From 02a37ea77a19c67c79b36c769f1bd5588a02c77d Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 27 Oct 2010 06:36:11 +0000
Subject: [PATCH] SE-308, SE-311 improved algorithm for gathering raw data
samples and data sets
SVN: 18453
---
.../client/api/v1/ProteomicsDataApiTest.java | 29 ++-
.../server/ProteomicsDataServiceInternal.java | 70 ++++--
.../server/api/v1/ProteomicsDataService.java | 54 ++++-
.../business/BusinessObjectFactory.java | 13 +-
.../server/business/DataSetManager.java | 167 -------------
.../server/business/ExperimentLoader.java | 77 ++++++
.../business/IBusinessObjectFactory.java | 2 +
.../server/business/ISampleLoader.java | 31 +++
.../server/business/SampleLoader.java | 121 +++++++++
.../shared/api/v1/dto/DataSet.java | 114 +++++++++
.../shared/api/v1/dto/Experiment.java | 2 +-
.../api/v1/dto/MsInjectionDataInfo.java | 29 ++-
.../validator/ParentSampleValidator.java | 48 ++++
.../validator/RawDataSampleValidator.java | 15 +-
.../shared/dto/MsInjectionSample.java | 25 +-
.../java/phosphonetx-applicationContext.xml | 3 +
.../web/server/RawDataSampleProviderTest.java | 4 +-
.../ProteomicsDataServiceInternalTest.java | 159 ++++++------
.../server/ProteomicsDataServiceTest.java | 6 -
.../business/AbstractLoaderTestCase.java | 56 +++++
.../server/business/DataSetManagerTest.java | 229 ------------------
.../server/business/ExperimentLoaderTest.java | 79 ++++++
.../server/business/SampleLoaderTest.java | 71 ++++++
.../validator/RawDataSampleValidatorTest.java | 3 +-
24 files changed, 883 insertions(+), 524 deletions(-)
delete mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetManager.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ExperimentLoader.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleLoader.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleLoader.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/DataSet.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/ParentSampleValidator.java
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbstractLoaderTestCase.java
delete mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetManagerTest.java
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ExperimentLoaderTest.java
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleLoaderTest.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiTest.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiTest.java
index f42913c27a1..0ed59a89edd 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiTest.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/api/v1/ProteomicsDataApiTest.java
@@ -19,8 +19,10 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.api.v1;
import java.util.Date;
import java.util.List;
import java.util.Map;
+import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
@@ -55,8 +57,20 @@ public class ProteomicsDataApiTest
{
System.out.println(" " + info.getMsInjectionSampleCode() + " -> "
+ info.getBiologicalSampleIdentifier() + " -> "
- + info.getBiologicalExperimentIdentifier() + ": latest data sets: "
- + latestDataSets);
+ + info.getBiologicalExperimentIdentifier());
+ Experiment experiment = info.getBiologicalExperiment();
+ if (experiment != null)
+ {
+ System.out.println(" biological experiment: "
+ + experiment.getCode() + " "
+ + experiment.getProperties());
+ }
+ System.out.println(" latest data sets: " + info.getLatestDataSetRegistrationDates());
+ Set<DataSet> dataSets = info.getDataSets();
+ for (DataSet dataSet : dataSets)
+ {
+ print(dataSet, " ");
+ }
}
}
@@ -100,4 +114,15 @@ public class ProteomicsDataApiTest
facade.logout();
}
+
+ private static void print(DataSet dataSet, String indentation)
+ {
+ System.out.println(indentation + dataSet.getCode() + " " + dataSet.getType() + " "
+ + dataSet.getRegistrationDate() + " " + dataSet.getProperties());
+ Set<DataSet> children = dataSet.getChildren();
+ for (DataSet child : children)
+ {
+ print(child, indentation + " ");
+ }
+ }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
index 61fc559f258..588908834ee 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternal.java
@@ -21,6 +21,7 @@ import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import ch.rinn.restrictions.Private;
@@ -30,7 +31,6 @@ import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataTable;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
@@ -41,8 +41,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
@@ -50,13 +48,14 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.DataSetManager;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ExperimentLoader;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleLoader;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.ParentSampleValidator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator.RawDataSampleValidator;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@@ -73,26 +72,34 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
@Private
static final String RAW_DATA_SAMPLE_TYPE = "MS_INJECTION";
+
+ private static final IValidator<Sample> PARENT_SAMPLE_VALIDATOR = new ParentSampleValidator();
private static final IValidator<MsInjectionSample> RAW_DATA_SAMPLE_VALIDATOR =
new RawDataSampleValidator();
private static final IValidator<Experiment> EXPERIMENT_VALIDATOR = new ExperimentValidator();
- private ICommonBusinessObjectFactory businessObjectFactory;
+ private ICommonBusinessObjectFactory commonBoFactory;
private ISessionManager<Session> sessionManagerFromConstructor;
+ private ExperimentLoader experimentLoader;
+
+ private IBusinessObjectFactory boFactory;
+
public ProteomicsDataServiceInternal()
{
}
public ProteomicsDataServiceInternal(ISessionManager<Session> sessionManager, IDAOFactory daoFactory,
- ICommonBusinessObjectFactory businessObjectFactory)
+ ICommonBusinessObjectFactory businessObjectFactory, IBusinessObjectFactory boFactory)
{
super(sessionManager, daoFactory);
sessionManagerFromConstructor = sessionManager;
- this.businessObjectFactory = businessObjectFactory;
+ this.commonBoFactory = businessObjectFactory;
+ this.boFactory = boFactory;
+ experimentLoader = new ExperimentLoader(getDAOFactory());
}
public void replaceAutoWiredSesseionManagerByConstructorSessionManager()
@@ -188,23 +195,38 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
private List<MsInjectionSample> loadAllRawDataSamples(Session session)
{
- ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
- ListSampleCriteria criteria = new ListSampleCriteria();
- SampleTypePE sampleTypePE =
- getDAOFactory().getSampleTypeDAO().tryFindSampleTypeByCode(RAW_DATA_SAMPLE_TYPE);
- criteria.setSampleType(SampleTypeTranslator.translate(sampleTypePE, null));
- criteria.setIncludeSpace(true);
- criteria.setSpaceCode(SPACE_CODE);
- ListOrSearchSampleCriteria criteria2 = new ListOrSearchSampleCriteria(criteria);
- criteria2.setEnrichDependentSamplesWithProperties(true);
- List<Sample> samples = sampleLister.list(criteria2);
- DataSetManager manager = new DataSetManager();
+ List<Sample> samples = loadAccessableSamples(session);
+ List<Sample> parentSamples = new ArrayList<Sample>();
for (Sample sample : samples)
{
- manager.addSample(sample);
+ parentSamples.add(sample.getGeneratedFrom());
+ }
+ experimentLoader.enrichWithExperiments(parentSamples);
+ Map<Sample, List<ExternalData>> dataSetsBySamples =
+ commonBoFactory.createDatasetLister(session).listAllDataSetsFor(samples);
+ List<MsInjectionSample> result = new ArrayList<MsInjectionSample>();
+ for (Entry<Sample, List<ExternalData>> entry : dataSetsBySamples.entrySet())
+ {
+ result.add(new MsInjectionSample(entry.getKey(), entry.getValue()));
+ }
+ return result;
+ }
+
+ protected List<Sample> loadAccessableSamples(Session session)
+ {
+ ISampleLoader sampleLoader = boFactory.createSampleLoader(session);
+ List<Sample> samples =
+ sampleLoader.listSamplesWithParentsByTypeAndSpace(RAW_DATA_SAMPLE_TYPE, SPACE_CODE);
+ PersonPE person = session.tryGetPerson();
+ List<Sample> validSamples = new ArrayList<Sample>();
+ for (Sample sample : samples)
+ {
+ if (PARENT_SAMPLE_VALIDATOR.isValid(person, sample))
+ {
+ validSamples.add(sample);
+ }
}
- manager.gatherDataSets(businessObjectFactory.createDatasetLister(session));
- return manager.getSamples();
+ return validSamples;
}
private void processDataSets(Session session, String dataSetProcessingKey,
@@ -212,7 +234,7 @@ public class ProteomicsDataServiceInternal extends AbstractServer<IProteomicsDat
{
String dataStoreServerCode = findDataStoreServer(dataSetProcessingKey);
IExternalDataTable externalDataTable =
- businessObjectFactory.createExternalDataTable(session);
+ commonBoFactory.createExternalDataTable(session);
externalDataTable.processDatasets(dataSetProcessingKey, dataStoreServerCode, dataSetCodes,
parameterBindings);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
index 4f94af701e8..3f9451803c2 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/api/v1/ProteomicsDataService.java
@@ -20,6 +20,7 @@ import java.io.Serializable;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -49,6 +50,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.generic.shared.util.DataTypeUtils;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.IProteomicsDataService;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataSet;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.DataStoreServerProcessingPluginInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.MsInjectionDataInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.PropertyKey;
@@ -122,8 +124,17 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
if (experiment != null)
{
info.setBiologicalExperimentIdentifier(experiment.getIdentifier());
+ info.setBiologicalExperiment(translate(experiment));
}
info.setBiologicalSampleProperties(translate(bioSample.getProperties()));
+ List<ExternalData> dataSets = sample.getDataSets();
+ Set<DataSet> transformedDataSets = new HashSet<DataSet>();
+ for (ExternalData dataSet : dataSets)
+ {
+ DataSet transformedDataSet = transform(dataSet);
+ transformedDataSets.add(transformedDataSet);
+ }
+ info.setDataSets(transformedDataSets);
Map<String, Date> latestDataSetRegistrationDates = new HashMap<String, Date>();
for (Entry<String, ExternalData> entry : sample.getLatestDataSets().entrySet())
{
@@ -133,6 +144,25 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
return info;
}
+ private DataSet transform(ExternalData dataSet)
+ {
+ DataSet transformedDataSet = new DataSet();
+ transformedDataSet.setId(dataSet.getId());
+ transformedDataSet.setCode(dataSet.getCode());
+ transformedDataSet.setType(dataSet.getDataSetType().getCode());
+ transformedDataSet.setRegistrationDate(dataSet.getRegistrationDate());
+ transformedDataSet.setProperties(translate(dataSet.getProperties()));
+ List<ExternalData> children = dataSet.getChildren();
+ if (children != null && children.isEmpty() == false)
+ {
+ for (ExternalData child : children)
+ {
+ transformedDataSet.addChild(transform(child));
+ }
+ }
+ return transformedDataSet;
+ }
+
public List<DataStoreServerProcessingPluginInfo> listDataStoreServerProcessingPluginInfos(
String sessionToken)
{
@@ -195,13 +225,7 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
for (Experiment experiment : experiments)
{
ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment e =
- new ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment();
- e.setId(experiment.getId());
- e.setCode(experiment.getCode());
- e.setProjectCode(experiment.getProject().getCode());
- e.setSpaceCode(experiment.getProject().getSpace().getCode());
- e.setRegistrationDate(experiment.getRegistrationDate());
- e.setProperties(translate(experiment.getProperties()));
+ translate(experiment);
result.add(e);
}
return result;
@@ -211,6 +235,20 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
}
}
+ private ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment translate(
+ Experiment experiment)
+ {
+ ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment e =
+ new ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto.Experiment();
+ e.setId(experiment.getId());
+ e.setCode(experiment.getCode());
+ e.setProjectCode(experiment.getProject().getCode());
+ e.setSpaceCode(experiment.getProject().getSpace().getCode());
+ e.setRegistrationDate(experiment.getRegistrationDate());
+ e.setProperties(translate(experiment.getProperties()));
+ return e;
+ }
+
public void processSearchData(String sessionToken, String userID, String dataSetProcessingKey,
long[] searchExperimentIDs)
{
@@ -260,7 +298,7 @@ public class ProteomicsDataService extends AbstractServer<IProteomicsDataService
public int getMinorVersion()
{
- return 2;
+ return 3;
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
index 966240e03b1..fab14dfcd6a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -31,11 +32,14 @@ public class BusinessObjectFactory extends AbstractPluginBusinessObjectFactory
{
private final IDAOFactory daoFactory;
private final IPhosphoNetXDAOFactory specificDAOFactory;
+ private final ICommonBusinessObjectFactory businessObjectFactory;
- public BusinessObjectFactory(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory)
+ public BusinessObjectFactory(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
+ ICommonBusinessObjectFactory businessObjectFactory)
{
this.daoFactory = daoFactory;
this.specificDAOFactory = specificDAOFactory;
+ this.businessObjectFactory = businessObjectFactory;
}
public ISampleLister createSampleLister(Session session)
@@ -88,4 +92,11 @@ public class BusinessObjectFactory extends AbstractPluginBusinessObjectFactory
return new SampleProvider(session, this);
}
+ public ISampleLoader createSampleLoader(Session session)
+ {
+ return new SampleLoader(session, daoFactory, businessObjectFactory);
+ }
+
+
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetManager.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetManager.java
deleted file mode 100644
index 01869aa2226..00000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetManager.java
+++ /dev/null
@@ -1,167 +0,0 @@
-/*
- * Copyright 2010 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.plugin.phosphonetx.server.business;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
-
-/**
- * Class managing indirect relation from Data Sets to Samples.
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetManager
-{
- private final Map<Long, MsInjectionSample> samples = new LinkedHashMap<Long, MsInjectionSample>();
-
- public void addSample(Sample plainSample)
- {
- MsInjectionSample sample = new MsInjectionSample(plainSample);
- samples.put(plainSample.getId(), sample);
- Experiment experiment = plainSample.getExperiment();
- if (experiment == null)
- {
- throw new UserFailureException("Sample '" + plainSample.getIdentifier() + "' of type '"
- + plainSample.getSampleType() + "' does not belong to an experiment.");
- }
- }
-
- public List<MsInjectionSample> getSamples()
- {
- return new ArrayList<MsInjectionSample>(samples.values());
- }
-
- public void gatherDataSets(IDatasetLister datasetLister)
- {
- List<ExternalData> dataSets = getDataSets(datasetLister);
- Map<Long, Long> dataSetSampleMap = mapDataSetsOnSamples(dataSets, datasetLister);
- for (ExternalData dataSet : dataSets)
- {
- Long sampleID = dataSetSampleMap.get(dataSet.getId());
- if (sampleID != null)
- {
- MsInjectionSample sample = samples.get(sampleID);
- if (sample != null)
- {
- sample.addLatestDataSet(dataSet);
- }
- }
- }
- }
-
- private List<ExternalData> getDataSets(IDatasetLister datasetLister)
- {
- Set<TechId> experimentIds = new LinkedHashSet<TechId>();
- for (MsInjectionSample sample : samples.values())
- {
- experimentIds.add(new TechId(sample.getSample().getExperiment().getId()));
- }
- List<ExternalData> result = new ArrayList<ExternalData>();
- List<ExternalData> dataSets = datasetLister.listByExperimentTechIds(experimentIds);
- for (ExternalData dataSet : dataSets)
- {
- result.add(dataSet);
- }
- return result;
- }
-
- private Map<Long, Long> mapDataSetsOnSamples(List<ExternalData> dataSets,
- IDatasetLister datasetLister)
- {
- List<ExternalData> descendentDataSets = new ArrayList<ExternalData>();
- Map<Long, Long> dataSetSampleMap = new HashMap<Long, Long>();
- Set<Long> ids = new LinkedHashSet<Long>();
- for (ExternalData dataSet : dataSets)
- {
- Sample sample = dataSet.getSample();
- if (sample != null)
- {
- dataSetSampleMap.put(dataSet.getId(), sample.getId());
- } else
- {
- descendentDataSets.add(dataSet);
- ids.add(dataSet.getId());
- }
- }
- Map<Long, Set<Long>> parentIds = datasetLister.listParentIds(ids);
- while (descendentDataSets.isEmpty() == false)
- {
- boolean nothingRemoved = true;
- for (Iterator<ExternalData> iterator = descendentDataSets.iterator(); iterator
- .hasNext();)
- {
- ExternalData dataSet = iterator.next();
- Set<Long> parent = parentIds.get(dataSet.getId());
- if (parent == null)
- {
- iterator.remove();
- nothingRemoved = false;
- continue;
- }
- if (parent.size() != 1)
- {
- throw new UserFailureException("Data set '" + dataSet.getCode() + "' has "
- + parent.size() + " instead of one parent data set.");
-
- }
- Long sampleID = dataSetSampleMap.get(parent.iterator().next());
- if (sampleID != null)
- {
- dataSetSampleMap.put(dataSet.getId(), sampleID);
- iterator.remove();
- nothingRemoved = false;
- }
- }
- assertSomeDataSetsAreRemoved(nothingRemoved, descendentDataSets);
- }
- return dataSetSampleMap;
- }
-
- private void assertSomeDataSetsAreRemoved(boolean nothingRemoved,
- List<ExternalData> descendentDataSets)
- {
- if (nothingRemoved)
- {
- StringBuilder builder = new StringBuilder();
- for (ExternalData externalData : descendentDataSets)
- {
- if (builder.length() > 0)
- {
- builder.append(", ");
- }
- builder.append(externalData.getCode());
- }
- throw new UserFailureException("Following data sets have wrong parents: "
- + builder.toString().trim());
- }
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ExperimentLoader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ExperimentLoader.java
new file mode 100644
index 00000000000..8243021f1a0
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ExperimentLoader.java
@@ -0,0 +1,77 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.server.business;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
+import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ExperimentLoader
+{
+ private final IDAOFactory daoFactory;
+
+ public ExperimentLoader(IDAOFactory daoFactory)
+ {
+ this.daoFactory = daoFactory;
+
+ }
+
+ public void enrichWithExperiments(Collection<Sample> samples)
+ {
+ Map<Long, List<Sample>> samplesByID = new LinkedHashMap<Long, List<Sample>>();
+ for (Sample sample : samples)
+ {
+ Experiment experiment = sample.getExperiment();
+ if (experiment != null)
+ {
+ Long id = experiment.getId();
+ List<Sample> list = samplesByID.get(id);
+ if (list == null)
+ {
+ list = new ArrayList<Sample>();
+ samplesByID.put(id, list);
+ }
+ list.add(sample);
+ }
+ }
+ List<ExperimentPE> experiments =
+ daoFactory.getExperimentDAO().listExperimentsWithProperties(samplesByID.keySet());
+ for (ExperimentPE experiment : experiments)
+ {
+ Experiment e = ExperimentTranslator.translate(experiment, "", LoadableFields.PROPERTIES);
+ List<Sample> list = samplesByID.get(experiment.getId());
+ for (Sample sample : list)
+ {
+ sample.setExperiment(e);
+ }
+ }
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
index 25acc3f21d6..8d649e2fd66 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
@@ -46,4 +46,6 @@ public interface IBusinessObjectFactory
public ISampleIDProvider createSampleIDProvider(Session session);
public ISampleProvider createSampleProvider(Session session);
+
+ public ISampleLoader createSampleLoader(Session session);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleLoader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleLoader.java
new file mode 100644
index 00000000000..bf65aba6af4
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ISampleLoader.java
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.server.business;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+
+/**
+ * Loader for sample having a parent.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface ISampleLoader
+{
+ public List<Sample> listSamplesWithParentsByTypeAndSpace(String sampleTypeCode, String spaceCode);
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleLoader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleLoader.java
new file mode 100644
index 00000000000..1ce33e6907c
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleLoader.java
@@ -0,0 +1,121 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.server.business;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.collections.IValidator;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleRelationShipSkeleton;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleSkeleton;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SampleLoader implements ISampleLoader
+{
+ private final Session session;
+ private final IDAOFactory daoFactory;
+ private final ICommonBusinessObjectFactory businessObjectFactory;
+
+ public SampleLoader(Session session, IDAOFactory daoFactory,
+ ICommonBusinessObjectFactory businessObjectFactory)
+ {
+ this.session = session;
+ this.daoFactory = daoFactory;
+ this.businessObjectFactory = businessObjectFactory;
+
+ }
+
+ public List<Sample> listSamplesWithParentsByTypeAndSpace(String sampleTypeCode, String spaceCode)
+ {
+ ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
+ Set<Long> filteredSampleIDs = getSampleIDs(sampleLister, sampleTypeCode, spaceCode);
+ ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(filteredSampleIDs);
+ criteria.setEnrichDependentSamplesWithProperties(true);
+ List<Sample> samples = sampleLister.list(criteria);
+ ArrayList<Sample> samplesWithParent = new ArrayList<Sample>();
+ for (Sample sample : samples)
+ {
+ if (sample.getParents().size() == 1)
+ {
+ samplesWithParent.add(sample);
+ }
+ }
+ return samplesWithParent;
+ }
+
+ private Set<Long> getSampleIDs(ISampleLister sampleLister, String sampleTypeCode,
+ String spaceCode)
+ {
+ SampleTypePE sampleTypePE =
+ daoFactory.getSampleTypeDAO().tryFindSampleTypeByCode(sampleTypeCode);
+ final Long sampleTypeID = sampleTypePE.getId();
+ GroupPE space =
+ daoFactory.getGroupDAO().tryFindGroupByCodeAndDatabaseInstance(spaceCode,
+ daoFactory.getHomeDatabaseInstance());
+ final Long spaceID = space.getId();
+ List<SampleSkeleton> sampleSkeletons =
+ sampleLister.listSampleBy(new IValidator<SampleSkeleton>()
+ {
+ public boolean isValid(SampleSkeleton sampleSkeleton)
+ {
+ return spaceID.equals(sampleSkeleton.getSpaceID())
+ && sampleTypeID.equals(sampleSkeleton.getTypeID());
+ }
+ });
+ final Set<Long> sampleIDs = new HashSet<Long>();
+ for (SampleSkeleton sampleSkeleton : sampleSkeletons)
+ {
+ sampleIDs.add(sampleSkeleton.getId());
+ }
+ final long relationshipTypeID =
+ sampleLister
+ .getRelationshipTypeID(BasicConstant.PARENT_CHILD_INTERNAL_RELATIONSHIP);
+ List<SampleRelationShipSkeleton> relationshipSkeletons =
+ sampleLister.listSampleRelationShipsBy(new IValidator<SampleRelationShipSkeleton>()
+ {
+ public boolean isValid(SampleRelationShipSkeleton skeleton)
+ {
+ return skeleton.getRelationShipTypeID() == relationshipTypeID
+ && sampleIDs.contains(skeleton.getChildSampleID());
+ }
+ });
+ Set<Long> filteredSampleIDs = new HashSet<Long>();
+ Set<Long> parentIDs = new HashSet<Long>();
+ for (SampleRelationShipSkeleton sampleRelationShipSkeleton : relationshipSkeletons)
+ {
+ filteredSampleIDs.add(sampleRelationShipSkeleton.getChildSampleID());
+ parentIDs.add(sampleRelationShipSkeleton.getParentSampleID());
+ }
+ return filteredSampleIDs;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/DataSet.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/DataSet.java
new file mode 100644
index 00000000000..c913ba615bd
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/DataSet.java
@@ -0,0 +1,114 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.shared.api.v1.dto;
+
+import java.io.Serializable;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+/**
+ * Date Set bean with properties, children and parents.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataSet implements Serializable
+{
+ private static final long serialVersionUID = 1L;
+
+ private long id;
+
+ private String code;
+
+ private String type;
+
+ private Date registrationDate;
+
+ private Map<PropertyKey, Serializable> properties;
+
+ private Set<DataSet> parents = new HashSet<DataSet>();
+
+ private Set<DataSet> children = new HashSet<DataSet>();
+
+ public final long getId()
+ {
+ return id;
+ }
+
+ public final void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public final String getCode()
+ {
+ return code;
+ }
+
+ public final void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ public final String getType()
+ {
+ return type;
+ }
+
+ public final void setType(String type)
+ {
+ this.type = type;
+ }
+
+ public final Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ public final void setRegistrationDate(Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ public final Map<PropertyKey, Serializable> getProperties()
+ {
+ return properties;
+ }
+
+ public final void setProperties(Map<PropertyKey, Serializable> properties)
+ {
+ this.properties = properties;
+ }
+
+ public final Set<DataSet> getParents()
+ {
+ return parents;
+ }
+
+ public final Set<DataSet> getChildren()
+ {
+ return children;
+ }
+
+ public void addChild(DataSet child)
+ {
+ getChildren().add(child);
+ child.getParents().add(this);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/Experiment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/Experiment.java
index a0d5e366092..be5e7ede90a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/Experiment.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/Experiment.java
@@ -21,7 +21,7 @@ import java.util.Date;
import java.util.Map;
/**
- *
+ * Experiment bean with properties.
*
* @author Franz-Josef Elmer
*/
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/MsInjectionDataInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/MsInjectionDataInfo.java
index 8bf75e5b448..12fb03700b8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/MsInjectionDataInfo.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/api/v1/dto/MsInjectionDataInfo.java
@@ -19,14 +19,17 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.api.v1.dto;
import java.io.Serializable;
import java.util.Date;
import java.util.Map;
+import java.util.Set;
/**
* Informations about an MS_INJECTION sample and its related biological sample. There are attributes
* for
* <ul><li>MS_INJECTION sample: ID, properties, code and registration date
* <li>Biological sample: identifier and properties
- * <li>Identifier of biological experiment (i.e. experiment of biological sample) if present
+ * <li>Biological experiment (i.e. experiment of biological sample) if present: identifier and properties
* <li>Registration dates of the most recently registered data sets for each data set type
+ * <li>All data sets including the derived ones of the MS_INJECTION sample with their type,
+ * registration date, and properties.
* </ul>
*
* @author Franz-Josef Elmer
@@ -49,8 +52,12 @@ public class MsInjectionDataInfo implements Serializable
private String biologicalExperimentIdentifier;
+ private Experiment biologicalExperiment;
+
private Map<PropertyKey, Serializable> biologicalSampleProperties;
+ private Set<DataSet> dataSets;
+
private Map<String, Date> latestDataSetRegistrationDates;
public long getMsInjectionSampleID()
@@ -124,6 +131,16 @@ public class MsInjectionDataInfo implements Serializable
this.biologicalExperimentIdentifier = biologicalExperimentIdentifier;
}
+ public final Experiment getBiologicalExperiment()
+ {
+ return biologicalExperiment;
+ }
+
+ public final void setBiologicalExperiment(Experiment biologicalExperiment)
+ {
+ this.biologicalExperiment = biologicalExperiment;
+ }
+
public Map<PropertyKey, Serializable> getBiologicalSampleProperties()
{
return biologicalSampleProperties;
@@ -134,6 +151,16 @@ public class MsInjectionDataInfo implements Serializable
this.biologicalSampleProperties = biologicalSampleProperties;
}
+ public final Set<DataSet> getDataSets()
+ {
+ return dataSets;
+ }
+
+ public final void setDataSets(Set<DataSet> dataSets)
+ {
+ this.dataSets = dataSets;
+ }
+
public Map<String, Date> getLatestDataSetRegistrationDates()
{
return latestDataSetRegistrationDates;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/ParentSampleValidator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/ParentSampleValidator.java
new file mode 100644
index 00000000000..7a1e1e77f1a
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/ParentSampleValidator.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.shared.authorization.validator;
+
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.IValidator;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.SpaceValidator;
+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.dto.PersonPE;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ParentSampleValidator implements IValidator<Sample>
+{
+ private IValidator<Space> validator = new SpaceValidator();
+
+ public boolean isValid(PersonPE person, Sample sample)
+ {
+ Sample parent = sample.getGeneratedFrom();
+ if (parent != null)
+ {
+ Space space = parent.getSpace();
+ if (space == null || validator.isValid(person, space))
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidator.java
index 5e51d404422..320c992f5aa 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidator.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidator.java
@@ -1,8 +1,6 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.authorization.validator;
-import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.SpaceValidator;
import ch.systemsx.cisd.openbis.generic.shared.authorization.validator.IValidator;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@@ -14,19 +12,10 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
*/
public final class RawDataSampleValidator implements IValidator<MsInjectionSample>
{
- private IValidator<Space> validator = new SpaceValidator();
+ private IValidator<Sample> validator = new ParentSampleValidator();
public boolean isValid(PersonPE person, MsInjectionSample sample)
{
- Sample parent = sample.getSample().getGeneratedFrom();
- if (parent != null)
- {
- Space space = parent.getSpace();
- if (space == null || validator.isValid(person, space))
- {
- return true;
- }
- }
- return false;
+ return validator.isValid(person, sample.getSample());
}
}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/MsInjectionSample.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/MsInjectionSample.java
index 45ef8105d4a..b13d6d86198 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/MsInjectionSample.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/MsInjectionSample.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
import java.util.Date;
import java.util.LinkedHashMap;
+import java.util.List;
import java.util.Map;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
@@ -32,10 +33,25 @@ public class MsInjectionSample
{
private final Sample sample;
private final Map<String, ExternalData> latestDataSets = new LinkedHashMap<String, ExternalData>();
+ private final List<ExternalData> dataSets;
- public MsInjectionSample(Sample sample)
+ public MsInjectionSample(Sample sample, List<ExternalData> dataSets)
{
this.sample = sample;
+ this.dataSets = dataSets;
+ add(dataSets);
+ }
+
+ private void add(List<ExternalData> datasets)
+ {
+ if (datasets != null)
+ {
+ for (ExternalData dataSet : datasets)
+ {
+ addLatestDataSet(dataSet);
+ add(dataSet.getChildren());
+ }
+ }
}
public Sample getSample()
@@ -43,12 +59,17 @@ public class MsInjectionSample
return sample;
}
+ public final List<ExternalData> getDataSets()
+ {
+ return dataSets;
+ }
+
public Map<String, ExternalData> getLatestDataSets()
{
return latestDataSets;
}
- public void addLatestDataSet(ExternalData dataSet)
+ private void addLatestDataSet(ExternalData dataSet)
{
String dataSetTypeCode = dataSet.getDataSetType().getCode();
Date registrationDate = dataSet.getRegistrationDate();
diff --git a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index 5bec6ae66f6..85eaadd8a99 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -38,6 +38,7 @@
class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.BusinessObjectFactory">
<constructor-arg ref="dao-factory"/>
<constructor-arg ref="phosphonetx-dao-factory"/>
+ <constructor-arg ref="common-business-object-factory" />
</bean>
<!--
@@ -66,6 +67,7 @@
</constructor-arg>
<constructor-arg ref="dao-factory"/>
<constructor-arg ref="common-business-object-factory" />
+ <constructor-arg ref="phosphonetx-bo-factory" />
</bean>
<bean id="proteomics-data-service-web"
@@ -73,6 +75,7 @@
<constructor-arg ref="session-manager" />
<constructor-arg ref="dao-factory"/>
<constructor-arg ref="common-business-object-factory" />
+ <constructor-arg ref="phosphonetx-bo-factory" />
</bean>
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
index 61c92451561..bc741c6a138 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/RawDataSampleProviderTest.java
@@ -21,6 +21,7 @@ import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDa
import static ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.RawDataSampleGridIDs.REGISTRATION_DATE;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Date;
import java.util.List;
@@ -33,6 +34,7 @@ import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
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.GenericValueEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
@@ -220,7 +222,7 @@ public class RawDataSampleProviderTest extends AbstractServerTestCase
List<MsInjectionSample> list = new ArrayList<MsInjectionSample>();
for (Sample sample : samples)
{
- list.add(new MsInjectionSample(sample));
+ list.add(new MsInjectionSample(sample, Arrays.<ExternalData>asList()));
}
will(returnValue(list));
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
index a6fc63ba091..56c4dae0fc6 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceInternalTest.java
@@ -31,10 +31,7 @@ import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -47,13 +44,14 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
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.ListOrSearchSampleCriteria;
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.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStoreServicePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentTypePE;
@@ -62,9 +60,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.RoleAssignmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.generic.shared.dto.properties.EntityKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleLoader;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IProteomicsDataServiceInternal;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
@@ -80,20 +79,37 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
private IProteomicsDataServiceInternal service;
- private ICommonBusinessObjectFactory boFactory;
+ private ICommonBusinessObjectFactory commonBoFactory;
private ExperimentTypePE experimentType;
+ private IBusinessObjectFactory boFactory;
+
+ private ISampleLoader sampleLoader;
+
@Override
@BeforeMethod
public final void setUp()
{
super.setUp();
- boFactory = context.mock(ICommonBusinessObjectFactory.class);
- service = new ProteomicsDataServiceInternal(sessionManager, daoFactory, boFactory);
+ commonBoFactory = context.mock(ICommonBusinessObjectFactory.class);
+ boFactory = context.mock(IBusinessObjectFactory.class);
+ sampleLoader = context.mock(ISampleLoader.class);
+ service = new ProteomicsDataServiceInternal(sessionManager, daoFactory, commonBoFactory, boFactory);
experimentType = new ExperimentTypePE();
experimentType.setCode(SEARCH_EXPERIMENT_TYPE);
experimentType.setDatabaseInstance(CommonTestUtils.createHomeDatabaseInstance());
+ PersonPE person = new PersonPE();
+ RoleAssignmentPE roleAssignment = new RoleAssignmentPE();
+ GroupPE group = new GroupPE();
+ group.setCode("Space-0");
+ DatabaseInstancePE databaseInstance = new DatabaseInstancePE();
+ databaseInstance.setCode("db");
+ databaseInstance.setUuid("UUID-db");
+ group.setDatabaseInstance(databaseInstance);
+ roleAssignment.setGroup(group);
+ person.setRoleAssignments(Collections.singleton(roleAssignment));
+ SESSION.setPerson(person);
}
@Test
@@ -117,8 +133,8 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
final long[] ids = new long[]
{ 2 };
HashMap<String, String> parameterBindings = new HashMap<String, String>();
- parameterBindings.put("ds-2", "s-2");
- prepareProcessDataSets(SESSION, parameterBindings, "ds-2");
+ parameterBindings.put("ds-21-child", "s-2");
+ prepareProcessDataSets(SESSION, parameterBindings, "ds-21-child");
service.processRawData(SESSION_TOKEN, COPY_PROCESSING_KEY, ids, "dt-0");
@@ -274,7 +290,7 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
DataStorePE s2 = store("s2", service(COPY_PROCESSING_KEY, PROCESSING));
will(returnValue(Arrays.asList(s1, s2)));
- one(boFactory).createExternalDataTable(session);
+ one(commonBoFactory).createExternalDataTable(session);
will(returnValue(externalDataTable));
one(externalDataTable).processDatasets(COPY_PROCESSING_KEY, "s2",
@@ -287,8 +303,8 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
private void prepareListRawDataSamples(final Long... sampleIDs)
{
final List<Sample> samples = new ArrayList<Sample>();
- final List<ExternalData> dataSets = new ArrayList<ExternalData>();
- final LinkedHashSet<TechId> experimentIds = new LinkedHashSet<TechId>();
+ final LinkedHashSet<Long> experimentIds = new LinkedHashSet<Long>();
+ final List<ExperimentPE> bioExperiments = new ArrayList<ExperimentPE>();
for (Long id : sampleIDs)
{
Sample sample = new Sample();
@@ -300,67 +316,74 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
sample.setExperiment(experiment);
Sample parent = new Sample();
parent.setId(id * 100);
+ Space space = new Space();
+ space.setCode("Space-" + id % 2);
+ DatabaseInstance instance = new DatabaseInstance();
+ instance.setCode("db");
+ instance.setUuid("UUID-db");
+ space.setInstance(instance);
+ parent.setSpace(space);
+ Experiment parentExperiment = new Experiment();
+ parentExperiment.setId(id * 20);
+ parent.setExperiment(parentExperiment);
sample.setGeneratedFrom(parent);
samples.add(sample);
- ExternalData dataSet = new ExternalData();
- dataSet.setId(id * 1000);
- dataSet.setCode("ds-" + id);
- dataSet.setDataSetType(new DataSetType("dt-" + id % 2));
- dataSet.setSample(sample);
- dataSets.add(dataSet);
- experimentIds.add(new TechId(id * 10));
+ if (id % 2 == 0)
+ {
+ ExperimentPE bioExperiment = createExperiment("e-type", "exp-" + id, space.getCode());
+ bioExperiment.setId(parentExperiment.getId());
+ bioExperiments.add(bioExperiment);
+ experimentIds.add(bioExperiment.getId());
+ }
}
context.checking(new Expectations()
{
{
- one(boFactory).createSampleLister(SESSION);
- will(returnValue(sampleLister));
-
- one(sampleTypeDAO).tryFindSampleTypeByCode(RAW_DATA_SAMPLE_TYPE);
- final SampleTypePE sampleType = new SampleTypePE();
- sampleType.setCode(RAW_DATA_SAMPLE_TYPE);
- sampleType.setId(20100104l);
- sampleType.setListable(Boolean.TRUE);
- sampleType.setAutoGeneratedCode(Boolean.FALSE);
- sampleType.setSubcodeUnique(Boolean.FALSE);
- sampleType.setGeneratedFromHierarchyDepth(0);
- sampleType.setContainerHierarchyDepth(0);
- sampleType.setSubcodeUnique(false);
- will(returnValue(sampleType));
-
- one(sampleLister).list(with(new BaseMatcher<ListOrSearchSampleCriteria>()
- {
- public boolean matches(Object item)
- {
- if (item instanceof ListOrSearchSampleCriteria)
- {
- ListOrSearchSampleCriteria criteria =
- (ListOrSearchSampleCriteria) item;
- assertEquals(SPACE_CODE, criteria.getSpaceCode());
- assertEquals(true, criteria.isIncludeSpace());
- SampleType type = criteria.getSampleType();
- assertEquals(RAW_DATA_SAMPLE_TYPE, type.getCode());
- assertEquals(sampleType.getId(), type.getId());
- return true;
- }
- return false;
- }
-
- public void describeTo(Description description)
- {
- description.appendValue(sampleType);
- }
- }));
+ one(boFactory).createSampleLoader(SESSION);
+ will(returnValue(sampleLoader));
+
+ one(sampleLoader).listSamplesWithParentsByTypeAndSpace(RAW_DATA_SAMPLE_TYPE, SPACE_CODE);
will(returnValue(samples));
-
- one(boFactory).createDatasetLister(SESSION);
+
+ one(experimentDAO).listExperimentsWithProperties(experimentIds);
+ will(returnValue(bioExperiments));
+
+ List<Sample> filteredSamples = new ArrayList<Sample>();
+ Map<Sample, List<ExternalData>> dataSetsBySamples = new HashMap<Sample, List<ExternalData>>();
+ for (Sample sample : samples)
+ {
+ if ("Space-0".equals(sample.getGeneratedFrom().getSpace().getCode()))
+ {
+ Long id = sample.getId();
+ ExternalData ds1 = new ExternalData();
+ ds1.setId(id * 1000);
+ ds1.setCode("ds-" + id);
+ ds1.setRegistrationDate(new Date(ds1.getId()));
+ ds1.setDataSetType(new DataSetType("dt-" + id % 2));
+ ds1.setSample(sample);
+ ExternalData ds2 = new ExternalData();
+ ds2.setId((id + 1) * 1001);
+ ds2.setCode("ds-" + id + 1);
+ ds2.setRegistrationDate(new Date(ds2.getId()));
+ ds2.setDataSetType(new DataSetType("dt-" + id % 2));
+ ds2.setSample(sample);
+ ExternalData ds2Child = new ExternalData();
+ ds2Child.setId(ds2.getId() + 1);
+ ds2Child.setCode(ds2.getCode() + "-child");
+ ds2Child.setRegistrationDate(new Date(ds2Child.getId()));
+ ds2Child.setDataSetType(new DataSetType("dt-" + id % 2));
+ ds2.setChildren(Arrays.asList(ds2Child));
+ dataSetsBySamples.put(sample, Arrays.asList(ds1, ds2));
+ filteredSamples.add(sample);
+ }
+ }
+
+ one(commonBoFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
-
- one(datasetLister).listByExperimentTechIds(experimentIds);
- will(returnValue(dataSets));
-
- one(datasetLister).listParentIds(Collections.<Long> emptySet());
- will(returnValue(Collections.<Long, Set<Long>> emptyMap()));
+
+ one(datasetLister).listAllDataSetsFor(filteredSamples);
+ will(returnValue(dataSetsBySamples));
+
}
});
}
@@ -390,7 +413,7 @@ public class ProteomicsDataServiceInternalTest extends AbstractServerTestCase
}
return experiment;
}
-
+
private DataStorePE store(String code, DataStoreServicePE... services)
{
DataStorePE store = new DataStorePE();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java
index df92f957408..ce66ea14cc9 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/ProteomicsDataServiceTest.java
@@ -157,12 +157,6 @@ public class ProteomicsDataServiceTest extends AbstractServerTestCase
{
{
one(internalService).listRawDataSamples(session2.getSessionToken());
- MsInjectionSample msInjectionSample = new MsInjectionSample(sample);
- msInjectionSample.addLatestDataSet(createDataSet(RAW_DATA, 10));
- msInjectionSample.addLatestDataSet(createDataSet(MZXML_DATA, 20));
- msInjectionSample.addLatestDataSet(createDataSet(MZXML_DATA, 15));
- msInjectionSample.addLatestDataSet(createDataSet(RAW_DATA, 30));
- will(returnValue(Arrays.asList(msInjectionSample)));
}
});
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbstractLoaderTestCase.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbstractLoaderTestCase.java
new file mode 100644
index 00000000000..5c10b7d8d75
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbstractLoaderTestCase.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.server.business;
+
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.transaction.TransactionConfiguration;
+
+import ch.systemsx.cisd.authentication.Principal;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOWithoutContextTest;
+import ch.systemsx.cisd.openbis.generic.shared.CommonTestUtils;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@ContextConfiguration(locations = "classpath:phosphonetx-applicationContext.xml")
+//In 'commonContext.xml', our transaction manager is called 'transaction-manager' (by default
+//Spring looks for 'transactionManager').
+@TransactionConfiguration(transactionManager = "transaction-manager")
+public abstract class AbstractLoaderTestCase extends AbstractDAOWithoutContextTest
+{
+ private static final Principal PRINCIPAL = new Principal(CommonTestUtils.USER_ID, "john",
+ "doe", "j@d");
+
+ private static final String SESSION_TOKEN = "session-token";
+
+ protected static final Session SESSION = new Session(CommonTestUtils.USER_ID, SESSION_TOKEN,
+ PRINCIPAL, "remote-host", 1);
+
+ protected ICommonBusinessObjectFactory boFactory;
+
+ @Autowired
+ public final void setBoFactory(final ICommonBusinessObjectFactory boFactory)
+ {
+ this.boFactory = boFactory;
+ }
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetManagerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetManagerTest.java
deleted file mode 100644
index 146f35188bd..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetManagerTest.java
+++ /dev/null
@@ -1,229 +0,0 @@
-/*
- * Copyright 2010 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.plugin.phosphonetx.server.business;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.Map.Entry;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-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.Sample;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.MsInjectionSample;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-public class DataSetManagerTest extends AssertJUnit
-{
- private static final long EXP1_ID = 11;
- private static final long SAMPLE1A_ID = 111;
- private static final long SAMPLE1B_ID = 112;
- private static final long EXP2_ID = 22;
- private static final long SAMPLE2A_ID = 221;
- private static final Sample SAMPLE1A = sample(EXP1_ID, SAMPLE1A_ID);
- private static final Sample SAMPLE1B = sample(EXP1_ID, SAMPLE1B_ID);
- private static final Sample SAMPLE2A = sample(EXP2_ID, SAMPLE2A_ID);
-
- private static Sample sample(long experimentID, long sampleID)
- {
- Sample sample = new Sample();
- sample.setId(sampleID);
- Experiment experiment = new Experiment();
- experiment.setId(experimentID);
- sample.setExperiment(experiment);
- return sample;
- }
-
- private Mockery context;
- private IDatasetLister dataSetLister;
- private DataSetManager manager;
-
- @BeforeMethod
- public void setUp()
- {
- context = new Mockery();
- dataSetLister = context.mock(IDatasetLister.class);
- manager = new DataSetManager();
- manager.addSample(SAMPLE1A);
- manager.addSample(SAMPLE1B);
- manager.addSample(SAMPLE2A);
- }
-
- @AfterMethod
- public void tearDown()
- {
- // To following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testNoDataSets()
- {
- prepareListByExperimentIds(Collections.<ExternalData>emptyList());
- prepareListParentIds(Collections.<Integer, Integer>emptyMap());
-
- manager.gatherDataSets(dataSetLister);
-
- List<MsInjectionSample> samples = manager.getSamples();
- for (MsInjectionSample msInjectionSample : samples)
- {
- assertEquals(0, msInjectionSample.getLatestDataSets().size());
- }
- assertEquals(3, samples.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testHappyCase()
- {
- Map<Integer, Integer> parentsMap = new HashMap<Integer, Integer>();
- List<ExternalData> dataSets = new ArrayList<ExternalData>();
- dataSets.add(dataSet(1, "A", SAMPLE1A));
- dataSets.add(dataSet(2, "A", SAMPLE1A));
- dataSets.add(dataSet(3, "A", SAMPLE1B));
- dataSets.add(dataSet(4, "A", SAMPLE2A));
- dataSets.add(dataSet(5, "B", null));
- parentsMap.put(5, 1);
- dataSets.add(dataSet(6, "B", null));
- parentsMap.put(6, 3);
- dataSets.add(dataSet(7, "B", null));
- parentsMap.put(7, 3);
- dataSets.add(dataSet(8, "B", null));
- parentsMap.put(8, 4);
- dataSets.add(dataSet(9, "C", null));
- parentsMap.put(9, 6);
- dataSets.add(dataSet(10, "C", null));
- parentsMap.put(10, 8);
- prepareListByExperimentIds(dataSets);
- prepareListParentIds(parentsMap);
-
- manager.gatherDataSets(dataSetLister);
-
- List<MsInjectionSample> samples = manager.getSamples();
- Map<Long, MsInjectionSample> map = new HashMap<Long, MsInjectionSample>();
- for (MsInjectionSample msInjectionSample : samples)
- {
- map.put(msInjectionSample.getSample().getId(), msInjectionSample);
- }
- assertEquals(3, samples.size());
- assertLatestDataSets(map.get(SAMPLE1A_ID), "A:2", "B:5");
- assertLatestDataSets(map.get(SAMPLE1B_ID), "A:3", "B:7", "C:9");
- assertLatestDataSets(map.get(SAMPLE2A_ID), "A:4", "B:8", "C:10");
- context.assertIsSatisfied();
- }
-
-
- @Test
- public void testWrongParent()
- {
- Map<Integer, Integer> parentsMap = new HashMap<Integer, Integer>();
- List<ExternalData> dataSets = new ArrayList<ExternalData>();
- dataSets.add(dataSet(1, "A", SAMPLE1A));
- dataSets.add(dataSet(2, "B", null));
- parentsMap.put(2, 42);
- prepareListByExperimentIds(dataSets);
- prepareListParentIds(parentsMap);
-
- try
- {
- manager.gatherDataSets(dataSetLister);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals("Following data sets have wrong parents: ds-2", ex.getMessage());
- }
-
- context.assertIsSatisfied();
- }
-
- private void assertLatestDataSets(MsInjectionSample sample, String... typesAndIDs)
- {
- Map<String, ExternalData> latestDataSets = sample.getLatestDataSets();
- for (String typeAndID : typesAndIDs)
- {
- String[] array = typeAndID.split(":");
- assertEquals(array[1], latestDataSets.get(array[0]).getId().toString());
- }
- assertEquals(typesAndIDs.length, latestDataSets.size());
- }
-
- private void prepareListByExperimentIds(final List<ExternalData> dataSets)
- {
- context.checking(new Expectations()
- {
- {
- one(dataSetLister).listByExperimentTechIds(
- new HashSet<TechId>(Arrays.asList(new TechId(EXP1_ID), new TechId(
- EXP2_ID))));
- will(returnValue(dataSets));
- }
- });
- }
-
- private void prepareListParentIds(final Map<Integer, Integer> parentIds)
- {
- context.checking(new Expectations()
- {
- {
- Set<Entry<Integer, Integer>> entrySet = parentIds.entrySet();
- Map<Long, Set<Long>> result = new HashMap<Long, Set<Long>>();
- Set<Long> keys = new HashSet<Long>();
- for (Entry<Integer, Integer> entry : entrySet)
- {
- long key = entry.getKey().longValue();
- keys.add(key);
- result.put(key, Collections.singleton(entry.getValue().longValue()));
- }
- one(dataSetLister).listParentIds(keys);
- will(returnValue(result));
- }
- });
- }
-
- private ExternalData dataSet(long id, String type, Sample sampleOrNull)
- {
- ExternalData dataSet = new ExternalData();
- dataSet.setId(id);
- dataSet.setCode("ds-" + id);
- dataSet.setRegistrationDate(new Date(100 * id));
- dataSet.setDataSetType(new DataSetType(type));
- dataSet.setSample(sampleOrNull);
- return dataSet;
- }
-}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ExperimentLoaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ExperimentLoaderTest.java
new file mode 100644
index 00000000000..9ffd83a789e
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ExperimentLoaderTest.java
@@ -0,0 +1,79 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.server.business;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleDAO;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Test(groups = "db")
+public class ExperimentLoaderTest extends AbstractLoaderTestCase
+{
+ @Test
+ public void test()
+ {
+ ExperimentLoader loader = new ExperimentLoader(daoFactory);
+ List<Sample> samples = loadSamples(980l, 981l, 982l, 983l, 984l);
+
+ loader.enrichWithExperiments(samples);
+
+ StringBuilder builder = new StringBuilder();
+ for (Sample sample : samples)
+ {
+ builder.append(sample.getId()).append(' ').append(sample.getCode());
+ Experiment experiment = sample.getExperiment();
+ if (experiment != null)
+ {
+ builder.append(": ").append(experiment.getCode()).append(' ');
+ builder.append(getSortedProperties(experiment));
+ }
+ builder.append('\n');
+ }
+ assertEquals("980 3V-126\n"
+ + "981 DP\n"
+ + "982 3VCP1: EXP1 [DESCRIPTION: A simple experiment, GENDER: MALE]\n"
+ + "983 3VCP2\n"
+ + "984 3VCP3: EXP1 [DESCRIPTION: A simple experiment, GENDER: MALE]\n",
+ builder.toString());
+ }
+
+ private List<Sample> loadSamples(Long... ids)
+ {
+ ISampleDAO sampleDAO = daoFactory.getSampleDAO();
+ List<Sample> list = new ArrayList<Sample>();
+ for (Long id : ids)
+ {
+ list.add(SampleTranslator.translate(sampleDAO.tryGetByTechId(new TechId(id)), ""));
+
+ }
+ return list;
+ }
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleLoaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleLoaderTest.java
new file mode 100644
index 00000000000..c806da68d06
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleLoaderTest.java
@@ -0,0 +1,71 @@
+/*
+ * Copyright 2010 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.plugin.phosphonetx.server.business;
+
+import static org.testng.AssertJUnit.assertEquals;
+
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Test(groups = "db")
+public class SampleLoaderTest extends AbstractLoaderTestCase
+{
+
+ @Test
+ public void test()
+ {
+ SampleLoader loader = new SampleLoader(SESSION, daoFactory, boFactory);
+ List<Sample> samples = loader.listSamplesWithParentsByTypeAndSpace("CELL_PLATE", "CISD");
+ Collections.sort(samples, new Comparator<Sample>()
+ {
+ public int compare(Sample s1, Sample s2)
+ {
+ return s1.getCode().compareTo(s2.getCode());
+ }
+ });
+ StringBuilder builder = new StringBuilder();
+ for (Sample sample : samples)
+ {
+ Sample parent = sample.getGeneratedFrom();
+ builder.append(sample.getCode()).append(" ").append(getSortedProperties(sample));
+ builder.append(" <- ").append(parent.getCode()).append(" ");
+ builder.append(getSortedProperties(parent)).append('\n');
+ }
+ assertEquals("3VCP1 [] <- 3V-123 [OFFSET: 42]\n"
+ + "3VCP2 [] <- 3V-123 [OFFSET: 42]\n"
+ + "3VCP4 [] <- 3V-125 [OFFSET: 49]\n"
+ + "3VCP5 [] <- 3V-125 [OFFSET: 49]\n"
+ + "3VCP6 [] <- 3V-125 [OFFSET: 49]\n"
+ + "3VCP7 [COMMENT: test comment, ORGANISM: RAT, SIZE: 4711] <- 3V-125 [OFFSET: 49]\n"
+ + "3VCP8 [] <- 3V-125 [OFFSET: 49]\n"
+ + "CP1-A1 [] <- DP1-A [OFFSET: 42]\n"
+ + "CP1-A2 [] <- DP1-A [OFFSET: 42]\n"
+ + "CP1-B1 [] <- DP1-B [OFFSET: 42]\n"
+ + "CP2-A1 [] <- DP2-A [OFFSET: 42]\n", builder.toString());
+ }
+
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidatorTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidatorTest.java
index 09b4f96dac0..708d3acbe70 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidatorTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/authorization/validator/RawDataSampleValidatorTest.java
@@ -23,6 +23,7 @@ import org.testng.AssertJUnit;
import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
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.dto.DatabaseInstancePE;
@@ -79,7 +80,7 @@ public class RawDataSampleValidatorTest extends AssertJUnit
}
sample.setGeneratedFrom(parent);
}
- return new MsInjectionSample(sample);
+ return new MsInjectionSample(sample, Arrays.<ExternalData>asList());
}
private static DatabaseInstance createDatabaseInstance(String code)
--
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