diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 3aefd8b58d26e8f6442408cfa3d407bf31a0b378..9d6194321e71be37f3cc8beda6f8745ab5e7f226 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -333,14 +333,14 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
}
public InputStream loadImages(String sessionToken, IDatasetIdentifier dataSetIdentifier,
- List<String> wellsOrNull, String channel, ImageSize thumbnailSizeOrNull)
+ List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull)
{
String datasetCode = dataSetIdentifier.getDatasetCode();
File rootDir = getRootDirectoryForDataSet(datasetCode);
IHCSImageDatasetLoader imageAccessor =
HCSImageDatasetLoaderFactory.create(rootDir, datasetCode);
List<PlateImageReference> imageReferences =
- createPlateImageReferences(imageAccessor, dataSetIdentifier, wellsOrNull, channel);
+ createPlateImageReferences(imageAccessor, dataSetIdentifier, wellPositions, channel);
Size size = null;
if (thumbnailSizeOrNull != null)
{
@@ -357,14 +357,14 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private List<PlateImageReference> createPlateImageReferences(
IHCSImageDatasetLoader imageAccessor, IDatasetIdentifier dataSetIdentifier,
- List<String> wellsOrNull, String channel)
+ List<WellPosition> wellPositions, String channel)
{
PlateImageParameters imageParameters = imageAccessor.getImageParameters();
int rowsNum = imageParameters.getRowsNum();
int colsNum = imageParameters.getColsNum();
List<PlateImageReference> imageReferences = new ArrayList<PlateImageReference>();
int numberOfTiles = imageParameters.getTileRowsNum() * imageParameters.getTileColsNum();
- if (wellsOrNull == null || wellsOrNull.isEmpty())
+ if (wellPositions == null || wellPositions.isEmpty())
{
// all wells
for (int i = 1; i <= rowsNum; i++)
@@ -377,69 +377,15 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
}
} else
{
- for (String well : wellsOrNull)
+ for (WellPosition wellPosition : wellPositions)
{
- int indexOfDot = well.indexOf('.');
- if (indexOfDot < 1)
- {
- throw createException("Expecting a '.'", well);
- }
- int row = getAndCheckRowNumber(indexOfDot, well, rowsNum);
- int col = getAndCheckColumnNumber(indexOfDot, well, colsNum);
- addImageReferencesForAllTiles(imageReferences, row, col, channel,
- dataSetIdentifier, numberOfTiles);
+ addImageReferencesForAllTiles(imageReferences, wellPosition.getWellRow(),
+ wellPosition.getWellColumn(), channel, dataSetIdentifier, numberOfTiles);
}
}
return imageReferences;
}
- private int getAndCheckColumnNumber(int indexOfDot, String well, int colsNum)
- {
- int col;
- try
- {
- col = Integer.parseInt(well.substring(indexOfDot + 1));
- } catch (NumberFormatException ex)
- {
- throw createException("String after '.' isn't a number", well);
- }
- if (col < 1)
- {
- throw createException("Column number starts with 1", well);
- }
- if (col > colsNum)
- {
- throw createException("There are only " + colsNum + " columns", well);
- }
- return col;
- }
-
- private int getAndCheckRowNumber(int indexOfDot, String well, int rowsNum)
- {
- int row;
- try
- {
- row = Integer.parseInt(well.substring(0, indexOfDot));
- } catch (NumberFormatException ex)
- {
- throw createException("String before '.' isn't a number", well);
- }
- if (row < 1)
- {
- throw createException("Row number starts with 1", well);
- }
- if (row > rowsNum)
- {
- throw createException("There are only " + rowsNum + " rows", well);
- }
- return row;
- }
-
- private UserFailureException createException(String description, String well)
- {
- return new UserFailureException("Invalid well description: " + description + ": " + well);
- }
-
private void addImageReferencesForAllTiles(List<PlateImageReference> imageReferences,
int wellRow, int wellColumn, String channel, IDatasetIdentifier dataset,
int numberOfTiles)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
index 7f9076fda7e87d7392bff31d696a54a5ac509c66..bb1395d28636340ee0eb52f66896e8f74ed489ad 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
@@ -33,6 +33,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDataset
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
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;
/**
* Public DSS API for screening. Since version 1.2 features are no longer identified by a name but
@@ -143,11 +144,28 @@ public interface IDssServiceRpcScreening extends IRpcService
public InputStream loadImages(
String sessionToken,
@AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<PlateImageReference> imageReferences);
-
+
+ /**
+ * Provide images for a specified data set, a list of well positions (empty list means all
+ * wells), a channel, and an optional thumb nail size. Images of all tiles are delivered. If
+ * thumb nail size isn't specified the original image is delivered otherwise a thumb nail image
+ * with same aspect ratio as the original image but which fits into specified size will be
+ * delivered.
+ * <p>
+ * The result is encoded into one stream, which consist of multiple blocks in a format:
+ * (<block-size><block-of-bytes>)*, where block-size is the block size in bytes encoded as one
+ * long number. The number of blocks is equal to the number of specified references and the
+ * order of blocks corresponds to the order of image references. The images will be converted to
+ * PNG format before being shipped.
+ *
+ * @since 1.4
+ */
+ @MinimalMinorVersion(4)
+ @DataSetAccessGuard
public InputStream loadImages(
String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
- List<String> wellsOrNull, String channel, ImageSize thumbnailSizeOrNull);
+ @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
+ List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull);
/**
* For a given set of image data sets, provide all image channels that have been acquired and
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/SingleDataSetIdentifierPredicate.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/SingleDataSetIdentifierPredicate.java
new file mode 100644
index 0000000000000000000000000000000000000000..ecdad6d7f1bcfa71b8d468c3e11726bd2fef66d0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/SingleDataSetIdentifierPredicate.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright 2010 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.screening.shared.api.v1;
+
+import java.util.Collections;
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.authorization.IAuthorizationGuardPredicate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SingleDataSetIdentifierPredicate implements
+ IAuthorizationGuardPredicate<IDssServiceRpcScreeningInternal, IDatasetIdentifier>
+
+{
+ private static final DatasetIdentifierPredicate PREDICATE = new DatasetIdentifierPredicate();
+
+ public Status evaluate(IDssServiceRpcScreeningInternal receiver, String sessionToken,
+ IDatasetIdentifier datasetIdentifier) throws UserFailureException
+ {
+ return PREDICATE.evaluate(receiver, sessionToken,
+ Collections.singletonList(datasetIdentifier));
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index dfdb77b9220ecb19174985bae896b48759de2dbe..2cb44013e12003fa2d9e1b44d547ad3a7710b0ff 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -38,6 +38,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifi
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
* A client side facade of openBIS and Datastore Server API. Since version 1.2 of the API features
@@ -250,8 +251,18 @@ public interface IScreeningOpenbisServiceFacade
IImageOutputStreamProvider outputStreamProvider, boolean convertToPNG)
throws IOException;
+ /**
+ * Loads original images or thumbnails for a specified data set, a list of well positions (empty
+ * list means all wells), a channel, and an optional thumb nail size. Images of all tiles are
+ * delivered. If thumb nail size isn't specified the original image is delivered otherwise a
+ * thumb nail image with same aspect ratio as the original image but which fits into specified
+ * size will be delivered.
+ *
+ * @return a list of byte arrays where each array contains a PNG encoded image.
+ */
public List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier,
- List<String> wellsOrNull, String channel, ImageSize thumbnailSizeOrNull) throws IOException;
+ List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull)
+ throws IOException;
/**
* For a given set of image data sets, provide all image channels that have been acquired and
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ImageViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ImageViewer.java
index c6f3378bf3ee20db94697ae6ffa25164c0078fff..a9ecceeef0ab053c18575f17c432c9be156d4c75 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ImageViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ImageViewer.java
@@ -31,8 +31,10 @@ import javax.swing.JPanel;
import org.apache.commons.lang.StringUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DataSetCodeAndWellPositions;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
/**
@@ -42,67 +44,46 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
*/
public class ImageViewer
{
-
- private static final class DataSetAndWells
- {
- private final String dataSetCode;
- private final List<String> wells = new ArrayList<String>();
-
- DataSetAndWells(String description)
- {
- int indexOfColon = description.indexOf(':');
- if (indexOfColon < 0)
- {
- dataSetCode = description;
- } else
- {
- dataSetCode = description.substring(0, indexOfColon);
- wells.addAll(Arrays.asList(StringUtils.split(description.substring(indexOfColon + 1))));
- }
- }
-
- public final String getDataSetCode()
- {
- return dataSetCode;
- }
-
- public final List<String> getWells()
- {
- return wells;
- }
- }
-
public static void main(String[] args)
{
String serviceURL = args[0];
String sessionToken = args[1];
long experimentID = Long.parseLong(args[2]);
String channel = args[3];
- Map<String, DataSetAndWells> dataSets = new HashMap<String, DataSetAndWells>();
+ Map<String, DataSetCodeAndWellPositions> dataSets =
+ new HashMap<String, DataSetCodeAndWellPositions>();
for (int i = 4; i < args.length; i++)
{
- DataSetAndWells dataSetAndWells = new DataSetAndWells(args[i]);
- dataSets.put(dataSetAndWells.getDataSetCode(), dataSetAndWells);
+ DataSetCodeAndWellPositions dw = new DataSetCodeAndWellPositions(args[i]);
+ dataSets.put(dw.getDataSetCode(), dw);
}
+
JFrame frame = new JFrame("Image Viewer");
frame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
Container contentPane = frame.getContentPane();
JPanel content = new JPanel();
content.setLayout(new BoxLayout(content, BoxLayout.Y_AXIS));
contentPane.add(content);
- ImageSize thumbnailSize = new ImageSize(200, 160);
+ ImageSize thumbnailSize = new ImageSize(100, 60);
try
{
- IScreeningOpenbisServiceFacade facade = ScreeningOpenbisServiceFacadeFactory.tryCreate(sessionToken, serviceURL);
- List<IDatasetIdentifier> dsIdentifier = facade.getDatasetIdentifiers(new ArrayList<String>(dataSets.keySet()));
+ IScreeningOpenbisServiceFacade facade =
+ ScreeningOpenbisServiceFacadeFactory.tryCreate(sessionToken, serviceURL);
+ List<IDatasetIdentifier> dsIdentifier =
+ facade.getDatasetIdentifiers(new ArrayList<String>(dataSets.keySet()));
for (IDatasetIdentifier identifier : dsIdentifier)
{
+ content.add(new JLabel("Images for data set " + identifier.getDatasetCode()));
+ JPanel imagePanel = new JPanel();
+ imagePanel.setLayout(new BoxLayout(imagePanel, BoxLayout.X_AXIS));
+ content.add(imagePanel);
+ List<WellPosition> wellPositions =
+ dataSets.get(identifier.getDatasetCode()).getWellPositions();
List<byte[]> imageBytes =
- facade.loadImages(identifier, dataSets.get(identifier.getDatasetCode())
- .getWells(), channel, thumbnailSize);
+ facade.loadImages(identifier, wellPositions, channel, thumbnailSize);
for (byte[] bytes : imageBytes)
{
- content.add(new JLabel(new ImageIcon(bytes)));
+ imagePanel.add(new JLabel(new ImageIcon(bytes)));
}
}
} catch (Exception ex)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
index 0fa30a1598d3f1cab04313d1481fee79aa2d8889..fab871c1ff6f16077f10dec0a6e4e5a9e0d7bcf8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
@@ -16,11 +16,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.api.v1;
-import java.awt.Component;
-import java.awt.Graphics;
-import java.awt.image.BufferedImage;
import java.io.BufferedOutputStream;
-import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
@@ -37,12 +33,6 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
-import javax.imageio.ImageIO;
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-
import org.apache.log4j.PropertyConfigurator;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
@@ -55,7 +45,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdent
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
@@ -70,7 +59,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellPosition;
*/
public class ScreeningClientApiTest
{
- public static void main(String[] args) throws Exception
+ public static void main(String[] args) throws IOException
{
if (args.length != 3)
{
@@ -94,24 +83,6 @@ public class ScreeningClientApiTest
System.exit(1);
return;
}
- IDatasetIdentifier dataSetID = facade.getDatasetIdentifiers(Arrays.asList("20101006020318852-10")).get(0);
- List<byte[]> images = facade.loadImages(dataSetID, Arrays.asList("1.3"), "DAPI", new ImageSize(100, 60));
- for (int i = 0; i < images.size(); i++)
- {
- byte[] imageBytes = images.get(i);
- BufferedImage image = ImageIO.read(new ByteArrayInputStream(imageBytes));
- JFrame frame = new JFrame("image " + i);
- frame.getContentPane().add(new JLabel(new ImageIcon(image)));
- frame.pack();
- frame.setLocation(10 * i, 10 * i);
- frame.setVisible(true);
-
- System.out.println(image.getWidth()+"x"+image.getHeight());
- }
- Thread.sleep(10000);
- System.exit(0);
-
-
List<ExperimentIdentifier> experiments = facade.listExperiments();
print("Experiments: " + experiments);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index 6d45d79f1ba50dde7dfc6b1fdcffc4ec73a27b49..47ccad7a181a161f110f71ed7b9ee2d1a6000adc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -540,14 +540,15 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
}
}
- public List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier, List<String> wellsOrNull,
- String channel, ImageSize thumbnailSizeOrNull) throws IOException
+ public List<byte[]> loadImages(IDatasetIdentifier dataSetIdentifier,
+ List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull)
+ throws IOException
{
DssServiceRpcScreeningHolder dssServiceHolder =
dssServiceCache.createDssService(dataSetIdentifier.getDatastoreServerUrl());
InputStream stream =
dssServiceHolder.getService().loadImages(sessionToken, dataSetIdentifier,
- wellsOrNull, channel, thumbnailSizeOrNull);
+ wellPositions, channel, thumbnailSizeOrNull);
ConcatenatedFileOutputStreamWriter imagesWriter =
new ConcatenatedFileOutputStreamWriter(stream);
List<byte[]> result = new ArrayList<byte[]>();
@@ -560,7 +561,6 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
{
result.add(outputStream.toByteArray());
}
- System.out.println("size "+ size);
} while (size >= 0);
return result;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DataSetCodeAndWellPositions.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DataSetCodeAndWellPositions.java
new file mode 100644
index 0000000000000000000000000000000000000000..8fd7171db531c1416dc677f97cb0a41128ed9a36
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DataSetCodeAndWellPositions.java
@@ -0,0 +1,78 @@
+/*
+ * Copyright 2010 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.api.v1.dto;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * Helper class for parsing strings containing data set code and well positions. Two forms are
+ * accepted:
+ * <pre>
+ * <data set code>
+ * </pre>
+ * and
+ * <pre>
+ * <data set code>:<row 1>.<col 1> <row 2>.<col 2> ...
+ * </pre>
+ *
+ * @since 1.4
+ * @author Franz-Josef Elmer
+ */
+public class DataSetCodeAndWellPositions
+{
+ private final String dataSetCode;
+ private final List<WellPosition> wellPositions = new ArrayList<WellPosition>();
+
+ /**
+ * Creates an instane from the specified description.
+ *
+ * @throws IllegalArgumentException in case of parsing error.
+ */
+ public DataSetCodeAndWellPositions(String dataSetCodeAndWellPositionsDescription)
+ {
+ int indexOfColon = dataSetCodeAndWellPositionsDescription.indexOf(':');
+ if (indexOfColon < 0)
+ {
+ dataSetCode = dataSetCodeAndWellPositionsDescription;
+ } else
+ {
+ dataSetCode = dataSetCodeAndWellPositionsDescription.substring(0, indexOfColon);
+ wellPositions.addAll(WellPosition
+ .parseWellPositions(dataSetCodeAndWellPositionsDescription
+ .substring(indexOfColon + 1)));
+ }
+ }
+
+ /**
+ * Returns the data set code.
+ */
+ public final String getDataSetCode()
+ {
+ return dataSetCode;
+ }
+
+ /**
+ * Returns the well positions. An empty list is returned in case of missing well position
+ * descriptions.
+ */
+ public final List<WellPosition> getWellPositions()
+ {
+ return wellPositions;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageSize.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageSize.java
index 8afed751f09a222c35953efb28590558d82c0d98..90a2db667086a3d61ee1fd575da11ffa70d6695a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageSize.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageSize.java
@@ -21,6 +21,7 @@ import java.io.Serializable;
/**
* Width and height of an image.
*
+ * @since 1.4
* @author Franz-Josef Elmer
*/
public class ImageSize implements Serializable
@@ -29,6 +30,9 @@ public class ImageSize implements Serializable
private final int width;
private final int height;
+ /**
+ * Creates an instance for specified width and height.
+ */
public ImageSize(int width, int height)
{
this.width = width;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellPosition.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellPosition.java
index 54bd1d5f66395f403b0c06c5726dc17d7fdfac8f..d970275dcb424c05206d716fd407358e8cbfacb0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellPosition.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellPosition.java
@@ -1,6 +1,9 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto;
import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.StringTokenizer;
/**
* Identifier of a well on a screening plate, contains row and column number.
@@ -11,6 +14,83 @@ public class WellPosition implements Serializable
{
private static final long serialVersionUID = 1L;
+ /**
+ * Parses a white-space separated list of well position descriptions. A well position
+ * description is of the form
+ * <code><it><row number></it>.<it><column number></it></code>.
+ *
+ * @throws IllegalArgumentException in case of parsing error.
+ * @since 1.4
+ */
+ public static List<WellPosition> parseWellPositions(String wellPositionDescriptions)
+ {
+ StringTokenizer tokenizer = new StringTokenizer(wellPositionDescriptions);
+ List<WellPosition> positions = new ArrayList<WellPosition>();
+ while (tokenizer.hasMoreTokens())
+ {
+ positions.add(parseWellPosition(tokenizer.nextToken()));
+ }
+ return positions;
+ }
+
+ /**
+ * Parses a well position description of the form
+ * <code><it><row number></it>.<it><column number></it></code>.
+ *
+ * @throws IllegalArgumentException in case of parsing error.
+ * @since 1.4
+ */
+ public static WellPosition parseWellPosition(String wellDescription)
+ {
+ int indexOfDot = wellDescription.indexOf('.');
+ if (indexOfDot < 1)
+ {
+ throw createException("Expecting a '.' in well description", wellDescription);
+ }
+ int row = getAndCheckRowNumber(indexOfDot, wellDescription);
+ int col = getAndCheckColumnNumber(indexOfDot, wellDescription);
+ return new WellPosition(row, col);
+ }
+
+ private static int getAndCheckColumnNumber(int indexOfDot, String well)
+ {
+ int col;
+ try
+ {
+ col = Integer.parseInt(well.substring(indexOfDot + 1));
+ } catch (NumberFormatException ex)
+ {
+ throw createException("String after '.' isn't a number", well);
+ }
+ if (col < 1)
+ {
+ throw createException("First column < 1", well);
+ }
+ return col;
+ }
+
+ private static int getAndCheckRowNumber(int indexOfDot, String well)
+ {
+ int row;
+ try
+ {
+ row = Integer.parseInt(well.substring(0, indexOfDot));
+ } catch (NumberFormatException ex)
+ {
+ throw createException("String before '.' isn't a number", well);
+ }
+ if (row < 1)
+ {
+ throw createException("First row < 1", well);
+ }
+ return row;
+ }
+
+ private static IllegalArgumentException createException(String description, String well)
+ {
+ return new IllegalArgumentException("Invalid well description: " + description + ": " + well);
+ }
+
private final int wellRow, wellColumn;
public WellPosition(int wellRow, int wellColumn)
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellPositionTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellPositionTest.java
index c1b3a74ea956869e603d0710cd35a7f24d370d6f..3318f08f1009905d2017c0f87b466327c35f4f67 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellPositionTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellPositionTest.java
@@ -32,4 +32,78 @@ public class WellPositionTest extends AssertJUnit
assertEquals(pos1, pos2);
assertEquals(pos1.hashCode(), pos2.hashCode());
}
+
+ @Test
+ public void testParseWellPositions()
+ {
+ assertEquals(0, WellPosition.parseWellPositions("").size());
+ assertEquals("[[1, 2]]", WellPosition.parseWellPositions("1.2").toString());
+ assertEquals("[[1, 2], [2, 3], [3, 4], [4, 5]]",
+ WellPosition.parseWellPositions("1.2 2.3 3.4\t4.5").toString());
+ }
+
+ @Test
+ public void testParseWellPoistionWithMissingDot()
+ {
+ try
+ {
+ WellPosition.parseWellPosition("A03");
+ fail("IllegalArgumentException expected");
+ } catch (IllegalArgumentException ex)
+ {
+ assertEquals("Invalid well description: Expecting a '.' in well description: A03", ex.getMessage());
+ }
+ }
+
+ @Test
+ public void testParseWellPoistionWithRowIsNotANumber()
+ {
+ try
+ {
+ WellPosition.parseWellPosition("a.1");
+ fail("IllegalArgumentException expected");
+ } catch (IllegalArgumentException ex)
+ {
+ assertEquals("Invalid well description: String before '.' isn't a number: a.1", ex.getMessage());
+ }
+ }
+
+ @Test
+ public void testParseWellPoistionWithRowIsLessThanOne()
+ {
+ try
+ {
+ WellPosition.parseWellPosition("0.1");
+ fail("IllegalArgumentException expected");
+ } catch (IllegalArgumentException ex)
+ {
+ assertEquals("Invalid well description: First row < 1: 0.1", ex.getMessage());
+ }
+ }
+
+ @Test
+ public void testParseWellPoistionWithColumnIsNotANumber()
+ {
+ try
+ {
+ WellPosition.parseWellPosition("1.a");
+ fail("IllegalArgumentException expected");
+ } catch (IllegalArgumentException ex)
+ {
+ assertEquals("Invalid well description: String after '.' isn't a number: 1.a", ex.getMessage());
+ }
+ }
+
+ @Test
+ public void testParseWellPoistionWithColumnIsLessThanOne()
+ {
+ try
+ {
+ WellPosition.parseWellPosition("1.0");
+ fail("IllegalArgumentException expected");
+ } catch (IllegalArgumentException ex)
+ {
+ assertEquals("Invalid well description: First column < 1: 1.0", ex.getMessage());
+ }
+ }
}