diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/HCSImageFileExtractor.java
new file mode 100644
index 0000000000000000000000000000000000000000..0b67c6d41eb7634d848df85da3bd81486e3153cc
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/HCSImageFileExtractor.java
@@ -0,0 +1,109 @@
+/*
+ * 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.genedata;
+
+import java.util.Properties;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.etlserver.HCSImageFileExtractionResult;
+import ch.systemsx.cisd.etlserver.IHCSImageFileAccepter;
+import ch.systemsx.cisd.etlserver.IHCSImageFileExtractor;
+import ch.systemsx.cisd.etlserver.plugins.AbstractHCSImageFileExtractor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor implements IHCSImageFileExtractor
+{
+ public HCSImageFileExtractor(final Properties properties)
+ {
+ super(properties);
+ }
+
+ @Private
+ HCSImageFileExtractor(Geometry wellGeometry)
+ {
+ super(wellGeometry);
+ }
+
+
+ public HCSImageFileExtractionResult process(IDirectory incomingDataSetDirectory,
+ DataSetInformation dataSetInformation, IHCSImageFileAccepter accepter)
+ {
+ assert incomingDataSetDirectory != null;
+ return process(incomingDataSetDirectory.listFiles(null, false), dataSetInformation, accepter);
+ }
+
+ @Override
+ protected String[] tryToSplitIntoTokens(String imageFileName)
+ {
+ String[] tokens = new String[4];
+ int indexOfChannelSeparator = imageFileName.indexOf('-');
+ if (indexOfChannelSeparator < 0)
+ {
+ return null;
+ }
+ tokens[3] = imageFileName.substring(indexOfChannelSeparator + 1);
+ String wellAndTileCoordinates = imageFileName.substring(0, indexOfChannelSeparator);
+ if (wellAndTileCoordinates.length() != 9)
+ {
+ return null;
+ }
+ tokens[1] = wellAndTileCoordinates.substring(0, 6);
+ tokens[2] = wellAndTileCoordinates.substring(6);
+ return tokens;
+ }
+
+ @Override
+ protected int getChannelWavelength(String channel)
+ {
+ try
+ {
+ return Integer.parseInt(channel) + 1;
+ } catch (NumberFormatException ex)
+ {
+ return 0;
+ }
+ }
+
+ @Override
+ protected Location tryGetWellLocation(String wellLocation)
+ {
+ return new Location(1, 1);
+ }
+
+ @Override
+ protected Location tryGetPlateLocation(String plateLocation)
+ {
+ try
+ {
+ int row = Integer.parseInt(plateLocation.substring(0, 3));
+ int column = Integer.parseInt(plateLocation.substring(3));
+ return new Location(row, column);
+ } catch (NumberFormatException ex)
+ {
+ return null;
+ }
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/lmc/HCSImageFileExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/lmc/HCSImageFileExtractor.java
index 2cff4ad2557579c5061a0a8009596b77e1d1908e..2a3cea2a142b6fd21655ed95623621837f0f84cb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/lmc/HCSImageFileExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/lmc/HCSImageFileExtractor.java
@@ -56,14 +56,13 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor impleme
}
@Override
- protected final int getChannelWavelength(final String value)
+ protected final int getChannelWavelength(final String channel)
{
- int channel;
- for (channel = 1; channel <= CHANNEL_NAMES.length; channel++)
+ for (int channelIndex = 1; channelIndex <= CHANNEL_NAMES.length; channelIndex++)
{
- if (value.equalsIgnoreCase(CHANNEL_NAMES[channel - 1]))
+ if (channel.equalsIgnoreCase(CHANNEL_NAMES[channelIndex - 1]))
{
- return channel;
+ return channelIndex;
}
}
return 0; // unknown channel name
@@ -81,11 +80,11 @@ public class HCSImageFileExtractor extends AbstractHCSImageFileExtractor impleme
* </p>
*/
@Override
- protected final Location tryGetWellLocation(final String value)
+ protected final Location tryGetWellLocation(final String wellLocation)
{
try
{
- int tileNumber = Integer.parseInt(value);
+ int tileNumber = Integer.parseInt(wellLocation);
Location letterLoc = Location.tryCreateLocationFromPosition(tileNumber, wellGeometry);
// transpose rows with columns
return new Location(letterLoc.getY(), letterLoc.getX());
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/genedata/HCSImageFileExtractorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/genedata/HCSImageFileExtractorTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..7a1d9d18fce3267f9150a70be1f24b764a26f9ba
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/genedata/HCSImageFileExtractorTest.java
@@ -0,0 +1,115 @@
+/*
+ * 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.genedata;
+
+import java.io.IOException;
+import java.util.Arrays;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.bds.hcs.WellGeometry;
+import ch.systemsx.cisd.bds.storage.IDirectory;
+import ch.systemsx.cisd.bds.storage.IFile;
+import ch.systemsx.cisd.etlserver.HCSImageFileExtractionResult;
+import ch.systemsx.cisd.etlserver.IHCSImageFileAccepter;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Friend(toClasses=HCSImageFileExtractor.class)
+public class HCSImageFileExtractorTest extends AssertJUnit
+{
+ private Mockery context;
+
+ private IHCSImageFileAccepter fileAccepter;
+
+ private HCSImageFileExtractor extractor;
+
+ private IDirectory directory;
+
+ private DataSetInformation dataSetInformation;
+
+ private IFile file1;
+
+ private IFile file2;
+
+ @BeforeMethod
+ public final void setUp() throws IOException
+ {
+ context = new Mockery();
+ directory = context.mock(IDirectory.class);
+ file1 = createImageFileMock("001001000-0.jpeg");
+ file2 = createImageFileMock("002005000-1.jpeg");
+ fileAccepter = context.mock(IHCSImageFileAccepter.class);
+ extractor = new HCSImageFileExtractor(new WellGeometry(1, 1));
+ dataSetInformation = new DataSetInformation();
+ }
+
+ @AfterMethod
+ public final void tearDown()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one do not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void test()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(directory).listFiles(null, false);
+ will(returnValue(Arrays.asList(file1, file2)));
+
+ one(fileAccepter).accept(1, new Location(1, 1), new Location(1, 1), file1);
+ one(fileAccepter).accept(2, new Location(2, 5), new Location(1, 1), file2);
+ }
+ });
+
+ HCSImageFileExtractionResult result = extractor.process(directory, dataSetInformation, fileAccepter);
+
+ assertEquals("[channel1[1=1], channel2[2=2]]", result.getChannels().toString());
+ assertEquals(2, result.getTotalFiles());
+ assertEquals(0, result.getInvalidFiles().size());
+ context.assertIsSatisfied();
+ }
+
+ private IFile createImageFileMock(final String fileName)
+ {
+ final IFile file = context.mock(IFile.class, fileName);
+ context.checking(new Expectations()
+ {
+ {
+ one(file).getPath();
+ will(returnValue(fileName));
+ }
+ });
+ return file;
+ }
+}
+