diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManager.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManager.java
index 38aff587293ea87e10e8597c904c19d5a5ce0c51..b78bf393bf7a9ca197c30ba26160f3cb298ebaf1 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManager.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManager.java
@@ -16,14 +16,15 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
+import java.util.ArrayList;
import java.util.Collection;
-import java.util.LinkedHashMap;
-import java.util.Map;
+import java.util.List;
import java.util.Set;
import java.util.TreeSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinAbundance;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
/**
@@ -31,8 +32,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundan
*/
class AbundanceManager
{
- private final Map<String, ProteinWithAbundances> proteins =
- new LinkedHashMap<String, ProteinWithAbundances>();
+ private final List<ProteinWithAbundances> proteins = new ArrayList<ProteinWithAbundances>();
private final ISampleProvider sampleProvider;
@@ -41,21 +41,29 @@ class AbundanceManager
AbundanceManager(ISampleProvider sampleProvider)
{
this.sampleProvider = sampleProvider;
-
}
-
- public void handle(ProteinReferenceWithProbability proteinReference)
+
+ public void handle(ProteinReferenceWithProtein proteinReference, List<ProteinAbundance> listOrNull)
{
- ProteinWithAbundances protein = getOrCreateProtein(proteinReference);
- String samplePermID = proteinReference.getSamplePermID();
- if (samplePermID != null)
+ String accessionNumber = proteinReference.getAccessionNumber();
+ ProteinWithAbundances protein = new ProteinWithAbundances();
+ protein.setCoverage(proteinReference.getCoverage());
+ protein.setId(proteinReference.getId());
+ protein.setDescription(proteinReference.getDescription());
+ protein.setAccessionNumber(accessionNumber);
+ proteins.add(protein);
+ if (listOrNull != null)
{
- Long sampleID = getSampleIDOrParentSampleID(samplePermID);
- sampleIDs.add(sampleID);
- protein.addAbundanceFor(sampleID, proteinReference.getAbundance());
+ for (ProteinAbundance proteinAbundance : listOrNull)
+ {
+ String samplePermID = proteinAbundance.getSamplePermID();
+ Long sampleID = getSampleIDOrParentSampleID(samplePermID);
+ sampleIDs.add(sampleID);
+ protein.addAbundanceFor(sampleID, proteinAbundance.getAbundance());
+ }
}
}
-
+
private Long getSampleIDOrParentSampleID(String samplePermID)
{
Sample sample = sampleProvider.getSample(samplePermID);
@@ -63,25 +71,9 @@ class AbundanceManager
return parent == null ? sample.getId() : parent.getId();
}
- private ProteinWithAbundances getOrCreateProtein(ProteinReferenceWithProbability proteinReference)
- {
- String accessionNumber = proteinReference.getAccessionNumber();
- ProteinWithAbundances protein = proteins.get(accessionNumber);
- if (protein == null)
- {
- protein = new ProteinWithAbundances();
- protein.setCoverage(proteinReference.getCoverage());
- protein.setId(proteinReference.getId());
- protein.setDescription(proteinReference.getDescription());
- protein.setAccessionNumber(accessionNumber);
- proteins.put(accessionNumber, protein);
- }
- return protein;
- }
-
public Collection<ProteinWithAbundances> getProteinsWithAbundances()
{
- return proteins.values();
+ return proteins;
}
public final Collection<Long> getSampleIDs()
@@ -89,4 +81,5 @@ class AbundanceManager
return sampleIDs;
}
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
index 209e514577fa40d7b5ec171fec47c3a768f97100..966240e03b13c22c83afa056ffa11c7142a4486e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
@@ -32,10 +32,10 @@ public class BusinessObjectFactory extends AbstractPluginBusinessObjectFactory
private final IDAOFactory daoFactory;
private final IPhosphoNetXDAOFactory specificDAOFactory;
- public BusinessObjectFactory(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory, String typeOfCaching)
+ public BusinessObjectFactory(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory)
{
this.daoFactory = daoFactory;
- this.specificDAOFactory = new DAOFactoryWithCache(specificDAOFactory, typeOfCaching);
+ this.specificDAOFactory = specificDAOFactory;
}
public ISampleLister createSampleLister(Session session)
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
deleted file mode 100644
index 818ed880788aa33e2374e76bef7d003057fd7679..0000000000000000000000000000000000000000
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DAOFactoryWithCache.java
+++ /dev/null
@@ -1,376 +0,0 @@
-/*
- * 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.server.business;
-
-import it.unimi.dsi.fastutil.longs.LongSet;
-
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.ListIterator;
-
-import net.lemnik.eodsql.DataSet;
-
-import org.apache.commons.lang.SerializationUtils;
-import org.apache.log4j.Logger;
-import org.springframework.jdbc.core.RowMapper;
-import org.springframework.jdbc.core.namedparam.NamedParameterJdbcOperations;
-import org.springframework.jdbc.core.namedparam.NamedParameterJdbcTemplate;
-import org.springframework.jdbc.core.simple.ParameterizedRowMapper;
-import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
-import org.springframework.jdbc.support.lob.LobHandler;
-
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-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.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;
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-class DAOFactoryWithCache implements IPhosphoNetXDAOFactory
-{
- private static final class ProteinQueryDAO implements IProteinQueryDAO
- {
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, ProteinQueryDAO.class);
-
- private static final class DataSetProxy<T> implements DataSet<T>
- {
- private List<T> list;
- DataSetProxy(List<T> list)
- {
- this.list = list;
- }
- public void add(int index, T element)
- {
- list.add(index, element);
- }
- public boolean add(T o)
- {
- return list.add(o);
- }
- public boolean addAll(Collection<? extends T> c)
- {
- return list.addAll(c);
- }
- public boolean addAll(int index, Collection<? extends T> c)
- {
- return list.addAll(index, c);
- }
- public void clear()
- {
- list.clear();
- }
- public boolean contains(Object o)
- {
- return list.contains(o);
- }
- public boolean containsAll(Collection<?> c)
- {
- return list.containsAll(c);
- }
- @Override
- public boolean equals(Object o)
- {
- return list.equals(o);
- }
- public T get(int index)
- {
- return list.get(index);
- }
- @Override
- public int hashCode()
- {
- return list.hashCode();
- }
- public int indexOf(Object o)
- {
- return list.indexOf(o);
- }
- public boolean isEmpty()
- {
- return list.isEmpty();
- }
- public Iterator<T> iterator()
- {
- return list.iterator();
- }
- public int lastIndexOf(Object o)
- {
- return list.lastIndexOf(o);
- }
- public ListIterator<T> listIterator()
- {
- return list.listIterator();
- }
- public ListIterator<T> listIterator(int index)
- {
- return list.listIterator(index);
- }
- public T remove(int index)
- {
- return list.remove(index);
- }
- public boolean remove(Object o)
- {
- return list.remove(o);
- }
- public boolean removeAll(Collection<?> c)
- {
- return list.removeAll(c);
- }
- public boolean retainAll(Collection<?> c)
- {
- return list.retainAll(c);
- }
- public T set(int index, T element)
- {
- return list.set(index, element);
- }
- public int size()
- {
- return list.size();
- }
- public List<T> subList(int fromIndex, int toIndex)
- {
- return list.subList(fromIndex, toIndex);
- }
- public Object[] toArray()
- {
- return list.toArray();
- }
- public <X> X[] toArray(X[] a)
- {
- return list.toArray(a);
- }
- public void close()
- {
- }
- public void disconnect()
- {
- }
- public boolean isConnected()
- {
- return false;
- }
-
- }
-
- private final IProteinQueryDAO dao;
-
- private final DatabaseConfigurationContext context;
-
- private final SimpleJdbcTemplate template;
-
- private NamedParameterJdbcTemplate namedTemplate;
-
- ProteinQueryDAO(final IProteinQueryDAO dao, DatabaseConfigurationContext context)
- {
- this.dao = dao;
- this.context = context;
- template = new SimpleJdbcTemplate(context.getDataSource());
- namedTemplate = new NamedParameterJdbcTemplate(context.getDataSource());
- }
-
- public void close()
- {
- dao.close();
- }
-
- public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID)
- {
- return dao.getProbabilityFDRMapping(dataSetID);
- }
-
- public boolean isClosed()
- {
- return dao.isClosed();
- }
-
- public DataSet<String> listAbundanceRelatedSamplePermIDsByExperiment(String experimentPermID)
- {
- return dao.listAbundanceRelatedSamplePermIDsByExperiment(experimentPermID);
- }
-
- public DataSet<IdentifiedPeptide> listIdentifiedPeptidesByProtein(long proteinID)
- {
- return dao.listIdentifiedPeptidesByProtein(proteinID);
- }
-
- public DataSet<ProteinReferenceWithProbability> listProteinsByExperiment(
- String experimentPermID)
- {
- long time = System.currentTimeMillis();
- final LobHandler lobHandler = context.getLobHandler();
- List<ProteinReferenceWithProbability> resultSet =
- template.queryForObject(
- "select blob from protein_view_cache where experiment_perm_id = ?",
- new ParameterizedRowMapper<List<ProteinReferenceWithProbability>>()
- {
-
- public List<ProteinReferenceWithProbability> mapRow(ResultSet rs,
- int rowNum) throws SQLException
- {
- return (List<ProteinReferenceWithProbability>) SerializationUtils
- .deserialize(lobHandler.getBlobAsBinaryStream(rs, 1));
- }
- }, experimentPermID);
- operationLog.info("(" + (System.currentTimeMillis() - time) + "ms) listProteinsByExperiment");
- return new DataSetProxy<ProteinReferenceWithProbability>(resultSet);
- }
-
- public DataSet<IdentifiedProtein> listProteinsByProteinReferenceAndExperiment(
- String experimentPermID, long proteinReferenceID)
- {
- return dao.listProteinsByProteinReferenceAndExperiment(experimentPermID,
- proteinReferenceID);
- }
-
- public DataSet<Sequence> listProteinSequencesByProteinReference(long proteinReferenceID)
- {
- return dao.listProteinSequencesByProteinReference(proteinReferenceID);
- }
-
- public DataSet<ProteinReferenceWithProbabilityAndPeptide> listProteinsWithProbabilityAndPeptidesByExperiment(
- String experimentPermID)
- {
- return dao.listProteinsWithProbabilityAndPeptidesByExperiment(experimentPermID);
- }
-
- public DataSet<SampleAbundance> listSampleAbundanceByProtein(String experimentPermID,
- long proteinReferenceID)
- {
- return dao.listSampleAbundanceByProtein(experimentPermID, proteinReferenceID);
- }
-
- public ProteinReference tryToGetProteinReference(long proteinReferenceID)
- {
- return dao.tryToGetProteinReference(proteinReferenceID);
- }
-
- public byte[] tryToGetCachedProteinView(String experimentPermID)
- {
- return dao.tryToGetCachedProteinView(experimentPermID);
- }
-
- public DataSet<ProteinReferenceWithProtein> listProteinReferencesByExperiment(
- String experimentPermID)
- {
- long time = System.currentTimeMillis();
- try
- {
- List<ProteinReferenceWithProtein> list = template.query("select d.id , p.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 = ?",
- new ParameterizedRowMapper<ProteinReferenceWithProtein>()
- {
-
- public ProteinReferenceWithProtein mapRow(ResultSet rs, int rowNum)
- throws SQLException
- {
- ProteinReferenceWithProtein protein =
- new ProteinReferenceWithProtein();
- protein.setDataSetID(rs.getLong(1));
- protein.setProteinID(rs.getLong(2));
- protein.setProbability(rs.getDouble(3));
- protein.setCoverage(rs.getDouble(4));
- protein.setId(rs.getLong(5));
- protein.setAccessionNumber(rs.getString(6));
- protein.setDescription(rs.getString(7));
- return protein;
- }
- }, experimentPermID);
- return new DataSetProxy<ProteinReferenceWithProtein>(list);
-// return dao.listProteinReferencesByExperiment(experimentPermID);
- } finally
- {
- operationLog.info("(" + (System.currentTimeMillis() - time )+ "ms) listProteinReferenceByExperiment");
- }
- }
-
- public DataSet<ProteinAbundance> listProteinWithAbundanceByExperiment(
- LongSet proteinIDs)
- {
- long time = System.currentTimeMillis();
- try
- {
- List<ProteinAbundance> list = namedTemplate.query("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 in (:ids)", Collections.singletonMap("ids", proteinIDs), new RowMapper()
- {
-
- public Object mapRow(ResultSet rs, int rowNum) throws SQLException
- {
- ProteinAbundance proteinAbundance = new ProteinAbundance();
- proteinAbundance.setId(rs.getLong(1));
- proteinAbundance.setAbundance(rs.getDouble(2));
- proteinAbundance.setSampleID(rs.getString(3));
- return proteinAbundance;
- }
- });
- return new DataSetProxy<ProteinAbundance>(list);
- } finally
- {
- operationLog.info("(" + (System.currentTimeMillis() - time)
- + "ms) listProteinWithAbundanceByExperiment");
- }
- }
- }
-
- private IProteinQueryDAO proteinQueryDAO;
- private DatabaseConfigurationContext context;
-
- DAOFactoryWithCache(IPhosphoNetXDAOFactory daoFactory, String typeOfCaching)
- {
- proteinQueryDAO = new ProteinQueryDAO(daoFactory.getProteinQueryDAO(), daoFactory.getContext());
- context = daoFactory.getContext();
- }
-
- public IProteinQueryDAO getProteinQueryDAO()
- {
- return proteinQueryDAO;
- }
-
- public DatabaseConfigurationContext getContext()
- {
- return context;
- }
-
-}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
index 945ecc7b86a560e6bca73ab47546d66b9dfc5c55..d1681f9b23d060b068b268fb8519f08ed181a805 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
@@ -26,7 +26,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQue
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ProbabilityToFDRCalculator;
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.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProtein;
/**
* @author Franz-Josef Elmer
@@ -43,7 +43,7 @@ class ErrorModel
this.specificDAOFactory = specificDAOFactory;
}
- boolean passProtein(ProteinReferenceWithProbability protein, double falseDiscoveryRate)
+ boolean passProtein(ProteinReferenceWithProtein protein, double falseDiscoveryRate)
{
ProbabilityToFDRCalculator calculator = getCalculator(protein.getDataSetID());
return calculator.calculateFDR(protein.getProbability()) <= falseDiscoveryRate;
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 337c15436f4adb1d937b1556694ce41a27c03c5d..53bb3ef4fbcb740847ea33a33e017846bc487175 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
@@ -38,7 +38,6 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceCol
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;
@@ -124,91 +123,60 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
double falseDiscoveryRate)
{
AbundanceManager abundanceManager = new AbundanceManager(sampleProvider);
- IPhosphoNetXDAOFactory daoFactory = getSpecificDAOFactory();
- ErrorModel errorModel = new ErrorModel(daoFactory);
- IProteinQueryDAO proteinQueryDAO = daoFactory.getProteinQueryDAO();
- DataSet<ProteinReferenceWithProtein> ds1 = proteinQueryDAO.listProteinReferencesByExperiment(experimentPermID);
- List<ProteinReferenceWithProtein> prs = new ArrayList<ProteinReferenceWithProtein>();
+ IPhosphoNetXDAOFactory specificDAOFactory = getSpecificDAOFactory();
+ IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO();
+ DataSet<ProteinReferenceWithProtein> dataSet =
+ dao.listProteinReferencesByExperiment(experimentPermID);
+ List<ProteinReferenceWithProtein> proteins = new ArrayList<ProteinReferenceWithProtein>();
LongOpenHashSet proteinIDs = new LongOpenHashSet();
try
{
- for (ProteinReferenceWithProtein protein : ds1)
+ for (ProteinReferenceWithProtein protein : dataSet)
{
- prs.add(protein);
+ proteins.add(protein);
proteinIDs.add(protein.getProteinID());
}
} finally
{
- ds1.close();
+ dataSet.close();
}
- DataSet<ProteinAbundance> ds2 = proteinQueryDAO.listProteinWithAbundanceByExperiment(proteinIDs);
- Map<Long, List<ProteinAbundance>> p2a = new HashMap<Long, List<ProteinAbundance>>();
+ Map<Long, List<ProteinAbundance>> abundancesPerProtein = getAbudancesPerProtein(proteinIDs);
+ ErrorModel errorModel = new ErrorModel(specificDAOFactory);
+ for (ProteinReferenceWithProtein protein : proteins)
+ {
+ if (errorModel.passProtein(protein, falseDiscoveryRate))
+ {
+ List<ProteinAbundance> list = abundancesPerProtein.get(protein.getProteinID());
+ abundanceManager.handle(protein, list);
+ }
+ }
+ return abundanceManager;
+ }
+
+ private Map<Long, List<ProteinAbundance>> getAbudancesPerProtein(LongOpenHashSet proteinIDs)
+ {
+ IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
+ DataSet<ProteinAbundance> dataSet = dao.listProteinWithAbundanceByExperiment(proteinIDs);
+ Map<Long, List<ProteinAbundance>> abundancesPerProtein =
+ new HashMap<Long, List<ProteinAbundance>>();
try
{
- for (ProteinAbundance proteinAbundance : ds2)
+ for (ProteinAbundance proteinAbundance : dataSet)
{
long proteinID = proteinAbundance.getId();
- List<ProteinAbundance> list = p2a.get(proteinID);
+ List<ProteinAbundance> list = abundancesPerProtein.get(proteinID);
if (list == null)
{
list = new ArrayList<ProteinAbundance>();
- p2a.put(proteinID, list);
+ abundancesPerProtein.put(proteinID, list);
}
list.add(proteinAbundance);
}
} finally
{
- 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.close();
}
-// 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;
+ return abundancesPerProtein;
}
private static double[] concatenate(double[] array1OrNull, double[] array2OrNull)
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 2e5a22a4d421e8c0b5add212039155f0c1276af1..3eb157ccf0c0ced52cf0d0612d6dc862eb2efdda 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
@@ -28,7 +28,6 @@ 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;
@@ -44,9 +43,6 @@ public interface IProteinQueryDAO extends BaseQuery
@Select(sql = "select * from probability_fdr_mappings where dase_id = ?{1}", disconnected = true)
public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID);
- @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 "
@@ -63,19 +59,6 @@ public interface IProteinQueryDAO extends BaseQuery
+ "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 "
- + "left join data_sets as d on p.dase_id = d.id "
- + "left join experiments as e on d.expe_id = e.id "
- + "left join sequences as s on ip.sequ_id = s.id "
- + "left join protein_references as pr on s.prre_id = pr.id "
- + "left join abundances as a on p.id = a.prot_id "
- + "left join samples on a.samp_id = samples.id "
- + "where e.perm_id = ?{1}")
- public DataSet<ProteinReferenceWithProbability> listProteinsByExperiment(String experimentPermID);
-
-
@Select(sql = "select p.dase_id as data_set_id, p.probability, s.prre_id as id, pe.sequence "
+ "from identified_proteins as ip left join sequences as s on ip.sequ_id = s.id "
+ "left join proteins as p on ip.prot_id = p.id "
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/migration/MigrationStepFrom002To003.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/migration/MigrationStepFrom002To003.java
index 7439043104d50ba0668446452a082f7da2b5605f..ec250df1430b26153ec3f8541cb5d2746c0d6d71 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/migration/MigrationStepFrom002To003.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/migration/MigrationStepFrom002To003.java
@@ -16,9 +16,6 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.db.migration;
-import java.io.ByteArrayOutputStream;
-import java.io.ObjectOutputStream;
-import java.io.Serializable;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
@@ -28,23 +25,17 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
-import org.apache.commons.lang.SerializationUtils;
import org.apache.log4j.Logger;
import org.springframework.dao.DataAccessException;
import org.springframework.jdbc.core.JdbcOperations;
import org.springframework.jdbc.core.ResultSetExtractor;
-import org.springframework.jdbc.core.simple.ParameterizedRowMapper;
import org.springframework.jdbc.core.simple.SimpleJdbcTemplate;
-import org.springframework.jdbc.support.JdbcUtils;
-
-import sun.print.PSPrinterJob.EPSPrinter;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.dbmigration.java.MigrationStepAdapter;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Occurrence;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.OccurrenceUtil;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
/**
*
@@ -64,7 +55,6 @@ public class MigrationStepFrom002To003 extends MigrationStepAdapter
List<Object[]> coverageValues = calculateCoverageValues(simpleJdbcTemplate);
operationLog.info("update " + coverageValues.size() + " identified proteins");
simpleJdbcTemplate.batchUpdate("update identified_proteins set coverage = ? where id = ?", coverageValues);
- createProteinView(simpleJdbcTemplate);
}
private List<Object[]> calculateCoverageValues(SimpleJdbcTemplate simpleJdbcTemplate)
@@ -99,67 +89,6 @@ public class MigrationStepFrom002To003 extends MigrationStepAdapter
return values;
}
- private void createProteinView(SimpleJdbcTemplate simpleJdbcTemplate)
- {
- List<String> experiments =
- simpleJdbcTemplate.query("select perm_id from experiments",
- new ParameterizedRowMapper<String>()
- {
- public String mapRow(ResultSet rs, int rowNum) throws SQLException
- {
- return rs.getString(1);
- }
- });
- operationLog.info("create protein views for " + experiments.size() + " experiments");
- logMemory();
- JdbcOperations jdbcOperations = simpleJdbcTemplate.getJdbcOperations();
- Object[] arguments = new Object[1];
- for (final String experiment : experiments)
- {
- arguments[0] = experiment;
- List<ProteinReferenceWithProbability> rows = simpleJdbcTemplate.query(
- "select pr.id, pr.accession_number, pr.description, d.id, p.probability, "
- + "ip.coverage, a.value, samples.perm_id "
- + "from identified_proteins as ip "
- + "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 "
- + "left join sequences as s on ip.sequ_id = s.id "
- + "left join protein_references as pr on s.prre_id = pr.id "
- + "left join abundances as a on p.id = a.prot_id "
- + "left join samples on a.samp_id = samples.id "
- + "where e.perm_id = ?", new ParameterizedRowMapper<ProteinReferenceWithProbability>()
- {
-
- public ProteinReferenceWithProbability mapRow(ResultSet rs,
- int rowNum) throws SQLException
- {
- ProteinReferenceWithProbability protein = new ProteinReferenceWithProbability();
- protein.setId(rs.getLong(1));
- protein.setAccessionNumber(rs.getString(2));
- protein.setDescription(rs.getString(3));
- protein.setDataSetID(rs.getLong(4));
- protein.setProbability(rs.getDouble(5));
- protein.setCoverage(rs.getDouble(6));
- protein.setAbundance(getDoubleOrNull(rs, 7));
- protein.setSamplePermID(rs.getString(8));
- return protein;
- }
- }, experiment);
- operationLog.info("insert " + rows.size() + " rows into protein_view_cache for experiment "
- + experiment);
- byte[] serializedRows = SerializationUtils.serialize((Serializable) rows);
- simpleJdbcTemplate.update("insert into protein_view_cache (experiment_perm_id, blob) "
- + "values(?, ?)", experiment, serializedRows);
- logMemory();
- }
- }
- private Double getDoubleOrNull(ResultSet rs, int index) throws SQLException
- {
- double result = rs.getDouble(index);
- return rs.wasNull() ? null : result;
- }
-
private Map<Long, List<String>> getPeptides(JdbcOperations jdbcOperations)
{
final Map<Long, List<String>> peptides = new HashMap<Long, List<String>>();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinWithAbundances.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinWithAbundances.java
index 8a16a8f4bbe98e8143accd2ea357a2727c11691b..4888189e7a8e98833ff7074ee5079bf13b9b53a8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinWithAbundances.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinWithAbundances.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+import it.unimi.dsi.fastutil.doubles.DoubleArrayList;
+
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Set;
@@ -33,7 +35,7 @@ public class ProteinWithAbundances extends ProteinReference
private double coverage;
- private final Map<Long, double[]> abundances = new LinkedHashMap<Long, double[]>();
+ private final Map<Long, DoubleArrayList> abundances = new LinkedHashMap<Long, DoubleArrayList>();
public double getCoverage()
{
@@ -47,15 +49,13 @@ public class ProteinWithAbundances extends ProteinReference
public void addAbundanceFor(long sampleID, double abundance)
{
- double[] array = abundances.get(sampleID);
- if (array == null)
+ DoubleArrayList list = abundances.get(sampleID);
+ if (list == null)
{
- array = EMPTY_ARRAY;
+ list = new DoubleArrayList();
+ abundances.put(sampleID, list);
}
- double[] newArray = new double[array.length + 1];
- System.arraycopy(array, 0, newArray, 0, array.length);
- newArray[array.length] = abundance;
- abundances.put(sampleID, newArray);
+ list.add(abundance);
}
public Set<Long> getSampleIDs()
@@ -65,7 +65,7 @@ public class ProteinWithAbundances extends ProteinReference
public double[] getAbundancesForSample(long sampleID)
{
- double[] values = abundances.get(sampleID);
- return values == null ? EMPTY_ARRAY : values;
+ DoubleArrayList list = abundances.get(sampleID);
+ return list == null ? EMPTY_ARRAY : list.toDoubleArray();
}
}
diff --git a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index f07dc588873328398414440d98db65fc985e08c6..6014a32b9ae6cdb42cb4e06a77f1d3331348461f 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -20,7 +20,7 @@
<property name="urlHostPart" value="${phosphonetx.database.url-host-part}" />
<property name="adminUser" value="${phosphonetx.database.admin-user}" />
<property name="owner" value="${phosphonetx.database.owner}" />
- <property name="readOnlyGroup" value="openbis_readonly" />
+ <property name="readOnlyGroup" value="phosphonetx_readonly" />
<property name="password" value="${phosphonetx.database.owner-password}" />
<property name="adminPassword" value="${phosphonetx.database.admin-password}" />
<property name="databaseKind" value="${phosphonetx.database.kind}" />
@@ -38,7 +38,6 @@
class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.BusinessObjectFactory">
<constructor-arg ref="dao-factory"/>
<constructor-arg ref="phosphonetx-dao-factory"/>
- <constructor-arg value="${type-of-caching}"/>
</bean>
<!--
diff --git a/rtd_phosphonetx/source/java/service.properties b/rtd_phosphonetx/source/java/service.properties
index 05992f1a3441496bfa8e5b9bbfac90fe178f6fd3..15fd9cc901bc7a00c0a2b1f157397d831eea90d5 100644
--- a/rtd_phosphonetx/source/java/service.properties
+++ b/rtd_phosphonetx/source/java/service.properties
@@ -66,5 +66,3 @@ query-database.label = Protein Data
query-database.databaseEngineCode = ${phosphonetx.database.engine}
query-database.basicDatabaseName = phosphonetx
query-database.databaseKind = ${phosphonetx.database.kind}
-
-#type-of-caching = file_system
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/sql/postgresql/003/grant-003.sql b/rtd_phosphonetx/source/sql/postgresql/003/grant-003.sql
new file mode 100644
index 0000000000000000000000000000000000000000..2e85f4fb1f6fcbb7f072005f9d1ab5ad9e1fe713
--- /dev/null
+++ b/rtd_phosphonetx/source/sql/postgresql/003/grant-003.sql
@@ -0,0 +1,18 @@
+-- Granting SELECT privilege to group PHOSPHONETX_READONLY
+
+GRANT SELECT ON TABLE EXPERIMENTS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE DATA_SETS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE MODIFICATIONS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE PEPTIDES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE PROTEINS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE SAMPLES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE SEQUENCES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE IDENTIFIED_PROTEINS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE ABUNDANCES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE PROBABILITY_FDR_MAPPINGS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE PROTEIN_REFERENCES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE DATABASES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE MODIFIED_PEPTIDES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE SPECTRUM_REFERENCES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE MODIFICATION_FRACTIONS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE EVENTS TO GROUP PHOSPHONETX_READONLY;
diff --git a/rtd_phosphonetx/source/sql/postgresql/003/schema-003.png b/rtd_phosphonetx/source/sql/postgresql/003/schema-003.png
new file mode 100755
index 0000000000000000000000000000000000000000..da8cae484122317fee9b24a68fa70670bec52989
Binary files /dev/null and b/rtd_phosphonetx/source/sql/postgresql/003/schema-003.png differ
diff --git a/rtd_phosphonetx/source/sql/postgresql/003/schema-003.sql b/rtd_phosphonetx/source/sql/postgresql/003/schema-003.sql
index 1c4cf2041d7e5a258b885a9ef9fd312bad247fa9..4dd90b2711ca06f202543708fd0d7e3caef40f6c 100755
--- a/rtd_phosphonetx/source/sql/postgresql/003/schema-003.sql
+++ b/rtd_phosphonetx/source/sql/postgresql/003/schema-003.sql
@@ -5,8 +5,8 @@
/* Project name: */
/* Author: */
/* Script type: Database creation script */
-/* Created on: 2009-12-07 11:03 */
-/* Model version: Version 2009-12-07 */
+/* Created on: 2010-03-31 16:10 */
+/* Model version: Version 2010-03-31 */
/* ---------------------------------------------------------------------- */
@@ -40,18 +40,6 @@ CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
/* Tables */
/* ---------------------------------------------------------------------- */
-/* ---------------------------------------------------------------------- */
-/* Add table "PROTEIN_VIEW" */
-/* ---------------------------------------------------------------------- */
-
-CREATE TABLE PROTEIN_VIEW_CACHE (
- ID BIGSERIAL NOT NULL,
- EXPERIMENT_PERM_ID CODE NOT NULL,
- BLOB BYTEA NOT NULL,
- CONSTRAINT PK_PROTEIN_VIEW PRIMARY KEY (ID)
-);
-
-
/* ---------------------------------------------------------------------- */
/* Add table "EXPERIMENTS" */
/* ---------------------------------------------------------------------- */
diff --git a/rtd_phosphonetx/source/sql/postgresql/migration/migration-002-003.sql b/rtd_phosphonetx/source/sql/postgresql/migration/migration-002-003.sql
index f2f9b1ecea66eadef5956f2781f1d56aac531eba..639f94657a5f066a34d862909c8e7ded53784ad6 100644
--- a/rtd_phosphonetx/source/sql/postgresql/migration/migration-002-003.sql
+++ b/rtd_phosphonetx/source/sql/postgresql/migration/migration-002-003.sql
@@ -2,10 +2,3 @@
ALTER TABLE IDENTIFIED_PROTEINS ADD COLUMN COVERAGE REAL_NUMBER;
-CREATE TABLE PROTEIN_VIEW_CACHE (
- ID BIGSERIAL NOT NULL,
- EXPERIMENT_PERM_ID CODE NOT NULL,
- BLOB BYTEA NOT NULL,
- CONSTRAINT PK_PROTEIN_VIEW PRIMARY KEY (ID)
-);
-
diff --git a/rtd_phosphonetx/source/sql/postgresql/schema.dez b/rtd_phosphonetx/source/sql/postgresql/schema.dez
index db19fe662755156618c655a908252c195dac69d8..f7c4d30fd3339b751c32db2d62671e1fa0e16fad 100755
--- a/rtd_phosphonetx/source/sql/postgresql/schema.dez
+++ b/rtd_phosphonetx/source/sql/postgresql/schema.dez
@@ -4,14 +4,14 @@
<VERSION>
<PROJECTSETTINGS>
<PROJECTFILENAME>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\phosphonetx.dez</PROJECTFILENAME>
-<MODIFIED>2009-12-07</MODIFIED>
+<MODIFIED>2010-03-31</MODIFIED>
<CREATED>2009-06-29</CREATED>
<CREATED2></CREATED2>
<PROJECTNAME></PROJECTNAME>
<DESCRIPTION></DESCRIPTION>
<AUTHOR></AUTHOR>
<COPYRIGHT></COPYRIGHT>
-<LASTGENERATEDFILES>N:\group\cisd\phosphonetx\datamodel\schema.sql;N:\group\cisd\phosphonetx\datamodel\drop.sql;C:\Users\felmer\Documents\CreateDBLog_200912073.txt</LASTGENERATEDFILES>
+<LASTGENERATEDFILES>N:\group\cisd\phosphonetx\datamodel\schema.sql;N:\group\cisd\phosphonetx\datamodel\drop.sql;\\d.ethz.ch\dfs\groups\bsse\users\cisd\felmer\Documents\CreateDBLog_201003311.txt</LASTGENERATEDFILES>
</PROJECTSETTINGS>
<CONNECTIONSETTINGS>
<SQLFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql</SQLFILE>
@@ -1209,7 +1209,7 @@
<POSNR>0</POSNR>
<SCHEMA></SCHEMA>
<DESC></DESC>
-<ATTRLASTID>5</ATTRLASTID>
+<ATTRLASTID>6</ATTRLASTID>
<IDXLASTID>1</IDXLASTID>
<TRGLASTID>1</TRGLASTID>
<CONLASTID>1</CONLASTID>
@@ -1309,6 +1309,19 @@
</ATTRIBUTEIDS>
</NNCON>
</ATTR>
+<ATTR>
+<NAME>COVERAGE</NAME>
+<ID>6</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>8</DOMAINID>
+<DT>
+<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+</ATTR>
</ATTRIBUTES>
</ENT>
<ENT>
@@ -2194,6 +2207,7 @@
</ENT>
<ENT>
<NAME>EVENTS</NAME>
+<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
<ID>176</ID>
<POSNR>0</POSNR>
<SCHEMA></SCHEMA>
@@ -2205,6 +2219,7 @@
<ATTRIBUTES>
<ATTR>
<NAME>LAST_SEEN_DELETION_EVENT_ID</NAME>
+<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
<ID>2</ID>
<POSNR>0</POSNR>
<SCHEMA></SCHEMA>
@@ -3061,9 +3076,9 @@
<ENTC>
<ID>47</ID>
<DIAGRAMID>1</DIAGRAMID>
-<W>142</W>
-<H>78</H>
-<L>541</L>
+<W>167</W>
+<H>93</H>
+<L>518</L>
<T>328</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
@@ -3087,7 +3102,7 @@
<ENTC>
<ID>96</ID>
<DIAGRAMID>1</DIAGRAMID>
-<W>245</W>
+<W>243</W>
<H>93</H>
<L>490</L>
<T>182</T>
@@ -3305,7 +3320,7 @@
<FROMRELATIVEX>5000</FROMRELATIVEX>
<FROMRELATIVEY>5000</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
-<TORELATIVEY>5000</TORELATIVEY>
+<TORELATIVEY>4194</TORELATIVEY>
<POINTS>
<POINT>
<X>454</X>
@@ -3320,7 +3335,7 @@
<Y>367</Y>
</POINT>
<POINT>
-<X>540</X>
+<X>517</X>
<Y>367</Y>
</POINT>
</POINTS>
@@ -3331,25 +3346,25 @@
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
<FROMRELATIVEX>2840</FROMRELATIVEX>
-<FROMRELATIVEY>3611</FROMRELATIVEY>
+<FROMRELATIVEY>4259</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
-<TORELATIVEY>5000</TORELATIVEY>
+<TORELATIVEY>4946</TORELATIVEY>
<POINTS>
<POINT>
<X>735</X>
-<Y>367</Y>
+<Y>374</Y>
</POINT>
<POINT>
-<X>705</X>
-<Y>367</Y>
+<X>722</X>
+<Y>374</Y>
</POINT>
<POINT>
-<X>705</X>
-<Y>367</Y>
+<X>722</X>
+<Y>374</Y>
</POINT>
<POINT>
-<X>683</X>
-<Y>367</Y>
+<X>685</X>
+<Y>374</Y>
</POINT>
</POINTS>
</RELC>
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
index 99d399a15d46a33e09024c784f7bd6ad5903a3f6..9c1b081cfd1aadfff3995142851993e397494c07 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/AbundanceManagerTest.java
@@ -16,7 +16,9 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
+import java.util.Arrays;
import java.util.Collection;
+import java.util.Collections;
import java.util.Iterator;
import org.jmock.Expectations;
@@ -25,7 +27,8 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerTestCase;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinAbundance;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundances;
/**
@@ -64,18 +67,19 @@ public class AbundanceManagerTest extends AbstractServerTestCase
public void testHandleTwoProteinReferencesButOnlyOneHasAnAbundance()
{
prepareSampleIDProvider();
- ProteinReferenceWithProbability protein1 = new ProteinReferenceWithProbability();
+ ProteinReferenceWithProtein protein1 = new ProteinReferenceWithProtein();
protein1.setId(1);
protein1.setAccessionNumber("abc1");
protein1.setDescription("abc one");
- protein1.setSamplePermID(PERM_ID1);
- protein1.setAbundance(1.5);
- abundanceManager.handle(protein1);
- ProteinReferenceWithProbability protein2 = new ProteinReferenceWithProbability();
+ ProteinAbundance proteinAbundance = new ProteinAbundance();
+ proteinAbundance.setSampleID(PERM_ID1);
+ proteinAbundance.setAbundance(1.5);
+ abundanceManager.handle(protein1, Collections.singletonList(proteinAbundance));
+ ProteinReferenceWithProtein protein2 = new ProteinReferenceWithProtein();
protein2.setId(2);
protein2.setAccessionNumber("abc2");
protein2.setDescription("abc two");
- abundanceManager.handle(protein2);
+ abundanceManager.handle(protein2, null);
assertEquals(1, abundanceManager.getSampleIDs().size());
Collection<ProteinWithAbundances> proteinsWithAbundances = abundanceManager.getProteinsWithAbundances();
@@ -103,11 +107,13 @@ public class AbundanceManagerTest extends AbstractServerTestCase
public void testHandleProteinReferencesWithManyAbundancesForTwoSamples()
{
prepareSampleIDProvider();
- abundanceManager.handle(createProteinReference(PERM_ID1, 1.5));
- abundanceManager.handle(createProteinReference(PERM_ID1, 2.25));
- abundanceManager.handle(createProteinReference(PERM_ID2, 42));
- abundanceManager.handle(createProteinReference(PERM_ID2, 4.75));
- abundanceManager.handle(createProteinReference(PERM_ID2, 7.5));
+ ProteinReferenceWithProtein protein1 = new ProteinReferenceWithProtein();
+ protein1.setId(1);
+ protein1.setAccessionNumber("abc1");
+ protein1.setDescription("abc one");
+
+ abundanceManager.handle(protein1, Arrays.asList(a(PERM_ID1, 1.5), a(PERM_ID1, 2.25), a(
+ PERM_ID2, 42), a(PERM_ID2, 4.75), a(PERM_ID2, 7.5)));
assertEquals(2, abundanceManager.getSampleIDs().size());
Collection<ProteinWithAbundances> proteinsWithAbundances = abundanceManager.getProteinsWithAbundances();
@@ -150,14 +156,11 @@ public class AbundanceManagerTest extends AbstractServerTestCase
});
}
- private ProteinReferenceWithProbability createProteinReference(String samplePermID, double abundance)
+ private ProteinAbundance a(String samplePermID, double abundance)
{
- ProteinReferenceWithProbability protein1 = new ProteinReferenceWithProbability();
- protein1.setId(1);
- protein1.setAccessionNumber("abc1");
- protein1.setDescription("abc one");
- protein1.setSamplePermID(samplePermID);
- protein1.setAbundance(abundance);
- return protein1;
+ ProteinAbundance protein = new ProteinAbundance();
+ protein.setSampleID(samplePermID);
+ protein.setAbundance(abundance);
+ return protein;
}
}
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 04c35faf6ca32b9353b6bde4928f6953ff9e1aae..6e2d588865e34fd9ea0b8ba58cba63d98f7b13b5 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
@@ -16,11 +16,16 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business;
+import it.unimi.dsi.fastutil.longs.LongArraySet;
+import it.unimi.dsi.fastutil.longs.LongSet;
+
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Map;
+import net.lemnik.eodsql.DataSet;
+
import org.jmock.Expectations;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -36,14 +41,14 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceCol
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.ProbabilityFDRMapping;
-import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinAbundance;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProtein;
/**
*
*
* @author Franz-Josef Elmer
*/
-@Test(groups="broken")
public class ProteinInfoTableTest extends AbstractServerTestCase
{
private static final double COVERAGE = 0.5;
@@ -52,7 +57,8 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
private static final long SAMPLE_ID_2 = 102L;
private static final long SAMPLE_ID_1 = 101L;
private static final Double ABUNDANCE = new Double(47.11);
- private static final long PROTEIN_ID = 41L;
+ private static final long PROTEIN_ID = 4141L;
+ private static final long PROTEIN_REFERENCE_ID = 41L;
private static final String SAMPLE_PERM_ID = "s47-11";
private static final long SAMPLE_ID = 4711;
private static final long DATA_SET_ID = 42L;
@@ -101,42 +107,50 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
@Test
public void testLoadLeadingToAnEmptyTable()
{
- final MockDataSet<ProteinReferenceWithProbability> dataSet =
- new MockDataSet<ProteinReferenceWithProbability>();
- prepareLoadDataSet(dataSet);
+ MockDataSet<ProteinReferenceWithProtein> proteinReferences = new MockDataSet<ProteinReferenceWithProtein>();
+ MockDataSet<ProteinAbundance> proteinAbundances = new MockDataSet<ProteinAbundance>();
+ prepareLoadDataSet(proteinReferences, proteinAbundances);
table.load(Arrays.<AbundanceColumnDefinition> asList(), EXPERIMENT_ID,
FALSE_DISCOVERY_RATE, AggregateFunction.MEAN, false);
assertEquals(0, table.getProteinInfos().size());
- assertEquals(true, dataSet.hasCloseBeenInvoked());
+ assertEquals(true, proteinReferences.hasCloseBeenInvoked());
+ assertEquals(true, proteinAbundances.hasCloseBeenInvoked());
context.assertIsSatisfied();
}
@Test
public void testSimpleLoad()
{
- final MockDataSet<ProteinReferenceWithProbability> dataSet =
- new MockDataSet<ProteinReferenceWithProbability>();
- ProteinReferenceWithProbability proteinReference = new ProteinReferenceWithProbability();
+ MockDataSet<ProteinReferenceWithProtein> proteinReferences =
+ new MockDataSet<ProteinReferenceWithProtein>();
+ MockDataSet<ProteinAbundance> abundances = new MockDataSet<ProteinAbundance>();
+ ProteinReferenceWithProtein proteinReference = new ProteinReferenceWithProtein();
proteinReference.setDataSetID(DATA_SET_ID);
- proteinReference.setSamplePermID(SAMPLE_PERM_ID);
+ proteinReference.setProteinID(PROTEIN_ID);
proteinReference.setAccessionNumber(ACCESSION_NUMBER);
- proteinReference.setId(PROTEIN_ID);
- proteinReference.setAbundance(ABUNDANCE);
- dataSet.add(proteinReference);
- proteinReference = new ProteinReferenceWithProbability();
+ proteinReference.setId(PROTEIN_REFERENCE_ID);
+ proteinReferences.add(proteinReference);
+ ProteinAbundance proteinAbundance = new ProteinAbundance();
+ proteinAbundance.setId(PROTEIN_ID);
+ proteinAbundance.setAbundance(ABUNDANCE);
+ proteinAbundance.setSampleID(SAMPLE_PERM_ID);
+ abundances.add(proteinAbundance);
+ proteinReference = new ProteinReferenceWithProtein();
+ proteinReference.setProteinID(PROTEIN_ID);
+ proteinReference.setId(PROTEIN_REFERENCE_ID);
proteinReference.setProbability(1);
proteinReference.setDataSetID(DATA_SET_ID);
- dataSet.add(proteinReference);
+ proteinReferences.add(proteinReference);
final MockDataSet<ProbabilityFDRMapping> mappings = new MockDataSet<ProbabilityFDRMapping>();
mappings.add(new ProbabilityFDRMapping());
ProbabilityFDRMapping mapping = new ProbabilityFDRMapping();
mapping.setProbability(1);
mapping.setFalseDiscoveryRate(1);
mappings.add(mapping);
- prepareLoadDataSet(dataSet);
+ prepareLoadDataSet(proteinReferences, abundances);
context.checking(new Expectations()
{
{
@@ -158,10 +172,10 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
Collection<ProteinInfo> proteins = table.getProteinInfos();
assertEquals(1, proteins.size());
ProteinInfo protein = proteins.iterator().next();
- assertEquals(PROTEIN_ID, protein.getId().getId().longValue());
+ assertEquals(PROTEIN_REFERENCE_ID, protein.getId().getId().longValue());
assertEquals(ACCESSION_NUMBER, protein.getAccessionNumber());
- assertEquals(true, dataSet.hasCloseBeenInvoked());
+ assertEquals(true, proteinReferences.hasCloseBeenInvoked());
assertEquals(true, mappings.hasCloseBeenInvoked());
context.assertIsSatisfied();
}
@@ -180,19 +194,27 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
private void checkAggregationType(double expectedAbundance, boolean aggregateOriginal)
{
- final MockDataSet<ProteinReferenceWithProbability> dataSet =
- new MockDataSet<ProteinReferenceWithProbability>();
- dataSet.add(createProtein(SAMPLE_ID_1, 1));
- dataSet.add(createProtein(SAMPLE_ID_1, 2));
- dataSet.add(createProtein(SAMPLE_ID_2, 3));
- dataSet.add(createProtein(SAMPLE_ID_3, 20));
+ final MockDataSet<ProteinReferenceWithProtein> proteinReferences =
+ new MockDataSet<ProteinReferenceWithProtein>();
+ ProteinReferenceWithProtein proteinReference = new ProteinReferenceWithProtein();
+ proteinReference.setProteinID(PROTEIN_ID);
+ proteinReference.setDataSetID(DATA_SET_ID);
+ proteinReference.setAccessionNumber(ACCESSION_NUMBER);
+ proteinReference.setId(PROTEIN_REFERENCE_ID);
+ proteinReference.setCoverage(COVERAGE);
+ proteinReferences.add(proteinReference);
+ MockDataSet<ProteinAbundance> proteinAbundances = new MockDataSet<ProteinAbundance>();
+ proteinAbundances.add(createProteinAbundance(SAMPLE_ID_1, 1));
+ proteinAbundances.add(createProteinAbundance(SAMPLE_ID_1, 2));
+ proteinAbundances.add(createProteinAbundance(SAMPLE_ID_2, 3));
+ proteinAbundances.add(createProteinAbundance(SAMPLE_ID_3, 20));
final MockDataSet<ProbabilityFDRMapping> mappings = new MockDataSet<ProbabilityFDRMapping>();
mappings.add(new ProbabilityFDRMapping());
ProbabilityFDRMapping mapping = new ProbabilityFDRMapping();
mapping.setProbability(1);
mapping.setFalseDiscoveryRate(1);
mappings.add(mapping);
- prepareLoadDataSet(dataSet);
+ prepareLoadDataSet(proteinReferences, proteinAbundances);
context.checking(new Expectations()
{
{
@@ -215,7 +237,7 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
Collection<ProteinInfo> proteins = table.getProteinInfos();
assertEquals(1, proteins.size());
ProteinInfo protein = proteins.iterator().next();
- assertEquals(PROTEIN_ID, protein.getId().getId().longValue());
+ assertEquals(PROTEIN_REFERENCE_ID, protein.getId().getId().longValue());
assertEquals(ACCESSION_NUMBER, protein.getAccessionNumber());
Map<Long, Double> abundances = protein.getAbundances();
assertEquals(2, abundances.size());
@@ -223,12 +245,14 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
assertEquals(20.0, abundances.get(SAMPLE_ID_3).doubleValue());
assertEquals(100 * COVERAGE, protein.getCoverage());
- assertEquals(true, dataSet.hasCloseBeenInvoked());
+ assertEquals(true, proteinReferences.hasCloseBeenInvoked());
assertEquals(true, mappings.hasCloseBeenInvoked());
context.assertIsSatisfied();
}
- private void prepareLoadDataSet(final MockDataSet<ProteinReferenceWithProbability> dataSet)
+ private void prepareLoadDataSet(
+ final MockDataSet<ProteinReferenceWithProtein> proteinReferences,
+ final DataSet<ProteinAbundance> proteinAbundances)
{
context.checking(new Expectations()
{
@@ -238,22 +262,27 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
experimentPE.setPermId(EXPERIMENT_PERM_ID);
will(returnValue(experimentPE));
- one(proteinDAO).listProteinsByExperiment(EXPERIMENT_PERM_ID);
- will(returnValue(dataSet));
+ one(proteinDAO).listProteinReferencesByExperiment(EXPERIMENT_PERM_ID);
+ will(returnValue(proteinReferences));
+
+ LongSet proteinIDs = new LongArraySet();
+ for (ProteinReferenceWithProtein p : proteinReferences)
+ {
+ proteinIDs.add(p.getProteinID());
+ }
+ one(proteinDAO).listProteinWithAbundanceByExperiment(proteinIDs);
+ will(returnValue(proteinAbundances));
}
});
}
- private ProteinReferenceWithProbability createProtein(long sampleID, double abundance)
+ private ProteinAbundance createProteinAbundance(long sampleID, double abundance)
{
- ProteinReferenceWithProbability proteinReference = new ProteinReferenceWithProbability();
- proteinReference.setDataSetID(DATA_SET_ID);
- proteinReference.setSamplePermID(PERM_ID_PREFIX + sampleID);
- proteinReference.setAccessionNumber(ACCESSION_NUMBER);
- proteinReference.setId(PROTEIN_ID);
- proteinReference.setAbundance(abundance);
- proteinReference.setCoverage(COVERAGE);
- return proteinReference;
+ ProteinAbundance proteinAbundance = new ProteinAbundance();
+ proteinAbundance.setSampleID(PERM_ID_PREFIX + sampleID);
+ proteinAbundance.setId(PROTEIN_ID);
+ proteinAbundance.setAbundance(abundance);
+ return proteinAbundance;
}
}