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<h1 class="releaseHeading" id="upgradeVersion-current">Upgrade to Release 1.7.12 from 1.7.09c</h1>
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Version Information
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Download
Description | i2b2 Released Version | Minimum Version Required | Download Link | Requirements |
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Files to upgrade the i2b2 server to 1.7.1212a | 1.7.1212a | 1.7.09c | | See Technical Details section on the i2b2 Upgrades page. |
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Notes
Release 1.7.12 contains changes to the i2b2 core Server, 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. Anchor |
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i2b2-upgrade-v1710-howTo | i2b2-upgrade-v1710-howTo- 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
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| Upgrade i2b2 |
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Knowing some sites have remained on JBoss 7 while some have upgraded to WildFly 10, we have gone ahead and provided Below are Step-by-Step Instructions for both scenarios. For the most part the overall process is very similar. What is different, is the path in which the files reside. Expand the box below to see an example of the differences between the two path namesafter you have upgraded to Wildfly.
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title | Example Paths to i2b2.war |
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language | powershell |
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title | JBoss 7 path |
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| /opt/jboss-as-7.1.1.Final/standalone/deployments/i2b2.war/ | Code Block |
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language | powershell |
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title | WildFly 10 path |
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| /opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war/ |
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| i2b2-upgrade-v1710-stepByStep-WildFly |
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| i2b2-upgrade-v1710-stepByStep-WildFly |
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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.
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Stop WildFly Code Block |
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language | powershell |
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title | Linux Example |
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collapse | true |
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| $ /opt/wildfly-{version}.Final/bin/jboss-cli.sh --connect command=:shutdown |
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Backup your existing i2b2.war directory |
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make a copy of move the /opt/wildfly-{version}.Final/standalone/deployments/ |
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i2b2.war/ and save it to a different location outside of /opt/wildfly-{version}.Final/
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make a copy of move the c:\opt\wildfly-{version}.Final\standalone\deployments\ |
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i2b2.war\ UI Step |
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Extract the download file i2b2core-war-1712.zip to a folder outside of wildfly folder.
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Copy the i2b2.war into your existing WildFly deployment directory.
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language | powershell |
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title | Linux Example |
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collapse | true |
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$ cp deployments/i2b2.war /and save it to a different location outside of c:\opt\wildfly-{version}.Final\
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Delete i2b2.war.deployed file
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language | powershell |
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title | Linux Example |
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collapse | true |
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$ rm /opt/wildfly-{version}.Final/standalone/deployments/i2b2.war.deployed |
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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-1712a.zip to a folder outside of wildfly folder.
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Copy all the files from the download war file deployment into your existing WildFly standalone directory. |
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Upgrade Database
Run the following upgrade scripts on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql In data folder | 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 | Crcdata/scripts/crc_create_query_{db}.sql Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql |
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.
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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> |
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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. UI Expand |
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| Properties files are stored at /opt/wildfly-{version}.Final/standalone/ |
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deploymentsconfiguration/ 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. |
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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. UI Expand |
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| On Linux, move the folder /var/www/html/webclient/ and save it to a different location outside of /var/wwww/html/webclient
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| On Windows, move the folder c:\inetpub\webclient and save it to a different location outside of c:\inetpub\webclient
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Install the new webclient on your web server
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| On Linux, extract the i2b2webclient- |
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17121712a.zip to the folder /var/www/html/webclient/ and copy the backup i2b2_config_data.js to /var/wwww/html/webclient
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| On Windows, extract the i2b2webclient- |
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1712 UI Step |
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1712a.zip c:\inetpub\webclient and copy the backup i2b2_config_data.js to c:\inetpub\webclient
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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 Code Block |
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language | powershell |
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title | Linux Example |
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collapse | true |
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| $ /opt/wildfly-{version}.Final/bin/standalone.sh -b 0.0.0.0 & |
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Verify your upgrade UI Expand |
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| 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.) |
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| i2b2-upgrade-zip-contents |
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Contents of the Zip File
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title | i2b2upgrade-1709c-to-1711.zip |
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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