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3.6 IM Tables

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Peter Rice
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3.6 IM Tables

Overview of the IM Data Installation Process

The Imdata tables are part of the Identity Management (IM) Cell. The following outlines the steps that will be taken during the Imdata installation.

Step 1:   Change your working directory

Step 2:   Configure the database properties for the Imdata

Step 3:   Create the Imdata tables, indexes and sequences

Step 4:   Load sample data into the tables

 

3.6.1 Working Directory

Step 1: Change Working Directory for Imdata Installation

During the IM Data Installation we will be working with the Imdata directory. Within this directory are the files we will be editing to define the database properties, create the IM tables and load the sample data provided with the data package.


To change your working directory to the Imdata directory enter the following command:

Change Directory Command

cd YOUR_I2B2_DATA_DIR/edu.harvard.i2b2.data/Release_1-7/NewInstall/Imdata
Important

The change directory command shown above is written for Linux. The command itself is the same for both Linux and Windows with the only exceptions being the slashes in the path name and Linux does not include the "drive".

  • Linux Path: use a forward slash.
  • Windows Path: use a backward slash.

EXAMPLES:

Windows Command:  cd C:\opt\data\edu.harvard.i2b2.data\Release_1-7\NewInstall\Imdata

Linux Command:  cd /opt/data/edu.harvard.i2b2.data/Release_1-7/NewInstall/Imdata

 

3.6.2 Set Database Properties

Step 2: Set Database Properties for Imdata Tables

As stated earlier each i2b2 database schema has a corresponding directory that contains the data files for installing the data. Each of these directories has a file called db.properties and it needs to be updated with your environment variables.

 

Steps for setting database properties


Assumptions:

  • You are logged into the command line application for your environment. (Linux: Terminal or Shell and Windows: Command Prompt)
  • You have already changed your working directory to the one that is appropriate for this installation.
  1. At the command prompt type the following:

 Linux Command

      open db.properties

Windows Command

      db.properties
  1. The db.properties file will open. Set the following properties for the DBMS at your site:
Important
When setting the database properties make sure you set the user to i2b2imdata and the project to demo.

 

Database Properties File

Oracle Database

db.type=oracle
db.username=i2b2imdata
db.password=demouser
db.server=LocationOfYourDatabase:1521:xe
db.driver=oracle.jdbc.driver.OracleDriver
db.url=jdbc:oracle:thin:@LocationOfYourDatabase:1521:xe
db.project=demo


PostgreSQL Database

db.type=postgresql
db.username=i2b2imdata
db.password=demouser
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://LocationOfYourDatabase/i2b2?searchpath=i2b2imdata
db.project=demo


SQL Server Database

db.type=sqlserver
db.username=i2b2imdata
db.password=demouser
db.driver=com.microsoft.sqlserver.jdbc.SQLServerDriver
db.url=jdbc:sqlserver://LocationOfYourDatabase:1433;database=demo
db.project=demo
  1. Save the changes and close the file.
Tip
To save yourself steps, DO NOT close your Command Prompt window as you will be continuing to use it throughout the remainder of the installation.

 

3.6.3 Create IM Tables

Step 3: Create Identity Management (IM) Tables

The third step in the Imdata installation process is to create the IM tables, indexes and sequences by running the following command:


Select the command line that is appropriate for your environment.

Linux Run Command

ant -f data_build.xml create_imdata_tables_release_1-7

Windows Run Command

%ANT_HOME%\bin\ant.bat -f data_build.xml create_imdata_tables_release_1-7
Note
If the command %ANT_HOME% does not work it may be because you did not set your environment variables as suggested in the Requirements Chapter. If you do not wish to set this variable then you will need to replace %ANT_HOME% with the full path to your Ant directory.

 

3.6.4 Load IM Tables

Step 4: Load Identity Management (IM) Tables

The fourth and final step in the Imdata installation process is to load the data into the IM tables by running the following command:

Important
  • The Imdata provided in the data package is a sampling of demonstration patients and projects that are by no means based on real patients. Its intended use is to provide you a sample of how you may setup the IM tables.
  • The data provided is intended to provide you a sample of how you may setup the IM tables.
  • If you have your own data and wish to load it instead of the i2b2 sample Imdata you can do it at this point of the installation.

 



Select the command line that is appropriate for your environment.

Linux Run Command

ant -f data_build.xml db_imdata_load_data

Windows Run Command

%ANT_HOME%\bin\ant.bat -f data_build.xml db_imdata_load_data

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