From 5a538377922b3e7ad72483c5885882593687129b Mon Sep 17 00:00:00 2001
From: izabel <izabel>
Date: Mon, 23 Aug 2010 11:17:23 +0000
Subject: [PATCH] [LMS-1708] Codes and labels for channels
SVN: 17575
---
.../etl/AbstractHCSImageFileExtractor.java | 37 +++---
.../openbis/dss/etl/AcquiredPlateImage.java | 10 +-
.../openbis/dss/etl/ChannelDescription.java | 61 +++++++++
.../openbis/dss/etl/HCSDatasetUploader.java | 14 +-
.../openbis/dss/etl/HCSImageCheckList.java | 22 ++--
.../dss/etl/HCSImageFileExtractionResult.java | 24 +++-
.../dss/etl/HCSImageFileExtractor.java | 31 ++---
.../dss/etl/IHCSImageDatasetLoader.java | 4 +-
.../dss/etl/PlateStorageProcessor.java | 120 +++++++++++++++---
.../ScreeningContainerDatasetInfoHelper.java | 20 +--
.../etl/dataaccess/HCSImageDatasetLoader.java | 10 +-
.../etl/dynamix/HCSImageFileExtractor.java | 13 +-
.../server/MergingImagesDownloadServlet.java | 4 +-
.../server/images/ImageChannelsUtils.java | 10 +-
.../server/DssServiceRpcScreening.java | 8 +-
.../detailviewers/ChannelComboBox.java | 10 +-
.../detailviewers/PlateMaterialReviewer.java | 2 +-
.../detailviewers/WellContentDialog.java | 6 +-
.../application/detailviewers/WellImages.java | 4 +-
.../api/v1/dto/ImageDatasetMetadata.java | 2 +-
.../api/v1/dto/PlateImageReference.java | 2 +-
.../basic/dto/PlateImageParameters.java | 12 +-
.../shared/imaging/HCSDatasetLoader.java | 18 +--
.../imaging/dataaccess/IImagingQueryDAO.java | 12 +-
.../imaging/dataaccess/ImgChannelDTO.java | 43 +++++--
.../dataaccess/ImagingQueryDAOTest.java | 10 +-
26 files changed, 336 insertions(+), 173 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ChannelDescription.java
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 a436a0a0456..e5f4dad6741 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
@@ -299,29 +299,36 @@ abstract public class AbstractHCSImageFileExtractor implements IHCSImageFileExtr
return components;
}
- protected final static List<String> extractChannelNames(final Properties properties)
- {
- return PropertyUtils.getMandatoryList(properties, PlateStorageProcessor.CHANNEL_NAMES);
- }
-
- protected final static Set<Channel> createChannels(List<String> channelNames)
+ protected final static Set<Channel> createChannels(List<ChannelDescription> channelDescriptions)
{
Set<Channel> channels = new HashSet<Channel>();
- for (String channelName : channelNames)
+ for (ChannelDescription channelDescription : channelDescriptions)
{
- channels.add(new Channel(channelName, null, null));
+ channels.add(new Channel(channelDescription.getCode(), null, null, channelDescription
+ .getLabel()));
}
return channels;
}
- protected final static void ensureChannelExist(List<String> channelNames, String channelName)
+ protected final static List<ChannelDescription> tryExtractChannelDescriptions(
+ final Properties properties)
+ {
+ return PlateStorageProcessor.extractChannelDescriptions(properties);
+ }
+
+ protected final static void ensureChannelExist(List<ChannelDescription> channelDescriptions,
+ String channelCode)
{
- if (channelNames.indexOf(channelName) == -1)
+ for (ChannelDescription channelDescription : channelDescriptions)
{
- throw UserFailureException.fromTemplate(
- "Channel '%s' is not one of: %s. Change the configuration.", channelName,
- channelNames);
+ if (channelDescription.getCode().equals(channelCode))
+ {
+ return;
+ }
}
+ throw UserFailureException.fromTemplate(
+ "Channel '%s' is not one of: %s. Change the configuration.", channelCode,
+ channelDescriptions);
}
protected final static Geometry getWellGeometry(final Properties properties)
@@ -342,10 +349,10 @@ abstract public class AbstractHCSImageFileExtractor implements IHCSImageFileExtr
}
protected static final AcquiredPlateImage createImage(Location plateLocation,
- Location wellLocation, String imageRelativePath, String channelName,
+ Location wellLocation, String imageRelativePath, String channelCode,
Float timepointOrNull, ColorComponent colorComponent)
{
- return new AcquiredPlateImage(plateLocation, wellLocation, channelName, timepointOrNull,
+ return new AcquiredPlateImage(plateLocation, wellLocation, channelCode, timepointOrNull,
null, new RelativeImageReference(imageRelativePath, null, colorComponent));
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredPlateImage.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredPlateImage.java
index b505fb4fd4e..b5612d067d1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredPlateImage.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredPlateImage.java
@@ -30,7 +30,7 @@ public class AcquiredPlateImage extends AbstractHashable
private final Location tileLocation;
- private final String channelName;
+ private final String channelCode;
// can be null
private final Float timePointOrNull, depthOrNull;
@@ -40,12 +40,12 @@ public class AcquiredPlateImage extends AbstractHashable
private RelativeImageReference thumbnailFilePathOrNull;
- public AcquiredPlateImage(Location wellLocation, Location tileLocation, String channelName,
+ public AcquiredPlateImage(Location wellLocation, Location tileLocation, String channelCode,
Float timePointOrNull, Float depthOrNull, RelativeImageReference imageFilePath)
{
this.wellLocation = wellLocation;
this.tileLocation = tileLocation;
- this.channelName = channelName.toUpperCase();
+ this.channelCode = channelCode.toUpperCase();
this.timePointOrNull = timePointOrNull;
this.depthOrNull = depthOrNull;
this.imageFilePath = imageFilePath;
@@ -71,9 +71,9 @@ public class AcquiredPlateImage extends AbstractHashable
return tileLocation.getX();
}
- public String getChannelName()
+ public String getChannelCode()
{
- return channelName;
+ return channelCode;
}
public Float tryGetTimePoint()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ChannelDescription.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ChannelDescription.java
new file mode 100644
index 00000000000..2596bee8eb1
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ChannelDescription.java
@@ -0,0 +1,61 @@
+/*
+ * Copyright 2010 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.dss.etl;
+
+/**
+ * @author Izabela Adamczyk
+ */
+public class ChannelDescription
+{
+
+ private final String code;
+
+ private final String label;
+
+ public ChannelDescription(String name)
+ {
+ assert name != null;
+ this.code = normalize(name);
+ this.label = name;
+ }
+
+ private String normalize(String name)
+ {
+ if (name == null)
+ {
+ return null;
+ }
+ return name.toUpperCase().replaceAll("[^A-Z0-9]", "_");
+ }
+
+ public ChannelDescription(String code, String label)
+ {
+ assert code != null && label != null;
+ this.code = code;
+ this.label = label;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public String getLabel()
+ {
+ return label;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
index da3e65569ab..a38c34bc0b7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
@@ -65,23 +65,23 @@ public class HCSDatasetUploader
private static class AcquiredImageInStack
{
- private final String channelName;
+ private final String channelCode;
private final RelativeImageReference imageFilePath;
private final RelativeImageReference thumbnailPathOrNull;
- public AcquiredImageInStack(String channelName, RelativeImageReference imageFilePath,
+ public AcquiredImageInStack(String channelCode, RelativeImageReference imageFilePath,
RelativeImageReference thumbnailPathOrNull)
{
- this.channelName = channelName.toUpperCase();
+ this.channelCode = channelCode.toUpperCase();
this.imageFilePath = imageFilePath;
this.thumbnailPathOrNull = thumbnailPathOrNull;
}
- public String getChannelName()
+ public String getChannelCode()
{
- return channelName;
+ return channelCode;
}
public RelativeImageReference getImageFilePath()
@@ -134,7 +134,7 @@ public class HCSDatasetUploader
private static AcquiredImageInStack makeAcquiredImageInStack(AcquiredPlateImage image)
{
- return new AcquiredImageInStack(image.getChannelName(), image.getImageReference(), image
+ return new AcquiredImageInStack(image.getChannelCode(), image.getImageReference(), image
.getThumbnailFilePathOrNull());
}
@@ -184,7 +184,7 @@ public class HCSDatasetUploader
List<ImgAcquiredImageDTO> acquiredImageDTOs = imagesToCreate.getAcquiredImages();
for (AcquiredImageInStack image : images)
{
- long channelTechId = channelsMap.get(image.getChannelName());
+ long channelTechId = channelsMap.get(image.getChannelCode());
ImgImageDTO imageDTO = mkImageWithIdDTO(image.getImageFilePath());
ImgImageDTO thumbnailDTO = tryMkImageWithIdDTO(image.getThumbnailPathOrNull());
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 73fa86b240c..e03a7b1337d 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
@@ -39,10 +39,10 @@ public final class HCSImageCheckList
private final Map<FullLocation, Check> imageMap;
- public HCSImageCheckList(final List<String> channelNames, final PlateDimension plateGeometry,
+ public HCSImageCheckList(final List<String> channelCodes, final PlateDimension plateGeometry,
final Geometry wellGeometry)
{
- if (channelNames.size() < 1)
+ if (channelCodes.size() < 1)
{
throw new IllegalArgumentException("Number of channels smaller than one.");
}
@@ -55,7 +55,7 @@ public final class HCSImageCheckList
throw new IllegalArgumentException("Unspecified well geometry.");
}
imageMap = new HashMap<FullLocation, Check>();
- for (String channelName : channelNames)
+ for (String channelCode : channelCodes)
{
for (int wellCol = 1; wellCol <= plateGeometry.getColsNum(); wellCol++)
{
@@ -66,13 +66,13 @@ public final class HCSImageCheckList
for (int tileRow = 1; tileRow <= wellGeometry.getRows(); tileRow++)
{
imageMap.put(new FullLocation(wellRow, wellCol, tileRow, tileCol,
- channelName), new Check());
+ channelCode), new Check());
}
}
}
}
}
- assert imageMap.size() == channelNames.size() * plateGeometry.getColsNum()
+ assert imageMap.size() == channelCodes.size() * plateGeometry.getColsNum()
* plateGeometry.getRowsNum() * wellGeometry.getColumns() * wellGeometry.getRows() : "Wrong map size";
}
@@ -95,7 +95,7 @@ public final class HCSImageCheckList
private static FullLocation createLocation(AcquiredPlateImage image)
{
return new FullLocation(image.getWellRow(), image.getWellColumn(), image.getTileRow(),
- image.getTileColumn(), image.getChannelName());
+ image.getTileColumn(), image.getChannelCode());
}
public final List<FullLocation> getCheckedOnFullLocations()
@@ -119,7 +119,7 @@ public final class HCSImageCheckList
{
private boolean checkedOff;
- private List<Float> timepoints = new ArrayList<Float>();
+ private final List<Float> timepoints = new ArrayList<Float>();
final void checkOff(Float timepointOrNull)
{
@@ -139,15 +139,15 @@ public final class HCSImageCheckList
final int tileRow, tileCol;
- final String channelName;
+ final String channelCode;
- public FullLocation(int wellRow, int wellCol, int tileRow, int tileCol, String channelName)
+ public FullLocation(int wellRow, int wellCol, int tileRow, int tileCol, String channelCode)
{
this.wellRow = wellRow;
this.wellCol = wellCol;
this.tileRow = tileRow;
this.tileCol = tileCol;
- this.channelName = channelName.toUpperCase();
+ this.channelCode = channelCode.toUpperCase();
}
private final static String toString(final int row, final int col, final String type)
@@ -162,7 +162,7 @@ public final class HCSImageCheckList
@Override
public final String toString()
{
- return "[channel=" + channelName + ", " + toString(wellRow, wellCol, "well") + ", "
+ return "[channel=" + channelCode + ", " + toString(wellRow, wellCol, "well") + ", "
+ toString(tileRow, tileCol, "tile") + "]";
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
index 5144c71ff54..2c2f5f365c7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
@@ -60,7 +60,7 @@ public final class HCSImageFileExtractionResult
/**
* A channel in which the image has been acquired.
* <p>
- * Each channel has its <code>name</code> which uniquely identifies it in one experiment or
+ * Each channel has its <code>code</code> which uniquely identifies it in one experiment or
* dataset.
* </p>
*
@@ -68,23 +68,27 @@ public final class HCSImageFileExtractionResult
*/
public static final class Channel
{
- private final String name;
+ private final String code;
+
+ private final String label;
private final String description;
private final Integer wavelength;
- public Channel(String name, String descriptionOrNull, Integer wavelengthOrNull)
+ public Channel(String code, String descriptionOrNull, Integer wavelengthOrNull, String label)
{
- assert name != null : "name is null";
- this.name = name;
+ assert code != null : "code is null";
+ assert label != null : "label is null";
+ this.label = label;
+ this.code = code;
this.description = descriptionOrNull;
this.wavelength = wavelengthOrNull;
}
- public String getName()
+ public String getCode()
{
- return name;
+ return code;
}
public String tryGetDescription()
@@ -96,6 +100,12 @@ public final class HCSImageFileExtractionResult
{
return wavelength;
}
+
+ public String getLabel()
+ {
+ return label;
+ }
+
}
}
\ No newline at end of file
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 2fa55ea0b2b..b21a5aa7689 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
@@ -25,7 +25,6 @@ import java.util.Set;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
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.imaging.dataaccess.ColorComponent;
@@ -50,7 +49,7 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
private final TileMapper tileMapperOrNull;
- private final List<String> channelNames;
+ private final List<ChannelDescription> channelDescriptions;
private final List<ColorComponent> channelColorComponentsOrNull;
@@ -59,7 +58,7 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
public HCSImageFileExtractor(final Properties properties)
{
super(properties);
- this.channelNames = extractChannelNames(properties);
+ this.channelDescriptions = tryExtractChannelDescriptions(properties);
this.channelColorComponentsOrNull = tryGetChannelComponents(properties);
checkChannelsAndColorComponents();
this.wellGeometry = getWellGeometry(properties);
@@ -70,7 +69,7 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
private void checkChannelsAndColorComponents()
{
if (channelColorComponentsOrNull != null
- && channelColorComponentsOrNull.size() != channelNames.size())
+ && channelColorComponentsOrNull.size() != channelDescriptions.size())
{
throw ConfigurationFailureException.fromTemplate(
"There should be exactly one color component for each channel name."
@@ -126,34 +125,24 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
for (int i = 0; i < channelColorComponentsOrNull.size(); i++)
{
ColorComponent colorComponent = channelColorComponentsOrNull.get(i);
- String channelName = channelNames.get(i);
- images.add(createImage(plateLocation, wellLocation, imageRelativePath, channelName,
- timepointOrNull, colorComponent));
+ ChannelDescription channelDescription = channelDescriptions.get(i);
+ images.add(createImage(plateLocation, wellLocation, imageRelativePath,
+ channelDescription.getCode(), timepointOrNull, colorComponent));
}
} else
{
- String channelName = channelToken.toUpperCase();
- ensureChannelExist(channelName);
- images.add(createImage(plateLocation, wellLocation, imageRelativePath, channelName,
+ String channelCode = channelToken.toUpperCase();
+ ensureChannelExist(channelDescriptions, channelCode);
+ images.add(createImage(plateLocation, wellLocation, imageRelativePath, channelCode,
timepointOrNull, null));
}
return images;
}
- private void ensureChannelExist(String channelName)
- {
- if (channelNames.indexOf(channelName) == -1)
- {
- throw UserFailureException.fromTemplate(
- "Channel '%s' is not one of: %s. Change the configuration.", channelName,
- channelNames);
- }
- }
-
@Override
protected Set<Channel> getAllChannels()
{
- return createChannels(channelNames);
+ return createChannels(channelDescriptions);
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java
index 4ac9f4aa60a..0a443b170ee 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java
@@ -26,9 +26,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoade
public interface IHCSImageDatasetLoader extends IHCSDatasetLoader
{
/**
- * @param chosenChannel start from 1
+ * @param chosenChannelCode start from 1
* @return image (with absolute path, page and color)
*/
- AbsoluteImageReference tryGetImage(String chosenChannel,
+ AbsoluteImageReference tryGetImage(String chosenChannelCode,
ImageChannelStackReference channelStackReference, Size thumbnailSizeOrNull);
}
\ No newline at end of file
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 e82fc4ec2b9..ada5d0c1423 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
@@ -42,6 +42,7 @@ import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.bds.storage.IFile;
import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileOperations;
@@ -78,7 +79,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImag
* registration, but increases the performance when the user wants to see the image. Can be 'true'
* or 'false', 'false' is the default value
* <li>thumbnail-max-width, thumbnail-max-height - thumbnails size in pixels
- * <li>channel-names - names of the channels in which images have been acquired
+ * <li>[deprecated] channel-names - names of the channels in which images have been acquired
+ * <li>channel-codes - codes of the channels in which images have been acquired
+ * <li>channel-labels - labels of the channels in which images have been acquired
* <li>well_geometry - format: [width]>x[height], e.g. 3x4. Specifies the grid into which a
* microscope divided the well to acquire images.
* <li>file-extractor - implementation of the {@link IHCSImageFileExtractor} interface which maps
@@ -122,16 +125,21 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private static final String DEPRECATED_FILE_EXTRACTOR_PROPERTY = "deprecated-file-extractor";
// comma separated list of channel names, order matters
+ @Deprecated
public static final String CHANNEL_NAMES = "channel-names";
+ // comma separated list of channel codes, order matters
+ public static final String CHANNEL_CODES = "channel-codes";
+
+ // comma separated list of channel labels, order matters
+ public static final String CHANNEL_LABELS = "channel-lables";
+
// -----------
private final DataSource dataSource;
private final Geometry spotGeometry;
- private final List<String> channelNames;
-
private final int thumbnailMaxWidth;
private final int thumbnailMaxHeight;
@@ -145,13 +153,14 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private IImagingQueryDAO currentTransaction;
+ private final List<ChannelDescription> channelDescriptions;
+
public PlateStorageProcessor(final Properties properties)
{
super(properties);
String spotGeometryText = getMandatoryProperty(SPOT_GEOMETRY_PROPERTY);
this.spotGeometry = Geometry.createFromString(spotGeometryText);
-
- this.channelNames = PropertyUtils.getMandatoryList(properties, CHANNEL_NAMES);
+ channelDescriptions = extractChannelDescriptions(properties);
thumbnailMaxWidth =
PropertyUtils.getInt(properties, THUMBNAIL_MAX_WIDTH_PROPERTY,
DEFAULT_THUMBNAIL_MAX_WIDTH);
@@ -179,6 +188,46 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
this.currentTransaction = null;
}
+ public final static List<ChannelDescription> extractChannelDescriptions(
+ final Properties properties)
+ {
+ List<String> names = PropertyUtils.tryGetList(properties, CHANNEL_NAMES);
+ List<String> codes = PropertyUtils.tryGetList(properties, CHANNEL_CODES);
+ List<String> labels = PropertyUtils.tryGetList(properties, CHANNEL_LABELS);
+ if (names != null && (codes != null || labels != null))
+ {
+ throw new ConfigurationFailureException(String.format(
+ "Configure either '%s' or ('%s','%s') but not both.", CHANNEL_NAMES,
+ CHANNEL_CODES, CHANNEL_LABELS));
+ }
+ if (names != null)
+ {
+ List<ChannelDescription> descriptions = new ArrayList<ChannelDescription>();
+ for (String name : names)
+ {
+ descriptions.add(new ChannelDescription(name));
+ }
+ return descriptions;
+ }
+ if (codes == null || labels == null)
+ {
+ throw new ConfigurationFailureException(String.format(
+ "Both '%s' and '%s' should be configured", CHANNEL_CODES, CHANNEL_LABELS));
+ }
+ if (codes.size() != labels.size())
+ {
+ throw new ConfigurationFailureException(String.format(
+ "Number of configured '%s' should be the same as number of '%s'.",
+ CHANNEL_CODES, CHANNEL_LABELS));
+ }
+ List<ChannelDescription> descriptions = new ArrayList<ChannelDescription>();
+ for (int i = 0; i < codes.size(); i++)
+ {
+ descriptions.add(new ChannelDescription(codes.get(i), labels.get(i)));
+ }
+ return descriptions;
+ }
+
private IImagingQueryDAO createQuery()
{
return QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
@@ -414,7 +463,12 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private HCSImageCheckList createImageCheckList(DataSetInformation dataSetInformation)
{
PlateDimension plateGeometry = getPlateGeometry(dataSetInformation);
- return new HCSImageCheckList(channelNames, plateGeometry, spotGeometry);
+ List<String> channelCodes = new ArrayList<String>();
+ for (ChannelDescription cd : channelDescriptions)
+ {
+ channelCodes.add(cd.getCode());
+ }
+ return new HCSImageCheckList(channelCodes, plateGeometry, spotGeometry);
}
private HCSImageFileExtractionResult extractImages(final DataSetInformation dataSetInformation,
@@ -424,7 +478,9 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
IHCSImageFileExtractor extractor = imageFileExtractor;
if (extractor == null)
{
- extractor = adapt(deprecatedImageFileExtractor, incomingDataSetDirectory, channelNames);
+ extractor =
+ adapt(deprecatedImageFileExtractor, incomingDataSetDirectory,
+ channelDescriptions);
}
final HCSImageFileExtractionResult result =
extractor.extract(incomingDataSetDirectory, dataSetInformation);
@@ -649,10 +705,30 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
return StorageFormat.PROPRIETARY;
}
+ private static List<String> extractChannelCodes(final List<ChannelDescription> descriptions)
+ {
+ List<String> channelCodes = new ArrayList<String>();
+ for (ChannelDescription cd : descriptions)
+ {
+ channelCodes.add(cd.getCode());
+ }
+ return channelCodes;
+ }
+
+ private static List<String> extractChannelLabels(final List<ChannelDescription> descriptions)
+ {
+ List<String> channelLabels = new ArrayList<String>();
+ for (ChannelDescription cd : descriptions)
+ {
+ channelLabels.add(cd.getLabel());
+ }
+ return channelLabels;
+ }
+
// adapts old-style image extractor to the new one which is stateless
private static IHCSImageFileExtractor adapt(
final ch.systemsx.cisd.etlserver.IHCSImageFileExtractor extractor,
- final File imageFileRootDirectory, final List<String> channelNames)
+ final File imageFileRootDirectory, final List<ChannelDescription> descriptions)
{
return new IHCSImageFileExtractor()
{
@@ -660,7 +736,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
DataSetInformation dataSetInformation)
{
HCSImageFileAccepter accepter =
- new HCSImageFileAccepter(imageFileRootDirectory, channelNames);
+ new HCSImageFileAccepter(imageFileRootDirectory,
+ extractChannelCodes(descriptions));
ch.systemsx.cisd.etlserver.HCSImageFileExtractionResult originalResult =
extractor.process(NodeFactory
.createDirectoryNode(incomingDataSetDirectory),
@@ -677,9 +754,10 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
new HashSet<HCSImageFileExtractionResult.Channel>();
for (Channel channel : channels)
{
- String name = getChannelName(channelNames, channel.getCounter());
- result.add(new HCSImageFileExtractionResult.Channel(name, null, channel
- .getWavelength()));
+ result.add(new HCSImageFileExtractionResult.Channel(getChannelCodeOrLabel(
+ extractChannelCodes(descriptions), channel.getCounter()), null,
+ channel.getWavelength(), getChannelCodeOrLabel(
+ extractChannelLabels(descriptions), channel.getCounter())));
}
return result;
}
@@ -696,15 +774,15 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
};
}
- private static String getChannelName(final List<String> channelNames, int channelId)
+ private static String getChannelCodeOrLabel(final List<String> channelCodes, int channelId)
{
- if (channelId > channelNames.size())
+ if (channelId > channelCodes.size())
{
throw UserFailureException.fromTemplate(
"Too large channel number %d, configured channels: %s.", channelId,
- CollectionUtils.abbreviate(channelNames, -1));
+ CollectionUtils.abbreviate(channelCodes, -1));
}
- return channelNames.get(channelId - 1);
+ return channelCodes.get(channelId - 1);
}
private static final class HCSImageFileAccepter implements IHCSImageFileAccepter
@@ -713,12 +791,12 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private final File imageFileRootDirectory;
- private final List<String> channelNames;
+ private final List<String> channelCodes;
- public HCSImageFileAccepter(File imageFileRootDirectory, List<String> channelNames)
+ public HCSImageFileAccepter(File imageFileRootDirectory, List<String> channelCodes)
{
this.imageFileRootDirectory = imageFileRootDirectory;
- this.channelNames = channelNames;
+ this.channelCodes = channelCodes;
}
public final void accept(final int channel, final Location wellLocation,
@@ -728,9 +806,9 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
FileUtilities.getRelativeFile(imageFileRootDirectory, new File(imageFile
.getPath()));
assert imageRelativePath != null : "Image relative path should not be null.";
- String channelName = getChannelName(channelNames, channel);
+ String channelCode = getChannelCodeOrLabel(channelCodes, channel);
AcquiredPlateImage imageDesc =
- new AcquiredPlateImage(wellLocation, tileLocation, channelName, null, null,
+ new AcquiredPlateImage(wellLocation, tileLocation, channelCode, null, null,
new RelativeImageReference(imageRelativePath, null, null));
images.add(imageDesc);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
index d8c418fc7c7..807d94a9d82 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfoHelper.java
@@ -257,7 +257,7 @@ public class ScreeningContainerDatasetInfoHelper
private static void addChannel(Map<String, Long> map, ImgChannelDTO channelDTO)
{
- map.put(channelDTO.getName(), channelDTO.getId());
+ map.put(channelDTO.getCode(), channelDTO.getId());
}
private static Map<String, ImgChannelDTO> asNameMap(List<ImgChannelDTO> channels)
@@ -265,7 +265,7 @@ public class ScreeningContainerDatasetInfoHelper
Map<String, ImgChannelDTO> nameMap = new HashMap<String, ImgChannelDTO>();
for (ImgChannelDTO channel : channels)
{
- nameMap.put(channel.getName(), channel);
+ nameMap.put(channel.getCode(), channel);
}
return nameMap;
}
@@ -274,11 +274,11 @@ public class ScreeningContainerDatasetInfoHelper
Map<String, ImgChannelDTO> existingChannels)
{
ImgChannelDTO channelDTO = makeChannelDTO(channel, expId);
- String channelName = channelDTO.getName();
- ImgChannelDTO existingChannel = existingChannels.get(channelName);
+ String channelCode = channelDTO.getCode();
+ ImgChannelDTO existingChannel = existingChannels.get(channelCode);
if (existingChannel == null)
{
- throw createInvalidNewChannelException(expId, existingChannels, channelName);
+ throw createInvalidNewChannelException(expId, existingChannels, channelCode);
}
// a channel with a specified name already exists for an experiment, its description
// will be updated. Wavelength will be updated only if it was null before.
@@ -291,8 +291,8 @@ public class ScreeningContainerDatasetInfoHelper
{
throw UserFailureException.fromTemplate(
"There are already datasets registered for the experiment "
- + "which use the same channel name, but with a different wavelength! "
- + "Channel %s, old wavelength %d, new wavelength %d.", channelName,
+ + "which use the same channel code, but with a different wavelength! "
+ + "Channel %s, old wavelength %d, new wavelength %d.", channelCode,
existingChannel.getWavelength(), channelDTO.getWavelength());
}
channelDTO.setId(existingChannel.getId());
@@ -305,7 +305,7 @@ public class ScreeningContainerDatasetInfoHelper
{
return UserFailureException.fromTemplate(
"Experiment with id '%d' has already some channels registered "
- + "and does not have a channel with a name '%s'. "
+ + "and does not have a channel with a code '%s'. "
+ "Register a new experiment to use new channels. "
+ "Available channel names in this experiment: %s.", expId, channelName,
existingChannels.keySet());
@@ -322,7 +322,7 @@ public class ScreeningContainerDatasetInfoHelper
private static ImgChannelDTO makeChannelDTO(HCSImageFileExtractionResult.Channel channel,
long expId)
{
- return ImgChannelDTO.createExperimentChannel(channel.getName(),
- channel.tryGetDescription(), channel.tryGetWavelength(), expId);
+ return ImgChannelDTO.createExperimentChannel(channel.getCode(),
+ channel.tryGetDescription(), channel.tryGetWavelength(), expId, channel.getLabel());
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
index 05f96a3579f..04caa8b4268 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
@@ -65,13 +65,13 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
}
/**
- * @param chosenChannel start from 1
+ * @param chosenChannelCode
* @return image (with absolute path, page and color)
*/
- public AbsoluteImageReference tryGetImage(String chosenChannel,
+ public AbsoluteImageReference tryGetImage(String chosenChannelCode,
ImageChannelStackReference channelStackReference, Size thumbnailSizeOrNull)
{
- assert StringUtils.isBlank(chosenChannel) == false;
+ assert StringUtils.isBlank(chosenChannelCode) == false;
LocationImageChannelStackReference stackLocations =
channelStackReference.tryGetChannelStackLocations();
if (stackLocations != null)
@@ -84,8 +84,8 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
}
Long chosenChannelId =
- query.tryGetChannelIdByChannelNameDatasetIdOrExperimentId(getDataset().getId(),
- getContainer().getExperimentId(), chosenChannel);
+ query.tryGetChannelIdByChannelCodeDatasetIdOrExperimentId(getDataset().getId(),
+ getContainer().getExperimentId(), chosenChannelCode);
if (chosenChannelId == null)
{
return null;
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 4361be170e0..44e38f70787 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
@@ -36,6 +36,7 @@ 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;
@@ -52,32 +53,32 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
private static final String POSITION_MAPPING_FILE_NAME = "pos2loc.tsv";
- private final List<String> channelNames;
+ private final List<ChannelDescription> channelDescriptions;
private final Map<File/* mapping file */, Map<DynamixWellPosition, WellLocation>> wellLocationMapCache;
public HCSImageFileExtractor(final Properties properties)
{
super(properties);
- this.channelNames = extractChannelNames(properties);
+ this.channelDescriptions = tryExtractChannelDescriptions(properties);
this.wellLocationMapCache = new HashMap<File, Map<DynamixWellPosition, WellLocation>>();
}
@Override
protected final Set<Channel> getAllChannels()
{
- return createChannels(channelNames);
+ return createChannels(channelDescriptions);
}
@Override
protected final List<AcquiredPlateImage> getImages(String channelToken, Location plateLocation,
Location wellLocation, Float timepointOrNull, String imageRelativePath)
{
- String channelName = channelToken.toUpperCase();
- ensureChannelExist(channelNames, channelName);
+ String channelCode = channelToken.toUpperCase();
+ ensureChannelExist(channelDescriptions, channelCode);
List<AcquiredPlateImage> images = new ArrayList<AcquiredPlateImage>();
- images.add(createImage(plateLocation, wellLocation, imageRelativePath, channelName,
+ images.add(createImage(plateLocation, wellLocation, imageRelativePath, channelCode,
timepointOrNull, null));
return images;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
index 7dab3727995..66e2891bb99 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java
@@ -48,8 +48,8 @@ public class MergingImagesDownloadServlet extends AbstractImagesDownloadServlet
List<AbsoluteImageReference> images =
ImageChannelsUtils.getImagePaths(datasetRoot, datasetCode, params);
BufferedImage image = ImageChannelsUtils.mergeImageChannels(params, images);
- String singleFileNameOrNull = images.size() == 1 ? images.get(0).getContent().getName() : null;
+ String singleFileNameOrNull =
+ images.size() == 1 ? images.get(0).getContent().getName() : null;
return createResponseContentStream(image, singleFileNameOrNull);
}
-
}
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 9b3f568fc19..e23282d2e1b 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
@@ -57,7 +57,7 @@ public class ImageChannelsUtils
Size thumbnailSizeOrNull = params.tryGetThumbnailSize();
if (params.isMergeAllChannels())
{
- for (String chosenChannel : imageAccessor.getImageParameters().getChannelsNames())
+ for (String chosenChannel : imageAccessor.getImageParameters().getChannelsCodes())
{
AbsoluteImageReference image =
getImage(imageAccessor, params.getChannelStack(), chosenChannel,
@@ -243,16 +243,16 @@ public class ImageChannelsUtils
// --------- common
/**
- * @param chosenChannel starts from 1
+ * @param chosenChannelCode starts from 1
* @throw {@link EnvironmentFailureException} when image does not exist
*/
public static AbsoluteImageReference getImage(IHCSImageDatasetLoader imageAccessor,
- ImageChannelStackReference channelStackReference, String chosenChannel,
+ ImageChannelStackReference channelStackReference, String chosenChannelCode,
Size thumbnailSizeOrNull)
{
AbsoluteImageReference image =
imageAccessor
- .tryGetImage(chosenChannel, channelStackReference, thumbnailSizeOrNull);
+ .tryGetImage(chosenChannelCode, channelStackReference, thumbnailSizeOrNull);
if (image != null)
{
return image;
@@ -261,7 +261,7 @@ public class ImageChannelsUtils
throw EnvironmentFailureException.fromTemplate("No "
+ (thumbnailSizeOrNull != null ? "thumbnail" : "image")
+ " found for channel stack %s and channel %s", channelStackReference,
- chosenChannel);
+ chosenChannelCode);
}
}
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 4e455a3a299..aec92e1894a 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
@@ -172,7 +172,7 @@ 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.getChannelsNames(), tilesNumber, image
+ return new ImageDatasetMetadata(dataset, params.getChannelsCodes(), tilesNumber, image
.getWidth(), image.getHeight());
}
@@ -185,12 +185,12 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
for (int col = 1; col <= params.getColsNum(); col++)
{
AbsoluteImageReference image;
- for (String channelName : params.getChannelsNames())
+ for (String channelCode : params.getChannelsCodes())
{
ImageChannelStackReference channelStackReference =
ImageChannelStackReference.createFromLocations(new Location(col, row),
new Location(1, 1));
- image = imageAccessor.tryGetImage(channelName, channelStackReference, null);
+ image = imageAccessor.tryGetImage(channelCode, channelStackReference, null);
if (image != null)
{
return image.getContent();
@@ -266,7 +266,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
}
return result;
}
-
+
private List<String> getCodes(FeatureTableBuilder builder)
{
List<CodeAndLabel> featureCodesAndLabels = builder.getCodesAndLabels();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelComboBox.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelComboBox.java
index a324e7318fc..bd940db43ad 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelComboBox.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelComboBox.java
@@ -50,7 +50,7 @@ public class ChannelComboBox extends SimpleComboBox<String>
public ChannelComboBox(List<String> names, String initialValue)
{
this();
- addUniqueNames(names);
+ addUniqueCodes(names);
if (initialValue != null)
{
setSimpleValue(initialValue);
@@ -74,11 +74,11 @@ public class ChannelComboBox extends SimpleComboBox<String>
/**
* Adds names to the combo box if they were not yet present.
*/
- private void addUniqueNames(List<String> names)
+ private void addUniqueCodes(List<String> codes)
{
List<String> withMerged = new ArrayList<String>();
withMerged.add(ScreeningConstants.MERGED_CHANNELS);
- withMerged.addAll(names);
+ withMerged.addAll(codes);
for (String s : withMerged)
{
if (findModel(s) == null)
@@ -88,10 +88,10 @@ public class ChannelComboBox extends SimpleComboBox<String>
}
}
- public void addNamesAndListener(List<String> newNames,
+ public void addCodesAndListener(List<String> newCodes,
SelectionChangedListener<SimpleComboValue<String>> listener)
{
- addUniqueNames(newNames);
+ addUniqueCodes(newCodes);
addSelectionChangedListener(listener);
autoselect();
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateMaterialReviewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateMaterialReviewer.java
index b851d3b98fc..bed0c97cd2b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateMaterialReviewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/PlateMaterialReviewer.java
@@ -391,7 +391,7 @@ public class PlateMaterialReviewer extends AbstractSimpleBrowserGrid<WellContent
new ChannelWidgetWithListener(viewerFactory);
widgetWithListener.update(channelChooser.getSimpleValue());
- channelChooser.addNamesAndListener(imageParameters.getChannelsNames(),
+ channelChooser.addCodesAndListener(imageParameters.getChannelsCodes(),
widgetWithListener.asSelectionChangedListener());
return widgetWithListener.asWidget();
}
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 263c9a1721b..d435ff38bf3 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
@@ -130,7 +130,7 @@ public class WellContentDialog extends Dialog
return new Text("Incorrect well code.");
}
PlateImageParameters imageParameters = imageDataset.getImageParameters();
- if (imageParameters.getChannelsNames().contains(channel) == false
+ if (imageParameters.getChannelsCodes().contains(channel) == false
&& channel.equals(ScreeningConstants.MERGED_CHANNELS) == false)
{
return new Text("No images available for this channel.");
@@ -197,7 +197,7 @@ public class WellContentDialog extends Dialog
}
};
return ChannelChooser.createViewerWithChannelChooser(viewerFactory, channelState, images
- .getChannelsNames());
+ .getChannelsCodes());
}
private static LayoutContainer createTilesGrid(final WellImages images, String channel,
@@ -266,7 +266,7 @@ public class WellContentDialog extends Dialog
}
};
return ChannelChooser.createViewerWithChannelChooser(viewerFactory, channelState, images
- .getChannelsNames());
+ .getChannelsCodes());
}
// ---------------- STATIC METHODS -------------------
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellImages.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellImages.java
index f6eb0f92499..a3873a74ee7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellImages.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellImages.java
@@ -55,9 +55,9 @@ public class WellImages
return imageParams.getTileColsNum();
}
- public List<String> getChannelsNames()
+ public List<String> getChannelsCodes()
{
- return imageParams.getChannelsNames();
+ return imageParams.getChannelsCodes();
}
public boolean isMultidimensional()
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 517b00b9d44..38e1627fa8d 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
@@ -50,7 +50,7 @@ public class ImageDatasetMetadata implements Serializable
}
/**
- * names of channels in which images have been acquired for the described dataset
+ * codes of channels in which images have been acquired for the described dataset
*/
public List<String> getChannelNames()
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateImageReference.java
index 6aad66651ec..88403903f3c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/PlateImageReference.java
@@ -42,7 +42,7 @@ public class PlateImageReference extends DatasetIdentifier
}
/**
- * channel name
+ * channel code
*/
public String getChannel()
{
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 5f3dbc41fcd..feca4ddf712 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
@@ -38,7 +38,7 @@ public class PlateImageParameters implements IsSerializable
private int tileColsNum;
- private List<String> channelsNames;
+ private List<String> channelsCodes;
// true if any well in the dataset has a time series (or depth stack) of images
private boolean isMultidimensional;
@@ -93,19 +93,19 @@ public class PlateImageParameters implements IsSerializable
this.datasetCode = datasetCode;
}
- public void setChannelsNames(List<String> channelsNames)
+ public void setChannelsCodes(List<String> channelsCodes)
{
- this.channelsNames = channelsNames;
+ this.channelsCodes = channelsCodes;
}
- public List<String> getChannelsNames()
+ public List<String> getChannelsCodes()
{
- return channelsNames;
+ return channelsCodes;
}
public int getChannelsNumber()
{
- return channelsNames.size();
+ return channelsCodes.size();
}
public boolean isMultidimensional()
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 dab333851d1..0f56582e1a1 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
@@ -47,7 +47,7 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
protected Integer channelCount;
- protected List<String> channelNames;
+ protected List<String> channelCodes;
public HCSDatasetLoader(IImagingQueryDAO query, String datasetPermId)
{
@@ -57,10 +57,10 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
{
throw new IllegalStateException(String.format("Dataset '%s' not found", datasetPermId));
}
- String[] namesAsArray =
- query.getChannelNamesByDatasetIdOrExperimentId(getDataset().getId(), getContainer()
+ String[] codesAsArray =
+ query.getChannelCodesByDatasetIdOrExperimentId(getDataset().getId(), getContainer()
.getExperimentId());
- this.channelNames = new ArrayList<String>(Arrays.asList(namesAsArray));
+ this.channelCodes = new ArrayList<String>(Arrays.asList(codesAsArray));
}
/** has to be called at the end */
@@ -85,7 +85,7 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
public int getChannelCount()
{
- return channelNames.size();
+ return channelCodes.size();
}
public List<WellImageChannelStack> listImageChannelStacks(WellLocation wellLocation)
@@ -122,12 +122,12 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
params.setTileRowsNum(getDataset().getFieldNumberOfRows());
params.setTileColsNum(getDataset().getFieldNumberOfColumns());
params.setIsMultidimensional(dataset.getIsMultidimensional());
- List<String> escapedChannelNames = new ArrayList<String>();
- for (String name : channelNames)
+ List<String> escapedChannelCodes = new ArrayList<String>();
+ for (String name : channelCodes)
{
- escapedChannelNames.add(StringEscapeUtils.escapeCsv(name));
+ escapedChannelCodes.add(StringEscapeUtils.escapeCsv(name));
}
- params.setChannelsNames(escapedChannelNames);
+ params.setChannelsCodes(escapedChannelCodes);
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 cc45c98716c..be84f753092 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 +108,8 @@ 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 label from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2} order by LABEL")
- public String[] getChannelNamesByDatasetIdOrExperimentId(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(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);
@@ -154,7 +154,7 @@ public interface IImagingQueryDAO extends TransactionQuery
public long addExperiment(String experimentPermId);
@Select("insert into CHANNELS (LABEL, CODE, DESCRIPTION, WAVELENGTH, DS_ID, EXP_ID) values "
- + "(?{1.name}, ?{1.name}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}) returning ID")
+ + "(?{1.label}, ?{1.code}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}) returning ID")
public long addChannel(ImgChannelDTO channel);
@Select("insert into CONTAINERS (PERM_ID, SPOTS_WIDTH, SPOTS_HEIGHT, EXPE_ID) values "
@@ -186,8 +186,8 @@ public interface IImagingQueryDAO extends TransactionQuery
+ "where ID = ?{1.id}")
public void updateChannel(ImgChannelDTO channel);
- @Select("select ID from CHANNELS where (DS_ID = ?{1} or EXP_ID = ?{2}) and LABEL = upper(?{3})")
- public Long tryGetChannelIdByChannelNameDatasetIdOrExperimentId(long id, long experimentId,
- String chosenChannel);
+ @Select("select ID from CHANNELS where (DS_ID = ?{1} or EXP_ID = ?{2}) and CODE = upper(?{3})")
+ public Long tryGetChannelIdByChannelCodeDatasetIdOrExperimentId(long id, long experimentId,
+ String chosenChannelCode);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
index 69ab6ac7936..0072348e2b1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
@@ -30,7 +30,10 @@ public class ImgChannelDTO extends AbstractHashable
private long id;
@ResultColumn("LABEL")
- private String name;
+ private String label;
+
+ @ResultColumn("CODE")
+ private String code;
@ResultColumn("DESCRIPTION")
private String descriptionOrNull;
@@ -46,16 +49,17 @@ public class ImgChannelDTO extends AbstractHashable
@ResultColumn("EXP_ID")
private Long experimentIdOrNull;
- public static ImgChannelDTO createDatasetChannel(String name, String descriptionOrNull,
- Integer wavelengthOrNull, long datasetId)
+ public static ImgChannelDTO createDatasetChannel(String code, String descriptionOrNull,
+ Integer wavelengthOrNull, long datasetId, String label)
{
- return new ImgChannelDTO(name, descriptionOrNull, wavelengthOrNull, datasetId, null);
+ return new ImgChannelDTO(code, descriptionOrNull, wavelengthOrNull, datasetId, null, label);
}
- public static ImgChannelDTO createExperimentChannel(String name, String descriptionOrNull,
- Integer wavelengthOrNull, long experimentId)
+ public static ImgChannelDTO createExperimentChannel(String code, String descriptionOrNull,
+ Integer wavelengthOrNull, long experimentId, String label)
{
- return new ImgChannelDTO(name, descriptionOrNull, wavelengthOrNull, null, experimentId);
+ return new ImgChannelDTO(code, descriptionOrNull, wavelengthOrNull, null, experimentId,
+ label);
}
private ImgChannelDTO()
@@ -63,12 +67,13 @@ public class ImgChannelDTO extends AbstractHashable
// All Data-Object classes must have a default constructor.
}
- private ImgChannelDTO(String name, String descriptionOrNull, Integer wavelengthOrNull,
- Long datasetIdOrNull, Long experimentIdOrNull)
+ private ImgChannelDTO(String code, String descriptionOrNull, Integer wavelengthOrNull,
+ Long datasetIdOrNull, Long experimentIdOrNull, String label)
{
assert (datasetIdOrNull == null && experimentIdOrNull != null)
|| (datasetIdOrNull != null && experimentIdOrNull == null);
- this.name = name.toUpperCase();
+ this.code = code.toUpperCase();
+ this.label = label;
this.descriptionOrNull = descriptionOrNull;
this.wavelengthOrNull = wavelengthOrNull;
this.datasetIdOrNull = datasetIdOrNull;
@@ -85,14 +90,14 @@ public class ImgChannelDTO extends AbstractHashable
this.id = id;
}
- public String getName()
+ public String getCode()
{
- return name;
+ return code;
}
- public void setName(String name)
+ public void setCode(String code)
{
- this.name = name;
+ this.code = code;
}
public String getDescription()
@@ -105,6 +110,16 @@ public class ImgChannelDTO extends AbstractHashable
this.descriptionOrNull = description;
}
+ public String getLabel()
+ {
+ return label;
+ }
+
+ public void setLabel(String label)
+ {
+ this.label = label;
+ }
+
/** can be null */
public Integer getWavelength()
{
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 7245fdbe9cc..e542bb1943d 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
@@ -42,6 +42,8 @@ import ch.systemsx.cisd.bds.hcs.Location;
public class ImagingQueryDAOTest extends AbstractDBTest
{
+ private static final String CHANNEL_LABEL = "Channel Label";
+
private static final int PAGE = 1;
private static final int Y_TILE_ROW = 2;
@@ -162,7 +164,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
// test countChannelByDatasetIdOrExperimentId
assertEquals(2, dao.countChannelByDatasetIdOrExperimentId(datasetId, experimentId));
String[] channelNames =
- dao.getChannelNamesByDatasetIdOrExperimentId(datasetId, experimentId);
+ dao.getChannelCodesByDatasetIdOrExperimentId(datasetId, experimentId);
assertEquals("DSCHANNEL", channelNames[0]);
assertEquals("EXPCHANNEL", channelNames[1]);
@@ -173,7 +175,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
|| channels[1] == channelId1 && channels[0] == channelId2);
// test get id of first channel
- assertEquals(channels[0], dao.tryGetChannelIdByChannelNameDatasetIdOrExperimentId(
+ assertEquals(channels[0], dao.tryGetChannelIdByChannelCodeDatasetIdOrExperimentId(
datasetId, experimentId, "dsChannel").intValue());
List<ImgChannelDTO> experimentChannels = dao.getChannelsByExperimentId(experimentId);
@@ -253,7 +255,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
{
final ImgChannelDTO channel =
ImgChannelDTO.createDatasetChannel(DS_CHANNEL, CHANNEL_DESCRIPTION, WAVELENGTH,
- datasetId);
+ datasetId, CHANNEL_LABEL);
return dao.addChannel(channel);
}
@@ -261,7 +263,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
{
final ImgChannelDTO channel =
ImgChannelDTO.createExperimentChannel(EXP_CHANNEL, CHANNEL_DESCRIPTION, WAVELENGTH,
- experimentId);
+ experimentId, CHANNEL_LABEL);
return dao.addChannel(channel);
}
--
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