Simple script taking spec of query as JSON and returning standard JSON report of each term found. Uses Brain

simple_json_query.py

from uk.ac.ebi.brain.core import Brain
import json
from owltools.graph import OWLGraphWrapper
import re
import sys


def write_json(json_var, path):
    """Writes json_var to file (path) with a nicely serialised layout."""
    json_file = open(path, "w")
    json_file.write(json.dumps(json_var ,sort_keys=True, indent=4, separators=(',', ': ')))
    json_file.close()
    
query = json.load(sys.argv[1])

# example query = { "query_type": 'descendant_class', "query" : "FBbt_0000001"}

    
def get_syns(ont, ID):
    ogw = OWLGraphWrapper(fbbto)
    obo_id = re.sub('_', ':', ID) 
    clazo = ogw.getOWLClassByIdentifier(obo_id)  # Needs to swith to get entity from ontology object in order to support individuals
    return ogw.getOBOSynonymStrings(clazo, [])

fbbt = Brain()
fbbt.learn("file:///repos/vfb-annotation-tools-gh/OWL/FBbt_query_classes_pre_reasoned.owl")
out = []
fbbto = fbbt.getOntology()

query_results = []
if query["query_type"] == 'descendant_classes':
    query_results = fbbt.getSubClasses(query[query], 0)
elif query["query_type"] == 'individuals;
    query_results = fbbt.getInstances(query[query], 0)


for ID in query_results:
    ni= {}
    ni['name'] = fbbt.getLabel(ID)
    ni['ID'] = ID
    synonyms = get_syns(fbbto, ID)
    ni['synonyms'] = list(synonyms)
    out.append(ni)

write_json(out, sys.argv[2])
fbbt.sleep()