diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
index ac9e797784c1524793a240de6869dbbab6d13893..d83d4107b1139605187c29ab2d61623e8f1687a6 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
@@ -167,7 +167,7 @@ public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtra
{
TechId sampleID = new TechId(sample.getId());
List<IEntityProperty> propertiesList =
- Util.getUpdatedProperties(sample, sampleType, properties);
+ Util.getProperties(properties, sampleType, new ArrayList<String>());
Set<NewAttachment> emptySet = Collections.<NewAttachment> emptySet();
Date version = sample.getModificationDate();
service.updateSample(new SampleUpdatesDTO(sampleID, propertiesList,
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Util.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Util.java
index 1edccd7f0f07b31a7f31b2013ad876abcf3fdce4..23f42c9f08d219bdeeb0f4afb7fc9a8da824a506 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Util.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/Util.java
@@ -18,9 +18,7 @@ package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import java.io.File;
import java.util.ArrayList;
-import java.util.LinkedHashMap;
import java.util.List;
-import java.util.Map;
import java.util.Properties;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -28,7 +26,6 @@ import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
@@ -43,32 +40,6 @@ class Util
{
}
- /**
- * Returns all updated properties of specified properties holder.
- *
- * @param entityType Entity type which knows all possible properties. Used to filter irrelevant
- * properties of <code>properties</code>.
- * @param properties Properties which might override properties provided by the properties
- * holder.
- */
- static List<IEntityProperty> getUpdatedProperties(IEntityPropertiesHolder propertiesHolder,
- EntityType entityType, Properties properties)
- {
- Map<String, IEntityProperty> map = new LinkedHashMap<String, IEntityProperty>();
- List<IEntityProperty> props = propertiesHolder.getProperties();
- for (IEntityProperty property : props)
- {
- map.put(property.getPropertyType().getCode(), property);
- }
- List<IEntityProperty> sampleProperties =
- getProperties(properties, entityType, new ArrayList<String>());
- for (IEntityProperty property : sampleProperties)
- {
- map.put(property.getPropertyType().getCode(), property);
- }
- return new ArrayList<IEntityProperty>(map.values());
- }
-
/**
* Returns an array of all entity properties defined by the specified entity type for which
* values are found in the specified {@link Properties} object.
@@ -88,7 +59,12 @@ class Util
return sampleProperties.toArray(new IEntityProperty[sampleProperties.size()]);
}
- private static List<IEntityProperty> getProperties(Properties properties,
+ /**
+ * Turns specified properties into a list of {@link IEntityProperty} instances in accordance to
+ * the property types assigned to the specified entity type. Keys of missing mandatory
+ * properties are added to the specified list.
+ */
+ static List<IEntityProperty> getProperties(Properties properties,
EntityType entityType, List<String> missingMandatoryProperties)
{
List<IEntityProperty> sampleProperties = new ArrayList<IEntityProperty>();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/UtilTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/UtilTest.java
index 81ca0f3aa7e0c7a870d41bdae7540bbd3546c739..96526ddff3c8efa9a3f75fd9a906c19d11d1b4b2 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/UtilTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/UtilTest.java
@@ -17,17 +17,14 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import java.util.Arrays;
-import java.util.List;
import java.util.Properties;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
@@ -38,43 +35,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
*/
public class UtilTest extends AssertJUnit
{
- @Test
- public void testGetUpdatedPropertiesForNoEntityProperties()
- {
- Sample sample = new Sample();
- sample.setProperties(Arrays.<IEntityProperty>asList());
- Properties properties = new Properties();
- properties.setProperty("blabla", "blub");
-
- List<IEntityProperty> props = Util.getUpdatedProperties(sample, new SampleType(), properties);
-
- assertEquals(0, props.size());
- }
-
- @Test
- public void testGetUpdatedProperties()
- {
- Sample sample = new Sample();
- EntityProperty p1 = createProperty("name", "Albert");
- EntityProperty p2 = createProperty("age", "26");
- sample.setProperties(Arrays.<IEntityProperty>asList(p1, p2));
- SampleType entityType = new SampleType();
- SampleTypePropertyType etpt1 = createETPT("name", false);
- SampleTypePropertyType etpt2 = createETPT("age", true);
- entityType.setSampleTypePropertyTypes(Arrays.asList(etpt1, etpt2));
- Properties properties = new Properties();
- properties.setProperty("blabla", "blub");
- properties.setProperty("age", "76");
-
- List<IEntityProperty> props = Util.getUpdatedProperties(sample, entityType, properties);
-
- assertEquals(2, props.size());
- assertEquals("name", props.get(0).getPropertyType().getCode());
- assertEquals("Albert", props.get(0).getValue());
- assertEquals("age", props.get(1).getPropertyType().getCode());
- assertEquals("76", props.get(1).getValue());
- }
-
@Test
public void testGetAndCheckProperties()
{
@@ -113,16 +73,6 @@ public class UtilTest extends AssertJUnit
}
}
- private EntityProperty createProperty(String name, String value)
- {
- EntityProperty entityProperty = new EntityProperty();
- PropertyType propertyType = new PropertyType();
- propertyType.setCode(name);
- entityProperty.setPropertyType(propertyType);
- entityProperty.setValue(value);
- return entityProperty;
- }
-
private SampleTypePropertyType createETPT(String code, boolean mandatory)
{
PropertyType propertyType = new PropertyType();