diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
index 2c9be62270839a25dff372619014a83c227b4da1..c52c9f02d36ef1d1d5f1478a9d95cc425dd72d22 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
@@ -27,9 +27,9 @@ import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
-import java.util.Map.Entry;
import org.apache.commons.lang.StringUtils;
import org.apache.log4j.Logger;
@@ -92,8 +92,8 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
static final String FILE_TYPE = ".srf";
- private final static Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, FlowLaneFeeder.class);
+ private final static Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+ FlowLaneFeeder.class);
private final IEncapsulatedOpenBISService service;
@@ -153,11 +153,11 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
String flowcellID = originalData.getName();
List<File> files = new ArrayList<File>();
FileUtilities.findFiles(originalData, files, createSrfFileFilter());
- if (files.size() < flowLaneSampleMap.size())
- {
- throw new EnvironmentFailureException("Only " + files.size()
- + " flow lane files found instead of " + flowLaneSampleMap.size() + ".");
- }
+ // if (files.size() < flowLaneSampleMap.size())
+ // {
+ // throw new EnvironmentFailureException("Only " + files.size()
+ // + " flow lane files found instead of " + flowLaneSampleMap.size() + ".");
+ // }
Set<String> processedFlowLanes = new LinkedHashSet<String>();
for (File file : files)
{
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
index 139e4310d4d53ac2605a434297857738b7eeb46b..d96c5c46b2198f51b8d09f1b2b14425483ad16a0 100644
--- 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
@@ -25,6 +25,7 @@ import javax.xml.bind.annotation.XmlElement;
* <clusterCountRaw>158466917</clusterCountRaw>
* <yield>3556528488</yield>
* </ChipResultsSummary>
+ * <Software>CASAVA-1.6.0</Software>
* </pre>
*
* @author Manuel Kohler
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
index bfc5917d9130de8859e9349e05b5d9eff2e2543b..e413f57456d7afe31cda5145edf3cacdd229c4e1 100644
--- 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
@@ -28,6 +28,8 @@ import javax.xml.bind.annotation.XmlRootElement;
* <yield>3556528488</yield>
* </ChipResultsSummary>
* ...
+ * <Software>CASAVA-1.6.0</Software>
+ * ...
* <Summary>
* </pre>
*
@@ -38,6 +40,8 @@ class IlluminaSummary
{
private ChipResultsSummary chipResultsSummary;
+ private String Software;
+
@XmlElement(name = "ChipResultsSummary")
public ChipResultsSummary getChipResultsSummary()
{
@@ -49,4 +53,14 @@ class IlluminaSummary
this.chipResultsSummary = chipResultsSummary;
}
+ @XmlElement(name = "Software")
+ public String getSoftware()
+ {
+ return Software;
+ }
+
+ public void setSoftware(String software)
+ {
+ Software = software;
+ }
}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java
index 634de2c5f80f021e21def1810a1dc0880ab4c54d..011daa0a753530edb6a891c368a245be969f9297 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/IlluminaSummaryReportingPlugin.java
@@ -58,6 +58,7 @@ public class IlluminaSummaryReportingPlugin extends AbstractDatastorePlugin impl
builder.addHeader("Clusters");
builder.addHeader("Clusters (PF)");
builder.addHeader("Yield (kbases)");
+ builder.addHeader("Software");
for (DatasetDescription dataset : datasets)
{
File originalData = getDataSubDir(dataset);
@@ -94,12 +95,20 @@ public class IlluminaSummaryReportingPlugin extends AbstractDatastorePlugin impl
DatasetDescription dataset, IlluminaSummary summary)
{
ChipResultsSummary chipResultSummary = summary.getChipResultsSummary();
+
+ String software_version = summary.getSoftware();
+ if (software_version == null)
+ {
+ software_version = "Not available";
+ }
+
List<ISerializableComparable> row =
Arrays.<ISerializableComparable> asList(
new StringTableCell(dataset.getSampleCode()), new IntegerTableCell(
- chipResultSummary.getClusterCountPF()), new IntegerTableCell(
chipResultSummary.getClusterCountRaw()), new IntegerTableCell(
- chipResultSummary.getYield()));
+ chipResultSummary.getClusterCountPF()), new IntegerTableCell(
+ chipResultSummary.getYield() / 1000), new StringTableCell(
+ software_version));
builder.addRow(row);
}
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
index cdd1ea121f8f65ac755f4c83e9b42b1f617b3d4d..b7aa0a88721814f03901909ea31b9470a7bcc648 100644
--- 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
@@ -39,26 +39,33 @@ public class IlluminaSummaryXMLLoaderTest extends AbstractFileSystemTestCase
assertEquals(new Long(98792458L), chipResultsSummary.getClusterCountPF());
assertEquals(new Long(158466917L), chipResultsSummary.getClusterCountRaw());
assertEquals(new Long(3556528488L), chipResultsSummary.getYield());
+ if (summary.getSoftware() == null)
+ {
+ assertEquals(null, summary.getSoftware());
+ } else
+ {
+ assertEquals("CASAVA-1.6.0", summary.getSoftware());
+ }
}
- 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>";
+ 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/> "
+ // + " <Software>CASAVA-1.6.0</Software> "
+ + "</Summary>";
}