[LMS-1690] screening erroneous solution

SVN: 17713

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java

@@ -16,6 +16,7 @@
 
 package ch.systemsx.cisd.openbis.plugin.screening.client.web.client;
 
+import java.util.Collection;
 import java.util.List;
 
 import ch.systemsx.cisd.openbis.generic.client.web.client.IClientService;
@@ -31,12 +32,12 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
@@ -74,6 +75,11 @@ public interface IScreeningClientService extends IClientService
      */
     public PlateImages getPlateContentForDataset(TechId datasetId);
 
+    /**
+     * @return ids of materials in experiment with specified id.
+     */
+    public Collection<Long> listExperimentMaterials(TechId experimentTechId);
+
     /**
      * @return well locations which belong to a parent plate connected to a specified experiment(s)
      *         and have specified material(s) inside.

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java

@@ -16,6 +16,7 @@
 
 package ch.systemsx.cisd.openbis.plugin.screening.client.web.client;
 
+import java.util.Collection;
 import java.util.List;
 
 import com.google.gwt.user.client.rpc.AsyncCallback;
@@ -31,12 +32,12 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
@@ -61,6 +62,12 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
     /** @see IScreeningClientService#getDataSetInfo(TechId) */
     public void getDataSetInfo(TechId datasetTechId, AsyncCallback<ExternalData> callback);
 
+    /**
+     * @see IScreeningClientService#listExperimentMaterials(TechId)
+     */
+    public void listExperimentMaterials(TechId experimentId,
+            AsyncCallback<Collection<Long>> callback);
+
     /**
      * @see IScreeningClientService#listPlateWells(DefaultResultSetConfig,
      *      PlateMaterialsSearchCriteria)

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ExperimentWellMaterialsSection.java

 package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
 
+import java.util.Collection;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.ICommonClientServiceAsync;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.DisposableSectionPanel;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.material.MaterialBrowserGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IDelegatedAction;
 import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolderWithIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientServiceAsync;
 import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
 import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.DisplayTypeIDGenerator;
@@ -18,12 +24,12 @@ public class ExperimentWellMaterialsSection extends DisposableSectionPanel
 {
     public static final String ID_SUFFIX = "ExperimentWellMaterialsSection";
 
-    @SuppressWarnings("unused")
     private final IViewContext<IScreeningClientServiceAsync> screeningViewContext;
 
-    @SuppressWarnings("unused")
     private final IEntityInformationHolderWithIdentifier experiment;
 
+    private Collection<Long> allowedMaterialIds;
+
     public ExperimentWellMaterialsSection(
             IViewContext<IScreeningClientServiceAsync> screeningViewContext,
             IEntityInformationHolderWithIdentifier experiment)
@@ -35,10 +41,51 @@ public class ExperimentWellMaterialsSection extends DisposableSectionPanel
         setDisplayID(DisplayTypeIDGenerator.PLATE_MATERIAL_BROWSER, ID_SUFFIX);
     }
 
+    @Override
+    protected void showContent()
+    {
+        IDelegatedAction onSuccessAction = new IDelegatedAction()
+            {
+                public void execute()
+                {
+                    ExperimentWellMaterialsSection.super.showContent();
+                }
+            };
+        screeningViewContext.getService().listExperimentMaterials(
+                TechId.create(experiment),
+                new ListMaterialIdsCallback(viewContext.getCommonViewContext(), this,
+                        onSuccessAction));
+    }
+
     @Override
     protected IDisposableComponent createDisposableContent()
     {
-        return MaterialBrowserGrid.createWithTypeChooser(viewContext.getCommonViewContext());
+        return MaterialBrowserGrid.createWithTypeChooser(viewContext.getCommonViewContext(),
+                allowedMaterialIds);
+    }
+
+    private final class ListMaterialIdsCallback extends AbstractAsyncCallback<Collection<Long>>
+    {
+
+        private final IDelegatedAction onSuccessAction;
+
+        private ExperimentWellMaterialsSection section;
+
+        public ListMaterialIdsCallback(final IViewContext<ICommonClientServiceAsync> viewContext,
+                ExperimentWellMaterialsSection section, IDelegatedAction onSuccessAction)
+        {
+            super(viewContext);
+            this.section = section;
+            this.onSuccessAction = onSuccessAction;
+        }
+
+        @Override
+        protected void process(Collection<Long> result)
+        {
+            section.allowedMaterialIds = result;
+            onSuccessAction.execute();
+        }
+
     }
 
 }
\ No newline at end of file

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java

@@ -16,6 +16,7 @@
 
 package ch.systemsx.cisd.openbis.plugin.screening.client.web.server;
 
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -57,13 +58,13 @@ import ch.systemsx.cisd.openbis.plugin.screening.BuildAndEnvironmentInfo;
 import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientService;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
@@ -185,6 +186,25 @@ public final class ScreeningClientService extends AbstractClientService implemen
         }
     }
 
+    public ResultSet<WellContent> listExperimentMaterials(
+            DefaultResultSetConfig<String, WellContent> gridCriteria,
+            final PlateMaterialsSearchCriteria materialCriteria)
+    {
+        try
+        {
+            return listEntities(gridCriteria, new IOriginalDataProvider<WellContent>()
+                {
+                    public List<WellContent> getOriginalData() throws UserFailureException
+                    {
+                        return server.listPlateWells(getSessionToken(), materialCriteria);
+                    }
+                });
+        } catch (final ch.systemsx.cisd.common.exceptions.UserFailureException e)
+        {
+            throw UserFailureExceptionTranslator.translate(e);
+        }
+    }
+
     public String prepareExportPlateLocations(TableExportCriteria<WellContent> criteria)
             throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
     {
@@ -290,4 +310,10 @@ public final class ScreeningClientService extends AbstractClientService implemen
         return server
                 .listImageChannelStacks(sessionToken, datasetCode, datastoreCode, wellLocation);
     }
+
+    public Collection<Long> listExperimentMaterials(TechId experimentId)
+    {
+        final String sessionToken = getSessionToken();
+        return server.listExperimentMaterials(sessionToken, experimentId);
+    }
 }

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java

@@ -16,10 +16,16 @@
 
 package ch.systemsx.cisd.openbis.plugin.screening.server;
 
+import java.sql.Connection;
+import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
 
 import javax.annotation.Resource;
 
+import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.QueryTool;
+
 import org.springframework.stereotype.Component;
 
 import ch.rinn.restrictions.Private;
@@ -28,6 +34,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
 import ch.systemsx.cisd.openbis.generic.server.AbstractServer;
 import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
 import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
 import ch.systemsx.cisd.openbis.generic.server.dataaccess.IVocabularyDAO;
 import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
@@ -44,6 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
 import ch.systemsx.cisd.openbis.generic.shared.dto.VocabularyPE;
 import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTranslator;
+import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQuery;
 import ch.systemsx.cisd.openbis.plugin.screening.server.logic.GenePlateLocationsLoader;
 import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader;
 import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningApiImpl;
@@ -59,11 +67,11 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
@@ -238,6 +246,25 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
                 materialTypeIdentifierOrNull);
     }
 
+    public Collection<Long> listExperimentMaterials(String sessionToken, TechId experimentId)
+    {
+        // TODO 2010-09-01, Piotr Buczek: move it to some BO when we have more queries like that
+        IScreeningQuery dao = createDAO(getDAOFactory());
+        DataIterator<Long> iterator = dao.getMaterialsForExperimentWells(experimentId.getId());
+        Collection<Long> result = new ArrayList<Long>();
+        for (Long l : iterator)
+        {
+            result.add(l);
+        }
+        return result;
+    }
+
+    private static IScreeningQuery createDAO(IDAOFactory daoFactory)
+    {
+        Connection connection = DatabaseContextUtils.getConnection(daoFactory);
+        return QueryTool.getQuery(connection, IScreeningQuery.class);
+    }
+
     private ScreeningApiImpl createScreeningApiImpl(String sessionToken)
     {
         final Session session = getSession(sessionToken);

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java

@@ -42,11 +42,11 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
@@ -208,6 +208,12 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
         return null;
     }
 
+    public Collection<Long> listExperimentMaterials(String sessionToken, TechId experimentId)
+    {
+        logAccess(sessionToken, "listExperimentMaterials", "experimentId(%s)", experimentId);
+        return null;
+    }
+
     public int getMajorVersion()
     {
         return MAJOR_VERSION;
@@ -217,4 +223,5 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
     {
         return ScreeningServer.MINOR_VERSION;
     }
+
 }

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/dataaccess/IScreeningQuery.java

@@ -210,4 +210,27 @@ public interface IScreeningQuery extends BaseQuery
             + "         and pt.is_internal_namespace = true and space.code = ?{1} and pl.code = ?{2}")
     public PlateGeometryContainer tryGetPlateGeometry(String spaceCode, String plateCode);
 
+    /**
+     * Returns the ids of all materials used in specified experiment.
+     */
+    @Select(sql = "SELECT distinct well_material.id            "
+            + "      FROM samples pl                           "
+            + "      JOIN samples well ON well.samp_id_part_of = pl.id"
+            + "      JOIN sample_properties well_props ON well_props.samp_id = well.id"
+            + "      JOIN materials well_material ON well_material.id = well_props.mate_prop_id"
+            + "     WHERE pl.expe_id = ?{1}", fetchSize = FETCH_SIZE)
+    public DataIterator<Long> getMaterialsForExperimentWells(long experimentId);
+
+    /**
+     * Returns the ids of materials of specified type and used in specified experiment.
+     */
+    @Select(sql = "SELECT distinct well_material.id            "
+            + "      FROM samples pl                           "
+            + "      JOIN samples well ON well.samp_id_part_of = pl.id"
+            + "      JOIN sample_properties well_props ON well_props.samp_id = well.id"
+            + "      JOIN materials well_material ON well_material.id = well_props.mate_prop_id"
+            + "     WHERE pl.expe_id = ?{1}                   "
+            + "       AND well_material.maty_id = {2}", fetchSize = FETCH_SIZE)
+    public DataIterator<Long> getMaterialsForExperimentWells(long experimentId, long materialTypeId);
+
 }

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java

@@ -16,6 +16,7 @@
 
 package ch.systemsx.cisd.openbis.plugin.screening.shared;
 
+import java.util.Collection;
 import java.util.List;
 
 import org.springframework.transaction.annotation.Transactional;
@@ -38,11 +39,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.PlateMaterialsSearchCriteriaPredicate;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellContentValidator;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellImageChannelStack;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
@@ -77,6 +78,14 @@ public interface IScreeningServer extends IServer
             String sessionToken,
             @AuthorizationGuard(guardClass = PlateMaterialsSearchCriteriaPredicate.class) PlateMaterialsSearchCriteria materialCriteria);
 
+    /**
+     * Loads all ids of materials connected with the specified experiment.
+     */
+    @Transactional(readOnly = true)
+    @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+    public Collection<Long> listExperimentMaterials(String sessionToken,
+            @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId);
+
     @Transactional
     @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
     public List<WellImageChannelStack> listImageChannelStacks(String sessionToken,