From de5991b3ddbb130759de6b809587ca801ac15888 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 8 Oct 2009 09:21:20 +0000
Subject: [PATCH] LMS-1219 add .MARKER_IS_FINISHED file
SVN: 12879
---
.../ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java | 12 ++++++++++--
.../ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java | 9 ++++++---
2 files changed, 16 insertions(+), 5 deletions(-)
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
index a9be637dad6..144306f2bb8 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
@@ -24,6 +24,7 @@ import java.util.List;
import java.util.Map;
import java.util.Properties;
+import ch.systemsx.cisd.common.Constants;
import ch.systemsx.cisd.common.TimingParameters;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
@@ -82,7 +83,8 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
{
String flowLine = extractFlowLine(file);
File dropBox = createDropBoxFile(flowLine);
- File flowLineDataSet = new File(dropBox, flowcellID + "_" + flowLine);
+ String fileName = flowcellID + "_" + flowLine;
+ File flowLineDataSet = new File(dropBox, fileName);
if (flowLineDataSet.exists())
{
throw new EnvironmentFailureException("There is already a data set for flow line "
@@ -103,6 +105,9 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
+ file.getAbsolutePath() + "' in folder '"
+ flowLineDataSet.getAbsolutePath() + "'.");
}
+ File markerFile = new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName);
+ flowLineDataSets.add(markerFile);
+ FileUtilities.writeToFile(markerFile, "");
}
}
@@ -198,7 +203,10 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
{
for (File file : flowLineDataSets)
{
- fileOperations.deleteRecursively(file);
+ if (file.exists())
+ {
+ fileOperations.deleteRecursively(file);
+ }
}
}
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
index 20698af13e3..b91f946efd5 100644
--- a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
@@ -31,6 +31,7 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.Constants;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.test.AssertionUtil;
@@ -186,8 +187,8 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
public void testUndoLastOperation()
{
testHappyCase();
- assertEquals(1, new File(workingDirectory, DROP_BOX_PREFIX + "1").list().length);
- assertEquals(1, new File(workingDirectory, DROP_BOX_PREFIX + "2").list().length);
+ assertEquals(2, new File(workingDirectory, DROP_BOX_PREFIX + "1").list().length);
+ assertEquals(2, new File(workingDirectory, DROP_BOX_PREFIX + "2").list().length);
flowLineFeeder.undoLastOperation();
@@ -245,7 +246,8 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
private void checkFlowLineDataSet(File originalFlowLine, String flowLineNumber)
{
File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLineNumber);
- File ds = new File(dropBox, "abc_" + flowLineNumber);
+ String fileName = "abc_" + flowLineNumber;
+ File ds = new File(dropBox, fileName);
assertEquals(true, ds.isDirectory());
File flowLine = new File(ds, originalFlowLine.getName());
@@ -257,6 +259,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
originalFlowLine.setLastModified(4711000);
assertEquals(4711000, flowLine.lastModified());
assertEquals(true, new File(ds, FlowLineFeeder.META_DATA_FILE_NAME).exists());
+ assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists());
}
private Sample createFlowLineSample(int flowLineNumber)
--
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