chemotion-converter-app

Development setup

First, ensure that basic Python development prerequisites are installed on the system. For Debian or Ubuntu this can be done using:

apt-get install build-essential python3-dev python3-pip python3-venv

After cloning the repository, we recommend to create a virtual environment for the application:

python3 -m venv env
source env/bin/activate  # this needs to be done in each new terminal session

Then, the application and its dependencies can be installed:

pip install -e .                     # installs the package in editable mode
pip install -r requirements/dev.txt  # only needed for the development setup

The application is configured using environment variables, which can be read from a .env file. The file .env.dev can be used as template. At least FLASK_APP=converter_app.app needs to be set.

The Flask development server can be started now:

flask run

Production setup

For the production deployment, we recommend to create a dedicated user:

groupadd chemotion -g 2002
useradd chemotion -u 2002 -g 2002 -c Chemotion -m -d /srv/chemotion -s /bin/bash

Again we create a virtual environment, but now we install the application directly from GitHub:

python3 -m venv env
source env/bin/activate
pip install git+https://github.com/ComPlat/converter-app

In production, HTTP basic auth is used to seperate clients. First, create a htpasswd file using the sha1 hashing algorithm:

htpasswd -s -c htpasswd client  # create a new file with the client_id "client"
htpasswd -s htpasswd client     # update an existing file for the client_id "client"

The path to this file needs to be provided in .env as HTPASSWD_PATH.

The development server is not suited for a production deployment. Instead we recomend to use a reverse-proxy setup using gunicorn and NGINX.

Create the .env file in /srv/chemotion/.env, but use .env.prod as template, since it contains the variables we need to set for gunicorn.

In order to create the needed log and run directories create a tmpfiles.d config in /etc/tmpfiles.d/chemotion-converter.conf. A sample file can be found in etc/tmpfiles.d/chemotion-converter.conf. Create the directories using:

systemd-tmpfiles --create

Next, create a systemd service file in /etc/systemd/system/chemotion-converter.service. Again, a sample file can be found in etc/systemd/system/chemotion-converter.service. Reload systemd and start (and enable) the service:

systemctl daemon-reload
systemctl start chemotion-converter
systemctl enable chemotion-converter

If the service won't start, journalctl -xf might indicate what is wrong.

The guincorn server listens on the port given in the env file (default: 9000) on localhost. Using the following code in your NGINX configuration, it can be reversed proxied to the /api/v1 route:

    location /api/v1 {
        proxy_pass         http://127.0.0.1:9000/;
        proxy_redirect     off;

        proxy_set_header   Host                 $host;
        proxy_set_header   X-Real-IP            $remote_addr;
        proxy_set_header   X-Forwarded-For      $proxy_add_x_forwarded_for;
        proxy_set_header   X-Forwarded-Proto    $scheme;
    }

    client_max_body_size 64M;  # set this to the maximum file size allowed for upload

jochenklar/chemotion-converter-app

chemotion-converter-app

Development setup

Production setup