This issue has surfaced a number of times in various flavors, particularly 
when an explicit upgrade (non-automatic requiring 
"allow_store_upgrade=true") is involved and the culprit seems to be this:

   - If you run Neo4j as a Windows Service (having installed via 
   Neo4jInstaller.bat and using recommended start/stop 'sc' commands, etc.) 
   there is no way to do a clean shutdown of a database.

(As long as no upgrade is involved, apparently Neo4j running as a Windows 
Service can start, stop, and restart databases with no problem (although 
the message logs reveal that a non-clean shutdown has been silently been 
detected and addressed on restart).

In the past, it has been suggested that this issue was from "jumping the 
gun" of not letting the Neo4j-Server instance shut down completely before 
restarting the Neo4j-Server Windows Service. But that is not the case.

To test the basic situation I did this with the same results on both 2.0 
and 2.1:

   1. Create an empty graph.db directory in my Neo4j data directory, then 
   start the Neo4j-Server Windows Service instance.
   2. Observe the fresh database being made. Make a copy of the 
   messages.log (called messages_onCreation.log
   3. Stop the Neo4j-Server Windows Service... wait, wait... wait (longer 
   than necessary)
   4. Compare the two messages logs... the same, no stopping messages.
   5. Delete the message.log and start the Neo4j-Server Windows Service.
   6. Observe the database directory during restart. Make a copy of the new 
   messages.log (called messages_on2ndStart.log

With no activity other than to create it, stop it, and then start it back 
up the messages.log shows multiple messages about detecting a non-clean 
shutdown. (The number of non-clean detection issues in the log depend on 
the Neo4j version being run.)

In the past, the recommendation was to use the deprecated Gremlin shell to 
do g.shutdown() then exit. But this doesn't seem to be (readily) available.

QUESTION 1: Does anyone know of a way to cleanly shut down a Neo4j database 
running under a Windows Service configuration?

QUESTION 2: Has anyone running Neo4j-Server as a Windows Service 
successfully upgraded a 2.0 DB to 2.1? If so, how?

I'm hoping to get a quick helpful reply or additional insights here before 
posting a question to S/O. Once I fully understand this issue, if it still 
appears that the fundamental problem is the Windows Service not cleanly 
shutting down, I'll enter an issue to this effect on the Neo4j GitHub Issue 
queue.

Thanks,
--Jim--

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