I am receiving a "not cleanly shutdown" log message when attempting to open a 2 year old Neo4j database posted on github at https://github.com/IGS/disease-ontology/tree/master/database/neo4j. How do I open/update this database?
Here's how I got it initialized: Downloaded the graph_db.tgz to my local win7-64 machine (neo4j-community-1.9.RC2), extracted the graph.db file to the data subfolder, renamed it graph_ontology.db, and edited the server config file to point to it as follows:
org.neo4j.server.database.location=data/graph_ontology.db
When starting Neo4j, the last entry in the log file is:
2013-05-21 17:23:33.418+0000 INFO [o.n.k.EmbeddedGraphDatabase]: Startup failed: Component 'org.neo4j.kernel.impl.transaction.XaDataSourceManager#1f91d41b' was successfully initialized, but failed to start. Please see attached cause exception.: Component 'org.neo4j.kernel.impl.nioneo.xa.NeoStoreXaDataSource#b86527e' was successfully initialized, but failed to start. Please see attached cause exception.: Mismatching store version found (Uknown while expecting v0.A.0) and the store is not cleanly shutdown. Recover the database with the previous database version and then attempt to upgrade
Thanks,
Jeff
Look at the messages.log of the database to determine which neo4j version it was started with last.
In this case it is 1.4
You can get it from here: http://dist.neo4j.org/neo4j-community-1.4.2-windows.zip
You can easily just point the neo4j-shell to it:
create an upgrade.properties that contains: allow_store_upgrade=true
and then use: bin/neo4j-shell -path graph_ontology.db -config upgrade.properties
Here is the converted db for 1.9.GA: https://dl.dropboxusercontent.com/u/14493611/disease_ontology_graphdb-1.9.tgz
Related
I am trying to import the Hetionet into the Neo4j and I follow the guidiance below:
https://github.com/hetio/hetionet/tree/master/hetnet/neo4j
While using the command
curl --insecure --location https://github.com/hetio/hetionet/raw/master/hetnet/neo4j/hetionet-v1.0.db.tar.bz2 | tar --extract --bzip2
The error “curl: (23) Failure writing output to destination” has been thrown.
Therefore I just downloaded the file directly and moved to the directory ".Neo4jDesktop\relate-data\dbmss\dbms-0d0d3324-d1a6-4d3e-b82c-0c4451a8c880\data\databases"
After I started the database, It showed that this database is currently offline. When I trying to do some operations to it, the error "Neo.TransientError.Database.DatabaseUnavailable" has been shown.
Some valuable informations in the log file debug.log are as below:
2022-07-19 23:11:53.896+0000 ERROR [c.n.d.DbmsReconciler] Encountered error when attempting to reconcile database graph.db (request by SystemGraph:1) to state 'online', database remains in state 'offline'
org.neo4j.dbms.api.DatabaseManagementException: Unable to start database DatabaseId{7a8c6b65[graph.db]}
Caused by: org.neo4j.kernel.lifecycle.LifecycleException: Component 'org.neo4j.kernel.database.Database#3da82075' was successfully initialized, but failed to start. Please see the attached cause exception "Unknown store version 'v0.A.7'".
The version of the dump you are trying to import is pretty old. From the readme
The database has been migrated to the Neo4j 3.0.1 Community Edition.
If you use a current 4.4 version of the database, the only thing you can do is to cascade through multiple versions and upgrade the store.
I am not yet sure if you really need each minor version to work properly.
Maybe it's already enough to go from 3.0 to 3.5 and follow this guide https://neo4j.com/docs/upgrade-migration-guide/current/migration/migrate-to-4.0/migrate-single-instance/
Otherwise starting 3.1-3.5 with allow_upgrade=true on the stores is the only option I see. There are Docker images available at
https://hub.docker.com/_/neo4j/ also for those older, unsupported versions.
Edit: You should be able to start/upgrade it with 3.3 and then again with 3.5 and then run a 4.4 neo4j-admin copy
I'm trying to remotely back up my Neo4J database for already 2 days and nothing works.
I run
sudo neo4j-admin backup --backup-dir=backup --name=graph.db-backup --from=1.1.1.1:1111 --timeout=50m
The files start to get saved and then simply erased after a while and there's no backup.
I tried setting up --pagecache=16M and HEAP_SIZE but it has no effect. Sometime it just stalls sometimes I get an error like this:
unexpected error: java.io.IOException: org.neo4j.com.ComException: Channel has been closed
The DB I'm backing up is Enterprise 3.3.3 and the one I'm backing up with is 3.5.14
Thank you for any help.
Is this the normal Neo4J behavior?
I try to install InfluxDB Enterprise Edition using this documentation: https://docs.influxdata.com/enterprise/v1.2/production_installation/. The Requirements suggest to either use a license-key or license-path, where I do it with the License Key.
In Step 2, after installing, configuring and starting the Data Nodes I try to join the data nodes to the cluster. But executing influxd-ctl add-data enterprise-data-01:8088 gives me the error:
add-data: operation exited with error: open /tmp/influx-enterprise.key.json: no such file or directory
although I configured not to use the license-key json but rather the license-key.
I also have the json file, so I tried it with the license-path but still getting the same error. Has somebody else encountered the same issues?
EDIT
Issue has been resolved, I had to restart the Data nodes after I changed the configuration to use the license-path facepalm. I went into this problem as I previously entered an old license key.
This is my problem. I have copied graph.db for a backup.
Neo4j was started when I did that.
After that I deleted graph.db and neo4j started a new one. Neo4j is working fine, no problems.
But when wanted to copy again graph.db (the backup one) I get:
Starting Neo4j Server...WARNING: not changing user
waiting for server to be ready... Failed to start within 120 seconds.
I have uninstalled and installed again neo4j and it does not work.
I think is a problem of permissions... If yes how to solve it? I have tried to change permissions with chmod but it does not work... Someone can help me with the code for changing the permissions or configure neo4j with good permissions.
On the log: this appears multiple times:
2014-08-14 15:27:58.102+0000 INFO [API] Setting startup timeout to: 120000ms based on -1
Detected incorrectly shut down database, performing recovery..
Any other suggestion?
Thank you for your help.
Try to use
bin/neo4j start-no-wait
instead of
bin/neo4j start
As commented before the data was corrupted. It was impossible to recover it.
The correct way to do the backup is: link
Never copy the files while running the database.
We need to zip the graph.db file and then copy it in another location as a backup.
For restore stop the database just delete recursively graph.db and unzip the backup.
Sadly the first data could not be restored...
I installed Neo4j as instructed in the site and was able to install and stat server. However I tried to copy the Beer example DB by stopping the server and deleting the current graph.db in the \data folder and replaced with the one Beer example downloaded from online (graph.db folder). This is the only step I did.
Now the issue is, when i tried to start the Server I get "StartService FAILED 1053"
I am using following command on the powershell in windows - c:\neo4j-community-2.0.0-M03> .\bat\Neo4j.bat start
Can someone please help if I have done anything wrong here.
Thank you!
You are running neo4j 2.0 against an older database file. You'll need to set the config parameter to allow the store to be upgraded before starting. See instructions here:
http://docs.neo4j.org/chunked/milestone/deployment-upgrading.html#_explicit_upgrade