Comments (5)
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.
from hetionet.
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/
from hetionet.
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?
from hetionet.
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"
from hetionet.
I looked into upgrading our docker image to use Neo4j 4.0 in #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 a95ae76, 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.
from hetionet.
Related Issues (20)
- Local files HOT 2
- Multiple Match Queries Not Working HOT 2
- Question About Hetionet's Dictionary HOT 3
- How to add new disease and anatomy nodes HOT 2
- Providing a dump version of Hetionet HOT 11
- http://neo4j.het.io/browser/ time out HOT 4
- Neo4J instance down (?) HOT 7
- Updated TSV version HOT 6
- graph.db database offline in neo4j HOT 3
- neo4j website down HOT 6
- Hetionet Browser is down HOT 4
- Mapping to original databases HOT 2
- Cannot map non-existing file HOT 5
- Do any relations imply another relation? HOT 1
- Connectivity Search Automated Query Question HOT 8
- Docker compatibility question HOT 4
- Question on metrics HOT 1
- What does it mean if something up regulates a disease in this context? HOT 3
- Speeding up data import to Neo4j v5 and CSV format data HOT 2
- Inquiry about metapaths from 2017 Paper "Systematic Integration of Biomedical Knowledge Prioritizes Drugs for Repurposing" HOT 7
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from hetionet.