From 7cd282c520f8dc0a8118b374f481fc0f4fdba704 Mon Sep 17 00:00:00 2001
From: izabel <izabel>
Date: Wed, 18 Mar 2009 08:25:43 +0000
Subject: [PATCH] [LMS-780] check sample consistency + server tests
SVN: 10274
---
.../openbis/generic/server/CommonServer.java | 61 +++++++-
.../server/business/bo/IExperimentBO.java | 2 +-
.../generic/server/CommonServerTest.java | 143 +++++++++++++++---
.../shared/AbstractServerTestCase.java | 10 +-
4 files changed, 182 insertions(+), 34 deletions(-)
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 8fbfc5f9d77..605e4b97ef5 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
@@ -648,20 +648,65 @@ public final class CommonServer extends AbstractServer<ICommonServer> implements
final Session session = getSessionManager().getSession(sessionToken);
if (newProjectIdentifier.equals(identifier) == false)
{
- final IExternalDataTable externalDataTable =
- businessObjectFactory.createExternalDataTable(session);
- externalDataTable.loadByExperimentIdentifier(identifier);
- if (externalDataTable.getExternalData().size() > 0)
- {
- throw new UserFailureException(
- "Changing the project of experiment containing data sets is not allowed.");
- }
+ checkExternalData(identifier, session);
+ checkSampleConsistency(identifier, newProjectIdentifier, session);
}
+
final IExperimentBO experimentBO = businessObjectFactory.createExperimentBO(session);
experimentBO.edit(identifier, properties, attachments, newProjectIdentifier);
experimentBO.save();
}
+ private void checkExternalData(ExperimentIdentifier identifier, final Session session)
+ {
+ final IExternalDataTable externalDataTable =
+ businessObjectFactory.createExternalDataTable(session);
+ externalDataTable.loadByExperimentIdentifier(identifier);
+ if (externalDataTable.getExternalData().size() > 0)
+ {
+ throw new UserFailureException(
+ "Changing the project of experiment containing data sets is not allowed.");
+ }
+ }
+
+ private void checkSampleConsistency(ExperimentIdentifier identifier,
+ ProjectIdentifier newProjectIdentifier, final Session session)
+ {
+ ListSampleCriteriaDTO criteria =
+ ListSampleCriteriaDTO.createExperimentIdentifier(identifier);
+ final ISampleTable sampleTable = businessObjectFactory.createSampleTable(session);
+ sampleTable.loadSamplesByCriteria(criteria);
+ final List<SamplePE> samples = sampleTable.getSamples();
+ if (samples.size() > 0)
+ {
+ checkExperimentGroupMatches(samples.get(0).getSampleIdentifier(),
+ newProjectIdentifier);
+ }
+ }
+
+ private void checkExperimentGroupMatches(SampleIdentifier sampleIdentifier,
+ ProjectIdentifier newProjectIdentifier)
+ {
+ assert sampleIdentifier != null : "Sample identifier not specified";
+ assert newProjectIdentifier != null : "Project identifier not specified";
+ final GroupIdentifier sampleGroup = sampleIdentifier.getGroupLevel();
+ if (sampleGroup == null)
+ {
+ throw new UserFailureException(
+ "Inconsistency detected: shared sample found in experiment.");
+ }
+ if (sampleGroup.getDatabaseInstanceCode().equals(
+ newProjectIdentifier.getDatabaseInstanceCode()) == false
+ || sampleGroup.getGroupCode().equals(newProjectIdentifier.getGroupCode()) == false)
+ {
+ throw new UserFailureException(
+ String
+ .format(
+ "Project cannot be changed to '%s' because experiment containes samples from group '%s'.",
+ newProjectIdentifier, sampleGroup));
+ }
+ }
+
public void editMaterial(String sessionToken, MaterialIdentifier identifier,
List<MaterialProperty> properties)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExperimentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExperimentBO.java
index e9154b16db9..0cbef8d614a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExperimentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/IExperimentBO.java
@@ -65,5 +65,5 @@ public interface IExperimentBO extends IBusinessObject
* Changes given experiment. Currently allowed changes: properties.
*/
public void edit(ExperimentIdentifier identifier, List<ExperimentProperty> properties,
- List<AttachmentPE> attachments, ProjectIdentifier newProjectIdentifierOrNull);
+ List<AttachmentPE> attachments, ProjectIdentifier newProjectIdentifier);
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
index bce3698b2af..0ef580f3401 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
@@ -31,8 +31,13 @@ import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServerSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
@@ -50,8 +55,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
@@ -61,14 +68,30 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
*/
public final class CommonServerTest extends AbstractServerTestCase
{
+ private static final String MATERIAL_TYPE_1 = "MATERIAL-TYPE-1";
+
+ private static final String MATERIAL_1 = "MATERIAL-1";
+
+ private static final String SAMPLE_1 = "SAMPLE-1";
+
+ private static final String EXP_1 = "EXP-1";
+
+ private static final String PROJECT_1 = "PROJECT-1";
+
+ private static final String GROUP_1 = "GROUP-1";
+
+ private static final String DATABASE_1 = "DATABASE-1";
+
private ICommonBusinessObjectFactory commonBusinessObjectFactory;
+
private DataStoreServerSessionManager dssSessionManager;
+
private IDataStoreService dataStoreService;
private final ICommonServer createServer()
{
- return new CommonServer(authenticationService, sessionManager,
- dssSessionManager, daoFactory, commonBusinessObjectFactory);
+ return new CommonServer(authenticationService, sessionManager, dssSessionManager,
+ daoFactory, commonBusinessObjectFactory);
}
private final static PersonPE createSystemUser()
@@ -489,8 +512,7 @@ public final class CommonServerTest extends AbstractServerTestCase
will(returnValue(new ArrayList<ExperimentPE>()));
}
});
- createServer()
- .listExperiments(SESSION_TOKEN, experimentType, projectIdentifier);
+ createServer().listExperiments(SESSION_TOKEN, experimentType, projectIdentifier);
context.assertIsSatisfied();
}
@@ -709,7 +731,7 @@ public final class CommonServerTest extends AbstractServerTestCase
will(returnValue(d1));
}
});
-
+
try
{
createServer().deleteDataSets(SESSION_TOKEN, Arrays.asList(d1.getCode()), "");
@@ -724,12 +746,13 @@ public final class CommonServerTest extends AbstractServerTestCase
context.assertIsSatisfied();
}
-
+
@Test
public void testDeleteDataSetsButOneDataSetIsUnknown()
{
prepareGetSession();
- dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url", dataStoreService));
+ dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
+ dataStoreService));
final ExternalDataPE d1 = createDataSet("d1");
final ExternalDataPE d2 = createDataSet("d2");
context.checking(new Expectations()
@@ -745,30 +768,104 @@ public final class CommonServerTest extends AbstractServerTestCase
one(dataStoreService).getKnownDataSets(with(any(String.class)),
with(equal(locations)));
will(returnValue(Arrays.asList(d1.getLocation())));
-
+
}
});
-
+
try
{
- createServer().deleteDataSets(SESSION_TOKEN, Arrays.asList(d1.getCode(), d2.getCode()), "");
+ createServer().deleteDataSets(SESSION_TOKEN, Arrays.asList(d1.getCode(), d2.getCode()),
+ "");
fail("UserFailureException expected");
} catch (UserFailureException e)
{
assertEquals(
"The following data sets are unknown by any registered Data Store Server. "
- + "May be the responsible Data Store Server is not running.\n[d2]", e
- .getMessage());
+ + "May be the responsible Data Store Server is not running.\n[d2]", e
+ .getMessage());
}
-
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testEditMaterialNothingChanged() throws Exception
+ {
+ final MaterialIdentifier identifier =
+ new MaterialIdentifier(MATERIAL_1, MATERIAL_TYPE_1);
+ final List<MaterialProperty> properties = new ArrayList<MaterialProperty>();
+ prepareGetSession();
+ context.checking(new Expectations()
+ {
+ {
+ one(commonBusinessObjectFactory).createMaterialBO(SESSION);
+ will(returnValue(materialBO));
+
+ one(materialBO).edit(identifier, properties);
+ one(materialBO).save();
+
+ }
+ });
+ createServer().editMaterial(SESSION_TOKEN, identifier, properties);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testEditSampleNothingChanged() throws Exception
+ {
+ final SampleIdentifier identifier =
+ SampleIdentifier.createOwnedBy(new SampleOwnerIdentifier(new GroupIdentifier(
+ DATABASE_1, GROUP_1)), SAMPLE_1);
+ final List<SampleProperty> properties = new ArrayList<SampleProperty>();
+ prepareGetSession();
+ context.checking(new Expectations()
+ {
+ {
+ one(commonBusinessObjectFactory).createSampleBO(SESSION);
+ will(returnValue(sampleBO));
+
+ one(sampleBO).edit(identifier, properties);
+ one(sampleBO).save();
+
+ }
+ });
+ createServer().editSample(SESSION_TOKEN, identifier, properties);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testEditExperimentNothingChanged() throws Exception
+ {
+ final ExperimentIdentifier identifier =
+ new ExperimentIdentifier(DATABASE_1, GROUP_1, PROJECT_1, EXP_1);
+ final List<ExperimentProperty> properties = new ArrayList<ExperimentProperty>();
+ final List<AttachmentPE> attachments = new ArrayList<AttachmentPE>();
+ final ProjectIdentifier newProjectIdentifier =
+ new ProjectIdentifier(DATABASE_1, GROUP_1, PROJECT_1);
+ prepareGetSession();
+ context.checking(new Expectations()
+ {
+ {
+ one(commonBusinessObjectFactory).createExperimentBO(SESSION);
+ will(returnValue(experimentBO));
+
+ one(experimentBO).edit(identifier, properties, attachments,
+ newProjectIdentifier);
+ one(experimentBO).save();
+
+ }
+ });
+ createServer().editExperiment(SESSION_TOKEN, identifier, properties, attachments,
+ newProjectIdentifier);
context.assertIsSatisfied();
}
-
- @Test
+
+ @Test
public void testDeleteDataSets()
{
prepareGetSession();
- dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url", dataStoreService));
+ dssSessionManager.registerDataStoreServer(new DataStoreServerSession("url",
+ dataStoreService));
final ExternalDataPE d1 = createDataSet("d1");
final ExternalDataPE d2 = createDataSet("d2");
context.checking(new Expectations()
@@ -784,18 +881,20 @@ public final class CommonServerTest extends AbstractServerTestCase
one(dataStoreService).getKnownDataSets(with(any(String.class)),
with(equal(locations)));
will(returnValue(locations));
-
+
one(externalDataDAO).markAsDeleted(d1, SESSION.tryGetPerson(), "reason");
one(externalDataDAO).markAsDeleted(d2, SESSION.tryGetPerson(), "reason");
- one(dataStoreService).deleteDataSets(with(any(String.class)), with(equal(locations)));
+ one(dataStoreService).deleteDataSets(with(any(String.class)),
+ with(equal(locations)));
}
});
-
- createServer().deleteDataSets(SESSION_TOKEN, Arrays.asList(d1.getCode(), d2.getCode()), "reason");
-
+
+ createServer().deleteDataSets(SESSION_TOKEN, Arrays.asList(d1.getCode(), d2.getCode()),
+ "reason");
+
context.assertIsSatisfied();
}
-
+
private ExternalDataPE createDataSet(String code)
{
ExternalDataPE data = new ExternalDataPE();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
index e0d43d80fb9..0e5f2083b1f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.IExperimentTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IGroupBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IProcedureBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IPropertyTypeBO;
@@ -70,9 +71,9 @@ public abstract class AbstractServerTestCase extends AssertJUnit
{
protected static final Principal PRINCIPAL =
new Principal(CommonTestUtils.USER_ID, "john", "doe", "j@d");
-
+
protected static final String SESSION_TOKEN = "session-token";
-
+
protected static final Session SESSION =
new Session(CommonTestUtils.USER_ID, SESSION_TOKEN, PRINCIPAL, "remote-host", 1);
@@ -104,6 +105,8 @@ public abstract class AbstractServerTestCase extends AssertJUnit
protected ISampleBO sampleBO;
+ protected IMaterialBO materialBO;
+
protected IExternalDataTable externalDataTable;
protected IExperimentTable experimentTable;
@@ -162,6 +165,7 @@ public abstract class AbstractServerTestCase extends AssertJUnit
// BO
groupBO = context.mock(IGroupBO.class);
sampleBO = context.mock(ISampleBO.class);
+ materialBO = context.mock(IMaterialBO.class);
experimentBO = context.mock(IExperimentBO.class);
propertyTypeBO = context.mock(IPropertyTypeBO.class);
vocabularyBO = context.mock(IVocabularyBO.class);
@@ -207,7 +211,7 @@ public abstract class AbstractServerTestCase extends AssertJUnit
// Otherwise one do not known which test failed.
context.assertIsSatisfied();
}
-
+
protected Session createSession()
{
return new Session(CommonTestUtils.USER_ID, SESSION_TOKEN, PRINCIPAL, "remote-host", 2);
--
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