diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
index bd31cad1aa7c6e9c70ef8b759b40ad8832ddba20..b59329d8cada9e899a2c9277db3c42b0b11bbfdc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/AbstractSampleBusinessObject.java
@@ -135,17 +135,13 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
samplePE.setGroup(sampleOwner.tryGetGroup());
samplePE.setDatabaseInstance(sampleOwner.tryGetDatabaseInstance());
defineSampleProperties(samplePE, newSample.getProperties());
- String parentIdentifier = newSample.getParentIdentifier();
- if (parentIdentifier != null)
- {
- setGeneratedFrom(sampleIdentifier, samplePE, parentIdentifier);
- } else if (newSample.getParents() != null)
+ String containerIdentifier = newSample.getContainerIdentifier();
+ setContainer(sampleIdentifier, samplePE, containerIdentifier);
+ if (newSample.getParentsOrNull() != null)
{
- final String[] parents = newSample.getParents();
+ final String[] parents = newSample.getParentsOrNull();
setParents(samplePE, parents);
}
- String containerIdentifier = newSample.getContainerIdentifier();
- setContainer(sampleIdentifier, samplePE, containerIdentifier);
samplePE.setPermId(getPermIdDAO().createPermId());
return samplePE;
}
@@ -202,18 +198,6 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
samplePE.setContainer(containerPE);
}
- protected void setGeneratedFrom(final SampleIdentifier sampleIdentifier,
- final SamplePE samplePE, String parentIdentifier)
- {
- final Set<SamplePE> newParents = new HashSet<SamplePE>();
- final SamplePE parentOrNull = tryGetValidParentSample(parentIdentifier, sampleIdentifier);
- if (parentOrNull != null)
- {
- newParents.add(parentOrNull);
- }
- replaceParents(samplePE, newParents);
- }
-
protected void setParents(final SamplePE childPE, final String[] parents)
{
final List<SampleIdentifier> parentIdentifiers =
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
index 50aacbf294a13c578df3150146dd32fb2068be13..39d859766e5eda315ea8cc5c149687543a6eac95 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleTable.java
@@ -246,11 +246,6 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
updateExperiment(sample, updates.getExperimentIdentifierOrNull(), experimentCache);
checkExperimentBusinessRules(getExternalDataDAO(), sample);
}
- if (details.isParentUpdateRequested())
- {
- setGeneratedFrom(updates.getSampleIdentifier(), sample,
- updates.getParentIdentifierOrNull());
- }
if (details.isParentsUpdateRequested())
{
final String[] parents = updates.getModifiedParentCodesOrNull();
@@ -266,8 +261,7 @@ public final class SampleTable extends AbstractSampleBusinessObject implements I
}
// NOTE: Checking business rules with relationships is expensive.
// Don't perform them unless relevant data were changed.
- if (details.isExperimentUpdateRequested() || details.isParentUpdateRequested()
- || details.isParentsUpdateRequested())
+ if (details.isExperimentUpdateRequested() || details.isParentsUpdateRequested())
{
checkParentBusinessRules(sample);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
index 39dad9bdc5ff89cb4722f157ba4621eff7c8d988..ecf885105fd05a92f3f32ffc60477d5404cbfd20 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewSample.java
@@ -46,14 +46,9 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
private SampleType sampleType;
/**
- * The parent identifier.
+ * Set of parent sample codes or identifiers. It will be assumed that all the samples belong
+ * to the same group as the child sample.
*/
- // TODO 2010-08-09, Piotr Buczek: remove
- private String parentIdentifier;
-
- // Set of parent sample codes or identifiers. It will be assumed that
- // all the samples belong to the same group as the child sample.
- // If equals to null then parentIdentifier should be used.
private String[] parentsOrNull;
/**
@@ -94,16 +89,15 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
final String containerIdentifier, final String[] parents)
{
NewSample result = new NewSample(identifier, sampleType, containerIdentifier);
- result.setParents(parents);
+ result.setParentsOrNull(parents);
return result;
}
public NewSample(final String identifier, SampleType sampleType, String containerIdentifier,
- String parentIdentifier, String[] parentsOrNull, String experimentIdentifier,
- IEntityProperty[] properties, List<NewAttachment> attachments)
+ String[] parentsOrNull, String experimentIdentifier, IEntityProperty[] properties,
+ List<NewAttachment> attachments)
{
this(identifier, sampleType, containerIdentifier);
- this.parentIdentifier = parentIdentifier;
this.parentsOrNull = parentsOrNull;
this.experimentIdentifier = experimentIdentifier;
this.properties = properties;
@@ -130,12 +124,12 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
this.sampleType = sampleType;
}
- public String[] getParents()
+ public String[] getParentsOrNull()
{
return parentsOrNull;
}
- public void setParents(String[] parents)
+ public void setParentsOrNull(String[] parents)
{
this.parentsOrNull = parents;
}
@@ -146,22 +140,27 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
if (parents != null)
{
String[] split = parents.split(",");
- setParents(split);
+ setParentsOrNull(split);
} else
{
- setParents((String[]) null);
+ setParentsOrNull(new String[0]);
}
}
+ /** @deprecated convenience method for tests - use {@link #getParentsOrNull()} instead */
+ @Deprecated
public final String getParentIdentifier()
{
- return parentIdentifier;
+ return getParentsOrNull() == null || getParentsOrNull().length == 0 ? null
+ : getParentsOrNull()[0];
}
+ /** @deprecated convenience method for tests - use {@link #setParents(String)} instead */
+ @Deprecated
@BeanProperty(label = PARENT, optional = true)
public final void setParentIdentifier(final String parent)
{
- this.parentIdentifier = parent;
+ setParents(parent);
}
public final String getContainerIdentifier()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleBatchUpdateDetails.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleBatchUpdateDetails.java
index 246ba61e934dd6d7329e6c2f620377d174a8efb9..87a06875a493102f1d32e18ffcb564106182437d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleBatchUpdateDetails.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/SampleBatchUpdateDetails.java
@@ -32,8 +32,6 @@ public class SampleBatchUpdateDetails implements IsSerializable, Serializable
private boolean experimentUpdateRequested;
- private boolean parentUpdateRequested;
-
private boolean parentsUpdateRequested;
private boolean containerUpdateRequested;
@@ -44,11 +42,10 @@ public class SampleBatchUpdateDetails implements IsSerializable, Serializable
{
}
- public SampleBatchUpdateDetails(boolean updateExperiment, boolean updateParent,
- boolean updateParents, boolean updateContainer, Set<String> propertiesToUpdate)
+ public SampleBatchUpdateDetails(boolean updateExperiment, boolean updateParents,
+ boolean updateContainer, Set<String> propertiesToUpdate)
{
this.experimentUpdateRequested = updateExperiment;
- this.parentUpdateRequested = updateParent;
this.parentsUpdateRequested = updateParents;
this.containerUpdateRequested = updateContainer;
this.propertiesToUpdate = propertiesToUpdate;
@@ -59,11 +56,6 @@ public class SampleBatchUpdateDetails implements IsSerializable, Serializable
return experimentUpdateRequested;
}
- public boolean isParentUpdateRequested()
- {
- return parentUpdateRequested;
- }
-
public boolean isParentsUpdateRequested()
{
return parentsUpdateRequested;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/UpdatedSample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/UpdatedSample.java
index 6a531d9baa29f0c93429636b79328348577e3cbf..a2d6ddfb5274b5cdbf58d6d0216d1d6625013f37 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/UpdatedSample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/UpdatedSample.java
@@ -40,9 +40,8 @@ public final class UpdatedSample extends NewSample
public UpdatedSample(NewSample newSample, SampleBatchUpdateDetails batchUpdateDetails)
{
super(newSample.getIdentifier(), newSample.getSampleType(), newSample
- .getContainerIdentifier(), newSample.getParentIdentifier(), newSample.getParents(),
- newSample.getExperimentIdentifier(), newSample.getProperties(), newSample
- .getAttachments());
+ .getContainerIdentifier(), newSample.getParentsOrNull(), newSample
+ .getExperimentIdentifier(), newSample.getProperties(), newSample.getAttachments());
this.batchUpdateDetails = batchUpdateDetails;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactory.java
index 67ea36da33a5e72a03a613026382647abd90ba2e..e1f17b0034fc6fe3c714c0413fbfcb9bb2a01254 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactory.java
@@ -93,6 +93,7 @@ class NewSampleParserObjectFactory extends AbstractParserObjectFactory<NewSample
return true;
}
+ @SuppressWarnings("deprecation")
@Override
public NewSample createObject(final String[] lineTokens) throws ParserException
{
@@ -116,7 +117,10 @@ class NewSampleParserObjectFactory extends AbstractParserObjectFactory<NewSample
setProperties(newSample, lineTokens);
newSample
.setContainerIdentifier(StringUtils.trimToNull(newSample.getContainerIdentifier()));
- newSample.setParentIdentifier(StringUtils.trimToNull(newSample.getParentIdentifier()));
+ if (newSample.getParentIdentifier() != null)
+ {
+ newSample.setParentIdentifier(StringUtils.trimToNull(newSample.getParentIdentifier()));
+ }
newSample.setExperimentIdentifier(StringUtils.trimToNull(newSample
.getExperimentIdentifier()));
return newSample;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
index 51a94ce4e0940617bb3b3a4cf0209dbe51285de1..7bb99f7df756ff1372f9e7c29028d6750a8b05f7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactory.java
@@ -55,9 +55,16 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
boolean updateExperiment = isColumnAvailable(UpdatedSample.EXPERIMENT);
boolean updateParent = isColumnAvailable(UpdatedSample.PARENT);
boolean updateParents = isColumnAvailable(UpdatedSample.PARENTS);
+ if (updateParent == updateParents == true)
+ {
+ throw new ParserException("Both '" + UpdatedSample.PARENT + "' and '"
+ + UpdatedSample.PARENTS
+ + "' columns were specified. One of them should be removed from the file.");
+ }
+ updateParents |= updateParent;
boolean updateContainer = isColumnAvailable(UpdatedSample.CONTAINER);
- return new SampleBatchUpdateDetails(updateExperiment, updateParent, updateParents,
- updateContainer, getUnmatchedProperties());
+ return new SampleBatchUpdateDetails(updateExperiment, updateParents, updateContainer,
+ getUnmatchedProperties());
}
//
@@ -86,12 +93,9 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
final boolean updateExperiment =
basicBatchUpdateDetails.isExperimentUpdateRequested()
&& isNotEmpty(newSample.getExperimentIdentifier());
- final boolean updateParent =
- basicBatchUpdateDetails.isParentUpdateRequested()
- && isNotEmpty(newSample.getParentIdentifier());
final boolean updateParents =
basicBatchUpdateDetails.isParentsUpdateRequested()
- && isNotEmpty(newSample.getParents());
+ && isNotEmpty(newSample.getParentsOrNull());
final boolean updateContainer =
basicBatchUpdateDetails.isContainerUpdateRequested()
&& isNotEmpty(newSample.getContainerIdentifier());
@@ -102,8 +106,8 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
propertiesToUpdate.add(property.getPropertyType().getCode());
}
- return new SampleBatchUpdateDetails(updateExperiment, updateParent, updateParents,
- updateContainer, propertiesToUpdate);
+ return new SampleBatchUpdateDetails(updateExperiment, updateParents, updateContainer,
+ propertiesToUpdate);
}
private boolean isNotEmpty(String[] parents)
@@ -118,13 +122,10 @@ final class UpdatedSampleParserObjectFactory extends NewSampleParserObjectFactor
{
newSample.setExperimentIdentifier(null);
}
- if (isDeletionMark(newSample.getParentIdentifier()))
- {
- newSample.setParentIdentifier(null);
- }
- if (newSample.getParents() != null && isDeletionMark(newSample.getParents()[0]))
+ if (newSample.getParentsOrNull() != null && newSample.getParentsOrNull().length > 0
+ && isDeletionMark(newSample.getParentsOrNull()[0]))
{
- newSample.setParents(new String[0]);
+ newSample.setParentsOrNull(new String[0]);
}
if (isDeletionMark(newSample.getContainerIdentifier()))
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
index 3e71b8aaba57fa3a2f48b874d59e5a8a668db29a..19efab7e69cc0707fe9dd146b826feaacf04e203 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServer.java
@@ -479,10 +479,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
experimentIdentifierOrNull = null;
newSampleIdentifier = oldSampleIdentifier;
}
- final String parentIdentifierOrNull = updatedSample.getParentIdentifier();
- final String[] parentsOrNull =
- (parentIdentifierOrNull == null) ? updatedSample.getParents() : new String[]
- { parentIdentifierOrNull };
+ final String[] parentsOrNull = updatedSample.getParentsOrNull();
final String containerIdentifierOrNull = updatedSample.getContainerIdentifier();
final SampleBatchUpdateDetails batchUpdateDetails =
createBatchUpdateDetails(updatedSample);
@@ -508,7 +505,7 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
propertyCodes.add(p.getPropertyType().getCode());
}
SampleBatchUpdateDetails result =
- new SampleBatchUpdateDetails(false, false, false, false, propertyCodes);
+ new SampleBatchUpdateDetails(false, false, false, propertyCodes);
return result;
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
index 419d06b3c34a203c440d0f1eab6e115590681687..18acefbd950ccc1c20a954dcee903bdc061eb490 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SampleBOTest.java
@@ -239,6 +239,7 @@ public final class SampleBOTest extends AbstractBOTest
context.assertIsSatisfied();
}
+ @SuppressWarnings("deprecation")
@Test
public final void testDefineSampleHappyCase()
{
@@ -739,6 +740,7 @@ public final class SampleBOTest extends AbstractBOTest
fail("The edition of stale sample should throw an exception");
}
+ @SuppressWarnings("deprecation")
public final void testFailToDefineSharedSampleWithParentInAGroup()
{
final SampleIdentifier sharedSampleIdentifier =
@@ -866,6 +868,7 @@ public final class SampleBOTest extends AbstractBOTest
context.assertIsSatisfied();
}
+ @SuppressWarnings("deprecation")
@Test
public final void testRegisterSampleWithUnknownParent()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAOTest.java
index 44a8accda2da19ee888efbc2740e318295a590d4..0ad2895ca0ccbc21dd657d5bfcbf0f6882b1a277 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/SampleDAOTest.java
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePropertyTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.EventType;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
@@ -52,7 +53,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationshipPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.EventPE.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
@@ -403,7 +403,7 @@ public final class SampleDAOTest extends AbstractDAOTest
deleteSample(deletedSample);
}
- @Test(groups = "broken")
+ @Test
public final void testDeleteWithGeneratedSamples()
{
final SamplePE deletedSample = findSample("3VCP2", "CISD");
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
index 78755ce9db0d90a2056caa76c636bdb450cc6b4a..97161fc191746d16973fe9cec5b10def7b67134f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientServiceTest.java
@@ -80,6 +80,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
private GenericClientService genericClientService;
+ @SuppressWarnings("deprecation")
private final static NewSample createNewSample(final String sampleIdentifier,
final String sampleTypeCode, final IEntityProperty[] properties, final String parent,
final String container)
@@ -125,7 +126,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
multipartFile = context.mock(MultipartFile.class);
genericClientService = new GenericClientService(genericServer, requestContextProvider);
}
-
+
@Test
public void testGetSampleGenerationInfo()
{
@@ -134,7 +135,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
{
{
prepareGetSessionToken(this);
-
+
one(genericServer).getSampleInfo(SESSION_TOKEN, sampleId);
SampleParentWithDerived parentWithDerived = new SampleParentWithDerived();
Sample sample = new Sample();
@@ -145,13 +146,14 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
});
SampleParentWithDerived info = genericClientService.getSampleGenerationInfo(sampleId);
-
+
IEntityProperty transformedXMLProperty = info.getParent().getProperties().get(0);
- assertEquals("<?xml version=\"1.0\" encoding=\"UTF-8\"?><b>hello</b>", transformedXMLProperty.tryGetAsString());
+ assertEquals("<?xml version=\"1.0\" encoding=\"UTF-8\"?><b>hello</b>",
+ transformedXMLProperty.tryGetAsString());
assertEquals("<root>hello</root>", transformedXMLProperty.tryGetOriginalValue());
context.assertIsSatisfied();
}
-
+
@Test
public void testGetSampleInfo()
{
@@ -184,51 +186,51 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
{
final TechId id = new TechId(4711L);
context.checking(new Expectations()
- {
{
- prepareGetSessionToken(this);
-
- one(genericServer).getDataSetInfo(SESSION_TOKEN, id);
- ExternalData dataSet = new ExternalData();
- dataSet.setDataSetProperties(Arrays.asList(createXmlProperty()));
- will(returnValue(dataSet));
- }
- });
-
+ {
+ prepareGetSessionToken(this);
+
+ one(genericServer).getDataSetInfo(SESSION_TOKEN, id);
+ ExternalData dataSet = new ExternalData();
+ dataSet.setDataSetProperties(Arrays.asList(createXmlProperty()));
+ will(returnValue(dataSet));
+ }
+ });
+
ExternalData info = genericClientService.getDataSetInfo(id);
-
+
IEntityProperty transformedXMLProperty = info.getProperties().get(0);
assertEquals("<?xml version=\"1.0\" encoding=\"UTF-8\"?><b>hello</b>",
transformedXMLProperty.tryGetAsString());
assertEquals("<root>hello</root>", transformedXMLProperty.tryGetOriginalValue());
context.assertIsSatisfied();
}
-
+
@Test
public void testGetMaterialInfo()
{
final TechId id = new TechId(4711L);
context.checking(new Expectations()
- {
{
- prepareGetSessionToken(this);
-
- one(genericServer).getMaterialInfo(SESSION_TOKEN, id);
- Material material = new Material();
- material.setProperties(Arrays.asList(createXmlProperty()));
- will(returnValue(material));
- }
- });
-
+ {
+ prepareGetSessionToken(this);
+
+ one(genericServer).getMaterialInfo(SESSION_TOKEN, id);
+ Material material = new Material();
+ material.setProperties(Arrays.asList(createXmlProperty()));
+ will(returnValue(material));
+ }
+ });
+
Material info = genericClientService.getMaterialInfo(id);
-
+
IEntityProperty transformedXMLProperty = info.getProperties().get(0);
assertEquals("<?xml version=\"1.0\" encoding=\"UTF-8\"?><b>hello</b>",
transformedXMLProperty.tryGetAsString());
assertEquals("<root>hello</root>", transformedXMLProperty.tryGetOriginalValue());
context.assertIsSatisfied();
}
-
+
@Test
public final void testRegisterSample()
{
@@ -276,6 +278,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
context.assertIsSatisfied();
}
+ @SuppressWarnings("deprecation")
@Test
public final void testRegisterSamples() throws IOException
{
@@ -326,7 +329,8 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
will(new CustomAction("check sample")
{
- @SuppressWarnings("unchecked")
+ @SuppressWarnings(
+ { "unchecked" })
public Object invoke(Invocation invocation) throws Throwable
{
final List<NewSamplesWithTypes> samplesSecions =
@@ -358,8 +362,8 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
assertEquals(1, result.size());
final BatchRegistrationResult batchRegistrationResult = result.get(0);
assertEquals(fileName, batchRegistrationResult.getFileName());
- assertEquals("Registration of 1 sample(s) is complete.", batchRegistrationResult
- .getMessage());
+ assertEquals("Registration of 1 sample(s) is complete.",
+ batchRegistrationResult.getMessage());
context.assertIsSatisfied();
}
@@ -406,7 +410,8 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
will(new CustomAction("check sample")
{
- @SuppressWarnings("unchecked")
+ @SuppressWarnings(
+ { "unchecked", "deprecation" })
public Object invoke(Invocation invocation) throws Throwable
{
final List<NewSamplesWithTypes> samplesSecions =
@@ -419,7 +424,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
final NewSample sample1 = samples.getNewSamples().get(0);
assertEquals("/G1/MP1", sample1.getIdentifier());
assertEquals("/G1/MP2", sample1.getContainerIdentifier());
- assertEquals(null, sample1.getParentIdentifier());
+ assertEquals(0, sample1.getParentsOrNull().length);
assertEquals("EXP1", sample1.getExperimentIdentifier());
assertEquals(1, sample1.getProperties().length);
final IEntityProperty prop1 = sample1.getProperties()[0];
@@ -448,7 +453,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
assertEquals("Update of 2 sample(s) is complete.", batchRegistrationResult.getMessage());
context.assertIsSatisfied();
}
-
+
@Test
public void testUpdateMaterials() throws IOException
{
@@ -465,7 +470,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
assertEquals(updateCount + " material(s) updated.", results.get(0).getMessage());
context.assertIsSatisfied();
}
-
+
@Test
public void testUpdateMaterialsIgnoringUnregisteredButNoUnregistered() throws IOException
{
@@ -473,16 +478,17 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
final boolean ignoreUnregisteredMaterials = true;
final int updateCount = 1;
prepareMaterialsUpdate(sessionKey, ignoreUnregisteredMaterials, updateCount);
-
+
List<BatchRegistrationResult> results =
- genericClientService.updateMaterials(MATERIAL_TYPE, sessionKey,
- ignoreUnregisteredMaterials);
-
+ genericClientService.updateMaterials(MATERIAL_TYPE, sessionKey,
+ ignoreUnregisteredMaterials);
+
assertEquals(1, results.size());
- assertEquals(updateCount + " material(s) updated, non ignored.", results.get(0).getMessage());
+ assertEquals(updateCount + " material(s) updated, non ignored.", results.get(0)
+ .getMessage());
context.assertIsSatisfied();
}
-
+
@Test
public void testUpdateMaterialsIgnoringUnregistered() throws IOException
{
@@ -490,11 +496,11 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
final boolean ignoreUnregisteredMaterials = true;
final int updateCount = 0;
prepareMaterialsUpdate(sessionKey, ignoreUnregisteredMaterials, updateCount);
-
+
List<BatchRegistrationResult> results =
- genericClientService.updateMaterials(MATERIAL_TYPE, sessionKey,
- ignoreUnregisteredMaterials);
-
+ genericClientService.updateMaterials(MATERIAL_TYPE, sessionKey,
+ ignoreUnregisteredMaterials);
+
assertEquals(1, results.size());
assertEquals(updateCount + " material(s) updated, 1 ignored.", results.get(0).getMessage());
context.assertIsSatisfied();
@@ -621,7 +627,7 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
property.setValue("<root>hello</root>");
return property;
}
-
+
/**
* A {@link BaseMatcher} extension for checking the list of {@link NewSample NewSamples}.
*
@@ -661,10 +667,10 @@ public final class GenericClientServiceTest extends AbstractClientServiceTest
private final boolean equals(final NewSample newSample, final NewSample thatNewSample)
{
return ObjectUtils.equals(newSample, thatNewSample)
- && StringUtils.equals(newSample.getContainerIdentifier(), thatNewSample
- .getContainerIdentifier())
- && StringUtils.equals(newSample.getParentIdentifier(), thatNewSample
- .getParentIdentifier())
+ && StringUtils.equals(newSample.getContainerIdentifier(),
+ thatNewSample.getContainerIdentifier())
+ && StringUtils.equals(Arrays.toString(newSample.getParentsOrNull()),
+ Arrays.toString(thatNewSample.getParentsOrNull()))
&& equals(newSample.getProperties(), thatNewSample.getProperties());
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactoryTest.java
index 717dc2a5ac46e1a3cfbdb598d709bf713bc4abe1..200f3e5436cea21a2b4da9bc9f85cc01c7789d73 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/NewSampleParserObjectFactoryTest.java
@@ -181,6 +181,7 @@ public final class NewSampleParserObjectFactoryTest
}
}
+ @SuppressWarnings("deprecation")
@Test(dataProvider = "getLineTokens")
public final void testCreateObject(final String[] lineTokens, final int numberOfProperties)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java
index ad9218f48bf5e3b3ff88c4a9539a19b52a94512f..ea811f8ad25471b9de2dd394401ef36e273090f3 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/UpdatedSampleParserObjectFactoryTest.java
@@ -113,9 +113,9 @@ public final class UpdatedSampleParserObjectFactoryTest
assertEquals(numOfPropertiestoUpdate, propertiesToUpdate.size());
assertEquals(StringUtils.isBlank(p1Token) == false, propertiesToUpdate.contains(PROPERTY_1));
assertEquals(StringUtils.isBlank(p2Token) == false, propertiesToUpdate.contains(PROPERTY_2));
- assertEquals(StringUtils.isBlank(containerToken) == false, batchUpdateDetails
- .isContainerUpdateRequested());
- assertFalse(batchUpdateDetails.isParentUpdateRequested());
+ assertEquals(StringUtils.isBlank(containerToken) == false,
+ batchUpdateDetails.isContainerUpdateRequested());
+ assertFalse(batchUpdateDetails.isParentsUpdateRequested());
assertFalse(batchUpdateDetails.isExperimentUpdateRequested());
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/SampleRegistrationTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/SampleRegistrationTest.java
index a1a56f27070142f1d43e3c632277f8ab1011af38..5b105dc74af016c03308980c1c639c2ed4376040 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/SampleRegistrationTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/plugin/generic/SampleRegistrationTest.java
@@ -73,7 +73,7 @@ public class SampleRegistrationTest extends GenericSystemTestCase
// - dealing with the same parent stated more than once
String[] parents = new String[]
{ "c1", "C2", "/CISD/C3", "CISD:/CISD/C3" };
- sample.setParents(parents);
+ sample.setParentsOrNull(parents);
genericClientService.registerSample("session", sample);
Sample s = getSpaceSample(identifier);
@@ -98,7 +98,7 @@ public class SampleRegistrationTest extends GenericSystemTestCase
final String identifier = CISD_SHORT + sampleCode;
sample.setIdentifier(identifier);
final String parent = "CISD:/CISD/C1";
- sample.setParents(new String[]
+ sample.setParentsOrNull(new String[]
{ parent });
final SampleType sampleType = new SampleType();
sampleType.setCode(DILUTION_PLATE);