This chapter describes security considerations and the installation process for the database tier. It contains the following topics:
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 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 following two additional database schemas are installed by the OHTR Installer. If desired, these schemas and their associated tablespaces can be created earlier in the OHF database by a DBA. If the schemas exist, the OHTR Installer uses them to store application and API objects. Otherwise it creates the tablespaces and schemas first.
APP - Application schema, which stores information used by user interface.
CGA - Clinical Genomics API schema, which stores objects used by query or data export API.
Download the OHTR installation package from the Media Pack and extract the files into a directory on the installation server.
Navigate 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
Navigate 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 |
| CGA | CGA_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 3.2.x 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 DB Connection 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 OHF Schema Details screen, enter values for the following fields and click Next.
Note:
Make sure that the username and password is 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 Service Schema Details screen, enter values for the following fields and click Next.
Services schema name
Services schema password
In the OHTR Schema Details screen, enter values for the following fields and click Next.
OHTR application schema name
OHTR application schema password
Clinical Genomics API schema name
Clinical Genomics API schema password
In the OHTR Tablespace Details screen, enter values for the following fields and click Next.
Default tablespace for APP schema
Temp tablespace for APP schema
In the Clinical Genomics Tablespace Details screen, enter values for the following fields and click Next.
Default tablespace for API schema
Temp tablespace for API schema
In the Database Verification screen, verify all the details.
Click Back to make any changes.
After verifying that all details are correct, click Install. Click Next.
In the Tablespace Datafile Location screen, specify the location of the tablespace data files. This is the directory on the database server where data files are created during installation. Click Next.
In the Summary screen, 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 resolve any errors.