def load_brain_from_file(path):
"""Created a Brain object from a file, preserving ontology metadata.
path = path to file. May be absolute or relative.
"""
m = createOWLOntologyManager()
o_file = File(path)
o = m.loadOntologyFromOntologyDocument(o_file)
return Brain(o)
def __init__(self, uri_or_fp):
self.b = Brain()
self.b.learn(uri_or_fp)
self.o = self.b.getOntology()
self.bsfp = self.b.getBidiShortFormProvider(
) # uses .getEntity(<string> shortForm), .getShortForm(OWLEntity entity)
self.ogw = OWLGraphWrapper(self.o)
self.start_auto_text = "---------------Text extracted from ontology: DO NOT EDIT---------------"
self.end_auto_text = "---------------END AUTO GENERATED SECTION---------------"
from uk.ac.ebi.brain.core import Brain
import sys
"""Runs verification tests on abstract patterns and generates markdown docs.
1st ARG specifies path to input/output files.
Second ARG specifies ontology file to use in validation."""
def load_json_from_file(path):
json_file = open(path, "r")
json_string = json_file.read()
json_file.close()
return json.loads(json_string)
# Testing abstract pattern validation and documentation
o = Brain()
o.learn(sys.argv[2]) # Running with local file for now.
# Switch this to specify path as argv
json_files = glob.glob(sys.argv[1] + "*.json") # Note - glob returns full file path
for f in json_files:
p = load_json_from_file(f)
m = re.search("(.+).json", f)
pattern_name = m.group(1)
print "Processing %s" % pattern_name
ap = pattern.abstract_pattern(p, o)
md = open(pattern_name + ".md", "w")
#print ap.gen_markdown_doc()
md.write(ap.gen_markdown_doc())
md.close()
o.sleep()
def __init__(self, uri_or_fp):
self.b = Brain()
self.b.learn(uri_or_fp)
self.o = self.b.getOntology()
self.bsfp = self.b.getBidiShortFormProvider(
) # uses .getEntity(<string> shortForm), .getShortForm(OWLEntity entity)
#!/usr/bin/env jython
from uk.ac.ebi.brain.core import Brain
import json
gorel = Brain()
gorel.learn("http://purl.obolibrary.org/obo/go/extensions/gorel.owl")
# Declaring AE rels as list for now.
relations = [ "GOREL_0001006" ]
# Would be better to pull list of AE rels automatically from file.
#With current structure, thus would require pulling subproperties. Can't do that with Brain.
# Iterate over list, pulling usage and saving to file named for relation:
for r in relations:
label = gorel.getLabel(r)
usage = gorel.getAnnotation(r, "usage")
usage_md = open("../.gitdown/" + label + "_usage.md", "w")
usage_md.write(usage)
usage_md.close()
gorel.sleep()
def load_ont(url):
ont = Brain()
ont.learn(url)
return ont
