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Configure CRC data source

Earlier during the data installation you created new crcdata tables and in order for the CRC to communicate with the database it needs to know where these tables reside. This information is configured in the crc-ds.xml file.

As part of the i2b2 on OMOP project there are specific crcdata tables that were created earlier in this installation process. Other than the metadata table, all other tables were created when you initially setup your i2b2 database using the standard i2b2 Installation Guide.

Steps to configure data sources

The following steps define how to add the data source for the new crcdata tables. The steps include example configurations for Oracle, PostgreSQL, and SQL Server.

Only 1 CRCBootStrapDS can reside in the crc-ds.xml file

  • If your file does contain the CRCBootStrapDS you can proceed with this section of the installation guide.
  • If your file does not contain the CRCBootStrapDS, you can go to the CRC Data Source Configuration chapter of the i2b2 Installation guide.

 

Step 1: Locate and open your crc-ds.xml file

File Location

YOUR_I2B2_SRC_DIR\edu.harvard.i2b2.crc\etc\

 

Step 2: Add a new datasource and update the following information: (see examples shown below)

    • Set the jndi-name and pool-name to OMOP_CDM_{ORACLE | POSTGRESQL | SQLSERVER}.
    • Update the connection-url to point to the location of the database containing the crcdata tables.
    • Update the user-name and password to accurately reflect the database user you setup during the Data Installation.
    • Verify the jdbc driver in the connection-url, driver-class, and driver accurately reflect the type of database you are connecting to.

Step 3: Save the changes and close the file.

Oracle Database
<datasource jta="false" jndi-name="java:/OMOP_CDM_ORACLE"
	pool-name="OMOP_CDM_ORACLE" 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>i2b2demodata</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>

 

PostgreSQL Database
<datasource jta="false" jndi-name="java:/OMOP_CDM_POSTGRESQL"
	pool-name="OMOP_CDM_POSTGRESQL" 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>i2b2demodata</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>

 

SQL Server Database
<datasource jta="false" jndi-name="java:/OMOP_CDM_SQLSERVER"
	pool-name="OMOP_CDM_SQLSERVER" 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>i2b2demodata</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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