From 3b6207bb5da0c0c0d6179efc5751ee2d66c99f22 Mon Sep 17 00:00:00 2001
From: izabel <izabel>
Date: Tue, 19 Oct 2010 09:13:15 +0000
Subject: [PATCH] [LMS-1818] don't allow to update dynamic properties;
automatically add placeholder property values to dynamic properties
SVN: 18342
---
.../AbstractExternalDataBusinessObject.java | 25 ++-
.../bo/AbstractMaterialBusinessObject.java | 18 +++
.../bo/AbstractSampleBusinessObject.java | 50 +++---
.../bo/EntityPropertiesConverter.java | 150 +++++++++++++++---
.../server/business/bo/ExperimentBO.java | 16 +-
.../server/business/bo/ExternalDataBO.java | 17 +-
.../bo/IEntityPropertiesConverter.java | 16 +-
.../server/business/bo/MaterialBO.java | 12 +-
.../server/business/bo/MaterialTable.java | 11 +-
.../generic/server/business/bo/SampleBO.java | 30 ++--
.../server/business/bo/SampleTable.java | 5 +-
.../experiment/PropertiesEditor.java | 12 +-
.../server/business/bo/ExperimentBOTest.java | 31 ++--
.../business/bo/ExternalDataBOTest.java | 57 ++++---
.../server/business/bo/SampleBOTest.java | 29 +++-
15 files changed, 331 insertions(+), 148 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractExternalDataBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractExternalDataBusinessObject.java
index df2bb470f93..da07e572cdd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractExternalDataBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractExternalDataBusinessObject.java
@@ -16,13 +16,15 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
+import java.util.HashSet;
import java.util.List;
import java.util.Set;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetPropertyPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -65,19 +67,32 @@ public abstract class AbstractExternalDataBusinessObject extends
List<IEntityProperty> newProperties, Set<String> set)
{
final Set<DataSetPropertyPE> existingProperties = externalData.getProperties();
- final EntityTypePE type = externalData.getDataSetType();
+ final DataSetTypePE type = externalData.getDataSetType();
final PersonPE registrator = findRegistrator();
externalData.setProperties(entityPropertiesConverter.updateProperties(existingProperties,
- type, newProperties, registrator, set));
+ type, newProperties, registrator, set, extractDynamicProperties(type)));
+ }
+
+ protected Set<String> extractDynamicProperties(final DataSetTypePE type)
+ {
+ Set<String> dynamicProperties = new HashSet<String>();
+ for (DataSetTypePropertyTypePE etpt : type.getDataSetTypePropertyTypes())
+ {
+ if (etpt.isDynamic())
+ {
+ dynamicProperties.add(etpt.getPropertyType().getCode());
+ }
+ }
+ return dynamicProperties;
}
protected void updateProperties(ExternalDataPE externalData, List<IEntityProperty> newProperties)
{
final Set<DataSetPropertyPE> existingProperties = externalData.getProperties();
- final EntityTypePE type = externalData.getDataSetType();
+ final DataSetTypePE type = externalData.getDataSetType();
final PersonPE registrator = findRegistrator();
externalData.setProperties(entityPropertiesConverter.updateProperties(existingProperties,
- type, newProperties, registrator));
+ type, newProperties, registrator, extractDynamicProperties(type)));
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractMaterialBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractMaterialBusinessObject.java
index 6ee3368197d..6f7ed0cc4bb 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractMaterialBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractMaterialBusinessObject.java
@@ -16,10 +16,15 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
+import java.util.HashSet;
+import java.util.Set;
+
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
@@ -60,4 +65,17 @@ public class AbstractMaterialBusinessObject extends AbstractBusinessObject
return result;
}
+ protected Set<String> extractDynamicProperties(final MaterialTypePE type)
+ {
+ Set<String> dynamicProperties = new HashSet<String>();
+ for (MaterialTypePropertyTypePE etpt : type.getMaterialTypePropertyTypes())
+ {
+ if (etpt.isDynamic())
+ {
+ dynamicProperties.add(etpt.getPropertyType().getCode());
+ }
+ }
+ return dynamicProperties;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
index 291c0caf046..f9582f2e637 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
@@ -43,6 +43,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationshipPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
@@ -237,8 +238,8 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
List<SampleRelationshipPE> oldParents = new ArrayList<SampleRelationshipPE>();
for (SampleRelationshipPE r : child.getParentRelationships())
{
- if (r.getRelationship().getCode().equals(
- BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP))
+ if (r.getRelationship().getCode()
+ .equals(BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP))
{
oldParents.add(r);
}
@@ -353,26 +354,26 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
{
if (cacheOrNull != null)
{
- entityPropertiesConverter.checkMandatoryProperties(sample.getProperties(), sample
- .getSampleType(), cacheOrNull);
+ entityPropertiesConverter.checkMandatoryProperties(sample.getProperties(),
+ sample.getSampleType(), cacheOrNull);
} else
{
- entityPropertiesConverter.checkMandatoryProperties(sample.getProperties(), sample
- .getSampleType());
+ entityPropertiesConverter.checkMandatoryProperties(sample.getProperties(),
+ sample.getSampleType());
}
final boolean hasDatasets = hasDatasets(externalDataDAO, sample);
if (hasDatasets && sample.getExperiment() == null)
{
throw UserFailureException.fromTemplate(
"Cannot detach the sample '%s' from the experiment "
- + "because there are already datasets attached to the sample.", sample
- .getIdentifier());
+ + "because there are already datasets attached to the sample.",
+ sample.getIdentifier());
}
if (hasDatasets && sample.getGroup() == null)
{
throw UserFailureException.fromTemplate("Cannot detach the sample '%s' from the space "
- + "because there are already datasets attached to the sample.", sample
- .getIdentifier());
+ + "because there are already datasets attached to the sample.",
+ sample.getIdentifier());
}
if (sample.getExperiment() != null
&& (sample.getGroup() == null || sample.getExperiment().getProject().getGroup()
@@ -423,8 +424,8 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
{
throw UserFailureException.fromTemplate(
"Cannot detach the sample '%s' from the experiment "
- + "because there are already datasets attached to the sample.", sample
- .getIdentifier());
+ + "because there are already datasets attached to the sample.",
+ sample.getIdentifier());
}
sample.setExperiment(null);
}
@@ -458,8 +459,8 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
if (sample.getGroup() == null)
{
throw UserFailureException.fromTemplate(
- "It is not allowed to connect a shared sample '%s' to the experiment.", sample
- .getIdentifier());
+ "It is not allowed to connect a shared sample '%s' to the experiment.",
+ sample.getIdentifier());
}
}
@@ -470,8 +471,8 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
{
throw UserFailureException.fromTemplate(
"The sample '%s' cannot be assigned to the experiment '%s' "
- + "because the experiment has been invalidated.", sample
- .getSampleIdentifier(), identOrNull);
+ + "because the experiment has been invalidated.",
+ sample.getSampleIdentifier(), identOrNull);
}
}
@@ -523,8 +524,8 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
{
throw UserFailureException.fromTemplate(
"Sample '%s' is an ancestor of Sample '%s' "
- + "and cannot be at the same time set as its child.", sample
- .getIdentifier(), parentToAdd.getIdentifier());
+ + "and cannot be at the same time set as its child.",
+ sample.getIdentifier(), parentToAdd.getIdentifier());
} else
{
final Set<TechId> nextToVisit = getSampleDAO().listParents(toVisit, relationship);
@@ -534,4 +535,17 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
}
}
}
+
+ protected Set<String> extractDynamicProperties(final SampleTypePE type)
+ {
+ Set<String> dynamicProperties = new HashSet<String>();
+ for (SampleTypePropertyTypePE etpt : type.getSampleTypePropertyTypes())
+ {
+ if (etpt.isDynamic())
+ {
+ dynamicProperties.add(etpt.getPropertyType().getCode());
+ }
+ }
+ return dynamicProperties;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityPropertiesConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityPropertiesConverter.java
index 93ef5b5b0ab..49ca722bfc3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityPropertiesConverter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/EntityPropertiesConverter.java
@@ -17,12 +17,16 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collection;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.commons.lang.StringUtils;
+
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.collections.IKeyExtractor;
import ch.systemsx.cisd.common.collections.TableMap;
@@ -31,9 +35,12 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.util.IPropertyValueValidator;
import ch.systemsx.cisd.openbis.generic.server.util.KeyExtractorFactory;
import ch.systemsx.cisd.openbis.generic.server.util.PropertyValidator;
+import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+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.MaterialIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
@@ -65,9 +72,12 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
private TableMap<String, EntityTypePE> entityTypesByCode;
+ private Map<String, Set<String>> dynamicPropertiesByEntityTypeCode =
+ new HashMap<String, Set<String>>();
+
private final TableMap<String, PropertyTypePE> propertyTypesByCode =
- new TableMap<String, PropertyTypePE>(KeyExtractorFactory
- .getPropertyTypeByCodeKeyExtractor());
+ new TableMap<String, PropertyTypePE>(
+ KeyExtractorFactory.getPropertyTypeByCodeKeyExtractor());
private TableMap<PropertyTypePE, EntityTypePropertyTypePE> entityTypePropertyTypesByPropertyTypes;
@@ -91,14 +101,35 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
this.propertyValueValidator = propertyValueValidator;
}
+ private final Set<String> getDynamicProperties(final EntityTypePE entityTypePE)
+ {
+ String code = entityTypePE.getCode();
+ if (dynamicPropertiesByEntityTypeCode.containsKey(code) == false)
+ {
+ HashSet<String> set = new HashSet<String>();
+ List<EntityTypePropertyTypePE> list =
+ daoFactory.getEntityPropertyTypeDAO(entityKind).listEntityPropertyTypes(
+ entityTypePE);
+ for (EntityTypePropertyTypePE etpt : list)
+ {
+ if (etpt.isDynamic())
+ {
+ set.add(etpt.getPropertyType().getCode());
+ }
+ }
+ dynamicPropertiesByEntityTypeCode.put(code, set);
+ }
+ return dynamicPropertiesByEntityTypeCode.get(code);
+ }
+
private final EntityTypePE getEntityType(final String entityTypeCode)
{
if (entityTypesByCode == null)
{
entityTypesByCode =
new TableMap<String, EntityTypePE>(daoFactory.getEntityTypeDAO(entityKind)
- .listEntityTypes(), KeyExtractorFactory
- .getEntityTypeByCodeKeyExtractor());
+ .listEntityTypes(),
+ KeyExtractorFactory.getEntityTypeByCodeKeyExtractor());
}
final EntityTypePE entityType = entityTypesByCode.tryGet(entityTypeCode.toUpperCase());
if (entityType == null)
@@ -246,8 +277,14 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
assert registrator != null : "Unspecified registrator";
assert properties != null : "Unspecified entity properties";
final EntityTypePE entityTypePE = getEntityType(entityTypeCode);
+ Set<String> dynamicProperties = getDynamicProperties(entityTypePE);
+ Set<String> propertiesToUpdate = extractPropertiesToUpdate(properties);
+ checkDynamicPropertiesNotManuallyUpdated(propertiesToUpdate, dynamicProperties);
+ List<IEntityProperty> newProperties =
+ new ArrayList<IEntityProperty>(Arrays.asList(properties));
+ addDynamicPropertiesPlaceholders(newProperties, propertiesToUpdate, dynamicProperties);
final List<T> list = new ArrayList<T>();
- for (final IEntityProperty property : properties)
+ for (final IEntityProperty property : newProperties)
{
final T convertedPropertyOrNull =
tryConvertProperty(registrator, entityTypePE, property);
@@ -259,20 +296,33 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
return list;
}
+ private Set<String> extractPropertiesToUpdate(IEntityProperty[] properties)
+ {
+ HashSet<String> result = new HashSet<String>();
+ for (IEntityProperty p : properties)
+ {
+ result.add(p.getPropertyType().getCode());
+ }
+ return result;
+ }
+
public <T extends EntityPropertyPE> void checkMandatoryProperties(Collection<T> properties,
EntityTypePE entityTypePE)
{
assert properties != null;
- checkMandatoryProperties(properties, entityTypePE, daoFactory.getEntityPropertyTypeDAO(
- entityKind).listEntityPropertyTypes(entityTypePE));
+ checkMandatoryProperties(
+ properties,
+ entityTypePE,
+ daoFactory.getEntityPropertyTypeDAO(entityKind).listEntityPropertyTypes(
+ entityTypePE));
}
public <T extends EntityPropertyPE> void checkMandatoryProperties(Collection<T> properties,
EntityTypePE entityTypePE, Map<EntityTypePE, List<EntityTypePropertyTypePE>> cache)
{
assert properties != null;
- checkMandatoryProperties(properties, entityTypePE, getAssignedPropertiesForEntityType(
- cache, entityTypePE));
+ checkMandatoryProperties(properties, entityTypePE,
+ getAssignedPropertiesForEntityType(cache, entityTypePE));
}
@@ -318,8 +368,8 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
{
if (entityTypPropertyType.isMandatory() && value == null)
{
- throw UserFailureException.fromTemplate(NO_ENTITY_PROPERTY_VALUE_FOR_S, propertyType
- .getCode());
+ throw UserFailureException.fromTemplate(NO_ENTITY_PROPERTY_VALUE_FOR_S,
+ propertyType.getCode());
}
if (value != null)
{
@@ -330,19 +380,22 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
return null;
}
- public final <T extends EntityPropertyPE> T createValidatedProperty(PropertyTypePE propertyType,
- EntityTypePropertyTypePE entityTypPropertyType, final PersonPE registrator,
- String validatedValue)
+ public final <T extends EntityPropertyPE> T createValidatedProperty(
+ PropertyTypePE propertyType, EntityTypePropertyTypePE entityTypPropertyType,
+ final PersonPE registrator, String validatedValue)
{
assert validatedValue != null;
return createEntityProperty(registrator, propertyType, entityTypPropertyType,
validatedValue);
}
- public <T extends EntityPropertyPE, P extends IEntityProperty> Set<T> updateProperties(
- Collection<T> oldProperties, EntityTypePE entityType, List<P> newProperties,
- PersonPE registrator)
+ public <T extends EntityPropertyPE> Set<T> updateProperties(Collection<T> oldProperties,
+ EntityTypePE entityType, List<IEntityProperty> newProperties, PersonPE registrator,
+ Set<String> dynamicProperties)
{
+ Set<String> propertiesToUpdate = extractPropertiesToUpdate(newProperties);
+ checkDynamicPropertiesNotManuallyUpdated(propertiesToUpdate, dynamicProperties);
+ addDynamicPropertiesPlaceholders(newProperties, propertiesToUpdate, dynamicProperties);
final List<T> convertedProperties =
convertProperties(newProperties, entityType.getCode(), registrator);
final Set<T> set = new HashSet<T>();
@@ -351,8 +404,8 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
T existingProperty = tryFind(oldProperties, newProperty);
if (existingProperty != null)
{
- existingProperty.setUntypedValue(newProperty.getValue(), newProperty
- .getVocabularyTerm(), newProperty.getMaterialValue());
+ existingProperty.setUntypedValue(newProperty.getValue(),
+ newProperty.getVocabularyTerm(), newProperty.getMaterialValue());
set.add(existingProperty);
} else
{
@@ -362,12 +415,26 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
return set;
}
- public <T extends EntityPropertyPE, P extends IEntityProperty> Set<T> updateProperties(
- Collection<T> oldProperties, EntityTypePE entityType, List<P> newProperties,
- PersonPE registrator, Set<String> propertiesToUpdate)
+ private <P extends IEntityProperty> Set<String> extractPropertiesToUpdate(List<P> newProperties)
{
+ Set<String> propertiesToUpdate = new HashSet<String>();
+ for (P np : newProperties)
+ {
+ propertiesToUpdate.add(np.getPropertyType().getCode());
+ }
+ return propertiesToUpdate;
+ }
+
+ public <T extends EntityPropertyPE> Set<T> updateProperties(Collection<T> oldProperties,
+ EntityTypePE entityType, List<IEntityProperty> newProperties, PersonPE registrator,
+ Set<String> propertiesToUpdate, Set<String> dynamicProperties)
+ {
+ checkDynamicPropertiesNotManuallyUpdated(propertiesToUpdate, dynamicProperties);
+ addDynamicPropertiesPlaceholders(newProperties, propertiesToUpdate, dynamicProperties);
// all new properties should be among propertiesToUpdate (no need to check it)
- final Set<T> set = updateProperties(oldProperties, entityType, newProperties, registrator);
+ final Set<T> set =
+ updateProperties(oldProperties, entityType, newProperties, registrator,
+ dynamicProperties);
// add old properties that are not among propertiesToUpdate (preserve those properties)
for (T oldProperty : oldProperties)
{
@@ -381,12 +448,45 @@ public final class EntityPropertiesConverter implements IEntityPropertiesConvert
return set;
}
+ private void addDynamicPropertiesPlaceholders(List<IEntityProperty> newProperties,
+ Set<String> propertiesToUpdate, Set<String> dynamicProperties)
+ {
+ propertiesToUpdate.addAll(dynamicProperties);
+ for (String dp : dynamicProperties)
+ {
+ final IEntityProperty entityProperty = new EntityProperty();
+ entityProperty.setValue(BasicConstant.PLACEHOLDER_PROPERTY_VALUE);
+ PropertyType propertyType = new PropertyType();
+ propertyType.setCode(dp);
+ entityProperty.setPropertyType(propertyType);
+ newProperties.add(entityProperty);
+ }
+ }
+
+ private void checkDynamicPropertiesNotManuallyUpdated(Set<String> propertiesToUpdate,
+ Set<String> dynamicProperties)
+ {
+ HashSet<String> allPropertiesToUpdate = new HashSet<String>();
+ for (String p : propertiesToUpdate)
+ {
+ allPropertiesToUpdate.add(p.toUpperCase());
+ }
+ HashSet<String> dynamicPropertiesToUpdate = new HashSet<String>(dynamicProperties);
+ dynamicPropertiesToUpdate.retainAll(allPropertiesToUpdate);
+ if (dynamicPropertiesToUpdate.isEmpty() == false)
+ {
+ throw new UserFailureException(String.format(
+ "Dynamic properties cannot be updated manually [%s]",
+ StringUtils.join(dynamicPropertiesToUpdate, ",")));
+ }
+ }
+
private static <T extends EntityPropertyPE> T tryFind(Collection<T> oldProperties, T p)
{
for (T oldProperty : oldProperties)
{
- if (oldProperty.getEntityTypePropertyType().getPropertyType().equals(
- p.getEntityTypePropertyType().getPropertyType()))
+ if (oldProperty.getEntityTypePropertyType().getPropertyType()
+ .equals(p.getEntityTypePropertyType().getPropertyType()))
{
return oldProperty;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
index 10f7a1fbb23..c1cc3eb88b4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
@@ -45,6 +45,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.EventType;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
@@ -561,7 +562,7 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
final ExperimentTypePE type = experiment.getExperimentType();
final PersonPE registrator = findRegistrator();
experiment.setProperties(propertiesConverter.updateProperties(existingProperties, type,
- properties, registrator));
+ properties, registrator, extractDynamicProperties(type)));
}
public void setGeneratedCode()
@@ -569,4 +570,17 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
final String code = createCode(EntityKind.EXPERIMENT);
experiment.setCode(code);
}
+
+ protected Set<String> extractDynamicProperties(final ExperimentTypePE type)
+ {
+ Set<String> dynamicProperties = new HashSet<String>();
+ for (ExperimentTypePropertyTypePE etpt : type.getExperimentTypePropertyTypes())
+ {
+ if (etpt.isDynamic())
+ {
+ dynamicProperties.add(etpt.getPropertyType().getCode());
+ }
+ }
+ return dynamicProperties;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
index 33eaeba898e..ac130c810ac 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBO.java
@@ -44,7 +44,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
@@ -212,8 +211,8 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
externalData.setRegistrator(tryToGetRegistrator(data));
DataStorePE dataStore = getDataStoreDAO().tryToFindDataStoreByCode(data.getDataStoreCode());
externalData.setDataStore(dataStore);
- defineDataSetProperties(externalData, convertToDataSetProperties(data
- .getDataSetProperties()));
+ defineDataSetProperties(externalData,
+ convertToDataSetProperties(data.getDataSetProperties()));
externalData.setDerived(sourceType == SourceType.DERIVED);
return dataStore;
}
@@ -353,11 +352,11 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
extractPropertyCodesToUpdate(properties, existingProperties);
List<NewProperty> propertyUpdates =
extractNewPropertiesToUpdate(properties, propertyUpdatesCodes);
- final EntityTypePE type = externalData.getDataSetType();
+ final DataSetTypePE type = externalData.getDataSetType();
final PersonPE registrator = findRegistrator();
externalData.setProperties(entityPropertiesConverter.updateProperties(existingProperties,
type, Arrays.asList(convertToDataSetProperties(propertyUpdates)), registrator,
- propertyUpdatesCodes));
+ propertyUpdatesCodes, extractDynamicProperties(type)));
}
private List<NewProperty> extractNewPropertiesToUpdate(List<NewProperty> properties,
@@ -487,8 +486,8 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
{
throw UserFailureException.fromTemplate(
"Data Set '%s' is an ancestor of Data Set '%s' "
- + "and cannot be at the same time set as its child.", externalData
- .getCode(), parentToAdd.getCode());
+ + "and cannot be at the same time set as its child.",
+ externalData.getCode(), parentToAdd.getCode());
} else
{
final Set<TechId> nextToVisit = findParentIds(toVisit);
@@ -553,8 +552,8 @@ public class ExternalDataBO extends AbstractExternalDataBusinessObject implement
if (missingDataSetCodes.size() > 0)
{
throw UserFailureException.fromTemplate(
- "Data Sets with following codes do not exist: '%s'.", CollectionUtils
- .abbreviate(missingDataSetCodes, 10));
+ "Data Sets with following codes do not exist: '%s'.",
+ CollectionUtils.abbreviate(missingDataSetCodes, 10));
} else
{
return dataSets;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityPropertiesConverter.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityPropertiesConverter.java
index 77a06a71c5b..0ed42020c17 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityPropertiesConverter.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IEntityPropertiesConverter.java
@@ -47,8 +47,8 @@ public interface IEntityPropertiesConverter
final PersonPE registrator);
/**
- * Returns given value validated and converted for given property type and entity type.
- * Result may be null if given value is null.
+ * Returns given value validated and converted for given property type and entity type. Result
+ * may be null if given value is null.
*/
public String tryCreateValidatedPropertyValue(PropertyTypePE propertyType,
EntityTypePropertyTypePE entityTypPropertyType, String value);
@@ -61,17 +61,17 @@ public interface IEntityPropertiesConverter
String validatedValue);
/** Updates Set<T> of properties. */
- public <T extends EntityPropertyPE, P extends IEntityProperty> Set<T> updateProperties(
- Collection<T> oldProperties, EntityTypePE entityType, List<P> newProperties,
- PersonPE registrator);
+ public <T extends EntityPropertyPE> Set<T> updateProperties(Collection<T> oldProperties,
+ EntityTypePE entityType, List<IEntityProperty> newProperties, PersonPE registrator,
+ Set<String> dynamicProperties);
/**
* Updates Set<T> of properties but preserve those old properties which codes are not among
* <var>propertiesToUpdate</var>.
*/
- public <T extends EntityPropertyPE, P extends IEntityProperty> Set<T> updateProperties(
- Collection<T> oldProperties, EntityTypePE entityType, List<P> newProperties,
- PersonPE registrator, Set<String> propertiesToUpdate);
+ public <T extends EntityPropertyPE> Set<T> updateProperties(Collection<T> oldProperties,
+ EntityTypePE entityType, List<IEntityProperty> newProperties, PersonPE registrator,
+ Set<String> propertiesToUpdate, Set<String> dynamicProperties);
/**
* Checks whether all mandatory properties are provided.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialBO.java
index d0dbd1d1819..0062a3e491b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialBO.java
@@ -26,14 +26,14 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventType;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
@@ -85,8 +85,8 @@ public final class MaterialBO extends AbstractMaterialBusinessObject implements
private void checkBusinessRules()
{
- entityPropertiesConverter.checkMandatoryProperties(material.getProperties(), material
- .getMaterialType());
+ entityPropertiesConverter.checkMandatoryProperties(material.getProperties(),
+ material.getMaterialType());
}
public void update(MaterialUpdateDTO materialUpdate)
@@ -103,10 +103,10 @@ public final class MaterialBO extends AbstractMaterialBusinessObject implements
private void updateProperties(List<IEntityProperty> properties)
{
final Set<MaterialPropertyPE> existingProperties = material.getProperties();
- final EntityTypePE type = material.getMaterialType();
+ final MaterialTypePE type = material.getMaterialType();
final PersonPE registrator = findRegistrator();
material.setProperties(entityPropertiesConverter.updateProperties(existingProperties, type,
- properties, registrator));
+ properties, registrator, extractDynamicProperties(type)));
}
public MaterialPE getMaterial()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialTable.java
index 09159836f71..be82676078e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/MaterialTable.java
@@ -108,8 +108,8 @@ public final class MaterialTable extends AbstractMaterialBusinessObject implemen
new HashMap<EntityTypePE, List<EntityTypePropertyTypePE>>();
for (MaterialPE m : materials)
{
- entityPropertiesConverter.checkMandatoryProperties(m.getProperties(), m
- .getMaterialType(), cache);
+ entityPropertiesConverter.checkMandatoryProperties(m.getProperties(),
+ m.getMaterialType(), cache);
}
}
@@ -177,17 +177,18 @@ public final class MaterialTable extends AbstractMaterialBusinessObject implemen
List<IEntityProperty> propertiesToUpdate, boolean deleteUntouchedProperties)
{
final Set<MaterialPropertyPE> existingProperties = material.getProperties();
- final EntityTypePE type = material.getMaterialType();
+ final MaterialTypePE type = material.getMaterialType();
final PersonPE registrator = findRegistrator();
if (deleteUntouchedProperties)
{
return entityPropertiesConverter.updateProperties(existingProperties, type,
- propertiesToUpdate, registrator);
+ propertiesToUpdate, registrator, extractDynamicProperties(type));
} else
{
Set<String> propertiesToUpdateNames = extractCodes(propertiesToUpdate);
return entityPropertiesConverter.updateProperties(existingProperties, type,
- propertiesToUpdate, registrator, propertiesToUpdateNames);
+ propertiesToUpdate, registrator, propertiesToUpdateNames,
+ extractDynamicProperties(type));
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
index 156fdbea070..ca9b60f6ee7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBO.java
@@ -32,11 +32,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.IdentifierHelper;
@@ -162,8 +162,10 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
} catch (final DataAccessException e)
{
final String fileName = property.getFileName();
- throwException(e, String.format("Filename '%s' for sample '%s'", fileName,
- sample.getSampleIdentifier()));
+ throwException(
+ e,
+ String.format("Filename '%s' for sample '%s'", fileName,
+ sample.getSampleIdentifier()));
}
}
attachments.clear();
@@ -186,8 +188,8 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
getSampleDAO().updateSample(sample);
} catch (final DataAccessException ex)
{
- throwException(ex, String.format("Couldn't update sample '%s'", sample
- .getSampleIdentifier()));
+ throwException(ex,
+ String.format("Couldn't update sample '%s'", sample.getSampleIdentifier()));
}
dataChanged = false;
}
@@ -196,8 +198,8 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
{
if (sample.getInvalidation() != null)
{
- throw UserFailureException.fromTemplate("Given sample '%s' is invalid.", sample
- .getSampleIdentifier());
+ throw UserFailureException.fromTemplate("Given sample '%s' is invalid.",
+ sample.getSampleIdentifier());
}
}
@@ -212,9 +214,9 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
if (experiment != null && experiment.getInvalidation() == null)
{
throw UserFailureException.fromTemplate(
- "Given sample code '%s' already registered for experiment '%s'.", sample
- .getSampleIdentifier(), IdentifierHelper
- .createExperimentIdentifier(experiment));
+ "Given sample code '%s' already registered for experiment '%s'.",
+ sample.getSampleIdentifier(),
+ IdentifierHelper.createExperimentIdentifier(experiment));
}
}
@@ -223,8 +225,8 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
if (sample.getGroup() == null)
{
throw UserFailureException.fromTemplate(
- "The sample '%s' is shared and cannot be assigned to any experiment.", sample
- .getSampleIdentifier());
+ "The sample '%s' is shared and cannot be assigned to any experiment.",
+ sample.getSampleIdentifier());
}
}
@@ -250,10 +252,10 @@ public final class SampleBO extends AbstractSampleBusinessObject implements ISam
private void updateProperties(List<IEntityProperty> properties)
{
final Set<SamplePropertyPE> existingProperties = sample.getProperties();
- final EntityTypePE type = sample.getSampleType();
+ final SampleTypePE type = sample.getSampleType();
final PersonPE registrator = findRegistrator();
sample.setProperties(entityPropertiesConverter.updateProperties(existingProperties, type,
- properties, registrator));
+ properties, registrator, extractDynamicProperties(type)));
}
private void updateParents(SampleUpdatesDTO updates)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
index 2be1156625d..4f186dd7e80 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
@@ -254,10 +254,11 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
Set<String> propertiesToUpdate)
{
final Set<SamplePropertyPE> existingProperties = sample.getProperties();
- final EntityTypePE type = sample.getSampleType();
+ final SampleTypePE type = sample.getSampleType();
final PersonPE registrator = findRegistrator();
+ Set<String> dynamicProperties = extractDynamicProperties(type);
sample.setProperties(entityPropertiesConverter.updateProperties(existingProperties, type,
- properties, registrator, propertiesToUpdate));
+ properties, registrator, propertiesToUpdate, dynamicProperties));
}
public void prepareForUpdate(List<SampleBatchUpdatesDTO> updates)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/PropertiesEditor.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/PropertiesEditor.java
index 9bdc91e1342..49c5c7f2d3e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/PropertiesEditor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/PropertiesEditor.java
@@ -34,7 +34,6 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.P
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.FieldUtil;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.GWTUtils;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.lang.StringEscapeUtils;
-import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
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;
@@ -166,16 +165,7 @@ abstract public class PropertiesEditor<T extends EntityType, S extends EntityTyp
Object value = field.get().getValue();
final S etpt = field.get().getData(ETPT); // null for section labels
- // dynamic property should always have a placeholder value
- // that will be filled later by by calculator
- if (etpt != null && etpt.isDynamic())
- {
- final IEntityProperty entityProperty = createEntityProperty();
- entityProperty.setValue(BasicConstant.PLACEHOLDER_PROPERTY_VALUE);
- entityProperty.setPropertyType(etpt.getPropertyType());
- properties.add(entityProperty);
- } else if (etpt != null && value != null
- && PropertyFieldFactory.valueToString(value) != null)
+ if (etpt != null && value != null && PropertyFieldFactory.valueToString(value) != null)
{
final IEntityProperty entityProperty = createEntityProperty();
entityProperty.setValue(PropertyFieldFactory.valueToString(value));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
index f0d6adaa245..4033ba6771d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPropertyPE;
@@ -101,7 +102,7 @@ public final class ExperimentBOTest extends AbstractBOTest
{
{
one(propertiesConverter).updateProperties(oldProperties, entityType,
- newProperties, registrator);
+ newProperties, registrator, new HashSet<String>());
will(returnValue(new HashSet<ExperimentPropertyPE>(updated)));
}
@@ -167,12 +168,16 @@ public final class ExperimentBOTest extends AbstractBOTest
expBO.loadByExperimentIdentifier(identifier);
// Get first attachment
- AssertJUnit.assertEquals(attachment1, expBO.getExperimentFileAttachment(attachment1
- .getFileName(), attachment1.getVersion()));
+ AssertJUnit.assertEquals(
+ attachment1,
+ expBO.getExperimentFileAttachment(attachment1.getFileName(),
+ attachment1.getVersion()));
// Get another version of attachment
- AssertJUnit.assertEquals(attachment2, expBO.getExperimentFileAttachment(attachment2
- .getFileName(), attachment2.getVersion()));
+ AssertJUnit.assertEquals(
+ attachment2,
+ expBO.getExperimentFileAttachment(attachment2.getFileName(),
+ attachment2.getVersion()));
// Try find not existing version of attachment
testThrowingExceptionOnUnknownFileVersion(attachment2, expBO);
@@ -291,6 +296,10 @@ public final class ExperimentBOTest extends AbstractBOTest
one(projectDAO).tryFindProject(dbCode, groupCode, projectCode);
will(returnValue(null));
+
+ one(entityPropertyTypeDAO).listEntityPropertyTypes(type);
+ will(returnValue(new ArrayList<EntityTypePropertyTypePE>()));
+
}
});
final ExperimentBO experimentBO = createExperimentBO();
@@ -302,8 +311,8 @@ public final class ExperimentBOTest extends AbstractBOTest
{
exceptionThrown = true;
assertTrue(e.getMessage().indexOf(
- String.format(ExperimentBO.ERR_PROJECT_NOT_FOUND, createIdentifier(dbCode,
- groupCode, projectCode, expCode))) > -1);
+ String.format(ExperimentBO.ERR_PROJECT_NOT_FOUND,
+ createIdentifier(dbCode, groupCode, projectCode, expCode))) > -1);
}
assertTrue(exceptionThrown);
@@ -417,8 +426,8 @@ public final class ExperimentBOTest extends AbstractBOTest
final List<IEntityProperty> newProperties = createDummyProperties();
prepareUpdateProperties(exp.getProperties(), newProperties, experimentType,
- ManagerTestTool.EXAMPLE_SESSION.tryGetPerson(), Arrays.asList(changedProperty,
- addedProperty));
+ ManagerTestTool.EXAMPLE_SESSION.tryGetPerson(),
+ Arrays.asList(changedProperty, addedProperty));
bo.updateProperties(newProperties);
assertTrue(bo.getExperiment().getProperties().contains(changedProperty));
@@ -735,9 +744,7 @@ public final class ExperimentBOTest extends AbstractBOTest
exceptionThrown = false;
try
{
- expBO
- .getExperimentFileAttachment("nonexistentAttachment.txt", attachment2
- .getVersion());
+ expBO.getExperimentFileAttachment("nonexistentAttachment.txt", attachment2.getVersion());
} catch (UserFailureException e)
{
exceptionThrown = true;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
index bfbc5abf8b6..9218af07cce 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExternalDataBOTest.java
@@ -23,6 +23,7 @@ import java.util.Arrays;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
+import java.util.HashSet;
import java.util.List;
import org.hamcrest.BaseMatcher;
@@ -43,6 +44,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SourceType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
@@ -76,16 +78,15 @@ public class ExternalDataBOTest extends AbstractBOTest
private static final DatabaseInstanceIdentifier DATABASE_INSTANCE_IDENTIFIER =
new DatabaseInstanceIdentifier(ManagerTestTool.EXAMPLE_DATABASE_INSTANCE.getCode());
- private static final GroupIdentifier GROUP_IDENTIFIER =
- new GroupIdentifier(DATABASE_INSTANCE_IDENTIFIER, ManagerTestTool.EXAMPLE_GROUP
- .getCode());
+ private static final GroupIdentifier GROUP_IDENTIFIER = new GroupIdentifier(
+ DATABASE_INSTANCE_IDENTIFIER, ManagerTestTool.EXAMPLE_GROUP.getCode());
- private static final SampleIdentifier SAMPLE_IDENTIFIER =
- new SampleIdentifier(GROUP_IDENTIFIER, "EXAMPLE_SAMPLE");
+ private static final SampleIdentifier SAMPLE_IDENTIFIER = new SampleIdentifier(
+ GROUP_IDENTIFIER, "EXAMPLE_SAMPLE");
- private static final ExperimentIdentifier EXPERIMENT_IDENTIFIER =
- new ExperimentIdentifier(new ProjectIdentifier(GROUP_IDENTIFIER,
- ManagerTestTool.EXAMPLE_PROJECT.getCode()), "EXPERIMENT_CODE");
+ private static final ExperimentIdentifier EXPERIMENT_IDENTIFIER = new ExperimentIdentifier(
+ new ProjectIdentifier(GROUP_IDENTIFIER, ManagerTestTool.EXAMPLE_PROJECT.getCode()),
+ "EXPERIMENT_CODE");
private static final String DATA_STORE_CODE = "dss1";
@@ -160,7 +161,7 @@ public class ExternalDataBOTest extends AbstractBOTest
assertEquals(null, externalData.getRegistrator());
context.assertIsSatisfied();
}
-
+
@Test
public void testDefineWithUserID()
{
@@ -186,11 +187,11 @@ public class ExternalDataBOTest extends AbstractBOTest
will(returnValue(registrator));
}
});
-
+
IExternalDataBO dataBO = createExternalDataBO();
dataBO.define(data, sample, SourceType.DERIVED);
ExternalDataPE externalData = dataBO.getExternalData();
-
+
assertEquals(DATA_SET_CODE, externalData.getCode());
assertEquals(BooleanOrUnknown.U, externalData.getComplete());
assertEquals(DATA_PRODUCER_CODE, externalData.getDataProducerCode());
@@ -208,7 +209,7 @@ public class ExternalDataBOTest extends AbstractBOTest
assertSame(registrator, externalData.getRegistrator());
context.assertIsSatisfied();
}
-
+
@Test
public void testDefineWithUserEMail()
{
@@ -229,17 +230,17 @@ public class ExternalDataBOTest extends AbstractBOTest
final PersonPE registrator = new PersonPE();
registrator.setEmail(data.getUserEMail());
context.checking(new Expectations()
- {
{
- one(personDAO).listPersons();
- will(returnValue(Arrays.asList(new PersonPE(), registrator)));
- }
- });
-
+ {
+ one(personDAO).listPersons();
+ will(returnValue(Arrays.asList(new PersonPE(), registrator)));
+ }
+ });
+
IExternalDataBO dataBO = createExternalDataBO();
dataBO.define(data, sample, SourceType.DERIVED);
ExternalDataPE externalData = dataBO.getExternalData();
-
+
assertEquals(DATA_SET_CODE, externalData.getCode());
assertEquals(BooleanOrUnknown.U, externalData.getComplete());
assertEquals(DATA_PRODUCER_CODE, externalData.getDataProducerCode());
@@ -424,7 +425,7 @@ public class ExternalDataBOTest extends AbstractBOTest
will(returnValue(fileFormatTypePE));
one(propertiesConverter).checkMandatoryProperties(
- Collections.<DataSetPropertyPE> emptySet(), null);
+ Collections.<DataSetPropertyPE> emptySet(), dataSet.getDataSetType());
one(externalDataDAO).validateAndSaveUpdatedEntity(dataSet);
}
@@ -432,7 +433,6 @@ public class ExternalDataBOTest extends AbstractBOTest
IExternalDataBO dataBO = createExternalDataBO();
dataBO.update(dataSetUpdatesDTO);
-
context.assertIsSatisfied();
}
@@ -491,8 +491,8 @@ public class ExternalDataBOTest extends AbstractBOTest
fail("UserFailureException expected");
} catch (UserFailureException e)
{
- assertEquals("Data Sets with following codes do not exist: '[" + PARENT_CODE + "]'.", e
- .getMessage());
+ assertEquals("Data Sets with following codes do not exist: '[" + PARENT_CODE + "]'.",
+ e.getMessage());
}
context.assertIsSatisfied();
@@ -508,8 +508,8 @@ public class ExternalDataBOTest extends AbstractBOTest
will(returnValue(dataSet));
one(propertiesConverter).updateProperties(
- Collections.<DataSetPropertyPE> emptySet(), null, null,
- ManagerTestTool.EXAMPLE_PERSON);
+ Collections.<DataSetPropertyPE> emptySet(), dataSet.getDataSetType(),
+ null, ManagerTestTool.EXAMPLE_PERSON, Collections.<String> emptySet());
will(returnValue(Collections.emptySet()));
one(databaseInstanceDAO).tryFindDatabaseInstanceByCode(
@@ -576,6 +576,13 @@ public class ExternalDataBOTest extends AbstractBOTest
dataSet.setModificationDate(PRODUCTION_DATE);
dataSet.setSample(sampleOrNull);
dataSet.setExperiment(experimentOrNull);
+ DataSetTypePE dataSetType = new DataSetTypePE();
+ dataSetType.setCode(DATA_SET_TYPE.getCode());
+ DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
+ databaseInstance.setCode("db");
+ dataSetType.setDatabaseInstance(databaseInstance);
+ dataSetType.setDataSetTypePropertyTypes(new HashSet<DataSetTypePropertyTypePE>());
+ dataSet.setDataSetType(dataSetType);
return dataSet;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
index 67f6dc3cd53..419d06b3c34 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
@@ -26,6 +26,7 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Date;
+import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -71,6 +72,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
*/
public final class SampleBOTest extends AbstractBOTest
{
+ private static final String SAMPLE_TYPE = "sample-type";
+
private static final TechId SAMPLE_TECH_ID = CommonTestUtils.TECH_ID;
private static final String DB = "DB";
@@ -91,18 +94,28 @@ public final class SampleBOTest extends AbstractBOTest
final SamplePE sample = new SamplePE();
sample.setCode(DEFAULT_SAMPLE_CODE);
sample.setModificationDate(new Date());
+ sample.setSampleType(createSampleTypePE(SAMPLE_TYPE));
return sample;
}
+ private static SampleTypePE createSampleTypePE(String typeCode)
+ {
+ SampleTypePE sampleType = new SampleTypePE();
+ sampleType.setCode(typeCode);
+ DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
+ databaseInstance.setCode(DB);
+ sampleType.setDatabaseInstance(databaseInstance);
+ sampleType.setSampleTypePropertyTypes(new HashSet<SampleTypePropertyTypePE>());
+ return sampleType;
+ }
+
private static SamplePE createSample(final SampleIdentifier sampleIdentifier,
final String sampleTypeCode)
{
final SamplePE sample = new SamplePE();
sample.setCode(sampleIdentifier.getSampleCode());
sample.setRegistrator(EXAMPLE_PERSON);
- final SampleTypePE sampleTypeDTO = new SampleTypePE();
- sampleTypeDTO.setCode(sampleTypeCode);
- sample.setSampleType(sampleTypeDTO);
+ sample.setSampleType(createSampleTypePE(sampleTypeCode));
return sample;
}
@@ -380,6 +393,7 @@ public final class SampleBOTest extends AbstractBOTest
sample.setCode("sampleCode");
sample.setExperiment(sampleExperiment);
sample.setGroup(EXAMPLE_GROUP);
+ sample.setSampleType(createSampleTypePE(SAMPLE_TYPE));
Date now = new Date();
sample.setModificationDate(now);
@@ -578,6 +592,7 @@ public final class SampleBOTest extends AbstractBOTest
sample.setId(SAMPLE_TECH_ID.getId());
sample.setCode(code);
sample.setGroup(group);
+ sample.setSampleType(createSampleTypePE(SAMPLE_TYPE));
return sample;
}
@@ -714,8 +729,8 @@ public final class SampleBOTest extends AbstractBOTest
try
{
SampleUpdatesDTO updates =
- new SampleUpdatesDTO(SAMPLE_TECH_ID, null, null, Collections
- .<NewAttachment> emptyList(), now, null, null, null);
+ new SampleUpdatesDTO(SAMPLE_TECH_ID, null, null,
+ Collections.<NewAttachment> emptyList(), now, null, null, null);
createSampleBO().update(updates);
} catch (UserFailureException e)
{
@@ -972,8 +987,8 @@ public final class SampleBOTest extends AbstractBOTest
context.checking(new Expectations()
{
{
- one(propertiesConverter).updateProperties(sample.getProperties(), null, null,
- EXAMPLE_PERSON);
+ one(propertiesConverter).updateProperties(sample.getProperties(),
+ sample.getSampleType(), null, EXAMPLE_PERSON, new HashSet<String>());
}
});
}
--
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