3.7 Metadata Tables

Overview of the Metadata Installation Process

The Metadata tables are part of the Ontology Management (ONT) Cell. The following outlines the steps that will be taken during the Metadata installation.

Step 1:   Change your working directory

Step 2:   Configure the database properties for the Metadata

Step 3:   Create the Metadata tables, indexes and sequences

Step 4:   Load sample data into the tables

 

3.7.1 Working Directory

Step1: Change Working Directory for Metadata Installation

During the Metadata Installation we will be working with the Metadata 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 Metadata directory enter the following command:

Change Directory Command

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

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\Metadata

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

 

3.7.2 Set Database Properties

Step 2: Set Database Properties for Metadata 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

2. 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 i2b2metadata and the project to demo.

 

Database Properties File

Oracle Database

db.type=oracle
db.username=i2b2metadata
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=i2b2metadata
db.password=demouser
db.driver=org.postgresql.Driver
db.url=jdbc:postgresql://LocationOfYourDatabase/i2b2?searchpath=i2b2metadata
db.project=demo

SQL Server Database

db.type=sqlserver
db.username=i2b2metadata
db.password=demouser
db.driver=com.microsoft.sqlserver.jdbc.SQLServerDriver
db.url=jdbc:sqlserver://LocationOfYourDatabase:1433;database=demo
db.project=demo

3. 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.

 

3.7.3 Create Metadata Tables

Step 3: Create Metadata Tables

The third step in the Metadata installation process is to create the Metadata 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_metadata_tables_release_1-7

Windows Run Command

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

 

3.7.4 Load Metadata Tables

Step 4: Load Metadata Tables

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

Important

The Metadata provided in the data package is a sampling of terms from various standard coding systems. There data is rather large but it is by no means a complete set of ICD-9, SNOMED, LOINC, or CPT codes. If you have your own Metadata and wish to load it instead of the i2b2 sample Metadata 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_metadata_load_data

Windows Run Command

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

Note

The loading of the Metadata may take an extended period of time (20 minutes) due to the amount of sample data provided.

Select the command line that is appropriate for your environment to load the identified data

Linux Run Command

ant -f data_build.xml db_metadata_load_identified_data

Windows Run Command

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