From 8275e6a1c91ac13244c245e38347bc03efb64026 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 10 May 2010 09:03:17 +0000
Subject: [PATCH] LMS-1531 yeastx: create DAOs (and connections) first time
when they are needed
SVN: 15860
---
.../cisd/yeastx/db/AbstractDatasetLoader.java | 35 +++++++++++++++--
.../cisd/yeastx/eicml/EICML2Database.java | 24 ++++--------
.../cisd/yeastx/etl/MLArchiverTask.java | 39 +++++++++++++------
.../cisd/yeastx/fiaml/FIAML2Database.java | 26 +++++--------
.../cisd/yeastx/mzxml/MzXml2Database.java | 25 ++++--------
.../cisd/yeastx/quant/QuantML2Database.java | 21 +++-------
.../cisd/yeastx/mzxml/MzXml2DatabaseTest.java | 2 +-
7 files changed, 90 insertions(+), 82 deletions(-)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/AbstractDatasetLoader.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/AbstractDatasetLoader.java
index a360f400414..da604dc960e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/AbstractDatasetLoader.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/AbstractDatasetLoader.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.yeastx.db;
+import javax.sql.DataSource;
+
import org.springframework.dao.DataAccessException;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
@@ -26,13 +28,40 @@ import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
*
* @author Tomasz Pylak
*/
-abstract public class AbstractDatasetLoader implements IDatasetLoader
+abstract public class AbstractDatasetLoader<T extends IGenericDAO> implements IDatasetLoader
{
- abstract protected IGenericDAO getDao();
-
// if false transaction has to be commited or rollbacked before the next dataset will be created
protected boolean isTransactionCompleted = true;
+ private final DataSource dataSource;
+
+ private final Class<T> queryClass;
+
+ private T daoOrNull; // created when used for the first time
+
+ protected AbstractDatasetLoader(DataSource dataSource, Class<T> queryClass)
+ {
+ this.dataSource = dataSource;
+ this.queryClass = queryClass;
+ }
+
+ // for tests only
+ protected AbstractDatasetLoader(DataSource dataSource, Class<T> queryClass, T dao)
+ {
+ this.dataSource = dataSource;
+ this.queryClass = queryClass;
+ this.daoOrNull = dao;
+ }
+
+ protected final T getDao()
+ {
+ if (daoOrNull == null)
+ {
+ this.daoOrNull = DBUtils.getQuery(dataSource, queryClass);
+ }
+ return daoOrNull;
+ }
+
/**
* Cannot be called twice in a row if {@link #commit()} or {@link #rollback()} has not been
* called in between.
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java
index 4856dfc6072..86441c7123f 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java
@@ -23,9 +23,7 @@ import java.util.List;
import javax.sql.DataSource;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
-import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IChromatogramObserver;
import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IMSRunObserver;
@@ -34,7 +32,7 @@ import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IMSRunObserver;
*
* @author Bernd Rinn
*/
-public class EICML2Database extends AbstractDatasetLoader
+public class EICML2Database extends AbstractDatasetLoader<IEICMSRunDAO>
{
private final static int CHROMATOGRAM_BATCH_SIZE = 100;
@@ -49,11 +47,9 @@ public class EICML2Database extends AbstractDatasetLoader
}
}
- private final IEICMSRunDAO dao;
-
- public EICML2Database(DataSource datasource)
+ public EICML2Database(DataSource dataSource)
{
- this.dao = DBUtils.getQuery(datasource, IEICMSRunDAO.class);
+ super(dataSource, IEICMSRunDAO.class);
}
/**
@@ -73,30 +69,26 @@ public class EICML2Database extends AbstractDatasetLoader
{
// add chromatograms from the last run to the database before setting the
// new run id
- addChromatograms(dao, eicMLId[0], chromatograms, 1);
+ addChromatograms(getDao(), eicMLId[0], chromatograms, 1);
run.setExperimentId(dataSet.getExperimentId());
run.setSampleId(dataSet.getSampleId());
run.setDataSetId(dataSet.getId());
- eicMLId[0] = dao.addMSRun(run);
+ eicMLId[0] = getDao().addMSRun(run);
}
}, new IChromatogramObserver()
{
public void observe(ChromatogramDTO chromatogram)
{
chromatograms.add(chromatogram);
- addChromatograms(dao, eicMLId[0], chromatograms, CHROMATOGRAM_BATCH_SIZE);
+ addChromatograms(getDao(), eicMLId[0], chromatograms,
+ CHROMATOGRAM_BATCH_SIZE);
}
});
- addChromatograms(dao, eicMLId[0], chromatograms, 1);
+ addChromatograms(getDao(), eicMLId[0], chromatograms, 1);
} catch (Throwable th)
{
rollbackAndRethrow(th);
}
}
- @Override
- protected IGenericDAO getDao()
- {
- return dao;
- }
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java
index 94ab1252646..7a0e3a8c3f4 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java
@@ -94,19 +94,9 @@ public class MLArchiverTask extends AbstractArchiverProcessingPlugin
Sample sample = null;
if (dataset.getSampleCode() != null)
{
- // NOTE: we assume that it is not a shared sample
- SampleIdentifier sampleIdentifier =
- new SampleIdentifier(new SpaceIdentifier(dataset.getDatabaseInstanceCode(),
- dataset.getGroupCode()), dataset.getSampleCode());
- sample =
- ServiceProvider.getOpenBISService().tryGetSampleWithExperiment(
- sampleIdentifier);
+ sample = fetchSample(dataset);
}
- ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifier(dataset.getDatabaseInstanceCode(), dataset
- .getGroupCode(), dataset.getProjectCode(), dataset.getExperimentCode());
- Experiment experiment =
- ServiceProvider.getOpenBISService().tryToGetExperiment(experimentIdentifier);
+ Experiment experiment = getOrFetchExperiment(dataset, sample);
databaseUploader = new ML2DatabaseUploader(properties);
databaseUploader.upload(getDataFile(dataset), sample, experiment, dataset
.getDatasetCode());
@@ -121,6 +111,31 @@ public class MLArchiverTask extends AbstractArchiverProcessingPlugin
}
}
+ private Sample fetchSample(DatasetDescription dataset)
+ {
+ Sample sample;
+ // NOTE: we assume that it is not a shared sample
+ SampleIdentifier sampleIdentifier =
+ new SampleIdentifier(new SpaceIdentifier(dataset.getDatabaseInstanceCode(), dataset
+ .getGroupCode()), dataset.getSampleCode());
+ sample = ServiceProvider.getOpenBISService().tryGetSampleWithExperiment(sampleIdentifier);
+ return sample;
+ }
+
+ private Experiment getOrFetchExperiment(DatasetDescription dataset, Sample sample)
+ {
+ if (sample != null && sample.getExperiment() != null)
+ {
+ return sample.getExperiment();
+ }
+ ExperimentIdentifier experimentIdentifier =
+ new ExperimentIdentifier(dataset.getDatabaseInstanceCode(), dataset.getGroupCode(),
+ dataset.getProjectCode(), dataset.getExperimentCode());
+ Experiment experiment =
+ ServiceProvider.getOpenBISService().tryToGetExperiment(experimentIdentifier);
+ return experiment;
+ }
+
private File getDataFile(DatasetDescription dataset)
{
File datasetDir = getDataSubDir(dataset);
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAML2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAML2Database.java
index d39c187757b..79246af8086 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAML2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAML2Database.java
@@ -23,9 +23,7 @@ import java.util.Iterator;
import javax.sql.DataSource;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
-import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
import ch.systemsx.cisd.yeastx.fiaml.FIAMLParser.IMSRunObserver;
/**
@@ -33,7 +31,7 @@ import ch.systemsx.cisd.yeastx.fiaml.FIAMLParser.IMSRunObserver;
*
* @author Bernd Rinn
*/
-public class FIAML2Database extends AbstractDatasetLoader
+public class FIAML2Database extends AbstractDatasetLoader<IFIAMSRunDAO>
{
private final static int PROFILE_CHUNK_SIZE = 250;
@@ -73,11 +71,9 @@ public class FIAML2Database extends AbstractDatasetLoader
};
}
- private final IFIAMSRunDAO dao;
-
- public FIAML2Database(DataSource datasource)
+ public FIAML2Database(DataSource dataSource)
{
- this.dao = DBUtils.getQuery(datasource, IFIAMSRunDAO.class);
+ super(dataSource, IFIAMSRunDAO.class);
}
/**
@@ -95,10 +91,12 @@ public class FIAML2Database extends AbstractDatasetLoader
run.setExperimentId(dataSet.getExperimentId());
run.setSampleId(dataSet.getSampleId());
run.setDataSetId(dataSet.getId());
- final long fiaMsRunId = dao.addMSRun(run);
- dao.addProfiles(fiaMsRunId, profileChunk(runData));
- dao.addCentroids(fiaMsRunId, runData.getCentroidMz(), runData
- .getCentroidIntensities(), runData.getCentroidCorrelations());
+ final long fiaMsRunId = getDao().addMSRun(run);
+ getDao().addProfiles(fiaMsRunId, profileChunk(runData));
+ getDao()
+ .addCentroids(fiaMsRunId, runData.getCentroidMz(),
+ runData.getCentroidIntensities(),
+ runData.getCentroidCorrelations());
}
});
} catch (Throwable th)
@@ -106,10 +104,4 @@ public class FIAML2Database extends AbstractDatasetLoader
rollbackAndRethrow(th);
}
}
-
- @Override
- protected IGenericDAO getDao()
- {
- return dao;
- }
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
index 876d18475c1..773f3870a3f 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
@@ -27,9 +27,7 @@ import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
-import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzPrecursorDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzRunDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzScanDTO;
@@ -41,19 +39,18 @@ import ch.systemsx.cisd.yeastx.utils.JaxbXmlParser;
*
* @author Tomasz Pylak
*/
-public class MzXml2Database extends AbstractDatasetLoader
+public class MzXml2Database extends AbstractDatasetLoader<IMzXmlDAO>
{
- private final IMzXmlDAO dao;
-
public MzXml2Database(DataSource datasource)
{
- this(DBUtils.getQuery(datasource, IMzXmlDAO.class));
+ super(datasource, IMzXmlDAO.class);
}
@Private
- MzXml2Database(IMzXmlDAO dao)
+ // for tests only
+ MzXml2Database(DataSource dataSource, IMzXmlDAO dao)
{
- this.dao = dao;
+ super(dataSource, IMzXmlDAO.class, dao);
}
/**
@@ -80,7 +77,7 @@ public class MzXml2Database extends AbstractDatasetLoader
@Private
void uploadRun(MzRunDTO run, DMDataSetDTO dataSet)
{
- long runId = dao.addRun(dataSet, run.getInstrument());
+ long runId = getDao().addRun(dataSet, run.getInstrument());
List<MzScanDTO> scans = run.getScans();
for (MzScanDTO scan : scans)
{
@@ -111,7 +108,7 @@ public class MzXml2Database extends AbstractDatasetLoader
scan.getNumber(), precursors.size());
}
}
- long scanId = dao.addScan(runId, scan, precursor1, precursor2);
+ long scanId = getDao().addScan(runId, scan, precursor1, precursor2);
uploadPeaks(scanId, scan.getPeaks());
}
@@ -119,7 +116,7 @@ public class MzXml2Database extends AbstractDatasetLoader
{
Iterable<Float> mzArray = createEverySecondIterator(peaks, 0);
Iterable<Float> intensityArray = createEverySecondIterator(peaks, 1);
- dao.addPeaks(scanId, mzArray, intensityArray);
+ getDao().addPeaks(scanId, mzArray, intensityArray);
}
// iterates on every second element of an array starting from the specified initial index
@@ -154,10 +151,4 @@ public class MzXml2Database extends AbstractDatasetLoader
}
};
}
-
- @Override
- protected IGenericDAO getDao()
- {
- return dao;
- }
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
index 4f314090303..fda48a38ce4 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
@@ -23,9 +23,7 @@ import java.util.List;
import javax.sql.DataSource;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
-import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
import ch.systemsx.cisd.yeastx.quant.dto.ConcentrationCompounds;
import ch.systemsx.cisd.yeastx.quant.dto.MSConcentrationDTO;
import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
@@ -37,13 +35,11 @@ import ch.systemsx.cisd.yeastx.utils.JaxbXmlParser;
*
* @author Tomasz Pylak
*/
-public class QuantML2Database extends AbstractDatasetLoader
+public class QuantML2Database extends AbstractDatasetLoader<IQuantMSDAO>
{
- private final IQuantMSDAO dao;
-
public QuantML2Database(DataSource datasource)
{
- this.dao = DBUtils.getQuery(datasource, IQuantMSDAO.class);
+ super(datasource, IQuantMSDAO.class);
}
/**
@@ -68,7 +64,7 @@ public class QuantML2Database extends AbstractDatasetLoader
for (MSQuantificationDTO quantification : quantifications.getQuantifications())
{
long quantificationId =
- dao.addQuantification(dataSet.getExperimentId(), dataSet.getId(),
+ getDao().addQuantification(dataSet.getExperimentId(), dataSet.getId(),
quantification);
uploadConcentrations(quantificationId, quantification.getConcentrations());
}
@@ -78,20 +74,13 @@ public class QuantML2Database extends AbstractDatasetLoader
{
for (MSConcentrationDTO concentration : concentrations)
{
- long concentrationId = dao.addConcentration(quantificationId, concentration);
+ long concentrationId = getDao().addConcentration(quantificationId, concentration);
uploadCompoundIds(concentrationId, concentration.getCompounds());
}
}
private void uploadCompoundIds(long concentrationId, ConcentrationCompounds compounds)
{
- dao.addCompoundIds(concentrationId, compounds.getCompoundIds());
+ getDao().addCompoundIds(concentrationId, compounds.getCompoundIds());
}
-
- @Override
- protected IGenericDAO getDao()
- {
- return dao;
- }
-
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
index e95c556e8ce..6837a6cf9c7 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
@@ -110,7 +110,7 @@ public class MzXml2DatabaseTest
}
});
- new MzXml2Database(dao).uploadRun(run, dataSet);
+ new MzXml2Database(null, dao).uploadRun(run, dataSet);
context.assertIsSatisfied();
}
}
--
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