On Linux, move the /opt/wildfly-{version}.Final/standalone/deployments/ and save it to a different location outside of /opt/wildfly-{version}.Final/
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\
Extract the download file i2b2core-war-1712.zip to a folder outside of wildfly folder.
Copy all the files from the download war file deployment into your existing WildFlystandalone directory.
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 /i2b2/data/ folder
CRC
Open the file: /i2b2/data/Crcdata/scripts/crc_create_query_{db}.sql and run the last 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' ;
Hive
Run /i2b2/data/Hivedata/scripts/upgrade_{db}_i2b2hive_tables.sql
Ontology
Open the file: /i2b2/data/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: /i2b2/data/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);
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>
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.
On Linux, move the folder /var/www/html/webclient/ and save it to a different location outside of /var/wwww/html/webclient
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
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
On Windows, extract the i2b2webclient-1712.zip c:\inetpub\webclient and copy the backup i2b2_config_data.js to c:\inetpub\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.)
