From 311c6ceb91fc8ec8c33a233ca6a24d8cd02fcedc Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Fri, 28 Aug 2009 16:12:29 +0000
Subject: [PATCH] add: support for providing the parent data set code as column
'parent' in the index.tsv file
SVN: 12316
---
.../yeastx/etl/BatchDataSetInfoExtractor.java | 1 +
.../yeastx/etl/DataSetMappingInformation.java | 16 +++++++++++
.../etl/DataSetInformationParserTest.java | 27 ++++++++++++++++---
3 files changed, 41 insertions(+), 3 deletions(-)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java
index f3ff856934c..95bc8ff912e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/BatchDataSetInfoExtractor.java
@@ -58,6 +58,7 @@ public class BatchDataSetInfoExtractor implements IDataSetInfoExtractor
info.setGroupCode(plainInfo.getGroupCode());
MLConversionType conversion = getConversion(plainInfo.getConversion());
info.setConversion(conversion);
+ info.setParentDataSetCode(plainInfo.getParentDataSetCode());
fileNameDecorator.enrich(info, incomingDataSetPath);
return info;
} else
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java
index 1dc4b89f3bc..675949f5652 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetMappingInformation.java
@@ -42,6 +42,8 @@ public class DataSetMappingInformation
private String groupCode;
private String conversion;
+
+ private String parentDataSetCode;
private List<NewProperty> properties;
@@ -67,6 +69,20 @@ public class DataSetMappingInformation
this.sampleCodeOrLabel = StringUtils.trimToNull(sampleCodeOrLabel);
}
+ /**
+ * Returns the code of the parent data set, if any.
+ */
+ public final String getParentDataSetCode()
+ {
+ return parentDataSetCode;
+ }
+
+ @BeanProperty(label="parent", optional = true)
+ public final void setParentDataSetCode(String parentCode)
+ {
+ this.parentDataSetCode = parentCode;
+ }
+
public String getExperimentName()
{
return experimentName;
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
index 443f1ad36a2..97275e3a8b7 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
@@ -36,9 +36,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
*/
public class DataSetInformationParserTest extends AbstractFileSystemTestCase
{
+ private static final String MANDATORY_HEADER = "file_name sample group\n";
+
private static final String HEADER =
// "# user@gmail.com\n+"+
- "file_name sample group experiment conversion dataset_property_1 dataset_property_2\n";
+ "file_name sample parent group experiment project conversion dataset_property_1 dataset_property_2\n";
private static final String TAB = "\t";
@@ -46,23 +48,42 @@ public class DataSetInformationParserTest extends AbstractFileSystemTestCase
public void testLoadIndexFile()
{
File indexFile =
- writeMappingFile(HEADER + "data.txt sample1 group1 experiment1 fiaML v1 v2");
+ writeMappingFile(HEADER
+ + "data.txt sample1 parentCode group1 experiment1 project1 fiaML v1 v2");
List<DataSetMappingInformation> list = tryParse(indexFile);
AssertJUnit.assertEquals(1, list.size());
DataSetMappingInformation elem = list.get(0);
AssertJUnit.assertEquals("group1", elem.getGroupCode());
+ AssertJUnit.assertEquals("parentCode", elem.getParentDataSetCode());
+ AssertJUnit.assertEquals("sample1", elem.getSampleCodeOrLabel());
AssertJUnit.assertEquals("data.txt", elem.getFileName());
+ AssertJUnit.assertEquals("experiment1", elem.getExperimentName());
+ AssertJUnit.assertEquals("project1", elem.getProjectCode());
AssertJUnit.assertEquals(2, elem.getProperties().size());
NewProperty prop1 = elem.getProperties().get(0);
AssertJUnit.assertEquals("v1", prop1.getValue());
AssertJUnit.assertEquals("dataset_property_1", prop1.getPropertyCode());
}
+ @Test
+ public void testLoadIndexFileMandatoryColumnsOnly()
+ {
+ File indexFile =
+ writeMappingFile(MANDATORY_HEADER
+ + "data2.txt sample2 group2");
+ List<DataSetMappingInformation> list = tryParse(indexFile);
+ AssertJUnit.assertEquals(1, list.size());
+ DataSetMappingInformation elem = list.get(0);
+ AssertJUnit.assertEquals("group2", elem.getGroupCode());
+ AssertJUnit.assertEquals("sample2", elem.getSampleCodeOrLabel());
+ AssertJUnit.assertEquals("data2.txt", elem.getFileName());
+ }
+
@Test
public void testLoadIndexFileWithMissingFieldValueFails() throws FileNotFoundException,
IOException
{
- File indexFile = writeMappingFile(HEADER + TAB + TAB + TAB + TAB + TAB + TAB);
+ File indexFile = writeMappingFile(HEADER + TAB + TAB + TAB + TAB + TAB + TAB + TAB + TAB);
List<DataSetMappingInformation> result = tryParse(indexFile);
AssertJUnit.assertNull("error during parsing expected", result);
List<String> logLines = readLogFile();
--
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