diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/CreateExperimentExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/CreateExperimentExecutor.java
index b59adb3a500f75b97bfe70bae9647b754fea9cdd..35e2a146e935e958d580452acda25b7227088c79 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/CreateExperimentExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/experiment/CreateExperimentExecutor.java
@@ -21,6 +21,7 @@ import java.util.List;
import org.apache.commons.lang.StringUtils;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.DataAccessException;
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
@@ -36,6 +37,7 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.experiment.ExperimentPer
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.ProjectByIdentiferValidator;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.DataAccessExceptionTranslator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
@@ -90,22 +92,29 @@ public class CreateExperimentExecutor implements ICreateExperimentExecutor
@Override
public List<ExperimentPermId> create(IOperationContext context, List<ExperimentCreation> creations)
{
- List<ExperimentPermId> result = new LinkedList<ExperimentPermId>();
-
- for (ExperimentCreation creation : creations)
+ try
{
- context.pushContextDescription(ExperimentContextDescription.creating(creation));
+ List<ExperimentPermId> result = new LinkedList<ExperimentPermId>();
- ExperimentPE experiment = createExperimentPE(context, creation);
- daoFactory.getExperimentDAO().createOrUpdateExperiment(experiment, context.getSession().tryGetPerson());
- createAttachmentExecutor.create(context, experiment, creation.getAttachments());
- addTagToEntityExecutor.add(context, experiment, creation.getTagIds());
- result.add(new ExperimentPermId(experiment.getPermId()));
+ for (ExperimentCreation creation : creations)
+ {
+ context.pushContextDescription(ExperimentContextDescription.creating(creation));
- context.popContextDescription();
- }
+ ExperimentPE experiment = createExperimentPE(context, creation);
+ daoFactory.getExperimentDAO().createOrUpdateExperiment(experiment, context.getSession().tryGetPerson());
+ createAttachmentExecutor.create(context, experiment, creation.getAttachments());
+ addTagToEntityExecutor.add(context, experiment, creation.getTagIds());
+ result.add(new ExperimentPermId(experiment.getPermId()));
+
+ context.popContextDescription();
+ }
- return result;
+ return result;
+ } catch (DataAccessException e)
+ {
+ DataAccessExceptionTranslator.throwException(e, "Experiment", EntityKind.EXPERIMENT);
+ return null;
+ }
}
private ExperimentPE createExperimentPE(IOperationContext context, ExperimentCreation experimentCreation)
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/CreateSampleExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/CreateSampleExecutor.java
index ab2f6b0327ddc455e2044f4965444cc58be27b4b..5f907a559a7f0cf5f21672cbe7779c36c6360e6b 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/CreateSampleExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/CreateSampleExecutor.java
@@ -25,7 +25,9 @@ import java.util.LinkedList;
import java.util.List;
import java.util.Map;
+import org.apache.commons.lang.StringUtils;
import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.dao.DataAccessException;
import org.springframework.stereotype.Component;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.IOperationContext;
@@ -33,11 +35,17 @@ import ch.ethz.sis.openbis.generic.server.api.v3.executor.attachment.ICreateAtta
import ch.ethz.sis.openbis.generic.server.api.v3.executor.property.IUpdateEntityPropertyExecutor;
import ch.ethz.sis.openbis.generic.server.api.v3.executor.tag.IAddTagToEntityExecutor;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.sample.SampleCreation;
+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.exceptions.UnauthorizedObjectAccessException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SampleByIdentiferValidator;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.DataAccessExceptionTranslator;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
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.identifier.SampleIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.util.RelationshipUtils;
/**
@@ -99,38 +107,44 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
@Override
public List<SamplePermId> create(IOperationContext context, List<SampleCreation> creations)
{
- List<SamplePermId> permIdsAll = new LinkedList<SamplePermId>();
- Map<SampleCreation, SamplePE> samplesAll = new LinkedHashMap<SampleCreation, SamplePE>();
-
- int batchSize = 1000;
- for (int batchStart = 0; batchStart < creations.size(); batchStart += batchSize)
+ try
{
- List<SampleCreation> creationsBatch = creations.subList(batchStart, Math.min(batchStart + batchSize, creations.size()));
- createSamples(context, creationsBatch, permIdsAll, samplesAll);
+ List<SamplePermId> permIdsAll = new LinkedList<SamplePermId>();
+ Map<SampleCreation, SamplePE> samplesAll = new LinkedHashMap<SampleCreation, SamplePE>();
- for (SampleCreation creation : creationsBatch)
+ int batchSize = 1000;
+ for (int batchStart = 0; batchStart < creations.size(); batchStart += batchSize)
{
- SamplePE sample = samplesAll.get(creation);
- createAttachmentExecutor.create(context, sample, creation.getAttachments());
- addTagToEntityExecutor.add(context, sample, creation.getTagIds());
+ List<SampleCreation> creationsBatch = creations.subList(batchStart, Math.min(batchStart + batchSize, creations.size()));
+ createSamples(context, creationsBatch, permIdsAll, samplesAll);
+
+ for (SampleCreation creation : creationsBatch)
+ {
+ SamplePE sample = samplesAll.get(creation);
+ createAttachmentExecutor.create(context, sample, creation.getAttachments());
+ addTagToEntityExecutor.add(context, sample, creation.getTagIds());
+ }
+
+ daoFactory.getSessionFactory().getCurrentSession().flush();
+ daoFactory.getSessionFactory().getCurrentSession().clear();
}
+ reloadSamples(samplesAll);
+
+ setSampleRelatedSamplesExecutor.set(context, samplesAll);
+ verifySampleExecutor.verify(context, samplesAll.values());
+
daoFactory.getSessionFactory().getCurrentSession().flush();
daoFactory.getSessionFactory().getCurrentSession().clear();
+ return permIdsAll;
+ } catch (DataAccessException e)
+ {
+ DataAccessExceptionTranslator.throwException(e, "Sample", EntityKind.SAMPLE);
+ return null;
}
-
- reloadSamples(samplesAll);
-
- setSampleRelatedSamplesExecutor.set(context, samplesAll);
- verifySampleExecutor.verify(context, samplesAll.values());
-
- daoFactory.getSessionFactory().getCurrentSession().flush();
- daoFactory.getSessionFactory().getCurrentSession().clear();
-
- return permIdsAll;
}
- private void createSamples(IOperationContext context, List<SampleCreation> creationsBatch,
+ private void createSamples(IOperationContext context, List<SampleCreation> creationsBatch,
List<SamplePermId> permIdsAll, Map<SampleCreation, SamplePE> samplesAll)
{
Map<SampleCreation, SamplePE> batchMap = new LinkedHashMap<SampleCreation, SamplePE>();
@@ -157,6 +171,12 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
for (Map.Entry<SampleCreation, SamplePE> batchEntry : batchMap.entrySet())
{
SamplePE sample = batchEntry.getValue();
+
+ if (false == new SampleByIdentiferValidator().doValidation(context.getSession().tryGetPerson(), sample))
+ {
+ throw new UnauthorizedObjectAccessException(new SampleIdentifier(sample.getIdentifier()));
+ }
+
Map<String, String> properties = batchEntry.getKey().getProperties();
updateEntityPropertyExecutor.update(context, sample, sample.getEntityType(), properties);
}
@@ -168,11 +188,13 @@ public class CreateSampleExecutor implements ICreateSampleExecutor
private SamplePE createSamplePE(IOperationContext context, SampleCreation sampleCreation)
{
- if (sampleCreation.getCode() == null)
+ if (StringUtils.isEmpty(sampleCreation.getCode()))
{
- throw new UserFailureException("No code for sample provided");
+ throw new UserFailureException("Code cannot be empty.");
}
-
+
+ SampleIdentifierFactory.assertValidCode(sampleCreation.getCode());
+
SamplePE sample = new SamplePE();
sample.setCode(sampleCreation.getCode());
String createdPermId = daoFactory.getPermIdDAO().createPermId();
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleTypeExecutor.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleTypeExecutor.java
index 4794d9e29e27dbaa3f06b38693683749152b6c26..1a69428aba8c4eeb9687169b45282a3fbb725d7c 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleTypeExecutor.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/api/v3/executor/sample/SetSampleTypeExecutor.java
@@ -68,7 +68,7 @@ public class SetSampleTypeExecutor implements ISetSampleTypeExecutor
if (creation.getTypeId() == null)
{
- throw new UserFailureException("No type for sample provided");
+ throw new UserFailureException("Type id cannot be null.");
} else
{
EntityTypePE type = typeMap.get(creation.getTypeId());
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateExperimentTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateExperimentTest.java
index 32f3e994ceb6e237f5a8cf4eba61dbde1aaac126..1d18ef8e8ae60e7825c8e9e4f9beef5a060c36c0 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateExperimentTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/api/v3/CreateExperimentTest.java
@@ -74,6 +74,28 @@ public class CreateExperimentTest extends AbstractExperimentTest
}, "Code cannot be empty", ExperimentContextDescription.creating(experiment));
}
+ @Test
+ public void testCreateExperimentWithExistingCode()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final ExperimentCreation experiment = new ExperimentCreation();
+ experiment.setCode("EXPERIMENT_WITH_EXISTING_CODE");
+ experiment.setTypeId(new EntityTypePermId("SIRNA_HCS"));
+ experiment.setProjectId(new ProjectIdentifier("/CISD/NEMO"));
+
+ v3api.createExperiments(sessionToken, Arrays.asList(experiment));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createExperiments(sessionToken, Arrays.asList(experiment));
+ }
+ }, "Experiment already exists in the database and needs to be unique", ExperimentContextDescription.creating(experiment));
+ }
+
@Test
public void testCreateExperimentWithIncorrectCode()
{
@@ -307,7 +329,7 @@ public class CreateExperimentTest extends AbstractExperimentTest
}
@Test
- public void testCreateExperimentWithIncorrectPropertyValue()
+ public void testCreateExperimentWithIncorrectDatePropertyValue()
{
final String sessionToken = v3api.login(TEST_USER, PASSWORD);
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 ede10d329ddee1e3f884d8da9184a69c0b074708..a787c72064304d9602cc11e3ec87204b8edc5770 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
@@ -17,6 +17,7 @@
package ch.ethz.sis.openbis.systemtest.api.v3;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNull;
import static org.testng.Assert.fail;
import java.util.ArrayList;
@@ -40,6 +41,8 @@ import ch.ethz.sis.openbis.generic.shared.api.v3.dto.entity.tag.Tag;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.fetchoptions.sample.SampleFetchOptions;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.CreationId;
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.experiment.IExperimentId;
import ch.ethz.sis.openbis.generic.shared.api.v3.dto.id.sample.ISampleId;
@@ -59,6 +62,477 @@ import ch.systemsx.cisd.common.test.AssertionUtil;
public class CreateSampleTest extends AbstractSampleTest
{
+ @Test
+ public void testCreateSampleWithoutCode()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ final SampleCreation sample = sampleCreation(null);
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Arrays.asList(sample));
+ }
+ }, "Code cannot be empty");
+ }
+
+ @Test
+ public void testCreateSampleWithExistingCode()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final SampleCreation sample = sampleCreation("SAMPLE_WITH_EXISTING_CODE");
+ v3api.createSamples(sessionToken, Arrays.asList(sample));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Arrays.asList(sample));
+ }
+ }, "Insert/Update of sample (code: SAMPLE_WITH_EXISTING_CODE) failed because sample with the same code already exists");
+ }
+
+ @Test
+ public void testCreateSampleWithIncorrectCode()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+ final SampleCreation sample = sampleCreation("?!*");
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Arrays.asList(sample));
+ }
+ }, "The code '?!*' contains illegal characters");
+ }
+
+ @Test
+ public void testCreateSampleWithoutType()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final SampleCreation sample = new SampleCreation();
+ sample.setCode("SAMPLE_WITHOUT_TYPE");
+ sample.setSpaceId(new SpacePermId("CISD"));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Arrays.asList(sample));
+ }
+ }, "Type id cannot be null");
+ }
+
+ @Test
+ public void testCreateSampleWithNonexistentType()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final IEntityTypeId typeId = new EntityTypePermId("IDONTEXIST");
+ final SampleCreation sample = new SampleCreation();
+ sample.setTypeId(typeId);
+ sample.setCode("SAMPLE_WITH_NONEXISTENT_TYPE");
+ sample.setSpaceId(new SpacePermId("CISD"));
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Arrays.asList(sample));
+ }
+ }, typeId);
+ }
+
+ @Test
+ public void testCreateSampleWithNonexistentPropertyCode()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("SAMPLE_WITH_NONEXISTENT_PROPERTY_CODE");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("CISD"));
+ creation.setProperty("NONEXISTENT_PROPERTY_CODE", "any value");
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Arrays.asList(creation));
+ }
+ }, "Property type with code 'NONEXISTENT_PROPERTY_CODE' does not exist");
+ }
+
+ @Test
+ public void testCreateSampleWithIncorrectVocabularyPropertyValue()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("SAMPLE_WITH_INCORRECT_PROPERTY_VALUE");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("CISD"));
+ creation.setProperty("ORGANISM", "NON_EXISTENT_ORGANISM");
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Arrays.asList(creation));
+ }
+ }, "Vocabulary value 'NON_EXISTENT_ORGANISM' is not valid. It must exist in 'ORGANISM' controlled vocabulary");
+ }
+
+ @Test
+ public void testCreateSampleWithoutMandatoryPropertyValue()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("SAMPLE_WITH_EMPTY_MANDATORY_PROPERTY");
+ creation.setTypeId(new EntityTypePermId("CONTROL_LAYOUT"));
+ creation.setSpaceId(new SpacePermId("CISD"));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Arrays.asList(creation));
+ }
+ }, "Value of mandatory property '$PLATE_GEOMETRY' not specified");
+ }
+
+ @Test
+ public void testCreateSampleWithoutSpaceButWithExperiment()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("SHARED_SAMPLE_TEST");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setExperimentId(new ExperimentIdentifier("/CISD/NEMO/EXP1"));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, "Shared samples cannot be attached to experiments");
+ }
+
+ @Test
+ public void testCreateSampleWithoutSpaceAsAdminUser()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("SHARED_SAMPLE_TEST");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+
+ List<SamplePermId> permIds = v3api.createSamples(sessionToken, Collections.singletonList(creation));
+
+ SampleFetchOptions fetchOptions = new SampleFetchOptions();
+ fetchOptions.fetchSpace();
+
+ Map<ISampleId, Sample> map = v3api.mapSamples(sessionToken, permIds, fetchOptions);
+ Sample sample = map.values().iterator().next();
+
+ assertEquals(sample.getCode(), "SHARED_SAMPLE_TEST");
+ assertNull(sample.getSpace());
+ }
+
+ @Test
+ public void testCreateSampleWithoutSpaceAsSpaceUser()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("SHARED_SAMPLE_TEST");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+
+ assertUnauthorizedObjectAccessException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, new SampleIdentifier("/SHARED_SAMPLE_TEST"));
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedSpace()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISpaceId spaceId = new SpacePermId("CISD");
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("UNAUTHORIZED_SPACE");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(spaceId);
+
+ assertUnauthorizedObjectAccessException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, spaceId);
+ }
+
+ @Test
+ public void testCreateSampleWithNonexistentSpace()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISpaceId spaceId = new SpacePermId("IDONTEXIST");
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("NONEXISTENT_SPACE");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(spaceId);
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, spaceId);
+ }
+
+ @Test
+ public void testCreateSampleWithInconsistentSpace()
+ {
+ final String sessionToken = v3api.login(TEST_USER, PASSWORD);
+
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("SAMPLE_WITH_INCONSISTENT_SPACE");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("TEST-SPACE"));
+ creation.setExperimentId(new ExperimentIdentifier("/CISD/NEMO/EXP1"));
+
+ assertUserFailureException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, "Sample space must be the same as experiment space");
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedExperiment()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final IExperimentId experimentId = new ExperimentPermId("200811050951882-1028");
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("UNAUTHORIZED_EXPERIMENT");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("TEST-SPACE"));
+ creation.setExperimentId(experimentId);
+
+ assertUnauthorizedObjectAccessException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, experimentId);
+ }
+
+ @Test
+ public void testCreateSampleWithNonexistentExperiment()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final IExperimentId experimentId = new ExperimentPermId("IDONTEXIST");
+ final SampleCreation creation = new SampleCreation();
+ creation.setCode("NONEXISTENT_EXPERIMENT");
+ creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
+ creation.setSpaceId(new SpacePermId("TEST-SPACE"));
+ creation.setExperimentId(experimentId);
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, experimentId);
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedParent()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISampleId parentId = createCisdSample("PARENT_SAMPLE");
+ final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_UNAUTHORIZED_PARENT");
+ creation.setParentIds(Collections.singletonList(parentId));
+
+ assertUnauthorizedObjectAccessException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, parentId);
+ }
+
+ @Test
+ public void testCreateSampleWithNonexistentParent()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISampleId parentId = new SamplePermId("IDONTEXIST");
+ final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_NONEXISTENT_PARENT");
+ creation.setParentIds(Collections.singletonList(parentId));
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, parentId);
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedChild()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISampleId childId = createCisdSample("CHILD_SAMPLE");
+ final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_UNAUTHORIZED_CHILD");
+ creation.setChildIds(Collections.singletonList(childId));
+
+ assertUnauthorizedObjectAccessException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, childId);
+ }
+
+ @Test
+ public void testCreateSampleWithNonexistentChild()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISampleId childId = new SamplePermId("IDONTEXIST");
+ final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_NONEXISTENT_CHILD");
+ creation.setChildIds(Collections.singletonList(childId));
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, childId);
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedContainer()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISampleId containerId = createCisdSample("CONTAINER_SAMPLE");
+ final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_UNAUTHORIZED_CONTAINER");
+ creation.setContainerId(containerId);
+
+ assertUnauthorizedObjectAccessException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, containerId);
+ }
+
+ @Test
+ public void testCreateSampleWithNonExistentContainer()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISampleId containerId = new SamplePermId("IDONTEXIST");
+ final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_NONEXISTENT_CONTAINER");
+ creation.setContainerId(containerId);
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, containerId);
+ }
+
+ @Test
+ public void testCreateSampleWithUnauthorizedContained()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISampleId containedId = createCisdSample("CONTAINED_SAMPLE");
+ final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_UNAUTHORIZED_CONTAINED");
+ creation.setContainedIds(Collections.singletonList(containedId));
+
+ assertUnauthorizedObjectAccessException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, containedId);
+ }
+
+ @Test
+ public void testCreateSampleWithNonexistentContained()
+ {
+ final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
+
+ final ISampleId containedId = new SamplePermId("IDONTEXIST");
+ final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_NONEXISTENT_CONTAINED");
+ creation.setContainedIds(Collections.singletonList(containedId));
+
+ assertObjectNotFoundException(new IDelegatedAction()
+ {
+ @Override
+ public void execute()
+ {
+ v3api.createSamples(sessionToken, Collections.singletonList(creation));
+ }
+ }, containedId);
+ }
+
@DataProvider(name = "tf-ft-tt")
Object[][] getDataProviderForRelationTest()
{
@@ -475,259 +949,6 @@ public class CreateSampleTest extends AbstractSampleTest
}
}
- @Test
- public void testCreateSampleWithoutCode()
- {
- String sessionToken = v3api.login(TEST_USER, PASSWORD);
- SampleCreation sample = sampleCreation(null);
- try
- {
- v3api.createSamples(sessionToken, Arrays.asList(sample));
- fail("Expected user failure exception");
- } catch (UserFailureException ufe)
- {
- AssertionUtil.assertContains("No code for sample provided", ufe.getMessage());
- }
- }
-
- @Test
- public void testCreateSampleWithUnauthorizedSpace()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISpaceId spaceId = new SpacePermId("CISD");
- final SampleCreation creation = new SampleCreation();
- creation.setCode("UNAUTHORIZED_SPACE");
- creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- creation.setSpaceId(spaceId);
-
- assertUnauthorizedObjectAccessException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, spaceId);
- }
-
- @Test
- public void testCreateSampleWithNonexistentSpace()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISpaceId spaceId = new SpacePermId("IDONTEXIST");
- final SampleCreation creation = new SampleCreation();
- creation.setCode("NONEXISTENT_SPACE");
- creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- creation.setSpaceId(spaceId);
-
- assertObjectNotFoundException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, spaceId);
- }
-
- @Test
- public void testCreateSampleWithUnauthorizedExperiment()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final IExperimentId experimentId = new ExperimentPermId("200811050951882-1028");
- final SampleCreation creation = new SampleCreation();
- creation.setCode("UNAUTHORIZED_EXPERIMENT");
- creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- creation.setSpaceId(new SpacePermId("TEST-SPACE"));
- creation.setExperimentId(experimentId);
-
- assertUnauthorizedObjectAccessException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, experimentId);
- }
-
- @Test
- public void testCreateSampleWithNonexistentExperiment()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final IExperimentId experimentId = new ExperimentPermId("IDONTEXIST");
- final SampleCreation creation = new SampleCreation();
- creation.setCode("NONEXISTENT_EXPERIMENT");
- creation.setTypeId(new EntityTypePermId("CELL_PLATE"));
- creation.setSpaceId(new SpacePermId("TEST-SPACE"));
- creation.setExperimentId(experimentId);
-
- assertObjectNotFoundException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, experimentId);
- }
-
- @Test
- public void testCreateSampleWithUnauthorizedParent()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISampleId parentId = createCisdSample("PARENT_SAMPLE");
- final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_UNAUTHORIZED_PARENT");
- creation.setParentIds(Collections.singletonList(parentId));
-
- assertUnauthorizedObjectAccessException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, parentId);
- }
-
- @Test
- public void testCreateSampleWithNonexistentParent()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISampleId parentId = new SamplePermId("IDONTEXIST");
- final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_NONEXISTENT_PARENT");
- creation.setParentIds(Collections.singletonList(parentId));
-
- assertObjectNotFoundException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, parentId);
- }
-
- @Test
- public void testCreateSampleWithUnauthorizedChild()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISampleId childId = createCisdSample("CHILD_SAMPLE");
- final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_UNAUTHORIZED_CHILD");
- creation.setChildIds(Collections.singletonList(childId));
-
- assertUnauthorizedObjectAccessException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, childId);
- }
-
- @Test
- public void testCreateSampleWithNonexistentChild()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISampleId childId = new SamplePermId("IDONTEXIST");
- final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_NONEXISTENT_CHILD");
- creation.setChildIds(Collections.singletonList(childId));
-
- assertObjectNotFoundException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, childId);
- }
-
- @Test
- public void testCreateSampleWithUnauthorizedContainer()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISampleId containerId = createCisdSample("CONTAINER_SAMPLE");
- final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_UNAUTHORIZED_CONTAINER");
- creation.setContainerId(containerId);
-
- assertUnauthorizedObjectAccessException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, containerId);
- }
-
- @Test
- public void testCreateSampleWithNonExistentContainer()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISampleId containerId = new SamplePermId("IDONTEXIST");
- final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_NONEXISTENT_CONTAINER");
- creation.setContainerId(containerId);
-
- assertObjectNotFoundException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, containerId);
- }
-
- @Test
- public void testCreateSampleWithUnauthorizedContained()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISampleId containedId = createCisdSample("CONTAINED_SAMPLE");
- final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_UNAUTHORIZED_CONTAINED");
- creation.setContainedIds(Collections.singletonList(containedId));
-
- assertUnauthorizedObjectAccessException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, containedId);
- }
-
- @Test
- public void testCreateSampleWithNonexistentContained()
- {
- final String sessionToken = v3api.login(TEST_SPACE_USER, PASSWORD);
-
- final ISampleId containedId = new SamplePermId("IDONTEXIST");
- final SampleCreation creation = sampleCreation("TEST-SPACE", "HAS_NONEXISTENT_CONTAINED");
- creation.setContainedIds(Collections.singletonList(containedId));
-
- assertObjectNotFoundException(new IDelegatedAction()
- {
- @Override
- public void execute()
- {
- v3api.createSamples(sessionToken, Collections.singletonList(creation));
- }
- }, containedId);
- }
-
private SampleCreation sampleCreation(String code)
{
SampleCreation sampleParent = new SampleCreation();