diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index bb7d43982d7e0a13a46bc5e049920a04dceb06c4..37d136ffbb28f17cc91dd88f1f834262ee4dec93 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -165,18 +165,16 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
public List<String> listAvailableFeatureCodes(String sessionToken,
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
{
+ List<ImgFeatureDefDTO> featureDefinitions = getFeatureDefinitions(featureDatasets);
+
+ // add only new feature names
List<String> result = new ArrayList<String>(); // keep the order
- for (IFeatureVectorDatasetIdentifier identifier : featureDatasets)
+ for (ImgFeatureDefDTO featureDefinition : featureDefinitions)
{
- // add only new feature names
- List<ImgFeatureDefDTO> featureDefinitions = getFeatureDefinitions(identifier);
- for (ImgFeatureDefDTO featureDefinition : featureDefinitions)
+ String featureCode = featureDefinition.getCode();
+ if (result.contains(featureCode) == false)
{
- String featureCode = featureDefinition.getCode();
- if (result.contains(featureCode) == false)
- {
- result.add(featureCode);
- }
+ result.add(featureCode);
}
}
return result;
@@ -771,6 +769,42 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
}
}
+ private List<ImgDatasetDTO> getDatasets(List<? extends IDatasetIdentifier> datasetIdents)
+ {
+ String[] permIds = extractPermIds(datasetIdents);
+ List<ImgDatasetDTO> datasets = getDAO().listDatasetsByPermId(permIds);
+ if (datasets.size() != datasetIdents.size())
+ {
+ Set<String> missing = new HashSet<String>(Arrays.asList(permIds));
+ for (ImgDatasetDTO dataset : datasets)
+ {
+ missing.remove(dataset.getPermId());
+ }
+ throw new UserFailureException("Following datasets could not be found: " + missing);
+ }
+ return datasets;
+ }
+
+ private long[] extractIds(List<ImgDatasetDTO> dataSets)
+ {
+ long[] ids = new long[dataSets.size()];
+ for (int i = 0; i < ids.length; i++)
+ {
+ ids[i] = dataSets.get(i).getId();
+ }
+ return ids;
+ }
+
+ private static String[] extractPermIds(List<? extends IDatasetIdentifier> datasets)
+ {
+ String[] permIds = new String[datasets.size()];
+ for (int i = 0; i < permIds.length; i++)
+ {
+ permIds[i] = datasets.get(i).getDatasetCode();
+ }
+ return permIds;
+ }
+
private ImgDatasetDTO getImagingDataset(IDatasetIdentifier datasetIdentifier)
{
ImgDatasetDTO dataset = getDAO().tryGetDatasetByPermId(datasetIdentifier.getDatasetCode());
@@ -1001,10 +1035,11 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
.matches(ScreeningConstants.ANY_MICROSCOPY_IMAGE_DATASET_TYPE_PATTERN);
}
- private List<ImgFeatureDefDTO> getFeatureDefinitions(IDatasetIdentifier identifier)
+ private List<ImgFeatureDefDTO> getFeatureDefinitions(
+ List<? extends IDatasetIdentifier> featureDatasets)
{
- ImgDatasetDTO dataSet = getImagingDataset(identifier);
- return getDAO().listFeatureDefsByDataSetId(dataSet.getId());
+ List<ImgDatasetDTO> dataSets = getDatasets(featureDatasets);
+ return getDAO().listFeatureDefsByDataSetIds(extractIds(dataSets));
}
private IImagingReadonlyQueryDAO getDAO()
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
index fbd9ef33486872402048480b64556514f6a1dc9e..267072a7d3c0d0b7b7f470cd89ca3d481644d695 100644
--- 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
@@ -115,7 +115,7 @@ class PlateDatasetLoader
private void loadDatasets()
{
- List<Long> sampleIds = extractSampleIds();
+ Set<Long> sampleIds = extractSampleIds();
IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
datasets = datasetLister.listBySampleIds(sampleIds);
datasets =
@@ -227,7 +227,7 @@ class PlateDatasetLoader
throw new UserFailureException("Sample '" + sample.getIdentifier() + "' has no property "
+ ScreeningConstants.PLATE_GEOMETRY);
}
-
+
protected Map<String, String> extractProperties(ExternalData dataSet)
{
final Map<String, String> properties = new HashMap<String, String>();
@@ -289,14 +289,9 @@ class PlateDatasetLoader
return sampleCodesArray;
}
- private List<Long> extractSampleIds()
+ private Set<Long> extractSampleIds()
{
- ArrayList<Long> sampleIds = new ArrayList<Long>(samples.size());
- for (Sample sample : samples)
- {
- sampleIds.add(sample.getId());
- }
- return sampleIds;
+ return samplesById.keySet();
}
protected static String getDataStoreUrlFromDataStore(DataStore dataStore)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
index 740eec7969eef4c8fd93fcddee6c87bbd4a6059a..5cd5ea43f46e8d790a94ab8fd3d6ed8fe61d5046 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoader.java
@@ -110,7 +110,8 @@ public class WellContentLoader
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
TechId geneMaterialId)
{
- final WellContentLoader loader = new WellContentLoader(session, businessObjectFactory, daoFactory);
+ final WellContentLoader loader =
+ new WellContentLoader(session, businessObjectFactory, daoFactory);
return loader.loadLocations(geneMaterialId);
}
@@ -123,12 +124,18 @@ public class WellContentLoader
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
WellSearchCriteria materialCriteria)
{
+ long start = System.currentTimeMillis();
WellContentLoader loader =
new WellContentLoader(session, businessObjectFactory, daoFactory);
-
List<WellContent> locations = loader.loadLocations(materialCriteria);
+
+ operationLog.info(String.format("[%d msec] Load %d locations.",
+ (System.currentTimeMillis() - start), locations.size()));
+
List<WellContent> withPropsAndDataSets = loader.enrichWithDatasets(locations);
- return loader.enrichWithFeatureVectors(withPropsAndDataSets);
+ List<WellContent> withFeatureVectors =
+ loader.enrichWithFeatureVectors(withPropsAndDataSets);
+ return withFeatureVectors;
}
/**
@@ -189,14 +196,24 @@ public class WellContentLoader
private List<WellContent> enrichWithDatasets(List<WellContent> locations)
{
+ long start = System.currentTimeMillis();
+
Collection<PlateIdentifier> plates = extractPlates(locations);
FeatureVectorDatasetLoader datasetsRetriever =
new FeatureVectorDatasetLoader(session, businessObjectFactory, null, plates);
Collection<ExternalData> imageDatasets = datasetsRetriever.getImageDatasets();
- Map<String, ImageDatasetParameters> imageParams = loadImagesReport(imageDatasets);
-
Collection<ExternalData> featureVectorDatasets =
datasetsRetriever.getFeatureVectorDatasets();
+
+ operationLog.info(String.format("[%d msec] load datasets (%d image, %d fv).",
+ (System.currentTimeMillis() - start), imageDatasets.size(),
+ featureVectorDatasets.size()));
+ start = System.currentTimeMillis();
+
+ Map<String, ImageDatasetParameters> imageParams = loadImagesReport(imageDatasets);
+ operationLog.info(String.format("[%d msec] loadImagesReport",
+ (System.currentTimeMillis() - start)));
+
Collection<ExternalData> childlessImageDatasets =
selectChildlessImageDatasets(imageDatasets, featureVectorDatasets);
@@ -557,6 +574,7 @@ public class WellContentLoader
return map;
}
+ // TODO 2011-04-04, Tomasz Pylak: inefficient, rewrite to use single queryfor all datasets
private Map<String/* dataset code */, ImageDatasetParameters> loadImagesReport(
Collection<ExternalData> imageDatasets)
{
@@ -581,7 +599,7 @@ public class WellContentLoader
private List<WellContent> loadLocations(WellSearchCriteria materialCriteria)
{
- DataIterator<WellContentQueryResult> locations;
+ Iterable<WellContentQueryResult> locations;
MaterialSearchCriteria materialSearchCriteria =
materialCriteria.getMaterialSearchCriteria();
ExperimentSearchCriteria experiment = materialCriteria.getExperimentCriteria();
@@ -592,7 +610,15 @@ public class WellContentLoader
materialSearchCriteria.tryGetMaterialCodesOrProperties();
Long expId = tryGetExperimentId(experiment);
+ long start = System.currentTimeMillis();
long[] materialIds = findMaterialIds(codesCriteria);
+
+ operationLog.info(String.format(
+ "[%d msec] Finding %d materials for criteria '%s'. Result: %s",
+ (System.currentTimeMillis() - start), materialIds.length, codesCriteria,
+ Arrays.toString(materialIds)));
+ start = System.currentTimeMillis();
+
if (expId == null)
{
locations =
@@ -705,22 +731,18 @@ public class WellContentLoader
return convert(locations);
}
- private List<WellContent> convert(DataIterator<WellContentQueryResult> queryResults)
+ private List<WellContent> convert(Iterable<WellContentQueryResult> queryResults)
{
- List<WellContentQueryResult> uniqueResults = removeDuplicateWells(queryResults);
+ List<WellContent> wellContents = removeDuplicateWells(queryResults);
- ArrayList<WellContent> wellContents = new ArrayList<WellContent>();
- for (WellContentQueryResult uniqueWell : uniqueResults)
- {
- wellContents.add(convert(uniqueWell));
- }
List<WellContent> withProperties = enrichWithWellProperties(wellContents);
IMaterialLister materialLister = businessObjectFactory.createMaterialLister(session);
List<Material> containedMaterials = getMaterialsWithDuplicates(withProperties);
materialLister.enrichWithProperties(containedMaterials);
+
return wellContents;
}
-
+
private static Set<Material> extractMaterials(List<WellContent> locations)
{
Set<Material> materials = new HashSet<Material>();
@@ -746,11 +768,10 @@ public class WellContentLoader
return materials;
}
- private List<WellContentQueryResult> removeDuplicateWells(
- DataIterator<WellContentQueryResult> queryResults)
+ private List<WellContent> removeDuplicateWells(Iterable<WellContentQueryResult> queryResults)
{
+ List<WellContent> wellContents = new ArrayList<WellContent>();
Set<String> seenWellPermIds = new HashSet<String>();
- List<WellContentQueryResult> result = new ArrayList<WellContentQueryResult>();
for (WellContentQueryResult queryResult : queryResults)
{
@@ -758,10 +779,10 @@ public class WellContentLoader
if (false == seenWellPermIds.contains(permId))
{
seenWellPermIds.add(permId);
- result.add(queryResult);
+ wellContents.add(convert(queryResult));
}
}
- return result;
+ return wellContents;
}
private static WellContent convert(WellContentQueryResult well)
@@ -769,11 +790,11 @@ public class WellContentLoader
WellLocation location =
ScreeningUtils.tryCreateLocationFromMatrixCoordinate(well.well_code);
EntityReference wellReference =
- new EntityReference(well.well_id, well.well_code,
- well.well_type_code, EntityKind.SAMPLE, well.well_perm_id);
+ new EntityReference(well.well_id, well.well_code, well.well_type_code,
+ EntityKind.SAMPLE, well.well_perm_id);
EntityReference plate =
- new EntityReference(well.plate_id, well.plate_code,
- well.plate_type_code, EntityKind.SAMPLE, well.plate_perm_id);
+ new EntityReference(well.plate_id, well.plate_code, well.plate_type_code,
+ EntityKind.SAMPLE, well.plate_perm_id);
return new WellContent(location, wellReference, plate, convertExperiment(well));
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureVectorLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureVectorLoader.java
index ef5d0aed6902ca71bbce0a60e1fa148969d2de61..e197893a4db84bafba46695221ac156fba80e4d5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureVectorLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureVectorLoader.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
+import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
@@ -30,6 +31,9 @@ import java.util.Set;
import org.apache.log4j.Logger;
+import ch.systemsx.cisd.common.collections.GroupByMap;
+import ch.systemsx.cisd.common.collections.IKeyExtractor;
+import ch.systemsx.cisd.common.collections.TableMap;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
@@ -43,6 +47,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellFeatureVec
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.FeatureTableRow;
import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.AbstractImgIdentifiable;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
@@ -71,6 +76,8 @@ public class FeatureVectorLoader
private Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> featureDefToValuesMap;
private FeatureVocabularyTermsMap featureDefToVocabularyTerms;
+
+ private ImgContainerDTO container;
}
public static interface IMetadataProvider
@@ -126,7 +133,7 @@ public class FeatureVectorLoader
throw new UserFailureException("Unkown data set " + dataSetCode);
}
- final List<ImgFeatureDefDTO> featureDefs = dao.listFeatureDefsByDataSetId(dataSet.getId());
+ final List<ImgFeatureDefDTO> featureDefs = dao.listFeatureDefsByDataSetIds(dataSet.getId());
final List<CodeAndLabel> result = new ArrayList<CodeAndLabel>();
for (ImgFeatureDefDTO featureDef : featureDefs)
{
@@ -165,7 +172,7 @@ public class FeatureVectorLoader
}
/**
- * fetches specified features of all wells
+ * Fetches specified features of all wells.
*
* @param featureCodes empty list means no filtering.
* @param metadataProviderOrNull if null plate identifiers in FeatureTableRow are not set
@@ -243,24 +250,22 @@ public class FeatureVectorLoader
}
}
- private void addFeatureVectorsOfDataSetsOrDie(Collection<String> datasetCodes)
+ private void addFeatureVectorsOfDataSetsIfPossible(Collection<String> datasetCodes)
{
- for (String datasetCode : datasetCodes)
+ final List<ImgDatasetDTO> dataSets = listDatasetsByPermId(datasetCodes);
+ if (dataSets.size() != datasetCodes.size())
{
- addFeatureVectorsOfDataSetOrDie(datasetCode);
+ operationLog.warn(createUnknownDatasetMessage(datasetCodes, dataSets));
}
+ addFeatureVectorsOfDataSets(dataSets);
}
- private void addFeatureVectorsOfDataSetsIfPossible(Collection<String> datasetCodes)
+ private String createUnknownDatasetMessage(Collection<String> requestedDatasetCodes,
+ final List<ImgDatasetDTO> existingDataSets)
{
- for (String datasetCode : datasetCodes)
- {
- if (addFeatureVectorsOfDataSet(datasetCode) == false)
- {
- operationLog.warn("Dataset " + datasetCode
- + " contains no feature vectors or does not exist.");
- }
- }
+ return String.format(
+ "Some of the datasets are unknown! Requested datasets: %s. Found datasets: %s.",
+ requestedDatasetCodes, existingDataSets);
}
private static Set<String> extractDatasetCodesFromSimpleReferences(
@@ -308,42 +313,56 @@ public class FeatureVectorLoader
* @throws UserFailureException if dataset with the specified code contains no feature vectors
* or does not exist.
*/
- void addFeatureVectorsOfDataSetOrDie(String dataSetCode)
+ void addFeatureVectorsOfDataSetsOrDie(Collection<String> datasetCodes)
{
- boolean added = addFeatureVectorsOfDataSet(dataSetCode);
- if (added == false)
+ final List<ImgDatasetDTO> dataSets = listDatasetsByPermId(datasetCodes);
+ if (dataSets.size() != datasetCodes.size())
{
- throw new UserFailureException("Unkown data set " + dataSetCode);
+ throw new UserFailureException(createUnknownDatasetMessage(datasetCodes, dataSets));
}
+ addFeatureVectorsOfDataSets(dataSets);
+ }
+
+ private List<ImgDatasetDTO> listDatasetsByPermId(Collection<String> datasetCodes)
+ {
+ return dao.listDatasetsByPermId(datasetCodes.toArray(new String[0]));
}
/**
- * Adds feature vectors for specified feature vector data set code.
- *
- * @return false if dataset with the specified code contains no feature vectors or does not
- * exist.<br>
- * true if feature vectors have been added.
+ * Adds feature vectors for specified feature vector data sets codes.
*/
- boolean addFeatureVectorsOfDataSet(String dataSetCode)
+ void addFeatureVectorsOfDataSets(List<ImgDatasetDTO> datasets)
{
- final ImgDatasetDTO dataSet = dao.tryGetDatasetByPermId(dataSetCode);
- if (dataSet == null)
+ long start = System.currentTimeMillis();
+ DatasetFeatureDefinitionCachedLister lister =
+ new DatasetFeatureDefinitionCachedLister(datasets, featureCodes, useAllFeatures,
+ dao);
+ for (ImgDatasetDTO dataset : datasets)
{
- return false;
- }
- final DatasetFeaturesBundle bundle = new DatasetFeaturesBundle();
- final Map<String, ImgFeatureDefDTO> featureCodeToDefMap =
- createFeatureCodeToDefMap(dao, dataSet);
- bundle.dataSet = dataSet;
- bundle.featureDefToValuesMap = new HashMap<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>>();
- bundle.featureDefToVocabularyTerms =
- createFeatureIdToVocabularyTermsMap(dao, dataSet,
- bundle.featureDefToValuesMap.keySet());
- bundles.add(bundle);
- if (useAllFeatures)
- {
- featureCodes.addAll(featureCodeToDefMap.keySet());
+ Map<String, ImgFeatureDefDTO> featureCodeToDefMap =
+ lister.getFeatureCodeToDefMap(dataset);
+
+ if (useAllFeatures)
+ {
+ featureCodes.addAll(featureCodeToDefMap.keySet());
+ }
+ assignIndicesToFeatures(featureCodeToDefMap);
+
+ DatasetFeaturesBundle bundle = new DatasetFeaturesBundle();
+ bundle.featureDefToValuesMap = lister.getFeatureValues(dataset);
+ bundle.dataSet = dataset;
+ bundle.container = lister.getContainer(dataset);
+ bundle.featureDefToVocabularyTerms =
+ createFeatureIdToVocabularyTermsMap(dataset,
+ bundle.featureDefToValuesMap.keySet(), lister);
+ bundles.add(bundle);
}
+ operationLog.info(String.format("[%d msec] Fetching %d features from %d datasets.",
+ (System.currentTimeMillis() - start), featureCodes.size(), datasets.size()));
+ }
+
+ private void assignIndicesToFeatures(final Map<String, ImgFeatureDefDTO> featureCodeToDefMap)
+ {
for (String featureCode : featureCodes)
{
final ImgFeatureDefDTO featureDefinition = featureCodeToDefMap.get(featureCode);
@@ -355,42 +374,213 @@ public class FeatureVectorLoader
featureCodeLabelToIndexMap.put(codeAndLabel, new Integer(
featureCodeLabelToIndexMap.size()));
}
- List<ImgFeatureValuesDTO> featureValueSets =
- dao.getFeatureValues(featureDefinition);
- if (featureValueSets.isEmpty())
+ }
+ }
+ }
+
+ /**
+ * Helper class which fetches all the results from the database at the beginning with one query,
+ * groups them and serves them from the cache.
+ */
+ private static class DatasetFeatureDefinitionCachedLister
+ {
+ private final GroupByMap<Long/* dataset id */, ImgFeatureDefDTO> requestedFeatureDefinitionsMap;
+
+ private final GroupByMap<Long/* dataset id */, ImgFeatureVocabularyTermDTO> featureVocabularyTermsMap;
+
+ // values for all datasets and requested features
+ private final GroupByMap</* feature def id */Long, ImgFeatureValuesDTO> featureValuesMap;
+
+ private final TableMap<Long/* container id */, ImgContainerDTO> containersByIdMap;
+
+ /**
+ * @datasets datasets in which we are interested
+ * @param featureCodes codes of features for which we want to fetch the values
+ * @param useAllFeatures if true the featureCodes param is ignored and values are fetched
+ * for all features
+ */
+ public DatasetFeatureDefinitionCachedLister(List<ImgDatasetDTO> datasets,
+ Set<String> featureCodes, boolean useAllFeatures, IImagingReadonlyQueryDAO dao)
+ {
+ this.containersByIdMap = createContainerByIdMap(datasets, dao);
+
+ long[] datasetIds = extractIds(datasets);
+ List<ImgFeatureDefDTO> requestedFeatureDefinitions =
+ listRequestedFeatureDefinitions(datasetIds, featureCodes, useAllFeatures, dao);
+ this.requestedFeatureDefinitionsMap =
+ GroupByMap.create(requestedFeatureDefinitions,
+ new IKeyExtractor<Long, ImgFeatureDefDTO>()
+ {
+ public Long getKey(ImgFeatureDefDTO featureDef)
+ {
+ return featureDef.getDataSetId();
+ }
+ });
+
+ List<ImgFeatureVocabularyTermDTO> featureVocabularyTerms =
+ dao.listFeatureVocabularyTermsByDataSetId(datasetIds);
+ this.featureVocabularyTermsMap =
+ GroupByMap.create(featureVocabularyTerms,
+ new IKeyExtractor<Long, ImgFeatureVocabularyTermDTO>()
+ {
+ public Long getKey(
+ ImgFeatureVocabularyTermDTO featureVocabularyTerm)
+ {
+ return featureVocabularyTerm.getDataSetId();
+ }
+ });
+
+ List<ImgFeatureValuesDTO> requestedFeatureValues =
+ dao.getFeatureValues(extractIds(requestedFeatureDefinitions));
+ this.featureValuesMap =
+ GroupByMap.create(requestedFeatureValues,
+ new IKeyExtractor<Long, ImgFeatureValuesDTO>()
+ {
+ public Long getKey(ImgFeatureValuesDTO featureVal)
+ {
+ return featureVal.getFeatureDefId();
+ }
+ });
+ }
+
+ private static TableMap<Long, ImgContainerDTO> createContainerByIdMap(
+ List<ImgDatasetDTO> datasets, IImagingReadonlyQueryDAO dao)
+ {
+ List<ImgContainerDTO> containers =
+ dao.listContainersByIds(extractContainerIds(datasets));
+ return new TableMap<Long, ImgContainerDTO>(containers,
+ new IKeyExtractor<Long, ImgContainerDTO>()
+ {
+ public Long getKey(ImgContainerDTO container)
+ {
+ return container.getId();
+ }
+ });
+ }
+
+ private List<ImgFeatureDefDTO> listRequestedFeatureDefinitions(long[] datasetIds,
+ Set<String> featureCodes, boolean useAllFeatures, IImagingReadonlyQueryDAO dao)
+ {
+ List<ImgFeatureDefDTO> allFeatureDefinitions =
+ dao.listFeatureDefsByDataSetIds(datasetIds);
+ List<ImgFeatureDefDTO> requestedFeatureDefinitions =
+ extractRequestedFeatureDefinitions(featureCodes, useAllFeatures,
+ allFeatureDefinitions);
+ return requestedFeatureDefinitions;
+ }
+
+ public ImgContainerDTO getContainer(ImgDatasetDTO dataset)
+ {
+ return containersByIdMap.getOrDie(dataset.getContainerId());
+ }
+
+ public Map<String, ImgFeatureDefDTO> getFeatureCodeToDefMap(ImgDatasetDTO dataset)
+ {
+ List<ImgFeatureDefDTO> featureDefinitions = getRequestedFeatureDefinitions(dataset);
+ return createCodeToDefMap(featureDefinitions);
+ }
+
+ private List<ImgFeatureDefDTO> getRequestedFeatureDefinitions(ImgDatasetDTO dataset)
+ {
+ return requestedFeatureDefinitionsMap.getOrDie(dataset.getId());
+ }
+
+ public List<ImgFeatureVocabularyTermDTO> getFeatureVocabularyTerms(ImgDatasetDTO dataSet)
+ {
+ List<ImgFeatureVocabularyTermDTO> terms =
+ featureVocabularyTermsMap.tryGet(dataSet.getId());
+ if (terms == null)
+ {
+ return Collections.emptyList();
+ }
+ return terms;
+ }
+
+ public Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> getFeatureValues(
+ ImgDatasetDTO dataset)
+ {
+ List<ImgFeatureDefDTO> datasetFeatureDefinitions =
+ getRequestedFeatureDefinitions(dataset);
+ Map<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>> defToValuesMap =
+ new HashMap<ImgFeatureDefDTO, List<ImgFeatureValuesDTO>>();
+ for (ImgFeatureDefDTO featureDef : datasetFeatureDefinitions)
+ {
+ List<ImgFeatureValuesDTO> values = featureValuesMap.getOrDie(featureDef.getId());
+ defToValuesMap.put(featureDef, values);
+ }
+ return defToValuesMap;
+ }
+
+ private static List<ImgFeatureDefDTO> extractRequestedFeatureDefinitions(
+ Set<String> featureCodes, boolean useAllFeatures,
+ List<ImgFeatureDefDTO> allFeatureDefinitions)
+ {
+ if (useAllFeatures)
+ {
+ return allFeatureDefinitions;
+ } else
+ {
+ return filterByCode(allFeatureDefinitions, featureCodes);
+ }
+ }
+
+ private static List<ImgFeatureDefDTO> filterByCode(
+ List<ImgFeatureDefDTO> allFeatureDefinitions, Set<String> featureCodes)
+ {
+ List<ImgFeatureDefDTO> result = new ArrayList<ImgFeatureDefDTO>();
+ for (ImgFeatureDefDTO featureDef : allFeatureDefinitions)
+ {
+ if (featureCodes.contains(featureDef.getCode()))
{
- throw new UserFailureException("At least one set of values for feature "
- + featureCode + " of data set " + dataSetCode + " expected.");
+ result.add(featureDef);
}
- bundle.featureDefToValuesMap.put(featureDefinition, featureValueSets);
}
+ return result;
+ }
+
+ private static long[] extractContainerIds(List<ImgDatasetDTO> datasets)
+ {
+ long[] ids = new long[datasets.size()];
+ int i = 0;
+ for (ImgDatasetDTO dataset : datasets)
+ {
+ ids[i++] = dataset.getContainerId();
+ }
+ return ids;
+ }
+
+ private static long[] extractIds(List<? extends AbstractImgIdentifiable> identifiables)
+ {
+ long[] ids = new long[identifiables.size()];
+ int i = 0;
+ for (AbstractImgIdentifiable identifiable : identifiables)
+ {
+ ids[i++] = identifiable.getId();
+ }
+ return ids;
+ }
+
+ private static Map<String, ImgFeatureDefDTO> createCodeToDefMap(
+ final List<ImgFeatureDefDTO> featureDefinitions)
+ {
+ final Map<String, ImgFeatureDefDTO> featureCodeToDefMap =
+ new LinkedHashMap<String, ImgFeatureDefDTO>();
+ for (ImgFeatureDefDTO def : featureDefinitions)
+ {
+ featureCodeToDefMap.put(def.getCode(), def);
+ }
+ return featureCodeToDefMap;
}
- return true;
}
private static FeatureVocabularyTermsMap createFeatureIdToVocabularyTermsMap(
- IImagingReadonlyQueryDAO dao, ImgDatasetDTO dataSet,
- Set<ImgFeatureDefDTO> datasetFeatureDefs)
+ ImgDatasetDTO dataSet, Set<ImgFeatureDefDTO> datasetFeatureDefs,
+ DatasetFeatureDefinitionCachedLister lister)
{
- List<ImgFeatureVocabularyTermDTO> allTerms =
- dao.listFeatureVocabularyTermsByDataSetId(dataSet.getId());
+ List<ImgFeatureVocabularyTermDTO> allTerms = lister.getFeatureVocabularyTerms(dataSet);
return FeatureVocabularyTermsMap.createVocabularyTermsMap(allTerms, datasetFeatureDefs);
}
- private static Map<String, ImgFeatureDefDTO> createFeatureCodeToDefMap(
- IImagingReadonlyQueryDAO dao, final ImgDatasetDTO dataSet)
- {
- final List<ImgFeatureDefDTO> featureDefinitions =
- dao.listFeatureDefsByDataSetId(dataSet.getId());
- final Map<String, ImgFeatureDefDTO> featureCodeToDefMap =
- new LinkedHashMap<String, ImgFeatureDefDTO>();
- for (ImgFeatureDefDTO def : featureDefinitions)
- {
- featureCodeToDefMap.put(def.getCode(), def);
- }
- return featureCodeToDefMap;
- }
-
/**
* Returns all feature codes/labels found. If the feature code list in the constructor is not
* empty the result will a list where the codes are a subset of this list.
@@ -409,7 +599,7 @@ public class FeatureVectorLoader
List<FeatureTableRow> rows = new ArrayList<FeatureTableRow>();
for (DatasetFeaturesBundle bundle : bundles)
{
- ImgContainerDTO container = dao.getContainerById(bundle.dataSet.getContainerId());
+ ImgContainerDTO container = bundle.container;
SampleIdentifier identifier = tryGetSampleIdentifier(container);
for (int rowIndex = 1; rowIndex <= container.getNumberOfRows(); rowIndex++)
{
@@ -471,7 +661,7 @@ public class FeatureVectorLoader
{
String dataSetCode = reference.getDatasetCode();
DatasetFeaturesBundle bundle = getDatasetFeaturesBundleOrDie(bundleMap, dataSetCode);
- ImgContainerDTO container = dao.getContainerById(bundle.dataSet.getContainerId());
+ ImgContainerDTO container = bundle.container;
SampleIdentifier identifier = tryGetSampleIdentifier(container);
final FeatureTableRow row =
createFeatureTableRow(bundle, identifier, reference,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
index 8e33b48e0187952cfac862318de230ca7fb53624..0f5fba7ee47f7877b185139eaffbfd9e122a8ac7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingReadonlyQueryDAO.java
@@ -22,6 +22,8 @@ import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.Select;
import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.LongArrayMapper;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.StringArrayMapper;
/**
* Operations on imaging database which are read-only.<br>
@@ -126,7 +128,7 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
* information about the spot to which it belongs.
*/
@Select("select i.*, ai.image_transformer_factory as image_transformer_factory, "
- +"s.id as spot_id, ai.id as acquired_image_id "
+ + "s.id as spot_id, ai.id as acquired_image_id "
+ " from data_sets d "
+ " join channel_stacks cs on cs.ds_id = d.id "
+ " join spots s on cs.spot_id = s.id "
@@ -215,6 +217,10 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
@Select("select * from DATA_SETS where PERM_ID = ?{1}")
public ImgDatasetDTO tryGetDatasetByPermId(String datasetPermId);
+ @Select(sql = "select * from DATA_SETS where PERM_ID = any(?{1})", parameterBindings =
+ { StringArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<ImgDatasetDTO> listDatasetsByPermId(String... datasetPermIds);
+
// ---------------- HCS - experiments, containers, channels ---------------------------------
@Select("select * from EXPERIMENTS where PERM_ID = ?{1}")
@@ -229,6 +235,10 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
@Select("select * from CONTAINERS where ID = ?{1}")
public ImgContainerDTO getContainerById(long containerId);
+ @Select(sql = "select * from CONTAINERS where ID = any(?{1})", parameterBindings =
+ { LongArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<ImgContainerDTO> listContainersByIds(long... containerIds);
+
// join with container is needed to use spots index
@Select("select cs.* from CHANNEL_STACKS cs "
+ "join SPOTS s on s.id = cs.spot_id "
@@ -252,15 +262,19 @@ public interface IImagingReadonlyQueryDAO extends BaseQuery
// ---------------- HCS - feature vectors ---------------------------------
- @Select("select * from FEATURE_DEFS where DS_ID = ?{1}")
- public List<ImgFeatureDefDTO> listFeatureDefsByDataSetId(long dataSetId);
+ @Select(sql = "select * from FEATURE_DEFS where DS_ID = any(?{1})", parameterBindings =
+ { LongArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<ImgFeatureDefDTO> listFeatureDefsByDataSetIds(long... dataSetIds);
- @Select("select t.* from FEATURE_VOCABULARY_TERMS t "
- + "join FEATURE_DEFS fd on fd.id = t.fd_id "
- + "where fd.DS_ID = ?{1} ")
- public List<ImgFeatureVocabularyTermDTO> listFeatureVocabularyTermsByDataSetId(long dataSetId);
+ @Select(sql = "select t.*, fd.ds_id as DS_ID from FEATURE_VOCABULARY_TERMS t "
+ + "join FEATURE_DEFS fd on fd.id = t.fd_id "
+ + "where fd.DS_ID = any(?{1}) ", parameterBindings =
+ { LongArrayMapper.class }, fetchSize = FETCH_SIZE)
+ public List<ImgFeatureVocabularyTermDTO> listFeatureVocabularyTermsByDataSetId(
+ long... dataSetIds);
- @Select(sql = "select * from FEATURE_VALUES where FD_ID = ?{1.id} order by T_in_SEC, Z_in_M", resultSetBinding = FeatureVectorDataObjectBinding.class)
- public List<ImgFeatureValuesDTO> getFeatureValues(ImgFeatureDefDTO featureDef);
+ @Select(sql = "select * from FEATURE_VALUES where FD_ID = any(?{1}) order by T_in_SEC, Z_in_M", parameterBindings =
+ { LongArrayMapper.class }, fetchSize = FETCH_SIZE, resultSetBinding = FeatureVectorDataObjectBinding.class)
+ public List<ImgFeatureValuesDTO> getFeatureValues(long... featureDefIds);
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java
index e456bfb5695e413edf2cf50acb95db1d5f19bf65..09dc14cf150a7f68f9424fb1d7dc54387cea8552 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/FeatureVectorDAOTest.java
@@ -103,7 +103,7 @@ public class FeatureVectorDAOTest extends AbstractDBTest
dataset = createDataSet();
createFeatureDef(dataset);
- List<ImgFeatureDefDTO> featureDefs = dao.listFeatureDefsByDataSetId(dataset.getId());
+ List<ImgFeatureDefDTO> featureDefs = dao.listFeatureDefsByDataSetIds(dataset.getId());
assertEquals(1, featureDefs.size());
ImgFeatureDefDTO featureDef = featureDefs.get(0);
@@ -113,7 +113,7 @@ public class FeatureVectorDAOTest extends AbstractDBTest
testCreateAndListFeatureVocabularyValues(featureDef);
createFeatureFloatValues(featureDef);
- List<ImgFeatureValuesDTO> featureValuesList = dao.getFeatureValues(featureDef);
+ List<ImgFeatureValuesDTO> featureValuesList = dao.getFeatureValues(featureDef.getId());
assertEquals(1, featureValuesList.size());
ImgFeatureValuesDTO featureValues = featureValuesList.get(0);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
index e3428dd866627daf9c57d35ea079856af0a09a90..aa8ef9b6b8ea79bb4a687c5b94717a9c456af281 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/ImagingQueryDAOTest.java
@@ -354,6 +354,10 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals(spotHeight, loadedContainer.getNumberOfRows());
assertEquals(experimentId, loadedContainer.getExperimentId());
+ List<ImgContainerDTO> containers = dao.listContainersByIds(containerId);
+ assertEquals(1, containers.size());
+ assertEquals(loadedContainer, containers.get(0));
+
return containerId;
}
@@ -372,6 +376,12 @@ public class ImagingQueryDAOTest extends AbstractDBTest
assertEquals(fieldsHeight, loadedDataset.getFieldNumberOfRows());
assertEquals(containerIdOrNull, loadedDataset.getContainerId());
+ // test listDatasetsByPermId
+ final List<ImgDatasetDTO> datasets = dao.listDatasetsByPermId(new String[]
+ { permId, "not existing" });
+ assertEquals(1, datasets.size());
+ assertEquals(loadedDataset, datasets.get(0));
+
return datasetId;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureDefinitionValuesTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureDefinitionValuesTest.java
index 62d64687c400b2f59f225182bbdf40dc67088931..7b878d8a7bd6f6a7a7b301cd834e0539658ebebb 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureDefinitionValuesTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureDefinitionValuesTest.java
@@ -96,17 +96,20 @@ public class FeatureDefinitionValuesTest extends AssertJUnit
List<ImgFeatureVocabularyTermDTO> terms = vector.getVocabularyTerms();
assertNotNull(terms);
assertEquals(2, terms.size());
- assertEquals("a", terms.get(0).getCode());
- assertEquals("b", terms.get(1).getCode());
+ int termIxA = terms.get(0).getCode().equals("a") ? 0 : 1;
+
+ assertEquals("a", terms.get(termIxA).getCode());
+ assertEquals("b", terms.get(1 - termIxA).getCode());
assertEquals(1, vector.getValues().size());
ImgFeatureValuesDTO featureValuesDTO = vector.getValues().get(0);
assertNull(featureValuesDTO.getT());
assertNull(featureValuesDTO.getZ());
PlateFeatureValues values = featureValuesDTO.getValues();
- assertEquals(terms.get(0).getSequenceNumber(), (int) values.getForWellLocation(1, 1));
- assertEquals(terms.get(1).getSequenceNumber(), (int) values.getForWellLocation(1, 2));
- assertEquals(terms.get(0).getSequenceNumber(), (int) values.getForWellLocation(1, 3));
+ assertEquals(terms.get(termIxA).getSequenceNumber(), (int) values.getForWellLocation(1, 1));
+ assertEquals(terms.get(1 - termIxA).getSequenceNumber(),
+ (int) values.getForWellLocation(1, 2));
+ assertEquals(terms.get(termIxA).getSequenceNumber(), (int) values.getForWellLocation(1, 3));
}
}
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
index 325c65dbb01c7d6f3c6ae4a5bdd3fa9bc1e27df1..4cb76b3ce14eb69fde557a1bf32c7989f64a28ef 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/FeatureVectorUploaderTest.java
@@ -98,7 +98,7 @@ public class FeatureVectorUploaderTest extends AbstractDBTest
private void verify()
{
- List<ImgFeatureDefDTO> featureDefs = dao.listFeatureDefsByDataSetId(datasetId);
+ List<ImgFeatureDefDTO> featureDefs = dao.listFeatureDefsByDataSetIds(datasetId);
assertEquals(2, featureDefs.size());
count = 0;
@@ -112,7 +112,7 @@ public class FeatureVectorUploaderTest extends AbstractDBTest
private void verifyFeatureDef()
{
assertEquals(TEST_FEATURE_NAME + count, featureDef.getLabel());
- List<ImgFeatureValuesDTO> featureValuesList = dao.getFeatureValues(featureDef);
+ List<ImgFeatureValuesDTO> featureValuesList = dao.getFeatureValues(featureDef.getId());
assertEquals(1, featureValuesList.size());
featureValues = featureValuesList.get(0);
verifyFeatureValues();
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapTest.java
index ef186bf518926ceb1a8e98e2bc81f7a1e57232e6..d6f80a39038333bb57512966ddbe8004262f3f0b 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHeatmapTest.java
@@ -64,7 +64,7 @@ public class TabularDataHeatmapTest extends AbstractTabularDataGraphTest
assertTrue(outputFile.length() > 0);
}
- @Test
+ @Test(groups = "slow")
public void testBigNumberHeatmap() throws IOException
{
File outputFile = getImageOutputFile();
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogramTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogramTest.java
index 96c4234dfb35a888349a52b8f2699971b4b6e30e..fab88d536379a2c570b42f1b734894a8df946ddb 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogramTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/graph/TabularDataHistogramTest.java
@@ -171,7 +171,7 @@ public class TabularDataHistogramTest extends AbstractTabularDataGraphTest
assertTrue(outputFile.length() > 0);
}
- @Test
+ @Test(groups = "slow")
public void testLotsOfBlanksHistogram() throws IOException
{
File outputFile = getImageOutputFile();
@@ -189,7 +189,7 @@ public class TabularDataHistogramTest extends AbstractTabularDataGraphTest
assertTrue(outputFile.length() > 0);
}
- @Test
+ @Test(groups = "slow")
public void testIncorrectlyConfiguredHistogram() throws IOException
{
File outputFile = getImageOutputFile();
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPluginTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPluginTest.java
index 19a1e540f413718b9f46613ef4896a3633c291c9..4b60d41b665da3cbe9798909732ef410c553331d 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPluginTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPluginTest.java
@@ -86,68 +86,56 @@ public class ImageAnalysisMergedRowsReportingPluginTest extends AssertJUnit
final DatasetDescription ds1 = new DatasetDescription();
ds1.setDatasetCode("ds1");
final ImgContainerDTO p1 = new ImgContainerDTO("p1", 3, 2, 0);
+ p1.setId(101);
final SampleIdentifier p1Identifier =
new SampleIdentifier(new SpaceIdentifier("1", "S"), "P1");
final DatasetDescription ds2 = new DatasetDescription();
ds2.setDatasetCode("ds2");
final ImgContainerDTO p2 = new ImgContainerDTO("p2", 2, 1, 0);
+ p2.setId(102);
final SampleIdentifier p2Identifier =
new SampleIdentifier(new SpaceIdentifier("1", "S"), "P2");
final ImgFeatureDefDTO ds1f1 = new ImgFeatureDefDTO("f1", "F1", "", 1);
+ ds1f1.setId(1);
final ImgFeatureDefDTO ds1f2 = new ImgFeatureDefDTO("f2", "F2", "", 1);
+ ds1f2.setId(2);
final ImgFeatureDefDTO ds2f2 = new ImgFeatureDefDTO("f2", "F2", "", 2);
+ ds2f2.setId(3);
final ImgFeatureDefDTO ds2f3 = new ImgFeatureDefDTO("f3", "F3", "", 2);
+ ds2f3.setId(4);
final ImgFeatureValuesDTO ds1f1Values =
- createFeatureValues("12, 2.5", "24, 3.25", "-1.5, 42");
+ createFeatureValues(ds1f1.getId(), "12, 2.5", "24, 3.25", "-1.5, 42");
final ImgFeatureValuesDTO ds1f2Values =
- createFeatureValues("-3.5, 12.5", "-2, 1", "5, 4.25");
- final ImgFeatureValuesDTO ds2f2Values = createFeatureValues("23", "5.75");
- final ImgFeatureValuesDTO ds2f3Values = createFeatureValues("-9", "44.125");
+ createFeatureValues(ds1f2.getId(), "-3.5, 12.5", "-2, 1", "5, 4.25");
+ final ImgFeatureValuesDTO ds2f2Values = createFeatureValues(ds2f2.getId(), "23", "5.75");
+ final ImgFeatureValuesDTO ds2f3Values = createFeatureValues(ds2f3.getId(), "-9", "44.125");
context.checking(new Expectations()
{
{
- one(dao).tryGetDatasetByPermId(ds1.getDatasetCode());
- will(returnValue(createDataSet(1)));
+ one(dao).listDatasetsByPermId(ds1.getDatasetCode(), ds2.getDatasetCode());
+ will(returnValue(Arrays.asList(createDataSet(1), createDataSet(2))));
- one(dao).listFeatureDefsByDataSetId(1);
- will(returnValue(Arrays.asList(ds1f1, ds1f2)));
+ one(dao).listFeatureDefsByDataSetIds(1, 2);
+ will(returnValue(Arrays.asList(ds1f1, ds1f2, ds2f2, ds2f3)));
- one(dao).listFeatureVocabularyTermsByDataSetId(1);
+ one(dao).listFeatureVocabularyTermsByDataSetId(1, 2);
will(returnValue(new ArrayList<ImgFeatureVocabularyTermDTO>()));
- one(dao).getContainerById(101);
- will(returnValue(p1));
+ one(dao).listContainersByIds(101, 102);
+ will(returnValue(Arrays.asList(p1, p2)));
one(service).tryGetSampleIdentifier(p1.getPermId());
will(returnValue(p1Identifier));
- one(dao).getFeatureValues(ds1f1);
- will(returnValue(Arrays.asList(ds1f1Values)));
-
- one(dao).getFeatureValues(ds1f2);
- will(returnValue(Arrays.asList(ds1f2Values)));
-
- one(dao).tryGetDatasetByPermId(ds2.getDatasetCode());
- will(returnValue(createDataSet(2)));
-
- one(dao).listFeatureDefsByDataSetId(2);
- will(returnValue(Arrays.asList(ds2f2, ds2f3)));
-
- one(dao).listFeatureVocabularyTermsByDataSetId(2);
- will(returnValue(new ArrayList<ImgFeatureVocabularyTermDTO>()));
-
- one(dao).getContainerById(102);
- will(returnValue(p2));
+ one(dao).getFeatureValues(ds1f1Values.getFeatureDefId(),
+ ds1f2Values.getFeatureDefId(), ds2f2Values.getFeatureDefId(),
+ ds2f3Values.getFeatureDefId());
+ will(returnValue(Arrays.asList(ds1f1Values, ds1f2Values, ds2f2Values,
+ ds2f3Values)));
one(service).tryGetSampleIdentifier(p2.getPermId());
will(returnValue(p2Identifier));
- one(dao).getFeatureValues(ds2f2);
- will(returnValue(Arrays.asList(ds2f2Values)));
-
- one(dao).getFeatureValues(ds2f3);
- will(returnValue(Arrays.asList(ds2f3Values)));
-
}
});
@@ -178,7 +166,7 @@ public class ImageAnalysisMergedRowsReportingPluginTest extends AssertJUnit
return datasetDTO;
}
- private ImgFeatureValuesDTO createFeatureValues(String... rows)
+ private ImgFeatureValuesDTO createFeatureValues(long featureDefId, String... rows)
{
float[][] matrix = new float[rows[0].split(",").length][rows.length];
for (int i = 0; i < rows.length; i++)
@@ -192,6 +180,6 @@ public class ImageAnalysisMergedRowsReportingPluginTest extends AssertJUnit
}
final MDFloatArray array = new MDFloatArray(matrix);
return new ImgFeatureValuesDTO(0.0, 0.0, new PlateFeatureValues(
- NativeTaggedArray.toByteArray(array)), 0L);
+ NativeTaggedArray.toByteArray(array)), featureDefId);
}
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 412db84bbd1252ea129d09ea16952721f7e5268f..a872a86b1be44711d8a791545f770703acfa4361 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -246,26 +246,15 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
{
prepareAssetDataSetsAreAccessible();
prepareLockDataSet("ds1", "ds2");
- prepareGetFeatureDefinitions(1, "f1", "f2");
- prepareGetFeatureDefinitions(2, "f2", "f3");
- @SuppressWarnings("deprecation")
- List<String> names =
- screeningService.listAvailableFeatureNames(SESSION_TOKEN, Arrays.asList(
- featureVectorDatasetIdentifier1, featureVectorDatasetIdentifier2));
-
- assertEquals("[f1, f2, f3]", names.toString());
- assertTrue(testMethodInterceptor.methodInvoked);
- context.assertIsSatisfied();
- }
-
- @Test
- public void testAuthorization()
- {
- prepareAssetDataSetsAreAccessible();
- prepareLockDataSet("ds1", "ds2");
- prepareGetFeatureDefinitions(1, "f1", "f2");
- prepareGetFeatureDefinitions(2, "f2", "f3");
+ long[] dataSetIDs = new long[]
+ { 1, 2 };
+ String[][] featureCodesPerDataset = new String[][]
+ {
+ { "f1", "f2" },
+ { "f2", "f3" } };
+ prepareListDatasets(dataSetIDs);
+ prepareGetFeatureDefinitions(dataSetIDs, featureCodesPerDataset);
List<String> names =
screeningService.listAvailableFeatureCodes(SESSION_TOKEN, Arrays.asList(
@@ -283,8 +272,16 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
prepareLockDataSet("ds1", "ds2");
FeatureVectorDatasetReference r1 = createFeatureVectorDatasetReference(DATASET_CODE);
FeatureVectorDatasetReference r2 = createFeatureVectorDatasetReference("ds2");
- prepareCreateFeatureVectorDataSet(1, "F1", "F2");
- prepareCreateFeatureVectorDataSet(2, "F2");
+ String[][] featureCodesPerDataset = new String[][]
+ {
+ { "F1", "F2" } };
+ prepareLoadFeatures(new long[]
+ { 1 }, featureCodesPerDataset);
+ featureCodesPerDataset = new String[][]
+ {
+ { "F2" } };
+ prepareLoadFeatures(new long[]
+ { 2 }, featureCodesPerDataset);
List<FeatureVectorDataset> dataSets =
screeningService.loadFeatures(SESSION_TOKEN, Arrays.asList(r1, r2),
@@ -308,6 +305,15 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
context.assertIsSatisfied();
}
+ private void prepareLoadFeatures(long[] dataSetIDs, String[][] featureCodesPerDataset)
+ {
+ prepareListDatasets(dataSetIDs);
+ prepareListContainers(dataSetIDs);
+ prepareGetFeatureDefinitions(dataSetIDs, featureCodesPerDataset);
+ prepareGetFeatureVocabularyTerms(dataSetIDs);
+ prepareCreateFeatureVectorDataSet(dataSetIDs, featureCodesPerDataset);
+ }
+
@Test
public void testLoadImages() throws IOException
{
@@ -590,71 +596,154 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
});
}
- private void prepareCreateFeatureVectorDataSet(final long dataSetID,
- final String... featureCodes)
+ private void prepareCreateFeatureVectorDataSet(final long[] dataSetIDs,
+ final String[]... featureCodesPerDataset)
{
- prepareGetFeatureDefinitions(dataSetID, featureCodes);
- prepareGetFeatureVocabularyTerms(dataSetID);
context.checking(new Expectations()
{
{
- one(dao).getContainerById(100 + dataSetID);
- will(returnValue(new ImgContainerDTO("12-34", 1, 2, 0)));
+ List<ImgFeatureValuesDTO> values = new ArrayList<ImgFeatureValuesDTO>();
+ long[] featureDefIds = new long[countFeatureCodes(featureCodesPerDataset)];
+ int featureDefIx = 0;
+ int datasetIx = 0;
- one(service).tryToGetSampleIdentifier("12-34");
- will(returnValue(new SampleIdentifier(new SpaceIdentifier("1", "S"), "P1")));
+ for (String[] featureCodes : featureCodesPerDataset)
+ {
+ long dataSetId = dataSetIDs[datasetIx++];
+ for (String featureCode : featureCodes)
+ {
+ featureDefIds[featureDefIx] = getFeatureDefId(featureCode);
+ int offset = getFeatureDefId(featureCode);
+ PlateFeatureValues matrixValues =
+ new PlateFeatureValues(NativeTaggedArray
+ .toByteArray(new MDFloatArray(new float[][]
+ {
+ { 3.5f * dataSetId + offset },
+ { 1.25f * dataSetId + offset } })));
+ ImgFeatureValuesDTO value =
+ new ImgFeatureValuesDTO(0.0, 0.0, matrixValues, 0L);
+ value.setFeatureDefId(featureDefIds[featureDefIx]);
+ values.add(value);
+
+ featureDefIx++;
+ }
+ }
+ one(dao).getFeatureValues(featureDefIds);
+ will(returnValue(values));
+ }
- for (String code : featureCodes)
+ });
+ }
+
+ private void prepareListContainers(final long[] dataSetIDs)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ long[] containerIds = new long[dataSetIDs.length];
+ List<ImgContainerDTO> containers = new ArrayList<ImgContainerDTO>();
+
+ for (int i = 0; i < dataSetIDs.length; i++)
{
- one(dao).getFeatureValues(new ImgFeatureDefDTO(code, code, "", 0));
- int offset = Integer.parseInt(code, 16);
- PlateFeatureValues array =
- new PlateFeatureValues(NativeTaggedArray
- .toByteArray(new MDFloatArray(new float[][]
- {
- { 3.5f * dataSetID + offset },
- { 1.25f * dataSetID + offset } })));
- will(returnValue(Arrays
- .asList(new ImgFeatureValuesDTO(0.0, 0.0, array, 0L))));
+ long id = dataSetIDs[i];
+ containerIds[i] = getContainerId(id);
+ ImgContainerDTO container = new ImgContainerDTO("12-34", 1, 2, 0);
+ container.setId(containerIds[i]);
+ containers.add(container);
+
+ one(service).tryToGetSampleIdentifier("12-34");
+ will(returnValue(new SampleIdentifier(new SpaceIdentifier("1", "S"), "P1")));
}
+
+ one(dao).listContainersByIds(containerIds);
+ will(returnValue(containers));
+ }
+ });
+ }
+
+ private void prepareListDatasets(final long[] dataSetIDs)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ String[] permIDs = new String[dataSetIDs.length];
+ List<ImgDatasetDTO> dataSets = new ArrayList<ImgDatasetDTO>();
+
+ for (int i = 0; i < dataSetIDs.length; i++)
+ {
+ long id = dataSetIDs[i];
+ permIDs[i] = "ds" + id;
+
+ ImgDatasetDTO dataSet =
+ new ImgDatasetDTO(permIDs[i], null, null, getContainerId(id), false);
+ dataSet.setId(id);
+ dataSets.add(dataSet);
+ }
+
+ one(dao).listDatasetsByPermId(permIDs);
+ will(returnValue(dataSets));
}
});
}
- private void prepareGetFeatureDefinitions(final long dataSetID, final String... featureCodes)
+ private void prepareGetFeatureDefinitions(final long[] dataSetIDs,
+ final String[]... featureCodesPerDataset)
{
context.checking(new Expectations()
{
{
- String permID = "ds" + dataSetID;
- one(dao).tryGetDatasetByPermId(permID);
- ImgDatasetDTO dataSet =
- new ImgDatasetDTO(permID, null, null, 100 + dataSetID, false);
- dataSet.setId(dataSetID);
- will(returnValue(dataSet));
-
- one(dao).listFeatureDefsByDataSetId(dataSetID);
List<ImgFeatureDefDTO> defs = new ArrayList<ImgFeatureDefDTO>();
- for (String code : featureCodes)
+ int datasetIx = 0;
+ for (String[] featureCodes : featureCodesPerDataset)
{
- defs.add(new ImgFeatureDefDTO(code, code, "", 0));
+ long dataSetID = dataSetIDs[datasetIx];
+ for (String code : featureCodes)
+ {
+ ImgFeatureDefDTO def = new ImgFeatureDefDTO(code, code, "", 0);
+ def.setDataSetId(dataSetID);
+ def.setId(getFeatureDefId(code));
+ defs.add(def);
+ }
+ datasetIx++;
}
+
+ one(dao).listFeatureDefsByDataSetIds(dataSetIDs);
will(returnValue(defs));
}
});
}
- private void prepareGetFeatureVocabularyTerms(final long dataSetID)
+ private void prepareGetFeatureVocabularyTerms(final long[] dataSetIDs)
{
context.checking(new Expectations()
{
{
- one(dao).listFeatureVocabularyTermsByDataSetId(dataSetID);
+ one(dao).listFeatureVocabularyTermsByDataSetId(dataSetIDs);
will(returnValue(new ArrayList<ImgFeatureVocabularyTermDTO>()));
}
});
}
+ private static long getContainerId(long datasetId)
+ {
+ return datasetId + 100;
+ }
+
+ private static int countFeatureCodes(String[][] featureCodesPerDataset)
+ {
+ int counter = 0;
+ for (String[] featureCodes : featureCodesPerDataset)
+ {
+ counter += featureCodes.length;
+ }
+ return counter;
+ }
+
+ private static int getFeatureDefId(String code)
+ {
+ return Integer.parseInt(code, 16);
+ }
+
private void prepareAssetDataSetIsAccessible(final String dsCode)
{
context.checking(new Expectations()
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoaderTest.java
index 99b15b63391805454f63289c22367faca1fe3456..a205f6ce48e26ed701a84b13e564a904bcb954aa 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoaderTest.java
@@ -21,6 +21,7 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -39,8 +40,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObject
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class FeatureVectorDatasetLoaderTest extends AbstractServerTestCase
@@ -52,18 +51,28 @@ public class FeatureVectorDatasetLoaderTest extends AbstractServerTestCase
{
screeningBOFactory = context.mock(IScreeningBusinessObjectFactory.class);
}
-
+
@Test
public void testGetFeatureVectorDatasets()
{
final RecordingMatcher<ListOrSearchSampleCriteria> recordingCriteriaMatcher =
new RecordingMatcher<ListOrSearchSampleCriteria>();
- final ExternalData ids1 = new DataSetBuilder(1l).code("ids1").type("HCS_IMAGE").getDataSet();
- final ExternalData fds1 = new DataSetBuilder(11l).code("fds1").type("HCS_ANALYSIS_WELL_FEATURES").getDataSet();
- final ExternalData fds2 = new DataSetBuilder(12l).code("fds2").type("HCS_ANALYSIS_WELL_FEATURES").getDataSet();
- final ExternalData ids2 = new DataSetBuilder(2l).code("ids2").type("HCS_IMAGE").getDataSet();
- final ExternalData fds3 = new DataSetBuilder(21l).code("fds3").type("HCS_ANALYSIS_WELL_FEATURES").getDataSet();
- final ExternalData fds4 = new DataSetBuilder(100l).code("fds4").type("HCS_ANALYSIS_WELL_FEATURES").getDataSet();
+ final ExternalData ids1 =
+ new DataSetBuilder(1l).code("ids1").type("HCS_IMAGE").getDataSet();
+ final ExternalData fds1 =
+ new DataSetBuilder(11l).code("fds1").type("HCS_ANALYSIS_WELL_FEATURES")
+ .getDataSet();
+ final ExternalData fds2 =
+ new DataSetBuilder(12l).code("fds2").type("HCS_ANALYSIS_WELL_FEATURES")
+ .getDataSet();
+ final ExternalData ids2 =
+ new DataSetBuilder(2l).code("ids2").type("HCS_IMAGE").getDataSet();
+ final ExternalData fds3 =
+ new DataSetBuilder(21l).code("fds3").type("HCS_ANALYSIS_WELL_FEATURES")
+ .getDataSet();
+ final ExternalData fds4 =
+ new DataSetBuilder(100l).code("fds4").type("HCS_ANALYSIS_WELL_FEATURES")
+ .getDataSet();
final ExternalData ds1 = new DataSetBuilder(101l).code("ds1").type("BLABLA").getDataSet();
context.checking(new Expectations()
{
@@ -72,18 +81,18 @@ public class FeatureVectorDatasetLoaderTest extends AbstractServerTestCase
will(returnValue(sampleLister));
allowing(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
-
+
one(sampleLister).list(with(recordingCriteriaMatcher));
ArrayList<Sample> samples = new ArrayList<Sample>();
samples.add(new SampleBuilder("/S/P1").id(42l).permID("s-1").getSample());
will(returnValue(samples));
-
- one(datasetLister).listBySampleIds(Arrays.asList(42l));
+
+ one(datasetLister).listBySampleIds(new HashSet<Long>(Arrays.asList(42l)));
will(returnValue(Arrays.asList(ids1, fds1, fds2, ids2, fds3, fds4, ds1)));
-
+
one(datasetLister).listByParentTechIds(Arrays.asList(1l, 2l));
will(returnValue(Arrays.asList(fds1, fds2, fds3, ds1)));
-
+
one(datasetLister).listParentIds(Arrays.asList(11l, 12l, 21l));
HashMap<Long, Set<Long>> map = new HashMap<Long, Set<Long>>();
map.put(11l, Collections.singleton(1l));
@@ -96,11 +105,15 @@ public class FeatureVectorDatasetLoaderTest extends AbstractServerTestCase
Arrays.<PlateIdentifier> asList(new PlateIdentifier("P1", "S", "s-1"));
FeatureVectorDatasetLoader loader =
new FeatureVectorDatasetLoader(SESSION, screeningBOFactory, null, plateIdentifiers);
-
- List<ExternalData> datasets = new ArrayList<ExternalData>(loader.getFeatureVectorDatasets());
-
- assertEquals("[]", Arrays.asList(recordingCriteriaMatcher.recordedObject().trySampleCodes()).toString());
- assertEquals("[s-1]", Arrays.asList(recordingCriteriaMatcher.recordedObject().trySamplePermIds()).toString());
+
+ List<ExternalData> datasets =
+ new ArrayList<ExternalData>(loader.getFeatureVectorDatasets());
+
+ assertEquals("[]", Arrays
+ .asList(recordingCriteriaMatcher.recordedObject().trySampleCodes()).toString());
+ assertEquals("[s-1]",
+ Arrays.asList(recordingCriteriaMatcher.recordedObject().trySamplePermIds())
+ .toString());
Collections.sort(datasets, new Comparator<ExternalData>()
{
public int compare(ExternalData o1, ExternalData o2)
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoaderTest.java
index 8ad5b2c618ae8be5591395974b29cb9e3bfaeac0..4bb9ead87afe95f7810efc01f2c9db03f7aab4af 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/HCSImageDatasetLoaderTest.java
@@ -21,6 +21,7 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -45,16 +46,16 @@ 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 HCSImageDatasetLoaderTest extends AbstractServerTestCase
{
private static final String STORE_CODE = "store-1";
+
private static final String DOWNLOAD_URL = "http://download";
+
private static final String HOST_URL = "http://host";
-
+
private IScreeningBusinessObjectFactory screeningBOFactory;
@BeforeMethod
@@ -62,7 +63,7 @@ public class HCSImageDatasetLoaderTest extends AbstractServerTestCase
{
screeningBOFactory = context.mock(IScreeningBusinessObjectFactory.class);
}
-
+
private DataSetBuilder dataSet(long id)
{
DataStoreBuilder dataStoreBuilder = new DataStoreBuilder(STORE_CODE);
@@ -70,24 +71,34 @@ public class HCSImageDatasetLoaderTest extends AbstractServerTestCase
Experiment experiment = new ExperimentBuilder().identifier("/S/P/E1").getExperiment();
return new DataSetBuilder(id).store(dataStoreBuilder.getStore()).experiment(experiment);
}
-
+
@Test
public void testGetSegmentationImageDatasetReferences()
{
final RecordingMatcher<ListOrSearchSampleCriteria> recordingCriteriaMatcher =
- new RecordingMatcher<ListOrSearchSampleCriteria>();
+ new RecordingMatcher<ListOrSearchSampleCriteria>();
SampleBuilder sampleBuilder = new SampleBuilder("/S/P1").id(42l).permID("s-1");
VocabularyTerm value = new VocabularyTerm();
value.setCode("96_WELLS_8X12");
sampleBuilder.property(ScreeningConstants.PLATE_GEOMETRY).value(value);
final Sample sample = sampleBuilder.getSample();
- final ExternalData ids1 = dataSet(1l).code("ids1").type("HCS_IMAGE").sample(sample).getDataSet();
- final ExternalData sds1 = dataSet(11l).code("sds1").type("HCS_IMAGE_SEGMENTATION").sample(sample).getDataSet();
- final ExternalData sds2 = dataSet(12l).code("sds2").type("HCS_IMAGE_SEGMENTATION").sample(sample).getDataSet();
- final ExternalData ids2 = dataSet(2l).code("ids2").type("HCS_IMAGE").sample(sample).getDataSet();
- final ExternalData sds3 = dataSet(21l).code("sds3").type("HCS_IMAGE_SEGMENTATION").sample(sample).getDataSet();
- final ExternalData sds4 = dataSet(100l).code("sds4").type("HCS_IMAGE_SEGMENTATION").getDataSet();
- final ExternalData ds1 = dataSet(101l).code("ds1").type("BLABLA").sample(sample).getDataSet();
+ final ExternalData ids1 =
+ dataSet(1l).code("ids1").type("HCS_IMAGE").sample(sample).getDataSet();
+ final ExternalData sds1 =
+ dataSet(11l).code("sds1").type("HCS_IMAGE_SEGMENTATION").sample(sample)
+ .getDataSet();
+ final ExternalData sds2 =
+ dataSet(12l).code("sds2").type("HCS_IMAGE_SEGMENTATION").sample(sample)
+ .getDataSet();
+ final ExternalData ids2 =
+ dataSet(2l).code("ids2").type("HCS_IMAGE").sample(sample).getDataSet();
+ final ExternalData sds3 =
+ dataSet(21l).code("sds3").type("HCS_IMAGE_SEGMENTATION").sample(sample)
+ .getDataSet();
+ final ExternalData sds4 =
+ dataSet(100l).code("sds4").type("HCS_IMAGE_SEGMENTATION").getDataSet();
+ final ExternalData ds1 =
+ dataSet(101l).code("ds1").type("BLABLA").sample(sample).getDataSet();
context.checking(new Expectations()
{
{
@@ -101,7 +112,7 @@ public class HCSImageDatasetLoaderTest extends AbstractServerTestCase
samples.add(sample);
will(returnValue(samples));
- one(datasetLister).listBySampleIds(Arrays.asList(42l));
+ one(datasetLister).listBySampleIds(new HashSet<Long>(Arrays.asList(42l)));
will(returnValue(Arrays.asList(ids1, sds1, sds2, ids2, sds3, sds4, ds1)));
one(datasetLister).listByParentTechIds(Arrays.asList(1l, 2l));
@@ -135,11 +146,14 @@ public class HCSImageDatasetLoaderTest extends AbstractServerTestCase
}
});
assertEquals("sds1 (plate: /S/P1 [s-1])", references.get(0).toString());
- assertEquals("ids1 (plate: /S/P1 [s-1])", references.get(0).getParentImageDatasetReference().toString());
+ assertEquals("ids1 (plate: /S/P1 [s-1])", references.get(0)
+ .getParentImageDatasetReference().toString());
assertEquals("sds2 (plate: /S/P1 [s-1])", references.get(1).toString());
- assertEquals("ids1 (plate: /S/P1 [s-1])", references.get(1).getParentImageDatasetReference().toString());
+ assertEquals("ids1 (plate: /S/P1 [s-1])", references.get(1)
+ .getParentImageDatasetReference().toString());
assertEquals("sds3 (plate: /S/P1 [s-1])", references.get(2).toString());
- assertEquals("ids2 (plate: /S/P1 [s-1])", references.get(2).getParentImageDatasetReference().toString());
+ assertEquals("ids2 (plate: /S/P1 [s-1])", references.get(2)
+ .getParentImageDatasetReference().toString());
assertEquals(3, references.size());
context.assertIsSatisfied();
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 25288f98a67b29cccf5c869e1b1067ce3da4cfbb..55cca8692e1a0c92bfd1b218cddada7f6575185f 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
@@ -150,6 +150,11 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
context.assertIsSatisfied();
}
+ private static HashSet<Long> asSet(long id)
+ {
+ return new HashSet<Long>(Arrays.asList(id));
+ }
+
@Test
public void testListImageDatasets()
{
@@ -165,7 +170,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
one(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
- one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
+ one(datasetLister).listBySampleIds(with(asSet(1)));
will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1),
imageAnalysisDataSet(p1, "2", 2))));
}
@@ -199,7 +204,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
one(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
- one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
+ one(datasetLister).listBySampleIds(with(asSet(1)));
will(returnValue(Arrays.asList(imageRawDataSet(p1, "1", 1),
imageRawDataSet(p1, "2", 2), imageAnalysisDataSet(p1, "3", 3))));
}
@@ -240,17 +245,17 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
allowing(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
- one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
+ one(datasetLister).listBySampleIds(with(asSet(1)));
final ExternalData rawImage = imageRawDataSet(p1, "2", 2);
- ExternalData imageSegmentationDataSet = imageSegmentationDataSet(p1, "3", 3, rawImage);
+ ExternalData imageSegmentationDataSet =
+ imageSegmentationDataSet(p1, "3", 3, rawImage);
ExternalData imageAnalysisDataSet = imageAnalysisDataSet(p1, "4", 4);
will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1), rawImage,
- imageSegmentationDataSet,
- imageAnalysisDataSet)));
-
+ imageSegmentationDataSet, imageAnalysisDataSet)));
+
one(datasetLister).listByParentTechIds(Arrays.asList(1l, 2l));
will(returnValue(Arrays.asList(imageSegmentationDataSet, imageAnalysisDataSet)));
-
+
one(datasetLister).listParentIds(Arrays.asList(3l));
HashMap<Long, Set<Long>> result = new HashMap<Long, Set<Long>>();
result.put(3l, Collections.singleton(2l));
@@ -295,7 +300,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
one(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
- one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
+ one(datasetLister).listBySampleIds(with(asSet(1)));
will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1))));
}
});
@@ -356,7 +361,8 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
exactly(2).of(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
long imageDatasetId = 1;
- one(datasetLister).listBySampleIds(with(Arrays.asList(imageDatasetId)));
+ one(datasetLister).listBySampleIds(
+ with(new HashSet<Long>(asSet(imageDatasetId))));
will(returnValue(Arrays.asList(
imageDataSet(p1, "" + imageDatasetId, imageDatasetId),
imageAnalysisDataSet(p1, "2", 2))));
@@ -411,7 +417,7 @@ public class ScreeningApiImplTest extends AbstractServerTestCase
one(screeningBOFactory).createDatasetLister(SESSION);
will(returnValue(datasetLister));
- one(datasetLister).listBySampleIds(with(Arrays.asList((long) 1)));
+ one(datasetLister).listBySampleIds(with(asSet(1)));
will(returnValue(Arrays.asList(imageDataSet(p1, "1", 1))));
}
});
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoaderTest.java
index 5afa9de28219954b76d5dcb05a86bd11a29e126c..5ef39a206fc1f79b3773f5655ae3059b72d56f3f 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellContentLoaderTest.java
@@ -52,7 +52,7 @@ public class WellContentLoaderTest extends AbstractScreeningDAOTest
@Autowired
IGenericServer server;
- @Test
+ @Test(groups = "slow")
public void testLoadWellContentsWithProperties()
{
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureTableBuilderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureTableBuilderTest.java
deleted file mode 100644
index a7964cd8a580cf6b672d9a6b72b198bbb3644745..0000000000000000000000000000000000000000
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureTableBuilderTest.java
+++ /dev/null
@@ -1,218 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.AssertJUnit;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.FeatureTableRow;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.IMetadataProvider;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureVocabularyTermDTO;
-
-/**
- * Tests of {@link FeatureVectorLoader}.
- *
- * @author Franz-Josef Elmer
- */
-public class FeatureTableBuilderTest extends AssertJUnit
-{
- private static final int EXPERIMENT_ID = 42;
-
- private static final String DATA_SET_CODE1 = "ds1";
-
- private static final String DATA_SET_CODE2 = "ds2";
-
- private static final String DATA_SET_CODE3 = "ds3";
-
- private Mockery context;
-
- private IMetadataProvider service;
-
- private IImagingReadonlyQueryDAO dao;
-
- @BeforeMethod
- public void beforeMethod()
- {
- context = new Mockery();
- service = context.mock(IMetadataProvider.class);
- dao = context.mock(IImagingReadonlyQueryDAO.class);
- }
-
- @AfterMethod
- public final void tearDown()
- {
- // The following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public void testNoFiltering()
- {
- prepareAddFeatureVectors(1, null, "<A>a", "<B>b");
- prepareAddFeatureVectors(2, null, "<B>beta", "c");
- prepareAddFeatureVectors(3, null, "<B>b");
-
- FeatureVectorLoader builder = createBuilder();
- builder.addFeatureVectorsOfDataSetOrDie(DATA_SET_CODE1);
- builder.addFeatureVectorsOfDataSetOrDie(DATA_SET_CODE2);
- builder.addFeatureVectorsOfDataSetOrDie(DATA_SET_CODE3);
- List<CodeAndLabel> codesAndLabels = builder.getCodesAndLabels();
- List<FeatureTableRow> rows = builder.createFeatureTableRows();
-
- assertEquals("[<A> a, <B> b, <B> beta, <C> c]", codesAndLabels.toString());
- assertFeatureTableRow(DATA_SET_CODE1, "A1", "db:/s/S1", "1.5, 11.5, NaN, NaN", rows.get(0));
- assertFeatureTableRow(DATA_SET_CODE1, "A2", "db:/s/S1", "0.5, 10.5, NaN, NaN", rows.get(1));
- assertFeatureTableRow(DATA_SET_CODE2, "A1", "db:/s/S2", "NaN, NaN, 2.5, 12.5", rows.get(2));
- assertFeatureTableRow(DATA_SET_CODE2, "A2", "db:/s/S2", "NaN, NaN, 1.5, 11.5", rows.get(3));
- assertFeatureTableRow(DATA_SET_CODE3, "A1", "db:/s/S3", "NaN, 3.5, NaN, NaN", rows.get(4));
- assertFeatureTableRow(DATA_SET_CODE3, "A2", "db:/s/S3", "NaN, 2.5, NaN, NaN", rows.get(5));
- assertEquals(6, rows.size());
- context.assertIsSatisfied();
- }
-
- @Test
- public void testFiltering()
- {
- prepareAddFeatureVectors(1, "B", "<A>a", "b");
- prepareAddFeatureVectors(2, "B", "<B>beta", "c");
- prepareAddFeatureVectors(3, "B", "b");
-
- FeatureVectorLoader builder = createBuilder("B");
- builder.addFeatureVectorsOfDataSetOrDie(DATA_SET_CODE1);
- builder.addFeatureVectorsOfDataSetOrDie(DATA_SET_CODE2);
- builder.addFeatureVectorsOfDataSetOrDie(DATA_SET_CODE3);
- List<CodeAndLabel> codesAndLabels = builder.getCodesAndLabels();
- List<FeatureTableRow> rows = builder.createFeatureTableRows();
-
- assertEquals("[<B> b, <B> beta]", codesAndLabels.toString());
- assertFeatureTableRow(DATA_SET_CODE1, "A1", "db:/s/S1", "11.5, NaN", rows.get(0));
- assertFeatureTableRow(DATA_SET_CODE1, "A2", "db:/s/S1", "10.5, NaN", rows.get(1));
- assertFeatureTableRow(DATA_SET_CODE2, "A1", "db:/s/S2", "NaN, 2.5", rows.get(2));
- assertFeatureTableRow(DATA_SET_CODE2, "A2", "db:/s/S2", "NaN, 1.5", rows.get(3));
- assertFeatureTableRow(DATA_SET_CODE3, "A1", "db:/s/S3", "3.5, NaN", rows.get(4));
- assertFeatureTableRow(DATA_SET_CODE3, "A2", "db:/s/S3", "2.5, NaN", rows.get(5));
- assertEquals(6, rows.size());
- context.assertIsSatisfied();
- }
-
- private void prepareAddFeatureVectors(final int dataSetID, final String filteredCodeOrNull,
- final String... featureCodesAndLabels)
- {
- context.checking(new Expectations()
- {
- {
- String dataSetCode = "ds" + dataSetID;
- one(dao).tryGetDatasetByPermId(dataSetCode);
- long containerId = dataSetID + 100;
- ImgDatasetDTO dataSet =
- new ImgDatasetDTO(dataSetCode, null, null, containerId, false);
- dataSet.setId(dataSetID);
- will(returnValue(dataSet));
-
- List<ImgFeatureDefDTO> defs = new ArrayList<ImgFeatureDefDTO>();
- Geometry geometry = Geometry.createFromCartesianDimensions(2, 1);
- for (int i = 0; i < featureCodesAndLabels.length; i++)
- {
- String codeAndLabels = featureCodesAndLabels[i];
- CodeAndLabel codeAndTitle = CodeAndLabelUtil.create(codeAndLabels);
- String title = codeAndTitle.getLabel();
- String code = codeAndTitle.getCode();
- if (filteredCodeOrNull == null || filteredCodeOrNull.equals(code))
- {
- ImgFeatureDefDTO def =
- new ImgFeatureDefDTO(title, code, title, dataSetID);
- def.setId(2 * dataSetID);
- defs.add(def);
- one(dao).getFeatureValues(def);
- PlateFeatureValues values = new PlateFeatureValues(geometry);
- values.setForWellLocation(dataSetID + 10 * i + 0.5f, 1, 1);
- values.setForWellLocation(dataSetID + 10 * i - 0.5f, 1, 2);
- will(returnValue(Arrays.asList(new ImgFeatureValuesDTO(0.0, 0.0,
- values, def.getId()))));
- }
- }
- one(dao).listFeatureDefsByDataSetId(dataSetID);
- will(returnValue(defs));
-
- one(dao).listFeatureVocabularyTermsByDataSetId(dataSetID);
- will(returnValue(new ArrayList<ImgFeatureVocabularyTermDTO>()));
-
- one(dao).getContainerById(containerId);
- String samplePermID = "s" + containerId;
- will(returnValue(new ImgContainerDTO(samplePermID, geometry.getNumberOfRows(),
- geometry.getNumberOfColumns(), EXPERIMENT_ID)));
-
- one(service).tryGetSampleIdentifier(samplePermID);
- will(returnValue(new SampleIdentifier(new SpaceIdentifier("db", "s"), "S"
- + dataSetID)));
- }
- });
- }
-
- private void assertFeatureTableRow(String expectedDataSetCode, String expectedWell,
- String expectedPlate, String expectedValues, FeatureTableRow row)
- {
- assertEquals(expectedDataSetCode, row.getDataSetCode());
- String rowLetter =
- PlateUtils.translateRowNumberIntoLetterCode(row.getWellLocation().getRow());
- assertEquals(expectedWell, rowLetter + row.getWellLocation().getColumn());
- assertEquals(expectedPlate, row.getPlateIdentifier().toString());
- assertEquals(expectedValues, render(row.getFeatureValues()));
- }
-
- private String render(FeatureValue[] values)
- {
- StringBuilder builder = new StringBuilder();
- for (FeatureValue value : values)
- {
- if (builder.length() > 0)
- {
- builder.append(", ");
- }
- builder.append(value);
- }
- return builder.toString();
- }
-
- private FeatureVectorLoader createBuilder(String... featureCodes)
- {
- return new FeatureVectorLoader(Arrays.asList(featureCodes), dao, service);
- }
-
-}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureVectorLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureVectorLoaderTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..4b976ab973a02703c20bca8945d00e8c5a05e95e
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/FeatureVectorLoaderTest.java
@@ -0,0 +1,344 @@
+/*
+ * 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.shared.imaging;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndLabelUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.FeatureTableRow;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.IMetadataProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingReadonlyQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureVocabularyTermDTO;
+
+/**
+ * Tests of {@link FeatureVectorLoader}.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FeatureVectorLoaderTest extends AssertJUnit
+{
+ private static final int EXPERIMENT_ID = 42;
+
+ private static final String DATA_SET_CODE1 = "ds1";
+
+ private static final String DATA_SET_CODE2 = "ds2";
+
+ private static final String DATA_SET_CODE3 = "ds3";
+
+ private Mockery context;
+
+ private IMetadataProvider service;
+
+ private IImagingReadonlyQueryDAO dao;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ service = context.mock(IMetadataProvider.class);
+ dao = context.mock(IImagingReadonlyQueryDAO.class);
+ }
+
+ @AfterMethod
+ public final void tearDown()
+ {
+ // The following line of code should also be called at the end of each test method.
+ // Otherwise one do not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testNoFiltering()
+ {
+ long[] dataSetIDs = new long[]
+ { 1, 2, 3 };
+ String[][] featureCodesPerDataset = new String[][]
+ {
+ { "<A>a", "<B>b" },
+ { "<B>beta", "c" },
+ { "<B>b" } };
+ prepareLoadFeatures(dataSetIDs, null, featureCodesPerDataset);
+
+ FeatureVectorLoader builder = createBuilder();
+ builder.addFeatureVectorsOfDataSetsOrDie(Arrays.asList(DATA_SET_CODE1, DATA_SET_CODE2,
+ DATA_SET_CODE3));
+ List<CodeAndLabel> codesAndLabels = builder.getCodesAndLabels();
+ List<FeatureTableRow> rows = builder.createFeatureTableRows();
+
+ assertEquals("[<A> a, <B> b, <B> beta, <C> c]", codesAndLabels.toString());
+ assertFeatureTableRow(DATA_SET_CODE1, "A1", "db:/s/S1", "1.5, 11.5, NaN, NaN", rows.get(0));
+ assertFeatureTableRow(DATA_SET_CODE1, "A2", "db:/s/S1", "0.5, 10.5, NaN, NaN", rows.get(1));
+ assertFeatureTableRow(DATA_SET_CODE2, "A1", "db:/s/S2", "NaN, NaN, 2.5, 12.5", rows.get(2));
+ assertFeatureTableRow(DATA_SET_CODE2, "A2", "db:/s/S2", "NaN, NaN, 1.5, 11.5", rows.get(3));
+ assertFeatureTableRow(DATA_SET_CODE3, "A1", "db:/s/S3", "NaN, 3.5, NaN, NaN", rows.get(4));
+ assertFeatureTableRow(DATA_SET_CODE3, "A2", "db:/s/S3", "NaN, 2.5, NaN, NaN", rows.get(5));
+ assertEquals(6, rows.size());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testFiltering()
+ {
+ long[] dataSetIDs = new long[]
+ { 1, 2, 3 };
+ String[][] featureCodesPerDataset = new String[][]
+ {
+ { "<A>a", "b" },
+ { "<B>beta", "c" },
+ { "b" } };
+ prepareLoadFeatures(dataSetIDs, "B", featureCodesPerDataset);
+
+ FeatureVectorLoader builder = createBuilder("B");
+ builder.addFeatureVectorsOfDataSetsOrDie(Arrays.asList(DATA_SET_CODE1, DATA_SET_CODE2,
+ DATA_SET_CODE3));
+ List<CodeAndLabel> codesAndLabels = builder.getCodesAndLabels();
+ List<FeatureTableRow> rows = builder.createFeatureTableRows();
+
+ assertEquals("[<B> b, <B> beta]", codesAndLabels.toString());
+ assertFeatureTableRow(DATA_SET_CODE1, "A1", "db:/s/S1", "11.5, NaN", rows.get(0));
+ assertFeatureTableRow(DATA_SET_CODE1, "A2", "db:/s/S1", "10.5, NaN", rows.get(1));
+ assertFeatureTableRow(DATA_SET_CODE2, "A1", "db:/s/S2", "NaN, 2.5", rows.get(2));
+ assertFeatureTableRow(DATA_SET_CODE2, "A2", "db:/s/S2", "NaN, 1.5", rows.get(3));
+ assertFeatureTableRow(DATA_SET_CODE3, "A1", "db:/s/S3", "3.5, NaN", rows.get(4));
+ assertFeatureTableRow(DATA_SET_CODE3, "A2", "db:/s/S3", "2.5, NaN", rows.get(5));
+ assertEquals(6, rows.size());
+ context.assertIsSatisfied();
+ }
+
+ private void prepareLoadFeatures(long[] dataSetIDs, String filteredCodeOrNull,
+ String[][] featureCodesPerDataset)
+ {
+ Geometry geometry = Geometry.createFromCartesianDimensions(2, 1);
+ prepareListDatasets(dataSetIDs);
+ prepareListContainers(dataSetIDs, geometry);
+ prepareGetFeatureDefinitions(dataSetIDs, featureCodesPerDataset);
+ prepareGetFeatureVocabularyTerms(dataSetIDs);
+ prepareAddFeatureVectors(dataSetIDs, filteredCodeOrNull, geometry, featureCodesPerDataset);
+ }
+
+ private void prepareAddFeatureVectors(final long dataSetIDs[], final String filteredCodeOrNull,
+ final Geometry geometry, final String[]... featureHeadersPerDataset)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ List<ImgFeatureValuesDTO> values = new ArrayList<ImgFeatureValuesDTO>();
+ List<Long> listedFeatureDefIds = new ArrayList<Long>();
+ long featureId = 0;
+ int datasetIx = 0;
+
+ for (String[] featureHeaders : featureHeadersPerDataset)
+ {
+ long dataSetId = dataSetIDs[datasetIx++];
+ long datasetFeatureIx = 0;
+ for (String featureHeader : featureHeaders)
+ {
+ String featureCode = CodeAndLabelUtil.create(featureHeader).getCode();
+ if (filteredCodeOrNull == null
+ || filteredCodeOrNull.equals(featureCode))
+ {
+ listedFeatureDefIds.add(featureId);
+
+ PlateFeatureValues matrixValues = new PlateFeatureValues(geometry);
+ matrixValues.setForWellLocation(dataSetId + 10 * datasetFeatureIx
+ + 0.5f, 1, 1);
+ matrixValues.setForWellLocation(dataSetId + 10 * datasetFeatureIx
+ - 0.5f, 1, 2);
+
+ ImgFeatureValuesDTO value =
+ new ImgFeatureValuesDTO(0.0, 0.0, matrixValues, featureId);
+ values.add(value);
+ }
+ featureId++;
+ datasetFeatureIx++;
+ }
+ }
+ one(dao).getFeatureValues(asPrimitiveArray(listedFeatureDefIds));
+ will(returnValue(values));
+ }
+
+ });
+ }
+
+ private static long[] asPrimitiveArray(List<Long> values)
+ {
+ long[] array = new long[values.size()];
+ for (int i = 0; i < array.length; i++)
+ {
+ array[i] = values.get(i);
+ }
+ return array;
+ }
+
+ private void prepareListContainers(final long[] dataSetIDs, final Geometry geometry)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ long[] containerIds = new long[dataSetIDs.length];
+ List<ImgContainerDTO> containers = new ArrayList<ImgContainerDTO>();
+
+ for (int i = 0; i < dataSetIDs.length; i++)
+ {
+ long id = dataSetIDs[i];
+ containerIds[i] = getContainerId(id);
+ String samplePermID = "s" + containerIds[i];
+ ImgContainerDTO container =
+ new ImgContainerDTO(samplePermID, geometry.getNumberOfRows(),
+ geometry.getNumberOfColumns(), EXPERIMENT_ID);
+ container.setId(containerIds[i]);
+ containers.add(container);
+
+ one(service).tryGetSampleIdentifier(samplePermID);
+ will(returnValue(createSpaceIdentifier(id)));
+ }
+
+ one(dao).listContainersByIds(containerIds);
+ will(returnValue(containers));
+ }
+
+ });
+ }
+
+ private void prepareListDatasets(final long[] dataSetIDs)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ String[] permIDs = new String[dataSetIDs.length];
+ List<ImgDatasetDTO> dataSets = new ArrayList<ImgDatasetDTO>();
+
+ for (int i = 0; i < dataSetIDs.length; i++)
+ {
+ long id = dataSetIDs[i];
+ permIDs[i] = "ds" + id;
+
+ ImgDatasetDTO dataSet =
+ new ImgDatasetDTO(permIDs[i], null, null, getContainerId(id), false);
+ dataSet.setId(id);
+ dataSets.add(dataSet);
+ }
+
+ one(dao).listDatasetsByPermId(permIDs);
+ will(returnValue(dataSets));
+ }
+ });
+ }
+
+ private void prepareGetFeatureDefinitions(final long[] dataSetIDs,
+ final String[]... featureCodesPerDataset)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ List<ImgFeatureDefDTO> defs = new ArrayList<ImgFeatureDefDTO>();
+ int datasetIx = 0;
+ int featureId = 0;
+ for (String[] featureCodes : featureCodesPerDataset)
+ {
+ long dataSetID = dataSetIDs[datasetIx];
+ for (String featureCode : featureCodes)
+ {
+ CodeAndLabel codeAndTitle = CodeAndLabelUtil.create(featureCode);
+ String title = codeAndTitle.getLabel();
+ String code = codeAndTitle.getCode();
+ ImgFeatureDefDTO def =
+ new ImgFeatureDefDTO(title, code, title, dataSetID);
+ def.setId(featureId++);
+ defs.add(def);
+ }
+ datasetIx++;
+ }
+
+ one(dao).listFeatureDefsByDataSetIds(dataSetIDs);
+ will(returnValue(defs));
+ }
+ });
+ }
+
+ private void prepareGetFeatureVocabularyTerms(final long[] dataSetIDs)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).listFeatureVocabularyTermsByDataSetId(dataSetIDs);
+ will(returnValue(new ArrayList<ImgFeatureVocabularyTermDTO>()));
+ }
+ });
+ }
+
+ private static long getContainerId(long datasetId)
+ {
+ return datasetId + 100;
+ }
+
+ private SampleIdentifier createSpaceIdentifier(long datasetId)
+ {
+ return new SampleIdentifier(new SpaceIdentifier("db", "s"), "S" + datasetId);
+ }
+
+ private void assertFeatureTableRow(String expectedDataSetCode, String expectedWell,
+ String expectedPlate, String expectedValues, FeatureTableRow row)
+ {
+ assertEquals(expectedDataSetCode, row.getDataSetCode());
+ String rowLetter =
+ PlateUtils.translateRowNumberIntoLetterCode(row.getWellLocation().getRow());
+ assertEquals(expectedWell, rowLetter + row.getWellLocation().getColumn());
+ assertEquals(expectedPlate, row.getPlateIdentifier().toString());
+ assertEquals(expectedValues, render(row.getFeatureValues()));
+ }
+
+ private String render(FeatureValue[] values)
+ {
+ StringBuilder builder = new StringBuilder();
+ for (FeatureValue value : values)
+ {
+ if (builder.length() > 0)
+ {
+ builder.append(", ");
+ }
+ builder.append(value);
+ }
+ return builder.toString();
+ }
+
+ private FeatureVectorLoader createBuilder(String... featureCodes)
+ {
+ return new FeatureVectorLoader(Arrays.asList(featureCodes), dao, service);
+ }
+
+}