diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
index a182385cdbf765ba6bedb33206d813c65973b138..02d17e343f119cb5b98b6016b2f71ba27c2b5155 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageDatasetUploader.java
@@ -285,7 +285,8 @@ abstract class AbstractImageDatasetUploader
private ImgImageZoomLevelDTO convert(long imageContainerDatasetId, ImageZoomLevel imageZoomLevel)
{
return new ImgImageZoomLevelDTO(imageZoomLevel.getPhysicalDatasetPermId(),
- imageZoomLevel.isOriginal(), imageContainerDatasetId);
+ imageZoomLevel.isOriginal(), imageZoomLevel.getRootPath(),
+ imageZoomLevel.getWidth(), imageZoomLevel.getHeight(), imageContainerDatasetId);
}
private static ImgImageDatasetDTO createImageDatasetDTO(String datasetPermId,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
index 9a6c7c0e54bde62f200adccd64c56325bfbd1c94..243858f2ffc9a28b8c74d231f46777c71296625a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AbstractImageFileExtractor.java
@@ -41,7 +41,7 @@ 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.dto.RelativeImageFile;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailFilePaths;
+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.etl.dto.api.v1.ImageIdentifier;
@@ -457,7 +457,7 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
}
public final static List<AcquiredSingleImage> createImagesWithNoColorComponent(
- ImageFileInfo imageInfo, ThumbnailFilePaths thumbnailFilePathsOrNull)
+ ImageFileInfo imageInfo, ThumbnailsInfo thumbnailFilePathsOrNull)
{
List<AcquiredSingleImage> images = new ArrayList<AcquiredSingleImage>();
images.add(createImage(imageInfo, imageInfo.getChannelCode(), null,
@@ -467,7 +467,7 @@ abstract public class AbstractImageFileExtractor implements IImageFileExtractor
public final static AcquiredSingleImage createImage(ImageFileInfo imageInfo,
String channelCode, ColorComponent colorComponentOrNull,
- ThumbnailFilePaths thumbnailFilePathsOrNull)
+ ThumbnailsInfo thumbnailFilePathsOrNull)
{
RelativeImageReference relativeImageRef =
new RelativeImageReference(imageInfo.getImageRelativePath(),
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 76bc4d5bf69712f2b22d7bf94ceec92e31ac28eb..b829a8713af74a64a430e9a4a20ce473876d0f6e 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
@@ -63,7 +63,7 @@ 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.impl.ImageDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetStructure;
-import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailFilePaths;
+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;
@@ -674,8 +674,9 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
new Geometry(imageDataSetStructure.getTileRowsNumber(),
imageDataSetStructure.getTileColumnsNumber());
- ThumbnailFilePaths thumbnailFilePaths = dataSetInformation.tryGetThumbnailFilePaths();
- List<AcquiredSingleImage> images = convertImages(imageDataSetStructure, thumbnailFilePaths);
+ ThumbnailsInfo thumbnailsInfo = dataSetInformation.getThumbnailsInfos();
+
+ List<AcquiredSingleImage> images = convertImages(imageDataSetStructure, thumbnailsInfo);
List<File> invalidFiles = new ArrayList<File>(); // handles in an earlier phase
ImageStorageConfiguraton imageStorageConfiguraton =
@@ -694,18 +695,15 @@ abstract class AbstractImageStorageProcessor extends AbstractStorageProcessor im
imageStorageConfiguraton.getStoreChannelsOnExperimentLevel(),
imageStorageConfiguraton.tryGetImageLibrary());
- String thumbnailDatasetPermIdOrNull =
- (thumbnailFilePaths == null) ? null : thumbnailFilePaths
- .getThumbnailPhysicalDatasetPermId();
ImageDatasetOwnerInformation imageDatasetOwner =
ImageDatasetOwnerInformation.create(dataSetInformation.getContainerDatasetPermId(),
- dataSetInformation, thumbnailDatasetPermIdOrNull);
+ dataSetInformation, thumbnailsInfo);
return new ImageFileExtractionWithConfig(imageDatasetOwner, extractionResult,
imageStorageConfiguraton);
}
private static List<AcquiredSingleImage> convertImages(
- ImageDataSetStructure imageDataSetStructure, ThumbnailFilePaths thumbnailFilePathsOrNull)
+ ImageDataSetStructure imageDataSetStructure, ThumbnailsInfo thumbnailFilePathsOrNull)
{
List<ImageFileInfo> imageInfos = imageDataSetStructure.getImages();
List<ChannelColorComponent> channelColorComponentsOrNull =
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 f3145f15c3af77f014aa659e739b142817c038a7..a77b2e34b0f864092c2b8d56c1c17cc0b04e54c8 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
@@ -46,7 +46,10 @@ 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.impl.ThumbnailFilePaths;
+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.ImageFileInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageIdentifier;
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.generic.shared.utils.ImageUtil;
@@ -58,41 +61,52 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
*/
public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
{
+ private static class ThumbnailData
+ {
+ private final byte[] data;
+
+ private final int width;
+
+ private final int height;
+
+ private ThumbnailData(byte[] data, int width, int height)
+ {
+ this.data = data;
+ this.width = width;
+ this.height = height;
+ }
+ }
+
/**
* Generates thumbnails of specified images whose paths are relative to the specified image
* parent directory.
*
- * @param images path to the images relative to the imagesParentDirectory
+ * @param imageDataSetStructure the images dataset structure, including paths relative to the
+ * imagesParentDirectory
* @param thumbnailFilePath absolute path to the file where thumbnails will be saved
* @param imageStorageConfiguraton describes how the thumbnails should be generated
- * @return null if thumbnails generation was not requested
*/
- public static ThumbnailFilePaths tryGenerateThumbnails(List<RelativeImageFile> images,
+ public static void tryGenerateThumbnails(ImageDataSetStructure imageDataSetStructure,
File imagesParentDirectory, String thumbnailFilePath,
ImageStorageConfiguraton imageStorageConfiguraton,
String thumbnailPhysicalDatasetPermId,
- ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
+ ThumbnailsStorageFormat thumbnailsStorageFormatOrNull, ThumbnailsInfo thumbnailPaths)
{
if (thumbnailsStorageFormatOrNull != null)
{
- ThumbnailFilePaths thumbnailPaths =
- new ThumbnailFilePaths(thumbnailPhysicalDatasetPermId);
-
+ thumbnailPaths.putDataSet(thumbnailPhysicalDatasetPermId,
+ thumbnailsStorageFormatOrNull.getThumbnailsFileName());
File thumbnailsFile = new File(thumbnailFilePath);
final String relativeThumbnailFilePath = thumbnailsFile.getName();
HDF5Container container = new HDF5Container(thumbnailsFile);
ImageLibraryInfo imageLibrary = imageStorageConfiguraton.tryGetImageLibrary();
Hdf5ThumbnailGenerator thumbnailsGenerator =
- new Hdf5ThumbnailGenerator(images, imagesParentDirectory,
- thumbnailsStorageFormatOrNull, imageLibrary, relativeThumbnailFilePath,
- thumbnailPaths, operationLog);
+ new Hdf5ThumbnailGenerator(imageDataSetStructure, imagesParentDirectory,
+ thumbnailPhysicalDatasetPermId, thumbnailsStorageFormatOrNull,
+ imageLibrary, relativeThumbnailFilePath, thumbnailPaths, operationLog);
container.runWriterClient(thumbnailsStorageFormatOrNull.isStoreCompressed(),
thumbnailsGenerator);
- return thumbnailPaths;
- } else
- {
- return null;
}
}
@@ -106,27 +120,31 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
private static final int MAX_RETRY_OF_FAILED_GENERATION = 3;
- private final List<RelativeImageFile> images;
+ private final ImageDataSetStructure imageDataSetStructure;
private final File imagesParentDirectory;
+ private String thumbnailPhysicalDatasetPermId;
+
private final ThumbnailsStorageFormat thumbnailsStorageFormat;
private final ImageLibraryInfo imageLibraryOrNull;
private final String relativeThumbnailFilePath;
- private final ThumbnailFilePaths thumbnailPathCollector;
+ private final ThumbnailsInfo thumbnailPathCollector;
private final Logger logger;
- private Hdf5ThumbnailGenerator(List<RelativeImageFile> images, File imagesParentDirectory,
+ private Hdf5ThumbnailGenerator(ImageDataSetStructure imageDataSetStructure,
+ File imagesParentDirectory, String thumbnailPhysicalDatasetPermId,
ThumbnailsStorageFormat thumbnailsStorageFormat, ImageLibraryInfo imageLibraryOrNull,
- String relativeThumbnailFilePath, ThumbnailFilePaths thumbnailPathCollector,
+ String relativeThumbnailFilePath, ThumbnailsInfo thumbnailPathCollector,
Logger operationLog)
{
- this.images = images;
+ this.imageDataSetStructure = imageDataSetStructure;
this.imagesParentDirectory = imagesParentDirectory;
+ this.thumbnailPhysicalDatasetPermId = thumbnailPhysicalDatasetPermId;
this.thumbnailsStorageFormat = thumbnailsStorageFormat;
this.imageLibraryOrNull = imageLibraryOrNull;
this.relativeThumbnailFilePath = relativeThumbnailFilePath;
@@ -139,7 +157,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
* the thumbnail. Using it allows not to allocate memory each time when a thumbnail
* is generated.
*/
- private Status generateThumbnail(IHDF5ContainerWriter writer, RelativeImageFile image,
+ private Status generateThumbnail(IHDF5ContainerWriter writer, ImageFileInfo image,
ByteArrayOutputStream bufferOutputStream)
{
String imagePath = image.getImageRelativePath();
@@ -149,24 +167,23 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
try
{
long start = System.currentTimeMillis();
- String imageIdOrNull = image.tryGetImageID();
- byte[] byteArray = generateThumbnail(bufferOutputStream, img, imageIdOrNull);
- String path =
- relativeThumbnailFilePath + AbstractImageStorageProcessor.ARCHIVE_DELIMITER
- + thumbnailPath;
- thumbnailPathCollector.saveThumbnailPath(image, path);
+ String imageIdOrNull = tryExtractImageID(image);
+ ThumbnailData thumbnailData = generateThumbnail(bufferOutputStream, img, imageIdOrNull);
+ thumbnailPathCollector.saveThumbnailPath(thumbnailPhysicalDatasetPermId,
+ RelativeImageFile.create(image), thumbnailPath, thumbnailData.width,
+ thumbnailData.height);
if (logger.isDebugEnabled())
{
long now = System.currentTimeMillis();
logger.debug(Thread.currentThread().getName() + " thumbnail " + thumbnailPath
- + " (" + byteArray.length + " bytes) generated in " + (now - start)
- + " msec");
+ + " (" + thumbnailData.data.length + " bytes) generated in "
+ + (now - start) + " msec");
}
synchronized (writer)
{
- writer.writeToHDF5Container(thumbnailPath, new ByteArrayInputStream(byteArray),
- byteArray.length);
+ writer.writeToHDF5Container(thumbnailPath, new ByteArrayInputStream(
+ thumbnailData.data), thumbnailData.data.length);
}
} catch (IOException ex)
{
@@ -175,7 +192,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
return Status.OK;
}
- private String createThumbnailPath(RelativeImageFile plateImage)
+ private String createThumbnailPath(ImageFileInfo plateImage)
{
String imagePath = plateImage.getImageRelativePath();
String newImagePath = imagePath;
@@ -184,7 +201,8 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
{
newImagePath = imagePath.substring(0, lastIndex);
}
- String imageIdOrNull = plateImage.tryGetImageID();
+
+ String imageIdOrNull = tryExtractImageID(plateImage);
if (imageIdOrNull != null)
{
newImagePath += "_" + imageIdOrNull;
@@ -193,37 +211,39 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
return newImagePath;
}
- private byte[] generateThumbnail(ByteArrayOutputStream bufferOutputStream, File img,
+ private static String tryExtractImageID(ImageFileInfo image)
+ {
+ ImageIdentifier imageIdentifier = image.tryGetImageIdentifier();
+ return imageIdentifier == null ? null : imageIdentifier.getUniqueStringIdentifier();
+ }
+
+ private ThumbnailData generateThumbnail(ByteArrayOutputStream bufferOutputStream, File img,
String imageIdOrNull) throws IOException
{
- byte[] byteArray;
+ ThumbnailData thumbnailData;
if (thumbnailsStorageFormat.isGenerateWithImageMagic())
{
- byteArray = generateThumbnailWithImageMagic(img);
+ thumbnailData = generateThumbnailWithImageMagic(img);
} else
{
- byteArray = generateThumbnailInternally(img, imageIdOrNull, bufferOutputStream);
+ thumbnailData = generateThumbnailInternally(img, imageIdOrNull, bufferOutputStream);
}
- return byteArray;
+ return thumbnailData;
}
- private byte[] generateThumbnailWithImageMagic(File imageFile) throws IOException
+ private ThumbnailData generateThumbnailWithImageMagic(File imageFile) throws IOException
{
- String size =
- thumbnailsStorageFormat.getMaxWidth() + "x"
- + thumbnailsStorageFormat.getMaxHeight();
+ int width = thumbnailsStorageFormat.getMaxWidth();
+ int height = thumbnailsStorageFormat.getMaxHeight();
if (thumbnailsStorageFormat.getZoomLevel() != null)
{
Dimension originalSize = loadUnchangedImageDimension(imageFile, null);
- long x =
- (int) Math.round(thumbnailsStorageFormat.getZoomLevel()
- * originalSize.getWidth());
- long y =
- (int) Math.round(thumbnailsStorageFormat.getZoomLevel()
- * originalSize.getHeight());
- size = x + "x" + y;
+ double zoomLevel = thumbnailsStorageFormat.getZoomLevel();
+ width = (int) Math.round(zoomLevel * originalSize.getWidth());
+ height = (int) Math.round(zoomLevel * originalSize.getHeight());
}
+ String size = width + "x" + height;
String imageFilePath = imageFile.getPath();
List<String> params = new ArrayList<String>();
@@ -245,28 +265,29 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
imageFilePath, result.getExitValue(), result.getProcessIOResult().getStatus()));
} else
{
- return result.getBinaryOutput();
+ return new ThumbnailData(result.getBinaryOutput(), width, height);
}
}
- private byte[] generateThumbnailInternally(File imageFile, String imageIdOrNull,
+ private ThumbnailData generateThumbnailInternally(File imageFile, String imageIdOrNull,
ByteArrayOutputStream bufferOutputStream) throws IOException
{
BufferedImage image = loadUnchangedImage(imageFile, imageIdOrNull);
- long x = thumbnailsStorageFormat.getMaxWidth();
- long y = thumbnailsStorageFormat.getMaxHeight();
+ int widht = thumbnailsStorageFormat.getMaxWidth();
+ int height = thumbnailsStorageFormat.getMaxHeight();
if (thumbnailsStorageFormat.getZoomLevel() != null)
{
- x = Math.round(thumbnailsStorageFormat.getZoomLevel() * image.getWidth());
- y = Math.round(thumbnailsStorageFormat.getZoomLevel() * image.getHeight());
+ widht = (int) Math.round(thumbnailsStorageFormat.getZoomLevel() * image.getWidth());
+ height = (int) Math.round(thumbnailsStorageFormat.getZoomLevel() * image.getHeight());
}
BufferedImage thumbnail =
- ImageUtil.rescale(image, (int) x, (int) y, false,
+ ImageUtil.rescale(image, widht, height, false,
thumbnailsStorageFormat.isHighQuality());
ImageUtil.writeImageToPng(thumbnail, bufferOutputStream);
- return bufferOutputStream.toByteArray();
+ return new ThumbnailData(bufferOutputStream.toByteArray(), thumbnail.getWidth(),
+ thumbnail.getHeight());
}
private BufferedImage loadUnchangedImage(File imageFile, String imageIdOrNull)
@@ -288,10 +309,9 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
thumbnailPath, ex.getMessage()));
}
- private ITaskExecutor<RelativeImageFile> createThumbnailGenerator(
- final IHDF5ContainerWriter writer)
+ private ITaskExecutor<ImageFileInfo> createThumbnailGenerator(final IHDF5ContainerWriter writer)
{
- return new ITaskExecutor<RelativeImageFile>()
+ return new ITaskExecutor<ImageFileInfo>()
{
private ThreadLocal<ByteArrayOutputStream> outputStreamBuffers =
new ThreadLocal<ByteArrayOutputStream>()
@@ -303,7 +323,7 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
}
};
- public Status execute(RelativeImageFile image)
+ public Status execute(ImageFileInfo image)
{
// each thread will get its own buffer to avoid allocating memory for the
// internal array each time
@@ -316,8 +336,9 @@ public class Hdf5ThumbnailGenerator implements IHDF5WriterClient
public void runWithSimpleWriter(IHDF5ContainerWriter writer)
{
- Collection<FailureRecord<RelativeImageFile>> errors =
- ParallelizedExecutor.process(images, createThumbnailGenerator(writer),
+ Collection<FailureRecord<ImageFileInfo>> errors =
+ ParallelizedExecutor.process(imageDataSetStructure.getImages(),
+ createThumbnailGenerator(writer),
thumbnailsStorageFormat.getAllowedMachineLoadDuringGeneration(), 100,
"Thumbnails generation", MAX_RETRY_OF_FAILED_GENERATION, true);
if (errors.size() > 0)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
index 79d1a850af5d97206d1753bfd7bdc9886075fb51..637641bf03caec39cf50925a98f19003d133af11 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IImagingDatasetLoader.java
@@ -72,9 +72,10 @@ public interface IImagingDatasetLoader extends IImageDatasetLoader
* @param channelCode channel code for which representative image is requested
* @param wellLocationOrNull if not null the returned images are restricted to one well.
* Otherwise the dataset is assumed to have no container and spots.
+ * @param imageSize
*/
AbsoluteImageReference tryGetRepresentativeThumbnail(String channelCode,
- Location wellLocationOrNull);
+ Location wellLocationOrNull, RequestedImageSize imageSize);
/**
* Returns the stored thumbnail for the given parameters, or <code>null</code>, if no thumbnail
@@ -85,8 +86,9 @@ public interface IImagingDatasetLoader extends IImageDatasetLoader
*
* @param channelCode The code of the channel to get the thumbnail for.
* @param channelStackReference Specifies well and tile of the thumbnail.
+ * @param imageSize
*/
AbsoluteImageReference tryGetThumbnail(String channelCode,
- ImageChannelStackReference channelStackReference);
+ ImageChannelStackReference channelStackReference, RequestedImageSize imageSize);
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
index f8d8f792c7fc7f75a3e543d90b5a4e0b0680b61a..7cc8191234f34f72c5cbc1c1c0d7a540447cbb95 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseVersionHolder.java
@@ -28,7 +28,7 @@ public class ImagingDatabaseVersionHolder implements IDatabaseVersionHolder
public String getDatabaseVersion()
{
- return "018"; // changed in S119
+ return "019"; // changed in S121
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingLoaderStrategyFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingLoaderStrategyFactory.java
index c7da4d9422045778dcec4a03ca04742a5e7b4aac..bdcd247549df44d3defb06f790a7ebdc9b01388c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingLoaderStrategyFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingLoaderStrategyFactory.java
@@ -59,14 +59,15 @@ public class ImagingLoaderStrategyFactory
ImageChannelStackReference channelStackReference,
RequestedImageSize imageSize)
{
- return this.imageAccessor.tryGetThumbnail(channelCode, channelStackReference);
+ return this.imageAccessor.tryGetThumbnail(channelCode, channelStackReference,
+ imageSize);
}
public AbsoluteImageReference tryGetRepresentativeImage(String channelCode,
Location wellLocationOrNull, RequestedImageSize imageSize)
{
return imageAccessor.tryGetRepresentativeThumbnail(channelCode,
- wellLocationOrNull);
+ wellLocationOrNull, imageSize);
}
};
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 5fd8d4e23a79fcdd7a77db17cc3b59d3d31798c5..1056eb91ddf65366f951b6ed05110729032f14c3 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
@@ -23,13 +23,16 @@ import java.util.Properties;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
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.impl.ThumbnailsInfo;
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;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -146,33 +149,47 @@ public final class PlateStorageProcessor extends AbstractImageStorageProcessor
public static class ImageDatasetOwnerInformation extends DatasetOwnerInformation
{
public static ImageDatasetOwnerInformation create(String containerDatasetPermId,
- DataSetInformation originalDataset, String thumbnailDatasetPermIdOrNull)
+ DataSetInformation originalDataset, ThumbnailsInfo thumbnailsInfosOrNull)
{
return new ImageDatasetOwnerInformation(containerDatasetPermId, originalDataset,
- thumbnailDatasetPermIdOrNull);
+ thumbnailsInfosOrNull);
}
private final List<ImageZoomLevel> imageZoomLevels;
private ImageDatasetOwnerInformation(String containerDatasetPermId,
- DataSetInformation originalDataset, String thumbnailDatasetPermIdOrNull)
+ DataSetInformation originalDataset, ThumbnailsInfo thumbnailsInfosOrNull)
{
super(containerDatasetPermId, originalDataset);
- this.imageZoomLevels = createZoomLevels(originalDataset, thumbnailDatasetPermIdOrNull);
+ this.imageZoomLevels = createZoomLevels(originalDataset, thumbnailsInfosOrNull);
}
private static List<ImageZoomLevel> createZoomLevels(DataSetInformation originalDataset,
- String thumbnailDatasetPermIdOrNull)
+ ThumbnailsInfo thumbnailsInfosOrNull)
{
List<ImageZoomLevel> zoomLevels = new ArrayList<ImageZoomLevel>();
+
ImageZoomLevel originalZoomLevel =
- new ImageZoomLevel(originalDataset.getDataSetCode(), true);
+ new ImageZoomLevel(originalDataset.getDataSetCode(), true,
+ StringUtils.EMPTY_STRING, null, null);
zoomLevels.add(originalZoomLevel);
- if (thumbnailDatasetPermIdOrNull != null)
+ if (thumbnailsInfosOrNull != null)
{
- ImageZoomLevel thumbnailZoomLevel =
- new ImageZoomLevel(thumbnailDatasetPermIdOrNull, false);
- zoomLevels.add(thumbnailZoomLevel);
+ for (String permId : thumbnailsInfosOrNull.getThumbnailPhysicalDatasetsPermIds())
+ {
+ Integer width = null, height = null;
+ Size dimension = thumbnailsInfosOrNull.tryGetDimension(permId);
+ if (dimension != null)
+ {
+ width = dimension.getWidth();
+ height = dimension.getHeight();
+ }
+ String rootPath = thumbnailsInfosOrNull.getRootPath(permId);
+
+ ImageZoomLevel thumbnailZoomLevel =
+ new ImageZoomLevel(permId, false, rootPath, width, height);
+ zoomLevels.add(thumbnailZoomLevel);
+ }
}
return zoomLevels;
}
@@ -193,7 +210,7 @@ public final class PlateStorageProcessor extends AbstractImageStorageProcessor
extractionResult, operationLog, notificationLog, notifyIfPlateIncomplete);
return validator.validateImages();
}
-
+
private void checkDataSetInformation(final DatasetOwnerInformation dataSetInformation)
{
assert dataSetInformation != null : "Unspecified data set information";
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PrefixedImage.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PrefixedImage.java
new file mode 100644
index 0000000000000000000000000000000000000000..47e56572bf4c96c88c36fa303b6b0d9375a175e8
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PrefixedImage.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright 2011 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;
+
+import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgImageDTO;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class PrefixedImage
+{
+ private final String pathPrefix;
+
+ private final ImgImageDTO image;
+
+ public PrefixedImage(String pathPrefix, ImgImageDTO image)
+ {
+ this.pathPrefix = pathPrefix;
+ this.image = image;
+ }
+
+ public String getFilePath()
+ {
+ if (StringUtils.isBlank(pathPrefix))
+ {
+ return image.getFilePath();
+ }
+ return pathPrefix + "/" + image.getFilePath();
+ }
+
+ public ColorComponent getColorComponent()
+ {
+ return image.getColorComponent();
+ }
+
+ public String getImageID()
+ {
+ return image.getImageID();
+ }
+
+ public IImageTransformerFactory tryGetImageTransformerFactory()
+ {
+ return image.tryGetImageTransformerFactory();
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
index 74f282d01400ab3e7564d2fb3a875a805684edf9..6861f592a41279730db71f26fa7f819032452f1c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingQueryDAO.java
@@ -90,8 +90,8 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
+ "?{1.imageLibraryName}, ?{1.imageReaderName}) returning ID")
public long addImageDataset(ImgImageDatasetDTO dataset);
- @Select("insert into image_zoom_levels (physical_dataset_perm_id, is_original, container_dataset_id) "
- + "values(?{1.physicalDatasetPermId}, ?{1.isOriginal}, ?{1.containerDatasetId}) returning ID")
+ @Select("insert into image_zoom_levels (physical_dataset_perm_id, is_original, container_dataset_id, path, width, height) "
+ + "values(?{1.physicalDatasetPermId}, ?{1.isOriginal}, ?{1.containerDatasetId}, ?{1.rootPath}, ?{1.width}, ?{1.height}) returning ID")
public long addImageZoomLevel(ImgImageZoomLevelDTO dataset);
@Select("insert into ANALYSIS_DATA_SETS (PERM_ID, CONT_ID) "
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageZoomLevel.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageZoomLevel.java
index 46844c2b06428307642191af3336ed5d9dee0f59..ff13e2ac6e252b7d785046f584365a8f20012662 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageZoomLevel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageZoomLevel.java
@@ -27,10 +27,20 @@ public class ImageZoomLevel
private final boolean isOriginal;
- public ImageZoomLevel(String physicalDatasetPermId, boolean isOriginal)
+ private final String rootPath;
+
+ private final Integer width;
+
+ private final Integer height;
+
+ public ImageZoomLevel(String physicalDatasetPermId, boolean isOriginal, String rootPath,
+ Integer width, Integer height)
{
this.physicalDatasetPermId = physicalDatasetPermId;
this.isOriginal = isOriginal;
+ this.rootPath = rootPath;
+ this.width = width;
+ this.height = height;
}
public String getPhysicalDatasetPermId()
@@ -43,4 +53,18 @@ public class ImageZoomLevel
return isOriginal;
}
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ public String getRootPath()
+ {
+ return rootPath;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
index 26514bce22ade9d2f97433585640063e31605989..3505d444113fa804968d8d89733d4bd8748b4cf3 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ImageDataSetInformation.java
@@ -42,7 +42,7 @@ public class ImageDataSetInformation extends BasicDataSetInformation
private ImageDataSetStructure imageDataSetStructure;
- private ThumbnailFilePaths thumbnailFilePathsOrNull;
+ private ThumbnailsInfo thumbnailsInfos;
private String containerDatasetPermId;
@@ -57,9 +57,9 @@ public class ImageDataSetInformation extends BasicDataSetInformation
}
/** @returns null if no thumbnails will be stored */
- public ThumbnailFilePaths tryGetThumbnailFilePaths()
+ public ThumbnailsInfo getThumbnailsInfos()
{
- return thumbnailFilePathsOrNull;
+ return thumbnailsInfos;
}
public ImageDataSetStructure getImageDataSetStructure()
@@ -88,9 +88,9 @@ public class ImageDataSetInformation extends BasicDataSetInformation
this.containerDatasetPermId = containerDatasetPermId;
}
- public void setThumbnailFilePaths(ThumbnailFilePaths thumbnailFilePathsOrNull)
+ public void setThumbnailsInfo(ThumbnailsInfo thumbnailsInfo)
{
- this.thumbnailFilePathsOrNull = thumbnailFilePathsOrNull;
+ this.thumbnailsInfos = thumbnailsInfo;
}
public void setImageDataSetStructure(ImageDataSetStructure imageDataSetStructure)
@@ -107,9 +107,9 @@ public class ImageDataSetInformation extends BasicDataSetInformation
appendNameAndObject(buffer, "images structure", imageDataSetStructure);
appendNameAndObject(buffer, "container dataset", containerDatasetPermId);
appendNameAndObject(buffer, "original dataset", this.getDataSetCode());
- if (this.tryGetThumbnailFilePaths() != null)
+ if (getThumbnailsInfos() != null)
{
- appendNameAndObject(buffer, "thumbnail", this.tryGetThumbnailFilePaths());
+ appendNameAndObject(buffer, "thumbnail", getThumbnailsInfos());
} else
{
appendNameAndObject(buffer, "thumbnail", "none");
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailFilePaths.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailFilePaths.java
deleted file mode 100644
index 1cb5d037e62a9600bd4b46bdbfc8ff5a80b768dc..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailFilePaths.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package ch.systemsx.cisd.openbis.dss.etl.dto.api.impl;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ToStringUtil;
-
-/**
- * Stores the mapping between image and their thumbnails paths. Thread-safe class.
- *
- * @author Tomasz Pylak
- */
-public class ThumbnailFilePaths
-{
- private final Map<RelativeImageFile, String> imageToThumbnailPathMap;
-
- private final String thumbnailPhysicalDatasetPermId;
-
- public ThumbnailFilePaths(String thumbnailPhysicalDatasetPermId)
- {
- assert thumbnailPhysicalDatasetPermId != null : "thumbnailPhysicalDatasetPermId is null";
-
- this.thumbnailPhysicalDatasetPermId = thumbnailPhysicalDatasetPermId;
- this.imageToThumbnailPathMap = new HashMap<RelativeImageFile, String>();
- }
-
- /**
- * Saves the path to the thumbnail for the specified image. The thumbnail path is relative and
- * starts with the name of the thumbnail file.
- */
- public synchronized void saveThumbnailPath(RelativeImageFile image, String thumbnailRelativePath)
- {
- imageToThumbnailPathMap.put(image, thumbnailRelativePath);
- }
-
- public synchronized String getThumbnailPath(RelativeImageFile image)
- {
- return imageToThumbnailPathMap.get(image);
- }
-
- public String getThumbnailPhysicalDatasetPermId()
- {
- return thumbnailPhysicalDatasetPermId;
- }
-
- @Override
- public String toString()
- {
- final StringBuilder buffer = new StringBuilder();
- ToStringUtil.appendNameAndObject(buffer, "number of thumbnails",
- imageToThumbnailPathMap.size());
- ToStringUtil.appendNameAndObject(buffer, "dataset perm id", thumbnailPhysicalDatasetPermId);
- return buffer.toString();
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailsInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailsInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..d72cb466a7622e4d99752a24daa577007c77565c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/ThumbnailsInfo.java
@@ -0,0 +1,117 @@
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.impl;
+
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ToStringUtil;
+
+/**
+ * Stores the mapping between image and their thumbnails paths. Thread-safe class.
+ *
+ * @author Tomasz Pylak
+ */
+public class ThumbnailsInfo
+{
+ public static class PhysicalDatasetInfo
+ {
+ private final String rootPath;
+
+ private int thumbnailsWidth;
+
+ private int thumbnailsHeight;
+
+ public PhysicalDatasetInfo(String rootPath)
+ {
+ this.rootPath = rootPath;
+ }
+ }
+
+ private final Map<RelativeImageFile, String> imageToThumbnailPathMap;
+
+ private final Map<String, PhysicalDatasetInfo> datasetInfos;
+
+ public ThumbnailsInfo()
+ {
+ this.imageToThumbnailPathMap = new HashMap<RelativeImageFile, String>();
+ this.datasetInfos = new HashMap<String, ThumbnailsInfo.PhysicalDatasetInfo>();
+ }
+
+ public void putDataSet(String permId, String rootPath)
+ {
+ datasetInfos.put(permId, new PhysicalDatasetInfo(rootPath));
+ }
+
+ /**
+ * Saves the path to the thumbnail for the specified image. The thumbnail path is relative and
+ * starts with the name of the thumbnail file.
+ */
+ public synchronized void saveThumbnailPath(String permId, RelativeImageFile image,
+ String thumbnailRelativePath, int width, int height)
+ {
+ imageToThumbnailPathMap.put(image, thumbnailRelativePath);
+
+ PhysicalDatasetInfo datasetInfo = datasetInfos.get(permId);
+ if (datasetInfo != null)
+ {
+ datasetInfo.thumbnailsWidth = Math.max(datasetInfo.thumbnailsWidth, width);
+ datasetInfo.thumbnailsHeight = Math.max(datasetInfo.thumbnailsHeight, height);
+ }
+ }
+
+ public synchronized String getThumbnailPath(RelativeImageFile image)
+ {
+ return imageToThumbnailPathMap.get(image);
+ }
+
+ public Set<String> getThumbnailPhysicalDatasetsPermIds()
+ {
+ return datasetInfos.keySet();
+ }
+
+ public Size tryGetDimension(String permId)
+ {
+ PhysicalDatasetInfo datasetInfo = datasetInfos.get(permId);
+ if (datasetInfo != null)
+ {
+ if (datasetInfo.thumbnailsWidth > 0 && datasetInfo.thumbnailsHeight > 0)
+ {
+ return new Size(datasetInfo.thumbnailsWidth, datasetInfo.thumbnailsHeight);
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public String toString()
+ {
+ final StringBuilder buffer = new StringBuilder();
+ ToStringUtil.appendNameAndObject(buffer, "number of thumbnails",
+ imageToThumbnailPathMap.size());
+ ToStringUtil.appendNameAndObject(buffer, "dataset perm ids: ", printPermIds());
+ return buffer.toString();
+ }
+
+ private String printPermIds()
+ {
+ StringBuilder sb = new StringBuilder("[");
+ boolean notFirst = false;
+ for (String permId : datasetInfos.keySet())
+ {
+ if (notFirst)
+ {
+ sb.append(";");
+ notFirst = true;
+ }
+ sb.append(" ").append(permId);
+ }
+ return sb.append(" ]").toString();
+ }
+
+ public String getRootPath(String permId)
+ {
+ return datasetInfos.get(permId).rootPath;
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
index 64351d4752db5a855348b1dbc57bf3f05bdab8ff..36b75120b11706c345f9f4644a0b6e582c2fa9ec 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDataSetHandler.java
@@ -30,14 +30,13 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTra
import ch.systemsx.cisd.openbis.dss.Constants;
import ch.systemsx.cisd.openbis.dss.etl.Hdf5ThumbnailGenerator;
import ch.systemsx.cisd.openbis.dss.etl.PlateGeometryOracle;
-import ch.systemsx.cisd.openbis.dss.etl.dto.RelativeImageFile;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageContainerDataSet;
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.ThumbnailFilePaths;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImagingDataSetRegistrationTransaction;
@@ -429,17 +428,17 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
imageDataSetStructure.getImageStorageConfiguraton()
.getThumbnailsStorageFormat();
+ ThumbnailsInfo thumbnailsInfo = new ThumbnailsInfo();
for (ThumbnailsStorageFormat thumbnailsStorageFormat : thumbnailsStorageFormatList)
{
IDataSet thumbnailDataset = createThumbnailDataset();
thumbnailDatasets.add(thumbnailDataset);
- ThumbnailFilePaths thumbnailPaths =
- generateThumbnails(imageDataSetStructure, incomingDirectory,
- thumbnailDataset, thumbnailsStorageFormat);
- imageDataSetInformation.setThumbnailFilePaths(thumbnailPaths);
+ generateThumbnails(imageDataSetStructure, incomingDirectory, thumbnailDataset,
+ thumbnailsStorageFormat, thumbnailsInfo);
containedDataSetCodes.add(thumbnailDataset.getDataSetCode());
}
+ imageDataSetInformation.setThumbnailsInfo(thumbnailsInfo);
}
// create main dataset (with original images)
@SuppressWarnings("unchecked")
@@ -470,9 +469,9 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
return new File(originalDirName + File.separator + directoryPath);
}
- private ThumbnailFilePaths generateThumbnails(ImageDataSetStructure imageDataSetStructure,
+ private void generateThumbnails(ImageDataSetStructure imageDataSetStructure,
File incomingDirectory, IDataSet thumbnailDataset,
- ThumbnailsStorageFormat thumbnailsStorageFormatOrNull)
+ ThumbnailsStorageFormat thumbnailsStorageFormatOrNull, ThumbnailsInfo thumbnailPaths)
{
String thumbnailFile;
if (thumbnailsStorageFormatOrNull == null)
@@ -487,22 +486,10 @@ public class JythonPlateDataSetHandler extends JythonTopLevelDataSetHandler<Data
thumbnailsStorageFormatOrNull.getThumbnailsFileName());
}
- List<RelativeImageFile> images = asRelativeImageFile(imageDataSetStructure.getImages());
- ThumbnailFilePaths thumbnailPaths =
- Hdf5ThumbnailGenerator.tryGenerateThumbnails(images, incomingDirectory,
- thumbnailFile, imageDataSetStructure.getImageStorageConfiguraton(),
- thumbnailDataset.getDataSetCode(), thumbnailsStorageFormatOrNull);
- return thumbnailPaths;
- }
-
- private static List<RelativeImageFile> asRelativeImageFile(List<ImageFileInfo> images)
- {
- List<RelativeImageFile> imageFiles = new ArrayList<RelativeImageFile>();
- for (ImageFileInfo image : images)
- {
- imageFiles.add(RelativeImageFile.create(image));
- }
- return imageFiles;
+ Hdf5ThumbnailGenerator.tryGenerateThumbnails(imageDataSetStructure, incomingDirectory,
+ thumbnailFile, imageDataSetStructure.getImageStorageConfiguraton(),
+ thumbnailDataset.getDataSetCode(), thumbnailsStorageFormatOrNull,
+ thumbnailPaths);
}
private IDataSet createThumbnailDataset()
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 2ed895dd957f9a04b875622604eca2cd86e6f08f..3ce22ddfcdd909f6c5ddd089f13f9340e15dad64 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
@@ -346,7 +346,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
for (String channelCode : params.getChannelsCodes())
{
AbsoluteImageReference image =
- imageAccessor.tryGetRepresentativeThumbnail(channelCode, null);
+ imageAccessor.tryGetRepresentativeThumbnail(channelCode, null, null);
if (image != null)
{
return image.getUnchangedImage();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
index c54e10e35d4b597f36cf5624bd28e7e3a693036a..52efb64ba2862c435339f1deefbd75430dfcd1af 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
@@ -235,9 +235,8 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
{ StringArrayMapper.class }, fetchSize = FETCH_SIZE)
public List<ImgImageDatasetDTO> listImageDatasetsByPermId(String... datasetPermIds);
- @Select(sql = "select * from IMAGE_ZOOM_LEVELS zoom, IMAGE_DATA_SETS img_ds "
- + "where zoom.CONTAINER_DATASET_ID = img_ds.id and img_ds.PERM_ID = ?{1}", fetchSize = FETCH_SIZE)
- public List<ImgImageZoomLevelDTO> listImageZoomLevels(String containerDatasetPermId);
+ @Select(sql = "select * from IMAGE_ZOOM_LEVELS zoom where zoom.CONTAINER_DATASET_ID = ?{1}", fetchSize = FETCH_SIZE)
+ public List<ImgImageZoomLevelDTO> listImageZoomLevels(long datasetId);
@Select(sql = "select * from ANALYSIS_DATA_SETS where PERM_ID = any(?{1})", parameterBindings =
{ StringArrayMapper.class }, fetchSize = FETCH_SIZE)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageZoomLevelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageZoomLevelDTO.java
index cb006c85e95ff04441e84251aa5f7b7ae1b47b15..ad1774d821f5b8df77b5c9bd306930b5e60eec28 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageZoomLevelDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageZoomLevelDTO.java
@@ -34,18 +34,30 @@ public class ImgImageZoomLevelDTO extends AbstractImgIdentifiable
@ResultColumn("container_dataset_id")
private long containerDatasetId;
+ @ResultColumn("path")
+ private String rootPath;
+
+ @ResultColumn("width")
+ private Integer width;
+
+ @ResultColumn("height")
+ private Integer height;
+
@SuppressWarnings("unused")
private ImgImageZoomLevelDTO()
{
// All Data-Object classes must have a default constructor.
}
- public ImgImageZoomLevelDTO(String physicalDatasetPermId, boolean isOriginal,
- long containerDatasetId)
+ public ImgImageZoomLevelDTO(String physicalDatasetPermId, boolean isOriginal, String rootPath,
+ Integer width, Integer height, long containerDatasetId)
{
this.physicalDatasetPermId = physicalDatasetPermId;
this.isOriginal = isOriginal;
this.containerDatasetId = containerDatasetId;
+ this.rootPath = rootPath;
+ this.width = width;
+ this.height = height;
}
public String getPhysicalDatasetPermId()
@@ -77,4 +89,34 @@ public class ImgImageZoomLevelDTO extends AbstractImgIdentifiable
{
this.containerDatasetId = containerDatasetId;
}
+
+ public String getRootPath()
+ {
+ return rootPath;
+ }
+
+ public void setRootPath(String rootPath)
+ {
+ this.rootPath = rootPath;
+ }
+
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ public void setWidth(Integer width)
+ {
+ this.width = width;
+ }
+
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ public void setHeight(Integer height)
+ {
+ this.height = height;
+ }
}
diff --git a/screening/source/sql/imaging/postgresql/019/schema-019.sql b/screening/source/sql/imaging/postgresql/019/schema-019.sql
new file mode 100644
index 0000000000000000000000000000000000000000..476e44e4a39043e60aae1f3c046e4ae4c8310bc5
--- /dev/null
+++ b/screening/source/sql/imaging/postgresql/019/schema-019.sql
@@ -0,0 +1,410 @@
+
+/* ---------------------------------------------------------------------- */
+/* Domains */
+/* ---------------------------------------------------------------------- */
+
+CREATE DOMAIN TECH_ID AS BIGINT;
+
+CREATE DOMAIN CODE AS VARCHAR(40);
+
+CREATE DOMAIN NAME AS VARCHAR(80);
+
+CREATE DOMAIN DESCRIPTION AS VARCHAR(200);
+
+CREATE DOMAIN FILE_PATH as VARCHAR(1000);
+
+CREATE DOMAIN COLOR_COMPONENT AS VARCHAR(40) CHECK (VALUE IN ('RED', 'GREEN', 'BLUE'));
+
+CREATE DOMAIN CHANNEL_COLOR AS VARCHAR(20) CHECK (VALUE IN ('BLUE', 'GREEN', 'RED', 'RED_GREEN', 'RED_BLUE', 'GREEN_BLUE'));
+
+CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
+
+/* ---------------------------------------------------------------------- */
+/* Tables */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE EXPERIMENTS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
+
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID)
+);
+
+CREATE TABLE CONTAINERS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+
+ SPOTS_WIDTH INTEGER,
+ SPOTS_HEIGHT INTEGER,
+
+ EXPE_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_SAMPLE_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX CONTAINERS_EXPE_IDX ON CONTAINERS(EXPE_ID);
+
+CREATE TABLE SPOTS (
+ ID BIGSERIAL NOT NULL,
+
+ -- position in the container, one-based
+ X INTEGER,
+ Y INTEGER,
+ CONT_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_SPOT_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX SPOTS_CONT_IDX ON SPOTS(CONT_ID);
+-- allows to select one spot of the container quicker
+CREATE INDEX SPOTS_COORDS_IDX ON SPOTS(CONT_ID, X, Y);
+
+CREATE TABLE ANALYSIS_DATA_SETS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+
+ CONT_ID TECH_ID,
+
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_ANALYSIS_DATA_SET_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX ANALYSIS_DATA_SETS_CONT_IDX ON ANALYSIS_DATA_SETS(CONT_ID);
+
+
+CREATE TABLE IMAGE_DATA_SETS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+
+ ---- image dataset specific fields (should be refactored)
+ FIELDS_WIDTH INTEGER,
+ FIELDS_HEIGHT INTEGER,
+ -- transformation for merged channels on the dataset level, overrides experiment level transformation
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
+ -- a redundant information if there are timepoint or depth stack data for any spots in this dataset
+ IS_MULTIDIMENSIONAL BOOLEAN_CHAR NOT NULL,
+
+ -- Which image library should be used to read the image?
+ -- If not specified, some heuristics are used, but it is slower and does not try with all the available libraries.
+ IMAGE_LIBRARY_NAME NAME,
+ -- Which reader in the library should be used? Valid only if the library name is specified.
+ -- Should be specified when library name is specified.
+ IMAGE_LIBRARY_READER_NAME NAME,
+ ---- END image dataset specific fields
+
+ CONT_ID TECH_ID,
+
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_IMAGE_DATA_SET_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX IMAGE_DATA_SETS_CONT_IDX ON IMAGE_DATA_SETS(CONT_ID);
+
+CREATE TABLE IMAGE_ZOOM_LEVELS (
+ ID BIGSERIAL NOT NULL,
+
+ IS_ORIGINAL BOOLEAN_CHAR NOT NULL,
+ CONTAINER_DATASET_ID TECH_ID NOT NULL,
+
+ -- Perm id of the 'physical' dataset which contains all images with this zoom.
+ -- Physical datasets are not stored in "image_data_sets" table, but we need the reference to them
+ -- when we delete or archive one zoom level.
+ PHYSICAL_DATASET_PERM_ID TEXT NOT NULL,
+
+ PATH FILE_PATH,
+ WIDTH INTEGER,
+ HEIGHT INTEGER,
+
+ PRIMARY KEY (ID),
+ UNIQUE (PHYSICAL_DATASET_PERM_ID),
+ CONSTRAINT FK_IMAGE_ZOOM_LEVELS_1 FOREIGN KEY (CONTAINER_DATASET_ID) REFERENCES IMAGE_DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX IMAGE_ZOOM_LEVELS_PHYS_DS_IDX ON IMAGE_ZOOM_LEVELS (PHYSICAL_DATASET_PERM_ID);
+CREATE INDEX IMAGE_ZOOM_LEVELS_CONT_FK_IDX ON IMAGE_ZOOM_LEVELS (CONTAINER_DATASET_ID);
+
+CREATE TABLE CHANNELS (
+ ID BIGSERIAL NOT NULL,
+
+ CODE NAME NOT NULL,
+ LABEL NAME NOT NULL,
+ DESCRIPTION DESCRIPTION,
+ WAVELENGTH INTEGER,
+
+ -- RGB color components specify the color in which channel should be displayed
+ RED_CC INTEGER NOT NULL,
+ GREEN_CC INTEGER NOT NULL,
+ BLUE_CC INTEGER NOT NULL,
+
+ DS_ID TECH_ID,
+ EXP_ID TECH_ID,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_CHANNELS_1 FOREIGN KEY (DS_ID) REFERENCES IMAGE_DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_CHANNELS_2 FOREIGN KEY (EXP_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT CHANNELS_DS_EXP_ARC_CK CHECK ((DS_ID IS NOT NULL AND EXP_ID IS NULL) OR (DS_ID IS NULL AND EXP_ID IS NOT NULL)),
+
+ CONSTRAINT CHANNELS_UK_1 UNIQUE(CODE, DS_ID),
+ CONSTRAINT CHANNELS_UK_2 UNIQUE(CODE, EXP_ID)
+);
+
+CREATE INDEX CHANNELS_DS_IDX ON CHANNELS(DS_ID);
+
+CREATE TABLE IMAGE_TRANSFORMATIONS (
+ ID BIGSERIAL NOT NULL,
+
+ CODE NAME NOT NULL,
+ LABEL NAME NOT NULL,
+ DESCRIPTION character varying(1000),
+ IMAGE_TRANSFORMER_FACTORY BYTEA NOT NULL,
+
+ -- For now there can be only one transformation for each channel which is editable by Image Viewer,
+ -- but when GUI will support more then this column will become really useful.
+ IS_EDITABLE BOOLEAN_CHAR NOT NULL,
+
+ -- The default choice to present the image.
+ -- If not present a 'hard-coded' default transformation will become available.
+ IS_DEFAULT BOOLEAN_CHAR NOT NULL DEFAULT 'F',
+
+ CHANNEL_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_IMAGE_TRANSFORMATIONS_CHANNEL FOREIGN KEY (CHANNEL_ID) REFERENCES CHANNELS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+
+ CONSTRAINT IMAGE_TRANSFORMATIONS_UK_1 UNIQUE(CODE, CHANNEL_ID)
+);
+
+CREATE INDEX IMAGE_TRANSFORMATIONS_CHANNELS_IDX ON IMAGE_TRANSFORMATIONS(CHANNEL_ID);
+
+CREATE TABLE CHANNEL_STACKS (
+ ID BIGSERIAL NOT NULL,
+
+ -- x and y are kind of a two dimensional sequence number, some use case may only use x and leave y alone
+ X INTEGER,
+ Y INTEGER,
+ -- We use the fixed dimension meters here.
+ Z_in_M REAL,
+ -- We use the fixed dimension seconds here.
+ T_in_SEC REAL,
+ SERIES_NUMBER INTEGER,
+
+ -- For all channel stacks of a well (HCS) or image dataset (microscopy) there should be exactly
+ -- one record with is_representative = true
+ is_representative BOOLEAN_CHAR NOT NULL DEFAULT 'F',
+
+ DS_ID TECH_ID NOT NULL,
+ SPOT_ID TECH_ID,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_CHANNEL_STACKS_1 FOREIGN KEY (SPOT_ID) REFERENCES SPOTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_CHANNEL_STACKS_2 FOREIGN KEY (DS_ID) REFERENCES IMAGE_DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX CHANNEL_STACKS_DS_IDX ON CHANNEL_STACKS(DS_ID);
+CREATE INDEX CHANNEL_STACKS_SPOT_IDX ON CHANNEL_STACKS(SPOT_ID);
+CREATE INDEX CHANNEL_STACKS_DIM_IDX ON CHANNEL_STACKS(X, Y, Z_in_M, T_in_SEC);
+
+CREATE TABLE IMAGES (
+ ID BIGSERIAL NOT NULL,
+
+ PATH FILE_PATH NOT NULL,
+ IMAGE_ID CODE,
+ COLOR COLOR_COMPONENT,
+
+ PRIMARY KEY (ID)
+);
+
+CREATE TABLE ACQUIRED_IMAGES (
+ ID BIGSERIAL NOT NULL,
+
+ IMG_ID TECH_ID,
+ THUMBNAIL_ID TECH_ID,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
+
+ CHANNEL_STACK_ID TECH_ID NOT NULL,
+ CHANNEL_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_IMAGES_1 FOREIGN KEY (CHANNEL_STACK_ID) REFERENCES CHANNEL_STACKS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_IMAGES_2 FOREIGN KEY (CHANNEL_ID) REFERENCES CHANNELS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_IMAGES_3 FOREIGN KEY (IMG_ID) REFERENCES IMAGES (ID) ON DELETE SET NULL ON UPDATE CASCADE,
+ CONSTRAINT FK_IMAGES_4 FOREIGN KEY (THUMBNAIL_ID) REFERENCES IMAGES (ID) ON DELETE SET NULL ON UPDATE CASCADE
+);
+
+CREATE INDEX IMAGES_CHANNEL_STACK_IDX ON ACQUIRED_IMAGES(CHANNEL_STACK_ID);
+CREATE INDEX IMAGES_CHANNEL_IDX ON ACQUIRED_IMAGES(CHANNEL_ID);
+CREATE INDEX IMAGES_IMG_IDX ON ACQUIRED_IMAGES(IMG_ID);
+CREATE INDEX IMAGES_THUMBNAIL_IDX ON ACQUIRED_IMAGES(THUMBNAIL_ID);
+
+CREATE TABLE EVENTS (
+ LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
+);
+
+/* ---------------------------------------------------------------------- */
+/* FEATURE VECTORS */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE FEATURE_DEFS (
+ ID BIGSERIAL NOT NULL,
+
+ CODE NAME NOT NULL,
+ LABEL NAME NOT NULL,
+ DESCRIPTION DESCRIPTION,
+
+ DS_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FEATURE_DEFS_1 FOREIGN KEY (DS_ID) REFERENCES ANALYSIS_DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FEATURE_DEFS_UK_1 UNIQUE(CODE, DS_ID)
+);
+
+CREATE INDEX FEATURE_DEFS_DS_IDX ON FEATURE_DEFS(DS_ID);
+
+CREATE TABLE FEATURE_VOCABULARY_TERMS (
+ ID BIGSERIAL NOT NULL,
+
+ CODE NAME NOT NULL,
+ SEQUENCE_NUMBER INTEGER NOT NULL,
+ FD_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FEATURE_VOCABULARY_TERMS_1 FOREIGN KEY (FD_ID) REFERENCES FEATURE_DEFS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX FEATURE_VOCABULARY_TERMS_FD_IDX ON FEATURE_VOCABULARY_TERMS(FD_ID);
+
+CREATE TABLE FEATURE_VALUES (
+ ID BIGSERIAL NOT NULL,
+
+ -- we use the fixed dimension meters here
+ Z_in_M REAL,
+ -- we use the fixed dimension seconds here
+ T_in_SEC REAL,
+ -- Serialized 2D matrix with values for each spot.
+ -- Contains floats which can be NaN.
+ -- It is never a case that the whole matrix contains NaN - in such a case we save nothing.
+ -- If feature definition has some connected vocabulary terms then the matrix
+ -- stores FEATURE_VOCABULARY_TERMS.SEQUENCE_NUMBER of the terms (should be casted from float to int).
+ -- If the term is null the Float.NaN is stored.
+ VALUES BYTEA NOT NULL,
+
+ FD_ID TECH_ID NOT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FEATURE_VALUES_1 FOREIGN KEY (FD_ID) REFERENCES FEATURE_DEFS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+ -- This constaint does not make any sense. Leave it out for now.
+ -- CONSTRAINT FEATURE_VALUES_UK_1 UNIQUE(Z_in_M, T_in_SEC)
+);
+
+CREATE INDEX FEATURE_VALUES_FD_IDX ON FEATURE_VALUES(FD_ID);
+CREATE INDEX FEATURE_VALUES_Z_AND_T_IDX ON FEATURE_VALUES(Z_in_M, T_in_SEC);
+
+
+/* ---------------------------------------------------------------------- */
+/* FUNCTIONS AND TRIGGERS */
+/* ---------------------------------------------------------------------- */
+
+CREATE OR REPLACE FUNCTION DELETE_UNUSED_IMAGES() RETURNS trigger AS $$
+BEGIN
+ delete from images where id = OLD.img_id or id = OLD.thumbnail_id;
+ RETURN NEW;
+END;
+$$ LANGUAGE 'plpgsql';
+
+CREATE TRIGGER UNUSED_IMAGES AFTER DELETE ON ACQUIRED_IMAGES
+ FOR EACH ROW EXECUTE PROCEDURE DELETE_UNUSED_IMAGES();
+
+CREATE OR REPLACE FUNCTION DELETE_UNUSED_NULLED_IMAGES() RETURNS trigger AS $$
+BEGIN
+ if NEW.img_id IS NULL then
+ if OLD.img_id IS NOT NULL then
+ delete from images where id = OLD.img_id;
+ end if;
+ end if;
+ if NEW.thumbnail_id IS NULL then
+ if OLD.thumbnail_id IS NOT NULL then
+ delete from images where id = OLD.thumbnail_id;
+ end if;
+ end if;
+ RETURN NEW;
+END;
+$$ LANGUAGE 'plpgsql';
+
+CREATE TRIGGER UNUSED_NULLED_IMAGES AFTER UPDATE ON ACQUIRED_IMAGES
+ FOR EACH ROW EXECUTE PROCEDURE DELETE_UNUSED_NULLED_IMAGES();
+
+CREATE OR REPLACE FUNCTION DELETE_EMPTY_ACQUIRED_IMAGES() RETURNS trigger AS $$
+BEGIN
+ delete from acquired_images where id = OLD.id;
+ RETURN NEW;
+END;
+$$ LANGUAGE 'plpgsql';
+
+CREATE TRIGGER EMPTY_ACQUIRED_IMAGES BEFORE UPDATE ON ACQUIRED_IMAGES
+ FOR EACH ROW
+ WHEN (NEW.img_id IS NULL AND NEW.thumbnail_id IS NULL)
+ EXECUTE PROCEDURE DELETE_EMPTY_ACQUIRED_IMAGES();
+
+
+------------------------------------------------------------------------------------
+-- Purpose: Create trigger CHANNEL_STACKS_CHECK which checks if both spot_id and dataset.cont_id
+-- are both null or not null.
+------------------------------------------------------------------------------------
+
+CREATE OR REPLACE FUNCTION CHANNEL_STACKS_CHECK() RETURNS trigger AS $$
+DECLARE
+ v_cont_id CODE;
+BEGIN
+
+ select cont_id into v_cont_id from image_data_sets where id = NEW.ds_id;
+
+ -- Check that if there is no spot than there is no dataset container as well
+ if v_cont_id IS NULL then
+ if NEW.spot_id IS NOT NULL then
+ RAISE EXCEPTION 'Insert/Update of CHANNEL_STACKS failed, as the dataset container is not set, but spot is (spot id = %).',NEW.spot_id;
+ end if;
+ else
+ if NEW.spot_id IS NULL then
+ RAISE EXCEPTION 'Insert/Update of CHANNEL_STACKS failed, as the dataset container is set (id = %), but spot is not set.',v_cont_id;
+ end if;
+ end if;
+ RETURN NEW;
+END;
+$$ LANGUAGE 'plpgsql';
+
+CREATE TRIGGER CHANNEL_STACKS_CHECK BEFORE INSERT OR UPDATE ON CHANNEL_STACKS
+ FOR EACH ROW EXECUTE PROCEDURE CHANNEL_STACKS_CHECK();
+
+------------------------------------------------------------------------------------
+-- Purpose: Create trigger IMAGE_TRANSFORMATIONS_DEFAULT_CHECK which checks
+-- if at most one channel's transformation is default
+------------------------------------------------------------------------------------
+
+CREATE OR REPLACE FUNCTION IMAGE_TRANSFORMATIONS_DEFAULT_CHECK() RETURNS trigger AS $$
+DECLARE
+ v_is_default boolean;
+BEGIN
+ if NEW.is_default = 'T' then
+ select is_default into v_is_default from IMAGE_TRANSFORMATIONS
+ where is_default = 'T'
+ and channel_id = NEW.channel_id
+ and id != NEW.id;
+ if v_is_default is NOT NULL then
+ RAISE EXCEPTION 'Insert/Update of image transformation (Code: %) failed, as the new record has is_default set to true and there is already a default record defined.', NEW.code;
+ end if;
+ end if;
+
+ RETURN NEW;
+END;
+$$ LANGUAGE 'plpgsql';
+
+CREATE TRIGGER IMAGE_TRANSFORMATIONS_DEFAULT_CHECK BEFORE INSERT OR UPDATE ON IMAGE_TRANSFORMATIONS
+ FOR EACH ROW EXECUTE PROCEDURE IMAGE_TRANSFORMATIONS_DEFAULT_CHECK();
+
\ No newline at end of file
diff --git a/screening/source/sql/imaging/postgresql/migration/migration-018-019.sql b/screening/source/sql/imaging/postgresql/migration/migration-018-019.sql
new file mode 100644
index 0000000000000000000000000000000000000000..4e727895a8047c5c995cd14844414d62ffed24e3
--- /dev/null
+++ b/screening/source/sql/imaging/postgresql/migration/migration-018-019.sql
@@ -0,0 +1,5 @@
+-- Migration from 018 to 019
+
+ALTER TABLE IMAGE_ZOOM_LEVELS ADD COLUMN PATH FILE_PATH;
+ALTER TABLE IMAGE_ZOOM_LEVELS ADD COLUMN WIDTH INTEGER;
+ALTER TABLE IMAGE_ZOOM_LEVELS ADD COLUMN HEIGHT INTEGER;
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
index 068607e700745c2063f4de82fb677d6898c97618..fc2f669aab8a7758701c1dcf09bcea59136341f1 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
@@ -428,9 +428,9 @@ public class ImagingQueryDAOTest extends AbstractDBTest
final long datasetId = dao.addImageDataset(dataset);
String physicalDatasetPermIdPrefix = permId + "666";
dao.addImageZoomLevel(new ImgImageZoomLevelDTO(physicalDatasetPermIdPrefix + "-123", true,
- datasetId));
+ "original", 800, 600, datasetId));
dao.addImageZoomLevel(new ImgImageZoomLevelDTO(physicalDatasetPermIdPrefix + "-666", false,
- datasetId));
+ "thumbs", 200, 150, datasetId));
final ImgImageDatasetDTO loadedDataset = dao.tryGetImageDatasetByPermId(permId);
assertNotNull(loadedDataset);
@@ -448,12 +448,23 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals(loadedDataset, datasets.get(0));
// test listImageZoomLevels
- List<ImgImageZoomLevelDTO> zoomLevels = dao.listImageZoomLevels(permId);
+ List<ImgImageZoomLevelDTO> zoomLevels = dao.listImageZoomLevels(datasetId);
assertEquals(2, zoomLevels.size());
for (ImgImageZoomLevelDTO zoomLevel : zoomLevels)
{
AssertionUtil.assertContains(physicalDatasetPermIdPrefix,
zoomLevel.getPhysicalDatasetPermId());
+ if (zoomLevel.getIsOriginal())
+ {
+ assertEquals("original", zoomLevel.getRootPath());
+ assertEquals(800, zoomLevel.getWidth().intValue());
+ assertEquals(600, zoomLevel.getHeight().intValue());
+ } else
+ {
+ assertEquals("thumbs", zoomLevel.getRootPath());
+ assertEquals(200, zoomLevel.getWidth().intValue());
+ assertEquals(150, zoomLevel.getHeight().intValue());
+ }
}
return datasetId;