From bffbc5898435a13fd2e3891e031abca0865af17f Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Thu, 24 Jun 2010 18:11:07 +0000
Subject: [PATCH] [LMS-1588] added access to the imaging db from openBIS
SVN: 16731
---
screening/dist/etc/service.properties | 2 -
screening/dist/server/service.properties | 11 ++
screening/etc/service.properties | 2 -
.../dss/etl/AbsoluteImageReference.java | 2 +-
.../etl/AbstractHCSImageFileExtractor.java | 2 +-
.../dss/etl/AbstractImageReference.java | 2 +-
.../openbis/dss/etl/HCSDatasetUploader.java | 16 +--
...java => HCSImageDatasetLoaderFactory.java} | 24 ++--
.../dss/etl/HCSImageFileExtractor.java | 2 +-
...oader.java => IHCSImageDatasetLoader.java} | 18 +--
.../dss/etl/PlateStorageProcessor.java | 8 +-
.../dss/etl/RelativeImageReference.java | 2 +-
.../ScreeningContainerDatasetInfoHelper.java | 28 ++---
.../BDSImagingDatabaseMigrator.java | 8 +-
.../bdsmigration/BDSImagingDbUploader.java | 16 +--
...Loader.java => HCSImageDatasetLoader.java} | 83 ++------------
.../dss/etl/dataaccess/IFeatureVectorDAO.java | 51 ---------
.../AbstractFeatureVectorMigrator.java | 12 +-
.../featurevector/CanonicalFeatureVector.java | 4 +-
.../CsvFeatureVectorMigrator.java | 4 +-
.../CsvToCanonicalFeatureVector.java | 4 +-
.../FeatureVectorStorageProcessor.java | 8 +-
.../featurevector/FeatureVectorUploader.java | 14 +--
.../etl/genedata/FeatureStorageProcessor.java | 8 +-
.../GenedataFeatureVectorMigrator.java | 4 +-
...enedataFormatToCanonicalFeatureVector.java | 4 +-
.../server/images/ImageChannelsUtils.java | 11 +-
...eeningPlateImageParamsReportingPlugin.java | 10 +-
.../server/DssServiceRpcScreening.java | 33 +++---
.../IScreeningBusinessObjectFactory.java | 3 +
.../ScreeningBusinessObjectFactory.java | 17 +++
.../dataaccess/IScreeningDAOFactory.java | 32 ++++++
.../dataaccess/db/ScreeningDAOFactory.java | 79 +++++++++++++
.../screening/shared/ResourceNames.java | 5 +-
.../shared/imaging/HCSDatasetLoader.java | 108 ++++++++++++++++++
.../shared/imaging/IHCSDatasetLoader.java} | 28 +++--
.../imaging}/dataaccess/ColorComponent.java | 2 +-
.../FeatureVectorDataObjectBinding.java | 2 +-
.../imaging/dataaccess/IImagingQueryDAO.java} | 4 +-
.../dataaccess/ImgAcquiredImageDTO.java | 2 +-
.../imaging}/dataaccess/ImgChannelDTO.java | 2 +-
.../dataaccess/ImgChannelStackDTO.java | 2 +-
.../imaging}/dataaccess/ImgContainerDTO.java | 2 +-
.../imaging}/dataaccess/ImgDatasetDTO.java | 2 +-
.../imaging}/dataaccess/ImgFeatureDefDTO.java | 2 +-
.../dataaccess/ImgFeatureValuesDTO.java | 2 +-
.../imaging}/dataaccess/ImgImageDTO.java | 2 +-
.../imaging}/dataaccess/ImgSpotDTO.java | 2 +-
.../java/screening-applicationContext.xml | 25 ++++
screening/source/java/service.properties | 11 ++
.../FeatureVectorUploaderTest.java | 14 +--
.../genedata/FeatureStorageProcessorTest.java | 14 +--
...ataFormatToCanonicalFeatureVectorTest.java | 4 +-
.../openbis/dss/screening/shared/.gitignore | 0
.../imaging}/dataaccess/AbstractDBTest.java | 2 +-
.../shared/imaging}/dataaccess/DBUtils.java | 2 +-
.../imaging}/dataaccess/DBUtilsForTests.java | 8 +-
.../dataaccess/FeatureVectorDAOTest.java | 15 ++-
.../dataaccess/ImagingQueryDAOTest.java} | 19 ++-
59 files changed, 488 insertions(+), 317 deletions(-)
rename screening/source/java/ch/systemsx/cisd/openbis/dss/etl/{HCSDatasetLoaderFactory.java => HCSImageDatasetLoaderFactory.java} (82%)
rename screening/source/java/ch/systemsx/cisd/openbis/dss/etl/{IHCSDatasetLoader.java => IHCSImageDatasetLoader.java} (78%)
rename screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/{HCSDatasetLoader.java => HCSImageDatasetLoader.java} (71%)
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IFeatureVectorDAO.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningDAOFactory.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/db/ScreeningDAOFactory.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl/dataaccess/ImagingDatabaseVersionHolder.java => plugin/screening/shared/imaging/IHCSDatasetLoader.java} (58%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ColorComponent.java (95%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/FeatureVectorDataObjectBinding.java (94%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl/dataaccess/IImagingUploadDAO.java => plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java} (98%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgAcquiredImageDTO.java (96%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgChannelDTO.java (97%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgChannelStackDTO.java (97%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgContainerDTO.java (96%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgDatasetDTO.java (97%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgFeatureDefDTO.java (96%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgFeatureValuesDTO.java (97%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgImageDTO.java (96%)
rename screening/source/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/ImgSpotDTO.java (96%)
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/shared/.gitignore
rename screening/sourceTest/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/AbstractDBTest.java (96%)
rename screening/sourceTest/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/DBUtils.java (96%)
rename screening/sourceTest/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/DBUtilsForTests.java (79%)
rename screening/sourceTest/java/ch/systemsx/cisd/openbis/{dss/etl => plugin/screening/shared/imaging}/dataaccess/FeatureVectorDAOTest.java (85%)
rename screening/sourceTest/java/ch/systemsx/cisd/openbis/{dss/etl/dataaccess/ImagingUploadDAOTest.java => plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java} (89%)
diff --git a/screening/dist/etc/service.properties b/screening/dist/etc/service.properties
index 062e3aa11b5..17ee8fab7ae 100644
--- a/screening/dist/etc/service.properties
+++ b/screening/dist/etc/service.properties
@@ -86,11 +86,9 @@ mail.smtp.host = file://${root-dir}
# ---------------------------------------------------------------------------
data-sources = imaging-db
-imaging-db.version-holder-class = ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImagingDatabaseVersionHolder
imaging-db.databaseEngineCode = postgresql
imaging-db.basicDatabaseName = imaging
imaging-db.databaseKind = productive
-imaging-db.scriptFolder = sql
# ---------------------------------------------------------------------------
# reporting and processing plugins configuration
diff --git a/screening/dist/server/service.properties b/screening/dist/server/service.properties
index e6ca7364f9b..342c6bf93b6 100644
--- a/screening/dist/server/service.properties
+++ b/screening/dist/server/service.properties
@@ -22,6 +22,17 @@ database.owner-password =
database.admin-user =
database.admin-password =
+imaging.database.engine = postgresql
+imaging.database.create-from-scratch = false
+imaging.database.script-single-step-mode = false
+imaging.database.url-host-part =
+imaging.database.kind = dev
+imaging.database.owner =
+imaging.database.owner-password =
+imaging.database.admin-user =
+imaging.database.admin-password =
+imaging.script-folder = source
+
#crowd.service.host = crowd-bsse.ethz.ch
#crowd.service.port = 8443
#crowd.application.name = <openbis_application_name_in_crowd>
diff --git a/screening/etc/service.properties b/screening/etc/service.properties
index ecc26319dbb..1719cd48f1d 100644
--- a/screening/etc/service.properties
+++ b/screening/etc/service.properties
@@ -86,11 +86,9 @@ mail.smtp.host = file://${root-dir}/emails
# ---------------------------------------------------------------------------
data-sources = imaging-db
-imaging-db.version-holder-class = ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImagingDatabaseVersionHolder
imaging-db.databaseEngineCode = postgresql
imaging-db.basicDatabaseName = imaging
imaging-db.databaseKind = dev
-imaging-db.scriptFolder = source/sql
# ---------------------------------------------------------------------------
# reporting and processing plugins configuration
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
index e5aaa9d311d..ad910197128 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java
@@ -17,7 +17,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
import ch.systemsx.cisd.common.io.IContent;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
* Reference to the image with an absolute path.
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 b2ed635b0c5..36a19c6fb3a 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
@@ -39,8 +39,8 @@ import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
* Abstract superclass for <code>IHCSImageFileExtractor</code> implementations.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageReference.java
index c0cbba98c90..2aaa9e6437d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageReference.java
@@ -17,7 +17,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
* Superclass for image reference.
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 a94af70cbfe..8ebc261c5d1 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
@@ -27,29 +27,29 @@ import java.util.Map.Entry;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfoHelper.ExperimentWithChannelsAndContainer;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgAcquiredImageDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgChannelStackDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgImageDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgSpotDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgAcquiredImageDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelStackDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSpotDTO;
/**
* @author Tomasz Pylak
*/
public class HCSDatasetUploader
{
- public static void upload(IImagingUploadDAO dao, ScreeningContainerDatasetInfo info,
+ public static void upload(IImagingQueryDAO dao, ScreeningContainerDatasetInfo info,
List<AcquiredPlateImage> images, Set<HCSImageFileExtractionResult.Channel> channels)
{
new HCSDatasetUploader(dao).upload(info, images, channels);
}
- private final IImagingUploadDAO dao;
+ private final IImagingQueryDAO dao;
- private HCSDatasetUploader(IImagingUploadDAO dao)
+ private HCSDatasetUploader(IImagingQueryDAO dao)
{
this.dao = dao;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetLoaderFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
similarity index 82%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetLoaderFactory.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
index 0ee4906d863..ac0b35df322 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetLoaderFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java
@@ -29,28 +29,28 @@ import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.io.FileBasedContent;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.HCSDatasetLoader;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.HCSImageDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
/**
* @author Tomasz Pylak
*/
-public class HCSDatasetLoaderFactory
+public class HCSImageDatasetLoaderFactory
{
private static final Map<String, IContentRepositoryFactory> repositoryFactories =
createFactories();
- private static final IImagingUploadDAO query = createQuery();
+ private static final IImagingQueryDAO query = createQuery();
- private static IImagingUploadDAO createQuery()
+ private static IImagingQueryDAO createQuery()
{
DataSource dataSource =
ServiceProvider.getDataSourceProvider().getDataSource(
ScreeningConstants.IMAGING_DATA_SOURCE);
- return QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ return QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
}
private static Map<String, IContentRepositoryFactory> createFactories()
@@ -61,30 +61,30 @@ public class HCSDatasetLoaderFactory
return factories;
}
- public static final IHCSDatasetLoader create(File datasetRootDir, String datasetCode)
+ public static final IHCSImageDatasetLoader create(File datasetRootDir, String datasetCode)
{
return createImageDBLoader(datasetRootDir, datasetCode);
// return createBDSLoader(datasetRootDir);
}
- private static HCSDatasetLoader createImageDBLoader(File datasetRootDir, String datasetCode)
+ private static HCSImageDatasetLoader createImageDBLoader(File datasetRootDir, String datasetCode)
{
IContentRepository repository = new ContentRepository(datasetRootDir, repositoryFactories);
- return new HCSDatasetLoader(query, datasetCode, repository);
+ return new HCSImageDatasetLoader(query, datasetCode, repository);
}
// remove when not needed
@SuppressWarnings("unused")
- private static IHCSDatasetLoader createBDSLoader(File datasetRootDir)
+ private static IHCSImageDatasetLoader createBDSLoader(File datasetRootDir)
{
final ch.systemsx.cisd.bds.hcs.HCSDatasetLoader loader =
new ch.systemsx.cisd.bds.hcs.HCSDatasetLoader(datasetRootDir);
return adapt(loader);
}
- private static IHCSDatasetLoader adapt(final ch.systemsx.cisd.bds.hcs.HCSDatasetLoader loader)
+ private static IHCSImageDatasetLoader adapt(final ch.systemsx.cisd.bds.hcs.HCSDatasetLoader loader)
{
- return new IHCSDatasetLoader()
+ return new IHCSImageDatasetLoader()
{
public void close()
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 418e0183604..7752e5a16a4 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
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.common.filesystem.FileOperations;
import ch.systemsx.cisd.openbis.dss.etl.AbstractHCSImageFileExtractor;
import ch.systemsx.cisd.openbis.dss.etl.AcquiredPlateImage;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
* Generic image extractor implementation. The images names should have an extension present in
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java
similarity index 78%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSDatasetLoader.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java
index b671bc722ae..65bfd6d728e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java
@@ -16,29 +16,15 @@
package ch.systemsx.cisd.openbis.dss.etl;
-import java.util.List;
-
-import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
/**
* @author Tomasz Pylak
*/
-public interface IHCSDatasetLoader
+public interface IHCSImageDatasetLoader extends IHCSDatasetLoader
{
-
- /** has to be called at the end */
- void close();
-
- Geometry getPlateGeometry();
-
- Geometry getWellGeometry();
-
- int getChannelCount();
-
- List<String> getChannelsNames();
-
/**
* @param chosenChannel start from 1
* @return image (with absolute path, page and color)
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 6fdf41fa9a9..9ce83fdb48f 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
@@ -61,12 +61,12 @@ import ch.systemsx.cisd.hdf5.HDF5FactoryProvider;
import ch.systemsx.cisd.hdf5.IHDF5Writer;
import ch.systemsx.cisd.openbis.dss.Constants;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageCheckList.FullLocation;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
/**
* Storage processor which stores HCS images in a special-purpose database.
@@ -142,7 +142,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private final ch.systemsx.cisd.etlserver.IHCSImageFileExtractor deprecatedImageFileExtractor;
- private IImagingUploadDAO currentTransaction;
+ private IImagingQueryDAO currentTransaction;
public PlateStorageProcessor(final Properties properties)
{
@@ -178,9 +178,9 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
this.currentTransaction = null;
}
- private IImagingUploadDAO createQuery()
+ private IImagingQueryDAO createQuery()
{
- return QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ return QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
}
private final static void checkDataSetInformation(final DataSetInformation dataSetInformation)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/RelativeImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/RelativeImageReference.java
index 1d9f12fdbd9..99b2ec918cb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/RelativeImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/RelativeImageReference.java
@@ -16,7 +16,7 @@
package ch.systemsx.cisd.openbis.dss.etl;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
* Reference to the image with a path relative to the folder with all the images.
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 6fb56512fb1..3a0b66ff09f 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
@@ -23,10 +23,10 @@ import java.util.Set;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgChannelDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgContainerDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgDatasetDTO;
+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.ImgContainerDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
/**
* Helper class for retrieving and/or creating entities associated with the screening container data
@@ -36,9 +36,9 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgDatasetDTO;
*/
public class ScreeningContainerDatasetInfoHelper
{
- private final IImagingUploadDAO dao;
+ private final IImagingQueryDAO dao;
- public ScreeningContainerDatasetInfoHelper(IImagingUploadDAO dao)
+ public ScreeningContainerDatasetInfoHelper(IImagingQueryDAO dao)
{
this.dao = dao;
}
@@ -55,7 +55,7 @@ public class ScreeningContainerDatasetInfoHelper
}
// Package-visible static methods
- public static long createDataset(IImagingUploadDAO dao, ScreeningContainerDatasetInfo info,
+ public static long createDataset(IImagingQueryDAO dao, ScreeningContainerDatasetInfo info,
long contId)
{
ImgDatasetDTO dataset =
@@ -71,10 +71,10 @@ public class ScreeningContainerDatasetInfoHelper
* transaction will be rolled back sample and experiment created in first transaction will stay
* in the DB.
*/
- public static ExperimentAndContainerIds getOrCreateExperimentAndContainer(
- IImagingUploadDAO dao, ScreeningContainerDatasetInfo info)
+ public static ExperimentAndContainerIds getOrCreateExperimentAndContainer(IImagingQueryDAO dao,
+ ScreeningContainerDatasetInfo info)
{
- synchronized (IImagingUploadDAO.class)
+ synchronized (IImagingQueryDAO.class)
{
CreatedOrFetchedEntity exp = getOrCreateExperiment(dao, info);
CreatedOrFetchedEntity cont = getOrCreateContainer(dao, info, exp.getId());
@@ -96,11 +96,11 @@ public class ScreeningContainerDatasetInfoHelper
* in the DB.
*/
public static ExperimentWithChannelsAndContainer getOrCreateExperimentWithChannelsAndContainer(
- IImagingUploadDAO dao, ScreeningContainerDatasetInfo info,
+ IImagingQueryDAO dao, ScreeningContainerDatasetInfo info,
Set<HCSImageFileExtractionResult.Channel> channels)
{
ScreeningContainerDatasetInfoHelper helper = new ScreeningContainerDatasetInfoHelper(dao);
- synchronized (IImagingUploadDAO.class)
+ synchronized (IImagingQueryDAO.class)
{
CreatedOrFetchedEntity exp = getOrCreateExperiment(dao, info);
long expId = exp.getId();
@@ -117,7 +117,7 @@ public class ScreeningContainerDatasetInfoHelper
}
}
- private static CreatedOrFetchedEntity getOrCreateContainer(IImagingUploadDAO dao,
+ private static CreatedOrFetchedEntity getOrCreateContainer(IImagingQueryDAO dao,
ScreeningContainerDatasetInfo info, long expId)
{
String containerPermId = info.getContainerPermId();
@@ -135,7 +135,7 @@ public class ScreeningContainerDatasetInfoHelper
}
}
- private static CreatedOrFetchedEntity getOrCreateExperiment(IImagingUploadDAO dao,
+ private static CreatedOrFetchedEntity getOrCreateExperiment(IImagingQueryDAO dao,
ScreeningContainerDatasetInfo info)
{
String experimentPermId = info.getExperimentPermId();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDatabaseMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDatabaseMigrator.java
index 6284cc4dad7..3f4f132f37d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDatabaseMigrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDatabaseMigrator.java
@@ -28,16 +28,16 @@ import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.etl.AbstractHCSImageFileExtractor;
import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
/**
* @author Franz-Josef Elmer
*/
public class BDSImagingDatabaseMigrator extends AbstractBDSMigrator
{
- private IImagingUploadDAO dao;
+ private IImagingQueryDAO dao;
private List<String> channelNames;
@@ -75,7 +75,7 @@ public class BDSImagingDatabaseMigrator extends AbstractBDSMigrator
public BDSImagingDatabaseMigrator(Properties properties)
{
DataSource dataSource = ServiceProvider.getDataSourceProvider().getDataSource(properties);
- dao = QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ dao = QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
channelNames =
PropertyUtils.getMandatoryList(properties, PlateStorageProcessor.CHANNEL_NAMES);
channelColorComponentsOrNull =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java
index 3e3679ddbfc..6ef193e48af 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java
@@ -49,9 +49,9 @@ import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor;
import ch.systemsx.cisd.openbis.dss.etl.RelativeImageReference;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
/**
* Uploads data to the imaging database.
@@ -62,7 +62,7 @@ class BDSImagingDbUploader
{
public static IMigrator createImagingDbUploaderMigrator(Properties properties)
{
- final IImagingUploadDAO dao = createQuery(properties);
+ final IImagingQueryDAO dao = createQuery(properties);
final List<String> channelNames =
PropertyUtils.getMandatoryList(properties, PlateStorageProcessor.CHANNEL_NAMES);
final List<ColorComponent> channelColorComponentsOrNull =
@@ -101,13 +101,13 @@ class BDSImagingDbUploader
}
}
- private static IImagingUploadDAO createQuery(Properties properties)
+ private static IImagingQueryDAO createQuery(Properties properties)
{
DataSource dataSource = ServiceProvider.getDataSourceProvider().getDataSource(properties);
- return QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ return QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
}
- private static boolean migrateDataset(File dataset, IImagingUploadDAO dao,
+ private static boolean migrateDataset(File dataset, IImagingQueryDAO dao,
List<String> channelNames, List<ColorComponent> channelColorComponentsOrNull)
{
String originalDatasetDirName = tryGetOriginalDatasetDirName(dataset);
@@ -121,7 +121,7 @@ class BDSImagingDbUploader
private final File dataset;
- private final IImagingUploadDAO dao;
+ private final IImagingQueryDAO dao;
private final String originalDatasetDirName;
@@ -129,7 +129,7 @@ class BDSImagingDbUploader
private final List<ColorComponent> channelColorComponentsOrNull;
- BDSImagingDbUploader(File dataset, IImagingUploadDAO dao, String originalDatasetDirName,
+ BDSImagingDbUploader(File dataset, IImagingQueryDAO dao, String originalDatasetDirName,
List<String> channelNames, List<ColorComponent> channelColorComponentsOrNull)
{
this.dataset = dataset;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
similarity index 71%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java
rename to screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
index 0b7dee61ddf..ec93ee30c00 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java
@@ -21,94 +21,38 @@ import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
import javax.imageio.ImageIO;
import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IContentRepository;
-import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.HCSDatasetLoader;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDTO;
/**
- * Helper class for easy handling of HCS image dataset standard structure.
+ * {@link HCSDatasetLoader} extension with code for handling images.
*
* @author Tomasz Pylak
* @author Piotr Buczek
*/
-public class HCSDatasetLoader implements IHCSDatasetLoader
+public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImageDatasetLoader
{
- private final IImagingUploadDAO query;
-
- private final ImgDatasetDTO dataset;
-
private final IContentRepository contentRepository;
- private ImgContainerDTO container;
-
- private Integer channelCount;
-
- private List<String> channelNames;
-
- public HCSDatasetLoader(IImagingUploadDAO query, String datasetPermId,
+ public HCSImageDatasetLoader(IImagingQueryDAO query, String datasetPermId,
IContentRepository contentRepository)
{
+ super(query, datasetPermId);
this.contentRepository = contentRepository;
- this.query = query;
- this.dataset = query.tryGetDatasetByPermId(datasetPermId);
- if (dataset == null)
- {
- throw new IllegalStateException(String.format("Dataset '%s' not found", datasetPermId));
- }
- }
-
- /** has to be called at the end */
- public void close()
- {
- query.close();
- }
-
- private ImgContainerDTO getContainer()
- {
- if (container == null)
- {
- container = query.getContainerById(dataset.getContainerId());
- }
- return container;
- }
-
- public Geometry getPlateGeometry()
- {
- return new Geometry(getContainer().getNumberOfRows(), getContainer().getNumberOfColumns());
- }
-
- private ImgDatasetDTO getDataset()
- {
- return dataset;
- }
-
- public Geometry getWellGeometry()
- {
- return new Geometry(getDataset().getFieldNumberOfRows(), getDataset()
- .getFieldNumberOfColumns());
- }
-
- public int getChannelCount()
- {
- if (channelCount == null)
- {
- channelCount = getChannelsNames().size();
- }
- return channelCount;
}
/**
@@ -224,15 +168,4 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
}
}
- public List<String> getChannelsNames()
- {
- if (channelNames == null)
- {
- String[] namesAsArray =
- query.getChannelNamesByDatasetIdOrExperimentId(getDataset().getId(),
- getContainer().getExperimentId());
- channelNames = new ArrayList<String>(Arrays.asList(namesAsArray));
- }
- return channelNames;
- }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IFeatureVectorDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IFeatureVectorDAO.java
deleted file mode 100644
index d6bbc3895e9..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IFeatureVectorDAO.java
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * 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.dataaccess;
-
-import java.util.List;
-
-import net.lemnik.eodsql.Select;
-import net.lemnik.eodsql.TransactionQuery;
-
-import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.ByteArrayMapper;
-
-/**
- * DAO for interacting with feature vector tables.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public interface IFeatureVectorDAO extends TransactionQuery
-{
- public static final int FETCH_SIZE = 1000;
-
- // Simple Getters
- @Select("SELECT * from FEATURE_DEFS where DS_ID = ?{1}")
- public List<ImgFeatureDefDTO> listFeatureDefsByDataSetId(long dataSetId);
-
- @Select(value = "SELECT * from FEATURE_VALUES where FD_ID = ?{1.id}", resultSetBinding = FeatureVectorDataObjectBinding.class)
- public List<ImgFeatureValuesDTO> getFeatureValues(ImgFeatureDefDTO featureDef);
-
- // Inserts
- @Select("INSERT into FEATURE_DEFS (NAME, DESCRIPTION, DS_ID) values "
- + "(?{1.name}, ?{1.description}, ?{1.dataSetId}) RETURNING ID")
- public long addFeatureDef(ImgFeatureDefDTO featureDef);
-
- @Select(value = "INSERT into FEATURE_VALUES (VALUES, Z_in_M, T_in_SEC, FD_ID) values "
- + "(?{1.values}, ?{1.z}, ?{1.t}, ?{1.featureDefId}) RETURNING ID", parameterBindings =
- { ByteArrayMapper.class })
- public long addFeatureValues(ImgFeatureValuesDTO featureValues);
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java
index ce06b80ce70..e43840968c9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java
@@ -28,8 +28,6 @@ import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.etlserver.plugins.IMigrator;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgDatasetDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
@@ -40,6 +38,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
/**
* Imports individual data sets into the imaging db.
@@ -48,7 +48,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst
*/
public abstract class AbstractFeatureVectorMigrator implements IMigrator
{
- protected final IImagingUploadDAO dao;
+ protected final IImagingQueryDAO dao;
protected final IEncapsulatedOpenBISService openBisService;
@@ -59,7 +59,7 @@ public abstract class AbstractFeatureVectorMigrator implements IMigrator
public AbstractFeatureVectorMigrator(Properties properties)
{
DataSource dataSource = ServiceProvider.getDataSourceProvider().getDataSource(properties);
- dao = QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ dao = QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
openBisService = ServiceProvider.getOpenBISService();
knownDataSets = openBisService.listDataSets();
knownDataSetsByCode =
@@ -247,7 +247,7 @@ public abstract class AbstractFeatureVectorMigrator implements IMigrator
*/
protected abstract static class AbstractImageDbImporter
{
- protected final IImagingUploadDAO dao;
+ protected final IImagingQueryDAO dao;
protected final ScreeningContainerDatasetInfo screeningDataSetInfo;
@@ -255,7 +255,7 @@ public abstract class AbstractFeatureVectorMigrator implements IMigrator
protected boolean isSuccessful = false;
- protected AbstractImageDbImporter(IImagingUploadDAO dao,
+ protected AbstractImageDbImporter(IImagingQueryDAO dao,
ScreeningContainerDatasetInfo screeningDataSetInfo, File fileToMigrate)
{
this.dao = dao;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CanonicalFeatureVector.java
index 555a8e75a99..e77f3823826 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CanonicalFeatureVector.java
@@ -19,8 +19,8 @@ package ch.systemsx.cisd.openbis.dss.etl.featurevector;
import java.util.ArrayList;
import java.util.List;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
/**
* Image feature vectors stored in a standardized form.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java
index 816657cea5a..07f9511253b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java
@@ -25,10 +25,10 @@ import java.util.Properties;
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.etlserver.DefaultStorageProcessor;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvToCanonicalFeatureVector.CsvToCanonicalFeatureVectorConfiguration;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.utils.CsvFileReaderHelper;
/**
@@ -120,7 +120,7 @@ public class CsvFeatureVectorMigrator extends AbstractFeatureVectorMigrator
private final CsvToCanonicalFeatureVectorConfiguration convertorConfig;
- protected ImporterCsv(IImagingUploadDAO dao,
+ protected ImporterCsv(IImagingQueryDAO dao,
ScreeningContainerDatasetInfo screeningDataSetInfo, File fileToMigrate,
FeatureVectorStorageProcessorConfiguration configuration,
CsvToCanonicalFeatureVectorConfiguration convertorConfig)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
index 3b9faf97c4c..d297d9904a1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
@@ -24,9 +24,9 @@ import java.util.List;
import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.geometry.Point;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
/**
* Converts feature vectors from CSV files to CanonicaFeatureVector objects.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
index 2d0ae122776..e68f87a4eb8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorStorageProcessor.java
@@ -31,7 +31,6 @@ import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.etlserver.AbstractDelegatingStorageProcessor;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvToCanonicalFeatureVector.CsvToCanonicalFeatureVectorConfiguration;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -39,6 +38,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.utils.CsvFileReaderHelper;
/**
@@ -59,7 +59,7 @@ public class FeatureVectorStorageProcessor extends AbstractDelegatingStorageProc
private final IEncapsulatedOpenBISService openBisService;
// Execution state of this object -- set to null after an execution is finished.
- private IImagingUploadDAO dataAccessObject = null;
+ private IImagingQueryDAO dataAccessObject = null;
public FeatureVectorStorageProcessor(Properties properties)
{
@@ -138,9 +138,9 @@ public class FeatureVectorStorageProcessor extends AbstractDelegatingStorageProc
return sampleOrNull;
}
- private IImagingUploadDAO createDAO()
+ private IImagingQueryDAO createDAO()
{
- return QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ return QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploader.java
index 9d2a93642e8..fa698dca418 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploader.java
@@ -20,9 +20,9 @@ import java.util.List;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfoHelper;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
/**
* Helper class for uploading feature vectors from the file system into the data base.
@@ -31,11 +31,11 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
*/
public class FeatureVectorUploader
{
- private final IImagingUploadDAO dao;
+ private final IImagingQueryDAO dao;
private final ScreeningContainerDatasetInfo info;
- public FeatureVectorUploader(IImagingUploadDAO imagingDao, ScreeningContainerDatasetInfo info)
+ public FeatureVectorUploader(IImagingQueryDAO imagingDao, ScreeningContainerDatasetInfo info)
{
this.dao = imagingDao;
this.info = info;
@@ -58,13 +58,13 @@ public class FeatureVectorUploader
private static class FeatureVectorUploaderHelper
{
- private final IImagingUploadDAO dao;
+ private final IImagingQueryDAO dao;
private final long dataSetId;
private final CanonicalFeatureVector fvec;
- FeatureVectorUploaderHelper(IImagingUploadDAO dao, ScreeningContainerDatasetInfo info,
+ FeatureVectorUploaderHelper(IImagingQueryDAO dao, ScreeningContainerDatasetInfo info,
long dataSetId, CanonicalFeatureVector fvec)
{
this.dao = dao;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessor.java
index 90797bd2ddc..bc898ea13d6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessor.java
@@ -37,7 +37,6 @@ import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.utils.Column;
import ch.systemsx.cisd.etlserver.utils.TableBuilder;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorUploader;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -45,6 +44,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
/**
* @author Franz-Josef Elmer
@@ -60,7 +60,7 @@ public class FeatureStorageProcessor extends AbstractDelegatingStorageProcessor
private final IEncapsulatedOpenBISService openBisService;
// Execution state of this object -- set to null after an execution is finished.
- private IImagingUploadDAO dataAccessObject = null;
+ private IImagingQueryDAO dataAccessObject = null;
private final class ColumnsBuilder
{
@@ -260,9 +260,9 @@ public class FeatureStorageProcessor extends AbstractDelegatingStorageProcessor
return sampleOrNull;
}
- protected IImagingUploadDAO createDAO()
+ protected IImagingQueryDAO createDAO()
{
- return QueryTool.getQuery(dataSource, IImagingUploadDAO.class);
+ return QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
}
private String convertColumnsToString(String barCode, ColumnsBuilder columnsBuilder)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFeatureVectorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFeatureVectorMigrator.java
index 4d956f9fe71..668b94c3af6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFeatureVectorMigrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFeatureVectorMigrator.java
@@ -25,11 +25,11 @@ import java.util.Properties;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.etlserver.DefaultStorageProcessor;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.AbstractFeatureVectorMigrator;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorUploader;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
/**
* Imports Genedata feature vectors into the database.
@@ -112,7 +112,7 @@ public class GenedataFeatureVectorMigrator extends AbstractFeatureVectorMigrator
/**
* @param fileToMigrate
*/
- private ImporterGenedata(IImagingUploadDAO dao,
+ private ImporterGenedata(IImagingQueryDAO dao,
ScreeningContainerDatasetInfo screeningDataSetInfo, File fileToMigrate)
{
super(dao, screeningDataSetInfo, fileToMigrate);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
index ae2a11c49a4..66b820fec50 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
@@ -27,9 +27,9 @@ import org.apache.commons.lang.StringUtils;
import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.geometry.Point;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
/**
* Converts currentFeature vectors from the Genedata currentFeature vector file format to
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 808b22874e8..649a762c2f5 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
@@ -26,11 +26,11 @@ import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
-import ch.systemsx.cisd.openbis.dss.etl.HCSDatasetLoaderFactory;
-import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
/**
* Utility classes to create an image of a specified size containing one channel or a subset of all
@@ -49,7 +49,8 @@ public class ImageChannelsUtils
public static List<AbsoluteImageReference> getImagePaths(File datasetRoot, String datasetCode,
TileImageReference params)
{
- IHCSDatasetLoader imageAccessor = HCSDatasetLoaderFactory.create(datasetRoot, datasetCode);
+ IHCSImageDatasetLoader imageAccessor =
+ HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
Location wellLocation = params.getWellLocation();
Location tileLocation = params.getTileLocation();
List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
@@ -218,7 +219,7 @@ public class ImageChannelsUtils
* @param chosenChannel starts from 1
* @throw {@link EnvironmentFailureException} when image does not exist
*/
- public static AbsoluteImageReference getImage(IHCSDatasetLoader imageAccessor,
+ public static AbsoluteImageReference getImage(IHCSImageDatasetLoader imageAccessor,
Location wellLocation, Location tileLocation, String chosenChannel,
Size thumbnailSizeOrNull)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
index 058a401cd27..e7273040dae 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
@@ -27,8 +27,8 @@ import java.util.Properties;
import org.apache.commons.lang.StringEscapeUtils;
import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.openbis.dss.etl.HCSDatasetLoaderFactory;
-import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
@@ -74,8 +74,8 @@ public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastoreP
for (DatasetDescription dataset : datasets)
{
File datasetFile = new File(storeRoot, dataset.getDataSetLocation());
- IHCSDatasetLoader imageAccessor =
- HCSDatasetLoaderFactory.create(datasetFile, dataset.getDatasetCode());
+ IHCSImageDatasetLoader imageAccessor =
+ HCSImageDatasetLoaderFactory.create(datasetFile, dataset.getDatasetCode());
addReportRows(builder, dataset, imageAccessor);
imageAccessor.close();
}
@@ -94,7 +94,7 @@ public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastoreP
}
private void addReportRows(SimpleTableModelBuilder builder, DatasetDescription dataset,
- IHCSDatasetLoader imageAccessor)
+ IHCSImageDatasetLoader imageAccessor)
{
Geometry plateGeometry = imageAccessor.getPlateGeometry();
Geometry wellGeometry = imageAccessor.getWellGeometry();
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 38a0556b982..d1faeadb7ec 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
@@ -40,8 +40,8 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.io.ConcatenatedContentInputStream;
import ch.systemsx.cisd.common.io.IContent;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
-import ch.systemsx.cisd.openbis.dss.etl.HCSDatasetLoaderFactory;
-import ch.systemsx.cisd.openbis.dss.etl.IHCSDatasetLoader;
+import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory;
+import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDssServiceRpc;
import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
@@ -170,8 +170,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private static ImageDatasetMetadata extractImageMetadata(IImageDatasetIdentifier dataset,
File datasetRoot)
{
- IHCSDatasetLoader imageAccessor =
- HCSDatasetLoaderFactory.create(datasetRoot, dataset.getDatasetCode());
+ IHCSImageDatasetLoader imageAccessor =
+ HCSImageDatasetLoaderFactory.create(datasetRoot, dataset.getDatasetCode());
IContent imageFile = getAnyImagePath(imageAccessor, dataset);
Geometry wellGeometry = imageAccessor.getWellGeometry();
int channelsNumber = imageAccessor.getChannelCount();
@@ -181,7 +181,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
image.getHeight());
}
- private static IContent getAnyImagePath(IHCSDatasetLoader imageAccessor,
+ private static IContent getAnyImagePath(IHCSImageDatasetLoader imageAccessor,
IImageDatasetIdentifier dataset)
{
Geometry plateGeometry = imageAccessor.getPlateGeometry();
@@ -232,14 +232,14 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
public InputStream loadImages(String sessionToken, List<PlateImageReference> imageReferences)
{
- Map<String, IHCSDatasetLoader> imageLoadersMap =
+ Map<String, IHCSImageDatasetLoader> imageLoadersMap =
getImageDatasetsMap(sessionToken, imageReferences);
List<IContent> imageFiles = new ArrayList<IContent>();
try
{
for (PlateImageReference imageReference : imageReferences)
{
- IHCSDatasetLoader imageAccessor =
+ IHCSImageDatasetLoader imageAccessor =
imageLoadersMap.get(imageReference.getDatasetCode());
assert imageAccessor != null : "imageAccessor not found for: " + imageReference;
AbsoluteImageReference image = tryGetImage(imageAccessor, imageReference);
@@ -260,20 +260,20 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return new ConcatenatedContentInputStream(true, imageFiles);
}
- private static void closeDatasetLoaders(Collection<IHCSDatasetLoader> loaders)
+ private static void closeDatasetLoaders(Collection<IHCSImageDatasetLoader> loaders)
{
- for (IHCSDatasetLoader loader : loaders)
+ for (IHCSImageDatasetLoader loader : loaders)
{
loader.close();
}
}
// throws exception if some datasets cannot be found
- private Map<String/* image or feature vector dataset code */, IHCSDatasetLoader> getImageDatasetsMap(
+ private Map<String/* image or feature vector dataset code */, IHCSImageDatasetLoader> getImageDatasetsMap(
String sessionToken, List<PlateImageReference> imageReferences)
{
- Map<String/* dataset code */, IHCSDatasetLoader> imageDatasetsMap =
- new HashMap<String, IHCSDatasetLoader>();
+ Map<String/* dataset code */, IHCSImageDatasetLoader> imageDatasetsMap =
+ new HashMap<String, IHCSImageDatasetLoader>();
for (PlateImageReference imageReference : imageReferences)
{
if (imageDatasetsMap.containsKey(imageReference.getDatasetCode()) == false)
@@ -282,7 +282,8 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
tryFindImageDataset(sessionToken, imageReference.getDatasetCode());
if (imageDataset != null)
{
- IHCSDatasetLoader imageAccessor = createImageLoader(imageDataset.getCode());
+ IHCSImageDatasetLoader imageAccessor =
+ createImageLoader(imageDataset.getCode());
imageDatasetsMap.put(imageReference.getDatasetCode(), imageAccessor);
} else
{
@@ -294,7 +295,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return imageDatasetsMap;
}
- private AbsoluteImageReference tryGetImage(IHCSDatasetLoader imageAccessor,
+ private AbsoluteImageReference tryGetImage(IHCSImageDatasetLoader imageAccessor,
PlateImageReference imageRef)
{
Location wellLocation = asLocation(imageRef.getWellPosition());
@@ -328,10 +329,10 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
return new Location(wellPosition.getWellColumn(), wellPosition.getWellRow());
}
- private IHCSDatasetLoader createImageLoader(String datasetCode)
+ private IHCSImageDatasetLoader createImageLoader(String datasetCode)
{
File datasetRoot = getRootDirectoryForDataSet(datasetCode);
- return HCSDatasetLoaderFactory.create(datasetRoot, datasetCode);
+ return HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
}
private ExternalData tryFindImageDataset(String sessionToken, String datasetCode)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
index cfc006f87e5..97248a938d6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatase
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
/**
* A <i>screening</i> plugin specific business object factory.
@@ -33,6 +34,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
*/
public interface IScreeningBusinessObjectFactory
{
+ public IHCSDatasetLoader createHCSDatasetLoader(final String datasetPermId);
+
public ISampleBO createSampleBO(final Session session);
public IExternalDataTable createExternalDataTable(final Session session);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
index 56bf93ad896..e5dc92736c6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.server;
+import javax.annotation.Resource;
+
import org.springframework.stereotype.Component;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentBO;
@@ -28,7 +30,10 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMater
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.AbstractPluginBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningDAOFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.HCSDatasetLoader;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
/**
* The unique {@link IScreeningBusinessObjectFactory} implementation.
@@ -40,6 +45,18 @@ public final class ScreeningBusinessObjectFactory extends AbstractPluginBusiness
implements IScreeningBusinessObjectFactory
{
+ @Resource(name = ResourceNames.SCREENING_DAO_FACTORY)
+ private IScreeningDAOFactory specificDAOFactory;
+
+ public ScreeningBusinessObjectFactory()
+ {
+ }
+
+ public final IHCSDatasetLoader createHCSDatasetLoader(final String datasetPermId)
+ {
+ return new HCSDatasetLoader(specificDAOFactory.getImagingQueryDAO(), datasetPermId);
+ }
+
public final ISampleBO createSampleBO(final Session session)
{
return getCommonBusinessObjectFactory().createSampleBO(session);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningDAOFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningDAOFactory.java
new file mode 100644
index 00000000000..e37c8c943b1
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningDAOFactory.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess;
+
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+
+/**
+ * A factory for Screening specific DAOs.
+ *
+ * @author Piotr Buczek
+ */
+public interface IScreeningDAOFactory
+{
+ public DatabaseConfigurationContext getContext();
+
+ public IImagingQueryDAO getImagingQueryDAO();
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/db/ScreeningDAOFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/db/ScreeningDAOFactory.java
new file mode 100644
index 00000000000..9a8095fdcf5
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/db/ScreeningDAOFactory.java
@@ -0,0 +1,79 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.db;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+
+import net.lemnik.eodsql.QueryTool;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningDAOFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+
+/**
+ * @author Piotr Buczek
+ */
+public class ScreeningDAOFactory implements IScreeningDAOFactory
+{
+ /** Current version of the database. */
+ public static final String DATABASE_VERSION = "003"; // S83
+
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, ScreeningDAOFactory.class);
+
+ private final IImagingQueryDAO imagingQueryDAO;
+
+ private final DatabaseConfigurationContext imagingDatabaseContext;
+
+ public ScreeningDAOFactory(DatabaseConfigurationContext context)
+ {
+ this.imagingDatabaseContext = context;
+ DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context, DATABASE_VERSION);
+ Connection connection = null;
+ try
+ {
+ connection = context.getDataSource().getConnection();
+ } catch (SQLException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ // TODO this is the same solution as in PhosphoNetX - is it ok to use connection here?
+ // shouldn't it be a data source passed here in constructor?
+ imagingQueryDAO = QueryTool.getQuery(connection, IImagingQueryDAO.class);
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("DAO factory for Screening created.");
+ }
+ }
+
+ public DatabaseConfigurationContext getContext()
+ {
+ return imagingDatabaseContext;
+ }
+
+ public IImagingQueryDAO getImagingQueryDAO()
+ {
+ return imagingQueryDAO;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
index 3890e439958..cba01cf953c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
@@ -37,8 +37,9 @@ public final class ResourceNames
public final static String SCREENING_PLUGIN_SERVER = "screening-plugin-server";
- public final static String SCREENING_BUSINESS_OBJECT_FACTORY =
- "screening-business-object-factory";
+ public final static String SCREENING_BUSINESS_OBJECT_FACTORY = "screening-bo-factory";
+
+ public final static String SCREENING_DAO_FACTORY = "screening-dao-factory";
public final static String SCREENING_SAMPLE_SERVER_PLUGIN = "screening-sample-server-plugin";
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
new file mode 100644
index 00000000000..11b03d9d39b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
@@ -0,0 +1,108 @@
+/*
+ * 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.plugin.screening.shared.imaging;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
+
+/**
+ * Helper class for easy handling of HCS image dataset standard structure with no code for handling
+ * images.
+ *
+ * @author Tomasz Pylak
+ * @author Piotr Buczek
+ */
+public class HCSDatasetLoader implements IHCSDatasetLoader
+{
+ protected final IImagingQueryDAO query;
+
+ protected final ImgDatasetDTO dataset;
+
+ protected ImgContainerDTO container;
+
+ protected Integer channelCount;
+
+ protected List<String> channelNames;
+
+ public HCSDatasetLoader(IImagingQueryDAO query, String datasetPermId)
+ {
+ this.query = query;
+ this.dataset = query.tryGetDatasetByPermId(datasetPermId);
+ if (dataset == null)
+ {
+ throw new IllegalStateException(String.format("Dataset '%s' not found", datasetPermId));
+ }
+ }
+
+ /** has to be called at the end */
+ public void close()
+ {
+ query.close();
+ }
+
+ protected final ImgContainerDTO getContainer()
+ {
+ if (container == null)
+ {
+ container = query.getContainerById(dataset.getContainerId());
+ }
+ return container;
+ }
+
+ public Geometry getPlateGeometry()
+ {
+ return new Geometry(getContainer().getNumberOfRows(), getContainer().getNumberOfColumns());
+ }
+
+ protected final ImgDatasetDTO getDataset()
+ {
+ return dataset;
+ }
+
+ public Geometry getWellGeometry()
+ {
+ return new Geometry(getDataset().getFieldNumberOfRows(), getDataset()
+ .getFieldNumberOfColumns());
+ }
+
+ public int getChannelCount()
+ {
+ if (channelCount == null)
+ {
+ channelCount = getChannelsNames().size();
+ }
+ return channelCount;
+ }
+
+ public List<String> getChannelsNames()
+ {
+ if (channelNames == null)
+ {
+ String[] namesAsArray =
+ query.getChannelNamesByDatasetIdOrExperimentId(getDataset().getId(),
+ getContainer().getExperimentId());
+ channelNames = new ArrayList<String>(Arrays.asList(namesAsArray));
+ }
+ return channelNames;
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatabaseVersionHolder.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
similarity index 58%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatabaseVersionHolder.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
index d5ce9a1180e..80756fb4bde 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatabaseVersionHolder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
@@ -14,23 +14,27 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IDatabaseVersionHolder;
+import java.util.List;
+
+import ch.systemsx.cisd.bds.hcs.Geometry;
/**
- * Stores current version of special purpose imaging database.
- *
* @author Tomasz Pylak
*/
-public class ImagingDatabaseVersionHolder implements IDatabaseVersionHolder
+public interface IHCSDatasetLoader
{
- /** Current version of the database. */
- static final String DATABASE_VERSION = "003"; // S83
- public String getDatabaseVersion()
- {
- return DATABASE_VERSION;
- }
+ /** has to be called at the end */
+ void close();
+
+ Geometry getPlateGeometry();
+
+ Geometry getWellGeometry();
+
+ int getChannelCount();
+
+ List<String> getChannelsNames();
-}
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ColorComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ColorComponent.java
similarity index 95%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ColorComponent.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ColorComponent.java
index ad63813c897..140dfe5af19 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ColorComponent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ColorComponent.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import java.awt.Color;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDataObjectBinding.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDataObjectBinding.java
similarity index 94%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDataObjectBinding.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDataObjectBinding.java
index 3b8476fd48b..1fe2ee36435 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDataObjectBinding.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDataObjectBinding.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import java.sql.ResultSet;
import java.sql.SQLException;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
similarity index 98%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
index c4a421f49c9..8fed686e6bc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import java.util.List;
@@ -28,7 +28,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.ByteArrayMapper;
/**
* @author Tomasz Pylak
*/
-public interface IImagingUploadDAO extends TransactionQuery
+public interface IImagingQueryDAO extends TransactionQuery
{
public static final int FETCH_SIZE = 1000;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageDTO.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageDTO.java
index 235e525767d..9ef3b0e381c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgAcquiredImageDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
index 48336231307..f473c2d7789 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
index 44ff7859cef..2fd24910d0b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgContainerDTO.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgContainerDTO.java
index 4427208dd42..e5932271494 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgContainerDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgDatasetDTO.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgDatasetDTO.java
index 18a1ee6d109..58cf4871a10 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgDatasetDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgFeatureDefDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureDefDTO.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgFeatureDefDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureDefDTO.java
index 166b39c1847..7ba947e07c6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgFeatureDefDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureDefDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgFeatureValuesDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureValuesDTO.java
similarity index 97%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgFeatureValuesDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureValuesDTO.java
index 0cda1a2925f..b3d418f221f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgFeatureValuesDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureValuesDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
index 19ad6ed07cb..ebdeabae3cb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgSpotDTO.java
similarity index 96%
rename from screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgSpotDTO.java
index 2927d99d3ca..57546b6dbe3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgSpotDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
diff --git a/screening/source/java/screening-applicationContext.xml b/screening/source/java/screening-applicationContext.xml
index 3a5e07e65e5..c8f42648252 100644
--- a/screening/source/java/screening-applicationContext.xml
+++ b/screening/source/java/screening-applicationContext.xml
@@ -9,6 +9,31 @@
<import resource="applicationContext.xml"/>
+ <bean id="imaging-db-configuration-context"
+ class="ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext">
+ <property name="basicDatabaseName" value="imaging" />
+ <property name="createFromScratch" value="${imaging.database.create-from-scratch}" />
+ <property name="scriptSingleStepMode" value="${imaging.database.script-single-step-mode}" />
+ <property name="sequenceNameMapper">
+ <bean class="ch.systemsx.cisd.openbis.generic.server.dataaccess.db.SequenceNameMapper" />
+ </property>
+ <property name="urlHostPart" value="${imaging.database.url-host-part}" />
+ <property name="adminUser" value="${imaging.database.admin-user}" />
+ <property name="owner" value="${imaging.database.owner}" />
+ <property name="readOnlyGroup" value="imaging_readonly" />
+ <property name="password" value="${imaging.database.owner-password}" />
+ <property name="adminPassword" value="${imaging.database.admin-password}" />
+ <property name="databaseKind" value="${imaging.database.kind}" />
+ <property name="databaseEngineCode" value="${imaging.database.engine}" />
+ <property name="scriptFolder" value="${imaging.script-folder}/sql" />
+ <property name="databaseInstance" value="${imaging.database-instance}" />
+ </bean>
+
+ <bean id="screening-dao-factory"
+ class="ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.db.ScreeningDAOFactory">
+ <constructor-arg ref="imaging-db-configuration-context"/>
+ </bean>
+
<!--
//Mail Client Parameters
-->
diff --git a/screening/source/java/service.properties b/screening/source/java/service.properties
index 3db582c2b93..1d4aa1792ce 100644
--- a/screening/source/java/service.properties
+++ b/screening/source/java/service.properties
@@ -21,6 +21,17 @@ database.owner-password =
database.admin-user =
database.admin-password =
+imaging.database.engine = postgresql
+imaging.database.create-from-scratch = false
+imaging.database.script-single-step-mode = false
+imaging.database.url-host-part =
+imaging.database.kind = dev
+imaging.database.owner =
+imaging.database.owner-password =
+imaging.database.admin-user =
+imaging.database.admin-password =
+imaging.script-folder = source
+
crowd.service.host = crowd-bsse.ethz.ch
crowd.service.port = 8443
crowd.application.name = lims
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
index 29d73a330bd..cc1195ae175 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
@@ -28,11 +28,11 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.AbstractDBTest;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.DBUtils;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.AbstractDBTest;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.DBUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
/**
* @author Chandrasekhar Ramakrishnan
@@ -47,12 +47,12 @@ public class FeatureVectorUploaderTest extends AbstractDBTest
private static final String TEST_FEATURE_NAME = "test";
- private IImagingUploadDAO dao;
+ private IImagingQueryDAO dao;
@BeforeClass(alwaysRun = true)
public void init() throws SQLException
{
- dao = DBUtils.getQuery(datasource, IImagingUploadDAO.class);
+ dao = DBUtils.getQuery(datasource, IImagingQueryDAO.class);
}
@Test
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
index 560164ab8f7..5b859884376 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
@@ -33,10 +33,6 @@ import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.etlserver.IStorageProcessor;
import ch.systemsx.cisd.etlserver.PlateDimensionParser;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgDatasetDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
@@ -44,6 +40,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericValueEntityPrope
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
/**
* @author Franz-Josef Elmer
@@ -63,7 +63,7 @@ public class FeatureStorageProcessorTest extends AbstractFileSystemTestCase
private Mockery context;
- private IImagingUploadDAO dao;
+ private IImagingQueryDAO dao;
private DataSource dataSource;
@@ -76,7 +76,7 @@ public class FeatureStorageProcessorTest extends AbstractFileSystemTestCase
super.setUp();
context = new Mockery();
- dao = context.mock(IImagingUploadDAO.class);
+ dao = context.mock(IImagingQueryDAO.class);
dataSource = context.mock(DataSource.class);
openBisService = context.mock(IEncapsulatedOpenBISService.class);
@@ -128,7 +128,7 @@ public class FeatureStorageProcessorTest extends AbstractFileSystemTestCase
// For Testing
@Override
- protected IImagingUploadDAO createDAO()
+ protected IImagingQueryDAO createDAO()
{
return dao;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVectorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVectorTest.java
index 2427bd798e6..a35e0b1e23e 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVectorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVectorTest.java
@@ -25,9 +25,9 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgFeatureValuesDTO;
import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
/**
* Check that Genedata feature vectors can be converted to the canonical form.
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/shared/.gitignore b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/shared/.gitignore
new file mode 100644
index 00000000000..e69de29bb2d
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/AbstractDBTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractDBTest.java
similarity index 96%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/AbstractDBTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractDBTest.java
index 4b2c4bcf666..1c6adfba799 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/AbstractDBTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/AbstractDBTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import java.sql.SQLException;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/DBUtils.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/DBUtils.java
similarity index 96%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/DBUtils.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/DBUtils.java
index 4b6845f2aa8..1206b6ee82e 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/DBUtils.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/DBUtils.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import javax.sql.DataSource;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/DBUtilsForTests.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/DBUtilsForTests.java
similarity index 79%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/DBUtilsForTests.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/DBUtilsForTests.java
index 4d6d2293d41..702e5448ec2 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/DBUtilsForTests.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/DBUtilsForTests.java
@@ -14,25 +14,25 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImagingDatabaseVersionHolder;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.db.ScreeningDAOFactory;
/**
* Utilities for dealing with databases in tests.
*
* @author Piotr Buczek
*/
-@Friend(toClasses = ImagingDatabaseVersionHolder.class)
+@Friend(toClasses = ScreeningDAOFactory.class)
public class DBUtilsForTests
{
public static void init(DatabaseConfigurationContext context)
{
DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context,
- ImagingDatabaseVersionHolder.DATABASE_VERSION);
+ ScreeningDAOFactory.DATABASE_VERSION);
}
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
similarity index 85%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
index d436277100c..9ead171b158 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import static org.testng.AssertJUnit.assertEquals;
@@ -25,9 +25,14 @@ import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
/**
- * Tests for {@link IImagingUploadDAO} methods that deal with feature vectors.
+ * Tests for {@link IImagingQueryDAO} methods that deal with feature vectors.
*
* @author Chandrasekhar Ramakrishnan
*/
@@ -35,7 +40,7 @@ import ch.systemsx.cisd.base.mdarray.MDDoubleArray;
{ "db", "screening" })
public class FeatureVectorDAOTest extends AbstractDBTest
{
- private IImagingUploadDAO dao;
+ private IImagingQueryDAO dao;
private ImgDatasetDTO dataset;
@@ -50,12 +55,12 @@ public class FeatureVectorDAOTest extends AbstractDBTest
@BeforeClass(alwaysRun = true)
public void init() throws SQLException
{
- dao = DBUtils.getQuery(datasource, IImagingUploadDAO.class);
+ dao = DBUtils.getQuery(datasource, IImagingQueryDAO.class);
}
private ImgDatasetDTO createDataSet()
{
- IImagingUploadDAO imagingDao = dao;
+ IImagingQueryDAO imagingDao = dao;
// Create an Experiment
final long experimentId = imagingDao.addExperiment(EXP_PERM_ID);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
similarity index 89%
rename from screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
index c78efa3c113..7d3496c9c8f 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
+package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
@@ -27,15 +27,24 @@ import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgAcquiredImageDTO;
+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;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSpotDTO;
/**
- * Tests for {@link IImagingUploadDAO}.
+ * Tests for {@link IImagingQueryDAO}.
*
* @author Piotr Buczek
*/
@Test(groups =
{ "db", "screening" })
-public class ImagingUploadDAOTest extends AbstractDBTest
+public class ImagingQueryDAOTest extends AbstractDBTest
{
private static final String PERM_ID = "PERM_ID";
@@ -68,12 +77,12 @@ public class ImagingUploadDAOTest extends AbstractDBTest
private static final String EXP_CHANNEL = "expChannel";
- private IImagingUploadDAO dao;
+ private IImagingQueryDAO dao;
@BeforeClass(alwaysRun = true)
public void init() throws SQLException
{
- dao = DBUtils.getQuery(datasource, IImagingUploadDAO.class);
+ dao = DBUtils.getQuery(datasource, IImagingQueryDAO.class);
}
@Test
--
GitLab