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17 Oracle Healthcare Foundation Omics Data Bank Loaders

You can load Omics data files by using REST APIs or PL/SQL loaders.

For information on how to load Omics data files using REST APIs, see the Oracle Healthcare Foundation Application Programming Interface Guide.

For information on how to load Omics data files using PL/SQL loaders, follow the instructions below:

1. Prerequisites

2. Installing the Oracle Healthcare Foundation Omics Data Bank Loaders

17.1 Prerequisites

To install Omics Data Bank Loaders, the Data Model must be installed. For Data Model installation instructions, see Chapter 2.

Installing Java

1. Download JRE 1.8 from http://www.oracle.com/technetwork/java/javase/downloads/index-jsp-138363.html

2. Install JRE on the system that you will use as the client tier. The EMBL and Swissprot loaders require JRE 1.8 to be installed on the machine from where they will be run.

3. Make sure that the path for Java 1.8 is set in the environment variable.

   Note:

   If you plan to execute multiple loaders, make sure that you execute each loader from a separate directory. You must copy .sh/.bat files to another directory to execute the loaders in parallel.

17.2 Installing the Oracle Healthcare Foundation Omics Data Bank Loaders

Copy the ODB Loaders folder or ODB_Loaders.zip file from the OHF <INSTALL_HOME>/.

If you are executing the loaders on an operating system that supports the bash shell command language, make sure that the .sh files have execute privileges.

For example,

chmod +x <filename>

For more details, refer to the Omics Data Bank chapter in the Oracle Healthcare Foundation Programmer's Guide.