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deployment_notes.md

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NOTE: These are notes only, not instructions. See the READMEs in this repo for documentation.

Notes from manual deployment

These instructions based on installing on a Duke research toolkits VM (ubuntu 16.04.1 LTS)

Install and setup postgres; see PostgreSQL installation instructions

$ sudo apt-get install postgresql postgresql-contrib
$ sudo -u postgres psql postgres
$ \password postgres  # then exit using \q
$ sudo -u postgres createdb otindex  # create database

Install pip, virtualenv, apache, libpq-dev and create a virtual environment $ sudo apt-get install python-pip $ sudo apt-get install virtualenv $ sudo apt-get install libpq-dev $ sudo apt-get install apache2 $ sudo apt-get install libapache2-mod-wsgi $ virtualenv opentree $ source opentree/bin/activate

Install git $ sudo apt-get install git-core

Install a local copy of the phylesystem $ mkdir phylesystem $ mkdir phylesystem/shards $ cd ~/phylesystem/shards $ git clone https://github.com/OpenTreeOfLife/phylesystem-1.git

Download a copy of OTT (substitute URL of current version): $ wget http://files.opentreeoflife.org/ott/ott2.10/ott2.10draft11.tgz $ tar xfvz ott2.10draft11.tgz

Set up peyotl, following the installation and configuration instructions. All operations run against local copies of phylesystem and OTT, do you do not need any of the API settings.

Run the peyotl tests: $ python setup.py test

Clone and setup the otindex repo $ git clone https://github.com/OpenTreeOfLife/otindex.git $ cd otindex $ pip install -r requirements.in $ python setup.py install

Edit the otindex development.yml file for the local setup $ cp development-example.ini development.ini You will need to specify the postgres user (likely 'postgres'), DB name, and DB password.

Set up and load the database $ bash run_setup_scripts.sh config.yml

Apache configuration based on: http://docs.pylonsproject.org/projects/pyramid/en/latest/tutorials/modwsgi/

Enable WSGI $ sudo a2enmod wsgi $ sudo /usr/sbin/apachectl restart

Set up the production.ini file:

Run the application

Run the tests

Deploying on AWS

  • Select Debian from Community AMIs: debian-jessie-amd64-hvm-2016-09-19-ebs - ami-2a34e94a

  • Select instance: m3.medium

  • Select the security group: 'OpenTree... with ping' for development and 'OpenTree production' for production. Note that you can't change the security group after launch!

  • Choose key pair: 'opentree' for dev, 'opentree production' for production

  • log in and accept the fingerprint prompt:

    ssh -i <pem file> admin@<hostname>

  • edit the ansible playbook with the IP address of the EC2 host

  • run ansible, where server is either production or development:

    ansible-playbook otindex.yml -i hosts --limit <server>

  • run the tests (see TESTING.md)