MyWEST - Installation Instructions

MyWEST is a Java software package that can run on any operating system platform with an adequate Java Virtual Machine installed.
To use database functionalities implemented in MyWEST, a Relational Data Base Management System (RDBMS) must be available. Then, connection to a database, with a suitable schema, of the available RDBMS must be set either via TCP/IP or via Open Data Base Connectivity (ODBC), using a specific database driver.

Minimum system requirements

• Java 2 Runtime Environment (JRE) version 1.3.1 or above (see here for details).
  Macintosh users need at least Mac OS X to run MyWEST, since only Mac OS X includes, as a core component, a full version of Java 2, Standard Edition, version 1.4.2.
• Internet connection. A fast connection is recommendable since extraction time heavily depends on connection speed.
• To store the extracted data aggregated in a database, a Relational Data Base Management System (RDBMS) (e.g. MS-Access, MySQL, MS-SQL Server, Oracle, Informix, ...) is required. If a RDBMS is not available, the extracted data can only be saved in tab delimited text Excel file format (ASCII text files with ".xls" extension), a file for each extraction, web databank, and type of data.
  
• Currently, on some configurations of MS-Windows NT/2000/XP operating systems, the PC user must have administrator privileges to run MyWEST properly.
• MyWEST has been tested on a PC as weak as having Pentium 133 MHz CPU, 64 MB RAM, 1.2 GB hard disk, and MS-Windows '98 operating system, obtaining acceptable performances.

Installation steps (here for a tutorial)

1. For all platform users (i.e. MS-Windows, Macintosh, Unix):
   
   
   • Extract MyWEST program files from the downloadable MyWEST.zip file. The extraction operation creates working directories and copies inside them the required program files.
     
     
   • Extract testing result files from the downloadable TestingResults.zip file. The extraction operation copies inside the working data directories the corresponding testing result files.
   
   

   Expecially for MS-Windows users, to avoid possible runtime problems do not extract MyWEST package into a directory with a path including blanck spaces (i.e C:\Documents and Settings\[user]\Desktop).

   
   
   
2. If a Java 2 Virtual Machine is not installed on the used computer, download and install a Java 2 Runtime Environment (JRE), version 1.3.1 or above (see here for details).
   
   

Now MyWEST is ready to run, extract data from databank web pages, and save them in text Excel file format (ASCII text files with ".xls" extension).
In order to store MyWEST extracted data in a relational database, next point 3 of this installation steps must be considered.

3. To store MyWEST extracted data in a relational database:
   
   
   • For the initial default use of MyWEST in MS-Windows environment, a suitable MS-Access database, DBgene.mdb, is provided in the MyWEST\data\ subdirectory, and the "DRIVER" and "DBURL" parameters in the provided DatabasesURL.txt file are set accordingly to establish an ODBC connection to this DBgene database.
     Therefore, for the default use of MyWEST in MS-Windows environment, the only requirement is that MS-Access is installed and the DBgene database is registered in the local ODBC data source.
     
     
   • All platform users (e.g. MS-Windows, Unix, Macintosh), can employ different database types by modifying accordingly the "DRIVER" and "DBURL" parameters in DatabasesURL.txt file. Specific drivers for MySQL and MS-SQL Server 7 databases (mysql-connector-java-3.0.10-stable-bin.jar and jtds-0.5.jar, respectively) are provided in MyWEST main directory.
     For MySQL database users, it is necessary to have installed a MySQL server, to configure a user without a password in order to avoid problems with the new password authentication protocol in some MySQL servers, and to copy the provided GeneData MySQL database into the MySQL server data directory. Besides, the MySQL server binding option must be activated by deleting the comment character "#" at the beginning of corresponding line in the my.ini MySQL configuration file (Figure 1).
     
     

     Figure 1. MySQL binding option in my.ini configuration file

     
     
     
   • If default configuration provided for MS-Windows users is not suitable, default values of "DRIVER" and "DBURL" parameters in the DatabasesURL.txt file in MyWEST main directory can be changed.
     Following the guidelines below, edit with a text editor the DatabasesURL.txt file:
     
     
     • to establish an ODBC connection with the database, set "DRIVER" parameter with the default Java ODBC driver name (e.g. "DRIVER=sun.jdbc.odbc.JdbcOdbcDriver", either for MS-Access, MySQL, or MS-SQL Server 7 databases) and "DBURL" parameter with the URL for accessing the database (i.e. "DBURL=jdbc:odbc:DATABASE_NAME", e.g. "DBURL=jdbc:odbc:DBgene" for the DBgene database).
       In case of using an ODBC connection in MS-Windows environment, the database for storage of the extracted data must be registered in the ODBC data source with the same name set in "DBURL" parameter inside the DatabasesURL.txt file.
       
       
     • to establish a direct TCP/IP connection with the database, set "DRIVER" parameter with the specific database driver name (e.g. "DRIVER=com.mysql.jdbc.Driver" for a MySQL database, or "DRIVER=com.inet.tds.TdsDriver" for a MS-SQL Server 7 database) and "DBURL" parameter with the URL for accessing the database (i.e. "DBURL=jdbc:DRIVER_NAME:DATABASE_FULL_URL", e.g. "DBURL=jdbc:mysql://111.111.111.111:3306/GeneData" for the GeneData MySQL database listening on the default 3306 door of a computer with IP 111.111.111.111, and using the above MySQL driver; or "DBURL=jdbc:inetdae7://111.111.111.111:1433/GeneDB" for the GeneDB MS-SQL Server 7 database listening on the default 1433 door of a computer with IP 111.111.111.111, and using the above MS-SQL Server 7 driver).
     
     
     To support more database types where to store extracted data, add corresponding drivers by copying their java package (jar or zip file) in MyWEST main directory and modify MANIFEST.MF files both in MyWEST.jar and MyWEST-Up.jar packages.
     
     

Start MyWEST

• For MS-Windows users, run file MyWEST.bat in MyWEST main directory (Figure 2).
  
  

  Figure 2. MyWEST.bat starting file in MyWEST main directory

  
  
  
• For other platform users (e.g. Macintosh, Unix), from command line simply move to MyWEST main directory and execute "javaw -jar MyWEST.jar".
  
  

  Figure 3. MyWEST.on Macintosh OS X 10.3 Panther

Troubleshooting

If MyWEST does not run, ensure that:

• All files and working directories contained in the MyWEST.zip file have been correctly extracted.
• A Java 2 Virtual Machine is installed, otherwise download and install a Java 2 Runtime Environment (JRE), version 1.3.1 or above (see here for details).
• The javaw.exe is in the system path, otherwise modify the MyWEST.bat file in the MyWEST main directory adding the path where the javaw.exe file is located in the local file system (e.g. c:\programs\JRE\1.3.1\bin\javaw -jar MyWEST.jar).
  
  
  

If MyWEST does not save mined data in the local database and/or a database error occurs, ensure that:

• A suitable Relational Data Base Management System (RDBMS) (e.g. MS-Access, MySQL, MS-SQL Server, Oracle, ...) is available.
• For the available RDBMS, a relational database with a suitable schema is ready to use.
• A connection to the available database has been correctly set and configured in the DatabasesURL.txt file in MyWEST main directory.

MySQL client installation

To easily view and query MyWEST mined data stored in a MySQL database, one of the available MySQL clients can be installed.