diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractHCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractHCSImageFileExtractor.java
index e5f4dad6741b4282b585624934bda085d188571d..06328853bad0fbbdd2b026b1aa1c134630062bf0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractHCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractHCSImageFileExtractor.java
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
index b21a5aa7689733bdf34bedb774ec3aa7b444c070..ce716bdc53b941172bcb5ca663365a79dd34448c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
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 2e2a3a66c3c4f98463ec244c20c27b35e5404102..9c3a93a387b844b125b16406af5b448c106e3f79 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
@@ -67,6 +67,7 @@ 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.dto.StorageFormat;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
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/dynamix/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dynamix/HCSImageFileExtractor.java
index 44e38f70787dd2b4826ddf007edc3955d6d8663c..dc74be8fb950855020812978c4956f2c5501a5fe 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
@@ -36,10 +36,10 @@ import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.etl.AbstractHCSImageFileExtractor;
import ch.systemsx.cisd.openbis.dss.etl.AcquiredPlateImage;
-import ch.systemsx.cisd.openbis.dss.etl.ChannelDescription;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
import ch.systemsx.cisd.openbis.dss.etl.dynamix.WellLocationMappingUtils.DynamixWellPosition;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
/**
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 aec92e1894a26fb5e70ff1187d4146938b89e87c..82dcb6955f897ed9d07449ce0351e9af09a28c62 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
@@ -172,8 +172,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
PlateImageParameters params = imageAccessor.getImageParameters();
int tilesNumber = params.getTileColsNum() * params.getTileRowsNum();
BufferedImage image = ImageUtil.loadImage(imageFile.getInputStream());
- return new ImageDatasetMetadata(dataset, params.getChannelsCodes(), tilesNumber, image
- .getWidth(), image.getHeight());
+ return new ImageDatasetMetadata(dataset, params.getChannelsCodes(), params
+ .getChannelsLabels(), tilesNumber, image.getWidth(), image.getHeight());
}
private static IContent getAnyImagePath(IHCSImageDatasetLoader imageAccessor,
@@ -232,7 +232,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
List<String> labels = getLabels(builder);
return new FeatureVectorDataset(dataset, codes, labels, featureVectors);
}
-
+
private List<String> normalize(List<String> names)
{
ArrayList<String> codes = new ArrayList<String>(names.size());
@@ -288,7 +288,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
}
return labels;
}
-
+
private FeatureVectorWithDescription createFeatureVector(FeatureTableRow featureTableRow,
final List<String> featureCodes)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetMetadata.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetMetadata.java
index 38e1627fa8db0038b54115785f9259c47f1e9988..d74f46f1e0007fec7ba2bfdd2bf0dec2a3acc3d0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetMetadata.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetMetadata.java
@@ -18,17 +18,23 @@ public class ImageDatasetMetadata implements Serializable
private final List<String> channelNames;
+ private final List<String> channelCodes;
+
+ private final List<String> channelLabels;
+
private final int tilesNumber;
private final int width;
private final int height;
- public ImageDatasetMetadata(IImageDatasetIdentifier dataset, List<String> channelNames,
- int tilesNumber, int width, int height)
+ public ImageDatasetMetadata(IImageDatasetIdentifier dataset, List<String> channelCodes,
+ List<String> channelLabels, int tilesNumber, int width, int height)
{
this.imageDataset = dataset;
- this.channelNames = channelNames;
+ this.channelNames = channelCodes;
+ this.channelCodes = channelCodes;
+ this.channelLabels = channelLabels;
this.channelsNumber = channelNames.size();
this.tilesNumber = tilesNumber;
this.width = width;
@@ -50,13 +56,32 @@ public class ImageDatasetMetadata implements Serializable
}
/**
- * codes of channels in which images have been acquired for the described dataset
+ * names of channels in which images have been acquired for the described dataset
*/
+ @Deprecated
public List<String> getChannelNames()
{
return channelNames;
}
+ /**
+ * Returns channel codes. If channel codes are unspecified channel names are returned. This will
+ * be the case if a serialized instance of a previous of this class will be deserialized.
+ */
+ public List<String> getChannelCodes()
+ {
+ return channelCodes == null ? channelNames : channelCodes;
+ }
+
+ /**
+ * Returns channel labels. If channel labels are unspecified channel names are returned. This
+ * will be the case if a serialized instance of a previous of this class will be deserialized.
+ */
+ public List<String> getChannelLabels()
+ {
+ return channelLabels == null ? channelNames : channelLabels;
+ }
+
/**
* number of image tiles (aka fields) into which each well is splited
*/
@@ -80,7 +105,7 @@ public class ImageDatasetMetadata implements Serializable
@Override
public String toString()
{
- return "Dataset " + imageDataset + " has [" + channelNames + "] channels, " + tilesNumber
- + " tiles. Images resolution: " + width + "x" + height;
+ return "Dataset " + imageDataset + " has [" + getChannelCodes() + "] channels, "
+ + tilesNumber + " tiles. Images resolution: " + width + "x" + height;
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ChannelDescription.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ChannelDescription.java
similarity index 85%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ChannelDescription.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ChannelDescription.java
index 2596bee8eb14c2c063eedcb3e0341477d9ec6ea8..9775101ddaf3800b43370e2105aba3c9ce62f667 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ChannelDescription.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ChannelDescription.java
@@ -14,12 +14,16 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
/**
+ * Describes channel by code and label.
+ *
* @author Izabela Adamczyk
*/
-public class ChannelDescription
+public class ChannelDescription implements IsSerializable
{
private final String code;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImageParameters.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImageParameters.java
index feca4ddf712d82c7d043c99f271083456180b5c2..27ae3a545aff57ff282d21a54a835df68151880d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImageParameters.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/PlateImageParameters.java
@@ -40,6 +40,8 @@ public class PlateImageParameters implements IsSerializable
private List<String> channelsCodes;
+ private List<String> channelsLabels;
+
// true if any well in the dataset has a time series (or depth stack) of images
private boolean isMultidimensional;
@@ -118,4 +120,14 @@ public class PlateImageParameters implements IsSerializable
this.isMultidimensional = isMultidimensional;
}
+ public void setChannelsLabels(List<String> channelsLabels)
+ {
+ this.channelsLabels = channelsLabels;
+ }
+
+ public List<String> getChannelsLabels()
+ {
+ return channelsLabels;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
index 0f56582e1a16cb13afd5b751159af5913cb102ac..babbe25198037ff5f91e24c3e1b1fbae7eebae44 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import org.apache.commons.lang.StringEscapeUtils;
@@ -26,6 +25,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImagePara
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelStackDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
@@ -47,7 +47,7 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
protected Integer channelCount;
- protected List<String> channelCodes;
+ protected List<ImgChannelDTO> channels;
public HCSDatasetLoader(IImagingQueryDAO query, String datasetPermId)
{
@@ -57,10 +57,9 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
{
throw new IllegalStateException(String.format("Dataset '%s' not found", datasetPermId));
}
- String[] codesAsArray =
- query.getChannelCodesByDatasetIdOrExperimentId(getDataset().getId(), getContainer()
+ this.channels =
+ query.getChannelsByDatasetIdOrExperimentId(getDataset().getId(), getContainer()
.getExperimentId());
- this.channelCodes = new ArrayList<String>(Arrays.asList(codesAsArray));
}
/** has to be called at the end */
@@ -85,7 +84,7 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
public int getChannelCount()
{
- return channelCodes.size();
+ return channels.size();
}
public List<WellImageChannelStack> listImageChannelStacks(WellLocation wellLocation)
@@ -122,12 +121,15 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
params.setTileRowsNum(getDataset().getFieldNumberOfRows());
params.setTileColsNum(getDataset().getFieldNumberOfColumns());
params.setIsMultidimensional(dataset.getIsMultidimensional());
- List<String> escapedChannelCodes = new ArrayList<String>();
- for (String name : channelCodes)
+ List<String> channelsCodes = new ArrayList<String>();
+ List<String> channelsLabels = new ArrayList<String>();
+ for (ImgChannelDTO channel : channels)
{
- escapedChannelCodes.add(StringEscapeUtils.escapeCsv(name));
+ channelsCodes.add(StringEscapeUtils.escapeCsv(channel.getCode()));
+ channelsLabels.add(StringEscapeUtils.escapeCsv(channel.getLabel()));
}
- params.setChannelsCodes(escapedChannelCodes);
+ params.setChannelsCodes(channelsCodes);
+ params.setChannelsCodes(channelsLabels);
return params;
}
}
\ No newline at end of file
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 be84f753092167daaea6bf574bfa94ceec833090..b58b63073029cd2f7e7a368c73fab17696ff5395 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
@@ -108,8 +108,9 @@ public interface IImagingQueryDAO extends TransactionQuery
@Select("select count(*) from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2}")
public int countChannelByDatasetIdOrExperimentId(long datasetId, long experimentId);
- @Select("select code from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2} order by CODE")
- public String[] getChannelCodesByDatasetIdOrExperimentId(long datasetId, long experimentId);
+ @Select("select * from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2} order by CODE")
+ public List<ImgChannelDTO> getChannelsByDatasetIdOrExperimentId(long datasetId,
+ long experimentId);
@Select(sql = "select id from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2} order by LABEL", fetchSize = FETCH_SIZE)
public long[] getChannelIdsByDatasetIdOrExperimentId(long datasetId, long experimentId);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
index 542941acfc4d40ecab2d3da849a0b981ecd561a5..9132401f6fedde16021ac277052aad96072eda72 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
@@ -205,9 +205,9 @@ public class ScreeningOpenbisServiceFacadeTest extends AssertJUnit
final String geneCode = "MYGENE";
final MaterialIdentifier materialIdentifier =
new MaterialIdentifier(MaterialTypeIdentifier.GENE, geneCode);
- final PlateWellReferenceWithDatasets pwRef = new PlateWellReferenceWithDatasets(new Plate(
- null, null, null, ExperimentIdentifier.createFromPermId(null)),
- new WellPosition(1, 2));
+ final PlateWellReferenceWithDatasets pwRef =
+ new PlateWellReferenceWithDatasets(new Plate(null, null, null, ExperimentIdentifier
+ .createFromPermId(null)), new WellPosition(1, 2));
context.checking(new Expectations()
{
{
@@ -216,7 +216,8 @@ public class ScreeningOpenbisServiceFacadeTest extends AssertJUnit
}
});
- final List<PlateWellReferenceWithDatasets> ref = facade.listPlateWells(materialIdentifier, false);
+ final List<PlateWellReferenceWithDatasets> ref =
+ facade.listPlateWells(materialIdentifier, false);
assertEquals(1, ref.size());
assertEquals(pwRef, ref.get(0));
@@ -265,10 +266,14 @@ public class ScreeningOpenbisServiceFacadeTest extends AssertJUnit
@Test
public void testListImageMetaData()
{
- List<String> channelNames = Arrays.asList("channel1");
- final ImageDatasetMetadata m1 = new ImageDatasetMetadata(i1id, channelNames, 1, 1, 1);
- final ImageDatasetMetadata m2 = new ImageDatasetMetadata(i1id, channelNames, 1, 1, 1);
- final ImageDatasetMetadata m3 = new ImageDatasetMetadata(i2id, channelNames, 1, 1, 1);
+ List<String> channelCodes = Arrays.asList("channel1");
+ List<String> channelLabels = Arrays.asList("Channel 1");
+ final ImageDatasetMetadata m1 =
+ new ImageDatasetMetadata(i1id, channelCodes, channelLabels, 1, 1, 1);
+ final ImageDatasetMetadata m2 =
+ new ImageDatasetMetadata(i1id, channelCodes, channelLabels, 1, 1, 1);
+ final ImageDatasetMetadata m3 =
+ new ImageDatasetMetadata(i2id, channelCodes, channelLabels, 1, 1, 1);
context.checking(new Expectations()
{
{
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
index e542bb1943db64c28bd6d8c91bc4dd7af35f478d..7ca89ea5696ee4afa1d278d1e34284f3ea5f50f4 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
@@ -163,10 +163,12 @@ public class ImagingQueryDAOTest extends AbstractDBTest
{
// test countChannelByDatasetIdOrExperimentId
assertEquals(2, dao.countChannelByDatasetIdOrExperimentId(datasetId, experimentId));
- String[] channelNames =
- dao.getChannelCodesByDatasetIdOrExperimentId(datasetId, experimentId);
- assertEquals("DSCHANNEL", channelNames[0]);
- assertEquals("EXPCHANNEL", channelNames[1]);
+ List<ImgChannelDTO> channelDTOS =
+ dao.getChannelsByDatasetIdOrExperimentId(datasetId, experimentId);
+ assertEquals("DSCHANNEL", channelDTOS.get(0).getCode());
+ assertEquals(CHANNEL_LABEL, channelDTOS.get(0).getLabel());
+ assertEquals("EXPCHANNEL", channelDTOS.get(1).getCode());
+ assertEquals(CHANNEL_LABEL, channelDTOS.get(1).getLabel());
// test getChannelIdsByDatasetIdOrExperimentId
long[] channels = dao.getChannelIdsByDatasetIdOrExperimentId(datasetId, experimentId);