Developers Getting Started With i2b2
Space shortcuts
Space Tools
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 12 Next »

Steps 1 and 2:

 Set up a project as documented here:  

  1. Project Setup: Create a project. In this step, you define a project path which will be used to reference the project later.  
    1. When adding users to the project:
      1. Add the user AGG_SERVICE_ACCOUNT and assign it the role DATA_AGG.
      2. Add any regular users and assign them the role DATA_OBFSC
  2. 6.4.3 Cell DB-Lookup: Add new db_lookup entries for each of the core cells, to define how the project will connect to the db.
    • The core cells are Ontology, CRC, and Workplace.
    • Talk about the DATASOURCE
    • 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.
    • Note: for  ONT_DB_LOOKUP and workplace_db_look up, c_project path does not have a beginning backslash


Step 3:

 Update DATASOURCE XML files IN WILDFLY IF NEEDED …

The CRC cell communicates with your i2b2db instance via the configurations set in crc-ds.xml.

For detailed information refer to 2. Data Source Configuration, or, for an example of setting up data sources for OMOP: Configure Data Sources 

The datasource parameter should be set to  CRCBootStrapDS for the CRCBootStrapDS pool name. 


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)  

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>



Step 5:

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.

Step 6

Finally add project users. Make sure to add AGG_SERVICE_ACCOUNT

https://community.i2b2.org/wiki/display/ServerSideDesign/Project+Setup

  • No labels