From 15d6aee2e32eb879ca97beb382a6f0797cbc245e Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Fri, 15 Jul 2011 14:10:23 +0000
Subject: [PATCH] [LMS-2383] Analysis procedures can now be selected in the
"Analysis Summary" section. The layout is still not finished, but the
functionality is there.
SVN: 22154
---
.../cisd/openbis/public/css/openbis.css | 7 +-
.../web/client/IScreeningClientService.java | 9 +-
.../client/IScreeningClientServiceAsync.java | 12 +-
.../application/ClientPluginFactory.java | 6 +-
.../client/web/client/application/Dict.java | 2 +
.../AnalysisProcedureChooser.java | 185 ++++++++++++++++++
.../ExperimentAnalysisSummaryGrid.java | 16 +-
.../ExperimentAnalysisSummarySection.java | 56 +++++-
.../ExperimentAnalysisSummaryViewer.java | 21 +-
.../ExperimentAnalysisSummaryResolver.java | 5 +-
.../specific/ScreeningLinkExtractor.java | 9 +-
.../client/web/public/screening-dictionary.js | 1 +
.../web/server/ScreeningClientService.java | 11 +-
.../FeatureVectorSummaryProvider.java | 8 +-
.../screening/server/ScreeningServer.java | 16 +-
.../server/ScreeningServerLogger.java | 13 +-
.../server/dataaccess/IScreeningQuery.java | 13 ++
.../server/logic/AbstractContentLoader.java | 5 +-
.../ExperimentFeatureVectorSummaryLoader.java | 37 +++-
.../logic/FeatureVectorDatasetLoader.java | 45 ++++-
.../MaterialFeatureVectorSummaryLoader.java | 4 +-
...erialFeaturesFromAllExperimentsLoader.java | 3 +-
.../server/logic/WellContentLoader.java | 3 +-
.../logic/WellFeatureCollectionLoader.java | 5 +-
.../screening/shared/IScreeningServer.java | 14 +-
.../shared/basic/dto/AnalysisProcedures.java | 54 +++++
26 files changed, 510 insertions(+), 50 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/AnalysisProcedureChooser.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/AnalysisProcedures.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/public/css/openbis.css b/openbis/source/java/ch/systemsx/cisd/openbis/public/css/openbis.css
index d350922c8ae..5707176ada4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/public/css/openbis.css
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/public/css/openbis.css
@@ -1,8 +1,13 @@
-body,div,td {
+body,div,td, .default-text {
font-family: verdana, tahoma, helvetica;
font-size: 12px;
}
+.default-text {
+ font-weight: normal;
+ color: black;
+}
+
.link-style {
color: blue;
text-decoration: underline;
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 9e19e30b3eb..f2760142ef2 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
@@ -33,6 +33,7 @@ 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.AnalysisProcedures;
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.FeatureVectorValues;
@@ -196,7 +197,7 @@ public interface IScreeningClientService extends IClientService
*/
public TypedTableResultSet<MaterialFeatureVectorSummary> listExperimentFeatureVectorSummary(
IResultSetConfig<String, TableModelRowWithObject<MaterialFeatureVectorSummary>> resultSetConfig,
- TechId experimentId) throws UserFailureException;
+ TechId experimentId, String analysisProcedureOrNull) throws UserFailureException;
public String prepareExportFeatureVectorSummary(
TableExportCriteria<TableModelRowWithObject<MaterialFeatureVectorSummary>> criteria)
@@ -225,4 +226,10 @@ public interface IScreeningClientService extends IClientService
public String prepareExportMaterialFeaturesFromAllExperiments(
TableExportCriteria<TableModelRowWithObject<MaterialSimpleFeatureVectorSummary>> criteria)
throws UserFailureException;
+
+ /**
+ * Return all analysis procedures for an experiment.
+ */
+ public AnalysisProcedures listAnalysisProcedures(TechId experimentId);
+
}
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 0d925aad185..5600a738368 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
@@ -34,6 +34,7 @@ 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.AnalysisProcedures;
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.FeatureVectorValues;
@@ -173,11 +174,12 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
AsyncCallback<ResultSet<Material>> callback);
/**
- * @see IScreeningClientService#listExperimentFeatureVectorSummary(IResultSetConfig, TechId)
+ * @see IScreeningClientService#listExperimentFeatureVectorSummary(IResultSetConfig, TechId,
+ * String)
*/
public void listExperimentFeatureVectorSummary(
IResultSetConfig<String, TableModelRowWithObject<MaterialFeatureVectorSummary>> resultSetConfig,
- TechId experimentId,
+ TechId experimentId, String analysisProcedureOrNull,
AsyncCallback<TypedTableResultSet<MaterialFeatureVectorSummary>> callback);
/**
@@ -219,4 +221,10 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
TableExportCriteria<TableModelRowWithObject<MaterialSimpleFeatureVectorSummary>> criteria,
AsyncCallback<String> callback);
+ /**
+ * @see IScreeningClientService#listAnalysisProcedures(TechId)
+ */
+ public void listAnalysisProcedures(TechId experimentId,
+ AsyncCallback<AnalysisProcedures> callback);
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
index 6f86cdbfb82..4ac26fd3d01 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ClientPluginFactory.java
@@ -67,8 +67,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.d
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.sample.LibrarySampleBatchRegistrationForm;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchByProjectCriteria;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.SingleExperimentSearchCriteria;
/**
@@ -192,7 +192,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
if (viewContext.getModel().isEmbeddedMode())
{
ExperimentAnalysisSummaryViewer.openTab(viewContext, new TechId(experiment),
- restrictGlobalScopeLinkToProject);
+ restrictGlobalScopeLinkToProject, null);
} else
{
new OpenEntityDetailsTabAction(experiment, viewContext).execute();
@@ -211,7 +211,7 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
if (viewContext.getModel().isEmbeddedMode())
{
return ScreeningLinkExtractor.createExperimentAnalysisSummaryBrowserLink(
- experiment.getPermId(), restrictGlobalScopeLinkToProject);
+ experiment.getPermId(), restrictGlobalScopeLinkToProject, null);
} else
{
return LinkExtractor.tryExtract(experiment);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
index 808f61b9ef4..a5b26bc8080 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
@@ -113,6 +113,8 @@ public final class Dict extends ch.systemsx.cisd.openbis.generic.client.web.clie
public static final String MATERIAL_IN_ALL_ASSAYS = "MATERIAL_IN_ALL_ASSAYS";
+ public static final String ANALYSIS_PROCEDURE = "ANALYSIS_PROCEDURE";
+
private Dict()
{
// Can not be instantiated.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/AnalysisProcedureChooser.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/AnalysisProcedureChooser.java
new file mode 100644
index 00000000000..782b13b57a0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/AnalysisProcedureChooser.java
@@ -0,0 +1,185 @@
+/*
+ * 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.client.web.client.application.detailviewers;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import com.extjs.gxt.ui.client.event.BaseEvent;
+import com.extjs.gxt.ui.client.event.Events;
+import com.extjs.gxt.ui.client.event.Listener;
+import com.extjs.gxt.ui.client.widget.Component;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.form.ComboBox.TriggerAction;
+import com.extjs.gxt.ui.client.widget.form.SimpleComboBox;
+import com.extjs.gxt.ui.client.widget.toolbar.FillToolItem;
+import com.extjs.gxt.ui.client.widget.toolbar.LabelToolItem;
+
+import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
+
+/**
+ * An UI panel for selecting analysis procedures.
+ *
+ * @author Kaloyan Enimanev
+ */
+class AnalysisProcedureChooser extends LayoutContainer
+{
+
+ /**
+ * Can be used from external classes wishing to be notified when the analysis procedure
+ * selection changes.
+ */
+ public static interface IAnalysisProcedureSelectionListener
+ {
+ void analysisProcedureSelected(String analysisProcedureOrNull);
+ }
+
+ private final static String UNSPECIFIED_ANALYSIS_PROCEDURE = "unspecified";
+
+ private final IViewContext<IScreeningClientServiceAsync> viewContext;
+ private final IAnalysisProcedureSelectionListener selectionListener;
+
+ private SimpleComboBox<String> analysisProceduresComboBox;
+
+ private final Listener<BaseEvent> selectionChangeListener = new Listener<BaseEvent>()
+ {
+
+ public void handleEvent(BaseEvent be)
+ {
+ selectionChanged();
+ }
+
+ };
+
+ public AnalysisProcedureChooser(IViewContext<IScreeningClientServiceAsync> viewContext,
+ List<String> analysisProcedures,
+ String selectedAnalysisProcedureOrNull,
+ IAnalysisProcedureSelectionListener selectionListener)
+ {
+ this.viewContext = viewContext;
+ this.selectionListener = selectionListener;
+ analysisProceduresComboBox = createProceduresComboBox();
+
+ setAutoHeight(true);
+ setAutoWidth(true);
+
+ add(createComboLabel());
+ add(analysisProceduresComboBox);
+ add(new FillToolItem());
+ addAnalysisProcedures(analysisProcedures);
+
+
+ setInitialSelection(selectedAnalysisProcedureOrNull);
+ }
+
+ private Component createComboLabel()
+ {
+ final LabelToolItem label =
+ new LabelToolItem(viewContext.getMessage(Dict.ANALYSIS_PROCEDURE)
+ + GenericConstants.LABEL_SEPARATOR);
+ label.addStyleName("default-text");
+ return label;
+ }
+
+ private SimpleComboBox<String> createProceduresComboBox()
+ {
+ SimpleComboBox<String> comboBox = new SimpleComboBox<String>();
+
+ comboBox.setTriggerAction(TriggerAction.ALL);
+ comboBox.setAllowBlank(false);
+ comboBox.setEditable(false);
+ comboBox.setEmptyText("No data sets found...");
+ comboBox.addListener(Events.SelectionChange, selectionChangeListener);
+
+ return comboBox;
+ }
+
+ private void addAnalysisProcedures(List<String> codes)
+ {
+ for (String code : transformAndSortCodes(codes))
+ {
+ addCodeToComboBox(code);
+ }
+ }
+
+ private List<String> transformAndSortCodes(List<String> codes)
+ {
+ List<String> sortedCodes = new ArrayList<String>();
+ for (String code : codes)
+ {
+ sortedCodes.add(analysisCodeToComboBoxValue(code));
+ }
+ Collections.sort(sortedCodes);
+
+ // unspecified is always an option and is always displayed at the end
+ sortedCodes.remove(UNSPECIFIED_ANALYSIS_PROCEDURE);
+ sortedCodes.add(UNSPECIFIED_ANALYSIS_PROCEDURE);
+
+ return sortedCodes;
+ }
+
+ private void addCodeToComboBox(String code)
+ {
+ if (analysisProceduresComboBox.findModel(code) == null)
+ {
+ analysisProceduresComboBox.add(code);
+ }
+ }
+
+ private void setInitialSelection(String analysisProcedureOrNull)
+ {
+ String comboBoxValue = analysisCodeToComboBoxValue(analysisProcedureOrNull);
+ if (UNSPECIFIED_ANALYSIS_PROCEDURE.equals(comboBoxValue))
+ {
+ comboBoxValue = getFirstValueFromCombo();
+ }
+ analysisProceduresComboBox.setSimpleValue(comboBoxValue);
+ }
+
+ private String getFirstValueFromCombo()
+ {
+ return analysisProceduresComboBox.getStore().getAt(0).getValue();
+ }
+
+ private void selectionChanged()
+ {
+ String selection = analysisProceduresComboBox.getSimpleValue();
+ notifySelectionListener(selection);
+ }
+
+ private void notifySelectionListener(String selection)
+ {
+ String analysisProcedureOrNull = comboBoxValueToAnalysisProcedure(selection);
+ selectionListener.analysisProcedureSelected(analysisProcedureOrNull);
+ }
+
+ private String analysisCodeToComboBoxValue(String analysisProcedureOrNull)
+ {
+ return StringUtils.isBlank(analysisProcedureOrNull) ? UNSPECIFIED_ANALYSIS_PROCEDURE
+ : analysisProcedureOrNull;
+ }
+
+ private String comboBoxValueToAnalysisProcedure(String comboBoxValue)
+ {
+ return UNSPECIFIED_ANALYSIS_PROCEDURE.equals(comboBoxValue) ? null : comboBoxValue;
+ }
+}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummaryGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummaryGrid.java
index 97cbbf5568f..012dcf70619 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummaryGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummaryGrid.java
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.C
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Constants;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.DisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.AnalysisProcedureChooser.IAnalysisProcedureSelectionListener;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
@@ -52,6 +53,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.FeatureV
* @author Kaloyan Enimanev
*/
public class ExperimentAnalysisSummaryGrid extends TypedTableGrid<MaterialFeatureVectorSummary>
+ implements IAnalysisProcedureSelectionListener
{
private static final String PREFIX = GenericConstants.ID_PREFIX
+ "experiment-feature-vector-summary";
@@ -64,6 +66,8 @@ public class ExperimentAnalysisSummaryGrid extends TypedTableGrid<MaterialFeatur
private final boolean restrictGlobalScopeLinkToProject;
+ private String analysisProcedureOrNull = null;
+
public static IDisposableComponent create(
IViewContext<IScreeningClientServiceAsync> viewContext,
IEntityInformationHolderWithIdentifier experiment,
@@ -137,13 +141,14 @@ public class ExperimentAnalysisSummaryGrid extends TypedTableGrid<MaterialFeatur
setBorders(true);
}
+
@Override
protected void listTableRows(
DefaultResultSetConfig<String, TableModelRowWithObject<MaterialFeatureVectorSummary>> resultSetConfig,
AsyncCallback<TypedTableResultSet<MaterialFeatureVectorSummary>> callback)
{
screeningViewContext.getService().listExperimentFeatureVectorSummary(resultSetConfig,
- new TechId(experiment), callback);
+ new TechId(experiment), analysisProcedureOrNull, callback);
}
@@ -172,4 +177,13 @@ public class ExperimentAnalysisSummaryGrid extends TypedTableGrid<MaterialFeatur
{
asDisposableWithoutToolbar().dispose();
}
+
+ //
+ // IAnalysisProcedureSelectionListener
+ //
+ public void analysisProcedureSelected(String analysisProcedure)
+ {
+ this.analysisProcedureOrNull = analysisProcedure;
+ refresh(true);
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummarySection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummarySection.java
index 0cee03edc13..b8b956c811c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummarySection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummarySection.java
@@ -1,12 +1,16 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.DisposableTabContent;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.DisplayTypeIDGenerator;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.AnalysisProcedureChooser.IAnalysisProcedureSelectionListener;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.AnalysisProcedures;
/**
* Experiment section panel which shows all feature vector summary for a given experiment.
@@ -20,6 +24,8 @@ public class ExperimentAnalysisSummarySection extends DisposableTabContent
private final IEntityInformationHolderWithIdentifier experiment;
+ private final IDisposableComponent analysisGridDisposableComponent;
+
public ExperimentAnalysisSummarySection(
IViewContext<IScreeningClientServiceAsync> screeningViewContext,
IEntityInformationHolderWithIdentifier experiment)
@@ -29,12 +35,60 @@ public class ExperimentAnalysisSummarySection extends DisposableTabContent
this.screeningViewContext = screeningViewContext;
this.experiment = experiment;
setIds(DisplayTypeIDGenerator.EXPERIMENT_FEATURE_VECTOR_SUMMARY_SECTION);
+
+ analysisGridDisposableComponent =
+ ExperimentAnalysisSummaryGrid.create(screeningViewContext, experiment, false);
}
@Override
protected IDisposableComponent createDisposableContent()
{
- return ExperimentAnalysisSummaryGrid.create(screeningViewContext, experiment, false);
+ return null;
+ }
+
+ private IAnalysisProcedureSelectionListener getGridAsListener()
+ {
+ return (IAnalysisProcedureSelectionListener) (analysisGridDisposableComponent
+ .getComponent());
+ }
+
+ @Override
+ protected void showContent()
+ {
+ super.showContent();
+
+ showAnalysisProcedureChooser();
+ }
+
+ private void showAnalysisProcedureChooser()
+ {
+ TechId experimentId = new TechId(experiment.getId());
+ screeningViewContext.getService().listAnalysisProcedures(experimentId,
+ new AbstractAsyncCallback<AnalysisProcedures>(screeningViewContext)
+ {
+ @Override
+ protected void process(AnalysisProcedures analysisProcedures)
+ {
+ setHeading("");
+ getHeader().setVisible(true);
+ final AnalysisProcedureChooser analysisProcedureChooser =
+ createAnalysisProcedureChooser(analysisProcedures);
+ getHeader().addTool(analysisProcedureChooser);
+ // WORKAROUND to GXT private widgetPanel in Header with fixed
+ // "float: right" set onRender
+ analysisProcedureChooser.addStyleName("force-float-left");
+
+ replaceContent(analysisGridDisposableComponent);
+ }
+ });
+ }
+
+ private AnalysisProcedureChooser createAnalysisProcedureChooser(
+ AnalysisProcedures analysisProcedures)
+ {
+ return new AnalysisProcedureChooser(screeningViewContext,
+ analysisProcedures.getProcedureCodes(), null,
+ getGridAsListener());
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummaryViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummaryViewer.java
index 5843e2e7454..3525dff9319 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummaryViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentAnalysisSummaryViewer.java
@@ -45,7 +45,8 @@ public class ExperimentAnalysisSummaryViewer
public static void openTab(
final IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- String experimentPermId, final boolean restrictGlobalScopeLinkToProject)
+ String experimentPermId, final boolean restrictGlobalScopeLinkToProject,
+ final String analysisProcedureOrNull)
{
screeningViewContext.getCommonService().getEntityInformationHolder(EntityKind.EXPERIMENT,
experimentPermId,
@@ -56,14 +57,15 @@ public class ExperimentAnalysisSummaryViewer
{
TechId experimentId = new TechId(experiment);
openTab(screeningViewContext, experimentId,
- restrictGlobalScopeLinkToProject);
+ restrictGlobalScopeLinkToProject, analysisProcedureOrNull);
}
});
}
public static void openTab(
final IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- TechId experimentId, final boolean restrictGlobalScopeLinkToProject)
+ TechId experimentId, final boolean restrictGlobalScopeLinkToProject,
+ final String analysisProcedureOrNull)
{
screeningViewContext.getCommonService().getExperimentInfo(experimentId,
new AbstractAsyncCallback<Experiment>(screeningViewContext)
@@ -73,7 +75,8 @@ public class ExperimentAnalysisSummaryViewer
{
AbstractTabItemFactory factory =
createTabFactory(screeningViewContext, result,
- restrictGlobalScopeLinkToProject);
+ restrictGlobalScopeLinkToProject,
+ analysisProcedureOrNull);
DispatcherHelper.dispatchNaviEvent(factory);
}
});
@@ -82,7 +85,7 @@ public class ExperimentAnalysisSummaryViewer
private static AbstractTabItemFactory createTabFactory(
final IViewContext<IScreeningClientServiceAsync> viewContext,
final IEntityInformationHolderWithProperties experiment,
- final boolean restrictGlobalScopeLinkToProject)
+ final boolean restrictGlobalScopeLinkToProject, final String analysisProcedureOrNull)
{
return new AbstractTabItemFactory()
{
@@ -99,7 +102,8 @@ public class ExperimentAnalysisSummaryViewer
public ITabItem create()
{
IDisposableComponent tabComponent =
- createViewer(viewContext, experiment, restrictGlobalScopeLinkToProject);
+ createViewer(viewContext, experiment, restrictGlobalScopeLinkToProject,
+ analysisProcedureOrNull);
return DefaultTabItem.create(getTabTitle(), tabComponent, viewContext);
}
@@ -107,7 +111,8 @@ public class ExperimentAnalysisSummaryViewer
public String tryGetLink()
{
return ScreeningLinkExtractor.createExperimentAnalysisSummaryBrowserLink(
- experiment.getPermId(), restrictGlobalScopeLinkToProject);
+ experiment.getPermId(), restrictGlobalScopeLinkToProject,
+ analysisProcedureOrNull);
}
@Override
@@ -128,7 +133,7 @@ public class ExperimentAnalysisSummaryViewer
private static IDisposableComponent createViewer(
IViewContext<IScreeningClientServiceAsync> viewContext,
IEntityInformationHolderWithProperties experiment,
- boolean restrictGlobalScopeLinkToProject)
+ boolean restrictGlobalScopeLinkToProject, String analysisProcedureOrNull)
{
String headingText = viewContext.getMessage(Dict.ASSAY_HEADER, experiment.getCode());
final IDisposableComponent gridComponent =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ExperimentAnalysisSummaryResolver.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ExperimentAnalysisSummaryResolver.java
index 1755c635664..5d471dc39fd 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ExperimentAnalysisSummaryResolver.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ExperimentAnalysisSummaryResolver.java
@@ -32,8 +32,11 @@ public class ExperimentAnalysisSummaryResolver extends AbstractViewLocatorResolv
boolean restrictGlobalScopeLinkToProject =
getOptionalBooleanParameter(locator,
ScreeningLinkExtractor.RESTRICT_GLOBAL_SEARCH_TO_PROJECT, false);
+
+ String analysisProcedureOrNull =
+ getOptionalParameter(locator, ScreeningLinkExtractor.ANALYSIS_PROCEDURE_KEY);
ExperimentAnalysisSummaryViewer.openTab(viewContext, experimentPermId,
- restrictGlobalScopeLinkToProject);
+ restrictGlobalScopeLinkToProject, analysisProcedureOrNull);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
index c859c699825..ac8681465e5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ui/columns/specific/ScreeningLinkExtractor.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific;
+import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.LinkExtractor;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.URLListEncoder;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.lang.StringEscapeUtils;
@@ -85,6 +86,8 @@ public class ScreeningLinkExtractor extends LinkExtractor
// false by default
public static final String RESTRICT_GLOBAL_SEARCH_TO_PROJECT = "restrictGlobalSearchToProject";
+ public static final String ANALYSIS_PROCEDURE_KEY = "analysisProcedure";
+
public static final String createPlateMetadataBrowserLink(String platePermId)
{
URLMethodWithParameters url = new URLMethodWithParameters("");
@@ -94,7 +97,7 @@ public class ScreeningLinkExtractor extends LinkExtractor
}
public static final String createExperimentAnalysisSummaryBrowserLink(String experimentPermId,
- boolean restrictGlobalScopeLinkToProject)
+ boolean restrictGlobalScopeLinkToProject, String analysisProcedureOrNull)
{
URLMethodWithParameters url = new URLMethodWithParameters("");
url.addParameter(BasicConstant.LOCATOR_ACTION_PARAMETER, EXPERIMENT_ANALYSIS_SUMMARY_ACTION);
@@ -105,6 +108,10 @@ public class ScreeningLinkExtractor extends LinkExtractor
url.addParameterWithoutEncoding(RESTRICT_GLOBAL_SEARCH_TO_PROJECT,
restrictGlobalScopeLinkToProject);
}
+ if (StringUtils.isNotBlank(analysisProcedureOrNull))
+ {
+ url.addParameter(ANALYSIS_PROCEDURE_KEY, analysisProcedureOrNull);
+ }
return tryPrint(url);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
index 34b53f1bef3..ae30526965b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
@@ -21,6 +21,7 @@ WELL: "Well",
WELL_IMAGES: "Well Images",
PREVIEW: "Preview",
PLATE_VIEWER_TITLE: "Plate {0}",
+ANALYSIS_PROCEDURE: "Analysis Procedure",
//
// Menu items
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 6604df83fa9..e8ba0078cef 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
@@ -56,6 +56,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.server.resultset.Pla
import ch.systemsx.cisd.openbis.plugin.screening.client.web.server.resultset.WellContentProvider;
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.AnalysisProcedures;
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.FeatureVectorValues;
@@ -294,10 +295,11 @@ public final class ScreeningClientService extends AbstractClientService implemen
public TypedTableResultSet<MaterialFeatureVectorSummary> listExperimentFeatureVectorSummary(
IResultSetConfig<String, TableModelRowWithObject<MaterialFeatureVectorSummary>> criteria,
- TechId experimentId)
+ TechId experimentId, String analysisProcedureOrNull)
{
FeatureVectorSummaryProvider provider =
- new FeatureVectorSummaryProvider(server, getSessionToken(), experimentId);
+ new FeatureVectorSummaryProvider(server, getSessionToken(), experimentId,
+ analysisProcedureOrNull);
return listEntities(provider, criteria);
}
@@ -345,4 +347,9 @@ public final class ScreeningClientService extends AbstractClientService implemen
return prepareExportEntities(criteria);
}
+ public AnalysisProcedures listAnalysisProcedures(TechId experimentId)
+ {
+ return server.listAnalysisProcedures(getSessionToken(), experimentId);
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/FeatureVectorSummaryProvider.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/FeatureVectorSummaryProvider.java
index 1a7e18d4880..492be321346 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/FeatureVectorSummaryProvider.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/resultset/FeatureVectorSummaryProvider.java
@@ -49,12 +49,15 @@ public class FeatureVectorSummaryProvider extends AbstractTableModelProvider<Mat
private final TechId experimentId;
+ private final String analysisProcedureOrNull;
+
public FeatureVectorSummaryProvider(IScreeningServer server, String sessionToken,
- TechId experimentId)
+ TechId experimentId, String analysisProcedureOrNull)
{
this.server = server;
this.sessionToken = sessionToken;
this.experimentId = experimentId;
+ this.analysisProcedureOrNull = analysisProcedureOrNull;
}
@Override
@@ -63,7 +66,8 @@ public class FeatureVectorSummaryProvider extends AbstractTableModelProvider<Mat
TypedTableModelBuilder<MaterialFeatureVectorSummary> builder =
new TypedTableModelBuilder<MaterialFeatureVectorSummary>();
ExperimentFeatureVectorSummary fvSummary =
- server.getExperimentFeatureVectorSummary(sessionToken, experimentId);
+ server.getExperimentFeatureVectorSummary(sessionToken, experimentId,
+ analysisProcedureOrNull);
builder.addColumn(MATERIAL_ID);
builder.columnGroup(MATERIAL_PROPS_GROUP);
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 37460453df3..d7f3ee5ebde 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
@@ -72,8 +72,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQue
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ExperimentFeatureVectorSummaryLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.FeatureVectorValuesLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.LogicalImageLoader;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.MaterialFeaturesFromAllExperimentsLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.MaterialFeatureVectorSummaryLoader;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.MaterialFeaturesFromAllExperimentsLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningApiImpl;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellContentLoader;
@@ -91,6 +91,7 @@ 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.AnalysisProcedures;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
@@ -302,13 +303,14 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
}
public ExperimentFeatureVectorSummary getExperimentFeatureVectorSummary(String sessionToken,
- TechId experimentId)
+ TechId experimentId, String analysisProcedureOrNull)
{
Session session = getSession(sessionToken);
// NOTE: we want the settings to be passed form the client in future
MaterialSummarySettings settings = createDefaultSettings();
return ExperimentFeatureVectorSummaryLoader.loadExperimentFeatureVectors(session,
- businessObjectFactory, getDAOFactory(), experimentId, settings);
+ businessObjectFactory, getDAOFactory(), experimentId, analysisProcedureOrNull,
+ settings);
}
public List<MaterialSimpleFeatureVectorSummary> getMaterialFeatureVectorsFromAllExperiments(
@@ -451,6 +453,14 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return createScreeningApiImpl(sessionToken).getDatasetIdentifiers(datasetCodes);
}
+ public AnalysisProcedures listAnalysisProcedures(String sessionToken, TechId experimentId)
+ {
+ checkSession(sessionToken);
+ IScreeningQuery dao = createDAO(getDAOFactory());
+ List<String> procedureCodes = dao.listAnalysisProcedures(experimentId.getId());
+ return new AnalysisProcedures(procedureCodes);
+ }
+
public List<PlateWellMaterialMapping> listPlateMaterialMapping(String sessionToken,
List<? extends PlateIdentifier> plates,
MaterialTypeIdentifier materialTypeIdentifierOrNull)
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 389f3524ec1..24ab08ab04c 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
@@ -50,6 +50,7 @@ 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.AnalysisProcedures;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
@@ -348,10 +349,11 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
}
public ExperimentFeatureVectorSummary getExperimentFeatureVectorSummary(String sessionToken,
- TechId experimentId)
+ TechId experimentId, String analysisProcedureOrNull)
{
logAccess(sessionToken, "getExperimentFeatureVectorSummary",
- "sessionToken(%s), experimentId(%s)", sessionToken, experimentId);
+ "sessionToken(%s), experimentId(%s), analysisProcedure(%s)", sessionToken,
+ experimentId, analysisProcedureOrNull);
return null;
}
@@ -373,4 +375,11 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
experimentSearchCriteria);
return null;
}
+
+ public AnalysisProcedures listAnalysisProcedures(String sessionToken, TechId experimentId)
+ {
+ logAccess(sessionToken, "listAnalysisProcedures", "sessionToken(%s), experimentId(%s)",
+ sessionToken, experimentId);
+ return null;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
index 3ca0cfaad02..47c51623cc4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java
@@ -305,4 +305,17 @@ public interface IScreeningQuery extends BaseQuery
public List<ExperimentReferenceQueryResult> getExperimentsWithMaterial(long materialId,
long projectId);
+ @Select(sql = "select distinct "
+ + " ds_props.value as value"
+ + " from experiments exp "
+ + " join data ds on ds.expe_id = exp.id "
+ + " join data_set_types ds_type on ds.dsty_id = ds_type.id "
+ + " join data_set_type_property_types dst_pt on dst_pt.dsty_id = ds_type.id "
+ + " left outer join data_set_properties ds_props on ds_props.ds_id = ds.id "
+ + " where "
+ + " exp.id = ?{1} "
+ + " and "
+ + " dst_pt.prty_id = (select id from property_types where code='ANALYSIS_PROCEDURE' and is_internal_namespace=true)")
+ public List<String> listAnalysisProcedures(long experimentId);
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
index 8de33f1da2d..4badb30efd7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/AbstractContentLoader.java
@@ -100,8 +100,9 @@ abstract class AbstractContentLoader
}
protected final FeatureVectorDatasetLoader createFeatureVectorDatasetsRetriever(
- Set<PlateIdentifier> plates)
+ Set<PlateIdentifier> plates, String analysisProcedureOrNull)
{
- return new FeatureVectorDatasetLoader(session, businessObjectFactory, null, plates);
+ return new FeatureVectorDatasetLoader(session, businessObjectFactory, null, plates,
+ analysisProcedureOrNull);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
index 07baa2ae640..9e5951d90e9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
@@ -63,15 +63,30 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoa
*/
public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
{
+
+ static class LoaderParameters
+ {
+ TechId experimentId;
+
+ String analysisProcedureOrNull;
+
+ LoaderParameters(TechId experimentId, String analysisProcedureOrNull)
+ {
+ this.experimentId = experimentId;
+ this.analysisProcedureOrNull = analysisProcedureOrNull;
+ }
+ }
+
/**
* Loads feature vectors summaries for all the materials in the specified experiment.
*/
public static ExperimentFeatureVectorSummary loadExperimentFeatureVectors(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
- TechId experimentId, MaterialSummarySettings settings)
+ TechId experimentId, String analysisProcedureOrNull, MaterialSummarySettings settings)
{
+ LoaderParameters params = new LoaderParameters(experimentId, analysisProcedureOrNull);
return new ExperimentFeatureVectorSummaryLoader(session, businessObjectFactory, daoFactory,
- settings).loadExperimentFeatureVectors(experimentId);
+ settings).loadExperimentFeatureVectors(params);
}
protected final MaterialSummarySettings settings;
@@ -84,10 +99,10 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
this.settings = settings;
}
- private ExperimentFeatureVectorSummary loadExperimentFeatureVectors(TechId experimentId)
+ private ExperimentFeatureVectorSummary loadExperimentFeatureVectors(LoaderParameters params)
{
- WellDataCollection wellDataCollection = tryLoadWellData(experimentId);
- ExperimentReference experiment = loadExperimentByTechId(experimentId);
+ WellDataCollection wellDataCollection = tryLoadWellData(params);
+ ExperimentReference experiment = loadExperimentByTechId(params.experimentId);
if (wellDataCollection == null)
{
@@ -160,10 +175,11 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
}, UniqueKeyViolationStrategy.KEEP_FIRST);
}
- protected final WellDataCollection tryLoadWellData(TechId experimentId)
+ protected final WellDataCollection tryLoadWellData(LoaderParameters params)
{
ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
- List<Sample> plates = sampleLister.list(createExperientCriteria(experimentId.getId()));
+ List<Sample> plates =
+ sampleLister.list(createExperientCriteria(params.experimentId.getId()));
List<Sample> wells = sampleLister.list(createWellsCriteria(plates));
if (wells.isEmpty())
{
@@ -173,7 +189,7 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
Set<PlateIdentifier> plateIdentifiers = extractIdentifiers(plates);
WellFeatureCollection<FeatureVectorValues> featureVectorsCollection =
- tryLoadWellSingleFeatureVectors(plateIdentifiers);
+ tryLoadWellSingleFeatureVectors(plateIdentifiers, params.analysisProcedureOrNull);
if (featureVectorsCollection == null)
{
return null; // no feature vector datasets connected to plates in this experiment
@@ -185,10 +201,11 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
}
private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
- Set<PlateIdentifier> plateIdentifiers)
+ Set<PlateIdentifier> plateIdentifiers, String analysisProcedureOrNull)
{
return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory)
- .tryLoadWellSingleFeatureVectors(plateIdentifiers, settings.getFeatureCodes());
+ .tryLoadWellSingleFeatureVectors(plateIdentifiers, settings.getFeatureCodes(),
+ analysisProcedureOrNull);
}
private static ExperimentFeatureVectorSummary createEmptySummary(ExperimentReference experiment)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
index c1a65e51143..40544e10eae 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/FeatureVectorDatasetLoader.java
@@ -16,6 +16,10 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+import static ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningUtils.isTypeMatching;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN;
+
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
@@ -27,6 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
@@ -42,17 +47,27 @@ class FeatureVectorDatasetLoader extends HCSImageDatasetLoader
// Parameter state
private final String featureVectorDatasetTypeCode;
+ private final String analysisProcedureOrNull;
+
// Running state
private Collection<ExternalData> featureVectorDatasets;
FeatureVectorDatasetLoader(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, String homeSpaceOrNull,
Set<? extends PlateIdentifier> plates)
+ {
+ this(session, businessObjectFactory, homeSpaceOrNull, plates, null);
+ }
+
+ FeatureVectorDatasetLoader(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, String homeSpaceOrNull,
+ Set<? extends PlateIdentifier> plates, String analysisProcedureOrNull)
{
super(session, businessObjectFactory, homeSpaceOrNull, plates,
ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN,
ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN);
featureVectorDatasetTypeCode = ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN;
+ this.analysisProcedureOrNull = analysisProcedureOrNull;
}
public static class FeatureVectorExternalData
@@ -106,12 +121,10 @@ class FeatureVectorDatasetLoader extends HCSImageDatasetLoader
List<ExternalData> imageDatasets = new ArrayList<ExternalData>();
for (ExternalData dataset : getDatasets())
{
- if (ScreeningUtils.isTypeMatching(dataset,
- ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN))
+ if (isMatchingAnalysisDataSet(dataset))
{
featureVectorDatasetSet.put(dataset.getId(), dataset);
- } else if (ScreeningUtils.isTypeMatching(dataset,
- ScreeningConstants.ANY_HCS_IMAGE_DATASET_TYPE_PATTERN))
+ } else if (isMatchingImageDataset(dataset))
{
imageDatasets.add(dataset);
}
@@ -121,6 +134,30 @@ class FeatureVectorDatasetLoader extends HCSImageDatasetLoader
featureVectorDatasets = featureVectorDatasetSet.values();
}
+ private boolean isMatchingImageDataset(ExternalData dataset)
+ {
+ return isTypeMatching(dataset, ANY_HCS_IMAGE_DATASET_TYPE_PATTERN);
+ }
+
+ private boolean isMatchingAnalysisProcedure(ExternalData dataset)
+ {
+ String dataSetAnalysisProcedure =
+ EntityHelper.tryFindPropertyValue(dataset, ScreeningConstants.ANALYSIS_PROCEDURE);
+ if (analysisProcedureOrNull == null)
+ {
+ return dataSetAnalysisProcedure == null;
+ } else
+ {
+ return analysisProcedureOrNull.equals(dataSetAnalysisProcedure);
+ }
+ }
+
+ private boolean isMatchingAnalysisDataSet(ExternalData dataset)
+ {
+ return isTypeMatching(dataset, HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN)
+ && isMatchingAnalysisProcedure(dataset);
+ }
+
private List<FeatureVectorDatasetReference> asFeatureVectorDatasetReferences()
{
List<FeatureVectorDatasetReference> result = new ArrayList<FeatureVectorDatasetReference>();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
index e0eb9b912cf..75b8031116b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
@@ -176,7 +176,9 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
private MaterialAllReplicasFeatureVectors tryLoadMaterialFeatureVectors(TechId materialId,
TechId experimentId)
{
- WellDataCollection experimentWells = tryLoadWellData(experimentId);
+ // TODO KE: 2011-07-15 this should also be changed
+ LoaderParameters params = new LoaderParameters(experimentId, null);
+ WellDataCollection experimentWells = tryLoadWellData(params);
if (experimentWells == null)
{
return null;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeaturesFromAllExperimentsLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeaturesFromAllExperimentsLoader.java
index 83cf56f5a51..2e72507c65d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeaturesFromAllExperimentsLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeaturesFromAllExperimentsLoader.java
@@ -358,8 +358,9 @@ public class MaterialFeaturesFromAllExperimentsLoader extends AbstractContentLoa
private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
Set<PlateIdentifier> plateIdentifiers)
{
+ // TODO KE: 2011-07-15 specify analysis procedure here ?
return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory)
- .tryLoadWellSingleFeatureVectors(plateIdentifiers, settings.getFeatureCodes());
+ .tryLoadWellSingleFeatureVectors(plateIdentifiers, settings.getFeatureCodes(), null);
}
}
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 4b3eb9c3c6e..1613b14b2f3 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
@@ -356,7 +356,8 @@ public class WellContentLoader extends AbstractContentLoader
List<WellContent> locations)
{
Set<PlateIdentifier> plates = extractPlates(locations);
- return createFeatureVectorDatasetsRetriever(plates);
+ // TODO KE: 2011-07-15 add analysis procedure support here
+ return createFeatureVectorDatasetsRetriever(plates, null);
}
private static Collection<ExternalData> selectChildlessImageDatasets(
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
index 18dff4c124d..66a8e59df6f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
@@ -56,11 +56,12 @@ public class WellFeatureCollectionLoader extends AbstractContentLoader
/** Loads feature vectors for chosen plates and set of features */
public WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
- Set<PlateIdentifier> plates, List<String> featureCodes)
+ Set<PlateIdentifier> plates, List<String> featureCodes, String analysisProcedureOrNull)
{
StopWatch watch = new StopWatch();
watch.start();
- FeatureVectorDatasetLoader datasetsRetriever = createFeatureVectorDatasetsRetriever(plates);
+ FeatureVectorDatasetLoader datasetsRetriever =
+ createFeatureVectorDatasetsRetriever(plates, analysisProcedureOrNull);
Collection<ExternalData> featureVectorDatasets =
datasetsRetriever.getFeatureVectorDatasets();
if (featureVectorDatasets.isEmpty())
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 6aea09c6871..14092853b95 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
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.DatasetRef
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.MaterialExperimentFeatureVectorSummaryValidator;
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.AnalysisProcedures;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorDataset;
@@ -219,7 +220,8 @@ public interface IScreeningServer extends IServer
@Transactional(readOnly = true)
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public ExperimentFeatureVectorSummary getExperimentFeatureVectorSummary(String sessionToken,
- @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId);
+ @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId,
+ String analysisProcedureOrNull);
/**
* Returns a feature vector summary (with details for each replica) for the given experiment and
@@ -241,4 +243,14 @@ public interface IScreeningServer extends IServer
String sessionToken, TechId materialId,
ExperimentSearchByProjectCriteria experimentSearchCriteria);
+ /**
+ * Return a list of all different analysis procedures applied to the data sets of an experiment.
+ * The result contains unique values. It can contain NULL (which can be used for data sets
+ * having no ANALYSIS_PROCEDURE value specified).
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ public AnalysisProcedures listAnalysisProcedures(String sessionToken,
+ @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId);
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/AnalysisProcedures.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/AnalysisProcedures.java
new file mode 100644
index 00000000000..8862f38ca0a
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/AnalysisProcedures.java
@@ -0,0 +1,54 @@
+/*
+ * 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.shared.basic.dto;
+
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ * A holder class for analysis procedures. The codes list contains unique values. It can contain
+ * NULL (which can be used for data sets having no ANALYSIS_PROCEDURE value specified).
+ *
+ * @author Kaloyan Enimanev
+ */
+public class AnalysisProcedures implements ISerializable
+{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+ private List<String> procedureCodes;
+
+ // GWT only
+ @SuppressWarnings("unused")
+ private AnalysisProcedures()
+ {
+ }
+
+ public AnalysisProcedures(List<String> procedureCodes)
+ {
+ this.procedureCodes = new ArrayList<String>(procedureCodes);
+ }
+
+ public List<String> getProcedureCodes()
+ {
+ return Collections.unmodifiableList(procedureCodes);
+ }
+
+}
--
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