This chapter describes security considerations and the installation process for the database tier. You will learn how to:
Install or upgrade the Oracle Healthcare Foundation (OHF) database tier to the release required for the OHTR release you are installing or upgrading to. See the release notes for more information.
The installation environment can be either:
the database server (Exadata computing node) where the OHF database is installed
a stand-alone Linux server that has the following additional software available:
Python 2x (2.6.6 or later)
Oracle 12c client with net services configured to access the OHF database
The following five database schemas are required to store OHTR objects. They are installed during the OHF database installation. Each schema and tablespace may have the default name or a name provided during OHF installation. Note these details, which you will need when you run the OHTR Installer.
CDM - Cohort Data Mart (CDM) schema stores the clinical information that is refreshed by ETLs.
ODB - Omics Data Bank (ODB) schema stores the omics data linked to patients as well as genetic reference data to link.
SVC - Services schema is used by ODB loader APIs.
ENT - The Enterprise (ENT) schema stores system-wide configuration information like product version.
JOB_ENGINE - Job Engine (JOB) schema tracks all jobs executed and provides templates for jobs.
The APP - Application schema is an additional database schema installed by the OHTR Installer, which stores information used in the UI. If desired, this schema and its associated tablespaces can be created earlier in the OHF database by a DBA. If the schema exists, the OHTR Installer uses it to store the application. Otherwise it creates the tablespaces and schemas first.
Download the OHTR installation package from the Media Pack and extract the files into a directory on the installation server.
Go to the <media_pack_location>/ folder.
Using the following command, unzip the OHTR_Linux-x64.zip file to the folder where you want to launch the installer:
unzip -a OHTR_Linux-x64.zip
Go to the Disk1/install folder.
Change the protection on files using the following command:
chmod 755 *
Important:
Ensure that all prerequisites (Section 2.1) have been fulfilled.To install the OHTR database framework:
Start the Oracle Universal Installer (OUI) using the following command:
If the database server is on the machine where the Installer is running, execute:
sh runInstaller.sh
If the database server is on a different machine, execute:
sh runInstaller.sh remote_installation=true
If you are executing the Installer on Linux, change the directory to Disk1/install and run the following command:
bash$ chmod +x unzip runInstaller runInstaller.sh
If the schema name provided here already exists in the OHF database, then that schema is used to install OHTR objects. If it does not exist, the schema will be created.
While creating the OHTR application schema, the Installer prompts for the default and temporary tablespaces for this user. If these tablespaces already exist, they are assigned to the user and quota unlimited is granted on them. Otherwise these tablespaces are created with the datafile located in the user-supplied file destinations:
| Database Schema | Default Tablespace | Temporary Tablespace |
|---|---|---|
| APP | APP_DATA | TRC_TEMP_TS |
The Welcome screen appears. Click Next.
In the Select a Product to Install screen, select the Oracle Healthcare Translational Research DB Tier 3.3 option, and click Next.
In the Specify Home Details screen, enter the installation home name and location, and click Next.
In the Verify Installation Prerequisites screen, verify if all the prerequisites are met before proceeding. Click Next.
In the Oracle Client Home Configuration screen, specify the Oracle client home path. The installer validates this path. Click Next.
In the Enter DB Connection details screen, enter values for the following fields and click Next:
Hostname: by default, the system host name appears.
Port: by default, the port number is 1521. You can edit this field if required.
Service name
System user password
Sys user password
In the Enter OHF Schema Details screen, enter values for the following fields and click Next:
Note:
Make sure that the user names and passwords are not the same for all entered schemas.Omics data bank schema name
Omics data bank schema password
Common data mart schema name
Common data mart schema password
Enterprise schema name
Enterprise schema password
Job Engine schema name
Job Engine schema password
In the Enter OHF Schema Details screen, enter values for the following fields and click Next.
Services schema name
Services schema password
In the Enter Schema Details screen, enter values for the following fields and click Next.
OHTR application schema name
OHTR application schema password
In the Specify Tablespace details screen, enter values for the following fields and click Next.
Default tablespace for APP schema
Temp tablespace for APP schema
In the Database Verification screen, verify all the details.
Click Back to make any changes.
After verifying that all details are correct, click Next.
In the Verify Configuration Parameters screen, verify all the details.
Click Back to make any changes.
After verifying that all details are correct, click Next.
In the Summary screen, take one last look at the details. If everything is alright, click Install.
When the installation is complete, the End of Installation screen appears. Review the information and click Exit.
At the confirmation prompt, click Yes to exit the Installer.
Review the generated installation log files for errors. If necessary, contact Oracle support to fix any errors.
For upgrading the Database Tier, follow the same steps as in section Section 2.3, "Install the Database Tier", except for step 11.
For an upgrade, in the Enter Schema details screen, if you use existing app schema values, you will no longer go through the Specify Tablespace details screen that is mentioned in step 11.