From d818c852df2abfb38da3550c3d07e17fbc95b7bf Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Mon, 18 May 2009 06:39:58 +0000
Subject: [PATCH] [SE-112] add: some code to parse eicML files and write them
into the database
SVN: 11069
---
rtd_yeastx/.classpath | 13 ++
rtd_yeastx/.project | 17 ++
rtd_yeastx/{ => .settings}/.gitignore | 0
.../cisd/yeastx/eicml/ChromatogramDTO.java | 52 +++++
.../systemsx/cisd/yeastx/eicml/DBFactory.java | 50 +++++
.../cisd/yeastx/eicml/EICML2Database.java | 79 ++++++++
.../cisd/yeastx/eicml/EICML2TabConverter.java | 162 ++++++++++++++++
.../yeastx/eicml/EICMLFilenameFilter.java | 33 ++++
.../cisd/yeastx/eicml/EICMLParser.java | 180 ++++++++++++++++++
.../cisd/yeastx/eicml/FloatArrayMapper.java | 75 ++++++++
.../systemsx/cisd/yeastx/eicml/IMSRunDAO.java | 84 ++++++++
.../yeastx/eicml/ListChromatogramLabels.java | 75 ++++++++
.../systemsx/cisd/yeastx/eicml/MSRunDTO.java | 102 ++++++++++
rtd_yeastx/source/sql/schema.sql | 38 ++++
.../ReadChromatogramsPerformanceTest.java | 53 ++++++
15 files changed, 1013 insertions(+)
create mode 100644 rtd_yeastx/.classpath
create mode 100644 rtd_yeastx/.project
rename rtd_yeastx/{ => .settings}/.gitignore (100%)
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ChromatogramDTO.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/DBFactory.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2TabConverter.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLFilenameFilter.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/FloatArrayMapper.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IMSRunDAO.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ListChromatogramLabels.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/MSRunDTO.java
create mode 100644 rtd_yeastx/source/sql/schema.sql
create mode 100644 rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/ReadChromatogramsPerformanceTest.java
diff --git a/rtd_yeastx/.classpath b/rtd_yeastx/.classpath
new file mode 100644
index 00000000000..cca51acedab
--- /dev/null
+++ b/rtd_yeastx/.classpath
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="src" path="source/java"/>
+ <classpathentry kind="src" path="sourceTest/java"/>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
+ <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="output" path="targets/classes"/>
+</classpath>
diff --git a/rtd_yeastx/.project b/rtd_yeastx/.project
new file mode 100644
index 00000000000..a5a0d918eb0
--- /dev/null
+++ b/rtd_yeastx/.project
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>rtd_yeastx</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>
diff --git a/rtd_yeastx/.gitignore b/rtd_yeastx/.settings/.gitignore
similarity index 100%
rename from rtd_yeastx/.gitignore
rename to rtd_yeastx/.settings/.gitignore
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ChromatogramDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ChromatogramDTO.java
new file mode 100644
index 00000000000..cecd4b786b8
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ChromatogramDTO.java
@@ -0,0 +1,52 @@
+/*
+ * 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.eicml;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+
+/**
+ * A class that represents a chromatogram in an eicML file.
+ */
+public class ChromatogramDTO
+{
+ @AutoGeneratedKeys
+ public long chromId;
+
+ public long msRunId;
+
+ public float q1Mz = Float.NaN;
+
+ public float q3LowMz = Float.NaN;
+
+ public float q3HighMz = Float.NaN;
+
+ public String label;
+
+ public char polarity = '?';
+
+ public float[] runTimes;
+
+ public float[] intensities;
+
+ @Override
+ public String toString()
+ {
+ return ToStringBuilder.reflectionToString(this);
+ }
+}
\ No newline at end of file
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/DBFactory.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/DBFactory.java
new file mode 100644
index 00000000000..3118e909354
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/DBFactory.java
@@ -0,0 +1,50 @@
+/*
+ * 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.eicml;
+
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.SQLException;
+
+import net.lemnik.eodsql.QueryTool;
+
+/**
+ * Factory for database objects.
+ *
+ * @author Bernd Rinn
+ */
+public class DBFactory
+{
+ static
+ {
+ QueryTool.getTypeMap().put(float[].class, new FloatArrayMapper());
+ }
+
+ public static Connection getConnection() throws SQLException
+ {
+ final Connection conn =
+ DriverManager.getConnection("jdbc:postgresql:metabol", System.getProperties()
+ .getProperty("user.name"), "");
+ conn.setAutoCommit(false);
+ return conn;
+ }
+
+ public static IMSRunDAO getDAO(Connection conn)
+ {
+ return QueryTool.getQuery(conn, IMSRunDAO.class);
+ }
+}
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
new file mode 100644
index 00000000000..89d66a975c1
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java
@@ -0,0 +1,79 @@
+/*
+ * 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.eicml;
+
+import java.io.File;
+import java.io.IOException;
+import java.sql.Connection;
+import java.sql.SQLException;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.xml.sax.SAXException;
+
+import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IChromatogramObserver;
+import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IMSRunObserver;
+
+/**
+ * Tool for uploading eicML files to the database.
+ *
+ * @author Bernd Rinn
+ */
+public class EICML2Database
+{
+
+ public static void main(String[] args) throws ParserConfigurationException, SAXException,
+ IOException, SQLException
+ {
+ final Connection conn = DBFactory.getConnection();
+ try
+ {
+ final String dir = args[0];
+ int permId = 0;
+ for (String f : new File(dir).list(new EICMLFilenameFilter()))
+ {
+ final long[] id = new long[1];
+ try
+ {
+ final IMSRunDAO dao = DBFactory.getDAO(conn);
+ new EICMLParser(dir + "/" + f, Integer.toString(++permId), new IMSRunObserver()
+ {
+ public void observe(MSRunDTO run)
+ {
+ id[0] = dao.addMSRun(run);
+ }
+ }, new IChromatogramObserver()
+ {
+ public void observe(ChromatogramDTO chromatogram)
+ {
+ chromatogram.msRunId = id[0];
+ dao.addChromatogram(chromatogram);
+ }
+ });
+ conn.commit();
+ } catch (Throwable th)
+ {
+ conn.rollback();
+ th.printStackTrace();
+ }
+ }
+ } finally
+ {
+ conn.close();
+ }
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2TabConverter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2TabConverter.java
new file mode 100644
index 00000000000..63ce5cce5c8
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2TabConverter.java
@@ -0,0 +1,162 @@
+/*
+ * 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.eicml;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.io.PrintStream;
+
+import javax.xml.parsers.ParserConfigurationException;
+
+import org.apache.commons.lang.StringUtils;
+import org.xml.sax.SAXException;
+
+/**
+ * A converter from eicML files to tab files.
+ *
+ * @author Bernd Rinn
+ */
+public class EICML2TabConverter
+{
+
+ public static void main(String[] args) throws IOException, ParserConfigurationException,
+ SAXException
+ {
+ final String dir = args[0];
+ for (String f : new File(dir).list(new EICMLFilenameFilter()))
+ {
+ final String[] msRunName = new String[1];
+ new EICMLParser(dir + "/" + f, null, new EICMLParser.IMSRunObserver()
+ {
+ public void observe(MSRunDTO run)
+ {
+ String runName = run.rawDataFileName;
+ if (runName.endsWith(".RAW"))
+ {
+ runName = runName.substring(0, runName.length() - 4);
+ }
+ String runDir = dir + "/" + runName;
+ new File(runDir).mkdir();
+ msRunName[0] = runDir;
+ PrintStream out;
+ try
+ {
+ out =
+ new PrintStream(new File(runDir + "/msrun_" + runName
+ + ".tsv"));
+ if (StringUtils.isNotBlank(run.rawDataFilePath))
+ {
+ out.println("filePath\t" + run.rawDataFilePath);
+ }
+ if (StringUtils.isNotBlank(run.rawDataFileName))
+ {
+ out.println("fileName\t" + run.rawDataFileName);
+ }
+ if (StringUtils.isNotBlank(run.instrumentType))
+ {
+ out.println("instrumentType\t" + run.instrumentType);
+ }
+ if (StringUtils.isNotBlank(run.instrumentManufacturer))
+ {
+ out.println("instrumentManufacturer\t"
+ + run.instrumentManufacturer);
+ }
+ if (StringUtils.isNotBlank(run.instrumentModel))
+ {
+ out.println("instrumentModel\t" + run.instrumentModel);
+ }
+ if (StringUtils.isNotBlank(run.methodIonisation))
+ {
+ out.println("methodIonisation\t" + run.methodIonisation);
+ }
+ if (StringUtils.isNotBlank(run.methodSeparation))
+ {
+ out.println("methodSeparation\t" + run.methodSeparation);
+ }
+ if (StringUtils.isNotBlank(run.acquisitionDate))
+ {
+ out.println("acquisitionDate\t" + run.acquisitionDate);
+ }
+ if (run.chromCount >= 0)
+ {
+ out.println("chromCount\t" + run.chromCount);
+ }
+ if (Float.isNaN(run.startTime) == false)
+ {
+ out.println("startTime\t" + run.startTime);
+ }
+ if (Float.isNaN(run.endTime) == false)
+ {
+ out.println("endTime\t" + run.endTime);
+ }
+ if (run.msRunId >= 0)
+ {
+ out.println("msRunId\t" + run.msRunId);
+ }
+ out.close();
+ } catch (FileNotFoundException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ }, new EICMLParser.IChromatogramObserver()
+ {
+ public void observe(ChromatogramDTO chromatogram)
+ {
+ PrintStream out;
+ try
+ {
+ out =
+ new PrintStream(new File(msRunName[0] + "/"
+ + chromatogram.label + ".tsv"));
+ if (Float.isNaN(chromatogram.q1Mz) == false)
+ {
+ out.println("#\tQ1Mz\t" + chromatogram.q1Mz);
+ }
+ if (Float.isNaN(chromatogram.q3LowMz) == false)
+ {
+ out.println("#\tQ3LowMz\t" + chromatogram.q3LowMz);
+ }
+ if (Float.isNaN(chromatogram.q3HighMz) == false)
+ {
+ out.println("#\tQ3HighMz\t" + chromatogram.q3HighMz);
+ }
+ if (StringUtils.isNotBlank(chromatogram.label))
+ {
+ out.println("#\tLabel\t" + chromatogram.label);
+ }
+ if (chromatogram.polarity != '\0')
+ {
+ out.println("#\tPolarity\t" + chromatogram.polarity);
+ }
+ for (int i = 0; i < chromatogram.runTimes.length; ++i)
+ {
+ out.println(chromatogram.runTimes[i] + "\t"
+ + chromatogram.intensities[i]);
+ }
+ out.close();
+ } catch (FileNotFoundException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ });
+ }
+ }
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLFilenameFilter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLFilenameFilter.java
new file mode 100644
index 00000000000..44940b080f6
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLFilenameFilter.java
@@ -0,0 +1,33 @@
+/*
+ * 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.eicml;
+
+import java.io.File;
+import java.io.FilenameFilter;
+
+/**
+ * A {@link FilenameFilter} for <code>eicML</code> files.
+ *
+ * @author Bernd Rinn
+ */
+final class EICMLFilenameFilter implements FilenameFilter
+{
+ public boolean accept(File myDir, String name)
+ {
+ return name.endsWith(".eicML");
+ }
+}
\ No newline at end of file
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
new file mode 100644
index 00000000000..e9e334bc00c
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
@@ -0,0 +1,180 @@
+/*
+ * 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.eicml;
+
+import java.io.IOException;
+
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParser;
+import javax.xml.parsers.SAXParserFactory;
+
+
+import org.apache.commons.codec.binary.Base64;
+import org.xml.sax.Attributes;
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.DefaultHandler;
+
+import ch.systemsx.cisd.base.convert.NativeData;
+import ch.systemsx.cisd.base.convert.NativeData.ByteOrder;
+
+
+/**
+ * A file for parsing <code>eicML</code> files.
+ *
+ * @author Bernd Rinn
+ */
+public class EICMLParser extends DefaultHandler
+{
+
+ /** A role that observes {@Link MSRun}s. */
+ public interface IMSRunObserver
+ {
+ void observe(MSRunDTO run);
+ }
+
+ /** A role that observes {@Link Chromatogram}s. */
+ public interface IChromatogramObserver
+ {
+ void observe(ChromatogramDTO chromatogram);
+ }
+
+ private StringBuilder buffer = new StringBuilder();
+
+ private String permIdOrNull;
+
+ private MSRunDTO msRun;
+
+ private ChromatogramDTO chromatogram;
+
+ private boolean parsingMsRun;
+
+ private boolean parsingChromatogram;
+
+ private final IMSRunObserver msRunObserverOrNull;
+
+ private final IChromatogramObserver chromatogramObserverOrNull;
+
+ public EICMLParser(String fileName, String permIdOrNull, IMSRunObserver msRunObserverOrNull,
+ IChromatogramObserver chromatogramObserverOrNull) throws ParserConfigurationException,
+ SAXException, IOException
+ {
+ assert fileName != null;
+
+ this.permIdOrNull = permIdOrNull;
+ this.msRunObserverOrNull = msRunObserverOrNull;
+ this.chromatogramObserverOrNull = chromatogramObserverOrNull;
+ parseDocument(fileName);
+ }
+
+ private void parseDocument(String fileName) throws ParserConfigurationException, SAXException,
+ IOException
+ {
+ final SAXParserFactory spf = SAXParserFactory.newInstance();
+ final SAXParser sp = spf.newSAXParser();
+ sp.parse(fileName, this);
+ }
+
+ @Override
+ public void startElement(String uri, String localName, String name, Attributes attributes)
+ throws SAXException
+ {
+ buffer.setLength(0);
+ if ("msRun".equals(name))
+ {
+ msRun = new MSRunDTO();
+ msRun.permId = permIdOrNull;
+ parsingMsRun = true;
+ } else if ("chromatogram".equals(name))
+ {
+ chromatogram = new ChromatogramDTO();
+ parsingChromatogram = true;
+ }
+ }
+
+ private float[] convert(String b64)
+ {
+ final byte[] decoded = Base64.decodeBase64(b64.getBytes());
+ return NativeData.byteToFloat(decoded, ByteOrder.BIG_ENDIAN);
+ }
+
+ void set(String name, String value) throws SAXException
+ {
+ if ("Q1Mz".equals(name) && value.length() > 0)
+ {
+ chromatogram.q1Mz = Float.parseFloat(value);
+ } else if ("Q3LowMz".equals(name) && value.length() > 0)
+ {
+ chromatogram.q3LowMz = Float.parseFloat(value);
+ } else if ("Q3HighMz".equals(name) && value.length() > 0)
+ {
+ chromatogram.q3HighMz = Float.parseFloat(value);
+ } else if ("label".equals(name) && value.length() > 0)
+ {
+ chromatogram.label = value;
+ } else if ("polarity".equals(name) && value.length() > 0)
+ {
+ if (value.length() != 1)
+ {
+ throw new SAXException("Illegal polarity: must be of length 1");
+ }
+ chromatogram.polarity = value.charAt(0);
+ } else if ("RT".equals(name) && value.length() > 0)
+ {
+ chromatogram.runTimes = convert(value);
+ } else if ("INT".equals(name) && value.length() > 0)
+ {
+ chromatogram.intensities = convert(value);
+ }
+ }
+
+ @Override
+ public void endElement(String uri, String localName, String name) throws SAXException
+ {
+ if ("msRun".equals(name))
+ {
+ parsingMsRun = false;
+ if (msRunObserverOrNull != null)
+ {
+ msRunObserverOrNull.observe(msRun);
+ }
+ msRun = null;
+ } else if ("chromatogram".equals(name))
+ {
+ parsingChromatogram = false;
+ if (chromatogramObserverOrNull != null)
+ {
+ chromatogramObserverOrNull.observe(chromatogram);
+ }
+ chromatogram = null;
+ }
+ if (parsingMsRun && msRun != null)
+ {
+ msRun.set(name, buffer.toString());
+ } else if (parsingChromatogram && chromatogram != null)
+ {
+ set(name, buffer.toString());
+ }
+ buffer.setLength(0);
+ }
+
+ @Override
+ public void characters(char[] ch, int start, int length) throws SAXException
+ {
+ buffer.append(new String(ch, start, length));
+ }
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/FloatArrayMapper.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/FloatArrayMapper.java
new file mode 100644
index 00000000000..3d9ccffc22e
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/FloatArrayMapper.java
@@ -0,0 +1,75 @@
+/*
+ * 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.eicml;
+
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.sql.Types;
+
+import net.lemnik.eodsql.TypeMapper;
+
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * {@link TypeMapper} for <code>float[]</var> columns.
+ *
+ * @author Bernd Rinn
+ */
+class FloatArrayMapper implements TypeMapper<float[]>
+{
+
+ public float[] get(ResultSet results, int column) throws SQLException
+ {
+ final String[] floatStr = StringUtils.split(results.getString(column), ',');
+ final float[] floatArr = new float[floatStr.length];
+ for (int i = 0; i < floatStr.length; ++i)
+ {
+ floatArr[i] = Float.parseFloat(floatStr[i]);
+ }
+ return floatArr;
+ }
+
+ public void set(ResultSet results, int column, float[] obj) throws SQLException
+ {
+ results.updateString(column, toString(obj));
+ }
+
+ public void set(PreparedStatement statement, int column, float[] obj) throws SQLException
+ {
+ if (obj != null)
+ {
+ statement.setString(column, toString(obj));
+ } else
+ {
+ statement.setNull(column, Types.VARCHAR);
+ }
+ }
+
+ private String toString(float[] array)
+ {
+ StringBuilder b = new StringBuilder();
+ for (float v : array)
+ {
+ b.append(v);
+ b.append(',');
+ }
+ b.setLength(b.length() - 1);
+ return b.toString();
+ }
+
+}
\ No newline at end of file
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IMSRunDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IMSRunDAO.java
new file mode 100644
index 00000000000..a1840e54ea2
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IMSRunDAO.java
@@ -0,0 +1,84 @@
+/*
+ * 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.eicml;
+
+import net.lemnik.eodsql.BaseQuery;
+import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.Select;
+
+/**
+ * Interface for querying / updating the metabol database.
+ *
+ * @author Bernd Rinn
+ */
+public interface IMSRunDAO extends BaseQuery
+{
+ final String ALL_MSRUN_COLUMNS =
+ "msruns.msRunId, msruns.permId, msruns.rawDataFileName, msruns.rawDataFilePath, "
+ + "msruns.acquisitionDate, msruns.instrumentType, msruns.instrumentManufacturer, "
+ + "msruns.instrumentModel, msruns.methodIonisation, msruns.methodSeparation, "
+ + "msruns.startTime, msruns.endTime";
+
+ @Select("INSERT INTO msruns (permId, rawDataFileName, rawDataFilePath, acquisitionDate, "
+ + "instrumentType, instrumentManufacturer, instrumentModel, methodIonisation, "
+ + "methodSeparation, startTime, endTime) values (?{1.permId}, ?{1.rawDataFileName}, "
+ + "?{1.rawDataFilePath}, ?{1.acquisitionDate}, ?{1.instrumentType}, "
+ + "?{1.instrumentManufacturer}, ?{1.instrumentModel}, ?{1.methodIonisation}, "
+ + "?{1.methodSeparation}, ?{1.startTime}, ?{1.endTime}) returning msRunId")
+ public long addMSRun(MSRunDTO msRun);
+
+ @Select("INSERT INTO chromatograms (msRunId, Q1MZ, Q3LowMz, Q3HighMz, label, polarity, runTimes, "
+ + "intensities) values (?{1.msRunId}, ?{1.q1Mz}, "
+ + "?{1.q3LowMz}, ?{1.q3HighMz}, ?{1.label}, "
+ + "?{1.polarity}, ?{1.runTimes}, ?{1.intensities}) returning chromId")
+ public long addChromatogram(ChromatogramDTO chromatogram);
+
+ @Select(sql = "SELECT * from msruns", rubberstamp = true)
+ public DataIterator<MSRunDTO> getMSRuns();
+
+ @Select(sql = "SELECT * from msruns where rawDataFileName=?{1}", rubberstamp = true)
+ public DataIterator<MSRunDTO> getMSRunsForRawDataFile(String rawDataFileName);
+
+ @Select("SELECT msruns.*, count(chromatograms.*) AS chromCount from msruns "
+ + "LEFT JOIN chromatograms USING(msRunId) where msruns.msRunId=?{1} GROUP BY "
+ + ALL_MSRUN_COLUMNS)
+ public MSRunDTO getMSRunById(long id);
+
+ @Select("SELECT msruns.*, count(chromatograms.*) AS chromCount from msruns "
+ + "LEFT JOIN chromatograms USING(msRunId) where msruns.permId=?{1} GROUP BY "
+ + ALL_MSRUN_COLUMNS)
+ public MSRunDTO getMSRunByPermId(String permId);
+
+ @Select("SELECT msruns.* FROM msrun LEFT JOIN chromatograms USING(msRunId) "
+ + "where chromatograms.chromId = ?{1.chromId}")
+ public MSRunDTO getMSRunForChromatogram(ChromatogramDTO chromatogram);
+
+ @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 msruns USING(msRunId) "
+ + "where msRunId=?{1.msRunId}", rubberstamp = true)
+ public DataIterator<ChromatogramDTO> getChromatogramsForRun(MSRunDTO msRun);
+
+ @Select(sql = "SELECT chromId, msRunId, Q1Mz, Q3LowMz, Q3HighMz, label, polarity FROM chromatograms "
+ + "LEFT JOIN msruns USING(msRunId) " + "where msRunId=?{1.msRunId}", rubberstamp = true)
+ public DataIterator<ChromatogramDTO> getChromatogramsForRunNoData(MSRunDTO 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
new file mode 100644
index 00000000000..583b9deb56c
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ListChromatogramLabels.java
@@ -0,0 +1,75 @@
+/*
+ * 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.eicml;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+
+import net.lemnik.eodsql.DataIterator;
+
+/**
+ * A method for listing all chromatogram labels of all run.
+ *
+ * @author Bernd Rinn
+ */
+public class ListChromatogramLabels
+{
+
+ public static void main(String[] args) throws SQLException
+ {
+ final Connection conn = DBFactory.getConnection();
+ try
+ {
+ final IMSRunDAO dao = DBFactory.getDAO(conn);
+ if (args.length > 0)
+ {
+ for (String fn : args)
+ {
+ String rawFile = fn;
+ if (rawFile.endsWith(".RAW") == false)
+ {
+ rawFile += ".RAW";
+ }
+ listChromatogramsForRuns(dao, dao.getMSRunsForRawDataFile(rawFile));
+ }
+ } else
+ {
+ listChromatogramsForRuns(dao, dao.getMSRuns());
+ }
+ } finally
+ {
+ conn.close();
+ }
+ }
+
+ private static void listChromatogramsForRuns(final IMSRunDAO dao, DataIterator<MSRunDTO> runs)
+ {
+ for (MSRunDTO run : runs)
+ {
+ String msRunName = run.rawDataFileName;
+ if (msRunName.endsWith(".RAW"))
+ {
+ msRunName = msRunName.substring(0, msRunName.length() - 4);
+ }
+ for (ChromatogramDTO chrom : dao.getChromatogramsForRunNoData(run))
+ {
+ System.out.println(msRunName + "\t" + chrom.label);
+ }
+ }
+ }
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/MSRunDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/MSRunDTO.java
new file mode 100644
index 00000000000..24dd268e69d
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/MSRunDTO.java
@@ -0,0 +1,102 @@
+/*
+ * 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.eicml;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.xml.sax.SAXException;
+
+/**
+ * A class that represents a MSRun in an eicML file.
+ */
+public class MSRunDTO
+{
+ @AutoGeneratedKeys
+ public long msRunId;
+
+ public String permId;
+
+ public String rawDataFilePath;
+
+ public String rawDataFileName;
+
+ public String instrumentType;
+
+ public String instrumentManufacturer;
+
+ public String instrumentModel;
+
+ public String methodIonisation;
+
+ public String methodSeparation;
+
+ public String acquisitionDate;
+
+ public int chromCount = -1;
+
+ public float startTime = Float.NaN;
+
+ public float endTime = Float.NaN;
+
+ void set(String name, String value) throws SAXException
+ {
+ if ("filePath".equals(name))
+ {
+ rawDataFilePath = value;
+ } else if ("fileName".equals(name))
+ {
+ rawDataFileName = value;
+ } else if ("instrumentType".equals(name))
+ {
+ instrumentType = value;
+ } else if ("instrumentManufacturer".equals(name))
+ {
+ instrumentManufacturer = value;
+ } else if ("instrumentModel".equals(name))
+ {
+ instrumentModel = value;
+ } else if ("methodIonisation".equals(name))
+ {
+ methodIonisation = value;
+ } else if ("methodSeparation".equals(name))
+ {
+ methodSeparation = value;
+ } else if ("acquisitionDate".equals(name))
+ {
+ acquisitionDate = value;
+ } else if ("chromCount".equals(name) && value.length() > 0)
+ {
+ chromCount = Integer.parseInt(value);
+ } else if ("msRunId".equals(name) && value.length() > 0)
+ {
+ msRunId = Long.parseLong(value);
+ } else if ("startTime".equals(name) && value.length() > 0)
+ {
+ startTime = Float.parseFloat(value);
+ } else if ("endTime".equals(name) && value.length() > 0)
+ {
+ endTime = Float.parseFloat(value);
+ }
+ }
+
+ @Override
+ public String toString()
+ {
+ return ToStringBuilder.reflectionToString(this);
+ }
+}
\ No newline at end of file
diff --git a/rtd_yeastx/source/sql/schema.sql b/rtd_yeastx/source/sql/schema.sql
new file mode 100644
index 00000000000..130a3cc3653
--- /dev/null
+++ b/rtd_yeastx/source/sql/schema.sql
@@ -0,0 +1,38 @@
+CREATE DATABASE metabol OWNER BRINN ENCODING 'UTF8';
+
+\c metabol
+
+SET ROLE 'brinn';
+
+CREATE TABLE msruns (
+ msRunId BIGSERIAL NOT NULL,
+ permId VARCHAR(40),
+ rawDataFileName VARCHAR(255) NOT NULL,
+ rawDataFilePath VARCHAR(1000) DEFAULT NULL,
+ acquisitionDate VARCHAR(30) DEFAULT NULL,
+ instrumentType VARCHAR(20) DEFAULT NULL,
+ instrumentManufacturer VARCHAR(50) DEFAULT NULL,
+ instrumentModel VARCHAR(100) DEFAULT NULL,
+ methodIonisation VARCHAR(10) DEFAULT NULL,
+ methodSeparation VARCHAR(100) DEFAULT NULL,
+ startTime REAL NOT NULL,
+ endTime REAL NOT NULL,
+ PRIMARY KEY (msRunId),
+ UNIQUE(permId)
+);
+
+CREATE TABLE chromatograms (
+ chromId BIGSERIAL NOT NULL,
+ msRunId BIGINT NOT NULL,
+ Q1Mz REAL NOT NULL,
+ Q3LowMz REAL NOT NULL,
+ Q3HighMz REAL NOT NULL,
+ label VARCHAR(100) DEFAULT NULL,
+ polarity VARCHAR(1) DEFAULT NULL,
+ runTimes TEXT NOT NULL,
+ intensities TEXT NOT NULL,
+ PRIMARY KEY (chromId),
+ CONSTRAINT FK_chromatogram_1 FOREIGN KEY (msRunId) REFERENCES msruns (msRunId) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX chromatogram_fk on chromatograms(msRunId);
\ No newline at end of file
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
new file mode 100644
index 00000000000..017b58885da
--- /dev/null
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/ReadChromatogramsPerformanceTest.java
@@ -0,0 +1,53 @@
+/*
+ * 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.eicml;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+
+/**
+ * A performance test of reading all chromatograms from the database.
+ *
+ * @author Bernd Rinn
+ */
+public class ReadChromatogramsPerformanceTest
+{
+
+ public static void main(String[] args) throws SQLException
+ {
+ long start = System.currentTimeMillis();
+ final Connection conn = DBFactory.getConnection();
+ try
+ {
+ final IMSRunDAO dao = DBFactory.getDAO(conn);
+ for (MSRunDTO run : dao.getMSRuns())
+ {
+ // We need to iterate over the chromatograms to make sure they are really read.
+ for (@SuppressWarnings("unused")
+ ChromatogramDTO chromatogram : dao.getChromatogramsForRun(run))
+ {
+ // Nothing to do.
+ }
+ }
+ } finally
+ {
+ conn.close();
+ }
+ System.out.println((System.currentTimeMillis() - start) / 1000.0f);
+ }
+
+}
--
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