From 598199dbb0779590c0b1a93c13d0458a99a596d4 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Mon, 25 May 2009 11:02:31 +0000
Subject: [PATCH] add: support for schema versioning change: use new batch
update support of eodsql
SVN: 11131
---
rtd_yeastx/.classpath | 28 ++---
.../ch/systemsx/cisd/yeastx/db/DBFactory.java | 40 +++++--
.../cisd/yeastx/eicml/EICML2Database.java | 34 ++++--
.../cisd/yeastx/eicml/IEICMSRunDAO.java | 21 ++--
.../yeastx/eicml/ListChromatogramLabels.java | 2 +-
.../cisd/yeastx/fiaml/FIAML2Database.java | 104 ++++++------------
.../cisd/yeastx/fiaml/IFIAMSRunDAO.java | 15 +--
.../cisd/yeastx/fiaml/ProfileDTO.java | 87 +++++++++++++++
.../001/schema-001.sql} | 24 ++--
.../ReadChromatogramsPerformanceTest.java | 2 +-
10 files changed, 227 insertions(+), 130 deletions(-)
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/ProfileDTO.java
rename rtd_yeastx/source/sql/{schema.sql => postgresql/001/schema-001.sql} (87%)
diff --git a/rtd_yeastx/.classpath b/rtd_yeastx/.classpath
index ecca2a6ee13..eb162b4b474 100644
--- a/rtd_yeastx/.classpath
+++ b/rtd_yeastx/.classpath
@@ -1,13 +1,15 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" path="source/java"/>
- <classpathentry kind="src" path="sourceTest/java"/>
- <classpathentry kind="lib" path="/libraries/commons-codec/commons-codec.jar" sourcepath="/libraries/commons-codec/src.zip"/>
- <classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
- <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 kind="output" path="targets/classes"/>
-</classpath>
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="source/java"/>
+ <classpathentry kind="src" path="sourceTest/java"/>
+ <classpathentry kind="lib" path="/libraries/commons-codec/commons-codec.jar" sourcepath="/libraries/commons-codec/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/commons-io/commons-io.jar" sourcepath="/libraries/commons-io/src.zip"/>
+ <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="/dbmigration"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/common"/>
+ <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/DBFactory.java
index 2381ba6ac2f..a4090b816f6 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java
@@ -17,11 +17,13 @@
package ch.systemsx.cisd.yeastx.db;
import java.sql.Connection;
-import java.sql.DriverManager;
import java.sql.SQLException;
import net.lemnik.eodsql.QueryTool;
+import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+
/**
* Factory for database connections.
*
@@ -29,25 +31,39 @@ import net.lemnik.eodsql.QueryTool;
*/
public class DBFactory
{
+ /** Current version of the database. */
+ public static final String DATABASE_VERSION = "001";
+
static
{
QueryTool.getTypeMap().put(float[].class, new FloatArrayMapper());
}
- public static Connection getConnection() throws SQLException
+ private final DatabaseConfigurationContext context;
+
+ public DBFactory(DatabaseConfigurationContext context)
+ {
+ this.context = context;
+ DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context, DATABASE_VERSION);
+ }
+
+ public Connection getConnection() throws SQLException
{
- try
- {
- Class.forName("org.postgresql.Driver");
- } catch (ClassNotFoundException ex)
- {
- throw new SQLException("No suitable driver.");
- }
- final Connection conn =
- DriverManager.getConnection("jdbc:postgresql:metabol", System.getProperties()
- .getProperty("user.name"), "");
+ final Connection conn = context.getDataSource().getConnection();
conn.setAutoCommit(false);
return conn;
}
+ public static DatabaseConfigurationContext createDefaultDBContext()
+ {
+ final DatabaseConfigurationContext context = new DatabaseConfigurationContext();
+ context.setDatabaseEngineCode("postgresql");
+ context.setBasicDatabaseName("metabol");
+ context.setDatabaseKind("dev");
+ context.setReadOnlyGroup("metabol_readonly");
+ context.setReadWriteGroup("metabol_readwrite");
+ context.setScriptFolder("source/sql");
+ return context;
+ }
+
}
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 43c5ef19f56..624930e02a9 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
@@ -20,6 +20,8 @@ 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.xml.parsers.ParserConfigurationException;
@@ -40,18 +42,32 @@ import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IMSRunObserver;
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)
+ {
+ if (chromatograms.size() >= CHROMATOGRAM_BATCH_SIZE)
+ {
+ dao.addChromatograms(eicMLId, chromatograms);
+ chromatograms.clear();
+ }
+ }
+
/**
* Method for uploading an <var>eicMLFile</var> to the database.
*/
- public static void uploadEicMLFile(final Connection conn, final File eicMLFile,
- String permId) throws SQLException
+ public static void uploadEicMLFile(final Connection conn, final File eicMLFile, String permId)
+ throws SQLException
{
- final long[] id = new long[1];
+ final long[] eicMLId = new long[1];
+ final List<ChromatogramDTO> chromatograms =
+ new ArrayList<ChromatogramDTO>(CHROMATOGRAM_BATCH_SIZE);
try
{
final IEICMSRunDAO dao = getDAO(conn);
@@ -59,16 +75,18 @@ public class EICML2Database
{
public void observe(EICMSRunDTO run)
{
- id[0] = dao.addMSRun(run);
+ eicMLId[0] = dao.addMSRun(run);
+ addChromatograms(dao, eicMLId[0], chromatograms, 1);
}
}, new IChromatogramObserver()
{
public void observe(ChromatogramDTO chromatogram)
{
- chromatogram.setEicMsRunId(id[0]);
- dao.addChromatogram(chromatogram);
+ chromatograms.add(chromatogram);
+ addChromatograms(dao, eicMLId[0], chromatograms, CHROMATOGRAM_BATCH_SIZE);
}
});
+ addChromatograms(dao, eicMLId[0], chromatograms, 1);
conn.commit();
} catch (Throwable th)
{
@@ -86,7 +104,8 @@ public class EICML2Database
public static void main(String[] args) throws ParserConfigurationException, SAXException,
IOException, SQLException
{
- final Connection conn = DBFactory.getConnection();
+ final long start = System.currentTimeMillis();
+ final Connection conn = new DBFactory(DBFactory.createDefaultDBContext()).getConnection();
try
{
final String dir = args[0];
@@ -99,6 +118,7 @@ public class EICML2Database
{
conn.close();
}
+ 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 1e7d0ecfd22..a32d0a685b6 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
@@ -16,9 +16,12 @@
package ch.systemsx.cisd.yeastx.eicml;
+import java.util.List;
+
import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
+import net.lemnik.eodsql.Update;
/**
* Interface for querying / updating the metabol database.
@@ -42,11 +45,11 @@ public interface IEICMSRunDAO extends BaseQuery
+ "?{1.methodSeparation}, ?{1.setId}, ?{1.operator}, ?{1.startTime}, ?{1.endTime}) returning eicMsRunId")
public long addMSRun(EICMSRunDTO msRun);
- @Select("INSERT INTO chromatograms (eicMsRunId, Q1MZ, Q3LowMz, Q3HighMz, label, polarity, runTimes, "
- + "intensities) values (?{1.eicMsRunId}, ?{1.q1Mz}, "
- + "?{1.q3LowMz}, ?{1.q3HighMz}, ?{1.label}, "
- + "?{1.polarity}, ?{1.runTimes}, ?{1.intensities}) returning chromId")
- public long addChromatogram(ChromatogramDTO chromatogram);
+ @Update(sql = "INSERT INTO chromatograms (eicMsRunId, Q1MZ, Q3LowMz, Q3HighMz, label, polarity, runTimes, "
+ + "intensities) values (?{1}, ?{2.q1Mz}, ?{2.q3LowMz}, ?{2.q3HighMz}, ?{2.label}, "
+ + "?{2.polarity}, ?{2.runTimes}, ?{2.intensities})", batchUpdate = true, parameterTypes =
+ { Long.class, ChromatogramDTO.class })
+ public void addChromatograms(long eicMsRunId, List<ChromatogramDTO> chromatogram);
@Select(sql = "SELECT * from eicmsruns", rubberstamp = true)
public DataIterator<EICMSRunDTO> getMsRuns();
@@ -70,16 +73,16 @@ public interface IEICMSRunDAO extends BaseQuery
@Select("SELECT chromatograms.* FROM chromatograms where chromId=?{1}")
public ChromatogramDTO getChromatogramById(long id);
-
+
@Select("SELECT chromatograms.* FROM chromatograms where label=?{1}")
public ChromatogramDTO getChromatogramByLabel(String label);
- @Select(sql = "SELECT chromatograms.* FROM chromatograms LEFT JOIN eicmsruns USING(eicMsRunId) "
- + "where eicMsRunId=?{1.eicMsRunId}", rubberstamp = true)
+ @Select("SELECT chromatograms.* FROM chromatograms LEFT JOIN eicmsruns USING(eicMsRunId) "
+ + "where eicMsRunId=?{1.eicMsRunId}")
public DataIterator<ChromatogramDTO> getChromatogramsForRun(EICMSRunDTO msRun);
@Select(sql = "SELECT chromId, eicMsRunId, Q1Mz, Q3LowMz, Q3HighMz, label, polarity FROM chromatograms "
- + "LEFT JOIN eicmsruns USING(eicMsRunId) " + "where eicMsRunId=?{1.eicMsRunId}", rubberstamp = true)
+ + "LEFT JOIN eicmsruns USING(eicMsRunId) " + "where eicMsRunId=?{1.eicMsRunId}")
public DataIterator<ChromatogramDTO> getChromatogramsForRunNoData(EICMSRunDTO msRun);
}
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 7ac602839b7..e5b50a783bd 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
@@ -33,7 +33,7 @@ public class ListChromatogramLabels
public static void main(String[] args) throws SQLException
{
- final Connection conn = DBFactory.getConnection();
+ final Connection conn = new DBFactory(DBFactory.createDefaultDBContext()).getConnection();
try
{
final IEICMSRunDAO dao = EICML2Database.getDAO(conn);
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 d8856dc148f..f017266053b 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
@@ -17,10 +17,9 @@
package ch.systemsx.cisd.yeastx.fiaml;
import java.io.File;
-import java.sql.BatchUpdateException;
import java.sql.Connection;
-import java.sql.PreparedStatement;
import java.sql.SQLException;
+import java.util.Iterator;
import net.lemnik.eodsql.QueryTool;
@@ -43,67 +42,39 @@ public class FIAML2Database
return QueryTool.getQuery(conn, IFIAMSRunDAO.class);
}
- private static void addProfilesForRun(final Connection conn, final long fiaMsRunId,
- FIAMSRunDataDTO runData) throws SQLException
+ private static Iterable<ProfileDTO> profileChunk(final FIAMSRunDataDTO runData)
{
- try
- {
- final PreparedStatement prepProfile =
- conn.prepareStatement("INSERT INTO profiles "
- + "(fiaMsRunId, lowMz, highMz, mz, "
- + "intensities) values (?, ?, ?, ?, ?)");
- final float[] mz = runData.getProfileMz();
- final float[] intensities = runData.getProfileIntensities();
- for (int i = 0; i < mz.length; i += PROFILE_CHUNK_SIZE)
+ return new Iterable<ProfileDTO>()
{
- final int imax = Math.min(mz.length, i + PROFILE_CHUNK_SIZE);
- prepProfile.setLong(1, fiaMsRunId);
- prepProfile.setFloat(2, mz[i]);
- prepProfile.setFloat(3, mz[imax - 1]);
- prepProfile.setString(4, toString(mz, i, imax));
- prepProfile.setString(5, toString(intensities, i, imax));
- prepProfile.addBatch();
- }
- prepProfile.executeBatch();
- } catch (BatchUpdateException ex)
- {
- throw ex.getNextException();
- }
- }
+ public Iterator<ProfileDTO> iterator()
+ {
+ return new Iterator<ProfileDTO>()
+ {
+ int i = 0;
- private static String toString(float[] array, int start, int end)
- {
- StringBuilder b = new StringBuilder();
- for (int i = start; i < end; ++i)
- {
- b.append(array[i]);
- b.append(',');
- }
- b.setLength(b.length() - 1);
- return b.toString();
- }
+ public boolean hasNext()
+ {
+ return i < runData.getProfileMz().length;
+ }
- private static void addCentroidsForRun(final Connection conn, final long fiaMsRunId,
- FIAMSRunDataDTO runData) throws SQLException
- {
- try
- {
- final PreparedStatement prepCentroid =
- conn.prepareStatement("INSERT INTO centroids (fiaMsRunId, mz, "
- + "intensity, correlation) values (?, ?, ?, ?)");
- for (int i = 0; i < runData.getCentroidMz().length; ++i)
- {
- prepCentroid.setLong(1, fiaMsRunId);
- prepCentroid.setFloat(2, runData.getCentroidMz()[i]);
- prepCentroid.setFloat(3, runData.getCentroidIntensities()[i]);
- prepCentroid.setFloat(4, runData.getCentroidCorrelations()[i]);
- prepCentroid.addBatch();
- }
- prepCentroid.executeBatch();
- } catch (BatchUpdateException ex)
- {
- throw ex.getNextException();
- }
+ public ProfileDTO next()
+ {
+ final int imax =
+ Math.min(runData.getProfileMz().length, i
+ + PROFILE_CHUNK_SIZE);
+ final int imin = i;
+ i = imax;
+ return ProfileDTO.split(runData.getProfileMz(), runData
+ .getProfileIntensities(), imin, imax);
+ }
+
+ public void remove()
+ {
+ throw new UnsupportedOperationException();
+ }
+ };
+ }
+ };
}
/**
@@ -120,14 +91,11 @@ public class FIAML2Database
public void observe(FIAMSRunDTO run, FIAMSRunDataDTO runData)
{
final long fiaMsRunId = dao.addMSRun(run);
- try
- {
- addProfilesForRun(conn, fiaMsRunId, runData);
- addCentroidsForRun(conn, fiaMsRunId, runData);
- } catch (SQLException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
+ getDAO(conn).addProfiles(fiaMsRunId, profileChunk(runData));
+ getDAO(conn)
+ .addCentroids(fiaMsRunId, runData.getCentroidMz(),
+ runData.getCentroidIntensities(),
+ runData.getCentroidCorrelations());
}
});
conn.commit();
@@ -147,7 +115,7 @@ public class FIAML2Database
public static void main(String[] args) throws SQLException
{
final long start = System.currentTimeMillis();
- final Connection conn = DBFactory.getConnection();
+ final Connection conn = new DBFactory(DBFactory.createDefaultDBContext()).getConnection();
try
{
final String dir = args[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 796b8db17a2..a5359fdeac2 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
@@ -44,12 +44,13 @@ public interface IFIAMSRunDAO extends BaseQuery
+ "?{1.internalStandard}, ?{1.od}, ?{1.operator}) returning fiaMsRunId")
public long addMSRun(FIAMSRunDTO msRun);
- // Too slow as eodsql 2.0 doesn't support batch updates.
- @Update("INSERT INTO profiles (fiaMsRunId, mz, intensity) values (?{1}, ?{2}, ?{3})")
- public void addProfileEntry(long fiaMsRunId, float mz, float intensity);
+ @Update(sql = "INSERT INTO centroids (fiaMsRunId, mz, intensity, correlation) "
+ + "values (?{1}, ?{2}, ?{3}, ?{4})", batchUpdate = true)
+ public void addCentroids(long fiaMsRunId, float[] mz, float[] intensity, float[] correlation);
+
+ @Update(sql = "INSERT INTO profiles (fiaMsRunId, lowMz, highMz, mz, intensities) "
+ + "values (?{1}, ?{2.lowMz}, ?{2.highMz}, ?{2.mz}, ?{2.intensities})", batchUpdate = true, parameterTypes =
+ { Long.class, ProfileDTO.class })
+ public void addProfiles(long fiaMsRunId, Iterable<ProfileDTO> profiles);
- // Too slow as eodsql 2.0 doesn't support batch updates.
- @Update("INSERT INTO centroids (fiaMsRunId, mz, intensity, correlation) "
- + "values (?{1}, ?{2}, ?{3}, ?{4})")
- public void addCentroidEntry(long fiaMsRunId, float mz, float intensity, float correlation);
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/ProfileDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/ProfileDTO.java
new file mode 100644
index 00000000000..8d9a06abee7
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/ProfileDTO.java
@@ -0,0 +1,87 @@
+/*
+ * Copyright 2009 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.yeastx.fiaml;
+
+/**
+ * A data transfer object for "mz over intensity" profiles.
+ *
+ * @author Bernd Rinn
+ */
+public class ProfileDTO
+{
+ private float lowMz;
+
+ private float highMz;
+
+ private float[] mz;
+
+ private float[] intensities;
+
+ public static ProfileDTO split(float[] mz, float[] intensities, int imin, int imax)
+ {
+ final ProfileDTO dto = new ProfileDTO();
+ final float[] mzChunk = new float[imax - imin];
+ System.arraycopy(mz, imin, mzChunk, 0, imax - imin);
+ dto.setMz(mzChunk);
+ dto.setLowMz(mzChunk[0]);
+ dto.setHighMz(mzChunk[mzChunk.length - 1]);
+ final float[] intChunk = new float[imax - imin];
+ System.arraycopy(intensities, imin, intChunk, 0, imax - imin);
+ dto.setIntensities(intChunk);
+ return dto;
+ }
+
+ public float getLowMz()
+ {
+ return lowMz;
+ }
+
+ public void setLowMz(float lowMz)
+ {
+ this.lowMz = lowMz;
+ }
+
+ public float getHighMz()
+ {
+ return highMz;
+ }
+
+ public void setHighMz(float highMz)
+ {
+ this.highMz = highMz;
+ }
+
+ public float[] getMz()
+ {
+ return mz;
+ }
+
+ public void setMz(float[] mz)
+ {
+ this.mz = mz;
+ }
+
+ public float[] getIntensities()
+ {
+ return intensities;
+ }
+
+ public void setIntensities(float[] intensities)
+ {
+ this.intensities = intensities;
+ }
+}
\ No newline at end of file
diff --git a/rtd_yeastx/source/sql/schema.sql b/rtd_yeastx/source/sql/postgresql/001/schema-001.sql
similarity index 87%
rename from rtd_yeastx/source/sql/schema.sql
rename to rtd_yeastx/source/sql/postgresql/001/schema-001.sql
index cd1301e9484..94f5cc3ec0c 100644
--- a/rtd_yeastx/source/sql/schema.sql
+++ b/rtd_yeastx/source/sql/postgresql/001/schema-001.sql
@@ -1,12 +1,6 @@
-CREATE DATABASE metabol ENCODING 'UTF8';
-
-CREATE ROLE metabol_readonly;
-
-CREATE ROLE metabol_readwrite;
-
-GRANT metabol_readwrite to brinn;
-
-\c metabol
+-----------------------------------
+-- Version 001
+-----------------------------------
CREATE TABLE eicmsruns (
eicMsRunId BIGSERIAL NOT NULL,
@@ -66,26 +60,30 @@ CREATE TABLE fiamsruns (
);
CREATE TABLE profiles (
+ profileId BIGSERIAL NOT NULL,
fiaMsRunId BIGINT NOT NULL,
lowMz REAL NOT NULL,
highMz REAL NOT NULL,
mz TEXT NOT NULL,
intensities TEXT NOT NULL,
- PRIMARY KEY (fiaMsRunId, lowMz),
+ PRIMARY KEY (profileId),
CONSTRAINT FK_profiles_1 FOREIGN KEY (fiaMsRunId) REFERENCES fiamsruns (fiaMsRunId) ON DELETE CASCADE ON UPDATE CASCADE
);
-CREATE INDEX profile_idx on profiles(fiaMsRunId, lowMz, highMz);
+CREATE INDEX profile_i on profiles(fiaMsRunId, lowMz, highMz);
CREATE TABLE centroids (
+ centroidId BIGSERIAL NOT NULL,
fiaMsRunId BIGINT NOT NULL,
mz REAL NOT NULL,
intensity REAL NOT NULL,
correlation REAL NOT NULL,
- PRIMARY KEY (fiaMsRunId, mz),
+ PRIMARY KEY (centroidId),
CONSTRAINT FK_centroids_1 FOREIGN KEY (fiaMsRunId) REFERENCES fiamsruns (fiaMsRunId) ON DELETE CASCADE ON UPDATE CASCADE
);
+CREATE INDEX centroid_i on centroids(fiaMsRunId, mz);
+
GRANT SELECT ON TABLE eicmsruns TO GROUP metabol_readonly;
GRANT SELECT ON TABLE chromatograms TO GROUP metabol_readonly;
GRANT SELECT ON TABLE fiamsruns TO GROUP metabol_readonly;
@@ -103,3 +101,5 @@ GRANT ALL PRIVILEGES ON TABLE centroids TO GROUP metabol_readwrite;
GRANT ALL PRIVILEGES ON SEQUENCE eicmsruns_eicmsrunid_seq TO GROUP metabol_readwrite;
GRANT ALL PRIVILEGES ON SEQUENCE chromatograms_chromid_seq TO GROUP metabol_readwrite;
GRANT ALL PRIVILEGES ON SEQUENCE fiamsruns_fiamsrunid_seq TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE profiles_profileid_seq TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE centroids_centroidid_seq TO GROUP metabol_readwrite;
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 783a5c309bd..ba7fb6d009c 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
@@ -31,8 +31,8 @@ public class ReadChromatogramsPerformanceTest
public static void main(String[] args) throws SQLException
{
+ final Connection conn = new DBFactory(DBFactory.createDefaultDBContext()).getConnection();
long start = System.currentTimeMillis();
- final Connection conn = DBFactory.getConnection();
try
{
final IEICMSRunDAO dao = EICML2Database.getDAO(conn);
--
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