[LMS-1634] xml beans and JAXB stuff

SVN: 16981

deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/ChipResultsSummary.java

+/*
+ * 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>
+ *   &lt;ChipResultsSummary&gt;
+ *     &lt;clusterCountPF&gt;98792458&lt;/clusterCountPF&gt;
+ *     &lt;clusterCountRaw&gt;158466917&lt;/clusterCountRaw&gt;
+ *     &lt;yield&gt;3556528488&lt;/yield&gt;
+ *   &lt;/ChipResultsSummary&gt;
+ * </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;
+    }
+
+}

deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummary.java

+/*
+ * 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>
+ *   &lt;Summary&gt;
+ *     &lt;ChipResultsSummary&gt;
+ *       &lt;clusterCountPF&gt;98792458&lt;/clusterCountPF&gt;
+ *       &lt;clusterCountRaw&gt;158466917&lt;/clusterCountRaw&gt;
+ *       &lt;yield&gt;3556528488&lt;/yield&gt;
+ *     &lt;/ChipResultsSummary&gt;
+ *     ...
+ *   &lt;Summary&gt;
+ * </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;
+    }
+
+}

deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoader.java

+/*
+ * 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);
+        }
+    }
+
+}

deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryXMLLoaderTest.java

+/*
+ * 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>";
+}