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 0e504f5cd824656f7a71ea8baf80bf861ae2de2b..2c5f832622b408a95a9cba711f6932b3f7699db0 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 @@ -18,7 +18,7 @@ package ch.systemsx.cisd.openbis.dss.etl; import java.awt.image.BufferedImage; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +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; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java index 1dd59b4475d6afd77e4d613e3bd1d918723890ff..9caeadb389572c4d40d8e9c512dae4c7d55afc8c 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageStorageProcessor.java @@ -42,8 +42,8 @@ import ch.systemsx.cisd.common.filesystem.FileOperations; import ch.systemsx.cisd.common.filesystem.FileUtilities; import ch.systemsx.cisd.common.filesystem.IFileOperations; import ch.systemsx.cisd.common.filesystem.SoftLinkMaker; -import ch.systemsx.cisd.common.hdf5.HDF5Container; -import ch.systemsx.cisd.common.hdf5.HierarchicalStructureDuplicatorFileToHDF5; +import ch.systemsx.cisd.openbis.common.hdf5.HDF5Container; +import ch.systemsx.cisd.openbis.common.hdf5.HierarchicalStructureDuplicatorFileToHDF5; import ch.systemsx.cisd.common.logging.LogCategory; import ch.systemsx.cisd.common.logging.LogFactory; import ch.systemsx.cisd.common.mail.IMailClient; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java index 23c3159efa9294f4e8f3eb15f30f1c978fc64229..dc52f723e6d7836f2ed204b70816a610706f36e0 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ComputeIntensityLevelTransformationsMaintenanceTask.java @@ -32,7 +32,7 @@ import ch.systemsx.cisd.common.exception.ConfigurationFailureException; import ch.systemsx.cisd.common.image.IntensityRescaling.Levels; import ch.systemsx.cisd.common.io.PersistentExtendedBlockingQueueDecorator; import ch.systemsx.cisd.common.io.PersistentExtendedBlockingQueueFactory; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.common.logging.LogCategory; import ch.systemsx.cisd.common.logging.LogFactory; import ch.systemsx.cisd.common.maintenance.IMaintenanceTask; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java index 7f4bc17aaad996e25382568e3a1f4404aa5db076..a8eda14b07185f0087b4fbe6fcea5250e9523b0d 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageDatasetLoaderFactory.java @@ -16,7 +16,7 @@ package ch.systemsx.cisd.openbis.dss.etl; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImagingDatasetLoader; import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java index 41f4deb4c78340db3aa14c2f059a2133b1d3c295..61d86f02ca4d6ca017e6852bab96287d04f54582 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Hdf5ThumbnailGenerator.java @@ -39,12 +39,12 @@ import ch.systemsx.cisd.common.concurrent.ITaskExecutor; import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor; import ch.systemsx.cisd.common.exception.Status; import ch.systemsx.cisd.common.filesystem.FileUtilities; -import ch.systemsx.cisd.common.hdf5.HDF5Container; -import ch.systemsx.cisd.common.hdf5.HDF5Container.IHDF5WriterClient; -import ch.systemsx.cisd.common.hdf5.IHDF5ContainerWriter; -import ch.systemsx.cisd.common.io.ByteArrayBasedContentNode; -import ch.systemsx.cisd.common.io.FileBasedContentNode; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.hdf5.HDF5Container; +import ch.systemsx.cisd.openbis.common.hdf5.HDF5Container.IHDF5WriterClient; +import ch.systemsx.cisd.openbis.common.hdf5.IHDF5ContainerWriter; +import ch.systemsx.cisd.openbis.common.io.ByteArrayBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.common.logging.LogCategory; import ch.systemsx.cisd.common.logging.LogFactory; import ch.systemsx.cisd.common.process.ProcessExecutionHelper; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTask.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTask.java index 67f6803cd3ff38a9ec11528b19767b3e9f35371e..5018818c01acb8ee9ba553dc94880822576ac7fc 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTask.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTask.java @@ -27,7 +27,7 @@ import net.lemnik.eodsql.QueryTool; import org.apache.log4j.Logger; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.common.logging.LogCategory; import ch.systemsx.cisd.common.logging.LogFactory; import ch.systemsx.cisd.common.maintenance.IDataStoreLockingMaintenanceTask; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Utils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Utils.java index b5e2ad8a59e88cbe9ace15be20c54909c364f70d..ed3298feb6beffe9aef2d36e23837f8732d11f5d 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Utils.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/Utils.java @@ -21,7 +21,7 @@ import java.awt.image.BufferedImage; import org.apache.log4j.Logger; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; import ch.systemsx.cisd.common.logging.LogCategory; import ch.systemsx.cisd.common.logging.LogFactory; import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java index 24228c187ae97304384d5dbd66b360edda346721..eaa873ee51577b9e4d9cd99ad2c71fafa5fcfa98 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingDatasetLoader.java @@ -27,8 +27,8 @@ import org.apache.commons.lang.StringUtils; import ch.systemsx.cisd.base.image.IImageTransformerFactory; import ch.systemsx.cisd.common.exception.UserFailureException; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; import ch.systemsx.cisd.hcs.Location; import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference; import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java index 627b5b01396e177dc19b4c3081d47ae7f675c15c..172d946588aef135e45087402496b351a2d698c1 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java @@ -32,8 +32,8 @@ import java.util.Properties; import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel; import ch.systemsx.cisd.common.exception.UserFailureException; -import ch.systemsx.cisd.common.io.FileBasedContentNode; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails; import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationService; import ch.systemsx.cisd.etlserver.registrator.IDataSetRegistrationDetailsFactory; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java index fb25add12190163f08cdb5beaa9ac43435520948..fe2bf44d6ac4ae99abb21d01c8bb8a62f5407b7a 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java @@ -39,7 +39,7 @@ import ch.systemsx.cisd.common.filesystem.FileUtilities; import ch.systemsx.cisd.common.image.IntensityRescaling; import ch.systemsx.cisd.common.image.IntensityRescaling.Levels; import ch.systemsx.cisd.common.image.IntensityRescaling.PixelHistogram; -import ch.systemsx.cisd.common.io.FileBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode; import ch.systemsx.cisd.common.logging.LogCategory; import ch.systemsx.cisd.common.logging.LogFactory; import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java index 30000b8b8ecda4ed14870938a65d7f49060cb745..96ceae363c94f90cf8bc33c6c126ed081412d784 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/MergingImagesDownloadServlet.java @@ -20,7 +20,7 @@ import java.io.IOException; import java.util.Properties; import ch.systemsx.cisd.common.exception.EnvironmentFailureException; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils; import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageGenerationDescription; import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider; 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 4eaa8a059801d987df56212aa83fcc5267e04d0e..9ac6fe3a76fce41bbe3a8d37581d96de546fcd1a 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 @@ -32,9 +32,9 @@ import ch.systemsx.cisd.base.image.IImageTransformerFactory; import ch.systemsx.cisd.common.exception.EnvironmentFailureException; import ch.systemsx.cisd.common.exception.UserFailureException; import ch.systemsx.cisd.common.image.MixColors; -import ch.systemsx.cisd.common.io.ByteArrayBasedContentNode; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.ByteArrayBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; import ch.systemsx.cisd.common.logging.LogCategory; import ch.systemsx.cisd.common.logging.LogFactory; import ch.systemsx.cisd.hcs.Location; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/AbstractSpotImagesTransformerProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/AbstractSpotImagesTransformerProcessingPlugin.java index d4b445c3ec2700f22f5feab81e1191fb4bee2d4a..55d97206a61844ee3af6e6f65797140be1a4bc3d 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/AbstractSpotImagesTransformerProcessingPlugin.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/AbstractSpotImagesTransformerProcessingPlugin.java @@ -22,7 +22,7 @@ import java.util.Properties; import ch.systemsx.cisd.base.image.IImageTransformerFactory; import ch.systemsx.cisd.common.exception.Status; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.common.properties.PropertyUtils; import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin; import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java index 1bf3c248199025ba37f16b478a7b949908e3d2b0..e717168b0438acfcc47bdbecc786f5c382c1ac6c 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/DynamixWellBrightnessEqualizerProcessingPlugin.java @@ -24,8 +24,8 @@ import java.util.Map; import java.util.Properties; import ch.systemsx.cisd.base.image.IImageTransformerFactory; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; import ch.systemsx.cisd.common.properties.PropertyUtils; import ch.systemsx.cisd.openbis.dss.etl.dynamix.IntensityRangeReductionFactory; import ch.systemsx.cisd.openbis.dss.generic.server.plugins.ColorRangeCalculator.ImagePixelsRange; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ExampleImageTransformationProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ExampleImageTransformationProcessingPlugin.java index 3583a28f25530bebdb9556346611b7a646f0a1cd..650001649a7613b23d53a996747250ac643f1f90 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ExampleImageTransformationProcessingPlugin.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ExampleImageTransformationProcessingPlugin.java @@ -22,7 +22,7 @@ import java.util.List; import java.util.Properties; import ch.systemsx.cisd.base.image.IImageTransformerFactory; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.common.properties.PropertyUtils; import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ExampleImageTransformerFactory; import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageEnrichedDTO; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FeatureListsAggregationServicePlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FeatureListsAggregationServicePlugin.java index 064bb1ed70aecf713d885c1c7af762625cafdbea..021215fb9ca8d133578cf562b2279600f98c570b 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FeatureListsAggregationServicePlugin.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/FeatureListsAggregationServicePlugin.java @@ -25,7 +25,7 @@ import java.util.Properties; import org.apache.commons.io.IOUtils; import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AggregationService; import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext; import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ResetImageLevelTransformationProcessingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ResetImageLevelTransformationProcessingPlugin.java index 7081bfbb43c18d76867a8cc2fe64c16e960734b3..49e9550098907cb886af15807f1dcbac14f0d159 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ResetImageLevelTransformationProcessingPlugin.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ResetImageLevelTransformationProcessingPlugin.java @@ -20,7 +20,7 @@ import java.io.File; import java.util.List; import java.util.Properties; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageEnrichedDTO; /** 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 f37082d1ba85dae1084aa77f6c446595c8dc984e..0e173fddb902b0e4572299e13a21fec92cc529b3 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 @@ -38,15 +38,15 @@ import com.googlecode.jsonrpc4j.Base64; import ch.systemsx.cisd.base.image.IImageTransformerFactory; import ch.systemsx.cisd.common.api.RpcServiceInterfaceVersionDTO; -import ch.systemsx.cisd.common.api.server.RpcServiceNameServer; +import ch.systemsx.cisd.openbis.common.api.server.RpcServiceNameServer; import ch.systemsx.cisd.common.exception.EnvironmentFailureException; import ch.systemsx.cisd.common.exception.UserFailureException; -import ch.systemsx.cisd.common.io.ConcatenatedContentInputStream; +import ch.systemsx.cisd.openbis.common.io.ConcatenatedContentInputStream; import ch.systemsx.cisd.common.io.ConcatenatedFileOutputStreamWriter; -import ch.systemsx.cisd.common.io.HierarchicalContentNodeBasedHierarchicalContentNode; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; -import ch.systemsx.cisd.common.spring.IInvocationLoggerContext; +import ch.systemsx.cisd.openbis.common.io.HierarchicalContentNodeBasedHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext; import ch.systemsx.cisd.hcs.Location; import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference; import ch.systemsx.cisd.openbis.dss.etl.HCSImageDatasetLoaderFactory; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java index b8c0e703c65decf9e6a3a1152b3cdc4e0d5b85ce..6a4997d93fe1e1a31be103f85b1f73809f07cc99 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java @@ -21,7 +21,7 @@ import java.util.Arrays; import java.util.List; import ch.systemsx.cisd.base.image.IImageTransformerFactory; -import ch.systemsx.cisd.common.spring.IInvocationLoggerContext; +import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext; import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening; import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration; import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java index 03a6eeb45a33e0ad9f7db8f047a0183f03d30cc6..3ebe87908e82d084c64c8a27f14f7767aaa3564b 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java @@ -23,7 +23,7 @@ import org.apache.commons.lang.time.DateUtils; import ch.systemsx.cisd.base.image.IImageTransformerFactory; import ch.systemsx.cisd.common.api.MinimalMinorVersion; -import ch.systemsx.cisd.common.api.client.ServiceFinder; +import ch.systemsx.cisd.openbis.common.api.client.ServiceFinder; import ch.systemsx.cisd.common.api.retry.RetryCaller; import ch.systemsx.cisd.common.api.retry.RetryProxyFactory; import ch.systemsx.cisd.common.exception.EnvironmentFailureException; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java index abe560a67625d9f4b7fa1e7eb9370fd69e94b9ee..9ab1a4f3c0124ca3027320c0b3f81594b6f33d0d 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java @@ -25,7 +25,7 @@ import org.springframework.stereotype.Component; import ch.rinn.restrictions.Private; import ch.systemsx.cisd.common.servlet.IRequestContextProvider; -import ch.systemsx.cisd.common.spring.IUncheckedMultipartFile; +import ch.systemsx.cisd.openbis.common.spring.IUncheckedMultipartFile; import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig; import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ListMaterialDisplayCriteria; import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningApiServiceJsonServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningApiServiceJsonServer.java index f5281d602fb6cf6b6c81abd5b5ffc068b487378e..80b9353253a2db46e03a522ba666edec243a3a22 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningApiServiceJsonServer.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningApiServiceJsonServer.java @@ -21,7 +21,7 @@ import javax.annotation.Resource; import org.springframework.stereotype.Controller; import org.springframework.web.bind.annotation.RequestMapping; -import ch.systemsx.cisd.common.api.server.AbstractApiJsonServiceExporter; +import ch.systemsx.cisd.openbis.common.api.server.AbstractApiJsonServiceExporter; import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames; import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningApiServiceServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningApiServiceServer.java index cada48212898370590f1fc71a33cf0629b0b479e..6b9d910b56a1f6c8cab024a3a3379ef61171c229 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningApiServiceServer.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningApiServiceServer.java @@ -21,7 +21,7 @@ import javax.annotation.Resource; import org.springframework.stereotype.Controller; import org.springframework.web.bind.annotation.RequestMapping; -import ch.systemsx.cisd.common.api.server.AbstractApiServiceExporter; +import ch.systemsx.cisd.openbis.common.api.server.AbstractApiServiceExporter; import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames; import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java index b49f255398523858251d98eb13485da28bedb1ff..8cfc2ce74bd253c7aa18a2da118e9cd0c2045a03 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java @@ -32,7 +32,7 @@ import org.springframework.stereotype.Component; import ch.rinn.restrictions.Private; import ch.systemsx.cisd.authentication.ISessionManager; import ch.systemsx.cisd.common.exception.UserFailureException; -import ch.systemsx.cisd.common.spring.IInvocationLoggerContext; +import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext; import ch.systemsx.cisd.openbis.generic.server.AbstractServer; import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.AuthorizationGuard; import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.Capability; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java index f290fd2e2a3b7f176606407e7dd0ab322b51f3ab..5bca96d061761576ec847d68578801ebce49a754 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java @@ -21,7 +21,7 @@ import java.util.List; import ch.systemsx.cisd.authentication.ISessionManager; import ch.systemsx.cisd.common.exception.UserFailureException; -import ch.systemsx.cisd.common.spring.IInvocationLoggerContext; +import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext; import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger; import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample; import ch.systemsx.cisd.openbis.generic.shared.basic.TechId; diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/json/ScreeningJsonClassValueToClassObjectsMapping.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/json/ScreeningJsonClassValueToClassObjectsMapping.java index 686a969c618d4f12a7cd0b0e35d6527c37088020..256ccc441164fa63c1497838c06f1f8d00c8e111 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/json/ScreeningJsonClassValueToClassObjectsMapping.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/json/ScreeningJsonClassValueToClassObjectsMapping.java @@ -18,7 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.api.json; import java.util.List; -import ch.systemsx.cisd.common.api.server.json.mapping.JsonStaticClassValueToClassObjectsMapping; +import ch.systemsx.cisd.openbis.common.api.server.json.mapping.JsonStaticClassValueToClassObjectsMapping; import ch.systemsx.cisd.openbis.generic.shared.api.json.GenericJsonClassValueToClassObjectsMapping; /** diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/json/ScreeningObjectMapper.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/json/ScreeningObjectMapper.java index b4500d9ee871d6193d0a7274b9b70a8042ad1ccc..4b9849b9a93d6d60abd5d2a93c1af6a747064401 100644 --- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/json/ScreeningObjectMapper.java +++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/json/ScreeningObjectMapper.java @@ -19,11 +19,11 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.api.json; import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.deser.DefaultDeserializationContext; -import ch.systemsx.cisd.common.api.server.json.deserializer.JsonDeserializerFactory; -import ch.systemsx.cisd.common.api.server.json.introspector.JsonTypeAndClassAnnotationIntrospector; -import ch.systemsx.cisd.common.api.server.json.mapping.JsonReflectionsBaseTypeToSubTypesMapping; -import ch.systemsx.cisd.common.api.server.json.resolver.JsonReflectionsSubTypeResolver; -import ch.systemsx.cisd.common.api.server.json.serializer.JsonSerializerFactory; +import ch.systemsx.cisd.openbis.common.api.server.json.deserializer.JsonDeserializerFactory; +import ch.systemsx.cisd.openbis.common.api.server.json.introspector.JsonTypeAndClassAnnotationIntrospector; +import ch.systemsx.cisd.openbis.common.api.server.json.mapping.JsonReflectionsBaseTypeToSubTypesMapping; +import ch.systemsx.cisd.openbis.common.api.server.json.resolver.JsonReflectionsSubTypeResolver; +import ch.systemsx.cisd.openbis.common.api.server.json.serializer.JsonSerializerFactory; /** * Jackson library object mapper used in screening OpenBIS. diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java index 17f415dcc4247b49dc5ef257616c3ea3f92b2123..949f4a094716f81f2714b48ade2e767956291a20 100644 --- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java +++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/ImageSizeFeedingMaintenanceTaskTest.java @@ -28,7 +28,7 @@ import org.testng.annotations.AfterMethod; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.common.logging.BufferedAppender; import ch.systemsx.cisd.common.test.RecordingMatcher; import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO; diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java index 3bf5b36bfcedcd36952de1bb10b3b9cd110f757e..50e3cfa7f48ec0f097b24f2c34e7e79e8a15845f 100644 --- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java +++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java @@ -38,8 +38,8 @@ import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel; import ch.systemsx.cisd.base.image.IImageTransformer; import ch.systemsx.cisd.base.image.IImageTransformerFactory; import ch.systemsx.cisd.common.exception.EnvironmentFailureException; -import ch.systemsx.cisd.common.io.FileBasedContentNode; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; import ch.systemsx.cisd.imagereaders.ImageReaderConstants; import ch.systemsx.cisd.imagereaders.ImageReadersTestHelper; import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference; diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java index 60436be0fb5d54a8a59feda3b17d52822180620e..96a32830f64ac5e7b837a38e19267bc6bd46ac01 100644 --- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java +++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java @@ -46,11 +46,11 @@ import ch.systemsx.cisd.base.image.IImageTransformerFactory; import ch.systemsx.cisd.base.mdarray.MDFloatArray; import ch.systemsx.cisd.common.exception.AuthorizationFailureException; import ch.systemsx.cisd.common.exception.UserFailureException; -import ch.systemsx.cisd.common.io.ByteArrayBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.ByteArrayBasedContentNode; import ch.systemsx.cisd.common.io.ConcatenatedFileOutputStreamWriter; -import ch.systemsx.cisd.common.io.FileBasedContentNode; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.FileBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; import ch.systemsx.cisd.hcs.Location; import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference; import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader; diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPluginTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPluginTest.java index 5f5aaa34bf5a7609c4f81229459d0cf7c6c5fe8d..2a0c603e089fca5f1eb3ac645d3dc6535e3f9b90 100644 --- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPluginTest.java +++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/plugins/jython/ScreeningJythonBasedReportingPluginTest.java @@ -28,7 +28,7 @@ import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent; import ch.systemsx.cisd.common.logging.LogInitializer; import ch.systemsx.cisd.common.test.RecordingMatcher; import ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.IPluginScriptRunnerFactory; diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java index 2621019cff096c700959597d03725a52f811822b..b58dff3e827b8c65b8b44b9c14390bc5e10da0e5 100644 --- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java +++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java @@ -39,9 +39,9 @@ import ch.rinn.restrictions.Friend; import ch.systemsx.cisd.base.image.IImageTransformerFactory; import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase; import ch.systemsx.cisd.common.filesystem.FileUtilities; -import ch.systemsx.cisd.common.io.ByteArrayBasedContentNode; -import ch.systemsx.cisd.common.io.ConcatenatedContentInputStream; -import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode; +import ch.systemsx.cisd.openbis.common.io.ByteArrayBasedContentNode; +import ch.systemsx.cisd.openbis.common.io.ConcatenatedContentInputStream; +import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode; import ch.systemsx.cisd.common.test.RecordingMatcher; import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss; import ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent; diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/JsonAnnotationTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/JsonAnnotationTest.java index 564ee3c415956927558083764e59dd6fe5c6c9f6..ff4282d51fc9f3610e18c088fd4da6df968d1122 100644 --- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/JsonAnnotationTest.java +++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/JsonAnnotationTest.java @@ -33,8 +33,8 @@ import com.fasterxml.jackson.annotation.JsonSubTypes; import com.fasterxml.jackson.annotation.JsonSubTypes.Type; import ch.systemsx.cisd.base.annotation.JsonObject; -import ch.systemsx.cisd.common.api.server.json.JsonUniqueCheckIgnore; -import ch.systemsx.cisd.common.api.server.json.util.ClassReferences; +import ch.systemsx.cisd.openbis.common.api.server.json.JsonUniqueCheckIgnore; +import ch.systemsx.cisd.openbis.common.api.server.json.util.ClassReferences; import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.IDssServiceRpcGeneric; import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening; import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;