diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
index 31e5069afa5a9f3b680208a3c8a5356040650203..9dc994cc37ad6880ec22344578b3ffa8dca8005b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ImagingDatabaseHelper.java
@@ -23,6 +23,8 @@ import java.util.Map;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.Channel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgExperimentDTO;
@@ -92,8 +94,7 @@ public class ImagingDatabaseHelper
* in the DB.
*/
public static ExperimentWithChannelsAndContainer getOrCreateExperimentWithChannelsAndContainer(
- IImagingQueryDAO dao, HCSContainerDatasetInfo info,
- List<Channel> channels)
+ IImagingQueryDAO dao, HCSContainerDatasetInfo info, List<Channel> channels)
{
ImagingDatabaseHelper helper = new ImagingDatabaseHelper(dao);
synchronized (IImagingQueryDAO.class)
@@ -289,9 +290,16 @@ public class ImagingDatabaseHelper
private Map<String, Long> createChannels(ChannelOwner channelOwner, List<Channel> channels)
{
+ int colorIndex = 0;
Map<String, Long> map = new HashMap<String, Long>();
for (Channel channel : channels)
{
+ if (channel.tryGetChannelColor() == null)
+ {
+ ChannelColor channelColor = ChannelColor.createFromIndex(colorIndex);
+ channel.setChannelColor(channelColor);
+ colorIndex++;
+ }
ImgChannelDTO channelDTO = createChannel(channel, channelOwner);
addChannel(map, channelDTO);
}
@@ -313,8 +321,8 @@ public class ImagingDatabaseHelper
return nameMap;
}
- private ImgChannelDTO updateExperimentChannel(Channel channel,
- long expId, Map<String, ImgChannelDTO> existingChannels)
+ private ImgChannelDTO updateExperimentChannel(Channel channel, long expId,
+ Map<String, ImgChannelDTO> existingChannels)
{
ImgChannelDTO channelDTO =
makeChannelDTO(channel, ChannelOwner.createExperiment(expId));
@@ -358,8 +366,7 @@ public class ImagingDatabaseHelper
channelName, existingChannels.keySet());
}
- private ImgChannelDTO createChannel(Channel channel,
- ChannelOwner channelOwner)
+ private ImgChannelDTO createChannel(Channel channel, ChannelOwner channelOwner)
{
ImgChannelDTO channelDTO = makeChannelDTO(channel, channelOwner);
long channelId = dao.addChannel(channelDTO);
@@ -367,12 +374,15 @@ public class ImagingDatabaseHelper
return channelDTO;
}
- private static ImgChannelDTO makeChannelDTO(Channel channel,
- ChannelOwner channelOwner)
+ private static ImgChannelDTO makeChannelDTO(Channel channel, ChannelOwner channelOwner)
{
+ ChannelColor channelColor = channel.tryGetChannelColor();
+ assert channelColor != null : "channel color should be specified at this point";
+ ImageChannelColor imageChannelColor = ImageChannelColor.valueOf(channelColor.name());
+
return new ImgChannelDTO(channel.getCode(), channel.tryGetDescription(),
channel.tryGetWavelength(), channelOwner.tryGetDatasetId(),
- channelOwner.tryGetExperimentId(), channel.getLabel());
+ channelOwner.tryGetExperimentId(), channel.getLabel(), imageChannelColor);
}
}
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 c3522838478e6a338d98b54773de3e945f99393d..0601f6bdab0774a72b4407b73cb86c9ec58ce84e 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 "011"; // changed in S105
+ return "012"; // changed in S106
}
}
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 ae5b3d5b9be7175068fe289d9ae31b4c0c8e17e5..7e5fd32086497b5900dca6bab4781b268296c691 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
@@ -69,8 +69,8 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
@Select("insert into EXPERIMENTS (PERM_ID) values (?{1}) returning ID")
public long addExperiment(String experimentPermId);
- @Select("insert into CHANNELS (LABEL, CODE, DESCRIPTION, WAVELENGTH, DS_ID, EXP_ID) values "
- + "(?{1.label}, ?{1.code}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}) returning ID")
+ @Select("insert into CHANNELS (LABEL, CODE, DESCRIPTION, WAVELENGTH, DS_ID, EXP_ID, COLOR) values "
+ + "(?{1.label}, ?{1.code}, ?{1.description}, ?{1.wavelength}, ?{1.datasetId}, ?{1.experimentId}, ?{1.dbChannelColor}) returning ID")
public long addChannel(ImgChannelDTO channel);
@Select("insert into CONTAINERS (PERM_ID, SPOTS_WIDTH, SPOTS_HEIGHT, EXPE_ID) values "
@@ -105,7 +105,7 @@ public interface IImagingQueryDAO extends TransactionQuery, IImagingReadonlyQuer
// updates
@Update("update CHANNELS "
- + "set DESCRIPTION = ?{1.description}, WAVELENGTH = ?{1.wavelength} "
+ + "set DESCRIPTION = ?{1.description}, WAVELENGTH = ?{1.wavelength}, COLOR = ?{1.dbChannelColor} "
+ "where ID = ?{1.id}")
public void updateChannel(ImgChannelDTO channel);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
index 845f51b144947cf3754b2426896f42835f9bfb0d..189ff38116c6bfef83c3b2738de970be3f971140 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/Channel.java
@@ -20,13 +20,28 @@ public final class Channel extends AbstractHashable
private Integer wavelength;
- /** Constructs a channel with a specified code and label. */
+ private ChannelColor channelColorOrNull;
+
+ /**
+ * Constructs a channel with a specified code and label. The channel will be presented in a
+ * default color.
+ */
public Channel(String code, String label)
+ {
+ this(code, label, null);
+ }
+
+ /**
+ * Constructs a channel with a specified code and label. The channel will be presented in a
+ * specified color.
+ */
+ public Channel(String code, String label, ChannelColor channelColorOrNull)
{
assert code != null : "code is null";
assert label != null : "label is null";
this.label = label;
this.code = code;
+ this.channelColorOrNull = channelColorOrNull;
}
public String getCode()
@@ -49,6 +64,16 @@ public final class Channel extends AbstractHashable
return label;
}
+ /**
+ * @return color for the specified channel which will be used to display merged channels images.
+ * null only during dataset registration wheb default color should be used, afterwards
+ * never null.
+ */
+ public ChannelColor tryGetChannelColor()
+ {
+ return channelColorOrNull;
+ }
+
/** Sets the description of the channel.Optional. */
public void setDescription(String description)
{
@@ -60,4 +85,11 @@ public final class Channel extends AbstractHashable
{
this.wavelength = wavelength;
}
+
+ /** Sets the color in which this channel will be displayed. */
+ public void setChannelColor(ChannelColor channelColor)
+ {
+ this.channelColorOrNull = channelColor;
+ }
+
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java
new file mode 100644
index 0000000000000000000000000000000000000000..0a10cf74204457afb80fbb0b4cc9d82472cf340e
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColor.java
@@ -0,0 +1,38 @@
+package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
+
+/**
+ * Allowed colors in which channels can be presented.
+ *
+ * @author Tomasz Pylak
+ */
+public enum ChannelColor
+{
+ BLUE(0), GREEN(1), RED(2), RED_GREEN(3), RED_BLUE(4), GREEN_BLUE(5);
+
+ // If no mapping between channels and colors has been provided then channels get consecutive
+ // colors. This field determines the order in which colors are assigned.
+ // It is important for backward compatibility as well.
+ private final int orderIndex;
+
+ private ChannelColor(int orderIndex)
+ {
+ this.orderIndex = orderIndex;
+ }
+
+ public int getColorOrderIndex()
+ {
+ return orderIndex;
+ }
+
+ public static ChannelColor createFromIndex(int colorIndex)
+ {
+ for (ChannelColor color : values())
+ {
+ if (color.getColorOrderIndex() == colorIndex)
+ {
+ return color;
+ }
+ }
+ throw new IllegalStateException("Invalid color index: " + colorIndex + "!");
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
index 7f92f26718906ca535cb6114d49e7a275f1ced2c..1ff5f95da8eb40b5b74ca83632315190fbb0775b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/SimpleImageDataConfig.java
@@ -76,12 +76,29 @@ abstract public class SimpleImageDataConfig
}
/**
- * Creates channel description for a given code. The channel label will be equal to the code.
- * Can be overridden in subclasses.
+ * <p>
+ * Creates channel description for a given code. Can be overridden in subclasses.
+ * </p>
+ * By default rhe channel label will be equal to the code. Channel color returned by
+ * {@link #getChannelColor(String)} will be used.
*/
public Channel createChannel(String channelCode)
{
- return new Channel(channelCode, channelCode);
+ ChannelColor channelColor = getChannelColor(channelCode);
+ return new Channel(channelCode, channelCode, channelColor);
+ }
+
+ /**
+ * Returns color for the specified channel. It will be used to display merged channels images.
+ * <p>
+ * Can be overridden in subclasses. It is ignored if {@link #createChannel(String)} is
+ * overridden as well.
+ * </p>
+ * By default returns null (the arbitrary color will be set).
+ */
+ public ChannelColor getChannelColor(String channelCode)
+ {
+ return null;
}
// --- auxiliary structures ----------------------------------------------
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
index f26648c429a4e0059b8435d5fecfaff4a7b3eb54..425a2d6faabf39648777073099d7ca70c45566d0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/SimpleImageDataSetRegistrator.java
@@ -172,7 +172,8 @@ public class SimpleImageDataSetRegistrator
List<Channel> channels = new ArrayList<Channel>();
for (String channelCode : channelCodes)
{
- channels.add(simpleImageConfig.createChannel(channelCode));
+ Channel channel = simpleImageConfig.createChannel(channelCode);
+ channels.add(channel);
}
return channels;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
index 460320b878eca1ea2c2a859971964bdb785eed8e..1dc3935f1472e1d011fa4d1733a6aa61bccb3a61 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.d
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.utils.GuiUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
/**
@@ -148,12 +149,11 @@ class ChannelChooser
for (DatasetImagesReference overlayDataset : overlayDatasets)
{
ImageDatasetParameters imageParams = overlayDataset.getImageParameters();
- List<String> channelsCodes = imageParams.getChannelsCodes();
- List<String> channelsLabels = imageParams.getChannelsLabels();
for (int i = 0; i < imageParams.getChannelsNumber(); i++)
{
- String channelCode = channelsCodes.get(i);
- String channelLabel = channelsLabels.get(i);
+ ImageChannel channel = imageParams.getChannels().get(i);
+ String channelCode = channel.getCode();
+ String channelLabel = channel.getLabel();
LabeledItem<ImageDatasetChannel> item =
createLabeledItem(overlayDataset, channelCode, channelLabel);
items.add(item);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java
new file mode 100644
index 0000000000000000000000000000000000000000..e51a89aeb830e3bdc2983812ffe2771bd92471d8
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannel.java
@@ -0,0 +1,87 @@
+/*
+ * 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.plugin.screening.shared.basic.dto;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ * A channel in which the image has been acquired.
+ * <p>
+ * Each channel has its <code>code</code> which uniquely identifies it in one experiment or dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageChannel implements ISerializable
+{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+ private String code;
+
+ private String label;
+
+ private String description;
+
+ private Integer wavelength;
+
+ private ImageChannelColor channelColor;
+
+ // GWT only
+ @SuppressWarnings("unused")
+ private ImageChannel()
+ {
+ }
+
+ public ImageChannel(String code, String label, String description, Integer wavelength,
+ ImageChannelColor channelColor)
+ {
+ this.code = code;
+ this.label = label;
+ this.description = description;
+ this.wavelength = wavelength;
+ this.channelColor = channelColor;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public String tryGetDescription()
+ {
+ return description;
+ }
+
+ public Integer tryGetWavelength()
+ {
+ return wavelength;
+ }
+
+ public String getLabel()
+ {
+ return label;
+ }
+
+ /**
+ * @return color for the specified channel which will be used to display merged channels images.
+ */
+ public ImageChannelColor getChannelColor()
+ {
+ return channelColor;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelColor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelColor.java
new file mode 100644
index 0000000000000000000000000000000000000000..e1fd8c8af465c1c59d06a8af262d42b39dbfb180
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelColor.java
@@ -0,0 +1,27 @@
+/*
+ * 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.plugin.screening.shared.basic.dto;
+
+/**
+ * Allowed colors in which channels can be presented.
+ *
+ * @author Tomasz Pylak
+ */
+public enum ImageChannelColor
+{
+ BLUE, GREEN, RED, RED_GREEN, RED_BLUE, GREEN_BLUE;
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
index dddc6de6a39aa526799f5399413eb1b2d75dbe8c..78b70ff5e6242f4568b353e30e32862dea2c6655 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
+import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -44,9 +45,7 @@ public class ImageDatasetParameters implements ISerializable
private int tileColsNum;
- private List<String> channelsCodes;
-
- private List<String> channelsLabels;
+ private List<ImageChannel> channels;
private Map<String/* channel code */, String/* signature */> channelsTransformerFactorySignatures =
new HashMap<String, String>();
@@ -104,19 +103,29 @@ public class ImageDatasetParameters implements ISerializable
this.datasetCode = datasetCode;
}
- public void setChannelsCodes(List<String> channelsCodes)
+ public List<String> getChannelsCodes()
{
- this.channelsCodes = channelsCodes;
+ List<String> channelCodes = new ArrayList<String>();
+ for (ImageChannel channel : channels)
+ {
+ channelCodes.add(channel.getCode());
+ }
+ return channelCodes;
}
- public List<String> getChannelsCodes()
+ public List<String> getChannelsLabels()
{
- return channelsCodes;
+ List<String> channelLabels = new ArrayList<String>();
+ for (ImageChannel channel : channels)
+ {
+ channelLabels.add(channel.getLabel());
+ }
+ return channelLabels;
}
public int getChannelsNumber()
{
- return channelsCodes.size();
+ return channels.size();
}
public boolean isMultidimensional()
@@ -129,14 +138,14 @@ public class ImageDatasetParameters implements ISerializable
this.isMultidimensional = isMultidimensional;
}
- public void setChannelsLabels(List<String> channelsLabels)
+ public void setChannels(List<ImageChannel> channels)
{
- this.channelsLabels = channelsLabels;
+ this.channels = channels;
}
- public List<String> getChannelsLabels()
+ public List<ImageChannel> getChannels()
{
- return channelsLabels;
+ return channels;
}
public void addTransformerFactorySignatureFor(String channelCode, String signatureOrNull)
@@ -148,5 +157,4 @@ public class ImageDatasetParameters implements ISerializable
{
return channelsTransformerFactorySignatures.get(channelCode);
}
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
index 72422a5d8f02c05efcecb393d72f2bc1b9550596..a127fd776492d681289777686c9e27e2da04c440 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
@@ -20,6 +20,8 @@ import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.common.utilities.MD5ChecksumCalculator;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannel;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStack;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -160,21 +162,29 @@ public class HCSDatasetLoader implements IImageDatasetLoader
params.setIsMultidimensional(dataset.getIsMultidimensional());
params.addTransformerFactorySignatureFor(ScreeningConstants.MERGED_CHANNELS,
mergedChannelTransformerFactorySignatureOrNull);
- List<String> channelsCodes = new ArrayList<String>();
- List<String> channelsLabels = new ArrayList<String>();
- for (ImgChannelDTO channel : channels)
+
+ List<ImageChannel> convertedChannels = new ArrayList<ImageChannel>();
+ for (ImgChannelDTO channelDTO : channels)
{
- String channelCode = channel.getCode();
- channelsCodes.add(channelCode);
- channelsLabels.add(channel.getLabel());
- params.addTransformerFactorySignatureFor(channelCode,
- tryGetSignature(channel.getSerializedImageTransformerFactory()));
+ ImageChannel channel = convert(channelDTO);
+ convertedChannels.add(channel);
+
+ String transformationSignature =
+ tryGetSignature(channelDTO.getSerializedImageTransformerFactory());
+ params.addTransformerFactorySignatureFor(channelDTO.getCode(), transformationSignature);
}
- params.setChannelsCodes(channelsCodes);
- params.setChannelsLabels(channelsLabels);
+ params.setChannels(convertedChannels);
return params;
}
+ private static ImageChannel convert(ImgChannelDTO channelDTO)
+ {
+ ImageChannelColor imageChannelColor =
+ ImageChannelColor.valueOf(channelDTO.getDbChannelColor());
+ return new ImageChannel(channelDTO.getCode(), channelDTO.getLabel(),
+ channelDTO.getDescription(), channelDTO.getWavelength(), imageChannelColor);
+ }
+
private String tryGetSignature(byte[] bytesOrNull)
{
if (bytesOrNull == null)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
index eaae5838b523ee5536a82afd1125cd0f6834c5a9..3393eabfa401566ef923f43aad9dda78f05dfde8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgChannelDTO.java
@@ -18,6 +18,8 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess;
import net.lemnik.eodsql.ResultColumn;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
+
/**
* @author Tomasz Pylak
*/
@@ -43,6 +45,10 @@ public class ImgChannelDTO extends AbstractImageTransformerFactoryHolder
@ResultColumn("EXP_ID")
private Long experimentIdOrNull;
+ /** Value for the {@link ImageChannelColor} enum. Not null. */
+ @ResultColumn("COLOR")
+ private String channelColor;
+
// GWT only
@SuppressWarnings("unused")
private ImgChannelDTO()
@@ -51,7 +57,8 @@ public class ImgChannelDTO extends AbstractImageTransformerFactoryHolder
}
public ImgChannelDTO(String code, String descriptionOrNull, Integer wavelengthOrNull,
- Long datasetIdOrNull, Long experimentIdOrNull, String label)
+ Long datasetIdOrNull, Long experimentIdOrNull, String label,
+ ImageChannelColor channelColor)
{
assert (datasetIdOrNull == null && experimentIdOrNull != null)
|| (datasetIdOrNull != null && experimentIdOrNull == null);
@@ -61,6 +68,7 @@ public class ImgChannelDTO extends AbstractImageTransformerFactoryHolder
this.wavelengthOrNull = wavelengthOrNull;
this.datasetIdOrNull = datasetIdOrNull;
this.experimentIdOrNull = experimentIdOrNull;
+ this.channelColor = channelColor.name();
}
public String getCode()
@@ -124,4 +132,14 @@ public class ImgChannelDTO extends AbstractImageTransformerFactoryHolder
this.experimentIdOrNull = experimentId;
}
+ /** Can be converted to {@link ImageChannelColor}. */
+ public String getDbChannelColor()
+ {
+ return channelColor;
+ }
+
+ public void setDbChannelColor(String channelColor)
+ {
+ this.channelColor = channelColor;
+ }
}
diff --git a/screening/source/sql/postgresql/012/data.sql b/screening/source/sql/postgresql/012/data.sql
new file mode 100644
index 0000000000000000000000000000000000000000..f08222c48c2932180be40863f775e14dac5267bc
--- /dev/null
+++ b/screening/source/sql/postgresql/012/data.sql
@@ -0,0 +1,275 @@
+-- Note that these data has to be loaded manually into the openBIS Core database.
+
+-- TODO: this sql should be converted to a generic sql without refering to technical ids.
+-- Now the ids should be updated if some new records will be added in the generic data.
+
+--
+-- PostgreSQL database dump
+--
+
+SET statement_timeout = 0;
+SET client_encoding = 'UTF8';
+SET standard_conforming_strings = off;
+SET check_function_bodies = false;
+SET client_min_messages = warning;
+SET escape_string_warning = off;
+
+SET search_path = public, pg_catalog;
+
+--
+-- Data for Name: controlled_vocabularies; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY controlled_vocabularies (id, code, description, registration_timestamp, pers_id_registerer, is_managed_internally, is_internal_namespace, dbin_id, modification_timestamp, is_chosen_from_list, source_uri) FROM stdin;
+2 PLATE_GEOMETRY The geometry or dimensions of a plate 2008-06-17 16:38:30.723292+02 1 t t 1 2009-11-27 16:02:26.451046+01 t \N
+3 MICROSCOPE Microscope used in an experiment. 2009-11-29 23:55:18.978884+01 1 f f 1 2009-12-17 01:50:54.68+01 t \N
+\.
+
+
+--
+-- Data for Name: controlled_vocabulary_terms; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY controlled_vocabulary_terms (id, code, registration_timestamp, covo_id, pers_id_registerer, label, description, ordinal) FROM stdin;
+3 384_WELLS_16X24 2008-06-17 16:38:30.723292+02 2 1 384 Wells, 16x24 \N 1
+4 96_WELLS_8X12 2008-06-17 16:38:31.101031+02 2 1 96 Wells, 8x12 \N 2
+5 1536_WELLS_32X48 2008-06-17 16:38:31.101031+02 2 1 1536 Wells, 32x48 \N 3
+6 BD_PATHWAY_855 2009-11-29 23:55:18.978884+01 3 1 \N \N 1
+7 MD_IMAGEXPRESS_MICROLIVE 2009-11-29 23:55:18.978884+01 3 1 \N \N 2
+8 MD_IMAGEXPRESS_MICRO_2 2009-11-29 23:55:18.978884+01 3 1 \N \N 3
+\.
+
+
+--
+-- Data for Name: data_set_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY data_set_types (id, code, description, dbin_id, modification_timestamp) FROM stdin;
+3 HCS_IMAGE_ANALYSIS_DATA Data derived from analysis of HCS images 1 2009-11-27 16:02:26.451046+01
+2 HCS_IMAGE HCS raw images acquired by microscopes 1 2009-11-27 16:02:26.451046+01
+4 HCS_ANALYSIS_PER_GENE Image analysis data aggregated per gene. 1 2009-12-16 16:59:50.743029+01
+\.
+
+
+--
+-- Data for Name: material_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY material_types (id, code, description, dbin_id, modification_timestamp) FROM stdin;
+1 VIRUS Virus 1 2009-11-27 16:02:26.451046+01
+2 CELL_LINE Cell Line or Cell Culture. The growing of cells under controlled conditions. 1 2009-11-27 16:02:26.451046+01
+3 GENE Gene 1 2009-11-27 16:02:26.451046+01
+4 SIRNA siRNA nucleotide 1 2009-11-27 16:02:26.451046+01
+5 CONTROL Control of a control layout 1 2009-11-27 16:02:26.451046+01
+6 BACTERIUM Bacterium 1 2009-11-27 16:02:26.451046+01
+7 COMPOUND Compound 1 2009-11-27 16:02:26.451046+01
+\.
+
+
+--
+-- Data for Name: property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY property_types (id, code, description, label, daty_id, registration_timestamp, pers_id_registerer, covo_id, is_managed_internally, is_internal_namespace, dbin_id, maty_prop_id) FROM stdin;
+3 NUCLEOTIDE_SEQUENCE A sequence of nucleotides Nucleotide Sequence 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N
+4 REFSEQ NCBI Reference Sequence code, applicable to sequences of type: DNA, RNA, protein RefSeq 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N
+13 MICROSCOPE Microscope 7 2009-11-29 23:57:05.85618+01 1 3 f f 1 \N
+7 INHIBITOR_OF Inhibitor Of Inhibitor Of 8 2009-11-27 16:02:45.060699+01 1 \N f f 1 3
+11 SIRNA siRNA siRNA 8 2009-11-29 23:56:19.39967+01 1 \N f f 1 4
+12 CONTROL Control Control 8 2009-11-29 23:56:37.355313+01 1 \N f f 1 5
+6 PLATE_GEOMETRY Plate Geometry Plate Geometry 7 2008-06-17 16:38:30.723292+02 1 2 t t 1 \N
+15 NUMBER_OF_CHANNEL Channels 3 2009-12-17 10:56:17.239319+01 1 \N f f 1 \N
+16 LIBRARY_ID Library id Id from the master plate library 1 2008-02-28 13:03:03.358532+01 1 \N f f 1 \N
+\.
+
+
+--
+-- Data for Name: data_set_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY data_set_type_property_types (id, dsty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, section, ordinal) FROM stdin;
+\.
+
+
+--
+-- Data for Name: experiment_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY experiment_types (id, code, description, dbin_id, modification_timestamp) FROM stdin;
+2 COMPOUND_HCS Compound High Content Screening 1 2009-11-27 16:02:26.451046+01
+1 SIRNA_HCS Small Interfering RNA High Content Screening 1 2009-11-27 16:02:26.451046+01
+\.
+
+
+--
+-- Data for Name: experiment_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY experiment_type_property_types (id, exty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, section, ordinal) FROM stdin;
+1 1 1 t t 1 2008-06-17 16:38:49.023295+02 \N 1
+2 2 1 t t 1 2008-06-17 16:38:49.301922+02 \N 1
+5 1 13 f f 1 2009-12-17 10:54:01.261178+01 \N 2
+\.
+
+
+--
+-- Data for Name: file_format_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY file_format_types (id, code, description, dbin_id) FROM stdin;
+7 PNG \N 1
+8 CSV files with values separated by comma or semicolon 1
+9 JPG \N 1
+\.
+
+
+--
+-- Data for Name: filters; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY filters (id, dbin_id, name, description, registration_timestamp, pers_id_registerer, modification_timestamp, expression, is_public, grid_id) FROM stdin;
+9 1 Infection index \N 2009-12-16 21:19:19.012657+01 1 2009-12-16 22:41:56.863+01 float(row.col('colIndex_5')) > float(${threshold}) t data-set-reporting-gridplate-image-analysis-merger
+8 1 Total number of cells \N 2009-12-16 21:18:05.161964+01 1 2009-12-16 22:42:31.707+01 int(row.col('colIndex_3')) > int(${threshold}) t data-set-reporting-gridplate-image-analysis-merger
+7 1 Number of infected cells \N 2009-12-16 21:17:40.765083+01 1 2009-12-16 22:42:46.052+01 int(row.col('colIndex_4')) > int(${threshold}) t data-set-reporting-gridplate-image-analysis-merger
+\.
+
+
+--
+-- Data for Name: material_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY material_type_property_types (id, maty_id, prty_id, is_mandatory, registration_timestamp, pers_id_registerer, is_managed_internally, section, ordinal) FROM stdin;
+10 4 7 t 2009-11-27 16:02:45.060699+01 1 f \N 4
+9 5 1 f 2008-02-28 13:03:03.358532+01 1 f \N 1
+8 4 1 f 2008-02-28 13:03:03.358532+01 1 f \N 3
+6 4 3 t 2008-02-28 13:03:03.358532+01 1 f \N 1
+12 4 16 f 2008-02-28 13:03:03.358532+01 1 f \N 1
+5 3 1 f 2008-02-28 13:03:03.358532+01 1 f \N 2
+3 7 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1
+2 6 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1
+1 1 1 t 2008-02-28 13:03:03.358532+01 1 f \N 1
+\.
+
+
+--
+-- Data for Name: sample_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY sample_types (id, code, description, dbin_id, is_listable, generated_from_depth, part_of_depth, modification_timestamp, is_auto_generated_code, generated_code_prefix) FROM stdin;
+3 PLATE Cell Plate 1 t 2 0 2009-11-27 16:02:26.451046+01 f S
+7 SIRNA_WELL \N 1 f 0 1 2009-11-27 19:42:03.483115+01 f O
+8 CONTROL_WELL \N 1 f 0 1 2009-11-27 19:42:25.791288+01 f C
+9 LIBRARY \N 1 f 0 0 2009-11-27 19:42:25.791288+01 f L
+\.
+
+
+--
+-- Data for Name: sample_type_property_types; Type: TABLE DATA; Schema: public; Owner: -
+--
+
+COPY sample_type_property_types (id, saty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, is_displayed, section, ordinal) FROM stdin;
+8 7 11 f f 1 2009-11-29 23:57:38.268212+01 t \N 1
+9 8 12 f f 1 2009-11-29 23:57:49.098187+01 t \N 1
+10 3 6 f f 1 2009-11-30 01:28:20.972263+01 t \N 1
+\.
+
+--
+-- PostgreSQL database dump complete
+--
+
+--------------------------------------------------
+-- update sequences values
+--------------------------------------------------
+
+select setval('controlled_vocabulary_id_seq', 100);
+select setval('cvte_id_seq', 100);
+select setval('property_type_id_seq', 100);
+select setval('file_format_type_id_seq', 100);
+select setval('filter_id_seq', 100);
+select setval('experiment_type_id_seq', 100);
+select setval('sample_type_id_seq', 100);
+select setval('data_set_type_id_seq', 100);
+select setval('material_type_id_seq', 100);
+select setval('etpt_id_seq', 100);
+select setval('stpt_id_seq', 100);
+select setval('mtpt_id_seq', 100);
+
+
+--------------------------------------------------
+-- create a gene property and assign it to sirna well
+--------------------------------------------------
+
+insert into property_types(
+ id,
+ code, description, label,
+ daty_id,
+ pers_id_registerer,
+ dbin_id,
+ maty_prop_id)
+values(
+ nextval('PROPERTY_TYPE_ID_SEQ'),
+ 'GENE','Inhibited gene','Gene',
+ (select id from data_types where code = 'MATERIAL'),
+ (select id from persons where user_id ='system'),
+ (select id from database_instances where is_original_source = 'T'),
+ (select id from material_types where code = 'GENE')
+ );
+
+insert into sample_type_property_types(
+ id,
+ saty_id,
+ prty_id,
+ is_mandatory,
+ pers_id_registerer,
+ ordinal
+) values(
+ nextval('stpt_id_seq'),
+ (select id from sample_types where code = 'SIRNA_WELL'),
+ (select id from property_types where code = 'GENE'),
+ false,
+ (select id from persons where user_id ='system'),
+ (select max(ordinal)+1 from sample_type_property_types
+ where saty_id = (select id from sample_types where code = 'SIRNA_WELL'))
+ );
+
+
+--------------------------------------------------
+-- Create gene property: gene_symbols
+--------------------------------------------------
+
+
+ insert into property_types
+ (id
+ ,code
+ ,description
+ ,label
+ ,daty_id
+ ,pers_id_registerer
+ ,dbin_id)
+ values
+ (nextval('PROPERTY_TYPE_ID_SEQ')
+ ,'GENE_SYMBOLS'
+ ,'Gene symbols'
+ ,'Gene symbols'
+ ,(select id from data_types where code ='VARCHAR')
+ ,(select id from persons where user_id ='system')
+ ,(select id from database_instances where is_original_source = 'T')
+ );
+
+ insert into material_type_property_types(
+ id,
+ maty_id,
+ prty_id,
+ is_mandatory,
+ pers_id_registerer,
+ ordinal
+ ) values(
+ nextval('mtpt_id_seq'),
+ (select id from material_types where code = 'GENE'),
+ (select id from property_types where code = 'GENE_SYMBOLS'),
+ false,
+ (select id from persons where user_id ='system'),
+ (select max(ordinal)+1 from material_type_property_types
+ where maty_id = (select id from material_types where code = 'GENE'))
+ );
+
diff --git a/screening/source/sql/postgresql/012/schema-012.sql b/screening/source/sql/postgresql/012/schema-012.sql
new file mode 100644
index 0000000000000000000000000000000000000000..c798e6d3ba6a294b6e578ac27d2d90bbc3cac884
--- /dev/null
+++ b/screening/source/sql/postgresql/012/schema-012.sql
@@ -0,0 +1,285 @@
+
+/* ---------------------------------------------------------------------- */
+/* 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 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_DATA_SET_1 FOREIGN KEY (CONT_ID) REFERENCES CONTAINERS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX DATA_SETS_CONT_IDX ON DATA_SETS(CONT_ID);
+
+CREATE TABLE CHANNELS (
+ ID BIGSERIAL NOT NULL,
+
+ CODE NAME NOT NULL,
+ LABEL NAME NOT NULL,
+ DESCRIPTION DESCRIPTION,
+ WAVELENGTH INTEGER,
+ IMAGE_TRANSFORMER_FACTORY BYTEA,
+ COLOR CHANNEL_COLOR NOT NULL,
+
+ 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)),
+
+ 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 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 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,
+ PAGE INTEGER,
+ COLOR COLOR_COMPONENT,
+
+ PRIMARY KEY (ID)
+);
+
+CREATE TABLE ACQUIRED_IMAGES (
+ ID BIGSERIAL NOT NULL,
+
+ IMG_ID TECH_ID NOT NULL,
+ 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 CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_IMAGES_4 FOREIGN KEY (THUMBNAIL_ID) REFERENCES IMAGES (ID) ON DELETE CASCADE 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 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();
+
+------------------------------------------------------------------------------------
+-- 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 $$
+DECLARE
+ v_cont_id CODE;
+BEGIN
+
+ select cont_id into v_cont_id from data_sets where id = NEW.ds_id;
+
+ -- Check that if there is no spot than there is no dataset container as well
+ if v_cont_id IS NULL then
+ if NEW.spot_id IS NOT NULL then
+ RAISE EXCEPTION 'Insert/Update of CHANNEL_STACKS failed, as the dataset container is not set, but spot is (spot id = %).',NEW.spot_id;
+ end if;
+ else
+ if NEW.spot_id IS NULL then
+ RAISE EXCEPTION 'Insert/Update of CHANNEL_STACKS failed, as the dataset container is set (id = %), but spot is not set.',v_cont_id;
+ end if;
+ end if;
+ RETURN NEW;
+END;
+$$ LANGUAGE 'plpgsql';
+
+CREATE TRIGGER CHANNEL_STACKS_CHECK BEFORE INSERT OR UPDATE ON CHANNEL_STACKS
+ FOR EACH ROW EXECUTE PROCEDURE CHANNEL_STACKS_CHECK();
\ No newline at end of file
diff --git a/screening/source/sql/postgresql/012/upload-screening-metadata.sh b/screening/source/sql/postgresql/012/upload-screening-metadata.sh
new file mode 100755
index 0000000000000000000000000000000000000000..1a8a1969f1ef9d83fafdeb766696b9c5eef14fe7
--- /dev/null
+++ b/screening/source/sql/postgresql/012/upload-screening-metadata.sh
@@ -0,0 +1,2 @@
+DB=$1
+psql -U postgres -d openbis_$DB -f data.sql
diff --git a/screening/source/sql/postgresql/migration/migration-011-012.sql b/screening/source/sql/postgresql/migration/migration-011-012.sql
new file mode 100644
index 0000000000000000000000000000000000000000..4197da7db0dba79e3d371c83c5bcc9516c6d3cb0
--- /dev/null
+++ b/screening/source/sql/postgresql/migration/migration-011-012.sql
@@ -0,0 +1,22 @@
+-- Migration from 011 to 012
+CREATE DOMAIN CHANNEL_COLOR AS VARCHAR(20) CHECK (VALUE IN ('BLUE', 'GREEN', 'RED', 'RED_GREEN', 'RED_BLUE', 'GREEN_BLUE'));
+
+ALTER TABLE channels ADD COLUMN color CHANNEL_COLOR;
+
+update channels upd_ch
+set color =
+ ( select
+ CASE
+ WHEN (upd_ch.id - min(id)) % 6 = 0 THEN 'BLUE'
+ WHEN (upd_ch.id - min(id)) % 6 = 1 THEN 'GREEN'
+ WHEN (upd_ch.id - min(id)) % 6 = 2 THEN 'RED'
+ WHEN (upd_ch.id - min(id)) % 6 = 3 THEN 'RED_GREEN'
+ WHEN (upd_ch.id - min(id)) % 6 = 4 THEN 'RED_BLUE'
+ WHEN (upd_ch.id - min(id)) % 6 = 5 THEN 'GREEN_BLUE'
+ END color
+ from channels cc
+ where upd_ch.exp_id = cc.exp_id or upd_ch.ds_id = cc.ds_id
+ group by cc.exp_id, cc.ds_id
+ );
+
+ALTER TABLE channels ALTER COLUMN color SET NOT NULL;
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ChannelColorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ChannelColorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..9f14f9af3b0a3748c5b107cb9ad7941f51e35b8c
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ChannelColorTest.java
@@ -0,0 +1,41 @@
+/*
+ * 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.dataaccess;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.test.AssertionUtil;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ChannelColor;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class ChannelColorTest extends AssertJUnit
+{
+ @Test
+ public void testEnumsEqual()
+ {
+ List<ChannelColor> values1 = Arrays.asList(ChannelColor.values());
+ List<ImageChannelColor> values2 = Arrays.asList(ImageChannelColor.values());
+ AssertionUtil.assertEnumsEqual(values1, values2);
+ }
+}
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 f4702198da5d214f7a929fb4cb7447410ade5bc5..00ac1faf50d3d2f92d2c2ebd3d56a287f21f4c72 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
@@ -31,6 +31,7 @@ import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.AbstractDBTest;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgAcquiredImageDTO;
@@ -54,6 +55,8 @@ public class ImagingQueryDAOTest extends AbstractDBTest
private static final String CHANNEL_LABEL = "Channel Label";
+ private static final ImageChannelColor CHANNEL_COLOR = ImageChannelColor.RED;
+
private static final int PAGE = 1;
private static final int Y_TILE_ROW = 2;
@@ -299,6 +302,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals("DSCHANNEL", datasetChannel.getCode());
assertEquals(CHANNEL_LABEL, datasetChannel.getLabel());
+ assertEquals(CHANNEL_COLOR.name(), datasetChannel.getDbChannelColor());
assertEquals(datasetChannelId, datasetChannel.getId());
assertEquals(datasetChannel, dao.tryGetChannelForDataset(datasetId, "dsChannel"));
@@ -308,6 +312,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
ImgChannelDTO experimentChannel = experimentChannels.get(0);
assertEquals("EXPCHANNEL", experimentChannel.getCode());
assertEquals(CHANNEL_LABEL, experimentChannel.getLabel());
+ assertEquals(CHANNEL_COLOR.name(), experimentChannel.getDbChannelColor());
assertEquals(experimentChannelId, experimentChannel.getId());
assertEquals(experimentChannel, dao.tryGetChannelForExperiment(experimentId, "expChannel"));
@@ -400,7 +405,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
{
final ImgChannelDTO channel =
new ImgChannelDTO(DS_CHANNEL, CHANNEL_DESCRIPTION, WAVELENGTH, datasetId, null,
- CHANNEL_LABEL);
+ CHANNEL_LABEL, CHANNEL_COLOR);
return dao.addChannel(channel);
}
@@ -408,7 +413,7 @@ public class ImagingQueryDAOTest extends AbstractDBTest
{
final ImgChannelDTO channel =
new ImgChannelDTO(EXP_CHANNEL, CHANNEL_DESCRIPTION, WAVELENGTH, null, experimentId,
- CHANNEL_LABEL);
+ CHANNEL_LABEL, CHANNEL_COLOR);
return dao.addChannel(channel);
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
index 3306e9b6d49da7fc4607126ffb6b281278da5b0c..eb2a160d7cbf03b2cfae696c68449ef8f914a765 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtilsTest.java
@@ -47,6 +47,7 @@ import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.ImageChannelStackR
import ch.systemsx.cisd.openbis.dss.generic.server.images.dto.RequestedImageSize;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtilTest;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
/**
@@ -165,7 +166,8 @@ public class ImageChannelsUtilsTest extends AssertJUnit
{
one(loader).getImageParameters();
ImageDatasetParameters imgParams = new ImageDatasetParameters();
- imgParams.setChannelsCodes(Arrays.asList(CHANNEL));
+ imgParams.setChannels(Arrays.asList(new ImageChannel(CHANNEL, CHANNEL, null,
+ null, null)));
will(returnValue(imgParams));
RequestedImageSize requestedSize =
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 55da96f177bbdf02f68d05bbf0596163cf87139f..cd6cb792052dee44963a18c47beeed4cf55b6fd4 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -79,6 +79,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IFeatureVecto
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannel;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelColor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
@@ -169,7 +171,8 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
imageParameters.setTileRowsNum(1);
imageParameters.setTileColsNum(2);
imageParameters.setDatasetCode(DATASET_CODE);
- imageParameters.setChannelsCodes(Arrays.asList(CHANNEL_CODE));
+ imageParameters.setChannels(Arrays.asList(new ImageChannel(CHANNEL_CODE, CHANNEL_CODE,
+ null, null, null)));
context.checking(new Expectations()
{
{
@@ -384,7 +387,8 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
{
one(dao).tryGetChannelForExperimentPermId(EXPERIMENT_PERM_ID, channel);
ImgChannelDTO channelDTO =
- new ImgChannelDTO("dapi", null, null, new Long(42), null, "dapi");
+ new ImgChannelDTO("dapi", null, null, new Long(42), null, "dapi",
+ ImageChannelColor.BLUE);
channelDTO.setSerializedImageTransformerFactory(SerializationUtils
.serialize(transformerFactory));
will(returnValue(channelDTO));