1 Data Model Installation

select * from v$parameter where name = 'compatible';

If the parameter is not set to 12.2.0.1.0, ask your database administrator to set it.

For Oracle Healthcare Foundation Globalization Support information, see Oracle Database Globalization Support Guide and set your database character set accordingly.

Verify the database connectivity using the following command:

SQL>connect <username>@<hostname>:<port number>/<service name>

or

sqlplus <username>@'(DESCRIPTION=(ADDRESS=(PROTOCOL=TCP)(HOST=<dbhost>)(PORT=<dbport>))(CONNECT_DATA=(SERVICE_NAME=<dbservicename>)))'

• Oracle Linux 6.7 (64-bit) OS or above

• Oracle Database 12.2.0.1.0 client

unzip -a OHF_721_Linux-x64.zip

chmod 755 *

• Hostname - By default, the system host name appears. For remote installations, set this value to the host name of the remote machine.

• Port - By default, the port number is 1521. You can edit this field if required.

• Service name

• System user password

• Sys user password

Interface Tables schema

• Hybrid columnar compression (default)

• No Compression

Data Warehouse schema

• No Compression (default)

• Advanced Compression: Preferred if updates are high. If you don't have a license for Advanced Compression, select Hybrid Columnar Compression.

• Hybrid Columnar Compression

Common Data Mart schema

• No Compression (default)

• Advanced Compression

Cohort Data Mart schema

• No Compression (default)

• Advanced Compression

Omics Data Bank schema

• Hybrid columnar compression (default)

On a non-Exadata setup, for each of the above schemas, choose either No Compression (default) or Advanced Compression.

• Interface Tables schema name

• Interface Tables schema password

• Data Warehouse schema name

• Data Warehouse schema password

• Common Data Mart schema name

• Common Data Mart schema password

• Omics Data Bank schema name

• Omics Data Bank schema password

• Cohort Data Mart schema name

• Cohort Data Mart password

• Enterprise schema name

• Enterprise schema password

• Job Engine schema name

• Job Engine schema password

• Services schema name

• Services schema password

• Clinical Genomics (cga) schema name

• Clinical Genomics (cga) schema password

For example,

Unix: /u01/oradata/dbname

ASM: +DATA_EX02/hashas01/datafile

Note:

• The ASM location must always start with +.

• The path should not end with /.

• hdi_ts - Default tablespace used for Interface tables (hdi) schema

• hdm_ts - Default tablespace used for Data Warehouse (hdm) schema

• hcd_ts - Default tablespace used for Common Data Mart (hcd) schema

• odb_data_ts - Default tablespace used for Omics Data Bank (odb) schema

• odb_index_ts - Tablespace used for indexes of the Omics Data Bank (odb) schema

• odb_lob_ts - Tablespace used for LOB columns in the Omics Data Bank (odb) schema

• cdm_data_ts - Default tablespace used for Cohort Data Mart (cdm) schema

• cdm_index_ts - Tablespace used for indexes of the Cohort Data Mart (cdm) schema

• ent_ts - Default tablespace used for Enterprise (ent) schema

• job_data_ts - Default tablespace for Job Engine (job) schema

• job_index_ts - Tablespace used for indexes of the Job Engine (job) schema

• job_store_ts - Database File System (DBFS) store is created as part of the Job Engine installation

• job_lob_ts - Tablespace used to store LOB data in the DBFS store created for the JOB ENGINE schema user

• job_tbs_ts - Tablespace used for the DBFS store created for the JOB_ENGINE schema

• svc_ts - Default tablespace used for services schema (svc)

• api_ts - Default tablespace used for Clinical Genomics schema (cga)

For each schema, you can edit the default tablespace name, initial size, max size, and tablespace encryption.

• hdi_temp - Temporary tablespace for the Interface tables schema (hdi)

• hdm_temp - Temporary tablespace for the Data warehouse schema (hdm)

• hcd_temp - Temporary tablespace for the Common data mart schema (hcd)

• odb_temp - Temporary tablespace for the Omics Data bank schema (odb)

• cdm_temp - Temporary tablespace for the Cohort data mart schema (cdm)

• ent_temp - Temporary tablespace for the Enterprise schema (ent)

• job_temp - Temporary tablespace for the Job Engine schema (job)

• svc_temp - Temporary tablespace for the Services schema (svc)

• api_ts - Temporary tablespace used for Clinical Genomics schema (cga)

For each schema, you can edit the temporary tablespace name, initial size and max size.

• Result Partition - Used to partition result tables in the ODB schema. The available options are:

  • GENE (Default)

  • STUDY (Deprecated. Use GENE instead)

• Promoter Offset - Numerical value to specify a portion of the gene used as a promoter in the ODB schema. The default value is 200.

• Flanking Offset - Numerical value to specify the region before and after a gene to link results to a gene in the ODB schema. The default value is 200.

• Max Parallel Degree - An option to specify the maximum degree of parallelism to be set on tables or used in the SQL statements for the CDM or ODB schema. It is dependent on the machine configuration of the database server. The default value is 2.

• Job Store Name - Use the job schema name.

If you are using the same database instance for multiple environments, enter a unique job store name for each job schema.

select * from v$parameter where name = 'compatible';

If the parameter is not set to 12.2.0.1.0, ask your database administrator to set it.

For Oracle Healthcare Foundation Globalization Support information, see Oracle Database Globalization Support Guide and set your database character set accordingly.

Verify the database connectivity using the following command:

SQL>connect <username>@<hostname>:<port number>/<service name>

or

sqlplus <username>@'(DESCRIPTION=(ADDRESS=(PROTOCOL=TCP)(HOST=<dbhost>)(PORT=<dbport>))(CONNECT_DATA=(SERVICE_NAME=<dbservicename>)))'

• Oracle Linux 6.7 (64-bit) OS or above

• Oracle Database 12.2.0.1.0 client

unzip -a OHF_721_Linux-x64.zip

Execute the following commands:

> ALTER USER <odb> QUOTA UNLIMITED on <odb_index_ts>

> ALTER USER <odb> QUOTA UNLIMITED on <odb_lob_ts>

Execute the following command:

> ALTER USER <cdm> QUOTA UNLIMITED on <cdm_index_ts>

Execute the following commands:

> ALTER USER <job> QUOTA UNLIMITED on <job_index_ts>

> ALTER USER <job> QUOTA UNLIMITED on <job_store_ts>

> ALTER USER <job> QUOTA UNLIMITED on <job_lob_ts>

> ALTER USER <job> QUOTA UNLIMITED on <job_tbs_ts>

select * from sys.gv_$session where status <> 'KILLED' and username in ('<OHF Schemas>');

chmod 755 *

• If the database server is on the machine where the installer is running and is an Exadata instance:

  sh runInstaller.sh -local dba_tasks=false db_platform=exadata

• If the database server is on the machine where the installer is running and is a non-Exadata instance:

  sh runInstaller.sh -local dba_tasks=false db_platform=default

• If the database server is on a different machine and is an Exadata instance:

  sh runInstaller.sh -local remote_installation=true dba_tasks=false db_platform=exadata

• If the database server is on a different machine and is a non-Exadata instance:

  sh runInstaller.sh -local dba_tasks=false db_platform=default remote_installation=true

The -local option tells the installer to install on the local node, irrespective of the cluster nodes specified on the installer machine.

The dba_tasks=false option tells the installer not to create user schemas and tablespaces.

• Hostname - By default, the system host name appears. For remote installations, set this value to the host name of the remote machine.

• Port - By default, the port number is 1521. You can edit this field if required.

• Service name

The installer will not validate the database connectivity. Make sure that you are able to connect to the database from SQLPlus.

Interface Tables schema

• Hybrid columnar compression (default)

• No Compression

Data Warehouse schema

• No Compression (default)

• Advanced Compression: Preferred if updates are high. If you don't have a license for Advanced Compression, select Hybrid Columnar Compression.

• Hybrid Columnar Compression

Common Data Mart schema

• No Compression (default)

• Advanced Compression

Cohort Data Mart schema

• No Compression (default)

• Advanced Compression

Omics Data Bank schema

• Hybrid columnar compression (default)

On a non-Exadata setup, for each of the above schemas, choose either No Compression (default) or Advanced Compression.

• Interface Tables schema name

• Interface Tables schema password

• Data Warehouse schema name

• Data Warehouse schema password

• Common Data Mart schema name

• Common Data Mart schema password

• Omics Data Bank schema name

• Omics Data Bank schema password

• Cohort Data Mart schema name

• Cohort Data Mart password

• Enterprise schema name

• Enterprise schema password

• Job Engine schema name

• Job Engine schema password

• Services schema name

• Services schema password

• Clinical Genomics (cga) schema name

• Clinical Genomics (cga) schema password

• Result Partition - Used to partition result tables in the ODB schema. The available options are:

  • GENE (Default)

  • STUDY (Deprecated. Use GENE instead)

• Promoter Offset - Numerical value to specify a portion of the gene used as a promoter in the ODB schema. The default value is 200.

• Flanking Offset - Numerical value to specify the region before and after a gene to link results to a gene in the ODB schema. The default value is 200.

• Max Parallel Degree - An option to specify the maximum degree of parallelism to be set on tables or used in the SQL statements for the CDM or ODB schema. It is dependent on the machine configuration of the database server. The default value is 2.

• Job Store Name - Use the job schema name.

Execute the following query to find all store names in the database (created by all previous installations) by connecting to the SYS user:

SELECT DISTINCT owner,object_type,object_name,created FROM all_objects WHERE object_name LIKE '%JOB_STORE%';

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:

SELECT DISTINCT owner,object_type,object_name,created FROM all_objects WHERE owner =<Job Username/schemaname> AND object_type IN ('TABLE','VIEW');

• cdm_index_ts_name

• odb_index_ts_name

• odb_lob_ts_name

• job_index_ts_name

• job_lob_ts_name

• job_tbs_ts_name