From ed90978ce4911c3286477529de2cc61d8aca0092 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 20 Mar 2012 15:21:37 +0000
Subject: [PATCH] LMS-2846 tests for AnalysisSettings and
ExperimentFeatureVectorSummaryLoader added.
SVN: 24756
---
.../screening/server/ScreeningServer.java | 2 +-
.../server/logic/AbstractContentLoader.java | 4 +-
.../server/logic/AnalysisSettings.java | 1 +
.../ExperimentFeatureVectorSummaryLoader.java | 34 +-
.../MaterialFeatureVectorSummaryLoader.java | 10 +-
...erialFeaturesFromAllExperimentsLoader.java | 10 +-
.../server/logic/WellContentLoader.java | 17 +-
.../server/logic/WellDataLoader.java | 7 +-
.../logic/WellFeatureCollectionLoader.java | 6 +-
.../server/logic/AnalysisSettingsTest.java | 73 ++++
...erimentFeatureVectorSummaryLoaderTest.java | 334 ++++++++++++++++++
...aterialFeatureVectorSummaryLoaderTest.java | 2 +-
12 files changed, 462 insertions(+), 38 deletions(-)
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AnalysisSettingsTest.java
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoaderTest.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 1e859e6f1e7..918cdf4206a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -330,7 +330,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
MaterialSummarySettings settings = createDefaultSettings();
ExperimentFeatureVectorSummaryLoader experimentFeatureVectorSummaryLoader =
new ExperimentFeatureVectorSummaryLoader(session, businessObjectFactory,
- getDAOFactory(), settings);
+ getDAOFactory(), null, settings);
return experimentFeatureVectorSummaryLoader.loadExperimentFeatureVectors(experimentId,
analysisProcedureCriteria, analysisSettings);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
index b30a9b41855..62333474dc0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
@@ -58,11 +58,13 @@ abstract class AbstractContentLoader
private IScreeningQuery screeningDao = null;
protected AbstractContentLoader(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory)
+ IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
+ IScreeningQuery screeningDaoOrNull)
{
this.session = session;
this.businessObjectFactory = businessObjectFactory;
this.daoFactory = daoFactory;
+ screeningDao = screeningDaoOrNull;
}
protected IScreeningQuery getScreeningDAO()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AnalysisSettings.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AnalysisSettings.java
index a3b52678825..91c153ee061 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AnalysisSettings.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AnalysisSettings.java
@@ -48,6 +48,7 @@ public class AnalysisSettings
String[] splittedProperty = property.split(",");
for (String dataSetTypeSetting : splittedProperty)
{
+ dataSetTypeSetting = dataSetTypeSetting.trim();
int indexOfColon = dataSetTypeSetting.indexOf(':');
if (indexOfColon < 0)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
index 274a9f9c398..3e88ac38407 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellDataLoader.MaterialIdSummariesAndFeatures;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentFeatureVectorSummary;
@@ -60,12 +61,13 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
public ExperimentFeatureVectorSummaryLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- MaterialSummarySettings settings)
+ IScreeningQuery screeningQuery, MaterialSummarySettings settings)
{
- super(session, businessObjectFactory, daoFactory);
+ super(session, businessObjectFactory, daoFactory, screeningQuery);
this.settings = settings;
this.wellDataLoader =
- new WellDataLoader(session, businessObjectFactory, daoFactory, settings);
+ new WellDataLoader(session, businessObjectFactory, daoFactory, screeningQuery,
+ settings);
}
public ExperimentFeatureVectorSummary loadExperimentFeatureVectors(TechId experimentId,
@@ -101,7 +103,7 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
message +=
"\n\nHint: The file pattern for the data set type "
+ ds.getDataSetType().getCode()
- + " could be wrong.";
+ + " might be wrong.";
}
throw decorateException(ex, ds, "Reason: " + message);
} catch (Exception ex)
@@ -112,6 +114,12 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
}
}
+ return calculatedSummary(experimentId, analysisProcedureCriteria, experiment);
+ }
+
+ ExperimentFeatureVectorSummary calculatedSummary(TechId experimentId,
+ AnalysisProcedureCriteria analysisProcedureCriteria, ExperimentReference experiment)
+ {
MaterialIdSummariesAndFeatures summaries =
wellDataLoader.tryCalculateExperimentFeatureVectorSummaries(experimentId,
settings.getReplicaMaterialTypeSubstrings(), analysisProcedureCriteria,
@@ -126,19 +134,18 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
summaries.getFeatureNames(), null);
}
- UserFailureException decorateException(Exception ex, ExternalData dataSet, String message)
+ private UserFailureException decorateException(Exception ex, ExternalData dataSet, String message)
{
- return new UserFailureException(
- "Analysis summary for data set "
- + dataSet.getCode()
- + " couldn't retrieved from Data Store Server. "
- + message, ex);
+ return new UserFailureException("Analysis summary for data set " + dataSet.getCode()
+ + " couldn't retrieved from Data Store Server. " + message, ex);
}
- List<ExternalData> getMatchingDataSets(TechId experimentId,
+ private List<ExternalData> getMatchingDataSets(TechId experimentId,
AnalysisProcedureCriteria analysisProcedureCriteria)
{
- List<ExternalData> dataSets = businessObjectFactory.createDatasetLister(session).listByExperimentTechId(experimentId, true);
+ List<ExternalData> dataSets =
+ businessObjectFactory.createDatasetLister(session).listByExperimentTechId(
+ experimentId, true);
List<ExternalData> matchingDataSets = new ArrayList<ExternalData>();
for (ExternalData dataSet : dataSets)
{
@@ -213,6 +220,7 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
{
List<MaterialFeatureVectorSummary> materialsSummary = Collections.emptyList();
List<CodeAndLabel> featureDescriptions = Collections.emptyList();
- return new ExperimentFeatureVectorSummary(experiment, materialsSummary, featureDescriptions, null);
+ return new ExperimentFeatureVectorSummary(experiment, materialsSummary,
+ featureDescriptions, null);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
index baddb66e429..0ff99e1cfcc 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.utils.GroupByMap;
import ch.systemsx.cisd.openbis.generic.shared.basic.utils.IGroupKeyExtractor;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellDataLoader.MaterialIdSummariesAndFeatures;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialAllReplicasFeatureVectors;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialBiologicalReplicateFeatureVector;
@@ -63,7 +64,7 @@ public class MaterialFeatureVectorSummaryLoader extends AbstractContentLoader
{
MaterialAllReplicasFeatureVectors resultOrNull =
new MaterialFeatureVectorSummaryLoader(session, businessObjectFactory, daoFactory,
- settings).tryLoadMaterialFeatureVectors(criteria);
+ null, settings).tryLoadMaterialFeatureVectors(criteria);
List<MaterialReplicaFeatureSummary> replicaRows = convertToFeatureRows(resultOrNull);
List<String> subgroupLabels = tryGetSubgroupLabels(resultOrNull);
@@ -183,12 +184,13 @@ public class MaterialFeatureVectorSummaryLoader extends AbstractContentLoader
@Private
MaterialFeatureVectorSummaryLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- MaterialSummarySettings settings)
+ IScreeningQuery screeningQuery, MaterialSummarySettings settings)
{
- super(session, businessObjectFactory, daoFactory);
+ super(session, businessObjectFactory, daoFactory, screeningQuery);
this.settings = settings;
this.wellDataLoader =
- new WellDataLoader(session, businessObjectFactory, daoFactory, settings);
+ new WellDataLoader(session, businessObjectFactory, daoFactory, screeningQuery,
+ settings);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeaturesFromAllExperimentsLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeaturesFromAllExperimentsLoader.java
index 7fc4f354217..97f5b9f5f26 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeaturesFromAllExperimentsLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeaturesFromAllExperimentsLoader.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import org.apache.commons.lang.time.StopWatch;
@@ -55,7 +54,7 @@ public class MaterialFeaturesFromAllExperimentsLoader extends AbstractContentLoa
{
MaterialFeaturesFromAllExperimentsLoader loader =
new MaterialFeaturesFromAllExperimentsLoader(session, businessObjectFactory,
- daoFactory, settings);
+ daoFactory, null, settings);
List<ExperimentReference> experiments =
loader.fetchExperiments(materialId, projectTechIdOrNull);
return loader.loadMaterialFeatureVectorsFromAllAssays(materialId,
@@ -103,11 +102,12 @@ public class MaterialFeaturesFromAllExperimentsLoader extends AbstractContentLoa
private MaterialFeaturesFromAllExperimentsLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- MaterialSummarySettings settings)
+ IScreeningQuery screeningQuery, MaterialSummarySettings settings)
{
- super(session, businessObjectFactory, daoFactory);
+ super(session, businessObjectFactory, daoFactory, screeningQuery);
this.wellDataLoader =
- new WellDataLoader(session, businessObjectFactory, daoFactory, settings);
+ new WellDataLoader(session, businessObjectFactory, daoFactory, screeningQuery,
+ settings);
}
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
index f2e86eee98f..bdbbb2e706e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
@@ -99,7 +99,7 @@ public class WellContentLoader extends AbstractContentLoader
TechId materialId, TechId experimentId)
{
WellContentLoader loader =
- new WellContentLoader(session, businessObjectFactory, daoFactory);
+ new WellContentLoader(session, businessObjectFactory, daoFactory, null);
return loader.loadLocations(materialId, experimentId);
}
@@ -109,7 +109,7 @@ public class WellContentLoader extends AbstractContentLoader
TechId materialId)
{
final WellContentLoader loader =
- new WellContentLoader(session, businessObjectFactory, daoFactory);
+ new WellContentLoader(session, businessObjectFactory, daoFactory, null);
return loader.loadLocations(materialId);
}
@@ -119,7 +119,7 @@ public class WellContentLoader extends AbstractContentLoader
TechId materialId, TechId projectId)
{
final WellContentLoader loader =
- new WellContentLoader(session, businessObjectFactory, daoFactory);
+ new WellContentLoader(session, businessObjectFactory, daoFactory, null);
return loader.loadLocationsForProject(materialId, projectId);
}
@@ -134,7 +134,7 @@ public class WellContentLoader extends AbstractContentLoader
{
long start = System.currentTimeMillis();
WellContentLoader loader =
- new WellContentLoader(session, businessObjectFactory, daoFactory);
+ new WellContentLoader(session, businessObjectFactory, daoFactory, null);
List<WellContent> locations = loader.loadLocations(materialCriteria);
operationLog.info(String.format("[%d msec] Load %d locations.",
@@ -161,7 +161,7 @@ public class WellContentLoader extends AbstractContentLoader
TechId materialId, TechId experimentId, MaterialSummarySettings settings)
{
WellContentLoader loader =
- new WellContentLoader(session, businessObjectFactory, daoFactory);
+ new WellContentLoader(session, businessObjectFactory, daoFactory, null);
List<WellContent> locations = loader.loadLocations(materialId, experimentId);
locations = loader.enrichWithSingleImageDatasets(locations);
return annotateWithReplicaLabels(locations, settings);
@@ -277,7 +277,7 @@ public class WellContentLoader extends AbstractContentLoader
WellSearchCriteria materialCriteria)
{
Iterable<WellContentQueryResult> locations =
- new WellContentLoader(session, businessObjectFactory, daoFactory)
+ new WellContentLoader(session, businessObjectFactory, daoFactory, null)
.loadRawLocations(materialCriteria);
Collection<Long> materialIds = extractMaterialIds(locations);
return businessObjectFactory.createMaterialLister(session).list(
@@ -296,9 +296,10 @@ public class WellContentLoader extends AbstractContentLoader
}
private WellContentLoader(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory)
+ IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
+ IScreeningQuery screeningQuery)
{
- super(session, businessObjectFactory, daoFactory);
+ super(session, businessObjectFactory, daoFactory, screeningQuery);
}
private List<WellContent> enrichWithWellProperties(List<WellContent> locations)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataLoader.java
index af7796e0944..a7cfbf7afde 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataLoader.java
@@ -42,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.BasicWellContentQueryResult;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IWellReference;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.PatternMatchingUtils;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContentQueryResult;
@@ -69,9 +70,9 @@ class WellDataLoader extends AbstractContentLoader
private final MaterialSummarySettings settings;
public WellDataLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
- IDAOFactory daoFactory, MaterialSummarySettings settings)
+ IDAOFactory daoFactory, IScreeningQuery screeningQuery, MaterialSummarySettings settings)
{
- super(session, businessObjectFactory, daoFactory);
+ super(session, businessObjectFactory, daoFactory, screeningQuery);
this.settings = settings;
}
@@ -490,7 +491,7 @@ class WellDataLoader extends AbstractContentLoader
private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
Set<PlateIdentifier> plates, AnalysisProcedureCriteria analysisProcedureCriteria)
{
- return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory)
+ return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory, null)
.tryLoadWellSingleFeatureVectors(plates, settings.getFeatureCodes(),
analysisProcedureCriteria);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
index d4b83bfbd05..ea81651cfe6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
@@ -36,6 +36,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.utils.GroupByMap;
import ch.systemsx.cisd.openbis.generic.shared.basic.utils.IGroupKeyExtractor;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
@@ -52,9 +53,10 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSFeatureVecto
public class WellFeatureCollectionLoader extends AbstractContentLoader
{
public WellFeatureCollectionLoader(Session session,
- IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory)
+ IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
+ IScreeningQuery screeningQuery)
{
- super(session, businessObjectFactory, daoFactory);
+ super(session, businessObjectFactory, daoFactory, screeningQuery);
}
/** Loads feature vectors for chosen plates and set of features */
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AnalysisSettingsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AnalysisSettingsTest.java
new file mode 100644
index 00000000000..d83b38efea5
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AnalysisSettingsTest.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.plugin.screening.server.logic;
+
+import java.util.Properties;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class AnalysisSettingsTest extends AssertJUnit
+{
+ @Test
+ public void testNoSettings()
+ {
+ AnalysisSettings analysisSettings = new AnalysisSettings(new Properties());
+
+ assertEquals(true, analysisSettings.noAnalysisSettings());
+ }
+
+ @Test
+ public void testInvalidSettings()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(AnalysisSettings.KEY, "TYPE1");
+ try
+ {
+ new AnalysisSettings(properties);
+ fail("ConfigurationFailureException expected");
+ } catch (ConfigurationFailureException ex)
+ {
+ assertEquals(
+ "Invalid property '" + AnalysisSettings.KEY + "': missing ':' in 'TYPE1'.",
+ ex.getMessage());
+ }
+ }
+
+ @Test
+ public void testSettings()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(AnalysisSettings.KEY, "TYPE1:viewer1, TYPE2:viewer2");
+ AnalysisSettings analysisSettings = new AnalysisSettings(properties);
+
+ assertEquals("viewer1", analysisSettings.tryToGetReportingPluginKey(new DataSetBuilder().type("TYPE1").getDataSet()));
+ assertEquals("viewer2", analysisSettings.tryToGetReportingPluginKey(new DataSetBuilder().type("TYPE2").getDataSet()));
+ assertEquals(null, analysisSettings.tryToGetReportingPluginKey(new DataSetBuilder().type("TYPE3").getDataSet()));
+ assertEquals(false, analysisSettings.noAnalysisSettings());
+ }
+
+
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoaderTest.java
new file mode 100644
index 00000000000..d7906782b9a
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoaderTest.java
@@ -0,0 +1,334 @@
+/*
+ * 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.plugin.screening.server.logic;
+
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Properties;
+
+import org.jmock.Expectations;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataStoreBuilder;
+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.ProjectPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SpacePE;
+import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.server.ScreeningServer;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentFeatureVectorSummary;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class ExperimentFeatureVectorSummaryLoaderTest extends AbstractServerTestCase
+{
+ private static final class ExperimentFeatureVectorSummaryLoaderWithNoCalculation extends ExperimentFeatureVectorSummaryLoader
+ {
+ public ExperimentFeatureVectorSummaryLoaderWithNoCalculation(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
+ IScreeningQuery screeningQuery, MaterialSummarySettings settings)
+ {
+ super(session, businessObjectFactory, daoFactory, screeningQuery, settings);
+ }
+
+ @Override
+ ExperimentFeatureVectorSummary calculatedSummary(TechId experimentId,
+ AnalysisProcedureCriteria analysisProcedureCriteria, ExperimentReference experiment)
+ {
+ return null;
+ }
+ }
+
+ private static final String DATA_STORE_CODE = "DSS";
+
+ private static final TechId EXPERIMENT_ID = new TechId(42);
+
+ private IScreeningBusinessObjectFactory screeningBOFactory;
+
+ private IScreeningQuery screeningQuery;
+
+ private MaterialSummarySettings materialSummarySettings;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ screeningBOFactory = context.mock(IScreeningBusinessObjectFactory.class);
+ screeningQuery = context.mock(IScreeningQuery.class);
+ materialSummarySettings = ScreeningServer.createDefaultSettings();
+ }
+
+ @Test
+ public void testLoadAnalysisSummaryFromReport()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(AnalysisSettings.KEY, "T1:viewer1");
+ prepareLoadExperiment();
+ DataSet ds1 =
+ new DataSetBuilder().code("ds1").type("T1")
+ .property(ScreeningConstants.ANALYSIS_PROCEDURE, "extern")
+ .store(new DataStoreBuilder(DATA_STORE_CODE).getStore()).getDataSet();
+ DataSet ds2 = new DataSetBuilder().code("ds2").type("T2").getDataSet();
+ prepareListDataSetsByExperiment(ds1, ds2);
+ TableModel tabelModel =
+ new TableModel(Collections.<TableModelColumnHeader> emptyList(),
+ Collections.<TableModelRow> emptyList());
+ prepareCreateReport(tabelModel, "viewer1", ds1);
+
+ ExperimentFeatureVectorSummary summary =
+ createLoaderWithoutCalculation().loadExperimentFeatureVectors(EXPERIMENT_ID,
+ AnalysisProcedureCriteria.createFromCode("extern"),
+ new AnalysisSettings(properties));
+
+ assertSame(tabelModel, summary.getTableModelOrNull());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadAnalysisSummaryFromReportWithFileNotFound()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(AnalysisSettings.KEY, "T1:viewer1");
+ prepareLoadExperiment();
+ DataSet ds1 =
+ new DataSetBuilder().code("ds1").type("T1")
+ .property(ScreeningConstants.ANALYSIS_PROCEDURE, "extern")
+ .store(new DataStoreBuilder(DATA_STORE_CODE).getStore()).getDataSet();
+ prepareListDataSetsByExperiment(ds1);
+ prepareCreateReportFails(new UserFailureException("Main TSV file could not be found."),
+ "viewer1", ds1);
+
+ try
+ {
+ createLoaderWithoutCalculation().loadExperimentFeatureVectors(EXPERIMENT_ID,
+ AnalysisProcedureCriteria.createFromCode("extern"),
+ new AnalysisSettings(properties));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Analysis summary for data set ds1 couldn't retrieved from "
+ + "Data Store Server. Reason: Main TSV file could not be found.\n" + "\n"
+ + "Hint: The file pattern for the data set type T1 might be wrong.",
+ ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadAnalysisSummaryFromReportWithOtherUserFailureException()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(AnalysisSettings.KEY, "T1:viewer1");
+ prepareLoadExperiment();
+ DataSet ds1 =
+ new DataSetBuilder().code("ds1").type("T1")
+ .property(ScreeningConstants.ANALYSIS_PROCEDURE, "extern")
+ .store(new DataStoreBuilder(DATA_STORE_CODE).getStore()).getDataSet();
+ prepareListDataSetsByExperiment(ds1);
+ prepareCreateReportFails(new UserFailureException("Oohps!"), "viewer1", ds1);
+
+ try
+ {
+ createLoaderWithoutCalculation().loadExperimentFeatureVectors(EXPERIMENT_ID,
+ AnalysisProcedureCriteria.createFromCode("extern"),
+ new AnalysisSettings(properties));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Analysis summary for data set ds1 couldn't retrieved from "
+ + "Data Store Server. Reason: Oohps!",
+ ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadAnalysisSummaryFromReportWithOtherException()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(AnalysisSettings.KEY, "T1:viewer1");
+ prepareLoadExperiment();
+ DataSet ds1 =
+ new DataSetBuilder().code("ds1").type("T1")
+ .property(ScreeningConstants.ANALYSIS_PROCEDURE, "extern")
+ .store(new DataStoreBuilder(DATA_STORE_CODE).getStore()).getDataSet();
+ prepareListDataSetsByExperiment(ds1);
+ prepareCreateReportFails(new IllegalArgumentException("Oohps!"), "viewer1", ds1);
+
+ try
+ {
+ createLoaderWithoutCalculation().loadExperimentFeatureVectors(EXPERIMENT_ID,
+ AnalysisProcedureCriteria.createFromCode("extern"),
+ new AnalysisSettings(properties));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Analysis summary for data set ds1 couldn't retrieved from "
+ + "Data Store Server. See server logs for the reason.",
+ ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadAnalysisForMoreThanOne()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(AnalysisSettings.KEY, "T1:viewer1");
+ prepareLoadExperiment();
+ DataSet ds1 =
+ new DataSetBuilder().code("ds1").type("T1")
+ .property(ScreeningConstants.ANALYSIS_PROCEDURE, "extern").getDataSet();
+ DataSet ds2 =
+ new DataSetBuilder().code("ds2").type("T1")
+ .property(ScreeningConstants.ANALYSIS_PROCEDURE, "extern").getDataSet();
+ prepareListDataSetsByExperiment(ds1, ds2);
+
+ ExperimentFeatureVectorSummary summary =
+ createLoaderWithoutCalculation().loadExperimentFeatureVectors(EXPERIMENT_ID,
+ AnalysisProcedureCriteria.createFromCode("extern"),
+ new AnalysisSettings(properties));
+
+ assertEquals(null, summary);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadAnalysisForWrongAnalysisProcedure()
+ {
+ Properties properties = new Properties();
+ properties.setProperty(AnalysisSettings.KEY, "T1:viewer1");
+ prepareLoadExperiment();
+ DataSet ds1 =
+ new DataSetBuilder().code("ds1").type("T1")
+ .property(ScreeningConstants.ANALYSIS_PROCEDURE, "extern")
+ .store(new DataStoreBuilder(DATA_STORE_CODE).getStore()).getDataSet();
+ DataSet ds2 = new DataSetBuilder().code("ds2").type("T2").getDataSet();
+ prepareListDataSetsByExperiment(ds1, ds2);
+
+ ExperimentFeatureVectorSummary summary =
+ createLoaderWithoutCalculation().loadExperimentFeatureVectors(EXPERIMENT_ID,
+ AnalysisProcedureCriteria.createFromCode("intern"),
+ new AnalysisSettings(properties));
+
+ assertEquals(null, summary);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testLoadAnalysisForNoAnalysisSetting()
+ {
+ Properties properties = new Properties();
+ prepareLoadExperiment();
+
+ ExperimentFeatureVectorSummary summary = createLoaderWithoutCalculation().loadExperimentFeatureVectors(EXPERIMENT_ID,
+ AnalysisProcedureCriteria.createFromCode("extern"), new AnalysisSettings(properties));
+
+ assertEquals(null, summary);
+ context.assertIsSatisfied();
+ }
+
+ private ExperimentFeatureVectorSummaryLoader createLoaderWithoutCalculation()
+ {
+ return new ExperimentFeatureVectorSummaryLoaderWithNoCalculation(SESSION,
+ screeningBOFactory, daoFactory, screeningQuery, materialSummarySettings);
+ }
+
+ private void prepareLoadExperiment()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(experimentDAO).tryGetByTechId(EXPERIMENT_ID);
+ ExperimentPE experiment = new ExperimentPE();
+ experiment.setId(EXPERIMENT_ID.getId());
+ experiment.setPermId("123-" + EXPERIMENT_ID);
+ experiment.setExperimentType(new ExperimentTypePE());
+ ProjectPE project = new ProjectPE();
+ project.setSpace(new SpacePE());
+ experiment.setProject(project);
+ will(returnValue(experiment));
+ }
+ });
+ }
+
+ private void prepareListDataSetsByExperiment(final DataSet... dataSets)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(screeningBOFactory).createDatasetLister(SESSION);
+ will(returnValue(datasetLister));
+
+ one(datasetLister).listByExperimentTechId(EXPERIMENT_ID, true);
+ will(returnValue(Arrays.asList(dataSets)));
+ }
+ });
+ }
+
+ private void prepareCreateReport(final TableModel report, final String reportingPluginKey,
+ final DataSet dataSet)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(screeningBOFactory).createDataSetTable(SESSION);
+ will(returnValue(dataSetTable));
+
+ one(dataSetTable).createReportFromDatasets(reportingPluginKey, DATA_STORE_CODE,
+ Arrays.asList(dataSet.getCode()));
+ will(returnValue(report));
+ }
+ });
+ }
+
+ private void prepareCreateReportFails(final Exception exception, final String reportingPluginKey,
+ final DataSet dataSet)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(screeningBOFactory).createDataSetTable(SESSION);
+ will(returnValue(dataSetTable));
+
+ one(dataSetTable).createReportFromDatasets(reportingPluginKey, DATA_STORE_CODE,
+ Arrays.asList(dataSet.getCode()));
+ will(throwException(exception));
+ }
+ });
+ }
+
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
index 3bdb054b34d..9da51222ca1 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
@@ -80,7 +80,7 @@ public class MaterialFeatureVectorSummaryLoaderTest extends AssertJUnit
Arrays.asList(new CodeAndLabel("A", "A"), new CodeAndLabel("B", "B"));
MaterialAllReplicasFeatureVectors featureVectors =
- new MaterialFeatureVectorSummaryLoader(null, null, null, settings)
+ new MaterialFeatureVectorSummaryLoader(null, null, null, null, settings)
.createMaterialFeatureVectors(new TechId(replId), wellDataList, null,
featuresDesc);
--
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