def test_dgraph_bulk_basics_path(dgraph_bundled_helper: DgraphBundledHelper):
dg = dgraph_bundled_helper
tmp_dir = tempfile.mkdtemp()
r1 = pathlib.Path(tmp_dir, 'r1.rdf')
with open(r1, 'a') as f:
f.write('_:a <{n}> "ATCG" . \n_:b <{n}> "TCGG" . \n'.format(
n=DEFAULT_NODE_TYPE))
f.write('_:a <{e}> _:e . \n_:e <{e}> _:b . \n'.format(
e=DEFAULT_EDGE_PREDICATE))
f.write('_:e <type> "contig1" . \n')
f.write('_:e <value> "0" . \n')
try:
dg.load(tmp_dir)
connected, starting_edges = dg.g.connected('ATCG', 'TCGG')
assert connected
log.info("Connectivity check passed")
assert len(starting_edges) == 1
log.info("Length of starting edges check passed")
paths, _ = dg.g.path('ATCG', 'TCGG')
assert len(paths) == 1
log.info("Length of paths check passed")
path = paths[0]
assert path[0].value == 'ATCG'
assert path[1].value == 'TCGG'
log.info("Path value checks passed")
joined = concat_values(path)
assert joined == 'ATCGG'
log.info("Joined path check passed")
except Exception as e:
log.critical("Couldn't find one of the expected nodes")
files = glob.glob('{}/**'.format(dg.g.out_dir), recursive=True)
log.critical("Files is out_dir are:\n{}".format(files))
raise e
def test_lemongraph_connected_distant_path(prebuilt_graph: Graph):
paths, _ = prebuilt_graph.path('ATACGACGCCA', 'CGTCCGGACGT')
assert len(paths) == 1
path = paths[0]
assert path[0].value == 'ATACGACGCCA'
assert path[-1].value == 'CGTCCGGACGT'
kmer = concat_values(path)
assert kmer == 'ATACGACGCCAGCGAACGTCCGGACGT'
def test_lemongraph_connected_path(prebuilt_graph: Graph):
paths, _ = prebuilt_graph.path('CCGGAAGAAAA', 'CGGAAGAAAAA')
assert len(paths) == 1
path = paths[0]
assert path[0].value == 'CCGGAAGAAAA'
assert path[1].value == 'CGGAAGAAAAA'
kmer = concat_values(path)
assert kmer == 'CCGGAAGAAAAA'
def query(self, src: str, dst: str):
log.info("Looking for all strings between {} and {} ...".format(
src, dst))
paths, paths_meta = self.g.path(src, dst)
list_hits = []
for i in range(len(paths)):
path = paths[i]
meta = paths_meta[i]
string = concat_values(path)
list_hits.append({'string': string, **meta})
ph = PrettyHits(list_hits)
log.info("Found: {}".format(ph))
def test_graph_connected_path(g: Graph):
_setup_connected(g)
paths, _ = g.path("ABC", "BCD")
# There should be 1 path in paths
assert len(paths) == 1
path = paths[0]
if path[0].value != "ABC" or path[1].value != "BCD":
raise GraphException(g=g)
else:
assert True
joined = concat_values(path)
assert joined == "ABCD"
def test_graph_connected_distant_path(g: Graph):
_setup_connected_distant(g)
paths, _ = g.path('ABC', 'CDE')
assert len(paths) == 1
path = paths[0]
assert len(path) == 3
assert path[0].value == "ABC"
assert path[1].value == "BCD"
assert path[2].value == "CDE"
joined = concat_values(path)
assert joined == "ABCDE"