mySCILHS i2b2 Setup

Owned by Stanley Boykin
Last updated: Jul 26, 2019 by Marc Natter

This document describes the steps to setup an i2b2 installation to receive and store myARCH survey responses.  All operations are performed on the i2b2 server.

Restore Missing Libraries

  1. 1.7.04 removed these libraries from the default VM installation, but they are required for the i2b2Loader to successfully upload to i2b2.

  2. Download commons-dbcp.jar version 1.4 (link)

  3. Download commons-pool.jar version 1.6 (link)

  4. Add the jars to /opt/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/WEB-INF/lib/

  5. Restart the i2b2 node

Add DestDir to File Repository

  1. Go to the i2b2 admin panel (http:/<my-i2b2-hostname>/admin/)

  2. Select Manage Cells > File Repository > Params > Add Param

  3. Add a param named DestDir with the value of a directory (ie: /opt/FRC) and save

  4. Verify the directory (ie: /opt/FRC) exists and if not, create it.

Upload Ontology and Concept Dimension Data

  • Run the following scripts as the i2b2metadata (or equivalent) user:

    • SCILHS_table_access.sql: appends the root metadata and points to the PCORI_SURVEY table for the survey ontology metadata.

    • PCORI_SURVEY_ontology_table.sql: creates the PCORI_SURVEY table and populates it with mySCILHS root ontology metadata (for the PAH and OA studies).

  • Run the following script as the i2b2demodata user (or whichever user that owns the CONCEPT_DIMENSION table):

    • SCILHS_concept_dimension_data.sql: loads the concepts from the PAH and OA surveys into the CONCEPT_DIMENSION table.