From a34e9e38e40310185ba52c8fc91c6099bd0c6cc5 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Wed, 9 Feb 2011 20:43:50 +0000
Subject: [PATCH] [LMS-2035] refactoring, use: - feature labels instead of
indexes, - map <feature label -> feature value> instead of feature value
array;
SVN: 19850
---
.../plugin/screening/OpenBISIE.gwt.xml | 13 +++
.../detailviewers/dto/WellData.java | 32 ++++--
.../heatmaps/HeatmapPresenter.java | 99 ++++++++++---------
.../detailviewers/heatmaps/PlateLayouter.java | 37 ++++---
.../heatmaps/PlateLayouterModel.java | 55 ++++++-----
.../shared/basic/dto/FeatureVectorValues.java | 20 ++--
.../screening/shared/dto/FeatureTableRow.java | 2 +-
.../shared/imaging/FeatureVectorLoader.java | 19 +++-
.../server/DssServiceRpcScreeningTest.java | 11 ++-
.../heatmaps/WellTooltipGeneratorTest.java | 54 +++++++---
10 files changed, 216 insertions(+), 126 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/OpenBISIE.gwt.xml
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/OpenBISIE.gwt.xml b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/OpenBISIE.gwt.xml
new file mode 100644
index 00000000000..3f5f98dea52
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/OpenBISIE.gwt.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE module PUBLIC "-//Google Inc.//DTD Google Web Toolkit 1.7.1//EN" "http://google-web-toolkit.googlecode.com/svn/tags/1.7.1/distro-source/core/src/gwt-module.dtd">
+<module rename-to="ch.systemsx.cisd.openbis.plugin.screening.OpenBIS">
+ <inherits name='ch.systemsx.cisd.openbis.OpenBIS-without-entry-point' />
+ <set-property name="user.agent" value="ie8" />
+
+ <entry-point class='ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningClient' />
+
+ <script src="screening-dictionary.js" />
+ <public path="client/web/public" />
+ <source path="client/web/client" />
+ <source path="shared/basic" />
+</module>
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/WellData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/WellData.java
index 556b9c2c1df..384cdba664c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/WellData.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/WellData.java
@@ -16,6 +16,10 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Set;
+
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
@@ -34,7 +38,10 @@ public class WellData
private WellMetadata wellMetadataOrNull;
- private FeatureValue[] featureValuesOrNull;
+ // ordered map from feature labels to feature values
+ // NOTE: it contains a subset of all feature values of a well (only the ones that were loaded)
+ private Map<String /* feature label */, FeatureValue> featureValuesMap =
+ new LinkedHashMap<String, FeatureValue>();
public WellData(WellLocation wellLocation, Experiment experiment)
{
@@ -42,18 +49,25 @@ public class WellData
this.experiment = experiment;
}
- public void setFeatureValues(FeatureValue[] featureValues)
+ public void addFeatureValue(String featureName, FeatureValue value)
+ {
+ featureValuesMap.put(featureName, value);
+ }
+
+ public void resetFeatureValues()
+ {
+ featureValuesMap.clear();
+ }
+
+ public FeatureValue tryGetFeatureValue(String featureLabel)
{
- this.featureValuesOrNull = featureValues;
+ return featureValuesMap.get(featureLabel);
}
- public FeatureValue tryGetFeatureValue(int featureVectorIndex)
+ // ordered set of feature labels for which we have loaded feature values
+ public Set<String> getFeatureLabels()
{
- if (featureValuesOrNull == null)
- {
- return null;
- }
- return featureValuesOrNull[featureVectorIndex];
+ return featureValuesMap.keySet();
}
public void setMetadata(WellMetadata well)
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 e90ecca5705..f6597b8bf2d 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
@@ -71,49 +71,48 @@ class HeatmapPresenter
}
/**
- * Changes the presented heatmap to the one which shows the feature which appears in all
- * {@link WellData} on a specified index.
+ * Changes the presented heatmap to the one which shows the feature with given label.
*/
- public void setFeatureValueMode(int featureIndex)
+ public void setFeatureValueMode(String featureName)
{
- IHeatmapRenderer<WellData> renderer = createFeatureHeatmapRenderer(featureIndex);
- refreshHeatmap(renderer, featureIndex);
+ IHeatmapRenderer<WellData> renderer = createFeatureHeatmapRenderer(featureName);
+ refreshHeatmap(renderer, featureName);
}
- private IHeatmapRenderer<WellData> createFeatureHeatmapRenderer(int featureIndex)
+ private IHeatmapRenderer<WellData> createFeatureHeatmapRenderer(String featureLabel)
{
List<WellData> wellList = model.getWellList();
- if (model.isVocabularyFeature(featureIndex))
+ if (model.isVocabularyFeature(featureLabel))
{
- return createVocabularyFeatureHeatmapRenderer(wellList, featureIndex);
+ return createVocabularyFeatureHeatmapRenderer(wellList, featureLabel);
} else
{
- return createFloatFeatureHeatmapRenderer(wellList, featureIndex, realNumberRenderer);
+ return createFloatFeatureHeatmapRenderer(wellList, featureLabel, realNumberRenderer);
}
}
- // here we are sure that all wells have a vocabulary feature at featureIndex index
+ // here we are sure that all wells have a vocabulary feature with given featureLabel
private static IHeatmapRenderer<WellData> createVocabularyFeatureHeatmapRenderer(
- List<WellData> wellList, final int featureIndex)
+ List<WellData> wellList, final String featureLabel)
{
- List<String> uniqueValues = extractUniqueVocabularyTerms(wellList, featureIndex);
+ List<String> uniqueValues = extractUniqueVocabularyTerms(wellList, featureLabel);
return new DetegatingStringHeatmapRenderer<WellData>(uniqueValues, null)
{
@Override
protected String extractLabel(WellData well)
{
- return tryAsVocabularyFeature(well, featureIndex);
+ return tryAsVocabularyFeature(well, featureLabel);
}
};
}
private static List<String> extractUniqueVocabularyTerms(List<WellData> wellList,
- int featureIndex)
+ String featureLabel)
{
Set<String> uniqueValues = new HashSet<String>();
for (WellData well : wellList)
{
- String term = tryAsVocabularyFeature(well, featureIndex);
+ String term = tryAsVocabularyFeature(well, featureLabel);
if (term != null)
{
uniqueValues.add(term);
@@ -125,7 +124,7 @@ class HeatmapPresenter
}
// updates color of all well components
- private void refreshHeatmap(IHeatmapRenderer<WellData> renderer, Integer featureIndexOrNull)
+ private void refreshHeatmap(IHeatmapRenderer<WellData> renderer, String featureLabelOrNull)
{
WellData[][] wellMatrix = model.getWellMatrix();
for (int rowIx = 0; rowIx < wellMatrix.length; rowIx++)
@@ -136,7 +135,7 @@ class HeatmapPresenter
Color color = renderer.getColor(wellData);
String tooltipOrNull =
WellTooltipGenerator.tryGenerateTooltip(model, rowIx, colIx,
- featureIndexOrNull, realNumberRenderer);
+ featureLabelOrNull, realNumberRenderer);
viewManipulations.refreshWellStyle(rowIx, colIx, color, tooltipOrNull);
}
}
@@ -151,15 +150,15 @@ class HeatmapPresenter
viewManipulations.updateLegend(legend);
}
- // here we are sure that all wells have a float feature at featureIndex index
+ // here we are sure that all wells have a float feature with given featureLabel
private static IHeatmapRenderer<WellData> createFloatFeatureHeatmapRenderer(
- List<WellData> wells, final int featureIndex, IRealNumberRenderer realNumberRenderer)
+ List<WellData> wells, final String featureLabel, IRealNumberRenderer realNumberRenderer)
{
float min = Float.MAX_VALUE;
float max = Float.MIN_VALUE;
for (WellData well : wells)
{
- Float value = tryAsFloatFeature(well, featureIndex);
+ Float value = tryAsFloatFeature(well, featureLabel);
if (value != null && Float.isNaN(value) == false && Float.isInfinite(value) == false)
{
min = Math.min(min, value);
@@ -171,20 +170,20 @@ class HeatmapPresenter
@Override
protected Float convert(WellData well)
{
- return tryAsFloatFeature(well, featureIndex);
+ return tryAsFloatFeature(well, featureLabel);
}
};
}
- private static float tryAsFloatFeature(WellData well, final int featureIndex)
+ private static float tryAsFloatFeature(WellData well, final String featureLabel)
{
- FeatureValue value = well.tryGetFeatureValue(featureIndex);
+ FeatureValue value = well.tryGetFeatureValue(featureLabel);
return value != null ? value.asFloat() : null;
}
- private static String tryAsVocabularyFeature(WellData well, final int featureIndex)
+ private static String tryAsVocabularyFeature(WellData well, final String featureLabel)
{
- FeatureValue value = well.tryGetFeatureValue(featureIndex);
+ FeatureValue value = well.tryGetFeatureValue(featureLabel);
return value != null ? value.tryAsVocabularyTerm() : null;
}
@@ -311,14 +310,14 @@ class HeatmapPresenter
/**
* Generates a short description of the well, which can be used as e.g. a tooltip
*
- * @param featureIndexOrNull if not null contains an index of the feature which should be
+ * @param featureLabelOrNull if not null contains label of the feature which should be
* distinguished.
*/
public static String tryGenerateTooltip(PlateLayouterModel model, int rowIx, int colIx,
- Integer featureIndexOrNull, IRealNumberRenderer realNumberRenderer)
+ String featureLabelOrNull, IRealNumberRenderer realNumberRenderer)
{
return new WellTooltipGenerator(model, realNumberRenderer).tryGenerateShortDescription(
- rowIx, colIx, featureIndexOrNull);
+ rowIx, colIx, featureLabelOrNull);
}
private final PlateLayouterModel model;
@@ -332,19 +331,21 @@ class HeatmapPresenter
this.realNumberRenderer = realNumberRenderer;
}
- private String tryGenerateShortDescription(int rowIx, int colIx, Integer featureIndexOrNull)
+ private String tryGenerateShortDescription(int rowIx, int colIx,
+ String distinguishedLabelOrNull)
{
WellData wellData = model.getWellMatrix()[rowIx][colIx];
String tooltip = "";
- if (featureIndexOrNull != null)
+ if (distinguishedLabelOrNull != null)
{
- tooltip += generateOneFeatureDescription(wellData, featureIndexOrNull, true);
+ tooltip += generateOneFeatureDescription(wellData, distinguishedLabelOrNull, true);
}
tooltip += generateMetadataDescription(wellData);
- int featuresNum = getNumberOfFeatures();
- if (featuresNum - (featureIndexOrNull != null ? 1 : 0) > 0)
+ int allFeaturesNum = getNumberOfAllFeatures();
+ int loadedFeaturesNum = getNumberOfLoadedFeatures(wellData);
+ if (loadedFeaturesNum - (distinguishedLabelOrNull != null ? 1 : 0) > 0)
{
if (tooltip.length() == 0)
{
@@ -353,15 +354,21 @@ class HeatmapPresenter
{
tooltip += NEWLINE; // separate metadata from the text below
}
- int describedFeaturesNum = Math.min(MAX_DESCRIBED_FEATURES, featuresNum);
- for (int ix = 0; ix < describedFeaturesNum; ix++)
+ int describedFeaturesNum = Math.min(MAX_DESCRIBED_FEATURES, loadedFeaturesNum);
+ int fCounter = 0;
+ for (String featureLabel : wellData.getFeatureLabels())
{
- if (featureIndexOrNull == null || ix != featureIndexOrNull.intValue())
+ if (featureLabel.equals(distinguishedLabelOrNull) == false)
{
- tooltip += generateOneFeatureDescription(wellData, ix, false);
+ tooltip += generateOneFeatureDescription(wellData, featureLabel, false);
+ }
+ fCounter++;
+ if (fCounter == describedFeaturesNum)
+ {
+ break;
}
}
- if (featuresNum > describedFeaturesNum)
+ if (allFeaturesNum > describedFeaturesNum)
{
tooltip += "...";
}
@@ -370,19 +377,21 @@ class HeatmapPresenter
}
- private int getNumberOfFeatures()
+ private int getNumberOfLoadedFeatures(WellData wellData)
+ {
+ return wellData.getFeatureLabels().size();
+ }
+
+ private int getNumberOfAllFeatures()
{
List<String> featureLabels = model.tryGetFeatureLabels();
return featureLabels == null ? 0 : featureLabels.size();
}
- private String generateOneFeatureDescription(WellData wellData, int featureIndex,
+ private String generateOneFeatureDescription(WellData wellData, String featureLabel,
boolean distinguished)
{
- List<String> featureLabels = model.tryGetFeatureLabels();
- assert featureLabels != null : "feature labels not set";
-
- FeatureValue value = wellData.tryGetFeatureValue(featureIndex);
+ FeatureValue value = wellData.tryGetFeatureValue(featureLabel);
// if the value should be distinguished we show it even if it's null
if (value == null && distinguished == false)
{
@@ -393,7 +402,7 @@ class HeatmapPresenter
{
textValue = "<b>" + textValue + "</b>";
}
- return featureLabels.get(featureIndex) + ": " + textValue + NEWLINE;
+ return featureLabel + ": " + textValue + NEWLINE;
}
private String renderValue(FeatureValue value)
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 71252b3f483..adf5209da84 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
@@ -99,7 +99,7 @@ public class PlateLayouter
private final Widget view;
- private final SimpleModelComboBox<Integer> heatmapKindChooser;
+ private final SimpleModelComboBox<String> heatmapKindChooser;
public PlateLayouter(ScreeningViewContext viewContext, PlateMetadata plateMetadata)
{
@@ -173,7 +173,7 @@ public class PlateLayouter
* re-rendering.
*/
private static Widget renderView(Component[][] renderedWells,
- SimpleModelComboBox<Integer> heatmapKindChooser, LayoutContainer legendContainer)
+ SimpleModelComboBox<String> heatmapKindChooser, LayoutContainer legendContainer)
{
LayoutContainer container = new LayoutContainer();
container.setScrollMode(Scroll.AUTO);
@@ -370,54 +370,51 @@ public class PlateLayouter
// ---------
- private static SimpleModelComboBox<Integer> createHeatmapKindComboBox(
+ private static SimpleModelComboBox<String> createHeatmapKindComboBox(
final HeatmapPresenter presenter, IMessageProvider messageProvider)
{
- List<LabeledItem<Integer>> items = createHeatmapKindModel(null);
- final SimpleModelComboBox<Integer> chooser =
- new SimpleModelComboBox<Integer>(messageProvider, items,
+ List<LabeledItem<String>> items = createHeatmapKindModel(null);
+ final SimpleModelComboBox<String> chooser =
+ new SimpleModelComboBox<String>(messageProvider, items,
HEATMAP_KIND_COMBOBOX_CHOOSER_WIDTH_PX);
- chooser.addSelectionChangedListener(new SelectionChangedListener<SimpleComboValue<LabeledItem<Integer>>>()
+ chooser.addSelectionChangedListener(new SelectionChangedListener<SimpleComboValue<LabeledItem<String>>>()
{
@Override
public void selectionChanged(
- SelectionChangedEvent<SimpleComboValue<LabeledItem<Integer>>> se)
+ SelectionChangedEvent<SimpleComboValue<LabeledItem<String>>> se)
{
- Integer value = SimpleModelComboBox.getChosenItem(se);
- if (value == null)
+ String featureName = SimpleModelComboBox.getChosenItem(se);
+ if (featureName == null)
{
presenter.setWellMetadataMode();
} else
{
- presenter.setFeatureValueMode(value);
+ presenter.setFeatureValueMode(featureName);
}
}
});
return chooser;
}
- private static void updateHeatmapKindComboBox(SimpleModelComboBox<Integer> chooser,
+ private static void updateHeatmapKindComboBox(SimpleModelComboBox<String> chooser,
List<String> featureLabelsOrNull)
{
- List<LabeledItem<Integer>> items = createHeatmapKindModel(featureLabelsOrNull);
+ List<LabeledItem<String>> items = createHeatmapKindModel(featureLabelsOrNull);
chooser.removeAll();
chooser.add(items);
GWTUtils.autoselect(chooser, false);
}
- private static List<LabeledItem<Integer>> createHeatmapKindModel(
- List<String> featureLabelsOrNull)
+ private static List<LabeledItem<String>> createHeatmapKindModel(List<String> featureLabelsOrNull)
{
- List<LabeledItem<Integer>> items = new ArrayList<LabeledItem<Integer>>();
- items.add(new LabeledItem<Integer>(null, METADATA_HEATMAP_KIND_MSG));
+ List<LabeledItem<String>> items = new ArrayList<LabeledItem<String>>();
+ items.add(new LabeledItem<String>(null, METADATA_HEATMAP_KIND_MSG));
if (featureLabelsOrNull != null)
{
- int i = 0;
for (String featureLabel : featureLabelsOrNull)
{
String label = FEATURE_HEATMAP_KIND_PREFIX_MSG + featureLabel;
- items.add(new LabeledItem<Integer>(i, label));
- i++;
+ items.add(new LabeledItem<String>(featureLabel, 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 9575b487417..564851df0dd 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
@@ -17,7 +17,10 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.heatmaps;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map.Entry;
+import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.WellData;
@@ -44,9 +47,9 @@ class PlateLayouterModel
private ImageDatasetEnrichedReference imageDatasetOrNull;
- private List<String> featureLabelsOrNull;
+ private List<String> featureLabelsOrNull; // names of all features
- private boolean[] isVocabularyFeatureMapOrNull;
+ private Set<String> vocabularyFeatureLabels = new HashSet<String>();
// ---
@@ -81,15 +84,9 @@ class PlateLayouterModel
return featureLabelsOrNull;
}
- public boolean isVocabularyFeature(int featureVectorIndex)
+ public boolean isVocabularyFeature(String featureLabel)
{
- if (isVocabularyFeatureMapOrNull == null)
- {
- return false;
- } else
- {
- return isVocabularyFeatureMapOrNull[featureVectorIndex];
- }
+ return vocabularyFeatureLabels.contains(featureLabel);
}
// --- some logic
@@ -97,7 +94,7 @@ class PlateLayouterModel
public void setFeatureVectorDataset(FeatureVectorDataset featureVectorDatasetOrNull)
{
unsetFeatureVectors();
- this.isVocabularyFeatureMapOrNull = null;
+ this.vocabularyFeatureLabels.clear(); // TODO PTR: don't clear on update
if (featureVectorDatasetOrNull == null)
{
this.featureLabelsOrNull = null;
@@ -106,32 +103,42 @@ class PlateLayouterModel
this.featureLabelsOrNull = featureVectorDatasetOrNull.getFeatureLabels();
List<? extends FeatureVectorValues> features =
featureVectorDatasetOrNull.getDatasetFeatures();
+ if (features.isEmpty() == false)
+ {
+ // NOTE: for each feature vector in the dataset this set is the same
+ this.vocabularyFeatureLabels = extractVocabularyFeatureLabels(features.get(0));
+ }
for (FeatureVectorValues featureVector : features)
{
- if (this.isVocabularyFeatureMapOrNull == null)
- {
- // NOTE: for each feature vector in the dataset this map would be the same
- this.isVocabularyFeatureMapOrNull = createIsVocabularyMap(featureVector);
- }
WellLocation loc = featureVector.getWellLocation();
WellData wellData = tryGetWellData(loc);
if (wellData != null)
{
- wellData.setFeatureValues(featureVector.getFeatureValues());
+ for (Entry<String, FeatureValue> entry : featureVector.getFeatureMap()
+ .entrySet())
+ {
+ String featureLabel = entry.getKey();
+ FeatureValue value = entry.getValue();
+ wellData.addFeatureValue(featureLabel, value);
+ }
}
}
}
}
- private static boolean[] createIsVocabularyMap(FeatureVectorValues featureVector)
+ private static Set<String> extractVocabularyFeatureLabels(FeatureVectorValues featureVector)
{
- FeatureValue[] values = featureVector.getFeatureValues();
- boolean[] map = new boolean[values.length];
- for (int i = 0; i < map.length; i++)
+ final Set<String> result = new HashSet<String>();
+ for (Entry<String, FeatureValue> entry : featureVector.getFeatureMap().entrySet())
{
- map[i] = values[i].isVocabularyTerm();
+ String featureLabel = entry.getKey();
+ FeatureValue featureValue = entry.getValue();
+ if (featureValue.isVocabularyTerm())
+ {
+ result.add(featureLabel);
+ }
}
- return map;
+ return result;
}
private WellData tryGetWellData(WellLocation loc)
@@ -152,7 +159,7 @@ class PlateLayouterModel
{
for (WellData well : wellList)
{
- well.setFeatureValues(null);
+ well.resetFeatureValues(); // TODO PTR: needed? keep values of all datasets
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/FeatureVectorValues.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/FeatureVectorValues.java
index e0c8a21abba..0c76c12be1c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/FeatureVectorValues.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/FeatureVectorValues.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
+import java.util.Map;
+
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.ServiceVersionHolder;
@@ -33,7 +35,7 @@ public class FeatureVectorValues implements ISerializable
private WellFeatureVectorReference featureVectorReference;
- private FeatureValue[] featureValues;
+ private Map<String /* feature label */, FeatureValue /* value */> featureMap;
// GWT only
@SuppressWarnings("unused")
@@ -42,21 +44,27 @@ public class FeatureVectorValues implements ISerializable
}
public FeatureVectorValues(String dataSetCode, WellLocation wellLocation,
- FeatureValue[] featureValues)
+ Map<String, FeatureValue> featureMap)
{
- this(new WellFeatureVectorReference(dataSetCode, wellLocation), featureValues);
+ this(new WellFeatureVectorReference(dataSetCode, wellLocation), featureMap);
}
public FeatureVectorValues(WellFeatureVectorReference featureVectorReference,
- FeatureValue[] featureValues)
+ Map<String, FeatureValue> featureMap)
{
this.featureVectorReference = featureVectorReference;
- this.featureValues = featureValues;
+ this.featureMap = featureMap;
}
+ // NOTE: don't use this method multiple times for performance reasons
public FeatureValue[] getFeatureValues()
{
- return featureValues;
+ return featureMap.values().toArray(new FeatureValue[0]);
+ }
+
+ public Map<String, FeatureValue> getFeatureMap()
+ {
+ return featureMap;
}
public String getDataSetCode()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/FeatureTableRow.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/FeatureTableRow.java
index f4003b95aca..28d791d3dd6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/FeatureTableRow.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/dto/FeatureTableRow.java
@@ -38,7 +38,7 @@ public class FeatureTableRow extends FeatureVectorValues
public FeatureTableRow(FeatureVectorValues featureVector)
{
super(featureVector.getDataSetCode(), featureVector.getWellLocation(), featureVector
- .getFeatureValues());
+ .getFeatureMap());
}
public FeatureVectorDatasetWellReference getReference()
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 f6e908fbd5b..921c7a9592d 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
@@ -134,12 +134,13 @@ public class FeatureVectorLoader
List<FeatureVectorValues> fvs = new ArrayList<FeatureVectorValues>();
for (FeatureTableRow row : featureRows)
{
- fvs.add(new FeatureVectorValues(row.getFeatureVectorReference(), row.getFeatureValues()));
+ fvs.add(new FeatureVectorValues(row.getFeatureVectorReference(), row.getFeatureMap()));
}
return new WellFeatureCollection<FeatureVectorValues>(fvs,
featureRowsCollection.getFeatureCodesAndLabels());
}
+ // TODO PTR use filtering by codes
/**
* fetches specified features of all wells
*
@@ -499,10 +500,24 @@ public class FeatureVectorLoader
WellLocation wellLocation)
{
String permId = bundle.dataSet.getPermId();
+
FeatureValue[] valueArray =
createFeatureValueArray(bundle.featureDefToValuesMap,
bundle.featureDefToVocabularyTerms, wellLocation);
- return new FeatureVectorValues(permId, wellLocation, valueArray);
+ return new FeatureVectorValues(permId, wellLocation, asValueMap(valueArray));
+ }
+
+ private Map<String, FeatureValue> asValueMap(FeatureValue[] valueArray)
+ {
+ List<CodeAndLabel> features = getCodesAndLabels();
+ assert features.size() == valueArray.length;
+
+ Map<String, FeatureValue> result = new LinkedHashMap<String, FeatureValue>();
+ for (int i = 0; i < valueArray.length; i++)
+ {
+ result.put(features.get(i).getLabel(), valueArray[i]);
+ }
+ return result;
}
private FeatureValue[] createFeatureValueArray(
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 5e1f8958769..bb399189139 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
@@ -45,7 +45,6 @@ import ch.systemsx.cisd.common.io.ByteArrayBasedContent;
import ch.systemsx.cisd.common.io.ConcatenatedFileOutputStreamWriter;
import ch.systemsx.cisd.common.io.FileBasedContent;
import ch.systemsx.cisd.common.io.IContent;
-import ch.systemsx.cisd.etlserver.Constants;
import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
import ch.systemsx.cisd.openbis.dss.etl.IImagingDatasetLoader;
import ch.systemsx.cisd.openbis.dss.generic.server.DssServiceRpcAuthorizationAdvisor;
@@ -203,7 +202,7 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
final String channel = "dapi";
prepareGetHomeDatabaseInstance();
prepareListDataSetsByCode();
-
+
List<PlateImageReference> plateImageReferences =
screeningService
.listPlateImageReferences(SESSION_TOKEN, ds, wellPositions, channel);
@@ -610,8 +609,12 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
{
{
one(service).listDataSetsByCode(Arrays.asList(DATASET_CODE));
- will(returnValue(Arrays.asList(new DataSetBuilder().code(DATASET_CODE)
- .shareId(ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID).getDataSet())));
+ will(returnValue(Arrays
+ .asList(new DataSetBuilder()
+ .code(DATASET_CODE)
+ .shareId(
+ ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID)
+ .getDataSet())));
}
});
}
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 c6deebb9add..2a88079fcb2 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
@@ -20,7 +20,9 @@ import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.applic
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
import org.testng.AssertJUnit;
import org.testng.annotations.Test;
@@ -73,9 +75,9 @@ public class WellTooltipGeneratorTest extends AssertJUnit
}
private static String tryGenerateShortDescription(PlateLayouterModel model, int rowIx,
- int colIx, Integer featureIndexOrNull)
+ int colIx, String featureLabelOrNull)
{
- return WellTooltipGenerator.tryGenerateTooltip(model, rowIx, colIx, featureIndexOrNull,
+ return WellTooltipGenerator.tryGenerateTooltip(model, rowIx, colIx, featureLabelOrNull,
createDummyRealNumberRenderer());
}
@@ -102,7 +104,7 @@ public class WellTooltipGeneratorTest extends AssertJUnit
assertEquals(METADATA_EXPECTED_DESC_A2 + "\n" + ALL_FEATURES_DESC, desc);
// one feature distingushed
- desc = tryGenerateShortDescription(model, 0, 1, 1);
+ desc = tryGenerateShortDescription(model, 0, 1, "FeatureY");
assertEquals("FeatureY: <b>2.0</b>\n" + METADATA_EXPECTED_DESC_A2 + "\n" + FEATURE_X_DESC,
desc);
@@ -118,7 +120,7 @@ public class WellTooltipGeneratorTest extends AssertJUnit
String desc = tryGenerateShortDescription(model, 0, 1, null);
assertEquals(ALL_FEATURES_DESC, desc);
- desc = tryGenerateShortDescription(model, 0, 1, 0);
+ desc = tryGenerateShortDescription(model, 0, 1, "FeatureX");
assertEquals("FeatureX: <b>1.0</b>\n" + "\n" + FEATURE_Y_DESC, desc);
}
@@ -134,7 +136,7 @@ public class WellTooltipGeneratorTest extends AssertJUnit
AssertionUtil.assertStarts("Feature0: 0.0", desc);
AssertionUtil.assertEnds("Feature29: 29.0\n" + "...", desc);
- desc = tryGenerateShortDescription(model, 0, 1, 4);
+ desc = tryGenerateShortDescription(model, 0, 1, "Feature4");
AssertionUtil.assertStarts("Feature4: <b>4.0</b>", desc);
AssertionUtil.assertEnds("Feature29: 29.0\n" + "...", desc);
}
@@ -153,27 +155,49 @@ public class WellTooltipGeneratorTest extends AssertJUnit
{
int size = 40;
List<String> featureLabels = new ArrayList<String>(size);
- FeatureValue[] featureValues = new FeatureValue[size];
- for (int i = 0; i < featureValues.length; i++)
+ Map<String, FeatureValue> featureValuesMap = new LinkedHashMap<String, FeatureValue>();
+ for (int i = 0; i < size; i++)
{
- featureValues[i] = FeatureValue.createFloat(i);
+ final String label = "Feature" + i;
+ final FeatureValue featureValue = FeatureValue.createFloat(i);
featureLabels.add("Feature" + i);
+ featureValuesMap.put(label, featureValue);
}
List<FeatureVectorValues> features = new ArrayList<FeatureVectorValues>();
- features.add(new FeatureVectorValues(null, getLocation(WELL_A2), featureValues));
+ features.add(new FeatureVectorValues(null, getLocation(WELL_A2), featureValuesMap));
return new FeatureVectorDataset(createDatasetReference(), features, featureLabels);
}
private static FeatureVectorDataset createFeatureVectorDataset()
{
- List<String> featureLabels = Arrays.asList("FeatureX", "FeatureY");
+
+ String[] featureLabels =
+ { "FeatureX", "FeatureY" };
List<FeatureVectorValues> features = new ArrayList<FeatureVectorValues>();
- features.add(new FeatureVectorValues(null, getLocation(WELL_A2), new FeatureValue[]
- { FeatureValue.createFloat(1), FeatureValue.createFloat(2) }));
- features.add(new FeatureVectorValues(null, getLocation(WELL_B3), new FeatureValue[]
- { FeatureValue.createFloat(-1), FeatureValue.createFloat(-2) }));
- return new FeatureVectorDataset(createDatasetReference(), features, featureLabels);
+ features.add(new FeatureVectorValues(null, getLocation(WELL_A2), createFeatureVectorMap(
+ featureLabels, new FeatureValue[]
+ { FeatureValue.createFloat(1), FeatureValue.createFloat(2) })));
+ 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));
+ }
+
+ private static Map<String, FeatureValue> createFeatureVectorMap(String[] labels,
+ FeatureValue[] values)
+ {
+ assert labels.length == values.length;
+
+ Map<String, FeatureValue> result = new LinkedHashMap<String, FeatureValue>();
+ for (int i = 0; i < labels.length; i++)
+ {
+ final String label = labels[i];
+ final FeatureValue featureValue = values[i];
+ result.put(label, featureValue);
+ }
+ return result;
}
private static DatasetReference createDatasetReference()
--
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