From a5b00b8bf82178e33cf3f108ca2112c6548d82a8 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 18 Aug 2010 14:50:54 +0000
Subject: [PATCH] LMS-1707 tests fixed, name -> label
SVN: 17516
---
.../CsvToCanonicalFeatureVector.java | 3 ++-
.../GenedataFormatToCanonicalFeatureVector.java | 3 ++-
.../dss/generic/server/FeatureTableBuilder.java | 12 ++++++------
.../screening/server/DssServiceRpcScreening.java | 2 +-
.../imaging/dataaccess/ImgFeatureDefDTO.java | 16 ++++++++--------
.../CsvToCanonicalFeatureVectorTest.java | 4 ++--
.../featurevector/FeatureVectorUploaderTest.java | 2 +-
.../genedata/FeatureStorageProcessorTest.java | 2 ++
...nedataFormatToCanonicalFeatureVectorTest.java | 2 +-
.../imaging/dataaccess/FeatureVectorDAOTest.java | 2 +-
10 files changed, 26 insertions(+), 22 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
index ae694fa3221..692c1634205 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVector.java
@@ -134,7 +134,8 @@ public class CsvToCanonicalFeatureVector
CanonicalFeatureVector featureVector = new CanonicalFeatureVector();
CodeAndTitle codeAndTitle = new CodeAndTitle(column.name);
ImgFeatureDefDTO featureDef = new ImgFeatureDefDTO();
- featureDef.setName(codeAndTitle.getTitle());
+ featureDef.setLabel(codeAndTitle.getTitle());
+ featureDef.setDescription(codeAndTitle.getTitle());
String code = codeAndTitle.getCode();
int count = counters.count(code);
featureDef.setCode(count == 1 ? code : code + count);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
index c898db97178..9b215c2b5b2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVector.java
@@ -84,7 +84,8 @@ public class GenedataFormatToCanonicalFeatureVector
int count = counters.count(name);
ImgFeatureDefDTO featureDef = new ImgFeatureDefDTO();
featureDef.setCode(count == 1 ? name : name + count);
- featureDef.setName(name);
+ featureDef.setLabel(name);
+ featureDef.setDescription(name);
featureVector.setFeatureDef(featureDef);
PlateFeatureValues valuesValues = convertColumnToValues(geometry, feature);
ImgFeatureValuesDTO values = new ImgFeatureValuesDTO(0., 0., valuesValues, 0);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
index b8d9a74d66e..d1298b70a01 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
@@ -116,18 +116,18 @@ public class FeatureTableBuilder
final Bundle bundle = new Bundle();
final List<ImgFeatureDefDTO> featureDefinitions =
dao.listFeatureDefsByDataSetId(dataSet.getId());
- final Map<String, ImgFeatureDefDTO> featureNameToDefMap =
+ final Map<String, ImgFeatureDefDTO> featureCodeToDefMap =
new LinkedHashMap<String, ImgFeatureDefDTO>();
for (ImgFeatureDefDTO def : featureDefinitions)
{
- featureNameToDefMap.put(def.getName(), def);
+ featureCodeToDefMap.put(def.getCode(), def);
}
bundle.dataSet = dataSet;
bundle.featureDefToValuesMap = new HashMap<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>>();
bundles.add(bundle);
if (useAllFeatures)
{
- featureNames.addAll(featureNameToDefMap.keySet());
+ featureNames.addAll(featureCodeToDefMap.keySet());
}
for (String featureName : featureNames)
{
@@ -136,7 +136,7 @@ public class FeatureTableBuilder
featureNameToIndexMap.put(featureName,
new Integer(featureNameToIndexMap.size()));
}
- final ImgFeatureDefDTO featureDefinition = featureNameToDefMap.get(featureName);
+ final ImgFeatureDefDTO featureDefinition = featureCodeToDefMap.get(featureName);
if (featureDefinition != null)
{
List<ImgFeatureValuesDTO> featureValueSets =
@@ -222,8 +222,8 @@ public class FeatureTableBuilder
{
break;
}
- Integer index = featureNameToIndexMap.get(featureDefinition.getName());
- assert index != null : "No index for feature " + featureDefinition.getName();
+ Integer index = featureNameToIndexMap.get(featureDefinition.getCode());
+ assert index != null : "No index for feature " + featureDefinition.getCode();
valueArray[index] =
featureValues.getForWellLocation(wellPosition.getWellRow(), wellPosition
.getWellColumn());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index ce3d7bba1cf..a83dfdca794 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -123,7 +123,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
List<ImgFeatureDefDTO> featureDefinitions = getFeatureDefinitions(identifier);
for (ImgFeatureDefDTO featureDefinition : featureDefinitions)
{
- String featureName = featureDefinition.getName();
+ String featureName = featureDefinition.getLabel();
if (result.contains(featureName) == false)
{
result.add(featureName);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureDefDTO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureDefDTO.java
index f805891426e..402505c40f1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureDefDTO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/ImgFeatureDefDTO.java
@@ -32,8 +32,8 @@ public class ImgFeatureDefDTO extends AbstractHashable
@AutoGeneratedKeys
private long id;
- @ResultColumn("NAME")
- private String name;
+ @ResultColumn("LABEL")
+ private String label;
@ResultColumn("CODE")
private String code;
@@ -48,9 +48,9 @@ public class ImgFeatureDefDTO extends AbstractHashable
{
}
- public ImgFeatureDefDTO(String name, String description, long dataSetId)
+ public ImgFeatureDefDTO(String label, String description, long dataSetId)
{
- this.name = name;
+ this.label = label;
this.description = description;
this.dataSetId = dataSetId;
}
@@ -65,14 +65,14 @@ public class ImgFeatureDefDTO extends AbstractHashable
this.id = id;
}
- public String getName()
+ public String getLabel()
{
- return name;
+ return label;
}
- public void setName(String name)
+ public void setLabel(String label)
{
- this.name = name;
+ this.label = label;
}
public void setCode(String code)
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVectorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVectorTest.java
index 9575906ecd1..7b22060aa29 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVectorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvToCanonicalFeatureVectorTest.java
@@ -54,7 +54,7 @@ public class CsvToCanonicalFeatureVectorTest extends AssertJUnit
// Check total cells feature
CanonicalFeatureVector totalCells = fvs.get(0);
ImgFeatureDefDTO def = totalCells.getFeatureDef();
- assertEquals("TotalCells", def.getName());
+ assertEquals("TotalCells", def.getLabel());
assertEquals(1, totalCells.getValues().size());
ImgFeatureValuesDTO values = totalCells.getValues().get(0);
PlateFeatureValues darr = values.getValues();
@@ -66,7 +66,7 @@ public class CsvToCanonicalFeatureVectorTest extends AssertJUnit
// Check InfectionIndex
CanonicalFeatureVector infectionIndex = fvs.get(2);
def = infectionIndex.getFeatureDef();
- assertEquals("InfectionIndex", def.getName());
+ assertEquals("InfectionIndex", def.getLabel());
assertEquals(1, infectionIndex.getValues().size());
values = infectionIndex.getValues().get(0);
darr = values.getValues();
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
index c6bf246977a..ef6e7b5eeff 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
@@ -111,7 +111,7 @@ public class FeatureVectorUploaderTest extends AbstractDBTest
private void verifyFeatureDef()
{
- assertEquals(TEST_FEATURE_NAME + count, featureDef.getName());
+ assertEquals(TEST_FEATURE_NAME + count, featureDef.getLabel());
List<ImgFeatureValuesDTO> featureValuesList = dao.getFeatureValues(featureDef);
assertEquals(1, featureValuesList.size());
featureValues = featureValuesList.get(0);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
index bd5de1755f2..268f2ae6430 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/FeatureStorageProcessorTest.java
@@ -100,6 +100,7 @@ public class FeatureStorageProcessorTest extends AbstractFileSystemTestCase
will(returnValue(datasetId));
ImgFeatureDefDTO featureDTO = new ImgFeatureDefDTO("alpha", "alpha", datasetId);
+ featureDTO.setCode("alpha");
one(dao).addFeatureDef(with(equal(featureDTO)));
will(returnValue((long) 1));
@@ -107,6 +108,7 @@ public class FeatureStorageProcessorTest extends AbstractFileSystemTestCase
will(returnValue((long) 1));
featureDTO = new ImgFeatureDefDTO("beta", "beta", datasetId);
+ featureDTO.setCode("beta");
one(dao).addFeatureDef(with(equal(featureDTO)));
will(returnValue((long) 2));
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVectorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVectorTest.java
index 17ff9db8c62..c91cf5e3999 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVectorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFormatToCanonicalFeatureVectorTest.java
@@ -66,7 +66,7 @@ public class GenedataFormatToCanonicalFeatureVectorTest extends AbstractFileSyst
private void verifyFeature(CanonicalFeatureVector feature, String featureName, float[] values)
{
ImgFeatureDefDTO featureDef = feature.getFeatureDef();
- assertEquals(featureName, featureDef.getName());
+ assertEquals(featureName, featureDef.getLabel());
List<ImgFeatureValuesDTO> featureValues = feature.getValues();
assertEquals(1, featureValues.size());
ImgFeatureValuesDTO featureValue = featureValues.get(0);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
index e12e0316b4c..124fe4e0833 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/FeatureVectorDAOTest.java
@@ -104,7 +104,7 @@ public class FeatureVectorDAOTest extends AbstractDBTest
assertEquals(1, featureDefs.size());
ImgFeatureDefDTO featureDef = featureDefs.get(0);
- assertEquals(TEST_FEATURE_NAME, featureDef.getName());
+ assertEquals(TEST_FEATURE_NAME, featureDef.getLabel());
createFeatureValues(featureDef);
List<ImgFeatureValuesDTO> featureValuesList = dao.getFeatureValues(featureDef);
--
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