1 Installation Overview

1.1 Supported Platforms

1.2 Supported Browser

The supported browser for TRC is Windows Internet Explorer IE 11or later, Mozilla Firefox v17 or later, and Google Chrome v12 or later.

1.3 Technology Stack

Following is the required technology stack for TRC:

• Oracle Database 11.2.0.4.0 with Partitioning Option (required) and Advanced Compression Option (recommended for Non-Exadata)

• Oracle Healthcare Data Warehouse Foundation (HDWF) 6.1

• Oracle Data Integrator (ODI) 11.1.1.7 or Informatica 9.5.1 Hot Fix 3

• Oracle Business Intelligence Enterprise Edition (OBIEE) 11.1.1.7.151020

• Oracle Application Development Framework (ADF) Runtime 12.1.3

• Oracle WebLogic Server 12.1.3

• Java Development Kit (JDK)

  • The TRC 3.1 web application requires JDK 1.7

  • Java Based loaders require JDK 1.8

• Python 2 (2.6 or higher). Python 3 is not compatible.

1.4 Before You Begin

TRC requires the following pre-installation tasks to be completed:

1. Install Oracle Database 11.2.0.4 according to platform-specific installation instructions available at the following location. The Oracle database Partitioning Option is required and the Advance Compression Option is highly recommended for Non-Exadata systems.

   http://www.oracle.com/pls/db112/portal.portal_db?selected=11&frame=

2. Install Oracle Healthcare Data Warehouse Foundation 6.1 according to instructions in the Oracle® Healthcare Data Warehouse Foundation Secure Installation and Configuration Guide.

3. Depending on whether you want to use Oracle Data Integrator or Informatica as your ETL tool, install either:

   • Oracle Data Integrator 11.1.1.7 according to instructions in the Oracle® Fusion Middleware Installation Guide for Oracle Data Integrator.

     
     

     Important: Do not create ODI repositories during installation.

     
     

   • Informatica 9.5.1 Hot Fix 3 according to the Informatica installation documentation.

4. Install Oracle Business Intelligence 11.1.1.7 according to Oracle® Fusion Middleware Installation Guide for Oracle Business Intelligence. Create a separate middleware home with WebLogic Server 10.3.6 for OBIEE.

   
   

   Important: See the document OBIEE 11g: Required and Recommended Bundle Patches and Patch Sets (Doc ID 1488475.1) on MOS to apply the OBIEE bundle patch 11.1.1.7.151020. Currently, TRC 3.1 is certified only with this patch version.

   
   

5. Install Oracle WebLogic Server 12.1.3 according to the instructions in the Oracle® Fusion Middleware Installation Guide for Oracle WebLogic Server 12c (12.1.3).

   
   

   Note: Make sure middleware homes are separate for Cohort Explorer and BI. For example, WebLogic 12c (12.1.3) - [CE mwhome] -CE_DOMAIN -CE_SERVER1 Weblogic 11g (10.3.6) - [BI mwhome] -[BI domain] -[BI server]

   
   

6. Install ADF runtime 12.1.3 and JSF 2.1 on the WebLogic server where TrcApp.ear will be deployed.

   
   

   Important: To address the exported file name issue in Internet Explorer 11, install patch 20587347 on top of ADF 12.1.3. For details, see Doc ID 1599898.1 on MOS.

   
   

7. Install Application Development Runtime (ADR) 12.1.3.0. For details, see the Oracle® Fusion Middleware Installation Guide for Application Developer 12c (12.1.3).

8. If you are upgrading from a previous version of TRC, ensure that you complete the following activities before running the upgrade:

   • Ensure that the following unique constraints introduced in TRC 3.1 are enforced in CDM:

     • Races are unique for every Subject

     • Races are unique for every Patient

     • Ethnicities are unique for every Subject

     • Ethnicities are unique for every Patient

     If this uniqueness is violated in CDM, fix the data in HDWF. Then load the corrected data into CDM using existing ETLs.

   • The ODB upgrade has Assembly (Alignment) concept which would link all the EMBL records with their respective assemblies. This happens by checking the ACCESSION column in W_EHA_DNA_SOURCE table which is populated by the EMBL loader. Some patch chromosome EMBL files might be loaded through the EMBL loader, which may not have a proper ACCESSION value in the table W_EHA_DNA_SOURCE. Update the ACCESSION column with proper values as follows:

     If you have older data loaded for which an ALIGNMENT cannot be determined because of the older version of the EMBL loader, update the ACCESSION records for previously loaded DNA_SOURCE records. The current version of EMBL loader handles the ACCESSION field for all types of files and the ALIGNMENT is created correctly.

     The Accession values should contain assembly name, chromosome name, start position, end position and the strand information separated by colons. For example, {Assembly name}:{chromosome or alternative DNA segment name}:{start position on chromosome or segment}:{end position on chromosome or segment}:{strand as 0 or 1}.

     Following are example accession values:

     GRCh37:18:72067284:73067283:1
     GRCh37:HSCHR6_MHC_DBB:1988144:2959211:1
     

1.5 Known Issues

• While upgrading from previous releases, some schemas do not have IQ checks.

• After the database bounces, you cannot log into TRC again. To fix this, perform the following steps after the database bounces:

  1. Stop the WebLogic server.

  2. Log in as the CDM user.

  3. Execute the following VPD_UTIL stored procedure:

     begin 
     vpd_util.refresh_vpd_policies; 
      end; 
      / 
     

  4. Restart WebLogic.

  5. Log into TRC with your username and password.