- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2018-11-15 17:55:53+13:00
- Desc:
- Adding initial attempt at basic provenance classes and properties.
* Treating existing 'Resource' class as the core entity as per PROV-O
* Adding new 'Agent' and 'Activity' classes
* Make the existing 'Researcher' class a subclass of Agent
* Adding new 'Software' class as a subclass of the Agent class
* Defining the relevant properties to describe the provenance linkages
* Software can be described with a text description and/or a URI pointing to the software
- Permanent Source URI:
- http://models.cellml.org/workspace/526/rawfile/c664f73a3975f999b8369a2bbc02aa9ead9f1329/draft01_schema.py
import owlready2
def load_owl(filename):
return owlready2.get_ontology("file://" + filename).load()
def map_properties_classes(ontology):
"""
Return a map of all things
"""
cls_prop_map = {cls: {} for cls in ontology.classes()}
for prop in ontology.properties():
for domain in prop.domain:
cls = cls_prop_map.get(domain)
if cls is None:
continue
cls[prop] = prop.range
return cls_prop_map
def to_name(thing):
if thing is str:
return 'string'
return '.'.join(str(thing).split('.')[1:])
def range_to_type_name(thing):
# a very lazy/naive implementation for the mean time.
if len(thing) == 1:
if thing[0] is str:
return "string"
else:
return to_name(thing[0])
# laziest possible conversion.
return str([to_name(item) for item in thing])
def build_schema(cls_prop_map):
results = {}
for cls, cls_prop in cls_prop_map.items():
key, value = build_schema_cls(cls, cls_prop)
results[key] = value
return results
def build_schema_cls(cls, cls_prop):
schema_properties = {}
schema = {
"$id": "",
"$schema": "http://schema.blackfynn.io/model/draft-01/schema",
"name": to_name(cls),
"description": "",
"category": "",
"properties": schema_properties,
"required": [],
}
for prop, range_ in cls_prop.items():
schema_properties[to_name(prop)] = {
"description": "",
"type": range_to_type_name(range_),
}
return to_name(cls), schema
if __name__ == '__main__':
import sys
import json
from os.path import basename
if len(sys.argv) < 2:
sys.stderr.write('usage: %s <owl_file>\n' % basename(sys.argv[0]))
sys.exit(1)
ontology = load_owl(sys.argv[1])
cls_prop_map = map_properties_classes(ontology)
schemas = build_schema(cls_prop_map)
print(json.dumps(schemas, indent=4))
