Developers Getting Started With i2b2
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  • The core cells are Ontology, CRC, and Workplace.
  • In i2b2 1.7.13 and below, this step is more easily done directly in the database. Add entries to xxx_db_lookup, for each of ONT, CRC, and WORK.
  • Add entries as below, with the project path you defined. It is easiest to copy these from an existing project.

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For  ONT_DB_LOOKUP and workplace_db_look up, c_project path does not have a beginning backslash

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Step 3:

 Update DATASOURCE XML files IN WILDFLY IF NEEDED. The data source is defined in the ds-xml file  file with parameters to connect to the hive and  data tables. The DB_Lookup.C_DB_Data source value  should be the same for  the poolname as well as the  jndi-name connection values

The CRC cell uses these configuration values to communicate with your i2b2db instance

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The datasource parameter value can be found in the CRC_DB_LOOKUP.C_DB_DATASOURCE (this is built at the time of datamart creation) to point to the datasource of your Crcdata tables location (star-schema and QT tables)  

Note: Example: SQL Server  crc-ds.xml 

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The pool-name parameter

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and the jndi-name value for the Bootstrap connection section  should be set

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Example crc-ds.xml 

<datasource jta="false" jndi-name="java:/CRCBootStrapDS"
    pool-name="CRCBootStrapDS" 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>i2b2hive</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>
<datasource jta="false" jndi-name="java:/<CRC_DB_LOOKUP.C_DB_DATASOURCE value>"
    pool-name="<CRC_DB_LOOKUP.C_DB_DATASOURCE value>" 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>

to constant value as  CRCBootStrapDS

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The pool-name parameter and the jndi-name value for the db connection section  should be set to the parameter  DB_Lookup.C_DB_Data source value 


Step 4:

Load i2b2 tables into the database(s) used for the project as needed, making sure to update db properties file with the  db parameters (e.g., 3.4 Crcdata Tables3.7.4 Load Metadata Tables). For example, you might specify an existing database in the ontology db-lookup, but a new database in the CRC db lookup. In this case, you only need to create/load the tables in the CRC database.

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