import yaml
import requests
from os.path import join, dirname, abspath
from rdflib import Graph, Namespace, Literal

bb_ont_url = ('https://raw.githubusercontent.com/BBN-E/Hume/master/resource/'
              'ontologies/hume_ontology.yaml')

eidos_ns = Namespace('https://github.com/clulab/eidos/wiki/JSON-LD/Grounding#')
indra_ns = 'http://sorger.med.harvard.edu/indra/'
indra_rel_ns = Namespace(indra_ns + 'relations/')
isa = indra_rel_ns.term('isa')

def save_hierarchy(g, path):
    with open(path, 'wb') as out_file:
        g_bytes = g.serialize(format='nt')
        # Replace extra new lines in string and get rid of empty line at end
        g_bytes = g_bytes.replace(b'\n\n', b'\n').strip()
        # Split into rows and sort
        rows = g_bytes.split(b'\n')
        rows.sort()
        g_bytes = b'\n'.join(rows)
        out_file.write(g_bytes)


def get_term(node, prefix):
    node = node.replace(' ', '_')
    path = prefix + '/' + node if prefix else node
    return eidos_ns.term(path)


def build_relations(G, node, tree, prefix):
    this_term = get_term(node, prefix)
    node = node.replace(' ', '_')
    if prefix is not None:
        prefix = prefix.replace(' ', '_')
    this_prefix = prefix + '/' + node if prefix else node
    for entry in tree:
        if isinstance(entry, str) and entry[0] != '_':
            child = entry
        elif isinstance(entry, dict):
            for child in entry.keys():
                if child[0] != '_' and child != 'examples' \
                   and any(isinstance(entry[child], t) for t in [list, dict]):
                    build_relations(G, child, entry[child], this_prefix)

        if child[0] != '_' and child != 'examples':
            child_term = get_term(child, this_prefix)
            rel = (child_term, isa, this_term)
            G.add(rel)


if __name__ == '__main__':
    yml = requests.get(bb_ont_url).content
    root = yaml.load(yml)
    G = Graph()
    for top_entry in root:
        for node in top_entry.keys():
            build_relations(G, node, top_entry[node], None)
    rdf_path = join(dirname(abspath(__file__)), 'bbn_ontology.rdf')
    save_hierarchy(G, rdf_path)
Create separate bbn ontology retriever.
Create separate bbn ontology retriever.
