OpenTreeOfLife/otindex

Name: otindex

Owner: OpenTreeOfLife

Description: opentree index using postgres and pyramid

Created: 2015-10-29 21:13:24.0

Updated: 2017-03-10 22:27:19.0

Pushed: 2017-05-09 20:34:04.0

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Size: 234

Language: Python

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README

otindex

A pyramid + postgres implementation of a treestore index for Open Tree of Life. Provides API access to the JSON files in the OpenTree phylesystem data store.

These instructions assume you are doing development setup on your local machine. For deploying otindex on a server, we have ansible playbook.

Tech used in development

• python 2.7.10
• pyramid v 1.5.7
• postgres v 9.5.2
• peyotl: opentree python library for interacting with the opentree tree store

Configuration

First copy the configuration template:

`$ cp development-example.ini development.ini`

Then adjust the new file for your local settings:

• In the connection_info section, add the database username, database name
  and password
• In the [app:main] section, edit sqlalchemy.url to match the settings in connection_info
• Optionally, change the logging level for various components

Installation

Install otindex and set up the database tables

You probably want to be using a virtualenv.

p install -r requirements.txt
thon setup.py develop
itialize_otindex_db development.ini

where initialize_otindex_db is in the bin directory of your virtualenv. This last step creates the database tables defined in models.py. It clears any existing tables.

Load data into the database The otindex/scripts directory contains scripts for loading data into the database. See the README file in that directory for detailed setup information.

Running the application

In the top-level directory, run:

$ pserve development.ini --reload

You should now be able to access the methods on http://0.0.0.0:6543.

Running tests

See TESTING.md in this repo.

Development notes

The top-level dev_scripts directory contains scripts for testing out new features. Some implement peyotl functions, while others allow database testing from the CLI without deploying pyramid. No promises that anything in that directory works property.