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biocypher / clinical-knowledge-graph

GNU General Public License v3.0
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CKG dump import utility #13

Open winternewt opened 4 weeks ago

winternewt commented 4 weeks ago

Aiming to address https://github.com/biocypher/clinical-knowledge-graph/issues/9 Made a downloader script and docker-compose config to download and spin-up CKG dump instance in a docker-container, eliminating the pitfalls and entry-threshold all at once for better reproducibility.

slobentanzer commented 4 weeks ago

Hi @winternewt, many thanks for the PR, and looks good in principle, but I can't get the Docker to work on ARM. Seems to be a problem of this older version of Neo4j, 4.2.19, which I also can't seem to find on the Dockerhub page of Neo4j. I get no matching manifest for linux/arm64/v8 in the manifest list entries for all 4.2 and 4.3 versions. We always used 4.4-enterprise or newer in our pipelines, which solves the manifest problem, but then I get a separate error (probably a packaging difference between 4.2 and 4.4):

Attaching to neo4j
neo4j  | Changed password for user 'neo4j'. IMPORTANT: this change will only take effect if performed before the database is started for the first time.
neo4j  | Fetching versions.json for Plugin 'apoc' from https://neo4j-contrib.github.io/neo4j-apoc-procedures/versions.json
neo4j  | Installing Plugin 'apoc' from https://github.com/neo4j-contrib/neo4j-apoc-procedures/releases/download/4.4.0.28/apoc-4.4.0.28-all.jar to /plugins/apoc.jar 
neo4j  | Applying default values for plugin apoc to neo4j.conf
neo4j  | Skipping dbms.security.procedures.unrestricted for plugin apoc because it is already set.
neo4j  | You may need to add apoc.* to the dbms.security.procedures.unrestricted setting in your configuration file.
neo4j  | Fetching versions.json for Plugin 'graph-data-science' from https://graphdatascience.ninja/versions.json
neo4j  | Installing Plugin 'graph-data-science' from https://graphdatascience.ninja/neo4j-graph-data-science-2.6.8.jar to /plugins/graph-data-science.jar 
neo4j  | Applying default values for plugin graph-data-science to neo4j.conf
neo4j  | Skipping dbms.security.procedures.unrestricted for plugin graph-data-science because it is already set.
neo4j  | You may need to add gds.* to the dbms.security.procedures.unrestricted setting in your configuration file.
neo4j  | /backups/neo4j-init.sh: line 4: gosu: command not found
neo4j exited with code 127

Is there a specific reason you want to use 4.2? And BTW, is there also a reason for using the community edition? We usually use enterprise, which is fine for open source projects.

antonkulaga commented 3 weeks ago

I can't get the Docker to work on ARM

Are there any use cases of running it in ARM?

We usually use enterprise,

Is it not overly restrictive for the users? The majority of people need help to afford enterprise licenses.

slobentanzer commented 3 weeks ago

Are there any use cases of running it in ARM?

Of course, all modern Macs and many current Linux machines are on ARM. I think it will rather increase than decrease as well because of their efficiency, even in data centres.

Is it not overly restrictive for the users? The majority of people need help to afford enterprise licenses.

Not at all. Neo4j enterprise is free of charge for non-profit research and open source.