Updating neo4j hanging

[explodecomputer]

Hey @mcgml can you help me with this - I'm trying to update the neo4j db but when I run the map_from_csv.py script it's hanging

gh13047@ieu-db-interface:~/mr-base-api/app/igd-metadata$ docker cp data/groups.tsv mr-base-api-v3_mr-base-api-v3-private_1:/tmp
gh13047@ieu-db-interface:~/mr-base-api/app/igd-metadata$ docker cp data/permissions.tsv mr-base-api-v3_mr-base-api-v3-private_1:/tmp
gh13047@ieu-db-interface:~/mr-base-api/app/igd-metadata$ docker cp data/memberships.tsv mr-base-api-v3_mr-base-api-v3-private_1:/tmp
gh13047@ieu-db-interface:~/mr-base-api/app/igd-metadata$ docker cp data/batches.tsv mr-base-api-v3_mr-base-api-v3-private_1:/tmp
gh13047@ieu-db-interface:~/mr-base-api/app/igd-metadata$ # import data to graph
gh13047@ieu-db-interface:~/mr-base-api/app/igd-metadata$ docker exec -it mr-base-api-v3_mr-base-api-v3-private_1 \
> python map_from_csv.py \
> --study /tmp/study.tsv \
> --groups /tmp/groups.tsv \
> --permissions_e /tmp/permissions.tsv \
> --memberships /tmp/memberships.tsv \
> --batches /tmp/batches.tsv
Production
Params: 

At this point it just hangs. I noticed a lot of analysis calls being made to this private repo, I'm not sure who is doing this or who has access to do it, and I wondered if this is essentially slowing it down, but I've left it running for several minutes and no progress

[mcgml]

Hi @explodecomputer does the script print logs? And can you curl Neo4J? If it is hanging then it sounds like a connection problem. Are you running from interface node?

[explodecomputer]

@mcgml thanks good questions

It doesn't print logs from this command beyond what was pasted above. However, these are the logs from the container itself

gh13047@ieu-db-interface:~/mr-base-api/app/igd-metadata$ docker logs --tail 10  mr-base-api-v3_mr-base-api-v3-private_1
[pid: 61329|app: 0|req: 163312/348110] 127.0.0.1 () {32 vars in 328 bytes} [Mon May 23 13:29:17 2022] GET / => generated 9626 bytes in 645 msecs (HTTP/1.1 200) 2 headers in 81 bytes (1 switches on core 1)
127.0.0.1 - - [23/May/2022:13:29:18 +0000] "GET / HTTP/1.1" 200 9626 "-" "curl/7.52.1" "-"
[pid: 75685|app: 0|req: 36670/348111] 127.0.0.1 () {32 vars in 328 bytes} [Mon May 23 13:29:48 2022] GET / => generated 9626 bytes in 629 msecs (HTTP/1.1 200) 2 headers in 81 bytes (1 switches on core 0)
127.0.0.1 - - [23/May/2022:13:29:49 +0000] "GET / HTTP/1.1" 200 9626 "-" "curl/7.52.1" "-"
[pid: 61329|app: 0|req: 163313/348112] 127.0.0.1 () {32 vars in 328 bytes} [Mon May 23 13:30:19 2022] GET / => generated 9626 bytes in 1420 msecs (HTTP/1.1 200) 2 headers in 81 bytes (1 switches on core 0)
127.0.0.1 - - [23/May/2022:13:30:20 +0000] "GET / HTTP/1.1" 200 9626 "-" "curl/7.52.1" "-"
[pid: 75685|app: 0|req: 36671/348113] 127.0.0.1 () {32 vars in 328 bytes} [Mon May 23 13:30:51 2022] GET / => generated 9626 bytes in 1218 msecs (HTTP/1.1 200) 2 headers in 81 bytes (1 switches on core 1)
127.0.0.1 - - [23/May/2022:13:30:52 +0000] "GET / HTTP/1.1" 200 9626 "-" "curl/7.52.1" "-"
[pid: 75685|app: 0|req: 36672/348114] 127.0.0.1 () {32 vars in 328 bytes} [Mon May 23 13:31:22 2022] GET / => generated 9626 bytes in 1709 msecs (HTTP/1.1 200) 2 headers in 81 bytes (1 switches on core 0)
127.0.0.1 - - [23/May/2022:13:31:24 +0000] "GET / HTTP/1.1" 200 9626 "-" "curl/7.52.1" "-"

I don't know what these are but it doesn't relate to the map_from_csv.py script.

I am running this on the interface node, and I can actually curl using this command -

curl -X POST -H 'Content-type: application/json' http://username:password@localhost:37474/db/data/transaction/commit -d '{"statements": [{"statement": "MATCH (n:User) RETURN n LIMIT 25;"}]}'