From fd709509bada2ceb36011ce5c153656d4a47549b Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 27 May 2010 07:42:53 +0000
Subject: [PATCH] LMS-1544 Improved performace of listImages and
listFeatureVectors.
SVN: 16139
---
.../screening/server/ScreeningServer.java | 3 +-
.../logic/FeatureVectorDatasetLoader.java | 108 ++++++++
.../server/logic/ImageDatasetLoader.java | 72 +++++
.../server/logic/PlateDatasetLoader.java | 258 ++++++++++++++++++
.../server/logic/ScreeningApiImpl.java | 214 +--------------
.../server/logic/ScreeningUtils.java | 20 ++
.../server/logic/ScreeningApiImplTest.java | 58 ++--
7 files changed, 499 insertions(+), 234 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.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 88134d36778..8c8f91858ce 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
@@ -199,7 +199,8 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
private ScreeningApiImpl createScreeningApiImpl(String sessionToken)
{
final Session session = getSession(sessionToken);
- return new ScreeningApiImpl(session, businessObjectFactory, getDAOFactory());
+ return new ScreeningApiImpl(session, businessObjectFactory, getDAOFactory(),
+ getDataStoreBaseURL());
}
public void logoutScreening(String sessionToken)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
new file mode 100644
index 00000000000..f1fc3a5e4a9
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
@@ -0,0 +1,108 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
+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.shared.api.v1.dto.FeatureVectorDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+class FeatureVectorDatasetLoader extends ImageDatasetLoader
+{
+ // TODO 2010-05-27, CR : See PlateDatasetLoader todo comment
+
+ // Parameter state
+ private final String featureVectorDatasetTypeCode;
+
+ // Running state
+ private List<ExternalData> featureVectorDatasets;
+
+ FeatureVectorDatasetLoader(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, String dataStoreBaseURL,
+ List<? extends PlateIdentifier> plates)
+ {
+ super(session, businessObjectFactory, dataStoreBaseURL, plates);
+ featureVectorDatasetTypeCode = ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE;
+ }
+
+ public List<FeatureVectorDatasetReference> getFeatureVectorDatasets()
+ {
+ // Load the image data sets
+ load();
+ loadFeatureVectorDatasets();
+ return asFeatureVectorDatasets();
+ }
+
+ private void loadFeatureVectorDatasets()
+ {
+ // TODO 2010-05-26, CR, : This is slow if there are a large number of image data sets
+ // Need to add a query to the dataset lister that returns, for a collection of tech ids, a
+ // child datasets and their parents.
+ featureVectorDatasets = new ArrayList<ExternalData>();
+ IDatasetLister datasetLister =
+ businessObjectFactory.createDatasetLister(session, dataStoreBaseURL);
+
+ for (ExternalData data : getDatasets())
+ {
+ List<ExternalData> children =
+ datasetLister.listByParentTechId(new TechId(data.getId()));
+ ArrayList<ExternalData> parentList = new ArrayList<ExternalData>();
+ parentList.add(data);
+ for (ExternalData child : children)
+ {
+ child.setParents(parentList);
+ }
+ featureVectorDatasets.addAll(children);
+ }
+
+ featureVectorDatasets =
+ ScreeningUtils.filterExternalDataByType(featureVectorDatasets,
+ featureVectorDatasetTypeCode);
+ }
+
+ private List<FeatureVectorDatasetReference> asFeatureVectorDatasets()
+ {
+ List<FeatureVectorDatasetReference> result = new ArrayList<FeatureVectorDatasetReference>();
+ for (ExternalData externalData : featureVectorDatasets)
+ {
+ result.add(asFeatureVectorDataset(externalData));
+ }
+ return result;
+ }
+
+ protected FeatureVectorDatasetReference asFeatureVectorDataset(ExternalData externalData)
+ {
+ DataStore dataStore = externalData.getDataStore();
+ ExternalData parentDataset = externalData.getParents().iterator().next();
+ return new FeatureVectorDatasetReference(externalData.getCode(),
+ dataStore.getDownloadUrl(), createPlateIdentifier(parentDataset),
+ extractPlateGeometry(parentDataset), externalData.getRegistrationDate(),
+ asImageDataset(parentDataset));
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
new file mode 100644
index 00000000000..2dee96c43c8
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ImageDatasetLoader.java
@@ -0,0 +1,72 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
+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.shared.api.v1.dto.ImageDatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Utility class for loading image datasets.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+class ImageDatasetLoader extends PlateDatasetLoader
+{
+ // TODO 2010-05-27, CR : See PlateDatasetLoader todo comment
+
+ ImageDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
+ String dataStoreBaseURL, List<? extends PlateIdentifier> plates)
+ {
+ super(session, businessObjectFactory, dataStoreBaseURL, plates,
+ ScreeningConstants.IMAGE_DATASET_TYPE);
+ }
+
+ /**
+ * Return the image datasets for the specified plates.
+ */
+ public List<ImageDatasetReference> getImageDatasets()
+ {
+ load();
+ return asImageDatasets();
+ }
+
+ private List<ImageDatasetReference> asImageDatasets()
+ {
+ List<ImageDatasetReference> result = new ArrayList<ImageDatasetReference>();
+ for (ExternalData externalData : getDatasets())
+ {
+ result.add(asImageDataset(externalData));
+ }
+ return result;
+ }
+
+ protected ImageDatasetReference asImageDataset(ExternalData externalData)
+ {
+ DataStore dataStore = externalData.getDataStore();
+ return new ImageDatasetReference(externalData.getCode(), dataStore.getDownloadUrl(),
+ createPlateIdentifier(externalData), extractPlateGeometry(externalData),
+ externalData.getRegistrationDate());
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java
new file mode 100644
index 00000000000..891e0309cf7
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateDatasetLoader.java
@@ -0,0 +1,258 @@
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+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.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * A helper class for retrieving data sets assocaiated with plates.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+class PlateDatasetLoader
+{
+ // TODO 2010-05-27, CR : This class and its subclasses should be refactored. The subclasses
+ // should become independent and use the dataset loader, instead of being dataset loaders.
+
+ // Infrastructure state
+ protected final Session session;
+
+ protected final IScreeningBusinessObjectFactory businessObjectFactory;
+
+ protected final String dataStoreBaseURL;
+
+ // Parameter state
+ private final List<? extends PlateIdentifier> plates;
+
+ private final String datasetTypeCode;
+
+ // Running state
+ private List<Sample> samples;
+
+ private List<ExternalData> datasets;
+
+ private HashMap<SampleIdentifier, Sample> samplesByIdentifier;
+
+ private HashMap<Long, Sample> samplesById;
+
+ PlateDatasetLoader(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
+ String dataStoreBaseURL, List<? extends PlateIdentifier> plates, String datasetTypeCode)
+ {
+ this.session = session;
+ this.businessObjectFactory = businessObjectFactory;
+ this.dataStoreBaseURL = dataStoreBaseURL;
+ this.plates = plates;
+ this.datasetTypeCode = datasetTypeCode;
+ }
+
+ protected List<ExternalData> getDatasets()
+ {
+ return datasets;
+ }
+
+ /**
+ * Loads the samples and datasets. Call the method before calling {@link #getDatasets()}.
+ */
+ protected void load()
+ {
+ loadSamples();
+ loadDatasets();
+ }
+
+ private void loadSamples()
+ {
+ String[] sampleCodesArray = extractSampleCodes();
+ ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(sampleCodesArray);
+ ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
+ samples = sampleLister.list(criteria);
+ // After loading the samples, we need to initialize the maps because other methods rely
+ // on this.
+ initializeSampleMaps();
+ filterSamplesByPlateIdentifiers();
+ }
+
+ private void loadDatasets()
+ {
+ List<Long> sampleIds = extractSampleIds();
+ IDatasetLister datasetLister =
+ businessObjectFactory.createDatasetLister(session, dataStoreBaseURL);
+ datasets = datasetLister.listBySampleIds(sampleIds);
+ datasets = ScreeningUtils.filterExternalDataByType(datasets, datasetTypeCode);
+ }
+
+ private void initializeSampleMaps()
+ {
+ samplesByIdentifier = new HashMap<SampleIdentifier, Sample>();
+ samplesById = new HashMap<Long, Sample>();
+ for (Sample sample : samples)
+ {
+ samplesByIdentifier.put(createSampleIdentifier(sample), sample);
+ samplesById.put(sample.getId(), sample);
+ }
+ }
+
+ /**
+ * Filter the list of samples, which were selected by code, to those that exactly match the
+ * identifiers in the plates
+ */
+ private void filterSamplesByPlateIdentifiers()
+ {
+ for (PlateIdentifier plate : plates)
+ {
+ Sample sample = samplesByIdentifier.get(createSampleIdentifier(plate));
+ // Make sure the sample and plate have the same *identifier* not just code
+ String plateSpaceCodeOrNull = plate.tryGetSpaceCode();
+ Space sampleSpaceOrNull = sample.getSpace();
+ String sampleSpaceCodeOrNull =
+ (null == sampleSpaceOrNull) ? null : sampleSpaceOrNull.getCode();
+
+ // Remove the sample if they don't match
+ if (plateSpaceCodeOrNull == null)
+ {
+ if (sampleSpaceCodeOrNull != null)
+ {
+ removeSample(sample);
+ }
+ } else if (false == plateSpaceCodeOrNull.equals(sampleSpaceCodeOrNull))
+ {
+ removeSample(sample);
+ }
+ }
+ }
+
+ private void removeSample(Sample sample)
+ {
+ samplesByIdentifier.remove(createSampleIdentifier(sample));
+ samplesById.remove(sample.getId());
+ samples.remove(sample);
+ }
+
+ protected PlateIdentifier createPlateIdentifier(ExternalData parentDataset)
+ {
+ Sample sample = getSample(parentDataset);
+ final String plateCode = sample.getCode();
+ Space space = sample.getSpace();
+ final String spaceCodeOrNull = (space != null) ? space.getCode() : null;
+ return new PlateIdentifier(plateCode, spaceCodeOrNull);
+ }
+
+ protected Geometry extractPlateGeometry(ExternalData dataSet)
+ {
+ Sample sample = getSample(dataSet);
+ List<IEntityProperty> properties = sample.getProperties();
+ for (IEntityProperty property : properties)
+ {
+ PropertyType propertyType = property.getPropertyType();
+ if (propertyType.getCode().equals(ScreeningConstants.PLATE_GEOMETRY))
+ {
+ String code = property.getVocabularyTerm().getCode();
+ int lastIndexOfUnderscore = code.lastIndexOf('_');
+ int lastIndexOfX = code.lastIndexOf('X');
+ if (lastIndexOfUnderscore < 0 || lastIndexOfX < 0)
+ {
+ throw new UserFailureException("Invalid property "
+ + ScreeningConstants.PLATE_GEOMETRY + ": " + code);
+ }
+ try
+ {
+ int width =
+ Integer.parseInt(code
+ .substring(lastIndexOfUnderscore + 1, lastIndexOfX));
+ int height = Integer.parseInt(code.substring(lastIndexOfX + 1));
+ return new Geometry(width, height);
+ } catch (NumberFormatException ex)
+ {
+ throw new UserFailureException("Invalid property "
+ + ScreeningConstants.PLATE_GEOMETRY + ": " + code);
+ }
+
+ }
+ }
+ throw new UserFailureException("Sample " + sample.getIdentifier() + " has no property "
+ + ScreeningConstants.PLATE_GEOMETRY);
+ }
+
+ private Sample getSample(ExternalData dataset)
+ {
+ // Sample may be NULL even though the selector does not begin with try
+ Sample sample = dataset.getSample();
+ assert sample != null : "dataset not connected to a sample: " + dataset;
+
+ // The dataset's reference to the sample is not complete, get the one from the map
+ return samplesById.get(sample.getId());
+ }
+
+ private String[] extractSampleCodes()
+ {
+ ArrayList<String> sampleCodes = new ArrayList<String>();
+ for (PlateIdentifier plate : plates)
+ {
+ sampleCodes.add(plate.getPlateCode());
+ }
+
+ String[] sampleCodesArray = new String[sampleCodes.size()];
+ sampleCodes.toArray(sampleCodesArray);
+
+ return sampleCodesArray;
+ }
+
+ private List<Long> extractSampleIds()
+ {
+ ArrayList<Long> sampleIds = new ArrayList<Long>();
+ for (Sample sample : samples)
+ {
+ sampleIds.add(sample.getId());
+ }
+ return sampleIds;
+ }
+
+ protected static SampleIdentifier createSampleIdentifier(PlateIdentifier plate)
+ {
+ SampleOwnerIdentifier owner;
+ String spaceCode = plate.tryGetSpaceCode();
+ if (spaceCode != null)
+ {
+ SpaceIdentifier space = new SpaceIdentifier(DatabaseInstanceIdentifier.HOME, spaceCode);
+ owner = new SampleOwnerIdentifier(space);
+ } else
+ {
+ owner = new SampleOwnerIdentifier(DatabaseInstanceIdentifier.createHome());
+ }
+ return SampleIdentifier.createOwnedBy(owner, plate.getPlateCode());
+ }
+
+ protected static SampleIdentifier createSampleIdentifier(Sample sample)
+ {
+ SampleOwnerIdentifier owner;
+ Space spaceOrNull = sample.getSpace();
+ String spaceCode = (null == spaceOrNull) ? null : spaceOrNull.getCode();
+ if (spaceCode != null)
+ {
+ SpaceIdentifier space = new SpaceIdentifier(DatabaseInstanceIdentifier.HOME, spaceCode);
+ owner = new SampleOwnerIdentifier(space);
+ } else
+ {
+ owner = new SampleOwnerIdentifier(DatabaseInstanceIdentifier.createHome());
+ }
+ return SampleIdentifier.createOwnedBy(owner, sample.getCode());
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index b52e5304008..f5077638af0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -17,13 +17,10 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
-import java.util.HashSet;
import java.util.List;
-import java.util.Set;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
-import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleTypeDAO;
@@ -34,25 +31,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PropertyTypePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleOwnerIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IDatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
@@ -72,211 +57,32 @@ public class ScreeningApiImpl
private final IDAOFactory daoFactory;
+ private final String dataStoreBaseURL;
+
public ScreeningApiImpl(Session session, IScreeningBusinessObjectFactory businessObjectFactory,
- IDAOFactory daoFactory)
+ IDAOFactory daoFactory, String dataStoreBaseURL)
{
this.session = session;
this.businessObjectFactory = businessObjectFactory;
this.daoFactory = daoFactory;
+ this.dataStoreBaseURL = dataStoreBaseURL;
}
public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
List<? extends PlateIdentifier> plates)
{
- List<FeatureVectorDatasetReference> result = new ArrayList<FeatureVectorDatasetReference>();
- List<ImageDatasetReference> imageDatasets = listImageDatasets(plates);
- ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
- Set<ExperimentPE> visitedExperiments = new HashSet<ExperimentPE>();
- for (PlateIdentifier plate : plates)
- {
- ExperimentPE experiment = tryGetExperiment(sampleBO, plate);
- if (experiment != null && visitedExperiments.contains(experiment) == false)
- {
- List<ExternalDataPE> datasets =
- daoFactory.getExternalDataDAO().listExternalData(experiment);
- List<ExternalDataPE> childrenDatasets = filterChildren(imageDatasets, datasets);
- List<ExternalDataPE> featureVectorDatasets =
- ScreeningUtils.filterDatasetsByType(childrenDatasets,
- ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE);
- result.addAll(asFeatureVectorDatasets(featureVectorDatasets));
- visitedExperiments.add(experiment);
- }
- }
- return result;
- }
+ FeatureVectorDatasetLoader datasetRetriever =
+ new FeatureVectorDatasetLoader(session, businessObjectFactory, dataStoreBaseURL,
+ plates);
+ List<FeatureVectorDatasetReference> result = datasetRetriever.getFeatureVectorDatasets();
- // return those datasets which have exactly one parent, which is contained in the parent set
- private static List<ExternalDataPE> filterChildren(
- List<? extends IDatasetIdentifier> parentDatasets, List<ExternalDataPE> datasets)
- {
- Set<String> parentDatasetCodes = createDatasetCodesSet(parentDatasets);
- List<ExternalDataPE> children = new ArrayList<ExternalDataPE>();
- for (ExternalDataPE dataset : datasets)
- {
- Set<DataPE> parents = dataset.getParents();
- if (parents.size() == 1)
- {
- DataPE parent = parents.iterator().next();
- if (parentDatasetCodes.contains(parent.getCode()))
- {
- children.add(dataset);
- }
- }
- }
- return children;
- }
-
- private static Set<String> createDatasetCodesSet(List<? extends IDatasetIdentifier> datasets)
- {
- Set<String> result = new HashSet<String>();
- for (IDatasetIdentifier dataset : datasets)
- {
- result.add(dataset.getDatasetCode());
- }
return result;
}
- private ExperimentPE tryGetExperiment(ISampleBO sampleBO, PlateIdentifier plate)
- {
- sampleBO.loadBySampleIdentifier(createSampleIdentifier(plate));
- SamplePE sample = sampleBO.getSample();
- return sample.getExperiment();
- }
-
public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates)
{
- List<ExternalDataPE> datasets = loadDatasets(plates, ScreeningConstants.IMAGE_DATASET_TYPE);
- return asImageDatasets(datasets);
- }
-
- // NOTE: this method is slow when a number of plates is big
- private List<ExternalDataPE> loadDatasets(List<? extends PlateIdentifier> plates,
- String datasetTypeCode)
- {
- ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
- List<ExternalDataPE> datasets = new ArrayList<ExternalDataPE>();
- for (PlateIdentifier plate : plates)
- {
- List<ExternalDataPE> plateDatasets = loadDatasets(plate, datasetTypeCode, sampleBO);
- datasets.addAll(plateDatasets);
- }
- return datasets;
- }
-
- private List<ExternalDataPE> loadDatasets(PlateIdentifier plate, String datasetTypeCode,
- ISampleBO sampleBO)
- {
- sampleBO.loadBySampleIdentifier(createSampleIdentifier(plate));
- SamplePE sample = sampleBO.getSample();
- List<ExternalDataPE> datasets = daoFactory.getExternalDataDAO().listExternalData(sample);
- datasets = ScreeningUtils.filterDatasetsByType(datasets, datasetTypeCode);
- return datasets;
- }
-
- private static List<FeatureVectorDatasetReference> asFeatureVectorDatasets(
- List<ExternalDataPE> datasets)
- {
- List<FeatureVectorDatasetReference> result = new ArrayList<FeatureVectorDatasetReference>();
- for (ExternalDataPE externalData : datasets)
- {
- result.add(asFeatureVectorDataset(externalData));
- }
- return result;
- }
-
- private static FeatureVectorDatasetReference asFeatureVectorDataset(ExternalDataPE externalData)
- {
- DataStorePE dataStore = externalData.getDataStore();
- DataPE parentDataset = externalData.getParents().iterator().next();
- return new FeatureVectorDatasetReference(externalData.getCode(),
- dataStore.getDownloadUrl(), createPlateIdentifier(parentDataset),
- extractPlateGeometry(parentDataset), externalData.getRegistrationDate(),
- asImageDataset(parentDataset));
- }
-
- private static List<ImageDatasetReference> asImageDatasets(List<ExternalDataPE> datasets)
- {
- List<ImageDatasetReference> result = new ArrayList<ImageDatasetReference>();
- for (ExternalDataPE externalData : datasets)
- {
- result.add(asImageDataset(externalData));
- }
- return result;
- }
-
- private static ImageDatasetReference asImageDataset(DataPE parentDataset)
- {
- DataStorePE dataStore = parentDataset.getDataStore();
- return new ImageDatasetReference(parentDataset.getCode(), dataStore.getDownloadUrl(),
- createPlateIdentifier(parentDataset), extractPlateGeometry(parentDataset),
- parentDataset.getRegistrationDate());
- }
-
- private static PlateIdentifier createPlateIdentifier(DataPE parentDataset)
- {
- SamplePE sample = getSample(parentDataset);
- final String plateCode = sample.getCode();
- GroupPE group = sample.getGroup();
- final String spaceCodeOrNull = (group != null) ? group.getCode() : null;
- return new PlateIdentifier(plateCode, spaceCodeOrNull);
- }
-
- private static SamplePE getSample(DataPE dataset)
- {
- SamplePE sample = dataset.tryGetSample();
- assert sample != null : "dataset not connected to a sample: " + dataset;
- return sample;
- }
-
- private static Geometry extractPlateGeometry(DataPE dataSet)
- {
- SamplePE sample = getSample(dataSet);
- Set<SamplePropertyPE> properties = sample.getProperties();
- for (SamplePropertyPE property : properties)
- {
- PropertyTypePE propertyType = property.getEntityTypePropertyType().getPropertyType();
- if (propertyType.getCode().equals(ScreeningConstants.PLATE_GEOMETRY))
- {
- String code = property.getVocabularyTerm().getCode();
- int lastIndexOfUnderscore = code.lastIndexOf('_');
- int lastIndexOfX = code.lastIndexOf('X');
- if (lastIndexOfUnderscore < 0 || lastIndexOfX < 0)
- {
- throw new UserFailureException("Invalid property "
- + ScreeningConstants.PLATE_GEOMETRY + ": " + code);
- }
- try
- {
- int width =
- Integer.parseInt(code
- .substring(lastIndexOfUnderscore + 1, lastIndexOfX));
- int height = Integer.parseInt(code.substring(lastIndexOfX + 1));
- return new Geometry(width, height);
- } catch (NumberFormatException ex)
- {
- throw new UserFailureException("Invalid property "
- + ScreeningConstants.PLATE_GEOMETRY + ": " + code);
- }
-
- }
- }
- throw new UserFailureException("Sample " + sample.getIdentifier() + " has no property "
- + ScreeningConstants.PLATE_GEOMETRY);
- }
-
- private static SampleIdentifier createSampleIdentifier(PlateIdentifier plate)
- {
- SampleOwnerIdentifier owner;
- String spaceCode = plate.tryGetSpaceCode();
- if (spaceCode != null)
- {
- SpaceIdentifier space = new SpaceIdentifier(DatabaseInstanceIdentifier.HOME, spaceCode);
- owner = new SampleOwnerIdentifier(space);
- } else
- {
- owner = new SampleOwnerIdentifier(DatabaseInstanceIdentifier.createHome());
- }
- return SampleIdentifier.createOwnedBy(owner, plate.getPlateCode());
+ return new ImageDatasetLoader(session, businessObjectFactory, dataStoreBaseURL, plates)
+ .getImageDatasets();
}
public List<Plate> listPlates()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
index 9b3725c9f8d..62ac9b54693 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningUtils.java
@@ -20,6 +20,7 @@ import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
@@ -81,4 +82,23 @@ public class ScreeningUtils
return dataset.getDataSetType().getCode().equals(datasetType);
}
+ public static List<ExternalData> filterExternalDataByType(List<ExternalData> datasets,
+ String datasetTypeCode)
+ {
+ List<ExternalData> chosenDatasets = new ArrayList<ExternalData>();
+ for (ExternalData dataset : datasets)
+ {
+ if (isTypeEqual(dataset, datasetTypeCode))
+ {
+ chosenDatasets.add(dataset);
+ }
+ }
+ return chosenDatasets;
+ }
+
+ private static boolean isTypeEqual(ExternalData dataset, String datasetType)
+ {
+ return dataset.getDataSetType().getCode().equals(datasetType);
+ }
+
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
index 0a648d3d203..43a2a1ffd2f 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImplTest.java
@@ -44,23 +44,23 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifi
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class ScreeningApiImplTest extends AbstractServerTestCase
{
private static final String SERVER_URL = "server-url";
+
private IScreeningBusinessObjectFactory screeningBOFactory;
+
private ScreeningApiImpl screeningApi;
@BeforeMethod
public void beforeMethod()
{
screeningBOFactory = context.mock(IScreeningBusinessObjectFactory.class);
- screeningApi = new ScreeningApiImpl(SESSION, screeningBOFactory, daoFactory);
+ screeningApi = new ScreeningApiImpl(SESSION, screeningBOFactory, daoFactory, "");
}
-
+
@Test
public void testListImageDatasets()
{
@@ -82,8 +82,8 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
}
});
- List<ImageDatasetReference> dataSets = screeningApi.listImageDatasets(Arrays.asList(pi1));
-
+ List<ImageDatasetReference> dataSets = screeningApi.listImageDatasets(Arrays.asList(pi1));
+
assertEquals("1", dataSets.get(0).getDatasetCode());
assertEquals(new Geometry(16, 24), dataSets.get(0).getPlateGeometry());
assertEquals(new Date(100), dataSets.get(0).getRegistrationDate());
@@ -92,7 +92,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
assertEquals(1, dataSets.size());
context.assertIsSatisfied();
}
-
+
@Test
public void testListImageDatasetsWithMissingPlateGeometry()
{
@@ -124,7 +124,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
}
context.assertIsSatisfied();
}
-
+
@Test
public void testListImageDatasetsWithPlateGeometryWithMissingUnderscore()
{
@@ -138,40 +138,40 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
assertListImageDatasetsFailsFor("abc_2.4");
context.assertIsSatisfied();
}
-
+
@Test
public void testListImageDatasetsWithPlateGeometryWithWidthNotANumber()
{
assertListImageDatasetsFailsFor("abc_aX4");
context.assertIsSatisfied();
}
-
+
@Test
public void testListImageDatasetsWithPlateGeometryWithHeightNotANumber()
{
assertListImageDatasetsFailsFor("abc_2Xb");
context.assertIsSatisfied();
}
-
+
private void assertListImageDatasetsFailsFor(final String plateGeometry)
{
final PlateIdentifier pi1 = new PlateIdentifier("p1", null);
context.checking(new Expectations()
- {
{
- one(screeningBOFactory).createSampleBO(SESSION);
- will(returnValue(sampleBO));
-
- one(sampleBO).loadBySampleIdentifier(asSampleIdentifier(pi1));
- one(sampleBO).getSample();
- SamplePE p1 = plate(pi1, plateGeometry);
- will(returnValue(p1));
-
- one(externalDataDAO).listExternalData(p1);
- will(returnValue(Arrays.asList(imageDataSet(p1, "1"))));
- }
- });
-
+ {
+ one(screeningBOFactory).createSampleBO(SESSION);
+ will(returnValue(sampleBO));
+
+ one(sampleBO).loadBySampleIdentifier(asSampleIdentifier(pi1));
+ one(sampleBO).getSample();
+ SamplePE p1 = plate(pi1, plateGeometry);
+ will(returnValue(p1));
+
+ one(externalDataDAO).listExternalData(p1);
+ will(returnValue(Arrays.asList(imageDataSet(p1, "1"))));
+ }
+ });
+
try
{
screeningApi.listImageDatasets(Arrays.asList(pi1));
@@ -182,7 +182,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
+ plateGeometry.toUpperCase(), ex.getMessage());
}
}
-
+
private SampleIdentifier asSampleIdentifier(PlateIdentifier plateIdentifier)
{
String spaceCode = plateIdentifier.tryGetSpaceCode();
@@ -194,7 +194,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
return new SampleIdentifier(new SpaceIdentifier(DatabaseInstanceIdentifier.createHome(),
spaceCode), plateIdentifier.getPlateCode());
}
-
+
private SamplePE plate(PlateIdentifier plateIdentifier, String plateGeometryOrNull)
{
SamplePE sample = new SamplePE();
@@ -228,7 +228,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
dataSet.setDataSetType(dataSetType(ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE));
return dataSet;
}
-
+
private ExternalDataPE createDataSet(SamplePE sample, String code)
{
ExternalDataPE dataSet = new ExternalDataPE();
@@ -240,7 +240,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
dataSet.setRegistrationDate(new Date(Long.parseLong(code) * 100));
return dataSet;
}
-
+
private DataSetTypePE dataSetType(String code)
{
DataSetTypePE type = new DataSetTypePE();
--
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