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Commit b3ab46f4 authored by felmer's avatar felmer
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BIS-142 Moving authorization annotations from IScreeningServer and... 

BIS-142 Moving authorization annotations from IScreeningServer and IScreeningApiServer to ScreeningServer. Introducing system test ScreeningServerAuthorizationTest. Moving ServerInterfaceRegressionTest from shared to server package.

SVN: 26577
parent 571d1fd3
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screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+ 150
− 44
View file @ b3ab46f4
......@@ -32,7 +32,6 @@ import org.springframework.stereotype.Component;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.spring.ExposablePropertyPlaceholderConfigurer;
import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.business.IPropertiesBatchManager;
......@@ -44,6 +43,15 @@ import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlu
import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlugin;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.Capability;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.DataSetTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodeCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
......@@ -54,6 +62,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
......@@ -78,6 +87,13 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningUtils;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellContentLoader;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.ExperimentIdentifierPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.PlateIdentifierPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.PlateWellReferenceWithDatasetsValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.ScreeningExperimentValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.ScreeningPlateListReadOnlyPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.ScreeningPlateValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.WellIdentifierPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata;
......@@ -92,6 +108,12 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateMetadata
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.DatasetReferencePredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.ExperimentSearchCriteriaPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.MaterialExperimentFeatureVectorSummaryValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.MaterialFeaturesOneExpPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellContentValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellSearchCriteriaPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.AnalysisProcedures;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentFeatureVectorSummary;
......@@ -133,9 +155,6 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
*/
public static final int MINOR_VERSION = 9;
@Resource(name = ExposablePropertyPlaceholderConfigurer.PROPERTY_CONFIGURER_BEAN_NAME)
private ExposablePropertyPlaceholderConfigurer configurer;
@Resource(name = ResourceNames.SCREENING_BUSINESS_OBJECT_FACTORY)
private IScreeningBusinessObjectFactory businessObjectFactory;
......@@ -194,8 +213,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
//
@Override
public final SampleParentWithDerived getSampleInfo(final String sessionToken,
final TechId sampleId)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public SampleParentWithDerived getSampleInfo(final String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
final TechId sampleId) throws UserFailureException
{
final Session session = getSession(sessionToken);
final ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
......@@ -206,14 +227,19 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public PlateContent getPlateContent(String sessionToken, TechId plateId)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public PlateContent getPlateContent(String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
TechId plateId)
{
Session session = getSession(sessionToken);
return PlateContentLoader.loadImagesAndMetadata(session, businessObjectFactory, plateId);
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public FeatureVectorDataset getFeatureVectorDataset(String sessionToken,
@AuthorizationGuard(guardClass = DatasetReferencePredicate.class)
DatasetReference dataset, CodeAndLabel featureName)
{
Session session = getSession(sessionToken);
......@@ -222,7 +248,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public PlateImages getPlateContentForDataset(String sessionToken, TechId datasetId)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public PlateImages getPlateContentForDataset(String sessionToken,
@AuthorizationGuard(guardClass = DataSetTechIdPredicate.class)
TechId datasetId)
{
Session session = getSession(sessionToken);
return PlateContentLoader.loadImagesAndMetadataForDataset(session, businessObjectFactory,
......@@ -230,7 +259,11 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public List<WellContent> listPlateWells(String sessionToken, WellSearchCriteria materialCriteria)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = WellContentValidator.class)
public List<WellContent> listPlateWells(String sessionToken,
@AuthorizationGuard(guardClass = WellSearchCriteriaPredicate.class)
WellSearchCriteria materialCriteria)
{
Session session = getSession(sessionToken);
return WellContentLoader.load(session, businessObjectFactory, getDAOFactory(),
......@@ -238,7 +271,9 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<WellReplicaImage> listWellImages(String sessionToken, TechId materialId,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
TechId experimentId)
{
Session session = getSession(sessionToken);
......@@ -247,7 +282,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public List<Material> listMaterials(String sessionToken, WellSearchCriteria materialCriteria)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<Material> listMaterials(String sessionToken,
@AuthorizationGuard(guardClass = WellSearchCriteriaPredicate.class)
WellSearchCriteria materialCriteria)
{
Session session = getSession(sessionToken);
return WellContentLoader.loadMaterials(session, businessObjectFactory, getDAOFactory(),
......@@ -255,8 +293,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public FeatureVectorValues getWellFeatureVectorValues(String sessionToken, String datasetCode,
String datastoreCode, WellLocation wellLocation)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public FeatureVectorValues getWellFeatureVectorValues(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
String datasetCode, String datastoreCode, WellLocation wellLocation)
{
getSession(sessionToken);
return FeatureVectorValuesLoader.loadFeatureVectorValues(businessObjectFactory,
......@@ -264,8 +304,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public LogicalImageInfo getImageDatasetInfo(String sessionToken, String datasetCode,
String datastoreCode, WellLocation wellLocationOrNull)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public LogicalImageInfo getImageDatasetInfo(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
String datasetCode, String datastoreCode, WellLocation wellLocationOrNull)
{
Session session = getSession(sessionToken);
return LogicalImageLoader.loadLogicalImageInfo(session, businessObjectFactory, datasetCode,
......@@ -273,7 +315,9 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ImageDatasetEnrichedReference getImageDatasetReference(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
String datasetCode, String datastoreCode)
{
Session session = getSession(sessionToken);
......@@ -282,7 +326,9 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<ImageResolution> getImageDatasetResolutions(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
String datasetCode, String datastoreCode)
{
checkSession(sessionToken);
......@@ -292,8 +338,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public ImageSampleContent getImageDatasetInfosForSample(String sessionToken, TechId sampleId,
WellLocation wellLocationOrNull)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ImageSampleContent getImageDatasetInfosForSample(String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
TechId sampleId, WellLocation wellLocationOrNull)
{
Session session = getSession(sessionToken);
return PlateContentLoader.getImageDatasetInfosForSample(session, businessObjectFactory,
......@@ -301,18 +349,23 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public ExternalData getDataSetInfo(String sessionToken, TechId datasetId)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ExternalData getDataSetInfo(String sessionToken,
@AuthorizationGuard(guardClass = DataSetTechIdPredicate.class)
TechId datasetId)
{
return commonServer.getDataSetInfo(sessionToken, datasetId);
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public Material getMaterialInfo(String sessionToken, TechId materialId)
{
return commonServer.getMaterialInfo(sessionToken, materialId);
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public Vocabulary getVocabulary(String sessionToken, String code) throws UserFailureException
{
checkSession(sessionToken);
......@@ -322,6 +375,8 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_ADMIN)
@Capability("WRITE_EXPERIMENT_SAMPLE_MATERIAL")
public void registerLibrary(String sessionToken, String userEmail,
List<NewMaterial> newGenesOrNull, List<NewMaterial> newOligosOrNull,
List<NewSamplesWithTypes> newSamplesWithType)
......@@ -331,8 +386,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public List<Material> listExperimentMaterials(String sessionToken, TechId experimentId,
MaterialType materialType)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<Material> listExperimentMaterials(String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
TechId experimentId, MaterialType materialType)
{
// TODO 2010-09-01, Piotr Buczek: move it to some BO when we have more queries like that
IScreeningQuery dao = createDAO(getDAOFactory());
......@@ -348,7 +405,9 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ExperimentFeatureVectorSummary getExperimentFeatureVectorSummary(String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
TechId experimentId, AnalysisProcedureCriteria analysisProcedureCriteria)
{
Session session = getSession(sessionToken);
......@@ -362,6 +421,8 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = MaterialExperimentFeatureVectorSummaryValidator.class)
public List<MaterialSimpleFeatureVectorSummary> getMaterialFeatureVectorsFromAllExperiments(
String sessionToken, MaterialFeaturesManyExpCriteria criteria)
{
......@@ -409,7 +470,9 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public MaterialReplicaFeatureSummaryResult getMaterialFeatureVectorSummary(String sessionToken,
@AuthorizationGuard(guardClass = MaterialFeaturesOneExpPredicate.class)
MaterialFeaturesOneExpCriteria criteria)
{
Session session = getSession(sessionToken);
......@@ -422,36 +485,50 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
// --------- IScreeningOpenbisServer - method signature should be changed with care
@Override
public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(String sessionToken,
List<? extends PlateIdentifier> plates)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException
{
return createScreeningApiImpl(sessionToken).listFeatureVectorDatasets(plates);
}
@Override
public List<ImageDatasetReference> listImageDatasets(String sessionToken,
List<? extends PlateIdentifier> plates)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<ImageDatasetReference> listImageDatasets(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException
{
return createScreeningApiImpl(sessionToken).listImageDatasets(plates);
}
@Override
public List<ImageDatasetReference> listRawImageDatasets(String sessionToken,
List<? extends PlateIdentifier> plates)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<ImageDatasetReference> listRawImageDatasets(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException
{
return createScreeningApiImpl(sessionToken).listRawImageDatasets(plates);
}
@Override
public List<ImageDatasetReference> listSegmentationImageDatasets(String sessionToken,
List<? extends PlateIdentifier> plates)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<ImageDatasetReference> listSegmentationImageDatasets(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException
{
return createScreeningApiImpl(sessionToken).listSegmentationImageDatasets(plates);
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<PlateWellReferenceWithDatasets> listPlateWells(
String sessionToken,
@AuthorizationGuard(guardClass = ExperimentIdentifierPredicate.class)
ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier experimentIdentifer,
MaterialIdentifier materialIdentifier, boolean findDatasets)
{
......@@ -460,6 +537,8 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = PlateWellReferenceWithDatasetsValidator.class)
public List<PlateWellReferenceWithDatasets> listPlateWells(String sessionToken,
MaterialIdentifier materialIdentifier, boolean findDatasets)
{
......@@ -468,58 +547,78 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public List<WellIdentifier> listPlateWells(String sessionToken, PlateIdentifier plateIdentifier)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<WellIdentifier> listPlateWells(
String sessionToken,
@AuthorizationGuard(guardClass = PlateIdentifierPredicate.class) PlateIdentifier plateIdentifier)
{
return createScreeningApiImpl(sessionToken).listPlateWells(plateIdentifier);
}
@Override
public Sample getWellSample(String sessionToken, WellIdentifier wellIdentifier)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public Sample getWellSample(
String sessionToken,
@AuthorizationGuard(guardClass = WellIdentifierPredicate.class) WellIdentifier wellIdentifier)
{
return createScreeningApiImpl(sessionToken).getWellSample(wellIdentifier, true);
}
@Override
public Sample getPlateSample(String sessionToken, PlateIdentifier plateIdentifier)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public Sample getPlateSample(
String sessionToken,
@AuthorizationGuard(guardClass = PlateIdentifierPredicate.class) PlateIdentifier plateIdentifier)
{
return createScreeningApiImpl(sessionToken).getPlateSample(plateIdentifier);
}
@Override
public List<Plate> listPlates(String sessionToken)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = ScreeningPlateValidator.class)
public List<Plate> listPlates(String sessionToken) throws IllegalArgumentException
{
return createScreeningApiImpl(sessionToken).listPlates();
}
@Override
public List<Plate> listPlates(String sessionToken, ExperimentIdentifier experiment)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<Plate> listPlates(
String sessionToken,
@AuthorizationGuard(guardClass = ExperimentIdentifierPredicate.class) ExperimentIdentifier experiment)
throws IllegalArgumentException
{
return createScreeningApiImpl(sessionToken).listPlates(experiment);
}
@Override
public List<ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier> listExperiments(
String sessionToken)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = ScreeningExperimentValidator.class)
public List<ExperimentIdentifier> listExperiments(String sessionToken)
{
return createScreeningApiImpl(sessionToken).listExperiments();
}
@Override
public List<ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier> listExperiments(
String sessionToken, String userId)
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
public List<ExperimentIdentifier> listExperiments(String sessionToken, String userId)
{
return createScreeningApiImpl(sessionToken).listExperiments(userId);
}
@Override
public List<IDatasetIdentifier> getDatasetIdentifiers(String sessionToken,
List<String> datasetCodes)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<IDatasetIdentifier> getDatasetIdentifiers(
String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> datasetCodes)
{
return createScreeningApiImpl(sessionToken).getDatasetIdentifiers(datasetCodes);
}
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public AnalysisProcedures listNumericalDatasetsAnalysisProcedures(String sessionToken,
@AuthorizationGuard(guardClass = ExperimentSearchCriteriaPredicate.class)
ExperimentSearchCriteria experimentSearchCriteria)
{
checkSession(sessionToken);
......@@ -542,8 +641,10 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public List<PlateWellMaterialMapping> listPlateMaterialMapping(String sessionToken,
List<? extends PlateIdentifier> plates,
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<PlateWellMaterialMapping> listPlateMaterialMapping(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates,
MaterialTypeIdentifier materialTypeIdentifierOrNull)
{
return createScreeningApiImpl(sessionToken).listPlateMaterialMapping(plates,
......@@ -594,15 +695,20 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
@Override
public List<PlateMetadata> getPlateMetadataList(String sessionToken,
List<? extends PlateIdentifier> plateIdentifiers) throws IllegalArgumentException
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<PlateMetadata> getPlateMetadataList(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plateIdentifiers)
throws IllegalArgumentException
{
return createScreeningApiImpl(sessionToken).getPlateMetadata(plateIdentifiers);
}
@Override
public ExperimentImageMetadata getExperimentImageMetadata(String sessionToken,
ExperimentIdentifier experimentIdentifer)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ExperimentImageMetadata getExperimentImageMetadata(
String sessionToken,
@AuthorizationGuard(guardClass = ExperimentIdentifierPredicate.class) ExperimentIdentifier experimentIdentifer)
{
checkSession(sessionToken);
return createScreeningApiImpl(sessionToken).getExperimentImageMetadata(experimentIdentifer);
......
screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
+ 1
− 57
View file @ b3ab46f4
......@@ -22,14 +22,6 @@ import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.Capability;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.DataSetTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
......@@ -37,16 +29,9 @@ 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.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
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.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.DatasetReferencePredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.ExperimentSearchCriteriaPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.MaterialExperimentFeatureVectorSummaryValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.MaterialFeaturesOneExpPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellContentValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellSearchCriteriaPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.AnalysisProcedures;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentFeatureVectorSummary;
......@@ -81,18 +66,14 @@ public interface IScreeningServer extends IServer
* image analysis only if one dataset with such a data exist.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public PlateContent getPlateContent(String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
TechId plateId);
/**
* Loads feature vector of specified dataset with one feature specified by name.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public FeatureVectorDataset getFeatureVectorDataset(String sessionToken,
@AuthorizationGuard(guardClass = DatasetReferencePredicate.class)
DatasetReference dataset, CodeAndLabel featureName);
/**
......@@ -100,9 +81,7 @@ public interface IScreeningServer extends IServer
*/
// TODO can return null
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public FeatureVectorValues getWellFeatureVectorValues(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
String datasetCode, String datastoreCode, WellLocation wellLocation);
/**
......@@ -110,9 +89,7 @@ public interface IScreeningServer extends IServer
* specified dataset, which is supposed to contain images in BDS-HCS format.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public PlateImages getPlateContentForDataset(String sessionToken,
@AuthorizationGuard(guardClass = DataSetTechIdPredicate.class)
TechId datasetId);
/**
......@@ -120,10 +97,7 @@ public interface IScreeningServer extends IServer
* image dataset and feature vectors.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = WellContentValidator.class)
public List<WellContent> listPlateWells(String sessionToken,
@AuthorizationGuard(guardClass = WellSearchCriteriaPredicate.class)
WellSearchCriteria materialCriteria);
/**
......@@ -133,9 +107,7 @@ public interface IScreeningServer extends IServer
* the whole well is ignored.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<WellReplicaImage> listWellImages(String sessionToken, TechId materialId,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
TechId experimentId);
/**
......@@ -144,9 +116,7 @@ public interface IScreeningServer extends IServer
* specified experiment(s) will be returned.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<Material> listMaterials(String sessionToken,
@AuthorizationGuard(guardClass = WellSearchCriteriaPredicate.class)
WellSearchCriteria materialCriteria);
/**
......@@ -155,33 +125,23 @@ public interface IScreeningServer extends IServer
* @param materialType
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<Material> listExperimentMaterials(String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
TechId experimentId, MaterialType materialType);
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public LogicalImageInfo getImageDatasetInfo(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
String datasetCode, String datastoreCode, WellLocation wellLocationOrNull);
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ImageDatasetEnrichedReference getImageDatasetReference(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
String datasetCode, String datastoreCode);
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
List<ImageResolution> getImageDatasetResolutions(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class)
public List<ImageResolution> getImageDatasetResolutions(String sessionToken,
String datasetCode, String datastoreCode);
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ImageSampleContent getImageDatasetInfosForSample(String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
TechId sampleId, WellLocation wellLocationOrNull);
/**
......@@ -192,40 +152,32 @@ public interface IScreeningServer extends IServer
* uniquely identified by given <var>sampleId</var> does not exist.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public SampleParentWithDerived getSampleInfo(final String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class)
final TechId sampleId) throws UserFailureException;
/**
* For given {@link TechId} returns the corresponding {@link ExternalData}.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ExternalData getDataSetInfo(String sessionToken,
@AuthorizationGuard(guardClass = DataSetTechIdPredicate.class)
TechId datasetId);
/**
* For given {@link TechId} returns the corresponding {@link Material}.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public Material getMaterialInfo(String sessionToken, TechId materialId);
/**
* Returns vocabulary with given code.
*/
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public Vocabulary getVocabulary(String sessionToken, String code) throws UserFailureException;
/**
* Registers the contents of an uploaded library.
*/
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_ADMIN)
@Capability("WRITE_EXPERIMENT_SAMPLE_MATERIAL")
public void registerLibrary(String sessionToken, String userEmail,
List<NewMaterial> newGenesOrNull, List<NewMaterial> newOligosOrNull,
List<NewSamplesWithTypes> newSamplesWithType);
......@@ -235,9 +187,7 @@ public interface IScreeningServer extends IServer
* materials.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ExperimentFeatureVectorSummary getExperimentFeatureVectorSummary(String sessionToken,
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
TechId experimentId, AnalysisProcedureCriteria analysisProcedureCriteria);
/**
......@@ -245,17 +195,13 @@ public interface IScreeningServer extends IServer
* material.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public MaterialReplicaFeatureSummaryResult getMaterialFeatureVectorSummary(String sessionToken,
@AuthorizationGuard(guardClass = MaterialFeaturesOneExpPredicate.class)
MaterialFeaturesOneExpCriteria criteria);
/**
* Returns feature vectors from all experiments for a specified material.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = MaterialExperimentFeatureVectorSummaryValidator.class)
public List<MaterialSimpleFeatureVectorSummary> getMaterialFeatureVectorsFromAllExperiments(
String sessionToken, MaterialFeaturesManyExpCriteria criteria);
......@@ -271,9 +217,7 @@ public interface IScreeningServer extends IServer
* </p>
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public AnalysisProcedures listNumericalDatasetsAnalysisProcedures(String sessionToken,
@AuthorizationGuard(guardClass = ExperimentSearchCriteriaPredicate.class)
ExperimentSearchCriteria experimentSearchCriteria);
}
screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
+ 26
− 81
View file @ b3ab46f4
......@@ -23,18 +23,6 @@ import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.api.IRpcService;
import ch.systemsx.cisd.common.api.MinimalMinorVersion;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodeCollectionPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.ExperimentIdentifierPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.PlateIdentifierPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.PlateWellReferenceWithDatasetsValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.ScreeningExperimentValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.ScreeningPlateListReadOnlyPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.ScreeningPlateValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.internal.authorization.WellIdentifierPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentImageMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
......@@ -71,7 +59,7 @@ public interface IScreeningApiServer extends IRpcService
* Service part of the URL to access this service remotely.
*/
public static final String SERVICE_URL = "/rmi-" + SERVICE_NAME + "-api-v1";
public static final String JSON_SERVICE_URL = SERVICE_URL + ".json";
/**
......@@ -94,22 +82,16 @@ public interface IScreeningApiServer extends IRpcService
* hierarchical context (space, project, experiment).
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = ScreeningPlateValidator.class)
List<Plate> listPlates(String sessionToken) throws IllegalArgumentException;
/**
* Return the list of all plates assigned to the given experiment.
*
* @since 1.5
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(5)
List<Plate> listPlates(
String sessionToken,
@AuthorizationGuard(guardClass = ExperimentIdentifierPredicate.class) ExperimentIdentifier experiment)
List<Plate> listPlates(String sessionToken, ExperimentIdentifier experiment)
throws IllegalArgumentException;
/**
......@@ -119,12 +101,9 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.8
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(8)
List<PlateMetadata> getPlateMetadataList(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException;
List<PlateMetadata> getPlateMetadataList(String sessionToken,
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
* Return the list of all visible experiments, along with their hierarchical context (space,
......@@ -133,8 +112,6 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.1
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = ScreeningExperimentValidator.class)
@MinimalMinorVersion(1)
List<ExperimentIdentifier> listExperiments(String sessionToken);
......@@ -145,7 +122,6 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.6
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
@MinimalMinorVersion(6)
List<ExperimentIdentifier> listExperiments(String sessionToken, String userId);
......@@ -154,22 +130,16 @@ public interface IScreeningApiServer extends IRpcService
* sets containing feature vectors for each of these plates.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException;
List<FeatureVectorDatasetReference> listFeatureVectorDatasets(String sessionToken,
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
* For a given set of plates provide the list of all data sets containing images for each of
* these plates.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
List<ImageDatasetReference> listImageDatasets(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException;
List<ImageDatasetReference> listImageDatasets(String sessionToken,
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
* For a given set of plates provide the list of all data sets containing raw images for each of
......@@ -178,12 +148,9 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.6
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(6)
List<ImageDatasetReference> listRawImageDatasets(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException;
List<ImageDatasetReference> listRawImageDatasets(String sessionToken,
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
* For a given set of plates provide the list of all data sets containing segmentation images
......@@ -192,21 +159,15 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.6
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(6)
List<ImageDatasetReference> listSegmentationImageDatasets(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates)
throws IllegalArgumentException;
List<ImageDatasetReference> listSegmentationImageDatasets(String sessionToken,
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
* Converts a given list of dataset codes to dataset identifiers.
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
List<IDatasetIdentifier> getDatasetIdentifiers(
String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodeCollectionPredicate.class) List<String> datasetCodes);
List<IDatasetIdentifier> getDatasetIdentifiers(String sessionToken, List<String> datasetCodes);
/**
* For the given <var>experimentIdentifier</var>, find all plate locations that are connected to
......@@ -216,12 +177,10 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.1
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(1)
List<PlateWellReferenceWithDatasets> listPlateWells(
String sessionToken,
@AuthorizationGuard(guardClass = ExperimentIdentifierPredicate.class) ExperimentIdentifier experimentIdentifer,
MaterialIdentifier materialIdentifier, boolean findDatasets);
List<PlateWellReferenceWithDatasets> listPlateWells(String sessionToken,
ExperimentIdentifier experimentIdentifer, MaterialIdentifier materialIdentifier,
boolean findDatasets);
/**
* For the given <var>materialIdentifier</var>, find all plate locations that are connected to
......@@ -231,8 +190,6 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.2
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@ReturnValueFilter(validatorClass = PlateWellReferenceWithDatasetsValidator.class)
@MinimalMinorVersion(2)
List<PlateWellReferenceWithDatasets> listPlateWells(String sessionToken,
MaterialIdentifier materialIdentifier, boolean findDatasets);
......@@ -243,35 +200,27 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.3
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(3)
public List<WellIdentifier> listPlateWells(
String sessionToken,
@AuthorizationGuard(guardClass = PlateIdentifierPredicate.class) PlateIdentifier plateIdentifier);
public List<WellIdentifier> listPlateWells(String sessionToken, PlateIdentifier plateIdentifier);
/**
* For a given <var>wellIdentifier</var>, return the corresponding {@link Sample} including properties.
* For a given <var>wellIdentifier</var>, return the corresponding {@link Sample} including
* properties.
*
* @since 1.3
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(3)
public Sample getWellSample(
String sessionToken,
@AuthorizationGuard(guardClass = WellIdentifierPredicate.class) WellIdentifier wellIdentifier);
public Sample getWellSample(String sessionToken, WellIdentifier wellIdentifier);
/**
* For a given <var>plateIdentifier</var>, return the corresponding {@link Sample}.
*
* @since 1.7
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(7)
public Sample getPlateSample(
String sessionToken,
@AuthorizationGuard(guardClass = PlateIdentifierPredicate.class) PlateIdentifier plateIdentifier);
public Sample getPlateSample(String sessionToken, PlateIdentifier plateIdentifier);
/**
* For a given list of <var>plates</var>, return the mapping of plate wells to materials
......@@ -284,11 +233,9 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.2
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(2)
List<PlateWellMaterialMapping> listPlateMaterialMapping(
String sessionToken,
@AuthorizationGuard(guardClass = ScreeningPlateListReadOnlyPredicate.class) List<? extends PlateIdentifier> plates,
List<PlateWellMaterialMapping> listPlateMaterialMapping(String sessionToken,
List<? extends PlateIdentifier> plates,
MaterialTypeIdentifier materialTypeIdentifierOrNull);
/**
......@@ -297,10 +244,8 @@ public interface IScreeningApiServer extends IRpcService
* @since 1.9
*/
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
@MinimalMinorVersion(1)
ExperimentImageMetadata getExperimentImageMetadata(
String sessionToken,
@AuthorizationGuard(guardClass = ExperimentIdentifierPredicate.class) ExperimentIdentifier experimentIdentifer);
ExperimentImageMetadata getExperimentImageMetadata(String sessionToken,
ExperimentIdentifier experimentIdentifer);
}
screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ServerInterfaceRegressionTest.java → screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/ServerInterfaceRegressionTest.java
+ 11
− 2
View file @ b3ab46f4
......@@ -14,11 +14,13 @@
* limitations under the License.
*/
package ch.systemsx.cisd.openbis.plugin.screening.shared;
package ch.systemsx.cisd.openbis.plugin.screening.server;
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.RegressionTestCase;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
/**
* @author Tomasz Pylak
......@@ -28,6 +30,13 @@ public class ServerInterfaceRegressionTest extends RegressionTestCase
@Test
public void testServerAnnotations()
{
assertMandatoryMethodAnnotations(IScreeningServer.class);
assertMandatoryMethodAnnotations(IScreeningServer.class, ScreeningServer.class);
}
@Test
public void testApiServerAnnotations()
{
assertMandatoryMethodAnnotations(IScreeningApiServer.class, ScreeningServer.class,
"tryLoginScreening: RolesAllowed\n" + "logoutScreening: RolesAllowed\n");
}
}
screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/ScreeningServerAuthorizationTest.java 0 → 100644
+ 127
− 0
View file @ b3ab46f4
/*
* 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.screening.systemtests;
import java.util.Collections;
import java.util.List;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
import ch.systemsx.cisd.openbis.generic.server.ICommonServerForInternalUse;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Grantee;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSamplesWithTypes;
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.Space;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
/**
*
*
* @author Franz-Josef Elmer
*/
public class ScreeningServerAuthorizationTest extends AbstractScreeningSystemTestCase
{
private static final String TEST_USER = "test-user";
private static final String SPACE_CODE = "CISD";
private ICommonServerForInternalUse commonServer;
private IScreeningServer screeningServer;
private IScreeningApiServer screeningApiServer;
private String userSessionToken;
@BeforeMethod
public void setUp()
{
commonServer =
(ICommonServerForInternalUse) applicationContext
.getBean(ch.systemsx.cisd.openbis.generic.shared.ResourceNames.COMMON_SERVER);
Object serverBean = applicationContext
.getBean(ResourceNames.SCREENING_PLUGIN_SERVER);
screeningServer = (IScreeningServer) serverBean;
screeningApiServer = (IScreeningApiServer) serverBean;
String sessionToken = commonServer.tryToAuthenticateAsSystem().getSessionToken();
if (hasSpace(sessionToken, SPACE_CODE) == false)
{
commonServer.registerSpace(sessionToken, SPACE_CODE, null);
}
if (hasPerson(sessionToken, TEST_USER) == false)
{
commonServer.registerPerson(sessionToken, TEST_USER);
Grantee grantee = Grantee.createPerson(TEST_USER);
commonServer.registerSpaceRole(sessionToken, RoleCode.OBSERVER, new SpaceIdentifier(
SPACE_CODE), grantee);
}
userSessionToken = commonServer.tryToAuthenticate(TEST_USER, "abc").getSessionToken();
}
private boolean hasSpace(String sessionToken, String spaceCode)
{
List<Space> spaces =
commonServer.listSpaces(sessionToken, DatabaseInstanceIdentifier.HOME_INSTANCE);
for (Space space : spaces)
{
if (space.getCode().equals(spaceCode))
{
return true;
}
}
return false;
}
private boolean hasPerson(String sessionToken, String personID)
{
List<Person> persons = commonServer.listPersons(sessionToken);
for (Person person : persons)
{
if (person.getUserId().equals(personID))
{
return true;
}
}
return false;
}
@Test(expectedExceptions = AuthorizationFailureException.class)
public void testSetSessionUserFailsBecauseOfNonAuthorized()
{
screeningServer.setSessionUser(userSessionToken, "system");
}
@Test(expectedExceptions = AuthorizationFailureException.class)
public void testListPlatesFailsBecauseOfAuthorization()
{
screeningApiServer.listPlates(userSessionToken, new ExperimentIdentifier("a", "b", "c", "d"));
}
@Test(expectedExceptions = AuthorizationFailureException.class)
public void testRegisterLibraryFailsBecauseOfNonAuthorized()
{
screeningServer.registerLibrary(userSessionToken, "",
Collections.<NewMaterial> emptyList(), Collections.<NewMaterial> emptyList(),
Collections.<NewSamplesWithTypes> emptyList());
}
}
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