diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
index b1fe18a94e1bf76644bb482961f5f38d88bc4be8..e6abc22586510c1f543a0c84d496577303d829a9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
@@ -25,7 +25,6 @@ import java.util.Set;
import java.util.Map.Entry;
import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfoHelper.ExperimentWithChannelsAndContainer;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
@@ -62,6 +61,7 @@ public class HCSDatasetUploader
dao, info, channels);
long contId = basicStruct.getContainerId();
Map<String, Long/* (tech id */> channelsMap = basicStruct.getChannelsMap();
+
Long[][] spotIds = getOrCreateSpots(contId, info, images);
long datasetId = createDataset(contId, info);
@@ -105,11 +105,11 @@ public class HCSDatasetUploader
{
Map<ImgChannelStackDTO, List<AcquiredImageInStack>> stackImagesMap =
makeStackImagesMap(images, spotIds, datasetId);
- createChannelStacks(stackImagesMap.keySet());
+ dao.addChannelStacks(new ArrayList<ImgChannelStackDTO>(stackImagesMap.keySet()));
createImages(stackImagesMap, channelsMap);
}
- private static Map<ImgChannelStackDTO, List<AcquiredImageInStack>> makeStackImagesMap(
+ private Map<ImgChannelStackDTO, List<AcquiredImageInStack>> makeStackImagesMap(
List<AcquiredPlateImage> images, Long[][] spotIds, long datasetId)
{
Map<ImgChannelStackDTO, List<AcquiredImageInStack>> map =
@@ -134,11 +134,12 @@ public class HCSDatasetUploader
.getThumbnailFilePathOrNull());
}
- private static ImgChannelStackDTO makeStackDTO(AcquiredPlateImage image, Long[][] spotIds,
+ private ImgChannelStackDTO makeStackDTO(AcquiredPlateImage image, Long[][] spotIds,
long datasetId)
{
long spotId = getSpotId(image, spotIds);
- return new ImgChannelStackDTO(image.getTileRow(), image.getTileColumn(), datasetId, spotId);
+ return new ImgChannelStackDTO(dao.createChannelStackId(), image.getTileRow(), image
+ .getTileColumn(), datasetId, spotId);
}
private static long getSpotId(AcquiredPlateImage image, Long[][] spotIds)
@@ -153,62 +154,103 @@ public class HCSDatasetUploader
private void createImages(Map<ImgChannelStackDTO, List<AcquiredImageInStack>> stackImagesMap,
Map<String, Long> channelsMap)
{
+ ImagesToCreate imagesToCreate =
+ new ImagesToCreate(new ArrayList<ImgImageDTO>(),
+ new ArrayList<ImgAcquiredImageDTO>());
for (Entry<ImgChannelStackDTO, List<AcquiredImageInStack>> entry : stackImagesMap
.entrySet())
{
long stackId = entry.getKey().getId();
- createImages(stackId, channelsMap, entry.getValue());
+ addImagesToCreate(imagesToCreate, stackId, channelsMap, entry.getValue());
}
+ dao.addImages(imagesToCreate.getImages());
+ dao.addAcquiredImages(imagesToCreate.getAcquiredImages());
}
- private void createImages(long stackId, Map<String, Long> channelsMap,
- List<AcquiredImageInStack> images)
+ /**
+ * Because we can have millions of images, we have to create them in batches. That is why we
+ * create all the DTOs first and generate ids for them before they are created in the database.
+ * Then we can save everything in one go.
+ */
+ private void addImagesToCreate(ImagesToCreate imagesToCreate, long stackId,
+ Map<String, Long> channelsMap, List<AcquiredImageInStack> images)
{
+ List<ImgImageDTO> imageDTOs = imagesToCreate.getImages();
+ List<ImgAcquiredImageDTO> acquiredImageDTOs = imagesToCreate.getAcquiredImages();
for (AcquiredImageInStack image : images)
{
- String channelName = image.getChannelName();
- Long channelTechId = channelsMap.get(channelName);
- if (channelTechId == null)
+ long channelTechId = channelsMap.get(image.getChannelName());
+
+ ImgImageDTO imageDTO = mkImageWithIdDTO(image.getImageFilePath());
+ ImgImageDTO thumbnailDTO = tryMkImageWithIdDTO(image.getThumbnailPathOrNull());
+ Long thumbnailId = thumbnailDTO == null ? null : thumbnailDTO.getId();
+ ImgAcquiredImageDTO acquiredImage =
+ mkAcquiredImage(stackId, channelTechId, imageDTO.getId(), thumbnailId);
+
+ imageDTOs.add(imageDTO);
+ if (thumbnailDTO != null)
{
- throw new EnvironmentFailureException("Invalid channel name " + channelName
- + ". Available channels: " + channelsMap.keySet());
+ imageDTOs.add(thumbnailDTO);
}
- createImage(stackId, channelTechId, image);
+ acquiredImageDTOs.add(acquiredImage);
+ }
+ }
+
+ private static class ImagesToCreate
+ {
+ private final List<ImgImageDTO> images;
+
+ private final List<ImgAcquiredImageDTO> acquiredImages;
+
+ public ImagesToCreate(List<ImgImageDTO> images, List<ImgAcquiredImageDTO> acquiredImages)
+ {
+ super();
+ this.images = images;
+ this.acquiredImages = acquiredImages;
+ }
+
+ public List<ImgImageDTO> getImages()
+ {
+ return images;
+ }
+
+ public List<ImgAcquiredImageDTO> getAcquiredImages()
+ {
+ return acquiredImages;
}
}
- private void createImage(long stackId, long channelTechId, AcquiredImageInStack image)
+ private ImgAcquiredImageDTO mkAcquiredImage(long stackId, long channelTechId, long imageId,
+ Long thumbnailId)
{
- long imageId = addImage(image.getImageFilePath());
- Long thumbnailId = addImage(image.getThumbnailPathOrNull());
ImgAcquiredImageDTO acquiredImage = new ImgAcquiredImageDTO();
acquiredImage.setImageId(imageId);
acquiredImage.setThumbnailId(thumbnailId);
acquiredImage.setChannelStackId(stackId);
acquiredImage.setChannelId(channelTechId);
- dao.addAcquiredImage(acquiredImage);
+ return acquiredImage;
}
- private Long addImage(RelativeImageReference imageReferenceOrNull)
+ private ImgImageDTO tryMkImageWithIdDTO(RelativeImageReference imageReferenceOrNull)
{
if (imageReferenceOrNull == null)
{
return null;
}
- return dao.addImage(new ImgImageDTO(imageReferenceOrNull.getRelativeImagePath(),
- imageReferenceOrNull.tryGetPage(), imageReferenceOrNull.tryGetColorComponent()));
+ return mkImageWithIdDTO(imageReferenceOrNull);
}
- private void createChannelStacks(Set<ImgChannelStackDTO> stacks)
+ private ImgImageDTO mkImageWithIdDTO(RelativeImageReference imageReferenceOrNull)
{
- for (ImgChannelStackDTO stack : stacks)
- {
- long id = dao.addChannelStack(stack);
- stack.setId(id);
- }
+ ImgImageDTO dto =
+ new ImgImageDTO(dao.createImageId(), imageReferenceOrNull.getRelativeImagePath(),
+ imageReferenceOrNull.tryGetPage(), imageReferenceOrNull
+ .tryGetColorComponent());
+ return dto;
}
- // returns a matrix of spot tech ids. The matrix[row][col] contains null is spot at (row,col)
+ // returns a matrix of spot tech ids. The matrix[row][col] contains null is
+ // spot at (row,col)
// does not exist. Spot coordinates are 0-based in the matrix.
private Long[][] getOrCreateSpots(long contId, ScreeningContainerDatasetInfo info,
List<AcquiredPlateImage> images)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java
index 5eeb050f3f60f19b10e36c7b397989fc96c7e07d..62002ba11310bd76f6e99f8e4b35c935c302256e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java
@@ -59,7 +59,7 @@ class BDSImagingDbUploader
private final IImagingQueryDAO dao;
- BDSImagingDbUploader(File dataset, IImagingQueryDAO dao, String originalDatasetDirName,
+ public BDSImagingDbUploader(File dataset, IImagingQueryDAO dao, String originalDatasetDirName,
List<String> channelNames, List<ColorComponent> channelColorComponentsOrNull)
{
this.dao = dao;
@@ -70,7 +70,7 @@ class BDSImagingDbUploader
}
- boolean migrate()
+ public boolean migrate()
{
List<AcquiredPlateImage> images = tryExtractMappings();
if (images == null)
@@ -154,7 +154,14 @@ class BDSImagingDbUploader
private static List<String> readLines(File mappingFile) throws IOException,
FileNotFoundException
{
- return IOUtils.readLines(new FileInputStream(mappingFile));
+ FileInputStream stream = new FileInputStream(mappingFile);
+ try
+ {
+ return IOUtils.readLines(stream);
+ } finally
+ {
+ stream.close();
+ }
}
private List<AcquiredPlateImage> tryParseMappings(List<String> lines)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
index 701c67e4647833430a3edf4e84d07c8a1c00a42f..9dbd16559629fda602f51996540a4d5da20f1588 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
@@ -93,23 +93,37 @@ public interface IImagingQueryDAO extends TransactionQuery
@Select(value = "SELECT * from FEATURE_VALUES where FD_ID = ?{1.id}", resultSetBinding = FeatureVectorDataObjectBinding.class)
public List<ImgFeatureValuesDTO> getFeatureValues(ImgFeatureDefDTO featureDef);
+ // generate ids
+
+ @Select("select nextval('images_id_seq')")
+ public long createImageId();
+
+ @Select("select nextval('channel_stacks_id_seq')")
+ public long createChannelStackId();
+
+ // batch updates
+
+ @Update(sql = "insert into CHANNEL_STACKS (ID, X, Y, Z_in_M, T_in_SEC, DS_ID, SPOT_ID) values "
+ + "(?{1.id}, ?{1.column}, ?{1.row}, ?{1.z}, ?{1.t}, ?{1.datasetId}, ?{1.spotId})", batchUpdate = true)
+ public void addChannelStacks(List<ImgChannelStackDTO> channelStacks);
+
+ @Update(sql = "insert into IMAGES (ID, PATH, PAGE, COLOR) values "
+ + "(?{1.id}, ?{1.filePath}, ?{1.page}, ?{1.colorComponentAsString})", batchUpdate = true)
+ public void addImages(List<ImgImageDTO> images);
+
+ @Update(sql = "insert into ACQUIRED_IMAGES (IMG_ID, THUMBNAIL_ID, CHANNEL_STACK_ID, CHANNEL_ID) values "
+ + "(?{1.imageId}, ?{1.thumbnailId}, ?{1.channelStackId}, ?{1.channelId})", batchUpdate = true)
+ public void addAcquiredImages(List<ImgAcquiredImageDTO> acquiredImages);
+
// inserts
@Select("insert into EXPERIMENTS (PERM_ID) values (?{1}) returning ID")
public long addExperiment(String experimentPermId);
- @Select("insert into ACQUIRED_IMAGES (IMG_ID, THUMBNAIL_ID, CHANNEL_STACK_ID, CHANNEL_ID) values "
- + "(?{1.imageId}, ?{1.thumbnailId}, ?{1.channelStackId}, ?{1.channelId}) returning ID")
- public long addAcquiredImage(ImgAcquiredImageDTO acquiredImage);
-
@Select("insert into CHANNELS (NAME, DESCRIPTION, WAVELENGTH, DS_ID, EXP_ID) values "
+ "(?{1.name}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}) returning ID")
public long addChannel(ImgChannelDTO channel);
- @Select("insert into CHANNEL_STACKS (X, Y, Z_in_M, T_in_SEC, DS_ID, SPOT_ID) values "
- + "(?{1.column}, ?{1.row}, ?{1.z}, ?{1.t}, ?{1.datasetId}, ?{1.spotId}) returning ID")
- public long addChannelStack(ImgChannelStackDTO channelStack);
-
@Select("insert into CONTAINERS (PERM_ID, SPOTS_WIDTH, SPOTS_HEIGHT, EXPE_ID) values "
+ "(?{1.permId}, ?{1.numberOfColumns}, ?{1.numberOfRows}, ?{1.experimentId}) returning ID")
public long addContainer(ImgContainerDTO container);
@@ -119,10 +133,6 @@ public interface IImagingQueryDAO extends TransactionQuery
+ "?{1.fieldNumberOfRows}, ?{1.containerId}) returning ID")
public long addDataset(ImgDatasetDTO dataset);
- @Select("insert into IMAGES (PATH, PAGE, COLOR) values "
- + "(?{1.filePath}, ?{1.page}, ?{1.colorComponentAsString}) returning ID")
- public long addImage(ImgImageDTO image);
-
@Select("insert into SPOTS (X, Y, CONT_ID, PERM_ID) values "
+ "(?{1.column}, ?{1.row}, ?{1.containerId}, ?{1.permId}) returning ID")
public long addSpot(ImgSpotDTO spot);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
index 2fd24910d0be2fc6abf6685fc661c802d5aa762a..8d616e35a6d4d6361218399057c5c18bb152abb6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelStackDTO.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
-import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
@@ -26,7 +25,7 @@ import ch.systemsx.cisd.common.utilities.AbstractHashable;
*/
public class ImgChannelStackDTO extends AbstractHashable
{
- @AutoGeneratedKeys
+ @ResultColumn("ID")
private long id;
// x and y are kind of a two dimensional sequence number, (e.g. tile column)
@@ -58,8 +57,9 @@ public class ImgChannelStackDTO extends AbstractHashable
// All Data-Object classes must have a default constructor.
}
- public ImgChannelStackDTO(int row, int column, long datasetId, long spotId)
+ public ImgChannelStackDTO(long id, int row, int column, long datasetId, long spotId)
{
+ this.id = id;
this.row = row;
this.column = column;
this.datasetId = datasetId;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
index ebdeabae3cb8941c8d0248e80129fd49a9fa32a1..3c0d33c38e19dde1dfb22f43da9c58c2d58ac92c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgImageDTO.java
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
-
-import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
import ch.systemsx.cisd.common.utilities.AbstractHashable;
@@ -27,7 +25,7 @@ import ch.systemsx.cisd.common.utilities.AbstractHashable;
*/
public class ImgImageDTO extends AbstractHashable
{
- @AutoGeneratedKeys
+ @ResultColumn("id")
private long id;
@ResultColumn("PATH")
@@ -45,8 +43,10 @@ public class ImgImageDTO extends AbstractHashable
// All Data-Object classes must have a default constructor.
}
- public ImgImageDTO(String filePath, Integer pageOrNull, ColorComponent colorComponentOrNull)
+ public ImgImageDTO(long id, String filePath, Integer pageOrNull,
+ ColorComponent colorComponentOrNull)
{
+ this.id = id;
this.filePath = filePath;
this.pageOrNull = pageOrNull;
this.colorComponentOrNull =
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
index 2bd4945d1a1b5eb96380d11614bac2bbfce42286..054d6c65b919a3e4294a6a2e572152e0f15721af 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImagingQueryDAOTest.java
@@ -20,6 +20,7 @@ import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import java.sql.SQLException;
+import java.util.Arrays;
import java.util.List;
import org.testng.AssertJUnit;
@@ -148,8 +149,8 @@ public class ImagingQueryDAOTest extends AbstractDBTest
|| channels[1] == channelId1 && channels[0] == channelId2);
// test get id of first channel
- assertEquals(channels[0], dao.tryGetChannelIdByChannelNameDatasetIdOrExperimentId(datasetId,
- experimentId, "dsChannel").intValue());
+ assertEquals(channels[0], dao.tryGetChannelIdByChannelNameDatasetIdOrExperimentId(
+ datasetId, experimentId, "dsChannel").intValue());
List<ImgChannelDTO> experimentChannels = dao.getChannelsByExperimentId(experimentId);
assertEquals(1, experimentChannels.size());
@@ -164,8 +165,9 @@ public class ImagingQueryDAOTest extends AbstractDBTest
private long addImage(String path, ColorComponent colorComponent)
{
- final ImgImageDTO image = new ImgImageDTO(path, PAGE, colorComponent);
- return dao.addImage(image);
+ final ImgImageDTO image = new ImgImageDTO(dao.createImageId(), path, PAGE, colorComponent);
+ dao.addImages(Arrays.asList(image));
+ return image.getId();
}
private long addExperiment()
@@ -243,17 +245,20 @@ public class ImagingQueryDAOTest extends AbstractDBTest
private long addChannelStack(long datasetId, long spotId)
{
final ImgChannelStackDTO channelStack =
- new ImgChannelStackDTO(Y_TILE_ROW, X_TILE_COLUMN, datasetId, spotId);
- return dao.addChannelStack(channelStack);
+ new ImgChannelStackDTO(dao.createChannelStackId(), Y_TILE_ROW, X_TILE_COLUMN,
+ datasetId, spotId);
+ dao.addChannelStacks(Arrays.asList(channelStack));
+ return channelStack.getId();
}
- private long addAcquiredImage(long imageId, long channelStackId, long channelId)
+ private void addAcquiredImage(long imageId, long channelStackId, long channelId)
{
final ImgAcquiredImageDTO acquiredImage = new ImgAcquiredImageDTO();
acquiredImage.setImageId(imageId);
acquiredImage.setChannelStackId(channelStackId);
acquiredImage.setChannelId(channelId);
- return dao.addAcquiredImage(acquiredImage);
+
+ dao.addAcquiredImages(Arrays.asList(acquiredImage));
}
}