From ce15c2bf2be2766afc362a93e1bf1e6574fbe43c Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Fri, 19 Oct 2012 11:17:01 +0000
Subject: [PATCH] SP-345 BIS-178: initial, incomplete commit
SVN: 27245
---
.../generic/server/UploadingCommandTest.java | 13 ++--
.../openbis/generic/server/CommonServer.java | 69 ++++++++++++++---
.../openbis/generic/server/ETLService.java | 70 +++++++++++++----
.../generic/server/MaterialHelper.java | 5 +-
.../api/v1/GeneralInformationService.java | 28 ++++---
.../server/business/bo/DataSetTable.java | 4 +-
.../EntityMetaprojectRelationRecord.java | 27 +++++++
.../common/MetaprojectCreator.java | 41 ++++++++++
.../common/MetaprojectRecord.java | 35 +++++++++
.../datasetlister/DataSetLister.java | 22 ++++--
.../samplelister/ISampleListingQuery.java | 15 ++++
.../samplelister/SampleLister.java | 77 +++++++++++++++++--
.../samplelister/SampleRecord.java | 3 +
.../server/dataaccess/IMetaprojectDAO.java | 9 +++
.../server/dataaccess/db/MetaprojectDAO.java | 22 ++++++
.../generic/shared/basic/dto/Experiment.java | 13 ++++
.../basic/dto/ExperimentFetchOption.java | 2 +-
.../shared/basic/dto/ExternalData.java | 13 +++-
.../generic/shared/basic/dto/Material.java | 14 +++-
.../generic/shared/basic/dto/Sample.java | 13 ++++
.../shared/translator/DataSetTranslator.java | 25 ++++--
.../translator/EntityHistoryTranslator.java | 13 ++--
.../translator/EntityPropertyTranslator.java | 2 +-
.../translator/ExperimentTranslator.java | 23 ++++--
.../shared/translator/MaterialTranslator.java | 22 ++++--
.../translator/MetaprojectTranslator.java | 55 ++++++++++++-
.../shared/translator/SampleTranslator.java | 38 +++++----
.../plugin/generic/server/GenericServer.java | 10 +++
.../generic/server/CommonServerTest.java | 17 +++-
.../api/v1/GeneralInformationServiceTest.java | 9 ++-
.../validator/ExperimentValidatorTest.java | 15 ++--
.../validator/ExternalDataValidatorTest.java | 5 +-
.../validator/SampleValidatorTest.java | 25 +++---
.../bo/datasetlister/DatasetListerTest.java | 4 +-
.../datasetlister/DataSetListerTest.java | 34 ++++----
.../dataaccess/db/MetaprojectDAOTest.java | 23 ++++++
.../shared/AbstractServerTestCase.java | 6 ++
.../translator/DataSetTranslatorTest.java | 9 ++-
.../api/v1/GeneralInformationServiceTest.java | 46 +++++++++++
.../124/042=metaproject_assignments_all.tsv | 1 +
.../shared/api/v1/dto/DataSetFetchOption.java | 2 +-
.../generic/shared/api/v1/dto/Sample.java | 42 ++++++++++
.../shared/api/v1/dto/SampleFetchOption.java | 11 ++-
.../server/ProteomicsDataServiceInternal.java | 24 ++++--
.../server/business/ExperimentLoader.java | 9 +--
.../server/business/ExperimentLoaderTest.java | 18 ++---
.../server/logic/LogicalImageLoader.java | 2 +-
.../server/logic/PlateContentLoader.java | 2 +-
.../server/logic/ScreeningApiImpl.java | 15 ++--
.../server/logic/ScreeningUtils.java | 2 +-
50 files changed, 819 insertions(+), 185 deletions(-)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/EntityMetaprojectRelationRecord.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/MetaprojectCreator.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/MetaprojectRecord.java
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
index 6b9a4900f58..efd0745a6ae 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/UploadingCommandTest.java
@@ -240,11 +240,11 @@ public class UploadingCommandTest extends AssertJUnit
createTestData(LOCATION1);
ds2 = createTestData(LOCATION2);
ExternalData dataSet1 =
- DataSetTranslator.translate(createDataSet("1"), "?",
+ DataSetTranslator.translate(createDataSet("1"), "?", null,
ExperimentTranslator.LoadableFields.PROPERTIES);
System.out.println("ds1:" + dataSet1.getExperiment().getProperties());
ExternalData dataSet2 =
- DataSetTranslator.translate(createDataSet("2"), "?",
+ DataSetTranslator.translate(createDataSet("2"), "?", null,
ExperimentTranslator.LoadableFields.PROPERTIES);
dataSets = Arrays.<ExternalData> asList(dataSet1, dataSet2);
command =
@@ -388,8 +388,7 @@ public class UploadingCommandTest extends AssertJUnit
one(uploader).upload(
Collections.singletonList(new FileWithOverrideName(new File(TMP,
- ZIP_FILENAME + ".zip"), null)),
- "id:user", null);
+ ZIP_FILENAME + ".zip"), null)), "id:user", null);
will(new CustomAction("report 'finish' to listener")
{
@Override
@@ -447,8 +446,7 @@ public class UploadingCommandTest extends AssertJUnit
one(uploader).upload(
Collections.singletonList(new FileWithOverrideName(new File(TMP,
- ZIP_FILENAME + ".zip"), null)),
- "id:user", null);
+ ZIP_FILENAME + ".zip"), null)), "id:user", null);
will(new CustomAction("report 'finish' to listener")
{
@Override
@@ -546,8 +544,7 @@ public class UploadingCommandTest extends AssertJUnit
one(uploader).upload(
Collections.singletonList(new FileWithOverrideName(new File(TMP,
- ZIP_FILENAME + ".zip"), null)),
- "id:user", null);
+ ZIP_FILENAME + ".zip"), null)), "id:user", null);
will(new CustomAction("report 'abort' to listener")
{
@Override
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index 1f61940f265..7111ca7b595 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -874,8 +874,17 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
experimentTable.load(experimentIdentifiers);
List<ExperimentPE> experiments = experimentTable.getExperiments();
+ final Collection<MetaprojectAssignmentPE> assignmentPEs =
+ getDAOFactory()
+ .getMetaprojectDAO()
+ .listMetaprojectAssignmentsForEntities(
+ session.tryGetPerson(),
+ experiments,
+ ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind.EXPERIMENT);
+ Map<Long, Set<Metaproject>> assignments =
+ MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs);
Collections.sort(experiments);
- return ExperimentTranslator.translate(experiments, session.getBaseIndexURL());
+ return ExperimentTranslator.translate(experiments, session.getBaseIndexURL(), assignments);
}
private final List<Experiment> listExperiments(final String sessionToken,
@@ -895,8 +904,17 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
experimentTable.load(experimentType.getCode(), spaceIdentifierOrNull);
}
final List<ExperimentPE> experiments = experimentTable.getExperiments();
+ final Collection<MetaprojectAssignmentPE> assignmentPEs =
+ getDAOFactory()
+ .getMetaprojectDAO()
+ .listMetaprojectAssignmentsForEntities(
+ session.tryGetPerson(),
+ experiments,
+ ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind.EXPERIMENT);
+ Map<Long, Set<Metaproject>> assignments =
+ MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs);
Collections.sort(experiments);
- return ExperimentTranslator.translate(experiments, session.getBaseIndexURL());
+ return ExperimentTranslator.translate(experiments, session.getBaseIndexURL(), assignments);
}
@Override
@@ -1259,7 +1277,11 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
datasetBO.enrichWithContainedDataSets();
datasetBO.enrichWithProperties();
final DataPE dataset = datasetBO.getData();
- return DataSetTranslator.translate(dataset, session.getBaseIndexURL(), false);
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), dataset);
+ return DataSetTranslator.translate(dataset, session.getBaseIndexURL(), false,
+ MetaprojectTranslator.translate(metaprojectPEs));
}
@Override
@@ -1296,7 +1318,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
for (final DataPE hit : resultSet)
{
HibernateUtils.initialize(hit.getChildRelationships());
- list.add(DataSetTranslator.translate(hit, session.getBaseIndexURL(), withDetails));
+ list.add(DataSetTranslator.translate(hit, session.getBaseIndexURL(), withDetails, null));
}
return list;
}
@@ -1919,7 +1941,13 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
throw UserFailureException.fromTemplate(
"No experiment could be found with given identifier '%s'.", identifier);
}
+
+ Collection<MetaprojectPE> metaprojects =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), experiment);
+
return ExperimentTranslator.translate(experiment, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojects),
ExperimentTranslator.LoadableFields.PROPERTIES,
ExperimentTranslator.LoadableFields.ATTACHMENTS);
}
@@ -1936,7 +1964,13 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
experimentBO.enrichWithProperties();
experimentBO.enrichWithAttachments();
final ExperimentPE experiment = experimentBO.getExperiment();
+
+ Collection<MetaprojectPE> metaprojects =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), experiment);
+
return ExperimentTranslator.translate(experiment, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojects),
ExperimentTranslator.LoadableFields.PROPERTIES,
ExperimentTranslator.LoadableFields.ATTACHMENTS);
}
@@ -2005,7 +2039,13 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
IMaterialBO materialBO = getBusinessObjectFactory().createMaterialBO(session);
materialBO.loadByMaterialIdentifier(identifier);
materialBO.enrichWithProperties();
- return MaterialTranslator.translate(materialBO.getMaterial());
+ MaterialPE materialPE = materialBO.getMaterial();
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), materialPE);
+
+ return MaterialTranslator.translate(materialPE,
+ MetaprojectTranslator.translate(metaprojectPEs));
}
@Override
@@ -2017,7 +2057,11 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
materialBO.loadDataByTechId(materialId);
materialBO.enrichWithProperties();
final MaterialPE material = materialBO.getMaterial();
- return MaterialTranslator.translate(material, true);
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), material);
+ return MaterialTranslator.translate(material, true,
+ MetaprojectTranslator.translate(metaprojectPEs));
}
@Override
@@ -3484,19 +3528,19 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
if (authorizationUtils.canAccessExperiment(metaprojectAssignment.getExperiment()))
{
experiments.add(ExperimentTranslator.translate(
- metaprojectAssignment.getExperiment(), baseIndexURL,
+ metaprojectAssignment.getExperiment(), baseIndexURL, null,
LoadableFields.PROPERTIES));
} else
{
- experiments.add(ExperimentTranslator
- .translateWithoutRevealingData(metaprojectAssignment.getExperiment()));
+ experiments.add(ExperimentTranslator.translateWithoutRevealingData(
+ metaprojectAssignment.getExperiment(), null));
}
} else if (metaprojectAssignment.getSample() != null)
{
if (authorizationUtils.canAccessSample(metaprojectAssignment.getSample()))
{
samples.add(SampleTranslator.translate(metaprojectAssignment.getSample(),
- baseIndexURL));
+ baseIndexURL, null));
} else
{
samples.add(SampleTranslator
@@ -3507,7 +3551,7 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
if (authorizationUtils.canAccessDataSet(metaprojectAssignment.getDataSet()))
{
dataSets.add(DataSetTranslator.translate(metaprojectAssignment.getDataSet(),
- baseIndexURL));
+ baseIndexURL, null));
} else
{
dataSets.add(DataSetTranslator
@@ -3515,7 +3559,8 @@ public final class CommonServer extends AbstractCommonServer<ICommonServerForInt
}
} else if (metaprojectAssignment.getMaterial() != null)
{
- materials.add(MaterialTranslator.translate(metaprojectAssignment.getMaterial()));
+ materials.add(MaterialTranslator.translate(metaprojectAssignment.getMaterial(),
+ null));
}
}
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 e96753666fe..b25a4601835 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
@@ -126,6 +126,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
@@ -165,7 +166,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataManagementSystemPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewContainerDataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
@@ -199,6 +203,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.L
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTypeTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExternalDataManagementSystemTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.MetaprojectTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.PersonTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ProjectTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
@@ -394,7 +399,10 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
throw new IllegalArgumentException("ExperimentFetchOptions were null");
}
- if (experimentFetchOptions.isSubsetOf(ExperimentFetchOption.BASIC))
+ checkSession(sessionToken);
+
+ if (experimentFetchOptions.isSubsetOf(ExperimentFetchOption.BASIC,
+ ExperimentFetchOption.METAPROJECTS))
{
ExperimentLister lister =
new ExperimentLister(getDAOFactory(), getSession(sessionToken)
@@ -438,7 +446,10 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
throw new IllegalArgumentException("ExperimentFetchOptions were null");
}
- if (experimentFetchOptions.isSubsetOf(ExperimentFetchOption.BASIC))
+ checkSession(sessionToken);
+
+ if (experimentFetchOptions.isSubsetOf(ExperimentFetchOption.BASIC,
+ ExperimentFetchOption.METAPROJECTS))
{
ExperimentLister lister =
new ExperimentLister(daoFactory, getSession(sessionToken).getBaseIndexURL());
@@ -485,8 +496,13 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
return null;
}
enrichWithProperties(experiment);
+
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), experiment);
+
return ExperimentTranslator.translate(experiment, session.getBaseIndexURL(),
- LoadableFields.PROPERTIES);
+ MetaprojectTranslator.translate(metaprojectPEs), LoadableFields.PROPERTIES);
}
@Override
@@ -518,7 +534,11 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
HibernateUtils.initialize(sample.getProperties());
enrichWithProperties(sample.getExperiment());
}
- return SampleTranslator.translate(sample, session.getBaseIndexURL(), true, true);
+ Collection<MetaprojectPE> metaprojects =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), sample);
+ return SampleTranslator.translate(sample, session.getBaseIndexURL(), true, true,
+ MetaprojectTranslator.translate(metaprojects));
}
@Override
@@ -711,8 +731,13 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
businessObjectFactory.createExperimentTable(session);
experimentTable.load(EntityType.ALL_TYPES_CODE, projectIdentifier);
final List<ExperimentPE> experiments = experimentTable.getExperiments();
+ final Collection<MetaprojectAssignmentPE> assignmentPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
+ session.tryGetPerson(), experiments, EntityKind.EXPERIMENT);
+ Map<Long, Set<Metaproject>> assignments =
+ MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs);
Collections.sort(experiments);
- return ExperimentTranslator.translate(experiments, session.getBaseIndexURL());
+ return ExperimentTranslator.translate(experiments, session.getBaseIndexURL(), assignments);
}
@Override
@@ -989,7 +1014,11 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
DataPE dataPE = dataBO.tryGetData();
if (null == dataPE)
return null;
- return DataSetTranslator.translate(dataPE, session.getBaseIndexURL());
+ Collection<MetaprojectPE> metaprojects =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), dataPE);
+ return DataSetTranslator.translate(dataPE, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojects));
}
@Override
@@ -1051,7 +1080,15 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
Session session = getSession(sessionToken);
ISampleTable sampleTable = businessObjectFactory.createSampleTable(session);
sampleTable.loadSamplesByCriteria(criteria);
- return SampleTranslator.translate(sampleTable.getSamples(), "");
+ List<SamplePE> samples = sampleTable.getSamples();
+
+ final Collection<MetaprojectAssignmentPE> assignmentPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
+ session.tryGetPerson(), samples, EntityKind.SAMPLE);
+ Map<Long, Set<Metaproject>> assignments =
+ MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs);
+
+ return SampleTranslator.translate(samples, "", assignments);
}
@Override
@@ -1233,9 +1270,7 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
// Register the data set
registerDataSetInternal(sessionToken, externalData, samplePE);
- Sample result =
- SampleTranslator.translate(Collections.singletonList(samplePE),
- session.getBaseIndexURL()).get(0);
+ Sample result = SampleTranslator.translate(samplePE, session.getBaseIndexURL(), null);
return result;
}
@@ -1254,9 +1289,13 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
final SamplePE samplePE = sampleBO.getSample();
registerDataSetInternal(sessionToken, externalData, samplePE);
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), samplePE);
+
Sample result =
- SampleTranslator.translate(Collections.singletonList(samplePE),
- session.getBaseIndexURL()).get(0);
+ SampleTranslator.translate(samplePE, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojectPEs));
return result;
}
@@ -1367,7 +1406,12 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
{
bo.loadByMaterialIdentifier(materialIdentifier);
bo.enrichWithProperties();
- return MaterialTranslator.translate(bo.getMaterial());
+ MaterialPE materialPE = bo.getMaterial();
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), materialPE);
+ return MaterialTranslator.translate(materialPE,
+ MetaprojectTranslator.translate(metaprojectPEs));
} catch (UserFailureException ufe)
{
// material does not exist
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/MaterialHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/MaterialHelper.java
index ae169a397f1..9085e39ece6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/MaterialHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/MaterialHelper.java
@@ -22,6 +22,7 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import java.util.concurrent.atomic.AtomicInteger;
import org.apache.log4j.Logger;
@@ -41,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
@@ -139,7 +141,8 @@ public class MaterialHelper
};
BatchOperationExecutor.executeInBatches(strategy);
- return MaterialTranslator.translate(registeredMaterials);
+ return MaterialTranslator.translate(registeredMaterials,
+ new HashMap<Long, Set<Metaproject>>());
}
public int updateMaterials(String materialTypeCode, final List<NewMaterial> newMaterials,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
index 3510f8d3200..92e7a6034e2 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
@@ -99,6 +99,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
@@ -109,6 +110,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
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.translator.DataSetTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.MetaprojectTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
/**
@@ -319,7 +321,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
Collection<Long> sampleIDs =
new SampleSearchManager(getDAOFactory().getHibernateSearchDAO(), sampleLister)
.searchForSampleIDs(detailedSearchCriteria);
- return createSampleLister().getSamples(sampleIDs, sampleFetchOptions);
+ return createSampleLister(session.tryGetPerson()).getSamples(sampleIDs, sampleFetchOptions);
}
@Override
@@ -369,9 +371,9 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
return samples;
}
- protected ISampleLister createSampleLister()
+ protected ISampleLister createSampleLister(PersonPE person)
{
- return new SampleLister(getDAOFactory());
+ return new SampleLister(getDAOFactory(), person);
}
@Override
@@ -585,9 +587,9 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
{ RoleWithHierarchy.SPACE_OBSERVER, RoleWithHierarchy.SPACE_ETL_SERVER })
public String tryGetDataStoreBaseURL(String sessionToken, String dataSetCode)
{
- checkSession(sessionToken);
+ Session session = getSession(sessionToken);
- final IDataSetLister lister = new DataSetLister(getDAOFactory());
+ final IDataSetLister lister = new DataSetLister(getDAOFactory(), session.tryGetPerson());
final List<DataStoreURLForDataSets> dataStores =
lister.getDataStoreDownloadURLs(Collections.singletonList(dataSetCode));
if (dataStores.isEmpty())
@@ -604,9 +606,9 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
public List<DataStoreURLForDataSets> getDataStoreBaseURLs(String sessionToken,
List<String> dataSetCodes)
{
- checkSession(sessionToken);
+ Session session = getSession(sessionToken);
- final IDataSetLister lister = new DataSetLister(getDAOFactory());
+ final IDataSetLister lister = new DataSetLister(getDAOFactory(), session.tryGetPerson());
return lister.getDataStoreDownloadURLs(dataSetCodes);
}
@@ -771,7 +773,12 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
}
HibernateUtils.initialize(dataPE.getChildRelationships());
HibernateUtils.initialize(dataPE.getProperties());
- ExternalData ds = DataSetTranslator.translate(dataPE, session.getBaseIndexURL());
+ Collection<MetaprojectPE> metaprojects =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), dataPE);
+ ExternalData ds =
+ DataSetTranslator.translate(dataPE, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojects));
result.add(Translator.translate(ds, connections));
}
return result;
@@ -806,8 +813,9 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
if (dataSetFetchOptions.isSubsetOf(DataSetFetchOption.BASIC, DataSetFetchOption.PARENTS,
DataSetFetchOption.CHILDREN))
{
- checkSession(sessionToken);
- final IDataSetLister lister = new DataSetLister(getDAOFactory());
+ Session session = getSession(sessionToken);
+ final IDataSetLister lister =
+ new DataSetLister(getDAOFactory(), session.tryGetPerson());
return lister.getDataSetMetaData(dataSetCodes, dataSetFetchOptions);
} else
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index 8af1c4fb582..fa1509aa989 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -60,6 +60,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetBatchUpdateDetails;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkModel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
@@ -521,7 +522,8 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
getConversationClient().getDataStoreService(dataStore.getRemoteUrl(),
session.getSessionToken());
String sessionToken = dataStore.getSessionToken();
- List<ExternalData> cleanDataSets = DataSetTranslator.translate(list, "?", "?");
+ List<ExternalData> cleanDataSets =
+ DataSetTranslator.translate(list, "?", "?", new HashMap<Long, Set<Metaproject>>());
service.uploadDataSetsToCIFEX(sessionToken, cleanDataSets, context);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/EntityMetaprojectRelationRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/EntityMetaprojectRelationRecord.java
new file mode 100644
index 00000000000..6824073ba5f
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/EntityMetaprojectRelationRecord.java
@@ -0,0 +1,27 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class EntityMetaprojectRelationRecord
+{
+ public Long metaproject_id;
+
+ public Long entity_id;
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/MetaprojectCreator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/MetaprojectCreator.java
new file mode 100644
index 00000000000..03829e60b60
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/MetaprojectCreator.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class MetaprojectCreator
+{
+ public static Metaproject createMetaproject(MetaprojectRecord metaprojectRecord, PersonPE owner)
+ {
+ Metaproject metaproject = new Metaproject();
+
+ metaproject.setId(metaprojectRecord.id);
+ metaproject.setName(metaprojectRecord.name);
+ metaproject.setDescription(metaprojectRecord.description);
+ metaproject.setPrivate(metaprojectRecord.is_private);
+ metaproject.setCreationDate(metaprojectRecord.creation_date);
+
+ metaproject.setOwnerId(owner.getUserId());
+
+ return metaproject;
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/MetaprojectRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/MetaprojectRecord.java
new file mode 100644
index 00000000000..0bfb85f77d4
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/common/MetaprojectRecord.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common;
+
+import java.util.Date;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class MetaprojectRecord
+{
+ public Long id;
+
+ public String name;
+
+ public String description;
+
+ public Boolean is_private;
+
+ public Date creation_date;
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
index b28ba6d2040..187d21e1916 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetLister.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalDataManagementSystem;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkDataSetUrl;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.IdentifierHelper;
@@ -55,19 +56,26 @@ public class DataSetLister implements IDataSetLister
private IDataSetListingQuery query;
- public DataSetLister(IAuthorizationDAOFactory daoFactory)
+ private PersonPE person;
+
+ public DataSetLister(IAuthorizationDAOFactory daoFactory, PersonPE person)
{
this(QueryTool.getQuery(DatabaseContextUtils.getConnection(daoFactory),
- IDataSetListingQuery.class));
+ IDataSetListingQuery.class), person);
}
- public DataSetLister(IDataSetListingQuery query)
+ public DataSetLister(IDataSetListingQuery query, PersonPE person)
{
if (query == null)
{
throw new IllegalArgumentException("Query was null");
}
+ if (person == null)
+ {
+ throw new IllegalArgumentException("Person was null");
+ }
this.query = query;
+ this.person = person;
}
@Override
@@ -82,11 +90,13 @@ public class DataSetLister implements IDataSetLister
{
throw new IllegalArgumentException("DataSetFetchOptions were null");
}
- if (!dataSetFetchOptions.isSubsetOf(DataSetFetchOption.BASIC, DataSetFetchOption.PARENTS,
- DataSetFetchOption.CHILDREN))
+ if (false == dataSetFetchOptions.isSubsetOf(DataSetFetchOption.BASIC,
+ DataSetFetchOption.PARENTS, DataSetFetchOption.CHILDREN,
+ DataSetFetchOption.METAPROJECTS))
{
throw new IllegalArgumentException("Currently only " + DataSetFetchOption.BASIC + ","
- + DataSetFetchOption.PARENTS + " and " + DataSetFetchOption.CHILDREN
+ + DataSetFetchOption.PARENTS + ", and " + DataSetFetchOption.CHILDREN + " and "
+ + DataSetFetchOption.METAPROJECTS
+ " fetch options are supported by this method");
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
index 7b0c3eafe23..8ba3dc549f9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/ISampleListingQuery.java
@@ -24,6 +24,8 @@ import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.TypeMapper;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.EntityMetaprojectRelationRecord;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.MetaprojectRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.PropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.LongSetMapper;
@@ -95,4 +97,17 @@ public interface ISampleListingQuery extends BaseQuery
{ LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<PropertyRecord> getProperties(LongSet entityIDs);
+ @Select(sql = "select ma.mepr_id as metaproject_id, ma.samp_id as entity_id "
+ + " from metaproject_assignments as ma "
+ + " join metaprojects as m on ma.mepr_id = m.id "
+ + "where ma.samp_id = any(?{1}) and m.owner = ?{2}", parameterBindings =
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public List<EntityMetaprojectRelationRecord> getMetaprojectAssignments(LongSet sampleIDs,
+ Long ownerId);
+
+ @Select(sql = "select id as id, name as name, description as description, "
+ + " private as is_private, creation_date as creation_date " + " from metaprojects"
+ + " where id = any(?{1})", parameterBindings =
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public List<MetaprojectRecord> getMetaprojects(LongSet metaprojectIDs);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
index 3e097c74416..a27da73de8d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleLister.java
@@ -35,6 +35,9 @@ import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.common.collection.IKeyExtractor;
import ch.systemsx.cisd.common.collection.TableMap;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.EntityMetaprojectRelationRecord;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.MetaprojectCreator;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.MetaprojectRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.PropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
@@ -43,6 +46,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
/**
* @author Franz-Josef Elmer
@@ -90,15 +94,18 @@ public class SampleLister implements ISampleLister
private Long relationID;
- public SampleLister(IDAOFactory daoFactory)
+ private PersonPE person;
+
+ public SampleLister(IDAOFactory daoFactory, PersonPE person)
{
this(QueryTool.getQuery(DatabaseContextUtils.getConnection(daoFactory),
- ISampleListingQuery.class));
+ ISampleListingQuery.class), person);
}
- SampleLister(ISampleListingQuery query)
+ SampleLister(ISampleListingQuery query, PersonPE person)
{
this.query = query;
+ this.person = person;
}
private Long getRelationShipType()
@@ -165,6 +172,11 @@ public class SampleLister implements ISampleLister
enrichWithAncestors(ancestors, sampleRecords,
fetchOptions.contains(SampleFetchOption.ANCESTORS));
List<Sample> samples = new ArrayList<Sample>();
+ if (fetchOptions.contains(SampleFetchOption.METAPROJECTS))
+ {
+ enrichWithMetaprojects(sampleRecords, sampleIdSet);
+ }
+
Map<Long, Sample> repository = new HashMap<Long, Sample>(); // Repository of all unlinked
// samples
for (Long rootSampleID : sampleIDs)
@@ -289,6 +301,48 @@ public class SampleLister implements ISampleLister
}
}
+ private void enrichWithMetaprojects(TableMap<Long, SampleRecord> sampleRecords,
+ LongSet sampleIdSet)
+ {
+ List<EntityMetaprojectRelationRecord> sampleMetaprojectRelations =
+ query.getMetaprojectAssignments(sampleIdSet, person.getId());
+ LongSet metaprojectIdSet = new LongOpenHashSet();
+ for (EntityMetaprojectRelationRecord record : sampleMetaprojectRelations)
+ {
+ metaprojectIdSet.add(record.metaproject_id);
+ }
+
+ List<MetaprojectRecord> metaprojects = query.getMetaprojects(metaprojectIdSet);
+ TableMap<Long, MetaprojectRecord> metaprojectRecords =
+ new TableMap<Long, MetaprojectRecord>(metaprojects,
+ new IKeyExtractor<Long, MetaprojectRecord>()
+ {
+ @Override
+ public Long getKey(MetaprojectRecord mr)
+ {
+ return mr.id;
+ }
+ });
+
+ for (EntityMetaprojectRelationRecord record : sampleMetaprojectRelations)
+ {
+ SampleRecord sampleRecord = sampleRecords.tryGet(record.entity_id);
+ if (sampleRecord != null)
+ {
+ if (sampleRecord.metaprojects == null)
+ {
+ sampleRecord.metaprojects = new ArrayList<MetaprojectRecord>();
+ }
+ MetaprojectRecord metaprojectRecord =
+ metaprojectRecords.tryGet(record.metaproject_id);
+ if (metaprojectRecord != null)
+ {
+ sampleRecord.metaprojects.add(metaprojectRecord);
+ }
+ }
+ }
+ }
+
private Sample createSample(SampleRecord sampleRecord, Map<Long, Sample> repository)
{
Sample sample = repository.get(sampleRecord.s_id);
@@ -339,6 +393,14 @@ public class SampleLister implements ISampleLister
initializer.putProperty(entry.getKey(), entry.getValue());
}
}
+ if (sampleRecord.metaprojects != null)
+ {
+ for (MetaprojectRecord metaprojectRecord : sampleRecord.metaprojects)
+ {
+ initializer.addMetaproject(MetaprojectCreator.createMetaproject(metaprojectRecord,
+ person));
+ }
+ }
initializer.setRetrievedFetchOptions(sampleRecord.fetchOptions);
List<SampleRecord> linkedSampleRecords = new ArrayList<SampleRecord>();
if (sampleRecord.children != null)
@@ -376,9 +438,14 @@ public class SampleLister implements ISampleLister
private EnumSet<SampleFetchOption> createAppropriateFetchOptions(
EnumSet<SampleFetchOption> fetchOptions)
{
- return EnumSet
- .of(fetchOptions.contains(SampleFetchOption.PROPERTIES) ? SampleFetchOption.PROPERTIES
+ EnumSet<SampleFetchOption> result =
+ EnumSet.of(fetchOptions.contains(SampleFetchOption.PROPERTIES) ? SampleFetchOption.PROPERTIES
: SampleFetchOption.BASIC);
+ if (fetchOptions.contains(SampleFetchOption.METAPROJECTS))
+ {
+ result.add(SampleFetchOption.METAPROJECTS);
+ }
+ return result;
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleRecord.java
index 8bcb991feec..daf6fdfc28b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/samplelister/SampleRecord.java
@@ -21,6 +21,7 @@ import java.util.EnumSet;
import java.util.List;
import java.util.Map;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.fetchoptions.common.MetaprojectRecord;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
/**
@@ -75,6 +76,8 @@ public class SampleRecord
public Map<String, String> properties;
+ public List<MetaprojectRecord> metaprojects;
+
public EnumSet<SampleFetchOption> fetchOptions;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMetaprojectDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMetaprojectDAO.java
index 54248625ac8..10194a5a49c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMetaprojectDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IMetaprojectDAO.java
@@ -20,8 +20,10 @@ import java.util.Collection;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropertiesHolder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
* @author Pawel Glyzewski
@@ -49,4 +51,11 @@ public interface IMetaprojectDAO extends IGenericDAO<MetaprojectPE>
*/
public Collection<MetaprojectPE> listMetaprojectsForEntity(PersonPE owner,
IEntityInformationWithPropertiesHolder entity);
+
+ /**
+ * Lists all metaprojects owned by given user, connected with given entities.
+ */
+ public Collection<MetaprojectAssignmentPE> listMetaprojectAssignmentsForEntities(
+ PersonPE owner, Collection<? extends IEntityInformationWithPropertiesHolder> entities,
+ EntityKind entityKind);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAO.java
index dc1c8e4315f..f6c29ed9252 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAO.java
@@ -38,6 +38,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropert
import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
* @author Pawel Glyzewski
@@ -132,4 +133,25 @@ public class MetaprojectDAO extends AbstractGenericEntityDAO<MetaprojectPE> impl
return metaprojects;
}
+
+ @Override
+ public Collection<MetaprojectAssignmentPE> listMetaprojectAssignmentsForEntities(
+ PersonPE owner, Collection<? extends IEntityInformationWithPropertiesHolder> entities,
+ EntityKind entityKind)
+ {
+ final DetachedCriteria criteria = DetachedCriteria.forClass(MetaprojectAssignmentPE.class);
+ criteria.createAlias("metaproject", "m");
+ criteria.add(Restrictions.eq("m.owner", owner));
+ criteria.add(Restrictions.in(entityKind.getLabel(), entities));
+ final List<MetaprojectAssignmentPE> assignments =
+ cast(getHibernateTemplate().findByCriteria(criteria));
+
+ if (operationLog.isDebugEnabled())
+ {
+ operationLog.debug(String.format("%s(%s, %s): %d metaproject(s) have been found.",
+ MethodUtils.getCurrentMethod().getName(), owner, entities, assignments.size()));
+ }
+
+ return assignments;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Experiment.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Experiment.java
index 12222f952a6..9ebece2b244 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Experiment.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Experiment.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
+import java.util.Collection;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.IAttachmentHolder;
@@ -57,6 +58,8 @@ public class Experiment extends CodeWithRegistrationAndModificationDate<Experime
private final boolean isStub;
+ private Collection<Metaproject> metaprojects;
+
public Experiment()
{
this(false);
@@ -221,4 +224,14 @@ public class Experiment extends CodeWithRegistrationAndModificationDate<Experime
{
return isStub;
}
+
+ public Collection<Metaproject> getMetaprojecs()
+ {
+ return metaprojects;
+ }
+
+ public void setMetaprojects(final Collection<Metaproject> metaprojects)
+ {
+ this.metaprojects = metaprojects;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExperimentFetchOption.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExperimentFetchOption.java
index 990f58da5e4..7ba1e6ecb86 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExperimentFetchOption.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExperimentFetchOption.java
@@ -22,6 +22,6 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
public enum ExperimentFetchOption implements FetchOption
{
- BASIC, PROPERTIES, PROPERTIES_OF_PROPERTIES, SCRIPTS;
+ BASIC, PROPERTIES, PROPERTIES_OF_PROPERTIES, SCRIPTS, METAPROJECTS;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
index 6685c6ad41a..0f32c3c0dd9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
@@ -86,6 +86,8 @@ public abstract class ExternalData extends CodeWithRegistrationAndModificationDa
private final boolean isStub;
+ private Collection<Metaproject> metaprojects;
+
public ExternalData(boolean isStub)
{
this.isStub = isStub;
@@ -384,6 +386,16 @@ public abstract class ExternalData extends CodeWithRegistrationAndModificationDa
this.storageConfirmation = storageConfirmation;
}
+ public void setMetaprojects(Collection<Metaproject> metaprojects)
+ {
+ this.metaprojects = metaprojects;
+ }
+
+ public Collection<Metaproject> getMetaprojects()
+ {
+ return metaprojects;
+ }
+
public DataSetKind getDataSetKind()
{
return DataSetKind.PHYSICAL;
@@ -416,5 +428,4 @@ public abstract class ExternalData extends CodeWithRegistrationAndModificationDa
return order1.compareTo(order2);
}
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Material.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Material.java
index 57dc91f324d..afb892ee83f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Material.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Material.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
+import java.util.Collection;
import java.util.Date;
import java.util.List;
@@ -41,6 +42,8 @@ public class Material extends CodeWithRegistration<Material> implements
private List<IEntityProperty> properties;
+ private Collection<Metaproject> metaprojects;
+
public MaterialType getMaterialType()
{
return materialType;
@@ -115,6 +118,16 @@ public class Material extends CodeWithRegistration<Material> implements
return new MaterialIdentifier(getCode(), getMaterialType().getCode()).print();
}
+ public void setMetaprojects(Collection<Metaproject> metaprojects)
+ {
+ this.metaprojects = metaprojects;
+ }
+
+ public Collection<Metaproject> getMetaprojects()
+ {
+ return metaprojects;
+ }
+
//
// Comparable
//
@@ -155,5 +168,4 @@ public class Material extends CodeWithRegistration<Material> implements
{
return getIdentifier();
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Sample.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Sample.java
index d23119999e6..e97cfce8f12 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Sample.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/Sample.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import java.util.Set;
import java.util.TreeSet;
@@ -75,6 +76,8 @@ public final class Sample extends CodeWithRegistrationAndModificationDate<Sample
private final boolean isStub;
+ private Collection<Metaproject> metaprojects;
+
public Sample()
{
this(false);
@@ -322,6 +325,16 @@ public final class Sample extends CodeWithRegistrationAndModificationDate<Sample
return isStub;
}
+ public void setMetaprojects(Collection<Metaproject> metaprojects)
+ {
+ this.metaprojects = metaprojects;
+ }
+
+ public Collection<Metaproject> getMetaprojects()
+ {
+ return metaprojects;
+ }
+
@Override
public String toString()
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
index b9c43184dfb..61ac7df294d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
@@ -21,6 +21,8 @@ import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import ch.systemsx.cisd.common.types.BooleanOrUnknown;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
@@ -35,6 +37,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.LinkDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PlaceholderDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
@@ -122,13 +125,14 @@ public class DataSetTranslator
}
public static List<ExternalData> translate(List<? extends DataPE> list,
- String defaultDataStoreBaseURL, String baseIndexURL)
+ String defaultDataStoreBaseURL, String baseIndexURL,
+ Map<Long, Set<Metaproject>> metaprojects)
{
ArrayList<ExternalData> result = new ArrayList<ExternalData>(list.size());
for (DataPE dataPE : list)
{
ExternalData data =
- translate(dataPE, baseIndexURL, true,
+ translate(dataPE, baseIndexURL, true, metaprojects.get(dataPE.getId()),
ExperimentTranslator.LoadableFields.PROPERTIES);
result.add(data);
}
@@ -161,13 +165,13 @@ public class DataSetTranslator
}
public static ExternalData translate(DataPE dataPE, String baseIndexURL,
- final LoadableFields... withExperimentFields)
+ Collection<Metaproject> metaprojects, final LoadableFields... withExperimentFields)
{
- return translate(dataPE, baseIndexURL, true, withExperimentFields);
+ return translate(dataPE, baseIndexURL, true, metaprojects, withExperimentFields);
}
public static ExternalData translate(DataPE dataPE, String baseIndexURL, boolean withDetails,
- final LoadableFields... withExperimentFields)
+ Collection<Metaproject> metaprojects, final LoadableFields... withExperimentFields)
{
ExternalData externalData = null;
if (dataPE.isContainer())
@@ -212,8 +216,13 @@ public class DataSetTranslator
externalData.setPermlink(PermlinkUtilities.createPermlinkURL(baseIndexURL,
EntityKind.DATA_SET, externalData.getIdentifier()));
setProperties(dataPE, externalData);
- externalData.setExperiment(ExperimentTranslator.translate(experiment, baseIndexURL,
+ externalData.setExperiment(ExperimentTranslator.translate(experiment, baseIndexURL, null,
withExperimentFields));
+
+ if (metaprojects != null)
+ {
+ externalData.setMetaprojects(metaprojects);
+ }
externalData.setDeletion(DeletionTranslator.translate(dataPE.getDeletion()));
return externalData;
}
@@ -222,7 +231,7 @@ public class DataSetTranslator
String baseIndexURL)
{
return containerOrNull != null ? (ContainerDataSet) translate(containerOrNull,
- baseIndexURL, false) : null;
+ baseIndexURL, false, null) : null;
}
private static ExternalData translateContainerDataSetProperties(DataPE dataPE,
@@ -316,7 +325,7 @@ public class DataSetTranslator
{
for (DataPE childPE : dataPE.getContainedDataSets())
{
- containedDataSets.add(translate(childPE, baseIndexURL));
+ containedDataSets.add(translate(childPE, baseIndexURL, null));
}
}
containerDataSet.setContainedDataSets(containedDataSets);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/EntityHistoryTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/EntityHistoryTranslator.java
index 78e4314358d..87c0ed0f087 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/EntityHistoryTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/EntityHistoryTranslator.java
@@ -21,8 +21,8 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityHistory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.AbstractEntityHistoryPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.AbstractEntityPropertyHistoryPE;
@@ -36,8 +36,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
*/
public class EntityHistoryTranslator
{
- public static List<EntityHistory> translate(
- List<AbstractEntityPropertyHistoryPE> history, String baseIndexURL)
+ public static List<EntityHistory> translate(List<AbstractEntityPropertyHistoryPE> history,
+ String baseIndexURL)
{
List<EntityHistory> result = new ArrayList<EntityHistory>();
HashMap<PropertyTypePE, PropertyType> cache = new HashMap<PropertyTypePE, PropertyType>();
@@ -48,8 +48,7 @@ public class EntityHistoryTranslator
return result;
}
- private static EntityHistory translate(
- AbstractEntityPropertyHistoryPE entityPropertyHistory,
+ private static EntityHistory translate(AbstractEntityPropertyHistoryPE entityPropertyHistory,
Map<PropertyTypePE, PropertyType> cache, String baseIndexURL)
{
EntityHistory result = new EntityHistory();
@@ -82,12 +81,12 @@ public class EntityHistoryTranslator
case EXPERIMENT:
entityType = EntityKind.EXPERIMENT.getDescription();
result.setRelatedEntity(ExperimentTranslator.translate(
- (ExperimentPE) entityHistory.getRelatedEntity(), baseIndexURL));
+ (ExperimentPE) entityHistory.getRelatedEntity(), baseIndexURL, null));
break;
case SAMPLE:
entityType = EntityKind.SAMPLE.getDescription();
result.setRelatedEntity(SampleTranslator.translate(
- (SamplePE) entityHistory.getRelatedEntity(), baseIndexURL));
+ (SamplePE) entityHistory.getRelatedEntity(), baseIndexURL, null));
break;
case MATERIAL:
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/EntityPropertyTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/EntityPropertyTranslator.java
index 4865f674c0e..277f4383e3d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/EntityPropertyTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/EntityPropertyTranslator.java
@@ -66,7 +66,7 @@ public final class EntityPropertyTranslator
break;
case MATERIAL:
basicProperty.setMaterial(MaterialTranslator.translate(
- propertyPE.getMaterialValue(), false));
+ propertyPE.getMaterialValue(), false, null));
break;
default:
basicProperty.setValue(propertyPE.tryGetUntypedValue());
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExperimentTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExperimentTranslator.java
index a8f062cf0b3..4bd5cd6c0e6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExperimentTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExperimentTranslator.java
@@ -17,15 +17,18 @@
package ch.systemsx.cisd.openbis.generic.shared.translator;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
@@ -70,25 +73,28 @@ public final class ExperimentTranslator
}
}
- public final static Experiment translateWithoutRevealingData(final ExperimentPE experiment)
+ public final static Experiment translateWithoutRevealingData(final ExperimentPE experiment,
+ Collection<Metaproject> metaprojects)
{
final Experiment result = new Experiment(true);
result.setId(HibernateUtils.getId(experiment));
result.setPermId(experiment.getPermId());
result.setProperties(new ArrayList<IEntityProperty>());
+ result.setMetaprojects(metaprojects);
return result;
}
public final static Experiment translate(final ExperimentPE experiment, String baseIndexURL,
- final LoadableFields... withFields)
+ Collection<Metaproject> metaprojects, final LoadableFields... withFields)
{
- return translate(experiment, baseIndexURL, false, withFields);
+ return translate(experiment, baseIndexURL, false, metaprojects, withFields);
}
public final static Experiment translate(final ExperimentPE experiment, String baseIndexURL,
- final boolean rawManagedProperties, final LoadableFields... withFields)
+ final boolean rawManagedProperties, Collection<Metaproject> metaprojects,
+ final LoadableFields... withFields)
{
if (experiment == null)
{
@@ -125,19 +131,24 @@ public final class ExperimentTranslator
}
}
+ if (metaprojects != null)
+ {
+ result.setMetaprojects(metaprojects);
+ }
+
return result;
}
// NOTE: when translating list of experiments managed properties will contain raw value
public final static List<Experiment> translate(final List<ExperimentPE> experiments,
- String baseIndexURL)
+ String baseIndexURL, Map<Long, Set<Metaproject>> metaprojects)
{
final List<Experiment> result = new ArrayList<Experiment>(experiments.size());
for (final ExperimentPE experiment : experiments)
{
HibernateUtils.initialize(experiment.getProperties());
result.add(ExperimentTranslator.translate(experiment, baseIndexURL, true,
- LoadableFields.PROPERTIES));
+ metaprojects.get(experiment.getId()), LoadableFields.PROPERTIES));
}
return result;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MaterialTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MaterialTranslator.java
index ef007939d8f..bcd66659d77 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MaterialTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MaterialTranslator.java
@@ -17,11 +17,15 @@
package ch.systemsx.cisd.openbis.generic.shared.translator;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialPE;
@@ -49,22 +53,25 @@ public final class MaterialTranslator
return newMaterial;
}
- public final static List<Material> translate(final List<MaterialPE> materials)
+ public final static List<Material> translate(final List<MaterialPE> materials,
+ Map<Long, Set<Metaproject>> metaprojects)
{
final List<Material> result = new ArrayList<Material>();
for (final MaterialPE material : materials)
{
- result.add(MaterialTranslator.translate(material));
+ result.add(MaterialTranslator.translate(material, metaprojects.get(material.getId())));
}
return result;
}
- public final static Material translate(final MaterialPE materialPE)
+ public final static Material translate(final MaterialPE materialPE,
+ Collection<Metaproject> metaprojects)
{
- return translate(materialPE, true);
+ return translate(materialPE, true, metaprojects);
}
- public final static Material translate(final MaterialPE materialPE, final boolean withProperties)
+ public final static Material translate(final MaterialPE materialPE,
+ final boolean withProperties, Collection<Metaproject> metaprojects)
{
if (materialPE == null)
{
@@ -85,6 +92,11 @@ public final class MaterialTranslator
setProperties(materialPE, result);
}
+ if (metaprojects != null)
+ {
+ result.setMetaprojects(metaprojects);
+ }
+
return result;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MetaprojectTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MetaprojectTranslator.java
index 488f6b183cc..9304b8f805b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MetaprojectTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/MetaprojectTranslator.java
@@ -17,9 +17,15 @@
package ch.systemsx.cisd.openbis.generic.shared.translator;
import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
/**
@@ -29,7 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
*/
public class MetaprojectTranslator
{
- public static List<Metaproject> translate(List<MetaprojectPE> metaprojectPEs)
+ public static List<Metaproject> translate(Collection<MetaprojectPE> metaprojectPEs)
{
List<Metaproject> metaprojects = new ArrayList<Metaproject>(metaprojectPEs.size());
@@ -64,4 +70,51 @@ public class MetaprojectTranslator
return metaprojectPE;
}
+ public static Map<Long, Set<Metaproject>> translateMetaprojectAssignments(
+ Collection<MetaprojectAssignmentPE> assignments)
+ {
+ Map<Long, Metaproject> metaprojects = new HashMap<Long, Metaproject>();
+ for (MetaprojectAssignmentPE assignment : assignments)
+ {
+ Long metaprojectId = assignment.getMetaproject().getId();
+ if (false == metaprojects.containsKey(metaprojectId))
+ {
+ metaprojects.put(metaprojectId, translate(assignment.getMetaproject()));
+ }
+ }
+
+ Map<Long, Set<Metaproject>> translatedAssignments = new HashMap<Long, Set<Metaproject>>();
+ for (MetaprojectAssignmentPE assignment : assignments)
+ {
+ Long entityId = tryGetEntityId(assignment);
+ Set<Metaproject> metaprojectsSet = translatedAssignments.get(entityId);
+ if (metaprojectsSet == null)
+ {
+ metaprojectsSet = new HashSet<Metaproject>();
+ translatedAssignments.put(entityId, metaprojectsSet);
+ }
+ metaprojectsSet.add(metaprojects.get(assignment.getMetaproject().getId()));
+ }
+
+ return translatedAssignments;
+ }
+
+ private static final Long tryGetEntityId(MetaprojectAssignmentPE assignment)
+ {
+ if (assignment.getExperiment() != null)
+ {
+ return assignment.getExperiment().getId();
+ } else if (assignment.getSample() != null)
+ {
+ return assignment.getSample().getId();
+ } else if (assignment.getDataSet() != null)
+ {
+ return assignment.getDataSet().getId();
+ } else if (assignment.getMaterial() != null)
+ {
+ return assignment.getMaterial().getId();
+ }
+
+ return null;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/SampleTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/SampleTranslator.java
index be92ba845ee..87b8453a58f 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/SampleTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/SampleTranslator.java
@@ -17,14 +17,18 @@
package ch.systemsx.cisd.openbis.generic.shared.translator;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
import ch.systemsx.cisd.openbis.generic.shared.basic.SearchlinkUtilities;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Attachment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
@@ -47,12 +51,13 @@ public final class SampleTranslator
// Can not be instantiated.
}
- public static List<Sample> translate(final List<SamplePE> samples, String baseIndexURL)
+ public static List<Sample> translate(final List<SamplePE> samples, String baseIndexURL,
+ Map<Long, Set<Metaproject>> metaprojects)
{
final List<Sample> list = new ArrayList<Sample>(samples.size());
for (final SamplePE sample : samples)
{
- list.add(translate(sample, baseIndexURL));
+ list.add(translate(sample, baseIndexURL, metaprojects.get(sample.getId())));
}
return list;
}
@@ -68,13 +73,15 @@ public final class SampleTranslator
return result;
}
- public final static Sample translate(final SamplePE samplePE, String baseIndexURL)
+ public final static Sample translate(final SamplePE samplePE, String baseIndexURL,
+ Collection<Metaproject> metaprojects)
{
- return translate(samplePE, baseIndexURL, true, false);
+ return translate(samplePE, baseIndexURL, true, false, metaprojects);
}
public final static Sample translate(final SamplePE samplePE, String baseIndexURL,
- final boolean withDetails, boolean withContainedSamples)
+ final boolean withDetails, boolean withContainedSamples,
+ Collection<Metaproject> metaprojects)
{
if (samplePE == null)
{
@@ -86,13 +93,13 @@ public final class SampleTranslator
final int generatedFromDep =
getPositiveIntegerValue(samplePE.getSampleType().getGeneratedFromHierarchyDepth());
return translate(samplePE, baseIndexURL, containerDep, generatedFromDep, withDetails,
- withContainedSamples);
+ withContainedSamples, metaprojects);
}
private final static Sample translate(final SamplePE samplePE, String baseIndexURL,
final int containerDep, final int generatedFromDep, final boolean withDetails,
- final boolean withContainedSamples)
+ final boolean withContainedSamples, Collection<Metaproject> metaprojects)
{
final Sample result = new Sample();
setCodes(result, samplePE);
@@ -118,7 +125,7 @@ public final class SampleTranslator
result.setRegistrationDate(samplePE.getRegistrationDate());
setProperties(result, samplePE);
result.setExperiment(ExperimentTranslator.translate(samplePE.getExperiment(),
- baseIndexURL, LoadableFields.PROPERTIES));
+ baseIndexURL, null, LoadableFields.PROPERTIES));
List<Attachment> attachments;
if (samplePE.attachmentsInitialized() == false)
{
@@ -135,7 +142,7 @@ public final class SampleTranslator
if (HibernateUtils.isInitialized(samplePE.getContainer()))
{
result.setContainer(translate(samplePE.getContainer(), baseIndexURL,
- containerDep - 1, 0, false, false));
+ containerDep - 1, 0, false, false, null));
}
}
if (generatedFromDep > 0 && samplePE.getParentRelationships() != null)
@@ -145,7 +152,7 @@ public final class SampleTranslator
for (SamplePE parent : samplePE.getParents())
{
result.addParent(translate(parent, baseIndexURL, 0, generatedFromDep - 1,
- false, false));
+ false, false, null));
}
}
}
@@ -155,12 +162,17 @@ public final class SampleTranslator
ArrayList<Sample> containedSamples = new ArrayList<Sample>();
for (SamplePE containedPE : samplePE.getContained())
{
- Sample containedSample = translate(containedPE, baseIndexURL, 0, 0, false, false);
+ Sample containedSample =
+ translate(containedPE, baseIndexURL, 0, 0, false, false, null);
containedSamples.add(containedSample);
}
result.setContainedSample(containedSamples);
}
+ if (metaprojects != null)
+ {
+ result.setMetaprojects(metaprojects);
+ }
result.setDeletion(DeletionTranslator.translate(samplePE.getDeletion()));
return result;
}
@@ -190,12 +202,12 @@ public final class SampleTranslator
final SampleParentWithDerived sampleGeneration = new SampleParentWithDerived();
sampleGeneration.setParent(SampleTranslator.translate(sampleGenerationDTO.getParent(),
- baseIndexURL));
+ baseIndexURL, null));
final List<Sample> generated = new ArrayList<Sample>();
for (SamplePE samplePE : sampleGenerationDTO.getDerived())
{
- generated.add(SampleTranslator.translate(samplePE, baseIndexURL, false, false));
+ generated.add(SampleTranslator.translate(samplePE, baseIndexURL, false, false, null));
}
sampleGeneration.setDerived(generated.toArray(new Sample[generated.size()]));
return sampleGeneration;
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 8eafe12f7ab..15cd7c215c8 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
@@ -101,6 +101,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentBatchUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleBatchUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
@@ -116,6 +117,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.translator.AttachmentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.MetaprojectTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.ServerUtils;
import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
@@ -226,12 +228,16 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
experimentBO.enrichWithProperties();
experimentBO.enrichWithAttachments();
final ExperimentPE experiment = experimentBO.getExperiment();
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), experiment);
if (experiment == null)
{
throw UserFailureException.fromTemplate(
"No experiment could be found with given identifier '%s'.", identifier);
}
return ExperimentTranslator.translate(experiment, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojectPEs),
ExperimentTranslator.LoadableFields.PROPERTIES,
ExperimentTranslator.LoadableFields.ATTACHMENTS);
}
@@ -244,7 +250,11 @@ public final class GenericServer extends AbstractServer<IGenericServer> implemen
experimentBO.enrichWithProperties();
experimentBO.enrichWithAttachments();
final ExperimentPE experiment = experimentBO.getExperiment();
+ Collection<MetaprojectPE> metaprojectPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectsForEntity(
+ session.tryGetPerson(), experiment);
return ExperimentTranslator.translate(experiment, session.getBaseIndexURL(),
+ MetaprojectTranslator.translate(metaprojectPEs),
ExperimentTranslator.LoadableFields.PROPERTIES,
ExperimentTranslator.LoadableFields.ATTACHMENTS);
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
index d1597f2ea89..6d034293708 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/CommonServerTest.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.generic.server;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
@@ -82,6 +83,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.FileFormatTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.LocatorTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
@@ -573,7 +575,7 @@ public final class CommonServerTest extends AbstractServerTestCase
dataStorePE.setCode("DST");
externalDataPE.setDataStore(dataStorePE);
final ExternalData externalData =
- DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL, null);
prepareGetSession();
final boolean showOnlyDirectlyConnected = true;
context.checking(new Expectations()
@@ -612,7 +614,7 @@ public final class CommonServerTest extends AbstractServerTestCase
dataStorePE.setCode("DST");
externalDataPE.setDataStore(dataStorePE);
final ExternalData externalData =
- DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL, null);
prepareGetSession();
context.checking(new Expectations()
{
@@ -638,6 +640,7 @@ public final class CommonServerTest extends AbstractServerTestCase
return EqualsBuilder.reflectionEquals(data1, data2);
}
+ @SuppressWarnings("unchecked")
@Test
public void testListExperiments()
{
@@ -657,6 +660,12 @@ public final class CommonServerTest extends AbstractServerTestCase
one(experimentTable).getExperiments();
will(returnValue(new ArrayList<ExperimentPE>()));
+
+ one(metaprojectDAO)
+ .listMetaprojectAssignmentsForEntities(
+ with(any(PersonPE.class)),
+ with(any(Collection.class)),
+ with(any(ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind.class)));
}
});
createServer().listExperiments(SESSION_TOKEN, experimentType, projectIdentifier);
@@ -1646,6 +1655,10 @@ public final class CommonServerTest extends AbstractServerTestCase
one(experimentBO).getExperiment();
will(returnValue(experimentPE));
+
+ one(metaprojectDAO).listMetaprojectsForEntity(session.tryGetPerson(),
+ experimentPE);
+ will(returnValue(new HashSet<MetaprojectPE>()));
}
});
final Experiment experiment =
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
index 023755fa857..6bbeabc0f46 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java
@@ -59,6 +59,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchAssociationCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy.RoleCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@@ -108,7 +109,7 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
propertiesBatchManager, commonServer)
{
@Override
- protected ISampleLister createSampleLister()
+ protected ISampleLister createSampleLister(PersonPE person)
{
return sampleLister2;
}
@@ -629,6 +630,9 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
.property("alpha", DataTypeCode.REAL, "3.14159")
.property("status", DataTypeCode.VARCHAR, "normal");
will(returnValue(ds1.getDataSet()));
+ one(metaprojectDAO).listMetaprojectsForEntity(session.tryGetPerson(),
+ ds1.getDataSet());
+ will(returnValue(new HashSet<Metaproject>()));
one(dataSetDAO).tryToFindDataSetByCode("ds2");
ExternalDataPEBuilder ds2 =
@@ -637,6 +641,9 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
.property("status", DataTypeCode.VARCHAR, "low")
.parent(ds1.getDataSet());
will(returnValue(ds2.getDataSet()));
+ one(metaprojectDAO).listMetaprojectsForEntity(session.tryGetPerson(),
+ ds2.getDataSet());
+ will(returnValue(new HashSet<Metaproject>()));
}
});
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExperimentValidatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExperimentValidatorTest.java
index 3ea8a7c21ab..67dfc5803ce 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExperimentValidatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExperimentValidatorTest.java
@@ -19,9 +19,8 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.server.authorization.AuthorizationTestCase;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExperimentValidator;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
/**
@@ -39,7 +38,7 @@ public class ExperimentValidatorTest extends AuthorizationTestCase
ExperimentValidator validator = new ExperimentValidator();
PersonPE person = createPersonWithRoleAssignments();
assertEquals(true, validator.isValid(person, ExperimentTranslator.translate(
- createExperiment(createAnotherGroup()), BASE_URL)));
+ createExperiment(createAnotherGroup()), BASE_URL, null)));
}
@Test
@@ -47,8 +46,8 @@ public class ExperimentValidatorTest extends AuthorizationTestCase
{
ExperimentValidator validator = new ExperimentValidator();
PersonPE person = createPersonWithRoleAssignments();
- assertEquals(true, validator.isValid(person, ExperimentTranslator.translate(
- createExperiment(createGroup()), BASE_URL)));
+ assertEquals(true, validator.isValid(person,
+ ExperimentTranslator.translate(createExperiment(createGroup()), BASE_URL, null)));
}
@Test
@@ -57,7 +56,9 @@ public class ExperimentValidatorTest extends AuthorizationTestCase
ExperimentValidator validator = new ExperimentValidator();
PersonPE person = createPersonWithRoleAssignments();
SpacePE group = createGroup("blabla", createAnotherDatabaseInstance());
- assertEquals(false, validator.isValid(person, ExperimentTranslator.translate(
- createExperiment(group), BASE_URL)));
+ assertEquals(
+ false,
+ validator.isValid(person,
+ ExperimentTranslator.translate(createExperiment(group), BASE_URL, null)));
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidatorTest.java
index 8c7c443de16..8d40e16768c 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/ExternalDataValidatorTest.java
@@ -19,7 +19,6 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.server.authorization.AuthorizationTestCase;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExternalDataValidator;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
@@ -33,8 +32,8 @@ public class ExternalDataValidatorTest extends AuthorizationTestCase
private DataSet createData(SpacePE group)
{
DataSet data = new DataSet();
- data.setExperiment(ExperimentTranslator
- .translate(createExperiment(group), "http://someURL"));
+ data.setExperiment(ExperimentTranslator.translate(createExperiment(group),
+ "http://someURL", null));
return data;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SampleValidatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SampleValidatorTest.java
index 0236a830d1c..661693337a0 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SampleValidatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/authorization/validator/SampleValidatorTest.java
@@ -19,9 +19,8 @@ package ch.systemsx.cisd.openbis.generic.server.authorization.validator;
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.server.authorization.AuthorizationTestCase;
-import ch.systemsx.cisd.openbis.generic.server.authorization.validator.SampleValidator;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
/**
@@ -38,8 +37,8 @@ public class SampleValidatorTest extends AuthorizationTestCase
{
SampleValidator validator = new SampleValidator();
PersonPE person = createPersonWithRoleAssignments();
- assertEquals(true, validator.isValid(person, SampleTranslator.translate(
- createSample(createAnotherGroup()), BASE_URL)));
+ assertEquals(true, validator.isValid(person,
+ SampleTranslator.translate(createSample(createAnotherGroup()), BASE_URL, null)));
}
@Test
@@ -47,8 +46,8 @@ public class SampleValidatorTest extends AuthorizationTestCase
{
SampleValidator validator = new SampleValidator();
PersonPE person = createPersonWithRoleAssignments();
- assertEquals(true, validator.isValid(person, SampleTranslator.translate(
- createSample(createDatabaseInstance()), BASE_URL)));
+ assertEquals(true, validator.isValid(person,
+ SampleTranslator.translate(createSample(createDatabaseInstance()), BASE_URL, null)));
}
@Test
@@ -57,7 +56,7 @@ public class SampleValidatorTest extends AuthorizationTestCase
SampleValidator validator = new SampleValidator();
PersonPE person = createPersonWithRoleAssignments();
assertEquals(false, validator.isValid(person, SampleTranslator.translate(
- createSample(createDatabaseInstance("blabla")), BASE_URL)));
+ createSample(createDatabaseInstance("blabla")), BASE_URL, null)));
}
@Test
@@ -65,8 +64,10 @@ public class SampleValidatorTest extends AuthorizationTestCase
{
SampleValidator validator = new SampleValidator();
PersonPE person = createPersonWithRoleAssignments();
- assertEquals(true, validator.isValid(person, SampleTranslator.translate(
- createSample(createGroup()), BASE_URL)));
+ assertEquals(
+ true,
+ validator.isValid(person,
+ SampleTranslator.translate(createSample(createGroup()), BASE_URL, null)));
}
@Test
@@ -75,7 +76,9 @@ public class SampleValidatorTest extends AuthorizationTestCase
SampleValidator validator = new SampleValidator();
PersonPE person = createPersonWithRoleAssignments();
SpacePE group = createGroup("blabla", createAnotherDatabaseInstance());
- assertEquals(false, validator.isValid(person, SampleTranslator.translate(
- createSample(group), BASE_URL)));
+ assertEquals(
+ false,
+ validator.isValid(person,
+ SampleTranslator.translate(createSample(group), BASE_URL, null)));
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
index 81b06885675..40163f97957 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
@@ -51,6 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IDatasetLocationNode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetShareId;
@@ -142,7 +143,8 @@ public class DatasetListerTest extends AbstractDAOTest
HashSet<String> samplePermIDs =
new HashSet<String>(Arrays.asList("200902091250077-1026", "200902091225616-1027"));
List<SamplePE> samplePEs = daoFactory.getSampleDAO().listByPermID(samplePermIDs);
- List<Sample> samples = SampleTranslator.translate(samplePEs, "");
+ List<Sample> samples =
+ SampleTranslator.translate(samplePEs, "", new HashMap<Long, Set<Metaproject>>());
Map<Sample, List<ExternalData>> dataSets = lister.listAllDataSetsFor(samples);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetListerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetListerTest.java
index def6af530c3..3d0225c818a 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetListerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/fetchoptions/datasetlister/DataSetListerTest.java
@@ -81,8 +81,7 @@ public class DataSetListerTest extends AbstractDAOTest
{
sessionToken = service.tryToAuthenticateForAllServices("test", "password");
query = EntityListingTestUtils.createQuery(daoFactory, IDataSetListingQueryDynamic.class);
- lister =
- new DataSetLister(query);
+ lister = new DataSetLister(query, getTestPerson());
}
@Test
@@ -130,15 +129,12 @@ public class DataSetListerTest extends AbstractDAOTest
+ " where code='STANDARD'");
final long newDataStoreId =
(Long) query
- .select(
- "insert into data_stores (id,dbin_id,code,download_url,remote_url,session_token)"
- + " values (nextval('data_store_id_seq'),1,'DSS2','http://download_2','http://remote_2','') returning id")
+ .select("insert into data_stores (id,dbin_id,code,download_url,remote_url,session_token)"
+ + " values (nextval('data_store_id_seq'),1,'DSS2','http://download_2','http://remote_2','') returning id")
.get(0).get("id");
- query.update(
- "update data set dast_id = ?{1} where code = ?{2}", newDataStoreId,
+ query.update("update data set dast_id = ?{1} where code = ?{2}", newDataStoreId,
"20081105092259000-20");
- query.update(
- "update data set dast_id = ?{1} where code = ?{2}", newDataStoreId,
+ query.update("update data set dast_id = ?{1} where code = ?{2}", newDataStoreId,
"20081105092259000-21");
List<String> codes = new ArrayList<String>();
@@ -153,14 +149,12 @@ public class DataSetListerTest extends AbstractDAOTest
{
if (url.getDataStoreURL().equals("http://download_1"))
{
- assertEquals(
- Arrays.asList("20081105092159188-3", "20081105092159111-1",
- "20081105092259000-19"),
- url.getDataSetCodes());
+ assertEquals(Arrays.asList("20081105092159188-3", "20081105092159111-1",
+ "20081105092259000-19"), url.getDataSetCodes());
} else if (url.getDataStoreURL().equals("http://download_2"))
{
- assertEquals(Arrays.asList("20081105092259000-20", "20081105092259000-21"), url
- .getDataSetCodes());
+ assertEquals(Arrays.asList("20081105092259000-20", "20081105092259000-21"),
+ url.getDataSetCodes());
} else
{
fail("URL " + url + " not expected.");
@@ -173,14 +167,12 @@ public class DataSetListerTest extends AbstractDAOTest
{
if (url.getDataStoreURL().equals("http://remote_1"))
{
- assertEquals(
- Arrays.asList("20081105092159188-3", "20081105092159111-1",
- "20081105092259000-19"),
- url.getDataSetCodes());
+ assertEquals(Arrays.asList("20081105092159188-3", "20081105092159111-1",
+ "20081105092259000-19"), url.getDataSetCodes());
} else if (url.getDataStoreURL().equals("http://remote_2"))
{
- assertEquals(Arrays.asList("20081105092259000-20", "20081105092259000-21"), url
- .getDataSetCodes());
+ assertEquals(Arrays.asList("20081105092259000-20", "20081105092259000-21"),
+ url.getDataSetCodes());
} else
{
fail("URL " + url + " not expected.");
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAOTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAOTest.java
index 11e6e96ccb3..1da3f963328 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAOTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/MetaprojectDAOTest.java
@@ -21,6 +21,7 @@ import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
+import java.util.Arrays;
import java.util.Collection;
import java.util.List;
@@ -28,7 +29,10 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.IEntityInformationWithPropertiesHolder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
* @author Pawel Glyzewski
@@ -181,4 +185,23 @@ public class MetaprojectDAOTest extends AbstractDAOTest
|| metaproject.getId().longValue() == 3l);
}
}
+
+ @Test
+ public void testListMetaprojectsForEntities()
+ {
+ ExperimentPE experiment1 = daoFactory.getExperimentDAO().getByTechId(new TechId(4));
+ ExperimentPE experiment2 = daoFactory.getExperimentDAO().getByTechId(new TechId(23));
+
+ Collection<MetaprojectAssignmentPE> assignments =
+ daoFactory.getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
+ getTestPerson(), Arrays.asList(new IEntityInformationWithPropertiesHolder[]
+ { experiment1, experiment2 }), EntityKind.EXPERIMENT);
+
+ assertEquals(3, assignments.size());
+ for (MetaprojectAssignmentPE assignment : assignments)
+ {
+ assertTrue(assignment.getMetaproject().getId().longValue() == 1l
+ || assignment.getMetaproject().getId().longValue() == 3l);
+ }
+ }
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
index 50d3de4f59c..627446d199e 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/AbstractServerTestCase.java
@@ -65,6 +65,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IFileFormatTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IHibernateSearchDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IMetaprojectDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IPersonDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IProjectDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IPropertyTypeDAO;
@@ -200,6 +201,8 @@ public abstract class AbstractServerTestCase extends AssertJUnit
protected IEntityOperationsLogDAO entityOperationsLogDAO;
+ protected IMetaprojectDAO metaprojectDAO;
+
private MaterialConfigurationProvider oldProvider;
@BeforeMethod
@@ -236,6 +239,7 @@ public abstract class AbstractServerTestCase extends AssertJUnit
deletionDAO = context.mock(IDeletionDAO.class);
hibernateSearchDAO = context.mock(IHibernateSearchDAO.class);
entityOperationsLogDAO = context.mock(IEntityOperationsLogDAO.class);
+ metaprojectDAO = context.mock(IMetaprojectDAO.class);
// BO
groupBO = context.mock(ISpaceBO.class);
entityTypeBO = context.mock(IEntityTypeBO.class);
@@ -297,6 +301,8 @@ public abstract class AbstractServerTestCase extends AssertJUnit
will(returnValue(hibernateSearchDAO));
allowing(daoFactory).getEntityOperationsLogDAO();
will(returnValue(entityOperationsLogDAO));
+ allowing(daoFactory).getMetaprojectDAO();
+ will(returnValue(metaprojectDAO));
}
});
oldProvider = MaterialConfigurationProvider.initializeForTesting(false);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslatorTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslatorTest.java
index 5bb670f747e..d41eb71e9ac 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslatorTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslatorTest.java
@@ -64,7 +64,7 @@ public class DataSetTranslatorTest extends AssertJUnit
{
ExternalDataPE externalDataPE = new ExternalDataPE();
externalDataPE.setDataStore(createStore());
- ExternalData data = DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ ExternalData data = DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL, null);
DataSet translated = data.tryGetAsDataSet();
@@ -129,7 +129,7 @@ public class DataSetTranslatorTest extends AssertJUnit
deletionPE.setRegistrator(personPE);
externalDataPE.setDeletion(deletionPE);
externalDataPE.setSampleAcquiredFrom(samplePE);
- ExternalData data = DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ ExternalData data = DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL, null);
DataSet translated = data.tryGetAsDataSet();
@@ -185,7 +185,8 @@ public class DataSetTranslatorTest extends AssertJUnit
externalDataPE.addParentRelationship(createParentRelationship(externalDataPE, "parent-1"));
externalDataPE.addParentRelationship(createParentRelationship(externalDataPE, "parent-2"));
- ExternalData externalData = DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL);
+ ExternalData externalData =
+ DataSetTranslator.translate(externalDataPE, BASE_INDEX_URL, null);
assertEquals("my-experiment", externalData.getExperiment().getCode());
assertEquals(2, externalData.getParents().size());
@@ -227,7 +228,7 @@ public class DataSetTranslatorTest extends AssertJUnit
linkDataPE.addParentRelationship(createParentRelationship(linkDataPE, "parent-1"));
linkDataPE.addParentRelationship(createParentRelationship(linkDataPE, "parent-2"));
- ExternalData externalData = DataSetTranslator.translate(linkDataPE, BASE_INDEX_URL);
+ ExternalData externalData = DataSetTranslator.translate(linkDataPE, BASE_INDEX_URL, null);
assertEquals("my-experiment", externalData.getExperiment().getCode());
assertEquals(2, externalData.getParents().size());
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
index c653bff1c07..ed53a3908f7 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.systemtest.api.v1;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
@@ -199,6 +200,51 @@ public class GeneralInformationServiceTest extends SystemTestCase
assertEntities("[]", samples);
}
+ @Test
+ public void testSearchForSamplesWithMetaprojects()
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE,
+ "DILUTION_PLATE"));
+
+ EnumSet<SampleFetchOption> fetchOptions =
+ EnumSet.of(SampleFetchOption.PROPERTIES, SampleFetchOption.METAPROJECTS);
+ List<Sample> samples =
+ generalInformationService.searchForSamples(sessionToken, searchCriteria,
+ fetchOptions);
+
+ assertEntities("[/CISD/3V-125, /CISD/3V-126, /CISD/DP1-A, /CISD/DP1-B, /CISD/DP2-A, /DP]",
+ samples);
+ assertEquals(fetchOptions, samples.get(0).getRetrievedFetchOptions());
+ assertEquals("3V-125", samples.get(0).getCode());
+ assertEquals("CISD", samples.get(0).getSpaceCode());
+ assertEquals(979L, samples.get(0).getId().longValue());
+ assertEquals("200811050945092-976", samples.get(0).getPermId());
+ assertEquals("DILUTION_PLATE", samples.get(0).getSampleTypeCode());
+ assertEquals(2L, samples.get(0).getSampleTypeId().longValue());
+ assertEquals("test", samples.get(0).getRegistrationDetails().getUserId());
+ assertEquals("John", samples.get(0).getRegistrationDetails().getUserFirstName());
+ assertEquals("Doe", samples.get(0).getRegistrationDetails().getUserLastName());
+ assertEquals("franz-josef.elmer@systemsx.ch", samples.get(0).getRegistrationDetails()
+ .getUserEmail());
+ assertEquals("{OFFSET=49}", samples.get(0).getProperties().toString());
+ assertEquals(1, samples.get(0).getMetaprojects().size());
+
+ Metaproject metaproject = samples.get(0).getMetaprojects().get(0);
+ assertEquals(3l, metaproject.getId().longValue());
+ assertEquals("ANOTHER_TEST_METAPROJECTS", metaproject.getName());
+ assertEquals("Another example metaproject", metaproject.getDescription());
+ assertTrue(metaproject.isPrivate());
+ assertNotNull(metaproject.getCreationDate());
+
+ loginAsObserver();
+ samples =
+ generalInformationService.searchForSamples(sessionToken, searchCriteria,
+ fetchOptions);
+
+ assertEntities("[]", samples);
+ }
+
@Test
public void testSearchForSamplesWithParents()
{
diff --git a/openbis/sourceTest/sql/postgresql/124/042=metaproject_assignments_all.tsv b/openbis/sourceTest/sql/postgresql/124/042=metaproject_assignments_all.tsv
index c405d1ac7c8..ca14a3027cc 100644
--- a/openbis/sourceTest/sql/postgresql/124/042=metaproject_assignments_all.tsv
+++ b/openbis/sourceTest/sql/postgresql/124/042=metaproject_assignments_all.tsv
@@ -11,3 +11,4 @@
11 1 \N 978 \N \N 3 2012-09-05 10:18:10.581+02
12 1 \N \N 2 \N 1 2012-09-05 10:18:10.581+02
13 3 4 \N \N \N \N 2012-09-05 10:18:10.581+02
+14 3 \N 979 \N \N \N 2012-09-05 10:18:10.581+02
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetFetchOption.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetFetchOption.java
index ece756283d3..a0f02bab4b1 100644
--- a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetFetchOption.java
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSetFetchOption.java
@@ -26,6 +26,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FetchOption;
public enum DataSetFetchOption implements FetchOption
{
- BASIC, PROPERTIES, PROPERTIES_OF_PROPERTIES, PARENTS, CHILDREN, CONTAINED
+ BASIC, PROPERTIES, PROPERTIES_OF_PROPERTIES, PARENTS, CHILDREN, CONTAINED, METAPROJECTS
}
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Sample.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Sample.java
index adb2f442f3a..90fe02f3fc2 100644
--- a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Sample.java
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Sample.java
@@ -35,6 +35,7 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdentifierHolder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
/**
* Immutable value object representing a sample.
@@ -94,6 +95,8 @@ public final class Sample implements Serializable, IIdentifierHolder, IIdHolder
private HashMap<String, String> properties = new HashMap<String, String>();
+ private List<Metaproject> metaprojects = new ArrayList<Metaproject>();
+
private EntityRegistrationDetails registrationDetails;
private EnumSet<SampleFetchOption> retrievedFetchOptions = EnumSet
@@ -199,6 +202,16 @@ public final class Sample implements Serializable, IIdentifierHolder, IIdHolder
properties.put(propCode, value);
}
+ public List<Metaproject> getMetaprojects()
+ {
+ return metaprojects;
+ }
+
+ public void addMetaproject(Metaproject metaproject)
+ {
+ metaprojects.add(metaproject);
+ }
+
public void setRegistrationDetails(EntityRegistrationDetails registrationDetails)
{
this.registrationDetails = registrationDetails;
@@ -297,6 +310,8 @@ public final class Sample implements Serializable, IIdentifierHolder, IIdHolder
private boolean isStub;
+ private List<Metaproject> metaprojects;
+
/**
* Creates a new instance with the provided initializer
*
@@ -338,6 +353,8 @@ public final class Sample implements Serializable, IIdentifierHolder, IIdHolder
this.properties = initializer.getProperties();
+ this.metaprojects = initializer.getMetaprojects();
+
InitializingChecks.checkValidRegistrationDetails(initializer.getRegistrationDetails(),
"Unspecified entity registration details.");
this.registrationDetails = initializer.getRegistrationDetails();
@@ -435,6 +452,19 @@ public final class Sample implements Serializable, IIdentifierHolder, IIdHolder
}
}
+ @JsonIgnore
+ public List<Metaproject> getMetaprojects() throws IllegalArgumentException
+ {
+ if (getRetrievedFetchOptions().contains(SampleFetchOption.METAPROJECTS))
+ {
+ return Collections.unmodifiableList(metaprojects);
+ } else
+ {
+ throw new IllegalArgumentException("Metaprojects were not retrieved for sample "
+ + getIdentifier() + ".");
+ }
+ }
+
/**
* Return the sample registration details.
*
@@ -638,6 +668,18 @@ public final class Sample implements Serializable, IIdentifierHolder, IIdHolder
this.properties = properties;
}
+ @JsonProperty("metaprojects")
+ public List<Metaproject> getMetaprojectsJson()
+ {
+ return retrievedFetchOptions.contains(SampleFetchOption.METAPROJECTS) ? metaprojects : null;
+ }
+
+ @JsonProperty("metaprojects")
+ private void setMetaprojectsJson(List<Metaproject> metaprojects)
+ {
+ this.metaprojects = metaprojects;
+ }
+
private void setRegistrationDetails(EntityRegistrationDetails registrationDetails)
{
this.registrationDetails = registrationDetails;
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleFetchOption.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleFetchOption.java
index db2483b08f4..0c26e79b41f 100644
--- a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleFetchOption.java
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SampleFetchOption.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto;
import ch.systemsx.cisd.base.annotation.JsonObject;
-
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FetchOption;
@@ -30,7 +29,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FetchOption;
* @author Franz-Josef Elmer
*/
@JsonObject("SampleFetchOption")
-public enum SampleFetchOption implements FetchOption
+public enum SampleFetchOption implements FetchOption
{
/**
* Samples will have only basic attributes (id, code, type, space code, experiment identifier,
@@ -48,7 +47,7 @@ public enum SampleFetchOption implements FetchOption
/**
* Samples contain also their children samples.
*/
- CHILDREN,
+ CHILDREN,
/**
* Ask for all ancestors.
*/
@@ -60,5 +59,9 @@ public enum SampleFetchOption implements FetchOption
/**
* Ask for contained samples. This is not supported in search operations
*/
- CONTAINED
+ CONTAINED,
+ /**
+ * Ask for metaprojects this sample belongs to.
+ */
+ METAPROJECTS
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternal.java
index a0adeed4e49..1acd4f96b82 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/ProteomicsDataServiceInternal.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.plugin.proteomics.server;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
@@ -32,8 +33,8 @@ import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.ReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.server.authorization.annotation.RolesAllowed;
-import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodeCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
+import ch.systemsx.cisd.openbis.generic.server.authorization.predicate.DataSetCodeCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.ExperimentValidator;
import ch.systemsx.cisd.openbis.generic.server.authorization.validator.IValidator;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
@@ -48,6 +49,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
@@ -55,11 +57,13 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectAssignmentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.translator.DataSetTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.MetaprojectTranslator;
import ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator.ParentSampleValidator;
import ch.systemsx.cisd.openbis.plugin.proteomics.server.authorization.validator.RawDataSampleValidator;
import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ExperimentLoader;
@@ -177,7 +181,7 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
@ReturnValueFilter(validatorClass = ExperimentValidator.class)
public List<Experiment> listExperiments(String sessionToken, String experimentTypeCode)
{
- checkSession(sessionToken);
+ Session session = getSession(sessionToken);
IDAOFactory daoFactory = getDAOFactory();
IEntityTypeDAO entityTypeDAO = daoFactory.getEntityTypeDAO(EntityKind.EXPERIMENT);
@@ -185,7 +189,12 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
(ExperimentTypePE) entityTypeDAO.tryToFindEntityTypeByCode(experimentTypeCode);
List<ExperimentPE> experiments =
daoFactory.getExperimentDAO().listExperimentsWithProperties(type, null, null);
- return ExperimentTranslator.translate(experiments, "");
+ final Collection<MetaprojectAssignmentPE> assignmentPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
+ session.tryGetPerson(), experiments, EntityKind.EXPERIMENT);
+ Map<Long, Set<Metaproject>> assignments =
+ MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs);
+ return ExperimentTranslator.translate(experiments, "", assignments);
}
@Override
@@ -198,7 +207,12 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
IDataSetTable dataSetTable = commonBoFactory.createDataSetTable(session);
dataSetTable.loadByExperimentTechId(experimentID);
- return DataSetTranslator.translate(dataSetTable.getDataSets(), "", "");
+ List<DataPE> dataSetPEs = dataSetTable.getDataSets();
+ Collection<MetaprojectAssignmentPE> assignmentPEs =
+ getDAOFactory().getMetaprojectDAO().listMetaprojectAssignmentsForEntities(
+ session.tryGetPerson(), dataSetPEs, EntityKind.DATA_SET);
+ return DataSetTranslator.translate(dataSetPEs, "", "",
+ MetaprojectTranslator.translateMetaprojectAssignments(assignmentPEs));
}
@Override
@@ -222,7 +236,7 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
+ " [" + experiment.getIdentifier() + "] is not of type " + experimentType
+ " but of type " + actualExperimentTypeCode + ".");
}
- Experiment translatedExperiment = ExperimentTranslator.translate(experiment, "");
+ Experiment translatedExperiment = ExperimentTranslator.translate(experiment, "", null);
if (EXPERIMENT_VALIDATOR.isValid(person, translatedExperiment))
{
List<DataPE> dataSets = dataSetDAO.listDataSets(experiment);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoader.java
index 5c1e6c49cc3..cba31196ff7 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoader.java
@@ -30,8 +30,6 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ExperimentLoader
@@ -41,9 +39,9 @@ public class ExperimentLoader
public ExperimentLoader(IDAOFactory daoFactory)
{
this.daoFactory = daoFactory;
-
+
}
-
+
public void enrichWithExperiments(Collection<Sample> samples)
{
Map<Long, List<Sample>> samplesByID = new LinkedHashMap<Long, List<Sample>>();
@@ -66,7 +64,8 @@ public class ExperimentLoader
daoFactory.getExperimentDAO().listExperimentsWithProperties(samplesByID.keySet());
for (ExperimentPE experiment : experiments)
{
- Experiment e = ExperimentTranslator.translate(experiment, "", LoadableFields.PROPERTIES);
+ Experiment e =
+ ExperimentTranslator.translate(experiment, "", null, LoadableFields.PROPERTIES);
List<Sample> list = samplesByID.get(experiment.getId());
for (Sample sample : list)
{
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoaderTest.java
index 4a92d677da4..12cc28d0cfc 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/proteomics/server/business/ExperimentLoaderTest.java
@@ -28,11 +28,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
-import ch.systemsx.cisd.openbis.plugin.proteomics.server.business.ExperimentLoader;
/**
- *
- *
* @author Franz-Josef Elmer
*/
@Test(groups = "db")
@@ -43,9 +40,9 @@ public class ExperimentLoaderTest extends AbstractLoaderTestCase
{
ExperimentLoader loader = new ExperimentLoader(daoFactory);
List<Sample> samples = loadSamples(980L, 981L, 986L);
-
+
loader.enrichWithExperiments(samples);
-
+
StringBuilder builder = new StringBuilder();
for (Sample sample : samples)
{
@@ -58,20 +55,19 @@ public class ExperimentLoaderTest extends AbstractLoaderTestCase
}
builder.append('\n');
}
- assertEquals("980 3V-126\n"
- + "981 DP\n"
- + "986 3VCP5: EXP10 [DESCRIPTION: A simple experiment, GENDER: MALE]\n",
+ assertEquals("980 3V-126\n" + "981 DP\n"
+ + "986 3VCP5: EXP10 [DESCRIPTION: A simple experiment, GENDER: MALE]\n",
builder.toString());
}
-
+
private List<Sample> loadSamples(Long... ids)
{
ISampleDAO sampleDAO = daoFactory.getSampleDAO();
List<Sample> list = new ArrayList<Sample>();
for (Long id : ids)
{
- list.add(SampleTranslator.translate(sampleDAO.tryGetByTechId(new TechId(id)), ""));
-
+ list.add(SampleTranslator.translate(sampleDAO.tryGetByTechId(new TechId(id)), "", null));
+
}
return list;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/LogicalImageLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/LogicalImageLoader.java
index 97bc5de618e..20e520e655f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/LogicalImageLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/LogicalImageLoader.java
@@ -223,6 +223,6 @@ public class LogicalImageLoader
private ExternalData translate(DataPE dataSet)
{
- return DataSetTranslator.translate(dataSet, session.getBaseIndexURL());
+ return DataSetTranslator.translate(dataSet, session.getBaseIndexURL(), null);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index f1cc4064865..b186c7e7a72 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -390,7 +390,7 @@ public class PlateContentLoader
private Sample translate(SamplePE sample)
{
- return SampleTranslator.translate(sample, session.getBaseIndexURL());
+ return SampleTranslator.translate(sample, session.getBaseIndexURL(), null);
}
private List<WellMetadata> loadWells(TechId plateId)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index 9a25d00294a..010d7760d61 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -442,7 +442,7 @@ public class ScreeningApiImpl
SampleIdentifier sampleIdentifier = createSampleIdentifier(plateIdentifier);
ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
sampleBO.loadBySampleIdentifier(sampleIdentifier);
- sample = SampleTranslator.translate(sampleBO.getSample(), "");
+ sample = SampleTranslator.translate(sampleBO.getSample(), "", null);
}
return sample;
}
@@ -474,7 +474,7 @@ public class ScreeningApiImpl
private Sample translate(SamplePE sample)
{
- return SampleTranslator.translate(sample, session.getBaseIndexURL());
+ return SampleTranslator.translate(sample, session.getBaseIndexURL(), null);
}
private static SampleIdentifier createSampleIdentifier(PlateIdentifier plate)
@@ -954,8 +954,9 @@ public class ScreeningApiImpl
if (apiMaterial == null)
{
apiMaterial = asApiMaterial(material, materialsCache);
- // FIXME: Caching disabled because a not fully filled Material could be cached
-// materialsCache.put(material.getId(), apiMaterial);
+ // FIXME: Caching disabled because a not fully filled Material could be
+ // cached
+ // materialsCache.put(material.getId(), apiMaterial);
}
String propCode = property.getPropertyType().getCode();
result.put(propCode, apiMaterial);
@@ -966,14 +967,16 @@ public class ScreeningApiImpl
}
private Material asApiMaterial(
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material materialDto, Map<Long, Material> materialsCache)
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material materialDto,
+ Map<Long, Material> materialsCache)
{
MaterialTypeIdentifier typeIdentifier =
new MaterialTypeIdentifier(materialDto.getMaterialType().getCode());
List<IEntityProperty> originalProperties = materialDto.getProperties();
Map<String, String> properties = EntityHelper.convertToStringMap(originalProperties);
- Map<String, Material> materialProperties = convertMaterialProperties(originalProperties, materialsCache);
+ Map<String, Material> materialProperties =
+ convertMaterialProperties(originalProperties, materialsCache);
return new Material(typeIdentifier, materialDto.getCode(), properties, materialProperties);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
index 5dcc9255939..9f809a96e20 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
@@ -67,7 +67,7 @@ public class ScreeningUtils
String dataTypeCode = dataset.getDataSetType().getCode();
String fileTypeCode = null;
Experiment experiment =
- ExperimentTranslator.translate(dataset.getExperiment(), baseIndexURL);
+ ExperimentTranslator.translate(dataset.getExperiment(), baseIndexURL, null);
String analysisProcedureOrNull =
EntityHelper.tryFindPropertyValue(dataset, ScreeningConstants.ANALYSIS_PROCEDURE);
return createDatasetReference(dataset.getId(), dataset.getCode(), analysisProcedureOrNull,
--
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