diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index 20db614b3cd84f8ef0051d06429793b8aa27ecf7..1f3be2df8d235b043edef01d1f35ed824366fd5e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -1576,7 +1576,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
columns.add(NewSample.IDENTIFIER_COLUMN);
}
columns.add(NewSample.CONTAINER);
- columns.add(NewSample.PARENT);
+ columns.add(NewSample.PARENTS);
if (withExperiments)
columns.add(NewSample.EXPERIMENT);
addProperties(columns, ((SampleTypePE) entityType).getSampleTypePropertyTypes());
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 0fa57e1cb497d584126a93a1927032e53c872e6c..bd31cad1aa7c6e9c70ef8b759b40ad8832ddba20 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
@@ -206,7 +206,7 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
final SamplePE samplePE, String parentIdentifier)
{
final Set<SamplePE> newParents = new HashSet<SamplePE>();
- final SamplePE parentOrNull = tryGetValidSample(parentIdentifier, sampleIdentifier);
+ final SamplePE parentOrNull = tryGetValidParentSample(parentIdentifier, sampleIdentifier);
if (parentOrNull != null)
{
newParents.add(parentOrNull);
@@ -230,6 +230,7 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
final Set<SamplePE> parentPEs = new HashSet<SamplePE>();
for (SampleIdentifier si : parentIdentifiers)
{
+ // TODO 2010-11-10, Piotr Buczek: use cache
SamplePE parent = getSampleByIdentifier(si);
parentPEs.add(parent);
}
@@ -238,6 +239,10 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
private void replaceParents(SamplePE child, Set<SamplePE> newParents)
{
+ for (SamplePE parent : newParents)
+ {
+ checkParentInvalidation(parent, child.getSampleIdentifier());
+ }
List<SampleRelationshipPE> oldParents = new ArrayList<SampleRelationshipPE>();
for (SampleRelationshipPE r : child.getParentRelationships())
{
@@ -280,8 +285,8 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
return result;
}
- private SamplePE tryGetValidSample(final String parentIdentifierOrNull,
- final SampleIdentifier sampleIdentifier)
+ private SamplePE tryGetValidParentSample(final String parentIdentifierOrNull,
+ final SampleIdentifier childIdentifier)
{
if (parentIdentifierOrNull == null)
{
@@ -289,19 +294,24 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
}
final SamplePE parentPE =
getSampleByIdentifier(SampleIdentifierFactory.parse(parentIdentifierOrNull));
+ checkParentInvalidation(parentPE, childIdentifier);
+ return parentPE;
+ }
+
+ private void checkParentInvalidation(final SamplePE parentPE, final SampleIdentifier child)
+ {
if (parentPE.getInvalidation() != null)
{
throw UserFailureException.fromTemplate(
- "Cannot register sample '%s': parent '%s' has been invalidated.",
- sampleIdentifier, parentIdentifierOrNull);
+ "Sample '%s' has been invalidated and can't become a parent of sample '%s'.",
+ parentPE.getIdentifier(), child);
}
- return parentPE;
}
private SamplePE tryGetValidNotContainedSample(final String parentIdentifierOrNull,
final SampleIdentifier sampleIdentifier)
{
- SamplePE sample = tryGetValidSample(parentIdentifierOrNull, sampleIdentifier);
+ SamplePE sample = tryGetValidParentSample(parentIdentifierOrNull, sampleIdentifier);
if (sample != null && sample.getContainer() != null)
{
throw UserFailureException.fromTemplate(
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleIdentifierBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleIdentifierBusinessObject.java
index 767854451664157a48de29c90bc4183e8e07c281..b504e0c0ffba7fbc15a414dca287bf4b24008f2f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleIdentifierBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleIdentifierBusinessObject.java
@@ -70,6 +70,7 @@ abstract class AbstractSampleIdentifierBusinessObject extends AbstractBusinessOb
protected SamplePE tryToGetSampleByIdentifier(final SampleIdentifier sampleIdentifier)
{
+ // TODO 2010-11-10, Piotr Buczek: use cache
assert sampleIdentifier != null : "Sample identifier unspecified.";
final SampleOwner sampleOwner = sampleOwnerFinder.figureSampleOwner(sampleIdentifier);
final String sampleCode = sampleIdentifier.getSampleCode();
@@ -78,8 +79,8 @@ abstract class AbstractSampleIdentifierBusinessObject extends AbstractBusinessOb
if (sampleOwner.isDatabaseInstanceLevel())
{
sample =
- sampleDAO.tryFindByCodeAndDatabaseInstance(sampleCode, sampleOwner
- .tryGetDatabaseInstance());
+ sampleDAO.tryFindByCodeAndDatabaseInstance(sampleCode,
+ sampleOwner.tryGetDatabaseInstance());
} else
{
assert sampleOwner.isGroupLevel() : "Must be of space level.";
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 7b3b58b875ba85f46cf8187eaf8e5abc42df2c48..50aacbf294a13c578df3150146dd32fb2068be13 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
@@ -251,6 +251,14 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
setGeneratedFrom(updates.getSampleIdentifier(), sample,
updates.getParentIdentifierOrNull());
}
+ if (details.isParentsUpdateRequested())
+ {
+ final String[] parents = updates.getModifiedParentCodesOrNull();
+ if (parents != null)
+ {
+ setParents(sample, parents);
+ }
+ }
if (details.isContainerUpdateRequested())
{
setContainer(updates.getSampleIdentifier(), sample,
@@ -258,7 +266,8 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
}
// NOTE: Checking business rules with relationships is expensive.
// Don't perform them unless relevant data were changed.
- if (details.isExperimentUpdateRequested() || details.isParentUpdateRequested())
+ if (details.isExperimentUpdateRequested() || details.isParentUpdateRequested()
+ || details.isParentsUpdateRequested())
{
checkParentBusinessRules(sample);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
index 4fd95b58100507e36fdfa890e2d8b26ceb6fd621..39dad9bdc5ff89cb4722f157ba4621eff7c8d988 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
@@ -39,6 +39,8 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
public static final String PARENT = "parent";
+ public static final String PARENTS = "parents";
+
public static final String EXPERIMENT = "experiment";
private SampleType sampleType;
@@ -97,11 +99,12 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
}
public NewSample(final String identifier, SampleType sampleType, String containerIdentifier,
- String parentIdentifier, String experimentIdentifier, IEntityProperty[] properties,
- List<NewAttachment> attachments)
+ String parentIdentifier, String[] parentsOrNull, String experimentIdentifier,
+ IEntityProperty[] properties, List<NewAttachment> attachments)
{
this(identifier, sampleType, containerIdentifier);
this.parentIdentifier = parentIdentifier;
+ this.parentsOrNull = parentsOrNull;
this.experimentIdentifier = experimentIdentifier;
this.properties = properties;
this.attachments = attachments;
@@ -137,6 +140,19 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
this.parentsOrNull = parents;
}
+ @BeanProperty(label = PARENTS, optional = true)
+ public void setParents(String parents)
+ {
+ if (parents != null)
+ {
+ String[] split = parents.split(",");
+ setParents(split);
+ } else
+ {
+ setParents((String[]) null);
+ }
+ }
+
public final String getParentIdentifier()
{
return parentIdentifier;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RelationshipType.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RelationshipType.java
new file mode 100644
index 0000000000000000000000000000000000000000..478f951659a9d3840b09d37360c043404d2baa5d
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/RelationshipType.java
@@ -0,0 +1,123 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
+
+import java.io.Serializable;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+/**
+ * The <i>GWT</i> version of RelationshipTypePE.
+ *
+ * @author Piotr Buczek
+ */
+public class RelationshipType extends Code<PropertyType> implements IsSerializable, Serializable
+{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+ private Long id;
+
+ /**
+ * Only used for displaying/viewing. With <code>managedInternally</code> is unambiguous (meaning
+ * that <code>simpleCode</code> alone could be not unique).
+ * <p>
+ * We have to use it, partly because <i>Javascript</i> handle '.' in an object-oriented way.
+ * </p>
+ */
+ private String simpleCode;
+
+ private boolean internalNamespace;
+
+ private boolean managedInternally;
+
+ private String description;
+
+ private String label;
+
+ private DatabaseInstance databaseInstance;
+
+ public Long getId()
+ {
+ return id;
+ }
+
+ public void setId(Long id)
+ {
+ this.id = id;
+ }
+
+ public String getSimpleCode()
+ {
+ return simpleCode;
+ }
+
+ public void setSimpleCode(String simpleCode)
+ {
+ this.simpleCode = simpleCode;
+ }
+
+ public boolean isInternalNamespace()
+ {
+ return internalNamespace;
+ }
+
+ public void setInternalNamespace(boolean internalNamespace)
+ {
+ this.internalNamespace = internalNamespace;
+ }
+
+ public boolean isManagedInternally()
+ {
+ return managedInternally;
+ }
+
+ public void setManagedInternally(boolean managedInternally)
+ {
+ this.managedInternally = managedInternally;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ public String getLabel()
+ {
+ return label;
+ }
+
+ public void setLabel(String label)
+ {
+ this.label = label;
+ }
+
+ public DatabaseInstance getDatabaseInstance()
+ {
+ return databaseInstance;
+ }
+
+ public void setDatabaseInstance(DatabaseInstance databaseInstance)
+ {
+ this.databaseInstance = databaseInstance;
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleBatchUpdateDetails.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleBatchUpdateDetails.java
index a67c64b290d373761158a9e6d748980705122c84..246ba61e934dd6d7329e6c2f620377d174a8efb9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleBatchUpdateDetails.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleBatchUpdateDetails.java
@@ -34,6 +34,8 @@ public class SampleBatchUpdateDetails implements IsSerializable, Serializable
private boolean parentUpdateRequested;
+ private boolean parentsUpdateRequested;
+
private boolean containerUpdateRequested;
private Set<String> propertiesToUpdate; // codes of properties to update
@@ -43,10 +45,11 @@ public class SampleBatchUpdateDetails implements IsSerializable, Serializable
}
public SampleBatchUpdateDetails(boolean updateExperiment, boolean updateParent,
- boolean updateContainer, Set<String> propertiesToUpdate)
+ boolean updateParents, boolean updateContainer, Set<String> propertiesToUpdate)
{
this.experimentUpdateRequested = updateExperiment;
this.parentUpdateRequested = updateParent;
+ this.parentsUpdateRequested = updateParents;
this.containerUpdateRequested = updateContainer;
this.propertiesToUpdate = propertiesToUpdate;
}
@@ -61,6 +64,11 @@ public class SampleBatchUpdateDetails implements IsSerializable, Serializable
return parentUpdateRequested;
}
+ public boolean isParentsUpdateRequested()
+ {
+ return parentsUpdateRequested;
+ }
+
public boolean isContainerUpdateRequested()
{
return containerUpdateRequested;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/UpdatedSample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/UpdatedSample.java
index c028671370816ef1b291ebb5b65e6ba67fbd5c80..6a531d9baa29f0c93429636b79328348577e3cbf 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/UpdatedSample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/UpdatedSample.java
@@ -40,8 +40,9 @@ public final class UpdatedSample extends NewSample
public UpdatedSample(NewSample newSample, SampleBatchUpdateDetails batchUpdateDetails)
{
super(newSample.getIdentifier(), newSample.getSampleType(), newSample
- .getContainerIdentifier(), newSample.getParentIdentifier(), newSample
- .getExperimentIdentifier(), newSample.getProperties(), newSample.getAttachments());
+ .getContainerIdentifier(), newSample.getParentIdentifier(), newSample.getParents(),
+ newSample.getExperimentIdentifier(), newSample.getProperties(), newSample
+ .getAttachments());
this.batchUpdateDetails = batchUpdateDetails;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
index 17558aa8b83083ed2a16380e086301cd16dd2057..51a94ce4e0940617bb3b3a4cf0209dbe51285de1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
@@ -54,9 +54,10 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
{
boolean updateExperiment = isColumnAvailable(UpdatedSample.EXPERIMENT);
boolean updateParent = isColumnAvailable(UpdatedSample.PARENT);
+ boolean updateParents = isColumnAvailable(UpdatedSample.PARENTS);
boolean updateContainer = isColumnAvailable(UpdatedSample.CONTAINER);
- return new SampleBatchUpdateDetails(updateExperiment, updateParent, updateContainer,
- getUnmatchedProperties());
+ return new SampleBatchUpdateDetails(updateExperiment, updateParent, updateParents,
+ updateContainer, getUnmatchedProperties());
}
//
@@ -88,6 +89,9 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
final boolean updateParent =
basicBatchUpdateDetails.isParentUpdateRequested()
&& isNotEmpty(newSample.getParentIdentifier());
+ final boolean updateParents =
+ basicBatchUpdateDetails.isParentsUpdateRequested()
+ && isNotEmpty(newSample.getParents());
final boolean updateContainer =
basicBatchUpdateDetails.isContainerUpdateRequested()
&& isNotEmpty(newSample.getContainerIdentifier());
@@ -98,8 +102,13 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
propertiesToUpdate.add(property.getPropertyType().getCode());
}
- return new SampleBatchUpdateDetails(updateExperiment, updateParent, updateContainer,
- propertiesToUpdate);
+ return new SampleBatchUpdateDetails(updateExperiment, updateParent, updateParents,
+ updateContainer, propertiesToUpdate);
+ }
+
+ private boolean isNotEmpty(String[] parents)
+ {
+ return parents != null && parents.length > 0 && isNotEmpty(parents[0]);
}
/** Cleans properties and connections of the specified sample that are marked for deletion. */
@@ -113,6 +122,10 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
{
newSample.setParentIdentifier(null);
}
+ if (newSample.getParents() != null && isDeletionMark(newSample.getParents()[0]))
+ {
+ newSample.setParents(new String[0]);
+ }
if (isDeletionMark(newSample.getContainerIdentifier()))
{
newSample.setContainerIdentifier(null);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index e7c8a5ba4e62936dfbbec6a9de0c8f9ad3829805..3e71b8aaba57fa3a2f48b874d59e5a8a668db29a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -481,7 +481,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
}
final String parentIdentifierOrNull = updatedSample.getParentIdentifier();
final String[] parentsOrNull =
- (parentIdentifierOrNull == null) ? new String[0] : new String[]
+ (parentIdentifierOrNull == null) ? updatedSample.getParents() : new String[]
{ parentIdentifierOrNull };
final String containerIdentifierOrNull = updatedSample.getContainerIdentifier();
final SampleBatchUpdateDetails batchUpdateDetails =
@@ -508,7 +508,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
propertyCodes.add(p.getPropertyType().getCode());
}
SampleBatchUpdateDetails result =
- new SampleBatchUpdateDetails(false, false, false, propertyCodes);
+ new SampleBatchUpdateDetails(false, false, false, false, propertyCodes);
return result;
}
}