From 4106fea342a63cea362b623c3f5b80dceb4baf16 Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Mon, 3 Dec 2012 09:12:01 +0000
Subject: [PATCH] SP-416 BIS-270 extract read only methods from transaction to
search service
SVN: 27823
---
.../api/v1/impl/AuthorizationHelper.java | 16 ++-
.../v2/IDataSetRegistrationTransactionV2.java | 20 ++-
.../api/v2/impl/AbstractTransactionState.java | 12 --
.../impl/DataSetRegistrationTransaction.java | 47 ++-----
.../api/v2/impl/SearchService.java | 86 ++++++++++++
...capsulatedFilteredBasicOpenBISService.java | 124 +++++++++++++-----
.../server/EncapsulatedOpenBISService.java | 7 +
.../IEncapsulatedBasicOpenBISService.java | 54 ++++++++
.../shared/IEncapsulatedOpenBISService.java | 59 +--------
.../api/internal/v2/ISearchService.java | 53 ++++++++
10 files changed, 337 insertions(+), 141 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AuthorizationHelper.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AuthorizationHelper.java
index a06983aa502..ae246ce1f67 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AuthorizationHelper.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AuthorizationHelper.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
+import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
@@ -62,9 +63,20 @@ public class AuthorizationHelper
String user, List<String> codes);
}
+ /**
+ * Returns null if given entity is not visible, or the entity if it is visible
+ */
+ public static <T> T filterToVisible(IEncapsulatedOpenBISService openBisService, String user,
+ T entity, IMapper<T, String> codeMapper, EntityKind entityKind)
+ {
+ List<String> visible =
+ entityKind.filterToVisible(openBisService, user,
+ Collections.singletonList(codeMapper.map(entity)));
+ return visible.size() == 1 ? entity : null;
+ }
+
public static <T> List<T> filterToVisible(IEncapsulatedOpenBISService openBisService,
- String user, List<T> entities,
- IMapper<T, String> codeMapper, EntityKind entityKind)
+ String user, List<T> entities, IMapper<T, String> codeMapper, EntityKind entityKind)
{
// create a list of codes
List<String> codes = new LinkedList<String>();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/IDataSetRegistrationTransactionV2.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/IDataSetRegistrationTransactionV2.java
index e2a8512b50c..9311ca858b2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/IDataSetRegistrationTransactionV2.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/IDataSetRegistrationTransactionV2.java
@@ -22,6 +22,7 @@ import net.lemnik.eodsql.DynamicTransactionQuery;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationContext;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.impl.SearchService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IDataSetImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExternalDataManagementSystemImmutable;
@@ -59,7 +60,9 @@ public interface IDataSetRegistrationTransactionV2
* Get a data set from the openBIS AS. Returns null if the data set does not exist.
*
* @return A data set or null
+ * @deprecated Use {@link SearchService#getDataSet(String)}
*/
+ @Deprecated
IDataSetImmutable getDataSet(String dataSetCode);
/**
@@ -81,7 +84,9 @@ public interface IDataSetRegistrationTransactionV2
* Get a sample from the openBIS AS. Returns null if the sample does not exist.
*
* @return A sample or null
+ * @deprecated Use {@link SearchService#getSample(String)}
*/
+ @Deprecated
ISampleImmutable getSample(String sampleIdentifierString);
/**
@@ -118,7 +123,10 @@ public interface IDataSetRegistrationTransactionV2
/**
* Get an experiment from the openBIS AS.
+ *
+ * @deprecated Use {@link SearchService#getExperiment(String)}
*/
+ @Deprecated
IExperimentImmutable getExperiment(String experimentIdentifierString);
/**
@@ -152,7 +160,9 @@ public interface IDataSetRegistrationTransactionV2
* Get a project from the openBIS AS. Returns null if the project does not exist.
*
* @return A project or null
+ * @deprecated Use {@link SearchService#getProject(String)}
*/
+ @Deprecated
IProjectImmutable getProject(String projectIdentifier);
/**
@@ -180,7 +190,9 @@ public interface IDataSetRegistrationTransactionV2
* Get a space from the openBIS AS. Returns null if the space does not exist.
*
* @return A space or null
+ * @deprecated Use {@link SearchService#getSpace(String)}
*/
+ @Deprecated
ISpaceImmutable getSpace(String spaceCode);
/**
@@ -194,7 +206,9 @@ public interface IDataSetRegistrationTransactionV2
* Get a material from the openBIS AS. Returns null if the material does not exist.
*
* @return A material or null
+ * @deprecated Use {@link SearchService#getMaterial(String)}
*/
+ @Deprecated
IMaterialImmutable getMaterial(String identifier);
/**
@@ -243,14 +257,14 @@ public interface IDataSetRegistrationTransactionV2
/**
* Only allowed when the user is available.
*
- * @return Read-only metaproject with given name for current user.
+ * @return metaproject with given name for current user.
*/
IMetaproject getMetaproject(String name);
/**
* Only allowed when the user is not available.
*
- * @return Read-only metaproject with given name for specified user.
+ * @return metaproject with given name for specified user.
*/
IMetaproject getMetaproject(String name, String ownerId);
@@ -258,7 +272,9 @@ public interface IDataSetRegistrationTransactionV2
* Get the read-only vocabulary with given code
*
* @returns null if the vocabulary is not found
+ * @deprecated Use {@link SearchService#getVocabulary(String)}
*/
+ @Deprecated
IVocabularyImmutable getVocabulary(String code);
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/AbstractTransactionState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/AbstractTransactionState.java
index aa61040dfec..fc8595803d2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/AbstractTransactionState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/AbstractTransactionState.java
@@ -407,18 +407,6 @@ public abstract class AbstractTransactionState<T extends DataSetInformation>
}
}
- public IDataSetImmutable getDataSet(String dataSetCode)
- {
- ExternalData dataSet = openBisService.tryGetDataSet(dataSetCode);
- if (dataSet == null)
- {
- return null;
- } else
- {
- return new DataSetImmutable(dataSet, openBisService);
- }
- }
-
public IDataSetUpdatable getDataSetForUpdate(String dataSetCode)
{
// See if we already have an updatable version of the data set
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSetRegistrationTransaction.java
index 8edf2d99385..c9fbe9b92db 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/DataSetRegistrationTransaction.java
@@ -78,13 +78,6 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInform
import ch.systemsx.cisd.openbis.generic.shared.basic.EntityOperationsState;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
* The implementation of a transaction. This class is designed to be used in one thread.
@@ -275,7 +268,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
@Override
public IDataSetImmutable getDataSet(String dataSetCode)
{
- return getStateAsLiveState().getDataSet(dataSetCode);
+ return getSearchServiceUnfiltered().getDataSet(dataSetCode);
}
@Override
@@ -293,11 +286,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
@Override
public ISampleImmutable getSample(String sampleIdentifierString)
{
- SampleIdentifier sampleIdentifier =
- new SampleIdentifierFactory(sampleIdentifierString).createIdentifier();
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sampleOrNull =
- openBisService.tryGetSampleWithExperiment(sampleIdentifier);
- return (null == sampleOrNull) ? null : new SampleImmutable(sampleOrNull);
+ return getSearchServiceUnfiltered().getSample(sampleIdentifierString);
}
@Override
@@ -339,11 +328,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
@Override
public IExperimentImmutable getExperiment(String experimentIdentifierString)
{
- ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifierFactory(experimentIdentifierString).createIdentifier();
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experimentOrNull =
- openBisService.tryGetExperiment(experimentIdentifier);
- return (null == experimentOrNull) ? null : new ExperimentImmutable(experimentOrNull);
+ return getSearchServiceUnfiltered().getExperiment(experimentIdentifierString);
}
@Override
@@ -361,13 +346,9 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
}
@Override
- public IProjectImmutable getProject(String projectIdentifierString)
+ public IProjectImmutable getProject(String projectIdentifier)
{
- ProjectIdentifier projectIdentifier =
- new ProjectIdentifierFactory(projectIdentifierString).createIdentifier();
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project projectOrNull =
- openBisService.tryGetProject(projectIdentifier);
- return (null == projectOrNull) ? null : new ProjectImmutable(projectOrNull);
+ return getSearchServiceUnfiltered().getProject(projectIdentifier);
}
@Override
@@ -391,31 +372,19 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
@Override
public ISpaceImmutable getSpace(String spaceCode)
{
- SpaceIdentifier spaceIdentifier = new SpaceIdentifier(spaceCode);
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space spaceOrNull =
- openBisService.tryGetSpace(spaceIdentifier);
- return (null == spaceOrNull) ? null : new SpaceImmutable(spaceOrNull);
+ return getSearchServiceUnfiltered().getSpace(spaceCode);
}
@Override
public IMaterialImmutable getMaterial(String materialCode, String materialType)
{
- MaterialIdentifier materialIdentifier = new MaterialIdentifier(materialCode, materialType);
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material materialOrNull =
- openBisService.tryGetMaterial(materialIdentifier);
- return (null == materialOrNull) ? null : new MaterialImmutable(materialOrNull);
+ return getSearchServiceUnfiltered().getMaterial(materialCode, materialType);
}
@Override
public IMaterialImmutable getMaterial(String identifier)
{
- MaterialIdentifier materialId = MaterialIdentifier.tryParseIdentifier(identifier);
- if (materialId == null)
- {
- throw new IllegalArgumentException("Incorrect material identifier format " + identifier
- + ". Expected code (type)");
- }
- return getMaterial(materialId.getCode(), materialId.getTypeCode());
+ return getSearchServiceUnfiltered().getMaterial(identifier);
}
@Override
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/SearchService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/SearchService.java
index 4fdf53af288..ed1a2620a80 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/SearchService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/SearchService.java
@@ -35,9 +35,11 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMaterialImmu
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMetaprojectAssignments;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMetaprojectContent;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IMetaprojectImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IProjectImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IPropertyAssignmentImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISpaceImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IVocabularyImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.MaterialIdentifierCollection;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
@@ -54,8 +56,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
@@ -70,6 +77,25 @@ public class SearchService implements ISearchService
this.openBisService = openBisService;
}
+ @Override
+ public IProjectImmutable getProject(String projectIdentifierString)
+ {
+ ProjectIdentifier projectIdentifier =
+ new ProjectIdentifierFactory(projectIdentifierString).createIdentifier();
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project projectOrNull =
+ openBisService.tryGetProject(projectIdentifier);
+ return (null == projectOrNull) ? null : new ProjectImmutable(projectOrNull);
+ }
+
+ @Override
+ public ISpaceImmutable getSpace(String spaceCode)
+ {
+ SpaceIdentifier spaceIdentifier = new SpaceIdentifier(spaceCode);
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space spaceOrNull =
+ openBisService.tryGetSpace(spaceIdentifier);
+ return (null == spaceOrNull) ? null : new SpaceImmutable(spaceOrNull);
+ }
+
@Override
public List<IExperimentImmutable> listExperiments(String projectIdentifierString)
{
@@ -290,6 +316,12 @@ public class SearchService implements ISearchService
return ConversionUtils.convertToMetaprojectsImmutable(metaprojects);
}
+ @Override
+ public IMetaprojectImmutable getMetaproject(String name)
+ {
+ return new MetaprojectImmutable(openBisService.tryGetMetaproject(name));
+ }
+
@Override
public IMetaprojectAssignments getMetaprojectAssignments(String name)
{
@@ -305,4 +337,58 @@ public class SearchService implements ISearchService
openBisService.listMetaprojectsForEntity(entity.getEntityId());
return ConversionUtils.convertToMetaprojectsImmutable(metaprojects);
}
+
+ @Override
+ public IDataSetImmutable getDataSet(String dataSetCode)
+ {
+ ExternalData dataSet = openBisService.tryGetDataSet(dataSetCode);
+ if (dataSet == null)
+ {
+ return null;
+ } else
+ {
+ return new DataSetImmutable(dataSet, openBisService);
+ }
+ }
+
+ @Override
+ public IExperimentImmutable getExperiment(String experimentIdentifierString)
+ {
+ ExperimentIdentifier experimentIdentifier =
+ new ExperimentIdentifierFactory(experimentIdentifierString).createIdentifier();
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experimentOrNull =
+ openBisService.tryGetExperiment(experimentIdentifier);
+ return (null == experimentOrNull) ? null : new ExperimentImmutable(experimentOrNull);
+ }
+
+ @Override
+ public ISampleImmutable getSample(String sampleIdentifierString)
+ {
+ SampleIdentifier sampleIdentifier =
+ new SampleIdentifierFactory(sampleIdentifierString).createIdentifier();
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sampleOrNull =
+ openBisService.tryGetSampleWithExperiment(sampleIdentifier);
+ return (null == sampleOrNull) ? null : new SampleImmutable(sampleOrNull);
+ }
+
+ @Override
+ public IMaterialImmutable getMaterial(String materialCode, String materialType)
+ {
+ MaterialIdentifier materialIdentifier = new MaterialIdentifier(materialCode, materialType);
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material materialOrNull =
+ openBisService.tryGetMaterial(materialIdentifier);
+ return (null == materialOrNull) ? null : new MaterialImmutable(materialOrNull);
+ }
+
+ @Override
+ public IMaterialImmutable getMaterial(String identifier)
+ {
+ MaterialIdentifier materialId = MaterialIdentifier.tryParseIdentifier(identifier);
+ if (materialId == null)
+ {
+ throw new IllegalArgumentException("Incorrect material identifier format " + identifier
+ + ". Expected code (type)");
+ }
+ return getMaterial(materialId.getCode(), materialId.getTypeCode());
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedFilteredBasicOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedFilteredBasicOpenBISService.java
index 1c6db5b7534..cec395ee9a9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedFilteredBasicOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedFilteredBasicOpenBISService.java
@@ -35,13 +35,19 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MetaprojectAssignments;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MetaprojectAssignmentsFetchOption;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
/**
@@ -71,6 +77,47 @@ public class EncapsulatedFilteredBasicOpenBISService implements IEncapsulatedBas
this.userName = userName;
}
+ private final static IMapper<ExternalData, String> externalDataCodeMapper =
+ new IMapper<ExternalData, String>()
+ {
+ @Override
+ public String map(ExternalData item)
+ {
+ return item.getCode();
+ }
+ };
+
+ private final static IMapper<Sample, String> sampleIdMapper = new IMapper<Sample, String>()
+ {
+ @Override
+ public String map(Sample item)
+ {
+ return item.getIdentifier();
+ }
+ };
+
+ private final static IMapper<Experiment, String> experimentIdMapper =
+ new IMapper<Experiment, String>()
+ {
+ @Override
+ public String map(Experiment item)
+ {
+ return item.getIdentifier();
+ }
+ };
+
+ @Override
+ public Project tryGetProject(ProjectIdentifier projectIdentifier) throws UserFailureException
+ {
+ return encapsulatedService.tryGetProject(projectIdentifier);
+ }
+
+ @Override
+ public Space tryGetSpace(SpaceIdentifier spaceIdentifier) throws UserFailureException
+ {
+ return encapsulatedService.tryGetSpace(spaceIdentifier);
+ }
+
@Override
public DataSetTypeWithVocabularyTerms getDataSetType(String dataSetTypeCode)
{
@@ -81,58 +128,52 @@ public class EncapsulatedFilteredBasicOpenBISService implements IEncapsulatedBas
@Override
public List<Sample> searchForSamples(SearchCriteria searchCriteria)
{
- IMapper<Sample, String> idMapper = new IMapper<Sample, String>()
- {
- @Override
- public String map(Sample item)
- {
- return item.getIdentifier();
- }
- };
List<Sample> samples = etlService.searchForSamples(systemSessionToken, searchCriteria);
return AuthorizationHelper.filterToVisible(encapsulatedService, userName, samples,
- idMapper, AuthorizationHelper.EntityKind.SAMPLE);
+ sampleIdMapper, AuthorizationHelper.EntityKind.SAMPLE);
+ }
+ @Override
+ @ManagedAuthentication
+ public Sample tryGetSampleWithExperiment(SampleIdentifier sampleIdentifier)
+ throws UserFailureException
+ {
+ Sample sample = encapsulatedService.tryGetSampleWithExperiment(sampleIdentifier);
+ return AuthorizationHelper.filterToVisible(encapsulatedService, userName, sample,
+ sampleIdMapper, AuthorizationHelper.EntityKind.SAMPLE);
}
@Override
public List<ExternalData> searchForDataSets(SearchCriteria searchCriteria)
{
- IMapper<ExternalData, String> codeMapper = new IMapper<ExternalData, String>()
- {
- @Override
- public String map(ExternalData item)
- {
- return item.getCode();
- }
- };
-
List<ExternalData> datasets =
etlService.searchForDataSets(systemSessionToken, searchCriteria);
return AuthorizationHelper.filterToVisible(encapsulatedService, userName, datasets,
- codeMapper, AuthorizationHelper.EntityKind.DATA_SET);
+ externalDataCodeMapper, AuthorizationHelper.EntityKind.DATA_SET);
}
@Override
public List<Experiment> listExperiments(ProjectIdentifier projectIdentifier)
{
- IMapper<Experiment, String> codeMapper = new IMapper<Experiment, String>()
- {
- @Override
- public String map(Experiment item)
- {
- return item.getIdentifier();
- }
- };
- List<Experiment> datasets =
+ List<Experiment> experiments =
etlService.listExperiments(systemSessionToken, projectIdentifier);
- return AuthorizationHelper.filterToVisible(encapsulatedService, userName, datasets,
- codeMapper, AuthorizationHelper.EntityKind.EXPERIMENT);
+ return AuthorizationHelper.filterToVisible(encapsulatedService, userName, experiments,
+ experimentIdMapper, AuthorizationHelper.EntityKind.EXPERIMENT);
+ }
+
+ @Override
+ @ManagedAuthentication
+ public Experiment tryGetExperiment(ExperimentIdentifier experimentIdentifier)
+ throws UserFailureException
+ {
+ Experiment experiment = encapsulatedService.tryGetExperiment(experimentIdentifier);
+ return AuthorizationHelper.filterToVisible(encapsulatedService, userName, experiment,
+ experimentIdMapper, AuthorizationHelper.EntityKind.EXPERIMENT);
}
@Override
@@ -154,6 +195,13 @@ public class EncapsulatedFilteredBasicOpenBISService implements IEncapsulatedBas
return etlService.listMaterials(systemSessionToken, criteria, withProperties);
}
+ @Override
+ @ManagedAuthentication
+ public Material tryGetMaterial(MaterialIdentifier materialIdentifier)
+ {
+ return encapsulatedService.tryGetMaterial(materialIdentifier);
+ }
+
@Override
public List<? extends EntityTypePropertyType<?>> listPropertyDefinitionsForEntityType(
String code, EntityKind entityKind)
@@ -168,7 +216,12 @@ public class EncapsulatedFilteredBasicOpenBISService implements IEncapsulatedBas
}
@Override
- @ManagedAuthentication
+ public Metaproject tryGetMetaproject(String name)
+ {
+ return etlService.tryGetMetaproject(systemSessionToken, name, userName);
+ }
+
+ @Override
public MetaprojectAssignments getMetaprojectAssignments(String name)
{
return etlService.getMetaprojectAssignments(systemSessionToken, name, userName,
@@ -176,9 +229,16 @@ public class EncapsulatedFilteredBasicOpenBISService implements IEncapsulatedBas
}
@Override
- @ManagedAuthentication
public List<Metaproject> listMetaprojectsForEntity(IObjectId entityId)
{
return etlService.listMetaprojectsForEntity(systemSessionToken, userName, entityId);
}
+
+ @Override
+ public ExternalData tryGetDataSet(String dataSetCode) throws UserFailureException
+ {
+ ExternalData data = encapsulatedService.tryGetDataSet(dataSetCode);
+ return AuthorizationHelper.filterToVisible(encapsulatedService, userName, data,
+ externalDataCodeMapper, AuthorizationHelper.EntityKind.DATA_SET);
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index ade9004e3fa..3e25a0c7e1d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -820,6 +820,13 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
"Listing metaprojects is available only for the user-filtered version of service");
}
+ @Override
+ public Metaproject tryGetMetaproject(String name)
+ {
+ throw new UnsupportedOperationException(
+ "Getting metaproject is available only for the user-filtered version of service");
+ }
+
@Override
@ManagedAuthentication
public MetaprojectAssignments getMetaprojectAssignments(String name)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedBasicOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedBasicOpenBISService.java
index d11db413829..c350b7728b8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedBasicOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedBasicOpenBISService.java
@@ -29,12 +29,18 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MetaprojectAssignments;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
* The basic subset of the {@link IEncapsulatedOpenBISService}, that requires only service and a
@@ -44,6 +50,18 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
*/
public interface IEncapsulatedBasicOpenBISService
{
+ /**
+ * Tries to get the space of specified identifier or <code>null</code> if not found.
+ */
+ @ManagedAuthentication
+ public Space tryGetSpace(SpaceIdentifier spaceIdentifier) throws UserFailureException;
+
+ /**
+ * Tries to get the project of specified identifier or <code>null</code> if not found.
+ */
+ @ManagedAuthentication
+ public Project tryGetProject(ProjectIdentifier projectIdentifier) throws UserFailureException;
+
/**
* Returns the data set type together with assigned property types for the specified data set
* type code.
@@ -51,12 +69,29 @@ public interface IEncapsulatedBasicOpenBISService
@ManagedAuthentication
public DataSetTypeWithVocabularyTerms getDataSetType(String dataSetTypeCode);
+ /**
+ * Tries to get the data set for the specified data set code, using the ETL server's session
+ * token.
+ */
+ @ManagedAuthentication
+ public ExternalData tryGetDataSet(final String dataSetCode) throws UserFailureException;
+
/**
* {@link IETLLIMSService#searchForSamples(String, SearchCriteria)}
*/
@ManagedAuthentication
public List<Sample> searchForSamples(SearchCriteria searchCriteria);
+ /**
+ * Gets a sample with the specified identifier. Sample is enriched with properties and the
+ * experiment with properties.
+ *
+ * @return <code>null</code> if no sample could be found for given <var>sampleIdentifier</var>.
+ */
+ @ManagedAuthentication
+ public Sample tryGetSampleWithExperiment(final SampleIdentifier sampleIdentifier)
+ throws UserFailureException;
+
/**
* {@link IETLLIMSService#searchForDataSets(String, SearchCriteria)}
*/
@@ -69,6 +104,13 @@ public interface IEncapsulatedBasicOpenBISService
@ManagedAuthentication
public List<Experiment> listExperiments(ProjectIdentifier projectIdentifier);
+ /**
+ * Tries to get the experiment of specified identifier or <code>null</code> if not found.
+ */
+ @ManagedAuthentication
+ public Experiment tryGetExperiment(ExperimentIdentifier experimentIdentifier)
+ throws UserFailureException;
+
/**
* Lists vocabulary terms.
*/
@@ -90,6 +132,12 @@ public interface IEncapsulatedBasicOpenBISService
@ManagedAuthentication
public List<Material> listMaterials(ListMaterialCriteria criteria, boolean withProperties);
+ /**
+ * For given {@link MaterialIdentifier} returns the corresponding {@link Material}.
+ */
+ @ManagedAuthentication
+ public Material tryGetMaterial(MaterialIdentifier materialIdentifier);
+
/**
* List property definitions for the given entity type
*/
@@ -104,6 +152,12 @@ public interface IEncapsulatedBasicOpenBISService
@ManagedAuthentication
public List<Metaproject> listMetaprojects();
+ /**
+ * For given (@code name} and current user returns the corresponding {@link Metaproject}
+ */
+ @ManagedAuthentication
+ public Metaproject tryGetMetaproject(String name);
+
/**
* List metaproject assignments for given metaproject and current user.
*/
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index fd71893a3f5..dea973ce2bf 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -29,15 +29,12 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalDataManagementSystem;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IDatasetLocationNode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Metaproject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
@@ -46,7 +43,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
@@ -58,8 +54,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
@@ -89,13 +83,6 @@ public interface IEncapsulatedOpenBISService extends IEncapsulatedBasicOpenBISSe
public IDatasetLocationNode tryGetDataSetLocation(final String dataSetCode)
throws UserFailureException;
- /**
- * Tries to get the data set for the specified data set code, using the ETL server's session
- * token.
- */
- @ManagedAuthentication
- public ExternalData tryGetDataSet(final String dataSetCode) throws UserFailureException;
-
/**
* Tries to get the data set for the specified data set code and specified session.
*/
@@ -132,55 +119,19 @@ public interface IEncapsulatedOpenBISService extends IEncapsulatedBasicOpenBISSe
public void checkDataSetCollectionAccess(String sessionToken, List<String> dataSetCodes)
throws UserFailureException;
- /**
- * Tries to get the experiment of specified identifier or <code>null</code> if not found.
- */
- @ManagedAuthentication
- public Experiment tryGetExperiment(ExperimentIdentifier experimentIdentifier)
- throws UserFailureException;
-
- /**
- * Tries to get the space of specified identifier or <code>null</code> if not found.
- */
- @ManagedAuthentication
- public Space tryGetSpace(SpaceIdentifier spaceIdentifier) throws UserFailureException;
-
- /**
- * Tries to get the project of specified identifier or <code>null</code> if not found.
- */
- @ManagedAuthentication
- public Project tryGetProject(ProjectIdentifier projectIdentifier) throws UserFailureException;
-
/**
* Gets all sample in accordance to the specified criteria.
*/
@ManagedAuthentication
public List<Sample> listSamples(final ListSampleCriteria criteria) throws UserFailureException;
- /**
- * Gets a sample with the specified identifier. Sample is enriched with properties and the
- * experiment with properties.
- *
- * @return <code>null</code> if no sample could be found for given <var>sampleIdentifier</var>.
- */
- @ManagedAuthentication
- public Sample tryGetSampleWithExperiment(final SampleIdentifier sampleIdentifier)
- throws UserFailureException;
-
/**
* Tries to get the sample identifier for the sample with specified permanent ID.
*
* @return <code>null</code> if nothing found.
*/
@ManagedAuthentication
- public SampleIdentifier tryGetSampleIdentifier(String samplePermID)
- throws UserFailureException;
-
- /**
- * For given {@link MaterialIdentifier} returns the corresponding {@link Material}.
- */
- @ManagedAuthentication
- public Material tryGetMaterial(MaterialIdentifier materialIdentifier);
+ public SampleIdentifier tryGetSampleIdentifier(String samplePermID) throws UserFailureException;
/**
* For given (@code name} and {@code ownerId} returns the corresponding {@link Metaproject}
@@ -276,8 +227,8 @@ public interface IEncapsulatedOpenBISService extends IEncapsulatedBasicOpenBISSe
* sample is found with no properties.
*/
@ManagedAuthentication
- public IEntityProperty[] tryGetPropertiesOfTopSample(
- final SampleIdentifier sampleIdentifier) throws UserFailureException;
+ public IEntityProperty[] tryGetPropertiesOfTopSample(final SampleIdentifier sampleIdentifier)
+ throws UserFailureException;
/**
* Tries to return the properties of the sample with given <var>sampleIdentifier</var>.. If
@@ -288,8 +239,8 @@ public interface IEncapsulatedOpenBISService extends IEncapsulatedBasicOpenBISSe
* sample found with no properties.
*/
@ManagedAuthentication
- public IEntityProperty[] tryGetPropertiesOfSample(
- final SampleIdentifier sampleIdentifier) throws UserFailureException;
+ public IEntityProperty[] tryGetPropertiesOfSample(final SampleIdentifier sampleIdentifier)
+ throws UserFailureException;
/** See {@link IETLLIMSService#listSamplesByCriteria(String, ListSamplesByPropertyCriteria)} */
@ManagedAuthentication
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISearchService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISearchService.java
index 1286bb33d6d..570995643b9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISearchService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v2/ISearchService.java
@@ -142,6 +142,11 @@ public interface ISearchService
*/
public List<IMetaprojectImmutable> listMetaprojects();
+ /**
+ * Get the given metaproject for the current user
+ */
+ IMetaprojectImmutable getMetaproject(String name);
+
/**
* @return the assignments for the given metaproject for current user.
*/
@@ -151,4 +156,52 @@ public interface ISearchService
* @return metaprojects for current user, which are assigned to the given entity
*/
public List<IMetaprojectImmutable> listMetaprojectsForEntity(IMetaprojectContent entity);
+
+ /**
+ * Get a data set from the openBIS AS. Returns null if the data set does not exist.
+ *
+ * @return A data set or null
+ */
+ IDataSetImmutable getDataSet(String dataSetCode);
+
+ /**
+ * Get a sample from the openBIS AS. Returns null if the sample does not exist.
+ *
+ * @return A sample or null
+ */
+ ISampleImmutable getSample(String sampleIdentifierString);
+
+ /**
+ * Get an experiment from the openBIS AS.
+ */
+ IExperimentImmutable getExperiment(String experimentIdentifierString);
+
+ /**
+ * Get a project from the openBIS AS. Returns null if the project does not exist.
+ *
+ * @return A project or null
+ */
+ IProjectImmutable getProject(String projectIdentifier);
+
+ /**
+ * Get a space from the openBIS AS. Returns null if the space does not exist.
+ *
+ * @return A space or null
+ */
+ ISpaceImmutable getSpace(String spaceCode);
+
+ /**
+ * Get a material from the openBIS AS. Returns null if the material does not exist.
+ *
+ * @return A material or null
+ */
+ IMaterialImmutable getMaterial(String materialCode, String materialType);
+
+ /**
+ * Get a material from the openBIS AS. Returns null if the material does not exist.
+ *
+ * @return A material or null
+ */
+ IMaterialImmutable getMaterial(String identifier);
+
}
--
GitLab