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Oracle Healthcare FoundationInstallation GuideRelease 8.0F37037-01November 2020
Oracle Healthcare Foundation Installation Guide, Release 8.0F37037-01Copyright 2020, 2020, Oracle and/or its affiliates.This software and related documentation are provided under a license agreement containing restrictions onuse and disclosure and are protected by intellectual property laws. Except as expressly permitted in yourlicense agreement or allowed by law, you may not use, copy, reproduce, translate, broadcast, modify, license,transmit, distribute, exhibit, perform, publish, or display any part, in any form, or by any means. Reverseengineering, disassembly, or decompilation of this software, unless required by law for interoperability, isprohibited.The information contained herein is subject to change without notice and is not warranted to be error-free. Ifyou find any errors, please report them to us in writing.If this is software or related documentation that is delivered to the U.S. Government or anyone licensing it onbehalf of the U.S. Government, then the following notice is applicable:U.S. GOVERNMENT END USERS: Oracle programs (including any operating system, integrated software,any programs embedded, installed or activated on delivered hardware, and modifications of such programs)and Oracle computer documentation or other Oracle data delivered to or accessed by U.S. Governmentend users are "commercial computer software" or "commercial computer software documentation" pursuantto the applicable Federal Acquisition Regulation and agency-specific supplemental regulations. As such,the use, reproduction, duplication, release, display, disclosure, modification, preparation of derivative works,and/or adaptation of i) Oracle programs (including any operating system, integrated software, any programsembedded, installed or activated on delivered hardware, and modifications of such programs), ii) Oraclecomputer documentation and/or iii) other Oracle data, is subject to the rights and limitations specified in thelicense contained in the applicable contract. The terms governing the U.S. Government’s use of Oracle cloudservices are defined by the applicable contract for such services. No other rights are granted to the U.S.Government.This software or hardware is developed for general use in a variety of information management applications.It is not developed or intended for use in any inherently dangerous applications, including applications thatmay create a risk of personal injury. If you use this software or hardware in dangerous applications, then youshall be responsible to take all appropriate fail-safe, backup, redundancy, and other measures to ensure itssafe use. Oracle Corporation and its affiliates disclaim any liability for any damages caused by use of thissoftware or hardware in dangerous applications.Oracle and Java are registered trademarks of Oracle and/or its affiliates. Other names may be trademarks oftheir respective owners.Intel and Intel Inside are trademarks or registered trademarks of Intel Corporation. All SPARC trademarks areused under license and are trademarks or registered trademarks of SPARC International, Inc. AMD, Epyc,and the AMD logo are trademarks or registered trademarks of Advanced Micro Devices. UNIX is a registeredtrademark of The Open Group.This software or hardware and documentation may provide access to or information about content, products,and services from third parties. Oracle Corporation and its affiliates are not responsible for and expresslydisclaim all warranties of any kind with respect to third-party content, products, and services unless otherwiseset forth in an applicable agreement between you and Oracle. Oracle Corporation and its affiliates will notbe responsible for any loss, costs, or damages incurred due to your access to or use of third-party content,products, or services, except as set forth in an applicable agreement between you and Oracle.
ContentsPreface1Documentation accessibilityixRelated resourcesixAccess to Oracle SupportixAdditional copyright informationixOverviewSoftware Requirements1-1Media Pack Content1-2General Guidelines for Installation1-2Supported Upgrade Paths1-3Where to Find the Product Documentation1-3Part I2InstallationData Model InstallationInstall the Data Model without Pre-created User Schemas2-1Check Prerequisites2-1Prepare the Installer2-2Run the Installer2-3Check the Installation2-6Install the Data Model with Pre-created User Schemas2-7Check Prerequisites2-7Oracle Healthcare Foundation Tablespaces2-8Temporary Tablespaces2-9Prepare the Installation Files2-9Create Database Roles2-10Create User Schemas2-10Run the Installation Scripts2-10Start the Installer2-11iii
3Run the Installer2-12Check the Installation2-14Revoke Privileges2-15Data Management Assembly for Oracle Data Integrator InstallationInstalling the Data Management Assembly without Pre-Created User SchemasCheck Prerequisites3-1Prepare the Installer3-3Run the Installer3-3Check the Installation3-7Create a New Oracle Data Integrator Repository Login3-7Installing the Data Management Assembly with Pre-Created User SchemasCheck Prerequisites43-83-9Create Default and Temporary Tablespaces3-10Create User Schemas3-11Prepare the Installer3-11Run the Installer3-12Check the Installation3-16Revoke Privileges3-16Data Management Assembly for Informatica InstallationInstalling the Data Management Assembly without Pre-Created User Schemas4-1Check Prerequisites4-1Prepare the Installer4-3Run the Installer4-3Check the Installation4-7Installing the Data Management Assembly with Pre-Created User Schemas4-7Check Prerequisites4-8Create Default and Temporary Tablespaces4-9Create User Schemas4-10Prepare the Installer4-10Run the Installer4-11Check the Installation4-14Revoke Privileges4-15Assigning the Integration Service53-14-15Middle-Tier InstallationInstalling the Middle-Tier on the Primary NodeCheck Prerequisites5-15-1iv
Prepare the Installer5-2Run the Installer5-2Check the Installation5-4Installing the Middle-Tier on a Secondary Node678Check Prerequisites5-5Prepare the Installer5-5Run the Installer5-5Check the Installation5-6JDBC GridLink Data Source Configuration (optional)Edit the Existing Generic Data Source6-1Create the JDBC GridLink Data Source6-1Oracle Healthcare Foundation Omics Data Bank LoadersInstallationPrerequisites7-1Installing the Oracle Healthcare Foundation Omics Data Bank Loaders7-1Oracle Healthcare Foundation Self-Service Analytics InstallationInstallation Overview8-1Prerequisites8-1Install the Oracle Healthcare Foundation Self-Service Analytics8-2Deploy the Oracle Healthcare Foundation Catalog in Oracle Business IntelligenceEnterprise Edition8-3Part II95-4UpgradeData Model UpgradeCheck Prerequisites9-1Upgrading from Healthcare Data Warehouse Foundation or a Previous OracleHealthcare Foundation Version9-4Prepare the Installer9-5Run the Installer9-5Check the Installation9-7Data MigrationCheck the Migration ScriptsUpgrading from Oracle Healthcare Foundation versions earlier than 7.0.19-79-89-8v
Upgrading from an Oracle Healthcare Foundation Version before 7.1Upgrading from Oracle Healthcare Foundation Versions Earlier than 8.0Execute Schema Migration Scripts After Modifications1011129-99-109-10Data Management Assembly for Oracle Data Integrator UpgradeCheck Prerequisites10-1Prepare the Installer10-3Run the Installer10-3Check the Installation and Delete E tables10-8Create a New Oracle Data Integrator Repository Login10-8Data Management Assembly for Informatica UpgradeCheck Prerequisites11-1Prepare the Installer11-3Run the Installer11-3Check the Installation11-7Middle-Tier Upgrade on the Primary NodeCheck Prerequisites12-1Prepare the Installer12-1Run the Installer12-2Check the Installation12-3Part IIIUninstall13Data Model Uninstall14Data Management Assembly for Oracle Data Integrator Uninstall15Data Management Assembly for Informatica Uninstallvi
16Middle-Tier UninstallPart IV17TroubleshootingData Model TroubleshootingInstallation Log Files181920A17-1Data Management Assembly for Oracle Data IntegratorTroubleshootingInstallation Log Files18-1Troubleshooting Timezone Errors18-2Troubleshooting Guidelines18-2Data Management Assembly for Informatica TroubleshootingInstallation Log Files19-1Troubleshooting Timezone Errors19-2Troubleshooting Guidelines19-2Troubleshooting19-2Middle-Tier TroubleshootingInstallation Log Files20-1Troubleshooting the Primary Node Installation20-1Troubleshooting the Secondary Node Installation20-2Troubleshooting Coherence Cluster Errors20-2Configuration Guide for ExadataSystem ConfigurationA-1Exadata Component ConfigurationA-1Database ConfigurationA-1Database I/O CalibrationA-2Resource ManagerA-2Database ParametersA-2Parallel Degree PolicyA-3Oracle Automatic Stats JobA-4Tablespace and Redo Log RecommendationsA-4vii
ASM RecommendationsA-5Maximum Availability RecommendationsA-5Application ConsiderationsBA-5General RecommendationsA-5Oracle Healthcare FoundationA-5Cohort Data ModelA-6Omics LoadersA-6Configuration Guide for Non-ExadataDatabase ConfigurationB-1Database I/O CalibrationB-1Resource ManagerB-1Database ParametersB-2Parallel Degree PolicyB-2Parallel Degree LimitB-3Adaptive TuningB-3Parallel Max ServersB-3Parallel Min ServersB-3Memory SettingsB-3Optimizer Features EnableB-4ProcessesB-4Oracle Automatic Stats JobB-4Tablespace and Redo Log RecommendationsB-4ASM RecommendationsB-4Application ConsiderationsB-5General RecommendationsB-5Oracle Healthcare FoundationB-5Cohort Data ModelB-5Omics LoadersB-5viii
PrefaceThis preface contains the following sections: Documentation accessibility Related resources Access to Oracle Support Additional copyright informationDocumentation accessibilityFor information about Oracle's commitment to accessibility, visit theOracle Accessibility Program website at http://www.oracle.com/pls/topic/lookup?ctx acc&id docacc.Related resourcesAll documentation and other supporting materials are available on the Oracle HelpCenter.Access to Oracle SupportOracle customers that have purchased support have access to electronic supportthrough Support Cloud.Contact our Oracle Customer Support Services team by logging requests in one of thefollowing locations: English interface of Oracle Health Sciences Customer Support Portal (https://hsgbu.custhelp.com/) Japanese interface of Oracle Health Sciences Customer Support Portal (https://hsgbu-jp.custhelp.com/)You can also call our 24x7 help desk. For information, visit iences-cloud-support/index.html or visithttp://www.oracle.com/pls/topic/lookup?ctx acc&id trs if you are hearing impaired.Additional copyright informationThis documentation may include references to materials, offerings, or products thatwere previously offered by Phase Forward Inc. Certain materials, offerings, services,or products may no longer be offered or provided. Oracle and its affiliates cannot beheld responsible for any such references should they appear in the text provided.ix
1OverviewThis document explains the installation and initial setup of Oracle HealthcareFoundation. The user installing Oracle Healthcare Foundation (OHF) should haveknowledge of Oracle, Informatica or Oracle Data Integrator, Oracle WebLogic Server,and the Linux operating system.The Oracle Healthcare Foundation installer lets you install the components below onthe Linux OS in the following order:1.Oracle Healthcare Foundation Data Model2.Oracle Healthcare Foundation Data Management Assembly for Oracle DataIntegratororOracle Healthcare Foundation Data Management Assembly for Informatica3.Oracle Healthcare Foundation Middle-TierNote:Oracle Healthcare Foundation should be installed by the same user whoinstalled the RDBMS or Oracle WebLogic Server.This chapter contains the following topics: Software Requirements Media Pack Content General Guidelines for Installation Supported Upgrade Paths Where to Find the Product DocumentationSoftware RequirementsComponentSoftware RequiredCommon requirements for allcomponents Data ModelOracle Linux 6.7 (64-bit) or above, or Oracle Linux 7 (64bit) operating system (OS)Oracle Database 12.2.0.1 Enterprise Edition, certified onOracle Database 19.3Python 2 (version 2.6.6 or above) or Python 3 (version3.6.4 or above)No additional requirements1-1
Chapter 1Media Pack ContentComponentSoftware RequiredData Management Assembly(Oracle Data Integrator) Oracle Data Integrator (ODI) 12.2.1.4 Standalone orEnterprise editionOracle Fusion Middleware Infrastructure 12.2.1.4 isrequired for Oracle Data Integrator Enterprise editionJava Development Kit (JDK) 1.8Oracle WebLogic Server 12.2.1.4 (optional)Data Management Assembly(Informatica) Informatica PowerCenter 10.2 or 10.4Middle-TierYou must install the Middle-Tier on a different Oracle WebLogicServer than the Oracle Data Integrator server. Self-Service Analytics(optional) Oracle Fusion Middleware Infrastructure 12.2.1.4.0 withOracle WebLogic Server 12.2.1.4.0Java Development Kit (JDK) 1.8 Update 111 (JDK 1.8u111) or aboveOracle Business Intelligence Enterprise Edition (OBIEE)12.2.1.4.0 (Oracle Business Intelligence Enterprise Edition12.2.1.4.0 is compatible with Oracle Fusion MiddlewareInfrastructure 12.2.1.3.0)Oracle Business Intelligence Developer Client Tools12.2.1.4.0Java Runtime Environment (JRE) 1.8 Update 111 (JRE1.8 u111) or aboveMedia Pack ContentThe media pack from the Oracle Software Delivery Cloud (OSDC) contains theinstaller for: Oracle Healthcare Foundation Linux (OHF V80 Linux-x64.zip)General Guidelines for Installation Linux X-windows should be used for the Linux Oracle Universal Installer (OUI)installation (Linux Graphical User Interface). Before running the installer, be sure to backup all existing Oracle HealthcareFoundation schemas and any customizations. Before running the installer, make sure that the ORACLE HOME and PATHenvironment variables are setup in your session.For example,export ORACLE HOME /u01/app/oracle/product/122010export PATH PATH: ORACLE HOME/bin When re-executing the installer due to a failure, enter the same details in thequestion prompting phase at all times. Do not delete any objects in the installationfolder. When re-executing the installer, if you receive OUI-10030 error messages, ignorethe messages to continue using the existing Oracle Healthcare Foundationinstallation HOME path.1-2
Chapter 1Supported Upgrade Paths Convert the installer execution shell to an SH shell as the installer script executesin the SH shell of the Linux OS. Text enclosed within in the following chapters indicate parameters and youmust provide an appropriate value.Supported Upgrade PathsThe following are the supported upgrade paths: HDWF 6.1/OHADI 3.1 to Oracle Healthcare Foundation 8.0 Oracle Healthcare Foundation 7.0.1 to Oracle Healthcare Foundation 8.0 Oracle Healthcare Foundation 7.1 to Oracle Healthcare Foundation 8.0 Oracle Healthcare Foundation 7.1.x to Oracle Healthcare Foundation 8.0 Oracle Healthcare Translational Research 3.1.0.2/3.1.0.3/3.1.0.4 to OracleHealthcare Foundation 8.0The Oracle Healthcare Foundation 8.0 Middle Tier upgrade is supported fromOracle Healthcare Foundation 7.1.x (see Middle-Tier Upgrade on the Primary Node ).To upgrade the Middle Tier from Oracle Healthcare Foundation 7.0.1 or 7.1,uninstall the existing oh domain and applications and install Oracle WebLogicServer 12.2.1.4.0, then do a fresh Oracle Healthcare Foundation 8.0 Middle tierinstallation (see Middle-Tier Installation).Where to Find the Product DocumentationThe product documentation is available from the following locations: My Oracle Support (https://support.oracle.com) Oracle Help Center ces/oracle-healthcare-foundation/index.html)If the software is available for download, the documentation set is available from theOracle Software Delivery Cloud (https://edelivery.oracle.com). All documents maynot be updated for every release. Therefore, the version numbers for the documents ina release may differ.1-3
Part IInstallationIn this chapter: Data Model Installation Data Management Assembly for Oracle Data Integrator Installation Data Management Assembly for Informatica Installation Middle-Tier Installation JDBC GridLink Data Source Configuration (optional) Oracle Healthcare Foundation Omics Data Bank Loaders Installation Oracle Healthcare Foundation Self-Service Analytics Installation
2Data Model InstallationThis chapter describes how to install the Oracle Healthcare Foundation Data Model.There are two ways to install the Data Model, depending on how you create the userschemas. The installer can create the user schemas during the installation or you cancreate them manually, prior to the installationFor more information, see: Install the Data Model without Pre-created User Schemas Install the Data Model with Pre-created User SchemasInstall the Data Model without Pre-created User SchemasThis section describes how to install the Data Model by using the installer to createfresh user schemas. Please complete the following: Check Prerequisites Prepare the Installer Run the Installer Check the InstallationCheck Prerequisites-PrerequisitesInstall Oracle Database 12.2.0.1.0 or 19.3 Enterprise Edition.Make sure that the database compatible parameter is set to 12.2.0.1.0 or higher byconnecting to the DBA user and running the query below:select * from v parameter where name 'compatible';Ensure the parameter is set to 12.2.0.1.0 or higher.If you are installing Oracle Healthcare Foundation on an Exadata environment, apply theOracle database patch 19562381 (Doc ID 19562381.8) and patch 31182793.Ensure the latest database patches are applied on Oracle Database version 12.2.0.1.0: Patch 30116802 - GI Oct 2019 Release Update 12.2.0.1.191015 or laterNote:Apply the latest CPU patch for the Oracle Database.Create a container database with a single pluggable database instance with the help of aOracle Database Administrator (optional).2-1
Chapter 2Install the Data Model without Pre-created User Schemas-PrerequisitesMake sure the database initialization parameter MAX STRING SIZE is set toSTANDARD (default value).Note that this parameter cannot be changed to STANDARD if the database is created withMAX-STRING SIZE set to EXTENDED.Set the NLS LENGTH SEMANTICS parameter to either CHAR or BYTE, based on yourrequirements.For Oracle Healthcare Foundation Globalization Support information, see Oracle DatabaseGlobalization Support Guide and set your database character set accordingly.Make sure that the password expiry notification message does not display for the sys andsystem schemas.To create an encrypted tablespace during the installation, set up your environment fortablespace encryption. For more information, see Oracle Database Advanced SecurityGuide 12.2. The installer only creates the tablespace and does not handle prerequisiteslike setting up the keystore, opening it, and so forth. The installer only checks whether thekeystore is open if the sys and system passwords are provided during the installation.Verify if you have a database license for Advanced Compression.Set the GLOBAL NAMES database initialization parameter to false.If you are installing Oracle Healthcare Foundation on an Exadata database machine, seethe Exadata Machine and Exadata Implementation sections in the Oracle HealthcareFoundation Programmer's Guide.For remote installations, make sure the following are available on the client machine: Oracle Linux 6.7 (64-bit) OS or aboveOracle Database 12.2.0.1.0 client with the Sqlplus utilityVerify the database connectivity through SERVICE NAME. Make sure that you areconnecting to the pluggable database (PDB) if installing in a container-based environment.Verify the database connectivity using the following command:SQL connect username@hostname:port number/servicename orsqlplususername@'(DESCRIPTION (ADDRESS (PROTOCOL TCP)(HOST dbhost)(PORT dbport)
Run the Installer 2-12 Check the Installation 2-14 Revoke Privileges 2-15. 3 . Data Management Assembly for Oracle Data Integrator Installation. Installing the Data Management Ass
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