diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredPlateImage.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredPlateImage.java
index 4dc8e01d49c054fa585bcdee22cb750d4cc9caf3..ce4fafbf9aaa0692dfa740c0fe5383a0497d5019 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredPlateImage.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/AcquiredPlateImage.java
@@ -17,49 +17,60 @@
package ch.systemsx.cisd.openbis.dss.etl;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
/**
* Describes properties extracted for one screening image.
*
* @author Tomasz Pylak
*/
-public class AcquiredPlateImage
+public class AcquiredPlateImage extends AbstractHashable
{
private final Location wellLocation;
private final Location tileLocation;
- private final int channel;
+ private final String channelName;
// can be null
private final Float timePointOrNull, depthOrNull;
private final RelativeImagePath imageFilePath; // relative to the dataset directory
- public AcquiredPlateImage(Location wellLocation, Location tileLocation, int channel,
+ public AcquiredPlateImage(Location wellLocation, Location tileLocation, String channelName,
Float timePointOrNull, Float depthOrNull, RelativeImagePath imageFilePath)
{
this.wellLocation = wellLocation;
this.tileLocation = tileLocation;
- this.channel = channel;
+ this.channelName = channelName;
this.timePointOrNull = timePointOrNull;
this.depthOrNull = depthOrNull;
this.imageFilePath = imageFilePath;
}
- public Location getWellLocation()
+ public int getWellRow()
{
- return wellLocation;
+ return wellLocation.getY();
}
- public Location getTileLocation()
+ public int getWellColumn()
{
- return tileLocation;
+ return wellLocation.getX();
}
- public int getChannel()
+ public int getTileRow()
{
- return channel;
+ return tileLocation.getY();
+ }
+
+ public int getTileColumn()
+ {
+ return tileLocation.getX();
+ }
+
+ public String getChannelName()
+ {
+ return channelName;
}
public Float tryGetTimePoint()
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 683605fad5758e71bf89da9dc386fd260fea1224..cabfa96ee3375c98d9921dc3b5e4269aa2b19e2b 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
@@ -17,13 +17,20 @@
package ch.systemsx.cisd.openbis.dss.etl;
import java.util.ArrayList;
-import java.util.HashSet;
+import java.util.HashMap;
import java.util.List;
+import java.util.Map;
import java.util.Set;
+import java.util.Map.Entry;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgAcquiredImageDTO;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgChannelDTO;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgChannelStackDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgDatasetDTO;
+import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgImageDTO;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgSpotDTO;
/**
@@ -32,9 +39,9 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.ImgSpotDTO;
class HCSDatasetUploader
{
public static void upload(IImagingUploadDAO dao, ScreeningContainerDatasetInfo info,
- List<AcquiredPlateImage> images)
+ List<AcquiredPlateImage> images, Set<HCSImageFileExtractionResult.Channel> channels)
{
- new HCSDatasetUploader(dao).upload(info, images);
+ new HCSDatasetUploader(dao).upload(info, images, channels);
}
private final IImagingUploadDAO dao;
@@ -44,100 +51,276 @@ class HCSDatasetUploader
this.dao = dao;
}
- private void upload(ScreeningContainerDatasetInfo info, List<AcquiredPlateImage> images)
+ private void upload(ScreeningContainerDatasetInfo info, List<AcquiredPlateImage> images,
+ Set<HCSImageFileExtractionResult.Channel> channels)
{
long expId = getOrCreateExperiment(info);
long contId = getOrCreateContainer(expId, info);
- Long[][] spotIds = getOrCreateSpots(contId, info);
+ Long[][] spotIds = getOrCreateSpots(contId, info, images);
+ Map<String, Long/* (tech id */> channelsMap = getOrCreateChannels(expId, channels);
long datasetId = createDataset(contId, info);
- createImages(images, spotIds, datasetId);
+
+ createImages(images, spotIds, channelsMap, datasetId);
}
- private void createImages(List<AcquiredPlateImage> images, Long[][] spotIds, long datasetId)
+ private Map<String, Long> getOrCreateChannels(long expId,
+ Set<HCSImageFileExtractionResult.Channel> channels)
{
- // TODO 2010-05-18, Tomasz Pylak: create immages and channels
+ Map<String/* name */, ImgChannelDTO> existingChannels =
+ asNameMap(dao.getChannelsByExperimentId(expId));
+ Map<String, Long> map = new HashMap<String, Long>();
+ for (HCSImageFileExtractionResult.Channel channel : channels)
+ {
+ ImgChannelDTO channelDTO = getOrCreateChannel(channel, expId, existingChannels);
+ map.put(channelDTO.getName(), channelDTO.getId());
+ }
+ return map;
}
- // 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)
+ private static Map<String, ImgChannelDTO> asNameMap(List<ImgChannelDTO> channels)
{
- String[][] wantedSpotPermIds = info.getSpotPermIds();
- List<ImgSpotDTO> spots = dao.listSpots(asList(wantedSpotPermIds));
- List<ImgSpotDTO> newSpots = findSpotsToCreate(spots, wantedSpotPermIds, contId);
- addSpotsAndSetIds(newSpots);
- spots.addAll(newSpots);
- return createPermIdMatrix(spots, info.getContainerWidth(), info.getContainerHeight());
+ Map<String, ImgChannelDTO> nameMap = new HashMap<String, ImgChannelDTO>();
+ for (ImgChannelDTO channel : channels)
+ {
+ nameMap.put(channel.getName(), channel);
+ }
+ return nameMap;
}
- private static Long[][] createPermIdMatrix(List<ImgSpotDTO> spots, int width, int height)
+ private ImgChannelDTO getOrCreateChannel(HCSImageFileExtractionResult.Channel channel,
+ long expId, Map<String, ImgChannelDTO> existingChannels)
{
- Long[][] matrix = new Long[width][height];
- for (ImgSpotDTO spot : spots)
+ ImgChannelDTO channelDTO = createChannelDTO(channel, expId);
+ ImgChannelDTO existingChannel = existingChannels.get(channelDTO.getName());
+ if (existingChannel != null)
+ {
+ // if a channel with a specified name already exists for an experiment, its description
+ // will be updated
+ if (existingChannel.getWavelength() != channelDTO.getWavelength())
+ {
+ throw UserFailureException
+ .fromTemplate(
+ "There are already datasets registered for the experiment "
+ + "which use the same channel name, but with a different wavelength! "
+ + "Channel %s, old wavelength %d, new wavelength %d.",
+ channelDTO.getName(), existingChannel.getWavelength(), channelDTO
+ .getWavelength());
+ }
+ channelDTO.setId(existingChannel.getId());
+ dao.updateChannel(channelDTO);
+ } else
{
- matrix[spot.getY() - 1][spot.getX() - 1] = spot.getId();
+ // if a channel with a specified name does not exists for an experiment, it's created
+ long channelId = dao.addChannel(channelDTO);
+ channelDTO.setId(channelId);
}
- return matrix;
+ return channelDTO;
+ }
+
+ private static ImgChannelDTO createChannelDTO(HCSImageFileExtractionResult.Channel channel,
+ long expId)
+ {
+ return ImgChannelDTO.createExperimentChannel(channel.getName(), channel.getDescription(),
+ channel.getWavelength(), expId);
}
- private void addSpotsAndSetIds(List<ImgSpotDTO> spots)
+ private static class AcquiredImageInStack
{
- for (ImgSpotDTO spot : spots)
+ private final String channelName;
+
+ private final RelativeImagePath imageFilePath;
+
+ public AcquiredImageInStack(String channelName, RelativeImagePath imageFilePath)
{
- long id = dao.addSpot(spot);
- spot.setId(id);
+ this.channelName = channelName;
+ this.imageFilePath = imageFilePath;
+ }
+
+ public String getChannelName()
+ {
+ return channelName;
+ }
+
+ public RelativeImagePath getImageFilePath()
+ {
+ return imageFilePath;
}
}
- private static List<ImgSpotDTO> findSpotsToCreate(List<ImgSpotDTO> existingSpots,
- String[][] wantedSpotPermIds, long contId)
+ private void createImages(List<AcquiredPlateImage> images, Long[][] spotIds,
+ Map<String, Long> channelsMap, long datasetId)
{
- List<ImgSpotDTO> newSpots = new ArrayList<ImgSpotDTO>();
- Set<String> existingPermIds = asPermIdSet(existingSpots);
- for (int row = 0; row < wantedSpotPermIds.length; row++)
+ Map<ImgChannelStackDTO, List<AcquiredImageInStack>> stackImagesMap =
+ makeStackImagesMap(images, spotIds, datasetId);
+ createChannelStacks(stackImagesMap.keySet());
+ createImages(stackImagesMap, channelsMap);
+ }
+
+ private Map<ImgChannelStackDTO, List<AcquiredImageInStack>> makeStackImagesMap(
+ List<AcquiredPlateImage> images, Long[][] spotIds, long datasetId)
+ {
+ Map<ImgChannelStackDTO, List<AcquiredImageInStack>> map =
+ new HashMap<ImgChannelStackDTO, List<AcquiredImageInStack>>();
+ for (AcquiredPlateImage image : images)
{
- String[] spotRow = wantedSpotPermIds[row];
- for (int col = 0; col < spotRow.length; col++)
+ ImgChannelStackDTO stackDTO = makeStackDTO(image, spotIds, datasetId);
+ List<AcquiredImageInStack> stackImages = map.get(stackDTO);
+ if (stackImages == null)
{
- String spotPermId = spotRow[col];
- if (spotPermId != null && existingPermIds.contains(spotPermId) == false)
- {
- newSpots.add(new ImgSpotDTO(spotPermId, col + 1, row + 1, contId));
- }
+ stackImages = new ArrayList<AcquiredImageInStack>();
}
+ stackImages.add(makeAcquiredImageInStack(image));
+ map.put(stackDTO, stackImages);
+ }
+ return map;
+ }
+
+ private static AcquiredImageInStack makeAcquiredImageInStack(AcquiredPlateImage image)
+ {
+ return new AcquiredImageInStack(image.getChannelName(), image.getImageFilePath());
+ }
+
+ private static ImgChannelStackDTO makeStackDTO(AcquiredPlateImage image, Long[][] spotIds,
+ long datasetId)
+ {
+ long spotId = getSpotId(image, spotIds);
+ return new ImgChannelStackDTO(image.getTileRow(), image.getTileColumn(), datasetId, spotId);
+ }
+
+ private static long getSpotId(AcquiredPlateImage image, Long[][] spotIds)
+ {
+ int wellRow = image.getWellRow();
+ int wellColumn = image.getWellColumn();
+ Long spotId = spotIds[wellRow - 1][wellColumn - 1];
+ assert spotId != null : "no spot for " + image;
+ return spotId;
+ }
+
+ private void createImages(Map<ImgChannelStackDTO, List<AcquiredImageInStack>> stackImagesMap,
+ Map<String, Long> channelsMap)
+ {
+ for (Entry<ImgChannelStackDTO, List<AcquiredImageInStack>> entry : stackImagesMap
+ .entrySet())
+ {
+ long stackId = entry.getKey().getId();
+ createImages(stackId, channelsMap, entry.getValue());
+ }
+ }
+
+ private void createImages(long stackId, Map<String, Long> channelsMap,
+ List<AcquiredImageInStack> images)
+ {
+ for (AcquiredImageInStack image : images)
+ {
+ long channelTechId = channelsMap.get(image.getChannelName());
+ createImage(stackId, channelTechId, image);
+ }
+ }
+
+ private void createImage(long stackId, long channelTechId, AcquiredImageInStack image)
+ {
+ long imageId = dao.addImage(new ImgImageDTO(image.getImageFilePath().getImagePath()));
+ ImgAcquiredImageDTO acquiredImage =
+ new ImgAcquiredImageDTO(imageId, stackId, channelTechId);
+ dao.addAcquiredImage(acquiredImage);
+ }
+
+ private void createChannelStacks(Set<ImgChannelStackDTO> stacks)
+ {
+ for (ImgChannelStackDTO stack : stacks)
+ {
+ long id = dao.addChannelStack(stack);
+ stack.setId(id);
+ }
+ }
+
+ // 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)
+ {
+ List<ImgSpotDTO> allSpots = dao.listSpots(contId);
+ List<ImgSpotDTO> newSpots =
+ createNewSpots(contId, images, allSpots, info.getContainerRows(), info
+ .getContainerColumns());
+ allSpots.addAll(newSpots);
+ return makeTechIdMatrix(allSpots, info.getContainerRows(), info.getContainerColumns());
+ }
+
+ private List<ImgSpotDTO> createNewSpots(long contId, List<AcquiredPlateImage> images,
+ List<ImgSpotDTO> existingSpots, int rows, int columns)
+ {
+ Boolean[][] newSpotMatrix = extractNewSpots(rows, columns, images, existingSpots);
+ List<ImgSpotDTO> newSpots = makeSpotDTOs(newSpotMatrix, contId);
+ for (ImgSpotDTO spot : newSpots)
+ {
+ long id = dao.addSpot(spot);
+ spot.setId(id);
}
return newSpots;
}
- private static Set<String> asPermIdSet(List<ImgSpotDTO> spots)
+ private Boolean[][] extractNewSpots(int rows, int columns, List<AcquiredPlateImage> images,
+ List<ImgSpotDTO> existingSpots)
+ {
+ Boolean[][] spots = extractExistingSpots(rows, columns, images);
+ unmarkSpots(existingSpots, spots);
+ return spots;
+ }
+
+ private static Boolean[][] extractExistingSpots(int rows, int columns,
+ List<AcquiredPlateImage> images)
{
- Set<String> set = new HashSet<String>();
- for (ImgSpotDTO spot : spots)
+ Boolean[][] spots = new Boolean[rows][columns];
+ for (AcquiredPlateImage image : images)
{
- set.add(spot.getPermId());
+ spots[image.getWellRow() - 1][image.getWellColumn() - 1] = true;
}
- return set;
+ return spots;
}
- private static List<String> asList(String[][] spotPermIds)
+ private static Long[][] makeTechIdMatrix(List<ImgSpotDTO> existingSpots, int rows, int columns)
{
- List<String> result = new ArrayList<String>();
- for (int row = 0; row < spotPermIds.length; row++)
+ Long[][] matrix = new Long[rows][columns];
+ for (ImgSpotDTO spot : existingSpots)
{
- String[] spotRow = spotPermIds[row];
+ matrix[spot.getRow() - 1][spot.getColumn() - 1] = spot.getId();
+ }
+ return matrix;
+ }
+
+ private static List<ImgSpotDTO> makeSpotDTOs(Boolean[][] spots, long contId)
+ {
+
+ List<ImgSpotDTO> newSpots = new ArrayList<ImgSpotDTO>();
+ for (int row = 0; row < spots.length; row++)
+ {
+ Boolean[] spotRow = spots[row];
for (int col = 0; col < spotRow.length; col++)
{
- result.add(spotRow[col]);
+ Boolean wanted = spotRow[col];
+ if (wanted != null && wanted)
+ {
+ newSpots.add(new ImgSpotDTO(row + 1, col + 1, contId));
+ }
}
}
- return result;
+ return newSpots;
+ }
+
+ private static void unmarkSpots(List<ImgSpotDTO> existingSpots, Boolean[][] spotMatrix)
+ {
+ for (ImgSpotDTO existingSpot : existingSpots)
+ {
+ spotMatrix[existingSpot.getRow()][existingSpot.getColumn()] = false;
+ }
}
private long createDataset(long contId, ScreeningContainerDatasetInfo info)
{
ImgDatasetDTO dataset =
- new ImgDatasetDTO(info.getDatasetPermId(), info.getTileWidth(), info
- .getTileHeight(), contId);
+ new ImgDatasetDTO(info.getDatasetPermId(), info.getTileRows(), info
+ .getTileColumns(), contId);
return dao.addDataset(dataset);
}
@@ -151,8 +334,8 @@ class HCSDatasetUploader
} else
{
ImgContainerDTO container =
- new ImgContainerDTO(containerPermId, info.getContainerWidth(), info
- .getContainerHeight(), expId);
+ new ImgContainerDTO(containerPermId, info.getContainerRows(), info
+ .getContainerColumns(), expId);
return dao.addContainer(container);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
new file mode 100644
index 0000000000000000000000000000000000000000..70b6872723a9490090b889088d7d2cdbd1cd62ad
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageCheckList.java
@@ -0,0 +1,164 @@
+/*
+ * Copyright 2008 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 java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
+/**
+ * Helper class to set the <code>is_complete</code> flag in the <i>BDS</i> library.
+ * <p>
+ * All the possible combinations are computed in the constructor. This class is also able to spot
+ * images which have already been handled.
+ * </p>
+ *
+ * @author Franz-Josef Elmer
+ */
+public final class HCSImageCheckList
+{
+
+ private final Map<FullLocation, Check> imageMap;
+
+ public HCSImageCheckList(final String[] channelNames, final Geometry plateGeometry,
+ final Geometry wellGeometry)
+ {
+ if (channelNames.length < 1)
+ {
+ throw new IllegalArgumentException("Number of channels smaller than one.");
+ }
+ if (plateGeometry == null)
+ {
+ throw new IllegalArgumentException("Unspecified plate geometry.");
+ }
+ if (wellGeometry == null)
+ {
+ throw new IllegalArgumentException("Unspecified well geometry.");
+ }
+ imageMap = new HashMap<FullLocation, Check>();
+ for (String channelName : channelNames)
+ {
+ for (int wellCol = 1; wellCol <= plateGeometry.getColumns(); wellCol++)
+ {
+ for (int wellRow = 1; wellRow <= plateGeometry.getRows(); wellRow++)
+ {
+ for (int tileCol = 1; tileCol <= wellGeometry.getColumns(); tileCol++)
+ {
+ for (int tileRow = 1; tileRow <= wellGeometry.getRows(); tileRow++)
+ {
+ imageMap.put(new FullLocation(wellRow, wellCol, tileRow, tileCol,
+ channelName), new Check());
+ }
+ }
+ }
+ }
+ }
+ assert imageMap.size() == channelNames.length * plateGeometry.getColumns()
+ * plateGeometry.getRows() * wellGeometry.getColumns() * wellGeometry.getRows() : "Wrong map size";
+ }
+
+ public final void checkOff(AcquiredPlateImage image)
+ {
+ assert image != null : "Unspecified image.";
+ final Check check = imageMap.get(createLocation(image));
+ if (check == null)
+ {
+ throw new IllegalArgumentException("Invalid channel/well/tile: " + image);
+ }
+ if (check.isCheckedOff())
+ {
+ throw new IllegalArgumentException("Image already handled: " + image);
+ }
+ check.checkOff();
+ }
+
+ private static FullLocation createLocation(AcquiredPlateImage image)
+ {
+ return new FullLocation(image.getWellRow(), image.getWellColumn(), image.getTileRow(),
+ image.getTileColumn(), image.getChannelName());
+ }
+
+ public final List<FullLocation> getCheckedOnFullLocations()
+ {
+ final List<FullLocation> fullLocations = new ArrayList<FullLocation>();
+ for (final Map.Entry<FullLocation, Check> entry : imageMap.entrySet())
+ {
+ if (entry.getValue().isCheckedOff() == false)
+ {
+ fullLocations.add(entry.getKey());
+ }
+ }
+ return fullLocations;
+ }
+
+ //
+ // Helper classes
+ //
+
+ private static final class Check
+ {
+ private boolean checkedOff;
+
+ final void checkOff()
+ {
+ checkedOff = true;
+ }
+
+ final boolean isCheckedOff()
+ {
+ return checkedOff;
+ }
+ }
+
+ public final static class FullLocation extends AbstractHashable
+ {
+ final int wellRow, wellCol;
+
+ final int tileRow, tileCol;
+
+ final String channelName;
+
+ public FullLocation(int wellRow, int wellCol, int tileRow, int tileCol, String channelName)
+ {
+ this.wellRow = wellRow;
+ this.wellCol = wellCol;
+ this.tileRow = tileRow;
+ this.tileCol = tileCol;
+ this.channelName = channelName;
+ }
+
+ private final static String toString(final int row, final int col, final String type)
+ {
+ return type + "= (" + row + ", " + col + ")";
+ }
+
+ //
+ // AbstractHashable
+ //
+
+ @Override
+ public final String toString()
+ {
+ return "[ channel = " + channelName + "," + toString(wellRow, wellCol, "well") + ","
+ + toString(tileRow, tileCol, "tile") + "]";
+ }
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
index 66b14cb63ea7daf38a01b9e624f7479165108775..25d3cd0ece4d0c2d710d7b944170136e848d52d9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
@@ -19,8 +19,6 @@ import java.io.File;
import java.util.List;
import java.util.Set;
-import ch.systemsx.cisd.bds.hcs.Channel;
-
/**
* Class which contains the image extraction process results.
*
@@ -58,4 +56,46 @@ public final class HCSImageFileExtractionResult
{
return channels;
}
+
+ /**
+ * A channel in which the image has been acquired.
+ * <p>
+ * Each channel has its <code>name</code> which uniquely identifies it in one experiment or
+ * dataset.
+ * </p>
+ *
+ * @author Tomasz Pylak
+ */
+ public static final class Channel
+ {
+ private final String name;
+
+ private final String description;
+
+ private final int wavelength;
+
+ public Channel(String name, String description, int wavelength)
+ {
+ assert name != null : "name is null";
+ this.name = name;
+ this.description = description;
+ this.wavelength = wavelength;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public int getWavelength()
+ {
+ return wavelength;
+ }
+ }
+
}
\ No newline at end of file
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 3d05045fb308754ac7a85eac7e12459ca395a731..4017a3dda27298e899bf88451d9a92137e154189 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
@@ -19,8 +19,10 @@ package ch.systemsx.cisd.openbis.dss.etl;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.List;
import java.util.Properties;
+import java.util.Set;
import javax.sql.DataSource;
@@ -30,6 +32,7 @@ import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang.time.DurationFormatUtils;
import org.apache.log4j.Logger;
+import ch.systemsx.cisd.bds.hcs.Channel;
import ch.systemsx.cisd.bds.hcs.Geometry;
import ch.systemsx.cisd.bds.hcs.Location;
import ch.systemsx.cisd.bds.hcs.PlateGeometry;
@@ -48,12 +51,11 @@ import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.ClassUtils;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.AbstractStorageProcessor;
-import ch.systemsx.cisd.etlserver.HCSImageCheckList;
import ch.systemsx.cisd.etlserver.IHCSImageFileAccepter;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.PlateDimension;
import ch.systemsx.cisd.etlserver.PlateDimensionParser;
-import ch.systemsx.cisd.etlserver.HCSImageCheckList.FullLocation;
+import ch.systemsx.cisd.openbis.dss.etl.HCSImageCheckList.FullLocation;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingUploadDAO;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -77,21 +79,24 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private static final Logger notificationLog =
LogFactory.getLogger(LogCategory.OPERATION, PlateStorageProcessor.class);
- private static final String NUMBER_OF_CHANNELS_PROPERTY = "number_of_channels";
-
private static final String SPOT_GEOMETRY_PROPERTY = "well_geometry";
private static final String FILE_EXTRACTOR_PROPERTY = "file-extractor";
private static final String DEPRECATED_FILE_EXTRACTOR_PROPERTY = "deprecated-file-extractor";
+ // comma separated list of channel names, order matters
+ private static final String CHANNEL_NAMES = "channel-names";
+
+ private static final String CHANNEL_SEPARATOR = ",";
+
// -----------
private final DataSource dataSource;
private final Geometry spotGeometry;
- private final int numberOfChannels;
+ private final String[] channelNames;
// one of the extractors is always null and one not null
private final IHCSImageFileExtractor imageFileExtractor;
@@ -106,7 +111,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
String spotGeometryText = getMandatoryProperty(SPOT_GEOMETRY_PROPERTY);
this.spotGeometry = Geometry.createFromString(spotGeometryText);
- this.numberOfChannels = extractNumberOfChannels();
+ this.channelNames = extractChannelNames(properties);
String fileExtractorClass = PropertyUtils.getProperty(properties, FILE_EXTRACTOR_PROPERTY);
if (fileExtractorClass != null)
@@ -126,16 +131,10 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
this.currentTransaction = null;
}
- private int extractNumberOfChannels()
+ private static String[] extractChannelNames(Properties properties)
{
- int channels = PropertyUtils.getInt(properties, NUMBER_OF_CHANNELS_PROPERTY, -1);
- if (channels == -1)
- {
- throw UserFailureException.fromTemplate(
- "Unconfigured property %s for storage processor %s.",
- NUMBER_OF_CHANNELS_PROPERTY, getClass().getName());
- }
- return channels;
+ String names = PropertyUtils.getMandatoryProperty(properties, CHANNEL_NAMES);
+ return names.split(CHANNEL_SEPARATOR);
}
private IImagingUploadDAO createQuery()
@@ -176,33 +175,17 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
info.setDatasetPermId(dataSetInformation.getDataSetCode());
Geometry plateGeometry = getPlateGeometry(dataSetInformation);
- int plateCols = plateGeometry.getColumns();
int plateRows = plateGeometry.getRows();
- info.setContainerWidth(plateCols);
- info.setContainerHeight(plateRows);
-
- info.setTileWidth(spotGeometry.getColumns());
- info.setTileHeight(spotGeometry.getRows());
+ int plateCols = plateGeometry.getColumns();
+ info.setContainerRows(plateRows);
+ info.setContainerColumns(plateCols);
- // TODO 2010-05-18, Tomasz Pylak: fetch spots from openBIS
- info.setSpotPermIds(createDummySpotPermIds(plateRows, plateCols));
+ info.setTileRows(spotGeometry.getRows());
+ info.setTileColumns(spotGeometry.getColumns());
return info;
}
- private String[][] createDummySpotPermIds(int plateRows, int plateCols)
- {
- String[][] spots = new String[plateRows][plateCols];
- for (int row = 0; row < plateRows; row++)
- {
- for (int col = 0; col < plateCols; col++)
- {
- spots[row][col] = "dummy_" + row + "_" + col + "_" + System.currentTimeMillis();
- }
- }
- return spots;
- }
-
private Geometry getPlateGeometry(final DataSetInformation dataSetInformation)
{
final IEntityProperty[] sampleProperties = dataSetInformation.getProperties();
@@ -284,17 +267,17 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
{
throw new UserFailureException("Experiment unknown for data set " + dataSetInformation);
}
- ScreeningContainerDatasetInfo info =
- createScreeningDatasetInfo(experiment, dataSetInformation);
-
HCSImageFileExtractionResult extractionResult =
extractImages(dataSetInformation, incomingDataSetDirectory);
+ ScreeningContainerDatasetInfo info =
+ createScreeningDatasetInfo(experiment, dataSetInformation);
+
validateImages(dataSetInformation, mailClient, incomingDataSetDirectory, info,
extractionResult);
moveFileToDirectory(incomingDataSetDirectory, originalFolder);
- storeInDatabase(info, extractionResult.getImages());
+ storeInDatabase(info, extractionResult.getImages(), extractionResult.getChannels());
return rootDirectory;
}
@@ -326,8 +309,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
List<AcquiredPlateImage> images = extractionResult.getImages();
for (AcquiredPlateImage image : images)
{
- imageCheckList.checkOff(image.getChannel(), image.getWellLocation(), image
- .getTileLocation());
+ imageCheckList.checkOff(image);
}
}
@@ -335,7 +317,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
{
Geometry plateGeometry = getPlateGeometry(info);
HCSImageCheckList imageCheckList =
- new HCSImageCheckList(numberOfChannels, plateGeometry, spotGeometry);
+ new HCSImageCheckList(channelNames, plateGeometry, spotGeometry);
return imageCheckList;
}
@@ -346,7 +328,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
IHCSImageFileExtractor extractor = imageFileExtractor;
if (extractor == null)
{
- extractor = adapt(deprecatedImageFileExtractor, incomingDataSetDirectory);
+ extractor = adapt(deprecatedImageFileExtractor, incomingDataSetDirectory, channelNames);
}
final HCSImageFileExtractionResult result =
extractor.extract(incomingDataSetDirectory, dataSetInformation);
@@ -361,7 +343,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
private static Geometry getPlateGeometry(ScreeningContainerDatasetInfo info)
{
- return new Geometry(info.getContainerHeight(), info.getContainerWidth());
+ return new Geometry(info.getContainerRows(), info.getContainerColumns());
}
@Override
@@ -433,14 +415,15 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
}
}
- private void storeInDatabase(ScreeningContainerDatasetInfo info, List<AcquiredPlateImage> images)
+ private void storeInDatabase(ScreeningContainerDatasetInfo info,
+ List<AcquiredPlateImage> images, Set<HCSImageFileExtractionResult.Channel> channels)
{
if (currentTransaction != null)
{
throw new IllegalStateException("previous transaction has not been commited!");
}
currentTransaction = createQuery();
- HCSDatasetUploader.upload(currentTransaction, info, images);
+ HCSDatasetUploader.upload(currentTransaction, info, images, channels);
}
private void rollbackDatabaseChanges()
@@ -566,7 +549,7 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
// adapts old-style image extractor to the new one which is stateless
private static IHCSImageFileExtractor adapt(
final ch.systemsx.cisd.etlserver.IHCSImageFileExtractor extractor,
- final File imageFileRootDirectory)
+ final File imageFileRootDirectory, final String[] channelNames)
{
return new IHCSImageFileExtractor()
{
@@ -574,14 +557,28 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
DataSetInformation dataSetInformation)
{
HCSImageFileAccepter accepter =
- new HCSImageFileAccepter(imageFileRootDirectory);
+ new HCSImageFileAccepter(imageFileRootDirectory, channelNames);
ch.systemsx.cisd.etlserver.HCSImageFileExtractionResult originalResult =
extractor.process(NodeFactory
.createDirectoryNode(incomingDataSetDirectory),
dataSetInformation, accepter);
+ Set<HCSImageFileExtractionResult.Channel> channels =
+ convert(originalResult.getChannels());
return new HCSImageFileExtractionResult(accepter.getImages(),
- asRelativePaths(originalResult.getInvalidFiles()), originalResult
- .getChannels());
+ asRelativePaths(originalResult.getInvalidFiles()), channels);
+ }
+
+ private Set<HCSImageFileExtractionResult.Channel> convert(Set<Channel> channels)
+ {
+ Set<HCSImageFileExtractionResult.Channel> result =
+ new HashSet<HCSImageFileExtractionResult.Channel>();
+ for (Channel channel : channels)
+ {
+ String name = getChannelName(channelNames, channel.getCounter());
+ result.add(new HCSImageFileExtractionResult.Channel(name, null, channel
+ .getWavelength()));
+ }
+ return result;
}
private List<File> asRelativePaths(List<IFile> files)
@@ -596,15 +593,29 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
};
}
+ private static String getChannelName(final String[] channelNames, int channelId)
+ {
+ if (channelId > channelNames.length)
+ {
+ throw UserFailureException.fromTemplate(
+ "Too large channel number %d, configured channels: %s.", channelId,
+ CollectionUtils.abbreviate(channelNames, -1));
+ }
+ return channelNames[channelId - 1];
+ }
+
private static final class HCSImageFileAccepter implements IHCSImageFileAccepter
{
private final List<AcquiredPlateImage> images = new ArrayList<AcquiredPlateImage>();
private final File imageFileRootDirectory;
- public HCSImageFileAccepter(File imageFileRootDirectory)
+ private final String[] channelNames;
+
+ public HCSImageFileAccepter(File imageFileRootDirectory, String[] channelNames)
{
this.imageFileRootDirectory = imageFileRootDirectory;
+ this.channelNames = channelNames;
}
public final void accept(final int channel, final Location wellLocation,
@@ -614,8 +625,9 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
FileUtilities.getRelativeFile(imageFileRootDirectory, new File(imageFile
.getPath()));
assert imageRelativePath != null : "Image relative path should not be null.";
+ String channelName = getChannelName(channelNames, channel);
AcquiredPlateImage imageDesc =
- new AcquiredPlateImage(wellLocation, tileLocation, channel, null, null,
+ new AcquiredPlateImage(wellLocation, tileLocation, channelName, null, null,
new RelativeImagePath(imageRelativePath));
images.add(imageDesc);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
index 176f9b3c09559b0d575da60b6f66588eb7f9d8d3..46a5705dbdf843bfd5a03f051543d31d1adc41ba 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
@@ -29,12 +29,9 @@ class ScreeningContainerDatasetInfo
private String datasetPermId;
- // [row][col]
- private String[][] spotPermIds;
+ private int containerRows, containerColumns;
- private int containerWidth, containerHeight;
-
- private int tileWidth, tileHeight;
+ private int tileRows, tileColumns;
public String getExperimentPermId()
{
@@ -66,54 +63,44 @@ class ScreeningContainerDatasetInfo
this.datasetPermId = datasetPermId;
}
- public String[][] getSpotPermIds()
- {
- return spotPermIds;
- }
-
- public void setSpotPermIds(String[][] spotPermIds)
- {
- this.spotPermIds = spotPermIds;
- }
-
- public int getContainerWidth()
+ public int getContainerRows()
{
- return containerWidth;
+ return containerRows;
}
- public void setContainerWidth(int containerWidth)
+ public void setContainerRows(int containerRows)
{
- this.containerWidth = containerWidth;
+ this.containerRows = containerRows;
}
- public int getContainerHeight()
+ public int getContainerColumns()
{
- return containerHeight;
+ return containerColumns;
}
- public void setContainerHeight(int containerHeight)
+ public void setContainerColumns(int containerColumns)
{
- this.containerHeight = containerHeight;
+ this.containerColumns = containerColumns;
}
- public int getTileWidth()
+ public int getTileRows()
{
- return tileWidth;
+ return tileRows;
}
- public void setTileWidth(int tileWidth)
+ public void setTileRows(int tileRows)
{
- this.tileWidth = tileWidth;
+ this.tileRows = tileRows;
}
- public int getTileHeight()
+ public int getTileColumns()
{
- return tileHeight;
+ return tileColumns;
}
- public void setTileHeight(int tileHeight)
+ public void setTileColumns(int tileColumns)
{
- this.tileHeight = tileHeight;
+ this.tileColumns = tileColumns;
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java
index 90c54cf78d461da52cdd2da3126987524072d1b5..c4742d1454a76c272ed0285deb757638d51da7a0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSDatasetLoader.java
@@ -71,7 +71,7 @@ public class HCSDatasetLoader
public Geometry getPlateGeometry()
{
- return new Geometry(getContainer().getSpotHeight(), getContainer().getSpotWidth());
+ return new Geometry(getContainer().getNumberOfRows(), getContainer().getNumberOfColumns());
}
private ImgDatasetDTO getDataset()
@@ -81,7 +81,8 @@ public class HCSDatasetLoader
public Geometry getWellGeometry()
{
- return new Geometry(getDataset().getFieldsHeight(), getDataset().getFieldsWidth());
+ return new Geometry(getDataset().getFieldNumberOfRows(), getDataset()
+ .getFieldNumberOfColumns());
}
public long getChannelCount()
@@ -103,10 +104,10 @@ public class HCSDatasetLoader
Location tileLocation)
{
assert chosenChannel > 0;
- assert tileLocation.getX() <= getDataset().getFieldsWidth();
- assert tileLocation.getY() <= getDataset().getFieldsHeight();
- assert wellLocation.getX() <= getContainer().getSpotWidth();
- assert wellLocation.getY() <= getContainer().getSpotHeight();
+ assert tileLocation.getX() <= getDataset().getFieldNumberOfColumns();
+ assert tileLocation.getY() <= getDataset().getFieldNumberOfRows();
+ assert wellLocation.getX() <= getContainer().getNumberOfColumns();
+ assert wellLocation.getY() <= getContainer().getNumberOfRows();
long[] channelIds =
query.getChannelIdsByDatasetIdOrExperimentId(getDataset().getId(), getContainer()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
index 2e572ac15f463a4b0ecf21372926d7d3b434db79..299b774adea26d6ea9950bb95f286a8b69e9ab62 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/IImagingUploadDAO.java
@@ -20,6 +20,7 @@ import java.util.List;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.TransactionQuery;
+import net.lemnik.eodsql.Update;
import ch.systemsx.cisd.bds.hcs.Location;
@@ -68,6 +69,12 @@ public interface IImagingUploadDAO extends TransactionQuery
@Select(sql = "select id from CHANNELS where DS_ID = ?{1} or EXP_ID = ?{2} order by name", fetchSize = FETCH_SIZE)
public long[] getChannelIdsByDatasetIdOrExperimentId(long datasetId, long experimentId);
+ @Select(sql = "select * from CHANNELS where EXP_ID = ?{1} order by name", fetchSize = FETCH_SIZE)
+ public List<ImgChannelDTO> getChannelsByExperimentId(long experimentId);
+
+ @Select("select * from SPOTS where cont_id = ?{1}")
+ public List<ImgSpotDTO> listSpots(long contId);
+
// inserts
@Select("insert into EXPERIMENTS (PERM_ID) values (?{1}) returning ID")
@@ -82,27 +89,30 @@ public interface IImagingUploadDAO extends TransactionQuery
public long addChannel(ImgChannelDTO channel);
@Select("insert into CHANNEL_STACKS (X, Y, Z_in_M, T_in_SEC, DS_ID, SPOT_ID) values "
- + "(?{1.x}, ?{1.y}, ?{1.z}, ?{1.t}, ?{1.datasetId}, ?{1.spotId}) returning ID")
+ + "(?{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.spotWidth}, ?{1.spotHeight}, ?{1.experimentId}) returning ID")
+ + "(?{1.permId}, ?{1.numberOfColumns}, ?{1.numberOfRows}, ?{1.experimentId}) returning ID")
public long addContainer(ImgContainerDTO container);
@Select("insert into DATA_SETS (PERM_ID, FIELDS_WIDTH, FIELDS_HEIGHT, CONT_ID) values "
- + "(?{1.permId}, ?{1.fieldsWidth}, ?{1.fieldsHeight}, ?{1.containerId}) returning ID")
+ + "(?{1.permId}, ?{1.fieldNumberOfColumns}, ?{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 (PERM_ID, X, Y, CONT_ID) values "
- + "(?{1.permId}, ?{1.x}, ?{1.y}, ?{1.containerId}) returning ID")
+ @Select("insert into SPOTS (X, Y, CONT_ID) values "
+ + "(?{1.column}, ?{1.row}, ?{1.containerId}) returning ID")
public long addSpot(ImgSpotDTO spot);
- // TODO 2010-05-19, Tomasz Pylak: implement me
- @Select("select * from SPOTS where TODO")
- public List<ImgSpotDTO> listSpots(List<String> spotPermIds);
+ // updates
+
+ @Update("update CHANNELS "
+ + "set DESCRIPTION = ?{1.description}, WAVELENGTH = ?{1.wavelength} "
+ + "where ID = ?{1.id}")
+ public void updateChannel(ImgChannelDTO channel);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java
index 85d16ddca110e5e184f579da7fc60a242e31234c..72f54157aef2b0a601f11523f0b5d5666558d364 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgAcquiredImageDTO.java
@@ -19,10 +19,12 @@ package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
/**
* @author Tomasz Pylak
*/
-public class ImgAcquiredImageDTO
+public class ImgAcquiredImageDTO extends AbstractHashable
{
@AutoGeneratedKeys
private long id;
@@ -40,6 +42,12 @@ public class ImgAcquiredImageDTO
@ResultColumn("THUMBNAIL_ID")
private Long thumbnailId;
+ @SuppressWarnings("unused")
+ private ImgAcquiredImageDTO()
+ {
+ // All Data-Object classes must have a default constructor.
+ }
+
public ImgAcquiredImageDTO(long imageId, long channelStackId, long channelId)
{
this.imageId = imageId;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java
index 0178d712b7e135622ef5480c5b028c2b8d852337..fbc44eb0088f223217f885323f14cf0140ac8187 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelDTO.java
@@ -19,28 +19,12 @@ package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
/**
* @author Tomasz Pylak
*/
-// CREATE TABLE CHANNELS (
-// ID BIGSERIAL NOT NULL,
-//
-// NAME NAME NOT NULL,
-// DESCRIPTION DESCRIPTION,
-// WAVELENGTH INTEGER,
-//
-// DS_ID TECH_ID,
-// EXP_ID TECH_ID,
-//
-// PRIMARY KEY (ID),
-// CONSTRAINT FK_CHANNELS_1 FOREIGN KEY (DS_ID) REFERENCES 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))
-// );
-public class ImgChannelDTO
+public class ImgChannelDTO extends AbstractHashable
{
@AutoGeneratedKeys
private long id;
@@ -74,6 +58,11 @@ public class ImgChannelDTO
return new ImgChannelDTO(name, descriptionOrNull, wavelengthOrNull, null, experimentId);
}
+ private ImgChannelDTO()
+ {
+ // All Data-Object classes must have a default constructor.
+ }
+
private ImgChannelDTO(String name, String descriptionOrNull, Integer wavelengthOrNull,
Long datasetIdOrNull, Long experimentIdOrNull)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java
index d92339eb5028a12d28f77bc2fc831a79ba97b499..44ff7859cef51079ce5b332482710249e8494998 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgChannelStackDTO.java
@@ -19,22 +19,24 @@ package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
/**
* @author Tomasz Pylak
*/
-public class ImgChannelStackDTO
+public class ImgChannelStackDTO extends AbstractHashable
{
@AutoGeneratedKeys
private long id;
// x and y are kind of a two dimensional sequence number, (e.g. tile column)
@ResultColumn("X")
- private Integer x;
+ private Integer column;
// x and y are kind of a two dimensional sequence number, (e.g. tile row, 1 is the first row)
// Some use case may only use x and leave y alone.
@ResultColumn("Y")
- private Integer y;
+ private Integer row;
// can be null
@ResultColumn("Z_in_M")
@@ -50,10 +52,16 @@ public class ImgChannelStackDTO
@ResultColumn("SPOT_ID")
private long spotId;
- public ImgChannelStackDTO(int x, int y, long datasetId, long spotId)
+ @SuppressWarnings("unused")
+ private ImgChannelStackDTO()
{
- this.x = x;
- this.y = y;
+ // All Data-Object classes must have a default constructor.
+ }
+
+ public ImgChannelStackDTO(int row, int column, long datasetId, long spotId)
+ {
+ this.row = row;
+ this.column = column;
this.datasetId = datasetId;
this.spotId = spotId;
}
@@ -68,24 +76,14 @@ public class ImgChannelStackDTO
this.id = id;
}
- public Integer getX()
- {
- return x;
- }
-
- public void setX(Integer x)
- {
- this.x = x;
- }
-
- public Integer getY()
+ public Integer getColumn()
{
- return y;
+ return column;
}
- public void setY(Integer y)
+ public Integer getRow()
{
- this.y = y;
+ return row;
}
public Float getZ()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java
index 84a8a25e06b0eb1fd9697b4dc98509a47d7a288b..4427208dd4286348d36ff2e3b5f6de64fc85be92 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgContainerDTO.java
@@ -19,12 +19,14 @@ package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
/**
* DTO holding information about the container in the imaging database.
*
* @author Tomasz Pylak
*/
-public class ImgContainerDTO
+public class ImgContainerDTO extends AbstractHashable
{
@AutoGeneratedKeys
private long id;
@@ -33,10 +35,10 @@ public class ImgContainerDTO
private String permId;
@ResultColumn("SPOTS_WIDTH")
- private Integer spotWidth;
+ private Integer numberOfColumns;
@ResultColumn("SPOTS_HEIGHT")
- private Integer spotHeight;
+ private Integer numberOfRows;
@ResultColumn("EXPE_ID")
private long experimentId;
@@ -46,11 +48,12 @@ public class ImgContainerDTO
{
}
- public ImgContainerDTO(String permId, Integer spotWidth, Integer spotHeight, long experimentId)
+ public ImgContainerDTO(String permId, Integer numberOfRows, Integer numberOfColumns,
+ long experimentId)
{
this.permId = permId;
- this.spotWidth = spotWidth;
- this.spotHeight = spotHeight;
+ this.numberOfRows = numberOfRows;
+ this.numberOfColumns = numberOfColumns;
this.experimentId = experimentId;
}
@@ -74,24 +77,24 @@ public class ImgContainerDTO
this.permId = permId;
}
- public Integer getSpotWidth()
+ public Integer getNumberOfColumns()
{
- return spotWidth;
+ return numberOfColumns;
}
- public void setSpotWidth(Integer spotWidth)
+ public void setNumberOfColumns(Integer spotNumberOfColumns)
{
- this.spotWidth = spotWidth;
+ this.numberOfColumns = spotNumberOfColumns;
}
- public Integer getSpotHeight()
+ public Integer getNumberOfRows()
{
- return spotHeight;
+ return numberOfRows;
}
- public void setSpotHeight(Integer spotHeight)
+ public void setNumberOfRows(Integer spotNumberOfRows)
{
- this.spotHeight = spotHeight;
+ this.numberOfRows = spotNumberOfRows;
}
public long getExperimentId()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
index ede179f6edae390898ad2639a6f244c841525f4d..18a1ee6d1090b95769835af1ab91297690146f5f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgDatasetDTO.java
@@ -19,10 +19,12 @@ package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
/**
* @author Tomasz Pylak
*/
-public class ImgDatasetDTO
+public class ImgDatasetDTO extends AbstractHashable
{
@AutoGeneratedKeys
private long id;
@@ -31,10 +33,10 @@ public class ImgDatasetDTO
private String permId;
@ResultColumn("FIELDS_WIDTH")
- private Integer fieldsWidthOrNull;
+ private Integer fieldNumberOfColumnsOrNull;
@ResultColumn("FIELDS_HEIGHT")
- private Integer fieldsHeightOrNull;
+ private Integer fieldNumberOfRowsOrNull;
@ResultColumn("CONT_ID")
private long containerId;
@@ -45,12 +47,12 @@ public class ImgDatasetDTO
// All Data-Object classes must have a default constructor.
}
- public ImgDatasetDTO(String permId, Integer fieldsWidthOrNull, Integer fieldsHeightOrNull,
- long containerId)
+ public ImgDatasetDTO(String permId, Integer fieldNumberOfRowsOrNull,
+ Integer fieldNumberOfColumnsOrNull, long containerId)
{
this.permId = permId;
- this.fieldsWidthOrNull = fieldsWidthOrNull;
- this.fieldsHeightOrNull = fieldsHeightOrNull;
+ this.fieldNumberOfColumnsOrNull = fieldNumberOfColumnsOrNull;
+ this.fieldNumberOfRowsOrNull = fieldNumberOfRowsOrNull;
this.containerId = containerId;
}
@@ -74,24 +76,24 @@ public class ImgDatasetDTO
this.permId = permId;
}
- public Integer getFieldsWidth()
+ public Integer getFieldNumberOfColumns()
{
- return fieldsWidthOrNull;
+ return fieldNumberOfColumnsOrNull;
}
- public void setFieldsWidth(Integer fieldsWidth)
+ public void setFieldNumberOfColumns(Integer numberOfColumns)
{
- this.fieldsWidthOrNull = fieldsWidth;
+ this.fieldNumberOfColumnsOrNull = numberOfColumns;
}
- public Integer getFieldsHeight()
+ public Integer getFieldNumberOfRows()
{
- return fieldsHeightOrNull;
+ return fieldNumberOfRowsOrNull;
}
- public void setFieldsHeight(Integer fieldsHeight)
+ public void setFieldNumberOfRows(Integer numberOfRows)
{
- this.fieldsHeightOrNull = fieldsHeight;
+ this.fieldNumberOfRowsOrNull = numberOfRows;
}
public long getContainerId()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java
index 2ec7299980782cfd717bb78e30e3f6c14d988ea6..efc4c58517b575ff742f68ea59c7da6404c0e362 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgImageDTO.java
@@ -19,10 +19,12 @@ package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
/**
* @author Tomasz Pylak
*/
-public class ImgImageDTO
+public class ImgImageDTO extends AbstractHashable
{
@AutoGeneratedKeys
private long id;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
index 1a0acb4a05ad624e154b709a305d5ebf6cbe3ba7..8815546b8ab69e95dba889e296c9296b8d461b25 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImgSpotDTO.java
@@ -19,24 +19,23 @@ package ch.systemsx.cisd.openbis.dss.etl.dataaccess;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
/**
* @author Tomasz Pylak
*/
-public class ImgSpotDTO
+public class ImgSpotDTO extends AbstractHashable
{
@AutoGeneratedKeys
private long id;
- @ResultColumn("PERM_ID")
- private String permId;
-
// position in the container, one-based (e.g. well column)
@ResultColumn("X")
- private Integer x;
+ private Integer column;
// position in the container, one-based (e.g. well row, 1 is the first row)
@ResultColumn("Y")
- private Integer y;
+ private Integer row;
@ResultColumn("CONT_ID")
private long containerId;
@@ -47,11 +46,10 @@ public class ImgSpotDTO
// All Data-Object classes must have a default constructor.
}
- public ImgSpotDTO(String permId, Integer x, Integer y, long containerId)
+ public ImgSpotDTO(Integer row, Integer column, long containerId)
{
- this.permId = permId;
- this.x = x;
- this.y = y;
+ this.column = column;
+ this.row = row;
this.containerId = containerId;
}
@@ -65,34 +63,24 @@ public class ImgSpotDTO
this.id = id;
}
- public String getPermId()
- {
- return permId;
- }
-
- public void setPermId(String permId)
- {
- this.permId = permId;
- }
-
- public Integer getX()
+ public Integer getColumn()
{
- return x;
+ return column;
}
- public void setX(Integer x)
+ public void setColumn(Integer column)
{
- this.x = x;
+ this.column = column;
}
- public Integer getY()
+ public Integer getRow()
{
- return y;
+ return row;
}
- public void setY(Integer y)
+ public void setRow(Integer row)
{
- this.y = y;
+ this.row = row;
}
public long getContainerId()
diff --git a/screening/source/sql/postgresql/001/schema-001.sql b/screening/source/sql/postgresql/001/schema-001.sql
index 87fdd3993029413dc6c8b3001b68dbe95d72c7dc..11f5df79d0cd95e60481487e8f984723a84c1975 100644
--- a/screening/source/sql/postgresql/001/schema-001.sql
+++ b/screening/source/sql/postgresql/001/schema-001.sql
@@ -45,7 +45,6 @@ CREATE INDEX CONTAINERS_EXPE_IDX ON CONTAINERS(EXPE_ID);
CREATE TABLE SPOTS (
ID BIGSERIAL NOT NULL,
- PERM_ID CODE NOT NULL,
-- position in the container, one-based
X INTEGER,
@@ -53,7 +52,6 @@ CREATE TABLE SPOTS (
CONT_ID TECH_ID NOT NULL,
PRIMARY KEY (ID),
- UNIQUE (PERM_ID),
CONSTRAINT FK_SPOT_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
index 49b0e489923f3cbbcd2b1731d45317ab74ea1879..1d94d01c45116ea9ced5a15671d067e436a752ce 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingUploadDAOTest.java
@@ -20,6 +20,7 @@ import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import java.sql.SQLException;
+import java.util.List;
import org.testng.AssertJUnit;
import org.testng.annotations.BeforeClass;
@@ -60,11 +61,9 @@ public class ImagingUploadDAOTest extends AbstractDBTest
private static final String DS_PERM_ID = "dsId";
- private static final String SPOT_ID = "sId";
-
private static final String DS_CHANNEL = "dsChannel";
- private static final String DESCRIPTION = "desc";
+ private static final String CHANNEL_DESCRIPTION = "channel desc";
private static final String EXP_CHANNEL = "expChannel";
@@ -95,14 +94,7 @@ public class ImagingUploadDAOTest extends AbstractDBTest
final long channelId1 = addDatasetChannel(datasetId);
final long channelId2 = addExperimentChannel(experimentId);
- // test countChannelByDatasetIdOrExperimentId
- assertEquals(2, dao.countChannelByDatasetIdOrExperimentId(datasetId, experimentId));
-
- // test getChannelIdsByDatasetIdOrExperimentId
- long[] channels = dao.getChannelIdsByDatasetIdOrExperimentId(datasetId, experimentId);
- assertEquals(2, channels.length);
- AssertJUnit.assertTrue(channels[0] == channelId1 && channels[1] == channelId2
- || channels[1] == channelId1 && channels[0] == channelId2);
+ testChannelMethods(experimentId, datasetId, channelId1, channelId2);
// create channel stack, images and acquired images
final long channelStackId = addChannelStack(datasetId, spotId);
@@ -111,7 +103,11 @@ public class ImagingUploadDAOTest extends AbstractDBTest
addAcquiredImage(imageId1, channelStackId, channelId1);
addAcquiredImage(imageId2, channelStackId, channelId2);
- // test getImage
+ testGetImage(datasetId, channelId1, channelId2);
+ }
+
+ private void testGetImage(final long datasetId, final long channelId1, final long channelId2)
+ {
ImgImageDTO image1 =
dao.getImage(channelId1, datasetId, new Location(X_WELL_COLUMN, Y_WELL_ROW),
new Location(X_TILE_COLUMN, Y_TILE_ROW));
@@ -125,6 +121,29 @@ public class ImagingUploadDAOTest extends AbstractDBTest
assertEquals(ColorComponent.RED, image2.getColorComponent());
}
+ private void testChannelMethods(final long experimentId, final long datasetId,
+ final long channelId1, final long channelId2)
+ {
+ // test countChannelByDatasetIdOrExperimentId
+ assertEquals(2, dao.countChannelByDatasetIdOrExperimentId(datasetId, experimentId));
+
+ // test getChannelIdsByDatasetIdOrExperimentId
+ long[] channels = dao.getChannelIdsByDatasetIdOrExperimentId(datasetId, experimentId);
+ assertEquals(2, channels.length);
+ AssertJUnit.assertTrue(channels[0] == channelId1 && channels[1] == channelId2
+ || channels[1] == channelId1 && channels[0] == channelId2);
+
+ List<ImgChannelDTO> experimentChannels = dao.getChannelsByExperimentId(experimentId);
+ assertEquals(1, experimentChannels.size());
+
+ // test update
+ ImgChannelDTO channel = experimentChannels.get(0);
+ channel.setDescription("new " + CHANNEL_DESCRIPTION);
+ channel.setWavelength(WAVELENGTH + 100);
+ dao.updateChannel(channel);
+ assertEquals(channel, dao.getChannelsByExperimentId(experimentId).get(0));
+ }
+
private long addImage(String path, ColorComponent colorComponent)
{
final ImgImageDTO image = new ImgImageDTO(path, PAGE, colorComponent);
@@ -147,15 +166,15 @@ public class ImagingUploadDAOTest extends AbstractDBTest
final Integer spotWidth = 1;
final Integer spotHeight = 2;
final ImgContainerDTO container =
- new ImgContainerDTO(permId, spotWidth, spotHeight, experimentId);
+ new ImgContainerDTO(permId, spotHeight, spotWidth, experimentId);
final Long containerId = dao.addContainer(container);
// test tryGetContainerIdPermId
assertEquals(containerId, dao.tryGetContainerIdPermId(permId));
final ImgContainerDTO loadedContainer = dao.getContainerById(containerId);
assertNotNull(loadedContainer);
assertEquals(permId, loadedContainer.getPermId());
- assertEquals(spotWidth, loadedContainer.getSpotWidth());
- assertEquals(spotHeight, loadedContainer.getSpotHeight());
+ assertEquals(spotWidth, loadedContainer.getNumberOfColumns());
+ assertEquals(spotHeight, loadedContainer.getNumberOfRows());
assertEquals(experimentId, loadedContainer.getExperimentId());
return containerId;
@@ -167,14 +186,14 @@ public class ImagingUploadDAOTest extends AbstractDBTest
final Integer fieldsWidth = 1;
final Integer fieldsHeight = 2;
final ImgDatasetDTO dataset =
- new ImgDatasetDTO(permId, fieldsWidth, fieldsHeight, containerId);
+ new ImgDatasetDTO(permId, fieldsHeight, fieldsWidth, containerId);
final long datasetId = dao.addDataset(dataset);
final ImgDatasetDTO loadedDataset = dao.tryGetDatasetByPermId(DS_PERM_ID);
assertNotNull(loadedDataset);
assertEquals(permId, loadedDataset.getPermId());
- assertEquals(fieldsWidth, loadedDataset.getFieldsWidth());
- assertEquals(fieldsHeight, loadedDataset.getFieldsHeight());
+ assertEquals(fieldsWidth, loadedDataset.getFieldNumberOfColumns());
+ assertEquals(fieldsHeight, loadedDataset.getFieldNumberOfRows());
assertEquals(containerId, loadedDataset.getContainerId());
return datasetId;
@@ -182,21 +201,22 @@ public class ImagingUploadDAOTest extends AbstractDBTest
private long addSpot(long containerId)
{
- final ImgSpotDTO spot = new ImgSpotDTO(SPOT_ID, X_WELL_COLUMN, Y_WELL_ROW, containerId);
+ final ImgSpotDTO spot = new ImgSpotDTO(Y_WELL_ROW, X_WELL_COLUMN, containerId);
return dao.addSpot(spot);
}
private long addDatasetChannel(long datasetId)
{
final ImgChannelDTO channel =
- ImgChannelDTO.createDatasetChannel(DS_CHANNEL, DESCRIPTION, WAVELENGTH, datasetId);
+ ImgChannelDTO.createDatasetChannel(DS_CHANNEL, CHANNEL_DESCRIPTION, WAVELENGTH,
+ datasetId);
return dao.addChannel(channel);
}
private long addExperimentChannel(long experimentId)
{
final ImgChannelDTO channel =
- ImgChannelDTO.createExperimentChannel(EXP_CHANNEL, DESCRIPTION, WAVELENGTH,
+ ImgChannelDTO.createExperimentChannel(EXP_CHANNEL, CHANNEL_DESCRIPTION, WAVELENGTH,
experimentId);
return dao.addChannel(channel);
}
@@ -204,7 +224,7 @@ public class ImagingUploadDAOTest extends AbstractDBTest
private long addChannelStack(long datasetId, long spotId)
{
final ImgChannelStackDTO channelStack =
- new ImgChannelStackDTO(X_TILE_COLUMN, Y_TILE_ROW, datasetId, spotId);
+ new ImgChannelStackDTO(Y_TILE_ROW, X_TILE_COLUMN, datasetId, spotId);
return dao.addChannelStack(channelStack);
}