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<!DOCTYPE html>
<html>
<head>
    <title>Upgrade i2b2 Software</title>
    <meta charset="UTF-8">
    <meta name="description" content="Upgrading the i2b2 Software to the latest version" />
    <meta name="keywords" content="i2b2, release, upgrade, 1.7.12" />
<!--    <link rel="stylesheet" type="text/css" media="all" href="/stylesheets/i2b2-wiki.css" /> -->
</head>
<body>
    <h1 class="releaseHeading" id="upgradeVersion-current">Upgrading i2b2 from version 1.7.09c to 1.7.12</h1>
</body>
</html>


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i2b2-upgrade-v1712-info
i2b2-upgrade-v1712-info

Version Information

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


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i2b2-upgrade-v1712-download
i2b2-upgrade-v1712-download

Download

Descriptioni2b2 Released VersionMinimum Version RequiredDownload LinkRequirements
Files to upgrade the i2b2 server to 1.7.121.7.121.7.09c
2b2core-war-1712.zip
See Technical Details section on the i2b2 Upgrades page.


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i2b2-upgrade-v1712-note
i2b2-upgrade-v1712-note

 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.


UI Expand
titleExample Paths to i2b2.war



Code Block
languagepowershell
titleWildFly 10 path
/opt/wildfly-10.0.0.Final/standalone/deployments/i2b2.war/





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i2b2-upgrade-v1710-stepByStep-WildFly
i2b2-upgrade-v1710-stepByStep-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.

UI Steps
sizesmall





UI Step

Stop WildFly

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ /opt/wildfly-{version}.Final/bin/jboss-cli.sh --connect command=:shutdown



UI Step

Backup your existing i2b2.war directory

UI Expand
titleLinux

On Linux, move the /opt/wildfly-{version}.Final/standalone/deployments/ and save it to a different location outside of /opt/wildfly-{version}.Final/ 



UI Expand
titleWindows

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





UI Step

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




UI Step

Copy all the files from the download war file deployment into your existing WildFly standalone directory.


UI Step

Upgrade i2b2 Databases to 1.7.12

Run the following upgrade scripts on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql

In /upgradei2b2/databasedata/ folder

CRC

Open the file: /upgradei2b2/databasedata/Crcdata/scripts/crc_create_query_{db}.sql  and run the last two three relevant sections (upgrading from 1.7.09c all the way to 1.7.12):

For example, for SQL server:

--==============================================================
-- Database Script to upgrade CRC from 1.7.09c to 1.7.10 
--==============================================================

-- New column added to support new SQL breakdowns - roles based access

alter table QT_QUERY_RESULT_TYPE add USER_ROLE_CD VARCHAR(255);

--==============================================================
-- Database Script to upgrade CRC from 1.7.10 to 1.7.11 
--==============================================================

insert into QT_PRIVILEGE(PROTECTION_LABEL_CD, DATAPROT_CD, HIVEMGMT_CD) values ('SETFINDER_QRY_PROTECTED','DATA_PROT','USER')

--==============================================================
-- Database Script to upgrade CRC from 1.7.11 to 1.7.12 
--==============================================================

alter table QT_QUERY_RESULT_TYPE add CLASSNAME VARCHAR(200)
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientSetGenerator' where NAME='PATIENTSET'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultEncounterSetGenerator' where NAME='PATIENT_ENCOUNTER_SET'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientCountGenerator' where NAME='PATIENT_COUNT_XML'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultGenerator' where NAME='PATIENT_GENDER_COUNT_XML'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultGenerator' where NAME='PATIENT_VITALSTATUS_COUNT_XML'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultGenerator' where NAME='PATIENT_RACE_COUNT_XML'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultGenerator' where NAME='PATIENT_AGE_COUNT_XML'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientSQLCountGenerator' where NAME='PATIENT_LOS_XML'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientSQLCountGenerator' where NAME='PATIENT_TOP20MEDS_XML'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientSQLCountGenerator' where NAME='PATIENT_TOP20DIAG_XML'
;
update QT_QUERY_RESULT_TYPE set CLASSNAME='edu.harvard.i2b2.crc.dao.setfinder.QueryResultPatientSQLCountGenerator' where NAME='PATIENT_INOUT_XML'
;


HiveRun /i2b2/data/Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql

Ontology

Open the file: /upgradei2b2/databasedata/Metadata/scripts/ont_{db}.sql  and run the script:

For example, for SQL server:

alter table TABLE_ACCESS add C_ONTOLOGY_PROTECTION VARCHAR(MAX);

PM

Open the file: /upgradei2b2/databasedata/Pmdata/scripts/upgrade_{db}_i2b2pm_tables.sql  and run the last relevant section (upgrading from 1.7.09c):

For example, for SQL server:

ALTER TABLE PM_USER_LOGIN
DROP PRIMARY KEY;

CREATE INDEX PM_USER_LOGIN_IDX ON PM_USER_LOGIN(USER_ID, ENTRY_DATE);




UI Step

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>




UI Step

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
titleLinux Example

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


UI Expand
titleWindows

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




UI Step

Install the new webclient on your web server

UI Expand
titleLinux

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


UI Expand
titleWindows

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




UI Step

Start WildFly

Code Block
languagepowershell
titleLinux Example
collapsetrue
$ /opt/wildfly-{version}.Final/bin/standalone.sh -b 0.0.0.0 &




UI Step

Verify your upgrade

UI Expand
titleTest 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.)






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i2b2-upgrade-zip-contents
i2b2-upgrade-zip-contents







Accrual to Clinical Trials ACT