[SOLVED] Neo4j : EntityNotFoundException: Node with id + Inconsistencies

Issue

I successfully migrated from Neo4J 2.0.0.M6 Community Edition to 2.0.0.RC1 Enterprise Edition.

But...
When i'm doing this query :

neo4j-sh (?)$ START n=node(4) RETURN n;

The answer is

EntityNotFoundException: Node with id 4

When I'm doing a neo4j-backup, It generate Inconsistencies errors

2014-01-25 21:19:58.808+0000 INFO  [org.neo4j]: ERROR: This label scan document refers to a node record that is not in use.
NodeLabelRange[docId=2; {Node[3]: Labels[0], Node[4]: Labels[1], Node[5]: Labels[1], Node[6]: Labels[1], Node[7]: Labels[1], Node[8]: Labels[0], Node[9]: Labels[1], Node[10]: Labels[1], Node[11]: Labels[1], Node[12]: Labels[0], Node[13]: Labels[1], Node[14]: Labels[1], Node[15]: Labels[0], Node[17]: Labels[1], Node[16]: Labels[1], Node[19]: Labels[1], Node[18]: Labels[0], Node[21]: Labels[1], Node[20]: Labels[1], Node[23]: Labels[1], Node[22]: Labels[1], Node[25]: Labels[1], Node[24]: Labels[1], Node[27]: Labels[1], Node[26]: Labels[0], Node[29]: Labels[1], Node[28]: Labels[1], Node[31]: Labels[0], Node[30]: Labels[1]}
Inconsistent with: Node[30,used=false,rel=0,prop=0,labels=Inline(0x0:[]),light]. 100% 

2014-01-25 21:19:58.809+0000 INFO  [org.neo4j]: Inconsistencies found:
    ConsistencySummaryStatistics{
    Number of errors: 28
    Number of warnings: 0
    Number of inconsistent LABEL_SCAN_DOCUMENT records: 1

I have inconsistencies on nodes 3 -> 30.
I'n not using those nodes anymore so I tried to delete them without success...

So... How can I remove them or fix the problem ?

Thank you !
Bons baisers de France :D

Solution

The manual upgrade neded to move from 2.0.0-M06 to 2.0.0-RC1 (or 2.0.0) is documented here:

http://blog.neo4j.org/2013/11/neo4j-200-rc1-final-preparations.html

Caution: manual upgrade between milestones

Data stores created with any previous milestone version can not be used with 2.0.0-RC1 unless a manual upgrade is performed. This is due to incompatible changes made to the store files. Please proceed with caution, backing up your data before attempting to manually upgrade.

Manual upgrade (only from 2.0.0-M06, and after you've backed up):

• Cleanly shut down on the old version on Neo4j 2.0.0-M06

  bin/neo4j stop

• Navigate to the database directory

  cd data/graph.db

• Delete the label scan store (this is the critical part that has a new format). It will be recreated on startup.

  rm -rf schema/label

• Start with the new version of Neo4j 2.0.0-RC1

  bin/neo4j start

Answered By - Michael Hunger