LMS-967 business layer for ProteinByExperiment viewer

SVN: 11666

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java

@@ -22,8 +22,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteri
 import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 
 /**
  * 

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java

@@ -23,8 +23,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
 import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 
 /**
  * 

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java

@@ -34,8 +34,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.propert
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 
 /**
  * 
@@ -86,6 +86,7 @@ public class ProteinViewer extends ContentPanel implements IDatabaseModification
             TechId proteinReferenceID)
     {
         widgetID = createWidgetID(proteinReferenceID);
+        setId(widgetID);
         this.viewContext = viewContext;
         this.experimentID = experimentID;
         this.proteinreferenceID = proteinReferenceID;
@@ -101,8 +102,9 @@ public class ProteinViewer extends ContentPanel implements IDatabaseModification
     private void recreateUI(ProteinByExperiment protein)
     {
         final Map<String, Object> properties = new LinkedHashMap<String, Object>();
+        properties.put("Protein Description", protein.getDescription());
+        properties.put("UniProt ID", protein.getUniprotID());
         final PropertyGrid propertyGrid = new PropertyGrid(viewContext, properties.size());
-        properties.put("ID", proteinreferenceID);
         add(propertyGrid);
     }
 

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java

@@ -20,31 +20,31 @@ import javax.annotation.Resource;
 
 import org.springframework.stereotype.Component;
 
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
 import ch.systemsx.cisd.common.servlet.IRequestContextProvider;
 import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
 import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
-import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
 import ch.systemsx.cisd.openbis.generic.client.web.server.AbstractClientService;
+import ch.systemsx.cisd.openbis.generic.client.web.server.translator.UserFailureExceptionTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.IServer;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinInfo;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 
 /**
- * 
- *
  * @author Franz-Josef Elmer
  */
 @Component(value = ResourceNames.PHOSPHONETX_PLUGIN_SERVICE)
-public class PhosphoNetXClientService extends AbstractClientService implements IPhosphoNetXClientService
+public class PhosphoNetXClientService extends AbstractClientService implements
+        IPhosphoNetXClientService
 {
     @Resource(name = ResourceNames.PHOSPHONETX_PLUGIN_SERVER)
     private IPhosphoNetXServer server;
-    
+
     public PhosphoNetXClientService()
     {
         super();
@@ -61,23 +61,32 @@ public class PhosphoNetXClientService extends AbstractClientService implements I
         return server;
     }
 
-    public ResultSet<ProteinInfo> listProteinsByExperiment(ListProteinByExperimentCriteria criteria) throws UserFailureException
+    public ResultSet<ProteinInfo> listProteinsByExperiment(ListProteinByExperimentCriteria criteria)
+            throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
     {
         final String sessionToken = getSessionToken();
-        return listEntities(criteria, new ListProteinOriginalDataProvider(server,
-                sessionToken, criteria.getExperimentID(), criteria.getFalseDiscoveryRate()));
+        return listEntities(criteria, new ListProteinOriginalDataProvider(server, sessionToken,
+                criteria.getExperimentID(), criteria.getFalseDiscoveryRate()));
     }
 
     public String prepareExportProteins(TableExportCriteria<ProteinInfo> exportCriteria)
-            throws UserFailureException
+            throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
     {
         return prepareExportEntities(exportCriteria);
     }
 
     public ProteinByExperiment getProteinByExperiment(TechId experimentID, TechId proteinReferenceID)
-            throws UserFailureException
+            throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
     {
-        return new ProteinByExperiment();
+        final String sessionToken = getSessionToken();
+        try
+        {
+            return server.getProteinByExperiment(sessionToken, experimentID, proteinReferenceID);
+        } catch (final UserFailureException e)
+        {
+            throw UserFailureExceptionTranslator.translate(e);
+        }
+
     }
 
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java

@@ -20,6 +20,8 @@ import java.util.List;
 
 import javax.annotation.Resource;
 
+import net.lemnik.eodsql.DataSet;
+
 import org.springframework.stereotype.Component;
 
 import ch.rinn.restrictions.Private;
@@ -35,9 +37,13 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IBusinessObjectFactory;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinReferenceTable;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
 
 /**
  * @author Franz-Josef Elmer
@@ -90,4 +96,31 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
         return table.getProteinReferences();
     }
 
+    public ProteinByExperiment getProteinByExperiment(String sessionToken, TechId experimentId,
+            TechId proteinReferenceID) throws UserFailureException
+    {
+        getSessionManager().getSession(sessionToken);
+        IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO();
+        ProteinByExperiment proteinByExperiment = new ProteinByExperiment();
+        ProteinReference proteinReference =
+                proteinQueryDAO.tryToGetProteinReference(proteinReferenceID.getId());
+        if (proteinReference == null)
+        {
+            throw new UserFailureException("No protein reference found for ID: " + proteinReferenceID);
+        }
+        proteinByExperiment.setUniprotID(proteinReference.getUniprotID());
+        proteinByExperiment.setDescription(proteinReference.getDescription());
+        DataSet<Sequence> sequences =
+                proteinQueryDAO.listProteinSequencesByProteinReference(proteinReferenceID.getId());
+        for (Sequence sequence : sequences)
+        {
+            ProteinSequence proteinSequence = new ProteinSequence();
+            proteinSequence.setId(new TechId(sequence.getId()));
+            proteinSequence.setSequence(sequence.getSequence());
+            proteinSequence.setDatabaseNameAndVersion(sequence.getDatabaseNameAndVersion());
+            proteinByExperiment.addSequence(proteinSequence);
+        }
+        return proteinByExperiment;
+    }
+
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java

@@ -28,6 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.SampleGenerationDTO;
 import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
 
 /**
@@ -70,4 +71,12 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
         return null;
     }
 
+    public ProteinByExperiment getProteinByExperiment(String sessionToken, TechId experimentId,
+            TechId proteinReferenceID) throws UserFailureException
+    {
+        logAccess(sessionToken, "get_protein_by_experiment",
+                "EXPERIMENT_ID(%s) PROTEIN_REFERENCE_ID(%s)", experimentId, proteinReferenceID);
+        return null;
+    }
+
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java

@@ -21,7 +21,9 @@ import net.lemnik.eodsql.DataSet;
 import net.lemnik.eodsql.Select;
 
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
 
 /**
  * 
@@ -40,4 +42,11 @@ public interface IProteinQueryDAO extends BaseQuery
             + "sequences as s left join protein_references as pr on s.prre_id = pr.id "
             + "where e.perm_id = ?{1} and ip.sequ_id = s.id order by pr.description")
     public DataSet<ProteinReferenceWithProbability> listProteinsByExperiment(String experimentPermID);
+    
+    @Select("select * from protein_references where id = ?{1}")
+    public ProteinReference tryToGetProteinReference(long proteinReferenceID);
+    
+    @Select("select s.id, s.amino_acid_sequence, d.name_and_version "
+            + "from sequences as s left join databases as d on s.db_id = d.id where s.prre_id = ?{1}")
+    public DataSet<Sequence> listProteinSequencesByProteinReference(long proteinReferenceID);
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java

@@ -27,6 +27,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
 
 /**
@@ -41,4 +42,12 @@ public interface IPhosphoNetXServer extends IServer
     public List<ProteinReference> listProteinsByExperiment(String sessionToken,
             @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
             TechId experimentId, double falseDiscoveryRate) throws UserFailureException;
+    
+    @Transactional
+    @RolesAllowed(RoleSet.OBSERVER)
+    public ProteinByExperiment getProteinByExperiment(String sessionToken,
+            @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
+            TechId experimentId, TechId proteinReferenceID) throws UserFailureException;
+    
+    
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinByExperiment.java

+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.List;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinByExperiment implements IsSerializable, Serializable
+{
+
+    private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+    
+    private String uniprotID;
+    
+    private String description;
+    
+    private List<ProteinSequence> sequences = new ArrayList<ProteinSequence>();
+
+    public final String getUniprotID()
+    {
+        return uniprotID;
+    }
+
+    public final void setUniprotID(String uniprotID)
+    {
+        this.uniprotID = uniprotID;
+    }
+
+    public final String getDescription()
+    {
+        return description;
+    }
+
+    public final void setDescription(String description)
+    {
+        this.description = description;
+    }
+
+    public final List<ProteinSequence> getSequences()
+    {
+        return sequences;
+    }
+    
+    public final void addSequence(ProteinSequence proteinSequence)
+    {
+        this.sequences.add(proteinSequence);
+    }
+    
+    
+}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java

+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto;
+
+import java.io.Serializable;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinSequence implements IsSerializable, Serializable
+{
+    private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+    
+    private TechId id;
+    
+    private String sequence;
+    
+    private String databaseNameAndVersion;
+
+    public final TechId getId()
+    {
+        return id;
+    }
+
+    public final void setId(TechId id)
+    {
+        this.id = id;
+    }
+
+    public final String getSequence()
+    {
+        return sequence;
+    }
+
+    public final void setSequence(String sequence)
+    {
+        this.sequence = sequence;
+    }
+
+    public final String getDatabaseNameAndVersion()
+    {
+        return databaseNameAndVersion;
+    }
+
+    public final void setDatabaseNameAndVersion(String databaseNameAndVersion)
+    {
+        this.databaseNameAndVersion = databaseNameAndVersion;
+    }
+
+}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReference.java

@@ -23,23 +23,14 @@ import net.lemnik.eodsql.ResultColumn;
  *
  * @author Franz-Josef Elmer
  */
-public abstract class ProteinReference extends AbstractDTOWithID
+public class ProteinReference extends AbstractDTOWithID
 {
-
     @ResultColumn("uniprot_id")
     private String uniprotID;
+    
     @ResultColumn("description")
     private String description;
 
-    /**
-     *
-     *
-     */
-    public ProteinReference()
-    {
-        super();
-    }
-
     public final String getUniprotID()
     {
         return uniprotID;

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinByExperiment.java → rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/Sequence.java

@@ -14,16 +14,43 @@
  * limitations under the License.
  */
 
-package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto;
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+
+import net.lemnik.eodsql.ResultColumn;
 
-import com.google.gwt.user.client.rpc.IsSerializable;
 
 /**
  * 
  *
  * @author Franz-Josef Elmer
  */
-public class ProteinByExperiment implements IsSerializable
+public class Sequence extends AbstractDTOWithID
 {
+    @ResultColumn("amino_acid_sequence")
+    private String sequence;
+    
+    @ResultColumn("name_and_version")
+    private String databaseNameAndVersion;
+
+    public final String getSequence()
+    {
+        return sequence;
+    }
+
+    public final void setSequence(String sequence)
+    {
+        this.sequence = sequence;
+    }
+
+    public final String getDatabaseNameAndVersion()
+    {
+        return databaseNameAndVersion;
+    }
+
+    public final void setDatabaseNameAndVersion(String databaseNameAndVersion)
+    {
+        this.databaseNameAndVersion = databaseNameAndVersion;
+    }
+
 
 }