From 211defe0a80622983ec848ea47f8079ba211064e Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 7 Jun 2011 15:35:23 +0000
Subject: [PATCH] LMS-2268 allow to specify project in 'all assays for a gene'
view (only with the URL). Keep this setting when navigating between different
views.
SVN: 21624
---
.../application/ClientPluginFactory.java | 89 ++++----
.../application/ScreeningViewContext.java | 4 -
.../ExperimentAnalysisSummaryGrid.java | 22 +-
.../ExperimentAnalysisSummarySection.java | 2 +-
.../ExperimentAnalysisSummaryViewer.java | 26 ++-
.../ExperimentWellMaterialBrowserGrid.java | 15 +-
.../detailviewers/ImagingMaterialViewer.java | 34 +++-
.../MaterialDisambiguationGrid.java | 2 +-
...aterialFeaturesFromAllExperimentsGrid.java | 23 ++-
...erialFeaturesFromAllExperimentsViewer.java | 20 +-
...erialFeaturesFromAllExpermentsSection.java | 10 +-
.../MaterialReplicaSummaryComponent.java | 80 +++++---
.../MaterialReplicaSummarySection.java | 19 +-
.../MaterialReplicaSummaryViewer.java | 69 ++++---
.../detailviewers/WellContentDialog.java | 12 +-
.../detailviewers/WellSearchGrid.java | 47 +++--
.../ExperimentAnalysisSummaryResolver.java | 7 +-
.../ImagingMaterialLocatorResolver.java | 76 ++++---
...ialFeaturesFromAllExperimentsResolver.java | 67 ------
.../MaterialReplicaSummaryResolver.java | 48 -----
.../locator/WellSearchLocatorResolver.java | 19 +-
.../specific/ScreeningLinkExtractor.java | 192 +++++++-----------
.../ExperimentIdentifierSearchCriteria.java | 46 ++++-
.../screening/server/ScreeningServer.java | 32 ++-
.../server/dataaccess/IScreeningQuery.java | 21 ++
.../server/logic/WellContentLoader.java | 44 ++--
.../WellSearchCriteriaPredicate.java | 66 ++++--
.../shared/basic/dto/WellSearchCriteria.java | 131 ++++++++++--
.../java/BiozentrumMatLabApiTest.java | 108 ++++++++--
.../utils/EntityTypeLabelUtilsTest.java | 8 +-
.../server/dataaccess/ScreeningDAOTest.java | 19 +-
31 files changed, 794 insertions(+), 564 deletions(-)
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/MaterialFeaturesFromAllExperimentsResolver.java
delete mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/MaterialReplicaSummaryResolver.java
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 df48e2f1c88..6f86cdbfb82 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
@@ -48,6 +48,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWit
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
@@ -65,9 +66,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.d
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.PlateSampleViewer;
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.ExperimentReference;
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.SingleExperimentSearchCriteria;
/**
@@ -185,11 +186,13 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
*/
public static final void openImagingExperimentViewer(
final IEntityInformationHolderWithPermId experiment,
+ boolean restrictGlobalScopeLinkToProject,
final IViewContext<IScreeningClientServiceAsync> viewContext)
{
if (viewContext.getModel().isEmbeddedMode())
{
- ExperimentAnalysisSummaryViewer.openTab(viewContext, new TechId(experiment));
+ ExperimentAnalysisSummaryViewer.openTab(viewContext, new TechId(experiment),
+ restrictGlobalScopeLinkToProject);
} else
{
new OpenEntityDetailsTabAction(experiment, viewContext).execute();
@@ -200,13 +203,15 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
* Creates a link to experiment detail viewer. In embedded mode the link will lead to the tab
* which has only the content of the analysis summary panel.
*/
- public static String createImagingExperimentViewerLink(ExperimentReference experiment,
+ public static String createImagingExperimentViewerLink(
+ IEntityInformationHolderWithPermId experiment,
+ boolean restrictGlobalScopeLinkToProject,
IViewContext<IScreeningClientServiceAsync> viewContext)
{
if (viewContext.getModel().isEmbeddedMode())
{
- return ScreeningLinkExtractor.createExperimentAnalysisSummaryBrowserLink(experiment
- .getPermId());
+ return ScreeningLinkExtractor.createExperimentAnalysisSummaryBrowserLink(
+ experiment.getPermId(), restrictGlobalScopeLinkToProject);
} else
{
return LinkExtractor.tryExtract(experiment);
@@ -225,18 +230,26 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
final ExperimentSearchCriteria experimentCriteriaOrNull,
final IViewContext<IScreeningClientServiceAsync> viewContext)
{
- String experimentPermId = tryGetExperimentPermId(experimentCriteriaOrNull);
if (viewContext.getModel().isEmbeddedMode())
{
MaterialIdentifier materialIdentifier = asMaterialIdentifier(material);
- if (experimentPermId != null)
+ ExperimentSearchByProjectCriteria multipleExperimentsScope =
+ tryAsMultipleExperimentsCriteria(experimentCriteriaOrNull);
+ if (multipleExperimentsScope != null)
{
- MaterialReplicaSummaryViewer.openTab(viewContext, experimentPermId,
- materialIdentifier);
+ MaterialFeaturesFromAllExperimentsViewer.openTab(viewContext, materialIdentifier,
+ multipleExperimentsScope);
} else
{
- MaterialFeaturesFromAllExperimentsViewer.openTab(viewContext, materialIdentifier,
- null);
+ assert experimentCriteriaOrNull != null;
+ SingleExperimentSearchCriteria experiment =
+ experimentCriteriaOrNull.tryGetExperiment();
+ assert experiment != null;
+
+ MaterialReplicaSummaryViewer.openTab(viewContext, experiment.getExperimentPermId(),
+ experimentCriteriaOrNull.getRestrictGlobalSearchLinkToProject(),
+ materialIdentifier);
+
}
} else
{
@@ -244,35 +257,23 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
}
}
- /**
- * Creates a link to material detail viewer. In embedded mode the link will lead to the tab
- * which has only the replica summary panel (for a chosen experiment or for all of them,
- * depending on the criteria).
- */
- public static String createImagingMaterialViewerLink(
- final IEntityInformationHolderWithPermId material,
- final ExperimentSearchCriteria experimentCriteria,
- IViewContext<IScreeningClientServiceAsync> viewContext)
+ private static ExperimentSearchByProjectCriteria tryAsMultipleExperimentsCriteria(
+ ExperimentSearchCriteria experimentCriteriaOrNull)
{
- if (viewContext.getModel().isEmbeddedMode())
+ if (experimentCriteriaOrNull == null)
{
- SingleExperimentSearchCriteria experiment = experimentCriteria.tryGetExperiment();
- String materialCode = material.getCode();
- String materialTypeCode = material.getEntityType().getCode();
- if (experiment != null)
- {
- return ScreeningLinkExtractor.createMaterialReplicaSummaryLink(
- experiment.getExperimentPermId(), materialCode, materialTypeCode);
- } else
- {
- return ScreeningLinkExtractor.createMaterialFeaturesFromAllExperimentsLink(
- materialCode, materialTypeCode);
- }
- } else
+ return ExperimentSearchByProjectCriteria.createAllExperimentsForAllProjects();
+ }
+ if (experimentCriteriaOrNull.tryGetExperiment() != null)
+ {
+ return null;
+ }
+ BasicProjectIdentifier project = experimentCriteriaOrNull.tryGetProjectIdentifier();
+ if (project != null)
{
- return ScreeningLinkExtractor
- .tryCreateMaterialDetailsLink(material, experimentCriteria);
+ return ExperimentSearchByProjectCriteria.createAllExperimentsForProject(project);
}
+ return ExperimentSearchByProjectCriteria.createAllExperimentsForAllProjects();
}
private static void openImagingMaterialGenericViewer(
@@ -286,22 +287,6 @@ public final class ClientPluginFactory extends AbstractClientPluginFactory<Scree
DispatcherHelper.dispatchNaviEvent(tab);
}
- private static String tryGetExperimentPermId(ExperimentSearchCriteria criteriaOrNull)
- {
- if (criteriaOrNull == null)
- {
- return null;
- }
- SingleExperimentSearchCriteria singleExperiment = criteriaOrNull.tryGetExperiment();
- if (singleExperiment != null)
- {
- return singleExperiment.getExperimentPermId();
- } else
- {
- return null;
- }
- }
-
private static MaterialIdentifier asMaterialIdentifier(
IEntityInformationHolderWithPermId material)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningViewContext.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningViewContext.java
index c6cdaaa0a9a..49d083e5d1b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningViewContext.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningViewContext.java
@@ -11,8 +11,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningCli
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.ExperimentAnalysisSummaryResolver;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.GlobalWellSearchLocatorResolver;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.ImagingMaterialLocatorResolver;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.MaterialFeaturesFromAllExperimentsResolver;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.MaterialReplicaSummaryResolver;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.PlateMetadataBrowserLocatorResolver;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator.WellSearchLocatorResolver;
@@ -52,8 +50,6 @@ public final class ScreeningViewContext extends
handlerRegistry.registerHandler(new WellSearchLocatorResolver(this));
handlerRegistry.registerHandler(new GlobalWellSearchLocatorResolver(this));
handlerRegistry.registerHandler(new ExperimentAnalysisSummaryResolver(this));
- handlerRegistry.registerHandler(new MaterialReplicaSummaryResolver(this));
- handlerRegistry.registerHandler(new MaterialFeaturesFromAllExperimentsResolver(this));
}
public static ScreeningDisplaySettingsManager getTechnologySpecificDisplaySettingsManager(
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 ba24315c542..dc24816f0f9 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
@@ -54,20 +54,21 @@ public class ExperimentAnalysisSummaryGrid extends TypedTableGrid<MaterialFeatur
private static final String PREFIX = GenericConstants.ID_PREFIX
+ "experiment-feature-vector-summary";
- public static final String BROWSER_ID = PREFIX + "_main";
-
- public static final String GRID_ID = PREFIX + TypedTableGrid.GRID_POSTFIX;
+ private static final String BROWSER_ID = PREFIX + "_main";
private final IViewContext<IScreeningClientServiceAsync> screeningViewContext;
private final IEntityInformationHolderWithIdentifier experiment;
+ private final boolean restrictGlobalScopeLinkToProject;
+
public static IDisposableComponent create(
IViewContext<IScreeningClientServiceAsync> viewContext,
- IEntityInformationHolderWithIdentifier experiment)
+ IEntityInformationHolderWithIdentifier experiment,
+ boolean restrictGlobalScopeLinkToProject)
{
- return new ExperimentAnalysisSummaryGrid(viewContext, experiment)
- .asDisposableWithoutToolbar();
+ return new ExperimentAnalysisSummaryGrid(viewContext, experiment,
+ restrictGlobalScopeLinkToProject).asDisposableWithoutToolbar();
}
private ICellListenerAndLinkGenerator<MaterialFeatureVectorSummary> createMaterialReplicaSummaryLinkGenerator()
@@ -87,7 +88,7 @@ public class ExperimentAnalysisSummaryGrid extends TypedTableGrid<MaterialFeatur
ISerializableComparable comparableValue)
{
IEntityInformationHolder material = entity.getMaterial();
- return ScreeningLinkExtractor.tryCreateMaterialDetailsLink(material,
+ return ScreeningLinkExtractor.createMaterialDetailsLink(material,
getExperimentAsSearchCriteria());
}
};
@@ -101,16 +102,19 @@ public class ExperimentAnalysisSummaryGrid extends TypedTableGrid<MaterialFeatur
private ExperimentSearchCriteria getExperimentAsSearchCriteria()
{
- return ExperimentSearchCriteria.createExperiment(experiment);
+ return ExperimentSearchCriteria.createExperiment(experiment,
+ restrictGlobalScopeLinkToProject);
}
ExperimentAnalysisSummaryGrid(IViewContext<IScreeningClientServiceAsync> viewContext,
- final IEntityInformationHolderWithIdentifier experiment)
+ final IEntityInformationHolderWithIdentifier experiment,
+ boolean restrictGlobalScopeLinkToProject)
{
super(viewContext.getCommonViewContext(), BROWSER_ID, true,
DisplayTypeIDGenerator.EXPERIMENT_FEATURE_VECTOR_SUMMARY_SECTION);
this.screeningViewContext = viewContext;
this.experiment = experiment;
+ this.restrictGlobalScopeLinkToProject = restrictGlobalScopeLinkToProject;
ICellListenerAndLinkGenerator<MaterialFeatureVectorSummary> linkGenerator =
createMaterialReplicaSummaryLinkGenerator();
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 1a55399b350..0cee03edc13 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
@@ -34,7 +34,7 @@ public class ExperimentAnalysisSummarySection extends DisposableTabContent
@Override
protected IDisposableComponent createDisposableContent()
{
- return ExperimentAnalysisSummaryGrid.create(screeningViewContext, experiment);
+ return ExperimentAnalysisSummaryGrid.create(screeningViewContext, experiment, false);
}
}
\ 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 5cddaa40882..079d2cbe37d 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
@@ -44,7 +44,7 @@ public class ExperimentAnalysisSummaryViewer
public static void openTab(
final IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- String experimentPermId)
+ String experimentPermId, final boolean restrictGlobalScopeLinkToProject)
{
screeningViewContext.getCommonService().getEntityInformationHolder(EntityKind.EXPERIMENT,
experimentPermId,
@@ -54,14 +54,15 @@ public class ExperimentAnalysisSummaryViewer
protected void process(IEntityInformationHolderWithPermId experiment)
{
TechId experimentId = new TechId(experiment);
- openTab(screeningViewContext, experimentId);
+ openTab(screeningViewContext, experimentId,
+ restrictGlobalScopeLinkToProject);
}
});
}
public static void openTab(
final IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- TechId experimentId)
+ TechId experimentId, final boolean restrictGlobalScopeLinkToProject)
{
screeningViewContext.getCommonService().getExperimentInfo(experimentId,
new AbstractAsyncCallback<Experiment>(screeningViewContext)
@@ -70,7 +71,8 @@ public class ExperimentAnalysisSummaryViewer
protected void process(Experiment result)
{
AbstractTabItemFactory factory =
- createTabFactory(screeningViewContext, result);
+ createTabFactory(screeningViewContext, result,
+ restrictGlobalScopeLinkToProject);
DispatcherHelper.dispatchNaviEvent(factory);
}
});
@@ -78,7 +80,8 @@ public class ExperimentAnalysisSummaryViewer
private static AbstractTabItemFactory createTabFactory(
final IViewContext<IScreeningClientServiceAsync> viewContext,
- final IEntityInformationHolderWithProperties experiment)
+ final IEntityInformationHolderWithProperties experiment,
+ final boolean restrictGlobalScopeLinkToProject)
{
return new AbstractTabItemFactory()
{
@@ -94,15 +97,16 @@ public class ExperimentAnalysisSummaryViewer
@Override
public ITabItem create()
{
- IDisposableComponent tabComponent = createViewer(viewContext, experiment);
+ IDisposableComponent tabComponent =
+ createViewer(viewContext, experiment, restrictGlobalScopeLinkToProject);
return DefaultTabItem.create(getTabTitle(), tabComponent, viewContext);
}
@Override
public String tryGetLink()
{
- return ScreeningLinkExtractor
- .createExperimentAnalysisSummaryBrowserLink(experiment.getPermId());
+ return ScreeningLinkExtractor.createExperimentAnalysisSummaryBrowserLink(
+ experiment.getPermId(), restrictGlobalScopeLinkToProject);
}
@Override
@@ -122,11 +126,13 @@ public class ExperimentAnalysisSummaryViewer
private static IDisposableComponent createViewer(
IViewContext<IScreeningClientServiceAsync> viewContext,
- IEntityInformationHolderWithProperties experiment)
+ IEntityInformationHolderWithProperties experiment,
+ boolean restrictGlobalScopeLinkToProject)
{
String headingText = "Assay " + experiment.getCode();
final IDisposableComponent gridComponent =
- ExperimentAnalysisSummaryGrid.create(viewContext, experiment);
+ ExperimentAnalysisSummaryGrid.create(viewContext, experiment,
+ restrictGlobalScopeLinkToProject);
return MaterialComponentUtils.createExperimentViewer(viewContext, experiment, headingText,
gridComponent);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentWellMaterialBrowserGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentWellMaterialBrowserGrid.java
index 8c2308389bb..20dc5a0417c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentWellMaterialBrowserGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentWellMaterialBrowserGrid.java
@@ -108,23 +108,26 @@ public class ExperimentWellMaterialBrowserGrid extends MaterialBrowserGrid
{
if (editMode == false)
{
- ExperimentSearchCriteria experimentCriteria =
- ExperimentSearchCriteria.createExperiment(experiment);
- ClientPluginFactory.openImagingMaterialViewer(material, experimentCriteria,
- screeningViewContext);
+ ClientPluginFactory.openImagingMaterialViewer(material,
+ createExperimentSearchCriteria(), screeningViewContext);
} else
{
super.showEntityViewer(material, editMode, active);
}
}
+ private ExperimentSearchCriteria createExperimentSearchCriteria()
+ {
+ return ExperimentSearchCriteria.createExperiment(experiment);
+ }
+
@Override
protected BaseEntityModel<Material> createModel(GridRowModel<Material> entity)
{
BaseEntityModel<Material> basicModel = super.createModel(entity);
basicModel.set(ModelDataPropertyNames.link(CommonMaterialColDefKind.CODE.id()),
- ScreeningLinkExtractor.tryCreateMaterialDetailsLink(entity.getOriginalObject(),
- experiment.getIdentifier()));
+ ScreeningLinkExtractor.createMaterialDetailsLink(entity.getOriginalObject(),
+ createExperimentSearchCriteria()));
return basicModel;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImagingMaterialViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImagingMaterialViewer.java
index b22df360e54..5854c2f0432 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImagingMaterialViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImagingMaterialViewer.java
@@ -30,6 +30,7 @@ import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.Gen
import ch.systemsx.cisd.openbis.plugin.generic.client.web.client.application.material.GenericMaterialViewer;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
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.SingleExperimentSearchCriteria;
/**
@@ -87,17 +88,46 @@ public class ImagingMaterialViewer extends GenericMaterialViewer
String experimentPermId = tryGetExperimentPermId();
if (experimentPermId != null)
{
+ boolean restrictGlobalScopeLinkToProject =
+ isRestrictGlobalScopeLinkToProject(experimentCriteriaOrNull);
MaterialReplicaSummarySection replicaSummarySection =
new MaterialReplicaSummarySection(screeningViewContext, material,
- experimentPermId);
+ experimentPermId, restrictGlobalScopeLinkToProject);
sections.add(replicaSummarySection);
}
+ ExperimentSearchByProjectCriteria experimentCriteria = tryConvert(experimentCriteriaOrNull);
MaterialFeaturesFromAllExpermentsSection featuresFromAllExperimentsSection =
- new MaterialFeaturesFromAllExpermentsSection(screeningViewContext, material);
+ new MaterialFeaturesFromAllExpermentsSection(screeningViewContext, material,
+ experimentCriteria);
sections.add(featuresFromAllExperimentsSection);
return sections;
}
+ private static boolean isRestrictGlobalScopeLinkToProject(
+ ExperimentSearchCriteria experimentCriteriaOrNull)
+ {
+
+ if (experimentCriteriaOrNull == null)
+ {
+ return false;
+ } else
+ {
+ return experimentCriteriaOrNull.getRestrictGlobalSearchLinkToProject();
+ }
+ }
+
+ private static ExperimentSearchByProjectCriteria tryConvert(
+ ExperimentSearchCriteria experimentCriteriaOrNull)
+ {
+ if (experimentCriteriaOrNull == null)
+ {
+ return null;
+ } else
+ {
+ return experimentCriteriaOrNull.tryAsSearchByProjectCriteria();
+ }
+ }
+
private String tryGetExperimentPermId()
{
if (experimentCriteriaOrNull != null)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDisambiguationGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDisambiguationGrid.java
index 4ee85f27003..41cb88bc66d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDisambiguationGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialDisambiguationGrid.java
@@ -221,7 +221,7 @@ public class MaterialDisambiguationGrid extends TypedTableGrid<Material>
{
public String tryGetLink(Material material, ISerializableComparable value)
{
- return ScreeningLinkExtractor.tryCreateMaterialDetailsLink(material,
+ return ScreeningLinkExtractor.createMaterialDetailsLink(material,
searchCriteria.getExperimentCriteria());
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsGrid.java
index cc5198251ad..170c59d756e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsGrid.java
@@ -38,8 +38,8 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.D
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.ExperimentReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSimpleFeatureVectorSummary;
-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.ExperimentSearchByProjectCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.grids.MaterialFeatureVectorsFromAllExperimentsGridColumnIDs;
/**
@@ -96,14 +96,16 @@ public class MaterialFeaturesFromAllExperimentsGrid extends
boolean specialKeyPressed)
{
ClientPluginFactory.openImagingExperimentViewer(rowItem
- .getObjectOrNull().getExperiment(), screeningViewContext);
+ .getObjectOrNull().getExperiment(),
+ getRestrictGlobalScopeLinkToProject(), screeningViewContext);
}
public String tryGetLink(MaterialSimpleFeatureVectorSummary entity,
ISerializableComparable value)
{
return ClientPluginFactory.createImagingExperimentViewerLink(
- entity.getExperiment(), screeningViewContext);
+ entity.getExperiment(), getRestrictGlobalScopeLinkToProject(),
+ screeningViewContext);
}
});
}
@@ -126,24 +128,31 @@ public class MaterialFeaturesFromAllExperimentsGrid extends
// in material detail view and the possibility of switching tabs is not
// implemented there.
MaterialReplicaSummaryViewer.openTab(screeningViewContext,
- experimentPermId, new MaterialIdentifier(material));
+ experimentPermId, getRestrictGlobalScopeLinkToProject(),
+ new MaterialIdentifier(material));
}
public String tryGetLink(MaterialSimpleFeatureVectorSummary entity,
ISerializableComparable value)
{
ExperimentSearchCriteria experiment = getExperimentCriteria(entity);
- return ScreeningLinkExtractor.tryCreateMaterialDetailsLink(material,
+ return ScreeningLinkExtractor.createMaterialDetailsLink(material,
experiment);
}
});
}
- private static ExperimentSearchCriteria getExperimentCriteria(
+ private boolean getRestrictGlobalScopeLinkToProject()
+ {
+ return experimentSearchCriteria.tryGetProjectIdentifier() != null;
+ }
+
+ private ExperimentSearchCriteria getExperimentCriteria(
MaterialSimpleFeatureVectorSummary summary)
{
ExperimentReference experimentRef = summary.getExperiment();
- return ExperimentSearchCriteria.createExperiment(experimentRef);
+ return ExperimentSearchCriteria.createExperiment(experimentRef,
+ getRestrictGlobalScopeLinkToProject());
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsViewer.java
index a7c6ebc6be0..ff908a3f943 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExperimentsViewer.java
@@ -24,7 +24,6 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.ITabItem;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpPageIdentifier;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
@@ -85,8 +84,7 @@ public class MaterialFeaturesFromAllExperimentsViewer
@Override
public String getId()
{
- return ScreeningModule.ID
- + ScreeningLinkExtractor.MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS_ACTION
+ return ScreeningModule.ID + "MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS"
+ material.getPermId();
}
@@ -102,20 +100,8 @@ public class MaterialFeaturesFromAllExperimentsViewer
@Override
public String tryGetLink()
{
- String materialCode = material.getCode();
- String materialTypeCode = material.getEntityType().getCode();
- String spaceCodeOrNull = null;
- String projectCodeOrNull = null;
- BasicProjectIdentifier projectIdentifier =
- experimentCriteria.tryGetProjectIdentifier();
- if (projectIdentifier != null)
- {
- spaceCodeOrNull = projectIdentifier.getSpaceCode();
- projectCodeOrNull = projectIdentifier.getProjectCode();
- }
-
- return ScreeningLinkExtractor.createMaterialFeaturesFromAllExperimentsLink(
- materialCode, materialTypeCode, spaceCodeOrNull, projectCodeOrNull);
+ return ScreeningLinkExtractor.createMaterialDetailsLink(material,
+ experimentCriteria.asExtendedCriteria());
}
@Override
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExpermentsSection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExpermentsSection.java
index adc7441b7f1..f1af043ef38 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExpermentsSection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialFeaturesFromAllExpermentsSection.java
@@ -21,22 +21,26 @@ public class MaterialFeaturesFromAllExpermentsSection extends DisposableTabConte
private final IEntityInformationHolderWithIdentifier material;
+ private final ExperimentSearchByProjectCriteria experimentCriteria;
+
public MaterialFeaturesFromAllExpermentsSection(
IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- IEntityInformationHolderWithIdentifier material)
+ IEntityInformationHolderWithIdentifier material,
+ ExperimentSearchByProjectCriteria experimentCriteria)
{
super(screeningViewContext.getMessage(Dict.MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS_SECTION),
screeningViewContext, material);
this.screeningViewContext = screeningViewContext;
this.material = material;
+ this.experimentCriteria = experimentCriteria;
setIds(DisplayTypeIDGenerator.MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS_SECTION);
}
@Override
protected IDisposableComponent createDisposableContent()
{
- return MaterialFeaturesFromAllExperimentsGrid.create(screeningViewContext,
- material, ExperimentSearchByProjectCriteria.createAllExperimentsForAllProjects());
+ return MaterialFeaturesFromAllExperimentsGrid.create(screeningViewContext, material,
+ experimentCriteria);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
index 55c529d44c5..3472dcfb3a5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
@@ -45,8 +45,11 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ID
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.NotScrollableContainer;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ClientPluginFactory;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningDisplayTypeIDGenerator;
@@ -78,19 +81,26 @@ public class MaterialReplicaSummaryComponent
private static final int ONE_IMAGE_SIZE_FACTOR_PX = 60;
public static IDisposableComponent createViewer(
- IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- IEntityInformationHolderWithPermId experiment, Material material)
+ IViewContext<IScreeningClientServiceAsync> screeningViewContext, Experiment experiment,
+ Material material, boolean restrictGlobalScopeLinkToProject)
{
- return new MaterialReplicaSummaryComponent(screeningViewContext).createViewer(experiment,
- material);
+ return new MaterialReplicaSummaryComponent(screeningViewContext,
+ restrictGlobalScopeLinkToProject, experiment).createViewer(material);
}
private final IViewContext<IScreeningClientServiceAsync> screeningViewContext;
+ private final boolean restrictGlobalScopeLinkToProject;
+
+ private final Experiment experiment;
+
private MaterialReplicaSummaryComponent(
- IViewContext<IScreeningClientServiceAsync> screeningViewContext)
+ IViewContext<IScreeningClientServiceAsync> screeningViewContext,
+ boolean restrictGlobalScopeLinkToProject, Experiment experiment)
{
this.screeningViewContext = screeningViewContext;
+ this.restrictGlobalScopeLinkToProject = restrictGlobalScopeLinkToProject;
+ this.experiment = experiment;
}
private class ImagesFoundCallback extends AbstractAsyncCallback<List<WellReplicaImage>>
@@ -299,14 +309,13 @@ public class MaterialReplicaSummaryComponent
return widgetWithListener.asWidget();
}
- private IDisposableComponent createViewer(IEntityInformationHolderWithPermId experiment,
- Material material)
+ private IDisposableComponent createViewer(Material material)
{
final LayoutContainer panel = new LayoutContainer();
panel.setLayout(new RowLayout(Orientation.VERTICAL));
panel.setScrollMode(Scroll.AUTO);
- Widget materialInfo = createMaterialInfo(screeningViewContext, experiment, material);
+ Widget materialInfo = createMaterialInfo(material);
panel.add(materialInfo, new RowData(-1, -1, PropertiesUtil.createHeaderInfoMargin()));
TechId materialTechId = new TechId(material);
@@ -348,14 +357,12 @@ public class MaterialReplicaSummaryComponent
};
}
- private static Widget createMaterialInfo(
- final IViewContext<IScreeningClientServiceAsync> viewContext,
- final IEntityInformationHolderWithPermId experiment, final Material material)
+ private Widget createMaterialInfo(final Material material)
{
LayoutContainer panel = new LayoutContainer();
panel.setLayout(new RowLayout());
- Widget headerWidget = createHeaderWithLinks(viewContext, experiment, material);
+ Widget headerWidget = createHeaderWithLinks(material);
panel.add(headerWidget, PropertiesUtil.createHeaderTitleLayoutData());
LayoutContainer materialPropertiesPanel = createMaterialPropertiesPanel(material);
@@ -364,9 +371,7 @@ public class MaterialReplicaSummaryComponent
return panel;
}
- private static Widget createHeaderWithLinks(
- final IViewContext<IScreeningClientServiceAsync> viewContext,
- final IEntityInformationHolderWithPermId experiment, final Material material)
+ private Widget createHeaderWithLinks(final Material material)
{
LayoutContainer headerPanel = new LayoutContainer();
headerPanel.setLayout(new TableLayout(2));
@@ -380,28 +385,24 @@ public class MaterialReplicaSummaryComponent
// in non-embedded mode there is a separate tab in material detail view with all assays
// information, so we do not display this link there
- if (viewContext.getModel().isEmbeddedMode())
+ if (screeningViewContext.getModel().isEmbeddedMode())
{
- Widget materialInAllAssaysSummaryLink =
- createMaterialInAllAssaysSummaryLink(viewContext, material);
+ Widget materialInAllAssaysSummaryLink = createMaterialInAllAssaysSummaryLink(material);
rightLinksPanel.add(materialInAllAssaysSummaryLink, linkMargins);
}
- Widget assayAnalysisSummaryLink =
- createAssayAnalysisSummaryLink(viewContext, experiment, material);
+ Widget assayAnalysisSummaryLink = createAssayAnalysisSummaryLink(material);
rightLinksPanel.add(assayAnalysisSummaryLink, linkMargins);
headerPanel.add(rightLinksPanel);
return headerPanel;
}
- private static Widget createMaterialInAllAssaysSummaryLink(
- final IViewContext<IScreeningClientServiceAsync> viewContext, final Material material)
+ private Widget createMaterialInAllAssaysSummaryLink(final Material material)
{
- // add link to feature vector summary for the experiment
+ final ExperimentSearchCriteria experimentCriteria = createAllAssaysExperimentCriteria();
String linkUrl =
- ClientPluginFactory.createImagingMaterialViewerLink(material,
- ExperimentSearchCriteria.createAllExperiments(), viewContext);
+ ScreeningLinkExtractor.createMaterialDetailsLink(material, experimentCriteria);
String linkText =
"Find " + MaterialComponentUtils.getMaterialFullName(material, false)
+ " in all assays";
@@ -409,13 +410,27 @@ public class MaterialReplicaSummaryComponent
{
public void onClick(ClickEvent event)
{
- ClientPluginFactory.openImagingMaterialViewer(material,
- ExperimentSearchCriteria.createAllExperiments(), viewContext);
+ ClientPluginFactory.openImagingMaterialViewer(material, experimentCriteria,
+ screeningViewContext);
}
}, linkUrl);
return linkWidget;
}
+ private ExperimentSearchCriteria createAllAssaysExperimentCriteria()
+ {
+ if (restrictGlobalScopeLinkToProject)
+ {
+ Project project = experiment.getProject();
+ BasicProjectIdentifier projectIdentifier =
+ new BasicProjectIdentifier(project.getSpace().getCode(), project.getCode());
+ return ExperimentSearchCriteria.createAllExperimentsForProject(projectIdentifier);
+ } else
+ {
+ return ExperimentSearchCriteria.createAllExperiments();
+ }
+ }
+
private static Html createHeaderTitle(final IEntityInformationHolderWithPermId experiment,
final Material material)
{
@@ -424,20 +439,19 @@ public class MaterialReplicaSummaryComponent
return PropertiesUtil.createHeaderTitle(headingText);
}
- private static Widget createAssayAnalysisSummaryLink(
- final IViewContext<IScreeningClientServiceAsync> viewContext,
- final IEntityInformationHolderWithPermId experiment, final Material material)
+ private Widget createAssayAnalysisSummaryLink(final Material material)
{
// add link to feature vector summary for the experiment
String linkUrl =
- ScreeningLinkExtractor.createExperimentAnalysisSummaryBrowserLink(experiment
- .getPermId());
+ ClientPluginFactory.createImagingExperimentViewerLink(experiment,
+ restrictGlobalScopeLinkToProject, screeningViewContext);
String linkText = "Show assay " + experiment.getCode();
Widget linkWidget = LinkRenderer.getLinkWidget(linkText, new ClickHandler()
{
public void onClick(ClickEvent event)
{
- ClientPluginFactory.openImagingExperimentViewer(experiment, viewContext);
+ ClientPluginFactory.openImagingExperimentViewer(experiment,
+ restrictGlobalScopeLinkToProject, screeningViewContext);
}
}, linkUrl);
return linkWidget;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummarySection.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummarySection.java
index 48b37409b9d..b96b8c2a36a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummarySection.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummarySection.java
@@ -4,8 +4,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAs
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.TabContent;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
@@ -24,17 +23,20 @@ class MaterialReplicaSummarySection extends TabContent
private final String experimentPermId;
+ private final boolean restrictGlobalScopeLinkToProject;
+
private IDisposableComponent viewer;
public MaterialReplicaSummarySection(
IViewContext<IScreeningClientServiceAsync> screeningViewContext, Material material,
- String experimentPermId)
+ String experimentPermId, boolean restrictGlobalScopeLinkToProject)
{
super(screeningViewContext.getMessage(Dict.MATERIAL_REPLICA_SUMMARY_SECTION_TITLE, ""),
screeningViewContext, material);
this.screeningViewContext = screeningViewContext;
this.material = material;
this.experimentPermId = experimentPermId;
+ this.restrictGlobalScopeLinkToProject = restrictGlobalScopeLinkToProject;
setHeaderVisible(false);
setIds(DisplayTypeIDGenerator.REPLICA_SUMMARY_MATERIAL_SECTION);
@@ -43,12 +45,11 @@ class MaterialReplicaSummarySection extends TabContent
@Override
protected void showContent()
{
- screeningViewContext.getCommonService().getEntityInformationHolder(EntityKind.EXPERIMENT,
- experimentPermId,
- new AbstractAsyncCallback<IEntityInformationHolderWithPermId>(screeningViewContext)
+ screeningViewContext.getCommonService().getExperimentInfoByPermId(experimentPermId,
+ new AbstractAsyncCallback<Experiment>(screeningViewContext)
{
@Override
- protected void process(IEntityInformationHolderWithPermId experiment)
+ protected void process(Experiment experiment)
{
setHeading(screeningViewContext.getMessage(
Dict.MATERIAL_REPLICA_SUMMARY_SECTION_TITLE,
@@ -62,11 +63,11 @@ class MaterialReplicaSummarySection extends TabContent
});
}
- private void createAndShowViewer(IEntityInformationHolderWithPermId experiment)
+ private void createAndShowViewer(Experiment experiment)
{
this.viewer =
MaterialReplicaSummaryComponent.createViewer(screeningViewContext, experiment,
- material);
+ material, restrictGlobalScopeLinkToProject);
add(viewer.getComponent());
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryViewer.java
index 4eac08af93f..ac2f43a63f1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryViewer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryViewer.java
@@ -26,13 +26,14 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.help.HelpP
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningModule;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.utils.MaterialComponentUtils;
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.WellSearchCriteria.ExperimentSearchCriteria;
/**
* Opens an independent tab with {@link MaterialReplicaSummaryComponent}.
@@ -47,11 +48,12 @@ public class MaterialReplicaSummaryViewer
* @param material should be enriched with properties
*/
public static void openTab(IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- String experimentPermId, Material material)
+ String experimentPermId, boolean restrictGlobalScopeLinkToProject, Material material)
{
MaterialReplicaSummaryViewer viewer =
- new MaterialReplicaSummaryViewer(screeningViewContext);
- AbstractAsyncCallback<IEntityInformationHolderWithPermId> experimentFoundCallback =
+ new MaterialReplicaSummaryViewer(screeningViewContext,
+ restrictGlobalScopeLinkToProject);
+ AbstractAsyncCallback<Experiment> experimentFoundCallback =
viewer.createExperimentFoundCallback(material);
viewer.fetchExperimentByPermId(experimentPermId, experimentFoundCallback);
}
@@ -60,38 +62,43 @@ public class MaterialReplicaSummaryViewer
* Fetches material and experiment and opens a tab with {@link MaterialReplicaSummaryComponent}.
*/
public static void openTab(IViewContext<IScreeningClientServiceAsync> screeningViewContext,
- String experimentPermId, MaterialIdentifier materialIdentifier)
+ String experimentPermId, boolean restrictGlobalScopeLinkToProject,
+ MaterialIdentifier materialIdentifier)
{
MaterialReplicaSummaryViewer viewer =
- new MaterialReplicaSummaryViewer(screeningViewContext);
- AbstractAsyncCallback<IEntityInformationHolderWithPermId> experimentFoundCallback =
+ new MaterialReplicaSummaryViewer(screeningViewContext,
+ restrictGlobalScopeLinkToProject);
+ AbstractAsyncCallback<Experiment> experimentFoundCallback =
viewer.createExperimentFoundCallback(materialIdentifier);
viewer.fetchExperimentByPermId(experimentPermId, experimentFoundCallback);
}
private final IViewContext<IScreeningClientServiceAsync> screeningViewContext;
+ private final boolean restrictGlobalScopeLinkToProject;
+
private MaterialReplicaSummaryViewer(
- IViewContext<IScreeningClientServiceAsync> screeningViewContext)
+ IViewContext<IScreeningClientServiceAsync> screeningViewContext,
+ boolean restrictGlobalScopeLinkToProject)
{
this.screeningViewContext = screeningViewContext;
+ this.restrictGlobalScopeLinkToProject = restrictGlobalScopeLinkToProject;
}
private void fetchExperimentByPermId(String experimentPermId,
- AbstractAsyncCallback<IEntityInformationHolderWithPermId> experimentFoundCallback)
+ AbstractAsyncCallback<Experiment> experimentFoundCallback)
{
- screeningViewContext.getCommonService().getEntityInformationHolder(EntityKind.EXPERIMENT,
- experimentPermId, experimentFoundCallback);
+ screeningViewContext.getCommonService().getExperimentInfoByPermId(experimentPermId,
+ experimentFoundCallback);
}
// NOTE: material is already fetched
- private AbstractAsyncCallback<IEntityInformationHolderWithPermId> createExperimentFoundCallback(
- final Material material)
+ private AbstractAsyncCallback<Experiment> createExperimentFoundCallback(final Material material)
{
- return new AbstractAsyncCallback<IEntityInformationHolderWithPermId>(screeningViewContext)
+ return new AbstractAsyncCallback<Experiment>(screeningViewContext)
{
@Override
- protected void process(IEntityInformationHolderWithPermId experiment)
+ protected void process(Experiment experiment)
{
openTab(experiment, material);
}
@@ -99,13 +106,13 @@ public class MaterialReplicaSummaryViewer
}
// NOTE: material has to be still fetched
- private AbstractAsyncCallback<IEntityInformationHolderWithPermId> createExperimentFoundCallback(
+ private AbstractAsyncCallback<Experiment> createExperimentFoundCallback(
final MaterialIdentifier materialIdentifier)
{
- return new AbstractAsyncCallback<IEntityInformationHolderWithPermId>(screeningViewContext)
+ return new AbstractAsyncCallback<Experiment>(screeningViewContext)
{
@Override
- protected void process(IEntityInformationHolderWithPermId experiment)
+ protected void process(Experiment experiment)
{
viewContext.getCommonService().getMaterialInformationHolder(materialIdentifier,
new MaterialFoundCallback(experiment));
@@ -116,9 +123,9 @@ public class MaterialReplicaSummaryViewer
private class MaterialFoundCallback extends
AbstractAsyncCallback<IEntityInformationHolderWithPermId>
{
- private final IEntityInformationHolderWithPermId experiment;
+ private final Experiment experiment;
- MaterialFoundCallback(IEntityInformationHolderWithPermId experiment)
+ MaterialFoundCallback(Experiment experiment)
{
super(screeningViewContext);
this.experiment = experiment;
@@ -139,24 +146,22 @@ public class MaterialReplicaSummaryViewer
}
}
- private void openTab(IEntityInformationHolderWithPermId experiment, Material material)
+ private void openTab(Experiment experiment, Material material)
{
AbstractTabItemFactory factory = createTabFactory(experiment, material);
DispatcherHelper.dispatchNaviEvent(factory);
}
- private AbstractTabItemFactory createTabFactory(
- final IEntityInformationHolderWithPermId experiment, final Material material)
+ private AbstractTabItemFactory createTabFactory(final Experiment experiment,
+ final Material material)
{
return new AbstractTabItemFactory()
{
-
@Override
public String getId()
{
- return ScreeningModule.ID
- + ScreeningLinkExtractor.MATERIAL_REPLICA_SUMMARY_ACTION
- + experiment.getCode() + material.getPermId();
+ return ScreeningModule.ID + "MATERIAL_REPLICA_SUMMARY" + experiment.getPermId()
+ + "-" + material.getPermId();
}
@Override
@@ -164,15 +169,18 @@ public class MaterialReplicaSummaryViewer
{
IDisposableComponent tabComponent =
MaterialReplicaSummaryComponent.createViewer(screeningViewContext,
- experiment, material);
+ experiment, material, restrictGlobalScopeLinkToProject);
return DefaultTabItem.create(getTabTitle(), tabComponent, screeningViewContext);
}
@Override
public String tryGetLink()
{
- return ScreeningLinkExtractor.createMaterialReplicaSummaryLink(experiment
- .getPermId(), material.getCode(), material.getEntityType().getCode());
+ ExperimentSearchCriteria experimentCriteria =
+ ExperimentSearchCriteria.createExperiment(experiment,
+ restrictGlobalScopeLinkToProject);
+ return ScreeningLinkExtractor.createMaterialDetailsLink(material,
+ experimentCriteria);
}
@Override
@@ -190,5 +198,4 @@ public class MaterialReplicaSummaryViewer
};
}
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
index f0ebd4f8193..9dbad35db48 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
@@ -425,18 +425,17 @@ public class WellContentDialog extends Dialog
final IEntityInformationHolderWithPermId material)
{
final String href =
- ScreeningLinkExtractor.tryCreateMaterialDetailsLink(material,
- experimentCriteria.getExperimentIdentifier());
+ ScreeningLinkExtractor.createMaterialDetailsLink(material, getExperimentCriteria());
final ClickHandler listener = new ClickHandler()
{
public void onClick(ClickEvent event)
{
WellContentDialog.this.hide();
ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ClientPluginFactory
- .openImagingMaterialViewer(material,
- ExperimentSearchCriteria.createExperiment(experimentCriteria),
+ .openImagingMaterialViewer(material, getExperimentCriteria(),
viewContext);
}
+
};
Anchor link = (Anchor) LinkRenderer.getLinkWidget(material.getCode(), listener, href);
if (viewContext.isSimpleOrEmbeddedMode())
@@ -452,6 +451,11 @@ public class WellContentDialog extends Dialog
return link;
}
+ private ExperimentSearchCriteria getExperimentCriteria()
+ {
+ return ExperimentSearchCriteria.createExperiment(experimentCriteria, false);
+ }
+
private Widget createEntityLink(IEntityInformationHolderWithPermId entity)
{
final ClickHandler listener = new OpenEntityDetailsTabClickListener(entity, viewContext);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
index 9aa497c7870..4f8179277ce 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
@@ -61,6 +61,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetCo
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TypedTableResultSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
@@ -79,7 +80,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.d
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.DatasetImagesReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria;
@@ -362,17 +362,26 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
private static String tryCreateMaterialDetailsLink(WellContent wellContent, Material material)
{
- String experimentIdentifier = wellContent.getExperiment().getIdentifier();
- return ScreeningLinkExtractor.tryCreateMaterialDetailsLink(material, experimentIdentifier);
+ return ScreeningLinkExtractor.createMaterialDetailsLink(material,
+ getExperimentCriteria(wellContent));
}
- private void openImagingMaterialViewer(WellContent wellContent, Material material)
+ private static ExperimentSearchCriteria getExperimentCriteria(WellContent wellContent)
{
- ExperimentReference experiment = wellContent.getExperiment();
- ExperimentSearchCriteria experimentCriteria =
- ExperimentSearchCriteria.createExperiment(experiment);
+ IEntityInformationHolderWithIdentifier experiment = wellContent.getExperiment();
+ return getExperimentCriteria(experiment);
+ }
- ClientPluginFactory.openImagingMaterialViewer(material, experimentCriteria, viewContext);
+ private static ExperimentSearchCriteria getExperimentCriteria(
+ IEntityInformationHolderWithIdentifier experiment)
+ {
+ return ExperimentSearchCriteria.createExperiment(experiment);
+ }
+
+ private void openImagingMaterialViewer(WellContent wellContent, Material material)
+ {
+ ClientPluginFactory.openImagingMaterialViewer(material, getExperimentCriteria(wellContent),
+ viewContext);
}
private void linkExperiment()
@@ -528,16 +537,17 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
ExperimentChooserFieldAdaptor experimentChooser =
ExperimentChooserField.create("", true, null, viewContext.getCommonViewContext());
final ExperimentChooserField chooserField = experimentChooser.getChooserField();
- chooserField.addChosenEntityListener(new IChosenEntityListener<TableModelRowWithObject<Experiment>>()
- {
- public void entityChosen(TableModelRowWithObject<Experiment> row)
- {
- if (row != null)
+ chooserField
+ .addChosenEntityListener(new IChosenEntityListener<TableModelRowWithObject<Experiment>>()
{
- chooseSingleExperiment(chooserField, row.getObjectOrNull());
- }
- }
- });
+ public void entityChosen(TableModelRowWithObject<Experiment> row)
+ {
+ if (row != null)
+ {
+ chooseSingleExperiment(chooserField, row.getObjectOrNull());
+ }
+ }
+ });
chooserField.setEditable(false);
if (experimentCriteriaOrNull != null && experimentCriteriaOrNull.tryGetExperiment() != null)
@@ -567,7 +577,8 @@ public class WellSearchGrid extends TypedTableGrid<WellContent>
new SingleExperimentSearchCriteria(experiment.getId(), experiment.getPermId(),
experiment.getIdentifier());
updateSingleExperimentChooser(chooserField, singleExperiment);
- this.experimentCriteriaOrNull = ExperimentSearchCriteria.createExperiment(singleExperiment);
+ this.experimentCriteriaOrNull =
+ ExperimentSearchCriteria.createExperiment(singleExperiment);
refresh();
}
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 ee700888df8..1755c635664 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
@@ -29,8 +29,11 @@ public class ExperimentAnalysisSummaryResolver extends AbstractViewLocatorResolv
getMandatoryParameter(
locator,
ScreeningLinkExtractor.EXPERIMENT_ANALYSIS_SUMMARY_EXPERIMENT_PERMID_PARAMETER_KEY);
-
- ExperimentAnalysisSummaryViewer.openTab(viewContext, experimentPermId);
+ boolean restrictGlobalScopeLinkToProject =
+ getOptionalBooleanParameter(locator,
+ ScreeningLinkExtractor.RESTRICT_GLOBAL_SEARCH_TO_PROJECT, false);
+ ExperimentAnalysisSummaryViewer.openTab(viewContext, experimentPermId,
+ restrictGlobalScopeLinkToProject);
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ImagingMaterialLocatorResolver.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ImagingMaterialLocatorResolver.java
index 57c52812dbf..47852aec211 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ImagingMaterialLocatorResolver.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/ImagingMaterialLocatorResolver.java
@@ -1,7 +1,5 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator;
-import java.util.Map;
-
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
@@ -9,6 +7,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.Ma
import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocator;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithPermId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
@@ -41,33 +40,44 @@ public class ImagingMaterialLocatorResolver extends MaterialLocatorResolver
assert (EntityKind.MATERIAL.name().equals(locator.tryGetEntity()));
ExperimentIdentifierSearchCriteria experimentCriteriaOrNull =
- tryGetExperimentIdentifierSearchCriteria(locator.getParameters());
+ tryGetExperimentIdentifierSearchCriteria(locator);
openInitialMaterialViewer(extractMaterialIdentifier(locator), experimentCriteriaOrNull);
}
private static ExperimentIdentifierSearchCriteria tryGetExperimentIdentifierSearchCriteria(
- Map<String, String> parameters)
+ ViewLocator locator)
{
+ // one experiment
String experimentIdentifierOrNull =
- parameters
- .get(ScreeningLinkExtractor.MATERIAL_DETAIL_EXPERIMENT_IDENT_PARAMETER_KEY);
- if (experimentIdentifierOrNull == null)
+ getOptionalParameter(locator,
+ ScreeningLinkExtractor.MATERIAL_DETAIL_EXPERIMENT_IDENT_PARAMETER_KEY);
+ if (experimentIdentifierOrNull != null)
{
- String searchAllExp =
- parameters
- .get(ScreeningLinkExtractor.MATERIAL_DETAIL_SEARCH_ALL_EXPERIMENTS_PARAMETER_KEY);
- if (StringUtils.isBlank(searchAllExp) == false
- && searchAllExp.equalsIgnoreCase("false") == false)
- {
- return ExperimentIdentifierSearchCriteria.createSearchAll();
- } else
- {
- return null;
- }
- } else
+ boolean restrictGlobalSearchToProject =
+ getOptionalBooleanParameter(locator,
+ ScreeningLinkExtractor.RESTRICT_GLOBAL_SEARCH_TO_PROJECT, false);
+ return ExperimentIdentifierSearchCriteria.createExperimentScope(
+ experimentIdentifierOrNull, restrictGlobalSearchToProject);
+ }
+ // project
+ String space = getOptionalParameter(locator, ScreeningLinkExtractor.SPACE_CODE_KEY);
+ String project = getOptionalParameter(locator, ScreeningLinkExtractor.PROJECT_CODE_KEY);
+ if (StringUtils.isBlank(space) == false && StringUtils.isBlank(project) == false)
{
- return new ExperimentIdentifierSearchCriteria(experimentIdentifierOrNull);
+ return ExperimentIdentifierSearchCriteria
+ .createProjectScope(new BasicProjectIdentifier(space, project));
}
+ // all experiments
+ boolean searchAllExp =
+ getOptionalBooleanParameter(
+ locator,
+ ScreeningLinkExtractor.MATERIAL_DETAIL_SEARCH_ALL_EXPERIMENTS_PARAMETER_KEY,
+ false);
+ if (searchAllExp)
+ {
+ return ExperimentIdentifierSearchCriteria.createSearchAll();
+ }
+ return null;
}
/**
@@ -87,15 +97,15 @@ public class ImagingMaterialLocatorResolver extends MaterialLocatorResolver
{
private final IViewContext<IScreeningClientServiceAsync> viewContext;
- private final ExperimentIdentifierSearchCriteria experimentCriteriaOrNull;
+ private final ExperimentIdentifierSearchCriteria scopeOrNull;
private OpenEntityDetailsTabCallback(
final IViewContext<IScreeningClientServiceAsync> viewContext,
- ExperimentIdentifierSearchCriteria experimentCriteriaOrNull)
+ ExperimentIdentifierSearchCriteria scopeOrNull)
{
super(viewContext);
this.viewContext = viewContext;
- this.experimentCriteriaOrNull = experimentCriteriaOrNull;
+ this.scopeOrNull = scopeOrNull;
}
//
@@ -108,19 +118,25 @@ public class ImagingMaterialLocatorResolver extends MaterialLocatorResolver
@Override
protected final void process(final IEntityInformationHolderWithPermId material)
{
- if (experimentCriteriaOrNull == null)
+ if (scopeOrNull == null)
{
openImagingMaterialViewer(material, null);
} else
{
- if (experimentCriteriaOrNull.searchAllExperiments())
+ String experimentIdentifier = scopeOrNull.tryGetExperimentIdentifier();
+ BasicProjectIdentifier project = scopeOrNull.tryGetProject();
+ if (experimentIdentifier != null)
+ {
+ fetchExperimentAndShowLocations(material, experimentIdentifier);
+ } else if (project != null)
{
openImagingMaterialViewer(material,
- ExperimentSearchCriteria.createAllExperiments());
+ ExperimentSearchCriteria
+ .createAllExperimentsForProject(project));
} else
{
- fetchExperimentAndShowLocations(material,
- experimentCriteriaOrNull.tryGetExperimentIdentifier());
+ openImagingMaterialViewer(material,
+ ExperimentSearchCriteria.createAllExperiments());
}
}
}
@@ -135,7 +151,9 @@ public class ImagingMaterialLocatorResolver extends MaterialLocatorResolver
protected void process(Experiment experiment)
{
ExperimentSearchCriteria experimentCriteria =
- ExperimentSearchCriteria.createExperiment(experiment);
+ ExperimentSearchCriteria.createExperiment(
+ experiment,
+ scopeOrNull.getRestrictGlobalSearchLinkToProject());
openImagingMaterialViewer(material, experimentCriteria);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/MaterialFeaturesFromAllExperimentsResolver.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/MaterialFeaturesFromAllExperimentsResolver.java
deleted file mode 100644
index 1f8d457fb30..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/MaterialFeaturesFromAllExperimentsResolver.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator;
-
-import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor.MATERIAL_CODE_KEY;
-import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor.MATERIAL_TYPE_CODE_KEY;
-import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor.PROJECT_CODE_KEY;
-import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor.SPACE_CODE_KEY;
-
-import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.AbstractViewLocatorResolver;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.MaterialFeaturesFromAllExperimentsViewer;
-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.WellSearchCriteria.ExperimentSearchByProjectCriteria;
-
-/**
- * Locator resolver for material summary from all experiments.
- *
- * @author Kaloyan Enimanev
- */
-public class MaterialFeaturesFromAllExperimentsResolver extends AbstractViewLocatorResolver
-{
- private final IViewContext<IScreeningClientServiceAsync> viewContext;
-
- public MaterialFeaturesFromAllExperimentsResolver(
- IViewContext<IScreeningClientServiceAsync> viewContext)
- {
- super(ScreeningLinkExtractor.MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS_ACTION);
- this.viewContext = viewContext;
- }
-
- public void resolve(final ViewLocator locator) throws UserFailureException
- {
- String materialCode = getMandatoryParameter(locator, MATERIAL_CODE_KEY);
-
- String materialTypeCode = getMandatoryParameter(locator, MATERIAL_TYPE_CODE_KEY);
-
- MaterialIdentifier materialIdentifier =
- new MaterialIdentifier(materialCode, materialTypeCode);
-
- String projectCodeOrNull = getOptionalParameter(locator, PROJECT_CODE_KEY);
- String spaceCodeOrNull = getOptionalParameter(locator, SPACE_CODE_KEY);
-
-
- ExperimentSearchByProjectCriteria experimentCriteria = null;
- if (StringUtils.isBlank(projectCodeOrNull) || StringUtils.isBlank(spaceCodeOrNull))
- {
- experimentCriteria =
- ExperimentSearchByProjectCriteria.createAllExperimentsForAllProjects();
- } else
- {
- BasicProjectIdentifier projectIdentifier =
- new BasicProjectIdentifier(spaceCodeOrNull, projectCodeOrNull);
- experimentCriteria =
- ExperimentSearchByProjectCriteria
- .createAllExperimentsForProject(projectIdentifier);
- }
-
- MaterialFeaturesFromAllExperimentsViewer.openTab(viewContext, materialIdentifier,
- experimentCriteria);
-
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/MaterialReplicaSummaryResolver.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/MaterialReplicaSummaryResolver.java
deleted file mode 100644
index 686a9e59190..00000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/MaterialReplicaSummaryResolver.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.locator;
-
-import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor.MATERIAL_REPLICA_SUMMARY_EXPERIMENT_PERM_ID_KEY;
-import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor.MATERIAL_CODE_KEY;
-import static ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor.MATERIAL_TYPE_CODE_KEY;
-
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.AbstractViewLocatorResolver;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocator;
-import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.MaterialReplicaSummaryViewer;
-import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
-
-/**
- * Locator resolver for material replica summary view.
- *
- * @author Kaloyan Enimanev
- */
-public class MaterialReplicaSummaryResolver extends AbstractViewLocatorResolver
-{
- private final IViewContext<IScreeningClientServiceAsync> viewContext;
-
- public MaterialReplicaSummaryResolver(IViewContext<IScreeningClientServiceAsync> viewContext)
- {
- super(ScreeningLinkExtractor.MATERIAL_REPLICA_SUMMARY_ACTION);
- this.viewContext = viewContext;
- }
-
- public void resolve(final ViewLocator locator) throws UserFailureException
- {
- String experimentPermId =
- getMandatoryParameter(locator, MATERIAL_REPLICA_SUMMARY_EXPERIMENT_PERM_ID_KEY);
-
- String materialCode =
- getMandatoryParameter(locator, MATERIAL_CODE_KEY);
-
- String materialTypeCode =
- getMandatoryParameter(locator, MATERIAL_TYPE_CODE_KEY);
-
- MaterialIdentifier materialIdentifier =
- new MaterialIdentifier(materialCode, materialTypeCode);
-
- MaterialReplicaSummaryViewer.openTab(viewContext, experimentPermId, materialIdentifier);
-
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/WellSearchLocatorResolver.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/WellSearchLocatorResolver.java
index e106ce6684b..3a4a7226536 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/WellSearchLocatorResolver.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/locator/WellSearchLocatorResolver.java
@@ -6,6 +6,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.Ab
import ch.systemsx.cisd.openbis.generic.client.web.client.application.locator.ViewLocator;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.URLListEncoder;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.WellSearchGrid;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ui.columns.specific.ScreeningLinkExtractor;
@@ -34,6 +35,9 @@ public class WellSearchLocatorResolver extends AbstractViewLocatorResolver
String experimentPermId =
getOptionalParameter(locator,
ScreeningLinkExtractor.WELL_SEARCH_EXPERIMENT_PERM_ID_PARAMETER_KEY);
+ String projectCode = getOptionalParameter(locator, ScreeningLinkExtractor.PROJECT_CODE_KEY);
+ String spaceCode = getOptionalParameter(locator, ScreeningLinkExtractor.SPACE_CODE_KEY);
+
String materialCodesOrProperties =
getMandatoryParameter(locator,
ScreeningLinkExtractor.WELL_SEARCH_MATERIAL_ITEMS_PARAMETER_KEY);
@@ -56,8 +60,19 @@ public class WellSearchLocatorResolver extends AbstractViewLocatorResolver
MaterialSearchCriteria.create(materialCodesCriteria);
if (StringUtils.isBlank(experimentPermId))
{
- WellSearchGrid.openTab(viewContext, ExperimentSearchCriteria.createAllExperiments(),
- materialSearchCriteria, showCombinedResults);
+ ExperimentSearchCriteria criteria;
+ if (StringUtils.isBlank(projectCode) || StringUtils.isBlank(spaceCode))
+ {
+ criteria = ExperimentSearchCriteria.createAllExperiments();
+ } else
+ {
+ criteria =
+ ExperimentSearchCriteria
+ .createAllExperimentsForProject(new BasicProjectIdentifier(
+ spaceCode, projectCode));
+ }
+ WellSearchGrid.openTab(viewContext, criteria, materialSearchCriteria,
+ showCombinedResults);
} else
{
WellSearchGrid.openTab(viewContext, experimentPermId, materialSearchCriteria,
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 c82d6ac543a..c859c699825 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
@@ -16,7 +16,6 @@
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;
@@ -24,6 +23,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.dto.ExperimentIdentifierSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
@@ -52,7 +52,7 @@ public class ScreeningLinkExtractor extends LinkExtractor
public final static String WELL_SEARCH_ACTION = "WELL_SEARCH";
- /** If not given then all experiments are searched. */
+ /** If not given then all experiments or experiments in the specified project are searched. */
public final static String WELL_SEARCH_EXPERIMENT_PERM_ID_PARAMETER_KEY = "experimentPermId";
public final static String WELL_SEARCH_IS_EXACT_PARAMETER_KEY = "isExactSearch";
@@ -72,21 +72,19 @@ public class ScreeningLinkExtractor extends LinkExtractor
public final static String EXPERIMENT_ANALYSIS_SUMMARY_EXPERIMENT_PERMID_PARAMETER_KEY =
"experimentPermId";
- public final static String MATERIAL_REPLICA_SUMMARY_ACTION = "MATERIAL_REPLICA_SUMMARY";
-
public final static String MATERIAL_REPLICA_SUMMARY_EXPERIMENT_PERM_ID_KEY = "experimentPermId";
public final static String MATERIAL_CODE_KEY = "materialCode";
public final static String MATERIAL_TYPE_CODE_KEY = "materialTypeCode";
- public final static String MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS_ACTION =
- "MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS";
-
public final static String PROJECT_CODE_KEY = "projectCode";
public final static String SPACE_CODE_KEY = "spaceCode";
+ // false by default
+ public static final String RESTRICT_GLOBAL_SEARCH_TO_PROJECT = "restrictGlobalSearchToProject";
+
public static final String createPlateMetadataBrowserLink(String platePermId)
{
URLMethodWithParameters url = new URLMethodWithParameters("");
@@ -95,46 +93,17 @@ public class ScreeningLinkExtractor extends LinkExtractor
return tryPrint(url);
}
- public static final String createExperimentAnalysisSummaryBrowserLink(String experimentPermId)
+ public static final String createExperimentAnalysisSummaryBrowserLink(String experimentPermId,
+ boolean restrictGlobalScopeLinkToProject)
{
URLMethodWithParameters url = new URLMethodWithParameters("");
url.addParameter(BasicConstant.LOCATOR_ACTION_PARAMETER, EXPERIMENT_ANALYSIS_SUMMARY_ACTION);
url.addParameter(EXPERIMENT_ANALYSIS_SUMMARY_EXPERIMENT_PERMID_PARAMETER_KEY,
experimentPermId);
- return tryPrint(url);
- }
-
- public static final String createMaterialReplicaSummaryLink(String experimentPermId,
- String materialCode, String materialTypeCode)
- {
- URLMethodWithParameters url = new URLMethodWithParameters("");
- url.addParameter(BasicConstant.LOCATOR_ACTION_PARAMETER, MATERIAL_REPLICA_SUMMARY_ACTION);
- url.addParameter(MATERIAL_REPLICA_SUMMARY_EXPERIMENT_PERM_ID_KEY, experimentPermId);
- url.addParameter(MATERIAL_CODE_KEY, materialCode);
- url.addParameter(MATERIAL_TYPE_CODE_KEY, materialTypeCode);
- return tryPrint(url);
- }
-
- public static final String createMaterialFeaturesFromAllExperimentsLink(String materialCode,
- String materialTypeCode)
- {
- return createMaterialFeaturesFromAllExperimentsLink(materialCode, materialTypeCode, null,
- null);
- }
-
- public static final String createMaterialFeaturesFromAllExperimentsLink(String materialCode,
- String materialTypeCode, String spaceCodeOrNull, String projectCodeOrNull)
- {
- URLMethodWithParameters url = new URLMethodWithParameters("");
- url.addParameter(BasicConstant.LOCATOR_ACTION_PARAMETER,
- MATERIAL_FEATURES_FROM_ALL_EXPERIMENTS_ACTION);
- url.addParameter(MATERIAL_CODE_KEY, materialCode);
- url.addParameter(MATERIAL_TYPE_CODE_KEY, materialTypeCode);
- if (false == StringUtils.isBlank(spaceCodeOrNull)
- && false == StringUtils.isBlank(projectCodeOrNull))
+ if (restrictGlobalScopeLinkToProject)
{
- url.addParameter(SPACE_CODE_KEY, spaceCodeOrNull);
- url.addParameter(PROJECT_CODE_KEY, projectCodeOrNull);
+ url.addParameterWithoutEncoding(RESTRICT_GLOBAL_SEARCH_TO_PROJECT,
+ restrictGlobalScopeLinkToProject);
}
return tryPrint(url);
}
@@ -154,71 +123,22 @@ public class ScreeningLinkExtractor extends LinkExtractor
materialCodesOrProperties, showCombinedResults);
}
- public static String createWellsSearchLink(ExperimentSearchCriteria experimentSearchCriteria,
+ public static String createWellsSearchLink(ExperimentSearchCriteria experimentCriteria,
MaterialSearchCodesCriteria materialCodesCriteria, Boolean showCombinedResults)
- {
- ExperimentPermIdSearchCriteria experimentCriteria =
- convertToPermIdExperimentCriteria(experimentSearchCriteria);
- return createWellsSearchLink(experimentCriteria, materialCodesCriteria, showCombinedResults);
- }
-
- private static class ExperimentPermIdSearchCriteria
- {
- public static ExperimentPermIdSearchCriteria createSearchAll()
- {
- return new ExperimentPermIdSearchCriteria(null);
- }
-
- // if null, all experiments are taken into account
- private final String experimentPermIdOrNull;
-
- public ExperimentPermIdSearchCriteria(String experimentPermIdOrNull)
- {
- this.experimentPermIdOrNull = experimentPermIdOrNull;
- }
-
- public String tryGetExperimentPermId()
- {
- return experimentPermIdOrNull;
- }
- }
-
- private static ExperimentPermIdSearchCriteria convertToPermIdExperimentCriteria(
- ExperimentSearchCriteria experimentSearchCriteria)
- {
- SingleExperimentSearchCriteria expOrNull = experimentSearchCriteria.tryGetExperiment();
- if (expOrNull == null)
- {
- return ExperimentPermIdSearchCriteria.createSearchAll();
- } else
- {
- return new ExperimentPermIdSearchCriteria(expOrNull.getExperimentPermId());
- }
- }
-
- private static ExperimentIdentifierSearchCriteria convertToIdentifierExperimentCriteria(
- ExperimentSearchCriteria experimentSearchCriteria)
- {
- SingleExperimentSearchCriteria experiment = experimentSearchCriteria.tryGetExperiment();
- if (experiment != null)
- {
- return new ExperimentIdentifierSearchCriteria(experiment.getExperimentIdentifier());
- } else
- {
- return ExperimentIdentifierSearchCriteria.createSearchAll();
- }
- }
-
- public static String createWellsSearchLink(
- final ExperimentPermIdSearchCriteria experimentCriteria,
- final MaterialSearchCodesCriteria materialCodesCriteria, boolean showCombinedResults)
{
URLMethodWithParameters url = new URLMethodWithParameters("");
url.addParameter(BasicConstant.LOCATOR_ACTION_PARAMETER, WELL_SEARCH_ACTION);
- if (false == StringUtils.isBlank(experimentCriteria.tryGetExperimentPermId()))
+ SingleExperimentSearchCriteria experiment = experimentCriteria.tryGetExperiment();
+ BasicProjectIdentifier project = experimentCriteria.tryGetProjectIdentifier();
+ if (experiment != null)
{
url.addParameter(WELL_SEARCH_EXPERIMENT_PERM_ID_PARAMETER_KEY,
- experimentCriteria.tryGetExperimentPermId());
+ experiment.getExperimentPermId());
+ }
+ if (project != null)
+ {
+ url.addParameterWithoutEncoding(SPACE_CODE_KEY, project.getSpaceCode());
+ url.addParameterWithoutEncoding(PROJECT_CODE_KEY, project.getProjectCode());
}
url.addParameter(WELL_SEARCH_IS_EXACT_PARAMETER_KEY,
materialCodesCriteria.isExactMatchOnly());
@@ -232,38 +152,49 @@ public class ScreeningLinkExtractor extends LinkExtractor
return tryPrint(url);
}
- /** Creates a link for material detail view where a single experiment is chosen */
- public static final String tryCreateMaterialDetailsLink(IEntityInformationHolder material,
- String experimentIdentifier)
+ private static ExperimentIdentifierSearchCriteria convertToIdentifierExperimentCriteria(
+ ExperimentSearchCriteria experimentSearchCriteria)
{
- assert experimentIdentifier != null : "experimentIdentifier is null";
- return tryCreateMaterialDetailsLink(material, new ExperimentIdentifierSearchCriteria(
- experimentIdentifier));
+ SingleExperimentSearchCriteria experiment = experimentSearchCriteria.tryGetExperiment();
+ BasicProjectIdentifier project = experimentSearchCriteria.tryGetProjectIdentifier();
+ if (experiment != null)
+ {
+ return ExperimentIdentifierSearchCriteria.createExperimentScope(
+ experiment.getExperimentIdentifier(),
+ experimentSearchCriteria.getRestrictGlobalSearchLinkToProject());
+ } else if (project != null)
+ {
+ return ExperimentIdentifierSearchCriteria.createProjectScope(project);
+ } else
+ {
+ return ExperimentIdentifierSearchCriteria.createSearchAll();
+ }
}
/**
- * Creates a link for material detail.
+ * Creates a link for material detail view.
*
* @param experimentCriteriaOrNull if null, no search for data about locations of the material
* takes place. Otherwise the search is performed in all or a single experiment.
*/
- public static final String tryCreateMaterialDetailsLink(IEntityInformationHolder material,
+ public static final String createMaterialDetailsLink(IEntityInformationHolder material,
ExperimentIdentifierSearchCriteria experimentCriteriaOrNull)
{
URLMethodWithParameters url =
- tryCreateMaterialDetailsLink(material.getCode(),
- material.getEntityType().getCode(), experimentCriteriaOrNull);
+ createMaterialDetailsLink(material.getCode(), material.getEntityType().getCode(),
+ experimentCriteriaOrNull);
return tryPrint(url);
}
- private static final URLMethodWithParameters tryCreateMaterialDetailsLink(String materialCode,
+ private static final URLMethodWithParameters createMaterialDetailsLink(String materialCode,
String materialTypeCode, ExperimentIdentifierSearchCriteria experimentCriteriaOrNull)
{
- if (materialCode == null || materialTypeCode == null)
- {
- return null;
- }
+ assert materialCode != null;
+ assert materialTypeCode != null;
+
URLMethodWithParameters url = tryCreateMaterialLink(materialCode, materialTypeCode);
+ assert url != null : "url is null";
+
if (experimentCriteriaOrNull != null)
{
if (experimentCriteriaOrNull.searchAllExperiments())
@@ -272,24 +203,37 @@ public class ScreeningLinkExtractor extends LinkExtractor
MATERIAL_DETAIL_SEARCH_ALL_EXPERIMENTS_PARAMETER_VALUE);
} else
{
- // We know that experiment identifier cannot contain characters that should be
- // encoded
- // apart from '/'. Encoding '/' makes the URL less readable and on the other hand
- // leaving it as it is doesn't cause us any problems.
- url.addParameterWithoutEncoding(MATERIAL_DETAIL_EXPERIMENT_IDENT_PARAMETER_KEY,
- StringEscapeUtils.unescapeHtml(experimentCriteriaOrNull
- .tryGetExperimentIdentifier()));
+ BasicProjectIdentifier project = experimentCriteriaOrNull.tryGetProject();
+ if (project != null)
+ {
+ url.addParameterWithoutEncoding(SPACE_CODE_KEY, project.getSpaceCode());
+ url.addParameterWithoutEncoding(PROJECT_CODE_KEY, project.getProjectCode());
+ } else
+ {
+ // We know that experiment identifier cannot contain characters that should be
+ // encoded
+ // apart from '/'. Encoding '/' makes the URL less readable and on the other
+ // hand
+ // leaving it as it is doesn't cause us any problems.
+ url.addParameterWithoutEncoding(MATERIAL_DETAIL_EXPERIMENT_IDENT_PARAMETER_KEY,
+ StringEscapeUtils.unescapeHtml(experimentCriteriaOrNull
+ .tryGetExperimentIdentifier()));
+ if (experimentCriteriaOrNull.getRestrictGlobalSearchLinkToProject())
+ {
+ url.addParameterWithoutEncoding(RESTRICT_GLOBAL_SEARCH_TO_PROJECT, "true");
+ }
+ }
}
}
return url;
}
- public static String tryCreateMaterialDetailsLink(IEntityInformationHolder material,
+ public static String createMaterialDetailsLink(IEntityInformationHolder material,
ExperimentSearchCriteria experimentSearchCriteria)
{
ExperimentIdentifierSearchCriteria experimentCriteria =
convertToIdentifierExperimentCriteria(experimentSearchCriteria);
- return tryCreateMaterialDetailsLink(material, experimentCriteria);
+ return createMaterialDetailsLink(material, experimentCriteria);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/dto/ExperimentIdentifierSearchCriteria.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/dto/ExperimentIdentifierSearchCriteria.java
index 58de6a1ea07..187b65ce721 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/dto/ExperimentIdentifierSearchCriteria.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/dto/ExperimentIdentifierSearchCriteria.java
@@ -17,25 +17,47 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.dto;
import ch.systemsx.cisd.common.shared.basic.utils.StringUtils;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
/**
* Allows to search in one experiment (given by identifier) or in all of them.
*
* @author Tomasz Pylak
*/
+// TODO 2011-06-07, Tomasz Pylak: rename to MaterialDetailViewScope
public class ExperimentIdentifierSearchCriteria
{
public static ExperimentIdentifierSearchCriteria createSearchAll()
{
- return new ExperimentIdentifierSearchCriteria(null);
+ return new ExperimentIdentifierSearchCriteria(null, null, false);
+ }
+
+ public static ExperimentIdentifierSearchCriteria createProjectScope(
+ BasicProjectIdentifier project)
+ {
+ return new ExperimentIdentifierSearchCriteria(null, project, false);
+ }
+
+ public static ExperimentIdentifierSearchCriteria createExperimentScope(
+ String experimentIdentifier, boolean restrictGlobalScopeLinkToProject)
+ {
+ return new ExperimentIdentifierSearchCriteria(experimentIdentifier, null,
+ restrictGlobalScopeLinkToProject);
}
// if null, all experiments are taken into account
private final String experimentIdentifierOrNull;
- public ExperimentIdentifierSearchCriteria(String experimentIdentifierOrNull)
+ private final BasicProjectIdentifier projectOrNull;
+
+ private final boolean restrictGlobalScopeLinkToProject;
+
+ private ExperimentIdentifierSearchCriteria(String experimentIdentifierOrNull,
+ BasicProjectIdentifier projectOrNull, boolean restrictGlobalScopeLinkToProject)
{
this.experimentIdentifierOrNull = experimentIdentifierOrNull;
+ this.projectOrNull = projectOrNull;
+ this.restrictGlobalScopeLinkToProject = restrictGlobalScopeLinkToProject;
}
public String tryGetExperimentIdentifier()
@@ -43,9 +65,27 @@ public class ExperimentIdentifierSearchCriteria
return experimentIdentifierOrNull;
}
+ /**
+ * Valid only if experiment identifier is present ({@link #tryGetExperimentIdentifier} is not
+ * null).<br>
+ * It determines the behavior of the link from material detail view in a single experiment
+ * context to the material detail view in 'global' context. If this parameter is true, the
+ * context will be the project to which the current experiment belongs, otherwise the context
+ * will be switched to all experiments.
+ */
+ public boolean getRestrictGlobalSearchLinkToProject()
+ {
+ return restrictGlobalScopeLinkToProject;
+ }
+
+ public BasicProjectIdentifier tryGetProject()
+ {
+ return projectOrNull;
+ }
+
public boolean searchAllExperiments()
{
- return StringUtils.isBlank(experimentIdentifierOrNull);
+ return StringUtils.isBlank(experimentIdentifierOrNull) && projectOrNull == null;
}
}
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 7941bbd2ec5..cb7254342b1 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -49,6 +49,7 @@ import ch.systemsx.cisd.openbis.generic.server.plugin.ISampleTypeSlaveServerPlug
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListMaterialCriteria;
@@ -317,21 +318,32 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
Session session = getSession(sessionToken);
// NOTE: we want the settings to be passed form the client in future
MaterialSummarySettings settings = createDefaultSettings();
-
- TechId projectTechIdOrNull;
- if (experimentCriteria.isAllExperiments()) {
- projectTechIdOrNull = null;
- } else {
- ProjectIdentifier projectIdentifier =
- new ProjectIdentifier(experimentCriteria.tryGetProjectIdentifier());
- Project project = commonServer.getProjectInfo(sessionToken, projectIdentifier);
- projectTechIdOrNull = new TechId(project);
- }
+
+ TechId projectTechIdOrNull = tryFetchProjectId(sessionToken, experimentCriteria);
return MaterialAllAssaysFeatureVectorSummaryLoader.loadMaterialFeatureVectorsFromAllAssays(
session, businessObjectFactory, getDAOFactory(), materialId, projectTechIdOrNull,
settings);
}
+ private TechId tryFetchProjectId(String sessionToken,
+ WellSearchCriteria.ExperimentSearchByProjectCriteria experimentCriteria)
+ {
+ if (experimentCriteria == null || experimentCriteria.isAllExperiments())
+ {
+ return null;
+ } else
+ {
+ return fetchProjectId(sessionToken, experimentCriteria.tryGetProjectIdentifier());
+ }
+ }
+
+ private TechId fetchProjectId(String sessionToken, BasicProjectIdentifier basicProjectIdentifier)
+ {
+ ProjectIdentifier projectIdentifier = new ProjectIdentifier(basicProjectIdentifier);
+ Project project = commonServer.getProjectInfo(sessionToken, projectIdentifier);
+ return new TechId(project);
+ }
+
public static MaterialSummarySettings createDefaultSettings()
{
MaterialSummarySettings settings = new MaterialSummarySettings();
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 20b378faf39..fc63e1dd5ee 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
@@ -74,6 +74,15 @@ public interface IScreeningQuery extends BaseQuery
public DataIterator<WellContentQueryResult> getPlateLocationsForMaterialId(long materialId,
long experimentId);
+ /**
+ * @return well locations which are connected to a given material (e.g. gene) and belong to the
+ * experiments within a given project.
+ */
+ @Select(sql = WELLS_FOR_MATERIAL_ID_SELECT
+ + " where well_material.id = ?{1} and spaces.code = ?{2} and projects.code = ?{3}")
+ public DataIterator<WellContentQueryResult> getPlateLocationsForMaterialId(long materialId,
+ String spaceCode, String projectCode);
+
/**
* @return well locations which are connected to a given material (e.g. gene) with the specified
* id.
@@ -90,6 +99,18 @@ public interface IScreeningQuery extends BaseQuery
public DataIterator<WellContentQueryResult> getPlateLocationsForMaterialAndProjectIds(
long materialId, long projectId);
+ /**
+ * @return well locations which belong to a parent plate connected to any experiment in the
+ * specified project. Each well will have a material property (e.g. gene) with one of
+ * the specified codes. The connected material will have one of the specified types.
+ */
+ @Select(sql = WELLS_FOR_MATERIAL_ID_SELECT + " where well_material.id = any(?{1}) and "
+ + "well_material_type.code = any(?{2}) and spaces.code = ?{3} and projects.code = ?{4}", parameterBindings =
+ { LongArrayMapper.class, StringArrayMapper.class, TypeMapper.class /* default mapper */,
+ TypeMapper.class })
+ public DataIterator<WellContentQueryResult> getPlateLocationsForMaterialCodesInProject(
+ long[] materialIds, String[] materialTypeCodes, String spaceCode, String projectCode);
+
/**
* @return well locations which belong to a parent plate connected to a specified experiment.
* Each well will have a material property (e.g. gene) with one of the specified codes.
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 1337d3c2f4e..2fd5caa4e82 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
@@ -40,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMater
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchAssociationCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriterion;
@@ -736,14 +737,18 @@ public class WellContentLoader extends AbstractContentLoader
Iterable<WellContentQueryResult> locations;
MaterialSearchCriteria materialSearchCriteria =
materialCriteria.getMaterialSearchCriteria();
- ExperimentSearchCriteria experiment = materialCriteria.getExperimentCriteria();
+
+ ExperimentSearchCriteria experimentCriteria =
+ materialCriteria.getExperimentCriteria();
+ SingleExperimentSearchCriteria experimentOrNull = experimentCriteria.tryGetExperiment();
+ BasicProjectIdentifier projectOrNull = experimentCriteria.tryGetProjectIdentifier();
+
IScreeningQuery dao = createDAO(daoFactory);
if (materialSearchCriteria.tryGetMaterialCodesOrProperties() != null)
{
MaterialSearchCodesCriteria codesCriteria =
materialSearchCriteria.tryGetMaterialCodesOrProperties();
- Long expId = tryGetExperimentId(experiment);
long start = System.currentTimeMillis();
long[] materialIds = findMaterialIds(codesCriteria);
@@ -753,28 +758,39 @@ public class WellContentLoader extends AbstractContentLoader
abbreviate(materialIds, 100)));
start = System.currentTimeMillis();
- if (expId == null)
+ if (experimentOrNull != null)
{
locations =
- dao.getPlateLocationsForMaterialCodes(materialIds,
- codesCriteria.getMaterialTypeCodes());
+ dao.getPlateLocationsForMaterialCodes(materialIds, codesCriteria
+ .getMaterialTypeCodes(), experimentOrNull.getExperimentId().getId());
+ } else if (projectOrNull != null)
+ {
+ locations =
+ dao.getPlateLocationsForMaterialCodesInProject(materialIds,
+ codesCriteria.getMaterialTypeCodes(), projectOrNull.getSpaceCode(),
+ projectOrNull.getProjectCode());
} else
{
locations =
dao.getPlateLocationsForMaterialCodes(materialIds,
- codesCriteria.getMaterialTypeCodes(), expId);
+ codesCriteria.getMaterialTypeCodes());
}
-
} else if (materialSearchCriteria.tryGetMaterialId() != null)
{
long materialId = materialSearchCriteria.tryGetMaterialId().getId();
- Long expId = tryGetExperimentId(experiment);
- if (expId == null)
+ if (experimentOrNull != null)
{
- locations = dao.getPlateLocationsForMaterialId(materialId);
+ locations =
+ dao.getPlateLocationsForMaterialId(materialId, experimentOrNull
+ .getExperimentId().getId());
+ } else if (projectOrNull != null)
+ {
+ locations =
+ dao.getPlateLocationsForMaterialId(materialId,
+ projectOrNull.getSpaceCode(), projectOrNull.getProjectCode());
} else
{
- locations = dao.getPlateLocationsForMaterialId(materialId, expId);
+ locations = dao.getPlateLocationsForMaterialId(materialId);
}
} else
{
@@ -863,12 +879,6 @@ public class WellContentLoader extends AbstractContentLoader
return criterion;
}
- private Long tryGetExperimentId(ExperimentSearchCriteria experiment)
- {
- SingleExperimentSearchCriteria exp = experiment.tryGetExperiment();
- return exp == null ? null : exp.getExperimentId().getId();
- }
-
private List<WellContent> loadLocations(TechId geneMaterialId, TechId experimentId)
{
DataIterator<WellContentQueryResult> locations =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/authorization/WellSearchCriteriaPredicate.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/authorization/WellSearchCriteriaPredicate.java
index 722f39481c8..3d9a6d6d498 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/authorization/WellSearchCriteriaPredicate.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/authorization/WellSearchCriteriaPredicate.java
@@ -16,40 +16,76 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.authorization;
-import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DelegatedPredicate;
+import java.util.List;
+
+import org.springframework.dao.DataAccessException;
+
+import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.IAuthorizationDataProvider;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.RoleWithIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.IPredicate;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SpaceIdentifierPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.SingleExperimentSearchCriteria;
/**
* @author Tomasz Pylak
*/
-public final class WellSearchCriteriaPredicate extends
- DelegatedPredicate<TechId, WellSearchCriteria>
+public final class WellSearchCriteriaPredicate implements IPredicate<WellSearchCriteria>
{
+ private final IPredicate<TechId> experimentPredicate;
+
+ private final SpaceIdentifierPredicate spacePredicate;
+
public WellSearchCriteriaPredicate()
{
- super(new ExperimentTechIdPredicate());
+ this.experimentPredicate = new ExperimentTechIdPredicate();
+ this.spacePredicate = new SpaceIdentifierPredicate();
}
- @Override
- public final String getCandidateDescription()
+ public final void init(IAuthorizationDataProvider provider)
{
- return "plate materials search criteria";
+ experimentPredicate.init(provider);
+ spacePredicate.init(provider);
}
- @Override
- public TechId tryConvert(WellSearchCriteria value)
+ public final Status evaluate(final PersonPE person,
+ final List<RoleWithIdentifier> allowedRoles, final WellSearchCriteria value)
{
- SingleExperimentSearchCriteria exp = value.getExperimentCriteria().tryGetExperiment();
- if (exp != null)
+ assert person != null : "Unspecified person";
+ assert allowedRoles != null : "Unspecified allowed roles";
+ if (value == null)
{
- return exp.getExperimentId();
- } else
+ throw UserFailureException.fromTemplate("No well search criteria specified.");
+ }
+ try
+ {
+ ExperimentSearchCriteria experimentCriteria = value.getExperimentCriteria();
+ SingleExperimentSearchCriteria experiment = experimentCriteria.tryGetExperiment();
+ BasicProjectIdentifier project = experimentCriteria.tryGetProjectIdentifier();
+ if (experiment != null)
+ {
+ return experimentPredicate.evaluate(person, allowedRoles,
+ experiment.getExperimentId());
+ } else if (project != null)
+ {
+ SpaceIdentifier space =
+ new SpaceIdentifier(project.getInstanceCode(), project.getSpaceCode());
+ return spacePredicate.evaluate(person, allowedRoles, space);
+ } else
+ {
+ return Status.OK;
+ }
+ } catch (DataAccessException ex)
{
- return null;
+ throw new UserFailureException(ex.getMessage(), ex);
}
}
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellSearchCriteria.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellSearchCriteria.java
index 3b7aee83ab6..2bcd06311fb 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellSearchCriteria.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/WellSearchCriteria.java
@@ -55,6 +55,11 @@ public class WellSearchCriteria implements ISerializable
{
}
+ public SingleExperimentSearchCriteria(IEntityInformationHolderWithIdentifier experiment)
+ {
+ this(experiment.getId(), experiment.getPermId(), experiment.getIdentifier());
+ }
+
public SingleExperimentSearchCriteria(long experimentId, String experimentPermId,
String experimentIdentifier)
{
@@ -85,54 +90,117 @@ public class WellSearchCriteria implements ISerializable
}
}
- /** points to one experiment or all of them */
- public static class ExperimentSearchCriteria implements IsSerializable, Serializable
+ /** Points to one experiment, all experiments of a project or all accessible experiments. */
+ public static final class ExperimentSearchCriteria implements IsSerializable, Serializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
- // if null, all experiments are taken into account
+ // if null, all experiments are taken into account (from one or all projects)
private SingleExperimentSearchCriteria experimentOrNull;
- public static final ExperimentSearchCriteria createAllExperiments()
+ private BasicProjectIdentifier projectIdOrNull;
+
+ /**
+ * Valid only if single experiment is used as a criteria.
+ */
+ // TODO 2011-06-07, Tomasz Pylak: Determines UI behaviour, should be refactored out from
+ // this server side DTO.
+ private boolean restrictGlobalScopeLinkToProject = false;
+
+ // GWT only
+ private ExperimentSearchCriteria()
+ {
+ }
+
+ public SingleExperimentSearchCriteria tryGetExperiment()
+ {
+ return experimentOrNull;
+ }
+
+ private ExperimentSearchCriteria(SingleExperimentSearchCriteria experimentOrNull,
+ boolean restrictGlobalScopeLinkToProject)
{
- return new ExperimentSearchCriteria(null);
+ this.experimentOrNull = experimentOrNull;
+ this.projectIdOrNull = null;
+ this.restrictGlobalScopeLinkToProject = restrictGlobalScopeLinkToProject;
+ }
+ private ExperimentSearchCriteria(BasicProjectIdentifier projectIdOrNull)
+ {
+ this.projectIdOrNull = projectIdOrNull;
}
public static ExperimentSearchCriteria createExperiment(
SingleExperimentSearchCriteria experiment)
{
- assert experiment != null : "experiment not specified";
- return new ExperimentSearchCriteria(experiment);
+ return createExperiment(experiment);
+ }
+
+ public static ExperimentSearchCriteria createExperiment(
+ SingleExperimentSearchCriteria experiment, boolean restrictGlobalScopeLinkToProject)
+ {
+ return new ExperimentSearchCriteria(experiment, restrictGlobalScopeLinkToProject);
}
- public static final ExperimentSearchCriteria createExperiment(
+ public static ExperimentSearchCriteria createExperiment(
IEntityInformationHolderWithIdentifier experiment)
{
- return createExperiment(experiment.getId(), experiment.getPermId(),
- experiment.getIdentifier());
+ return createExperiment(experiment, false);
}
- private static final ExperimentSearchCriteria createExperiment(long experimentId,
- String experimentPermId, String experimentIdentifier)
+ public static ExperimentSearchCriteria createExperiment(
+ IEntityInformationHolderWithIdentifier experiment,
+ boolean restrictGlobalScopeLinkToProject)
{
- return new ExperimentSearchCriteria(new SingleExperimentSearchCriteria(experimentId,
- experimentPermId, experimentIdentifier));
+ return createExperiment(new SingleExperimentSearchCriteria(experiment),
+ restrictGlobalScopeLinkToProject);
}
- // GWT only
- private ExperimentSearchCriteria()
+ public static ExperimentSearchCriteria createAllExperiments()
{
+ return new ExperimentSearchCriteria(null, false);
}
- private ExperimentSearchCriteria(SingleExperimentSearchCriteria experimentOrNull)
+ public static final ExperimentSearchCriteria createAllExperimentsForProject(
+ BasicProjectIdentifier projectIdentifier)
{
- this.experimentOrNull = experimentOrNull;
+ if (projectIdentifier == null)
+ {
+ throw new IllegalArgumentException("Project identifier cannot be null");
+ }
+ return new ExperimentSearchCriteria(projectIdentifier);
}
- public SingleExperimentSearchCriteria tryGetExperiment()
+ public BasicProjectIdentifier tryGetProjectIdentifier()
{
- return experimentOrNull;
+ return projectIdOrNull;
+ }
+
+ /**
+ * Valid only if single experiment is used as a criteria.<br>
+ * It determines the behavior of the link from material detail view in a single experiment
+ * context to the material detail view in 'global' context. If this parameter is true, the
+ * context will be the project to which the current experiment belongs, otherwise the
+ * context will be switched to all experiments.
+ */
+ public boolean getRestrictGlobalSearchLinkToProject()
+ {
+ return restrictGlobalScopeLinkToProject;
+ }
+
+ public ExperimentSearchByProjectCriteria tryAsSearchByProjectCriteria()
+ {
+ if (tryGetExperiment() != null)
+ {
+ return null;
+ } else if (projectIdOrNull != null)
+ {
+ return ExperimentSearchByProjectCriteria
+ .createAllExperimentsForProject(projectIdOrNull);
+ } else
+ {
+ return ExperimentSearchByProjectCriteria.createAllExperimentsForAllProjects();
+ }
}
@Override
@@ -140,12 +208,19 @@ public class WellSearchCriteria implements ISerializable
{
if (experimentOrNull == null)
{
- return "all experiments";
+ if (projectIdOrNull == null)
+ {
+ return "all experiments";
+ } else
+ {
+ return "all experiments from project " + projectIdOrNull;
+ }
} else
{
return experimentOrNull.toString();
}
}
+
}
public static final class ExperimentSearchByProjectCriteria implements IsSerializable,
@@ -171,10 +246,11 @@ public class WellSearchCriteria implements ISerializable
return new ExperimentSearchByProjectCriteria(null);
}
+ // GWT only
private ExperimentSearchByProjectCriteria()
{
}
-
+
private ExperimentSearchByProjectCriteria(BasicProjectIdentifier projectIdOrNull)
{
this.projectIdOrNull = projectIdOrNull;
@@ -190,6 +266,17 @@ public class WellSearchCriteria implements ISerializable
return projectIdOrNull == null;
}
+ public ExperimentSearchCriteria asExtendedCriteria()
+ {
+ if (projectIdOrNull != null)
+ {
+ return ExperimentSearchCriteria.createAllExperimentsForProject(projectIdOrNull);
+ } else
+ {
+ return ExperimentSearchCriteria.createAllExperiments();
+ }
+ }
+
@Override
public String toString()
{
diff --git a/screening/sourceTest/java/BiozentrumMatLabApiTest.java b/screening/sourceTest/java/BiozentrumMatLabApiTest.java
index 14e109d8d25..73d5620e5ab 100644
--- a/screening/sourceTest/java/BiozentrumMatLabApiTest.java
+++ b/screening/sourceTest/java/BiozentrumMatLabApiTest.java
@@ -41,19 +41,109 @@ public class BiozentrumMatLabApiTest
mountPoint = args[2];
}
- OpenBISScreeningML.login("admin", passwd, "http://bc2-openbis01.bc2.unibas.ch:8443");
+ OpenBISScreeningML.login("cisd", passwd, "http://bc2-openbis01.bc2.unibas.ch:8443");
+ String experiment = "/TEST/TEST-USER/MY-ASSAY";
+ Object[][] channels = OpenBISScreeningML.listChannels(experiment);
+ print2DArray(channels);
+
+ testLoadFeatures(chosenPlate, experiment);
+
+ testImagesMetadata(chosenPlate);
+ testLoadImage(chosenPlate);
+ testWellProperties(chosenPlate);
+ testLoadDataset(chosenPlate, mountPoint, datasetTypePattern);
+
+ OpenBISScreeningML.logout();
+ }
+
+ private static void testLoadFeatures(String chosenPlate, String experiment)
+ {
+ Object[][] features = OpenBISScreeningML.listFeatures(experiment);
+ print2DArray(features);
+
+ Object[][][] featureMatrix = OpenBISScreeningML.getFeatureMatrixForPlate(chosenPlate);
+ System.out.println("per plate features -------------------------------");
+ print3DArray(featureMatrix);
+
+ String[] featureNames = new String[]
+ { "OOF" };
+ featureMatrix = OpenBISScreeningML.getFeatureMatrixForPlate(chosenPlate, featureNames);
+ System.out.println("one per plate feature -------------------------------");
+ print3DArray(featureMatrix);
+
+ featureMatrix = OpenBISScreeningML.getFeatureMatrix(experiment, "149420", featureNames);
+ System.out.println("one per gene feature -------------------------------");
+ print3DArray(featureMatrix);
+ }
+
+ private static void print3DArray(Object[][][] array)
+ {
+ System.out.println("{");
+ for (int i = 0; i < array.length; i++)
+ {
+ print2DArray(array[i]);
+ }
+ System.out.println("}");
+ }
+
+ private static void print2DArray(Object[][] array)
+ {
+ System.out.println("[");
+ for (int i = 0; i < array.length; i++)
+ {
+ printAsRow(array[i]);
+ }
+ System.out.println("]");
+ }
+
+ private static void printAsRow(Object[] objects)
+ {
+ StringBuffer sb = new StringBuffer();
+ sb.append("[");
+ for (int i = 0; i < objects.length; i++)
+ {
+ sb.append(objects[i]);
+ sb.append(",");
+ }
+ sb.append("]");
+ System.out.println(sb.toString());
+ }
+
+ private static void testImagesMetadata(String chosenPlate)
+ {
Object[][] meta = OpenBISScreeningML.getImagesMetadata(chosenPlate);
- System.out.println(String.format("Number of tiles: %s. Plate geometry %sx%s", meta[1][3],
- meta[1][6], meta[1][7]));
+ System.out.println(String.format("Number of tiles: %s. Plate geometry %sx%s", meta[0][2],
+ meta[0][5], meta[0][6]));
+ }
+
+ private static void testLoadDataset(String chosenPlate, String mountPoint,
+ String datasetTypePattern)
+ {
+ // Loads dataset with classification results.
+ // OpenBIS store diretcory is mounted locally in "/mount/openbis/store", so no data are
+ // copied and just a path to the appropriate location
+ // is returned.
+ Object[][] datasets =
+ OpenBISScreeningML.loadDataSets(chosenPlate, datasetTypePattern, mountPoint);
+ System.out.println("Path to the first downloaded dataset: " + datasets[0][1]);
+ }
+ private static void testLoadImage(String chosenPlate)
+ {
// fetch 3ed tile of well (1,1). The second call to fetch this image will return it from the
// local cache.
// The last optional parameter can specify a list of channels to load (otherwise all
// channels are loaded).
- Object[][][] images = OpenBISScreeningML.loadImages(chosenPlate, 1, 1, 3);
- System.out.println("Image path: " + images[1][1]);
+ long start = System.currentTimeMillis();
+ Object[][][] images = OpenBISScreeningML.loadImages(chosenPlate, 1, 1, 3, new String[]
+ { "CY3" });
+ System.out.println("Image path: " + images[0][0][0]);
+ System.out.println("Took: " + (System.currentTimeMillis() - start));
+ }
+ private static void testWellProperties(String chosenPlate)
+ {
// properties of well (2,4)
Object[][] props = OpenBISScreeningML.getWellProperties(chosenPlate, 2, 4);
for (int i = 0; i < props.length; i++)
@@ -66,13 +156,5 @@ public class BiozentrumMatLabApiTest
{
{ "DESCRIPTION", "hello example" } };
OpenBISScreeningML.updateWellProperties(chosenPlate, 2, 4, props);
-
- // Loads dataset with classification results.
- // OpenBIS store diretcory is mounted locally in "/mount/openbis/store", so no data are
- // copied and just a path to the appropriate location
- // is returned.
- Object[][] datasets =
- OpenBISScreeningML.loadDataSets(chosenPlate, datasetTypePattern, mountPoint);
- System.out.println("Path to the first downloaded dataset: " + datasets[0][1]);
}
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/utils/EntityTypeLabelUtilsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/utils/EntityTypeLabelUtilsTest.java
index e8b91ae00bc..271c6da2bf0 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/utils/EntityTypeLabelUtilsTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/utils/EntityTypeLabelUtilsTest.java
@@ -33,9 +33,9 @@ public class EntityTypeLabelUtilsTest extends AssertJUnit
@Test
public void test()
{
- assertEquals("2011-05-30, Raw (DAT)", createLabel("HCS_IMAGE_RAW", true));
- assertEquals("2011-05-30, Features", createLabel("HCS_ANALYSIS_WELL_FEATURES", false));
- assertEquals("2011-05-30, Analysis cell classifications (DAT)",
+ assertEquals("Raw (DAT), 2011-05-30 12:34", createLabel("HCS_IMAGE_RAW", true));
+ assertEquals("Features, 2011-05-30 12:34", createLabel("HCS_ANALYSIS_WELL_FEATURES", false));
+ assertEquals("Analysis cell classifications (DAT), 2011-05-30 12:34",
createLabel("HCS_ANALYSIS_CELL_CLASSIFICATIONS", true));
}
@@ -44,7 +44,7 @@ public class EntityTypeLabelUtilsTest extends AssertJUnit
{
DatasetReference ref =
new DatasetReference(0, "code", typeCode, null, "DAT", null, null, null, null);
- return EntityTypeLabelUtils.createDatasetLabel(ref, withFileType, "2011-05-30");
+ return EntityTypeLabelUtils.createDatasetLabel(ref, withFileType, "2011-05-30 12:34");
}
}
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
index b03d89a8166..f589680be44 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/ScreeningDAOTest.java
@@ -79,11 +79,22 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
AssertJUnit.assertEquals(0, locations.size());
}
+ @Test
+ public void testGetPlateLocationsForOneMaterialAllExperimentsFromProject()
+ {
+ // it just tests if the sql runs
+ List<WellContentQueryResult> locations =
+ EntityListingTestUtils.asList(query.getPlateLocationsForMaterialId(1, "space",
+ "project"));
+ AssertJUnit.assertEquals(0, locations.size());
+ }
+
@Test
public void testGetPlateMappingAllTypes()
{
// it just tests if the sql runs
- List<WellContentQueryResult> locations = EntityListingTestUtils.asList(query.getPlateMapping("xxx"));
+ List<WellContentQueryResult> locations =
+ EntityListingTestUtils.asList(query.getPlateMapping("xxx"));
AssertJUnit.assertEquals(0, locations.size());
}
@@ -148,6 +159,12 @@ public class ScreeningDAOTest extends AbstractScreeningDAOTest
materialTypeCodes, 1));
AssertJUnit.assertEquals(0, locations.size());
+ // one project
+ locations =
+ EntityListingTestUtils.asList(query.getPlateLocationsForMaterialCodesInProject(ids,
+ materialTypeCodes, "space", "project"));
+ AssertJUnit.assertEquals(0, locations.size());
+
// all experiments
locations =
EntityListingTestUtils.asList(query.getPlateLocationsForMaterialCodes(ids,
--
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