From b93c02a3363dc81ccbbe1abb981adeaf34bfb8da Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 8 Dec 2009 14:52:07 +0000
Subject: [PATCH] LMS-1290 revert changes made since revision 13672
SVN: 13747
---
.../phosphonetx/server/PhosphoNetXServer.java | 45 +++------
.../server/business/DataSetProteinTable.java | 46 ++++------
.../server/business/ErrorModel.java | 26 ++----
.../server/business/ProteinDetailsBO.java | 85 +++++++----------
.../server/business/ProteinInfoTable.java | 92 +++++--------------
.../server/business/ProteinSequenceTable.java | 47 ++++------
.../server/business/ProteinSummaryTable.java | 48 +++++-----
.../server/business/SampleTable.java | 36 +++-----
.../dataaccess/IPhosphoNetXDAOFactory.java | 16 +---
.../dataaccess/db/PhosphoNetXDAOFactory.java | 50 ++--------
.../java/phosphonetx-applicationContext.xml | 1 -
.../source/java/service.properties | 4 -
.../server/PhosphoNetXServerTest.java | 3 +-
.../server/business/ErrorModelTest.java | 3 +-
.../server/business/ProteinInfoTableTest.java | 5 +-
.../business/ProteinSummaryTableTest.java | 3 +-
16 files changed, 161 insertions(+), 349 deletions(-)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
index 7fb1a68590c..677886ca746 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
@@ -108,27 +108,21 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
{
Session session = getSession(sessionToken);
String experimentPermID = getExperimentPermIDFor(experimentID);
- final IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAOFromPool();
+ IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO();
+ DataSet<String> samplePermIDs =
+ dao.listAbundanceRelatedSamplePermIDsByExperiment(experimentPermID);
try
{
- DataSet<String> samplePermIDs =
- dao.listAbundanceRelatedSamplePermIDsByExperiment(experimentPermID);
- try
+ IAbundanceColumnDefinitionTable table =
+ specificBOFactory.createAbundanceColumnDefinitionTable(session);
+ for (String samplePermID : samplePermIDs)
{
- IAbundanceColumnDefinitionTable table =
- specificBOFactory.createAbundanceColumnDefinitionTable(session);
- for (String samplePermID : samplePermIDs)
- {
- table.add(samplePermID);
- }
- return table.getSortedAndAggregatedDefinitions(treatmentTypeOrNull);
- } finally
- {
- samplePermIDs.close();
+ table.add(samplePermID);
}
+ return table.getSortedAndAggregatedDefinitions(treatmentTypeOrNull);
} finally
{
- specificDAOFactory.returnProteinQueryDAOToPool(dao);
+ samplePermIDs.close();
}
}
@@ -158,20 +152,13 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
TechId proteinReferenceID) throws UserFailureException
{
Session session = getSession(sessionToken);
+ IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO();
ProteinByExperiment proteinByExperiment = new ProteinByExperiment();
- final IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAOFromPool();
- final ProteinReference proteinReference;
- try
- {
- proteinReference = proteinQueryDAO.tryToGetProteinReference(proteinReferenceID.getId());
- } finally
- {
- specificDAOFactory.returnProteinQueryDAOToPool(proteinQueryDAO);
- }
+ ProteinReference proteinReference =
+ proteinQueryDAO.tryToGetProteinReference(proteinReferenceID.getId());
if (proteinReference == null)
{
- throw new UserFailureException("No protein reference found for ID: "
- + proteinReferenceID);
+ throw new UserFailureException("No protein reference found for ID: " + proteinReferenceID);
}
AccessionNumberBuilder builder =
new AccessionNumberBuilder(proteinReference.getAccessionNumber());
@@ -199,10 +186,8 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
final Session session = getSession(sessionToken);
IProteinSequenceTable sequenceTable = specificBOFactory.createProteinSequenceTable(session);
sequenceTable.loadByReference(proteinReferenceID);
- IDataSetProteinTable dataSetProteinTable =
- specificBOFactory.createDataSetProteinTable(session);
- dataSetProteinTable.load(getExperimentPermIDFor(experimentId), proteinReferenceID,
- sequenceTable);
+ IDataSetProteinTable dataSetProteinTable = specificBOFactory.createDataSetProteinTable(session);
+ dataSetProteinTable.load(getExperimentPermIDFor(experimentId), proteinReferenceID, sequenceTable);
return dataSetProteinTable.getDataSetProteins();
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetProteinTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetProteinTable.java
index 995562e8b33..de3f83c4db3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetProteinTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DataSetProteinTable.java
@@ -50,37 +50,25 @@ class DataSetProteinTable extends AbstractBusinessObject implements IDataSetProt
public void load(String experimentPermID, TechId proteinReferenceID,
IProteinSequenceTable sequenceTable)
{
- final ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
- final IProteinQueryDAO proteinQueryDAO =
- getSpecificDAOFactory().getProteinQueryDAOFromPool();
- try
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ DataSet<IdentifiedProtein> proteins =
+ proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
+ proteinReferenceID.getId());
+ dataSetProteins = new ArrayList<DataSetProtein>();
+ for (IdentifiedProtein protein : proteins)
{
- final DataSet<IdentifiedProtein> proteins =
- proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
- proteinReferenceID.getId());
- try
- {
- dataSetProteins = new ArrayList<DataSetProtein>();
- for (IdentifiedProtein protein : proteins)
- {
- errorModel.setFalseDiscoveryRateFor(protein);
- DataSetProtein dataSetProtein = new DataSetProtein();
- dataSetProtein.setDataSetID(new TechId(protein.getDataSetID()));
- dataSetProtein.setDataSetPermID(protein.getDataSetPermID());
- dataSetProtein.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
- dataSetProtein.setPeptideCount(protein.getPeptideCount());
- dataSetProtein.setProteinID(new TechId(protein.getProteinID()));
- dataSetProtein.setSequenceName(sequenceTable.getShortName(protein.getDatabaseID()));
- dataSetProteins.add(dataSetProtein);
- }
- } finally
- {
- proteins.close();
- }
- } finally
- {
- getSpecificDAOFactory().returnProteinQueryDAOToPool(proteinQueryDAO);
+ errorModel.setFalseDiscoveryRateFor(protein);
+ DataSetProtein dataSetProtein = new DataSetProtein();
+ dataSetProtein.setDataSetID(new TechId(protein.getDataSetID()));
+ dataSetProtein.setDataSetPermID(protein.getDataSetPermID());
+ dataSetProtein.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
+ dataSetProtein.setPeptideCount(protein.getPeptideCount());
+ dataSetProtein.setProteinID(new TechId(protein.getProteinID()));
+ dataSetProtein.setSequenceName(sequenceTable.getShortName(protein.getDatabaseID()));
+ dataSetProteins.add(dataSetProtein);
}
+ proteins.close();
}
}
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 8e0db8c2655..945ecc7b86a 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
@@ -69,27 +69,15 @@ class ErrorModel
if (calculator == null)
{
calculator = new ProbabilityToFDRCalculator();
- final IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAOFromPool();
- try
+ IProteinQueryDAO dao = specificDAOFactory.getProteinQueryDAO();
+ DataSet<ProbabilityFDRMapping> mappings = dao.getProbabilityFDRMapping(dataSetID);
+ for (ProbabilityFDRMapping probabilityFDRMapping : mappings)
{
- final DataSet<ProbabilityFDRMapping> mappings =
- dao.getProbabilityFDRMapping(dataSetID);
- try
- {
- for (ProbabilityFDRMapping probabilityFDRMapping : mappings)
- {
- double probability = probabilityFDRMapping.getProbability();
- double falseDiscoveryRate = probabilityFDRMapping.getFalseDiscoveryRate();
- calculator.add(probability, falseDiscoveryRate);
- }
- } finally
- {
- mappings.close();
- }
- } finally
- {
- specificDAOFactory.returnProteinQueryDAOToPool(dao);
+ double probability = probabilityFDRMapping.getProbability();
+ double falseDiscoveryRate = probabilityFDRMapping.getFalseDiscoveryRate();
+ calculator.add(probability, falseDiscoveryRate);
}
+ mappings.close();
calculator.init();
calculators.put(dataSetID, calculator);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
index 8ae15ff9eb1..20ce913bf62 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
@@ -54,74 +54,53 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
public void loadByExperimentAndReference(TechId experimentID, TechId proteinReferenceID)
{
String experimentPermID = getExperimentPermIDFor(experimentID);
- final IProteinQueryDAO proteinQueryDAO =
- getSpecificDAOFactory().getProteinQueryDAOFromPool();
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ DataSet<IdentifiedProtein> proteins =
+ proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
+ proteinReferenceID.getId());
try
{
- final DataSet<IdentifiedProtein> proteins =
- proteinQueryDAO.listProteinsByProteinReferenceAndExperiment(experimentPermID,
- proteinReferenceID.getId());
- try
+ if (proteins.size() == 1)
{
- if (proteins.size() == 1)
+ ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ IdentifiedProtein protein = proteins.get(0);
+ errorModel.setFalseDiscoveryRateFor(protein);
+ details = new ProteinDetails();
+ details.setSequence(protein.getSequence());
+ details.setDatabaseNameAndVersion(protein.getDatabaseNameAndVersion());
+ details.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
+ String dataSetPermID = protein.getDataSetPermID();
+ details.setDataSetPermID(dataSetPermID);
+ DataPE ds = getDaoFactory().getExternalDataDAO().tryToFindDataSetByCode(dataSetPermID);
+ if (ds != null)
{
- ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
- IdentifiedProtein protein = proteins.get(0);
- errorModel.setFalseDiscoveryRateFor(protein);
- details = new ProteinDetails();
- details.setSequence(protein.getSequence());
- details.setDatabaseNameAndVersion(protein.getDatabaseNameAndVersion());
- details.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
- String dataSetPermID = protein.getDataSetPermID();
- details.setDataSetPermID(dataSetPermID);
- DataPE ds =
- getDaoFactory().getExternalDataDAO().tryToFindDataSetByCode(
- dataSetPermID);
- if (ds != null)
- {
- details.setDataSetTechID(ds.getId());
- details.setDataSetTypeCode(ds.getDataSetType().getCode());
- }
- details.setPeptides(loadPeptides(protein));
- details.setProteinID(new TechId(protein.getProteinID()));
+ details.setDataSetTechID(ds.getId());
+ details.setDataSetTypeCode(ds.getDataSetType().getCode());
}
- } finally
- {
- proteins.close();
+ details.setPeptides(loadPeptides(protein));
+ details.setProteinID(new TechId(protein.getProteinID()));
}
} finally
{
- getSpecificDAOFactory().returnProteinQueryDAOToPool(proteinQueryDAO);
+ proteins.close();
}
}
private List<Peptide> loadPeptides(IdentifiedProtein protein)
{
- final IProteinQueryDAO proteinQueryDAO =
- getSpecificDAOFactory().getProteinQueryDAOFromPool();
- try
- {
- final DataSet<IdentifiedPeptide> identifiedPeptides =
- proteinQueryDAO.listIdentifiedPeptidesByProtein(protein.getProteinID());
- try
- {
- final List<Peptide> peptides = new ArrayList<Peptide>();
- for (IdentifiedPeptide identifiedPeptide : identifiedPeptides)
- {
- Peptide peptide = new Peptide();
- peptide.setSequence(identifiedPeptide.getSequence());
- peptide.setCharge(identifiedPeptide.getCharge());
- peptides.add(peptide);
- }
- return peptides;
- } finally
- {
- identifiedPeptides.close();
- }
- } finally
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ DataSet<IdentifiedPeptide> identifiedPeptides =
+ proteinQueryDAO.listIdentifiedPeptidesByProtein(protein.getProteinID());
+ List<Peptide> peptides = new ArrayList<Peptide>();
+ for (IdentifiedPeptide identifiedPeptide : identifiedPeptides)
{
- getSpecificDAOFactory().returnProteinQueryDAOToPool(proteinQueryDAO);
+ Peptide peptide = new Peptide();
+ peptide.setSequence(identifiedPeptide.getSequence());
+ peptide.setCharge(identifiedPeptide.getCharge());
+ peptides.add(peptide);
}
+ identifiedPeptides.close();
+ return peptides;
}
private String getExperimentPermIDFor(TechId experimentId)
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 d96357e3bba..22c16518f60 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
@@ -21,14 +21,9 @@ import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.concurrent.Callable;
-import java.util.concurrent.ExecutorService;
-import java.util.concurrent.Future;
import net.lemnik.eodsql.DataSet;
-import ch.systemsx.cisd.base.namedthread.NamingThreadPoolExecutor;
-import ch.systemsx.cisd.common.concurrent.ConcurrencyUtilities;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
@@ -49,9 +44,6 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinWithAbundan
*/
class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTable
{
- private static final ExecutorService executor =
- new NamingThreadPoolExecutor("ProteinInfoTableQuery").daemonize();
-
private List<ProteinInfo> infos;
ProteinInfoTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
@@ -72,50 +64,17 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
public void load(List<AbundanceColumnDefinition> definitions, TechId experimentID,
double falseDiscoveryRate, AggregateFunction function, boolean aggregateOnOriginal)
{
- final IExperimentDAO experimentDAO = getDaoFactory().getExperimentDAO();
- final String permID = experimentDAO.getByTechId(experimentID).getPermId();
- final CoverageCalculator coverageCalculator;
- final Collection<ProteinWithAbundances> proteins;
- final DataSet<ProteinReferenceWithPeptideSequence> proteinReferencesWithPeptides;
- final DataSet<ProteinReferenceWithProbability> proteinReferencesWithProbability;
- final IProteinQueryDAO dao1 = getSpecificDAOFactory().getProteinQueryDAOFromPool();
- final IProteinQueryDAO dao2OrNull = getSpecificDAOFactory().tryGetProteinQueryDAOFromPool();
- try
- {
- if (dao2OrNull != null)
- {
- // Run 2nd query in a separate thread in parallel to the 1st one
- final Future<DataSet<ProteinReferenceWithPeptideSequence>> proteinReferencesWithPeptidesFuture =
- getProteinReferencesWithPeptideAsynchronously(dao1, permID);
- proteinReferencesWithProbability = dao2OrNull.listProteinsByExperiment(permID);
- proteinReferencesWithPeptides =
- ConcurrencyUtilities.tryGetResult(proteinReferencesWithPeptidesFuture,
- ConcurrencyUtilities.NO_TIMEOUT);
- } else
- {
- // Run queries sequentially in the current thread
- proteinReferencesWithPeptides = dao1.listProteinsWithPeptidesByExperiment(permID);
- proteinReferencesWithProbability = dao1.listProteinsByExperiment(permID);
- }
- coverageCalculator = setUpCoverageCalculator(proteinReferencesWithPeptides);
- proteins =
- setUpAbundanceManager(proteinReferencesWithProbability, falseDiscoveryRate)
- .getProteinsWithAbundances();
- } finally
- {
- getSpecificDAOFactory().returnProteinQueryDAOToPool(dao1);
- if (dao2OrNull != null)
- {
- getSpecificDAOFactory().returnProteinQueryDAOToPool(dao2OrNull);
- }
- }
+ IExperimentDAO experimentDAO = getDaoFactory().getExperimentDAO();
+ String permID = experimentDAO.getByTechId(experimentID).getPermId();
+ CoverageCalculator coverageCalculator = setUpCoverageCalculator(permID);
+ AbundanceManager abundanceManager = setUpAbundanceManager(permID, falseDiscoveryRate);
+ Collection<ProteinWithAbundances> proteins = abundanceManager.getProteinsWithAbundances();
infos = new ArrayList<ProteinInfo>(proteins.size());
for (ProteinWithAbundances protein : proteins)
{
ProteinInfo proteinInfo = new ProteinInfo();
proteinInfo.setId(new TechId(protein.getId()));
- AccessionNumberBuilder builder =
- new AccessionNumberBuilder(protein.getAccessionNumber());
+ AccessionNumberBuilder builder = new AccessionNumberBuilder(protein.getAccessionNumber());
proteinInfo.setCoverage(coverageCalculator.calculateCoverageFor(protein.getId()));
proteinInfo.setAccessionNumber(builder.getAccessionNumber());
proteinInfo.setDescription(protein.getDescription());
@@ -130,8 +89,7 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
double[] values = protein.getAbundancesForSample(sampleID);
if (values != null && values.length > 0 && aggregateOnOriginal == false)
{
- values = new double[]
- { function.aggregate(values) };
+ values = new double[] {function.aggregate(values)};
}
abundanceValues = concatenate(abundanceValues, values);
}
@@ -146,14 +104,17 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
}
}
- private AbundanceManager setUpAbundanceManager(
- DataSet<ProteinReferenceWithProbability> proteinReferences, double falseDiscoveryRate)
+ private AbundanceManager setUpAbundanceManager(String experimentPermID,
+ double falseDiscoveryRate)
{
AbundanceManager abundanceManager = new AbundanceManager(getDaoFactory().getSampleDAO());
+ IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ DataSet<ProteinReferenceWithProbability> resultSet =
+ dao.listProteinsByExperiment(experimentPermID);
try
{
- for (ProteinReferenceWithProbability protein : proteinReferences)
+ for (ProteinReferenceWithProbability protein : resultSet)
{
if (errorModel.passProtein(protein, falseDiscoveryRate))
{
@@ -162,35 +123,24 @@ class ProteinInfoTable extends AbstractBusinessObject implements IProteinInfoTab
}
} finally
{
- proteinReferences.close();
+ resultSet.close();
}
return abundanceManager;
}
-
- private Future<DataSet<ProteinReferenceWithPeptideSequence>> getProteinReferencesWithPeptideAsynchronously(
- final IProteinQueryDAO dao, final String experimentPermID)
- {
- return executor.submit(new Callable<DataSet<ProteinReferenceWithPeptideSequence>>()
- {
- public DataSet<ProteinReferenceWithPeptideSequence> call() throws Exception
- {
- return dao.listProteinsWithPeptidesByExperiment(experimentPermID);
- }
- });
- }
-
- private CoverageCalculator setUpCoverageCalculator(
- DataSet<ProteinReferenceWithPeptideSequence> proteinReferences)
+
+ private CoverageCalculator setUpCoverageCalculator(String experimentPermID)
{
+ IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
+ DataSet<ProteinReferenceWithPeptideSequence> resultSet = dao.listProteinsWithPeptidesByExperiment(experimentPermID);
try
{
- return new CoverageCalculator(proteinReferences);
+ return new CoverageCalculator(resultSet);
} finally
{
- proteinReferences.close();
+ resultSet.close();
}
}
-
+
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/business/ProteinSequenceTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSequenceTable.java
index 5bc51e8d584..ffd31325cb7 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSequenceTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSequenceTable.java
@@ -72,37 +72,26 @@ class ProteinSequenceTable extends AbstractBusinessObject implements IProteinSeq
public void loadByReference(TechId proteinReferenceID)
{
- final IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAOFromPool();
- try
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ DataSet<Sequence> sequences =
+ proteinQueryDAO.listProteinSequencesByProteinReference(proteinReferenceID.getId());
+ proteinSequences = new ArrayList<ProteinSequence>(sequences.size());
+ databaseIDToShortNameMap = new HashMap<Long, String>();
+ int number = 0;
+ for (Sequence sequence : sequences)
{
- final DataSet<Sequence> sequences =
- proteinQueryDAO.listProteinSequencesByProteinReference(proteinReferenceID.getId());
- try
- {
- proteinSequences = new ArrayList<ProteinSequence>(sequences.size());
- databaseIDToShortNameMap = new HashMap<Long, String>();
- int number = 0;
- for (Sequence sequence : sequences)
- {
- ProteinSequence proteinSequence = new ProteinSequence();
- proteinSequence.setId(new TechId(sequence.getId()));
- String shortName = createShortName(number++);
- proteinSequence.setShortName(shortName);
- proteinSequence.setSequence(sequence.getSequence());
- long databaseID = sequence.getDatabaseID();
- proteinSequence.setDatabaseID(new TechId(databaseID));
- proteinSequence.setDatabaseNameAndVersion(sequence.getDatabaseNameAndVersion());
- proteinSequences.add(proteinSequence);
- databaseIDToShortNameMap.put(databaseID, shortName);
- }
- } finally
- {
- sequences.close();
- }
- } finally
- {
- getSpecificDAOFactory().returnProteinQueryDAOToPool(proteinQueryDAO);
+ ProteinSequence proteinSequence = new ProteinSequence();
+ proteinSequence.setId(new TechId(sequence.getId()));
+ String shortName = createShortName(number++);
+ proteinSequence.setShortName(shortName);
+ proteinSequence.setSequence(sequence.getSequence());
+ long databaseID = sequence.getDatabaseID();
+ proteinSequence.setDatabaseID(new TechId(databaseID));
+ proteinSequence.setDatabaseNameAndVersion(sequence.getDatabaseNameAndVersion());
+ proteinSequences.add(proteinSequence);
+ databaseIDToShortNameMap.put(databaseID, shortName);
}
+ sequences.close();
}
private String createShortName(int number)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java
index ec08d8e6c53..f15ea14ce74 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java
@@ -88,43 +88,37 @@ class ProteinSummaryTable extends AbstractBusinessObject implements IProteinSumm
public void load(TechId experimentID)
{
- final IExperimentDAO experimentDAO = getDaoFactory().getExperimentDAO();
- final String permID = experimentDAO.getByTechId(experimentID).getPermId();
- final ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
- final IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAOFromPool();
+ IExperimentDAO experimentDAO = getDaoFactory().getExperimentDAO();
+ String permID = experimentDAO.getByTechId(experimentID).getPermId();
+ IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
+ ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ DataSet<ProteinReferenceWithProbabilityAndPeptide> resultSet =
+ dao.listProteinsWithProbabilityAndPeptidesByExperiment(permID);
+ List<Counter> counters = new ArrayList<Counter>(FDR_LEVELS.length);
+ for (double fdrLevel : FDR_LEVELS)
+ {
+ counters.add(new Counter(fdrLevel));
+ }
try
{
- final DataSet<ProteinReferenceWithProbabilityAndPeptide> resultSet =
- dao.listProteinsWithProbabilityAndPeptidesByExperiment(permID);
- final List<Counter> counters = new ArrayList<Counter>(FDR_LEVELS.length);
- for (double fdrLevel : FDR_LEVELS)
- {
- counters.add(new Counter(fdrLevel));
- }
- try
+ for (ProteinReferenceWithProbabilityAndPeptide protein : resultSet)
{
- for (ProteinReferenceWithProbabilityAndPeptide protein : resultSet)
- {
- long dataSetID = protein.getDataSetID();
- double probability = protein.getProbability();
- double fdr = errorModel.calculateFalsDiscoveryRate(dataSetID, probability);
- for (Counter counter : counters)
- {
- counter.handle(fdr, protein);
- }
- }
- summaries = new ArrayList<ProteinSummary>(counters.size());
+ long dataSetID = protein.getDataSetID();
+ double probability = protein.getProbability();
+ double fdr = errorModel.calculateFalsDiscoveryRate(dataSetID, probability);
for (Counter counter : counters)
{
- summaries.add(counter.getProteinSummary());
+ counter.handle(fdr, protein);
}
- } finally
+ }
+ summaries = new ArrayList<ProteinSummary>(counters.size());
+ for (Counter counter : counters)
{
- resultSet.close();
+ summaries.add(counter.getProteinSummary());
}
} finally
{
- getSpecificDAOFactory().returnProteinQueryDAOToPool(dao);
+ resultSet.close();
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleTable.java
index 8431a210fd4..898e5efbda3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleTable.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/SampleTable.java
@@ -62,33 +62,27 @@ class SampleTable extends AbstractBusinessObject implements ISampleTable
public void loadSamplesWithAbundance(TechId experimentID, TechId proteinReferenceID)
{
samples = new ArrayList<SampleWithPropertiesAndAbundance>();
- final IDAOFactory daoFactory = getDaoFactory();
- final String experimentPermID = daoFactory.getExperimentDAO().getByTechId(experimentID).getPermId();
- final IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAOFromPool();
+ IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+ IDAOFactory daoFactory = getDaoFactory();
+ String experimentPermID = daoFactory.getExperimentDAO().getByTechId(experimentID).getPermId();
+ DataSet<SampleAbundance> sampleAbundances =
+ proteinQueryDAO.listSampleAbundanceByProtein(experimentPermID, proteinReferenceID.getId());
try
{
- final DataSet<SampleAbundance> sampleAbundances =
- proteinQueryDAO.listSampleAbundanceByProtein(experimentPermID, proteinReferenceID.getId());
- try
+ ISampleDAO sampleDAO = daoFactory.getSampleDAO();
+ for (SampleAbundance sampleAbundance : sampleAbundances)
{
- ISampleDAO sampleDAO = daoFactory.getSampleDAO();
- for (SampleAbundance sampleAbundance : sampleAbundances)
- {
- SampleWithPropertiesAndAbundance sample = new SampleWithPropertiesAndAbundance();
- sample.setAbundance(sampleAbundance.getAbundance());
- String samplePermID = sampleAbundance.getSamplePermID();
- long sampleID = sampleIDProvider.getSampleIDOrParentSampleID(samplePermID);
- SamplePE samplePE = sampleDAO.getByTechId(new TechId(sampleID));
- fillSampleData(sample, samplePE);
- samples.add(sample);
- }
- } finally
- {
- sampleAbundances.close();
+ SampleWithPropertiesAndAbundance sample = new SampleWithPropertiesAndAbundance();
+ sample.setAbundance(sampleAbundance.getAbundance());
+ String samplePermID = sampleAbundance.getSamplePermID();
+ long sampleID = sampleIDProvider.getSampleIDOrParentSampleID(samplePermID);
+ SamplePE samplePE = sampleDAO.getByTechId(new TechId(sampleID));
+ fillSampleData(sample, samplePE);
+ samples.add(sample);
}
} finally
{
- getSpecificDAOFactory().returnProteinQueryDAOToPool(proteinQueryDAO);
+ sampleAbundances.close();
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IPhosphoNetXDAOFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IPhosphoNetXDAOFactory.java
index 2b49f2c9b17..670a00f1c6b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IPhosphoNetXDAOFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IPhosphoNetXDAOFactory.java
@@ -23,19 +23,5 @@ package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess;
*/
public interface IPhosphoNetXDAOFactory
{
- /**
- * Retrieves a {@link IProteinQueryDAO} from the pool.
- */
- public IProteinQueryDAO getProteinQueryDAOFromPool();
-
- /**
- * Retrieves a {@link IProteinQueryDAO} from the pool or <code>null</code> if none is currently
- * available.
- */
- public IProteinQueryDAO tryGetProteinQueryDAOFromPool();
-
- /**
- * Returns the given <var>proteinQueryDAO</var> to the pool.
- */
- public void returnProteinQueryDAOToPool(IProteinQueryDAO proteinQueryDAO);
+ public IProteinQueryDAO getProteinQueryDAO();
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java
index 10f7fc1b068..63fe09c0b92 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java
@@ -16,9 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.db;
+import java.sql.Connection;
import java.sql.SQLException;
-import java.util.concurrent.BlockingQueue;
-import java.util.concurrent.LinkedBlockingQueue;
import net.lemnik.eodsql.QueryTool;
@@ -43,57 +42,28 @@ public class PhosphoNetXDAOFactory implements IPhosphoNetXDAOFactory
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, PhosphoNetXDAOFactory.class);
- private final BlockingQueue<IProteinQueryDAO> availableProteinQueryObjects =
- new LinkedBlockingQueue<IProteinQueryDAO>();
+ private IProteinQueryDAO proteinQueryDAO;
- public PhosphoNetXDAOFactory(DatabaseConfigurationContext context,
- int numberOfParallelQueriesHint)
+ public PhosphoNetXDAOFactory(DatabaseConfigurationContext context)
{
- final int numberOfParallelQueries =
- (numberOfParallelQueriesHint <= 0) ? Runtime.getRuntime().availableProcessors()
- : numberOfParallelQueriesHint;
DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context, DATABASE_VERSION);
- for (int i = 0; i < numberOfParallelQueries; ++i)
- {
- availableProteinQueryObjects.add(createQuery(context));
- }
- if (operationLog.isInfoEnabled())
- {
- operationLog.info("DAO factory for PhosphoNetX created.");
- }
- }
-
- private IProteinQueryDAO createQuery(DatabaseConfigurationContext context)
- {
+ Connection connection = null;
try
{
- return QueryTool.getQuery(context.getDataSource().getConnection(),
- IProteinQueryDAO.class);
+ connection = context.getDataSource().getConnection();
} catch (SQLException ex)
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
- }
-
- public IProteinQueryDAO getProteinQueryDAOFromPool()
- {
- try
- {
- return availableProteinQueryObjects.take();
- } catch (InterruptedException ex)
+ proteinQueryDAO = QueryTool.getQuery(connection, IProteinQueryDAO.class);
+ if (operationLog.isInfoEnabled())
{
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ operationLog.info("DAO factory for PhosphoNetX created.");
}
}
- public IProteinQueryDAO tryGetProteinQueryDAOFromPool()
+ public IProteinQueryDAO getProteinQueryDAO()
{
- return availableProteinQueryObjects.poll();
+ return proteinQueryDAO;
}
-
- public void returnProteinQueryDAOToPool(IProteinQueryDAO proteinQueryDAO)
- {
- availableProteinQueryObjects.add(proteinQueryDAO);
- }
-
}
diff --git a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index be242ac6f94..3af8c91f361 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -32,7 +32,6 @@
<bean id="phosphonetx-dao-factory"
class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.db.PhosphoNetXDAOFactory">
<constructor-arg ref="phosphonetx-db-configuration-context"/>
- <constructor-arg value="${phosphonetx.number-of-parallel-queries}"/>
</bean>
<bean id="phosphonetx-bo-factory"
diff --git a/rtd_phosphonetx/source/java/service.properties b/rtd_phosphonetx/source/java/service.properties
index 5f9578be35d..67190951302 100644
--- a/rtd_phosphonetx/source/java/service.properties
+++ b/rtd_phosphonetx/source/java/service.properties
@@ -35,10 +35,6 @@ phosphonetx.database.owner-password =
phosphonetx.database.admin-user =
phosphonetx.database.admin-password =
phosphonetx.script-folder = source
-# Provide here the number of long-running queries that should be executed in parallel on the database
-# 0 means: use number of CPUs in the system (which assumes that the database and the application
-# server are running on the same host).
-phosphonetx.number-of-parallel-queries = 0
crowd.service.host = crowd.systemsx.ch
crowd.service.port = 8443
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
index 4d1a7ea859e..a794e34a8c0 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerTest.java
@@ -70,9 +70,8 @@ public class PhosphoNetXServerTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- allowing(phosphoNetXDAOFactory).getProteinQueryDAOFromPool();
+ allowing(phosphoNetXDAOFactory).getProteinQueryDAO();
will(returnValue(proteinDAO));
- allowing(phosphoNetXDAOFactory).returnProteinQueryDAOToPool(proteinDAO);
}
});
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModelTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModelTest.java
index f027d67255b..3aace8dbac0 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModelTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModelTest.java
@@ -56,9 +56,8 @@ public class ErrorModelTest extends AssertJUnit
context.checking(new Expectations()
{
{
- allowing(specificDAOFactory).getProteinQueryDAOFromPool();
+ allowing(specificDAOFactory).getProteinQueryDAO();
will(returnValue(proteinQueryDAO));
- allowing(specificDAOFactory).returnProteinQueryDAOToPool(proteinQueryDAO);
atMost(1).of(proteinQueryDAO).getProbabilityFDRMapping(DATA_SET1_ID);
MockDataSet<ProbabilityFDRMapping> dataSet1 = new MockDataSet<ProbabilityFDRMapping>();
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 23bf9ae0c6a..350d680a55a 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
@@ -75,11 +75,8 @@ public class ProteinInfoTableTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- allowing(specificDAOFactory).getProteinQueryDAOFromPool();
+ allowing(specificDAOFactory).getProteinQueryDAO();
will(returnValue(proteinDAO));
- allowing(specificDAOFactory).tryGetProteinQueryDAOFromPool();
- will(returnValue(proteinDAO));
- allowing(specificDAOFactory).returnProteinQueryDAOToPool(proteinDAO);
}
});
table = new ProteinInfoTable(daoFactory, specificDAOFactory, SESSION);
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTableTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTableTest.java
index 9dadc30a08b..fd86e373abf 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTableTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTableTest.java
@@ -62,9 +62,8 @@ public class ProteinSummaryTableTest extends AbstractServerTestCase
context.checking(new Expectations()
{
{
- allowing(specificDAOFactory).getProteinQueryDAOFromPool();
+ allowing(specificDAOFactory).getProteinQueryDAO();
will(returnValue(proteinDAO));
- allowing(specificDAOFactory).returnProteinQueryDAOToPool(proteinDAO);
}
});
table = new ProteinSummaryTable(daoFactory, specificDAOFactory, SESSION);
--
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