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ChemTools-WebApp

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A Django webapp built around the functionality of chemtools [DEPRECATED]. This includes various utilities for parsing Gaussian log files, creating molecular structures, submitting jobs to Torque clusters, and predicting optoelectronic properties of benzobisazoles. These tools can be used through a django interface, or some of the tools can also just be used on the command line.

Here is a demo site.

Deploy

This setup assumes you are on a machine with the apt package manager. This will proceed to install the required dependencies and setup an nginx server to serve chemtools. Once this is done, you should be able to see it in your browser at http://localhost/.

$ cd chemtools-webapp
$ source install.sh

To remove chemtools, run the following commands.

$ cd chemtools-webapp
$ source install.sh remove

In addition to the parameter given to install.sh, there are also three environment variables that get used. They are INSTALL_USER, CHEMTOOLS_DIR, and HTTPS. INSTALL_USER is used to set the user that chemtools will install with (if no value is given this will default to USER). , CHEMTOOLS_DIR sets the path where chemtools is located (by default this is set to be the current directory). HTTPS specifices whether or not to use the https nginx config or not. This defaults to the regular nginx config. By giving HTTPS any non null value it will use the https configuration.

Vagrant Deploy

This assumes that you already have vagrant and virtualbox installed.

$ cd chemtools-webapp/vagrant
$ vagrant up
# Warning: This includes the test key from project/media/tests by default. This key MUST be removed if you plan on opening this server up to the internet. If you want to change the port, just change the value in the vagrant/Vagrantfile and reboot the vm.
Go to http://localhost:4567/

To spin up a vm from the local copy of chemtools-webapp can set the environmental variable DEV to true

$ DEV=true vagrant up

Development Setup

There are two ways to get a dev setup, either you can do a vagrant deployment, or you can run the install.sh script with the dev option.

$ cd chemtools-webapp
$ source install.sh dev
$ python manage.py runserver 0.0.0.0:8000
Go to http://localhost:8000/

To run the test server with ssl, you can run the following command:

$ python manage.py runsslserver\
    --key=project/media/tests/server.key\
    --certificate=project/media/tests/server.crt 0.0.0.0:8000
Go to https://localhost:8000/

If you want to get rid of the warning message when you connect to it, you can add the certificate to your browser's certificate manager.

Test

Currently, there are a few tests as a sanity check for some of the main features of chemtools. You can run them with the following command. Note: For some of the tests to pass they require a test Torque Cluster. This requirement can be satisfied using this repository which contains a Vagrant setup of a basic cluster. NOTE: These tests also assume that the test cluster is at localhost port 2222.

$ python manage.py test account chem chemtools cluster data docs

If you have coverage.py installed (if not you can install with pip install coverage), you can also run the following commands to see which parts of the code are covered by the tests.

$ coverage run manage.py test account chem chemtools cluster data docs
$ coverage html

Database

The database used can be changed in by going in project/settings.py and changing the DATABASE dictionary.