Project Description

Project Members

• Dave Angulo
• Dominic Battre
• Hussam Ala Eldeen
• Eric Puryear
• Jennifer Von Puymbrouck
• Rob Vogelbacher
• Lee Ann Hollenbeck

Employed Software

• Apache2 (documentation) with mod_jk
• Tomcat
  • Java Server Pages (tutorial)
  • Struts (documentation)
  • JDBC
• MySQL (documentation)
• Ant (documentation)

Resources

The primary development computer is histone.cti.depaul.edu. If you like to get an account, please follow the instructions of Getting Accounts.

The production system can be found in /home/dbattre/IBG-MSP-prod/, it uses the database MassSpec_prod. Be careful with these and discuss modifications with the other project members.

Getting started:

1. Install Tomcat. On histone you don't need to do that add a root account to tomcat by adding the following line:

         <user username="root" password="secret" roles="admin,manager"/>
         

   to your conf/tomcat-users.xml file.
2. Checkout a local copy of the IBG-MSP repository by executing svn co http://histone.cti.depaul.edu/svn/IBGWorkbench/trunk/web/IBG-MSP/ (for example directly into your home directory).
3. Copy build.properties.templates to build.properties and adapt it to your local system by setting your catalina.home and manager.password.
4. Copy src/log4j.properties.template to src/log4j.properties and adapt it by setting your log4j.appender.R.File.
5. Copy src/ibg_msp/config.properties.template to src/ibg_msp/config.properties and adapt it to your local system
6. (only on your home machine) Download MySQL
7. (only on your home machine) Specify the database name you want to use in database/tables.ddl, database/defaultvalues.dml, database/compareDB.ddl, src/ibg_msp/BeanHandler.java (we should move it from the latter), and src/ibg_msp/comparemassspec/ComparisonBeanHandler.java On Histone you can use the databases MassSpec_04 and Spectral_Comparison.
8. (only on your home machine) Execute mysql -u root -p <database/tables.ddl <database/defaultvalues.dml and mysql -u root -p <database/compareDB.ddl
9. (only on your home machine) Create a user account which can access the newly created databases in MySQL and make sure it has the same password as specified in src/ibg_msp/BeanHandler.java and src/ibg_msp/comparemassspec/ComparisonBeanHandler.java
10. (only on your home machine) Install Ant and add the jars to your CLASSPATH environment variable.
11. Execute ant install and you should be able to access your project at http://localhost:8080/IBG-MSP
    On histone, you have to set up mod_jk in /etc/apache2/workers2.properties and restart apache2.

In the future you should be able to compile and deploy you changes to tomcat by executing ant reload

This assumes the Java SDK is already installed.

1. Create IBG-MSP locally.
   1. Obtain an account to the primary development server histone.cti.depaul.edu – Get Account.
   2. Install a Subversion client such as TortoiseSVN and read its documentation. There is a section in the tutorial on Subversion.
   3. Checkout a local copy of the IBG-MSP repository from http://histone.cti.depaul.edu/svn/IBGWorkbench/trunk/web/IBG-MSP/ with the SVN client. (TortoiseSVN integrates into Windows Explorer. In Windows Explorer, create a folder locally for your local IBG-MSP repository. Right-click on the folder and select SVN Checkout. Complete the checkout.)
2. Install the latest stable Tomcat (it is platform independent.) Note where it is installed. In the Tomcat installation directory, find conf\tomcat-users.xml. Edit the file and insert:

         <user username="root" password="secret" roles="admin,manager"/>
         

   Make sure Tomcat works: start it up if it is not already started*, and try the Tomcat admin web application http://localhost:8080/admin/ .
3. Install the latest stable MySQL for the Windows platform. During the configuration, select for root to only be able to log on from localhost, and select to include bin directory in Windows PATH.
   Download the MySQL JDBC driver and put it (mysql-connector-java-3.1.6-bin.jar) in Tomcat\common\lib. Putting the driver in this folder will make it available to Tomcat internally and to any application run on Tomcat.
4. Modify files in the local IBG-MSP repository for the local environment.
   1. Copy build.properties.templates to build.properties and adapt it to your local system by setting your catalina.home and manager.password. In the path for catalina.home, use double backslashes.
      
      For example: catalina.home = C:\\Dev\\Tomcat 5.0
      
      
   2. Copy src\log4j.properties.template to src\log4j.properties and adapt it by setting your log4j.appender.R.File. Again, be sure to use double backslashes. If the directory does not exist, create it.
      
      For example: log4j.appender.R.File = C:\\Dev\\Tomcat 5.0\\logs\\ibg-msp.txt
      
      
   3. Copy src\ibg_msp\config.properties.template to src\ibg_msp\config.properties and adapt it to your local system. If the directory does not exist, create it.
      
      For example: msFileBaseDirectory = C:\\Dev\\tmp\\MS\\
      
      
   4. Specify the database name you want to use in database\tables.ddl, database\defaultvalues.dml, database\compareDB.ddl, src\ibg_msp\BeanHandler.java, and src\ibg_msp\comparemassspec\ComparisonBeanHandler.java (Note: the user name and password you specify in BeanHandler.java and ComparisonBeanHandler.java will be the user name and password you create in step 6 below).-- JenniferVanPuymbrouck - 23 Jun 2005
      
      For example in BeanHandler.java:
      return DriverManager.getConnection
("jdbc:mysql://localhost/MassSpec_04","mspecuser","YOUR_DB_PASSWORD");
      
      For example in ComparisonBeanHandler.java:
      return DriverManager.getConnection
("jdbc:mysql://localhost/Spectral_Comparison","mspecuser","YOUR_DB_PASSWORD");
      
      
5. Make sure MySQL is running* then open a command prompt in the local IBG-MSP repository directory. Execute:
   
   mysql -u root -p <database\tables.ddl
mysql -u root -p <database\defaultvalues.dml
mysql -u root -p <database\compareDB.ddl
   
   
6. Create a user account in MySQL which can access the newly created database and make sure it has the same password as specified in src\ibg_msp\BeanHandler.java

GRANT ALL ON MassSpec_04.* TO 'mspecuser'@'localhost' IDENTIFIED BY 'YOUR_DB_PASSWORD';
   
   
7. Download Ant. Extract it to the desired directory such as c:\Dev\ant. To run Ant, the ANT_HOME and JAVA_HOME environmental variables must be set and Ant's bin directory should be in the PATH. This can be accomplished by creating and executing a small batch file such as:

         set ANT_HOME=c:\Dev\ant
         set JAVA_HOME=c:\Dev\jdk1.2.2
         set PATH=%PATH%;%ANT_HOME%\bin
         

   or by setting the environmental variables in Window's system properties.
   Copy the file server/lib/catalina-ant.jar from the Tomcat 5 installation into the "lib" directory of your Ant installation.
8. From a command prompt opened in the local IBG-MSP repository directory, execute ant install. Access the project with a web browser at http://localhost:8080/IBG-MSP .
   In the future you should be able to compile and deploy your changes to tomcat by executing ant reload.
9. At http://localhost:8080/IBG-MSP , try to register. The application should complain of an invalid e-mail address.
   At a command prompt, log into MySQL. Use the MyMassSpec database. Execute DISPLAY users; In the users table exists a record for the e-mail address entered in the attempted registration. Note or change the password. Change the access level to 'a'. Try logging into the IBG-MSP application.
10. Amend these instructions to help the next person.

* MySQL and Tomcat 5.0 can be run as services. The services can be stopped or started in the Windows services console. Services can also be started and stopped at the command line:

   net start “apache tomcat”
   net stop “apache tomcat”
   net start mysql
   net stop mysql
   

Since these services take up resources, if they are not being used often, the services should be started and stopped manually, and they should not automatically run whenever Windows is started. This can be set in the services console. The services console can be found in administrative tools, which can be found in the control panel. Note that the services console displays which services are currently running and whether the startup type is automatic, manual, or disabled. If MySQL or Tomcat is started in another manner, this will not be reflected in the services console. It may be necessary to press F5 or go to actions>refresh to refresh the services console.

Database Documentation

Documentation on the database structure, field descriptions, and table relationships for the IBG database is currently in progress. An initial draft is available here: IBG Database Docs

Subprojects

This page contains several possible project ideas: MassSpecDatabaseSubprojects

Links

• Production System: http://histone.cti.depaul.edu/IBG-MSP
• Testing System: http://histone.cti.depaul.edu/IBG-MSP-domi (feel free to enter data (non-sense) data here)
• mzXML
• data formats
  • Considerations about parsing the data formats: MassSpecParsers

-- DaveAngulo - 25 Sep 2005
-- LeeAnnHollenbeck - 09 May 2005
-- DominicBattre - 19 Jan 2005