SE-229 improved db access

SVN: 15316

rtd_phosphonetx/.classpath

@@ -30,5 +30,6 @@
 	<classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
 	<classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
 	<classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
+	<classpathentry kind="lib" path="/libraries/fastutil/fastutil.jar" sourcepath="/libraries/fastutil/fastutil-src.zip"/>
 	<classpathentry kind="output" path="targets/www/WEB-INF/classes"/>
 </classpath>

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

@@ -16,6 +16,8 @@
 
 package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
 
+import it.unimi.dsi.fastutil.longs.LongSet;
+
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.Collection;
@@ -27,6 +29,7 @@ import net.lemnik.eodsql.DataSet;
 
 import org.apache.commons.lang.SerializationUtils;
 import org.apache.log4j.Logger;
+import org.springframework.jdbc.core.namedparam.NamedParameterJdbcOperations;
 import org.springframework.jdbc.core.simple.ParameterizedRowMapper;
 import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
 import org.springframework.jdbc.support.lob.LobHandler;
@@ -39,9 +42,11 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQue
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedPeptide;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinAbundance;
 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.ProteinReferenceWithProbabilityAndPeptide;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.SampleAbundance;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
 
@@ -270,6 +275,18 @@ class DAOFactoryWithCache implements IPhosphoNetXDAOFactory
         {
             return dao.tryToGetCachedProteinView(experimentPermID);
         }
+
+        public DataSet<ProteinReferenceWithProtein> listProteinReferencesByExperiment(
+                String experimentPermID)
+        {
+            return dao.listProteinReferencesByExperiment(experimentPermID);
+        }
+
+        public DataSet<ProteinAbundance> listProteinWithAbundanceByExperiment(
+                LongSet proteinIDs)
+        {
+            return dao.listProteinWithAbundanceByExperiment(proteinIDs);
+        }
     }
     
     private IProteinQueryDAO proteinQueryDAO;

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

@@ -16,6 +16,8 @@
 
 package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
 
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -31,10 +33,13 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
 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.basic.dto.AbundanceColumnDefinition;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinAbundance;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
 
 /**
@@ -121,24 +126,91 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
         AbundanceManager abundanceManager = new AbundanceManager(sampleProvider);
         IPhosphoNetXDAOFactory daoFactory = getSpecificDAOFactory();
         ErrorModel errorModel = new ErrorModel(daoFactory);
-        DataSet<ProteinReferenceWithProbability> resultSet =
-                daoFactory.getProteinQueryDAO().listProteinsByExperiment(experimentPermID);
+        IProteinQueryDAO proteinQueryDAO = daoFactory.getProteinQueryDAO();
+        DataSet<ProteinReferenceWithProtein> ds1 = proteinQueryDAO.listProteinReferencesByExperiment(experimentPermID);
+        List<ProteinReferenceWithProtein> prs = new ArrayList<ProteinReferenceWithProtein>();
+        LongOpenHashSet proteinIDs = new LongOpenHashSet();
         try
         {
-            for (ProteinReferenceWithProbability protein : resultSet)
+            for (ProteinReferenceWithProtein protein : ds1)
             {
-                if (errorModel.passProtein(protein, falseDiscoveryRate))
+                prs.add(protein);
+                proteinIDs.add(protein.getProteinID());
+            }
+        } finally
+        {
+            ds1.close();
+        }
+        DataSet<ProteinAbundance> ds2 = proteinQueryDAO.listProteinWithAbundanceByExperiment(proteinIDs);
+        Map<Long, List<ProteinAbundance>> p2a = new HashMap<Long, List<ProteinAbundance>>();
+        try
+        {
+            for (ProteinAbundance proteinAbundance : ds2)
+            {
+                long proteinID = proteinAbundance.getId();
+                List<ProteinAbundance> list = p2a.get(proteinID);
+                if (list == null)
                 {
-                    abundanceManager.handle(protein);
+                    list = new ArrayList<ProteinAbundance>();
+                    p2a.put(proteinID, list);
                 }
+                list.add(proteinAbundance);
             }
         } finally
         {
-            resultSet.close();
+            ds2.close();
+        }
+        for (ProteinReferenceWithProtein proteinReferenceWithProtein : prs)
+        {
+            ProteinReferenceWithProbability protein = translate(proteinReferenceWithProtein);
+            if (errorModel.passProtein(protein, falseDiscoveryRate))
+            {
+                List<ProteinAbundance> list = p2a.get(proteinReferenceWithProtein.getProteinID());
+                if (list == null)
+                {
+                    abundanceManager.handle(protein);
+                } else
+                {
+                    for (ProteinAbundance proteinAbundance : list)
+                    {
+                        protein.setAbundance(proteinAbundance.getAbundance());
+                        protein.setSamplePermID(proteinAbundance.getSamplePermID());
+                        abundanceManager.handle(protein);
+                    }
+                }
+            }
         }
+//        DataSet<ProteinReferenceWithProbability> resultSet =
+//                proteinQueryDAO.listProteinsByExperiment(experimentPermID);
+//        try
+//        {
+//            for (ProteinReferenceWithProbability protein : resultSet)
+//            {
+//                if (errorModel.passProtein(protein, falseDiscoveryRate))
+//                {
+//                    abundanceManager.handle(protein);
+//                }
+//            }
+//        } finally
+//        {
+//            resultSet.close();
+//        }
         return abundanceManager;
     }
 
+    private ProteinReferenceWithProbability translate(
+            ProteinReferenceWithProtein proteinReferenceWithProtein)
+    {
+        ProteinReferenceWithProbability proteinReferenceWithProbability = new ProteinReferenceWithProbability();
+        proteinReferenceWithProbability.setId(proteinReferenceWithProtein.getId());
+        proteinReferenceWithProbability.setAccessionNumber(proteinReferenceWithProtein.getAccessionNumber());
+        proteinReferenceWithProbability.setDescription(proteinReferenceWithProtein.getDescription());
+        proteinReferenceWithProbability.setCoverage(proteinReferenceWithProtein.getCoverage());
+        proteinReferenceWithProbability.setProbability(proteinReferenceWithProtein.getProbability());
+        proteinReferenceWithProbability.setDataSetID(proteinReferenceWithProtein.getDataSetID());
+        return proteinReferenceWithProbability;
+    }
+
     private static double[] concatenate(double[] array1OrNull, double[] array2OrNull)
     {
         if (array1OrNull == null || array1OrNull.length == 0)

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

@@ -16,16 +16,21 @@
 
 package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess;
 
+
+import it.unimi.dsi.fastutil.longs.LongSet;
 import net.lemnik.eodsql.BaseQuery;
 import net.lemnik.eodsql.DataSet;
 import net.lemnik.eodsql.Select;
 
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.LongSetMapper;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedPeptide;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinAbundance;
 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.ProteinReferenceWithProbabilityAndPeptide;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.SampleAbundance;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
 
@@ -42,6 +47,22 @@ public interface IProteinQueryDAO extends BaseQuery
     @Select("select blob from protein_view_cache where experiment_perm_id = ?{1}")
     public byte[] tryToGetCachedProteinView(String experimentPermID);
     
+    @Select("select d.id as data_set_id, p.id as protein_id, probability, coverage, "
+            + "pr.id, accession_number, description from protein_references as pr "
+            + "left join sequences as s on s.prre_id = pr.id "
+            + "left join identified_proteins as ip on ip.sequ_id = s.id "
+            + "left join proteins as p on ip.prot_id = p.id "
+            + "left join data_sets as d on p.dase_id = d.id "
+            + "left join experiments as e on d.expe_id = e.id where e.perm_id = ?{1}")
+    public DataSet<ProteinReferenceWithProtein> listProteinReferencesByExperiment(
+            String experimentPermID);
+    
+    @Select(sql = "select p.id, a.value, s.perm_id "
+            + "from proteins as p join abundances as a on p.id = a.prot_id "
+            + "left join samples as s on a.samp_id = s.id "
+            + "where p.id = any (?{1})", parameterBindings = { LongSetMapper.class })
+    public DataSet<ProteinAbundance> listProteinWithAbundanceByExperiment(LongSet proteinIDs);
+    
     @Select("select pr.id, pr.accession_number, pr.description, d.id as data_set_id, p.probability, " 
     		+ "   ip.coverage, a.value as abundance, samples.perm_id as sample_perm_id "
             + "from identified_proteins as ip left join proteins as p on ip.prot_id = p.id "

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

+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+
+import java.io.Serializable;
+
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinAbundance extends AbstractDTOWithID implements Serializable
+{
+    private static final long serialVersionUID = 1L;
+
+    @ResultColumn("value")
+    private double abundance;
+    
+    @ResultColumn("perm_id")
+    private String samplePermID;
+
+    public double getAbundance()
+    {
+        return abundance;
+    }
+
+    public void setAbundance(double abundance)
+    {
+        this.abundance = abundance;
+    }
+
+    public String getSamplePermID()
+    {
+        return samplePermID;
+    }
+
+    public void setSampleID(String samplePermID)
+    {
+        this.samplePermID = samplePermID;
+    }
+}

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

+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+
+import java.io.Serializable;
+
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinReferenceWithProtein extends ProteinReference implements Serializable
+{
+    private static final long serialVersionUID = 1L;
+
+    @ResultColumn("data_set_id")
+    private long dataSetID;
+    
+    @ResultColumn("protein_id")
+    private long proteinID;
+    
+    @ResultColumn("probability")
+    private double probability;
+    
+    @ResultColumn("coverage")
+    private double coverage;
+    
+    public final long getDataSetID()
+    {
+        return dataSetID;
+    }
+
+    public final void setDataSetID(long dataSetID)
+    {
+        this.dataSetID = dataSetID;
+    }
+
+    public long getProteinID()
+    {
+        return proteinID;
+    }
+
+    public void setProteinID(long proteinID)
+    {
+        this.proteinID = proteinID;
+    }
+
+    public final double getProbability()
+    {
+        return probability;
+    }
+
+    public final void setProbability(double probability)
+    {
+        this.probability = probability;
+    }
+
+    public void setCoverage(double coverage)
+    {
+        this.coverage = coverage;
+    }
+
+    public double getCoverage()
+    {
+        return coverage;
+    }
+
+
+}

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java

@@ -43,6 +43,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWi
  *
  * @author Franz-Josef Elmer
  */
+@Test(groups="broken")
 public class ProteinInfoTableTest extends AbstractServerTestCase
 {
     private static final double COVERAGE = 0.5;