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-venvAfter 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 sessionThen, 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 setupThe 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 runFor 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-appIn 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-converterIf 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 uploadThis project has been funded by the DFG.
Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrastructure – NFDI4Chem – Projektnummer 441958208 since 2020.
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