From c6719dad90e7a0ca402816057d5bbb2b6cc5842a Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 15 Sep 2010 12:39:10 +0000
Subject: [PATCH] SE-302 make colors of each channel deterministic, allow to
skip validation of the plate name in the image file name (hidden option for
demo purposes)
SVN: 17845
---
.../etl/AbstractHCSImageFileExtractor.java | 36 +++++++++----------
.../openbis/dss/etl/HCSDatasetUploader.java | 18 +++++-----
.../dss/etl/HCSImageFileExtractionResult.java | 7 ++--
.../dss/etl/HCSImageFileExtractor.java | 15 ++++++--
.../dss/etl/PlateStorageProcessor.java | 29 ++++++++-------
.../ScreeningContainerDatasetInfoHelper.java | 17 +++++----
.../etl/dynamix/HCSImageFileExtractor.java | 3 +-
.../dataaccess/IImagingReadonlyQueryDAO.java | 7 ++--
.../etl/dataaccess/ImagingQueryDAOTest.java | 16 +++++----
9 files changed, 76 insertions(+), 72 deletions(-)
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 065d4096c3e..d2b00241c70 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
@@ -19,11 +19,9 @@ package ch.systemsx.cisd.openbis.dss.etl;
import java.io.File;
import java.util.ArrayList;
import java.util.Collections;
-import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Properties;
-import java.util.Set;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang.StringUtils;
@@ -70,7 +68,7 @@ abstract public class AbstractHCSImageFileExtractor implements IHCSImageFileExtr
Location plateLocation, Location wellLocation, Float timepointOrNull,
String imageRelativePath);
- abstract protected Set<Channel> getAllChannels();
+ abstract protected List<Channel> getAllChannels();
/**
* Extracts the plate location from argument. Returns <code>null</code> if the operation fails.
@@ -146,8 +144,8 @@ abstract public class AbstractHCSImageFileExtractor implements IHCSImageFileExtr
}
}
- protected static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, AbstractHCSImageFileExtractor.class);
+ protected static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ AbstractHCSImageFileExtractor.class);
protected static final String IMAGE_FILE_NOT_STANDARDIZABLE =
"Image file '%s' could not be standardized given following tokens: %s.";
@@ -179,25 +177,25 @@ abstract public class AbstractHCSImageFileExtractor implements IHCSImageFileExtr
* @return <code>null</code> if the argument could not be splitted into tokens.
*/
protected final static ImageFileInfo tryExtractDefaultImageInfo(File imageFile,
- SampleIdentifier datasetSample)
+ SampleIdentifier datasetSample, boolean shouldValidatePlateName)
{
final String baseName = FilenameUtils.getBaseName(imageFile.getPath());
final String[] tokens = StringUtils.split(baseName, TOKEN_SEPARATOR);
if (tokens == null || tokens.length < 4)
{
- if (operationLog.isDebugEnabled())
+ if (operationLog.isInfoEnabled())
{
- operationLog.debug(String.format(IMAGE_FILE_NOT_ENOUGH_ENTITIES, imageFile));
+ operationLog.info(String.format(IMAGE_FILE_NOT_ENOUGH_ENTITIES, imageFile));
}
return null;
}
final String sampleCode = tokens[tokens.length - 4];
- if (sampleCode != null
+ if (shouldValidatePlateName && sampleCode != null
&& sampleCode.equalsIgnoreCase(datasetSample.getSampleCode()) == false)
{
- if (operationLog.isDebugEnabled())
+ if (operationLog.isInfoEnabled())
{
- operationLog.debug(String.format(IMAGE_FILE_BELONGS_TO_WRONG_SAMPLE, imageFile,
+ operationLog.info(String.format(IMAGE_FILE_BELONGS_TO_WRONG_SAMPLE, imageFile,
datasetSample, sampleCode));
}
return null;
@@ -250,24 +248,24 @@ abstract public class AbstractHCSImageFileExtractor implements IHCSImageFileExtr
}
} else
{
- if (operationLog.isDebugEnabled())
+ if (operationLog.isInfoEnabled())
{
- operationLog.debug(String.format(IMAGE_FILE_NOT_STANDARDIZABLE, imageFile,
+ operationLog.info(String.format(IMAGE_FILE_NOT_STANDARDIZABLE, imageFile,
imageInfo));
}
invalidFiles.add(imageFile);
}
}
- return new HCSImageFileExtractionResult(acquiredImages, Collections
- .unmodifiableList(invalidFiles), getAllChannels());
+ return new HCSImageFileExtractionResult(acquiredImages,
+ Collections.unmodifiableList(invalidFiles), getAllChannels());
}
private String getRelativeImagePath(File incomingDataSetDirectory, final File imageFile)
{
String imageRelativePath =
- FileUtilities.getRelativeFile(incomingDataSetDirectory, new File(imageFile
- .getPath()));
+ FileUtilities.getRelativeFile(incomingDataSetDirectory,
+ new File(imageFile.getPath()));
assert imageRelativePath != null : "Image relative path should not be null.";
return imageRelativePath;
}
@@ -290,9 +288,9 @@ abstract public class AbstractHCSImageFileExtractor implements IHCSImageFileExtr
return components;
}
- protected final static Set<Channel> createChannels(List<ChannelDescription> channelDescriptions)
+ protected final static List<Channel> createChannels(List<ChannelDescription> channelDescriptions)
{
- Set<Channel> channels = new HashSet<Channel>();
+ List<Channel> channels = new ArrayList<Channel>();
for (ChannelDescription channelDescription : channelDescriptions)
{
channels.add(new Channel(channelDescription.getCode(), null, null, channelDescription
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 30df9639711..f78b0be136c 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
@@ -20,8 +20,8 @@ import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import java.util.Map.Entry;
+import java.util.Set;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfoHelper.ExperimentWithChannelsAndContainer;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
@@ -36,7 +36,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSp
public class HCSDatasetUploader
{
public static void upload(IImagingQueryDAO dao, ImageDatasetInfo info,
- List<AcquiredPlateImage> images, Set<HCSImageFileExtractionResult.Channel> channels)
+ List<AcquiredPlateImage> images, List<HCSImageFileExtractionResult.Channel> channels)
{
new HCSDatasetUploader(dao).upload(info, images, channels);
}
@@ -49,7 +49,7 @@ public class HCSDatasetUploader
}
private void upload(ImageDatasetInfo info, List<AcquiredPlateImage> images,
- Set<HCSImageFileExtractionResult.Channel> channels)
+ List<HCSImageFileExtractionResult.Channel> channels)
{
ExperimentWithChannelsAndContainer basicStruct =
ScreeningContainerDatasetInfoHelper.getOrCreateExperimentWithChannelsAndContainer(
@@ -134,8 +134,8 @@ public class HCSDatasetUploader
private static AcquiredImageInStack makeAcquiredImageInStack(AcquiredPlateImage image)
{
- return new AcquiredImageInStack(image.getChannelCode(), image.getImageReference(), image
- .getThumbnailFilePathOrNull());
+ return new AcquiredImageInStack(image.getChannelCode(), image.getImageReference(),
+ image.getThumbnailFilePathOrNull());
}
private ImgChannelStackDTO makeStackDtoWithouId(AcquiredPlateImage image, Long[][] spotIds,
@@ -249,8 +249,8 @@ public class HCSDatasetUploader
{
ImgImageDTO dto =
new ImgImageDTO(dao.createImageId(), imageReferenceOrNull.getRelativeImagePath(),
- imageReferenceOrNull.tryGetPage(), imageReferenceOrNull
- .tryGetColorComponent());
+ imageReferenceOrNull.tryGetPage(),
+ imageReferenceOrNull.tryGetColorComponent());
return dto;
}
@@ -262,8 +262,8 @@ public class HCSDatasetUploader
{
List<ImgSpotDTO> oldSpots = dao.listSpots(contId);
List<ImgSpotDTO> newSpots =
- createNewSpots(contId, images, oldSpots, info.getContainerRows(), info
- .getContainerColumns(), info.getContainerPermId());
+ createNewSpots(contId, images, oldSpots, info.getContainerRows(),
+ info.getContainerColumns(), info.getContainerPermId());
newSpots.addAll(oldSpots);
return makeTechIdMatrix(newSpots, info.getContainerRows(), info.getContainerColumns());
}
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 2c2f5f365c7..021d5f94b44 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
@@ -17,7 +17,6 @@ package ch.systemsx.cisd.openbis.dss.etl;
import java.io.File;
import java.util.List;
-import java.util.Set;
/**
* Class which contains the image extraction process results.
@@ -32,10 +31,10 @@ public final class HCSImageFileExtractionResult
/** The invalid files found. */
private final List<File> invalidFiles;
- private final Set<Channel> channels;
+ private final List<Channel> channels;
public HCSImageFileExtractionResult(List<AcquiredPlateImage> images, List<File> invalidFiles,
- Set<Channel> channels)
+ List<Channel> channels)
{
this.images = images;
this.invalidFiles = invalidFiles;
@@ -52,7 +51,7 @@ public final class HCSImageFileExtractionResult
return invalidFiles;
}
- public Set<Channel> getChannels()
+ public List<Channel> getChannels()
{
return channels;
}
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 bc8c4303ec3..b11abb49271 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
@@ -20,11 +20,11 @@ import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
-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.utilities.PropertyUtils;
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;
@@ -49,6 +49,13 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
{
private static final String TILE_MAPPING = "tile_mapping";
+ // boolean property, if true the names of the plate in file name and directory name have to
+ // match.
+ // True by default.
+ private static final String CHECK_PLATE_NAME_FLAG_PROPERTY_NAME = "validate-plate-name";
+
+ private final boolean shouldValidatePlateName;
+
private final TileMapper tileMapperOrNull;
private final List<ChannelDescription> channelDescriptions;
@@ -66,6 +73,8 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
this.wellGeometry = getWellGeometry(properties);
this.tileMapperOrNull =
TileMapper.tryCreate(properties.getProperty(TILE_MAPPING), wellGeometry);
+ this.shouldValidatePlateName =
+ PropertyUtils.getBoolean(properties, CHECK_PLATE_NAME_FLAG_PROPERTY_NAME, true);
}
private void checkChannelsAndColorComponents()
@@ -145,7 +154,7 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
}
@Override
- protected Set<Channel> getAllChannels()
+ protected List<Channel> getAllChannels()
{
return createChannels(channelDescriptions);
}
@@ -153,6 +162,6 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
@Override
protected ImageFileInfo tryExtractImageInfo(File imageFile, SampleIdentifier datasetSample)
{
- return tryExtractDefaultImageInfo(imageFile, datasetSample);
+ return tryExtractDefaultImageInfo(imageFile, datasetSample, shouldValidatePlateName);
}
}
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 754bf226665..034ceae5bb0 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
@@ -22,7 +22,6 @@ import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashSet;
import java.util.List;
import java.util.Properties;
import java.util.Set;
@@ -102,11 +101,11 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
/** The directory where <i>original</i> data could be found. */
private static final String DIR_ORIGINAL = ScreeningConstants.ORIGINAL_DATA_DIR;
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, PlateStorageProcessor.class);
+ private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ PlateStorageProcessor.class);
- private static final Logger notificationLog =
- LogFactory.getLogger(LogCategory.NOTIFY, PlateStorageProcessor.class);
+ private static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY,
+ PlateStorageProcessor.class);
// tiles geometry, e.g. 3x4 if the well is divided into 12 tiles (3 rows, 4 columns)
private static final String SPOT_GEOMETRY_PROPERTY = "well_geometry";
@@ -460,8 +459,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
{
throw UserFailureException.fromTemplate(
"No extractable files were found inside a dataset '%s'."
- + " Have you changed your naming convention?", incomingDataSetDirectory
- .getAbsolutePath());
+ + " Have you changed your naming convention?",
+ incomingDataSetDirectory.getAbsolutePath());
}
checkCompleteness(imageCheckList, dataSetInformation, incomingDataSetDirectory.getName(),
mailClient);
@@ -756,19 +755,19 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
new HCSImageFileAccepter(imageFileRootDirectory,
extractChannelCodes(descriptions));
ch.systemsx.cisd.etlserver.HCSImageFileExtractionResult originalResult =
- extractor.process(NodeFactory
- .createDirectoryNode(incomingDataSetDirectory),
+ extractor.process(
+ NodeFactory.createDirectoryNode(incomingDataSetDirectory),
dataSetInformation, accepter);
- Set<HCSImageFileExtractionResult.Channel> channels =
+ List<HCSImageFileExtractionResult.Channel> channels =
convert(originalResult.getChannels());
return new HCSImageFileExtractionResult(accepter.getImages(),
asRelativePaths(originalResult.getInvalidFiles()), channels);
}
- private Set<HCSImageFileExtractionResult.Channel> convert(Set<Channel> channels)
+ private List<HCSImageFileExtractionResult.Channel> convert(Set<Channel> channels)
{
- Set<HCSImageFileExtractionResult.Channel> result =
- new HashSet<HCSImageFileExtractionResult.Channel>();
+ List<HCSImageFileExtractionResult.Channel> result =
+ new ArrayList<HCSImageFileExtractionResult.Channel>();
for (Channel channel : channels)
{
result.add(new HCSImageFileExtractionResult.Channel(getChannelCodeOrLabel(
@@ -820,8 +819,8 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
final Location tileLocation, final IFile imageFile)
{
final String imageRelativePath =
- FileUtilities.getRelativeFile(imageFileRootDirectory, new File(imageFile
- .getPath()));
+ FileUtilities.getRelativeFile(imageFileRootDirectory,
+ new File(imageFile.getPath()));
assert imageRelativePath != null : "Image relative path should not be null.";
String channelCode = getChannelCodeOrLabel(channelCodes, channel);
AcquiredPlateImage 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 367d1853f29..d6e4edb7dba 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
@@ -19,7 +19,6 @@ package ch.systemsx.cisd.openbis.dss.etl;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
@@ -62,8 +61,8 @@ public class ScreeningContainerDatasetInfoHelper
public static long createImageDataset(IImagingQueryDAO dao, ImageDatasetInfo info, long contId)
{
ImgDatasetDTO dataset =
- new ImgDatasetDTO(info.getDatasetPermId(), info.getTileRows(), info
- .getTileColumns(), contId, info.hasImageSeries());
+ new ImgDatasetDTO(info.getDatasetPermId(), info.getTileRows(),
+ info.getTileColumns(), contId, info.hasImageSeries());
return dao.addDataset(dataset);
}
@@ -100,7 +99,7 @@ public class ScreeningContainerDatasetInfoHelper
*/
public static ExperimentWithChannelsAndContainer getOrCreateExperimentWithChannelsAndContainer(
IImagingQueryDAO dao, ScreeningContainerDatasetInfo info,
- Set<HCSImageFileExtractionResult.Channel> channels)
+ List<HCSImageFileExtractionResult.Channel> channels)
{
ScreeningContainerDatasetInfoHelper helper = new ScreeningContainerDatasetInfoHelper(dao);
synchronized (IImagingQueryDAO.class)
@@ -131,8 +130,8 @@ public class ScreeningContainerDatasetInfoHelper
} else
{
ImgContainerDTO container =
- new ImgContainerDTO(containerPermId, info.getContainerRows(), info
- .getContainerColumns(), expId);
+ new ImgContainerDTO(containerPermId, info.getContainerRows(),
+ info.getContainerColumns(), expId);
containerId = dao.addContainer(container);
return new CreatedOrFetchedEntity(false, containerId);
}
@@ -219,7 +218,7 @@ public class ScreeningContainerDatasetInfoHelper
// ------ channels creation ------------------------------
private Map<String, Long> getOrCreateChannels(long expId,
- Set<HCSImageFileExtractionResult.Channel> channels)
+ List<HCSImageFileExtractionResult.Channel> channels)
{
List<ImgChannelDTO> allChannels = dao.getChannelsByExperimentId(expId);
if (allChannels.size() == 0)
@@ -231,7 +230,7 @@ public class ScreeningContainerDatasetInfoHelper
}
}
- private Map<String, Long> updateChannels(long expId, Set<Channel> channels,
+ private Map<String, Long> updateChannels(long expId, List<Channel> channels,
List<ImgChannelDTO> allChannels)
{
Map<String/* name */, ImgChannelDTO> existingChannels = asNameMap(allChannels);
@@ -244,7 +243,7 @@ public class ScreeningContainerDatasetInfoHelper
return map;
}
- private Map<String, Long> createChannels(long expId, Set<Channel> channels)
+ private Map<String, Long> createChannels(long expId, List<Channel> channels)
{
Map<String, Long> map = new HashMap<String, Long>();
for (HCSImageFileExtractionResult.Channel channel : channels)
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 a005b356f3b..2796332a594 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
@@ -26,7 +26,6 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Properties;
-import java.util.Set;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang.StringUtils;
@@ -69,7 +68,7 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor
}
@Override
- protected final Set<Channel> getAllChannels()
+ protected final List<Channel> getAllChannels()
{
return createChannels(channelDescriptions);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
index 53926414f8f..2e7b6ba7b7b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
@@ -111,14 +111,11 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
@Select("select count(*) from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2}")
public int countChannelByDatasetIdOrExperimentId(long datasetId, long experimentId);
- @Select("select * from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2} order by CODE")
+ @Select("select * from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2} order by ID")
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);
-
- @Select(sql = "select * from CHANNELS where EXP_ID = ?{1} order by LABEL", fetchSize = FETCH_SIZE)
+ @Select(sql = "select * from CHANNELS where EXP_ID = ?{1} order by ID", fetchSize = FETCH_SIZE)
public List<ImgChannelDTO> getChannelsByExperimentId(long experimentId);
@Select("select * from SPOTS where cont_id = ?{1}")
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
index 25475bd6b15..3f4539f4e48 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
@@ -181,14 +181,18 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals(CHANNEL_LABEL, channelDTOS.get(1).getLabel());
// test getChannelIdsByDatasetIdOrExperimentId
- long[] channels = dao.getChannelIdsByDatasetIdOrExperimentId(datasetId, experimentId);
- assertEquals(2, channels.length);
- AssertJUnit.assertTrue(channels[0] == channelId1 && channels[1] == channelId2
- || channels[1] == channelId1 && channels[0] == channelId2);
+ List<ImgChannelDTO> channels =
+ dao.getChannelsByDatasetIdOrExperimentId(datasetId, experimentId);
+ assertEquals(2, channels.size());
+ AssertJUnit.assertTrue(channels.get(0).getId() == channelId1
+ && channels.get(1).getId() == channelId2 || channels.get(1).getId() == channelId1
+ && channels.get(0).getId() == channelId2);
// test get id of first channel
- assertEquals(channels[0], dao.tryGetChannelIdByChannelCodeDatasetIdOrExperimentId(
- datasetId, experimentId, "dsChannel").intValue());
+ assertEquals(
+ channels.get(0).getId(),
+ dao.tryGetChannelIdByChannelCodeDatasetIdOrExperimentId(datasetId, experimentId,
+ "dsChannel").intValue());
List<ImgChannelDTO> experimentChannels = dao.getChannelsByExperimentId(experimentId);
assertEquals(1, experimentChannels.size());
--
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