Thanks for your reply Michael.
When I was shortening the 1.5k lines of my code into a form that coule be 
posted here I have found the solution to the problem.

The issue was that I stupidly created an object field thix.tx to save 
myself creating a new variable every time I wanted to do a transaction.
However at some point I've started using the same transaction in other 
functions called so I've been successing an closing the transactions 
somewhere in the middle of the bigger transaction I wanted to perform. See 
the code below.

class sth{
    private GraphDatabaseService db;
    private Transaction tx;
    private ExecutionEngine engine;

    public void sth(){
        this.engine = new ExecutionEngine(this.db);
        this.tx = this.db.beginTx();
        try{
            this.sth2();
            this.engine.execute(important_creating_query);
            this.tx.success();
        } finally {
            this.tx.close(); 
        }
    }

    public int sth2(){
        this.tx = this.db.beginTx();
        try{
            this.engine.execute(some_matching_query);
            this.tx.success();
        } finally {
            this.tx.close(); 
        }
    }
}

I sort of makes sense to me that the creating query in the sth() function 
wasn't saved in this case.

I'm sorry for bothering you.

Anyway, hopefully maybe someone will find a solution in this topic in 
future.

Cheers,
Adam


On Saturday, 12 July 2014 02:18:34 UTC+1, Michael Hunger wrote:
>
> Please post the code,
> how do you shut down the db?
> Are you by chance running a server and your embedded code on the same 
> database?
>
>
> On Fri, Jul 11, 2014 at 5:23 AM, Adam Golinski <[email protected] 
> <javascript:>> wrote:
>
>> Hi all!
>>
>> I am experiencing this strange issue of part of my relationships 
>> disappearing after shutting and reopening Java embedded neo4j db.
>> I am using neo4j community 2.1.2.
>>
>> The strangest part is that only part of relationships disappear - only 1 
>> out of 2 labels.
>> Relationships with this label are created last and it seems as if they 
>> were not 'commited' to the db.
>>
>> However I am sure they are created since as long as I create them and I 
>> don't shut the db I can perform other operations I need on them and I am 
>> getting the results I would expect.
>>
>> What could possibly be the reason of such behaviour?
>>
>> I can post the source code if necessary, it's a bit messy though.
>>
>> Cheers
>> Adam Golinski
>>  
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