Developers Getting Started With i2b2
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Steps 1:

 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

Step 2:

Update DB_Lookup tables to define the Wildfly XML datasource name for the project. Refer to 6.4.3 Cell DB-Lookup: for details.

Ontology and Workplace cells can also be set up using Project Setup. 

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.
  • In i2b2 1.7.13 and above, 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.

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 data source is defined in the ds-xml file with parameters to connect to the hive and  data tables.

i2b2 Server communicates with your i2b2db instance using ds.xml files. For detailed information refer to 2. Data Source Configuration


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: SQL Server  crc-ds.xml 

The pool-name parameter and the jndi-name value for the Bootstrap connection section  should be set to constant value as  CRCBootStrapDS

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.

Step 5:

Finally add project users. Make sure to add AGG_SERVICE_ACCOUNT

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