Upgrade to Release 1.7.13 from 1.7.09c
Download
| Description | i2b2 Released Version | Minimum Version Required | Download Link | Requirements |
|---|---|---|---|---|
| Files to upgrade the i2b2 server to 1.7.13 | 1.7.13 | 1.7.09c | See Technical Details section on the i2b2 Upgrades page. | |
| Files to upgrade the i2b2 db instance to 1.7.13 | 1.7.13 | 1.7.09c | i2b2core-upgrade-1.7.13.zip | |
| Files to upgrade the webclient | 1.7.13 | i2b2webclient-1713.zip |
Notes
Release 1.7.13 contains changes to the i2b2 core Server, database and Web Client.
- The db upgrade process is now automated to reduce the workload of manually running each individual sql script against your db instance.
- All the SQL script executions are incorporated into a single data_build.xml which can easily be run using ant commands.
Note: If you are running your application on JBoss, please upgrade to Wildfly before proceeding with the upgrade.
Upgrade Instructions
Below are Step-by-Step Instructions after you have upgraded to Wildfly.
Initial Steps:
- Download the i2b2core-upgrade-1713.zip from
- Extract the download file i2b2core-upgrade-1713.zip to a folder outside of your existing i2b2 installation folder
Then, follow the steps below to upgrade i2b2 server, database instance and the webclient.
Steps to Upgrade i2b2 Server
In the following instructions the variable { version } refers to your version of Wildfly installed. We now support Wildfly 17 version.
Stop WildFly
Backup your existing i2b2.war directory
Copy all the files from the extracted downloaded war file deployment into your existing WildFly standalone directory. The folder includes the upgraded war file and jdbc driver files
/opt/<wildfly-17.0.0.Final and above version>/standalone/deployments/
Update the datasource (*-ds.xml) files in your deployment directory
Copy *-ds.xml files from the backup folder to wildfly-17.0.#.Final/standalone/deployments
Edit the following files crc-ds.xml, ont-ds.xml, pm-ds.xml, work-ds.xml
and replace ALL the <driver>{something}.jar</driver> with
Oracle | SQL Server | PostgreSQL |
<driver>ojdbc8.jar</driver> | <driver>mssql-jdbc-7.4.1.jre8.jar</driver> | <driver>postgresql42.2.8.jar</driver> |
Migrate cell properties to 1.7.13, if needed. In 1.7.12, cell properties have been moved to the database, in a table called hive_cell_params. If any cell properties were previously changed, they will need to be manually updated in the database. After this, the properties files can be deleted to prevent confusion.
More documentation on setting cell properties is available at this page. Most commonly, the AGG_SERVICE_ACCOUNT password will need to be updated. Generally, the cell URLs do not need to be configured anymore, as the hostname and port is now auto-detected.
Steps to Upgrade i2b2 database
- Backup your existing data folder
- Copy all the folders from the extracted download data folder into your existing data Upgrade folder
Example .\2b2core-upgrade-1712a_ext\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\. This will replace the existing Crcdata, Hivedata, Metadata, PMdata folders .
Alternative to step 2, navigate to the edu.harvard.i2b2.data\Release_1-7\Upgrade\ directory of your extracted folder
3. Copy the db.properties files from your back up into the respective locations(namely Crcdata, Hivedata, Metadata, PMdata )
4. Open the command prompt and navigate to cell folders and run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql .
Alternative to Step 4, you can run individual SQL scripts on your db instance in place of ant commands.
In data folder\Release_1-7\Upgrade\ run the ant commands under each individual cell subfolder as below. | |
| Upgrade From Build | Upgrade to Latest build |
1.7.09c | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-09c upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-09c upgrade_hive_tables_release_1-7-10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-09c upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
1.7.10 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
1.7.11 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
| 1.7.12 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-12 |
Steps to Upgrade i2b2 Webclient
Backup your existing i2b2_config_data.js from your web server
On your webclient backup your existing i2b2_config_data.js to a folder outside of your web server.
Install the new webclient on your web server
Start WildFly
You can either run WildFly standalone or as a service.
Verify Your Upgrade
your upgrade
