Version Information
| Current Version: | 1.7.13 |
|---|---|
| Release Date: | June 2022 |
| License: | Mozilla 2 Open Source License |
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 | i2b2 data-source1.7.13.zip | |
| Files to upgrade the webclient | 1.7.13 | i2b2webclient-source1713.zip |
Notes
Release 1.7.13 contains changes to the i2b2 core Server, database and Web Client.
- User login using SAML Authentication
- User Account Registration Tool for local and SAML users
- Updated ACT Ontology v4
- Automated db upgrade process using single data_build.xml
- Improved patient counting scripts
- Log4J upgrade to latest 2.17.1 version to address security vulnerabilities
- Code changes as per veracode scan making i2b2 more secure
- i2b2-Synthea 1K syntheaMass data set in i2b2 format
- i2b2-Synthea data load scripts for loading Synthea data from scratch
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 binary upgrade distribution from i2b2core-upgrade-1713.zip
- 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 existing deployment directory containing i2b2.war file
Upgrade deployments folder
Copy all the files from the extracted downloaded deployment folder into your existing WildFly standalone/deployments directory.
Example your deployments folder: /opt/<wildfly-17.0.0.Final and above version>/standalone/deployments/
Example extracted deployments folder: i2b2core-upgrade-1713\i2b2\deployments
The folder includes the upgraded war file and upgraded jdbc driver files.
Update 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
Replace ALL the <driver>{something}.jar</driver> with latest drivers as below
Oracle | SQL Server | PostgreSQL |
|---|---|---|
<driver>ojdbc8.jar</driver> | <driver>mssql-jdbc--9.2.0jre8.jar</driver> | <driver>postgresql42.3.2.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.
Properties files are stored at /opt/wildfly-{version}.Final/standalone/configuration/ on Linux and c:\opt\wildfly-{version}.Final\standalone\configuration\ on Windows. The table can be edited with a SQL editor in hive_cell_params.
Steps to Upgrade i2b2 database
Steps to perform db upgrade:
- Backup your existing data folder
- Copy all the folders created by extracting the latest version into your existing data Upgrade folder. This will replace existing Crcdata, Hivedata, Metadata, PMdata folders. Example: Downloads\i2b2core-upgrade-1713\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\.
- Copy the db.properties files from your back up into the respective locations (namely Crcdata, Hivedata, Metadata, PMdata )
- Open the command prompt and navigate to each cell folder and run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql.
Alternative to above Step, you can run individual SQL scripts on your db instance in place of ant commands. - In datafolder\Release_1-7\Upgrade\ run the ant commands under each individual cell folder 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_tables_release_1-7-09c upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-12a In the Pmdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c |
1.7.10 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-12a |
1.7.11 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_table_release_1-7-12a In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12a In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a |
| 1.7.12a | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12a |
- Upgrade stored procedures
Run the below CRC and metadata Sql Procedures if your db instance is Postgres.
In Crcdata/scripts/procedures/<db instance>/*.sql
In Metadata/scripts/procedures/<db instance>/*.sql
HIVE_CELL_PARAMS configuration
Check HIVE_CELL_PARAMS table is updated with cell properties parameters as detailed here
Steps to Upgrade i2b2 Webclient
Backup existing webclient folder to a different location outside of your current webclient installation folder
Install new webclient
- Extract the i2b2webclient-1713.zip
- Replace your existing webclient folder on your web server with the extracted webclient folder
- Update i2b2_config_data.js using your existing i2b2_config_data.js from your backed up web directory. Details are provided here
Backup your entire webclient folder before proceeding with webclient upgrade
Start WildFly
You can either run WildFly standalone or as a service.
Verify Your Upgrade
Test Webclient
Navigate to your local i2b2 Web Client in your preferred browser and verify you are able to log on and perform standard i2b2 functions. (e.g. Run queries, retrieve previous queries, view breakdowns, etc.)
