From 25ba1a6289df35af77d509760e5855c7632fc66f Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 18 Jul 2011 22:02:34 +0000
Subject: [PATCH] LMS-2395 material summary bug, LMS-2355 preparation
refactoring (which also improves performance)
SVN: 22191
---
.../BasicWellContentQueryResult.java | 19 +-
.../server/dataaccess/IWellReference.java | 31 +
.../dataaccess/WellContentQueryResult.java | 18 +-
.../server/logic/AbstractContentLoader.java | 21 +-
.../ExperimentFeatureVectorSummaryLoader.java | 301 ++--------
.../MaterialFeatureVectorSummaryLoader.java | 125 ++--
...erialFeaturesFromAllExperimentsLoader.java | 228 +-------
.../server/logic/WellDataLoader.java | 541 ++++++++++++++++++
.../logic/WellReplicaSummaryCalculator.java | 4 +-
.../server/logic/dto/IWellExtendedData.java | 40 --
.../screening/server/logic/dto/WellData.java | 13 +-
.../server/logic/dto/WellExtendedData.java | 27 +-
.../basic/dto/MaterialSummarySettings.java | 10 +-
.../server/dataaccess/ScreeningDAOTest.java | 2 +-
...aterialFeatureVectorSummaryLoaderTest.java | 23 +-
.../server/logic}/WellDataCollection.java | 9 +-
.../WellReplicaSummaryCalculatorTest.java | 3 +-
17 files changed, 785 insertions(+), 630 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IWellReference.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataLoader.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/IWellExtendedData.java
rename screening/{source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto => sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic}/WellDataCollection.java (79%)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/BasicWellContentQueryResult.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/BasicWellContentQueryResult.java
index 76182c72cab..ade4dffa60b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/BasicWellContentQueryResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/BasicWellContentQueryResult.java
@@ -17,6 +17,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess;
import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
/**
* Basic information about well content which allows to compute rankings.
@@ -24,13 +26,24 @@ import ch.rinn.restrictions.Private;
* @author Tomasz Pylak
*/
@Private
-public class BasicWellContentQueryResult
+public class BasicWellContentQueryResult implements IWellReference
{
- public String well_code;
+ private String well_code;
- public String plate_perm_id;
+ private String plate_perm_id;
public String exp_perm_id;
public long material_content_id;
+
+ public String getPlatePermId()
+ {
+ return plate_perm_id;
+ }
+
+ public WellReference getWellReference()
+ {
+ WellLocation wellLocation = WellLocation.parseLocationStr(well_code);
+ return new WellReference(wellLocation, plate_perm_id);
+ }
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IWellReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IWellReference.java
new file mode 100644
index 00000000000..eb46139a5bd
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IWellReference.java
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2011 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.dataaccess;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
+
+/**
+ * Allows to reference a well.
+ *
+ * @author Tomasz Pylak
+ */
+public interface IWellReference
+{
+ String getPlatePermId();
+
+ WellReference getWellReference();
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
index fa5a0c7713e..1d3d174b821 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/WellContentQueryResult.java
@@ -17,12 +17,15 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess;
import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
/**
* @author Tomasz Pylak
*/
@Private
-public class WellContentQueryResult extends ExperimentReferenceQueryResult
+public class WellContentQueryResult extends ExperimentReferenceQueryResult implements
+ IWellReference
{
// well pointer
@@ -42,7 +45,7 @@ public class WellContentQueryResult extends ExperimentReferenceQueryResult
public String plate_type_code;
- public String plate_perm_id;
+ private String plate_perm_id;
// a pointer to a material which was being searched for inside a well
@@ -55,4 +58,15 @@ public class WellContentQueryResult extends ExperimentReferenceQueryResult
@Deprecated
public String material_content_type_code;
+
+ public String getPlatePermId()
+ {
+ return plate_perm_id;
+ }
+
+ public WellReference getWellReference()
+ {
+ WellLocation wellLocation = WellLocation.parseLocationStr(well_code);
+ return new WellReference(wellLocation, plate_perm_id);
+ }
}
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 2e4debdcaa4..b30a9b41855 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
@@ -21,6 +21,7 @@ import java.util.Set;
import net.lemnik.eodsql.QueryTool;
+import org.apache.commons.lang.time.StopWatch;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -54,6 +55,8 @@ abstract class AbstractContentLoader
protected final IDAOFactory daoFactory;
+ private IScreeningQuery screeningDao = null;
+
protected AbstractContentLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory)
{
@@ -62,10 +65,14 @@ abstract class AbstractContentLoader
this.daoFactory = daoFactory;
}
- protected static IScreeningQuery createDAO(IDAOFactory daoFactory)
+ protected IScreeningQuery getScreeningDAO()
{
- Connection connection = DatabaseContextUtils.getConnection(daoFactory);
- return QueryTool.getQuery(connection, IScreeningQuery.class);
+ if (screeningDao == null)
+ {
+ Connection connection = DatabaseContextUtils.getConnection(daoFactory);
+ screeningDao = QueryTool.getQuery(connection, IScreeningQuery.class);
+ }
+ return screeningDao;
}
protected final ExperimentReference loadExperimentByPermId(String experimentPermId)
@@ -106,4 +113,12 @@ abstract class AbstractContentLoader
return new FeatureVectorDatasetLoader(session, businessObjectFactory, null, plates,
analysisProcedureCriteria);
}
+
+ protected final StopWatch createWatchAndStart()
+ {
+ StopWatch watch = new StopWatch();
+ watch.start();
+ return watch;
+ }
+
}
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 121438dbc59..cacf849b982 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
@@ -16,13 +16,9 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
-import java.util.ArrayList;
-import java.util.Collection;
import java.util.Collections;
-import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
-import java.util.Map;
import java.util.Set;
import ch.systemsx.cisd.common.collections.CollectionUtils;
@@ -30,32 +26,20 @@ import ch.systemsx.cisd.common.collections.CollectionUtils.ICollectionMappingFun
import ch.systemsx.cisd.common.collections.IKeyExtractor;
import ch.systemsx.cisd.common.collections.TableMap;
import ch.systemsx.cisd.common.collections.TableMap.UniqueKeyViolationStrategy;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
-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.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.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.logic.dto.IWellData;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellExtendedData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellDataLoader.MaterialIdSummaryAndFeatures;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellDataCollection;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
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.FeatureVectorValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
/**
* {@See #loadExperimentFeatureVectors}.
@@ -64,20 +48,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoa
*/
public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
{
-
- static class LoaderParameters
- {
- TechId experimentId;
-
- AnalysisProcedureCriteria analysisProcedureCriteria;
-
- LoaderParameters(TechId experimentId, AnalysisProcedureCriteria analysisProcedureCriteria)
- {
- this.experimentId = experimentId;
- this.analysisProcedureCriteria = analysisProcedureCriteria;
- }
- }
-
/**
* Loads feature vectors summaries for all the materials in the specified experiment.
*/
@@ -86,57 +56,55 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
TechId experimentId, AnalysisProcedureCriteria analysisProcedureCriteria,
MaterialSummarySettings settings)
{
- LoaderParameters params = new LoaderParameters(experimentId, analysisProcedureCriteria);
return new ExperimentFeatureVectorSummaryLoader(session, businessObjectFactory, daoFactory,
- settings).loadExperimentFeatureVectors(params);
+ settings).loadExperimentFeatureVectors(experimentId, analysisProcedureCriteria);
}
protected final MaterialSummarySettings settings;
+ private final WellDataLoader wellDataLoader;
+
protected ExperimentFeatureVectorSummaryLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
MaterialSummarySettings settings)
{
super(session, businessObjectFactory, daoFactory);
this.settings = settings;
+ this.wellDataLoader =
+ new WellDataLoader(session, businessObjectFactory, daoFactory, settings);
}
- private ExperimentFeatureVectorSummary loadExperimentFeatureVectors(LoaderParameters params)
+ private ExperimentFeatureVectorSummary loadExperimentFeatureVectors(TechId experimentId,
+ AnalysisProcedureCriteria analysisProcedureCriteria)
{
- WellDataCollection wellDataCollection = tryLoadWellData(params);
- ExperimentReference experiment = loadExperimentByTechId(params.experimentId);
- if (wellDataCollection == null)
+ MaterialIdSummaryAndFeatures summaries =
+ wellDataLoader.tryCalculateExperimentFeatureVectorSummaries(experimentId,
+ settings.getReplicaMaterialTypeSubstrings(), analysisProcedureCriteria,
+ false);
+ ExperimentReference experiment = loadExperimentByTechId(experimentId);
+ if (summaries == null)
{
return createEmptySummary(experiment);
}
- List<MaterialFeatureVectorSummary> featureSummaries =
- calculateReplicasFeatureVectorSummaries(wellDataCollection);
-
- return new ExperimentFeatureVectorSummary(experiment, featureSummaries,
- wellDataCollection.getFeatureDescriptions());
- }
-
- private List<MaterialFeatureVectorSummary> calculateReplicasFeatureVectorSummaries(
- WellDataCollection wellDataCollection)
- {
- List<? extends IWellData> wellDataList = wellDataCollection.getWellDataList();
- List<MaterialIdFeatureVectorSummary> summaries =
- calculateReplicasFeatureVectorSummaries(wellDataList);
- return enrichWithMaterial(summaries, wellDataCollection);
+ List<MaterialFeatureVectorSummary> enrichedFeatureSummaries =
+ enrichWithMaterials(summaries.getFeatureSummaries());
+ return new ExperimentFeatureVectorSummary(experiment, enrichedFeatureSummaries,
+ summaries.getFeatureNames());
}
- private final List<MaterialIdFeatureVectorSummary> calculateReplicasFeatureVectorSummaries(
- List<? extends IWellData> wellDataList)
+ private List<MaterialFeatureVectorSummary> enrichWithMaterials(
+ List<MaterialIdFeatureVectorSummary> summaries)
{
- return WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(wellDataList,
- settings.getAggregationType(), false);
+ Set<Long> materialIds = extractMaterialIds(summaries);
+ List<Material> materials = fetchMaterials(materialIds);
+ return enrichWithMaterials(summaries, materials);
}
- private static List<MaterialFeatureVectorSummary> enrichWithMaterial(
- List<MaterialIdFeatureVectorSummary> summaries, WellDataCollection wellDataCollection)
+ private static List<MaterialFeatureVectorSummary> enrichWithMaterials(
+ List<MaterialIdFeatureVectorSummary> summaries, List<Material> materials)
{
- final TableMap<Long, Material> materialMap = createMaterialMap(wellDataCollection);
+ final TableMap<Long, Material> materialMap = createMaterialMap(materials);
return CollectionUtils
.map(summaries,
new ICollectionMappingFunction<MaterialFeatureVectorSummary, MaterialIdFeatureVectorSummary>()
@@ -149,6 +117,22 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
});
}
+ private List<Material> fetchMaterials(Set<Long> materialIds)
+ {
+ return businessObjectFactory.createMaterialLister(session).list(
+ new ListMaterialCriteria(materialIds), true);
+ }
+
+ private static Set<Long> extractMaterialIds(List<MaterialIdFeatureVectorSummary> summaries)
+ {
+ Set<Long> ids = new HashSet<Long>();
+ for (MaterialIdFeatureVectorSummary summary : summaries)
+ {
+ ids.add(summary.getMaterial());
+ }
+ return ids;
+ }
+
private static MaterialFeatureVectorSummary convert(MaterialIdFeatureVectorSummary summary,
TableMap<Long, Material> materialMap)
{
@@ -157,58 +141,15 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
}
private static TableMap<Long/* material id */, Material> createMaterialMap(
- WellDataCollection wellDataCollection)
+ List<Material> materials)
{
- List<Material> materials =
- CollectionUtils.map(wellDataCollection.getWellDataList(),
- new ICollectionMappingFunction<Material, IWellExtendedData>()
- {
- public Material map(IWellExtendedData wellData)
- {
- return wellData.getMaterial();
- }
- });
return new TableMap<Long, Material>(materials, new IKeyExtractor<Long, Material>()
{
public Long getKey(Material material)
{
return material.getId();
}
- }, UniqueKeyViolationStrategy.KEEP_FIRST);
- }
-
- protected final WellDataCollection tryLoadWellData(LoaderParameters params)
- {
- ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
- List<Sample> plates =
- sampleLister.list(createExperientCriteria(params.experimentId.getId()));
- List<Sample> wells = sampleLister.list(createWellsCriteria(plates));
- if (wells.isEmpty())
- {
- return null; // no wells in this experiment
- }
- enrichWithMaterialProperties(wells);
-
- Set<PlateIdentifier> plateIdentifiers = extractIdentifiers(plates);
- WellFeatureCollection<FeatureVectorValues> featureVectorsCollection =
- tryLoadWellSingleFeatureVectors(plateIdentifiers, params.analysisProcedureCriteria);
- if (featureVectorsCollection == null)
- {
- return null; // no feature vector datasets connected to plates in this experiment
- }
-
- List<IWellExtendedData> wellDataList = asWellData(wells, featureVectorsCollection);
- return new WellDataCollection(wellDataList,
- featureVectorsCollection.getFeatureCodesAndLabels());
- }
-
- private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
- Set<PlateIdentifier> plateIdentifiers,
- AnalysisProcedureCriteria analysisProcedureCriteria)
- {
- return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory)
- .tryLoadWellSingleFeatureVectors(plateIdentifiers, settings.getFeatureCodes(),
- analysisProcedureCriteria);
+ }, UniqueKeyViolationStrategy.ERROR);
}
private static ExperimentFeatureVectorSummary createEmptySummary(ExperimentReference experiment)
@@ -217,156 +158,4 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
List<CodeAndLabel> featureDescriptions = Collections.emptyList();
return new ExperimentFeatureVectorSummary(experiment, materialsSummary, featureDescriptions);
}
-
- private void enrichWithMaterialProperties(List<Sample> samples)
- {
- IMaterialLister materialLister = businessObjectFactory.createMaterialLister(session);
- List<Material> containedMaterials = extractMaterialsWithDuplicates(samples);
- materialLister.enrichWithProperties(containedMaterials);
- }
-
- private static List<Material> extractMaterialsWithDuplicates(List<Sample> samples)
- {
- List<Material> materials = new ArrayList<Material>();
- for (Sample sample : samples)
- {
- materials.addAll(extractMaterials(sample));
- }
- return materials;
- }
-
- private static Collection<? extends Material> extractMaterials(Sample sample)
- {
- List<Material> materials = new ArrayList<Material>();
- List<IEntityProperty> properties = sample.getProperties();
- for (IEntityProperty property : properties)
- {
- Material material = property.getMaterial();
- if (material != null)
- {
- materials.add(material);
- }
- }
- return materials;
- }
-
- private List<IWellExtendedData> asWellData(List<Sample> wells,
- WellFeatureCollection<FeatureVectorValues> featureVectorsCollection)
- {
- Map<WellReference, FeatureVectorValues> featureVectors =
- createWellToFeatureVectorMap(featureVectorsCollection);
- List<String> orderedFeatureLabels = featureVectorsCollection.getFeatureLabels();
- List<IWellExtendedData> wellDataList = new ArrayList<IWellExtendedData>();
- for (Sample well : wells)
- {
- IWellExtendedData wellData =
- tryCreateWellData(well, featureVectors, orderedFeatureLabels);
- if (wellData != null)
- {
- wellDataList.add(wellData);
- }
- }
- return wellDataList;
- }
-
- private IWellExtendedData tryCreateWellData(Sample well,
- Map<WellReference, FeatureVectorValues> featureVectorsMap,
- List<String> orderedFeatureLabels)
- {
- final float[] featureVectorNumbers =
- tryExtractFeatureVectorValues(well, featureVectorsMap, orderedFeatureLabels);
- if (featureVectorNumbers == null)
- {
- return null;
- }
- final Material replicaMaterial = tryFindReplicaMaterial(well, settings);
- if (replicaMaterial == null)
- {
- return null;
- }
- return new WellExtendedData(replicaMaterial.getId(), featureVectorNumbers, well,
- replicaMaterial);
- }
-
- private static Material tryFindReplicaMaterial(Sample well, MaterialSummarySettings settings)
- {
- String replicaMatrialTypePattern =
- ScreeningUtils.asJavaRegExpr(settings.getReplicaMatrialTypeSubstrings());
- if (replicaMatrialTypePattern == null)
- {
- return null;
- }
- for (Material material : extractMaterials(well))
- {
- if (material.getEntityType().getCode().matches(replicaMatrialTypePattern))
- {
- return material;
- }
- }
- return null;
- }
-
- private static float[] tryExtractFeatureVectorValues(Sample well,
- Map<WellReference, FeatureVectorValues> featureVectorsMap,
- List<String> orderedFeatureLabels)
- {
- WellReference wellReference = asWellReference(well);
- FeatureVectorValues featureVector = featureVectorsMap.get(wellReference);
- if (featureVector == null)
- {
- return null;
- }
- return WellFeatureCollectionLoader.asFeatureVectorValues(featureVector);
- }
-
- private static WellReference asWellReference(Sample well)
- {
- WellLocation location =
- ScreeningUtils.tryCreateLocationFromMatrixCoordinate(well.getSubCode());
- WellReference wellReference = new WellReference(location, well.getContainer().getPermId());
- return wellReference;
- }
-
- private static Set<PlateIdentifier> extractIdentifiers(List<Sample> plates)
- {
- Set<PlateIdentifier> idents = new HashSet<PlateIdentifier>();
- for (Sample plate : plates)
- {
- idents.add(PlateIdentifier.createFromPermId(plate.getPermId()));
- }
- return idents;
- }
-
- private static ListOrSearchSampleCriteria createWellsCriteria(List<Sample> plates)
- {
- Collection<Long> plateIds = new ArrayList<Long>();
- for (Sample plate : plates)
- {
- plateIds.add(plate.getId());
- }
- ListOrSearchSampleCriteria criteria =
- new ListOrSearchSampleCriteria(
- ListOrSearchSampleCriteria.createForContainers(plateIds));
- return criteria;
- }
-
- private static ListOrSearchSampleCriteria createExperientCriteria(long expId)
- {
- return new ListOrSearchSampleCriteria(
- ListOrSearchSampleCriteria.createForExperiment(new TechId(expId)));
- }
-
- private static Map<WellReference, FeatureVectorValues> createWellToFeatureVectorMap(
- WellFeatureCollection<FeatureVectorValues> featureVectors)
- {
- Map<WellReference, FeatureVectorValues> wellToFeatureVectorMap =
- new HashMap<WellReference, FeatureVectorValues>();
- for (FeatureVectorValues featureValues : featureVectors.getFeatures())
- {
- WellReference wellReference = featureValues.getWellReference();
- wellToFeatureVectorMap.put(wellReference, featureValues);
- }
- return wellToFeatureVectorMap;
- }
-
}
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 75b8031116b..f3d20c0efe6 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
@@ -29,21 +29,21 @@ import ch.systemsx.cisd.common.collections.IKeyExtractor;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
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.logic.dto.IWellData;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellExtendedData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellDataLoader.MaterialIdSummaryAndFeatures;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialAllReplicasFeatureVectors;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialBiologicalReplicateFeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialTechnicalReplicateFeatureVector;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellDataCollection;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialBiologicalReplicateFeatureSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaFeatureSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaFeatureSummaryResult;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
/**
* For the specified material in the specified experiment loads feature vectors (details and
@@ -52,7 +52,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummar
*
* @author Tomasz Pylak
*/
-public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorSummaryLoader
+public class MaterialFeatureVectorSummaryLoader extends AbstractContentLoader
{
/**
* For comments {@See MaterialFeatureVectorSummaryLoader}.
@@ -165,40 +165,56 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
// ----------------------
+ private final MaterialSummarySettings settings;
+
+ private final WellDataLoader wellDataLoader;
+
@Private
MaterialFeatureVectorSummaryLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
MaterialSummarySettings settings)
{
- super(session, businessObjectFactory, daoFactory, settings);
+ super(session, businessObjectFactory, daoFactory);
+ this.settings = settings;
+ this.wellDataLoader =
+ new WellDataLoader(session, businessObjectFactory, daoFactory, settings);
+
}
private MaterialAllReplicasFeatureVectors tryLoadMaterialFeatureVectors(TechId materialId,
TechId experimentId)
{
- // TODO KE: 2011-07-15 this should also be changed
- LoaderParameters params = new LoaderParameters(experimentId, null);
- WellDataCollection experimentWells = tryLoadWellData(params);
- if (experimentWells == null)
+ // TODO KE: 2011-07-15 specify analysis procedure
+ AnalysisProcedureCriteria analysisProcedureCriteria =
+ AnalysisProcedureCriteria.createAllProcedures();
+ MaterialIdSummaryAndFeatures summaries =
+ wellDataLoader.tryCalculateExperimentFeatureVectorSummaries(experimentId,
+ analysisProcedureCriteria, materialId, true);
+ if (summaries == null)
{
return null;
}
- return tryLoadMaterialFeatureVectors(materialId, experimentWells);
- }
-
- @Private
- MaterialAllReplicasFeatureVectors tryLoadMaterialFeatureVectors(TechId materialId,
- WellDataCollection experimentWells)
- {
- List<IWellExtendedData> experimentWellsData = experimentWells.getWellDataList();
MaterialIdFeatureVectorSummary materialGeneralSummary =
- tryCalculateMaterialSummary(materialId, experimentWellsData);
+ tryFindMaterialSummary(materialId, summaries.getFeatureSummaries());
if (materialGeneralSummary == null)
{
return null;
}
- List<IWellExtendedData> materialWellsData =
- filterWellsByMaterial(experimentWellsData, materialId);
+ List<WellExtendedData> materialWellsData =
+ wellDataLoader.tryLoadWellData(materialId, experimentId, analysisProcedureCriteria);
+ if (materialWellsData == null)
+ {
+ return null;
+ }
+ return createMaterialFeatureVectors(materialId, materialWellsData, materialGeneralSummary,
+ summaries.getFeatureNames());
+ }
+
+ @Private
+ MaterialAllReplicasFeatureVectors createMaterialFeatureVectors(TechId materialId,
+ List<WellExtendedData> materialWellsData,
+ MaterialIdFeatureVectorSummary materialGeneralSummary, List<CodeAndLabel> featureNames)
+ {
ReplicateSequenceProvider replicaSequences =
new ReplicateSequenceProvider(materialWellsData,
settings.getBiologicalReplicatePropertyTypeCodes());
@@ -208,14 +224,14 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
List<MaterialTechnicalReplicateFeatureVector> replicas =
filterDirectTechnicalReplicas(materialWellsData, replicaSequences);
- return new MaterialAllReplicasFeatureVectors(experimentWells.getFeatureDescriptions(),
- materialGeneralSummary, subgroups, replicas);
+ return new MaterialAllReplicasFeatureVectors(featureNames, materialGeneralSummary,
+ subgroups, replicas);
}
private List<MaterialBiologicalReplicateFeatureVector> createBiologicalReplicates(
- List<IWellExtendedData> materialWells, ReplicateSequenceProvider replicaSequences)
+ List<WellExtendedData> materialWells, ReplicateSequenceProvider replicaSequences)
{
- GroupByMap<Integer, IWellExtendedData> biologicalReplicateMap =
+ GroupByMap<Integer, WellExtendedData> biologicalReplicateMap =
groupByBiologicalReplicate(materialWells, replicaSequences);
List<MaterialBiologicalReplicateFeatureVector> subgroups =
@@ -223,7 +239,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
MaterialReplicaSummaryAggregationType aggregationType = settings.getAggregationType();
for (Integer biologicalReplicateSeq : replicaSequences.getBiologicalReplicateSequences())
{
- List<IWellExtendedData> technicalReplicateWells =
+ List<WellExtendedData> technicalReplicateWells =
biologicalReplicateMap.getOrDie(biologicalReplicateSeq);
MaterialBiologicalReplicateFeatureVector subgroup =
createBiologicalReplicate(technicalReplicateWells, replicaSequences,
@@ -234,7 +250,7 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
}
private MaterialBiologicalReplicateFeatureVector createBiologicalReplicate(
- List<IWellExtendedData> technicalReplicateWells,
+ List<WellExtendedData> technicalReplicateWells,
ReplicateSequenceProvider replicaSequences,
MaterialReplicaSummaryAggregationType aggregationType)
{
@@ -248,37 +264,28 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
aggregationType, subgroupLabel);
}
- private String getSubgroupLabel(List<IWellExtendedData> subgroupWellDataList,
+ private String getSubgroupLabel(List<WellExtendedData> subgroupWellDataList,
ReplicateSequenceProvider replicaSequences)
{
assert subgroupWellDataList.size() > 0 : "empty subgroup";
// all wells belong to the same subgroup, so it does not matter which one we take
- Sample well = subgroupWellDataList.get(0).getWell();
+ IEntityPropertiesHolder well = subgroupWellDataList.get(0);
String label = replicaSequences.tryGetBiologicalReplicateLabel(well);
assert label != null : "no biological replicates!";
return label;
}
- private MaterialIdFeatureVectorSummary tryCalculateMaterialSummary(TechId materialId,
- List<? extends IWellData> experimentWellDataList)
- {
- List<MaterialIdFeatureVectorSummary> featureSummaries =
- WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(
- experimentWellDataList, settings.getAggregationType(), true);
- return tryFindMaterialSummary(materialId, featureSummaries);
- }
-
// chooses wells which have no information about which biological replicate they are
private static List<MaterialTechnicalReplicateFeatureVector> filterDirectTechnicalReplicas(
- List<IWellExtendedData> materialWellDataList,
+ List<WellExtendedData> materialWellDataList,
final ReplicateSequenceProvider replicaSequences)
{
- List<IWellExtendedData> directTechnicalReplicas =
+ List<WellExtendedData> directTechnicalReplicas =
CollectionUtils.filter(materialWellDataList,
- new ICollectionFilter<IWellExtendedData>()
+ new ICollectionFilter<WellExtendedData>()
{
- public boolean isPresent(IWellExtendedData element)
+ public boolean isPresent(WellExtendedData element)
{
return replicaSequences.isBiologicalReplicate(element) == false;
}
@@ -288,11 +295,11 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
}
private static List<MaterialTechnicalReplicateFeatureVector> createTechnicalReplicates(
- List<IWellExtendedData> wells, final ReplicateSequenceProvider replicaSequences)
+ List<WellExtendedData> wells, final ReplicateSequenceProvider replicaSequences)
{
List<MaterialTechnicalReplicateFeatureVector> replicas =
new ArrayList<MaterialTechnicalReplicateFeatureVector>();
- for (IWellExtendedData wellData : wells)
+ for (WellExtendedData wellData : wells)
{
int replicaSequenceNumber = replicaSequences.getTechnicalReplicateSequence(wellData);
MaterialTechnicalReplicateFeatureVector featureVector =
@@ -304,12 +311,12 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
}
private static void sortByTechnicalReplicateSequence(
- List<IWellExtendedData> materialWellDataList,
+ List<WellExtendedData> materialWellDataList,
final ReplicateSequenceProvider replicaSequences)
{
- Collections.sort(materialWellDataList, new Comparator<IWellExtendedData>()
+ Collections.sort(materialWellDataList, new Comparator<WellExtendedData>()
{
- public int compare(IWellExtendedData w1, IWellExtendedData w2)
+ public int compare(WellExtendedData w1, WellExtendedData w2)
{
Integer replicaSequenceNumber1 =
replicaSequences.getTechnicalReplicateSequence(w1);
@@ -320,33 +327,19 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
});
}
- private static List<IWellExtendedData> filterWellsByMaterial(
- List<IWellExtendedData> wellDataList, final TechId materialTechId)
- {
- final Long materialId = materialTechId.getId();
- return CollectionUtils.filter(wellDataList, new ICollectionFilter<IWellExtendedData>()
- {
- public boolean isPresent(IWellExtendedData element)
- {
- return materialId.equals(element.getReplicaMaterialId());
- }
- });
- }
-
/**
* A subgroup can be e.g. oligo or compound concentration.
*/
- private GroupByMap<Integer, IWellExtendedData> groupByBiologicalReplicate(
- List<IWellExtendedData> materialWellDataList,
+ private GroupByMap<Integer, WellExtendedData> groupByBiologicalReplicate(
+ List<WellExtendedData> materialWellDataList,
final ReplicateSequenceProvider replicaSequences)
{
return GroupByMap.create(materialWellDataList,
- new IKeyExtractor<Integer, IWellExtendedData>()
+ new IKeyExtractor<Integer, WellExtendedData>()
{
- public Integer getKey(IWellExtendedData wellData)
+ public Integer getKey(WellExtendedData wellData)
{
- return replicaSequences.tryGetBiologicalReplicateSequence(wellData
- .getWell());
+ return replicaSequences.tryGetBiologicalReplicateSequence(wellData);
}
});
}
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 2e72507c65d..71b827dc71a 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
@@ -18,11 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
import org.apache.commons.lang.time.StopWatch;
@@ -34,21 +30,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
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.ExperimentReferenceQueryResult;
import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
-import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.PatternMatchingUtils;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSimpleFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
/**
* Finds all experiments where the given material is present and calculates summaries for feature
@@ -65,18 +51,17 @@ public class MaterialFeaturesFromAllExperimentsLoader extends AbstractContentLoa
IDAOFactory daoFactory, TechId materialId, TechId projectTechIdOrNull,
MaterialSummarySettings settings)
{
- IScreeningQuery dao = createDAO(daoFactory);
+ MaterialFeaturesFromAllExperimentsLoader loader =
+ new MaterialFeaturesFromAllExperimentsLoader(session, businessObjectFactory,
+ daoFactory, settings);
List<ExperimentReference> experiments =
- fetchExperiments(materialId, projectTechIdOrNull, dao);
-
- return new MaterialFeaturesFromAllExperimentsLoader(session, businessObjectFactory,
- daoFactory, dao, settings).loadMaterialFeatureVectorsFromAllAssays(materialId,
- experiments);
+ loader.fetchExperiments(materialId, projectTechIdOrNull);
+ return loader.loadMaterialFeatureVectorsFromAllAssays(materialId, experiments);
}
- private static List<ExperimentReference> fetchExperiments(TechId materialId,
- TechId projectTechIdOrNull, IScreeningQuery dao)
+ private List<ExperimentReference> fetchExperiments(TechId materialId, TechId projectTechIdOrNull)
{
+ IScreeningQuery dao = getScreeningDAO();
List<ExperimentReferenceQueryResult> experimentRefs;
if (projectTechIdOrNull == null)
{
@@ -111,42 +96,15 @@ public class MaterialFeaturesFromAllExperimentsLoader extends AbstractContentLoa
exp.exp_type_code, exp.proj_code, exp.space_code);
}
- private final MaterialSummarySettings settings;
-
- private final IScreeningQuery screeningQuery;
+ private final WellDataLoader wellDataLoader;
private MaterialFeaturesFromAllExperimentsLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- IScreeningQuery screeningQuery, MaterialSummarySettings settings)
+ MaterialSummarySettings settings)
{
super(session, businessObjectFactory, daoFactory);
- this.settings = settings;
- this.screeningQuery = screeningQuery;
- }
-
- private List<BasicWellContentQueryResult> fetchWellLocations(
- List<ExperimentReference> experiments)
- {
- StopWatch watch = createWatchAndStart();
- String materialTypePattern =
- PatternMatchingUtils.asPostgresSimilarExpression(settings
- .getReplicaMatrialTypeSubstrings());
- List<BasicWellContentQueryResult> wells =
- screeningQuery.getPlateLocationsForExperiment(extractIds(experiments),
- materialTypePattern);
- operationLog.info("[" + watch.getTime() + " msec] Fetching " + wells.size() + " wells.");
- return wells;
- }
-
- private static long[] extractIds(List<ExperimentReference> experiments)
- {
- long[] ids = new long[experiments.size()];
- int i = 0;
- for (ExperimentReference experiment : experiments)
- {
- ids[i++] = experiment.getId();
- }
- return ids;
+ this.wellDataLoader =
+ new WellDataLoader(session, businessObjectFactory, daoFactory, settings);
}
/**
@@ -182,7 +140,8 @@ public class MaterialFeaturesFromAllExperimentsLoader extends AbstractContentLoa
operationLog.info(String.format("Processing %d experiments with %d datasets: %s",
experimentsBatch.size(), datasetsInBatch, experimentsBatch));
List<MaterialSimpleFeatureVectorSummary> batchSummaries =
- loadMaterialFeatureVectorsFromAllAssaysBatch(materialId, experimentsBatch);
+ wellDataLoader.loadMaterialFeatureVectorsFromAllAssaysBatch(materialId,
+ experimentsBatch);
summaries.addAll(batchSummaries);
experimentsBatch.clear();
datasetsInBatch = 0;
@@ -194,54 +153,6 @@ public class MaterialFeaturesFromAllExperimentsLoader extends AbstractContentLoa
return summaries;
}
- // load all experiments in a constant number of selects
- private List<MaterialSimpleFeatureVectorSummary> loadMaterialFeatureVectorsFromAllAssaysBatch(
- TechId materialId, List<ExperimentReference> experiments)
- {
- List<MaterialSimpleFeatureVectorSummary> summaries =
- new ArrayList<MaterialSimpleFeatureVectorSummary>();
- StopWatch watch = createWatchAndStart();
- int totalWellsLoaded = 0;
- int totalFeatureVectorsLoaded = 0;
-
- List<BasicWellContentQueryResult> allWells = fetchWellLocations(experiments);
- totalWellsLoaded += allWells.size();
- Set<PlateIdentifier> plates = extractPlates(allWells);
- WellFeatureCollection<FeatureVectorValues> allWellFeaturesOrNull =
- tryLoadWellSingleFeatureVectors(plates);
-
- if (allWellFeaturesOrNull == null)
- {
- addEmptySummaries(summaries, experiments);
- } else
- {
- for (ExperimentReference experiment : experiments)
- {
- totalFeatureVectorsLoaded += allWellFeaturesOrNull.getFeatures().size();
- Map<WellReference, Long/* material id */> wellToMaterialMap =
- createWellToMaterialMapForExperiment(allWells, experiment);
-
- MaterialSimpleFeatureVectorSummary summary =
- calculateExperimentFeatureVectorSummary(materialId, experiment,
- allWellFeaturesOrNull, wellToMaterialMap);
- summaries.add(summary);
- }
- }
- operationLog.info(String.format(
- "[%d msec] Experiments batch: %d, wells loaded: %d, feature vectors: %d.",
- watch.getTime(), experiments.size(), totalWellsLoaded, totalFeatureVectorsLoaded));
- return summaries;
- }
-
- private void addEmptySummaries(List<MaterialSimpleFeatureVectorSummary> summaries,
- List<ExperimentReference> experiments)
- {
- for (ExperimentReference experiment : experiments)
- {
- summaries.add(new MaterialSimpleFeatureVectorSummary(experiment));
- }
- }
-
private int countAnalysisDatasets(ExperimentReference experiment)
{
List<TechId> experiments = Arrays.asList(new TechId(experiment.getId()));
@@ -250,117 +161,4 @@ public class MaterialFeaturesFromAllExperimentsLoader extends AbstractContentLoa
return ScreeningUtils.filterImageAnalysisDatasets(datasets).size();
}
- private StopWatch createWatchAndStart()
- {
- StopWatch watch = new StopWatch();
- watch.start();
- return watch;
- }
-
- private static Map<WellReference, Long/* material id */> createWellToMaterialMapForExperiment(
- List<BasicWellContentQueryResult> wells, ExperimentReference experiment)
- {
- Map<WellReference, Long> wellToMaterialMap = new HashMap<WellReference, Long>();
- for (BasicWellContentQueryResult well : wells)
- {
- if (belongsToExperiment(well, experiment))
- {
- WellReference wellReference = createWellReference(well);
- wellToMaterialMap.put(wellReference, well.material_content_id);
- }
- }
- return wellToMaterialMap;
- }
-
- private static boolean belongsToExperiment(BasicWellContentQueryResult well,
- ExperimentReference experiment)
- {
- return well.exp_perm_id.equals(experiment.getPermId());
- }
-
- private static WellReference createWellReference(BasicWellContentQueryResult well)
- {
- WellLocation wellLocation = WellLocation.parseLocationStr(well.well_code);
- return new WellReference(wellLocation, well.plate_perm_id);
- }
-
- /**
- * @param experimentWellToMaterialMap wells belonging to the specified experiment
- * @param allFeatures all features, not only for the specified experiment but possibly also for
- * few others
- */
- private MaterialSimpleFeatureVectorSummary calculateExperimentFeatureVectorSummary(
- TechId materialId, ExperimentReference experiment,
- WellFeatureCollection<FeatureVectorValues> allFeatures,
- Map<WellReference, Long> experimentWellToMaterialMap)
- {
- // we have to calculate summaries for all materials in the experiment to get the right
- // ranking of the specified material
- List<IWellData> experimentWellData =
- createWellData(experimentWellToMaterialMap, allFeatures.getFeatures());
- List<MaterialIdFeatureVectorSummary> experimentSummaries =
- WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(
- experimentWellData, settings.getAggregationType(), false);
-
- // select the summary of the right material
- MaterialIdFeatureVectorSummary materialSummary =
- findMaterialSummary(materialId, experimentSummaries);
- return new MaterialSimpleFeatureVectorSummary(experiment,
- allFeatures.getFeatureCodesAndLabels(), materialSummary.getFeatureVectorSummary(),
- materialSummary.getFeatureVectorRanks());
- }
-
- private MaterialIdFeatureVectorSummary findMaterialSummary(TechId materialId,
- List<MaterialIdFeatureVectorSummary> summaries)
- {
- for (MaterialIdFeatureVectorSummary summary : summaries)
- {
- if (summary.getMaterial().equals(materialId.getId()))
- {
- return summary;
- }
- }
- throw new IllegalStateException("It should not happen: no summary found for material "
- + materialId);
- }
-
- // connects each well with a material with its feature vector
- private static List<IWellData> createWellData(
- Map<WellReference, Long/* material id */> experimentWellToMaterialMap,
- List<FeatureVectorValues> allFeatures)
- {
- List<IWellData> experimentWellDataList = new ArrayList<IWellData>();
- for (FeatureVectorValues feature : allFeatures)
- {
- Long materialId = experimentWellToMaterialMap.get(feature.getWellReference());
- if (materialId != null)
- {
- float[] values = WellFeatureCollectionLoader.asFeatureVectorValues(feature);
- IWellData wellData = new WellData(materialId, values);
- experimentWellDataList.add(wellData);
- }
- }
- return experimentWellDataList;
- }
-
- private static Set<PlateIdentifier> extractPlates(List<BasicWellContentQueryResult> allWells)
- {
- Set<PlateIdentifier> plates = new HashSet<PlateIdentifier>();
- for (BasicWellContentQueryResult well : allWells)
- {
- String platePermId = well.plate_perm_id;
- PlateIdentifier plateIdent = PlateIdentifier.createFromPermId(platePermId);
- plates.add(plateIdent);
- }
- return plates;
- }
-
- private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
- Set<PlateIdentifier> plateIdentifiers)
- {
- // TODO KE: 2011-07-15 specify analysis procedure here ?
- return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory)
- .tryLoadWellSingleFeatureVectors(plateIdentifiers, settings.getFeatureCodes(), null);
- }
-
}
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
new file mode 100644
index 00000000000..24c755ace32
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataLoader.java
@@ -0,0 +1,541 @@
+/*
+ * Copyright 2011 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.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import net.lemnik.eodsql.DataIterator;
+
+import org.apache.commons.lang.time.StopWatch;
+
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.collections.CollectionUtils.ICollectionFilter;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.IMaterialBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
+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.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+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.IWellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.PatternMatchingUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.WellContentQueryResult;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorValues;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSimpleFeatureVectorSummary;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
+
+/**
+ * Loads well's feature vectors and materials and calculates summaries.
+ *
+ * @author Tomasz Pylak
+ */
+class WellDataLoader extends AbstractContentLoader
+{
+ private final MaterialSummarySettings settings;
+
+ public WellDataLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
+ IDAOFactory daoFactory, MaterialSummarySettings settings)
+ {
+ super(session, businessObjectFactory, daoFactory);
+ this.settings = settings;
+ }
+
+ /**
+ * Loads feature vectors of each well with the specified material in the specified experiment.
+ */
+ public List<WellExtendedData> tryLoadWellData(TechId materialId, TechId experimentId,
+ AnalysisProcedureCriteria analysisProcedureCriteria)
+ {
+ List<WellContentQueryResult> wells =
+ getPlateLocationsForMaterialId(materialId, experimentId);
+ List<WellData> wellsData =
+ tryCreateWellDataForMaterial(wells, materialId, analysisProcedureCriteria);
+ if (wellsData == null)
+ {
+ return null;
+ }
+ Map<WellReference, Sample> wellRefToSampleMap = loadEnrichedWellSamples(wells);
+ return createWellExtendedData(wellsData, wellRefToSampleMap);
+ }
+
+ private List<WellContentQueryResult> getPlateLocationsForMaterialId(TechId materialId,
+ TechId experimentId)
+ {
+ DataIterator<WellContentQueryResult> wellsIterator =
+ getScreeningDAO().getPlateLocationsForMaterialId(materialId.getId(),
+ experimentId.getId());
+
+ List<WellContentQueryResult> wells = new ArrayList<WellContentQueryResult>();
+ for (WellContentQueryResult well : wellsIterator)
+ {
+ wells.add(well);
+ }
+ return wells;
+ }
+
+ private Map<WellReference, Sample> loadEnrichedWellSamples(
+ Iterable<WellContentQueryResult> wells)
+ {
+ Set<Long> wellIds = extractWellIds(wells);
+ List<Sample> wellSamples = loadSamplesWithMaterialPropertiesEnriched(wellIds);
+ return asWellRefToSampleMap(wellSamples, wells);
+ }
+
+ private List<WellData> tryCreateWellDataForMaterial(Iterable<WellContentQueryResult> wells,
+ TechId materialId, AnalysisProcedureCriteria analysisProcedureCriteria)
+ {
+ WellFeatureCollection<FeatureVectorValues> allWellFeatures =
+ tryLoadWellSingleFeatureVectors(wells, analysisProcedureCriteria);
+ if (allWellFeatures == null)
+ {
+ return null;
+ }
+ List<FeatureVectorValues> features = allWellFeatures.getFeatures();
+ Map<WellReference, Long> dummyMaterialMap = createDummyMaterialMap(wells, materialId);
+ return createWellData(dummyMaterialMap, features);
+ }
+
+ private Map<WellReference, Long/* material id */> createDummyMaterialMap(
+ Iterable<WellContentQueryResult> wells, TechId materialId)
+ {
+ Map<WellReference, Long> experimentWellToMaterialMap = new HashMap<WellReference, Long>();
+ for (WellContentQueryResult well : wells)
+ {
+ WellReference wellReference = well.getWellReference();
+ experimentWellToMaterialMap.put(wellReference, materialId.getId());
+ }
+ return experimentWellToMaterialMap;
+ }
+
+ private static Map<WellReference, Sample> asWellRefToSampleMap(List<Sample> wellSamples,
+ Iterable<WellContentQueryResult> wells)
+ {
+ Map<WellReference, Sample> wellRefToSampleMap = new HashMap<WellReference, Sample>();
+ Map<Long, Sample> idToSampleMap = asSampleIdMap(wellSamples);
+ for (WellContentQueryResult well : wells)
+ {
+ Sample sample = idToSampleMap.get(well.well_id);
+ wellRefToSampleMap.put(well.getWellReference(), sample);
+ }
+ return wellRefToSampleMap;
+ }
+
+ private List<WellExtendedData> createWellExtendedData(List<WellData> wellsData,
+ final Map<WellReference, Sample> wellRefToSampleMap)
+ {
+ return CollectionUtils.map(wellsData,
+ new CollectionUtils.ICollectionMappingFunction<WellExtendedData, WellData>()
+ {
+ public WellExtendedData map(WellData wellData)
+ {
+ WellReference wellReference = wellData.tryGetWellReference();
+ assert wellReference != null : "wellReference not available for "
+ + wellData;
+ Sample wellSample = wellRefToSampleMap.get(wellReference);
+ assert wellSample != null : "Cannot find a sample for " + wellReference;
+
+ return new WellExtendedData(wellData, wellSample);
+ }
+ });
+ }
+
+ private static Map<Long, Sample> asSampleIdMap(List<Sample> samples)
+ {
+ Map<Long/* sample id */, Sample> map = new HashMap<Long, Sample>();
+ for (Sample sample : samples)
+ {
+ map.put(sample.getId(), sample);
+ }
+ return map;
+ }
+
+ private List<Sample> loadSamplesWithMaterialPropertiesEnriched(Set<Long> wellIds)
+ {
+ ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(wellIds);
+ ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
+ List<Sample> wellSamples = sampleLister.list(criteria);
+
+ IMaterialLister materialLister = businessObjectFactory.createMaterialLister(session);
+ List<Material> containedMaterials = getMaterialsWithDuplicates(wellSamples);
+ materialLister.enrichWithProperties(containedMaterials);
+
+ return wellSamples;
+ }
+
+ /**
+ * Return *all* material objects contained in the wells as list. The list can contained
+ * different objects representing the same entity in the database, but we need the duplication
+ * to be able to populate an object graph with wells correctly.
+ */
+ private static List<Material> getMaterialsWithDuplicates(List<Sample> samples)
+ {
+ List<Material> materials = new ArrayList<Material>();
+ for (Sample sample : samples)
+ {
+ for (IEntityProperty property : sample.getProperties())
+ {
+ Material materialOrNull = property.getMaterial();
+ if (materialOrNull != null)
+ {
+ materials.add(materialOrNull);
+ }
+ }
+ }
+ return materials;
+ }
+
+ private static Set<Long> extractWellIds(Iterable<WellContentQueryResult> wells)
+ {
+ Set<Long> ids = new HashSet<Long>();
+ for (WellContentQueryResult well : wells)
+ {
+ ids.add(well.well_id);
+ }
+ return ids;
+ }
+
+ /**
+ * Calculates summaries of feature vectors for each experiment and a specified material. Uses a
+ * constant number of selects.
+ */
+ public List<MaterialSimpleFeatureVectorSummary> loadMaterialFeatureVectorsFromAllAssaysBatch(
+ TechId materialId, List<ExperimentReference> experiments)
+ {
+ List<MaterialSimpleFeatureVectorSummary> summaries =
+ new ArrayList<MaterialSimpleFeatureVectorSummary>();
+ StopWatch watch = createWatchAndStart();
+ int totalWellsLoaded = 0;
+ int totalFeatureVectorsLoaded = 0;
+
+ List<BasicWellContentQueryResult> allWells =
+ fetchWellLocations(materialId, extractIds(experiments));
+ totalWellsLoaded += allWells.size();
+ // TODO KE: 2011-07-15 specify analysis procedure here
+ WellFeatureCollection<FeatureVectorValues> allWellFeaturesOrNull =
+ tryLoadWellSingleFeatureVectors(allWells,
+ AnalysisProcedureCriteria.createAllProcedures());
+
+ if (allWellFeaturesOrNull == null)
+ {
+ addEmptySummaries(summaries, experiments);
+ } else
+ {
+ for (ExperimentReference experiment : experiments)
+ {
+ totalFeatureVectorsLoaded += allWellFeaturesOrNull.getFeatures().size();
+ List<BasicWellContentQueryResult> experimentWells =
+ filterExperimentWells(allWells, experiment.getPermId());
+ List<MaterialIdFeatureVectorSummary> experimentSummaries =
+ calculateExperimentFeatureVectorSummaries(experimentWells,
+ allWellFeaturesOrNull, false);
+
+ MaterialSimpleFeatureVectorSummary summary =
+ findExperimentFeatureVectorSummary(materialId, experiment,
+ allWellFeaturesOrNull.getFeatureCodesAndLabels(),
+ experimentSummaries);
+ summaries.add(summary);
+ }
+ }
+ operationLog.info(String.format(
+ "[%d msec] Experiments batch: %d, wells loaded: %d, feature vectors: %d.",
+ watch.getTime(), experiments.size(), totalWellsLoaded, totalFeatureVectorsLoaded));
+ return summaries;
+ }
+
+ private static long[] extractIds(List<ExperimentReference> experiments)
+ {
+ long[] ids = new long[experiments.size()];
+ int i = 0;
+ for (ExperimentReference experiment : experiments)
+ {
+ ids[i++] = experiment.getId();
+ }
+ return ids;
+ }
+
+ private void addEmptySummaries(List<MaterialSimpleFeatureVectorSummary> summaries,
+ List<ExperimentReference> experiments)
+ {
+ for (ExperimentReference experiment : experiments)
+ {
+ summaries.add(new MaterialSimpleFeatureVectorSummary(experiment));
+ }
+ }
+
+ /**
+ * Fetches wells containing materials of the same type as the specified one in chosen
+ * experiment.
+ */
+ private List<BasicWellContentQueryResult> fetchWellLocations(TechId materialId,
+ TechId experimentId)
+ {
+ return fetchWellLocations(materialId, new long[]
+ { experimentId.getId() });
+ }
+
+ /**
+ * Fetches wells containing materials of the same type as the specified one in chosen
+ * experiments.
+ */
+ private List<BasicWellContentQueryResult> fetchWellLocations(TechId materialId,
+ long[] experimentIds)
+ {
+ String materialTypeCode = fetchMaterialTypeCode(materialId);
+ return fetchWellLocations(materialTypeCode, experimentIds);
+ }
+
+ private List<BasicWellContentQueryResult> fetchWellLocations(String materialTypeCodePattern,
+ long[] experimentIds)
+ {
+ StopWatch watch = createWatchAndStart();
+ List<BasicWellContentQueryResult> wells =
+ getScreeningDAO().getPlateLocationsForExperiment(experimentIds,
+ materialTypeCodePattern);
+ operationLog.info("[" + watch.getTime() + " msec] Fetching " + wells.size() + " wells.");
+ return wells;
+ }
+
+ private List<MaterialIdFeatureVectorSummary> calculateExperimentFeatureVectorSummaries(
+ Iterable<BasicWellContentQueryResult> wells,
+ WellFeatureCollection<FeatureVectorValues> allWellFeatures, boolean calculateDeviations)
+ {
+ List<? extends IWellData> experimentWellData = createWellData(wells, allWellFeatures);
+
+ // We have to calculate summaries for all materials in the experiment to get the
+ // right ranking of the specified material.
+ return calculateExperimentFeatureVectorSummaries(experimentWellData, calculateDeviations);
+ }
+
+ private List<WellData> createWellData(Iterable<BasicWellContentQueryResult> wells,
+ WellFeatureCollection<FeatureVectorValues> allWellFeatures)
+ {
+ Map<WellReference, Long/* material id */> wellToMaterialMap =
+ createWellToMaterialMap(wells);
+ return createWellData(wellToMaterialMap, allWellFeatures.getFeatures());
+ }
+
+ private String fetchMaterialTypeCode(TechId materialId)
+ {
+ IMaterialBO materialBO = businessObjectFactory.createMaterialBO(session);
+ materialBO.loadDataByTechId(materialId);
+ return materialBO.getMaterial().getEntityType().getCode();
+ }
+
+ // NOTE: if there are 2 materials in a well, a random one will be chosen
+ private static Map<WellReference, Long/* material id */> createWellToMaterialMap(
+ Iterable<BasicWellContentQueryResult> wells)
+ {
+ Map<WellReference, Long> wellToMaterialMap = new HashMap<WellReference, Long>();
+ for (BasicWellContentQueryResult well : wells)
+ {
+ WellReference wellReference = well.getWellReference();
+ wellToMaterialMap.put(wellReference, well.material_content_id);
+ }
+ return wellToMaterialMap;
+ }
+
+ private static List<BasicWellContentQueryResult> filterExperimentWells(
+ List<BasicWellContentQueryResult> wells, final String experimentPermId)
+ {
+ return CollectionUtils.filter(wells, new ICollectionFilter<BasicWellContentQueryResult>()
+ {
+ public boolean isPresent(BasicWellContentQueryResult well)
+ {
+ return belongsToExperiment(well, experimentPermId);
+ }
+ });
+ }
+
+ private static boolean belongsToExperiment(BasicWellContentQueryResult well,
+ String experimentPermId)
+ {
+ return well.exp_perm_id.equals(experimentPermId);
+ }
+
+ private MaterialSimpleFeatureVectorSummary findExperimentFeatureVectorSummary(
+ TechId materialId, ExperimentReference experiment, List<CodeAndLabel> features,
+ List<MaterialIdFeatureVectorSummary> experimentSummaries)
+ {
+ // select the summary of the right material
+ MaterialIdFeatureVectorSummary materialSummary =
+ findMaterialSummary(materialId, experimentSummaries);
+ return new MaterialSimpleFeatureVectorSummary(experiment, features,
+ materialSummary.getFeatureVectorSummary(), materialSummary.getFeatureVectorRanks());
+ }
+
+ private List<MaterialIdFeatureVectorSummary> calculateExperimentFeatureVectorSummaries(
+ List<? extends IWellData> experimentWellData, boolean calculateDeviations)
+ {
+ return WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(
+ experimentWellData, settings.getAggregationType(), calculateDeviations);
+ }
+
+ private static MaterialIdFeatureVectorSummary findMaterialSummary(TechId materialId,
+ List<MaterialIdFeatureVectorSummary> summaries)
+ {
+ for (MaterialIdFeatureVectorSummary summary : summaries)
+ {
+ if (summary.getMaterial().equals(materialId.getId()))
+ {
+ return summary;
+ }
+ }
+ throw new IllegalStateException("It should not happen: no summary found for material "
+ + materialId);
+ }
+
+ // connects each well with a material with its feature vector
+ private static List<WellData> createWellData(
+ Map<WellReference, Long/* material id */> experimentWellToMaterialMap,
+ List<FeatureVectorValues> allFeatures)
+ {
+ List<WellData> experimentWellDataList = new ArrayList<WellData>();
+ for (FeatureVectorValues feature : allFeatures)
+ {
+ WellReference wellReference = feature.getWellReference();
+ Long materialId = experimentWellToMaterialMap.get(wellReference);
+ if (materialId != null)
+ {
+ float[] values = WellFeatureCollectionLoader.asFeatureVectorValues(feature);
+ WellData wellData = new WellData(materialId, values, wellReference);
+ experimentWellDataList.add(wellData);
+ }
+ }
+ return experimentWellDataList;
+ }
+
+ private static Set<PlateIdentifier> extractPlates(Iterable<? extends IWellReference> allWells)
+ {
+ Set<PlateIdentifier> plates = new HashSet<PlateIdentifier>();
+ for (IWellReference well : allWells)
+ {
+ String platePermId = well.getPlatePermId();
+ PlateIdentifier plateIdent = PlateIdentifier.createFromPermId(platePermId);
+ plates.add(plateIdent);
+ }
+ return plates;
+ }
+
+ private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
+ Iterable<? extends IWellReference> allWells,
+ AnalysisProcedureCriteria analysisProcedureCriteria)
+ {
+ Set<PlateIdentifier> plates = extractPlates(allWells);
+ return tryLoadWellSingleFeatureVectors(plates, analysisProcedureCriteria);
+ }
+
+ private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
+ Set<PlateIdentifier> plates, AnalysisProcedureCriteria analysisProcedureCriteria)
+ {
+ return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory)
+ .tryLoadWellSingleFeatureVectors(plates, settings.getFeatureCodes(),
+ analysisProcedureCriteria);
+ }
+
+ /**
+ * Calculates summaries of feature vectors for each material of the specified type in the given
+ * experiment.
+ */
+ public MaterialIdSummaryAndFeatures tryCalculateExperimentFeatureVectorSummaries(
+ TechId experimentId, String[] replicaMaterialTypeSubstrings,
+ AnalysisProcedureCriteria analysisProcedureCriteria, boolean calculateDeviations)
+ {
+ String typePatterns =
+ PatternMatchingUtils.asPostgresSimilarExpression(settings
+ .getReplicaMaterialTypeSubstrings());
+ List<BasicWellContentQueryResult> wells = fetchWellLocations(typePatterns, new long[]
+ { experimentId.getId() });
+ return tryCalculateExperimentFeatureVectorSummaries(wells, analysisProcedureCriteria,
+ calculateDeviations);
+ }
+
+ /**
+ * Calculates summaries of feature vectors for each material in the given experiment. A material
+ * of one well is chosen by filtering materials of the same type as the specified one.
+ */
+ public MaterialIdSummaryAndFeatures tryCalculateExperimentFeatureVectorSummaries(
+ TechId experimentId, AnalysisProcedureCriteria analysisProcedureCriteria,
+ TechId materialId, boolean calculateDeviations)
+ {
+ List<BasicWellContentQueryResult> wells = fetchWellLocations(materialId, experimentId);
+ return tryCalculateExperimentFeatureVectorSummaries(wells, analysisProcedureCriteria,
+ calculateDeviations);
+ }
+
+ private MaterialIdSummaryAndFeatures tryCalculateExperimentFeatureVectorSummaries(
+ List<BasicWellContentQueryResult> wells,
+ AnalysisProcedureCriteria analysisProcedureCriteria, boolean calculateDeviations)
+ {
+ WellFeatureCollection<FeatureVectorValues> allWellFeatures =
+ tryLoadWellSingleFeatureVectors(wells, analysisProcedureCriteria);
+
+ if (allWellFeatures == null)
+ {
+ return null;
+ }
+ List<MaterialIdFeatureVectorSummary> featureSummaries =
+ calculateExperimentFeatureVectorSummaries(wells, allWellFeatures,
+ calculateDeviations);
+ return new MaterialIdSummaryAndFeatures(featureSummaries,
+ allWellFeatures.getFeatureCodesAndLabels());
+ }
+
+ static class MaterialIdSummaryAndFeatures
+ {
+ private final List<MaterialIdFeatureVectorSummary> featureSummaries;
+
+ private final List<CodeAndLabel> featureNames;
+
+ public MaterialIdSummaryAndFeatures(List<MaterialIdFeatureVectorSummary> featureSummaries,
+ List<CodeAndLabel> featureNames)
+ {
+ this.featureSummaries = featureSummaries;
+ this.featureNames = featureNames;
+ }
+
+ public List<MaterialIdFeatureVectorSummary> getFeatureSummaries()
+ {
+ return featureSummaries;
+ }
+
+ public List<CodeAndLabel> getFeatureNames()
+ {
+ return featureNames;
+ }
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
index 0168e77b0ba..d04db25a867 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.common.collections.GroupByMap;
import ch.systemsx.cisd.common.collections.IKeyExtractor;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
/**
@@ -196,7 +196,7 @@ public class WellReplicaSummaryCalculator
{
Long replicaId = entry.getKey();
float[] aggregates = entry.getValue().getAggregates();
- IWellData summaryWellData = new WellExtendedData(replicaId, aggregates, null, null);
+ IWellData summaryWellData = new WellData(replicaId, aggregates, null);
summaryWellDataList.add(summaryWellData);
}
return summaryWellDataList;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/IWellExtendedData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/IWellExtendedData.java
deleted file mode 100644
index b7b821b2fa5..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/IWellExtendedData.java
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2011 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.dto;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-
-/**
- * Enriches interface to access well feature vector with well sample and material metadata.
- *
- * @author Tomasz Pylak
- */
-public interface IWellExtendedData extends IEntityPropertiesHolder, IWellData
-{
- /** Well sample for which the data are provided. */
- Sample getWell();
-
- /**
- * Material in the well which allowed to find replicates (e.g. gene or compound).<br>
- * Note: if the replicaId is the same for two wellData then the returned material is also the
- * same.
- */
- Material getMaterial();
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellData.java
index 3dc98d7fbd3..aa0f33b76d6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellData.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellData.java
@@ -18,6 +18,8 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto;
import java.util.Arrays;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
+
/**
* The simplest implementation of {@Link IWellData}.
*
@@ -29,10 +31,14 @@ public class WellData implements IWellData
private final float[] featureVector;
- public WellData(long replicaId, float[] featureVector)
+ private final WellReference wellReferenceOrNull;
+
+ /** @param wellReferenceOrNull null if these are aggregated data */
+ public WellData(long replicaId, float[] featureVector, WellReference wellReferenceOrNull)
{
this.featureVector = featureVector;
this.replicaId = replicaId;
+ this.wellReferenceOrNull = wellReferenceOrNull;
}
public long getReplicaMaterialId()
@@ -45,6 +51,11 @@ public class WellData implements IWellData
return featureVector;
}
+ public WellReference tryGetWellReference()
+ {
+ return wellReferenceOrNull;
+ }
+
@Override
public String toString()
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellExtendedData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellExtendedData.java
index 32e62f85443..825e925243c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellExtendedData.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellExtendedData.java
@@ -18,36 +18,36 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto;
import java.util.List;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
- * The simplest implementation of {@Link IWellExtendedData}.
+ * Enriches {@link IWellData} interface with well sample.
+ * metadata.
*
* @author Tomasz Pylak
*/
-public class WellExtendedData extends WellData implements IWellExtendedData
+public class WellExtendedData extends WellData implements IEntityPropertiesHolder
{
- private Sample well;
+ private final Sample well;
- private final Material material;
-
- public WellExtendedData(long replicaId, float[] featureVector, Sample well, Material material)
+ public WellExtendedData(WellData wellData, Sample well)
{
- super(replicaId, featureVector);
+ super(wellData.getReplicaMaterialId(), wellData.getFeatureVector(), wellData
+ .tryGetWellReference());
this.well = well;
- this.material = material;
}
+ /** Properties of the well sample for which the data are provided. */
public Sample getWell()
{
return well;
}
- public Material getMaterial()
+ public Long getId()
{
- return material;
+ return well.getId();
}
public List<IEntityProperty> getProperties()
@@ -55,9 +55,4 @@ public class WellExtendedData extends WellData implements IWellExtendedData
return well.getProperties();
}
- public Long getId()
- {
- return well.getId();
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSummarySettings.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSummarySettings.java
index 3c05eae5d5a..08aceb09feb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSummarySettings.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSummarySettings.java
@@ -30,8 +30,8 @@ public class MaterialSummarySettings implements ISerializable
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
/**
- * the name of a material property type that can be rendered as a link to a details view. TODO
- * KE: this should be part of the display settings ?!
+ * The name of a material property type that can be rendered as a link to a details view when a
+ * material is shown.
*/
private String materialDetailsPropertyType;
@@ -39,8 +39,8 @@ public class MaterialSummarySettings implements ISerializable
private String[] replicaMatrialTypeSubstrings;
- // well property codes which links to the material which determins which biological replicate it
- // is, e.g. siRNA or compound
+ // well property codes which links to the material which determines which biological replicate
+ // it is, e.g. siRNA or compound
private List<String> biologicalReplicatePropertyTypeCodes;
private MaterialReplicaSummaryAggregationType aggregationType;
@@ -55,7 +55,7 @@ public class MaterialSummarySettings implements ISerializable
this.featureCodes = featureCodes;
}
- public String[] getReplicaMatrialTypeSubstrings()
+ public String[] getReplicaMaterialTypeSubstrings()
{
return replicaMatrialTypeSubstrings;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
index 1b06ae8365d..4ea1b80c18b 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
@@ -178,7 +178,7 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
{
List<BasicWellContentQueryResult> locations =
EntityListingTestUtils.asList(query.getPlateLocationsForExperiment(new long[]
- { 1, 2 }, "%GENE%"));
+ { 1, 2 }, "GENE"));
AssertJUnit.assertEquals(0, locations.size());
List<ExperimentReferenceQueryResult> experiments = query.getExperimentsWithMaterial(1);
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 709c5b62848..9bf4efbf043 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
@@ -35,12 +35,10 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellExtendedData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialAllReplicasFeatureVectors;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialBiologicalReplicateFeatureVector;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellDataCollection;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
@@ -61,7 +59,7 @@ public class MaterialFeatureVectorSummaryLoaderTest extends AssertJUnit
settings.setAggregationType(MaterialReplicaSummaryAggregationType.MEDIAN);
settings.setBiologicalReplicatePropertyTypeCodes(SIRNA_PROPERTY_TYPE_CODE);
int replId = 0;
- List<IWellExtendedData> wellDataList = Arrays.asList(
+ List<WellExtendedData> wellDataList = Arrays.asList(
// repl. 1 group 1
createSIRNAWellData(replId, 1, 10, 100),
@@ -80,18 +78,13 @@ public class MaterialFeatureVectorSummaryLoaderTest extends AssertJUnit
createSIRNAWellData(replId + 2, 1, 0, 500));
List<CodeAndLabel> featuresDesc =
Arrays.asList(new CodeAndLabel("A", "A"), new CodeAndLabel("B", "B"));
- WellDataCollection wellDataCollection = new WellDataCollection(wellDataList, featuresDesc);
MaterialAllReplicasFeatureVectors featureVectors =
new MaterialFeatureVectorSummaryLoader(null, null, null, settings)
- .tryLoadMaterialFeatureVectors(new TechId(replId), wellDataCollection);
+ .createMaterialFeatureVectors(new TechId(replId), wellDataList, null,
+ featuresDesc);
- MaterialIdFeatureVectorSummary generalSummary = featureVectors.getGeneralSummary();
- assertArraysEqual(new float[]
- { 65, 650 }, generalSummary.getFeatureVectorSummary());
- assertArraysEqual(new int[]
- { 2, 3 }, generalSummary.getFeatureVectorRanks());
- assertEquals(replId, generalSummary.getMaterial().longValue());
+ assertNull(featureVectors.getGeneralSummary());
assertEquals(featuresDesc, featureVectors.getFeatureDescriptions());
int groupId = 1;
@@ -120,7 +113,7 @@ public class MaterialFeatureVectorSummaryLoaderTest extends AssertJUnit
}
- private static IWellExtendedData createSIRNAWellData(long replicaId, long siRNAId,
+ private static WellExtendedData createSIRNAWellData(long replicaId, long siRNAId,
float... featureValues)
{
MaterialEntityProperty subgroupProperty = new MaterialEntityProperty();
@@ -135,7 +128,7 @@ public class MaterialFeatureVectorSummaryLoaderTest extends AssertJUnit
return createWellData(replicaId, subgroupProperty, featureValues);
}
- private static IWellExtendedData createWellData(long replicaId,
+ private static WellExtendedData createWellData(long replicaId,
IEntityProperty subgroupProperty, float... featureValues)
{
Material material = new Material();
@@ -147,6 +140,6 @@ public class MaterialFeatureVectorSummaryLoaderTest extends AssertJUnit
material.setProperties(properties);
well.setProperties(properties);
- return new WellExtendedData(replicaId, featureValues, well, material);
+ return new WellExtendedData(new WellData(replicaId, featureValues, null), well);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellDataCollection.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataCollection.java
similarity index 79%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellDataCollection.java
rename to screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataCollection.java
index 16bb94d2ad3..3053ff786e5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellDataCollection.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellDataCollection.java
@@ -14,11 +14,12 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto;
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
/**
* List of well data and description of each feature.
@@ -27,19 +28,19 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
*/
public class WellDataCollection
{
- private final List<IWellExtendedData> wellDataList;
+ private final List<WellExtendedData> wellDataList;
// has the same length as feature vectors in all wells
private final List<CodeAndLabel> featureDescriptions;
- public WellDataCollection(List<IWellExtendedData> wellDataList,
+ public WellDataCollection(List<WellExtendedData> wellDataList,
List<CodeAndLabel> featureDescriptions)
{
this.wellDataList = wellDataList;
this.featureDescriptions = featureDescriptions;
}
- public List<IWellExtendedData> getWellDataList()
+ public List<WellExtendedData> getWellDataList()
{
return wellDataList;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
index e7e6a9ff2ac..8951f6191e0 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
@@ -33,6 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellReplicaSummaryCalculator.SummaryFeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
@@ -206,7 +207,7 @@ public class WellReplicaSummaryCalculatorTest extends AssertJUnit
{
Material material = new Material();
material.setId(replicaId);
- return new WellExtendedData(replicaId, featureValues, null, material);
+ return new WellExtendedData(new WellData(replicaId, featureValues, null), null);
}
private List<MaterialIdFeatureVectorSummary> calculate(List<IWellData> wellDataList)
--
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