This repository holds the code that runs The Open Tree Of Life API, which talks to the backend datastore phylesystem.
This repo uses peyotl
to interact with a copy of the phylesystem data on a server.
The code here provides a web services API to that data store.
The best description of the phylesystem is in the published paper in Bioinformatics.
See docs/ for examples of how to use the API with curl
.
There are a dependencies installable from pypi using pip, and the open tree of life client-side python library is also used on the server side for handling some aspects of NexSON.
$ pip install -r requirements.txt
$ cd ..
The first time you run, you'll need to:
$ git clone https://github.com/OpenTreeOfLife/peyotl.git
$ cd peyotl
$ pip install -r requirements.txt
$ python setup.py develop
Subsequently changing to the peyotl
directory and running
$ git pull origin master
should be sufficient to get the latest changes.
$ cp private/config.exampl private/config
then open private/config in a text editor and tweak it.
repo_parent
should be a file path which holds 1 or more phyleystem-# repositories
with the data.
git_ssh
and pkey
The behavior of the log for functions run from with a request is determined by the config file. Specifically, the
[logging]
level = debug
filepath = /tmp/my-api.log
formatter = rich
section of that file.
If you are developer of the phylesystem-api, and you want to see logging for functions that are not called in the context of a request, you can use the environmental variables:
OT_API_LOG_FILE_PATH
filepath of log file (StreamHandler if omitted)OT_API_LOGGING_LEVEL
(NotSet, debug, info, warning, error, or critical)OT_API_LOGGING_FORMAT
"rich", "simple" or "None" (None is default)This git repository is meant to be a "web2py application", so you need to
create a symlink in $WEB2PY_ROOT/applications
to the API repo directory:
cd $WEB2PY_ROOT/application
ln -sf /dir/with/api.opentreeoflife.org api
See docs/ for examples of how to use the API with curl
.
See peyotl has wrappers for accessing phylesystem web services. See the peyotl wiki for details.
See the CREDITS file
Recommended .git/hooks/pre-commit
:
#!/bin/sh
if ! black --check phylesystem_api/phylesystem_api phylesystem_api/setup.py phylesystem_api/tests ; then
black phylesystem_api/phylesystem_api phylesystem_api/setup.py phylesystem_api/tests
echo "code reformatted. commit again!"
exit 1
fi