From 8a4a7337d0c4821610eb68b07ac08e6de6d1502a Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Thu, 10 Feb 2011 20:52:10 +0000
Subject: [PATCH] [LMS-2029] limit number of initially loaded features; load
subsequent features on demand
SVN: 19889
---
.../web/client/IScreeningClientService.java | 9 ++
.../client/IScreeningClientServiceAsync.java | 11 ++-
.../heatmaps/HeatmapPresenter.java | 65 ++++++++++++--
.../detailviewers/heatmaps/PlateLayouter.java | 44 +++++-----
.../heatmaps/PlateLayouterModel.java | 87 +++++++++++++++----
.../web/server/ScreeningClientService.java | 15 ++++
.../server/FeatureCountLimitProvider.java | 56 ++++++++++++
.../server/IFeatureCountLimitProvider.java | 29 +++++++
.../IScreeningBusinessObjectFactory.java | 5 +-
.../ScreeningBusinessObjectFactory.java | 8 ++
.../screening/server/ScreeningServer.java | 11 +++
.../server/ScreeningServerLogger.java | 11 +++
.../server/logic/PlateContentLoader.java | 78 +++++++++++++----
.../screening/shared/IScreeningServer.java | 16 +++-
.../screening/shared/ResourceNames.java | 2 +
.../DatasetReferencePredicate.java | 45 ++++++++++
.../basic/dto/FeatureVectorDataset.java | 13 +--
.../java/screening-applicationContext.xml | 4 +
screening/source/java/service.properties | 7 +-
.../heatmaps/WellTooltipGeneratorTest.java | 12 +--
20 files changed, 450 insertions(+), 78 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/FeatureCountLimitProvider.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IFeatureCountLimitProvider.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/authorization/DatasetReferencePredicate.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
index f4c27f69fbc..8ccc4f191b0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
@@ -25,11 +25,14 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteri
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSampleContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
@@ -70,6 +73,12 @@ public interface IScreeningClientService extends IClientService
*/
public PlateContent getPlateContent(TechId sampleId) throws UserFailureException;
+ /**
+ * Fetches feature vector of specified dataset with one feature specified by name.
+ */
+ public FeatureVectorDataset getFeatureVectorDataset(DatasetReference dataset,
+ CodeAndLabel featureName);
+
/**
* Fetches information about a plate: metadata and images for wells. The specified dataset is
* supposed to be in BDS-HCS format.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
index 18e0d5c31b9..4ccba731d5d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client;
+import com.google.gwt.user.client.rpc.AsyncCallback;
+
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.IResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ListMaterialDisplayCriteria;
@@ -23,11 +25,14 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRowWithObject;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSampleContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
@@ -39,8 +44,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria;
-import com.google.gwt.user.client.rpc.AsyncCallback;
-
/**
* Service interface for the <i>screening</i> <i>GWT</i> client.
*
@@ -56,6 +59,10 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
/** @see IScreeningClientService#getPlateContent(TechId) */
public void getPlateContent(TechId sampleId, final AsyncCallback<PlateContent> callback);
+ /** @see IScreeningClientService#getFeatureVectorDataset(DatasetReference, CodeAndLabel) */
+ public void getFeatureVectorDataset(DatasetReference dataset, CodeAndLabel featureName,
+ AsyncCallback<FeatureVectorDataset> callback);
+
/** @see IScreeningClientService#getPlateContentForDataset(TechId) */
public void getPlateContentForDataset(TechId datasetId,
AsyncCallback<PlateImages> createDisplayPlateCallback);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/HeatmapPresenter.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/HeatmapPresenter.java
index f6597b8bf2d..4f154d29f75 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/HeatmapPresenter.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/HeatmapPresenter.java
@@ -8,17 +8,24 @@ import java.util.Iterator;
import java.util.List;
import java.util.Set;
+import com.extjs.gxt.ui.client.widget.MessageBox;
+import com.google.gwt.user.client.rpc.AsyncCallback;
import com.google.gwt.user.client.ui.Widget;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.IRealNumberRenderer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.WellData;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.heatmaps.dto.Color;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.heatmaps.dto.HeatmapScaleElement;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
@@ -50,11 +57,15 @@ class HeatmapPresenter
private final IRealNumberRenderer realNumberRenderer;
+ private final ScreeningViewContext viewContext;
+
// ---
- public HeatmapPresenter(PlateLayouterModel model, IRealNumberRenderer realNumberRenderer,
+ public HeatmapPresenter(ScreeningViewContext viewContext, PlateLayouterModel model,
+ IRealNumberRenderer realNumberRenderer,
HeatmapPresenter.IHeatmapViewManipulator viewManipulations)
{
+ this.viewContext = viewContext;
this.model = model;
this.viewManipulations = viewManipulations;
this.realNumberRenderer = realNumberRenderer;
@@ -71,12 +82,53 @@ class HeatmapPresenter
}
/**
- * Changes the presented heatmap to the one which shows the feature with given label.
+ * Changes the presented heatmap to the one which shows the feature with given name.
*/
- public void setFeatureValueMode(String featureName)
+ public void setFeatureValueMode(CodeAndLabel featureName)
+ {
+ if (model.isFeatureAvailable(featureName.getLabel()))
+ {
+ doChangeFeatureValueMode(featureName);
+ } else
+ {
+ DatasetReference dataset = model.tryGetDatasetReference();
+ if (dataset != null)
+ {
+ viewContext.getService().getFeatureVectorDataset(dataset, featureName,
+ createChangeHeatmapCallback(viewContext, featureName));
+ } else
+ {
+ MessageBox.alert("Error", "No data set selected", null);
+ }
+ }
+ }
+
+ private void doChangeFeatureValueMode(CodeAndLabel featureName)
{
- IHeatmapRenderer<WellData> renderer = createFeatureHeatmapRenderer(featureName);
- refreshHeatmap(renderer, featureName);
+ IHeatmapRenderer<WellData> renderer = createFeatureHeatmapRenderer(featureName.getLabel());
+ refreshHeatmap(renderer, featureName.getLabel());
+ }
+
+ private AsyncCallback<FeatureVectorDataset> createChangeHeatmapCallback(
+ final ScreeningViewContext context, final CodeAndLabel featureName)
+ {
+ return new AbstractAsyncCallback<FeatureVectorDataset>(context)
+ {
+ @Override
+ protected void process(FeatureVectorDataset featureVector)
+ {
+ model.updateFeatureVectorDataset(featureVector);
+
+ if (model.isFeatureAvailable(featureName.getLabel()))
+ {
+ doChangeFeatureValueMode(featureName);
+ } else
+ {
+ MessageBox.alert("Error",
+ "No values found for feature " + featureName.getLabel(), null);
+ }
+ }
+ };
}
private IHeatmapRenderer<WellData> createFeatureHeatmapRenderer(String featureLabel)
@@ -384,8 +436,7 @@ class HeatmapPresenter
private int getNumberOfAllFeatures()
{
- List<String> featureLabels = model.tryGetFeatureLabels();
- return featureLabels == null ? 0 : featureLabels.size();
+ return model.getAllFeatureNames().size();
}
private String generateOneFeatureDescription(WellData wellData, String featureLabel,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/PlateLayouter.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/PlateLayouter.java
index adf5209da84..4f4e5e0b3ae 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/PlateLayouter.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/PlateLayouter.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.SimpleModelComboBox;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.GWTUtils;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.LayoutUtils;
@@ -99,7 +100,7 @@ public class PlateLayouter
private final Widget view;
- private final SimpleModelComboBox<String> heatmapKindChooser;
+ private final SimpleModelComboBox<CodeAndLabel> heatmapKindChooser;
public PlateLayouter(ScreeningViewContext viewContext, PlateMetadata plateMetadata)
{
@@ -108,7 +109,7 @@ public class PlateLayouter
LayoutContainer legendContainer = new LayoutContainer();
IRealNumberRenderer realNumberRenderer = createRealNumberRenderer(viewContext);
this.presenter =
- new HeatmapPresenter(model, realNumberRenderer, createViewManipulator(
+ new HeatmapPresenter(viewContext, model, realNumberRenderer, createViewManipulator(
renderedWells, legendContainer));
this.heatmapKindChooser = createHeatmapKindComboBox(presenter, viewContext);
this.view = renderView(renderedWells, heatmapKindChooser, legendContainer);
@@ -164,7 +165,7 @@ public class PlateLayouter
public void changeDisplayedFeatureVectorDataset(FeatureVectorDataset dataset)
{
this.model.setFeatureVectorDataset(dataset);
- updateHeatmapKindComboBox(heatmapKindChooser, model.tryGetFeatureLabels());
+ updateHeatmapKindComboBox(heatmapKindChooser, model.getAllFeatureNames());
}
/**
@@ -173,7 +174,7 @@ public class PlateLayouter
* re-rendering.
*/
private static Widget renderView(Component[][] renderedWells,
- SimpleModelComboBox<String> heatmapKindChooser, LayoutContainer legendContainer)
+ SimpleModelComboBox<CodeAndLabel> heatmapKindChooser, LayoutContainer legendContainer)
{
LayoutContainer container = new LayoutContainer();
container.setScrollMode(Scroll.AUTO);
@@ -370,20 +371,20 @@ public class PlateLayouter
// ---------
- private static SimpleModelComboBox<String> createHeatmapKindComboBox(
+ private static SimpleModelComboBox<CodeAndLabel> createHeatmapKindComboBox(
final HeatmapPresenter presenter, IMessageProvider messageProvider)
{
- List<LabeledItem<String>> items = createHeatmapKindModel(null);
- final SimpleModelComboBox<String> chooser =
- new SimpleModelComboBox<String>(messageProvider, items,
+ List<LabeledItem<CodeAndLabel>> items = createHeatmapKindModel(null);
+ final SimpleModelComboBox<CodeAndLabel> chooser =
+ new SimpleModelComboBox<CodeAndLabel>(messageProvider, items,
HEATMAP_KIND_COMBOBOX_CHOOSER_WIDTH_PX);
- chooser.addSelectionChangedListener(new SelectionChangedListener<SimpleComboValue<LabeledItem<String>>>()
+ chooser.addSelectionChangedListener(new SelectionChangedListener<SimpleComboValue<LabeledItem<CodeAndLabel>>>()
{
@Override
public void selectionChanged(
- SelectionChangedEvent<SimpleComboValue<LabeledItem<String>>> se)
+ SelectionChangedEvent<SimpleComboValue<LabeledItem<CodeAndLabel>>> se)
{
- String featureName = SimpleModelComboBox.getChosenItem(se);
+ CodeAndLabel featureName = SimpleModelComboBox.getChosenItem(se);
if (featureName == null)
{
presenter.setWellMetadataMode();
@@ -396,25 +397,26 @@ public class PlateLayouter
return chooser;
}
- private static void updateHeatmapKindComboBox(SimpleModelComboBox<String> chooser,
- List<String> featureLabelsOrNull)
+ private static void updateHeatmapKindComboBox(SimpleModelComboBox<CodeAndLabel> chooser,
+ List<CodeAndLabel> featureNames)
{
- List<LabeledItem<String>> items = createHeatmapKindModel(featureLabelsOrNull);
+ List<LabeledItem<CodeAndLabel>> items = createHeatmapKindModel(featureNames);
chooser.removeAll();
chooser.add(items);
GWTUtils.autoselect(chooser, false);
}
- private static List<LabeledItem<String>> createHeatmapKindModel(List<String> featureLabelsOrNull)
+ private static List<LabeledItem<CodeAndLabel>> createHeatmapKindModel(
+ List<CodeAndLabel> featureNamesOrNull)
{
- List<LabeledItem<String>> items = new ArrayList<LabeledItem<String>>();
- items.add(new LabeledItem<String>(null, METADATA_HEATMAP_KIND_MSG));
- if (featureLabelsOrNull != null)
+ List<LabeledItem<CodeAndLabel>> items = new ArrayList<LabeledItem<CodeAndLabel>>();
+ items.add(new LabeledItem<CodeAndLabel>(null, METADATA_HEATMAP_KIND_MSG));
+ if (featureNamesOrNull != null)
{
- for (String featureLabel : featureLabelsOrNull)
+ for (CodeAndLabel featureName : featureNamesOrNull)
{
- String label = FEATURE_HEATMAP_KIND_PREFIX_MSG + featureLabel;
- items.add(new LabeledItem<String>(featureLabel, label));
+ String label = FEATURE_HEATMAP_KIND_PREFIX_MSG + featureName.getLabel();
+ items.add(new LabeledItem<CodeAndLabel>(featureName, label));
}
}
return items;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/PlateLayouterModel.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/PlateLayouterModel.java
index 564851df0dd..d7933d2dc7f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/PlateLayouterModel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/PlateLayouterModel.java
@@ -18,12 +18,15 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.
import java.util.ArrayList;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map.Entry;
import java.util.Set;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.WellData;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorValues;
@@ -39,6 +42,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellMetadata;
*/
class PlateLayouterModel
{
+ private DatasetReference datasetReference; // currently shown dataset
+
private final WellData[][] wellMatrix;
private final List<WellData> wellList; // the same wells as in the matrix
@@ -47,8 +52,13 @@ class PlateLayouterModel
private ImageDatasetEnrichedReference imageDatasetOrNull;
- private List<String> featureLabelsOrNull; // names of all features
+ // names of all features
+ private List<CodeAndLabel> allFeatureNames = new ArrayList<CodeAndLabel>();
+
+ // labels of loaded features
+ private Set<String> availableFeatureLabels = new LinkedHashSet<String>();
+ // labels of loaded vocabulary features
private Set<String> vocabularyFeatureLabels = new HashSet<String>();
// ---
@@ -59,6 +69,11 @@ class PlateLayouterModel
this.wellList = asList(wellMatrix);
}
+ public DatasetReference tryGetDatasetReference()
+ {
+ return datasetReference;
+ }
+
public WellData[][] getWellMatrix()
{
return wellMatrix;
@@ -79,9 +94,14 @@ class PlateLayouterModel
this.imageDatasetOrNull = imageDataset;
}
- public List<String> tryGetFeatureLabels()
+ public List<CodeAndLabel> getAllFeatureNames()
{
- return featureLabelsOrNull;
+ return allFeatureNames;
+ }
+
+ public boolean isFeatureAvailable(String featureLabel)
+ {
+ return availableFeatureLabels.contains(featureLabel);
}
public boolean isVocabularyFeature(String featureLabel)
@@ -93,14 +113,12 @@ class PlateLayouterModel
public void setFeatureVectorDataset(FeatureVectorDataset featureVectorDatasetOrNull)
{
- unsetFeatureVectors();
- this.vocabularyFeatureLabels.clear(); // TODO PTR: don't clear on update
- if (featureVectorDatasetOrNull == null)
+ cleanFeatureVectors();
+ this.datasetReference = null;
+ if (featureVectorDatasetOrNull != null)
{
- this.featureLabelsOrNull = null;
- } else
- {
- this.featureLabelsOrNull = featureVectorDatasetOrNull.getFeatureLabels();
+ this.datasetReference = featureVectorDatasetOrNull.getDatasetReference();
+ this.allFeatureNames.addAll(featureVectorDatasetOrNull.getFeatureNames());
List<? extends FeatureVectorValues> features =
featureVectorDatasetOrNull.getDatasetFeatures();
if (features.isEmpty() == false)
@@ -118,6 +136,7 @@ class PlateLayouterModel
.entrySet())
{
String featureLabel = entry.getKey();
+ availableFeatureLabels.add(featureLabel);
FeatureValue value = entry.getValue();
wellData.addFeatureValue(featureLabel, value);
}
@@ -126,6 +145,46 @@ class PlateLayouterModel
}
}
+ private void cleanFeatureVectors()
+ {
+ this.vocabularyFeatureLabels.clear();
+ this.availableFeatureLabels.clear();
+ this.allFeatureNames.clear();
+ for (WellData well : wellList)
+ {
+ well.resetFeatureValues();
+ }
+ }
+
+ // add new feature to those already loaded
+ public void updateFeatureVectorDataset(FeatureVectorDataset featureVectorDataset)
+ {
+ assert datasetReference.getCode().equals(
+ featureVectorDataset.getDatasetReference().getCode());
+
+ List<? extends FeatureVectorValues> features = featureVectorDataset.getDatasetFeatures();
+ if (features.isEmpty() == false)
+ {
+ // NOTE: for each feature vector in the dataset this set is the same
+ this.vocabularyFeatureLabels.addAll(extractVocabularyFeatureLabels(features.get(0)));
+ }
+ for (FeatureVectorValues featureVector : features)
+ {
+ WellLocation loc = featureVector.getWellLocation();
+ WellData wellData = tryGetWellData(loc);
+ if (wellData != null)
+ {
+ for (Entry<String, FeatureValue> entry : featureVector.getFeatureMap().entrySet())
+ {
+ String featureLabel = entry.getKey();
+ availableFeatureLabels.add(featureLabel);
+ FeatureValue value = entry.getValue();
+ wellData.addFeatureValue(featureLabel, value);
+ }
+ }
+ }
+ }
+
private static Set<String> extractVocabularyFeatureLabels(FeatureVectorValues featureVector)
{
final Set<String> result = new HashSet<String>();
@@ -155,14 +214,6 @@ class PlateLayouterModel
}
}
- private void unsetFeatureVectors()
- {
- for (WellData well : wellList)
- {
- well.resetFeatureValues(); // TODO PTR: needed? keep values of all datasets
- }
- }
-
// ------------------------
// Elements will NOT contain null even if well is empty.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
index fe82d66ea8c..c64bd44667a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
@@ -40,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.ITableModelP
import ch.systemsx.cisd.openbis.generic.client.web.server.translator.UserFailureExceptionTranslator;
import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
@@ -50,6 +51,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.BuildAndEnvironmentInfo;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientService;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSampleContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
@@ -141,6 +144,18 @@ public final class ScreeningClientService extends AbstractClientService implemen
}
}
+ public FeatureVectorDataset getFeatureVectorDataset(DatasetReference dataset,
+ CodeAndLabel featureName) throws UserFailureException
+ {
+ try
+ {
+ return server.getFeatureVectorDataset(getSessionToken(), dataset, featureName);
+ } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
+ {
+ throw UserFailureExceptionTranslator.translate(e);
+ }
+ }
+
public PlateImages getPlateContentForDataset(TechId datasetId)
{
try
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/FeatureCountLimitProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/FeatureCountLimitProvider.java
new file mode 100644
index 00000000000..6f9d2224cce
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/FeatureCountLimitProvider.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2008 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;
+
+import org.apache.commons.lang.StringUtils;
+import org.springframework.stereotype.Component;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
+
+/**
+ * The unique {@link IFeatureCountLimitProvider} implementation.
+ *
+ * @author Piotr Buczek
+ */
+@Component(ResourceNames.FEATURE_COUNT_LIMIT_PROVIDER)
+public final class FeatureCountLimitProvider implements IFeatureCountLimitProvider
+{
+
+ private static int DEFAULT_FEATURE_COUNT_LIMIT = 5;
+
+ private int limit = DEFAULT_FEATURE_COUNT_LIMIT;
+
+ public FeatureCountLimitProvider()
+ {
+ }
+
+ public int getLimit()
+ {
+ return limit;
+ }
+
+ public void setLimitAsString(String limitAsString)
+ {
+ // This method is called by spring with value taken from properties file.
+ // Ignore the new value and keep default value when the property wasn't properly specified.
+ if (StringUtils.isNumeric(limitAsString))
+ {
+ limit = Integer.parseInt(limitAsString);
+ }
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IFeatureCountLimitProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IFeatureCountLimitProvider.java
new file mode 100644
index 00000000000..bde4a8b02a5
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IFeatureCountLimitProvider.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server;
+
+/**
+ * Provides limit of features to be initially fetched for dataset feature vectors.
+ *
+ * @author Piotr Buczek
+ */
+public interface IFeatureCountLimitProvider
+{
+
+ /** Returns max number of initially loaded features in total for all data sets. */
+ int getLimit();
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
index 38d205b8043..fffa130c737 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java
@@ -25,8 +25,8 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatase
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IImageDatasetLoader;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSFeatureVectorLoader;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IImageDatasetLoader;
/**
* A <i>screening</i> plugin specific business object factory.
@@ -58,4 +58,7 @@ public interface IScreeningBusinessObjectFactory
public IExternalDataBO createExternalDataBO(Session session);
public IDatasetLister createDatasetLister(Session session);
+
+ public IFeatureCountLimitProvider getFeatureCountLimitProvider();
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
index 3eae7165207..bee199d05a9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java
@@ -57,6 +57,9 @@ public final class ScreeningBusinessObjectFactory extends AbstractPluginBusiness
@Resource(name = ResourceNames.SCREENING_DAO_FACTORY)
private IScreeningDAOFactory specificDAOFactory;
+ @Resource(name = ResourceNames.FEATURE_COUNT_LIMIT_PROVIDER)
+ private IFeatureCountLimitProvider featureCountLimitProvider;
+
public ScreeningBusinessObjectFactory()
{
}
@@ -130,4 +133,9 @@ public final class ScreeningBusinessObjectFactory extends AbstractPluginBusiness
{
return getCommonBusinessObjectFactory().createDatasetLister(session);
}
+
+ public IFeatureCountLimitProvider getFeatureCountLimitProvider()
+ {
+ return featureCountLimitProvider;
+ }
}
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 925b0325d80..ea0c08a324f 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
@@ -49,6 +49,7 @@ import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlug
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
@@ -82,6 +83,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifi
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSampleContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LogicalImageInfo;
@@ -169,6 +172,14 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return PlateContentLoader.loadImagesAndMetadata(session, businessObjectFactory, plateId);
}
+ public FeatureVectorDataset getFeatureVectorDataset(String sessionToken,
+ DatasetReference dataset, CodeAndLabel featureName)
+ {
+ Session session = getSession(sessionToken);
+ return PlateContentLoader.loadFeatureVectorDataset(session, businessObjectFactory, dataset,
+ featureName);
+ }
+
public PlateImages getPlateContentForDataset(String sessionToken, TechId datasetId)
{
Session session = getSession(sessionToken);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
index 3ba6a08231e..68e8f864811 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
@@ -49,6 +50,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifi
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSampleContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LogicalImageInfo;
@@ -91,6 +94,14 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
logAccess(sessionToken, "getPlateContent", "PLATE(%s)", plateId.getId());
return null;
}
+
+ public FeatureVectorDataset getFeatureVectorDataset(String sessionToken,
+ DatasetReference dataset, CodeAndLabel featureName)
+ {
+ logAccess(sessionToken, "getFeatureVectorDataset", "DATA_SET(%s) FEATURE(%s)", dataset.getCode(), featureName);
+ return null;
+ }
+
public PlateImages getPlateContentForDataset(String sessionToken, TechId datasetId)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index 3a4f4f6269f..a04bba32f56 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.Collections;
import java.util.List;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -27,13 +28,13 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -70,9 +71,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IImageDatasetLoa
*/
public class PlateContentLoader
{
- // max number of initially loaded features
- @SuppressWarnings("unused")
- private static int MAX_FEATURES = 7;
/**
* Loads data about the plate for a specified sample id. Attaches information about images and
@@ -84,6 +82,17 @@ public class PlateContentLoader
return new PlateContentLoader(session, businessObjectFactory).getPlateContent(plateId);
}
+ /**
+ * Loads feature vector of specified dataset with one feature specified by name.
+ */
+ public static FeatureVectorDataset loadFeatureVectorDataset(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, DatasetReference dataset,
+ CodeAndLabel featureName)
+ {
+ return new PlateContentLoader(session, businessObjectFactory).fetchFeatureVector(dataset,
+ featureName);
+ }
+
/**
* Loads data about the plate for a specified dataset, which is supposed to contain images.
*/
@@ -270,36 +279,73 @@ public class PlateContentLoader
return fetchFeatureVectors(featureVectorDatasetReferences);
}
+ private FeatureVectorDataset fetchFeatureVector(DatasetReference datasetReference,
+ CodeAndLabel featureName)
+ {
+ IHCSFeatureVectorLoader loader =
+ businessObjectFactory.createHCSFeatureVectorLoader(datasetReference
+ .getDatastoreCode());
+ FeatureVectorDataset result = loadFeatureVector(datasetReference, featureName, loader);
+ return result;
+ }
+
private List<FeatureVectorDataset> fetchFeatureVectors(
List<DatasetReference> featureVectorDatasetReferences)
{
List<FeatureVectorDataset> featureVectorDatasets = new ArrayList<FeatureVectorDataset>();
- for (DatasetReference datasetReference : featureVectorDatasetReferences)
+ if (featureVectorDatasetReferences.isEmpty() == false)
{
- IHCSFeatureVectorLoader loader =
- businessObjectFactory.createHCSFeatureVectorLoader(datasetReference
- .getDatastoreCode());
- FeatureVectorDataset featureVectorDataset = loadFeatureVector(datasetReference, loader);
- featureVectorDatasets.add(featureVectorDataset);
+ int maxFeatures = businessObjectFactory.getFeatureCountLimitProvider().getLimit();
+ int maxFeaturesPerDataset =
+ Math.max(1, maxFeatures / featureVectorDatasetReferences.size());
+ for (DatasetReference datasetReference : featureVectorDatasetReferences)
+ {
+ IHCSFeatureVectorLoader loader =
+ businessObjectFactory.createHCSFeatureVectorLoader(datasetReference
+ .getDatastoreCode());
+ FeatureVectorDataset featureVectorDataset =
+ loadFeatureVector(datasetReference, loader, maxFeaturesPerDataset);
+ featureVectorDatasets.add(featureVectorDataset);
+ }
}
return featureVectorDatasets;
}
+ // loads feature vector with limited number of features
private FeatureVectorDataset loadFeatureVector(DatasetReference datasetReference,
- IHCSFeatureVectorLoader loader)
+ IHCSFeatureVectorLoader loader, int maxFeaturesPerDataset)
{
+ List<CodeAndLabel> allFeatureNames =
+ loader.fetchDatasetFeatureNames(datasetReference.getCode());
+ List<CodeAndLabel> featuresToLoad = allFeatureNames;
+ if (featuresToLoad.size() > maxFeaturesPerDataset)
+ {
+ featuresToLoad = featuresToLoad.subList(0, maxFeaturesPerDataset);
+ }
+ WellFeatureCollection<FeatureVectorValues> featureValues =
+ loader.fetchDatasetFeatureValues(datasetReference.getCode(), featuresToLoad);
+ List<FeatureVectorValues> featureVectors = featureValues.getFeatures();
+
+ FeatureVectorDataset featureVectorDataset =
+ new FeatureVectorDataset(datasetReference, featureVectors, allFeatureNames);
+ return featureVectorDataset;
+ }
- List<CodeAndLabel> featureNames =
+ // loads feature vector with only one feature specified by name
+ private FeatureVectorDataset loadFeatureVector(DatasetReference datasetReference,
+ CodeAndLabel featureName, IHCSFeatureVectorLoader loader)
+ {
+ List<CodeAndLabel> allFeatureNames =
loader.fetchDatasetFeatureNames(datasetReference.getCode());
- // TODO PTR limit names
+
WellFeatureCollection<FeatureVectorValues> featureValues =
- loader.fetchDatasetFeatureValues(datasetReference.getCode(), featureNames);
+ loader.fetchDatasetFeatureValues(datasetReference.getCode(),
+ Collections.singletonList(featureName));
List<FeatureVectorValues> featureVectors = featureValues.getFeatures();
- List<String> featureLabels = CodeAndLabel.asLabels(featureNames);
FeatureVectorDataset featureVectorDataset =
- new FeatureVectorDataset(datasetReference, featureVectors, featureLabels);
+ new FeatureVectorDataset(datasetReference, featureVectors, allFeatureNames);
return featureVectorDataset;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
index d0d16455309..befe4fbd8e9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractT
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
@@ -39,8 +40,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.DatasetReferencePredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellContentValidator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellSearchCriteriaPredicate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageSampleContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LogicalImageInfo;
@@ -58,7 +62,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCrit
public interface IScreeningServer extends IServer
{
/**
- * loads data about the plate for a specified sample id. Attaches information about images and
+ * Loads data about the plate for a specified sample id. Attaches information about images and
* image analysis only if one dataset with such a data exist.
*/
@Transactional(readOnly = true)
@@ -66,6 +70,16 @@ public interface IScreeningServer extends IServer
public PlateContent getPlateContent(String sessionToken,
@AuthorizationGuard(guardClass = SampleTechIdPredicate.class) TechId plateId);
+ /**
+ * Loads feature vector of specified dataset with one feature specified by name.
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ public FeatureVectorDataset getFeatureVectorDataset(
+ String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetReferencePredicate.class) DatasetReference dataset,
+ CodeAndLabel featureName);
+
/**
* Returns plate content for a specified HCS_IMAGE dataset. Loads data about the plate for a
* specified dataset, which is supposed to contain images in BDS-HCS format.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
index cba01cf953c..8b545d76ec7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/ResourceNames.java
@@ -43,5 +43,7 @@ public final class ResourceNames
public final static String SCREENING_SAMPLE_SERVER_PLUGIN = "screening-sample-server-plugin";
+ public final static String FEATURE_COUNT_LIMIT_PROVIDER = "feature-count-limit-provider";
+
public static final String MAIL_CLIENT_PARAMETERS = "mail-client-parameters";
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/authorization/DatasetReferencePredicate.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/authorization/DatasetReferencePredicate.java
new file mode 100644
index 00000000000..7572b2e9e99
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/authorization/DatasetReferencePredicate.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright 2008 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.authorization;
+
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DelegatedPredicate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+
+/**
+ * @author Piotr Buczek
+ */
+public final class DatasetReferencePredicate extends DelegatedPredicate<String, DatasetReference>
+{
+ public DatasetReferencePredicate()
+ {
+ super(new DataSetCodePredicate());
+ }
+
+ @Override
+ public final String getCandidateDescription()
+ {
+ return "dataset reference";
+ }
+
+ @Override
+ public String tryConvert(DatasetReference value)
+ {
+ return value.getCode();
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/FeatureVectorDataset.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/FeatureVectorDataset.java
index 8de439b7180..acbaa665f8a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/FeatureVectorDataset.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/FeatureVectorDataset.java
@@ -19,6 +19,8 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.annotation.DoNotEscape;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
@@ -26,13 +28,14 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
*
* @author Tomasz Pylak
*/
+@DoNotEscape
public class FeatureVectorDataset implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
private DatasetReference datasetReference;
- private List<String> featureLabels;
+ private List<CodeAndLabel> featureNames;
private List<FeatureVectorValues> datasetFeatures;
@@ -43,11 +46,11 @@ public class FeatureVectorDataset implements ISerializable
}
public FeatureVectorDataset(DatasetReference datasetReference,
- List<FeatureVectorValues> datasetFeatures, List<String> featureLabels)
+ List<FeatureVectorValues> datasetFeatures, List<CodeAndLabel> featureNames)
{
this.datasetReference = datasetReference;
this.datasetFeatures = datasetFeatures;
- this.featureLabels = featureLabels;
+ this.featureNames = featureNames;
}
public DatasetReference getDatasetReference()
@@ -55,9 +58,9 @@ public class FeatureVectorDataset implements ISerializable
return datasetReference;
}
- public List<String> getFeatureLabels()
+ public List<CodeAndLabel> getFeatureNames()
{
- return featureLabels;
+ return featureNames;
}
public List<? extends FeatureVectorValues> getDatasetFeatures()
diff --git a/screening/source/java/screening-applicationContext.xml b/screening/source/java/screening-applicationContext.xml
index fb7b1f1a948..45bc6c0bf0b 100644
--- a/screening/source/java/screening-applicationContext.xml
+++ b/screening/source/java/screening-applicationContext.xml
@@ -18,6 +18,10 @@
<constructor-arg ref="${data-source-provider}"/>
</bean>
+ <bean id="feature-count-limit-provider" class="ch.systemsx.cisd.openbis.plugin.screening.server.FeatureCountLimitProvider">
+ <property name="limitAsString" value="${feature-count-limit}"/>
+ </bean>
+
<!--
//Mail Client Parameters
-->
diff --git a/screening/source/java/service.properties b/screening/source/java/service.properties
index 68625e05929..803ff482785 100644
--- a/screening/source/java/service.properties
+++ b/screening/source/java/service.properties
@@ -55,7 +55,7 @@ cifex-recipient = id:cifexdatamanager
hibernate.search.index-base = ./targets/indices-${database.kind}
# One of NO_INDEX, SKIP_IF_MARKER_FOUND, INDEX_FROM_SCRATCH.
# If not specified, default (SKIP_IF_MARKER_FOUND) is taken.
-hibernate.search.index-mode = NO_INDEX
+hibernate.search.index-mode = SKIP_IF_MARKER_FOUND
#hibernate.search.index-mode = INDEX_FROM_SCRATCH
# Defines the maximum number of elements indexed before flushing the transaction-bound queue.
# Default is 1000.
@@ -66,4 +66,7 @@ hibernate.search.maxResults = 100000
hibernate.search.worker.execution=async
# Name of the file that stores Web Client configuration
-web-client-configuration-file = etc/web-client.properties
\ No newline at end of file
+web-client-configuration-file = etc/web-client.properties
+
+# (optional) max number of features to load initially for every Plate Layout view (default: 5)
+feature-count-limit = 10
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/WellTooltipGeneratorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/WellTooltipGeneratorTest.java
index 2a88079fcb2..05093da83b8 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/WellTooltipGeneratorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/heatmaps/WellTooltipGeneratorTest.java
@@ -29,6 +29,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.test.AssertionUtil;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.IRealNumberRenderer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -154,18 +155,18 @@ public class WellTooltipGeneratorTest extends AssertJUnit
private static FeatureVectorDataset createLargeFeatureVectorDataset()
{
int size = 40;
- List<String> featureLabels = new ArrayList<String>(size);
+ List<CodeAndLabel> featureNames = new ArrayList<CodeAndLabel>(size);
Map<String, FeatureValue> featureValuesMap = new LinkedHashMap<String, FeatureValue>();
for (int i = 0; i < size; i++)
{
final String label = "Feature" + i;
final FeatureValue featureValue = FeatureValue.createFloat(i);
- featureLabels.add("Feature" + i);
+ featureNames.add(new CodeAndLabel(label, label));
featureValuesMap.put(label, featureValue);
}
List<FeatureVectorValues> features = new ArrayList<FeatureVectorValues>();
features.add(new FeatureVectorValues(null, getLocation(WELL_A2), featureValuesMap));
- return new FeatureVectorDataset(createDatasetReference(), features, featureLabels);
+ return new FeatureVectorDataset(createDatasetReference(), features, featureNames);
}
private static FeatureVectorDataset createFeatureVectorDataset()
@@ -181,8 +182,9 @@ public class WellTooltipGeneratorTest extends AssertJUnit
features.add(new FeatureVectorValues(null, getLocation(WELL_B3), createFeatureVectorMap(
featureLabels, new FeatureValue[]
{ FeatureValue.createFloat(-1), FeatureValue.createFloat(-2) })));
- return new FeatureVectorDataset(createDatasetReference(), features,
- Arrays.asList(featureLabels));
+ return new FeatureVectorDataset(createDatasetReference(), features, Arrays.asList(
+ new CodeAndLabel(featureLabels[0], featureLabels[0]), new CodeAndLabel(
+ featureLabels[1], featureLabels[1])));
}
private static Map<String, FeatureValue> createFeatureVectorMap(String[] labels,
--
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