pyraphyletic - a pyramid implementation of phylesystem-api

This is an untested port of the phylesystem-api from web2py to pyramid.

See https://github.com/OpenTreeOfLife/phylesystem-api/blob/master/docs/README.md for as description of the API.

We don't have an immediate plan to replace the web2py version with this one. (see http://irclog.perlgeek.de/opentreeoflife/2014-06-13 )

Instructions

Prerequisites

This web app serves requests that interact with git-versioned data The repo_parent setting in your *.ini file should be set to be the filepath of a directory (often called a "shards" directory in Open Tree documentation) that is the parent of these git repos.

Setting up repos

for testing

For any tests that check the ability of the phylesystem-api to push new content to a remote version of the repositories, you'll need to a fork of the testing repos:

• https://github.com/snacktavish/mini_phyl
• https://github.com/snacktavish/mini_system
• https://github.com/jimallman/mini_amendments
• https://github.com/jimallman/mini_collections

Assuming that you have cloned those to a git server such that the repositories have those names and that the git clone prefix is common to all of them then you can bootstrap the local shards directory to serve as your repo_parent setting using the setup-testing-repos.bash script. For instance, @mtholder

1. Sets a PEYOTL_ROOT environmental variable to point to the top of the peyotl repository.

2. The he created a subdirectory inside of pyraphyletic called "shards" to serve as the repo parent by running:

bash setup-local-testing-repos.bash shards [email protected]:mtholder

for a production or dev server

When deploying on a new machine that will act as one of the Open Tree of Life's 2 servers you don't need to fork any repos to start the process. You should be able to set up a new machine with:

PEYOTL_ROOT="${HOME}/repo/peyotl" bash setup-dev-repos.bash "${HOME}/repo/dev-shards"

or

PEYOTL_ROOT="${HOME}/repo/peyotl" bash setup-production-repos.bash "${HOME}/repo/production-shards"

Note: peyotl is a prerequisite of pyraphyletic, but the PEYOTL_ROOT variable is only needed for the setup-*.bash scripts

Configuring pyraphyletic

1. copy development.ini.example to development.ini

2. tweak the settings in [app:main] as you would for the web2py impl.

3. Launch the dev server. For debugging, I like to use:

   $ while true ; do pserve development.ini --reload ; sleep 5 ; done

to start an infinite loop of relaunching (server crashes on launch if you have a SyntaxError)

Credits

See CREDITS file for author list.

thanks to http://stackoverflow.com/questions/21107057/pyramid-cors-for-ajax-requests