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Contents

List of Figures

List of Tables

Title and Copyright Information

Preface

• Audience
• Documentation Accessibility
• Finding Information and Patches on My Oracle Support
• Finding Oracle Documentation
• Related Documents
• Conventions

1 Preparing to Install Oracle Clinical

• 1.1 Installation and User Documentation
  • 1.1.1 My Oracle Support Articles
  • 1.1.2 User Documentation
• 1.2 Architecture
• 1.3 Technology Stack
  • 1.3.1 Planning an Oracle Clinical Database Tier Installation
    • 1.3.1.1 Character Set Requirements
    • 1.3.1.2 Critical Patch Update
    • 1.3.1.3 Database Tier Operating System Requirements
    • 1.3.1.4 Oracle Database Requirements and Options
      • 1.3.1.4.1 Oracle Database Partitioning Option
      • 1.3.1.4.2 Distributed Database Option and Advanced Replication Option
    • 1.3.1.5 Global Library Location
    • 1.3.1.6 Database Seed Numbers in a Replicated Environment
  • 1.3.2 Planning an Oracle Clinical Application Tier Installation
    • 1.3.2.1 Character Set Requirements
    • 1.3.2.2 Critical Patch Update
    • 1.3.2.3 Oracle Clinical Forms and Reports Servers
      • 1.3.2.3.1 Shared Directory
      • 1.3.2.3.2 Permanent IP Address
  • 1.3.3 Planning an Oracle Clinical Client Installation
• 1.4 Supported Configurations with Oracle Data Guard and RAC
  • 1.4.1 Supported Configurations with Oracle Real Application Clusters (RAC)
  • 1.4.2 Supported Configurations with Oracle Data Guard
• 1.5 Downloading and Extracting the Software
  • 1.5.1 Creating Staging Areas
    • 1.5.1.1 Database Server Staging Area
    • 1.5.1.2 Application Server Staging Area
  • 1.5.2 Downloading and Extracting the Oracle Clinical 5.1.0.0.x and Oracle Thesaurus Management System 5.1.0.0.x Media Pack
  • 1.5.3 Downloading and Extracting Patches from My Oracle Support
  • 1.5.4 Downloading Oracle Java Development Kit
  • 1.5.5 Downloading the Java Runtime Environment
  • 1.5.6 Downloading Adobe Reader
  • 1.5.7 Downloading JSpell (Optional)
• 1.6 Using the Silent Installer
• 1.7 Reviewing the Installation Log Files
• 1.8 Choosing a Character Set
• 1.9 Applying Oracle Critical Patch Updates
• 1.10 Applying the Latest Oracle Clinical Patch Set
• 1.11 Integrating Oracle Clinical with Other Products and Options
  • 1.11.1 Oracle Clinical Remote Data Capture Onsite
  • 1.11.2 Oracle Thesaurus Management System
  • 1.11.3 Siebel Clinical
  • 1.11.4 Oracle Life Sciences Data Hub
  • 1.11.5 SAS
  • 1.11.6 Custom Applications for Oracle Clinical

2 Installing Oracle Clinical Database Server on UNIX

• 2.1 Installing Oracle Clinical on a Real Applications Cluster (RAC) Database Configuration (Optional)
• 2.2 Perform Prerequisite Tasks for Installing Oracle Database
  • 2.2.1 Create Owners, Groups, and Mount Points
  • 2.2.2 Set Up the opapps User Account and oclsascr User Group
    • 2.2.2.1 Create the oclsascr User Group for SAS
    • 2.2.2.2 Create the opapps Account
  • 2.2.3 Configure Kernel Resources and Adjust Operating System Environment
  • 2.2.4 Test the C Compiler Installation
  • 2.2.5 Install Latest Operating System Patches
• 2.3 Install Oracle Database
  • 2.3.1 Install Oracle Database 12c Release 1 (12.1.0.1) Enterprise Edition
  • 2.3.2 Install Oracle Database 12c Release 1 (12.1.0.1) Examples
• 2.4 Set Permissions
  • 2.4.1 Change Permissions for Running oraenv Script
  • 2.4.2 Grant Access to the ORACLE_HOME Directory
  • 2.4.3 Set Permissions for the Oracle Inventory Directory
• 2.5 Install the Oracle Clinical Database Server
  • 2.5.1 Gather Required Information
  • 2.5.2 Prepare to Install the Oracle Clinical Database Server Software
  • 2.5.3 Install the Oracle Clinical Database Server Software
  • 2.5.4 Save the Installation Information
  • 2.5.5 Review the Installation Log Files
  • 2.5.6 Oracle Clinical Database Server Directory Structure for UNIX
  • 2.5.7 Remove Group Privileges from this Session
• 2.6 Perform Post-installation Tasks
  • 2.6.1 Complete the Setup of the opapps Account
  • 2.6.2 Review the opa_settings File

3 Installing the Oracle Clinical Database Server on Windows

• 3.1 Set Up the opapps User Account and the oclsascr User Group
  • 3.1.1 Create the oclsascr and oinstall User Groups
  • 3.1.2 Create the opapps Account and Add It to Groups
• 3.2 Set Up Local Policy Security Options
• 3.3 Install Oracle Database
  • 3.3.1 Install Oracle Database 12.1.0.1 Enterprise Edition
  • 3.3.2 Install Oracle Database 12.1.0.1 Examples
• 3.4 Install the Oracle Clinical Database Server
  • 3.4.1 Gather Required Information
  • 3.4.2 Install the Oracle Clinical 5.1 Database Server for Windows
  • 3.4.3 Review the Log Files
  • 3.4.4 Oracle Clinical Database Server Directory Structure for Windows
• 3.5 Perform Post-installation Tasks
  • 3.5.1 Limit Permissions on the XMLTEMP Folder
  • 3.5.2 Review the opa_settings.bat File

4 Creating an Oracle Clinical Database

• 4.1 Review Oracle Database Requirements and Recommendations
  • 4.1.1 Start with a New Database Instance
  • 4.1.2 Check Required Tablespaces
  • 4.1.3 Use the Database Configuration Assistant
  • 4.1.4 Decide Which Type of 12c Database to Create
  • 4.1.5 Select Required Components
  • 4.1.6 Use Automatic Memory Management
  • 4.1.7 Accept Connections as a Service
  • 4.1.8 Set Initialization Parameters
  • 4.1.9 Modify the tnsnames.ora File on the Database Server
• 4.2 Install Oracle Clinical Database Objects
  • 4.2.1 Customize the Installation
    • 4.2.1.1 Edit the Tablespace Size Scripts
    • 4.2.1.2 Edit the User Account Creation Script
    • 4.2.1.3 Create a Secret Store Directory
  • 4.2.2 Gather Required Information
  • 4.2.3 Start Installing the Oracle Clinical Database
    • 4.2.3.1 Start the Installer on a UNIX Server
    • 4.2.3.2 Start the Installer on a Windows Server
  • 4.2.4 Remove Group Privileges from this Session (UNIX Only)
• 4.3 Review the Log Files for Installation Errors
• 4.4 Perform Post-Installation Database Tasks
  • 4.4.1 Set the Database Time Zone
  • 4.4.2 Pin Database Packages
    • 4.4.2.1 Pin UNIX Database Packages
    • 4.4.2.2 Pin Windows Database Packages
  • 4.4.3 Set Up Disconnected Replication (Optional)
    • 4.4.3.1 Check Tablespace Size
    • 4.4.3.2 Create a Wallet Credential for the RXC_DISC_REP Database User
    • 4.4.3.3 Test Wallet Connection for RXC_DISC_REP
    • 4.4.3.4 Add Reference Codelist Value
  • 4.4.4 Consider Implementing Partitioning

5 Installing and Configuring the Application Tier

• 5.1 Before You Start
  • 5.1.1 Identify a Single Account to Perform All Application Tier Installation Tasks
  • 5.1.2 Get a CA Certificate for HTTPS
• 5.2 Install Adobe Reader
• 5.3 Install Oracle Java Development Kit
• 5.4 Install Oracle WebLogic Server 10.3.6
• 5.5 Install and Configure Oracle Application Server 11gR2
  • 5.5.1 Install Oracle Application Server 11gR2 (11.1.2.1)
  • 5.5.2 Stop Services
  • 5.5.3 Apply Patch
  • 5.5.4 Create ORACLE_INSTANCE Environment Variable
• 5.6 Enable SSL Between a Browser and Oracle HTTP Server
  • 5.6.1 Enabling SSL Between a Browser and Oracle HTTP Server Using a Certificate Authority
    • 5.6.1.1 Creating an Oracle Wallet and Generating a Certificate Request
    • 5.6.1.2 Obtain Trusted Certificate and User Certificate from Certificate Authority
    • 5.6.1.3 Import the User Certificate and Trusted Certificate to OWM
    • 5.6.1.4 Edit the Oracle HTTP Server Configuration File
      • 5.6.1.4.1 Add the New Wallet Location and Specify Port
      • 5.6.1.4.2 Make OHS Compatible with Internet Explorer 9 and Above
      • 5.6.1.4.3 Add Security Settings
  • 5.6.2 Enabling SSL Between a Browser and Oracle HTTP Server With Self Signing
• 5.7 Install Oracle Application Developer FrameWork and Apply Patches
  • 5.7.1 Install Oracle Application Developer Framework (ADF)
  • 5.7.2 Upgrade ADF
  • 5.7.3 Patch ADF to Support Internet Explorer 11
• 5.8 Modify the tnsnames.ora File on the Application Server
• 5.9 Test Connectivity to Databases for Forms and Reports Servers
  • 5.9.1 Test the Connection from the Application Servers to the Database
  • 5.9.2 Troubleshoot Network Connection Issues
• 5.10 Restart the Computer

6 Installing the Oracle Clinical Front End

• 6.1 Gather the Required Information
• 6.2 Restart Computer and Stop All Servers and Services
• 6.3 Install the Oracle Clinical Front End Components
  • 6.3.1 Review the Installation Log File
  • 6.3.2 Restart the Computer
  • 6.3.3 Add WebLogic Data Sources If Using Multiple Databases
• 6.4 Make the Java Runtime Environment Available for Download
• 6.5 Make the Oracle Clinical PDF Plug-in Available to Users
• 6.6 Share the RDC Directory for Image Access
  • 6.6.1 Sharing the Directory Across Multiple Computers
  • 6.6.2 Setting Up the Image Directory on a Single Computer
• 6.7 Install and Configure JSpell Spell Checker SDK (Optional)
  • 6.7.1 Install JSpell on Oracle Application Server
  • 6.7.2 Install the JSpell WAR File on the WebLogic Server
  • 6.7.3 Update the mod_wl_ohs.conf File for JSpell
  • 6.7.4 Restart Oracle HTTP Server (OHS)
  • 6.7.5 Test the JSpell Servlet
  • 6.7.6 Update the formsweb.cfg File for JSpell
  • 6.7.7 Update the Windows System Registry for JSpell
  • 6.7.8 Test JSpell in the Graphic Layout Editor
• 6.8 Verify and Fix Environment Variables
  • 6.8.1 Check Values
  • 6.8.2 Correct Values
• 6.9 Setting Up Automatic Startup
  • 6.9.1 Set Up Script to Execute Automatically at Machine Startup
  • 6.9.2 Verify Autostart Scripts
  • 6.9.3 Test Autostart
• 6.10 Starting Servers Manually
  • 6.10.1 Starting the FRDomain Admin Server
  • 6.10.2 Starting the Forms Server
  • 6.10.3 Starting the Reports Server
  • 6.10.4 Starting the OPADomain Admin Server
  • 6.10.5 Starting the OpaServer1 Server
• 6.11 Verify the Application Tier Installation
• 6.12 Stopping Servers
  • 6.12.1 Stopping the Forms Server
  • 6.12.2 Stopping the Reports Server
  • 6.12.3 Stopping the FRDomain Admin Server
  • 6.12.4 Stopping the OPADomain Admin Server
  • 6.12.5 Stopping the OpaServer1 Server

7 Installing the Oracle Clinical Reports Server

• 7.1 Gather Required Information
• 7.2 Restart Computer and Stop Servers
• 7.3 Start the WebLogic FRDomain Admin Server
• 7.4 Install the Oracle Clinical Reports Server
  • 7.4.1 Restart the Computer
• 7.5 Set Up the Reports Server for Access and File Viewing
  • 7.5.1 Create the Reports Server Root Directory
  • 7.5.2 Share and Grant Access to the Reports Server Root Directory
  • 7.5.3 Create Reports Server Log Directories for Each User
  • 7.5.4 Configure the Reports Server for DCI Forms and PDRs
• 7.6 Add the Reports Server to the Database Reference Codelist
• 7.7 Test the Reports Server Installation
• 7.8 Set Up Automatic Startup of Services

8 Setting Up the Parameterized Submission Process

• 8.1 Set Up PSUB
  • 8.1.1 Create Directories and Enter Values in OCL_STATE Local Reference Codelist
  • 8.1.2 Enable Users to Submit PSUB Jobs
  • 8.1.3 Enable opapps to Use the at Command (UNIX Only)
  • 8.1.4 Set Up Active Directory (Windows Only)
• 8.2 Starting and Stopping the PSUB Service
  • 8.2.1 Starting and Stopping PSUB Automatically in UNIX
    • 8.2.1.1 Starting PSUB Automatically in UNIX
    • 8.2.1.2 Stopping PSUB Automatically in UNIX
    • 8.2.1.3 Starting PSUB Automatically in Windows
      • 8.2.1.3.1 Creating a System Environment Variable
      • 8.2.1.3.2 Creating a Batch File
      • 8.2.1.3.3 Scheduling the Batch File and Testing the Setup
      • 8.2.1.3.4 Adding a Shortcut
  • 8.2.2 Starting PSUB Manually in UNIX
  • 8.2.3 Starting PSUB Manually in Windows
• 8.3 Testing the PSUB Installation
• 8.4 Customizing the PSUB Service
• 8.5 Running PSUB in a RAC Environment

9   Setting Up SAS

• 9.1 Setting Up SAS Data Extract
  • 9.1.1 Give Users Access to the opapps Account
  • 9.1.2 Add the opapps Account to the oclsascr User Group
  • 9.1.3 Give opapps Access to the Directory Specified in the RXC_SAS_VIEW Environment Variable
  • 9.1.4 Set Up SAS User Authentication and Set OCL_STATE Reference Codelist Values
• 9.2 Installing SAS on a UNIX Computer
  • 9.2.1 Modify SAS 9.3 and opa_settings on UNIX
    • 9.2.1.1 Prepare the SAS Template File
    • 9.2.1.2 Additional Modifications for Oracle Solaris
  • 9.2.2 Installing SAS on the Same UNIX Computer as Oracle Clinical
    • 9.2.2.1 Set REMOTE_OS_AUTHENT to FALSE
    • 9.2.2.2 Set Up a SAS Connection
      • 9.2.2.2.1 Oracle Wallet
      • 9.2.2.2.2 SAS Encryption
  • 9.2.3 Installing SAS on a Different UNIX Computer from Oracle Clinical
    • 9.2.3.1 Establish the Connection to SAS on a Different Computer
      • 9.2.3.1.1 NFS
      • 9.2.3.1.2 Create opapps on the SAS Server
      • 9.2.3.1.3 Check init.ora
      • 9.2.3.1.4 Create a Shell Script
    • 9.2.3.2 Set Up SAS Security on a Different Computer
      • 9.2.3.2.1 Oracle Wallet
      • 9.2.3.2.2 SAS Encryption
    • 9.2.3.3 Configure Private and Public Keys for Using SSH with SAS
• 9.3 Installing SAS on a Windows Computer
  • 9.3.1 Modify the opasettings.bat file
  • 9.3.2 Installing SAS on the Same Windows Server Computer
    • 9.3.2.1 Set REMOTE_OS_AUTHENT to FALSE
    • 9.3.2.2 Set System Path
    • 9.3.2.3 Edit the SAS Config File and Grant Permissions
  • 9.3.3 Installing SAS on a Different Windows Server Computer
    • 9.3.3.1 Set REMOTE_OS_AUTHENT to TRUE
    • 9.3.3.2 Enable Executing Data Extract PSUB Jobs
    • 9.3.3.3 Edit the SAS Config File and Grant Permissions
    • 9.3.3.4 Set Values in OCL_STATE Reference Codelist

10 Setting Up Clients

• 10.1 Configuring Personal Firewall
• 10.2 Using Safari on an iPad
• 10.3 Setting Internet Options for Microsoft Internet Explorer
  • 10.3.1 Set Up for Proxy Usage on Fully Qualified Application Tier Names
  • 10.3.2 Set Document Mode to Quirks (the Default Setting)
  • 10.3.3 Allow More Connections
  • 10.3.4 Turn Off Compatibility View in Internet Explorer
• 10.4 Download Required Applications for Clients
  • 10.4.1 Download the Java Runtime Environment
  • 10.4.2 Download the Oracle Clinical PDF Plug-in
  • 10.4.3 Download Adobe Reader
• 10.5 Mapping Network Drive for Image Browsing
• 10.6 Enabling Report Generation from the Command Line
• 10.7 Logging In

11 Upgrading an Oracle Clinical Installation to Release 5.1

• 11.1 Changes Introduced in Oracle Clinical 5.0
  • 11.1.1 Changes to Parameterized Submission (PSUB)
  • 11.1.2 Changes in SAS Data Extract Implementation
  • 11.1.3 Changes to File and Image Viewing
  • 11.1.4 Reset Application Account Passwords Proactively
• 11.2 Changes Introduced in Oracle Clinical and RDC 5.1
  • 11.2.1 Grant Users Access to New and Changed Oracle Clinical Menu Items
    • 11.2.1.1 Audited Study Data Deletion Menu Items
    • 11.2.1.2 Partial Source Data Verification Menu Items
  • 11.2.2 Grant RDC Onsite Users New Verify Privileges
  • 11.2.3 Set Up Custom Review Types and Assign Custom Review Privileges
• 11.3 Database Server
  • 11.3.1 Install Oracle Database Server 12.1.0.1
    • 11.3.1.1 Installing the Oracle Database Server on UNIX
    • 11.3.1.2 Installing the Oracle Database Server on Windows
  • 11.3.2 Install the Oracle Clinical Database Server
    • 11.3.2.1 Installing the Oracle Clinical 5.1 Database Server on UNIX
    • 11.3.2.2 Installing the Oracle Clinical 5.1 Database Server on Windows
  • 11.3.3 Preserving Your Database Customizations
• 11.4 Database
  • 11.4.1 Stop Processes
    • 11.4.1.1 Stop PSUB
    • 11.4.1.2 Prevent Access to Oracle Clinical Databases
    • 11.4.1.3 Stop Replication (If Applicable)
      • 11.4.1.3.1 Prepare All Replication Environments
      • 11.4.1.3.2 Stop Standard Replication
      • 11.4.1.3.3 Stop Symmetric Replication
  • 11.4.2 Back Up Your Database(s)
  • 11.4.3 Upgrade the Database to Oracle Database 12c Release 1 (12.1.0.1)
    • 11.4.3.1 Upgrade in Place
    • 11.4.3.2 Clone Your Database
  • 11.4.4 Set Initialization Parameters
  • 11.4.5 Create a Secret Store Directory
  • 11.4.6 Upgrade Databases to Oracle Clinical 5.1
    • 11.4.6.1 Gather the Required Information
    • 11.4.6.2 Running the Installer in UNIX
    • 11.4.6.3 Running the Installer in Windows
    • 11.4.6.4 Review the Log Files for Upgrade Results and Errors
      • 11.4.6.4.1 Finding Errors
      • 11.4.6.4.2 Known Error Messages
      • 11.4.6.4.3 Reencrypt Account Passwords
      • 11.4.6.4.4 Check If You Need to Prepare and Migrate Data
    • 11.4.6.5 Compile Invalid Objects
      • 11.4.6.5.1 Compile PL/SQL Code Before Running the Script
      • 11.4.6.5.2 Run the compile_schema_invalid.sql Script
      • 11.4.6.5.3 UNIX
      • 11.4.6.5.4 Windows
    • 11.4.6.6 Perform Post-Upgrade Database Tasks
      • 11.4.6.6.1 Set the Database Time Zone
      • 11.4.6.6.2 Pin Database Packages
      • 11.4.6.6.3 Migrate Users
      • 11.4.6.6.4 Run Scripts to Gather Schema Statistics for the Oracle Database Optimizer
  • 11.4.7 Check Internal Sequence Numbers
  • 11.4.8 Upgrade Installations that Use Replication
• 11.5 Application Tier
  • 11.5.1 Copy Any Customized Application Tier Files
  • 11.5.2 Install the Application Tier Technology Stack
    • 11.5.2.1 Upgrading from a Release Earlier than 5.0
    • 11.5.2.2 Upgrading from Release 5.0.x
  • 11.5.3 Install the Oracle Clinical Front End and Reports Server
  • 11.5.4 Set Remote Method Invocation (RMI) JDBC Security to Secure
  • 11.5.5 Preserve Your Customizations
    • 11.5.5.1 Oracle Clinical Forms
    • 11.5.5.2 Oracle Clinical Reports
    • 11.5.5.3 Formsweb.cfg
    • 11.5.5.4 RDC Onsite Customizable Files
    • 11.5.5.5 Customizable HTML Files
• 11.6 Postupgrade Steps
  • 11.6.1 Update Environment Variables (If Upgrading from 5.0.x)
  • 11.6.2 Manually Start the Advanced Queue Process (If You Cloned a Database)

Index