SNPSEQ Archive DB

A self contained (Tornado) REST service that serves as a frontend for a simple SQL db that contains the state of our uploads, verifications and removals done by other SNPSEQ archive services.

Trying it out

python3 -m venv --upgrade-deps .venv
source .venv/bin/activate
pip install .

Try running it:

 archive-db-ws --config=config/ --debug

And then you can find a simple API documentation by going to:

http://localhost:8888/api

Running tests

source .venv/bin/activate
pip install -e .[test]
nosetests tests/

REST endpoints

Creating a new Upload (and associated Archive if none exists):

curl -i -X "POST" -d '{"path": "/path/to/directory/", "host": "my-host", "description": "my-descr"}' http://localhost:8888/api/1.0/upload

Creating a new Verification (and associated Archive if none exists):

curl -i -X "POST" -d '{"path": "/path/to/directory/", "host": "my-host", "description": "my-descr"}' http://localhost:8888/api/1.0/verification

Getting a randomly picked Archive that has been uploaded within a certain timespan, but never verified before:

curl -i -X "GET" -d '{"age": "7", "safety_margin": "3"}' http://localhost:8888/api/1.0/randomarchive

Print the records from the database:

curl -i -X "GET" http://localhost:8888/api/1.0/view

Print the N (positive integer) latest uploads from the database:

curl -i -X "GET" http://localhost:8888/api/1.0/view/N

Query the database for uploads matching specific criteria:

curl -i -X "POST" -d '{"host": "biotank", "uploaded_before": "2023-03-01", "verified": "False"}' http://localhost:8888/api/1.0/query

Docker container

For testing purposes, you can also build a Docker container using the resources in the docker/ folder:

# build and start Docker container
docker/up

This will build and start a Docker container that the archive-db service and listens on port 8787:

# interact with archive-verify service on port 8787
curl 127.0.0.1:8787/api/1.0/version
    #   {"version": "1.2.0"}

The container log output can be followed:

# follow the container log output (Ctrl+C to stop)
docker/log

The docker container can be stopped and removed:

# stop and remove the running docker container
docker/down