From 97c292ce4899e8debc84e3f32738237f7ea4e47c Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Wed, 27 Jun 2012 19:24:37 +0000
Subject: [PATCH] BIS-94 SP-145 : Track and throw an exception of the contained
samples are not available in the DSS-side DTO.
SVN: 25901
---
.../api/v1/impl/SampleImmutable.java | 46 ++++++++++++
.../api/v1/impl/SearchService.java | 11 ++-
.../api/internal/v1/ISampleImmutable.java | 12 ++-
.../systemtests/SearchServiceTest.java | 73 +++++++++++++++++++
4 files changed, 138 insertions(+), 4 deletions(-)
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/SearchServiceTest.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
index bb5a0d23409..14f3ba7af66 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
@@ -17,12 +17,14 @@
package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
import java.util.ArrayList;
+import java.util.EnumSet;
import java.util.List;
import java.util.Set;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
@@ -32,17 +34,51 @@ public class SampleImmutable implements ISampleImmutable
{
private final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample;
+ private final EnumSet<SampleFetchOption> retrievedFetchOptions;
+
private final boolean existingSample;
+ /**
+ * Creates a new object that wraps the sample, which is assumed be an existing sample with all
+ * fetch options retrieved.
+ *
+ * @param sample The sample to wrap.
+ */
public SampleImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
{
this(sample, true);
}
+ /**
+ * Creates a new object that wraps the sample, which is assumed be an existing sample.
+ *
+ * @param sample The sample to wrap.
+ * @param retrievedFetchOptions The fetch options the sample includes.
+ */
+ public SampleImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample,
+ EnumSet<SampleFetchOption> retrievedFetchOptions)
+ {
+ this(sample, retrievedFetchOptions, true);
+ }
+
+ /**
+ * Creates a new object that wraps the sample, which is assumed to have all fetch options
+ * retrieved.
+ *
+ * @param sample The sample to wrap.
+ * @param existingSample True if the sample exists in the DB.
+ */
public SampleImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample,
boolean existingSample)
+ {
+ this(sample, EnumSet.allOf(SampleFetchOption.class), existingSample);
+ }
+
+ public SampleImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample,
+ EnumSet<SampleFetchOption> retrievedFetchOptions, boolean existingSample)
{
this.sample = sample;
+ this.retrievedFetchOptions = retrievedFetchOptions;
this.existingSample = existingSample;
}
@@ -120,6 +156,10 @@ public class SampleImmutable implements ISampleImmutable
@Override
public List<ISampleImmutable> getContainedSamples()
{
+ if (false == canGetContainedSamples())
+ {
+ throw new IllegalStateException("Contained samples were not returned by the server.");
+ }
List<ISampleImmutable> result = new ArrayList<ISampleImmutable>();
List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample> containedSamples =
sample.tryGetContainedSamples();
@@ -147,6 +187,12 @@ public class SampleImmutable implements ISampleImmutable
return parentIdentifiers;
}
+ @Override
+ public boolean canGetContainedSamples()
+ {
+ return retrievedFetchOptions.contains(SampleFetchOption.CONTAINED);
+ }
+
@Override
public int hashCode()
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
index e3819323d1c..b8319f52b86 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SearchService.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
import java.util.ArrayList;
+import java.util.EnumSet;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -30,6 +31,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IMaterialImmu
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISearchService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.MaterialIdentifierCollection;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SampleFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
@@ -46,7 +48,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierF
/**
* @author Chandrasekhar Ramakrishnan
*/
-class SearchService implements ISearchService
+public class SearchService implements ISearchService
{
private final IEncapsulatedOpenBISService openBisService;
@@ -134,7 +136,9 @@ class SearchService implements ISearchService
ArrayList<ISampleImmutable> samples = new ArrayList<ISampleImmutable>(serverSamples.size());
for (Sample sample : serverSamples)
{
- samples.add(new SampleImmutable(sample));
+ // Search for samples only returns the basic object with with properties.
+ samples.add(new SampleImmutable(sample, EnumSet.of(SampleFetchOption.BASIC,
+ SampleFetchOption.PROPERTIES)));
}
return samples;
}
@@ -185,7 +189,8 @@ class SearchService implements ISearchService
MaterialType materialType = new MaterialType();
materialType.setCode(typeCode);
List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material> materialsOfType =
- openBisService.listMaterials(ListMaterialCriteria.createFromMaterialType(materialType), true);
+ openBisService.listMaterials(
+ ListMaterialCriteria.createFromMaterialType(materialType), true);
accumulatedResults.addAll(materialsOfType);
}
return accumulatedResults;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/ISampleImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/ISampleImmutable.java
index eed9ca55fcc..5d685958688 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/ISampleImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/api/internal/v1/ISampleImmutable.java
@@ -63,10 +63,20 @@ public interface ISampleImmutable
/**
* Return the contained sample objects. Only available for samples existing prior the
- * transaction start.
+ * transaction start that were obtained from the server with their contained samples included.
+ * Call {@link #canReturnContainedSamples()} to see if these can be provided.
+ *
+ * @throws IllegalStateException If the contained samples cannot be returned.
*/
List<ISampleImmutable> getContainedSamples();
+ /**
+ * Return true if this sample object has contained samples available. This is independent of
+ * whether or not the sample has contained samples. This method only says if the contained
+ * samples were provided to this object by the application server.
+ */
+ public boolean canGetContainedSamples();
+
/**
* Returns the permId of this sample.
*/
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/SearchServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/SearchServiceTest.java
new file mode 100644
index 00000000000..36ef516e926
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/SearchServiceTest.java
@@ -0,0 +1,73 @@
+/*
+ * Copyright 2012 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.datastoreserver.systemtests;
+
+import java.util.List;
+
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.SampleImmutable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.SearchService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class SearchServiceTest extends SystemTestCase
+{
+ private IEncapsulatedOpenBISService openBis;
+
+ private SearchService searchService;
+
+ @BeforeTest
+ public void setUp()
+ {
+ openBis = ServiceProvider.getOpenBISService();
+ searchService = new SearchService(openBis);
+ }
+
+ @Test
+ public void testGettingContainedSamples()
+ {
+ List<ISampleImmutable> samples = searchService.searchForSamples("DESCRIPTION", "*", null);
+ assertTrue("Should have found at least one sample.", samples.size() > 0);
+
+ ISampleImmutable sampleFromSearch = samples.get(0);
+ // SampleSearch should return samples without contained samples
+ assertFalse(sampleFromSearch.canGetContainedSamples());
+ try
+ {
+ sampleFromSearch.getContainedSamples();
+ fail("getContainedSamples should have thrown an error");
+ } catch (IllegalStateException e)
+ {
+ // This is the correct behavior
+ }
+
+ // Getting the same sample from the openBis directly should include contained
+ ISampleImmutable sampleFromServer =
+ new SampleImmutable(openBis.tryGetSampleWithExperiment(SampleIdentifierFactory
+ .parse(sampleFromSearch.getSampleIdentifier())));
+ assertTrue(sampleFromServer.canGetContainedSamples());
+ assertTrue(sampleFromServer.getContainedSamples().size() > 0);
+
+ }
+}
--
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