Connecting BioNumerics to MySQL

Transcription

1 Connecting BioNumerics to MySQL A brief overview Applied Maths NV - KJ February 2010

2 MySQL server side MySQL settings file MySQL is a very flexible DBMS and has quite a number of settings that allows one to optimize it for a specific application. A few settings should be set correctly before it communicates correctly with BioNumerics, i.e. the SQL mode and maximum allowed packet size. 1. Locate the MySQL settings file (e.g. C:\Program Files\MySQL\MySQL Server 5.0\my.ini for Windows) 2. Change the line that specifies the sql-mode under the [mysqld] tag in the settings file to: sql-mode="mssql,no_backslash_escapes" 3. Add following line under the [mysqld] tag in the settings file: max_allowed_packet = 16M As an alternative to specifying these settings in the MySQL settings file, the SQL mode and maximum allowed packet size can also be set in the MySQL Command line client or as a startup statement in BioNumerics (see further). Creating a new empty database (Minimal Setup) 4. Open the MySQL Command line client 5. Connect to the correct server 6. Enter the command to create the new database: CREATE DATABASE MyBNdb; 7. If not specified so in the MySQL settings file, change the SQL-Mode to MSSQL and NO_BACKSLASH_ESCAPES : SET GLOBAL sql_mode='mssql,no_backslash_escapes'; 8. If not specified in the MySQL settings file, set the max_allowed_packet variable to 16Mb: SET GLOBAL max_allowed_packet= ; Page 2

3 9. Close the MySQL Command Line Client Page 3

4 BioNumerics Client Side Creating the linked BioNumerics database 1. Open the BioNumerics Startup screen and click on the Create new Database icon 2. Enter a name for your BioNumerics database (eg. the organism studied). This name can be different from the name specified in MySQL. Click Next>. 3. Leave the settings as they are, unless you want your link to the MySQL DB stored elsewhere. Please do not change unless you have good reasons to change this. Click Next>. Page 4

5 4. Change the logging option to Yes if you wish to keep track of the changed that have occurred in your BioNumerics/MySQL database. Click Finish. 5. In the Setup new database dialog, select New connected database (custom created) from the list. Specify MySQL as the database type and click Build to create the ODBC connection string. Please note that you must have the MySQL Client ODBC drivers installed before proceeding! 6. The creation of an ODBC connection string is OS dependent, so the following is based on Windows XP SP2 settings. In the Select Data Source window, select the second tab: Machine Data Source and click New... Page 5

6 7. Select User Data Source if you want to have this ODBC link only visible for the current Windows user, else select System Data Source. Click Next>. 8. Select the correct MySQL driver from the list, make sure you have the correct version for MySQL 3.51, MySQL 5.1 respectively. We are working with MySQL 5, so we select the MySQL ODBC 5.1 Driver. Click Next. 9. Click Finish Page 6

7 10. In the ODBC configuration fill out the dialog box according to your own preferences and select the correct server that hosts your empty SQL database. Specify the correct credentials and choose the authentication method that matches your setup. As we didn t create any other user yet for the SQL database we can only log on as the system administrator. Please use the authentication method according to your local IT policy and server setup. Change the database to your new empty SQL database. Click <Test>. If the result is successful, click <OK>. If you do not want the password saved with the ODBC connection, delete it before clicking <OK>. Page 7

8 11. Back in the Select Data Source dialog, select the newly created ODBC connection from the list. Click OK. 12. If needed re-enter your credentials for the database. Page 8

9 13. The ODBC string is nicely filled out in the BioNumerics setup wizard. As the username and password are managed by the DSN you have just created, you might need to delete everything after the SERVER or PORT part. BioNumerics will prompt for the password every time the database is opened. No unauthorized access to the DB can be made. Click Proceed. 14. You will be prompted several times to enter your password again in the MySQL Login prompt. BioNumerics will automatically create all necessary tables and referential integrity rules. 15. Just before opening the database you can choose to install some additional plugin tools. Click Proceed. Page 9

10 16. The new empty BioNumerics database opens. All ODBC settings can be verified by selecting Database>Connected databases... from the main menu. Page 10

11 17. Please note that in this panel, you can link the BioNumerics components to custom TableNames. If you have a SCHEMA in use that is different from the default SCHEMA for the connected user, make sure you have linked to the proper tables and add the SCHEMA-name to the tablename decoration. E.g. myschema.[tablename] Leave the [TABLENAME] in the expression, do not alter this. 18. The SQL statements to set the SQL mode and maximum allowed packet size (see higher) can also be entered as Startup statement(s) in this dialog box, instead of via the MySQL Command Line Client. Page 11