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Commit 8781accc authored by pkupczyk's avatar pkupczyk
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SSDM-127 : GENERAL - Delete project/experiment/sample/dataset 

SVN: 32549
parent 6628a906
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openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingService.java
+ 51
− 1
View file @ 8781accc
......@@ -37,6 +37,7 @@ import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.IOpenBisSessionManager;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.Translator;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings;
......@@ -59,7 +60,7 @@ public class GeneralInformationChangingService extends
AbstractServer<IGeneralInformationChangingService> implements
IGeneralInformationChangingService
{
public static final int MINOR_VERSION = 5;
public static final int MINOR_VERSION = 6;
@Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
private ICommonServer server;
......@@ -283,4 +284,53 @@ public class GeneralInformationChangingService extends
return info;
}
@Override
public void deleteProjects(String sessionToken, List<Long> projectIds, String reason)
{
server.deleteProjects(sessionToken, TechId.createList(projectIds), reason);
}
@Override
public void deleteExperiments(String sessionToken, List<Long> experimentIds, String reason, DeletionType deletionType)
{
server.deleteExperiments(sessionToken, TechId.createList(experimentIds), reason, Translator.translate(deletionType));
}
@Override
public void deleteSamples(String sessionToken, List<Long> sampleIds, String reason, DeletionType deletionType)
{
server.deleteSamples(sessionToken, TechId.createList(sampleIds), reason, Translator.translate(deletionType));
}
@Override
public void deleteDataSets(String sessionToken, List<String> dataSetCodes, String reason, DeletionType deletionType)
{
server.deleteDataSets(sessionToken, dataSetCodes, reason, Translator.translate(deletionType), false);
}
@Override
public void deleteDataSetsForced(String sessionToken, List<String> dataSetCodes, String reason, DeletionType deletionType)
{
server.deleteDataSetsForced(sessionToken, dataSetCodes, reason, Translator.translate(deletionType), false);
}
@Override
public void revertDeletions(String sessionToken, List<Long> deletionIds)
{
server.revertDeletions(sessionToken, TechId.createList(deletionIds));
}
@Override
public void deletePermanently(String sessionToken, List<Long> deletionIds)
{
server.deletePermanently(sessionToken, TechId.createList(deletionIds));
}
@Override
public void deletePermanentlyForced(String sessionToken, List<Long> deletionIds)
{
server.deletePermanentlyForced(sessionToken, TechId.createList(deletionIds));
}
}
openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationChangingServiceLogger.java
+ 52
− 0
View file @ 8781accc
......@@ -16,12 +16,14 @@
package ch.systemsx.cisd.openbis.generic.server.api.v1;
import java.util.List;
import java.util.Map;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.openbis.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings;
......@@ -167,6 +169,56 @@ class GeneralInformationChangingServiceLogger extends AbstractServerLogger imple
return null;
}
@Override
public void deleteProjects(String sessionToken, List<Long> projectIds, String reason)
{
logAccess(sessionToken, "deleteProjects", "projectIds(%s), reason(%s)", abbreviate(projectIds), reason);
}
@Override
public void deleteExperiments(String sessionToken, List<Long> experimentIds, String reason, DeletionType deletionType)
{
logAccess(sessionToken, "deleteExperiments", "experimentIds(%s), reason(%s), deletionType(%s)", abbreviate(experimentIds), reason,
deletionType);
}
@Override
public void deleteSamples(String sessionToken, List<Long> sampleIds, String reason, DeletionType deletionType)
{
logAccess(sessionToken, "deleteSamples", "sampleIds(%s), reason(%s), deletionType(%s)", abbreviate(sampleIds), reason, deletionType);
}
@Override
public void deleteDataSets(String sessionToken, List<String> dataSetCodes, String reason, DeletionType deletionType)
{
logAccess(sessionToken, "deleteDataSets", "dataSetCodes(%s), reason(%s), deletionType(%s)", abbreviate(dataSetCodes), reason, deletionType);
}
@Override
public void deleteDataSetsForced(String sessionToken, List<String> dataSetCodes, String reason, DeletionType deletionType)
{
logAccess(sessionToken, "deleteDataSetsForced", "dataSetCodes(%s), reason(%s), deletionType(%s)", abbreviate(dataSetCodes), reason,
deletionType);
}
@Override
public void revertDeletions(String sessionToken, List<Long> deletionIds)
{
logAccess(sessionToken, "revertDeletions", "deletionIds(%s)", abbreviate(deletionIds));
}
@Override
public void deletePermanently(String sessionToken, List<Long> deletionIds)
{
logAccess(sessionToken, "deletePermanently", "deletionIds(%s)", abbreviate(deletionIds));
}
@Override
public void deletePermanentlyForced(String sessionToken, List<Long> deletionIds)
{
logAccess(sessionToken, "deletePermanentlyForced", "deletionIds(%s)", abbreviate(deletionIds));
}
@Override
public int getMajorVersion()
{
......
openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+ 23
− 3
View file @ 8781accc
......@@ -83,6 +83,8 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOptions;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStoreURLForDataSets;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Deletion;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletionFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MaterialIdentifier;
......@@ -144,7 +146,7 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
public class GeneralInformationService extends AbstractServer<IGeneralInformationService> implements
IGeneralInformationService
{
public static final int MINOR_VERSION = 29;
public static final int MINOR_VERSION = 30;
@Resource(name = ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER)
private ICommonServer commonServer;
......@@ -966,14 +968,14 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
}
return result;
}
@Override
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<SearchDomain> listAvailableSearchDomains(String sessionToken)
{
checkSession(sessionToken);
return commonServer.listAvailableSearchDomains(sessionToken);
}
......@@ -1331,4 +1333,22 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
checkSession(sessionToken);
return new EntityCodeGenerator(getDAOFactory()).generateCode(prefix, EntityKind.valueOf(entityKind));
}
@Override
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_USER)
public List<Deletion> listDeletions(String sessionToken, EnumSet<DeletionFetchOption> fetchOptions)
{
if (fetchOptions != null && fetchOptions.contains(DeletionFetchOption.ALL_ENTITIES))
{
return Translator.translate(commonServer.listDeletions(sessionToken, true));
} else if (fetchOptions != null && fetchOptions.contains(DeletionFetchOption.ORIGINAL_ENTITIES))
{
return Translator.translate(commonServer.listOriginalDeletions(sessionToken));
} else
{
return Translator.translate(commonServer.listDeletions(sessionToken, false));
}
}
}
openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
+ 11
− 1
View file @ 8781accc
......@@ -34,6 +34,8 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStoreURLForDataSets;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Deletion;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletionFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
......@@ -297,7 +299,7 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
}
@Override
public List<SearchDomainSearchResult> searchOnSearchDomain(String sessionToken, String preferredSearchDomainOrNull,
public List<SearchDomainSearchResult> searchOnSearchDomain(String sessionToken, String preferredSearchDomainOrNull,
String searchString, Map<String, String> optionalParametersOrNull)
{
logAccess(sessionToken, "search-on-search-domain", "PREFERRED_SEARCH_DOMAIN(%s) SEARCH_STRING(%s)",
......@@ -496,4 +498,12 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
logAccess(sessionToken, "generateCode", "sessionToken(%s) prefix(%s) entityKind(%s)", sessionToken, prefix, entityKind);
return null;
}
@Override
public List<Deletion> listDeletions(String sessionToken, EnumSet<DeletionFetchOption> fetchOptions)
{
logAccess(sessionToken, "listDeletions", "fetchOptions(%s)", fetchOptions);
return null;
}
}
openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/Translator.java
+ 80
− 0
View file @ 8781accc
......@@ -43,6 +43,10 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetKind;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletedEntity;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Deletion;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityRegistrationDetails.EntityRegistrationDetailsInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityTypeInitializer;
......@@ -93,6 +97,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample.SamplePermId
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample.SampleTechIdId;
import ch.systemsx.cisd.openbis.generic.shared.basic.AttachmentDownloadConstants;
import ch.systemsx.cisd.openbis.generic.shared.basic.GenericSharedConstants;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
......@@ -1045,4 +1050,79 @@ public class Translator
return result;
}
public static ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType translate(DeletionType deletionType)
{
switch (deletionType)
{
case PERMANENT:
return ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType.PERMANENT;
case TRASH:
return ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType.TRASH;
default:
throw new IllegalArgumentException("Unknown deletion type: " + deletionType);
}
}
public static List<Deletion> translate(List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Deletion> deletions)
{
List<Deletion> result = new LinkedList<Deletion>();
if (deletions != null)
{
for (ch.systemsx.cisd.openbis.generic.shared.basic.dto.Deletion deletion : deletions)
{
result.add(translate(deletion));
}
}
return result;
}
public static Deletion translate(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Deletion deletion)
{
Deletion result = new Deletion();
result.setId(deletion.getId());
result.setReasonOrNull(deletion.getReason());
result.setTotalExperimentsCount(deletion.getTotalExperimentsCount());
result.setTotalDatasetsCount(deletion.getTotalDatasetsCount());
result.setTotalSamplesCount(deletion.getTotalSamplesCount());
List<DeletedEntity> entities = new LinkedList<DeletedEntity>();
for (IEntityInformationHolderWithIdentifier entity : deletion.getDeletedEntities())
{
entities.add(translate((ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedEntity) entity));
}
result.setDeletedEntities(entities);
return result;
}
public static DeletedEntity translate(ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedEntity entity)
{
DeletedEntity result = new DeletedEntity();
result.setId(entity.getId());
result.setCode(entity.getCode());
result.setPermId(entity.getPermId());
result.setIdentifier(entity.getIdentifier());
result.setEntityType(entity.getEntityType().getCode());
result.setEntityKind(translate(entity.getEntityKind()));
return result;
}
public static EntityKind translate(ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind kind)
{
switch (kind)
{
case EXPERIMENT:
return EntityKind.EXPERIMENT;
case SAMPLE:
return EntityKind.SAMPLE;
case DATA_SET:
return EntityKind.DATA_SET;
case MATERIAL:
return EntityKind.MATERIAL;
default:
throw new IllegalArgumentException("Unknown entity kind: " + kind);
}
}
}
openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationChangingServiceTest.java
+ 224
− 0
View file @ 8781accc
......@@ -22,9 +22,12 @@ import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import junit.framework.Assert;
import org.springframework.beans.factory.annotation.Autowired;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
......@@ -34,8 +37,17 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationChangingService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Deletion;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignments;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.dataset.DataSetCodeId;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.experiment.ExperimentIdentifierId;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.material.MaterialCodeAndTypeCodeId;
......@@ -497,4 +509,216 @@ public class GeneralInformationChangingServiceTest extends SystemTestCase
generalInformationChangingService);
}
@Test
public void testDeleteProject()
{
testDeletePermanent(new ProjectDeleteAction(), new ProjectListDeletedAction());
}
@Test
public void testDeleteExperientPermanent()
{
testDeletePermanent(new ExperimentDeleteAction(), new ExperimentListDeletedAction());
}
@Test
public void testDeleteExperientTrash()
{
testDeleteTrash(new ExperimentDeleteAction(), new ExperimentListDeletedAction());
}
@Test
public void testDeleteSamplePermanent()
{
testDeletePermanent(new SampleDeleteAction(), new SampleListDeletedAction());
}
@Test
public void testDeleteSampleTrash()
{
testDeleteTrash(new SampleDeleteAction(), new SampleListDeletedAction());
}
@Test
public void testDeleteDataSetPermanent()
{
testDeletePermanent(new DataSetDeleteAction(), new DataSetListDeletedAction());
}
@Test
public void testDeleteDataSetTrash()
{
testDeletePermanent(new DataSetDeleteAction(), new DataSetListDeletedAction());
}
private class ProjectDeleteAction implements DeleteAction<Project>
{
@Override
public void delete(Project project, String reason, DeletionType deletionType)
{
generalInformationChangingService.deleteProjects(sessionToken, Collections.singletonList(project.getId()), reason);
}
}
private class ProjectListDeletedAction implements ListDeletedAction<Project>
{
@Override
public List<Project> list()
{
List<Project> projects = generalInformationService.listProjects(sessionToken);
for (Project project : projects)
{
if (project.getIdentifier().equals("/TEST-SPACE/PROJECT-TO-DELETE"))
{
return Collections.singletonList(project);
}
}
return Collections.emptyList();
}
}
private class ExperimentDeleteAction implements DeleteAction<Experiment>
{
@Override
public void delete(Experiment experiment, String reason, DeletionType deletionType)
{
generalInformationChangingService.deleteExperiments(sessionToken, Collections.singletonList(experiment.getId()), reason,
deletionType);
}
}
private class ExperimentListDeletedAction implements ListDeletedAction<Experiment>
{
@Override
public List<Experiment> list()
{
return generalInformationService.listExperiments(sessionToken, Collections.singletonList("/TEST-SPACE/NOE/EXPERIMENT-TO-DELETE"));
}
}
private class SampleDeleteAction implements DeleteAction<Sample>
{
@Override
public void delete(Sample sample, String reason, DeletionType deletionType)
{
generalInformationChangingService.deleteSamples(sessionToken, Collections.singletonList(sample.getId()), reason,
deletionType);
}
}
private class SampleListDeletedAction implements ListDeletedAction<Sample>
{
@Override
public List<Sample> list()
{
SearchCriteria criteria = new SearchCriteria();
criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "SAMPLE-TO-DELETE"));
return generalInformationService.searchForSamples(sessionToken, criteria);
}
}
private class DataSetDeleteAction implements DeleteAction<DataSet>
{
@Override
public void delete(DataSet dataSet, String reason, DeletionType deletionType)
{
generalInformationChangingService.deleteDataSets(sessionToken, Collections.singletonList(dataSet.getCode()), reason,
deletionType);
}
}
private class DataSetListDeletedAction implements ListDeletedAction<DataSet>
{
@Override
public List<DataSet> list()
{
SearchCriteria criteria = new SearchCriteria();
criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "DATASET-TO-DELETE"));
return generalInformationService.searchForDataSets(sessionToken, criteria);
}
}
private <T> void testDeleteTrash(DeleteAction<T> deleteAction, ListDeletedAction<T> listAction)
{
List<T> beforeObjects = listAction.list();
List<Deletion> beforeDeletions = generalInformationService.listDeletions(sessionToken, null);
Assert.assertEquals(1, beforeObjects.size());
// move an object to trash
T deletedObject = beforeObjects.get(0);
String reason = "Test delete to trash: " + deletedObject;
deleteAction.delete(deletedObject, reason, DeletionType.TRASH);
List<T> afterObjects = listAction.list();
List<Deletion> afterDeletions = generalInformationService.listDeletions(sessionToken, null);
Deletion deletion = afterDeletions.get(afterDeletions.size() - 1);
// the object should not be listed and a new deletion should be appear
Assert.assertEquals(0, afterObjects.size());
Assert.assertEquals(beforeDeletions.size() + 1, afterDeletions.size());
Assert.assertEquals(reason, deletion.getReasonOrNull());
// revert the logical deletion
generalInformationChangingService.revertDeletions(sessionToken, Collections.singletonList(deletion.getId()));
afterObjects = listAction.list();
afterDeletions = generalInformationService.listDeletions(sessionToken, null);
// the object should be listed again and the deletion should be gone
Assert.assertEquals(1, afterObjects.size());
Assert.assertEquals(beforeDeletions.size(), afterDeletions.size());
// move the object again to trash
deleteAction.delete(deletedObject, reason, DeletionType.TRASH);
afterObjects = listAction.list();
afterDeletions = generalInformationService.listDeletions(sessionToken, null);
deletion = afterDeletions.get(afterDeletions.size() - 1);
// the object should be gone again and a new deletion should appear
Assert.assertEquals(0, afterObjects.size());
Assert.assertEquals(beforeDeletions.size() + 1, afterDeletions.size());
Assert.assertEquals(reason, deletion.getReasonOrNull());
// permanently confirm the deletion
generalInformationChangingService.deletePermanently(sessionToken, Collections.singletonList(deletion.getId()));
afterObjects = listAction.list();
afterDeletions = generalInformationService.listDeletions(sessionToken, null);
// both the object and the deletion should be gone
Assert.assertEquals(0, afterObjects.size());
Assert.assertEquals(beforeDeletions.size(), afterDeletions.size());
}
private <T> void testDeletePermanent(DeleteAction<T> deleteAction, ListDeletedAction<T> listAction)
{
List<T> beforeObjects = listAction.list();
List<Deletion> beforeDeletions = generalInformationService.listDeletions(sessionToken, null);
Assert.assertEquals(1, beforeObjects.size());
// delete an object permanently
T deletedObject = beforeObjects.get(0);
deleteAction.delete(deletedObject, "Test delete permanently: " + deletedObject, DeletionType.PERMANENT);
List<T> afterObjects = listAction.list();
List<Deletion> afterDeletions = generalInformationService.listDeletions(sessionToken, null);
// the object should be gone and no new deletions should appear
Assert.assertEquals(0, afterObjects.size());
Assert.assertEquals(beforeDeletions.size(), afterDeletions.size());
}
private interface DeleteAction<T>
{
public void delete(T object, String reason, DeletionType deletionType);
}
private interface ListDeletedAction<T>
{
public List<T> list();
}
}
openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
+ 4
− 4
View file @ 8781accc
......@@ -153,7 +153,7 @@ public class GeneralInformationServiceTest extends SystemTestCase
}
});
assertEquals(
"[/CISD/DEFAULT, /CISD/NEMO, /CISD/NOE, /TEST-SPACE/NOE, /TEST-SPACE/TEST-PROJECT, /TESTGROUP/TESTPROJ]",
"[/CISD/DEFAULT, /CISD/NEMO, /CISD/NOE, /TEST-SPACE/NOE, /TEST-SPACE/PROJECT-TO-DELETE, /TEST-SPACE/TEST-PROJECT, /TESTGROUP/TESTPROJ]",
projects.toString());
loginAsObserver();
......@@ -820,7 +820,7 @@ public class GeneralInformationServiceTest extends SystemTestCase
{
SearchCriteria criteria = new SearchCriteria();
List<Sample> samples = generalInformationService.searchForSamples(sessionToken, criteria);
assertEquals(700, samples.size());
assertEquals(701, samples.size());
}
@Test
......@@ -1355,7 +1355,7 @@ public class GeneralInformationServiceTest extends SystemTestCase
{
SearchCriteria criteria = new SearchCriteria();
List<DataSet> dataSets = generalInformationService.searchForDataSets(sessionToken, criteria);
assertEquals(30, dataSets.size());
assertEquals(31, dataSets.size());
}
@Test
......@@ -1457,7 +1457,7 @@ public class GeneralInformationServiceTest extends SystemTestCase
List<Experiment> experiments =
generalInformationService.searchForExperiments(sessionToken, searchCriteria);
assertEntities("[/CISD/NOE/EXP-TEST-2, /TEST-SPACE/NOE/EXP-TEST-2]", experiments);
assertEntities("[/CISD/NOE/EXP-TEST-2, /TEST-SPACE/NOE/EXP-TEST-2, /TEST-SPACE/NOE/EXPERIMENT-TO-DELETE]", experiments);
}
@Test
......
openbis/sourceTest/sql/postgresql/143/008=data_all.tsv
+ 1
− 0
View file @ 8781accc
......@@ -29,3 +29,4 @@
32 COMPONENT_1A 2 \N 2011-05-09 10:22:59.203+02 2011-05-09 10:22:59.313+02 f t 2011-05-09 16:34:44.462776+02 8 1 t \N \N \N \N 0 \N 2014-04-01 09:56:25.410678+02
33 COMPONENT_2A 2 \N 2011-05-09 10:22:59.203+02 2011-05-09 10:22:59.313+02 f t 2011-05-09 16:34:44.462776+02 8 1 t \N \N \N \N 0 \N 2014-04-01 09:56:25.410678+02
34 COMPONENT_1B 2 \N 2011-05-09 10:22:59.203+02 2011-05-09 10:22:59.313+02 f t 2011-05-09 16:34:44.462776+02 8 1 t \N \N \N \N 0 \N 2014-04-01 09:56:25.410678+02
35 DATASET-TO-DELETE 1 \N 2008-11-05 09:22:59.203+01 2008-11-05 09:22:59.313+01 f t 2009-03-23 15:34:44.462776+01 23 1 t \N 2 \N \N 0 \N 2014-04-01 09:56:25.410678+02
openbis/sourceTest/sql/postgresql/143/028=experiments_all.tsv
+ 1
− 0
View file @ 8781accc
......@@ -10,3 +10,4 @@
22 EXP-Y 1 2 2008-11-05 09:22:37.246+01 1 \N f 2009-03-18 10:50:19.475958+01 201108050937246-1031 \N 0 \N
23 EXP-SPACE-TEST 1 2 2008-11-05 09:22:40.555+01 5 \N f 2009-03-18 10:50:19.475958+01 201206190940555-1032 \N 0 \N
24 EXP-TEST-2 1 2 2009-02-09 12:17:55.058768+01 6 \N f 2009-03-18 10:50:19.475958+01 200902091255058-1037 \N 0 \N
25 EXPERIMENT-TO-DELETE 1 2 2009-02-09 12:17:55.058768+01 6 \N f 2009-03-18 10:50:19.475958+01 200902091255058-1038 \N 0 \N
openbis/sourceTest/sql/postgresql/143/029=external_data.tsv
+ 1
− 0
View file @ 8781accc
......@@ -20,3 +20,4 @@
32 contained/COMPONENT_1A 8 1 4 U \N AVAILABLE \N \N f -50 t
33 contained/COMPONENT_2A 8 1 4 U \N AVAILABLE \N \N f -50 t
34 contained/COMPONENT_1B 8 1 4 U \N AVAILABLE \N \N f -50 t
35 xml/dataset-to-delete 8 1 4 U \N AVAILABLE \N \N f -50 t
openbis/sourceTest/sql/postgresql/143/046=projects.tsv
+ 1
− 0
View file @ 8781accc
......@@ -4,3 +4,4 @@
4 20120814110011738-104 NOE 1 \N \N 2 2008-11-05 09:21:43.312+01 2009-04-03 15:56:37.675094+02 \N 0
5 20120814110011738-105 TEST-PROJECT 3 \N \N 2 2008-11-05 09:18:14.967+01 2009-04-03 15:56:37.675094+02 \N 0
6 20120814110011738-106 NOE 3 \N \N 2 2008-11-05 09:21:43.312+01 2009-04-03 15:56:37.675094+02 \N 0
7 20120814110011738-107 PROJECT-TO-DELETE 3 \N \N 2 2008-11-05 09:21:43.312+01 2009-04-03 15:56:37.675094+02 \N 0
openbis/sourceTest/sql/postgresql/143/057=samples_all.tsv
+ 1
− 0
View file @ 8781accc
......@@ -1029,3 +1029,4 @@
1058 EV-PARENT 10 2009-02-09 12:09:19.327518+01 2 \N 3 \N 2009-08-18 17:54:11.56+02 23 201206191219327-1058 \N EV-PARENT,-1,3,-1 \N 0 \N
1059 EV-PARENT-NORMAL 11 2009-02-09 12:09:19.327518+01 2 \N 3 \N 2009-08-18 17:54:11.56+02 23 201206191219327-1059 \N EV-PARENT-NORMAL,-1,3,-1 \N 0 \N
1060 CP-TEST-4 3 2009-02-09 12:09:50.077973+01 2 \N 3 \N 2009-08-18 17:54:36.929+02 24 200902091250077-1060 \N CP-TEST-4,-1,1,-1 \N 0 \N
1061 SAMPLE-TO-DELETE 11 2009-02-09 12:09:19.327518+01 2 \N 3 \N 2009-08-18 17:54:11.56+02 23 201206191219327-1061 \N SAMPLE-TO-DELETE,-1,3,-1 \N 0 \N
openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationChangingService.java
+ 84
− 0
View file @ 8781accc
......@@ -16,10 +16,12 @@
package ch.systemsx.cisd.openbis.generic.shared.api.v1;
import java.util.List;
import java.util.Map;
import ch.systemsx.cisd.common.api.IRpcService;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletionType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.MetaprojectAssignmentsIds;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.NewVocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.WebAppSettings;
......@@ -177,4 +179,86 @@ public interface IGeneralInformationChangingService extends IRpcService
final String sessionToken,
final String sampleTypeCode,
final String sessionKey);
/**
* Deletes the specified projects.
*
* @param projectIds Ids of projects to delete
* @param reason Reason of the deletion
* @since 1.6
*/
public void deleteProjects(String sessionToken, List<Long> projectIds, String reason);
/**
* Deletes or trashes the specified experiments depending on the chosen deletion type.
*
* @param experimentIds Ids of experiments to delete
* @param reason Reason of the deletion
* @param deletionType Type of the deletion
* @since 1.6
*/
public void deleteExperiments(String sessionToken, List<Long> experimentIds, String reason,
DeletionType deletionType);
/**
* Deletes or trashes the specified samples depending on the chosen deletion type.
*
* @param sampleIds Ids of samples to delete
* @param reason Reason of the deletion
* @param deletionType Type of the deletion
* @since 1.6
*/
public void deleteSamples(String sessionToken, List<Long> sampleIds, String reason,
DeletionType deletionType);
/**
* Deletes or trashes the specified data sets depending on the chosen deletion type. This method CANNOT delete data sets with deletion_disallow
* flag set to true in their type (compare with {@link #deleteDataSetsForced(String, List, String, DeletionType)}.
*
* @param dataSetCodes Codes of data sets to delete
* @param reason Reason of the deletion
* @param deletionType Type of the deletion
* @since 1.6
*/
public void deleteDataSets(String sessionToken, List<String> dataSetCodes, String reason,
DeletionType deletionType);
/**
* Deletes or trashes the specified data sets depending on the chosen deletion type. This method CAN delete data sets with deletion_disallow flag
* set to true in their type but requires special user privileges (compare with {@link #deleteDataSets(String, List, String, DeletionType)}.
*
* @param dataSetCodes Codes of data sets to delete
* @param reason Reason of the deletion
* @param deletionType Type of the deletion
* @since 1.6
*/
public void deleteDataSetsForced(String sessionToken, List<String> dataSetCodes, String reason,
DeletionType deletionType);
/**
* Reverts specified deletions (puts back all entities moved to trash in the deletions).
*
* @param deletionIds Ids of deletions to be reverted
* @since 1.6
*/
public void revertDeletions(String sessionToken, List<Long> deletionIds);
/**
* Permanently deletes entities moved to trash in specified deletions. This method CANNOT delete data sets with deletion_disallow flag set to true
* in their type (compare with {@link #deletePermanentlyForced(String, List)})
*
* @param deletionIds Ids of deletions to be deleted permanently
* @since 1.6
*/
public void deletePermanently(String sessionToken, List<Long> deletionIds);
/**
* Permanently deletes entities moved to trash in specified deletions. It CAN delete data sets with deletion_disallow flag set to true in their
* type (compare with {@link #deletePermanently(String, List)}).
*
* @param deletionIds Ids of deletions to be deleted permanently
* @since 1.6
*/
public void deletePermanentlyForced(String sessionToken, List<Long> deletionIds);
}
openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
+ 23
− 15
View file @ 8781accc
......@@ -32,6 +32,8 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataStoreURLForDataSets;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Deletion;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DeletionFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Material;
......@@ -54,7 +56,6 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.id.sample.ISampleId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
/**
* Service for retrieving general informations.
*
......@@ -399,28 +400,26 @@ public interface IGeneralInformationService extends IRpcService
EnumSet<DataSetFetchOption> fetchOptions);
/**
* Searches on a search domain. If no preferred search domain is specified the first available one will be used.
* If the preferred sequence search domain doesn't exist or isn't available also the first available one will be used.
* Searches on a search domain. If no preferred search domain is specified the first available one will be used. If the preferred sequence search
* domain doesn't exist or isn't available also the first available one will be used.
*
* @param preferredSearchDomainOrNull The key of the preferred search domain or <code>null</code>.
* @param searchString The search string.
* @param optionalParametersOrNull Optional parameters. Can be <code>null</code>.
* The semantics depends on the type of search domain.
* @param optionalParametersOrNull Optional parameters. Can be <code>null</code>. The semantics depends on the type of search domain.
* @since 1.29
*/
public List<SearchDomainSearchResult> searchOnSearchDomain(String sessionToken,
String preferredSearchDomainOrNull, String searchString,
public List<SearchDomainSearchResult> searchOnSearchDomain(String sessionToken,
String preferredSearchDomainOrNull, String searchString,
Map<String, String> optionalParametersOrNull);
/**
* Lists available search domains. Their name attribute can be used when invoking
* {@link #searchOnSearchDomain(String, String, String, Map)}.
* Lists available search domains. Their name attribute can be used when invoking {@link #searchOnSearchDomain(String, String, String, Map)}.
*
* @return empty list if no search domain is available.
* @since 1.29
*/
public List<SearchDomain> listAvailableSearchDomains(String sessionToken);
/**
* Return all data sets matching specified search criteria. Note, that for returned container data sets the contained data sets have only code,
* type and registration date set.
......@@ -429,7 +428,7 @@ public interface IGeneralInformationService extends IRpcService
* @since 1.8
*/
public List<DataSet> searchForDataSets(String sessionToken, SearchCriteria searchCriteria);
/**
* Return all data sets matching specified search criteria and visible to user <var>userId</var>. Note, that for returned container data sets the
* contained data sets have only code, type and registration date set.
......@@ -550,7 +549,7 @@ public interface IGeneralInformationService extends IRpcService
boolean allVersions);
public Map<String, String> getUserDisplaySettings(final String sessionToken);
/**
* Lists property types.
*
......@@ -558,7 +557,7 @@ public interface IGeneralInformationService extends IRpcService
* @since 1.26
*/
public List<PropertyType> listPropertyTypes(String sessionToken, boolean withRelations);
/**
* Generate Code.
*
......@@ -567,5 +566,14 @@ public interface IGeneralInformationService extends IRpcService
* @since 1.28
*/
public String generateCode(String sessionToken, String prefix, String entityKind);
}
/**
* Returns all deletions.
*
* @param fetchOptions Options that control which parts of the deletions are fetched.
* @return a sorted list of {@link Deletion}.
* @since 1.30
*/
public List<Deletion> listDeletions(String sessionToken, EnumSet<DeletionFetchOption> fetchOptions);
}
openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DeletedEntity.java 0 → 100644
+ 104
− 0
View file @ 8781accc
/*
* Copyright 2014 ETH Zuerich, Scientific IT Services
*
* 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.shared.api.v1.dto;
import java.io.Serializable;
import ch.systemsx.cisd.base.annotation.JsonObject;
/**
* @author pkupczyk
*/
@JsonObject("DeletedEntity")
public class DeletedEntity implements Serializable
{
private static final long serialVersionUID = 1L;
private Long id;
private String code;
private String permId;
private String identifier;
private String entityType;
private EntityKind entityKind;
public Long getId()
{
return id;
}
public void setId(Long id)
{
this.id = id;
}
public String getCode()
{
return code;
}
public void setCode(String code)
{
this.code = code;
}
public String getPermId()
{
return permId;
}
public void setPermId(String permId)
{
this.permId = permId;
}
public String getIdentifier()
{
return identifier;
}
public void setIdentifier(String identifier)
{
this.identifier = identifier;
}
public String getEntityType()
{
return entityType;
}
public void setEntityType(String entityType)
{
this.entityType = entityType;
}
public EntityKind getEntityKind()
{
return entityKind;
}
public void setEntityKind(EntityKind entityKind)
{
this.entityKind = entityKind;
}
}
openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/Deletion.java 0 → 100644
+ 106
− 0
View file @ 8781accc
/*
* Copyright 2014 ETH Zuerich, Scientific IT Services
*
* 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.shared.api.v1.dto;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.base.annotation.JsonObject;
/**
* @author pkupczyk
*/
@JsonObject("Deletion")
public class Deletion implements Serializable
{
private static final long serialVersionUID = 1L;
private Long id;
private int totalSamplesCount;
private int totalDatasetsCount;
private int totalExperimentsCount;
private String reasonOrNull;
private List<DeletedEntity> deletedEntities = new ArrayList<DeletedEntity>();
public Long getId()
{
return id;
}
public void setId(Long id)
{
this.id = id;
}
public int getTotalSamplesCount()
{
return totalSamplesCount;
}
public void setTotalSamplesCount(int totalSamplesCount)
{
this.totalSamplesCount = totalSamplesCount;
}
public int getTotalDatasetsCount()
{
return totalDatasetsCount;
}
public void setTotalDatasetsCount(int totalDatasetsCount)
{
this.totalDatasetsCount = totalDatasetsCount;
}
public int getTotalExperimentsCount()
{
return totalExperimentsCount;
}
public void setTotalExperimentsCount(int totalExperimentsCount)
{
this.totalExperimentsCount = totalExperimentsCount;
}
public String getReasonOrNull()
{
return reasonOrNull;
}
public void setReasonOrNull(String reasonOrNull)
{
this.reasonOrNull = reasonOrNull;
}
public List<DeletedEntity> getDeletedEntities()
{
return deletedEntities;
}
public void setDeletedEntities(List<DeletedEntity> deletedEntities)
{
this.deletedEntities = deletedEntities;
}
}
openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DeletionFetchOption.java 0 → 100644
+ 40
− 0
View file @ 8781accc
/*
* Copyright 2014 ETH Zuerich, Scientific IT Services
*
* 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.shared.api.v1.dto;
import java.io.Serializable;
import ch.systemsx.cisd.base.annotation.JsonObject;
/**
* @author pkupczyk
*/
@JsonObject("DeletionFetchOption")
public enum DeletionFetchOption implements Serializable
{
/**
* Deletions will contain only the originally deleted entities
*/
ORIGINAL_ENTITIES,
/**
* Deletions will contain the originally deleted entities and all the related entities that were also deleted by a cascade.
*/
ALL_ENTITIES
}
openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DeletionType.java 0 → 100644
+ 34
− 0
View file @ 8781accc
/*
* Copyright 2014 ETH Zuerich, Scientific IT Services
*
* 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.shared.api.v1.dto;
import java.io.Serializable;
import ch.systemsx.cisd.base.annotation.JsonObject;
/**
* Types of deletion operations.
*
* @author pkupczyk
*/
@JsonObject("DeletionType")
public enum DeletionType implements Serializable
{
PERMANENT, TRASH
}
openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/EntityKind.java 0 → 100644
+ 32
− 0
View file @ 8781accc
/*
* Copyright 2014 ETH Zuerich, Scientific IT Services
*
* 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.shared.api.v1.dto;
import java.io.Serializable;
import ch.systemsx.cisd.base.annotation.JsonObject;
/**
* @author pkupczyk
*/
@JsonObject("EntityKind")
public enum EntityKind implements Serializable
{
MATERIAL, EXPERIMENT, SAMPLE, DATA_SET
}
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