From 78347ace2bd6d0b4539dc87ab52c8cc3d498d6a8 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 14 Nov 2012 07:09:05 +0000
Subject: [PATCH] SP-367, BIS-242: Improved handling of simultaneous
adding/removing of samples in experiment edit form.
SVN: 27604
---
.../web/client/application/ui/CodesArea.java | 11 +-
.../server/business/bo/ExperimentBO.java | 67 ++--
.../basic/dto/BasicExperimentUpdates.java | 12 +
...ractGenericExperimentRegisterEditForm.java | 5 +
.../experiment/GenericExperimentEditForm.java | 1 +
.../web/server/GenericClientService.java | 1 +
.../server/business/bo/ExperimentBOTest.java | 300 ++++++++++--------
.../generic/shared/CommonTestUtils.java | 1 +
.../ExperimentOptimisticLockingTest.java | 75 +++--
.../optimistic_locking/ToolBox.java | 19 +-
10 files changed, 302 insertions(+), 190 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/CodesArea.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/CodesArea.java
index 4e017773638..c207df9d5ae 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/CodesArea.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/CodesArea.java
@@ -31,6 +31,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
*/
abstract public class CodesArea<T extends ICodeHolder> extends MultilineItemsField
{
+ private List<String> originalCodes;
+
public CodesArea(String emptyTextMsg)
{
super("", false);
@@ -39,8 +41,13 @@ abstract public class CodesArea<T extends ICodeHolder> extends MultilineItemsFie
public final void setCodeProviders(Collection<T> codeProviders)
{
- List<String> codes = Code.extractCodes(codeProviders);
- setItems(codes);
+ originalCodes = Code.extractCodes(codeProviders);
+ setItems(originalCodes);
+ }
+
+ public String[] getOriginalCodes()
+ {
+ return originalCodes.toArray(new String[0]);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
index 710d07404c3..cd657659ec0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBO.java
@@ -40,7 +40,6 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.Experime
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.ExperimentTechIdId;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.IExperimentId;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
@@ -492,54 +491,35 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
attachSamples(sampleCodes);
} else
{
- setExperimentSamples(sampleCodes);
+ String[] originalSampleCodes = updates.getOriginalSampleCodes();
+ updateSamples(originalSampleCodes, sampleCodes);
}
}
}
- @Private
- // attaches specified existing samples to the experiment
- void attachSamples(String[] sampleCodes)
+ private void updateSamples(String[] originalSampleCodes, String[] sampleCodes)
{
- List<SamplePE> samplesToAdd = findUnassignedSamplesByCodes(asSet(sampleCodes));
- addToExperiment(samplesToAdd);
+ Set<String> samplesToAdd = asSet(sampleCodes);
+ samplesToAdd.removeAll(Arrays.asList(originalSampleCodes));
+ addToExperiment(findSamplesByCodes(samplesToAdd, true));
+
+ Set<String> samplesToRemove = asSet(originalSampleCodes);
+ samplesToRemove.removeAll(Arrays.asList(sampleCodes));
+ removeFromExperiment(findSamplesByCodes(samplesToRemove, false));
}
@Private
- // changes the list of samples assigned to this experiment to the specified one
- void setExperimentSamples(String[] sampleCodes)
+ // attaches specified existing samples to the experiment
+ void attachSamples(String[] sampleCodes)
{
- List<SamplePE> samples = experiment.getSamples();
- String[] currentSampleCodes = Code.extractCodesToArray(samples);
- Set<String> currentSampleCodesSet = asSet(currentSampleCodes);
- Set<String> codesToAdd = asSet(sampleCodes);
- codesToAdd.removeAll(currentSampleCodesSet);
-
- List<SamplePE> samplesToAdd = findUnassignedSamplesByCodes(codesToAdd);
+ List<SamplePE> samplesToAdd = findSamplesByCodes(asSet(sampleCodes), true);
addToExperiment(samplesToAdd);
-
- Set<String> codesToRemove = asSet(currentSampleCodes);
- codesToRemove.removeAll(asSet(sampleCodes));
- removeFromExperiment(filterSamples(samples, codesToRemove));
}
- private List<SamplePE> findUnassignedSamplesByCodes(Set<String> codesToAdd)
+ private List<SamplePE> findSamplesByCodes(Set<String> codesToAdd, boolean unassigned)
{
- SpacePE group = experiment.getProject().getSpace();
- return findUnassignedSamples(getSampleDAO(), codesToAdd, group);
- }
-
- private static List<SamplePE> filterSamples(List<SamplePE> samples, Set<String> extractedCodes)
- {
- List<SamplePE> result = new ArrayList<SamplePE>();
- for (SamplePE sample : samples)
- {
- if (extractedCodes.contains(sample.getCode()))
- {
- result.add(sample);
- }
- }
- return result;
+ SpacePE space = experiment.getProject().getSpace();
+ return findSamples(getSampleDAO(), codesToAdd, space, unassigned);
}
private void removeFromExperiment(List<SamplePE> samples)
@@ -560,22 +540,25 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
}
}
- // Finds samples in the specified group. Throws exception if some samples do not exist.
+ // Finds samples in the specified space. Throws exception if some samples do not exist.
// Throws exception if any sample code specified is already assigned to an experiment.
- private static List<SamplePE> findUnassignedSamples(ISampleDAO sampleDAO,
- Set<String> sampleCodes, SpacePE group) throws UserFailureException
+ private static List<SamplePE> findSamples(ISampleDAO sampleDAO, Set<String> sampleCodes,
+ SpacePE space, boolean unassigned) throws UserFailureException
{
List<SamplePE> samples = new ArrayList<SamplePE>();
List<String> missingSamples = new ArrayList<String>();
for (String code : sampleCodes)
{
- SamplePE sample = sampleDAO.tryFindByCodeAndSpace(code, group);
+ SamplePE sample = sampleDAO.tryFindByCodeAndSpace(code, space);
if (sample == null)
{
missingSamples.add(code);
} else
{
- checkSampleUnassigned(code, sample);
+ if (unassigned)
+ {
+ checkSampleUnassigned(code, sample);
+ }
samples.add(sample);
}
}
@@ -583,7 +566,7 @@ public final class ExperimentBO extends AbstractBusinessObject implements IExper
{
throw UserFailureException.fromTemplate(
"Samples with following codes do not exist in the space '%s': '%s'.",
- group.getCode(), CollectionUtils.abbreviate(missingSamples, 10));
+ space.getCode(), CollectionUtils.abbreviate(missingSamples, 10));
} else
{
return samples;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicExperimentUpdates.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicExperimentUpdates.java
index 610ee016645..5218e5cca0a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicExperimentUpdates.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicExperimentUpdates.java
@@ -43,6 +43,8 @@ public class BasicExperimentUpdates implements Serializable
// if it does not have data sets attached yet. Otherwise an exception will be thrown.
private String[] sampleCodesOrNull;
+ private String[] originalSampleCodes;
+
// if true sampleCodesOrNull changes semantic - sample codes are the same as in newSamples and
// all of them will be attached to the experiment.
private boolean registerSamples;
@@ -82,6 +84,16 @@ public class BasicExperimentUpdates implements Serializable
this.sampleCodesOrNull = sampleCodes;
}
+ public String[] getOriginalSampleCodes()
+ {
+ return originalSampleCodes;
+ }
+
+ public void setOriginalSampleCodes(String[] originalSampleCodes)
+ {
+ this.originalSampleCodes = originalSampleCodes;
+ }
+
public void setNewSamples(List<NewSamplesWithTypes> list)
{
this.newSamples = list;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractGenericExperimentRegisterEditForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractGenericExperimentRegisterEditForm.java
index 7ac62518950..e77283a4b83 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractGenericExperimentRegisterEditForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/AbstractGenericExperimentRegisterEditForm.java
@@ -275,6 +275,11 @@ abstract public class AbstractGenericExperimentRegisterEditForm extends
return null;
}
+ protected String[] getOriginalSamples()
+ {
+ return samplesArea != null ? samplesArea.getOriginalCodes() : new String[0];
+ }
+
protected SampleType getSampleType()
{
if (existingSamplesRadio.getValue() == false)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentEditForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentEditForm.java
index b9ff6791d8d..fc39ed20b95 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentEditForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/experiment/GenericExperimentEditForm.java
@@ -96,6 +96,7 @@ public final class GenericExperimentEditForm extends AbstractGenericExperimentRe
updates.setProjectIdentifier(extractProjectIdentifier());
updates.setAttachmentSessionKey(attachmentsSessionKey);
updates.setAttachments(attachmentsManager.extractAttachments());
+ updates.setOriginalSampleCodes(getOriginalSamples());
updates.setSampleCodes(getSamples());
updates.setSampleType(getSampleType());
updates.setGenerateCodes(autoGenerateCodes.getValue().booleanValue());
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
index b2d429103e6..336f6578ee6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
@@ -607,6 +607,7 @@ public class GenericClientService extends AbstractClientService implements IGene
updatesDTO.setProjectIdentifier(project);
updatesDTO.setAttachments(attachments);
updatesDTO.setProperties(updates.getProperties());
+ updatesDTO.setOriginalSampleCodes(updates.getOriginalSampleCodes());
updatesDTO.setSampleCodes(updates.getSampleCodes());
updatesDTO.setVersion(updates.getVersion());
updatesDTO.setRegisterSamples(updates.isRegisterSamples());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
index 8ddb532349a..826687a8c67 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/ExperimentBOTest.java
@@ -35,7 +35,6 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.test.AssertionUtil;
import ch.systemsx.cisd.openbis.generic.server.business.ManagerTestTool;
import ch.systemsx.cisd.openbis.generic.server.util.TimeIntervalChecker;
import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
@@ -45,6 +44,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
@@ -52,7 +52,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.IAuthSession;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityPropertiesHolder;
import ch.systemsx.cisd.openbis.generic.shared.dto.IModifierAndModificationDateBean;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
@@ -60,6 +59,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
@@ -700,18 +700,10 @@ public final class ExperimentBOTest extends AbstractBOTest
updates.setProperties(Collections.<IEntityProperty> emptyList());
updates.setAttachments(Collections.<NewAttachment> emptyList());
prepareAnyDaoCreation();
+ prepareLoadingExperiment(exp);
context.checking(new Expectations()
{
{
- one(experimentDAO).tryGetByTechId(new TechId(exp.getId()),
- ExperimentBO.PROPERTY_TYPES);
- will(returnValue(exp));
-
- one(entityTypeDAO).listEntityTypes();
- will(returnValue(Arrays.asList(exp.getExperimentType())));
-
- allowing(entityPropertyTypeDAO)
- .listEntityPropertyTypes(exp.getExperimentType());
one(relationshipService).assignExperimentToProject(
ManagerTestTool.EXAMPLE_SESSION, exp, newProject);
}
@@ -727,137 +719,210 @@ public final class ExperimentBOTest extends AbstractBOTest
}
@Test
- public final void testEditSamples()
+ public void testUpdateByAddingASample()
{
- // we test if this sample will stay assigned to the experiment if it was assigned before
- SamplePE untouchedSample = createSampleWithCode("untouchedSample");
- // we test unasignment of this sample from the experiment
- SamplePE unassignedSample = createSampleWithCode("unassignedSample");
- // we test if this sample will be assigned to the experiment
- SamplePE assignedSample = createSampleWithCode("assignedSample");
+ ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
+ ExperimentPE experiment = CommonTestUtils.createExperiment(identifier);
+ experiment.setProperties(Collections.<EntityPropertyPE> emptySet());
+ prepareLoadingExperiment(identifier, experiment);
+ ExperimentUpdatesDTO update = createDefaultUpdateObject(experiment);
+ update.setOriginalSampleCodes(new String[]
+ { "S1" });
+ update.setSampleCodes(new String[]
+ { "S1", "S2" });
+ prepareAddSamplesToExperiment(experiment, false, "S2");
+ ExperimentBO experimentBO = loadExperiment(identifier, experiment);
+
+ experimentBO.update(update);
- final ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
- final ExperimentPE exp = CommonTestUtils.createExperiment(identifier);
- exp.setSamples(Arrays.asList(untouchedSample, unassignedSample));
+ context.assertIsSatisfied();
+ }
- prepareLoadExperimentByIdentifier(identifier, exp);
- prepareTryFindSample(exp.getProject().getSpace(), assignedSample.getCode(), assignedSample);
- prepareNoDatasetsFound();
- final ExperimentBO expBO = loadExperiment(identifier, exp);
+ @Test(expectedExceptionsMessageRegExp = "Sample 'S2' is already assigned.*", expectedExceptions = UserFailureException.class)
+ public void testUpdateByAddingAnAlreadyAssignedSample()
+ {
+ ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
+ ExperimentPE experiment = CommonTestUtils.createExperiment(identifier);
+ experiment.setProperties(Collections.<EntityPropertyPE> emptySet());
+ prepareLoadingExperiment(identifier, experiment);
+ ExperimentUpdatesDTO update = createDefaultUpdateObject(experiment);
+ update.setOriginalSampleCodes(new String[]
+ { "S1" });
+ update.setSampleCodes(new String[]
+ { "S1", "S2" });
+ prepareAddSamplesToExperiment(experiment, true, "S2");
+ ExperimentBO experimentBO = loadExperiment(identifier, experiment);
+
+ experimentBO.update(update);
- String[] editedSamples = new String[]
- { untouchedSample.getCode(), assignedSample.getCode() };
- expBO.setExperimentSamples(editedSamples);
- assertEquals(exp, untouchedSample.getExperiment());
+ context.assertIsSatisfied();
}
- private void prepareNoDatasetsFound()
+ @Test(expectedExceptionsMessageRegExp = "Samples with following codes do not exist "
+ + "in the space 'HOME_GROUP': '\\[S2\\]'\\.", expectedExceptions = UserFailureException.class)
+ public void testUpdateByAddingAnUnknownSample()
{
+ ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
+ final ExperimentPE experiment = CommonTestUtils.createExperiment(identifier);
+ experiment.setProperties(Collections.<EntityPropertyPE> emptySet());
+ prepareLoadingExperiment(identifier, experiment);
+ ExperimentUpdatesDTO update = createDefaultUpdateObject(experiment);
+ update.setOriginalSampleCodes(new String[]
+ { "S1" });
+ update.setSampleCodes(new String[]
+ { "S1", "S2" });
context.checking(new Expectations()
{
{
- allowing(dataDAO).hasDataSet((with(any(SamplePE.class))));
- will(returnValue(false));
-
- one(relationshipService).assignSampleToExperiment(
- with(any(IAuthSession.class)), with(any(SamplePE.class)),
- with(any(ExperimentPE.class)));
-
- one(relationshipService).unassignSampleFromExperiment(
- with(any(IAuthSession.class)), with(any(SamplePE.class)));
+ SpacePE space = experiment.getProject().getSpace();
+ one(sampleDAO).tryFindByCodeAndSpace("S2", space);
}
});
- }
+ ExperimentBO experimentBO = loadExperiment(identifier, experiment);
- @Test
- public final void testEditSamplesAddingAssignedSampleFails()
- {
- SamplePE assignedSample = createSampleWithCode("assignedSample");
- assignedSample.setExperiment(createExperiment("anotherExp"));
-
- final ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
- final ExperimentPE exp = CommonTestUtils.createExperiment(identifier);
- assert exp.getSamples().size() == 0 : "no samples expected";
+ experimentBO.update(update);
- prepareLoadExperimentByIdentifier(identifier, exp);
- prepareTryFindSample(exp.getProject().getSpace(), assignedSample.getCode(), assignedSample);
-
- final ExperimentBO expBO = loadExperiment(identifier, exp);
-
- String[] editedSamples = new String[]
- { assignedSample.getCode() };
-
- String errorMsg = "Sample 'assignedSample' is already assigned to the experiment";
- try
- {
- expBO.setExperimentSamples(editedSamples);
- } catch (UserFailureException e)
- {
-
- AssertionUtil.assertContains(errorMsg, e.getMessage());
- return;
- }
- fail("exception expected with the error msg: " + errorMsg);
+ context.assertIsSatisfied();
}
@Test
- public final void testEditSamplesAssigningUnexistingSampleFails()
+ public void testUpdateByAddingAndRemovingSamples()
{
- String unknownSampleCode = "unknownSampleCode";
+ ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
+ ExperimentPE experiment = CommonTestUtils.createExperiment(identifier);
+ experiment.setProperties(Collections.<EntityPropertyPE> emptySet());
+ prepareLoadingExperiment(identifier, experiment);
+ ExperimentUpdatesDTO update = createDefaultUpdateObject(experiment);
+ update.setOriginalSampleCodes(new String[]
+ { "S1", "S2" });
+ update.setSampleCodes(new String[]
+ { "S3", "S2" });
+ prepareRemoveSamplesFromExperiment(experiment, false, "S1");
+ prepareAddSamplesToExperiment(experiment, false, "S3");
+ ExperimentBO experimentBO = loadExperiment(identifier, experiment);
+
+ experimentBO.update(update);
- final ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
- final ExperimentPE exp = CommonTestUtils.createExperiment(identifier);
+ context.assertIsSatisfied();
+ }
- prepareLoadExperimentByIdentifier(identifier, exp);
- final ExperimentBO expBO = loadExperiment(identifier, exp);
+ @Test(expectedExceptionsMessageRegExp = ".*datasets.*", expectedExceptions = UserFailureException.class)
+ public void testUpdateByRemovingASampleWithDataSets()
+ {
+ ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
+ ExperimentPE experiment = CommonTestUtils.createExperiment(identifier);
+ experiment.setProperties(Collections.<EntityPropertyPE> emptySet());
+ prepareLoadingExperiment(identifier, experiment);
+ ExperimentUpdatesDTO update = createDefaultUpdateObject(experiment);
+ update.setOriginalSampleCodes(new String[]
+ { "S1", "S2" });
+ update.setSampleCodes(new String[]
+ { "S2" });
+ prepareRemoveSamplesFromExperiment(experiment, true, "S1");
+ ExperimentBO experimentBO = loadExperiment(identifier, experiment);
+
+ experimentBO.update(update);
- prepareTryFindSample(exp.getProject().getSpace(), unknownSampleCode, null);
- String errorMsg =
- "Samples with following codes do not exist in the space 'HOME_GROUP': '[unknownSampleCode]'.";
- try
- {
- expBO.setExperimentSamples(new String[]
- { unknownSampleCode });
- } catch (UserFailureException e)
- {
+ context.assertIsSatisfied();
+ }
- assertEquals(errorMsg, e.getMessage());
- return;
- }
- fail("exception expected with the error msg: " + errorMsg);
+ private ExperimentUpdatesDTO createDefaultUpdateObject(ExperimentPE experiment)
+ {
+ ExperimentUpdatesDTO update = new ExperimentUpdatesDTO();
+ update.setExperimentId(new TechId(experiment));
+ update.setProjectIdentifier(new ExperimentIdentifierFactory(experiment.getIdentifier())
+ .createIdentifier());
+ update.setAttachments(Collections.<NewAttachment> emptyList());
+ update.setProperties(Collections.<IEntityProperty> emptyList());
+ return update;
}
- @Test
- public final void testEditSamplesUnassigningSampleWithDatasetsFails()
+ private void prepareLoadingExperiment(ExperimentIdentifier identifier,
+ final ExperimentPE experiment)
{
- final SamplePE assignedSample = createSampleWithCode("assignedSample");
+ prepareLoadingExperiment(experiment);
+ prepareLoadExperimentByIdentifier(identifier, experiment);
+ context.checking(new Expectations()
+ {
+ {
+ ProjectPE projectPE = experiment.getProject();
+ SpacePE space = projectPE.getSpace();
+ one(projectDAO).tryFindProject(space.getDatabaseInstance().getCode(),
+ space.getCode(), projectPE.getCode());
+ will(returnValue(projectPE));
+ }
+ });
+ }
- final ExperimentIdentifier identifier = CommonTestUtils.createExperimentIdentifier();
- final ExperimentPE exp = CommonTestUtils.createExperiment(identifier);
- exp.setSamples(Arrays.asList(assignedSample));
+ private void prepareAddSamplesToExperiment(final ExperimentPE experiment,
+ final boolean alreadyAssignedToAnExperiment, final String... sampleCodes)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ SpacePE space = experiment.getProject().getSpace();
+ for (String sampleCode : sampleCodes)
+ {
+ one(sampleDAO).tryFindByCodeAndSpace(sampleCode, space);
+ SamplePE sample = createSampleWithCode(sampleCode);
+ if (alreadyAssignedToAnExperiment)
+ {
+ sample.setExperiment(experiment);
+ }
+ will(returnValue(sample));
+ if (alreadyAssignedToAnExperiment)
+ {
+ break;
+ }
+ one(relationshipService).assignSampleToExperiment(EXAMPLE_SESSION, sample,
+ experiment);
+ }
+ }
+ });
+ }
- prepareLoadExperimentByIdentifier(identifier, exp);
- final ExperimentBO expBO = loadExperiment(identifier, exp);
+ private void prepareRemoveSamplesFromExperiment(final ExperimentPE experiment,
+ final boolean samplesHaveDataSets, final String... sampleCodes)
+ {
context.checking(new Expectations()
{
{
- allowing(dataDAO).hasDataSet(with(assignedSample));
- will(returnValue(true));
+ SpacePE space = experiment.getProject().getSpace();
+ for (String sampleCode : sampleCodes)
+ {
+ one(sampleDAO).tryFindByCodeAndSpace(sampleCode, space);
+ SamplePE sample = createSampleWithCode(sampleCode);
+ will(returnValue(sample));
+
+ one(dataDAO).hasDataSet(sample);
+ will(returnValue(samplesHaveDataSets));
+ if (samplesHaveDataSets)
+ {
+ break;
+ }
+ one(relationshipService).unassignSampleFromExperiment(EXAMPLE_SESSION,
+ sample);
+ }
}
});
+ }
- String errorMsg =
- "Operation cannot be performed, because some datasets have been already produced for the sample 'assignedSample'.";
- try
- {
- expBO.setExperimentSamples(new String[] {}); // remove all samples
- } catch (UserFailureException e)
- {
+ private void prepareLoadingExperiment(final ExperimentPE experiment)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(experimentDAO).tryGetByTechId(new TechId(experiment),
+ ExperimentBO.PROPERTY_TYPES);
+ will(returnValue(experiment));
- assertEquals(errorMsg, e.getMessage());
- return;
- }
- fail("exception expected with the error msg: " + errorMsg);
+ one(entityTypeDAO).listEntityTypes();
+ will(returnValue(Arrays.asList(experiment.getExperimentType())));
+
+ allowing(entityPropertyTypeDAO).listEntityPropertyTypes(
+ experiment.getExperimentType());
+ }
+ });
}
@Test
@@ -881,13 +946,6 @@ public final class ExperimentBOTest extends AbstractBOTest
context.assertIsSatisfied();
}
- private static ExperimentPE createExperiment(String code)
- {
- ExperimentIdentifier ident =
- new ExperimentIdentifier(CommonTestUtils.createProjectIdentifier(), code);
- return CommonTestUtils.createExperiment(ident);
- }
-
private ExperimentBO loadExperiment(final ExperimentIdentifier identifier,
final ExperimentPE exp)
{
@@ -897,18 +955,6 @@ public final class ExperimentBOTest extends AbstractBOTest
return expBO;
}
- private void prepareTryFindSample(final SpacePE group, final String sampleCode,
- final SamplePE foundSample)
- {
- context.checking(new Expectations()
- {
- {
- one(sampleDAO).tryFindByCodeAndSpace(sampleCode, group);
- will(returnValue(foundSample));
- }
- });
- }
-
private static SamplePE createSampleWithCode(String code)
{
SamplePE s = CommonTestUtils.createSample();
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/CommonTestUtils.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/CommonTestUtils.java
index 9514eb31013..bdc3b8dc3d9 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/CommonTestUtils.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/CommonTestUtils.java
@@ -372,6 +372,7 @@ public class CommonTestUtils
final ExperimentPE exp = new ExperimentPE();
final ExperimentTypePE expType = new ExperimentTypePE();
expType.setCode("TEST-EXP-TYPE");
+ expType.setDatabaseInstance(new DatabaseInstancePE());
exp.setId(42L);
exp.setExperimentType(expType);
exp.setCode(ei.getExperimentCode());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ExperimentOptimisticLockingTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ExperimentOptimisticLockingTest.java
index 3f027e6a971..a781f37df5d 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ExperimentOptimisticLockingTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ExperimentOptimisticLockingTest.java
@@ -87,7 +87,7 @@ public class ExperimentOptimisticLockingTest extends OptimisticLockingTestCase
genericServer.updateExperiment(sessionToken, updates);
Experiment retrievedExperiment = toolBox.loadExperiment(experiment);
- checkModifierAndModificationDateOfExperiment(timeIntervalChecker, retrievedExperiment,
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, retrievedExperiment,
"test");
assertEquals("DESCRIPTION: testChangePropertyOfAnExistingExperiment", retrievedExperiment
.getProperties().get(0).toString());
@@ -141,7 +141,7 @@ public class ExperimentOptimisticLockingTest extends OptimisticLockingTestCase
Experiment retrievedExperiment =
commonServer.getExperimentInfo(systemSessionToken, new TechId(experiment));
- checkModifierAndModificationDateOfExperiment(timeIntervalChecker, retrievedExperiment,
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, retrievedExperiment,
"test");
assertEquals(toolBox.project2.getIdentifier(), retrievedExperiment.getProject()
.getIdentifier());
@@ -172,6 +172,32 @@ public class ExperimentOptimisticLockingTest extends OptimisticLockingTestCase
}
}
+ @Test
+ public void testAddMetaProject()
+ {
+ Experiment experiment = toolBox.createAndLoadExperiment(1);
+ ExperimentUpdatesDTO updates = new ExperimentUpdatesDTO();
+ updates.setVersion(experiment.getVersion());
+ updates.setExperimentId(new TechId(experiment));
+ updates.setProjectIdentifier(toolBox.createProjectIdentifier(experiment.getProject()
+ .getIdentifier()));
+ updates.setAttachments(ToolBox.NO_ATTACHMENTS);
+ updates.setProperties(experiment.getProperties());
+ updates.setMetaprojectsOrNull(new String[]
+ { "TEST_METAPROJECTS" });
+ String sessionToken = logIntoCommonClientService().getSessionID();
+ assertEquals("", toolBox.renderMetaProjects(toolBox
+ .loadExperiment(sessionToken, experiment).getMetaprojects()));
+
+ genericServer.updateExperiment(sessionToken, updates);
+
+ Experiment loadedExperiment = toolBox.loadExperiment(sessionToken, experiment);
+ assertEquals(experiment.getModifier(), loadedExperiment.getModifier());
+ assertEquals(experiment.getModificationDate(), loadedExperiment.getModificationDate());
+ assertEquals("/test/TEST_METAPROJECTS",
+ toolBox.renderMetaProjects(loadedExperiment.getMetaprojects()));
+ }
+
@Test
public void testMoveSampleBetweenExperiments()
{
@@ -193,14 +219,14 @@ public class ExperimentOptimisticLockingTest extends OptimisticLockingTestCase
etlService.performEntityOperations(sessionToken, details);
Experiment loadedExperiment1 = toolBox.loadExperiment(experiment1);
- checkModifierAndModificationDateOfExperiment(timeIntervalChecker, loadedExperiment1,
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, loadedExperiment1,
ToolBox.USER_ID);
List<Sample> samples1 =
commonServer.listSamples(systemSessionToken,
ListSampleCriteria.createForExperiment(new TechId(loadedExperiment1)));
assertEquals("[]", samples1.toString());
Experiment loadedExperiment2 = toolBox.loadExperiment(experiment2);
- checkModifierAndModificationDateOfExperiment(timeIntervalChecker, loadedExperiment2,
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, loadedExperiment2,
ToolBox.USER_ID);
List<Sample> samples2 =
commonServer.listSamples(systemSessionToken,
@@ -209,14 +235,19 @@ public class ExperimentOptimisticLockingTest extends OptimisticLockingTestCase
}
@Test
- public void testRemoveSampleFromExperiment()
+ public void testRemoveAndAddSamples()
{
Experiment experiment = toolBox.createAndLoadExperiment(1);
- toolBox.createAndLoadSample(1, experiment);
+ Sample sample1 = toolBox.createAndLoadSample(1, experiment);
+ Sample sample2 = toolBox.createAndLoadSample(2, experiment);
+ Sample sample3 = toolBox.createAndLoadSample(3, null);
ExperimentUpdatesDTO update = new ExperimentUpdatesDTO();
update.setVersion(toolBox.loadExperiment(experiment).getVersion());
update.setExperimentId(new TechId(experiment));
- update.setSampleCodes(new String[0]);
+ update.setOriginalSampleCodes(new String[]
+ { sample1.getCode(), sample2.getCode() });
+ update.setSampleCodes(new String[]
+ { sample2.getCode(), sample3.getCode() });
update.setProperties(ToolBox.NO_PROPERTIES);
update.setAttachments(ToolBox.NO_ATTACHMENTS);
update.setProjectIdentifier(toolBox.createProjectIdentifier(experiment.getProject()
@@ -227,11 +258,24 @@ public class ExperimentOptimisticLockingTest extends OptimisticLockingTestCase
genericServer.updateExperiment(sessionToken, update);
Experiment loadedExperiment = toolBox.loadExperiment(experiment);
- checkModifierAndModificationDateOfExperiment(timeIntervalChecker, loadedExperiment, "test");
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, loadedExperiment,
+ "test");
List<Sample> samples =
commonServer.listSamples(systemSessionToken,
ListSampleCriteria.createForExperiment(new TechId(loadedExperiment)));
- assertEquals("[]", samples.toString());
+ assertEquals("[" + sample2.getCode() + ", " + sample3.getCode() + "]", toolBox
+ .extractCodes(samples).toString());
+ Sample reloadedSample1 = toolBox.loadSample(sample1);
+ assertEquals(null, reloadedSample1.getExperiment());
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, reloadedSample1, "test");
+ Sample reloadedSample2 = toolBox.loadSample(sample2);
+ assertEquals(experiment.getIdentifier(), reloadedSample2.getExperiment().getIdentifier());
+ assertEquals(sample2.getModifier(), reloadedSample2.getModifier());
+ assertEquals(sample2.getModificationDate(), reloadedSample2.getModificationDate());
+ Sample reloadedSample3 = toolBox.loadSample(sample3);
+ assertEquals(experiment.getIdentifier(), reloadedSample3.getExperiment().getIdentifier());
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, reloadedSample3, "test");
+
}
@Test
@@ -259,22 +303,17 @@ public class ExperimentOptimisticLockingTest extends OptimisticLockingTestCase
genericServer.updateDataSet(sessionToken, update);
Experiment loadedExperiment1 = toolBox.loadExperiment(exp1);
- checkModifierAndModificationDateOfExperiment(timeIntervalChecker, loadedExperiment1, "test");
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, loadedExperiment1,
+ "test");
List<ExternalData> dataSets1 =
etlService.listDataSetsByExperimentID(systemSessionToken, new TechId(exp1));
assertEquals("[]", dataSets1.toString());
Experiment loadedExperiment2 = toolBox.loadExperiment(exp2);
- checkModifierAndModificationDateOfExperiment(timeIntervalChecker, loadedExperiment2, "test");
+ toolBox.checkModifierAndModificationDateOfBean(timeIntervalChecker, loadedExperiment2,
+ "test");
List<ExternalData> dataSets2 =
etlService.listDataSetsByExperimentID(systemSessionToken, new TechId(exp2));
assertEquals(dataSet.getCode(), dataSets2.get(0).getCode());
}
- private void checkModifierAndModificationDateOfExperiment(
- TimeIntervalChecker timeIntervalChecker, Experiment experiment, String userId)
- {
- assertEquals(userId, experiment.getModifier().getUserId());
- timeIntervalChecker.assertDateInInterval(experiment.getModificationDate());
- }
-
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ToolBox.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ToolBox.java
index d63c613253c..e1b547579ac 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ToolBox.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/optimistic_locking/ToolBox.java
@@ -24,6 +24,7 @@ import java.util.Collection;
import java.util.Collections;
import java.util.List;
+import ch.systemsx.cisd.common.shared.basic.string.CommaSeparatedListBuilder;
import ch.systemsx.cisd.openbis.generic.server.util.TimeIntervalChecker;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
@@ -40,6 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Grantee;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LocatorType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
@@ -294,7 +296,12 @@ public class ToolBox
public Experiment loadExperiment(final IIdentifierHolder experiment)
{
- return commonServer.getExperimentInfo(systemSessionToken,
+ return loadExperiment(systemSessionToken, experiment);
+ }
+
+ public Experiment loadExperiment(String sessionToken, final IIdentifierHolder experiment)
+ {
+ return commonServer.getExperimentInfo(sessionToken,
ExperimentIdentifierFactory.parse(experiment.getIdentifier()));
}
@@ -410,4 +417,14 @@ public class ToolBox
// ignored
}
}
+
+ public String renderMetaProjects(Collection<Metaproject> metaprojects)
+ {
+ CommaSeparatedListBuilder builder = new CommaSeparatedListBuilder();
+ for (Metaproject metaproject : metaprojects)
+ {
+ builder.append(metaproject.getIdentifier());
+ }
+ return builder.toString();
+ }
}
--
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