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Upgrade to Release 1.7.12 from 1.7.09c

Version Information

Current Version:1.7.12
Release Date:November, 2019
License:Mozilla 2 Open Source License

Download

Descriptioni2b2 Released VersionMinimum Version RequiredDownload LinkRequirements
Files to upgrade the i2b2 server to 1.7.121.7.121.7.09cSee Technical Details section on the i2b2 Upgrades page.

 Notes

    • Release 1.7.12 contains changes to the i2b2 database and Web Client.
    • If you are upgrading to 1.7.12 from a release prior to 1.7.09c it is important you read the upgrade documentation before upgrading your system because earlier upgrades had changes to properties files. When a release has a change to a property file as did 1.7.09 we will make note of it and outline the steps to merge the changes into your local properties file.


Upgrade Instructions

Below are Step-by-Step Instructions after you have  upgraded to Wildfly.


Example Paths to i2b2.war


WildFly 10 path
/opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war/





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

Linux Example
$ /opt/wildfly-{version}.Final/bin/jboss-cli.sh --connect command=:shutdown


Backup your existing i2b2.war directory

Linux

On Linux, make a copy of /opt/wildfly-{version}.Final/standalone/deployments/i2b2.war/ and save it to a different location outside of /opt/wildfly-{version}.Final/ 

Windows

On Windows, make a copy of c:\opt\wildfly-{version}.Final\standalone\deployments\i2b2.war\ and save it to a different location outside of c:\opt\wildfly-{version}.Final

Delete i2b2.war.deployed file

Linux Example
$ rm /opt/wildfly-{version}.Final/standalone/deployments/i2b2.war.deployed

Starting in 1.7.12 i2b2 will be using a .war file instead of the folder that contains the extension .war.   In future version the upgrade will be replacing the existing .war file with a new war file.

Extract the download file i2b2core-war-1712.zip to a folder outside of wildfly folder.

Copy the i2b2.war into your existing WildFly deployment directory.

Linux Example
$ cp deployments/i2b2.war /opt/wildfly-{version}.Final/standalone/deployments

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.

Linux Example

On Linux, move the folder /var/www/html/webclient/ and save it to a different location outside of /var/wwww/html/webclient

Windows

On Windows, move the folder c:\inetpub\webclient and save it to a different location outside of c:\inetpub\webclient

Install the new webclient on your web server

Linux

On Linux, extract the i2b2webclient-1712.zip to the folder /var/www/html/webclient/ and copy the backup i2b2_config_data.js  to /var/wwww/html/webclient

Windows

On Windows, extract the i2b2webclient-1712.zip c:\inetpub\webclient and copy the backup i2b2_config_data.js  to c:\inetpub\webclient

Run the database upgrade scripts based on the database vendor you are using.   Run the .sql scripts on your database using preferred client.  Within each file contains all the upgrade scripts from 1.7.09c to 1.7.12, run the required scripts for the version you are currently on.

Run the scripts to re created your stored procedures for the CRC Cell.   Modify the db.properties file to reflect your database information.   Than run the following

ant -f crcdata/data_build.xml create_procedures_release_1-7

Run the scripts to created your stored procedures for the Ontology Cell total number   Modify the db.properties file to reflect your database information.   Than run the following

ant -f metadata/data_build.xml create_procedures_release_1-7

Start WildFly

Linux Example
$ /opt/wildfly-{version}.Final/bin/standalone.sh -b 0.0.0.0 &

Verify your upgrade

Test Web Client

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.)




Contents of the Zip File

i2b2upgrade-1709c-to-1712.zip


database/

Crcdata/

scripts/

oracle/

query_demo_insert_data.sql

postgresql/

query_demo_insert_data.sql

sqlserver/

query_demo_insert_data.sql

crc_create_query_oracle.sql

crc_create_query_postgresql.sql

crc_create_qyert_sqlserver.sql

Metadata/

ont_oracle.sql

ony_postgresql.sql

ont_sqlserver.sql

Pmdata/

upgrade_oracle_i2b2pm_tables.sql

upgrade_postgresql_i2b2pm_tables.sql

upgrade_sqlserver_i2b2pm_tables.sql


deployments/

i2b2.war

i2b2webclient-1712.zip








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