From 2c90904c2c06ddb8753e2d7a10f924c939cf21c9 Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Thu, 5 Nov 2015 12:18:37 +0000
Subject: [PATCH] SSDM-2706 : V3 AS API - create data sets (only metadata) -
check that container is actually of container type (also during data set
update)
SVN: 34997
---
.../UpdateDataSetChildrenExecutor.java | 2 +-
.../UpdateDataSetContainedExecutor.java | 8 +-
.../UpdateDataSetContainersExecutor.java | 8 +-
.../dataset/UpdateDataSetParentsExecutor.java | 2 +-
...actUpdateEntityToManyRelationExecutor.java | 6 +-
.../sample/UpdateSampleChildrenExecutor.java | 2 +-
.../sample/UpdateSampleContainedExecutor.java | 2 +-
.../sample/UpdateSampleParentsExecutor.java | 2 +-
.../systemtest/api/v3/UpdateDataSetTest.java | 93 +++++++++++--------
9 files changed, 78 insertions(+), 47 deletions(-)
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetChildrenExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetChildrenExecutor.java
index 98c695ecf35..4bb8661d9f6 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetChildrenExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetChildrenExecutor.java
@@ -50,7 +50,7 @@ public class UpdateDataSetChildrenExecutor extends AbstractUpdateEntityToManyRel
}
@Override
- protected void check(IOperationContext context, IDataSetId relatedId, DataPE related)
+ protected void check(IOperationContext context, DataPE entity, IDataSetId relatedId, DataPE related)
{
if (false == new DataSetPEByExperimentOrSampleIdentifierValidator().doValidation(context.getSession().tryGetPerson(), related))
{
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetContainedExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetContainedExecutor.java
index 38e9b7d0e11..ebc4cc7f81f 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetContainedExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetContainedExecutor.java
@@ -26,6 +26,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.IdListUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.dataset.DataSetUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.dataset.IDataSetId;
import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnauthorizedObjectAccessException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.DataSetPEByExperimentOrSampleIdentifierValidator;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
@@ -50,12 +51,17 @@ public class UpdateDataSetContainedExecutor extends AbstractUpdateEntityToManyRe
}
@Override
- protected void check(IOperationContext context, IDataSetId relatedId, DataPE related)
+ protected void check(IOperationContext context, DataPE entity, IDataSetId relatedId, DataPE related)
{
if (false == new DataSetPEByExperimentOrSampleIdentifierValidator().doValidation(context.getSession().tryGetPerson(), related))
{
throw new UnauthorizedObjectAccessException(relatedId);
}
+ if (false == entity.isContainer())
+ {
+ throw new UserFailureException("Data set " + entity.getCode()
+ + " is not of a container type therefore cannot have contained data sets.");
+ }
}
@Override
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetContainersExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetContainersExecutor.java
index ff2c02d7631..ea2bf487edf 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetContainersExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetContainersExecutor.java
@@ -26,6 +26,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.IdListUpdateValue;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.dataset.DataSetUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.dataset.IDataSetId;
import ch.ethz.sis.openbis.generic.shared.api.v3.exceptions.UnauthorizedObjectAccessException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.DataSetPEByExperimentOrSampleIdentifierValidator;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
@@ -50,7 +51,7 @@ public class UpdateDataSetContainersExecutor extends AbstractUpdateEntityToManyR
}
@Override
- protected void check(IOperationContext context, IDataSetId relatedId, DataPE related)
+ protected void check(IOperationContext context, DataPE entity, IDataSetId relatedId, DataPE related)
{
if (false == new DataSetPEByExperimentOrSampleIdentifierValidator().doValidation(context.getSession().tryGetPerson(), related))
{
@@ -61,6 +62,11 @@ public class UpdateDataSetContainersExecutor extends AbstractUpdateEntityToManyR
@Override
protected void add(IOperationContext context, DataPE entity, DataPE related)
{
+ if (false == related.isContainer())
+ {
+ throw new UserFailureException("Data set " + related.getCode()
+ + " is not of a container type therefore cannot be set as a container of data set " + entity.getCode() + ".");
+ }
relationshipService.assignDataSetToContainer(context.getSession(), entity, related);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetParentsExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetParentsExecutor.java
index 18e9c620d73..45fa1be56b9 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetParentsExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/UpdateDataSetParentsExecutor.java
@@ -50,7 +50,7 @@ public class UpdateDataSetParentsExecutor extends AbstractUpdateEntityToManyRela
}
@Override
- protected void check(IOperationContext context, IDataSetId relatedId, DataPE related)
+ protected void check(IOperationContext context, DataPE entity, IDataSetId relatedId, DataPE related)
{
if (false == new DataSetPEByExperimentOrSampleIdentifierValidator().doValidation(context.getSession().tryGetPerson(), related))
{
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/AbstractUpdateEntityToManyRelationExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/AbstractUpdateEntityToManyRelationExecutor.java
index 3aea1576484..f0e393550c4 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/AbstractUpdateEntityToManyRelationExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/AbstractUpdateEntityToManyRelationExecutor.java
@@ -69,7 +69,7 @@ public abstract class AbstractUpdateEntityToManyRelationExecutor<ENTITY_UPDATE,
{
throw new ObjectNotFoundException((IObjectId) relatedId);
}
- check(context, relatedId, related);
+ check(context, entity, relatedId, related);
relatedCollection.add(related);
}
if (action instanceof ListUpdateActionSet<?>)
@@ -88,7 +88,7 @@ public abstract class AbstractUpdateEntityToManyRelationExecutor<ENTITY_UPDATE,
{
relatedCollection.add(related);
}
- check(context, relatedId, related);
+ check(context, entity, relatedId, related);
}
remove(context, entity, relatedCollection);
}
@@ -150,7 +150,7 @@ public abstract class AbstractUpdateEntityToManyRelationExecutor<ENTITY_UPDATE,
protected abstract IdListUpdateValue<? extends RELATED_ID> getRelatedUpdate(IOperationContext context, ENTITY_UPDATE update);
- protected abstract void check(IOperationContext context, RELATED_ID relatedId, RELATED_PE related);
+ protected abstract void check(IOperationContext context, ENTITY_PE entity, RELATED_ID relatedId, RELATED_PE related);
protected abstract void add(IOperationContext context, ENTITY_PE entity, RELATED_PE related);
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleChildrenExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleChildrenExecutor.java
index ce44efe248f..bc545a1e594 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleChildrenExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleChildrenExecutor.java
@@ -50,7 +50,7 @@ public class UpdateSampleChildrenExecutor extends AbstractUpdateEntityToManyRela
}
@Override
- protected void check(IOperationContext context, ISampleId relatedId, SamplePE related)
+ protected void check(IOperationContext context, SamplePE entity, ISampleId relatedId, SamplePE related)
{
if (false == new SampleByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), related))
{
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainedExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainedExecutor.java
index b953ab667ed..3c6b0e7f62a 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainedExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleContainedExecutor.java
@@ -54,7 +54,7 @@ public class UpdateSampleContainedExecutor extends AbstractUpdateEntityToManyRel
}
@Override
- protected void check(IOperationContext context, ISampleId relatedId, SamplePE related)
+ protected void check(IOperationContext context, SamplePE entity, ISampleId relatedId, SamplePE related)
{
if (false == new SampleByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), related))
{
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleParentsExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleParentsExecutor.java
index 3bb5a25881d..2957285e084 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleParentsExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/UpdateSampleParentsExecutor.java
@@ -50,7 +50,7 @@ public class UpdateSampleParentsExecutor extends AbstractUpdateEntityToManyRelat
}
@Override
- protected void check(IOperationContext context, ISampleId relatedId, SamplePE related)
+ protected void check(IOperationContext context, SamplePE entity, ISampleId relatedId, SamplePE related)
{
if (false == new SampleByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), related))
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateDataSetTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateDataSetTest.java
index 66a794e7dd8..d303760860e 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateDataSetTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/UpdateDataSetTest.java
@@ -27,9 +27,6 @@ import java.util.Map;
import org.testng.annotations.Test;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue.ListUpdateAction;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue.ListUpdateActionAdd;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.ListUpdateValue.ListUpdateActionRemove;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.dataset.DataSet;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.dataset.DataSetUpdate;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.dataset.PhysicalDataUpdate;
@@ -42,7 +39,6 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentIde
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.IExperimentId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
-import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.tag.ITagId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.tag.TagCode;
import ch.systemsx.cisd.common.action.IDelegatedAction;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -399,10 +395,7 @@ public class UpdateDataSetTest extends AbstractSampleTest
DataSetUpdate update = new DataSetUpdate();
update.setDataSetId(dataSetId);
- ListUpdateAction<IDataSetId> addAction = new ListUpdateActionAdd<IDataSetId>();
- addAction.setItems(Collections.singletonList(new DataSetPermId("20081105092259000-20")));
-
- update.setParentActions(Collections.singletonList(addAction));
+ update.getParentIds().add(new DataSetPermId("20081105092259000-20"));
v3api.updateDataSets(sessionToken, Collections.singletonList(update));
@@ -423,9 +416,7 @@ public class UpdateDataSetTest extends AbstractSampleTest
DataSetUpdate update = new DataSetUpdate();
update.setDataSetId(originalChild);
- ListUpdateAction<IDataSetId> removeAction = new ListUpdateActionRemove<IDataSetId>();
- removeAction.setItems(Collections.singletonList(originalParent));
- update.setParentActions(Collections.singletonList(removeAction));
+ update.getParentIds().remove(originalParent);
assertRemovingParent(originalChild, originalParent, update);
}
@@ -460,9 +451,7 @@ public class UpdateDataSetTest extends AbstractSampleTest
DataSetUpdate update = new DataSetUpdate();
update.setDataSetId(originalParent);
- ListUpdateAction<IDataSetId> removeAction = new ListUpdateActionRemove<IDataSetId>();
- removeAction.setItems(Collections.singletonList(originalChild));
- update.setChildActions(Collections.singletonList(removeAction));
+ update.getChildIds().remove(originalChild);
assertRemovingParent(originalChild, originalParent, update);
}
@@ -494,8 +483,8 @@ public class UpdateDataSetTest extends AbstractSampleTest
{
final String sessionToken = v3api.login(TEST_USER, PASSWORD);
- DataSetPermId dataSetId = new DataSetPermId("20081105092259000-8");
- final DataSetPermId componentId = new DataSetPermId("20081105092259000-9");
+ DataSetPermId dataSetId = new DataSetPermId("CONTAINER_1");
+ final DataSetPermId componentId = new DataSetPermId("CONTAINER_2");
final DataSetUpdate update = new DataSetUpdate();
update.setDataSetId(dataSetId);
@@ -509,7 +498,7 @@ public class UpdateDataSetTest extends AbstractSampleTest
{
v3api.updateDataSets(sessionToken, Collections.singletonList(update));
}
- }, "Circular dependency found: 20081105092259000-8");
+ }, "Circular dependency found: CONTAINER_1");
}
@Test
@@ -521,12 +510,8 @@ public class UpdateDataSetTest extends AbstractSampleTest
DataSetUpdate update = new DataSetUpdate();
update.setDataSetId(dataSetId);
- ListUpdateActionAdd<IDataSetId> addAction = new ListUpdateActionAdd<IDataSetId>();
- ListUpdateAction<IDataSetId> removeAction = new ListUpdateActionRemove<IDataSetId>();
- addAction.setItems(Collections.singletonList(new DataSetPermId("COMPONENT_2A")));
- removeAction.setItems(Collections.singletonList(new DataSetPermId("COMPONENT_1A")));
-
- update.setContainedActions(Arrays.asList(addAction, removeAction));
+ update.getContainedIds().add(new DataSetPermId("COMPONENT_2A"));
+ update.getContainedIds().remove(new DataSetPermId("COMPONENT_1A"));
v3api.updateDataSets(sessionToken, Collections.singletonList(update));
@@ -537,6 +522,25 @@ public class UpdateDataSetTest extends AbstractSampleTest
AssertionUtil.assertCollectionContainsOnly(dataSetCodes(result.getContained()), "COMPONENT_1B", "COMPONENT_2A");
}
+ @Test
+ public void testUpdateWithComponentWithNonContainerDataSet()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetUpdate update = new DataSetUpdate();
+ update.setDataSetId(new DataSetPermId("COMPONENT_1A"));
+ update.getContainedIds().add(new DataSetPermId("COMPONENT_2A"));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.updateDataSets(sessionToken, Collections.singletonList(update));
+ }
+ }, "Data set COMPONENT_1A is not of a container type therefore cannot have contained data sets.");
+ }
+
@Test
public void testUpdateWithContainerAddRemove()
{
@@ -550,12 +554,8 @@ public class UpdateDataSetTest extends AbstractSampleTest
DataSetUpdate update = new DataSetUpdate();
update.setDataSetId(dataSetId);
- ListUpdateActionAdd<IDataSetId> addAction = new ListUpdateActionAdd<IDataSetId>();
- ListUpdateAction<IDataSetId> removeAction = new ListUpdateActionRemove<IDataSetId>();
- addAction.setItems(Arrays.asList(cont2, cont3a));
- removeAction.setItems(Collections.singletonList(cont1));
-
- update.setContainerActions(Arrays.asList(addAction, removeAction));
+ update.getContainerIds().add(cont2, cont3a);
+ update.getContainerIds().remove(cont1);
v3api.updateDataSets(sessionToken, Collections.singletonList(update));
@@ -572,6 +572,28 @@ public class UpdateDataSetTest extends AbstractSampleTest
AssertionUtil.assertCollectionContains(dataSetCodes(map.get(cont3a).getContained()), dataSetId.getPermId());
}
+ @Test
+ public void testUpdateWithContainerAddNotContainerDataSet()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ DataSetPermId dataSetId = new DataSetPermId("CONTAINER_1");
+ DataSetPermId containerId = new DataSetPermId("COMPONENT_2A");
+
+ final DataSetUpdate update = new DataSetUpdate();
+ update.setDataSetId(dataSetId);
+ update.getContainerIds().add(containerId);
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.updateDataSets(sessionToken, Collections.singletonList(update));
+ }
+ }, "Data set COMPONENT_2A is not of a container type therefore cannot be set as a container of data set CONTAINER_1.");
+ }
+
@Test
public void testUpdateWithContainerUnauthorized()
{
@@ -610,9 +632,8 @@ public class UpdateDataSetTest extends AbstractSampleTest
// add tag1
DataSetUpdate firstUpdate = new DataSetUpdate();
firstUpdate.setDataSetId(dataSet);
- ListUpdateAction<ITagId> addAction = new ListUpdateActionAdd<ITagId>();
- addAction.setItems(Arrays.asList(newTag1));
- firstUpdate.setTagActions(Arrays.asList(addAction));
+ firstUpdate.getTagIds().add(newTag1);
+
v3api.updateDataSets(sessionToken, Arrays.asList(firstUpdate));
Map<IDataSetId, DataSet> result = v3api.mapDataSets(sessionToken, Arrays.asList(dataSet), fe);
@@ -621,11 +642,9 @@ public class UpdateDataSetTest extends AbstractSampleTest
// remove test_metaprojects and add a new tag2
DataSetUpdate secondUpdate = new DataSetUpdate();
secondUpdate.setDataSetId(dataSet);
- addAction = new ListUpdateActionAdd<ITagId>();
- ListUpdateAction<ITagId> removeAction = new ListUpdateActionRemove<ITagId>();
- addAction.setItems(Arrays.asList(newTag2));
- removeAction.setItems(Arrays.asList(existingTag));
- secondUpdate.setTagActions(Arrays.asList(addAction, removeAction));
+ secondUpdate.getTagIds().remove(existingTag);
+ secondUpdate.getTagIds().add(newTag2);
+
v3api.updateDataSets(sessionToken, Arrays.asList(secondUpdate));
result = v3api.mapDataSets(sessionToken, Arrays.asList(dataSet), fe);
--
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