There are a number of issues that can occur in an i2b2/SHRINE environment ultimately leading to queries not working correctly at your site. We've compiled a list of common things that you should try/verify at your site.
The first step is to disregard the SHRINE component altogether and verify that queries are working in your local i2b2. To do this, access your i2b2 webclient (not SHRINE web client), and login with the same service account credentials that your SHRINE uses. You can find this account defined in SHRINE's configuration file (e.g. /opt/shrine/tomcat/lib/shrine.conf). After you login to your i2b2 web client, try running a query–remember, this will action will only query your local i2b2. If you cannot get queries to run in your local i2b2 using the same i2b2 account that SHRINE uses, then the problem must be troubleshooted in i2b2, not SHRINE.
Remember, the SHRINE only uses one i2b2 account to execute all queries at your local site. If you are logged into the i2b2 webclient as this account, you should notice that your Previous Queries pane at the bottom-left is filled with queries run as this user. These are the local i2b2 queries that are behind every query that your site responds to in the SHRINE. Therefore, if you know the query name and/or date & time, you can find the corresponding i2b2 query from the problematic SHRINE query, and troubleshoot from there.
i2b2 runs in the Wildfly application server. Depending on your log level settings, it may be difficult to find the exact logs you are looking for. One quick way is to run your Wildfly "in the console" and not in the background. You can do this by first shutting down your Wildfly server. Once it's shutdown, you can type the following command:
# cd /opt/wildfly/bin (replace this directory with your Wildfly directory)
# ./standalone.sh -b 0.0.0.0
All of your log messages will be outputted on screen. After Wildfly starts, you should access your i2b2 web client, construct and run a query. If/when you encounter an error, you may see Java exceptions in the console screen. When you're done, be sure to Ctrl+C to break out of the process, and restart your Wildfly in the background your usual way.
There may be required core database changes in some i2b2 version upgrades. This means that one or more tables in your i2b2 installation will need to be modified (e.g. to add a new column, etc.) If you've verified that you've performed all the necessary database changes, please make sure to check your Cell Properties Migration. Starting with i2b2 1.7.12, all cell properties that used to be in /wildfly/standalone/configuration/{cell}/{cell}.properties (e.g. "crc,properties" file) have been migrated to the database. There is a new table called HIVE_CELL_PARAMS that stores all of your cell properties now. The most common issue is that the AGG_SERVICE_ACCOUNT password that used to be defined in crc.properties needs to be updated in the database. Please ensure that this is done, or no queries will work.