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".
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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.
- At the command prompt type the following:
Linux Command
open db.properties
Windows Command
db.properties
- 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
- 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
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