This is Mercury Sample Manager, a sample management tool that enables researchers to keep track of their samples from any PC in a laboratory. The programme is a Flask-based web service that runs on a central server on the local network of your research institute and that can be accessed from all other computers on the same network using the normal web browser (should be a recent browser though).

This programme should work an almost any platform (Linux, Windows, MacOS), but I only provide the installation instructions for Linux. Seeing that you should install it on a server, I suppose Linux is the target OS in most cases anyways.

You should have python 2.x and pip installed on your system. From there on it's quite straightforward:

$ sudo pip install virtualenv

installs virtualenv for python. This is not absolutely necessary, but I recommend it. You can now create a folder somewhere and clone the git repository:

$ git clone git@github.com:green-mercury/MSM.git

Now you enter this directory and you create a virtual environment for python - and activate it:

$ cd MSM
$ virtualenv venv
$ . venv/bin/activate

Finally, all that remains to do is to install the required python packages:

$ pip install -r requirements.txt

Now you have to initialise the database by running:

$ python manage.py db upgrade

This will also create the admin user that you will use for your first login (admin@admin.com, password is admin).

You can start the development server by simply executing the "run script":

$ ./run

Carry out the steps described above in order to set up the development server. Then configure gunicorn autostart by setting up a corresponding autostart file. This is explained below either for upstart or for systemd.

Create the file /etc/init/msm.conf and copy the following code into it:

description "Gunicorn application server running Mercury Sample Manager"

start on runlevel [2345]
stop on runlevel [!2345]

respawn
setuid [user name]
setgid www-data

env FLASK_CONFIG=production
env PATH=[path]/MSM/venv/bin:/usr/bin
chdir [path]/MSM
exec gunicorn --workers 4 --bind unix:msm.sock -m 007 manage:app

Where you will have to replace [user name] by your user name and [path] by the path where you installed the programme. The second path (/usr/bin) is where you should have installed the git executable.

Create the file /lib/systemd/system/msm.service and copy the following code into it:

[Unit]
Description=Gunicorn application server running Mercury Sample Manager

[Service]
Restart=on-failure
User=[user name]
Group=www-data

Environment=FLASK_CONFIG=production
Environment=PATH=[path]/MSM/venv/bin:/usr/bin
WorkingDirectory=[path]/MSM
ExecStart=[path]/MSM/venv/bin/gunicorn --workers 4 --bind unix:msm.sock -m 007 manage:app

[Install]
WantedBy=multi-user.target

Where you will have to replace [user name] by your user name and [path] by the path where you installed the programme. The second path (/usr/bin) is where you should have installed the git executable.

Now activate autostart:

sudo systemctl enable msm

Now install nginx:

$ sudo apt-get install nginx

Create an SSL certificate and key in the following folder:

$ sudo mkdir /etc/nginx/ssl
$ cd /etc/nginx/ssl

In order to create SSL certificate and key follow the steps given in https://www.digitalocean.com/community/tutorials/how-to-create-a-ssl-certificate-on-nginx-for-ubuntu-12-04

You then want to configure your nginx server. Create a file "msm" in /etc/nginx/sites-available and copy the following content into it:

server {
    listen 80;
    server_name localhost;
    rewrite        ^ https://$server_name$request_uri? permanent;
}


# HTTPS server

server {
    listen 443;
    server_name localhost;

    ssl on;
    ssl_certificate /etc/nginx/ssl/server.crt;
    ssl_certificate_key /etc/nginx/ssl/server.key;

    location / {
    include proxy_params;
      proxy_pass http://unix:[path]/MSM/msm.sock;
    }
}

Where - again - you have to replace [path] by the path to the application's directory. Then create a symbolic link to this file in /etc/nginx/sites-enabled and delete the default entry:

$ sudo ln -s /etc/nginx/sites-available/msm /etc/nginx/sites-enabled
$ sudo rm /etc/nginx/sites-enabled/default

If you want your server to support large file uploads, you have to change /etc/nginx/nginx.conf and add the following line to the http context to increase the size limit (in this example 5 Megabytes):

# set client body size to 5M #
client_max_body_size 5M;

You can now start your server by executing:

$ sudo start msm
$ sudo service nginx restart

If you use upstart, for systemd type:

$ sudo systemctl start msm
$ sudo systemctl restart nginx

The server will now automatically - i.e. also after a reboot - be available on localhost.

More details: https://www.digitalocean.com/community/tutorials/how-to-serve-flask-applications-with-gunicorn-and-nginx-on-ubuntu-14-04