IdentiPy Server - a Django-based web interface for IdentiPy

Citation

IdentiPy and IdentiPy Server are described in this JPR paper: http://dx.doi.org/10.1021/acs.jproteome.7b00640

Please cite it when using IdentiPy and/or IdentiPy Server or their parts.

License

IdentiPy Server is published under the Apache 2.0 license.

Requirements

• Python 3
• Django 2+
• identipy and its dependencies
  • pyteomics
  • pyteomics.cythonize
  • numpy
  • scipy
  • lxml
    • (if installed with pip, lxml will need development packages of libxml2 and libxslt to compile)
• Scavager and its dependencies
  • matplotlib
    • cycler, pyparsing, python-dateutil, functools32
  • CatBoost
  • Pandas
  • pyteomics.pepxmltk
• psutil
• Pillow

IdentiPy: https://github.com/levitsky/identipy

Scavager: https://github.com/markmipt/scavager

All dependencies can be installed using pip or the package manager of your operating system.

How to run IdentiPy Server

IdentiPy Server currently works on Unix-like operating systems only. IdentiPy and Scavager need to be properly installed to be imported by IdentiPy Server.

Setup

Clone this reposoitory into the location where you want to keep the uploads and results:

$ git clone https://github.com/levitsky/identipy_server.git

Download and install all dependencies, either globally or in a virtual environment:

$ cd identipy_server
$ pip install -r requirements.txt

Run these commands to initialize the database:

$ python manage.py makemigrations
$ python manage.py migrate

Then create a superuser account to manage the database...

$ python manage.py createsuperuser

You can also create a regular user account from Django admin site or from command line:

$ python manage.py createuser <username>

You can then run Django development server to test your setup:

$ python manage.py runserver

This will start a development server on 127.0.0.1:8000, so it will only be available locally. If you need to access the server from a local network, specify the IP address and port you need, e.g.:

$ python manage.py runserver 192.168.1.2:9000

While the development server is running, you can log into IdentiPy Server and use it in your browser. If you log in as superuser, you can add more users via the admin page, e.g. 192.168.1.2:9000/admin

Production use

For more reliable use (especially for multiple-user installations), we recommend running IndetiPy Server with a WSGI-compatible web server application like Apache or Nginx+uWSGI, instead of the Django development server:

https://docs.djangoproject.com/en/3.2/howto/deployment/wsgi/

Example configuration files are included:

• uwsgi_parameters and identipy.example.ini - for uWSGI;
• identipy.example.conf - for nginx;
• example-httpd-vhosts.conf - for Apache with mod_wsgi and virtual hosts.

You may need to edit the following settings in identipy_server/settings.py:

• Django settings:

  • SECRET_KEY
  • DEBUG
  • ALLOWED_HOSTS
  • STATIC_ROOT
  • DATABASES (repeat migration after changing this)
  • CACHES
  • LOGGING

• Project-specific settings:

  • EMAIL_*
  • NUMBER_OF_PARALLEL_RUNS
  • STATUS_UPDATE_INTERVAL
  • ZIP_COMPRESSION
  • ALLOW_ZIP64
  • LOCAL_IMPORT
  • URL_IMPORT

For explanation of Django settings see the official documentation: https://docs.djangoproject.com/en/4.0/ref/settings/