diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipResultsSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipResultsSummary.java
new file mode 100644
index 0000000000000000000000000000000000000000..cf07fd33f048cba6d8831455aa7eb92825de3ccf
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipResultsSummary.java
@@ -0,0 +1,74 @@
+/*
+ * 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * <pre>
+ * <ChipResultsSummary>
+ * <clusterCountPF>98792458</clusterCountPF>
+ * <clusterCountRaw>158466917</clusterCountRaw>
+ * <yield>3556528488</yield>
+ * </ChipResultsSummary>
+ * </pre>
+ *
+ * @author Manuel Kohler
+ */
+// @XmlType
+public class ChipResultsSummary
+{
+ private String clusterCountPF;
+
+ private String clusterCountRaw;
+
+ private String yield;
+
+ @XmlElement
+ public String getClusterCountPF()
+ {
+ return clusterCountPF;
+ }
+
+ public void setClusterCountPF(String clusterCountPF)
+ {
+ this.clusterCountPF = clusterCountPF;
+ }
+
+ @XmlElement
+ public String getClusterCountRaw()
+ {
+ return clusterCountRaw;
+ }
+
+ public void setClusterCountRaw(String clusterCountRaw)
+ {
+ this.clusterCountRaw = clusterCountRaw;
+ }
+
+ @XmlElement
+ public String getYield()
+ {
+ return yield;
+ }
+
+ public void setYield(String yield)
+ {
+ this.yield = yield;
+ }
+
+}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java
new file mode 100644
index 0000000000000000000000000000000000000000..c9e801b7cb0b51fcf8c8c430df5e6b41a2f18963
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java
@@ -0,0 +1,53 @@
+/*
+ * 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+
+/**
+ * <pre>
+ * <Summary>
+ * <ChipResultsSummary>
+ * <clusterCountPF>98792458</clusterCountPF>
+ * <clusterCountRaw>158466917</clusterCountRaw>
+ * <yield>3556528488</yield>
+ * </ChipResultsSummary>
+ * ...
+ * <Summary>
+ * </pre>
+ *
+ * @author Manuel Kohler
+ */
+@XmlRootElement(name = "Summary")
+// @XmlType
+public class IlluminaSummary
+{
+ private ChipResultsSummary chipResultsSummary;
+
+ @XmlElement(name = "ChipResultsSummary")
+ public ChipResultsSummary getChipResultsSummary()
+ {
+ return chipResultsSummary;
+ }
+
+ public void setChipResultsSummary(ChipResultsSummary chipResultsSummary)
+ {
+ this.chipResultsSummary = chipResultsSummary;
+ }
+
+}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoader.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoader.java
new file mode 100644
index 0000000000000000000000000000000000000000..4128e188937c5f1f3a698f3895f290b9b0821603
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoader.java
@@ -0,0 +1,94 @@
+/*
+ * Copyright 2009 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStream;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.Unmarshaller;
+import javax.xml.bind.UnmarshallerHandler;
+
+import org.xml.sax.EntityResolver;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.utilities.XMLInfraStructure;
+
+/**
+ * Loader of Illumina summary XML file.
+ *
+ * @author Manuel Kohler
+ */
+class IlluminaSummaryXMLLoader
+{
+
+ private final Unmarshaller unmarshaller;
+
+ private final XMLInfraStructure xmlInfraStructure;
+
+ IlluminaSummaryXMLLoader(boolean validating)
+ {
+ try
+ {
+ JAXBContext context = JAXBContext.newInstance(IlluminaSummary.class);
+ unmarshaller = context.createUnmarshaller();
+ xmlInfraStructure = new XMLInfraStructure(validating);
+ xmlInfraStructure.setEntityResolver(new EntityResolver()
+ {
+ public InputSource resolveEntity(String publicId, String systemId)
+ throws SAXException, IOException
+ {
+ String schemaVersion = systemId.substring(systemId.lastIndexOf('/'));
+ String resource =
+ "/"
+ + IlluminaSummaryXMLLoader.class.getPackage().getName()
+ .replace('.', '/') + schemaVersion;
+ InputStream inputStream =
+ IlluminaSummaryXMLLoader.class.getResourceAsStream(resource);
+ return inputStream == null ? null : new InputSource(inputStream);
+ }
+ });
+
+ } catch (Exception ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
+ IlluminaSummary readSummaryXML(File dataSet)
+ {
+ try
+ {
+ UnmarshallerHandler unmarshallerHandler = unmarshaller.getUnmarshallerHandler();
+ xmlInfraStructure.parse(new FileReader(dataSet), unmarshallerHandler);
+ Object object = unmarshallerHandler.getResult();
+ if (object instanceof IlluminaSummary == false)
+ {
+ throw new IllegalArgumentException("Wrong type: " + object);
+ }
+ return (IlluminaSummary) object;
+ } catch (Exception ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
+}
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..eb8f0494dad880ec468bc46dcf41039c9eb70eef
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright 2009 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import java.io.File;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class IlluminaSummaryXMLLoaderTest extends AbstractFileSystemTestCase
+{
+ @Test
+ public void test()
+ {
+ File file = new File(workingDirectory, "test.xml");
+ FileUtilities.writeToFile(file, EXAMPLE);
+ IlluminaSummary summary = new IlluminaSummaryXMLLoader(false).readSummaryXML(file);
+
+ ChipResultsSummary chipResultsSummary = summary.getChipResultsSummary();
+ assertEquals("98792458", chipResultsSummary.getClusterCountPF());
+ assertEquals("158466917", chipResultsSummary.getClusterCountRaw());
+ assertEquals("3556528488", chipResultsSummary.getYield());
+ }
+
+ protected static final String EXAMPLE = "<?xml version='1.0' ?>\n "
+ + "<?xml-stylesheet type='text/xsl' href='Summary.xsl' ?>\n "
+ + "<Summary> "
+ + " <ChipResultsSummary> "
+ + " <clusterCountPF>98792458</clusterCountPF> "
+ + " <clusterCountRaw>158466917</clusterCountRaw> "
+ + " <yield>3556528488</yield> "
+ + " </ChipResultsSummary> "
+ + " <ChipSummary> "
+ + " <ChipID>unknown</ChipID> "
+ + " <Machine>HWI-EAS264</Machine> "
+ + " <RunFolder>090916_42R0CAAXX</RunFolder> "
+ + " </ChipSummary> "
+ + " <Date>Tue Oct 20 18:15:43 2009</Date> "
+ + " <ExpandedLaneSummary/> "
+ + " <LaneParameterSummary/> "
+ + " <LaneResultsSummary/> "
+ + " <TileErrorsByLane/> "
+ + "</Summary>";
+}