Stream: troubleshooting

Topic: security patch: replacing 5.14 war file


view this post on Zulip jamie jamison (Jun 30 2026 at 02:35):

We're still on 5.14. I'm trying to replace the old dataverse-5.14.war file with the updated one. The deploy has been failing because the postgres database (dvndb) exists:
**PRIMARY KEY (SEQ_NAME))": org.postgresql.util.PSQLException: ERROR: relation "sequence" already exists PER01000: Got SQLException executing statement "INSERT INTO SEQUENCE(SEQ_NAME, SEQ_COUNT) values ('SEQ_GEN', 0)": org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "sequence_pkey" Detail: Key (seq_name)=(SEQ_GEN) already exists.
Command deploy failed. renamed the dvndb database as a backup. But the deploy now fails because dvndb doesn't exist: remote failure: Error occurred during deployment: Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.7.9.payara-p2): org.eclipse.persistence.exceptions.DatabaseException Internal Exception: java.sql.SQLException: Error in allocating a connection. Cause: Connection could not be allocated because: FATAL: database "dvndb" does not exist
Error Code: 0. Please see server.log for more details.
Command deploy failed.
**

Should there be an empty dvndb for the deploy? (I'll also copy this to the google group).

view this post on Zulip jamie jamison (Jun 30 2026 at 22:28):

Deploy then fails because there isn't a dvndb database. Created an empty dvndb database (the renamed backup also still exists). The deploy works but payara5 isn't coming up.

Caused by: javax.persistence.NoResultException: getSingleResult() did not retrieve any entities... findRootDataver

view this post on Zulip Philip Durbin ๐Ÿš€ (Jul 01 2026 at 01:02):

Sorry, sorry, been busy. You definitely should keep your database!

view this post on Zulip jamie jamison (Jul 01 2026 at 22:41):

I put the original dvndb database back. Then undeployed and redeployed the patched dataverse-5.14.war file.

sudo ./asadmin deploy /tmp/dataverse-5.14.war
Enter admin user name> admin
Enter admin password for user "admin">
No response from Domain Admin Server after 600 seconds.
The command is either taking too long to complete or the server has failed.
Please see the server log files for command status.
Command deploy failed.


payara5-server.log

view this post on Zulip Philip Durbin ๐Ÿš€ (Jul 08 2026 at 20:56):

I just caught up on how @Don Sizemore is helping at https://help.hmdc.harvard.edu/Ticket/Display.html?id=409936

Let's keep talking there. Or feel free to start a three way DM with me and Don.

view this post on Zulip jamie jamison (Jul 09 2026 at 20:33):

Tim and claude found the answer.

I don't know why but the the way deploy runs is a bit different then it was when 5.14 was initially deployed (the unpatched version).

I checked to be sure who 'owned' dataverse-5.14 and deployed by:
**
sudo -u dataverse ./asadmin deploy dataverse-5.14.war
**

view this post on Zulip Philip Durbin ๐Ÿš€ (Jul 09 2026 at 20:37):

ah, great!


Last updated: Aug 18 2026 at 08:27 UTC