From c59e82b5f9e1b518aeec1f06167bc057d14efe73 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 31 Mar 2010 09:28:55 +0000
Subject: [PATCH] SE-229 improved db access
SVN: 15316
---
rtd_phosphonetx/.classpath | 1 +
.../server/business/DAOFactoryWithCache.java | 17 ++++
.../server/business/ProteinInfoTable.java | 84 ++++++++++++++++--
.../server/dataaccess/IProteinQueryDAO.java | 21 +++++
.../shared/dto/ProteinAbundance.java | 57 +++++++++++++
.../dto/ProteinReferenceWithProtein.java | 85 +++++++++++++++++++
.../server/business/ProteinInfoTableTest.java | 1 +
7 files changed, 260 insertions(+), 6 deletions(-)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinAbundance.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProtein.java
diff --git a/rtd_phosphonetx/.classpath b/rtd_phosphonetx/.classpath
index e979a205d8b..ec186f0bf31 100644
--- a/rtd_phosphonetx/.classpath
+++ b/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>
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DAOFactoryWithCache.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DAOFactoryWithCache.java
index 0daa92f433b..5ee33d3391e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DAOFactoryWithCache.java
+++ b/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;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTable.java
index cb41376e3a8..337c15436f4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTable.java
+++ b/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)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
index e603085a1a5..2e5a22a4d42 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
+++ b/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 "
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinAbundance.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinAbundance.java
new file mode 100644
index 00000000000..92c9a6a2750
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinAbundance.java
@@ -0,0 +1,57 @@
+/*
+ * 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;
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProtein.java
new file mode 100644
index 00000000000..2eb03624586
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProtein.java
@@ -0,0 +1,85 @@
+/*
+ * 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;
+ }
+
+
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java
index 8fb2b940c65..04c35faf6ca 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinInfoTableTest.java
+++ b/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;
--
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