webapi for mindgames image server
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.



webapi for mindgames image server

Initially based on examples from eve-demo and mriqc's web api.

Currently super bare bones.

Start it up as follows:

cd docker-ever
docker-compose build
docker-compose up

Browse to localhost for the swagger api documentation, then promptly ignore that documentation for uploading images. Instead of doing what it says, you'll need to submit images as a form as described here.

Here's an example of posting an image and associated mask with the Python 3 requests library:

import requests
from pathlib import Path
import json
import os
# this code assumes that the jpg, the json describing it, 
# and the mask file have the same name with different extenstions
url = 'http://localhost/api/v1/'
i = Path('data/0ff016cefb9590eb8cc1e3f7afc74ac372a6e0c27f98d1373b54e244.jpg')
j = i.with_suffix('.json')
with open(j,'r') as h:
    manifest = json.load(h)
with open(i,'rb') as img:
    r = requests.post(url+'image',files={'pic':img},data=manifest, headers={'Authorization':os.environ.get('API_TOKEN','"testing_secret"')})
m = i.with_suffix('.mask')
image_id = r.json()['_id']
if m.exists():
    mask_dat = {'image_id':image_id,'mode':'truth'}
    with open(m,'rb') as h:
        mask_dat['pic'] = json.dumps(json.load(h))
        rm = requests.post(url+'mask',data=mask_dat, headers={'Authorization':os.environ.get('API_TOKEN','"testing_secret"')})

Here we use the id of the image we just uploaded to download an image and it's mask:

geti_url = url+'image?where={"_id":"%s"}'%image_id
res_i= requests.get(geti_url)

getm_url = url+'mask?where={"image_id":"%s"}'%image_id
res_m= requests.get(getm_url)

If you want to get statistics for all of the masks submitted for a training image send a get request like so:

get_aggmasks = url+'maskagg?aggregate={"$image_search":"%s"}'%image_id
res_aggm = requests.get(get_aggmasks)

This will return a json response like so:

{'_items': [{'_id': '599d87d0d52c9f00099b2aab',
   'avescore': 0.1,
   'nattempts': 1,
   'nusers': 1,
   'sumscore': 0.1}]}

Backend selection logic is now tentatively implemented. It depends on several variables being available in the config file:

ROLL_N = 10

If user_id and token parameters are set as parameters on the get item request, the backend will first decide if the user's rolling average score is above threshold. If it is and they don't randomly get assigned to training based on the test_per_train setting, then it will try to give them a novel test image, otherwise giving them an image seen the fewest number of times. If they are selected to get a training image, then they will get a repeated training image based on the train_repeat parameter or a novel or least seen training image.

The reqeust should look something like this:

geti_url = url+'image?where={"task":"dev"}&user_id=%s&token=%s'%(uid,token)
res_i= requests.get(geti_url)

Setting up certbot

First you've got to run the website with the pre_cert_bot docker-compose file: docker-compose -f docker-compose_pre_cert_bot.yml build; docker-compose -f docker-compose_pre_cert_bot.yml down -v; docker-compose -f docker-compose_pre_cert_bot.yml up Then, while the site is up with that config, run the certbot docker container: docker run -it --rm -v certs:/etc/letsencrypt -v certs-data:/data/letsencrypt certbot/certbot certonly --webroot --webroot-path=/data/letsencrypt -d test.medulina.com -d testapi.medulina.com This should create the certs and put them in the certs and certs-data folders. Then you can run docker-compose build; docker-compose down -v; docker-compose up. If you're on prod, there might be a different docker-compose file to use.

Renewing certbot manually

docker run -it --rm -v /home/mindr/le_log:/var/log/letsencrypt -v /home/mindr/certs:/etc/letsencrypt -v /home/mindr/certs-data:/data/letsencrypt certbot/certbot renew Then restart the docker containers.

Setting up a cron job for certbot renewal

Add user to /etc/cron.allow Then as the user you'd like to renew from run crontab -e Then just add the following line to the crontab:

1 1 1 * * docker run --rm -v /home/mindr/le_log:/var/log/letsencrypt -v /home/mindr/certs:/etc/letsencrypt -v /home/mindr/certs-data:/data/letsencrypt certbot/certbot renew > ~/cronlog 2>&1

Commands for clearing the DB of user data

db.mask.remove({'mode': {$ne: "truth"}})