From d04e374de31b1db689215cda7d211b6373287db1 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Mon, 9 Aug 2010 13:04:47 +0000
Subject: [PATCH] [LMS-1676] changes in new sample (only for single sample
registration and update)
SVN: 17370
---
.../client/web/client/dto/SampleUpdates.java | 7 +--
.../openbis/generic/server/ETLService.java | 7 +--
.../bo/AbstractSampleBusinessObject.java | 29 ++++++++++--
.../shared/basic/dto/BasicSampleUpdates.java | 5 ++-
.../generic/shared/basic/dto/NewSample.java | 44 ++++++++++++++++---
.../shared/basic/dto/UpdatedSample.java | 7 ++-
.../shared/dto/SampleBatchUpdatesDTO.java | 2 +-
.../generic/shared/dto/SampleUpdatesDTO.java | 7 +--
...AbstractGenericSampleRegisterEditForm.java | 2 +-
.../sample/GenericSampleEditForm.java | 8 ++--
.../sample/GenericSampleRegistrationForm.java | 19 ++++++--
.../web/server/GenericClientService.java | 3 +-
.../server/business/bo/SampleBOTest.java | 20 ++++-----
.../predicate/NewSamplePredicateTest.java | 15 ++++---
.../NewSamplesWithTypePredicateTest.java | 15 ++++---
.../generic/server/GenericServerTest.java | 2 +-
.../dss/bundle/BundleDataSetHelperRpc.java | 4 +-
.../DataSetInfoExtractorForMSInjection.java | 21 ++++++---
18 files changed, 153 insertions(+), 64 deletions(-)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/SampleUpdates.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/SampleUpdates.java
index de8b59062b2..eb92858099f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/SampleUpdates.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/dto/SampleUpdates.java
@@ -56,10 +56,11 @@ public class SampleUpdates extends BasicSampleUpdates
public SampleUpdates(String sessionKey, TechId sampleId, List<IEntityProperty> properties,
List<NewAttachment> attachments, ExperimentIdentifier experimentIdentifierOrNull,
- Date version, String sampleIdentifier, String parentIdentifierOrNull,
- String containerIdentifierOrNull)
+ Date version, String sampleIdentifier, String containerIdentifierOrNull,
+ String parentIdentifierOrNull, String[] parents)
{
- super(sampleId, properties, version, parentIdentifierOrNull, containerIdentifierOrNull);
+ super(sampleId, properties, version, containerIdentifierOrNull, parentIdentifierOrNull,
+ parents);
this.sessionKey = sessionKey;
this.attachments = attachments;
this.experimentIdentifierOrNull = experimentIdentifierOrNull;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index e88a045cd55..3ca33f98281 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -601,7 +601,8 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
{
Session session = getSession(sessionToken);
IExternalDataDAO externalDataDAO = getDAOFactory().getExternalDataDAO();
- ExternalDataPE dataSet = externalDataDAO.tryToFindFullDataSetByCode(dataSetCode, false, false);
+ ExternalDataPE dataSet =
+ externalDataDAO.tryToFindFullDataSetByCode(dataSetCode, false, false);
if (dataSet != null)
{
DataSetTypePE dataSetType = dataSet.getDataSetType();
@@ -768,8 +769,8 @@ public class ETLService extends AbstractCommonServer<IETLService> implements IET
String groupPrefix =
container.getGroup() != null ? ("/" + container.getGroup().getCode() + "/")
: "/";
- newSamples.add(new NewSample(groupPrefix + code, SampleTypeTranslator.translate(
- sampleTypePE, null), null, container.getIdentifier()));
+ newSamples.add(NewSample.createWithParent(groupPrefix + code, SampleTypeTranslator
+ .translate(sampleTypePE, null), null, container.getIdentifier()));
}
getSampleTypeSlaveServerPlugin(sampleTypePE).registerSamples(session, newSamples);
}
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 f7f40c9d9d7..d2797f354d9 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
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
@@ -45,6 +46,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
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.IdentifierHelper;
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.SampleIdentifierFactory;
@@ -130,7 +132,23 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
samplePE.setDatabaseInstance(sampleOwner.tryGetDatabaseInstance());
defineSampleProperties(samplePE, newSample.getProperties());
String parentIdentifier = newSample.getParentIdentifier();
- setGeneratedFrom(sampleIdentifier, samplePE, parentIdentifier);
+ if (parentIdentifier != null)
+ {
+ setGeneratedFrom(sampleIdentifier, samplePE, parentIdentifier);
+ } else if (newSample.getParents() != null)
+ {
+ final String[] parents = newSample.getParents();
+ final List<SampleIdentifier> parentIdentifiers =
+ IdentifierHelper.extractSampleIdentifiers(parents);
+ if (sampleIdentifier.isSpaceLevel())
+ {
+ final String spaceCode = sampleIdentifier.getSpaceLevel().getSpaceCode();
+ for (SampleIdentifier si : parentIdentifiers)
+ {
+ IdentifierHelper.fillAndCheckGroup(si, spaceCode);
+ }
+ }
+ }
String containerIdentifier = newSample.getContainerIdentifier();
setContainer(sampleIdentifier, samplePE, containerIdentifier);
samplePE.setPermId(getPermIdDAO().createPermId());
@@ -214,14 +232,19 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
private void removeParents(SamplePE child)
{
+ List<SampleRelationshipPE> parents = new ArrayList<SampleRelationshipPE>();
for (SampleRelationshipPE r : child.getParentRelationships())
{
if (r.getRelationship().getCode().equals(
BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP))
{
- child.removeParentRelationship(r);
+ parents.add(r);
}
}
+ for (SampleRelationshipPE r : parents)
+ {
+ child.removeParentRelationship(r);
+ }
}
// ineffective for adding a collection of parents
@@ -244,7 +267,7 @@ abstract class AbstractSampleBusinessObject extends AbstractSampleIdentifierBusi
RelationshipTypePE relationshipType)
{
final SampleRelationshipPE relationship =
- new SampleRelationshipPE(child, parent, relationshipType);
+ new SampleRelationshipPE(parent, child, relationshipType);
child.addParentRelationship(relationship);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicSampleUpdates.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicSampleUpdates.java
index 84552fab3aa..4fff987b9ab 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicSampleUpdates.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/BasicSampleUpdates.java
@@ -76,13 +76,14 @@ public class BasicSampleUpdates implements IsSerializable, Serializable
}
public BasicSampleUpdates(TechId sampleId, List<IEntityProperty> properties, Date version,
- String parentIdentifierOrNull, String containerIdentifierOrNull)
+ String containerIdentifierOrNull, String parentIdentifierOrNull, String[] parents)
{
this.sampleIdOrNull = sampleId;
this.properties = properties;
this.version = version;
- this.parentIdentifierOrNull = parentIdentifierOrNull;
this.containerIdentifierOrNull = containerIdentifierOrNull;
+ this.parentIdentifierOrNull = parentIdentifierOrNull;
+ this.modifiedParentCodesOrNull = parents;
}
public TechId getSampleIdOrNull()
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 12d7cabf22c..4fd95b58100 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
@@ -46,8 +46,14 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
/**
* The parent identifier.
*/
+ // 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;
+
/**
* The container identifier.
*/
@@ -66,20 +72,36 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
{
}
- public NewSample(final String identifier, final SampleType sampleType,
- final String parentIdentifier, final String containerIdentifier)
+ private NewSample(final String identifier, final SampleType sampleType,
+ final String containerIdentifier)
{
setIdentifier(identifier);
setSampleType(sampleType);
- setParentIdentifier(parentIdentifier);
setContainerIdentifier(containerIdentifier);
}
- public NewSample(final String identifier, SampleType sampleType, String parentIdentifier,
- String containerIdentifier, String experimentIdentifier, IEntityProperty[] properties,
+ public static NewSample createWithParent(final String identifier, final SampleType sampleType,
+ final String containerIdentifier, final String parentIdentifier)
+ {
+ NewSample result = new NewSample(identifier, sampleType, containerIdentifier);
+ result.setParentIdentifier(parentIdentifier);
+ return result;
+ }
+
+ public static NewSample createWithParents(final String identifier, final SampleType sampleType,
+ final String containerIdentifier, final String[] parents)
+ {
+ NewSample result = new NewSample(identifier, sampleType, containerIdentifier);
+ result.setParents(parents);
+ return result;
+ }
+
+ public NewSample(final String identifier, SampleType sampleType, String containerIdentifier,
+ String parentIdentifier, String experimentIdentifier, IEntityProperty[] properties,
List<NewAttachment> attachments)
{
- this(identifier, sampleType, parentIdentifier, containerIdentifier);
+ this(identifier, sampleType, containerIdentifier);
+ this.parentIdentifier = parentIdentifier;
this.experimentIdentifier = experimentIdentifier;
this.properties = properties;
this.attachments = attachments;
@@ -105,6 +127,16 @@ public class NewSample extends Identifier<NewSample> implements Comparable<NewSa
this.sampleType = sampleType;
}
+ public String[] getParents()
+ {
+ return parentsOrNull;
+ }
+
+ public void setParents(String[] parents)
+ {
+ this.parentsOrNull = parents;
+ }
+
public final String getParentIdentifier()
{
return parentIdentifier;
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 7a2686fda1c..e1cfb3838d2 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
@@ -39,10 +39,9 @@ public final class UpdatedSample extends NewSample
public UpdatedSample(NewSample newSample, SampleBatchUpdateDetails batchUpdateDetails)
{
- super(newSample.getIdentifier(), newSample.getSampleType(),
- newSample.getParentIdentifier(), newSample.getContainerIdentifier(), newSample
- .getExperimentIdentifier(), newSample.getProperties(), newSample
- .getAttachments());
+ super(newSample.getIdentifier(), newSample.getSampleType(), newSample
+ .getContainerIdentifier(), newSample.getParentIdentifier(), newSample
+ .getExperimentIdentifier(), newSample.getProperties(), newSample.getAttachments());
this.batchUpdateDetails = batchUpdateDetails;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleBatchUpdatesDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleBatchUpdatesDTO.java
index 33e78a97898..f366c194ba2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleBatchUpdatesDTO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleBatchUpdatesDTO.java
@@ -41,7 +41,7 @@ public class SampleBatchUpdatesDTO extends SampleUpdatesDTO
String containerIdentifierOrNull, SampleBatchUpdateDetails details)
{
super(null, properties, experimentIdentifierOrNull, null, null, sampleIdentifier,
- parentIdentifierOrNull, containerIdentifierOrNull);
+ containerIdentifierOrNull, parentIdentifierOrNull, null);
this.oldSampleIdentifierOrNull = oldSampleIdentifier;
this.details = details;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleUpdatesDTO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleUpdatesDTO.java
index 0a82f0e2d99..1c0d740fe4b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleUpdatesDTO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/SampleUpdatesDTO.java
@@ -43,10 +43,11 @@ public class SampleUpdatesDTO extends BasicSampleUpdates
public SampleUpdatesDTO(TechId sampleId, List<IEntityProperty> properties,
ExperimentIdentifier experimentIdentifierOrNull, Collection<NewAttachment> attachments,
- Date version, SampleIdentifier sampleIdentifier, String parentIdentifierOrNull,
- String containerIdentifierOrNull)
+ Date version, SampleIdentifier sampleIdentifier, String containerIdentifierOrNull,
+ String parentIdentifierOrNull, String[] parentsOrNull)
{
- super(sampleId, properties, version, parentIdentifierOrNull, containerIdentifierOrNull);
+ super(sampleId, properties, version, containerIdentifierOrNull, parentIdentifierOrNull,
+ parentsOrNull);
this.experimentIdentifierOrNull = experimentIdentifierOrNull;
this.attachments = attachments;
this.sampleIdentifier = sampleIdentifier;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/AbstractGenericSampleRegisterEditForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/AbstractGenericSampleRegisterEditForm.java
index 3a1504a4ad5..e7ab575cc8e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/AbstractGenericSampleRegisterEditForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/AbstractGenericSampleRegisterEditForm.java
@@ -270,7 +270,7 @@ abstract public class AbstractGenericSampleRegisterEditForm extends
return sampleType.getCode();
}
- protected String[] getSamples()
+ protected String[] getParents()
{
return parentsArea.tryGetSampleCodes();
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleEditForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleEditForm.java
index dc62f5740f3..11cf3cf3143 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleEditForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleEditForm.java
@@ -64,13 +64,15 @@ public final class GenericSampleEditForm extends AbstractGenericSampleRegisterEd
{
final List<IEntityProperty> properties = extractProperties();
final List<NewAttachment> attachments = attachmentsManager.extractAttachments();
- ExperimentIdentifier experimentIdent =
+ final ExperimentIdentifier experimentIdent =
experimentField != null ? experimentField.tryToGetValue() : null;
+ final String containerOrNull = StringUtils.trimToNull(container.getValue());
+ final String parentOrNull = StringUtils.trimToNull(parent.getValue());
+ final String[] parents = getParents();
viewContext.getService().updateSample(
new SampleUpdates(attachmentsSessionKey, techIdOrNull, properties, attachments,
experimentIdent, originalSample.getModificationDate(),
- createSampleIdentifier(), StringUtils.trimToNull(parent.getValue()),
- StringUtils.trimToNull(container.getValue())),
+ createSampleIdentifier(), containerOrNull, parentOrNull, parents),
new UpdateSampleCallback(viewContext));
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleRegistrationForm.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleRegistrationForm.java
index 97d9f97694e..29549e423d9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleRegistrationForm.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/client/application/sample/GenericSampleRegistrationForm.java
@@ -97,9 +97,22 @@ public final class GenericSampleRegistrationForm extends AbstractGenericSampleRe
(experimentField != null && experimentField.tryToGetValue() != null) ? experimentField
.tryToGetValue().getIdentifier()
: null;
- final NewSample newSample =
- new NewSample(createSampleIdentifier(), sampleType, StringUtils.trimToNull(parent
- .getValue()), StringUtils.trimToNull(container.getValue()));
+
+ final String containerOrNull = StringUtils.trimToNull(container.getValue());
+ final String parentOrNull = StringUtils.trimToNull(parent.getValue());
+ final NewSample newSample;
+ if (parentOrNull == null)
+ {
+ final String[] parents = getParents();
+ newSample =
+ NewSample.createWithParents(createSampleIdentifier(), sampleType,
+ containerOrNull, parents);
+ } else
+ {
+ newSample =
+ NewSample.createWithParent(createSampleIdentifier(), sampleType,
+ containerOrNull, parentOrNull);
+ }
final List<IEntityProperty> properties = extractProperties();
newSample.setProperties(properties.toArray(IEntityProperty.EMPTY_ARRAY));
newSample.setAttachments(attachmentsManager.extractAttachments());
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 7ccdaa4edc3..5ac80ef2c05 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
@@ -350,8 +350,9 @@ public class GenericClientService extends AbstractClientService implements IGene
.getSampleIdOrNull(), updates.getProperties(),
convExperimentIdentifierOrNull, attachments, updates
.getVersion(), sampleOwner, updates
+ .getContainerIdentifierOrNull(), updates
.getParentIdentifierOrNull(), updates
- .getContainerIdentifierOrNull()));
+ .getModifiedParentCodesOrNull()));
result.copyFrom(updateResult);
}
}.process(updates.getSessionKey(), getHttpSession(), updates.getAttachments());
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 5590b9218f5..9561416b7bf 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
@@ -409,7 +409,7 @@ public final class SampleBOTest extends AbstractBOTest
});
createSampleBO().update(
new SampleUpdatesDTO(SAMPLE_TECH_ID, null, experimentIdentifier, Collections
- .<NewAttachment> emptyList(), now, null, null, null));
+ .<NewAttachment> emptyList(), now, null, null, null, null));
assertEquals(experimentToAttach, sample.getExperiment());
context.assertIsSatisfied();
@@ -445,7 +445,7 @@ public final class SampleBOTest extends AbstractBOTest
createSampleBO().update(
new SampleUpdatesDTO(SAMPLE_TECH_ID, null, null, Collections
.<NewAttachment> emptyList(), now, SampleIdentifierFactory
- .parse(newSampleIdentifierWithoutDb), null, null));
+ .parse(newSampleIdentifierWithoutDb), null, null, null));
String newSampleIdentWithDb =
EXAMPLE_DATABASE_INSTANCE.getCode() + ":" + newSampleIdentifierWithoutDb;
assertEquals(newSampleIdentWithDb, sample.getSampleIdentifier().toString());
@@ -505,7 +505,7 @@ public final class SampleBOTest extends AbstractBOTest
assertNull(sample.getGeneratedFrom());
createSampleBO().update(
new SampleUpdatesDTO(SAMPLE_TECH_ID, null, null, Collections
- .<NewAttachment> emptyList(), now, null, parent.getSampleIdentifier()
+ .<NewAttachment> emptyList(), now, null, null, parent.getSampleIdentifier()
.toString(), null));
SamplePE newParent = sample.getGeneratedFrom();
assertNotNull(newParent);
@@ -557,8 +557,8 @@ public final class SampleBOTest extends AbstractBOTest
assertNull(sample.getContainer());
createSampleBO().update(
new SampleUpdatesDTO(SAMPLE_TECH_ID, null, null, Collections
- .<NewAttachment> emptyList(), now, null, null, container
- .getSampleIdentifier().toString()));
+ .<NewAttachment> emptyList(), now, null, container.getSampleIdentifier()
+ .toString(), null, null));
assertNotNull(sample.getContainer());
assertEquals(container, sample.getContainer());
context.assertIsSatisfied();
@@ -611,8 +611,8 @@ public final class SampleBOTest extends AbstractBOTest
assertNull(sample.getContainer());
SampleBO bo = createSampleBO();
bo.update(new SampleUpdatesDTO(SAMPLE_TECH_ID, null, null, Collections
- .<NewAttachment> emptyList(), now, null, null, container.getSampleIdentifier()
- .toString()));
+ .<NewAttachment> emptyList(), now, null,
+ container.getSampleIdentifier().toString(), null, null));
bo.save();
context.assertIsSatisfied();
}
@@ -643,7 +643,7 @@ public final class SampleBOTest extends AbstractBOTest
{
createSampleBO().update(
new SampleUpdatesDTO(SAMPLE_TECH_ID, null, null, Collections
- .<NewAttachment> emptyList(), now, null, null, null));
+ .<NewAttachment> emptyList(), now, null, null, null, null));
} catch (UserFailureException ex)
{
exceptionThrown = true;
@@ -671,7 +671,7 @@ public final class SampleBOTest extends AbstractBOTest
{
SampleUpdatesDTO updates =
new SampleUpdatesDTO(SAMPLE_TECH_ID, null, null, Collections
- .<NewAttachment> emptyList(), now, null, null, null);
+ .<NewAttachment> emptyList(), now, null, null, null, null);
createSampleBO().update(updates);
} catch (UserFailureException e)
{
@@ -993,6 +993,6 @@ public final class SampleBOTest extends AbstractBOTest
createSampleBO().update(
new SampleUpdatesDTO(sampleId, null, experimentIdentifier, Collections
.<NewAttachment> emptyList(), sample.getModificationDate(), null, null,
- null));
+ null, null));
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/NewSamplePredicateTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/NewSamplePredicateTest.java
index eca0a008ca2..808855c9bf1 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/NewSamplePredicateTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/NewSamplePredicateTest.java
@@ -43,7 +43,8 @@ public class NewSamplePredicateTest extends AuthorizationTestCase
SampleIdentifier sampleIdentifier =
new SampleIdentifier(new DatabaseInstanceIdentifier(ANOTHER_INSTANCE_CODE), "s1");
NewSample sample =
- new NewSample(sampleIdentifier.toString(), sampleType, "parent", "container");
+ NewSample.createWithParent(sampleIdentifier.toString(), sampleType, "parent",
+ "container");
prepareProvider(ANOTHER_INSTANCE_CODE, createAnotherDatabaseInstance(), createGroups());
predicate.init(provider);
@@ -61,7 +62,8 @@ public class NewSamplePredicateTest extends AuthorizationTestCase
SampleIdentifier sampleIdentifier =
new SampleIdentifier(new DatabaseInstanceIdentifier(INSTANCE_CODE), "s1");
NewSample sample =
- new NewSample(sampleIdentifier.toString(), sampleType, "parent", "container");
+ NewSample.createWithParent(sampleIdentifier.toString(), sampleType, "parent",
+ "container");
prepareProvider(INSTANCE_CODE, createDatabaseInstance(), createGroups());
predicate.init(provider);
@@ -81,7 +83,8 @@ public class NewSamplePredicateTest extends AuthorizationTestCase
SampleIdentifier sampleIdentifier =
new SampleIdentifier(new GroupIdentifier(INSTANCE_CODE, SPACE_CODE), "s1");
NewSample sample =
- new NewSample(sampleIdentifier.toString(), sampleType, "parent", "container");
+ NewSample.createWithParent(sampleIdentifier.toString(), sampleType, "parent",
+ "container");
prepareProvider(INSTANCE_CODE, createDatabaseInstance(), createGroups());
predicate.init(provider);
@@ -99,7 +102,8 @@ public class NewSamplePredicateTest extends AuthorizationTestCase
GroupIdentifier groupIdentifier = new GroupIdentifier(INSTANCE_CODE, ANOTHER_GROUP_CODE);
SampleIdentifier sampleIdentifier = new SampleIdentifier(groupIdentifier, "s1");
NewSample sample =
- new NewSample(sampleIdentifier.toString(), sampleType, "parent", "container");
+ NewSample.createWithParent(sampleIdentifier.toString(), sampleType, "parent",
+ "container");
List<GroupPE> groups = Arrays.asList(createGroup(groupIdentifier));
prepareProvider(INSTANCE_CODE, createDatabaseInstance(), groups);
predicate.init(provider);
@@ -107,7 +111,8 @@ public class NewSamplePredicateTest extends AuthorizationTestCase
Status status = predicate.evaluate(createPerson(), createRoles(false), sample);
assertEquals(true, status.isError());
- assertEquals("User 'megapixel' does not have enough privileges.", status.tryGetErrorMessage());
+ assertEquals("User 'megapixel' does not have enough privileges.", status
+ .tryGetErrorMessage());
context.assertIsSatisfied();
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/NewSamplesWithTypePredicateTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/NewSamplesWithTypePredicateTest.java
index 18d60a6fb3b..55c47a9d3b7 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/NewSamplesWithTypePredicateTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/authorization/predicate/NewSamplesWithTypePredicateTest.java
@@ -88,8 +88,9 @@ public class NewSamplesWithTypePredicateTest extends AuthorizationTestCase
predicate.init(provider);
Status status =
predicate.evaluate(person, roles, new NewSamplesWithTypes(new SampleType(), Arrays
- .asList(new NewSample(sampleIdentifier1.toString(), null, null, null),
- new NewSample(sampleIdentifier2.toString(), null, null, null))));
+ .asList(NewSample.createWithParent(sampleIdentifier1.toString(), null,
+ null, null), NewSample.createWithParent(sampleIdentifier2
+ .toString(), null, null, null))));
assertEquals(false, status.isError());
context.assertIsSatisfied();
}
@@ -116,8 +117,9 @@ public class NewSamplesWithTypePredicateTest extends AuthorizationTestCase
predicate.init(provider);
Status status =
predicate.evaluate(person, roles, new NewSamplesWithTypes(new SampleType(), Arrays
- .asList(new NewSample(sampleIdentifier1.toString(), null, null, null),
- new NewSample(sampleIdentifier2.toString(), null, null, null))));
+ .asList(NewSample.createWithParent(sampleIdentifier1.toString(), null,
+ null, null), NewSample.createWithParent(sampleIdentifier2
+ .toString(), null, null, null))));
assertEquals(true, status.isError());
context.assertIsSatisfied();
}
@@ -146,8 +148,9 @@ public class NewSamplesWithTypePredicateTest extends AuthorizationTestCase
predicate.init(provider);
Status status =
predicate.evaluate(person, roles, new NewSamplesWithTypes(new SampleType(), Arrays
- .asList(new NewSample(sampleIdentifier1.toString(), null, null, null),
- new NewSample(sampleIdentifier2.toString(), null, null, null))));
+ .asList(NewSample.createWithParent(sampleIdentifier1.toString(), null,
+ null, null), NewSample.createWithParent(sampleIdentifier2
+ .toString(), null, null, null))));
assertEquals(true, status.isError());
context.assertIsSatisfied();
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
index dc0ffee8f85..6e11b24efa1 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/plugin/generic/server/GenericServerTest.java
@@ -437,7 +437,7 @@ public final class GenericServerTest extends AbstractServerTestCase
sample.setModificationDate(newModificationDate);
final SampleUpdatesDTO updates =
new SampleUpdatesDTO(sampleId, properties, null, attachments, version, null, null,
- null);
+ null, null);
context.checking(new Expectations()
{
{
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelperRpc.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelperRpc.java
index 67a81ba60c3..9223893e704 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelperRpc.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/BundleDataSetHelperRpc.java
@@ -130,7 +130,7 @@ class BundleDataSetHelperRpc extends BundleDataSetHelper
Sample parentSample = getOpenbisService().tryGetSampleWithExperiment(parentIdOrNull);
sampleId = new SampleIdentifier(parentIdOrNull.getSpaceLevel(), sampleCode);
sample =
- new NewSample(sampleId.toString(), replicaSampleType,
+ NewSample.createWithParent(sampleId.toString(), replicaSampleType,
parentIdOrNull.toString(), null);
sample.setExperimentIdentifier(parentSample.getExperiment().getIdentifier());
} else if (experimentIdOrNull != null)
@@ -140,7 +140,7 @@ class BundleDataSetHelperRpc extends BundleDataSetHelper
new SpaceIdentifier(experimentIdOrNull.getDatabaseInstanceCode(),
experimentIdOrNull.getSpaceCode());
sampleId = new SampleIdentifier(spaceId, sampleCode);
- sample = new NewSample(sampleId.toString(), replicaSampleType, null, null);
+ sample = NewSample.createWithParent(sampleId.toString(), replicaSampleType, null, null);
sample.setExperimentIdentifier(experimentIdOrNull.toString());
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
index 873097a3060..9200822ad05 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForMSInjection.java
@@ -56,22 +56,27 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtractorWithService
{
static final String MS_INJECTION_PROPERTIES_FILE = "ms-injection.properties";
+
static final String DATA_SET_PROPERTIES_FILE = "data-set.properties";
static final String PROJECT_CODE_KEY = "PROJECT_CODE";
+
static final String EXPERIMENT_CODE_KEY = "EXPERIMENT_CODE";
+
static final String SAMPLE_CODE_KEY = "SAMPLE_CODE";
+
static final String USER_KEY = "USER";
-
+
static final String DATA_SET_TYPE_KEY = "DATA_SET_TYPE";
+
static final String FILE_TYPE_KEY = "FILE_TYPE";
+
static final String PARENT_TYPE_KEY = "PARENT_TYPE";
-
+
static final String EXPERIMENT_TYPE_CODE = "MS_INJECT";
static final String SAMPLE_TYPE_CODE = "MS_INJECTION";
-
public DataSetInfoExtractorForMSInjection(Properties properties)
{
this(ServiceProvider.getOpenBISService());
@@ -95,11 +100,13 @@ public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtra
ExperimentIdentifier experimentIdentifier = getExperimentIdentifier(sampleProperties);
getOrCreateExperiment(experimentIdentifier);
info.setExperimentIdentifier(experimentIdentifier);
- long sampleID = registerOrUpdateSample(sampleIdentifier, experimentIdentifier, sampleProperties);
-
+ long sampleID =
+ registerOrUpdateSample(sampleIdentifier, experimentIdentifier, sampleProperties);
+
Properties dataSetProperties =
Util.loadPropertiesFile(incomingDataSetPath, DATA_SET_PROPERTIES_FILE);
- String dataSetTypeCode = PropertyUtils.getMandatoryProperty(dataSetProperties, DATA_SET_TYPE_KEY);
+ String dataSetTypeCode =
+ PropertyUtils.getMandatoryProperty(dataSetProperties, DATA_SET_TYPE_KEY);
String parentTypeOrNull = dataSetProperties.getProperty(PARENT_TYPE_KEY);
dataSetProperties.remove(DATA_SET_TYPE_KEY);
dataSetProperties.remove(FILE_TYPE_KEY);
@@ -150,7 +157,7 @@ public class DataSetInfoExtractorForMSInjection extends AbstractDataSetInfoExtra
Set<NewAttachment> emptySet = Collections.<NewAttachment> emptySet();
Date version = sample.getModificationDate();
service.updateSample(new SampleUpdatesDTO(sampleID, propertiesList,
- experimentIdentifier, emptySet, version, sampleIdentifier, null, null));
+ experimentIdentifier, emptySet, version, sampleIdentifier, null, null, null));
return sample.getId();
}
}
--
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