From e6c63da077835782c1a7ad120f6f7924d5e55b15 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Sat, 17 Oct 2009 18:52:26 +0000
Subject: [PATCH] [SE-154] fixed race condition - 1v
SVN: 12993
---
.../ch/systemsx/cisd/yeastx/db/DBUtils.java | 32 ++++++++++++-------
.../cisd/yeastx/eicml/EICML2Database.java | 13 ++++++--
2 files changed, 31 insertions(+), 14 deletions(-)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
index 775f7f376a6..41884545224 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
@@ -89,20 +89,27 @@ public class DBUtils
* Creates the data set based on the information given in <var>dataSet</var>. The sample and
* experiment of the data set may already exist in the database. If they don't, they are created
* as well.
+ * <p>
+ * NOTE: Code responsible for trying to get sample and experiment from the DB and creating them
+ * if they don't exist is in synchronized block and uses currently opened transaction. Then the
+ * transaction is closed and data set is added to the DB in second transaction. If second
+ * transaction will be rolled back sample and experiment created in first transaction will stay
+ * in the DB.
*/
public static void createDataSet(IGenericDAO dao, DMDataSetDTO dataSet)
{
- DMExperimentDTO experiment = getOrCreateExperiment(dao, dataSet);
- dataSet.setExperimentId(experiment.getId()); // make sure all the ids are set correctly.
-
- if (dataSet.getSample() != null)
+ synchronized (IGenericDAO.class)
{
- String permId = dataSet.getSample().getPermId();
- DMSampleDTO sample;
- // it may have happened that the sample has been created by another thread after
- // we checked that it does not exist
- synchronized (IGenericDAO.class)
+ DMExperimentDTO experiment = getOrCreateExperiment(dao, dataSet);
+ dataSet.setExperimentId(experiment.getId()); // make sure all the ids are set correctly.
+
+ if (dataSet.getSample() != null)
{
+ String permId = dataSet.getSample().getPermId();
+ DMSampleDTO sample;
+ // it may have happened that the sample has been created by another thread after
+ // we checked that it does not exist
+
sample = dao.getSampleByPermId(permId);
if (sample == null)
{
@@ -110,10 +117,13 @@ public class DBUtils
sample.setExperiment(experiment);
sample = createSample(dao, sample, permId);
}
+
+ sample.setExperiment(experiment);
+ dataSet.setSample(sample); // make sure all the ids are set correctly.
}
- sample.setExperiment(experiment);
- dataSet.setSample(sample); // make sure all the ids are set correctly.
+ dao.close(true);
}
+
long dataSetId = dao.addDataSet(dataSet);
dataSet.setId(dataSetId);
}
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 d4ee22aa905..49d8a640634 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
@@ -28,6 +28,7 @@ import javax.xml.parsers.ParserConfigurationException;
import net.lemnik.eodsql.QueryTool;
import net.lemnik.eodsql.TransactionQuery;
+import org.springframework.dao.DataAccessException;
import org.xml.sax.SAXException;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
@@ -100,7 +101,13 @@ public class EICML2Database
transaction.close(true);
} catch (Throwable th)
{
- DBUtils.rollbackAndClose(transaction);
+ try
+ {
+ DBUtils.rollbackAndClose(transaction);
+ } catch (DataAccessException ex)
+ {
+ // Avoid this exception shadowing the original exception.
+ }
throw CheckedExceptionTunnel.wrapIfNecessary(th);
}
}
@@ -115,8 +122,8 @@ public class EICML2Database
int permId = 0;
for (String f : new File(dir).list(new EICMLFilenameFilter()))
{
- eicML2Database.uploadEicMLFile(new File(dir, f), new DMDataSetDTO(
- Integer.toString(++permId), "sample1", "the sample name", "experiment1",
+ eicML2Database.uploadEicMLFile(new File(dir, f), new DMDataSetDTO(Integer
+ .toString(++permId), "sample1", "the sample name", "experiment1",
"the experiment name"));
}
System.out.println((System.currentTimeMillis() - start) / 1000.0);
--
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