From d55a8a196020bf03a9bd0d974df1a89bbf61c238 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Tue, 19 Oct 2010 09:27:46 +0000
Subject: [PATCH] just take the first GERALD die which you found, just a bit
more robust
SVN: 18343
---
.../IlluminaSummaryReportingPlugin.java | 41 ++++++++-----------
1 file changed, 17 insertions(+), 24 deletions(-)
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 e66d9996558..5e576669063 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
@@ -61,7 +61,7 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
private static final String[] PROPERTIES =
{ "GENOME_ANALYZER", "END_TYPE", "ILLUMINA_PIPELINE_VERSION",
- "CYCLES_REQUESTED_BY_CUSTOMER" };
+ "CYCLES_REQUESTED_BY_CUSTOMER" };
public IlluminaSummaryReportingPlugin(Properties properties, File storeRoot)
{
@@ -94,27 +94,20 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
// set the directory containing the Summary.xml
File childDirectory =
- new File(originalData, dataset.getSampleCode()
- + DATA_INTENSITIES_BASE_CALLS_PATH);
+ new File(originalData, dataset.getSampleCode()
+ + DATA_INTENSITIES_BASE_CALLS_PATH);
File[] files = childDirectory.listFiles(new FileFilter()
- {
- public boolean accept(File file)
{
- return file.isDirectory() && file.getName().startsWith(GERALD_DIR);
- }
- });
-
- System.out.println(files[0]);
- if (files.length == 1)
- {
- File geraldDir = files[0];
- File summaryFile = new File(geraldDir, SUMMARY_FILE_NAME);
- describe(builder, dataset, summaryFile);
- } else
- {
- // throw new EnvironmentFailureException(String.format("More than one ..."));
- // removed because it doesn't help, so just do nothing
- }
+ public boolean accept(File file)
+ {
+ return file.isDirectory() && file.getName().startsWith(GERALD_DIR);
+ }
+ });
+
+ // just take the first GERALD folder which was found
+ File geraldDir = files[0];
+ File summaryFile = new File(geraldDir, SUMMARY_FILE_NAME);
+ describe(builder, dataset, summaryFile);
}
return builder.getTableModel();
}
@@ -194,10 +187,10 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
String sampleCode = dataset.getSampleCode();
String databaseInstanceCode = dataset.getDatabaseInstanceCode();
SampleIdentifier sampleIdentifier =
- new SampleIdentifier(new SpaceIdentifier(databaseInstanceCode, spaceCode),
- sampleCode);
+ new SampleIdentifier(new SpaceIdentifier(databaseInstanceCode, spaceCode),
+ sampleCode);
Sample sampleOrNull =
- ServiceProvider.getOpenBISService().tryGetSampleWithExperiment(sampleIdentifier);
+ ServiceProvider.getOpenBISService().tryGetSampleWithExperiment(sampleIdentifier);
if (sampleOrNull == null)
{
throw new EnvironmentFailureException(String.format(
@@ -220,7 +213,7 @@ public class IlluminaSummaryReportingPlugin extends AbstractTableModelReportingP
{
// we use one instance
private static JaxbXmlParser<IlluminaSummary> PARSER_INSTANCE =
- new JaxbXmlParser<IlluminaSummary>(IlluminaSummary.class, false);
+ new JaxbXmlParser<IlluminaSummary>(IlluminaSummary.class, false);
public static IlluminaSummary readSummaryXML(File summaryXml)
{
--
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