Install the Data Model with Pre-created User Schemas
This section describes how to install the Data Model by creating Oracle Healthcare Foundation user schemas and tablespaces outside the installer, then using the installer to create database objects in the respective user schemas. Please complete the following:
- Check Prerequisites
- Oracle Healthcare Foundation Tablespaces
- Temporary Tablespaces
- Prepare the Installation Files
- Create Database Roles
- Create User Schemas
- Run the Installation Scripts
- Start the Installer
- Run the Installer
- Check the Installation
- Revoke Privileges
Parent topic: Data Model Installation
Check Prerequisites
- | Prerequisites |
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Make sure Oracle Database 12.2.0.1 Enterprise Edition is installed. |
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Make sure that the database compatible parameter is set to 12.2.0.1.0 by connecting to the DBA user and running the query below:
If the parameter is not set to 12.2.0.1.0, ask your database administrator to set it. |
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If you are installing Oracle Healthcare Foundation on an Exadata environment, apply the Oracle database patch 19562381 (Doc ID 19562381.8) and patch 31182793. |
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Make sure the database initialization parameter MAX_STRING_SIZE is set to STANDARD (default value). This parameter cannot be changed to STANDARD if the database was created with MAX_STRING_SIZE set to EXTENDED. |
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Set the NLS_LENGTH_SEMANTICS parameter to either CHAR or BYTE, based on your requirements. For Oracle Healthcare Foundation Globalization Support information, see Oracle Database Globalization Support Guide and set your database character set accordingly. |
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Make sure that the password expiry notification message does not display for the sys and system schemas. |
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To create an encrypted tablespace during the installation, set up your environment for tablespace encryption. For more information, see Oracle Database Advanced Security Guide 12.2. The installer only creates the tablespace and does not handle prerequisites like setting up the keystore, opening it, and so forth. The installer only checks whether the keystore is open if the sys and system passwords are provided during the installation. |
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Verify if you have a database license for Advanced Compression. |
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Set the GLOBAL_NAMES database initialization parameter to false. |
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If you are installing Oracle Healthcare Foundation on an Exadata database machine, see the Exadata Machine and Exadata Implementation sections in the Oracle Healthcare Foundation Programmer's Guide. |
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For remote installations, make sure the following are available on the client machine:
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Enable a database connection through SERVICE_NAME. Make sure that you are connecting to the pluggable database (PDB) if you are installing in a container-based environment. Verify the database connectivity using the following commands:
or
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Make sure that the Sqlplus utility is available in the installation server. |
Parent topic: Install the Data Model with Pre-created User Schemas
Oracle Healthcare Foundation Tablespaces
Create the following default tablespaces. You can use different tablespace names than the ones listed below.
- | Tablespace Name | Big File Tablespace | Description |
---|---|---|---|
hdi_ts |
Yes |
Default tablespace for the Interface Tables (hdi) schema |
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hdm_ts |
Yes |
Default tablespace for the Data Warehouse (hdm) schema |
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hcd_ts |
Yes |
Default tablespace for the Common Data Mart (hcd) schema |
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odb_data_ts |
Yes |
Default tablespace for the Omics Data Bank (odb) schema |
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odb_index_ts |
Yes |
Used for indexes of the Omics Data Bank (odb) schema |
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odb_lob_ts |
Yes |
Used for LOB columns in the Omics Data Bank (odb) schema |
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cdm_data_ts |
Yes |
Default tablespace for the Cohort Data Mart (cdm) schema |
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cdm_index_ts |
Yes |
Used for indexes of the Cohort Data Mart (cdm) schema |
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ent_ts |
No |
Default tablespace for the Enterprise (ent) schema |
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job_data_ts |
No |
Default tablespace for the Job Engine (job) schema |
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job_index_ts |
No |
Used for indexes of the Job Engine (job) schema |
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job_store_ts |
No |
Database File System (DBFS) store created as part of the Job Engine installation |
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job_lob_ts |
No |
Name of the tablespace to store LOB data in the DBFS store created for the JOB ENGINE schema user |
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job_tbs_ts |
No |
Name of the tablespace to be used for the DBFS store created for the JOB_ENGINE schema |
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svc_ts |
No |
Default tablespace used for the Services (svc) schema |
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api_ts |
No |
Default tablespace for the Clinical Genomics (cga) API schema. |
Parent topic: Install the Data Model with Pre-created User Schemas
Temporary Tablespaces
Oracle Healthcare Foundation loaders and ETLs require a large temporary tablespace for sorting. A dedicated bigfile temporary tablespace or a single temporary tablespace group should be assigned to all Oracle Healthcare Foundation schemas.
Parent topic: Install the Data Model with Pre-created User Schemas
Prepare the Installation Files
- | Preparations |
---|---|
Extract the contents of the Oracle Healthcare Foundation media pack to your system. |
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Open the media_pack_location folder. |
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Unzip the
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Parent topic: Install the Data Model with Pre-created User Schemas
Create Database Roles
- | Instructions |
---|---|
Navigate to the directory |
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Unzip the
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Connect to Oracle SYS
from the extracted content and create database roles by
executing the |
Parent topic: Install the Data Model with Pre-created User Schemas
Create User Schemas
Create the following user schemas and assign the appropriate default and temporary
tablespaces. Refer to Oracle Healthcare Foundation Tablespaces
and Temporary Tablespaces
for details. If you created tablespaces
with different names, use those names instead.
- | Schema | Default Tablespace | Temporary Tablespace |
---|---|---|---|
Interface Tables (hdi) |
hdi_ts |
temp |
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Data Warehouse (hdm) |
hdm_ts |
temp |
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Common Data Mart (hcd) |
hcd_ts |
temp |
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Omics Data Bank (odb) |
odb_data_ts |
temp |
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Cohort Data Mart (cdm) |
cdm_data_ts |
temp |
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Enterprise (ent) |
ent_ts |
temp |
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Job Engine (job) |
job_data_ts |
temp |
|
Services (svc) |
svc_ts |
temp |
|
Clinical Genomics (cga) |
api_ts |
temp |
Parent topic: Install the Data Model with Pre-created User Schemas
Run the Installation Scripts
Execute the following scripts/commands as a DBA user. When prompted, enter the respective schema names.
When prompted for the application role, enter OHF_APPLICATION_ROLE.
- | Scripts |
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Execute the following commands: > > |
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Execute the following command: > |
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Execute the following commands:
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Parent topic: Install the Data Model with Pre-created User Schemas
Start the Installer
- | Steps |
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Make sure that all the Oracle Healthcare Foundation schemas are disconnected from the database by querying
|
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Navigate to the
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Change the protection on the files as follows: chmod 755 * |
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Start the Oracle Universal Installer (OUI) using the following command:
The The |
Parent topic: Install the Data Model with Pre-created User Schemas
Run the Installer
- | Screen | Action |
---|---|---|
Welcome |
Click Next. |
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Select a Product to Install |
Select the Oracle Healthcare Foundation Data Model 8.1.0.0.0 option. |
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Specify Home Details |
Enter the installation home name and location. |
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Verify Installation Prerequisites |
Verify if all the prerequisites are met before proceeding. |
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Oracle Client Home Configuration |
Specify the Oracle (version 12.2.0.1.0) client home path. The installer validates this path. |
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Database Configuration |
Enter values for the following fields:
The installer will not validate the database connectivity. Make sure that you are able to connect to the database from SQLPlus. |
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Table Compression |
On an Exadata setup, use the following compression options: Interface Tables schema
Data Warehouse schema
Common Data Mart schema
Cohort Data Mart schema
Omics Data Bank schema
On a non-Exadata setup, for each of the above schemas, choose either No Compression (default) or Advanced Compression. |
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Data Model Configuration |
Enter values for the pre-created schemas:
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Data Model Configuration |
Enter values for the pre-created schemas:
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Data Model Configuration |
Enter values for the pre-created schemas:
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Data Model Configuration Verification |
Click Next. |
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Tablespace Details |
Click Next. |
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Temporary Tablespace Details |
Click Next. |
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Omics Data Bank and Cohort Data Mart Parameters |
Enter values for the following fields:
Execute the following query to find all store names in the database (created by all previous installations) by connecting to the SYS user:
Note: If you have store names in the database that do not match the %JOB_STORE% pattern, run the following query to find the correct names:
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Tablespace Parameters |
Enter values for the fields below from the existing or pre-created CDM, ODB, and Job
engine schemas. Make sure that these tablespaces exist or were
created before the installation. Refer to
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Summary |
Click Install. |
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End of Installation |
Click Exit after reviewing the installation information. At the confirmation prompt, click Yes to exit the installer. |
Parent topic: Install the Data Model with Pre-created User Schemas
Check the Installation
- | Steps |
---|---|
Review the generated installation log files for errors. For details, see
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Contact Oracle support, if necessary, to resolve any errors. |
Parent topic: Install the Data Model with Pre-created User Schemas
Revoke Privileges
After the Cohort Data Mart (CDM) and Omics Data Bank (ODB) data model installation, connect to the database user with the DBA privilege, and execute the following scripts to revoke privileges:
REVOKE CREATE ANY DIRECTORY FROM odb user
REVOKE CREATE ANY CONTEXT FROM cdm user
where,
odb_user is the ODB schema name.
cdm_user is the CDM schema name.
Parent topic: Install the Data Model with Pre-created User Schemas