Oracle® Life Sciences Data Hub

Installation Guide

Release 3.1
F40563-03
June 2021
Oracle Life Sciences Data Hub Installation Guide, Release 3.1

F40563-03

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Contents
Preface
Documentation accessibility vi
Diversity and Inclusion vi
Related resources vi
Access to Oracle Support vi

1 Before You Begin

1.1 Check for the Most Recent Information 1-1
1.2 Get Your Company ID from Oracle 1-1
1.3 Assemble the Software 1-2
1.3.1 Get the Oracle Life Sciences Warehouse 3.1 Media Pack 1-2
1.3.2 Download Software to a Staging Area 1-3
1.4 Assemble the Documentation 1-4
1.4.1 Books 1-4
1.4.2 My Oracle Support Articles 1-5
1.4.2.1 System Requirements and Technology 1-5
1.4.2.2 Upgrading to Oracle Life Sciences Data Hub Release 3.1 1-5
1.4.2.3 Other Documents Related to Oracle Life Sciences Data Hub 1-6

2 System Requirements and Technology Stack

2.1 System Requirements 2-1
2.1.1 Operating Systems 2-1
2.1.1.1 Database Tier 2-1
2.1.1.2 Application Tier 2-2
2.1.1.3 Clients 2-2
2.1.2 Hardware 2-2
2.2 Technology Stack 2-3
2.3 Integrated External Systems 2-4

iii
3 The Two Supported Upgrade Paths

4 Upgrading E-Business Suite from 12.1.3 to 12.2.9

4.1 Upgrade E-Business Suite from 12.1.3 to 12.2.9 4-1
4.2 Apply the Database Patches 4-4
4.3 Apply the Additional EBS Patches 4-5
4.4 Revert Database Init Parameters and Grant Access to APPS 4-5

5 Upgrading to Oracle Life Sciences Data Hub Release 3.1

5.1 Run the Start Maintenance Script 5-1
5.2 Stop Server Processes 5-2
5.3 Back Up the Oracle E-Business Suite Database 5-2
5.4 Upgrade to Oracle Life Sciences Data Hub 3.1 5-2
5.4.1 Database Tier Preinstallation Steps 5-3
5.4.1.1 Abort the Long-Running Jobs 5-3
5.4.1.2 Cancel the Sessions Holding Locks on Application Objects 5-3
5.4.1.3 Disconnect Blocking Sessions 5-3
5.4.2 Provide Required Grants to the APPS Schema 5-4
5.4.3 Apply Oracle LSH Patch 31136807 5-4
5.4.4 Drop Non-edition Public Synonyms (cdrdropnepubsynonym.sql) 5-4
5.4.5 Create Tablespace cdr_data_ts 5-5
5.4.6 Install Oracle LSH 3.1 5-7
5.4.7 Install the CdrRuntime.jar File 5-7
5.4.8 Add clovi.gif to the EBS R12.2 File System 5-8
5.4.9 Create Oracle LSH UI JAR File 5-8
5.4.10 Set Up Resource Capping 5-9
5.4.11 Check Non-Default Service 5-10
5.4.12 Turn off EXE DEBUG 5-10
5.4.13 Run the Upgrade Script to Edition Existing Schemas 5-11
5.4.14 Enable Audit Trail 5-12
5.4.15 Reset Init Parameters 5-12
5.4.16 Execute the cdrretifytable.sql Script 5-12
5.5 Set Profile at the Site-Level 5-13
5.6 Run the Post-Installation Programs 5-13
5.6.1 Log On to Oracle Applications 5-14
5.6.2 Load the Adapter Files 5-14
5.6.3 Run the Post-Installation Concurrent Program 5-15
5.6.4 Grant Security Rights to Seeded Adapters 5-17
5.7 Run the Stop Maintenance Script 5-17

iv
 5.8 Start Server Processes 5-17
5.9 Regenerate the JAR Files 5-18
5.10 Run the Health Check Scripts 5-19
5.11 Migrate Secure File 5-19
5.11.1 Initiate the Secure File Migration 5-19
5.11.2 Monitor the Secure File Migration 5-19
5.11.3 Post Secure File Migration Task 5-20

6 What's Next

7 Change Record

A Architecture Overview
A.1 Client Tier A-1
A.2 Application Tier A-2
A.3 Database Tier A-3
A.4 Adapters to External Systems A-3
A.4.1 Source Data Systems A-4
A.4.2 Data Transformation and Reporting Tools A-5
A.4.3 Visualization Tools A-5
A.4.4 Data Export Tools A-5

v
 Preface

Preface
This preface contains the following sections:
• Documentation accessibility
• Diversity and Inclusion
• Related resources
• Access to Oracle Support

Documentation accessibility
For information about Oracle's commitment to accessibility, visit the Oracle
Accessibility Program website at http://www.oracle.com/pls/topic/lookup?
ctx=acc&id=docacc.

Diversity and Inclusion

Oracle is fully committed to diversity and inclusion. Oracle respects and values having
a diverse workforce that increases thought leadership and innovation. As part of our
initiative to build a more inclusive culture that positively impacts our employees,
customers, and partners, we are working to remove insensitive terms from our
products and documentation. We are also mindful of the necessity to maintain
compatibility with our customers' existing technologies and the need to ensure
continuity of service as Oracle's offerings and industry standards evolve. Because of
these technical constraints, our effort to remove insensitive terms is ongoing and will
take time and external cooperation.

Related resources
All documentation and other supporting materials are available on the Oracle Help
Center.

Access to Oracle Support

Oracle customers that have purchased support have access to electronic support
through My Oracle Support. For information, visit http://www.oracle.com/pls/topic/
lookup?ctx=acc&id=info or visit http://www.oracle.com/pls/topic/lookup?ctx=acc&id=trs
if you are hearing impaired.

vi
1
Before You Begin
If you are upgrading from a previous release, you may only need to check for the most recent
information, assemble the software, and upgrade to 3.0.
This section includes the following topics:
• Check for the Most Recent Information
• Get Your Company ID from Oracle
• Assemble the Software
• Assemble the Documentation

1.1 Check for the Most Recent Information

It is critical that you check that you have the most current information before you begin the
installation process.
• Latest Release Notes. Check for the most recent version of the Release Notes on My
Oracle Support with article ID 2617887.1.
• Known Installation and Configuration Issues. For up-to-date information, see My
Oracle Support article 2617887.1.
• Latest Critical Patch Updates and Technology Stack Updates. Check My Oracle
Support article 180430.1, Oracle Health Sciences Applications Supported Technology
Stack, for the latest quarterly Oracle Critical Patch Update (CPU) certified with Oracle
LSH, and apply it. This patch includes security fixes and should always be up to date.
• Installation Verification. After you have installed Oracle LSH, see My Oracle Support
article 1063225.1, Oracle Life Sciences Data Hub Installation Verification Test (also called
the "smoke test") to verify that all basic features are functioning properly.
• Check the Oracle LSH Product Information Page on My Oracle Support for the latest
information; see article ID 1318219.1

1.2 Get Your Company ID from Oracle

When you install Oracle LSH, you need to enter a parameter value for the company ID. The
company ID serves as part of the primary key for all the Oracle LSH objects you define in this
instance of Oracle LSH. If your company ever merges with another company and your Oracle
LSH data and metadata are merged with the data of another company, the company ID
distinguishes the objects created in each original company and prevents duplicate object
primary keys.
To ensure that you have a unique number relative to other Oracle LSH customers, Oracle
recommends that you use a number assigned to you by Oracle. Company IDs are tracked in
an Oracle bug that is not publicly viewable. Contact Oracle Support or ask your consultant to
reserve a range of ten numbers for your company. You can use these numbers for:

1-1
 Chapter 1
Assemble the Software

• Your company ID. If you have multiple instances of Oracle LSH, Oracle
recommends using a different company ID for each instance.
• The tech type ID of any adapters your company may create.

1.3 Assemble the Software

Use the technology stack product versions mentioned in this document. Even if newer
versions of the technology stack products become available, they may not be
compatible with Oracle LSH.
• Get the Oracle Life Sciences Warehouse 3.1 Media Pack
• Download Software to a Staging Area

1.3.1 Get the Oracle Life Sciences Warehouse 3.1 Media Pack
Oracle LSH, Oracle Health Sciences Data Management Workbench, and their
technology stacks are contained on the Oracle Health Sciences Data Management
Workbench 3.1 media pack for various platforms.
To receive a physical media pack with all the required DVDs, contact Oracle Support.
To expedite your request, you can call Oracle Support directly or open a Service
Request (SR) selecting problem category: Version Update Request.
To download the media pack from eDelivery:
1. Go to Oracle Software Delivery Cloud, http://edelivery.oracle.com, click Sign In,
and log in with your user ID.
2. Select Download Package from the All Categories drop-down list (or leave All
Categories selected). Enter Oracle Health Sciences Data Management
Workbench in the Search field and click Search.
3. Select DLP: Oracle Health Sciences Data Management Workbench 3.1.0.0.0
and click Add to Cart.
4. Click Checkout. You see a list of the selected software:
• Oracle Health Sciences Data Management Workbench 3.1.0.0.0 (Oracle
Standard Terms and Conditions)
• Oracle Life Sciences Data Hub 3.1.0.0.0
• Oracle Health Sciences Data Management Workbench 3.1.0.0.0
5. From the Platform drop-down list, select the appropriate operating system.
6. Click Continue.
7. Review the Terms and Restrictions and select I reviewed and accept the Oracle
License Agreement to continue. (Click Print from the top-right corner of the
screen to print the agreement.) Click Continue. You see a list of zipped files for
the Oracle Life Sciences Data Hub <your operating system> 3.1 release and
Oracle Health Sciences Data Management Workbench <your operating system>
3.1 release:
• Oracle Life Sciences Data Hub 3.1.0
• Oracle Health Sciences Data Management Workbench 3.1.0
• Oracle Thesaurus Management System 5.3.1

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 Chapter 1
Assemble the Software

8. Leave the list of zipped files selected to download the package of Oracle Health Sciences
Data Management Workbench 3.1.0.0.0 files or only select the files you need.
9. Click Download. Then browse to the location where you want to save the Oracle
executable.
10. Double-click the Oracle executable. Leave the default destination or click Browse to
select another one. Click Next. Oracle downloads the zipped files.
11. Move the zipped files to a staging area and unzip them. The full release contains a
software folder for Oracle DMW (p32003082_31000_Generic.zip), Oracle LSH
(p6114439_R12_GENERIC.zip, p27723788_R12_GENERIC.zip,
p31136807_R12_GENERIC.zip, p32078417_R12_GENERIC.zip) and Oracle TMS
(p30717198_53100_Generic.zip).
12. See Download Software to a Staging Area for details on downloading the software.

1.3.2 Download Software to a Staging Area

Creating a staging area is recommended, but not required.
To set up the staging area successfully, create a directory for each disk in the media pack and
then download and expand all the files that comprise a single disk in the media pack to the
same location.
See the spreadsheet on the documentation disk for a list of patches and their location on the
media pack.
To download patches from My Oracle Support, go to https://support.oracle.com.

Note:
See My Oracle Support article 1138053.1, Oracle Life Sciences Data Hub and
Oracle Clinical Development Analytics Known Install and Configuration Issues for
the latest information.

Table 1-1 Software to Download for Oracle LSH and Oracle DMW

Disk or Patch Name Source ID Number

Oracle E-Business Suite Release 12.2 software distribution Media pack 15 disks
Oracle Database 19c for Linux Media Pack V982063-01
Oracle Thesaurus Management System 5.3.1 Media Pack 30717198
Oracle LSH Splicer patch for Applications R12 Media Pack 6114439
Oracle Life Sciences Data Hub 3.1 Media Pack 32078417
Oracle Life Sciences Data Hub online help Media Pack 18551089
Oracle E-Business Suite SDK patch Media Pack 27723788
NOT ABLE TO ADD HTTPS URL TO FAVORITES LINK IN 12.1.2. My Oracle Support 11781531
HTTP IS PRE-PENDED TO URL
FND_NO_DATABASE_CONNECTION My Oracle Support 11832737

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 Chapter 1
Assemble the Documentation

Table 1-1 (Cont.) Software to Download for Oracle LSH and Oracle DMW

Disk or Patch Name Source ID Number

API TO PREVALIDATE EBS USERS for Oracle LSH (This patch is My Oracle Support 19357286
only required if you perform a full install of Oracle LSH 3.0 [not an
upgrade to 3.0 from a previous version].)
FND PRODUCT INSTALLATION IS NOT EXECUTING FOR GHR, My Oracle Support 16263414
OTL, IREC PRODUCTS (This patch is only required if you perform a
full install of Oracle LSH 3.0 [not an upgrade to 3.0 from a previous
version].)
Oracle Database 19c; for a list of patches required, see My Oracle My Oracle Support 2580629.1,
Support article 1058763.1. 2530680.1, and
2617850.1

If you use Oracle Health Sciences Data Management Workbench, download the
following software to a separate application server. For system requirements, see the
Oracle Health Sciences Data Management Workbench Installation Guide.

Table 1-2 Software to Download for Oracle DMW

Disk or Patch Name Source ID Number

Oracle WebLogic Server 12.2.1.4 and Coherence for Linux x86 Media Pack p30188255_122140
_Generic.zip
ADF patch My Oracle Support 32588679
Oracle Health Sciences Data Management Workbench 3.1 Media Pack 32078417

1.4 Assemble the Documentation

Installing Oracle LSH is a complex process because it includes installing, upgrading,
and patching a number of other products. This book guides you through the process,
but refers you to the documentation for other products along the way.
Oracle recommends that you gather all the documentation you will need and read it
before you begin the process of installing Oracle LSH.
• Books
• My Oracle Support Articles

1.4.1 Books
The books you need to install the technology stack are included in the media pack.
You can also find PDF and HTML copies online; see Documentation accessibility.
In addition to this guide, you need:
• Oracle Life Sciences Data Hub System Administrator's Guide Release
• Oracle Thesaurus Management System Installation Guide Release 5.3.1
• Oracle E-Business Suite Upgrade Guide Release 12.0 and 12.1 to 12.2
• Oracle E-Business Suite Release 12.1.1 Documentation Library which includes:

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 Chapter 1
Assemble the Documentation

– Oracle E-Business Suite Maintenance Utilities

– Oracle E-Business Suite Maintenance Procedures
– Oracle E-Business Suite Patching Procedures
– Oracle E-Business Suite System Administrator's Guide - Configuration
– Oracle E-Business Suite System Administrator's Guide - Maintenance
– Oracle E-Business Suite System Administrator's Guide - Security
– Oracle® Applications Upgrade Guide Release 11i to 12.1.1
• Oracle E-Business Suite Installation Guide: Using Rapid Install Release 12
• Oracle Business Intelligence Publisher Installation Guide Release 10.1.3.4
The rest of the Oracle LSH user documentation is also included. However, you should check
Oracle Help Center for the most current versions.

1.4.2 My Oracle Support Articles

The My Oracle Support Web site contains links to the most recent patches and updates for
Oracle products. This section lists all the My Oracle Support articles listed in subsequent
sections of this guide so that you can copy all of them to one place. See Documentation
accessibility.
• System Requirements and Technology
• Upgrading to Oracle Life Sciences Data Hub Release 3.1
• Other Documents Related to Oracle Life Sciences Data Hub

1.4.2.1 System Requirements and Technology

System Requirements and Technology Stack references the following My Oracle Support
articles:
• 180430.1, Oracle Life Sciences Applications Supported Technology Stacks

1.4.2.2 Upgrading to Oracle Life Sciences Data Hub Release 3.1

Upgrading to Oracle Life Sciences Data Hub Release 3.1 references the following My Oracle
Support article:
• 1320300.1, Oracle E-Business Suite Release Notes, Release 12.2
• 1330701.1, Oracle E-Business Suite Installation and Upgrade Notes Release 12 (12.2)
for Linux x86-64 Note
• 2495027.1, Oracle E-Business Suite Release 12.2.9 Readme
• 396009.1, Database Initialization Parameters for Oracle E-Business Suite Release 12
• 1531121.1, Using the Online Patching Readiness Report in Oracle E-Business Suite
Release 12.2
• 1375769.1, Sharing The Application Tier File System in Oracle E-Business Suite Release
12.2
• 1054417.1, Patch 6678700 Worker Fails On Applying MSDODPCODE.sql With
ORA-33292 Insufficient Permissions To Access Analytic Workspace APPS.ODPCODE;
ORA-33262: Analytic workspace ODPCODE does not exist.

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• 1314218.1, ORA-37002: Oracle OLAP failed to initialize while applying patch

6678700
• 2580629.1, Interoperability Notes: Oracle E-Business Suite Release 12.1 with
Oracle Database 19c
• 2530680.1, Using Oracle 19c RAC Multitenant (Single PDB) with Oracle E-
Business Suite Release 12.1 (for an Oracle RAC environment)
• 1333659.1, Applying The Patch 6678700 Worker 1 Failed: File Cskbcat.Ldt.
ERRORS: ORA-20000: Oracle Text error: DRG-50857: oracle error in
textindexmethods.ODCIIndexUpdate, DRG-13201: KOREAN_LEXER is
desupported
• 1281478.1, Script Czhist.Sql Fails During Application Of Patch 6678700
• 1083981.1, Script Pechktsk.Sql fails with, ORA-00979: Not A Group By
Expression when applying Patch 6678700 or Patch 3500000
• 1322144.1, Error - ORA-54015 : biv_b_age_h_sum_mv.xdf Failes with Duplicate
Column Expression was Specified
• 1284055.1, 12.1.1 Upgrade Fails on Fem_bal_nacc_hier_l2_mv.xdf with Oracle
11.2.0.2 Database
• 1106795.1, adapcctl.sh: exiting with status 150

1.4.2.3 Other Documents Related to Oracle Life Sciences Data Hub

The following related documents are available on My Oracle Support. See
Documentation accessibility.
• Oracle Life Science Data Hub (LSH) Summary of Patches Available (1376925.1)
• Oracle Life Sciences Data Hub 2.1.3, 2.1.4, 2.2, 2.2.1, 2.3, 2.3.1 and 2.4
Installation Verification Tests (1063225.1)
• Guide to Using Oracle VM Templates in an Oracle Life Sciences Data Hub 2.2
Installation (1450700.1)
• Oracle Life Sciences Data Hub 2.2 Data Guard Support (1342251.1)
• Oracle Life Sciences Data Hub Release 2.2 Performance Behavior and System
Recommendations (1369871.1)

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2
System Requirements and Technology Stack
If you install Oracle LSH for the first time or upgrade to a new version after December 31,
2010 and are using Oracle Enterprise Manager (OEM) 10.2.0.4 or 10.2.0.5 with Oracle LSH,
apply OEM patch 8350262.
For further information, see My Oracle Support article number 1217493.1.
This section contains the following topics:
• System Requirements
• Technology Stack
• Integrated External Systems

2.1 System Requirements

This section includes some general requirements for your Oracle Life Sciences Data Hub
installation. For requirements on other products you need to install, see the documentation
that came with them.
The general requirements topics include:
• Operating Systems
• Hardware

2.1.1 Operating Systems

To get the most current information on the Oracle LSH technology stack, see My Oracle
Support article 180430.1, Oracle Life Sciences Applications Supported Technology Stacks.
This section includes the folllowing topics:
• Database Tier
• Application Tier
• Clients

2.1.1.1 Database Tier

The Oracle LSH database tier can be installed on the following platforms:
• Linux x86-64 (64-Bit)
– Oracle Enterprise Linux 7.4 or later
– Red Hat Enterprise Linux 7.4 or later
• AIX 7.1 and 7.2 (64-Bit)
• Oracle Solaris 11 on SPARC (64-Bit)

2-1
 Chapter 2
System Requirements

Note:
The database global name cannot be greater than 64 characters.

2.1.1.2 Application Tier

You can install the Oracle LSH application tier on the following platforms:
• Linux x86-64 (64-Bit)
– Oracle Enterprise Linux 6 or later, and 7.4 or later
– Red Hat Enterprise AS/ES 5
– Red Hat Enterprise AS/ES 6
• HP Itanium 11i v3 (11.31) (64-bit)
• AIX 6.1 (64-Bit)
• Oracle Solaris 10 on SPARC (64-Bit)
• Oracle Solaris 11 on SPARC (64-Bit)

2.1.1.3 Clients
Oracle LSH supports the following browsers on Microsoft Windows operating systems:
• Google Chrome Version 89.0.4389.114 (Official Build) (64-bit)
• Mozilla Firefox Quantum Extended Support Release 78.9.0esr (64-bit)
• Mozilla Firefox Version 87.0 (64-bit)
• Microsoft Edge Chromium Version 89.0.774.68 (Official build) (64-bit)
For Oracle JRE, Oracle LSH supports the same versions as Oracle E-Business Suite
12.1.3. To get the latest information:
1. Go to My Oracle Support at https://support.oracle.com and sign in.
2. Click the Certifications tab.
3. In the Search area, enter Oracle E-Business Suite for Product and 12.1.3 for
Release, and click Search.
4. In the Search Results page, expand Management and Development Tools.
5. Check the Oracle JRE versions displayed and click the link to see more.

2.1.2 Hardware
Oracle Applications 12.2.9 and Oracle Database 19c can be installed on the same or
different servers.
In addition, you need one computer running on Windows for use in installing Oracle
Thesaurus Management System (Oracle TMS). You will not need this computer for
Oracle LSH after installing Oracle TMS except to install any Oracle TMS patches that
may be required in the future. You need at least one Windows computer if you plan to
use Oracle Business Intelligence Enterprise Edition to define Business Areas and
create data visualizations (Oracle Business Intelligence Enterprise Edition Answers).

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 Chapter 2
Technology Stack

You can use the same Windows computer for Oracle Business Intelligence Enterprise Edition
and Oracle TMS.

Note:
Oracle LSH does not support a Windows server for SAS.

In an installation where the application and database tiers are installed on different
computers, those computers are typically connected by a local area network (LAN), while the
application-tier computer is connected to clients in a wide area network (WAN).
Using Real Application Clusters (RAC) to install the database over several nodes is optional.
Oracle LSH uses Oracle XML Publisher (which is bundled with Oracle Applications) to
generate PDF-format Report Sets. If you plan to use this feature and if your Report Sets are
very large, you may want to dedicate one node to Oracle XML Publisher processing.
For system hardware requirements see the documentation for each component; see
Assemble the Documentation.
In addition:
• The TCP/IP network connection to the server should be at least at 1 GB.
• Be sure to allow for growth in database storage capacity.
• Oracle recommends installing a test environment as similar as possible to the production
environment, including all operating system and other patches and updates.

2.2 Technology Stack

To get the most current information on the Oracle LSH technology stack, see My Oracle
Support article 180430.1. At the time of publication of this document, the required technology
stack for Oracle LSH consists of the following products:
• Oracle Applications 12.2.9

Note:
Oracle Life Sciences Data Hub has been tested ONLY on Release 12.2.9 of
Oracle Applications. Do not install more recent releases unless explicitly
instructed to do so by an Oracle Life Sciences Data Hub note or alert on
My Oracle Support.

• Java Development Kit (JDK) 1.8.0_211 is required for the Oracle LSH Distributed
Processing Server.
• Oracle Database 19c
• XML DB, which is included with the 19c database, is required for Oracle LSH.
• Oracle Thesaurus Management System 5.3.1 Database Tier is used internally for the
Oracle LSH classification system.

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 Chapter 2
Integrated External Systems

• A zip utility and Java Development Kit (JDK) 1.8.0_211 are required for the
Oracle LSH Distributed Processing Server.
• WinZip or 7-Zip is required on clients used by Oracle LSH developers who launch
integrated development environments (IDEs) such as SAS or the Oracle BI
Administration Tool on their PC. Neither of these utilities is included on the media
pack.
For WinZip, use Pro 11.2 SR-1, WinZip 8.1, or any other WinZip version that
includes WZUNZIP.exe.

2.3 Integrated External Systems

Oracle LSH includes adapters to support integration with the following external
systems.
• Oracle Clinical 5.2.1 and 5.2.2
• SAS 9.1.3, SAS 9.2, SAS 9.3, and SAS 9.4: Optional and licensed separately.
• Oracle Business Intelligence Enterprise Edition (OBIEE) 12.2.1.4 can be used to
create OBIEE visualizations of Oracle LSH data. Optional and licensed separately.
The OBIEE Presentation Server, OBIEE Server, and the OBIEE Administrator's
Tool are required if you are using Oracle Business Intelligence Enterprise Edition.
The latter two run on Windows only.

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The Two Supported Upgrade Paths
For upgrading to Oracle LSH release 3.1, the following are the two supported upgrade paths:
• If you are upgrading from a release prior to Oracle LSH release 3.0:
1. Upgrade to Oracle LSH release 3.0 for both the technology stack and the Oracle LSH
product. Follow instructions in the Oracle Life Sciences Data Hub Installation Guide
Release 3.0.
2. Upgrade E-Business Suite. Follow instructions in Upgrading E-Business Suite from
12.1.3 to 12.2.9.
3. Upgrade to Oracle LSH release 3.1. Follow instructions in Upgrading to Oracle Life
Sciences Data Hub Release 3.1.
• If you are upgrading from Oracle LSH release 3.0:
1. Upgrade E-Business Suite. Follow instructions in Upgrading E-Business Suite from
12.1.3 to 12.2.9.
2. Upgrade to Oracle LSH release 3.1. Follow instructions in Upgrading to Oracle Life
Sciences Data Hub Release 3.1.

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4
Upgrading E-Business Suite from 12.1.3 to
12.2.9
This section includes the following topics:
• Upgrade E-Business Suite from 12.1.3 to 12.2.9
• Apply the Database Patches
• Apply the Additional EBS Patches
• Revert Database Init Parameters and Grant Access to APPS

4.1 Upgrade E-Business Suite from 12.1.3 to 12.2.9

For instruction on how to upgrade E-Business Suite (EBS) from release 12.1.3 to 12.2.9, see
Oracle E-Business Suite Upgrade Guide Release 12.0 and 12.1 to 12.2.

Note:
While following the instructions in the Oracle E-Business Suite Upgrade Guide, the
following are a few exceptions you must perform as these are required specifically
for Oracle DMW and Oracle LSH.

• Instead of instructions in chapter 4 Performing the Upgrade > section "Performing the
Upgrade to Release 12.2.0" > step 1 "Disable AOL Audit Trail (conditional)", perform the
following steps to back up the Oracle DMW and Oracle LSH audit tables and clean up the
audit tables to prepare for the upgrade:
1. Connect to the database as SYSDBA.
2. Execute the following query to determine the space required by audit tables:

select segment_name,segment_type,bytes/1024/1024/1024 GB
from dba_segments
where segment_type='TABLE' and segment_name IN
('CDR_BA_DB_PRIVILEGES_A',
'CDR_CONNECTIONS_A',
'CDR_NAMINGS_A',
'CDR_NAMING_VERSIONS_A',
'CDR_OBJECT_SUBTYPES_B_A',
'CDR_OBJECT_SUBTYPES_TL_A',
'CDR_OBJ_CLA_MAPPINGS_A',
'CDR_OBJ_UG_A',
'CDR_OUTPUTS_A',
'CDR_REMOTE_LOCATIONS_A',
'CDR_ROLES_B_A',
'CDR_ROLES_TL_A',

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'CDR_SECURITY_DBACCOUNT_A',
'CDR_SOURCE_CODES_A',
'CDR_SUBTYPE_OPR_ROLES_A',
'CDR_TABLE_REFS_A',
'CDR_TABLE_REF_JOBS_A',
'CDR_UG_ROLES_A',
'CDR_USER_GROUPS_B_A',
'CDR_USER_GROUPS_TL_A',
'CDR_USER_UG_ROLES_A',
'DME_FLAG_DATA_A');

3. Execute the following query to determine the total space (in GB) required in
the APPS_TS_TX_DATA tablespace to back up all the audit tables:

select sum(GB) from (select segment_name,segment_type,bytes/

1024/1024/1024 GB
from dba_segments
where segment_type='TABLE' and segment_name IN
('CDR_BA_DB_PRIVILEGES_A',
'CDR_CONNECTIONS_A',
'CDR_NAMINGS_A',
'CDR_NAMING_VERSIONS_A',
'CDR_OBJECT_SUBTYPES_B_A',
'CDR_OBJECT_SUBTYPES_TL_A',
'CDR_OBJ_CLA_MAPPINGS_A',
'CDR_OBJ_UG_A',
'CDR_OUTPUTS_A',
'CDR_REMOTE_LOCATIONS_A',
'CDR_ROLES_B_A',
'CDR_ROLES_TL_A',
'CDR_SECURITY_DBACCOUNT_A',
'CDR_SOURCE_CODES_A',
'CDR_SUBTYPE_OPR_ROLES_A',
'CDR_TABLE_REFS_A',
'CDR_TABLE_REF_JOBS_A',
'CDR_UG_ROLES_A',
'CDR_USER_GROUPS_B_A',
'CDR_USER_GROUPS_TL_A',
'CDR_USER_UG_ROLES_A',
'DME_FLAG_DATA_A')
) t ;

4. Allocate the required space (in GB) from the pervious step to the
APPS_TS_TX_DATA tablespace.
5. Download Oracle LSH 3.1 patch p32078417_R12_GENERIC.zip.
6. Unzip patch p32078417_R12_GENERIC.zip (DO NOT APPLY PATCH).
7. Go to PATCH_Folder/32078417/cdr/patch/115/sql.
8. Log in to SQL*Plus as the APPS user.
9. Execute the script cdr31ugppreauditscript.sql to back up the tables.
10. Set the audit groups (LSH_Audit and DMW_AUDIT) status to "Disable-Purge
Table".

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11. Run the Audit Table Update Request program. This will drop all triggers/views and
data from _A tables.
12. Go to PATCH_Folder/32078417/cdr/patch/115/sql.

13. Log in to SQL*Plus as the APPS user.

14. Execute the script cdr31ugppostauditscript.sql to drop the audit (_A) tables
and the corresponding synonyms.
15. Connect as APPS user and back up the CDR_REMOTE_LOCATIONS table data:
Create table CDR.CDR_REMOTE_LOCATIONS_BK31 as select * from
CDR.CDR_REMOTE_LOCATIONS;
• Before you disable the custom triggers in chapter 4 Performing the Upgrade > section
"Performing the Upgrade to Release 12.2.0" > step 5 Disable custom triggers,
constraints, indexes, business events, and VPD (conditional), drop the trigger
"OWBSYS.CDR_RTREPOS_TG". Then, execute the following command to find the
custom triggers that you must disable:
select trigger_name from dba_triggers where trigger_name like
'%CDR%';
Follow the remaining instructions in step 5 Disable custom triggers, constraints, indexes,
business events, and VPD (conditional).
• Instead of instructions in chapter 4 Performing the Upgrade > section "Database and
System Administration Tasks" > step 3 "Gather schema statistics (required)", perform the
instructions in Gathering Schema Statistics for DMW and LSH (Doc ID 2220975.1). For
all other EBS schemas, execute the following command:

Note:
To save some upgrade time, perform this task at least 1 or 2 weeks before
upgrading to Oracle LSH release 3.1.

FND_STATS.GATHER_SCHEMA_STATISTICS (<schema name>, <estimate

percent>, <degree of parallelism>, <backup flag>, <restart request
ID, if applicable>, <history mode>, <gather options>,
<modificationsthreshold>, <invalidate dependent cursors>);
For example: FND_STATS.GATHER_SCHEMA_STATISTICS('AK', 10, 8,
'NOBACKUP', NULL, 'LASTRUN', 'GATHER AUTO', 10, 'N');
You can get the schema details by executing the following query:

set lines 1000

set pages 1000
select 'FND_STATS.GATHER_SCHEMA_STATISTICS('''|| ORACLE_USERNAME ||''',
10, 8, ''NOBACKUP'', NULL, ''LASTRUN'', ''GATHER AUTO'', 10, ''N'')'
prep_statement
from fnd_oracle_userid where ORACLE_USERNAME not in
('APPS','CDR','APPLSYS');
;

• In chapter 4 Performing the Upgrade > section "Performing the Upgrade to Release
12.2.0" > step 13 "Apply AD 12.2 upgrade driver (required)", if any error occurs while

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Apply the Database Patches

applying the patch 10117518 as a prerequisite to run the adgrants.sql, see R12 E-
Business Suite On Oracle Cloud Administration Error "ORA-20000: ORA-01917:
user or role 'APPS' does not exist"When Running Adgrants.sql Against A Cloud
Multi Tenant Database (Doc ID 2447786.1).
• In chapter 4 Performing the Upgrade > section "Performing the Upgrade to
Release 12.2.0" > step 3 "Update init.ora with upgrade parameters (required)",
along with the instructions in See Database Initialization Parameters for Oracle
Applications Release 12.2 (Doc ID: 396009.1), execute the following query to
update the "container_data" parameter (in both CDB and PDB) and revoke the
administer database trigger:

alter system set audit_trail=NONE scope=spfile

Revoke ADMINISTER DATABASE TRIGGER from APPS ;
alter system set container_data=ALL scope=spfile;

After the EBS upgrade is complete, you must revert all the changes done in the
above query. For instruction on how to rever the changes, see Revert Database
Init Parameters and Grant Access to APPS.
• In chapter 4 Performing the Upgrade > section "Enabling Online Patching", while
reviewing the output of the script ADZDPSUM.sql, do not register any custom
schemas using the script ADZDREG.sql.
• Instead of instructions in chapter 4 Performing the Upgrade > section "Upgrading
to the Latest Code Level" > sub-section "Apply the Latest AD and TXK for Release
12.2" > step 3.1 "Running adsplice", apply the AD Splicer patch for Oracle LSH,
patch number 6114439, which is in the Oracle LSH media pack. For more
information, see Oracle Life Sciences Data Hub Installation Guide Release 3.0.
• Instead of instructions in chapter 4 Performing the Upgrade > section "Upgrading
to the Latest Code Level" > sub-section "Apply the Latest Oracle E-Business Suite
Release Update Pack for Release 12.2", perform instructions in Oracle E-Business
Suite Release 12.2.9 Readme (Doc ID 2495027.1) on My Oracle Support >
section "Section 8: Apply Oracle E-Business Suite 12.2.9 Release Update Pack" >
sub-section "8.1 Path A — Upgrade and New Installation Customers upgrading to
Oracle E-Business Suite 12.2.9 Release Update Pack"
After performing the instructions in sub-section "8.1 Path A — Upgrade and New
Installation Customers upgrading to Oracle E-Business Suite 12.2.9 Release
Update Pack", see Oracle E-Business Suite Upgrade Guide Release 12.0 and
12.1 to 12.2 > chapter 5 "Performing Post-Upgrade Tasks" > perform instructions
in sections "Database and System Administration TasksDatabase and System
Administration Tasks" through "Oracle XML Publisher Tasks". After that, instead of
performing the post-upgrade steps in chapter 5 "Performing Post-Upgrade Tasks",
perform instructions in Oracle E-Business Suite Release 12.2.9 Readme (Doc ID
2495027.1) on My Oracle Support > section "Section 9: Post-Update Steps".

4.2 Apply the Database Patches

1. Apply the database patch p31463613_1910000DBRU_Linux-x86-64.zip.
2. Apply the database patch p30808109_1910000DBRU_Linux-x86-64.zip.

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4.3 Apply the Additional EBS Patches

Apply the additional EBS patches using ADOP, if not already applied.

• Apply 31959538:R12.TXK.C, 31943873:R12.FWK.C, and 27222751:R12.FND.C

patches by executing the following command:

adop phase=prepare
adop phase=apply patches=31959538:R12.TXK.C, 31943873:R12.FWK.C,
27222751:R12.FND.C
adop phase=actualize_all
adop phase=finalize finalize_mode=full
adop phase=cutover
adop phase=cleanup cleanup_mode=full

4.4 Revert Database Init Parameters and Grant Access to APPS

Execute the following commands:

alter system set audit_trail=<orginal_value> scope=spfile;

Grant ADMINISTER DATABASE TRIGGER to APPS ;
alter system set container_data=<orginal_value> scope=spfile;

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Upgrading to Oracle Life Sciences Data Hub
Release 3.1
This section includes the following topics:
• Run the Start Maintenance Script
• Stop Server Processes
• Back Up the Oracle E-Business Suite Database
• Upgrade to Oracle Life Sciences Data Hub 3.1
• Set Profile at the Site-Level
• Run the Post-Installation Programs
• Run the Stop Maintenance Script
• Start Server Processes
• Regenerate the JAR Files
• Run the Health Check Scripts
• Migrate Secure File

5.1 Run the Start Maintenance Script

Before you upgrade any of the software, follow the steps in this procedure to start the
maintenance activity.
To run the Start Maintenace script:
1. Download or copy the maintenance start script file from the Oracle LSH application
server (EBS Middle Tier server) $CDR_TOP/patch/115/sql/cdrmaintstart.sql to
the database server’s ORACLE_HOME location or any other preferred location.
2. From the database server, log in to SQL*Plus (not SQL Developer) as the APPS
database user.
3. Enter this command to stop the study health monitor scheduler:
SQL> EXECUTE DBMS_SCHEDULER.DISABLE('STUDY_HEALTH_REFRESH', FORCE
=> TRUE);
4. Enter this command to execute the script:
SQL> @cdrmaintstart.sql
5. Check the log file.
The log file validates the success of the Start Maintenance process and provides a
maintenance ID. For example, it lists messages to show what it found up and running and
what it stopped (such as the message queue and job queue).

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5.2 Stop Server Processes

This step is required for all upgrade paths.
Before you begin the upgrade, stop the following servers:
• Oracle LSH Distributed Processing (DP) Server
• Application Server

5.3 Back Up the Oracle E-Business Suite Database

Oracle recommends that you make a cold backup of the Oracle E-Business Suite
database in case you encounter problems during the upgrade process. You can use
the backup to restore the database (if necessary).

Note:
Shut down the database using the NORMAL option to ensure you can use
the backup to restore the database. Do not use the IMMEDIATE or ABORT
option to shut down the database.

5.4 Upgrade to Oracle Life Sciences Data Hub 3.1

These steps are required for all upgrade paths.
• Database Tier Preinstallation Steps
• Provide Required Grants to the APPS Schema
• Apply Oracle LSH Patch 31136807
• Drop Non-edition Public Synonyms (cdrdropnepubsynonym.sql)
• Create Tablespace cdr_data_ts
• Install Oracle LSH 3.1
• Install the CdrRuntime.jar File
• Add clovi.gif to the EBS R12.2 File System
• Create Oracle LSH UI JAR File
• Set Up Resource Capping
• Check Non-Default Service
• Turn off EXE DEBUG
• Run the Upgrade Script to Edition Existing Schemas
• Enable Audit Trail
• Reset Init Parameters
• Execute the cdrretifytable.sql Script

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5.4.1 Database Tier Preinstallation Steps

This section contains the following topics:
• Abort the Long-Running Jobs
• Cancel the Sessions Holding Locks on Application Objects
• Disconnect Blocking Sessions

5.4.1.1 Abort the Long-Running Jobs

1. Log in to SQL*Plus as apps.
2. Run the following query to find the long running jobs:

select * from cdr_jobs where job_status_rc like '%EXECUTING%';

3. Log in to the Oracle LSH application.

4. Navigate to Life Sciences Data Hub > Job Execution.
5. Search for the job using the job ID and cancel it.

5.4.1.2 Cancel the Sessions Holding Locks on Application Objects

1. Run the following query:

SELECT 'alter system kill session'||''''||sid||','||serial#||''''||'

immediate;'from v$session where sid in ( select session_id FROM
sys.dba_ddl_locks
WHERE (name like 'CDR_%' or name like 'DME_%') );

2. Run the alter statement to cancel the active sessions.

5.4.1.3 Disconnect Blocking Sessions

Before you upgrade, check for and stop any current database sessions.
1. If WebLogic Server is running, stop it. See Oracle® Fusion Middleware Administering
Server Startup and Shutdown for Oracle WebLogic Server (12.2.1.3) at https://
docs.oracle.com/middleware/12213/wls/START/.
Log files for the AdminServer and the DMWServer are located in:

middleware_home/user_projects/domains/DMWDomain/servers/AdminServer/logs

and

middleware_home/user_projects/domains/DMWDomain/servers/DMWServer/logs

2. Log in to SQL*Plus as apps.

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3. Run the following query to find current sessions:

SELECT 'USER: '||s.username||' SID: '||s.sid||' SERIAL #: '||

S.SERIAL# "USER
HOLDING LOCK", s.inst_id
FROM gv$lock l
,dba_objects o
,gv$session s
WHERE l.id1 = o.object_id
AND s.sid = l.sid
AND o.owner = 'CDR'
AND o.object_name = 'DME_DISC_WORKTABLIST';

This query returns the user, SID, serial number, and instance ID of each current
session.
4. Disconnect each current session, passing in the SID and serial number:

alter system disconnect session 'SID, serial_number' IMMEDIATE

5.4.2 Provide Required Grants to the APPS Schema

• Connect to the PDB as sys user and execute the following commands:

grant execute any procedure to apps with admin option;

grant select any dictionary to apps;

grant ADMINISTER DATABASE TRIGGER to APPS;

5.4.3 Apply Oracle LSH Patch 31136807

• Apply patch 31136807 using ADOP, with options=forceapply.

5.4.4 Drop Non-edition Public Synonyms (cdrdropnepubsynonym.sql)

1. Download Oracle LSH 3.1 Patch p32078417_R12_GENERIC.zip.
2. Unzip patch p32078417_R12_GENERIC.zip (DO NOT APPLY PATCH).
3. Go to PATCH_Folder/32078417/cdr/patch/115/sql.
4. Connect to the database as APPS user and run the
cdrdropnepubsynonym.sql script.
5. In the promt, enter Y.

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6. To verify whether or not the script has completed, run the following query to make sure
there are no rows returned:

SELECT owner, object_name, object_type

FROM all_objects
WHERE owner = 'PUBLIC'
and (upper(object_name) like 'CDR_%' or upper(object_name) like
'DME_%')
and OBJECT_TYPE= 'SYNONYM'
and edition_name is null;

7. Check the log file for any errors, and save it for future references. If you need help to fix
any error, contact Health Sciences Support.

5.4.5 Create Tablespace cdr_data_ts

Create a separate tablespace cdr_data_ts for the LOB storage. You must calculate an
estimated size of the old implementation of the LOB basic file and allocate 25% more
tablespace size for the tablespace cdr_data_ts. This tablespace will store the migrated
secure file implementation.
1. Connect to Oracle DMW PDB as SYS or SYSTEM user.
2. Calculate the approximate size of the existing LOB by executing the following SQL
statement.

WITH lobs AS (
SELECT /*+ materialize cardinality(2) */
*
FROM
(
SELECT
owner,
segment_name
FROM
dba_lobs
WHERE
table_name = 'CDR_JOB_LOG'
UNION
SELECT
owner,
index_name segment_name
FROM
dba_lobs
WHERE
table_name = 'CDR_JOB_LOG'
)
)
SELECT
round(SUM(bytes) / 1024 / 1024) AS size_mb,
round(SUM(bytes) / 1024 / 1024/1024) AS size_gb,
round(SUM(bytes) / 1024 / 1024 / 1024 / 1024, 2) AS size_tb
FROM
dba_segments
WHERE

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( owner,
segment_name ) IN (
SELECT
*
FROM
lobs
);

The SQL provides output in MB, GB, and TB.

3. Calculate the number of datafiles.
Number of required datafiles = Estimated size from step 1 (note the number from
SIZE_GB) x 1.25 (25% over allocation) / OS max file size limit
For example, if the estimated size from step 1 is 875GB and the max file size limit
is 30GB, then:
Number of required datafiles = 875 x 1.25 / 30 = 36.45
Round this calculated decimal number to 37.
4. Make sure there is enough space available in the ASM disk group. In case you do
not use the ASM disk group, make sure there is enough disk space available at
the operating system directory where the datafiles will be created.
5. Create the tablespace cdr_data_ts by executing the following command:

CREATE TABLESPACE cdr_data_ts DATAFILE

'fully qualified datafile name' SIZE 500M
AUTOEXTEND ON NEXT 100M MAXSIZE max size limit of the file,
typically 30G on Linux OS
EXTENT MANAGEMENT LOCAL UNIFORM SIZE 100M SEGMENT SPACE
MANAGEMENT AUTO;

For example, assuming 30GB operating system file size limit using ASM storage
"+DATA":

CREATE TABLESPACE cdr_data_ts DATAFILE '+DATA' SIZE 500M

AUTOEXTEND ON NEXT 100M MAXSIZE 30G
EXTENT MANAGEMENT LOCAL UNIFORM SIZE 100M SEGMENT SPACE
MANAGEMENT AUTO;

6. Add the datafiles, as required by executing the following command:

ALTER TABLESPACE cdr_data_ts ADD DATAFILE 'fully qualified datafile
name' SIZE 500M AUTOEXTEND ON NEXT 100M MAXSIZE max size limit of the
file, typically 30G on Linux OS;
For example, assuming 30GB operating system file size limit using ASM storage
"+DATA":

ALTER TABLESPACE cdr_data_ts ADD DATAFILE '+DATA' SIZE 500M

AUTOEXTEND ON NEXT 100M MAXSIZE 30G;

7. Assign a quota for the tablespace cdr_data_ts to the user CDR and optionally to
APPS.

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ALTER USER CDR QUOTA UNLIMITED ON cdr_data_ts;

ALTER USER APPS QUOTA UNLIMITED ON cdr_data_ts;

5.4.6 Install Oracle LSH 3.1

Note:
You do not need to install the Oracle LSH online Help or create the system
administrator when upgrading Oracle LSH. You only need to complete those tasks
for a full installation.

You must install the Oracle LSH 3.1 as a patch to Oracle Applications using ADOP. The
patch, number 32078417, is on the media pack.
1. Unzip the patch to $NE_BASE/EBSapps/patch.
2. Run ADOP patch. See instructions to install patch using adop. for details.

5.4.7 Install the CdrRuntime.jar File

1. On the Oracle LSH server, navigate to the $CDR_TOP/jar folder. It contains the
CdrRuntime.zip file.
2. Copy the CdrRuntime.zip file to the Oracle Database server in any temporary location.
Then enter this command to unzip the file and extract CdrRuntime.jar:
unzip CdrRuntime.zip
3. Run these commands to load the java files to the database. First this command:
dropjava -force -thin -user apps/apps@"(DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)
(HOST=<DB hostname>)(PORT=<DB port number>))(CONNECT_DATA=(SERVICE_NAME=<DB
service name>)))" CdrRuntime.jar
Then this command:
loadjava -force -thin -user apps/apps@"(DESCRIPTION=(ADDRESS=(PROTOCOL=tcp)
(HOST=<DB host name>)(PORT=<DB port number>))(CONNECT_DATA=(SERVICE_NAME=<DB
service name>)))" CdrRuntime.jar
4. Run this query to return a set of alter java commands that should be run to compile
invalid classes:
SELECT
'alter java class "'
|| object_name
|| '" compile;'
FROM
dba_objects
WHERE
object_type = 'JAVA CLASS'
and object_name LIKE '%cdr%'

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AND status = 'INVALID';

5. Connect to the database as APPS and run the statements returned by the able
query.
6. Rerun the query and confirm that it does not return any rows.

Note:
If the query returns rows, execute the statements returned again. Repeat
this process until the SQL does not return any rows.

5.4.8 Add clovi.gif to the EBS R12.2 File System

1. Source the PATCH file system environment file.
2. Perform the following:
a. Copy clovi.gif from $CDR_TOP/media to $RUN_BASE/FMW_Home/
Oracle_EBS-app1/applications/oacore/html/cabo/images/
cache.
b. Copy clovi.gif from $CDR_TOP/media to $PATCH_BASE/FMW_Home/
Oracle_EBS-app1/applications/oacore/html/cabo/images/
cache.
3. Re-source the environment file, as required.

5.4.9 Create Oracle LSH UI JAR File

1. Create a directory $FND_TOP/admin/template/custom.
2. Copy the existing $FND_TOP/admin/template/
ebsProductManifest_xml.tmp to $FND_TOP/admin/template/custom.
3. Modify $FND_TOP/admin/template/custom/
ebsProductManifest_xml.tmp to add the following additional <classpath>
entry after the <classpath> section for the customall.jar file. This should be
after </classpath> and before the line </classpath-contents>.

<classpath>
<absolute-path>%s_current_base%/EBSapps/comn/java/classes/
oracle/apps/cdr/jar</absolute-path>
<relative-path>../../../../java/classes/oracle/apps/cdr/jar</
relative-path>
<windows-path>@BEA_HOME@/../EBSapps/comn/java/classes/oracle/
apps/cdr/jar</windows-path>
<libraries>
<library>cdrlshall.jar</library>
</libraries>
</classpath>

Replace EBSapps with your corresponding directory name if it is different.

4. Run AutoConfig.

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5. Bounce the application tier services.

Note:
These changes must be redone if ebsProductManifest_xml.tmp is
patched in future.

6. In order to to synchronize the changes (during the next prepare phase) between both the
file systems fs1 and fs2, back up the file <APPL_TOP_NE>/ad/custom/adop_sync.drv.
7. Add the following lines (after replacing EBSapps with your correct directory name) to the
original file just before the line "#End Customization".

# For LSH 3.1 : BEGIN

cp -R %s_current_base%/EBSapps/comn/java/classes/oracle/apps/cdr
%s_other_base%/EBSapps/comn/java/classes/oracle/apps
cp %s_current_base%/EBSapps/comn/java/classes/oracle/apps/cdr/jar/
cdrlshall.jar %s_other_base%/EBSapps/comn/java/classes/oracle/apps/cdr/jar
cp %s_current_base%/EBSapps/appl/fnd/12.0.0/admin/template/custom/
ebsProductManifest_xml.tmp %s_other_base%/EBSapps/appl/fnd/12.0.0/admin/
template/custom
# For LSH 3.1 : END

8. After the changes are synchronized, make sure you run Autoconfig for the latest template
changes to take effect.

5.4.10 Set Up Resource Capping

Resource capping of Oracle DMW and Oracle LSH jobs is required to ensure that you have
enough resources available for the UI activity especially when jobs demand a high CPU time.
If you do not set up the resource capping, the UI operations may suffer due to the CPU queue
length and resource crunch. The system routes the data processing jobs to a database
service specifically defined for that purpose. A resource plan which limits the CPU usage of
these jobs to 75% is applied on the sessions that connect to this service.
1. Log on to the database as SYS user.
2. Create a database service. Perform one of the following:
• For a non-RAC standalone database, run the following command. This service will be
used for executing the data processing jobs (for example, XFM , Oracle InForm and
so on).

begin
dbms_service.create_service('service_name','service_name');
end;
/
begin
dbms_service.start_service('service_name');
end;
/

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• For a RAC database, run the following command:

srvctl add service -d CDB NAME -s service_name -pdb PDB NAME -

preferred CDB Instance1,CDB Instance2
srvctl start service -db CDB NAME -service service_name

For example:

srvctl add service -d dmw3dvc -s service_name -pdb dmw3dv -

preferred dmw3dvc1,dmw3dvc2
srvctl start service -db dmw3dvc -service service_name

3. Navigate to $CDR_TOP/patch/115/sql.
4. Execute the script dmwRMSetup.sql.
The script prompts for the database service created for the data processing jobs.
5. Enter the service_name you have created.
The script prompts for the Oracle DMW PDB name.
6. Enter the Oracle DMW PDB name.
7. Type Y, and press Enter.
The script creates a resource limit plan for the data processing jobs.

5.4.11 Check Non-Default Service

1. Log in to Oracle Database 19c as sysdba user.
2. Execute this query to find all the service names with LONG:

select NAME, NETWORK_NAME, CON_NAME, CLB_GOAL

from gv$active_services
where CLB_GOAL='LONG';

3. Check that the non-default service name is not the same as the pdb / cdb name or
any sys service name.

5.4.12 Turn off EXE DEBUG

1. Log in to Oracle Database 19c.
2. Enter:

SQL> select FND_PROFILE.VALUE_SPECIFIC('LSH:ENABLE_DEBUGGING') from

dual;
FND_PROFILE.VALUE_SPECIFIC('LSH:ENABLE_DEBUGGING')

--------------------------------------------------------------------
------------
$YESNO$NO
SQL> select FND_PROFILE.VALUE_SPECIFIC('DMW:USER_DEBUGGING') from
dual;
FND_PROFILE.VALUE_SPECIFIC('DMW:USER_DEBUGGING')

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Upgrade to Oracle Life Sciences Data Hub 3.1

Note:
After you install Oracle DMW, you sign in and navigate to the Administration
page and click the Tracing & Logging tab to see that you disabled logging and
tracing in Active Sessions.

5.4.13 Run the Upgrade Script to Edition Existing Schemas

Run the dmeupg31runprgs.sql script to ensure that all the applicable Oracle DMW and
Oracle LSH schemas get editioned which were created in an earlier version of Oracle DMW
and Oracle LSH. You must plan a maintenance window to run the script.

Note:
Run this script only if you want to upgrade from Oracle DMW or Oracle LSH release
3.0 to release 3.1. For any other upgrade path, do not run this script.

This script generates a log file. For example, dmeupg31runprgs<YYYYMMDDHHMISS>.LST.

The script displays the output on the console and also writes in the log file.
Enable the Oracle DMW Maintenance Mode and perform the following steps to run the script
on a computer with an Oracle client that can connect to the Oracle DMW database server
using SQLPlus:
1. Before you run the dmeupg31runprgs.sql script, you must remove the obsolete editions
by executing the following commands:

adop phase=prepare
adop phase=actualize_all
adop phase=finalize finalize_mode=full
adop phase=cutover
adop phase=cleanup cleanup_mode=full

2. Download the dmeupg31runprgs.sql script file from $CDR_TOP/patch/115/sql/.

3. Log on to SQLPlus (not SQLDeveloper) as the APPS database user.
4. Invoke the script from your download directory. For example,
<download_directory>/ dmeupg31runprgs.sql.
This script submits the job DMEUPG31$EDITIONSCHS. To track the status of this job,
execute the following query:
SELECT * FROM DBA_SCHEDULER_JOBS WHERE JOB_NAME =
'DMEUPG31$EDITIONSCHS';

You can also monitor the job while it is executing:

SELECT * FROM DBA_SCHEDULER_RUNNING_JOBS WHERE JOB_NAME =
'DMEUPG31$EDITIONSCHS';

After the job execution completes, check the status of the job:

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Upgrade to Oracle Life Sciences Data Hub 3.1

SELECT * FROM DBA_SCHEDULER_JOB_RUN_DETAILS WHERE JOB_NAME =

'DMEUPG31$EDITIONSCHS';

The scripts displays the number of schemas to get editioned. If this number is high, job
execution may take more time to complete.
You can monitor the processed and remaining schemas using the below query
anytime in addition to the above queries:

Select Decode(Success_Flag, 'Y', 'processed_schema_Count', 'F',

'failed_schema_Count', 'remaining_schema_count') as status,
Count(*) as num_schemas
From DME_UPG31_SCH_TAB
Group By Success_Flag;

Note:
If you resubmit the script while the above job is already running, the script
will abort.

5.4.14 Enable Audit Trail

The system administrator must enable the audit trail.
1. Navigate to Security > Audit Trail > Groups.
2. Set the status of the audit groups (LSH_AUDIT and DMW_AUDIT) to Enable
Requested.
3. Run the Audit Table Update Request program.

5.4.15 Reset Init Parameters

• Execute the following command:
alter system set container_data=CURRENT_DICTIONARY
scope=spfile; alter system set audit_trail=DB scope=spfile

5.4.16 Execute the cdrretifytable.sql Script

If you are upgrading from Oracle LSH release 2.2.x or 2.4.9.x to release 3.1, you must
execute the cdrretifytable.sql script. However, if you have already executed
this script earlier successfully in release 2.4.9.x, you need not execute this script
again.
For executable objects like programs and data marts, the script validates that the
BLINDING_UPGRADABLE_RC attribute is set correctly for the LSH 2.2.x tables. If the
attribute is set incorrectly, the script updates it to use the correct value. In addition, if
the BLINDING_UPGRADABLE_RC attribute is set incorrectly, the script re-installs text
Load Sets and their target tables.
1. Log on to the application tier.
2. Source the environment file.

5-12
 Chapter 5
Set Profile at the Site-Level

3. Navigate to the $CDR_TOP/patch/115/sql directory.

4. Log in to SQL*Plus as the APPS user.
5. Execute the script cdrretifytable.sql.
This script validates whether or not the Oracle LSH 2.2.x or 2.4.9.x tables are compatible
with Oracle LSH 3.1. This script also submits the job "CDR_UPGRADEFROM22".
6. To track the job status, execute the following query:
select job_name,state from DBA_SCHEDULER_JOBS where
job_name='CDR_UPGRADEFROM22';
7. To monitor the job while it is executing, execute the following query:
SELECT job_name,session_id,running_instance FROM
DBA_SCHEDULER_RUNNING_JOBS WHERE JOB_NAME = 'CDR_UPGRADEFROM22';
8. To check the script execution status after the scheduler job is completed, execute the
following query:
select job_name,status,error#,additional_info from
dba_scheduler_job_run_details where job_name='CDR_UPGRADEFROM22';
9. After the script execution is completed, extract the output from the CDR_EXE_DEBUG
table by executing the following query:
select logentry from cdr_exe_debug where location='UPGRADEFROM22'
order by seq;

5.5 Set Profile at the Site-Level

Set the Manual Password Reset Enabled profile to Yes at the site-level.
1. Log on to Oracle E-Business Suite as sysadmin user.
2. Expand the System Administrator folder in the left panel.
3. Expand Profile, and select System.
The Find System Profile Values window appears.
4. In the Profile field, enter Manual Password Reset Enabled.
5. Click Find.
The system returns you to the System Profile Values window with Manual Password
Reset Enabled displayed in the Profile Option Name column.
6. Select Yes as the value at the site-level.
7. Click Save.

5.6 Run the Post-Installation Programs

You must run the Oracle LSH LOB Loader and post-installation concurrent programs.

5-13
 Chapter 5
Run the Post-Installation Programs

Note:
If you are using RAC, shut down all but one database node before running
the post-installation programs. If you leave more than one node up, the jobs
may run successfully but you may get errors.

• Log On to Oracle Applications

• Load the Adapter Files
• Run the Post-Installation Concurrent Program
• Grant Security Rights to Seeded Adapters

5.6.1 Log On to Oracle Applications

To run the jobs, you must log on to Oracle Applications as an Oracle LSH user with the
following roles:
• LSH Setup Admin
• LSH Adapter Security Admin
1. Open your Web browser.
2. Enter the eBusiness Suite SSWA (Self-Service Web Application) URL as follows:
http://<host name>.<domain name>:<HTTP port>/oa_servlets/AppsLogin
For example:
http://appshost.your_company.com:8000/oa_servlets/AppsLogin
The Applications Login screen appears.
3. Log in as a user with LSH Setup Admin and LSH Adapter Security Admin
privileges. An Oracle LSH page opens. Click Home from the links on the top right
corner of the page to reach the Oracle Applications Home Page.
4. Select the LSH Setup Admin Responsibility by clicking on it. Lookups appears in
the second column.
5. Click Lookups. (If necessary, click Grant This Session or Grant Always.) The
Oracle Life Sciences Data Hub Lookups window opens.
6. From the View menu, select Requests.

5.6.2 Load the Adapter Files

Oracle LSH includes predefined adapters that control the interaction between Oracle
LSH and other systems. The Oracle LSH LOB Loader concurrent program finds all the
adapter SQL files and loads them into a table in Oracle LSH.
To run the Oracle LSH LOB Loader:
1. Follow steps in Log On to Oracle Applications.
2. Click Submit a New Request. The Submit a New Request window opens.
3. Select Single Request and click OK. The Submit Request window opens.

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 Chapter 5
Run the Post-Installation Programs

4. Click the gray LOV button on the right of the Name field. The Reports List of Values
opens.
5. Select LSH LOB Loader Concurrent Program and click OK.
6. Click Submit. A window pops up with the job ID and asks if you want to submit another
request.
7. Click No.
To monitor the concurrent program's progress:
1. Click Find.
2. Click Refresh Data periodically to update the execution phase and status displayed on
screen.
When the status is Complete you can view the log file by clicking the View Log button.

Note:

• Always check the log file because the phase may be Complete and the status
Normal, but the program may not have successfully completed all its tasks.
• If you see this message in the log file: "ORA-20001: APP-FND-02901: You do
not have access privilege to any operating unit. Please check if your profile
option MO: Security Profile includes any operating unit or the profile option MO:
Operating Unit is set. has been detected in MO_GLOBAL.INIT," see this article
on My Oracle Support: ORA-20001: APP-FND-02901 Errors Running
Collections or Plan in 12.2 OR in Trying to View Request Log from Legacy
Collections Self Service In R12.0/12.1 (article 981828.1).

5.6.3 Run the Post-Installation Concurrent Program

Run the Job: To run the Oracle LSH post-installation concurrent process:
1. Click Submit a New Request under one of the following circumstances:
• in the Requests window you used to monitor the Oracle LSH LOB Loader concurrent
process
• after following the steps in Log On to Oracle Applications
2. Select Single Request and click OK. The Submit Request window opens.
3. Click the gray LOV button on the right of the Name field. The Reports List of Values
opens.
4. Select LSH: Post Installation Program and click OK. The Parameters pop-up window
appears.
5. Enter values for the following Parameters:

5-15
 Chapter 5
Run the Post-Installation Programs

Note:
Carefully set the following parameters. You cannot change the values for
some of the parameters after you run the job.

• Company ID. The company ID serves as part of the primary key for all the
Oracle LSH objects you define in this instance of Oracle LSH.
• Owning Location. Enter the name of your Oracle Applications instance.
• Object Sequence Start Value. Enter a single digit. The system will end all
object IDs with this digit to further distinguish objects created in this Oracle
LSH instance.
• Object Sequence Start Value. Leave blank. The system will end all object
IDs with the number 1.
• Database Host Name. Enter the machine name of the database server
instance.
• Database Port Number. Enter the port number of the database server
instance.
6. Click Submit. A window pops up with the job ID and asks if you want to submit
another request.
7. Note the job ID and click No.
Monitor the Process: To monitor the concurrent process's progress:
1. Click Find. Use the job ID to search for the process.
2. Click Refresh Data periodically to update the execution phase and status
displayed on screen.
3. When the phase is Complete, click the View Log.

Note:
Always check the log file, because the phase may be Complete and the
status Normal and yet the process may not have successfully completed
all its tasks.

Check the log file to make sure it did the following:

• Set the company ID
• Set the owning location
• Recreated the cdr_object_id_seq with the start value you provided
• Inserted one record each in the cdr_namings and cdr_naming_versions tables
for the instance domain

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Run the Stop Maintenance Script

Note:
The job does the above only the first time it runs.

• Set the profile to check if the post-installation has been run for this site.

5.6.4 Grant Security Rights to Seeded Adapters

In order to ensure that seeded adapters have the security rights they need to call APIs, do
the following:
1. Make sure that no LSH session is up and running.
2. Log in to SQL*Plus as apps.
3. Run $CDR_TOP/patch/115/sql/cdradaptergrants.sql

5.7 Run the Stop Maintenance Script

After you upgrade the software, follow the steps in this procedure to stop the maintenance
activity.
To run the Stop Maintenace script:
1. Download or copy the maintenance start script file from the Oracle LSH application
server (EBS Middle Tier server) $CDR_TOP/patch/115/sql/cdrmaintstop.sql to
the database server’s ORACLE_HOME location or any other preferred location.
2. From the database server, log in to SQL*Plus (not SQL Developer) as the APPS
database user.
3. Enter this command to execute the script:
SQL> @cdrmaintstop.sql
4. Check the log file.
The log file validates the success of the Stop Maintenance process and provides a
maintenance ID. For example, it lists the job report (ID, user name, job duration, job
type), Distributed Processing (DP) server report (location, description, and machine), and
service details. If you notice that any errors with stopping the maintenance script, contact
Oracle Support.

5.8 Start Server Processes

This step is required for all upgrade paths.
Start the following servers:
• Application Server
• Oracle LSH Distributed Processing (DP) Server

5-17
 Chapter 5
Regenerate the JAR Files

If the following issue occurs during the DP server start process, add an entry to
listener.ora and reload the listener (instructions are mentioned below):

[CdrExeJSExe] Exception thrown: Error in creating JDBC Connections

for ConnectionPool.
Related SQL Exception: Unable to start the Universal Connection
Pool: oracle.ucp.UniversalConnectionPoolException: Cannot get
Connection from Datasource: java.sql.SQLRecoverableException:
ORA-01034: ORACLE not available
ORA-27101: shared memory realm does not exist
Linux-x86_64 Error: 2: No such file or directory
Additional information: 4460
Additional information: -1725901513
oracle.apps.cdr.dpserver.exec.server.CdrExeJSException: Error in
creating JDBC Connections for ConnectionPool.
at
oracle.apps.cdr.dpserver.exec.server.CdrExeJSDataSource.getConnectio
n(CdrExeJSDataSource.java:191)
at
oracle.apps.cdr.dpserver.exec.server.CdrExeJSInitializer.<init>(CdrE
xeJSInitializer.java:92)
at
oracle.apps.cdr.dpserver.exec.server.CdrExeJSExe.startService(CdrExe
JSExe.java:263)
at
oracle.apps.cdr.dpserver.exec.server.CdrExeJSExe.main(CdrExeJSExe.ja
va:562)

1. Add the following entry to listener.ora:

USE_SID_AS_SERVICE_<Listener_Name> = ON
where, <Listener_Name> is the listener name that is in use.
2. Reload the listener:
lsnrctl reload

5.9 Regenerate the JAR Files

1. Log on to Oracle LSH with the same user that was used for submitting the Post
Install and the Lob Loader programs.
2. On the Home page, expand the Life Sciences Data Hub link.
3. Click on any link available to you, such as Home or Applications.
4. If the page is rendered properly, do not regenerate the JAR files. If the page is not
rendered properly and throws some error, regenerate the JAR files by performing
the following steps:
a. Source the Run File System environment file.
b. Run adadmin (provide SYSTEM and APPS password when prompted).
c. Select Generate Applications Files.
d. Select Generate product JAR Files.
e. Type ALL for all products when prompted.

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 Chapter 5
Run the Health Check Scripts

f. Type Yes for the force generation of JAR files when prompted.
g. Restart the Oracle LSH middle tier services.

5.10 Run the Health Check Scripts

Run the Health Check scripts for Oracle LSH and Oracle DMW as described in My Oracle
Support Article 2733714.1 (https://support.oracle.com).

5.11 Migrate Secure File

This section includes the following topics:
• Initiate the Secure File Migration
Instructions to initiate the secure file migration.
• Monitor the Secure File Migration
• Post Secure File Migration Task
Tasks that are required after the secure file migration completes.

5.11.1 Initiate the Secure File Migration

Instructions to initiate the secure file migration.
1. Log on to the application tier.
2. Source the environment file.
3. Navigate to the $CDR_TOP/patch/115/sql directory.
4. Log in to SQL*Plus as the APPS user.
5. Execute the script cdrsecfilepostinstscript.sql.
A prompt to enter the number of threads appears.
6. Enter 8.
A prompt to enter the logfile pathname appears.
7. Press Enter to select the default logfile pathname or enter a name of your choice.
8. After the script execution is complete, check for any errors. If case of an error, contact
Health Sciences Support.
Tthe migration process starts.

5.11.2 Monitor the Secure File Migration

1. Make sure at least two DBMS SCHEDULER JOBS are scheduled and running. These
jobs name starts with MIGRATE_BASICFILE_TO_SECUREFILE. Execute the following
command to confirm:

select
owner,
job_name,
JOB_ACTION,
START_DATE,
ENABLED,

5-19
 Chapter 5
Migrate Secure File

STATE
from dba_SCHEDULER_JOBS
where job_name like 'MIGRATE_BASICFILE_TO_SECUREFILE%'

2. Wait for the BASIC FILE to SECUREFILE migration to complete. You can monitor
the migration progress by executing the following command:.

select thread_id,
Number_of_batch_to_processe,
no_of_processed_batch,
case when THREAD_ID in (1,2) then 'DBMS JOB SHOULD BE RUNNING'
when Number_of_batch_to_processe > no_of_processed_batch then 'DBMS
JOB SHOULD BE RUNNING'
else 'DBMS JOB SHOULD NOT BE RUNNING' end as status
from
(
select thread_id,
count(distinct batchid) Number_of_batch_to_processe,
(select count(1) from cdr_job_log_sfm_tmp where
THREAD_ID=a.THREAD_ID and status in ('COMPLETE','FAILED'))
no_of_processed_batch
from cdr_job_log_sfm_tmp a
group by thread_id
);

5.11.3 Post Secure File Migration Task

Tasks that are required after the secure file migration completes.
To perform the next set of tasks, wait for at least 12 hours after the secure file
migration completes. A complete application downtime is required.
1. Stop all application tier services and job queue.

Note:
DO NOT stop the database.

2. If there is any cronjob related to Oracle LSH or Oracle DMW, suspend them.
Disable any custom scheduler or DBMS jobs related to Oracle LSH or Oracle
DMW.
3. Note the count of the invalid objects of APPS, APPLSYS, and CDR schema by
executing the following command:

select owner,
status,
count(1)
from dba_objects
where status <> 'VALID'
and owner in ('APPS','APPLSYS','CDR')
AND object_name <> 'CDR_SECUREFILE_MIGRATION'
AND object_name NOT LIKE 'CDR%SECFILE%'
AND object_name NOT LIKE 'CDR%SFM%'

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Migrate Secure File

group by owner,
status;

4. Once all application tier services are stopped, execute the cutover script by performing
the following steps:
a. Log in to the application tier.
b. Source the environment file.
c. Navigate to the $CDR_TOP/patch/115/sql directory.
d. Log in to SQL*Plus as the APPS user.
e. Execute the script cdrsecfilecutoff.sql.
A prompt to press enter to start the process appears.
f. Press Enter.
A prompt to enter the logfile pathname appears.
g. Press Enter to select the default logfile pathname or enter a name of your choice.
h. After the script execution is complete, check for any errors. If case of an error,
contact Health Sciences Support.
It will take some time for the script to execute.
5. After the script cdrsecfilecutoff.sql executes, make sure no DBMS SCHEDULER
JOBS are running related to secure file migration.
6. Make sure the new CDR_JOB_LOG table's LOB column LOG_MESSAGE is of type
SECUREFILE.
To do so, execute the following SQL command. The output of the SECUREFILE column
should be YES corresponding to the CDR_JOB_LOG table.

select
OWNER,
TABLE_NAME,
COLUMN_NAME,
SEGMENT_NAME,
LOGGING,
SECUREFILE
from dba_lobs
where table_name like 'CDR_JOB_LOG%';

7. If there is any new INVALID objects in the APPS, APPLSYS, or CDR schema, compile
those invalid objects.

select owner,
status,
count(1)
from dba_objects
where status <> 'VALID'
and owner in ('APPS','APPLSYS','CDR')
AND object_name <> 'CDR_SECUREFILE_MIGRATION'
AND object_name NOT LIKE 'CDR%SECFILE%'
AND object_name NOT LIKE 'CDR%SFM%'

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Migrate Secure File

group by owner,
status;

8. After all validations are successful, start all the application tier services and job
queue.

5-22
6
What's Next
After you have finished all the installation tasks outlined in this book, you must do the
following tasks before you can begin to use the Oracle Life Sciences Data Hub (Oracle LSH):

Note:
Oracle Health Sciences Data Management Warehouse customers can skip this
section and proceed to the Oracle Health Sciences Data Management Warehouse
Installation Guide.

• Define Oracle LSH Distributed Processing (DP) Server service locations and services to
integrate Oracle LSH with its processing engines and IDEs. See "Setting Up Services" in
the Oracle Life Sciences Data Hub System Administrator's Guide.
• Design an object security system, classification system, and organizational structure for
your implementation of Oracle LSH. See "Designing a Security System," "Designing a
Classification System," and "Designing an Organizational Structure" in the Oracle Life
Sciences Data Hub Implementation Guide.
• Set up the security system, see "Setting Up the Security System" in the Oracle Health
Sciences Data Management Workbench and Life Sciences Data Hub Security Guide.
• Set up the classification system and organizational domains. See "Setting Up the
Classification System" in the Oracle Life Sciences Data Hub System Administrator's
Guide and "Applications User Interface" in Oracle Life Sciences Data Hub Application
Developer's Guide.
• Define remote locations to integrate Oracle LSH with Oracle-based source data systems.
See "Registering Locations and Connections" in the Oracle Life Sciences Data Hub
System Administrator's Guide.
• If you plan to use OBIEE for visualizations or Oracle BIP for reports, do the additional
setup required for each system. See the Oracle Life Sciences Data Hub System
Administrator's Guide for information.

6-1
7
Change Record
• April 2021: First version of the guide.
• May 2021: Second version of the guide. In this version:
– Removed the support of Oracle Enterprise Linux and Red Hat Enterprise Linux
version 8 for the database tier; see Database Tier
– Added support for Oracle Enterprise Linux version 7.4 or later; see Application Tier
– Added the chapter The Two Supported Upgrade Paths
– In Upgrade E-Business Suite from 12.1.3 to 12.2.9:
* Added information to drop the trigger "OWBSYS.CDR_RTREPOS_TG"
* Added a note for gathering the schema statistics
* Added information on troubleshooting any error that occurs while applying the
patch 10117518 as a prerequisite to run the adgrants.sql
– Added a step to stop the study health monitor scheduler in Run the Start
Maintenance Script
– Removed a few topics from the guide that were not required for upgrading to Oracle
LSH release 3.1.
• June 2021: Third version of the guide. In this version:
– Added a step to apply the database patch p30808109_1910000DBRU_Linux-
x86-64.zip in Apply the Database Patches.
– Updated step to log in to Oracle Database 19c as sysdba user in Check Non-Default
Service.
– Updated the query to monitor the processed and remaining schemas in Run the
Upgrade Script to Edition Existing Schemas.
– Added a step to restart the Oracle LSH middle tier services in Regenerate the JAR
Files.
– Added the troubleshooting steps for the exception error that might occur during the
Oracle LSH Distributed Processing (DP) server start process in Start Server
Processes.

7-1
A
Architecture Overview
The following figure shows the logical Oracle Life Sciences Data Hub architecture described
in this section.

This section contains the following topics:

• Client Tier
• Application Tier
• Database Tier
• Adapters to External Systems

A.1 Client Tier

There are two ways to set up a client, depending on the type of user:

A-1
 Appendix A
Application Tier

Consumers and Administrators: Oracle Life Sciences Data Hub (Oracle LSH)
Consumers, who retrieve information in the form of reports and visualizations, and
Oracle LSH Administrators, who perform administrative tasks within Oracle LSH,
require the following on their personal computers:
• A Web browser
• Java Virtual Machine (JVM)
Administrators require either JInitiator or JVM to use any of the Oracle Forms screens
related to security, to run the post-installation jobs, and to set up user accounts and
functional roles.
Definers: A full-service client for users who create (define) the programs that operate
on Oracle LSH data and generate reports requires additional software:
• Oracle LSH plug-in for launching Integrated Development Environments (IDEs)
• WinZip
• Web browser
• In addition, Definers need one or more IDE clients. These may include: SAS PC,
SQL*Plus, SQL Developer, Oracle BI Administration Tool, Oracle Reports, and
Oracle Business Intelligence Publisher.

A.2 Application Tier

In addition to standard Oracle Applications components, the Oracle Life Sciences Data
Hub application tier includes the following:
Oracle LSH Application Server: The Oracle LSH Application Server renders the user
interface using the Oracle Applications Framework and handles the communication
between the user interface and the database using the Java Runtime Environment.
Oracle LSH Distributed Processing (DP) Server: The Oracle LSH DP Server
handles the communication between Oracle LSH and the external processing systems
required to support the IDEs.
Processing Systems
XML Publisher is required for internal Oracle LSH processing. The other systems are
required only if you are developing Oracle LSH Programs in those technologies:
• Oracle XML Publisher is used by Oracle LSH to run system reports. Oracle LSH
also uses XML Publisher to create Report Sets as a single PDF output with a
unified table of contents and custom templates.
• Oracle Reports executes user-developed Oracle Reports Programs.
• Oracle Business Intelligence Publisher executes user-developed Oracle BIP
Programs.
• SAS executes user-developed SAS Programs.
• Oracle Discoverer Plus. Accessed by Consumer clients through a Web browser,
this application generates data visualizations based on user-developed Oracle
LSH Discoverer Business Areas.

A-2
 Appendix A
Database Tier

A.3 Database Tier

The Oracle Life Sciences Data Hub database tier includes the following:
• Oracle Enterprise Edition RDBMS. All of the Oracle LSH database tier components use
the Oracle Enterprise Edition database server and database.
• Oracle Applications Schema. The Oracle Applications Schema is the schema installed
as part of the Oracle Applications installation.
• Oracle Workflow. Oracle LSH uses Oracle Workflow to allow users to create and
execute Workflow programs. Oracle Workflow is installed with Oracle Applications.
• Oracle Thesaurus Management System (TMS). Oracle LSH uses the TMS database
tier internally to run its classification system, which is a required part of Oracle LSH
functionality.

Oracle Enterprise Edition RDBMS

All of the Oracle LSH database tier components use the Oracle Enterprise Edition database
server and database.

Oracle Applications Schema

The Oracle Applications Schema is the schema installed as part of the Oracle Applications
installation. It contains the Oracle LSH schema.

Oracle LSH Database Server and Schema

These include the Oracle LSH business logic in PL/SQL packages, internal Oracle LSH
tables and views, security, adapters, and APIs; as well as Oracle LSH user-developed
metadata tables and packages.

Oracle Workflow
Oracle LSH uses Oracle Workflow to allow users to create and execute Oracle LSH Workflow
Programs. Oracle Workflow is installed with Oracle Applications.

Oracle Thesaurus Management System (TMS)

The Oracle LSH classification system is based on TMS.

A.4 Adapters to External Systems

Oracle Life Sciences Data Hub (Oracle LSH) is intended for integration with other systems for
a variety of purposes. Each external system integrated with Oracle LSH requires an adapter
to handle whatever communication and exchange is required, depending on the purpose of
the integration and the technical specifications of the external system. Oracle LSH is shipped
with built-in adapters for loading data into Oracle LSH from other systems, for developing and
executing programs operating on Oracle LSH data, and for exporting data out of Oracle LSH.
#GUID-F406D70F-BB51-42EE-B6DF-5AA0452F42C2/CBHGAICE shows the adapters that
are included with Oracle LSH. Adapters to other systems may be available from third parties.

A-3
 Appendix A
Adapters to External Systems

This section contains the following topics:

• Source Data Systems
• Data Transformation and Reporting Tools
• Visualization Tools
• Data Export Tools

A.4.1 Source Data Systems

Oracle Life Sciences Data Hub (Oracle LSH) includes adapters to external systems
that you can use to load data into Oracle LSH:
• SAS. The SAS adapter allows you to load SAS data sets into Oracle LSH.
• Text. The Text adapter allows you to load text files from any system into Oracle
LSH.
• Oracle Databases. The general Oracle Databases adapter allows you to load
data from any Oracle database into Oracle LSH.

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 Appendix A
Adapters to External Systems

• Oracle Clinical. The Oracle Clinical adapter family includes eight specialized adapters
for loading the following data and metadata from Oracle Clinical:
– Data Extract SAS Views
– Data Extract Oracle Views
– Global Library
– Labs
– Study Data
– Study Design and Definition
– Stable Interface Tables
– Randomization

A.4.2 Data Transformation and Reporting Tools

Oracle LSH includes adapters to set up the following systems as integrated development
environments (IDEs) for developing and generating programs:
• SAS
• PL/SQL
• Oracle Reports
• Oracle Business Intelligence Publisher

A.4.3 Visualization Tools

Oracle LSH includes adapters to allow the following systems to display visualizations of
Oracle LSH data:
• Oracle Discoverer
• Oracle Business Intelligence Enterprise Edition (OBIEE) Answers
• Oracle Clinical Development Analytics—to view visualizations in OBIEE Answers of
Oracle Clinical data in Oracle LSH
• Generic Visualization Adapter—to integrate other visualization tools

A.4.4 Data Export Tools

Oracle LSH includes adapters to allow exporting Oracle LSH data:
• Oracle Export
• SAS—Transport Files and Data Sets
• Text Files

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