2 Install Oracle Database

If you are upgrading TMS, skip to Chapter 6, "Upgrading Oracle Thesaurus Management System to Release 5.2.1".

If you have already performed these steps as part of installing or upgrading Oracle Clinical to Release 5.2, skip to Chapter 3, "Install and Configure the Oracle Application Tier".

If you are using Oracle Real Application Clusters (RAC) or Oracle Data Guard, see Section 1.5, "Supported Configurations with Oracle Data Guard and RAC".

This chapter includes:

2.1 Get the Oracle Database 12.1.0 Installation Guide

  1. Open or download the installation guide for your operating system:

2.2 Download and Extract the Oracle Database 12.1.0 Software

To download and extract the Oracle Database 12.1.0 software:

  1. Follow instructions in the Oracle Database Installation Guide.

Oracle Thesaurus Management System requires Oracle Database Enterprise Edition.

Oracle Database Grid Infrastructure is optional.

2.3 Performing Prerequisite Tasks for Installing Oracle Database

To ensure that your platform meets the minimum requirements for installing Oracle Database 12c Release 2 (12.1.0.2), you must perform the following preparatory tasks:

2.3.1 Create Owners, Groups, and Mount Points

To create the software owner, required groups, and mount points:

  1. Create the software owner and groups:

    • Create a UNIX user to own the Oracle software. Typically, the user name is oracle.

    • Create two groups: one is the Oracle Inventory group; the other is the operating system DBA group. Typically, the group names are oinstall and dba, respectively.

  2. Create mount points owned by the oracle user:

    • Create a software mount point of at least 10 GB.

    • Create mount points to hold the database files, control files, and log files, respectively.

  3. Test permissions. Ensure that the oracle user can write to the new mount points and all subdirectories.

2.3.2 Configure Kernel Resources and Adjust Operating System Environment

The performance of Oracle Database relies on proper tuning of operating system parameters. In addition, if you are creating several Oracle instances, you might have to increase the amount of shared memory and semaphores on the system by setting kernel parameters.

For details, see the "Configure Kernel Parameters" section of the Oracle Database 12c Release 2 Installation Guide for your operating system.

2.3.3 Install Latest Operating System Patches

Download and install the latest operating system patches required for Oracle, if necessary. Review the latest platform-specific install bulletins for Oracle Database 12c Release 1 (12.1.0.2).

2.4 Install Oracle Database 12.1.0

To install Oracle Database 12.1.0, follow the instructions in the Oracle Database Installation Guide, making selections appropriate for TMS as noted in the following sections.

TMS requires:

  • Oracle Database Enterprise Edition

  • Oracle Web Tier (Oracle Fusion Middleware Web Tier Utilities)

  • Oracle Database Text Option

Oracle Database Grid Infrastructure is optional.

You can configure database(s) as part of the database software installation or after, using the Database Configuration Assistant (DBCA).

Oracle Thesaurus Management System supports installation on either a Container Database (CDB) containing a Pluggable Database (PDB) or a non-CDB database.

Note:

For information on pluggable and container databases, see:

For an explanation of which options require an additional license, see the Database Licensing Information User Manual at https://docs.oracle.com/database/121/DBLIC/toc.htm.

2.4.1 Install and Configure Oracle Database

Oracle recommends that you set up a new database instance so that neither Oracle Thesaurus Management System nor its installation process interferes with other applications. However, you can install Oracle Thesaurus Management System on an existing database instance.

When you configure the database, select the following options for Oracle Thesaurus Management System:

  • Character Set: See Section 1.8, "Choose a Character Set".

  • Automatic Memory Management (recommended)

  • Oracle JVM (required)

  • Distributed Database Option and Advanced Replication Option (required only if you are using Oracle Clinical Distributed Study Conduct (Replication))

  • Oracle Partitioning (recommended)

  • Oracle Text (required)

  • Oracle XML DB (required)

  • Oracle Database Client (required)

  • Oracle Database Examples (required)

    Note:

    Oracle Text, Java Virtual Machine (JVM), and Oracle XML DB are configured automatically if you select a general purpose template.

  • Accept connections as a service instead of a SID. Service name requirements for Oracle Thesaurus Management System include:

    • The service name must be less than 15 characters long.

    • It must not include the domain.

    • It must be all lowercase.

      Note:

      If you are installing the Oracle Thesaurus Management System database on a pluggable Oracle 12.1.0.2 database (PDB), see My Oracle Support article ID 1910177.1, How To Configure TNS / SQLNET using the local_listener parameter for Pluggable Database In Oracle 12c, Allowing a SQLNET Connection to the PDB.

  • Check that required tablespaces exist, have Autoextend on, and have the following minimum sizes:

    • SYSTEM: 900 mb

    • TEMP: 100 mb

    • UNDOTBS1: 700 mb

    • USERS: 500 mb

    • SYSAUX: 600 mb

  • Initialization Parameters. Table 2-1 shows the required or recommended values for Oracle Thesaurus Management System. For parameters that accept a value within a range, the minimum values are given.

Tip:

Parameters are listed in alphabetical order. In the Database Configuration Assistant, you can click the Parameter column to display the parameters in the same order. You may need to select Advanced Parameters to see all of them.

Note:

If you make any changes to the initialization parameters, restart the database for the new settings to take effect.

Table 2-1 Required and Recommended Initialization Values in the init.ora File

Parameter Value Comments

COMPATIBLE

12.0.0.0

Specifies the release with which the Oracle server must maintain compatibility.

DB_BLOCK_SIZE

16384 bytes

You cannot change this value after you create the database.

DB_CACHE_SIZE

150 MB

Recommended value for 50 to 60 concurrent users. Adjust this value according to your organization's needs.

DB_DOMAIN

null

DO NOT set this value.

DB_FILES

200

Oracle adds needed space to the control files up to the number specified in the DB_FILES parameter.

EVENT

31151 trace name context forever, level 0x100

Required for HTML generation.

NOTE: Do not include the EVENT parameter when you create the database. Once the database is created, you can add the EVENT parameter to the init.ora file.

JAVA_POOL_SIZE

50 MB

Recommended value for 50 to 60 concurrent users. You can change the value of this parameter after installation.

JOB_QUEUE_PROCESSES

10

Developer-specific parameter. You can change the value of this parameter after installation.

LARGE_POOL_SIZE

50 MB

Recommended value for 50 to 60 concurrent users.

MEMORY_MAX_TARGET

1000 MB (minimum)

Adjust this value according to your organization's needs.

MEMORY_TARGET

1000 MB (minimum)

Adjust this value according to your organization's needs.

NLS_DATE_FORMAT

DD-MON-RRRR (default value)

Determines the format in which client applications running on the Windows server transfer date information to and from the database. The format must specify the year as RRRR.

NLS_LENGTH_SEMANTICS

BYTE

The CHAR value for this parameter is not supported.

OPEN_CURSORS

800 or greater

You can change the value of this parameter after installation.

OPTIMIZER_DYNAMIC_SAMPLING

2 or greater

The default setting is 2. Oracle recommends using dynamic sampling for Batch Data Load temporary tables; see the Oracle Clinical Administrator's Guide.

OPTIMIZER_FEATURES_ENABLE

12.1.0.2

Acts as an umbrella for enabling a series of optimizer features based on an Oracle release number.

NOTE: Oracle Thesaurus Management System 5.2.1 is certified on the Oracle Database 11g optimizer features.

OPTIMIZER_MODE

CHOOSE

If you run Oracle Thesaurus Management System's statistics gathering scripts, the CHOOSE value sets Oracle Optimizer to apply the execution plan that best minimizes response time. See the Oracle Database documentation for more information. (CHOOSE is the default value when you specify 11.2.0.4 as the value of OPTIMIZER_FEATURES_ENABLE.)

PGA_AGGREGATE_TARGET

200 MB

Recommended value for 50 to 60 concurrent users. You can change the value of this parameter after installation.

REMOTE_LOGIN_PASSWORDFILE

EXCLUSIVE

The database must be set up to use password file authentication.

SEC_CASE_SENSITIVE_LOGON

FALSE

Lets you enter passwords without case sensitivity.

SESSIONS

500 or greater

You can change the value of this parameter after installation.

SGA_MAX_SIZE

600 MB (minimum)

Recommended value for 50 to 60 concurrent users. Adjust this value according to your organization's needs.

SGA_TARGET

600 MB (minimum)

Recommended value for 50 to 60 concurrent users. Adjust this value according to your organization's needs.

SHARED_POOL_SIZE

150 MB (minimum)

Recommended value for 50 to 60 concurrent users. You can change the value of this parameter after installation.

UNDO_MANAGEMENT

AUTO

Specifies which undo space management mode the system uses. When set to AUTO, the instance starts in Automatic Undo Management (AUM) mode.

UTL_FILE_DIR

opa_home\xmltemp

Specifies each directory you access.

For Windows environments, samples of the valid syntax are as follows:

UTL_FILE_DIR=c:\e2b\import

UTL_FILE_DIR=c:\opapps\xmltemp

In a UNIX environment, UTL_FILE_DIR requires an entry with two specified paths: one with and one without a trailing slash. Add these lines before any other UTL_FILE_DIR entries:

UTL_FILE_DIR=/usr/opapps/oc/xmltemp/

UTL_FILE_DIR=/usr/opapps/oc/xmltemp

2.4.2 Modify the tnsnames.ora File on the Database Server

There is a tnsnames.ora file in at least two locations in the installation. Oracle recommends maintaining a master file and copying it to each location whenever you add a database. See Section 3.13, "Modify the tnsnames.ora File on the Application Server" for the application server locations.

  1. Navigate to the tnsnames.ora file in the following directory on the database server:

    Oracle_Home/network/admin

  2. Enter a connect string for each database that matches the database's service name.

  3. If there are multiple Oracle homes, maintain tns entries for all databases in a central location; for example: /etc/tnsnames.ora.

2.4.3 Create the oinstall User Group

Use instructions in the Oracle Database 12.1.0.2 Installation Guide chapter "Configuring Users, Groups and Environments for Oracle Database."

  1. Check if the oinstall user group exists.

  2. If it does not exist, create it.

2.4.4 Check Required Tablespaces

Table 2-2 lists the tablespaces, along with their minimum size, required for Oracle Clinical. Make sure the database contains these tablespaces. The best practice is to create them with the Autoextend On option, to avoid running out of space.

In addition, you may need to increase the minimum sizes for your installation.

Table 2-2 Required Tablespaces and Sizes

Tablespace Minimum Size

SYSTEM

900 MB

TEMP

100 MB

UNDOTBS1

700 MB

USERS

500 MB

SYSAUX

600 MB

2.4.5 Performance Tuning Step for Pluggable Databases

To prevent performance issues, specifically with accessing dba_synonyms view, take these steps. See My Oracle Support doc ID 2033658.1 for more information.

  1. Run the following statement:

    alter system set "_common_data_view_enabled" = false scope=both;

  2. Restart the database.

2.5 Install Oracle Database 12c Release 1 (12.1.0.2) Examples

Oracle Database Examples includes the following items:

  • Oracle JDBC Development Drivers (required)

  • Oracle Database Examples (required)

  • Oracle Product Demonstrations (optional)

Note:

You do not need to install any of the sample schemas. They are not required for either Oracle Clinical or TMS. You can add them later if you change your mind.

To install Oracle Database Examples:

  1. Extract the zip file containing Oracle Database Examples in the examples directory.

  2. Start Oracle Universal Installer from the examples directory.

    ./runInstaller

    Or, if the database server has multiple Oracle Homes, then enter:

    ./runInstaller -invPtrLoc ORACLE_HOME/oraInst.loc

  3. Accept all the default values during the installation.

For more information, see the Oracle Database Examples Installation Guide at http://docs.oracle.com/database/121/nav/portal_11.htm.

2.6 Install Oracle Critical Patch Update

  1. Check My Oracle Support article ID 180430.1, Oracle Health Sciences (Life Sciences/Pharmaceutical/Healthcare) Applications Supported Technology Stacks, for the latest quarterly Oracle CPU patches tested with Oracle Health Sciences applications.

  2. Install these patches on every computer with an Oracle Home.