Usage

Start the development server

docker build -t dist .
./scripts/run.sh

The script create a ./data directory to persist Neo4j's data to the host machine. The Docker image will load a sample database if the directory ./data/databases/graph.db does not exist (for example, at first run).

If you want to restore the sample data, simply delete ./data and run ./scripts/run.sh again.

Init a new sample database (20 seconds on 8 CPUs)

./scripts/regenerate_db.sh

Backup the current db

./scripts/backup_db.sh # will dump to ./data/init.db.bak on host machine

Tail application's logs

make logs

View the toy graph

• Visit http://localhost:7474
• Set Connect URL to bolt://localhost:7687
• Set Authentication type to No authentication
• Click the top left icon (Databases), it should show the currently existing node and relationship types. Click on one of them to view the graph.
• Drag the nodes far away from each other for clarity. You can also set colors for them.

Make a test request

• Nearest neighbors

curl --request GET 'localhost:8080/api/v1/samples/s1/nearest-neighbours'
# The result should be a JSON array of {experiement_id: str, distance: int}

• Nearest leaf in the phylogenetic tree

curl --request GET 'localhost:8080/api/v1/samples/s1/nearest-leaf-node'
# The result should look like
# {
#   "distance": 7,
#   "leaf_id": "l857"
# }

Stop (& destroy) the development server

docker stop dist

Development

Run tests

make test_db
make test