6 Upgrading Oracle Thesaurus Management System to Release 5.3

6.3.1 Before You Start

6.3.2 Gather Required Information

Have the following information ready.

Install the 12.2.1.3 Oracle WebLogic Server

• Home directory path for FMW 12.2.1.3; for example: C:\Oracle12213\Middleware\Oracle_Home

• Email address to receive the security updates specific to your installation

• My Oracle Support password if you wish to receive the security updates through My Oracle Support

Install the Oracle Fusion Middleware Infrastructure Software

• Home directory path for FMW 12.2.1.3; for example: C:\ Oracle12213\Middleware\Oracle_Home

• Email address to receive the security updates specific to your installation

• My Oracle Support password if you wish to receive the security updates through My Oracle Support

Install the Oracle Forms and Reports Servers

• Home directory path for FMW 12.2.1.3; for example: C:\ Oracle12213\Middleware\Oracle_Home

6.3.3 Restart Computer and Stop All Servers

1. Restart the computer before starting the upgrade to 12.2.1.3.

2. Before starting the upgrade to 12.2.1.3, stop all servers and components.

   For FRDomian, make sure Admin Server, WLS_FORMS, WLS_REPORTS, OHS, report server instance, and Node Manager are stopped.

   For OPADomain, make sure Admin Server, managed server, and Node Manager are stopped.

6.3.4 Install Oracle Application Tier 12.2.1.3

Install Oracle WebLogic Server, Oracle Fusion Middleware Infrastructure Software, and Oracle Forms and Reports Server in the new 12.2.1.3 ORACLE_HOME.

1. To install Oracle WebLogic Server, see Section 3.5, "Install Oracle WebLogic Server 12.2.1.3".

2. To install Oracle Fusion Middleware Infrastructure Software, see Section 3.6, "Install the Oracle Fusion Middleware Infrastructure Software".

3. To install Oracle Forms and Reports Server, see Section 3.7, "Install the Oracle Forms and Reports Servers".

6.3.5 Run Pre-Upgrade Readiness Check

Once the new 12.2.1.3 ORACLE_HOME is created and Oracle WebLogic Server, Oracle Fusion Middleware Infrastructure Software, and Oracle Forms and Reports Servers are installed, run a pre-upgrade readiness check. You must run this check separately for FRDomain and OPAdomain.

1. Run the following command to start the pre-upgrade readiness check:

   <12.2.1.3_Oracle_Home>\oracle_common\upgrade\bin\ua.bat -readiness
   

   1. Select the Domain Based option and enter the domain location.

   2. Select the Include checks for all schemas and Include checks for all configurations check boxes.

2. Enter the WebLogic domain directory where schemas and configurations will be checked. This will be the path to the domains directory from <12.2.1.2_Oracle_Home>. For example, C:\Oracle\Middleware\Oracle_Home\user_projects\domains\FRDomain.

3. Check schemas and configuration in FRDomain.

   Schemas to be checked:

   • Oracle Platform Security Services – OPSS

   • Oracle Audit Services – IAU

   • Common Infrastructure Services – STB

   Configuration to be checked:

   • System Components Infrastructure

   • Oracle HTTP Server

   • Oracle JRF

   • Common Infrastructure Services

   • Oracle Forms Services

   • Oracle Reports Services

4. Check schemas and configuration in OPADomain.

   Schemas to be checked:

   • Oracle Platform Security Services – OPSS

   • Oracle Audit Services – IAU

   • Common Infrastructure Services – STB

   Configuration to be checked:

   • System Components Infrastructure

   • Oracle HTTP Server

   • Oracle JRF

   • Common Infrastructure Services

   • Oracle Forms Services

5. Enter the administrator database account credentials for checking the RCU OPSS schema. The account need to have DBA privileges (can be system account).

   Note:

   Click Connect to make sure the credentials you entered are valid.

6. Enter the administrator database account credentials for checking account credentials for the RCU IAU and STB schemas. The account need to have DBA privileges (can be system account).

7. In the Readiness Progress screen, check that all the components should have a green status – upgrade not necessary or ready for upgrade.

For OPADomain in the Readiness Progress screen all the components should have a green status – upgrade not necessary or ready for upgrade; except for Oracle Forms Services. The Oracle Forms Service component for OPADomain will be marked as Failure but this can be ignored as Oracle Forms Service is not a part of OPADomain.

6.3.6 Upgrade the Domain Schema

Perform the following steps separately for both the FRDomain and OPADomain in the existing 12.2.1.2 User Projects Home.

1. Run the following command in the new 12.2.1.3 ORACLE_HOME.

   <12.2.1.3_Oracle_Home>\oracle_common\upgrade\bin\ua.bat
   

2. Select the All Schemas Used by a Domain check box and provide the domain location.

3. Upgrade the components in FRDomain/OPADomain.

   • Oracle Platform Security Services - OPSS

   • Oracle Audit Services - IAU

   • Common Infrastructure Services - STB

4. Create the component whose schema is missing in FRDomain/OPADomain.

   • Oracle WebLogic Services

5. Check all prerequisites.

6. Enter the administrator database account credentials for checking RCU. The account need to have DBA privileges (can be system account).

7. Select the Create missing schemas for specified domain check box and enter the schema password.

   Note:

   It is recommended to use the same password used for other RCU schema components.

8. In the Examine screen, make sure all the checks should be green and status is not failed.

9. In the Upgrade Summary screen, make sure all the information is correct.

10. Click Upgrade.

6.3.7 Run the Reconfiguration Wizard

Run the Reconfiguration Wizard For FRDomain

1. Open a DOS prompt and run:

   <12.2.1.3_Oracle_Home>\oracle_common\common\bin\reconfig.cmd -log  <path_to_log_file>\FRDomain_log.txt -log_priority=ALL
   

You can accept most default values, with the exception noted below.

Select Domain

1. Select the FRDomain location; for example:

   C:\Oracle\Middleware\Oracle_Home\user_projects\domains\FRDomain

Database Configuration Type

1. Select the RCU data check box under Specify AutoConfiguration Options Using.

2. Make sure the RCU database is correct.

3. Click Get RCU Configuration.

Component Datasources

1. Select all RCUs.

2. Click Next.

Advanced Configuration

1. Select all check boxes.

Make a note of the FRDomain defaultCoherenceCluster port because for OPADomain a different port needs to be used. By default, it is 7574.

Run the Reconfiguration Wizard For OPADomain

1. Open a DOS prompt and run:

   <12.2.1.3_Oracle_Home>\oracle_common\common\bin\reconfig.cmd -log  <path_to_log_file>\OPADomain_log.txt -log_priority=ALL
   

You can accept most default values, with the exception noted below.

Select Domain

1. Select the OPADomain location; for example:

   C:\Oracle\Middleware\Oracle_Home\user_projects\domains\OPADomain

Datasources

1. Select the existing data sources.

Database Configuration Type

1. Select the RCU data check box under Specify AutoConfiguration Options Using.

2. Make sure the RCU database is correct.

3. Click Get RCU Configuration.

Component Datasources

1. Select all RCUs.

2. Click Next.

Advanced Configuration

1. Select all check boxes.

Default Coherence Cluster

1. Use a different port number other than the one used for FRDomain. For example, 7575.

Domain Frontend Host

1. Deselect the Configure Domain Frontend Host check box.

6.3.8 Upgrade the Forms Server

Start the upgrade assistant in the new 12.2.1.3 Oracle Home to upgrade the Forms installation.

1. Run the following command:

   <12.2.1.3_Oracle_Home>\oracle_common\upgrade\bin\ua.bat
   

2. Select the All Configurations Used by a Domain check box, and provide the FRDomain location.

3. Upgrade the components in FRDomain:

   • System Components Infrastructure

   • Oracle HTTP Server

   • Oracle JRF

   • Oracle Forms Services

   • Oracle Reports Services

4. In the Prerequisites screen, select all the check boxes.

5. In the Examine screen, make sure all the checks have the status "ready for upgrade" or "upgrade not necessary".

6. Click Upgrade.

7. Start all components for FRDomain, except the report server you created for TMS 5.2.1 or OC 5.2.0.

   If OHS fails to start with exit status = 1 (startComponent ohs1), there is an issue in the httpd.conf files in the FRDomain.

   The httpd.conf files can be found under:

   • <12.2.1.2_Oracle_Home>\user_projects\domains\FRDomain\config\fmwconfig\components\OHS\instances\ohs1\

   • <12.2.1.2_Oracle_Home>\user_projects\domains\FRDomain\config\fmwconfig\components\OHS\ohs1\

   Note:

   Make sure the httpd.conf files have only one Listen directive for one specific port.

   Listen <machine_name>:<port_number>

6.5.1 Back Up Database Objects

Back up the following packages if you have customized them:

• tms_ud_activation_rules

• tms_sup_srchobj

6.5.2 Prevent Access to Oracle Thesaurus Management System Databases

You must ensure that no data entry is performed, and no jobs that update data (such as batch validation) run during the upgrade process.

To prevent users from accessing the data, place the database in restricted mode. Provide restricted session access to the following accounts:

• SYSTEM

• SYS

• OPA

• RXC

• TMS

• CTXSYS

• OPS$TMSBROWSER

• TDX

After you complete the upgrade, remove the restricted access from the databases and user accounts.

6.5.3 Upgrade to Oracle Database 12.1.0.2

Oracle recommends backing up your database(s) at this point.

6.5.4 Gather Required Information

Before you start the Installer, be sure you have the information it prompts for:

1. Home Details: The full path to the OPA_HOME or similar application home name on your application server; by default:

   C:\opapps53

   Note:

   If TMS 5.2.x or Oracle Clinical 5.2.x has already been installed on this application server, OPA_HOME may already be set to C:\opapps52 or similar path and you must use this for TMS 5.3 too. Do not create a new OPA_HOME if this was already created. The TMS 5.3 components will be placed by the installer under this OPA_HOME at the specified location for the TMS 5.3 release.

2. Oracle Database Client Home: Full path to ORACLE_HOME. For example, C:\Oracle\Middleware\Oracle_Home.

   If you upgraded the technology stack from version 12.2.1.2 to 12.2.1.3, use the new 12.2.1.3_ORACLE_HOME you created.

   Note:

   Make sure the tnsnames.ora from your ORACLE_HOME\network\admin has an entry for your database.

3. TMS Server Code Home Directory: The system detects the location and enters the value for you. By default, it is <OPA_HOME>\tms.

4. Database Service Name to connect: Enter the database name. It must be a valid TNS entry in your tnsnames.ora file.

5. Database Details: Enter the database server name and database port number.

6. NLS Settings: Enter the NLS settings for the database; see Section 1.8, "Choose a Character Set". Oracle strongly recommends that you use UTF8. The default values are:

   • American_America.UTF8

   • DD-MON-RRRR

7. Directory for data tablespace data files: Enter the path to the directory on the database server where the data tablespace datafiles for the application should be created during the installation. The Installer does not validate the value and you must use the following syntax, including a trailing slash, depending on your operating system; for example:

   • UNIX: /u01/oradata/dbname/

   • Windows: drive:\oradata\dbname\

8. Enter and confirm passwords for the following accounts:

   • SYS

   • SYSTEM

   • RXC

   • OPA

   • TMS

   • CTXSYS

   • TMSPROXY

6.5.5 Stop PSUB Process (If Integrated with Oracle Clinical)

If your TMS installation is integrated with Oracle Clinical, you must stop the PSUB process before upgrading the database. See the Oracle Clinical Administrator's Guide for instructions.

6.5.6 Start the Installer

To upgrade a TMS database:

1. Log in to the application server as a user with system administrator privileges.

2. In the staging area, locate the directory where you downloaded and extracted Oracle Thesaurus Management System (see Section 1.6, "Download the Software").

3. Run the following file as an administrator:

   Disk1\install\setup.exe

   The Installer opens to the Welcome screen.

   Note:

   See Section 1.7, "Use the Silent Installer (Optional)" for instructions for running the Installer as a file with pre-entered parameter values.

   Note:

   Although there is a button for deinstalling products on the Welcome screen, Oracle does not support using the Installer to deinstall Oracle Thesaurus Management System.

4. In the Select a Product to Install page, select TMS Database Upgrade 5.3.0.0.x.

6.5.7 Attend to the TMS Database Upgrade Installer Screens

The Oracle Universal Installer guides you through the database upgrade. Provide the information you assembled in Section 6.5.4, "Gather Required Information."

Ignore tablespace creation errors:

• Select Yes if the database already has the TMS tablespaces created.

• Select No if the TMS tablespaces do not exist.

The Installer gives you information that you should make a note of.

6.5.8 Set Initialization Parameters

After the upgrade completes, set the init.ora parameters according to the instructions in Section 2.4.1, "Install and Configure Oracle Database."

You must stop and then start the database to activate the changed init.ora parameters.

6.5.9 Check Installation Log for Errors

When you upgrade, the installation log file may report the following error:

".....
Connected.
BEGIN tms_dsi_xml_schema.InstallSchemas; END  

*
ERROR at line 1:
ORA-02303: cannot drop or replace a type with type or table dependents 
ORA-06512: at "XDB.DBMS_XMLSCHEMA_INT", line 3
ORA-06512: at "XDB.DBMS_XMLSCHEMA", line 14 
ORA-06512: at "TMS.TMS_DSI_XML_SCHEMA", line 35 
ORA-06512: at line 1
 
finished TMSUPG 
TMS will now attempt to validate any invalidate objects... 
...."

This error occurs because the tmsupg.sql upgrade script executes tms_dsi_xml_schema.InstallSchemas before attempting to validate any invalid objects. Execution of tms_dsi_xml_schema.InstallSchemas fails if the database has invalid objects.

If this error occurs, you need to:

1. Run compile invalid until all database objects have been made valid.

2. Run tms_dsi_xml_schema.InstallSchemas manually. See Section 6.5.10, "Configure DSI Import" for details.

6.5.10 Configure DSI Import

If you plan to use disconnected system integration (DSI), enter following commands:

set LOCAL=databasename
sqlplus tms/password
exec tms_dsi_xml_schema.InstallSchemas;
 

6.5.11 Load Dictionaries

You can load dictionaries at any time. See the Oracle Thesaurus Management System User's Guide for information about loading dictionaries.

6.5.12 Integration with Oracle Clinical

When a TMS database is cloned and TMS is integrated with Oracle Clinical, force rederivation must be executed for all Oracle Clinical studies.

6.8.1 Gather Required Information

Have the following information ready to enter in the Installer screens:

• Home Details: Enter the following:

  • Name: OPA_HOME

  • Path: C:\opapps53

  Note:

  If TMS 5.2.x or Oracle Clinical 5.2.x has already been installed on this application server, OPA_HOME may already be set to C:\opapps52 or similar path and you must use this for TMS 5.3 too. Do not create a new OPA_HOME if this was already created. The TMS 5.3 components will be placed by the installer under this OPA_HOME at the specified location for the TMS 5.3 release.

• Java Home is the location where JDK 1.8.0_191 or higher was installed

• Oracle Fusion Middleware home directory:

  • If the technology stack has been upgraded from version 12.2.1.2 to 12.2.1.3, use the new 12.2.1.3 Oracle Home (post upgrade one). The upgrade to 12.2.1.3 is an out-of-place upgrade and a new oracle_home is created; for example, C:\Oracle12213\Middleware\Oracle_Home.

  • If the technology stack was already at version 12.2.1.3, use the Oracle Home you had at the time of technology stack installation; for example, C:\Oracle\Middleware\Oracle_Home.

• Oracle Fusion Middleware User Project directory:

  • If the technology stack has been upgraded from version 12.2.1.2 to 12.2.1.3, use the initial 12.2.1.2 Oracle Home (pre upgrade one) to select the user projects directory. The upgrade to 12.2.1.3 is an out-of-place upgrade and the domains reside in the 12.2.1.2 oracle home; for example, C:\Oracle\Middleware\Oracle_Home\user_projects.

  • If the technology stack was already at version 12.2.1.3, use the Oracle Home you had at the time of technology stack installation; for example, C:\Oracle\Middleware\Oracle_Home\user_projects.

• OPA home directory: By default, it is C:\opapps53.

• OPADomain Administration Server configuration details:

  • Listen address

  • OPADomain Listen port number

  • OPADomain SSL listen port number

  • OPADomain WebLogic username

  • OPADomain WebLogic password

• OPADomain Node Manager configuration details:

  • Listen address

  • OPA Domain NodeManager Listen port number

  • WebLogic username

  • WebLogic Server password

• Database details (database used for data source created under OPADomain):

  • Server.Domain: for example, servername.your_company.com

  • Port number

  • Database service name

  • TMS Proxy Password (tmsproxy)—the password you created when installing Oracle Thesaurus Management System database objects.

• Managed Server configuration details:

  • Number of Managed Servers

  • Listen port start index

• Online help URL: If you have customized the online help, the URL where the customized online help is located.

6.8.2 Start the Installer

To install the TMS Front End:

1. Log in as a user with system administrator privileges.

2. In the staging area, locate the directory where you downloaded and extracted Oracle Thesaurus Management System (see Section 1.6, "Download the Software").

3. Run the following file as an administrator:

   Disk1\install\setup.exe

   The Installer opens to the Welcome screen.

   Note:

   See Section 1.7, "Use the Silent Installer (Optional)" for instructions for running the Installer as a file with pre-entered parameter values.

   Note:

   Although there is a button for deinstalling products on the Welcome screen, Oracle does not support using the Installer to deinstall Oracle Thesaurus Management System.

6.8.3 Attend to the TMS Front End Installer Screens

The Oracle Universal Installer guides you through the installation and configuration of the TMS Front End.

1. Select a Product to install: Oracle Thesaurus Management System Front End 5.3.0.0.x.

2. Home Details: From the Directory drop-down, select the OPA Home that corresponds to the Oracle Thesaurus Management System home (for example, C:\opapps53). When you select the directory, the value in the Home drop-down changes automatically.

3. Available Product Components: Select Oracle Thesaurus Management System Front End 5.3.0.0.x– Install status – Upgrade.

   Note:

   Although the Installer gives you the option install the TMS Server (database server code) at the same time, do not select this option. You must install the TMS Server first, then the database objects, and then the Front End.

4. Choose Install Type: Select No.

5. Follow the instructions on the installation screens, providing the information you assembled in Section 6.8.1, "Gather Required Information".

6. Summary: The Summary screen provides information about the global settings, languages, space requirements, and products for this installation.

   Review the installation details to verify that they are correct. To revisit earlier installation screens and make changes, click Back.

   When you are ready to continue, click Install.

7. Install: The Installer copies the files onto the server, completes the setup and configuration tasks, and generates a log file of this installation.

   In addition, the Install screen displays the location of the log file that records the results of the installation activities for this session. Make a note of this information so you can view the log file after the installation.

8. End of Installation: The End of Installation screen reports whether the installation was successful. In addition, this screen lists the URLs that you use to access the TMS application and TMS Lite Browser.

   The Installer saves the URL information in the following file:

   %OPA_HOME%\log\setup.txt

   When you have finished reviewing the installation information, click Exit.

6.8.4 Find the Installation Log Files

During the installation of an Oracle Health Sciences component, the Oracle Universal Installer generates the following log file:

installActionstimestamp.log

On a Windows installation, the log files are located at:

\Oracle\Inventory\logs

For example:

C:\Program Files\Oracle\Inventory\logs

All generated log files have a timestamp appended to the name. For example:

installActions2013-04-30_11-22-52AM.log

If you encounter any error, contact Health Sciences Support.

6.8.5 Set Remote Method Invocation (RMI) JDBC Security to Secure

1. Log in to the OPADomain WebLogic Server.

2. Go to Summary of Servers, select Managed Server of OPADomain, select General, and click Advanced.

3. Change the RMI JDBC Security setting to Secure.

4. Click Save.

5. Click Activate Changes.