Neuro API

Information

Quickly develop NEURON models from the web.

Running Neuro API

Docker Start

git clone https://github.com/cyneuro/neuroapi.git
cd neuroapi
sudo docker-compose up -d

Manual Start

Obtaining the code:

git clone https://github.com/cyneuro/neuroapi.git
cd neuroapi

If you don't have neuron or anaconda installed use the scripts located in the nrn_install folder. In the following example ubuntu is the user account. You MUST specify the full path of the install directory. TODO: realpath

cd neuroapi/nrn_install
mkdir /home/ubuntu/apps
./ubuntu_requirements.sh
./easy-conda-install.sh /home/ubuntu/apps
./easy-nrn-install.sh /home/ubuntu/apps

You will need to have NEURON installed and accessible by python for some of the functions.

cd neuroapi
pip install -r requirements.txt
python setup.py develop
neuroapi init
neuroapi run -h 0.0.0.0

Authentication

THIS IS NOT CURRENTLY ENABLED FOR THE FUNCTIONS CALL

To access protected resources, you will need an access token. You can generate an access and a refresh token using /auth/login endpoint, example using curl

curl -X POST -H "Content-Type: application/json" -d '{"username": "admin", "password": "admin"}' http://localhost:5000/auth/login

This will return something like this

{
  "access_token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ0eXBlIjoiYWNjZXNzIiwiaWRlbnRpdHkiOjEsImlhdCI6MTUxMDAwMDQ0MSwiZnJlc2giOmZhbHNlLCJqdGkiOiI2OTg0MjZiYi00ZjJjLTQ5MWItYjE5YS0zZTEzYjU3MzFhMTYiLCJuYmYiOjE1MTAwMDA0NDEsImV4cCI6MTUxMDAwMTM0MX0.P-USaEIs35CSVKyEow5UeXWzTQTrrPS_YjVsltqi7N4", 
  "refresh_token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6MSwiaWF0IjoxNTEwMDAwNDQxLCJ0eXBlIjoicmVmcmVzaCIsImp0aSI6IjRmMjgxOTQxLTlmMWYtNGNiNi05YmI1LWI1ZjZhMjRjMmU0ZSIsIm5iZiI6MTUxMDAwMDQ0MSwiZXhwIjoxNTEyNTkyNDQxfQ.SJPsFPgWpZqZpHTc4L5lG_4aEKXVVpLLSW1LO7g4iU0"
}

You can use access_token to access protected endpoints :

curl -X GET -H "Content-Type: application/json" -H "Authorization: Bearer eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpYXQiOjE1NzAwMzg2MzgsIm5iZiI6MTU3MDAzODYzOCwianRpIjoiNTQ3NTkwMWUtMWFiMC00ZDI1LWI4YjktZWYzMTc2OGFhN2YwIiwiZXhwIjoxNTcwMDM5NTM4LCJpZGVudGl0eSI6MSwiZnJlc2giOmZhbHNlLCJ0eXBlIjoiYWNjZXNzIn0.p8JB2hKutnbDXqfiGvK2gsyN6ENxLD0e1MBMag28RUQ" http://127.0.0.1:5000/api/v1/users

You can use refresh token to retreive a new access_token using the endpoint /auth/refresh

curl -X POST -H "Content-Type: application/json" -H "Authorization: Bearer eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpZGVudGl0eSI6MSwiaWF0IjoxNTEwMDAwNDQxLCJ0eXBlIjoicmVmcmVzaCIsImp0aSI6IjRmMjgxOTQxLTlmMWYtNGNiNi05YmI1LWI1ZjZhMjRjMmU0ZSIsIm5iZiI6MTUxMDAwMDQ0MSwiZXhwIjoxNTEyNTkyNDQxfQ.SJPsFPgWpZqZpHTc4L5lG_4aEKXVVpLLSW1LO7g4iU0" http://127.0.0.1:5000/auth/refresh

this will only return a new access token

{
  "access_token": "eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJ0eXBlIjoiYWNjZXNzIiwiaWRlbnRpdHkiOjEsImlhdCI6MTUxMDAwMDYxOCwiZnJlc2giOmZhbHNlLCJqdGkiOiIzODcxMzg4Ni0zNGJjLTRhOWQtYmFlYS04MmZiNmQwZjEyNjAiLCJuYmYiOjE1MTAwMDA2MTgsImV4cCI6MTUxMDAwMTUxOH0.cHuNf-GxVFJnUZ_k9ycoMMb-zvZ10Y4qbrW8WkXdlpw"
}

Calling Functions

With authentication - After obtaining your access token, "POST" or "GET" a request from the /functions location:

curl -X GET -H "Content-Type: application/json" -H "Authorization: Bearer eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpYXQiOjE1NzAwMzg2MzgsIm5iZiI6MTU3MDAzODYzOCwianRpIjoiNTQ3NTkwMWUtMWFiMC00ZDI1LWI4YjktZWYzMTc2OGFhN2YwIiwiZXhwIjoxNTcwMDM5NTM4LCJpZGVudGl0eSI6MSwiZnJlc2giOmZhbHNlLCJ0eXBlIjoiYWNjZXNzIn0.p8JB2hKutnbDXqfiGvK2gsyN6ENxLD0e1MBMag28RUQ" "http://127.0.0.1:5000/api/v1/function" --data '{"function":"a","params":{"a":"b"}}'

Notice the use of the required function and params parameters.

Without authentication , requests look like this:

curl -X GET -H "Content-Type: application/json" "http://127.0.0.1:5000/api/v1/function" --data '{"function":"return_params","params":{"params":{"a":33431}}}'

Available functions and return values

Any function placed in neuroapi.neuro.core.py will be accessible from the public API.

run_cell

Roughly 21 values supplied (see below), returns base64 encoded image text containing plots

curl -X GET -H "Content-Type: application/json" "http://127.0.0.1:5000/api/v1/function" --data '{"function":"run_cell","params":{"el":-70,"diam":200,"cm":1,"gl":30,"gna":120,"gh":10,"gk":12,"tstop":500,"dur":[100,400],"amp":0.1,"mhalf":-38.43,"hhalf":7.2,"mk":7.2,"hk":-8,"nhalf":-81,"kn":11,"multiply":1,"multiply1":1,"multiply2":1,"seg1":-60,"seg2":-61,"seg3":-62.5}}'

Return:

Tyler@DESKTOP MINGW64 ~/Desktop/git_stage
$ curl -X GET -H "Content-Type: application/json" "http://127.0.0.1:5000/api/v1/                   function" --data '{"function":"run_cell","params":{"el":-70,"diam":200,"cm":1,"g                   l":30,"gna":120,"gh":10,"gk":12,"tstop":500,"dur":[100,400],"amp":0.1,"mhalf":-3                   8.43,"hhalf":7.2,"mk":7.2,"hk":-8,"nhalf":-81,"kn":11,"multiply":1,"multiply1":1                   ,"multiply2":1,"seg1":-60,"seg2":-61,"seg3":-62.5}}'
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   273    0     0  100   273      0    169  0:00:01  0:00:01 --:--:--   169{
    "result": "b'iVBORw0KGgoAAAANSUhEUgAABkAAAAV4CAYAAAD4zRH6AAAABHNCSVQICAgIfAh                   kiAAAAAlwSFlzAAAPYQAAD2EBqD+naQAAADl0RVh0U29mdHdhcmUAbWF0cGxvdGxpYiB2ZXJzaW9uIDI                   uMi4zLCBodHRwOi8vbWF0cGxvdGxpYi5vcmcvIxREBQAAIABJREFUeJzs3X9wXXWdN/BPfjRJ201iS7B                   YGyio6y4WV2x3GJAVumCBUXkYXX48sDx2BhiRgjKBcaaoIzJiZ6RU1

Running tests

Simplest way to run tests is to use tox, it will create a virtualenv for tests, install all dependencies and run pytest

tox

But you can also run pytest manually, you just need to install tests dependencies before

pip install pytest pytest-runner pytest-flask pytest-factoryboy factory_boy
pytest

WARNING: you will need to set env variables