The PM cell needs to communicate with your i2b2 database and in order to do this it needs to know where the tables for the pmdata reside. Therefore the third and final step in the cell configuration process is to configure the data sources for the PM Cell. This information is configured in the pm-ds.xml file.
Things to keep in mind when configuring your datasources:
When configuring your data sources you want to make sure you edit the following:
- The pmdata tables were created during the chapter on Data Installation.
- The PMBootStrapDS points to the data source for your pm tables.
- The <user-name> and <password> need to match the database user you set up for your pmdata. In the i2b2 demo database this is i2b2pm and demouser.
- The <connection_url> needs to have the following:
- The correct JDBC information for your type of database.
- The correct location of the database containing your pmdata tables.
- Both the <driver-class> and <driver> need to accurately reflect the type of database you are connecting to.
The following steps define how to configure your data sources for the PM Cell.
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1. The pm-ds.xml file is located in the following directory: |
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YOUR_I2B2_SRC_DIR\edu.harvard.i2b2.pm\etc\jboss |
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2. Open the pm-ds.xml file to configure your data sources. |
Oracle Database
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<datasource jta="false" jndi-name="java:/PMBootStrapDS"
pool-name="PMBootStrapDS" enabled="true" use-ccm="false">
<connection-url>jdbc:oracle:thin:@localhost:1521:xe</connection-url>
<driver-class>oracle.jdbc.OracleDriver</driver-class>
<driver>ojdbc6.jar</driver>
<security>
<user-name>i2b2pm</user-name>
<password>demouser</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
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PostgreSQL Database
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<datasource jta="false" jndi-name="java:/PMBootStrapDS"
pool-name="PMBootStrapDS" enabled="true" use-ccm="false">
<connection-url>jdbc:postgresql://localhost:5432/i2b2</connection-url>
<driver-class>org.postgresql.Driver</driver-class>
<driver>postgresql-9.2-1002.jdbc4.jar</driver>
<security>
<user-name>i2b2pm</user-name>
<password>demouser</password>
</security>
<validation>
<validate-on-match>false</validate-on-match>
<background-validation>false</background-validation>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
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SQL Server Database
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<datasource jta="false" jndi-name="java:/PMBootStrapDS"
pool-name="PMBootStrapDS" enabled="true" use-ccm="false">
<connection-url>jdbc:sqlserver://localhost:1433</connection-url>
<driver-class>com.microsoft.sqlserver.jdbc.SQLServerDriver</driver-class>
<driver>sqljdbc4.jar</driver>
<security>
<user-name>i2b2pm</user-name>
<password>demouser</password>
</security>
<validation>
<valid-connection-checker class-name="org.jboss.jca.adapters.jdbc.extensions.mssql.MSSQLValidConnectionChecker"></valid-connection-checker>
<validate-on-match>false</validate-on-match>
</validation>
<statement>
<share-prepared-statements>false</share-prepared-statements>
</statement>
</datasource>
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3. Save the changes and close the file. |
