SP-416 BIS-270 finish the split of v1 and v2 in screening

SVN: 27818

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbsoluteImageReference.java

@@ -21,7 +21,7 @@ import java.awt.image.BufferedImage;
 import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java

@@ -41,9 +41,9 @@ import ch.systemsx.cisd.hcs.Geometry;
 import ch.systemsx.cisd.hcs.Location;
 import ch.systemsx.cisd.hcs.WellGeometry;
 import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java

@@ -61,15 +61,15 @@ import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor.DatasetOwnerInform
 import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor.ImageDatasetOwnerInformation;
 import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageSeriesPoint;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageStorageConfiguraton;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.OriginalDataStorageFormat;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetStructure;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorComponent;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageStorageConfiguraton;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.OriginalDataStorageFormat;
-import ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler;
+import ch.systemsx.cisd.openbis.dss.etl.jython.v1.JythonPlateDataSetHandler;
 import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java

@@ -37,9 +37,9 @@ import ch.systemsx.cisd.common.logging.LogCategory;
 import ch.systemsx.cisd.common.logging.LogFactory;
 import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
 import ch.systemsx.cisd.common.properties.PropertyUtils;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformationBuffer;
-import ch.systemsx.cisd.openbis.dss.etl.jython.SimpleImageDataSetRegistrator;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformationBuffer;
+import ch.systemsx.cisd.openbis.dss.etl.jython.v1.SimpleImageDataSetRegistrator;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
 import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/FlexibleHCSImageFileExtractor.java

@@ -20,7 +20,7 @@ import java.io.File;
 import java.util.Properties;
 
 import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
 
 /**

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetUploader.java

@@ -24,7 +24,7 @@ import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ExperimentWithChan
 import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ImagingChannelsMap;
 import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageZoomLevel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgSpotDTO;
 

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractor.java

@@ -25,7 +25,7 @@ import org.apache.commons.lang.StringUtils;
 import ch.systemsx.cisd.common.properties.PropertyUtils;
 import ch.systemsx.cisd.hcs.Location;
 import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
 import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
 

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java

@@ -52,14 +52,14 @@ import ch.systemsx.cisd.common.process.ProcessIOStrategy;
 import ch.systemsx.cisd.common.process.ProcessResult;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorComponent;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageStorageConfiguraton;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetStructure;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorComponent;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageStorageConfiguraton;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageFileExtractionResult.java

@@ -20,7 +20,7 @@ import java.util.List;
 
 import ch.systemsx.cisd.hcs.Geometry;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
 
 /**
  * Class which contains the image extraction process results.

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageValidator.java

@@ -29,7 +29,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.common.mail.IMailClient;
 import ch.systemsx.cisd.hcs.Geometry;
 import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor.DatasetOwnerInformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateDimension;
 

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java

@@ -26,10 +26,10 @@ import java.util.Set;
 import ch.rinn.restrictions.Private;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.transformations.ImageTransformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColor;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.ImageTransformation;
 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.ImgExperimentDTO;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyBlackboxSeriesStorageProcessor.java

@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor.ImageDatasetOwnerI
 import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageDatasetInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelDescription;
 

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageDatasetUploader.java

@@ -22,7 +22,7 @@ import java.util.Map;
 import ch.systemsx.cisd.openbis.dss.etl.ImagingDatabaseHelper.ImagingChannelsMap;
 import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageZoomLevel;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Channel;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageZoomLevelDTO;
 
 /**

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/MicroscopyImageFileExtractor.java

@@ -22,7 +22,7 @@ import java.util.Properties;
 import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
 import ch.systemsx.cisd.hcs.Location;
 import ch.systemsx.cisd.openbis.dss.etl.dto.UnparsedImageFileInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
 import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
 

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateGeometryOracle.java

@@ -28,8 +28,8 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.common.shared.basic.string.StringUtils;
 import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
 import ch.systemsx.cisd.hcs.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedBasicOpenBISService;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java

@@ -31,10 +31,10 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageDatasetInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageZoomLevel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ThumbnailsStorageFormat.FileFormat;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
 import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat.FileFormat;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/TileGeometryOracle.java

@@ -25,7 +25,7 @@ import java.util.Map;
 import java.util.Map.Entry;
 
 import ch.systemsx.cisd.common.geometry.SpatialPoint;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
 
 /**

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/biozentrum/ImageMetadataExtractor.java

@@ -27,7 +27,7 @@ import ch.systemsx.cisd.imagereaders.ImageID;
 import ch.systemsx.cisd.imagereaders.ImageReaderConstants;
 import ch.systemsx.cisd.imagereaders.ImageReaderFactory;
 import ch.systemsx.cisd.openbis.dss.etl.TileGeometryOracle;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Location;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.Location;
 
 /**
  * @author Kaloyan Enimanev

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java

@@ -35,7 +35,7 @@ import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
 import ch.systemsx.cisd.openbis.dss.etl.PrefixedImage;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
 import ch.systemsx.cisd.openbis.dss.etl.dto.ImageTransfomationFactories;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColorRGB;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ChannelColorRGB;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.HCSChannelStackByLocationReference;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackReference.MicroscopyChannelStackByLocationReference;

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/RelativeImageFile.java

@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.dss.etl.dto;
 import java.io.Serializable;
 
 import ch.systemsx.cisd.common.reflection.AbstractHashable;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.ImageFileInfo;
 
 /**
  * Points to one image on the file system.