From 75ad8a71a19b7c9118771934eeaa42a90d0b6619 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Mon, 7 Jun 2010 08:41:35 +0000
Subject: [PATCH] [SE-255] use subEntitySeparator for contained sample codes
SVN: 16290
---
.../DefaultDataSetInfoExtractor.java | 10 +++++-
.../DefaultDataSetInfoExtractorTest.java | 36 ++++++++++++++-----
2 files changed, 36 insertions(+), 10 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractor.java
index 60c64cee464..686d9db7bdf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractor.java
@@ -323,7 +323,7 @@ public class DefaultDataSetInfoExtractor extends AbstractDataSetInfoExtractor
dataSetInformation.setExperimentIdentifier(experimentIdentifier);
if (experimentIdentifier == null)
{
- dataSetInformation.setSampleCode(entitiesProvider.getEntity(indexOfSampleCode));
+ dataSetInformation.setSampleCode(extractSampleCode(entitiesProvider));
}
dataSetInformation.setParentDataSetCodes(getParentDataSetCodes(entitiesProvider));
dataSetInformation.setProducerCode(tryGetDataProducerCode(entitiesProvider));
@@ -358,6 +358,14 @@ public class DefaultDataSetInfoExtractor extends AbstractDataSetInfoExtractor
return identifier;
}
+ private String extractSampleCode(final DataSetNameEntitiesProvider entitiesProvider)
+ {
+ // subEntitySeparator can be used instead of ':' for contained sample code
+ // (':' is not an allowed char some OS and it is not achievable in Mac OS Finder)
+ String sampleCode = entitiesProvider.getEntity(indexOfSampleCode);
+ return sampleCode.replace(subEntitySeparator, ':');
+ }
+
private List<String> getParentDataSetCodes(final DataSetNameEntitiesProvider entitiesProvider)
{
if (indexOfParentDataSetCodes.isUndefined())
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractorTest.java
index 7e84f0db77e..cb485f04cc4 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DefaultDataSetInfoExtractorTest.java
@@ -54,6 +54,24 @@ public final class DefaultDataSetInfoExtractorTest extends CodeExtractortTestCas
assertTrue(WORKING_DIRECTORY.mkdirs());
}
+ @Test
+ public void testExtractContainedSampleIdentifier()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(asPropertyName(GROUP_CODE), "my-group");
+ final IDataSetInfoExtractor extractor = new DefaultDataSetInfoExtractor(properties);
+
+ final DataSetInformation dsInfo1 =
+ extractor.getDataSetInformation(new File("BOX_1&S_1"), null);
+ final DataSetInformation dsInfo2 =
+ extractor.getDataSetInformation(new File("BOX_1:S_1"), null);
+
+ assertEquals("BOX_1:S_1", dsInfo1.getSampleIdentifier().getSampleCode());
+ assertEquals("S_1", dsInfo1.getSampleIdentifier().getSampleSubCode());
+ assertEquals("BOX_1:S_1", dsInfo2.getSampleIdentifier().getSampleCode());
+ assertEquals("S_1", dsInfo2.getSampleIdentifier().getSampleSubCode());
+ }
+
@Test
public void testExtractExperimentIdentifierWithoutGroup()
{
@@ -70,32 +88,32 @@ public final class DefaultDataSetInfoExtractorTest extends CodeExtractortTestCas
assertEquals("123", dsInfo.getExperimentIdentifier().getExperimentCode());
assertEquals(null, dsInfo.getSampleIdentifier());
}
-
+
@Test
public void testExtractExperimentIdentifierWithGroup()
{
Properties properties = new Properties();
properties.setProperty(INDEX_OF_EXPERIMENT_IDENTIFIER, "1");
final IDataSetInfoExtractor extractor = new DefaultDataSetInfoExtractor(properties);
-
+
final DataSetInformation dsInfo =
- extractor.getDataSetInformation(new File("bla.abc&xy&123.bla"), null);
-
+ extractor.getDataSetInformation(new File("bla.abc&xy&123.bla"), null);
+
assertEquals("ABC", dsInfo.getExperimentIdentifier().getSpaceCode());
assertEquals("XY", dsInfo.getExperimentIdentifier().getProjectCode());
assertEquals("123", dsInfo.getExperimentIdentifier().getExperimentCode());
assertEquals(null, dsInfo.getSampleIdentifier());
}
-
+
@Test
public void testHappyCaseWithDefaultProperties()
{
final String barcode = "XYZ123";
final IDataSetInfoExtractor extractor = new DefaultDataSetInfoExtractor(new Properties());
-
+
final DataSetInformation dsInfo =
- extractor.getDataSetInformation(new File("bla.bla." + barcode), null);
-
+ extractor.getDataSetInformation(new File("bla.bla." + barcode), null);
+
assertNull(dsInfo.getExperimentIdentifier());
assertEquals(barcode, dsInfo.getSampleIdentifier().getSampleCode());
assertEquals(0, dsInfo.getParentDataSetCodes().size());
@@ -186,7 +204,7 @@ public final class DefaultDataSetInfoExtractorTest extends CodeExtractortTestCas
final Properties properties = new Properties();
final String separator = "=";
properties.setProperty(ENTITY_SEPARATOR, separator);
- String subSeparator = "%";
+ String subSeparator = "%";
properties.setProperty(SUB_ENTITY_SEPARATOR, subSeparator);
properties.setProperty(INDEX_OF_SAMPLE_CODE, "0");
properties.setProperty(INDEX_OF_PARENT_DATA_SET_CODE, "1");
--
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