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 |
Notes
Release 1.7.12 contains changes to the i2b2 core Server, database and Web Client.
- The upgrade process is now made easier using a pre-built war file and the properties files are now stored in the database.
- The prebuilt-war file has all the core, web and database files packaged together and available as single download zip file.
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.
Step-by-Step Instructions for WildFly
In the following instructions the variable { version } refers to your version of Wildfly installed. We have tested with Wildfly 10, 14, and 17.
Stop WildFly
Backup your existing i2b2.war directory
Extract the download file i2b2core-war-1712a.zip to a folder outside of wildfly folder.
Copy all the files from the download war file deployment into your existing WildFly standalone directory.
Steps to Upgrade Database
- Backup your existing data folder
- Download the upgrade zip folder from
- Extract the download file i2b2core-upgrade-1.7.13.zip to a folder outside of the data folder.
- Copy the db.properties files from your data back up sub folders, namely Crcdata, Hivedata, Metadata, PMdata to the respective locations of the new data folder
- Run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql .
Alternative to Step 5, 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 in the each individual cell folder as below. | |
1.7.09c | PmData/scripts/upgrade_{db}_i2b2pm_tables.sql Crcdata/scripts/crc_create_query_{db}.sql Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql |
1.7.10 | Metadata/scripts/ont_{db}.sql Crcdata/scripts/crc_create_query_{db}.sql Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql |
1.7.11 1.7.12 1.7.13 | Crcdata/scripts/crc_create_query_{db}.sql Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7 |
Run the ant scripts for Metadata and Crcdata for releases 1.7.09C to 1.7.12.
If you are upgrading from 1.7.12 to 1.7.12a, run the ant script for Crcdata.
Update the datasource (*-ds.xml) files in your deployment directory
Copy *-ds.xml files from the backup folder to wildfly-1#.0.1.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 1.7.12, 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.
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
Verify your upgrade
