Unable to import "graph.db" in Neo4j 4.0.4

[jshubhangi2697]

[dhimmel]

I wonder if hetionet-v1.0.db.tar.bz2 is too old to be imported into Neo4j 4.0. That database was exported from Neo4j 3.0.1

From https://neo4j.com/docs/migration-guide/4.0/important-information/#supported-upgrade-paths:

The following upgrade path is supported: 3.5.any → 4.0.x

Is it possible to see the neo4j logs when trying to load the database? Those would make it easier to diagnose the issue.

[jshubhangi2697]

Below is today's log:

Directories in use:
  home:         /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4
  config:       /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4/conf
  logs:         /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4/logs
  plugins:      /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4/plugins
  import:       /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4/import
  data:         /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4/data
  certificates: /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4/certificates
  run:          /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4/run
Starting Neo4j.
WARNING: Max 8192 open files allowed, minimum of 40000 recommended. See the Neo4j manual.
2020-06-18 07:38:58.216+0000 INFO  ======== Neo4j 4.0.4 ========
2020-06-18 07:38:58.343+0000 INFO  Starting...
2020-06-18 07:39:48.918+0000 INFO  Sending metrics to CSV file at /home/ubuntu-user/.config/Neo4j Desktop/Application/neo4jDatabases/database-40a013bb-9709-440c-a2d8-4be36145611d/installation-4.0.4/metrics
2020-06-18 07:39:49.259+0000 INFO  Bolt enabled on localhost:7687.
2020-06-18 07:39:49.259+0000 INFO  Started.
2020-06-18 07:39:52.102+0000 WARN  Server thread metrics not available (missing neo4j.server.threads.jetty.all)
2020-06-18 07:39:52.133+0000 WARN  Server thread metrics not available (missing neo4j.server.threads.jetty.idle)
2020-06-18 07:39:53.511+0000 INFO  Server thread metrics have been registered successfully
2020-06-18 07:40:06.319+0000 INFO  Remote interface available at http://localhost:7474/

[dhimmel]

The log output above looks okay to me. I don't see anything in it about loading the database.

For me to help further, I'll need to know a little bit about your setup. Can you describe the steps you took to install & launch neo4j and load Hetionet database?

[jshubhangi2697]

I followed the instructions given :

Make sure the Neo4j server is stopped. Navigate to the data/databases directory inside the Neo4j directory and run:

# Backup graph.db directory if it exists
if [ -d "graph.db" ]; then
  mv graph.db graph.db.backup_`date +%F`
fi

# Download and extract graph.db for Hetionet v1.0
curl --location https://github.com/hetio/hetionet/raw/master/hetnet/neo4j/hetionet-v1.0.db.tar.bz2 | tar --extract --bzip2

After this in the config file I changed the default db to "graph"

[dhimmel]

I looked into upgrading our docker image to use Neo4j 4.0 in https://github.com/hetio/hetionet/pull/33. I ran into an error that is unrelated to this. But until that error is fixed (or at least I can find additional info on it), I don't plan on working on Neo4j 4.0 support for the Hetionet database.

In https://github.com/hetio/hetionet/commit/a95ae76581af604e91d744680aee3f888fa18887, I updated the README to link to "Running the docker". Docker is another way to launch the database. It should work similarly across systems, so requires less user-specific support. Perhaps this will be sufficient for your needs.