Unable to upgrade from 2025-09 in Desktop2 MacOS
closed
roger.gordon@ithinking.co.uk
I have Databases (0) from the Local instances tab. Running on MacOS. Version Version 2.1.1 (2.1.1). Databases created with 2025-09. I made a separate post of the Database list issue.
NB: the Data directory is on an external drive, but I think this is a Desktop2 issue since neo4j-admin will back up all DBs and I can connect to all 3 of them (system, default neo4j and one more for testing)
When I try to upgrade I get a message that the Data folder must exist (it has been redirected in neo4j.conf to an external file using server.directories.data=....)
Nissanka Fernando
marked this post as
closed
Thanks for highlighting this issue, we will be adding the workaround instructions to the Desktop documentation
Angelo Gazzola
Hi Roger,
The two issues you're seeing are indeed related and more specifically they stem from the fact that Desktop assumes the default paths for the DBMS directories.
Unfortunately fixing this in Desktop won't be as straightforward as "just" reading these paths from the config. Happy to discuss more what a potential solution could be, but for now I see two options to unblock you from upgrading this Neo4j DBMS:
- Do the upgrade manually and in a way that Desktop picks up the upgraded DBMS.
- Move Desktop's data path to the same external drive, move the data directory to be in the default DBMS directory, and upgrade through Desktop.
I think you'll have a much easier time with the first option. It's less configuration to deal with, no moving around of files, it'll require less disk space if you already have a backup, and you'll get a better view of the progress status, which might be useful given the size of the database.
What you'd do in that case, assuming a migration from 2025.09.0 to one of the more recent versions, and assuming you already have a backup of that instance, is follow these steps (it's the same steps listed at https://neo4j.com/docs/upgrade-migration-guide/current/version-2025/#_standalone_servers but tweaked for your setup)
- Stop the old Neo4j instance.
- Update server.directories.datain the original instance to the default location (this is to avoid having two instances pointing to the same data directory).
- Create a new instance in Desktop with the version you want to upgrade to.
- Update server.directories.datain the new instance to point to the data directory in your external drive, and delete the default data directory for the new instance (this is to avoid having Desktop show you information about the default data directory even though you're not using it).
- Start the new Neo4j instance. You can monitor the logs to see how the upgrade is progressing. The neo4j.log file contains information on the upgrade.
Please let me know if this helps.
Nissanka Fernando
roger.gordon@ithinking.co.uk please let me know if you need any more help with this issue beyond Angelo's upgrade advice, otherwise we'll close it soon
roger.gordon@ithinking.co.uk
Hi all, ended up doing a complete reinstall and restoring the database. The restore of the database backup fails unless Desktop 2 is shutdown and restarted several times, but eventually got there. YMMV - make sure you have good backups!
Nissanka Fernando
Hi Roger,
Have you set the Desktop custom data path? Take a look here:
roger.gordon@ithinking.co.uk
Nissanka Fernando - disaster!
I followed instructions and a second desktop keeps popping up. Neo4j confused about where database files are. Now Neo4j not starting.
I have a full backup from before I tried the plist. There should be NO transactions pending btw....
I deleted the plist file after a launchctl unload and then a restart. no joy:
2025-12-30 11:48:19.396+0000 INFO ======== Neo4j 2025.09.0 ========
2025-12-30 11:48:19.428+0000 INFO This instance is ServerId{e30d7f67} (e30d7f67-a3f1-4f2a-96d7-b9efa8baf8fd)
2025-12-30 11:48:19.569+0000 INFO Resolved endpoints with LIST{endpoints:'[localhost:6000]'} to '[localhost:6000]'
2025-12-30 11:48:19.592+0000 INFO Resolved endpoints with LIST{endpoints:'[localhost:6000]'} to '[localhost:6000]'
2025-12-30 11:48:31.787+0000 ERROR Failed to start Neo4j on localhost:7474.
java.lang.RuntimeException: Error starting Neo4j database server at /Volumes/T7/neo4j/data/databases
...
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'com.neo4j.dbms.reconciler.operators.SystemOperator@31f295b6' was successfully initialized, but failed to start. Please see the attached cause exception "Fail to start 'DatabaseId{00000000[system]}' since transaction logs were found, while database files are missing.".
roger.gordon@ithinking.co.uk
Just looked in the external drive and Neo4j Desktop has
wiped
out the entire database. Nissanka Fernando any thoughts?Nissanka Fernando
roger.gordon@ithinking.co.uk: I'm very sorry about this and not sure what has happened. Please could you share the Desktop app logs from Developer > View main log.
My initial theory is there is either some inconsistency or incompatibility between the Desktop custom data path functionality and the neo4j.conf custom directories. I'm sharing with engineering now to take a look. cc Angelo Gazzola
Nissanka Fernando
Hello roger.gordon@ithinking.co.uk! I have a few more questions for you:
- Can you provide more details about the error message you receive when attempting to upgrade?
- Have you tried any troubleshooting steps, such as moving the Data directory back to the local drive, to see if the issue persists?
- Is there any specific reason for redirecting the Data directory to an external drive, and have you encountered similar issues with other versions?
roger.gordon@ithinking.co.uk
Nissanka Fernando thanks for your response...
There's that weird 0 Databases issue - don't know if that's relevant or just a quirky thing.
- The database is over 400gb so won't fit on my HD. Thats possibly an issue for the normal upgrade since it want to put a backup in
/Users/rogergordon/Library/Application%20Support/neo4j-desktop/Application/Data/backups
- same issue as 3 above, but do note that I have changed the original data directory under the install to data-old-- to be clearer this is on the hard drive -- the external drive is as expected: /data/....
- will run this again but the logs showed that it wanted the data directory (perhaps for the backup).
Is the neo4j.conf file read for the upgrade? The server.directories.dumps.root property is directed to and external drive and not the Application Support directory....
roger.gordon@ithinking.co.uk
Nissanka Fernando, the backup is successful (only about 80gb), but then Desktop flashes onto a create your first instance screen.
The log entry in the upgrade-logs folder has an empty neo4j.log file and the relate.debug.json shows:
{"os":"darwin","backup":"/Users/rogergordon/Library/Application Support/neo4j-desktop/Application/Data/backups/backup-ed192354-3194-4dfc-9bdf-c148ba37dd5c","sourceDbms":{"id":"c4a02801-2701-41c2-86d1-41a350923a00","version":"2025.09.0","path":"/Users/rogergordon/Library/Application Support/neo4j-desktop/Application/Data/dbmss/dbms-c4a02801-2701-41c2-86d1-41a350923a00","plugins":["apoc"]},"targetDbms":{"id":"51b1fe8e-b32c-434b-952d-495ea0699df1","version":"2025.11.2","path":"/Users/rogergordon/Library/Application Support/neo4j-desktop/Application/Data/dbmss/dbms-51b1fe8e-b32c-434b-952d-495ea0699df1"}}