auto-foundry-check.py

#!/usr/bin/env python3

# Read the ontologies.yml file
# check foundry criteria

__author__ = 'Chris Mungall'

import argparse, yaml

header = '''---
layout: doc
title: OBO Foundry Criteria Checker
---

[The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration](http://www.nature.com/nbt/journal/v25/n11/abs/nbt1346.html)

Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel, and Suzanna Lewis

*Nature Biotechnology* **25**, 1251 - 1255 (2007)

[Google Scholar list of papers citing The OBO Foundry.](https://scholar.google.ca/scholar?cites=13806088078865650870&as_sdt=2005&sciodt=0,5&hl=en)

### Ontology Project Publications

'''

template = '- {ontology} ({id}): [{title}]({link})\n'

IN_FOUNDRY_ORDER = 'in_foundry_order'

def main():
    parser = argparse.ArgumentParser(
        description='Extract foundry data')
    parser.add_argument('-i', '--ontologies',
        type=argparse.FileType('r'),
        help='the ontologies YAML file to read')
    #parser.add_argument(-'r','--review_path',
    #    type=str,
    #    help='the path to the review file')
    args = parser.parse_args()

    data = yaml.load(args.ontologies, Loader=yaml.SafeLoader)
    reviews = []
    for ontology in data['ontologies']:
        if 'is_obsolete' in ontology:
            continue
        reviews.append(review_ontology(ontology))

    print('## SUCCESS')
    for r in reviews:
        if r['fails'] == []:
            print(' * {}'.format(r['id']))
    print('## FAILS')
    for r in reviews:
        if len(r['fails']) > 0:
            conflict = ''
            if r['conflict']:
                conflict = '*CONFLICT*'
            print(' * {} FAILS: {} {}'.format(r['id'],r['fails'],conflict))


FAIL_LICENSE = 'license not CC-BY or CC-0'
FAIL_TRACKER = 'No tracker for community requests'
FAIL_USERS = 'No real users'
def review_ontology(ont):
    inject(ont)
    fails = []
    is_foundry = IN_FOUNDRY_ORDER in ont
    open_license = False
    if 'license' in ont:
        lurl = ont['license']['url']
        if 'creativecommons.org/licenses/by/' in lurl or 'creativecommons.org/publicdomain/zero' in lurl:
            open_license = True
    if not open_license:
        fails.append(FAIL_LICENSE)
    if 'tracker' not in ont:
        fails.append(FAIL_TRACKER)
    if 'usages' not in ont:
        fails.append(FAIL_USERS)
    conflict = is_foundry and len(fails)>0
    return dict(id=ont['id'], fails=fails, conflict=conflict)

def inject(ont):
    pass
    
if __name__ == "__main__":
    main()