Pyontutils 0.1.34

Description:

pyontutils 0.1.34

pyontutils

python utilities for working with ontologies
Installation
pyontutils is slowly approaching stability. You can obtain it and other related
packages from pypi and install them as you see fit (e.g. pip install --user pyontutils).
If you need a bleeding edge version I reccomend installing it into your environment
(virtual or otherwise) using pip install --user --editable .[dev,test] run from
from your local copy of this repo.
Configuration
pyontutils makes use of 3 configuration files:

~/.config/pyontutils/config.yaml.
This file can be used to augment the varibles defined in auth-config.py.
For more details about the config see the orthauth guide.
secrets.yaml that you can put wherever
you want by editing the auth-stores: secrets: path: entry in config.yaml.
The file mode needs to be set to 0600 so that only you can read and write it.
It is also advisable to place it inside a folder with a mode set to 0700 since
some editors do not preserve file modes. orthauth will fail loudly if this happens.
./nifstd/scigraph/curie_map.yaml or
~/.config/pyontutils/curie_map.yaml
if a pyontutils git repository is not found. pyontutils will retrieve the
latest version of this file from github on first run if it cannot find a local copy.
The full list of locations that are searched for curie_map.yaml are specified in
auth-config.py.

If you are going to use the SciCrunch SciGraph production instance follow the
instructions
in the sparc curation setup guide to obtain an API key and put it in the right place.
In short you can set the key in your secrets file and specify the path to it in
config.yaml under the =scigraph-api-key= variable.
Alternately you can set the key using the SCICRUNCH_API_KEY environment variable
(e.g., by running export SCICRUNCH_API_KEY=$(cat path/to/my/apikey)) or by whatever
means you prefer for managing your keys.
Development Installation
From the directory that contains this readme run the following.
Refer to .travis.yml for full details.
for f in {librdflib,htmlfn,ttlser,.,neurondm,nifstd}; do pushd $f; pip install --user --pre --editable . ; popd; done

If you need even more information there is fairly exhaustive doccumentation
located in the sparc curation setup doc.
Requirements
This repo requires PyPy3 or >=Python3.6.
See and setup.py and Pipfile for additional requirements.
ontload requires Java8 and >=maven3.3 in order to build SciGraph.
parcellation requires FSL
to be installed or you need to obtain the atlases in
some other way. In order to build the packages required by this repo you will need
gcc (and toolchain) installed and will need to have the development packages for
libxml installed. To build the development dependencies you will also need the
development packages for postgresql, and protobuf installed on your system.
Building the documentation for the ontology requires pandoc and emacs along
with orgstrap. See .travis.yml
for an example of how to bootstrap a working dev environment. Alternately see
pyontutils-9999.ebuild and
nifstd-tools-9999.ebuild in tgbugs-overlay.
Utility Scripts
pyontutils provides a set of scripts that are useful for maintaining and managing ontologies
using git, and making them available via SciGraph. Note that if you choose the development
installation option you will need to ln -sT the scripts to your preferred bin folder.
For the full list please see the documentation.

ttlfmt
Reserialize ontology files using deterministic turtle (spec).
ontutils
Various useful and frequently needed commands for ontology processes as well as less frequent refactorings.
ontload
Load an ontology managed by git into SciGraph for easy deployment of services.
qnamefix
Set qnames based on the curies defined for a given ontology.
necromancy
Find dead ids in an ontology and raise them to be owl:Classes again.
scigraph-codegen
Generate a rest client against a SciGraph services endpoint.
scig
Run queries against a SciGraph endpoint from the command line.
graphml_to_ttl
Convert yEd graphml files to ttl.
ontree
Run a webserver to query and view hierarchies from the ontology.

NIF-Ontology
Many of these scripts are written for working on the NIF standard ontology
found here.
SciGraph
scigraph_codegen.py is code geneator for creating a python client library against a
SciGraph REST endpoint.
scigraph_client.py is the client library generated against the nif development scigraph instance.
ontload can be used to load your ontology into SciGraph for local use.
Building releases
See release.org.