From 15f64e46d102ae3ee0e2c5d824d23c24c4fbf2a7 Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Mon, 2 Nov 2015 13:51:52 +0000
Subject: [PATCH] SSDM-2706 : V3 AS API - create data sets (only metadata) -
unit tests
SVN: 34962
---
.../dataset/CreateDataSetExecutor.java | 4 +
...ifyDataSetSampleAndExperimentExecutor.java | 28 ++
.../dataset/SetDataSetSampleExecutor.java | 50 --
.../dataset/VerifyDataSetExecutor.java | 4 +
...ifyDataSetSampleAndExperimentExecutor.java | 130 ++++++
.../entity/AbstractCreateEntityExecutor.java | 4 +-
openbis/source/java/service.properties | 2 +-
.../systemtest/api/v3/CreateDataSetTest.java | 441 ++++++++++++++++++
.../systemtest/api/v3/CreateSampleTest.java | 24 +-
.../sql/postgresql/149/014=data_set_types.tsv | 1 +
10 files changed, 623 insertions(+), 65 deletions(-)
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/IVerifyDataSetSampleAndExperimentExecutor.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/VerifyDataSetSampleAndExperimentExecutor.java
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/CreateDataSetExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/CreateDataSetExecutor.java
index f29740a75f9..16a766b65f6 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/CreateDataSetExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/CreateDataSetExecutor.java
@@ -105,6 +105,10 @@ public class CreateDataSetExecutor extends AbstractCreateEntityExecutor<DataSetC
{
throw new UserFailureException("Type id cannot be null.");
}
+ if (creation.getExperimentId() == null && creation.getSampleId() == null)
+ {
+ throw new UserFailureException("Experiment id and sample id cannot be both null.");
+ }
}
@Override
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/IVerifyDataSetSampleAndExperimentExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/IVerifyDataSetSampleAndExperimentExecutor.java
new file mode 100644
index 00000000000..26dfb39ea5a
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/IVerifyDataSetSampleAndExperimentExecutor.java
@@ -0,0 +1,28 @@
+/*
+ * Copyright 2015 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.ethz.sis.openbis.generic.server.api.v3.executor.dataset;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.entity.IVerifyEntityRelationsExecutor;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+
+/**
+ * @author pkupczyk
+ */
+public interface IVerifyDataSetSampleAndExperimentExecutor extends IVerifyEntityRelationsExecutor<DataPE>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/SetDataSetSampleExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/SetDataSetSampleExecutor.java
index 4de346e9243..2b8da7690b7 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/SetDataSetSampleExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/SetDataSetSampleExecutor.java
@@ -16,22 +16,13 @@
package ch.ethz.sis.openbis.generic.server.api.v3.executor.dataset;
-import java.util.Properties;
-
-import javax.annotation.PostConstruct;
-import javax.annotation.Resource;
-
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.entity.AbstractSetEntitySampleRelationExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.dataset.DataSetCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.spring.ExposablePropertyPlaceholderConfigurer;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.util.DataSetTypeWithoutExperimentChecker;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.util.RelationshipUtils;
@@ -43,17 +34,6 @@ public class SetDataSetSampleExecutor extends AbstractSetEntitySampleRelationExe
ISetDataSetSampleExecutor
{
- @Resource(name = ExposablePropertyPlaceholderConfigurer.PROPERTY_CONFIGURER_BEAN_NAME)
- protected ExposablePropertyPlaceholderConfigurer configurer;
-
- private DataSetTypeWithoutExperimentChecker dataSetTypeChecker;
-
- @PostConstruct
- public void init() throws Exception
- {
- dataSetTypeChecker = new DataSetTypeWithoutExperimentChecker(configurer == null ? new Properties() : configurer.getResolvedProps());
- }
-
@Override
protected ISampleId getRelatedId(DataSetCreation creation)
{
@@ -65,39 +45,9 @@ public class SetDataSetSampleExecutor extends AbstractSetEntitySampleRelationExe
{
if (related != null)
{
- assertAllowedSampleForDataSet(entity, related);
RelationshipUtils.setSampleForDataSet(entity, related, context.getSession());
RelationshipUtils.setExperimentForDataSet(entity, related.getExperiment(), context.getSession());
}
}
- private void assertAllowedSampleForDataSet(DataPE dataSet, SamplePE sample)
- {
- ExperimentPE experiment = sample.getExperiment();
-
- if (experiment == null)
- {
- if (dataSetTypeChecker.isDataSetTypeWithoutExperiment(dataSet.getDataSetType().getCode()))
- {
- if (sample.getSpace() == null)
- {
- throw new UserFailureException("Data set can not be registered because sample '"
- + sample.getSampleIdentifier() + "' is a shared sample.");
- } else if (sample.getDeletion() != null)
- {
- throw new UserFailureException("Data set can not be registered because sample '"
- + sample.getSampleIdentifier() + "' is in trash.");
- }
- } else
- {
- throw new UserFailureException("Data set can not be registered because no experiment "
- + "found for sample '" + sample.getSampleIdentifier() + "'.");
- }
- } else if (experiment.getDeletion() != null)
- {
- throw new UserFailureException("Data set can not be registered because experiment '"
- + experiment.getIdentifier() + "' is in trash.");
- }
- }
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/VerifyDataSetExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/VerifyDataSetExecutor.java
index 214acaeb7ff..e0f81e22dde 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/VerifyDataSetExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/VerifyDataSetExecutor.java
@@ -32,6 +32,9 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
public class VerifyDataSetExecutor implements IVerifyDataSetExecutor
{
+ @Autowired
+ private IVerifyDataSetSampleAndExperimentExecutor verifyDataSetSampleAndExperimentExecutor;
+
@Autowired
private IVerifyEntityPropertyExecutor verifyEntityPropertyExecutor;
@@ -44,6 +47,7 @@ public class VerifyDataSetExecutor implements IVerifyDataSetExecutor
@Override
public void verify(IOperationContext context, Collection<DataPE> dataSets)
{
+ verifyDataSetSampleAndExperimentExecutor.verify(context, dataSets);
verifyEntityPropertyExecutor.verify(context, dataSets);
verifyDataSetContainersExecutor.verify(context, dataSets);
verifyDataSetParentsExecutor.verify(context, dataSets);
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/VerifyDataSetSampleAndExperimentExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/VerifyDataSetSampleAndExperimentExecutor.java
new file mode 100644
index 00000000000..24a1f065d12
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/dataset/VerifyDataSetSampleAndExperimentExecutor.java
@@ -0,0 +1,130 @@
+/*
+ * Copyright 2015 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.ethz.sis.openbis.generic.server.api.v3.executor.dataset;
+
+import java.util.Collection;
+import java.util.Properties;
+
+import javax.annotation.PostConstruct;
+import javax.annotation.Resource;
+
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.spring.ExposablePropertyPlaceholderConfigurer;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.util.DataSetTypeWithoutExperimentChecker;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+
+/**
+ * @author pkupczyk
+ */
+@Component
+public class VerifyDataSetSampleAndExperimentExecutor implements IVerifyDataSetSampleAndExperimentExecutor
+{
+
+ @Resource(name = ExposablePropertyPlaceholderConfigurer.PROPERTY_CONFIGURER_BEAN_NAME)
+ private ExposablePropertyPlaceholderConfigurer configurer;
+
+ private DataSetTypeWithoutExperimentChecker dataSetTypeChecker;
+
+ @PostConstruct
+ public void init() throws Exception
+ {
+ dataSetTypeChecker = new DataSetTypeWithoutExperimentChecker(configurer == null ? new Properties() : configurer.getResolvedProps());
+ }
+
+ @Override
+ public void verify(IOperationContext context, Collection<DataPE> dataSets)
+ {
+ for (DataPE dataSet : dataSets)
+ {
+ verify(context, dataSet);
+ }
+ }
+
+ private void verify(IOperationContext context, DataPE dataSet)
+ {
+ ExperimentPE experiment = dataSet.getExperiment();
+ SamplePE sample = dataSet.tryGetSample();
+
+ verifyExperimentNotInTrash(experiment);
+ verifySampleNotInTrash(sample);
+
+ if (sample == null && experiment == null)
+ {
+ throw new UserFailureException("Data set cannot be registered because it is neither connected to a sample nor to an experiment.");
+ } else if (sample == null && experiment != null)
+ {
+ return;
+ } else if (sample != null && experiment == null)
+ {
+ verifySampleNotShared(sample);
+ verifyExperimentNotNeeded(dataSet);
+ } else if (sample != null && experiment != null)
+ {
+ verifySampleNotShared(sample);
+ verifySampleInExperiment(sample, experiment);
+ }
+ }
+
+ private void verifyExperimentNotInTrash(ExperimentPE experiment)
+ {
+ if (experiment != null && experiment.getDeletion() != null)
+ {
+ throw new UserFailureException("Data set can not be registered because experiment '"
+ + experiment.getIdentifier() + "' is in trash.");
+ }
+ }
+
+ private void verifyExperimentNotNeeded(DataPE dataSet)
+ {
+ if (false == dataSetTypeChecker.isDataSetTypeWithoutExperiment(dataSet.getDataSetType().getCode()))
+ {
+ throw new UserFailureException("Data set can not be registered because it is not connected to an experiment.");
+ }
+ }
+
+ private void verifySampleNotInTrash(SamplePE sample)
+ {
+ if (sample != null && sample.getDeletion() != null)
+ {
+ throw new UserFailureException("Data set can not be registered because sample '"
+ + sample.getSampleIdentifier() + "' is in trash.");
+ }
+ }
+
+ private void verifySampleNotShared(SamplePE sample)
+ {
+ if (sample.getSpace() == null)
+ {
+ throw new UserFailureException("Data set can not be registered because sample '"
+ + sample.getSampleIdentifier() + "' is a shared sample.");
+ }
+ }
+
+ private void verifySampleInExperiment(SamplePE sample, ExperimentPE experiment)
+ {
+ if (false == experiment.equals(sample.getExperiment()))
+ {
+ throw new UserFailureException("Data set can not be registered because it connected to a different experiment than its sample.");
+ }
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/AbstractCreateEntityExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/AbstractCreateEntityExecutor.java
index 7fa0089a153..9d90ecce5a1 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/AbstractCreateEntityExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/entity/AbstractCreateEntityExecutor.java
@@ -105,14 +105,14 @@ public abstract class AbstractCreateEntityExecutor<CREATION, PE, PERM_ID> implem
checkAccess(context, entity);
}
+ save(context, new ArrayList<PE>(batchMap.values()), false);
+
for (PE entity : entitiesAll.values())
{
PERM_ID permId = createPermId(context, entity);
permIdsAll.add(permId);
}
- save(context, new ArrayList<PE>(batchMap.values()), false);
-
daoFactory.setBatchUpdateMode(false);
}
diff --git a/openbis/source/java/service.properties b/openbis/source/java/service.properties
index 91606b1c989..e6fcba68c76 100644
--- a/openbis/source/java/service.properties
+++ b/openbis/source/java/service.properties
@@ -13,7 +13,7 @@ core-plugins-folder = source/core-plugins
project-samples-enabled = false
-data-set-types-with-no-experiment-needed = .*
+data-set-types-with-no-experiment-needed = (?!REQUIRES\\_EXPERIMENT).*
# Supported: currently only 'postgresql' is supported
database.engine = postgresql
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateDataSetTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateDataSetTest.java
index 511a473b9b8..11cc5666318 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateDataSetTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateDataSetTest.java
@@ -22,12 +22,17 @@ import static org.testng.Assert.assertNull;
import java.util.Arrays;
import java.util.List;
import java.util.Map;
+import java.util.UUID;
import org.testng.annotations.Test;
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.DataSetCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.dataset.PhysicalDataCreation;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.deletion.experiment.ExperimentDeletionOptions;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.deletion.sample.SampleDeletionOptions;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.experiment.ExperimentCreation;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.fetchoptions.dataset.DataSetFetchOptions;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.dataset.DataSetPermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.dataset.FileFormatTypePermId;
@@ -35,8 +40,15 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.dataset.IDataSetId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.dataset.LocatorTypePermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.datastore.DataStorePermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.EntityTypePermId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.entitytype.IEntityTypeId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentIdentifier;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPermId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.project.ProjectIdentifier;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SampleIdentifier;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.SamplePermId;
+import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.space.SpacePermId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.vocabulary.VocabularyTermCode;
+import ch.systemsx.cisd.common.action.IDelegatedAction;
/**
* @author pkupczyk
@@ -44,6 +56,393 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.vocabulary.VocabularyTer
public class CreateDataSetTest extends AbstractDataSetTest
{
+ @Test
+ public void testCreateWithCodeNull()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ final DataSetCreation dataSet = dataSetCreation();
+ dataSet.setCode(null);
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(dataSet));
+ }
+ }, "Code cannot be empty");
+ }
+
+ @Test
+ public void testCreateWithCodeExisting()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation dataSet = dataSetCreation();
+ dataSet.setCode("DATA_SET_WITH_EXISTING_CODE");
+ v3api.createDataSets(sessionToken, Arrays.asList(dataSet));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(dataSet));
+ }
+ }, "DataSet already exists in the database and needs to be unique");
+ }
+
+ @Test
+ public void testCreateWithCodeIncorrect()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ final DataSetCreation dataSet = dataSetCreation();
+ dataSet.setCode("?!*");
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(dataSet));
+ }
+ }, "Given code '?!*' contains illegal characters (allowed: A-Z, a-z, 0-9 and _, -, .)");
+ }
+
+ @Test
+ public void testCreateWithTypeNull()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation dataSet = dataSetCreation();
+ dataSet.setTypeId(null);
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(dataSet));
+ }
+ }, "Type id cannot be null");
+ }
+
+ @Test
+ public void testCreateWithTypeNonexistent()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final IEntityTypeId typeId = new EntityTypePermId("IDONTEXIST");
+ final DataSetCreation dataSet = dataSetCreation();
+ dataSet.setTypeId(typeId);
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(dataSet));
+ }
+ }, typeId);
+ }
+
+ @Test
+ public void testCreateWithPropertyCodeNonexistent()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setProperty("NONEXISTENT_PROPERTY_CODE", "any value");
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ }
+ }, "Property type with code 'NONEXISTENT_PROPERTY_CODE' does not exist");
+ }
+
+ @Test
+ public void testCreateWithPropertyValueIncorrect()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setTypeId(new EntityTypePermId("HCS_IMAGE"));
+ creation.setProperty("GENDER", "NON_EXISTENT_GENDER");
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ }
+ }, "Vocabulary value 'NON_EXISTENT_GENDER' is not valid. It must exist in 'GENDER' controlled vocabulary");
+ }
+
+ @Test
+ public void testCreateWithPropertyValueMandatoryButNull()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setTypeId(new EntityTypePermId("HCS_IMAGE"));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ }
+ }, "Value of mandatory property 'COMMENT' not specified");
+ }
+
+ @Test
+ public void testCreateWithExperimentNullAndSampleNull()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setExperimentId(null);
+ creation.setSampleId(null);
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ }
+ }, "Experiment id and sample id cannot be both null.");
+ }
+
+ @Test
+ public void testCreateWithExperimentNotNullAndSampleNull()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setExperimentId(new ExperimentIdentifier("/CISD/NEMO/EXP1"));
+ creation.setSampleId(null);
+
+ DataSetFetchOptions fo = new DataSetFetchOptions();
+ fo.withExperiment();
+ fo.withSample();
+
+ List<DataSetPermId> permIds = v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ Map<IDataSetId, DataSet> dataSets = v3api.mapDataSets(sessionToken, permIds, fo);
+ DataSet dataSet = dataSets.values().iterator().next();
+
+ assertEquals(dataSet.getCode(), creation.getCode().toUpperCase());
+ assertEquals(dataSet.getExperiment().getIdentifier().getIdentifier(), "/CISD/NEMO/EXP1");
+ assertEquals(dataSet.getSample(), null);
+ }
+
+ @Test
+ public void testCreateWithExperimentNullAndSampleInExperiment()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setExperimentId(null);
+ creation.setSampleId(new SampleIdentifier("/CISD/CP-TEST-1"));
+
+ DataSetFetchOptions fo = new DataSetFetchOptions();
+ fo.withExperiment();
+ fo.withSample();
+
+ List<DataSetPermId> permIds = v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ Map<IDataSetId, DataSet> dataSets = v3api.mapDataSets(sessionToken, permIds, fo);
+ DataSet dataSet = dataSets.values().iterator().next();
+
+ assertEquals(dataSet.getCode(), creation.getCode().toUpperCase());
+ assertEquals(dataSet.getExperiment().getIdentifier().getIdentifier(), "/CISD/NEMO/EXP-TEST-1");
+ assertEquals(dataSet.getSample().getIdentifier().getIdentifier(), "/CISD/CP-TEST-1");
+ }
+
+ @Test
+ public void testCreateWithExperimentNullAndSampleNotInExperimentWhenTypeAllows()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setTypeId(new EntityTypePermId("UNKNOWN"));
+ creation.setExperimentId(null);
+ creation.setSampleId(new SampleIdentifier("/CISD/3V-125"));
+
+ DataSetFetchOptions fo = new DataSetFetchOptions();
+ fo.withExperiment();
+ fo.withSample();
+
+ List<DataSetPermId> permIds = v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ Map<IDataSetId, DataSet> dataSets = v3api.mapDataSets(sessionToken, permIds, fo);
+ DataSet dataSet = dataSets.values().iterator().next();
+
+ assertEquals(dataSet.getCode(), creation.getCode().toUpperCase());
+ assertEquals(dataSet.getExperiment(), null);
+ assertEquals(dataSet.getSample().getIdentifier().getIdentifier(), "/CISD/3V-125");
+ }
+
+ @Test
+ public void testCreateWithExperimentNullAndSampleNotInExperimentWhenTypeDoesNotAllow()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setTypeId(new EntityTypePermId("REQUIRES_EXPERIMENT"));
+ creation.setExperimentId(null);
+ creation.setSampleId(new SampleIdentifier("/CISD/3V-125"));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ }
+ }, "Data set can not be registered because it is not connected to an experiment.");
+ }
+
+ @Test
+ public void testCreateWithExperimentNotNullAndSampleNotNullNotInExperiment()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setTypeId(new EntityTypePermId("UNKNOWN"));
+ creation.setExperimentId(new ExperimentIdentifier("/CISD/NEMO/EXP-TEST-1"));
+ creation.setSampleId(new SampleIdentifier("/CISD/3V-125"));
+
+ DataSetFetchOptions fo = new DataSetFetchOptions();
+ fo.withExperiment();
+ fo.withSample();
+
+ List<DataSetPermId> permIds = v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ Map<IDataSetId, DataSet> dataSets = v3api.mapDataSets(sessionToken, permIds, fo);
+ DataSet dataSet = dataSets.values().iterator().next();
+
+ assertEquals(dataSet.getCode(), creation.getCode().toUpperCase());
+ assertEquals(dataSet.getExperiment(), null);
+ assertEquals(dataSet.getSample().getIdentifier().getIdentifier(), "/CISD/3V-125");
+ }
+
+ @Test
+ public void testCreateWithExperimentNotNullAndSampleNotNullInSameExperiment()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setTypeId(new EntityTypePermId("UNKNOWN"));
+ creation.setExperimentId(new ExperimentIdentifier("/CISD/NEMO/EXP-TEST-1"));
+ creation.setSampleId(new SampleIdentifier("/CISD/CP-TEST-1"));
+
+ DataSetFetchOptions fo = new DataSetFetchOptions();
+ fo.withExperiment();
+ fo.withSample();
+
+ List<DataSetPermId> permIds = v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ Map<IDataSetId, DataSet> dataSets = v3api.mapDataSets(sessionToken, permIds, fo);
+ DataSet dataSet = dataSets.values().iterator().next();
+
+ assertEquals(dataSet.getCode(), creation.getCode().toUpperCase());
+ assertEquals(dataSet.getExperiment().getIdentifier().getIdentifier(), "/CISD/NEMO/EXP-TEST-1");
+ assertEquals(dataSet.getSample().getIdentifier().getIdentifier(), "/CISD/CP-TEST-1");
+ }
+
+ @Test
+ public void testCreateWithExperimentNotNullAndSampleNotNullInDifferentExperiment()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setTypeId(new EntityTypePermId("UNKNOWN"));
+ creation.setExperimentId(new ExperimentIdentifier("/CISD/DEFAULT/EXP-REUSE"));
+ creation.setSampleId(new SampleIdentifier("/CISD/CP-TEST-1"));
+
+ DataSetFetchOptions fo = new DataSetFetchOptions();
+ fo.withExperiment();
+ fo.withSample();
+
+ List<DataSetPermId> permIds = v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ Map<IDataSetId, DataSet> dataSets = v3api.mapDataSets(sessionToken, permIds, fo);
+ DataSet dataSet = dataSets.values().iterator().next();
+
+ assertEquals(dataSet.getCode(), creation.getCode().toUpperCase());
+ assertEquals(dataSet.getExperiment().getIdentifier().getIdentifier(), "/CISD/NEMO/EXP-TEST-1");
+ assertEquals(dataSet.getSample().getIdentifier().getIdentifier(), "/CISD/CP-TEST-1");
+ }
+
+ @Test
+ public void testCreateWithExperimentInTrash()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ List<ExperimentPermId> experimentIds = v3api.createExperiments(sessionToken, Arrays.asList(experimentCreation()));
+ ExperimentDeletionOptions deletion = new ExperimentDeletionOptions();
+ deletion.setReason("testing");
+ v3api.deleteExperiments(sessionToken, experimentIds, deletion);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setExperimentId(experimentIds.get(0));
+ creation.setSampleId(null);
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ }
+ }, experimentIds.get(0));
+ }
+
+ @Test
+ public void testCreateWithSampleInTrash()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ List<SamplePermId> sampleIds = v3api.createSamples(sessionToken, Arrays.asList(sampleCreation()));
+ SampleDeletionOptions deletion = new SampleDeletionOptions();
+ deletion.setReason("testing");
+ v3api.deleteSamples(sessionToken, sampleIds, deletion);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setExperimentId(null);
+ creation.setSampleId(sampleIds.get(0));
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ }
+ }, sampleIds.get(0));
+ }
+
+ @Test
+ public void testCreateWithSampleShared()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final DataSetCreation creation = dataSetCreation();
+ creation.setExperimentId(null);
+ creation.setSampleId(new SamplePermId("200811050947161-652"));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createDataSets(sessionToken, Arrays.asList(creation));
+ }
+ }, "Data set can not be registered because sample '/MP' is a shared sample.");
+ }
+
@Test
public void testCreatePhysicalData()
{
@@ -118,4 +517,46 @@ public class CreateDataSetTest extends AbstractDataSetTest
assertEquals(dataSet.getContained().iterator().next().getCode(), "20081105092159188-3");
}
+ private DataSetCreation dataSetCreation()
+ {
+ PhysicalDataCreation physicalCreation = new PhysicalDataCreation();
+ physicalCreation.setLocation("a/b/c");
+ physicalCreation.setFileFormatTypeId(new FileFormatTypePermId("TIFF"));
+ physicalCreation.setLocatorTypeId(new LocatorTypePermId("RELATIVE_LOCATION"));
+ physicalCreation.setStorageFormatId(new VocabularyTermCode("PROPRIETARY"));
+
+ DataSetCreation creation = new DataSetCreation();
+ creation.setCode(UUID.randomUUID().toString());
+ creation.setTypeId(new EntityTypePermId("UNKNOWN"));
+ creation.setExperimentId(new ExperimentIdentifier("/CISD/NEMO/EXP1"));
+ creation.setDataStoreId(new DataStorePermId("STANDARD"));
+ creation.setPhysicalData(physicalCreation);
+
+ return creation;
+ }
+
+ private ExperimentCreation experimentCreation()
+ {
+ ExperimentCreation creation = new ExperimentCreation();
+ creation.setCode(UUID.randomUUID().toString());
+ creation.setTypeId(new EntityTypePermId("SIRNA_HCS"));
+ creation.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
+ creation.setProperty("DESCRIPTION", "a description");
+ return creation;
+ }
+
+ private SampleCreation sampleCreation()
+ {
+ SampleCreation creation = new SampleCreation();
+ creation.setCode(UUID.randomUUID().toString());
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("CISD"));
+ return creation;
+ }
+
+ public static void main(String[] args)
+ {
+ System.out.println("REQUIRES_EXPERIMENT".matches("(?!REQUIRES\\_EXPERIMENT).*"));
+ }
+
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateSampleTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateSampleTest.java
index 8a1ec240b7e..c1fa9cbd308 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateSampleTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateSampleTest.java
@@ -941,22 +941,22 @@ public class CreateSampleTest extends AbstractSampleTest
private SampleCreation sampleCreation(String code)
{
- SampleCreation sampleParent = new SampleCreation();
- sampleParent.setCode(code);
- sampleParent.setTypeId(new EntityTypePermId("CELL_PLATE"));
- sampleParent.setSpaceId(new SpacePermId("CISD"));
- sampleParent.setCreationId(new CreationId("creation " + code));
- return sampleParent;
+ SampleCreation creation = new SampleCreation();
+ creation.setCode(code);
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("CISD"));
+ creation.setCreationId(new CreationId("creation " + code));
+ return creation;
}
private SampleCreation sampleCreation(String spaceCode, String code)
{
- SampleCreation sampleParent = new SampleCreation();
- sampleParent.setCode(code);
- sampleParent.setTypeId(new EntityTypePermId("CELL_PLATE"));
- sampleParent.setSpaceId(new SpacePermId(spaceCode));
- sampleParent.setCreationId(new CreationId("creation " + code));
- return sampleParent;
+ SampleCreation creation = new SampleCreation();
+ creation.setCode(code);
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId(spaceCode));
+ creation.setCreationId(new CreationId("creation " + code));
+ return creation;
}
private SamplePermId createCisdSample(String code)
diff --git a/openbis/sourceTest/sql/postgresql/149/014=data_set_types.tsv b/openbis/sourceTest/sql/postgresql/149/014=data_set_types.tsv
index 31b8fa819a2..310b618a6a3 100644
--- a/openbis/sourceTest/sql/postgresql/149/014=data_set_types.tsv
+++ b/openbis/sourceTest/sql/postgresql/149/014=data_set_types.tsv
@@ -6,3 +6,4 @@
6 VALIDATED_CONTAINER_TYPE A container test-validated data set type 2011-05-09 12:24:44.462776+02 \N \N f CONTAINER 11
7 VALIDATED_IMPOSSIBLE_TO_UPDATE_TYPE A dataset type impossible to updatea set type 2011-05-09 12:24:44.462776+02 \N \N f PHYSICAL 6
8 VALIDATED_NORMAL_TYPE A regular test-validated type 2011-05-09 12:24:00+02 \N \N f PHYSICAL 11
+9 REQUIRES_EXPERIMENT Requires experiment 2009-03-23 15:34:44.462776+01 \N \N f PHYSICAL \N
--
GitLab