guardgraph

Introduction

Species interaction graph analysis package for the European GUARDEN project.

To run this project:

docker compose up

When start-up is completed, visit http://localhost:8000/ To stop the application, run docker compose down

If neo4j container was not properly shutdown, the lock file needs to be removed rm ~/data/gg/databases/store_lock for a succesfull startup.

Sometimes this is not sufficient, and you need to remove any neo4j container:

NEO4J=$(docker container ps -a | grep neo4j | cut -f1 -d' ')
docker container rm $NEO4J

Development notes

docker ps -a # to see container id of python container
GUARDCON=$(docker ps -a | grep guardgraph-web | cut -f1 -d' ')
docker exec -it $GUARDCON /bin/sh

The above code block gives you a shell in the running container. There you can change dir to /code and work on the code for testing, provided you clone it to a subdir pf ~/repos

Example:

%load_ext autoreload
%autoreload 2
%cd /code
from guardgraph.graph import InteractionsGraph
ig = InteractionsGraph()
ig.load_interaction_data()

Time to load:

Entries	Time to load	Std.dev
10	37.7 ms	4.54 ms
100	191 ms	23.3 ms
1000	1.21 s	46.3 ms
10000	46.6 s	627 ms
100000	21min 28s

With cypher batches:

%%timeit -r1 -n1 ix.reset_graph(force=True)
ix.load_interaction_data(
    max_entries=10000, batch_size=5000, cypher_batched=True
)

Entries	Batch size	Time to load	Std.dev
10000	10	31.7 s	120 ms
10000	100	26.4 s	58.6 ms
10000	1000	25.1 s	45.2 ms
10000	10000	16 s	13.4 ms
100000	10000	23min 4s
100000	50000	22min 21s

Get database from minikube

scp -i $(minikube ssh-key) docker@$(minikube ip):/data/worker/db.sqlite backup