final String plateGeometryString =
+ tryFindProperty(properties, PLATE_GEOMETRY_PROPERTY_NAME);
+ if (plateGeometryString == null)
+ {
+ return null;
+ }
+ final PlateDimension dimension = tryParsePlateDimension(plateGeometryString);
+ if (dimension == null)
+ {
+ throw new IllegalArgumentException("Cannot parse plate geometry " + plateGeometryString);
+ }
+ return dimension;
+
+ }
+
+ // parses plate geometry - takes the token after the last "_" sign and assumes that the number
+ // of rows is separated
+ // from number of columns by the 'X' sign, e.g. XXX_YYY_16x24
+ private static PlateDimension tryParsePlateDimension(final String plateGeometryString)
+ {
+ final String[] tokens = plateGeometryString.split("_");
+ final String sizeToken = tokens[tokens.length - 1];
+ final String[] dims = sizeToken.split("X");
+ if (dims.length != 2)
+ {
+ return null;
+ }
+ final Integer rows = tryParseInteger(dims[0]);
+ final Integer cols = tryParseInteger(dims[1]);
+ if (rows == null || cols == null)
+ {
+ return null;
+ }
+ return new PlateDimension(rows, cols);
+ }
+
+ private static Integer tryParseInteger(final String value)
+ {
+ try
+ {
+ return Integer.parseInt(value);
+ } catch (final NumberFormatException e)
+ {
+ return null;
+ }
+ }
+
+ private static String tryFindProperty(final IEntityProperty[] properties,
+ final String propertyCode)
+ {
+ for (final IEntityProperty property : properties)
+ {
+ final PropertyType propertyType = property.getPropertyType();
+ if (propertyType.getCode().equals(propertyCode))
+ {
+ return property.tryGetAsString();
+ }
+ }
+ return null;
+ }
+
+ public static Geometry getPlateGeometry(List<IEntityProperty> properties)
+ {
+ return getPlateDimension(properties.toArray(new IEntityProperty[0])).getPlateGeometry();
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
index 096c8aac317..3be6357d8d2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
@@ -44,7 +44,11 @@ public interface IImagingQueryDAO extends TransactionQuery
// and acquired_images.channel_stack.spot.y = wellY
+ "cs.x = ?{3.x} and cs.y = ?{3.y} and s.x = ?{4.x} and s.y = ?{4.y} and "
// joins
- + "ai.CHANNEL_STACK_ID = cs.ID and cs.SPOT_ID = s.ID";
+ + "ai.CHANNEL_STACK_ID = cs.ID and cs.SPOT_ID = s.ID "
+ // TODO 2010-07-27, Tomasz Pylak: select the first image if there are many time
+ // points or depth scans.
+ // Should be deleted when support for time points will be added!
+ + "order by cs.T_in_SEC, cs.Z_in_M limit 1";
// select acquired_images.images.* from acquired_images
@Select("select i.* " + "from ACQUIRED_IMAGES as ai join IMAGES as i on ai.IMG_ID = i.ID "
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
index 1f233bf5b93..6cfc05a3cce 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
@@ -33,7 +33,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.etlserver.IStorageProcessor;
-import ch.systemsx.cisd.etlserver.PlateDimensionParser;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
@@ -41,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericValueEntityPrope
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimensionParser;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
--
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