5 Installing the Oracle Health Sciences Omics Data Bank Loaders

5.1 Prerequisite for Installing Oracle Health Sciences Omics Data Bank Loaders

You can install the loaders either on Windows or any other operating system that supports the bash shell command language. If installing on Windows, setup Oracle Wallet with Omics Data Model schema credentials. Setting up Oracle Wallet is optional on all other operating systems.

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. Ensure that the path for Java 1.8 is set in the environment variable.

   
   

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

   
   

Setting up Oracle Wallet

1. Add the following code to tnsnames.ora in $ORACLE_HOME\NETWORK\ADMIN:

   DB001_Wallet = (DESCRIPTION = (ADDRESS_LIST = (ADDRESS = (PROTOCOL = TCP)(HOST = <hostname>)(PORT = <port>)) ) (CONNECT_DATA = (SERVICE_NAME = < service name>) ) )
   

   
   

   Note: Set the SERVICE_NAME, PORT, and HOST values in this code to point to your database installation.

   
   

2. Execute the following commands to create Oracle Wallet either on the client or middle tier:

   >>mkdir wallets>mkstore -wrl <wallet_location> -create -nologoEnter password: <type a 8 alphanumeric-character password>Enter password again:<retype above password>>cd wallets>dirVolume in drive D is DataVolume Serial Number is C###Directory of <wallet_location>11/24/2011 09:24 PM <DIR> .11/24/2011 09:24 PM <DIR> ..11/24/2011 09:13 PM 3,965 cwallet.sso11/24/2011 09:13 PM 3,888 ewallet.p12
   

   The last command should list two files created by running mkstore -create, cwallet.sso and ewallet.p12.

3. Use the following syntax at the command line to create database connection credentials in the Wallet:

   mkstore -wrl <wallet_location> -createCredential <db_connect_string> <username>
   

   Enter the password when prompted.

   
   

   Note: For every user credential added to the Wallet, you must create a new dataset name in tnsnames.ora.

   
   

4. In the client sqlnet.ora file, enter the WALLET_LOCATION parameter and set it to the directory location of the wallet.

   For example,

   WALLET_LOCATION = (SOURCE=(METHOD=FILE)(METHOD_DATA=(DIRECTORY=D:\wallets)))SQLNET.WALLET_OVERRIDE = TRUE
   

5. Execute the following command to test connectivity through SQLPlus:

   >sqlplus /@DB001_WalletSQL*Plus: Release 11.2.0.1.0 Production on Fri Nov 25 15:54:35 2011Copyright (c) 1982, 2010, Oracle. All rights reserved.Connected to:Oracle Database 11g Enterprise Edition Release 11.2.0.1.0 - 64bit ProductionWith the Partitioning, OLAP, Data Mining and Real Application Testing optionsSQL>
   

5.2 Installing the Oracle Health Sciences Omics Data Bank Loaders

Copy the ODB loaders folder from the media pack to the location from where you want to run the loaders.

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

For example,

chmod +x <filename>