From 0cb4f4301c9594885a8ffb9c2bbcc1e8f68eb378 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Thu, 17 Dec 2009 14:34:13 +0000
Subject: [PATCH] change: replace the ":" in the flow lane sample name by a "_"
to make opening the files easier from a Perl / Bash script
SVN: 13995
---
.../bsse/cisd/dsu/dss/FlowLaneFeeder.java | 2 +-
.../bsse/cisd/dsu/dss/FlowLaneFeederTest.java | 28 ++++++-------------
2 files changed, 10 insertions(+), 20 deletions(-)
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 e7afa3d671a..61ec02480ac 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
@@ -160,7 +160,7 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
File dropBox = createDropBoxFile(flowLane);
String fileName =
flowLaneSample.getGroup().getCode() + entitySepaparator + flowcellID
- + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + flowLane;
+ + entitySepaparator + flowLane;
File flowLaneDataSet = new File(dropBox, fileName);
if (flowLaneDataSet.exists())
{
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
index 930fac45172..71f79a8b3eb 100644
--- a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
@@ -263,13 +263,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
File[] transferedFiles = transferDropBox.listFiles();
assertEquals(1, transferedFiles.length);
- String sampleName =
- SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + "2";
+ String sampleName = SAMPLE_CODE + "_2";
assertEquals("G2_" + sampleName, transferedFiles[0].getName());
File metaFile = getFile(transferedFiles[0], FlowLaneFeeder.META_DATA_FILE_TYPE);
- String myFileName =
- asFileName(sampleName + "_" + EXTERNAL_SAMPLE_NAME
- + FlowLaneFeeder.META_DATA_FILE_TYPE);
+ String myFileName = asFileName(sampleName + FlowLaneFeeder.META_DATA_FILE_TYPE);
assertEquals(myFileName, metaFile.getName());
assertHardLinkOnSameFile(originalFlowLane2, getFile(transferedFiles[0], "2.srf"));
@@ -306,12 +303,11 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
File[] transferedFiles = transferDropBox.listFiles();
assertEquals(1, transferedFiles.length);
- String sampleName =
- SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + "2";
+ String sampleName = SAMPLE_CODE + "_2";
assertEquals("G2_" + sampleName, transferedFiles[0].getName());
File metaFile = getFile(transferedFiles[0], FlowLaneFeeder.META_DATA_FILE_TYPE);
- assertEquals(asFileName(sampleName + "_" + EXTERNAL_SAMPLE_NAME
- + FlowLaneFeeder.META_DATA_FILE_TYPE), metaFile.getName());
+ assertEquals(asFileName(sampleName + FlowLaneFeeder.META_DATA_FILE_TYPE), metaFile
+ .getName());
List<String> metaData = FileUtilities.loadToStringList(metaFile);
String lastLine = metaData.remove(metaData.size() - 1);
assertEquals("[Parent\tnull, Code\tfc:2, Contact Person Email\tab@c.de, "
@@ -460,9 +456,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
private void checkFlowLaneDataSet(File originalFlowLane, String flowLaneNumber)
{
File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLaneNumber);
- String flowLaneSampleCode =
- SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING
- + flowLaneNumber;
+ String flowLaneSampleCode = SAMPLE_CODE + "_" + flowLaneNumber;
String fileName =
"G" + flowLaneNumber + FlowLaneFeeder.DEFAULT_ENTITY_SEPARATOR + flowLaneSampleCode;
File ds = new File(dropBox, fileName);
@@ -473,9 +467,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
assertEquals(FileUtilities.loadToString(originalFlowLane), FileUtilities
.loadToString(flowLane));
assertHardLinkOnSameFile(originalFlowLane, flowLane);
- String metaDataFileName =
- flowLaneSampleCode + (flowLaneNumber.equals("2") ? "_" + EXTERNAL_SAMPLE_NAME : "")
- + FlowLaneFeeder.META_DATA_FILE_TYPE;
+ String metaDataFileName = flowLaneSampleCode + FlowLaneFeeder.META_DATA_FILE_TYPE;
metaDataFileName = asFileName(metaDataFileName);
assertEquals(true, new File(ds, metaDataFileName).exists());
assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists());
@@ -492,8 +484,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
private Sample createFlowLaneSample(int flowLaneNumber)
{
Sample sample = new Sample();
- sample.setCode(SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING
- + flowLaneNumber);
+ sample.setCode(SAMPLE_CODE + ":" + flowLaneNumber);
Group group = new Group();
group.setCode("G" + flowLaneNumber);
sample.setGroup(group);
@@ -502,8 +493,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
Person registrator = new Person();
registrator.setEmail("ab@c.de");
sample.setRegistrator(registrator);
- sample.setIdentifier(SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING
- + flowLaneNumber);
+ sample.setIdentifier(SAMPLE_CODE + ":" + flowLaneNumber);
return sample;
}
--
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