<commit_before>opentree vagrant
################
This repo has the input files needed to bootstrap a vagrant ( http://www.vagrantup.com/ ) virtual
machine with the opentree of life software tools

Installation
############
After installing vagrant, 

    $ cp set-up-web2py-user.mysql.txt.Example set-up-web2py-user.mysql.txt

Then edit set-up-web2py-user.mysql.txt if you want to change the db passwords used by the web apps

The commands for booting the virtual machine and logging in are:

    $ vagrant up
    $ vagrant ssh

Launching software
##################

To launch phylografter:

    $ cd $OPEN_TREE/web2py
    $ echo 'your preferred web2py admin password here' | python web2py.py --nogui -i 192.168.33.10 & 

or:

    $ python web2py.py --nogui -a '<recycle>' -i 192.168.33.10 & 

if you have previously launched web2py and entered an admin password. 192.168.33.10 is the
IP listed in the Vagrantfile as the virtual machine's IP. After doing this, you should be able to see
open tree software at http://192.168.33.10:8000/phylografter and  http://192.168.33.10:8000/opentree

If you need to have access to the admin section of web2py, launch it without the -i and IP address.
This will cause web2py to bind to the loopback (localhost, or 127.0.0.1) address. Then you can
 log out of the virtual machine and use:
<commit_msg>moving mysql passwords to env vars in the scripts, because they are used in several spots. This should be OK if you the virtual instance is on a private netwark accessible to only the host machine<commit_after>opentree vagrant
################
This repo has the input files needed to bootstrap a vagrant ( http://www.vagrantup.com/ ) virtual machine with the opentree of life software tools. MTH has tested this with VirtualBox ( https://www.virtualbox.org/ ).

*NOTE* the mysql passwords are in plain text in the bootstrap file, so this should not be used for an outward-facing deployment. The default deployment should allow you to connect only via the host machine, so is should not introduce a security hole in your host machine.

Installation
############
After installing vagrant, the commands for booting the virtual machine and logging in are:

    $ vagrant up
    $ vagrant ssh

Launching software
##################

To launch phylografter:

    $ cd $OPEN_TREE/web2py
    $ echo 'your preferred web2py admin password here' | python web2py.py --nogui -i 192.168.33.10 & 

or:

    $ python web2py.py --nogui -a '<recycle>' -i 192.168.33.10 & 

if you have previously launched web2py and entered an admin password. 192.168.33.10 is the
IP listed in the Vagrantfile as the virtual machine's IP. After doing this, you should be able to see
open tree software at http://192.168.33.10:8000/phylografter and  http://192.168.33.10:8000/opentree

If you need to have access to the admin section of web2py, launch it without the -i and IP address.
This will cause web2py to bind to the loopback (localhost, or 127.0.0.1) address. Then you can
 log out of the virtual machine and use:

{'fraction_non_alphanumeric': 0.09523809523809523, 'fraction_numerical': 0.04794973544973545, 'mean_word_length': 3.771293375394322, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 5, 'https://': 1, 'lorem ipsum': 0, 'www.': 3, 'xml': 0}, 'pii_count': 12, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5668770', 'n_tokens_mistral': 980, 'n_tokens_neox': 869, 'n_words': 414}