diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/BasicDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/BasicDataSetInformation.java
new file mode 100644
index 0000000000000000000000000000000000000000..84e475238305917f81b2015dc3e1b314abde5ed2
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/BasicDataSetInformation.java
@@ -0,0 +1,82 @@
+/*
+ * 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.dto.api.v1;
+
+import java.util.Arrays;
+
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.IServer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+
+/**
+ * Basic attributes of a dataset connected to a sample and optionally to one parent dataset.
+ *
+ * @author Tomasz Pylak
+ */
+public class BasicDataSetInformation extends DataSetInformation
+{
+ private static final long serialVersionUID = IServer.VERSION;
+
+ private String fileFormatTypeCode;
+
+ // marks if a dataset is measured or derived from measured data
+ private boolean isMeasured = true;
+
+ /** Sets code of the dataset type */
+ public void setDatasetTypeCode(String datasetTypeCode)
+ {
+ DataSetType dataSetType = new DataSetType();
+ dataSetType.setCode(datasetTypeCode);
+ super.setDataSetType(dataSetType);
+ }
+
+ /** Mandatory: sets file format code. */
+ public void setFileFormatCode(String fileFormatCode)
+ {
+ this.fileFormatTypeCode = fileFormatCode;
+ }
+
+ /** Mandatory: sets attributes of the connected sample */
+ public void setSample(String sampleSpaceCode, String sampleCode)
+ {
+ super.setSpaceCode(sampleSpaceCode);
+ super.setSampleCode(sampleCode);
+ }
+
+ /** attributes of the parent dataset - optional */
+ public void setParentDatasetCode(String parentDatasetCode)
+ {
+ super.setParentDataSetCodes(Arrays.asList(parentDatasetCode));
+ }
+
+ /** marks if a dataset is measured or derived from measured data */
+ public void setMeasured(boolean isMeasured)
+ {
+ this.isMeasured = isMeasured;
+ }
+
+ public String getFileFormatTypeCode()
+ {
+ return fileFormatTypeCode;
+ }
+
+ public boolean isMeasured()
+ {
+ return isMeasured;
+ }
+
+}
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 65208142bb29a583eb6cc5b91b3c80f5ce512ff0..3107de89fdcb7382463b3cc8c35583db7b80f40a 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
@@ -20,6 +20,7 @@ public final class Channel extends AbstractHashable
private Integer wavelength;
+ /** Constructs a channel with a specified code and label. */
public Channel(String code, String label)
{
assert code != null : "code is null";
@@ -48,11 +49,13 @@ public final class Channel extends AbstractHashable
return label;
}
+ /** Optional. Sets the description of the channel. */
public void setDescription(String description)
{
this.description = description;
}
+ /** Optional. Sets the wavelength of the channel. */
public void setWavelength(Integer wavelength)
{
this.wavelength = wavelength;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponent.java
index b270a8d3ce46225a7ee86e62eea7ab603014b0d4..76ed3f99f42ffc6e87d713fc2ca38f856ce151ad 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ChannelColorComponent.java
@@ -17,8 +17,8 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.v1;
/**
- * Color component of an image which constitutes one channel (if the image consists of all channels
- * merged).
+ * Color component of an image which constitutes one channel. Useful if the image consists of all
+ * channels merged together.
*
* @author Tomasz Pylak
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageDataSetInformation.java
index ed350b0aadee8331b8a67f4e58bea2fd3a0fc7dd..3d51fa509ffc3af0ed5c667f36a127120cd02a4a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageDataSetInformation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageDataSetInformation.java
@@ -27,7 +27,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
*
* @author Tomasz Pylak
*/
-public class ImageDataSetInformation extends DataSetInformation
+public class ImageDataSetInformation extends BasicDataSetInformation
{
private static final long serialVersionUID = IServer.VERSION;
@@ -77,17 +77,20 @@ public class ImageDataSetInformation extends DataSetInformation
// ------ setters
+ /** Sets location of the tile (a.k.a. filed or side) on the 'well matrix'. */
public void setTileGeometry(int tileRowsNumber, int tileColumnsNumber)
{
this.tileRowsNumber = tileRowsNumber;
this.tileColumnsNumber = tileColumnsNumber;
}
+ /** Sets detailed description of the images in the dataset. */
public void setImages(List<ImageFileInfo> images)
{
this.images = images;
}
+ /** Sets all channels available in the dataset. */
public void setChannels(List<Channel> channels)
{
this.channels = channels;
@@ -111,8 +114,8 @@ public class ImageDataSetInformation extends DataSetInformation
}
/**
- * Allows to configure various image storage parameters. Set to null if the global configuration
- * of the storage processor should be used.
+ * Allows to configure various image storage parameters. Set to null if the configuration of the
+ * storage processor should be used.
*/
public void setImageStorageConfiguraton(ImageStorageConfiguraton imageStorageConfiguratonOrNull)
{
@@ -130,8 +133,8 @@ public class ImageDataSetInformation extends DataSetInformation
@Override
public String toString()
{
- return "[ dataset code = " + getDataSetCode() + ", tile Rows Number: " + tileRowsNumber
- + ", tile Columns Number: " + tileColumnsNumber + ", channels: "
+ return "[ dataset code: " + super.getDataSetCode() + ", tile Rows Number: "
+ + tileRowsNumber + ", tile Columns Number: " + tileColumnsNumber + ", channels: "
+ CollectionUtils.abbreviate(channels, -1) + ", images: "
+ CollectionUtils.abbreviate(images, 20);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
index fa1fcc9a06921754fcfe44c7d8e6d06005cefe0f..7dde8735f4be60b114029b91cda334299bc99f62 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ImageStorageConfiguraton.java
@@ -54,6 +54,15 @@ public class ImageStorageConfiguraton
this.thumbnailsStorageFormatOrNull = thumbnailsStorageFormatOrNull;
}
+ /**
+ * Convenience method to switch on thumbnails generation with default settings. Overrides the
+ * results of {@link #setThumbnailsStorageFormat(ThumbnailsStorageFormat)}!.
+ */
+ public void switchOnThumbnailsGeneration()
+ {
+ this.thumbnailsStorageFormatOrNull = new ThumbnailsStorageFormat();
+ }
+
public OriginalDataStorageFormat getOriginalDataStorageFormat()
{
return originalDataStorageFormat;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
index 1fab6f760ac8b47be594afd82c57459ca9cc62cf..75c26090baae1b7274ead73fc53f3faf14bd5fba 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v1/ThumbnailsStorageFormat.java
@@ -37,6 +37,14 @@ public class ThumbnailsStorageFormat
private boolean storeCompressed = DEFAULT_COMPRESS_THUMBNAILS;
+ /**
+ * Creates empty object which instructs that the thumbnails should be generated with default
+ * settings. Use setters to change default behaviour (you will probably not have to).
+ */
+ public ThumbnailsStorageFormat()
+ {
+ }
+
public int getMaxWidth()
{
return maxWidth;