def test_neo_to_graph_upload():
""" loads a neo4j graph from a json file
"""
jt = JsonTransformer()
jt.parse('resources/robodb2.json')
nt = NeoTransformer(jt.graph, host='localhost', port='7474', username='******', password='******')
nt.save_with_unwind()
nt.neo4j_report()
def test_load():
"""
Test for loading into JsonTransformer
"""
json_file = os.path.join(resource_dir, 'semmed/gene.json')
jt = JsonTransformer()
jt.parse(json_file)
edge_list = list(jt.graph.edges(data=True))
assert edge_list[0][-1]['subject'] == 'UMLS:C0948075'
assert edge_list[0][-1]['object'] == 'UMLS:C1290952'
def test_validate_json():
"""
Validate against a valid representative Biolink Model compliant JSON
"""
json_file = os.path.join(resource_dir, 'valid.json')
jt = JsonTransformer()
jt.parse(json_file)
validator = Validator()
e = validator.validate(jt.graph)
assert len(e) == 0
def test_neo_to_graph_upload():
""" loads a neo4j graph from a json file
"""
jt = JsonTransformer()
jt.parse('resources/robodb2.json')
nt = NeoTransformer(jt.graph,
uri=DEFAULT_NEO4J_URL,
username=DEFAULT_NEO4J_USERNAME,
password=DEFAULT_NEO4J_PASSWORD)
nt.save()
nt.neo4j_report()
def test_load():
"""
load tests
"""
t = ObanRdfTransformer()
t.parse("tests/resources/monarch/biogrid_test.ttl")
t.report()
w1 = PandasTransformer(t)
w1.save('target/biogrid-e.csv', type='e')
w1.save('target/biogrid-n.csv', type='n')
w2 = GraphMLTransformer(t)
w2.save("target/x1n.graphml")
w3 = JsonTransformer(t)
w3.save("target/x1n.json")
def test_owl_load():
"""
Load a test OWL and export as JSON
"""
input_file = os.path.join(resource_dir, 'mody.ttl')
output_archive_file = os.path.join(target_dir, 'mondo_test')
output_json_file = os.path.join(target_dir, 'mondo_test.json')
t = RdfOwlTransformer()
t.parse(input_file, input_format='ttl')
t.report()
pt = PandasTransformer(t.graph)
pt.save(output_archive_file)
jt = JsonTransformer(t.graph)
jt.save(output_json_file)
def test_load():
"""
load and save tests
"""
cwd = os.path.abspath(os.path.dirname(__file__))
src_path = os.path.join(cwd, 'resources', 'monarch', 'biogrid_test.ttl')
tpath = os.path.join(cwd, 'target')
os.makedirs(tpath, exist_ok=True)
tg_path = os.path.join(tpath, "test_output.ttl")
# execute ObanRdfTransformer's parse and save function
t = ObanRdfTransformer()
t.parse(src_path, input_format="turtle")
t.save(tg_path, output_format="turtle")
t.report()
w1 = PandasTransformer(t.graph)
w1.save(os.path.join(tpath, 'biogrid-e.csv'), type='e')
w1.save(os.path.join(tpath, 'biogrid-n.csv'), type='n')
# read again the source, test graph
src_graph = rdflib.Graph()
src_graph.parse(src_path, format="turtle")
# read again the dumped target graph
tg_graph = rdflib.Graph()
tg_graph.parse(tg_path, format="turtle")
# compare subgraphs from the source and the target graph.
OBAN = Namespace('http://purl.org/oban/')
for a in src_graph.subjects(RDF.type, OBAN.association):
oban_src_graph = rdflib.Graph()
oban_src_graph += src_graph.triples((a, None, None))
oban_tg_graph = rdflib.Graph()
oban_tg_graph += tg_graph.triples((a, None, None))
# see they are indeed identical (isomorphic)
if not oban_src_graph.isomorphic(oban_tg_graph):
raise RuntimeError('The subgraphs whose subject is ' + str(a) +
' are not isomorphic ones.')
w2 = GraphMLTransformer(t.graph)
w2.save(os.path.join(tpath, "x1n.graphml"))
w3 = JsonTransformer(t.graph)
w3.save(os.path.join(tpath, "x1n.json"))
def main(path, output, model):
if model is not None:
bmt.load(model)
t = JsonTransformer()
t.parse(path)
t = PandasTransformer(t.graph)
t.save(output)
def test_json_load():
t = JsonTransformer()
t.parse(os.path.join(resource_dir, 'valid.json'))
assert t.graph.number_of_nodes() == 6
assert t.graph.number_of_edges() == 5
n = t.graph.nodes['MONDO:0017148']
assert isinstance(n, dict)
assert 'id' in n and n['id'] == 'MONDO:0017148'
assert n['name'] == 'heritable pulmonary arterial hypertension'
assert n['category'][0] == 'biolink:Disease'
data = t.graph.get_edge_data('HGNC:11603', 'MONDO:0017148')
assert len(data.keys()) == 1
data = data.popitem()[1]
assert data['subject'] == 'HGNC:11603'
assert data['object'] == 'MONDO:0017148'
assert data['edge_label'] == 'biolink:related_to'
assert data['relation'] == 'RO:0004013'
def test_load():
"""
load tests
"""
cwd = os.path.abspath(os.path.dirname(__file__))
resdir = os.path.join(cwd, 'resources')
tdir = os.path.join(cwd, 'target')
os.makedirs(tdir, exist_ok=True)
t = RdfOwlTransformer()
fn = os.path.join(resdir, "mody.ttl.gz")
f = gzip.open(fn, 'rb')
t.parse(f, input_format='ttl')
t.report()
w1 = PandasTransformer(t.graph)
w1.save(os.path.join(tdir, 'mondo-e.csv'), type='e')
w1.save(os.path.join(tdir, 'mondo-n.csv'), type='n')
w3 = JsonTransformer(t.graph)
w3.save(os.path.join(tdir, "mondo.json"))
def test_load():
"""
load TTL and save as CSV
"""
input_file = os.path.join(resource_dir, 'monarch/biogrid_test.ttl')
output_file = os.path.join(target_dir, 'test_output.ttl')
t = ObanRdfTransformer()
t.parse(input_file, input_format="turtle")
t.report()
t.save(output_file, output_format="turtle")
output_archive_file = os.path.join(target_dir, 'biogrid_test')
pt = PandasTransformer(t.graph)
pt.save(output_archive_file)
# read again the source, test graph
src_graph = rdflib.Graph()
src_graph.parse(input_file, format="turtle")
# read again the dumped target graph
target_graph = rdflib.Graph()
target_graph.parse(output_file, format="turtle")
# compare subgraphs from the source and the target graph.
OBAN = Namespace('http://purl.org/oban/')
for a in src_graph.subjects(RDF.type, OBAN.association):
oban_src_graph = rdflib.Graph()
oban_src_graph += src_graph.triples((a, None, None))
oban_tg_graph = rdflib.Graph()
oban_tg_graph += target_graph.triples((a, None, None))
# see they are indeed identical (isomorphic)
if not oban_src_graph.isomorphic(oban_tg_graph):
print(
'The subgraphs whose subject is {} are not isomorphic'.format(
a))
# w2 = GraphMLTransformer(t.graph)
# w2.save(os.path.join(tpath, "x1n.graphml"))
w3 = JsonTransformer(t.graph)
w3.save(os.path.join(target_dir, "biogrid_test.json"))
def main(path, output):
G = JsonTransformer(path).graph
for u, v, attr_dict in G.edges(data=True):
edge_label = attr_dict['edge_label']
try:
predicate, category = edge_label.replace(' ', '_').rsplit('_', 1)
except ValueError:
continue
is_predicate = bmt.get_predicate(predicate) is not None
is_category = bmt.get_class(category) is not None
if is_predicate and is_category:
if 'category' not in G.node[v]:
G.node[v]['category'] = [category]
elif category not in G.node[v]['category']:
G.node[v]['category'].append(category)
logging.info('from {u} {p} {v} found {v} is a {c}'.format(
u=u, p=p, v=v, c=category))
def main(path, output, model):
if model is not None:
bmt.load(model)
t = JsonTransformer()
t.parse(path)
def curie_to_label(curie:str):
"""
Uses the biolink model toolkit to look up an
element (on the tree rooted at `named thing`
and `related to`) for a given curie. If none
can be found then returns the original curie.
"""
if isinstance(curie, (list, tuple, set)):
return [curie_to_label(c) for c in curie]
elif isinstance(curie, str):
e = bmt.get_by_mapping(curie)
return e if e is not None else curie
else:
return None
for n, attr in t.graph.nodes(data=True):
attr['category'] = curie_to_label(attr.get('category'))
for s, o, attr in t.graph.edges(data=True):
attr['predicate'] = curie_to_label(attr.get('predicate'))
t.save(output)
def test_json_save():
t = JsonTransformer()
t.parse(os.path.join(resource_dir, 'valid.json'))
assert t.graph.number_of_nodes() == 6
assert t.graph.number_of_edges() == 5
t.save(os.path.join(target_dir, 'graph.json'))
assert os.path.exists(os.path.join(target_dir, 'graph.json'))
def test_export():
"""
Test export behavior of JsonTransformer
"""
json_file = os.path.join(resource_dir, 'semmed/gene.json')
output_file = os.path.join(target_dir, 'semmeddb_export.json')
jt = JsonTransformer()
jt.parse(json_file)
jt.save(output_file)
assert os.path.isfile(output_file)
"""
Loads all the turtle files with their required ontologies and transforms them to
json. Then loads all these json files, along with the semmeddb edges.csv and
nodes.csv files, into a single NetworkX graph, and performs `clique_merge` on it.
Finally, saves the resulting NetworkX graph as `clique_merged.csv`
"""
from kgx import ObanRdfTransformer2, JsonTransformer, HgncRdfTransformer, RdfOwlTransformer2
from kgx import clique_merge, make_valid_types
t = RdfOwlTransformer2()
t.parse('data/hp.owl')
t = JsonTransformer(t)
t.save('results/hp.json')
t = RdfOwlTransformer2()
t.parse('data/mondo.owl')
t = JsonTransformer(t)
t.save('results/mondo.json')
t = HgncRdfTransformer()
t.parse('data/hgnc.ttl')
t = JsonTransformer(t)
t.save('results/hgnc.json')
t = ObanRdfTransformer2()
t.add_ontology('data/mondo.owl')
t.add_ontology('data/hp.owl')
t.parse('data/orphanet.ttl')
t = JsonTransformer(t)
t.save('results/orphanet.json')
"""
This script prepares the clique_merged.json file for uploading to Neo4j
- Removes nodes that cannot be categorized into the biolink model
- Renames edge labels that don't matche the biolink model to "related_to"
- Transforms into CSV format
"""
from kgx import JsonTransformer, PandasTransformer
import bmt
t = JsonTransformer()
t.parse('results/clique_merged.json')
t = PandasTransformer(t)
G = t.graph
size = len(G)
nodes = []
for n, data in G.nodes(data=True):
data['category'] = [
c for c in data.get('category', []) if bmt.get_class(c) is not None
]
if data['category'] == []:
if 'name' in data:
data['category'] = ['named thing']
else:
nodes.append(n)
G.remove_nodes_from(nodes)
from kgx import JsonTransformer
from pprint import pprint
from terminaltables import AsciiTable
import sys, numpy
if len(sys.argv) < 3:
min_frequency = 100
else:
min_frequency = int(sys.argv[2])
if len(sys.argv) < 2:
quit('Required argument: path to json knowledge graph')
else:
path = sys.argv[1]
t = JsonTransformer()
t.parse(path)
category_list = []
uncategorized_example = {}
uncategorized_frequency = {}
for n in t.graph.nodes():
c = t.graph.node[n].get('category')
if c is None:
iri = t.graph.node[n].get('iri')
k = iri.split('/')
if '_' in k[-1]:
prefix, _ = k[-1].split('_', 1)
k = tuple(k[:-1] + [prefix])
else:
from kgx import ObanRdfTransformer, JsonTransformer, HgncRdfTransformer
from kgx import clique_merge
t = JsonTransformer()
t.parse('hgnc.json')
t.parse('clinvar.json')
t.parse('omim.json')
t.parse('hpoa.json')
t.parse('orphanet.json')
t.save('merged.json')
t.graph = clique_merge(t.graph)
t.save('clique_merged.json')
def test_neo_to_graph_download():
""" downloads a neo4j graph
"""
return
subject_label = 'gene'
object_label = None
edge_type = None
stop_after = 100
output_transformer = JsonTransformer()
G = output_transformer.graph
driver = http_gdb('http://localhost:7474', username='', password='')
subject_label = ':`{}`'.format(subject_label) if isinstance(
subject_label, str) else ''
object_label = ':`{}`'.format(object_label) if isinstance(
object_label, str) else ''
edge_type = ':`{}`'.format(edge_type) if isinstance(edge_type, str) else ''
match = 'match (n{})-[e{}]->(m{})'.format(subject_label, edge_type,
object_label)
results = driver.query('{} return count(*)'.format(match))
print('Using cyper query: {} return n, e, m'.format(match))
for a, in results:
size = a
break
if size == 0:
print('No data available')
quit()
page_size = 1_000
skip_flag = False
for i in range(0, size, page_size):
q = '{} return n, e, m skip {} limit {}'.format(match, i, page_size)
results = driver.query(q)
for n, e, m in results:
subject_attr = n['data']
object_attr = m['data']
edge_attr = e['data']
if 'id' not in subject_attr or 'id' not in object_attr:
if not skip_flag:
print('Skipping records that have no id attribute')
skip_flag = True
continue
s = subject_attr['id']
o = object_attr['id']
if 'edge_label' not in edge_attr:
edge_attr['edge_label'] = e['metadata']['type']
if 'category' not in subject_attr:
subject_attr['category'] = n['metadata']['labels']
if 'category' not in object_attr:
object_attr['category'] = m['metadata']['labels']
if s not in G:
G.add_node(s, **subject_attr)
if o not in G:
G.add_node(o, **object_attr)
G.add_edge(s, o, key=edge_attr['edge_label'], **edge_attr)
if stop_after is not None and G.number_of_edges() > stop_after:
break
from kgx import JsonTransformer, clique_merge
t = JsonTransformer()
t.parse('results/hp.owl')
t.parse('results/mondo.json')
t.parse('results/hgnc.json')
t.parse('results/clinvar.json')
t.parse('results/omim.json')
t.parse('results/hpoa.json')
t.parse('results/orphanet.json')
#t = PandasTransformer(t.graph)
#t.parse('data/semmeddb_edges.csv')
#t.parse('data/semmeddb_nodes.csv')
t.graph = clique_merge(t.graph)
t.save('results/clique_merged.json')
from kgx import JsonTransformer, clique_merge
import sys
path = sys.argv[1]
t = JsonTransformer()
t.parse(path)
t.graph = clique_merge(t.graph)
t.save('clique_merged.json')
from kgx import ObanRdfTransformer, JsonTransformer, HgncRdfTransformer
from collections import Counter
#o = ObanRdfTransformer()
#o.add_ontology('data/mondo.owl')
#o.add_ontology('data/hp.owl')
#o.add_ontology('data/go.owl')
#o.add_ontology('data/so.owl')
#o.add_ontology('data/ordo.owl')
from rdflib import URIRef
t = HgncRdfTransformer()
t.parse('data/hgnc.ttl')
t = JsonTransformer(t)
t.save('hgnc.json')
quit()
t = ObanRdfTransformer()
t.ontologies = o.ontologies
t.parse('data/orphanet.ttl')
t = JsonTransformer(t)
t.save('orphanet.json')
t = ObanRdfTransformer()
t.ontologies = o.ontologies
t.parse('data/hpoa.ttl')
t = JsonTransformer(t)
t.save('hpoa.json')
t = ObanRdfTransformer()
from kgx import ObanRdfTransformer, JsonTransformer, HgncRdfTransformer
from kgx import clique_merge
t = JsonTransformer()
#t.parse('hgnc.json')
#t.parse('clinvar.json')
#t.parse('omim.json')
#t.parse('hpoa.json')
#t.parse('orphanet.json')
t.parse('semmeddb.json')
t.parse('merged.json')
t.save('merged.json')
t.graph = clique_merge(t.graph)
t.save('clique_merged.json')