diff --git a/rtd_yeastx/.classpath b/rtd_yeastx/.classpath
index 4f59ee85a035bcfdf1e0ebda06ea56bac6407856..6dd1e778a74d21fa8ae98dadc7c7b75e43abc82b 100644
--- a/rtd_yeastx/.classpath
+++ b/rtd_yeastx/.classpath
@@ -7,7 +7,6 @@
<classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
<classpathentry kind="lib" path="/libraries/postgresql/postgresql.jar" sourcepath="/libraries/postgresql/postgresql-src.zip"/>
- <classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
<classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
<classpathentry combineaccessrules="false" kind="src" path="/openbis"/>
@@ -19,5 +18,7 @@
<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base-test.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
<classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
<classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
+ <classpathentry kind="lib" path="/libraries/spring/spring.jar" sourcepath="/libraries/spring/src.jar"/>
+ <classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
similarity index 72%
rename from rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java
rename to rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
index e3ad8353745f533e576d6d1a612bfe2792618cb6..cca5144be55435c39f0c6f969d21310bf24e3028 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
@@ -16,20 +16,19 @@
package ch.systemsx.cisd.yeastx.db;
-import java.sql.Connection;
-import java.sql.SQLException;
-
import net.lemnik.eodsql.QueryTool;
+import net.lemnik.eodsql.TransactionQuery;
import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
/**
- * Factory for database connections.
+ * Database utilities. Call {@link #init(DatabaseConfigurationContext)} before working with the
+ * database.
*
* @author Bernd Rinn
*/
-public class DBFactory
+public class DBUtils
{
/** Current version of the database. */
public static final String DATABASE_VERSION = "001";
@@ -39,21 +38,6 @@ public class DBFactory
QueryTool.getTypeMap().put(float[].class, new FloatArrayMapper());
}
- private final DatabaseConfigurationContext context;
-
- public DBFactory(DatabaseConfigurationContext context)
- {
- this.context = context;
- DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context, DATABASE_VERSION);
- }
-
- public Connection getConnection() throws SQLException
- {
- final Connection conn = context.getDataSource().getConnection();
- conn.setAutoCommit(false);
- return conn;
- }
-
public static DatabaseConfigurationContext createDefaultDBContext()
{
final DatabaseConfigurationContext context = new DatabaseConfigurationContext();
@@ -67,11 +51,36 @@ public class DBFactory
}
/**
- * Returns the data access object for the generic tables of the data mart.
+ * Checks the database specified by <var>context</var> and migrates it to the current version if
+ * necessary.
+ */
+ public static void init(DatabaseConfigurationContext context)
+ {
+ DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context, DATABASE_VERSION);
+ }
+
+ /**
+ * Rolls backs and closes the given <var>transactionOrNull</var>, if it is not <code>null</code>
+ * .
+ */
+ public static void rollbackAndClose(TransactionQuery transactionOrNull)
+ {
+ if (transactionOrNull != null)
+ {
+ transactionOrNull.rollback();
+ transactionOrNull.close();
+ }
+ }
+
+ /**
+ * Closes the given <var>transactionOrNull</var>, if it is not <code>null</code> .
*/
- public static IGenericDAO getDAO(Connection conn)
+ public static void close(TransactionQuery transactionOrNull)
{
- return QueryTool.getQuery(conn, IGenericDAO.class);
+ if (transactionOrNull != null)
+ {
+ transactionOrNull.close();
+ }
}
/**
@@ -84,7 +93,8 @@ public class DBFactory
DMSampleDTO sample = dao.getSampleByPermId(dataSet.getSample().getPermId());
if (sample == null)
{
- DMExperimentDTO experiment = dao.getExperimentByPermId(dataSet.getExperiment().getPermId());
+ DMExperimentDTO experiment =
+ dao.getExperimentByPermId(dataSet.getExperiment().getPermId());
if (experiment == null)
{
experiment = dataSet.getExperiment();
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
index 04e25d50e164bd8e9edfe7c58a8e948c67d840e2..0faa99e2ba33e01027a4cf651e06737535a080b8 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
@@ -16,15 +16,15 @@
package ch.systemsx.cisd.yeastx.db;
-import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.Select;
+import net.lemnik.eodsql.TransactionQuery;
/**
* Interface for the "generic" methods (i.e. experiment, sample and data set).
*
* @author Bernd Rinn
*/
-public interface IGenericDAO extends BaseQuery
+public interface IGenericDAO extends TransactionQuery
{
@Select("select * from EXPERIMENTS where PERM_ID = ?{1}")
@@ -39,6 +39,9 @@ public interface IGenericDAO extends BaseQuery
@Select("select * from SAMPLES where PERM_ID = ?{1}")
public DMSampleDTO getSampleByPermId(String samplePermId);
+ @Select("select DS.* from DATA_SETS DS JOIN SAMPLES S on DS.SAMP_ID = S.ID where S.PERM_ID = ?{1}")
+ public DMDataSetDTO[] listDataSetsForSample(String samplePermId);
+
@Select("select * from SAMPLES where ID = ?{1}")
public DMSampleDTO getSampleById(long id);
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 e82fe396aaa1af195a5411cc2476c4c8bdd5e858..d4ee22aa905b2d68b84fe047d30636f534a94714 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
@@ -18,19 +18,20 @@ package ch.systemsx.cisd.yeastx.eicml;
import java.io.File;
import java.io.IOException;
-import java.sql.Connection;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.List;
+import javax.sql.DataSource;
import javax.xml.parsers.ParserConfigurationException;
import net.lemnik.eodsql.QueryTool;
+import net.lemnik.eodsql.TransactionQuery;
import org.xml.sax.SAXException;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.yeastx.db.DBFactory;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IChromatogramObserver;
import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IMSRunObserver;
@@ -45,11 +46,6 @@ public class EICML2Database
private final static int CHROMATOGRAM_BATCH_SIZE = 100;
- public static IEICMSRunDAO getDAO(Connection conn)
- {
- return QueryTool.getQuery(conn, IEICMSRunDAO.class);
- }
-
private static void addChromatograms(IEICMSRunDAO dao, long eicMLId,
List<ChromatogramDTO> chromatograms, int threshold)
{
@@ -60,19 +56,26 @@ public class EICML2Database
}
}
+ private final IEICMSRunDAO dao;
+
+ public EICML2Database(DataSource datasource)
+ {
+ this.dao = QueryTool.getQuery(datasource, IEICMSRunDAO.class);
+ }
+
/**
* Method for uploading an <var>eicMLFile</var> to the database.
*/
- public static void uploadEicMLFile(final Connection conn, final File eicMLFile,
- final DMDataSetDTO dataSet) throws SQLException
+ public void uploadEicMLFile(final File eicMLFile, final DMDataSetDTO dataSet)
{
final long[] eicMLId = new long[1];
final List<ChromatogramDTO> chromatograms =
new ArrayList<ChromatogramDTO>(CHROMATOGRAM_BATCH_SIZE);
+ TransactionQuery transaction = null;
try
{
- DBFactory.createDataSet(DBFactory.getDAO(conn), dataSet);
- final IEICMSRunDAO dao = getDAO(conn);
+ transaction = dao;
+ DBUtils.createDataSet(dao, dataSet);
new EICMLParser(eicMLFile.getPath(), new IMSRunObserver()
{
public void observe(EICMSRunDTO run)
@@ -94,17 +97,11 @@ public class EICML2Database
}
});
addChromatograms(dao, eicMLId[0], chromatograms, 1);
- conn.commit();
+ transaction.close(true);
} catch (Throwable th)
{
- conn.rollback();
- if (th instanceof SQLException)
- {
- throw (SQLException) th;
- } else
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(th);
- }
+ DBUtils.rollbackAndClose(transaction);
+ throw CheckedExceptionTunnel.wrapIfNecessary(th);
}
}
@@ -112,20 +109,15 @@ public class EICML2Database
IOException, SQLException
{
final long start = System.currentTimeMillis();
- final Connection conn = new DBFactory(DBFactory.createDefaultDBContext()).getConnection();
- try
- {
- final String dir = args[0];
- int permId = 0;
- for (String f : new File(dir).list(new EICMLFilenameFilter()))
- {
- uploadEicMLFile(conn, new File(dir, f), new DMDataSetDTO(
- Integer.toString(++permId), "sample1", "the sample name", "experiment1",
- "the experiment name"));
- }
- } finally
+ final EICML2Database eicML2Database =
+ new EICML2Database(DBUtils.createDefaultDBContext().getDataSource());
+ final String dir = args[0];
+ int permId = 0;
+ for (String f : new File(dir).list(new EICMLFilenameFilter()))
{
- conn.close();
+ 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);
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java
index 7fff59b2f0fb08a65c2d40cc1f87b6c0c71b8c6d..f11191925f3c343b3983bba1628e6730a1af2787 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java
@@ -18,7 +18,8 @@ package ch.systemsx.cisd.yeastx.eicml;
import java.util.List;
-import net.lemnik.eodsql.BaseQuery;
+import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
@@ -28,7 +29,7 @@ import net.lemnik.eodsql.Update;
*
* @author Bernd Rinn
*/
-public interface IEICMSRunDAO extends BaseQuery
+public interface IEICMSRunDAO extends IGenericDAO
{
final String ALL_EIC_MSRUN_COLUMNS =
"EIC_MS_RUNS.ID, EIC_MS_RUNS.EXPE_ID, EIC_MS_RUNS.SAMP_ID, EIC_MS_RUNS.DS_ID, "
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ListChromatogramLabels.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ListChromatogramLabels.java
index e5b50a783bdc0a89b65b606ab3dbac6667ba6ad9..26766eb781758431b71a40dbfcdf686e5caadaea 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ListChromatogramLabels.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ListChromatogramLabels.java
@@ -16,12 +16,14 @@
package ch.systemsx.cisd.yeastx.eicml;
-import java.sql.Connection;
import java.sql.SQLException;
-import ch.systemsx.cisd.yeastx.db.DBFactory;
-
import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.QueryTool;
+import net.lemnik.eodsql.TransactionQuery;
+
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
/**
* A method for listing all chromatogram labels of all runs.
@@ -33,10 +35,13 @@ public class ListChromatogramLabels
public static void main(String[] args) throws SQLException
{
- final Connection conn = new DBFactory(DBFactory.createDefaultDBContext()).getConnection();
+ final DatabaseConfigurationContext context = DBUtils.createDefaultDBContext();
+ DBUtils.init(context);
+ TransactionQuery transaction = null;
try
{
- final IEICMSRunDAO dao = EICML2Database.getDAO(conn);
+ final IEICMSRunDAO dao = QueryTool.getQuery(context.getDataSource(), IEICMSRunDAO.class);
+ transaction = dao;
if (args.length > 0)
{
for (String fn : args)
@@ -54,7 +59,7 @@ public class ListChromatogramLabels
}
} finally
{
- conn.close();
+ DBUtils.close(transaction);
}
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
index b9178b0da466fda78a2c936232920701d09e4c66..83d63f7dac025fed0b49c8576bb7c93273d28ee2 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
@@ -17,7 +17,6 @@
package ch.systemsx.cisd.yeastx.etl;
import java.io.File;
-import java.sql.Connection;
import java.sql.SQLException;
import java.util.Properties;
import java.util.Set;
@@ -32,7 +31,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.dto.EntityPropertyPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
-import ch.systemsx.cisd.yeastx.db.DBFactory;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.eicml.EICML2Database;
import ch.systemsx.cisd.yeastx.fiaml.FIAML2Database;
@@ -47,8 +46,10 @@ public class ML2DatabaseUploader
{
private static final String DATABASE_PROPERTIES_PREFIX = "database.";
- private final Connection connection;
-
+ private final EICML2Database eicML2Database;
+
+ private final FIAML2Database fiaML2Database;
+
private final String uniqueSampleNamePropertyCode;
private final String uniqueExperimentNamePropertyCode;
@@ -58,28 +59,17 @@ public class ML2DatabaseUploader
final Properties dbProps =
ExtendedProperties.getSubset(properties, DATABASE_PROPERTIES_PREFIX, true);
final DatabaseConfigurationContext dbContext =
- (dbProps.isEmpty() ? DBFactory.createDefaultDBContext() : BeanUtils.createBean(
+ (dbProps.isEmpty() ? DBUtils.createDefaultDBContext() : BeanUtils.createBean(
DatabaseConfigurationContext.class, dbProps));
- this.connection = getDatabaseConnection(dbContext);
+ DBUtils.init(dbContext);
+ this.eicML2Database = new EICML2Database(dbContext.getDataSource());
+ this.fiaML2Database = new FIAML2Database(dbContext.getDataSource());
this.uniqueExperimentNamePropertyCode =
DatasetMappingResolver.getUniqueExperimentNamePropertyCode(properties);
this.uniqueSampleNamePropertyCode =
DatasetMappingResolver.getUniqueSampleNamePropertyCode(properties);
}
- private static Connection getDatabaseConnection(DatabaseConfigurationContext dbContext)
- throws EnvironmentFailureException
- {
- try
- {
- return new DBFactory(dbContext).getConnection();
- } catch (SQLException e)
- {
- throw EnvironmentFailureException.fromTemplate(e,
- "Cannot connect to the database which stores transformed mzXML files.");
- }
- }
-
/** uploads files with recognized extensions to the additional database */
public void upload(File dataSet, DataSetInformation dataSetInformation)
throws EnvironmentFailureException
@@ -111,14 +101,14 @@ public class ML2DatabaseUploader
throws SQLException
{
DMDataSetDTO openbisBacklink = createBacklink(dataSetInformation);
- EICML2Database.uploadEicMLFile(connection, dataSet, openbisBacklink);
+ eicML2Database.uploadEicMLFile(dataSet, openbisBacklink);
}
private void translateFIA(File dataSet, DataSetInformation dataSetInformation)
throws SQLException
{
DMDataSetDTO openbisBacklink = createBacklink(dataSetInformation);
- FIAML2Database.uploadFiaMLFile(connection, dataSet, openbisBacklink);
+ fiaML2Database.uploadFiaMLFile(dataSet, openbisBacklink);
}
private DMDataSetDTO createBacklink(DataSetInformation dataSetInformation)
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 2d0db836a53216d554b89c58109f54845ab86459..fdfffd19bcf79e89b9dfc8ee6165f6a5d3702d3d 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
@@ -17,14 +17,18 @@
package ch.systemsx.cisd.yeastx.fiaml;
import java.io.File;
-import java.sql.Connection;
import java.sql.SQLException;
import java.util.Iterator;
+import javax.sql.DataSource;
+
import net.lemnik.eodsql.QueryTool;
+import net.lemnik.eodsql.TransactionQuery;
+
+import org.springframework.dao.DataAccessException;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.yeastx.db.DBFactory;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.fiaml.FIAMLParser.IMSRunObserver;
@@ -38,11 +42,6 @@ public class FIAML2Database
private final static int PROFILE_CHUNK_SIZE = 250;
- public static IFIAMSRunDAO getDAO(Connection conn)
- {
- return QueryTool.getQuery(conn, IFIAMSRunDAO.class);
- }
-
private static Iterable<ProfileDTO> profileChunk(final FIAMSRunDataDTO runData)
{
return new Iterable<ProfileDTO>()
@@ -78,16 +77,24 @@ public class FIAML2Database
};
}
+ private final IFIAMSRunDAO dao;
+
+ public FIAML2Database(DataSource datasource)
+ {
+ this.dao = QueryTool.getQuery(datasource, IFIAMSRunDAO.class);
+ }
+
/**
* Method for uploading an <var>fiaMLFile</var> to the database.
*/
- public static void uploadFiaMLFile(final Connection conn, final File fiaMLFile,
- final DMDataSetDTO dataSet) throws SQLException
+ public void uploadFiaMLFile(final File fiaMLFile, final DMDataSetDTO dataSet)
+ throws SQLException
{
+ TransactionQuery transaction = null;
try
{
- DBFactory.createDataSet(DBFactory.getDAO(conn), dataSet);
- final IFIAMSRunDAO dao = getDAO(conn);
+ transaction = dao;
+ DBUtils.createDataSet(dao, dataSet);
new FIAMLParser(fiaMLFile.getPath(), new IMSRunObserver()
{
public void observe(FIAMSRunDTO run, FIAMSRunDataDTO runData)
@@ -96,44 +103,38 @@ public class FIAML2Database
run.setSampleId(dataSet.getSampleId());
run.setDataSetId(dataSet.getId());
final long fiaMsRunId = dao.addMSRun(run);
- getDAO(conn).addProfiles(fiaMsRunId, profileChunk(runData));
- getDAO(conn)
- .addCentroids(fiaMsRunId, runData.getCentroidMz(),
- runData.getCentroidIntensities(),
- runData.getCentroidCorrelations());
+ dao.addProfiles(fiaMsRunId, profileChunk(runData));
+ dao.addCentroids(fiaMsRunId, runData.getCentroidMz(), runData
+ .getCentroidIntensities(), runData.getCentroidCorrelations());
}
});
- conn.commit();
+ transaction.close(true);
} catch (Throwable th)
{
- conn.rollback();
- if (th instanceof SQLException)
+ try
{
- throw (SQLException) th;
- } else
+ DBUtils.rollbackAndClose(transaction);
+ } catch (DataAccessException ex)
{
- throw CheckedExceptionTunnel.wrapIfNecessary(th);
+ // Avoid this exception shadowing the original exception.
}
+ throw CheckedExceptionTunnel.wrapIfNecessary(th);
}
}
public static void main(String[] args) throws SQLException
{
final long start = System.currentTimeMillis();
- final Connection conn = new DBFactory(DBFactory.createDefaultDBContext()).getConnection();
- try
- {
- final String dir = args[0];
- int permId = 0;
- for (String f : new File(dir).list(new FIAMLFilenameFilter()))
- {
- System.out.println(f);
- uploadFiaMLFile(conn, new File(dir, f), new DMDataSetDTO(Integer.toString(++permId),
- "sample perm id", "sample name", "experiment perm id", "experiment name"));
- }
- } finally
+ final FIAML2Database fiaML2Database =
+ new FIAML2Database(DBUtils.createDefaultDBContext().getDataSource());
+ final String dir = args[0];
+ int permId = 0;
+ for (String f : new File(dir).list(new FIAMLFilenameFilter()))
{
- conn.close();
+ System.out.println(f);
+ fiaML2Database.uploadFiaMLFile(new File(dir, f), new DMDataSetDTO(Integer
+ .toString(++permId), "sample perm id", "sample name", "experiment perm id",
+ "experiment name"));
}
System.out.println((System.currentTimeMillis() - start) / 1000.0);
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java
index f8de0f12da5c9fed258390ccf10da6e6ffe0a762..1d7c17b2ee0f45279590eef47b81225ab21c86d6 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java
@@ -16,7 +16,8 @@
package ch.systemsx.cisd.yeastx.fiaml;
-import net.lemnik.eodsql.BaseQuery;
+import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
@@ -26,7 +27,7 @@ import net.lemnik.eodsql.Update;
*
* @author Bernd Rinn
*/
-public interface IFIAMSRunDAO extends BaseQuery
+public interface IFIAMSRunDAO extends IGenericDAO
{
final String ALL_FIA_MSRUN_COLUMNS =
"FIA_MS_RUNS.ID, FIA_MS_RUNS.EXPE_ID, "
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/db/AbstractDBTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/db/AbstractDBTest.java
index 379ecbc97eb3a69a7601683a6230cf9fdecadf53..5362ec35c8b06aadaa5818eb6dc2717efaaf2184 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/db/AbstractDBTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/db/AbstractDBTest.java
@@ -16,19 +16,14 @@
package ch.systemsx.cisd.yeastx.db;
-import java.sql.Connection;
import java.sql.SQLException;
-import net.lemnik.eodsql.QueryTool;
+import javax.sql.DataSource;
-import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
import ch.systemsx.cisd.common.logging.LogInitializer;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-import ch.systemsx.cisd.yeastx.eicml.IEICMSRunDAO;
-import ch.systemsx.cisd.yeastx.fiaml.IFIAMSRunDAO;
/**
* Abstract test case for database related unit testing.
@@ -42,40 +37,16 @@ public abstract class AbstractDBTest
LogInitializer.init();
}
- protected Connection conn;
+ protected DataSource datasource;
@BeforeClass(alwaysRun = true)
public void setUpClass() throws SQLException
{
- final DatabaseConfigurationContext context = DBFactory.createDefaultDBContext();
+ final DatabaseConfigurationContext context = DBUtils.createDefaultDBContext();
context.setDatabaseKind("dbtest");
context.setCreateFromScratch(true);
- new DBFactory(context).getConnection();
- }
-
- @BeforeMethod(alwaysRun = true)
- public void setUpMethod() throws SQLException
- {
- final DatabaseConfigurationContext context = DBFactory.createDefaultDBContext();
- context.setDatabaseKind("dbtest");
- conn = new DBFactory(context).getConnection();
- }
-
- @AfterMethod(alwaysRun = true)
- public void closeConnection() throws SQLException
- {
- conn.close();
- conn = null;
- }
-
- protected IEICMSRunDAO getEICMLDAO()
- {
- return QueryTool.getQuery(conn, IEICMSRunDAO.class);
- }
-
- protected IFIAMSRunDAO getFIAMLDAO()
- {
- return QueryTool.getQuery(conn, IFIAMSRunDAO.class);
+ DBUtils.init(context);
+ datasource = context.getDataSource();
}
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
index 890c878184a26cd3e964e081be7277382467f38d..a66cedc8ef04ff63908de3864a8f1612a8628fd0 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
@@ -24,6 +24,7 @@ import java.sql.SQLException;
import java.text.ParseException;
import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.QueryTool;
import org.apache.commons.lang.ArrayUtils;
import org.testng.annotations.BeforeMethod;
@@ -45,13 +46,14 @@ public class EICMLTest extends AbstractDBTest
@BeforeMethod(alwaysRun = true)
public void setDAO() throws SQLException
{
- eicmlDAO = getEICMLDAO();
+ eicmlDAO = QueryTool.getQuery(datasource, IEICMSRunDAO.class);
}
@Test
public void testUploadEicML() throws SQLException
{
- EICML2Database.uploadEicMLFile(conn, new File("resource/examples/example.eicML"),
+ EICML2Database db = new EICML2Database(datasource);
+ db.uploadEicMLFile(new File("resource/examples/example.eicML"),
new DMDataSetDTO("data set perm id", "sample perm id", "sample name",
"experiment perm id", "experiment name"));
}
@@ -138,7 +140,6 @@ public class EICMLTest extends AbstractDBTest
assertEquals(17L, run.getMsRunId().longValue());
assertEquals(32L, run.getSetId().longValue());
assertEquals("???", run.getOperator());
- runs.close(); // Shoudn't be necessary, just to be sure.
final DataIterator<ChromatogramDTO> chromatograms = eicmlDAO.getChromatogramsForRun(run);
int count = 0;
while (chromatograms.hasNext())
@@ -148,6 +149,5 @@ public class EICMLTest extends AbstractDBTest
++count;
}
assertEquals(run.getChromCount(), count);
- chromatograms.close(); // Shoudn't be necessary, just to be sure.
}
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/ReadChromatogramsPerformanceTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/ReadChromatogramsPerformanceTest.java
index ba7fb6d009ce2c27f4b6faf1b5db54d83b784b08..54147631f26ab312e612c1df6fe0c1fc438b6fde 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/ReadChromatogramsPerformanceTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/ReadChromatogramsPerformanceTest.java
@@ -16,10 +16,13 @@
package ch.systemsx.cisd.yeastx.eicml;
-import java.sql.Connection;
import java.sql.SQLException;
-import ch.systemsx.cisd.yeastx.db.DBFactory;
+import net.lemnik.eodsql.QueryTool;
+import net.lemnik.eodsql.TransactionQuery;
+
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
/**
* A performance test of reading all chromatograms from the database.
@@ -31,11 +34,13 @@ public class ReadChromatogramsPerformanceTest
public static void main(String[] args) throws SQLException
{
- final Connection conn = new DBFactory(DBFactory.createDefaultDBContext()).getConnection();
+ final DatabaseConfigurationContext context = DBUtils.createDefaultDBContext();
+ DBUtils.init(context);
+ TransactionQuery transaction = null;
long start = System.currentTimeMillis();
try
{
- final IEICMSRunDAO dao = EICML2Database.getDAO(conn);
+ final IEICMSRunDAO dao = QueryTool.getQuery(context.getDataSource(), IEICMSRunDAO.class);
for (EICMSRunDTO run : dao.getMsRuns())
{
// We need to iterate over the chromatograms to make sure they are really read.
@@ -47,7 +52,7 @@ public class ReadChromatogramsPerformanceTest
}
} finally
{
- conn.close();
+ DBUtils.close(transaction);
}
System.out.println((System.currentTimeMillis() - start) / 1000.0f);
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
index 6b22e445e0d142c1de224b02c2b626fec18ed680..cfb4ed22690da413011a2d06e4f6be27786373f7 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
@@ -16,21 +16,26 @@
package ch.systemsx.cisd.yeastx.fiaml;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+
import java.io.File;
import java.sql.SQLException;
import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.QueryTool;
+import org.springframework.dao.DataIntegrityViolationException;
+import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.yeastx.db.AbstractDBTest;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
-import static org.testng.AssertJUnit.*;
-
/**
- * A test for thhe fiaML tables.
+ * A test for the fiaML tables.
*
* @author Bernd Rinn
*/
@@ -41,26 +46,33 @@ public class FIAMLTest extends AbstractDBTest
@BeforeMethod(alwaysRun = true)
public void setDAO() throws SQLException
{
- fiamsDAO = getFIAMLDAO();
+ fiamsDAO = QueryTool.getQuery(datasource, IFIAMSRunDAO.class);
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void close()
+ {
+ fiamsDAO.close();
}
- @Test(groups = "broken")
+ @Test
public void testUploadFiaML() throws SQLException
{
- FIAML2Database.uploadFiaMLFile(conn, new File("resource/examples/example.fiaML"),
+ FIAML2Database fiaML2Database = new FIAML2Database(datasource);
+ fiaML2Database.uploadFiaMLFile(new File("resource/examples/example.fiaML"),
new DMDataSetDTO("data set perm id", "sample perm id", "sample name",
"experiment perm id", "experiment name"));
}
- @Test(groups = "broken", dependsOnMethods = "testUploadFiaML")
+ @Test(dependsOnMethods = "testUploadFiaML")
public void testGetMsRuns()
{
final DataIterator<FIAMSRunDTO> runs = fiamsDAO.getMsRuns();
final FIAMSRunDTO run = runs.next();
assertFalse(runs.hasNext());
assertEquals(686, run.getProfileCount());
- runs.close(); // Shoudn't be necessary, just to be sure.
final DataIterator<ProfileDTO> profiles = fiamsDAO.getProfilesForRun(run);
+ assertFalse(profiles.isClosed());
int count = 0;
while (profiles.hasNext())
{
@@ -70,7 +82,6 @@ public class FIAMLTest extends AbstractDBTest
++count;
}
assertEquals(686, count);
- profiles.close(); // Shoudn't be necessary, just to be sure.
final DataIterator<CentroidDTO> centroids = fiamsDAO.getCentroidsForRun(run);
count = 0;
while (centroids.hasNext())
@@ -81,7 +92,46 @@ public class FIAMLTest extends AbstractDBTest
++count;
}
assertEquals(556, count);
- centroids.close(); // Shoudn't be necessary, just to be sure.
+ fiamsDAO.close();
+ }
+
+ @Test(dependsOnMethods = "testGetMsRuns")
+ public void testUploadFiaMLFileTwiceWithOneDAO() throws SQLException
+ {
+ FIAML2Database fiaML2Database = new FIAML2Database(datasource);
+ fiaML2Database.uploadFiaMLFile(new File("resource/examples/example.fiaML"),
+ new DMDataSetDTO("data set perm id2", "sample perm id2", "sample name",
+ "experiment perm id2", "experiment name"));
+ fiaML2Database.uploadFiaMLFile(new File("resource/examples/example.fiaML"),
+ new DMDataSetDTO("data set perm id3", "sample perm id", "sample name",
+ "experiment perm id", "experiment name"));
+ }
+
+ @Test(dependsOnMethods = "testUploadFiaMLFileTwiceWithOneDAO", expectedExceptions = DataIntegrityViolationException.class)
+ public void testCreateSameDataSetTwiceFailing() throws SQLException
+ {
+ try
+ {
+ DBUtils.createDataSet(fiamsDAO, new DMDataSetDTO("data set perm id 4",
+ "sample perm id4", "sample name", "experiment perm id", "experiment name"));
+ // This will fail with a DataIntegrityViolationException.
+ DBUtils.createDataSet(fiamsDAO, new DMDataSetDTO("data set perm id 4",
+ "sample perm id4", "sample name", "experiment perm id", "experiment name"));
+ } catch (RuntimeException ex)
+ {
+ // This isn't actually necessary for PostgreSQL, but e.g. Oracle does commit a
+ // transaction when no explicit rollback is given.
+ fiamsDAO.rollback();
+ throw ex;
+ }
+ }
+
+ @Test(dependsOnMethods = "testCreateSameDataSetTwiceFailing")
+ public void testDataSets() throws SQLException
+ {
+ assertEquals(2, fiamsDAO.listDataSetsForSample("sample perm id").length);
+ assertEquals(1, fiamsDAO.listDataSetsForSample("sample perm id2").length);
+ assertEquals(0, fiamsDAO.listDataSetsForSample("sample perm id4").length);
}
}