def test_graph_basics_nodes(g: Graph):
expected = ["ABC", "BCE", "CEF"]
expected = set(Node(value=v) for v in expected)
for node in expected:
g.upsert_node(node)
# We assume the backing store might change ordering and only care for the
# node values
assert set(n.value for n in g.nodes) == set(ne.value for ne in expected)
def _setup_connected_distant(g: Graph):
n1 = Node(value="ABC")
n2 = Node(value="BCD")
n3 = Node(value="CDE")
g.upsert_node(n1)
g.upsert_node(n2)
g.upsert_node(n3)
e1 = Edge(src="ABC", tgt="BCD", edge_value=0)
g.add_edge(e1)
e2 = Edge(src="BCD", tgt="CDE", edge_value=1)
g.add_edge(e2)
g.save()
def test_lemongraph_not_connected(prebuilt_graph: Graph):
connected, starting_edges = prebuilt_graph.connected(
'GCTGGATACGT', 'CGTCCGGACGT')
if connected:
raise GraphException(prebuilt_graph)
else:
assert True
assert len(starting_edges) == 0
def test_graph_connected_no_node(g: Graph):
_setup_connected_no_node(g)
connected, starting_edges = g.connected('ABC', 'BCD')
if connected:
raise GraphException(g)
else:
assert True
assert len(starting_edges) == 0
def test_lemongraph_connected_distant(prebuilt_graph: Graph):
connected, starting_edges = prebuilt_graph.connected(
'ATACGACGCCA', 'CGTCCGGACGT')
if not connected:
raise GraphException(prebuilt_graph)
else:
assert True
assert len(starting_edges) == 1
log.debug("Found starting_edges as {}".format(starting_edges[0]))
def test_graph_connected(g: Graph):
_setup_connected(g)
connected, starting_edges = g.connected('ABC', 'BCD')
if not connected:
raise GraphException(g)
else:
assert True
assert len(starting_edges) == 1
log.debug("Found starting_edges as {}".format(starting_edges[0]))
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 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_graph_node_labels(g: Graph):
# TODO: we dont support node labels yet for our Dgraph backend
if isinstance(g, Dgraph):
return
expected = [
Node(value="ABC", labels={"species": "dog"}),
Node(value="BCE", labels={"species": "cat"})
]
for node in expected:
g.upsert_node(node)
assert len(g.nodes) == 2
for node in g.nodes:
if node.value == "ABC":
assert node.labels == expected[0].labels
elif node.value == "BCE":
assert node.labels == expected[1].labels
else:
# Something went wrong
assert False
def test_graph_connected_shortcut(g: Graph):
_setup_connected_shortcut(g)
connected, starting_edges = g.connected('ABC', 'CDE')
if not connected:
raise GraphException(g)
else:
assert True
assert len(starting_edges) == 2
log.debug("Found starting_edges as:")
for e in starting_edges:
log.debug(e)
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 _setup_connected(g: Graph):
n1 = Node(value="ABC")
n2 = Node(value="BCD")
g.upsert_node(n1)
g.upsert_node(n2)
e = Edge(src="ABC", tgt="BCD", edge_value=0)
g.add_edge(e)
g.save()
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"
def test_graph_connected_multiple_path(g: Graph):
_setup_connected_multiple(g)
paths, _ = g.path('ABC', 'CDE')
assert len(paths) == 2
flagged_bcd = False
flagged_xyz = False
for path in paths:
assert path[0].value == "ABC"
assert path[2].value == "CDE"
# flagged to prevent reuse of same value
if path[1].value == "BCD" and not flagged_bcd:
flagged_bcd = True
assert True
elif path[1].value == "XYZ" and not flagged_xyz:
flagged_xyz = True
assert True
else:
log.fatal("Reached the end of path iteration unexpectedly.")
assert False
def test_graph_connected_shortcut_path(g: Graph):
_setup_connected_shortcut(g)
paths, _ = g.path('ABC', 'CDE')
assert len(paths) == 2
flagged_shortcut = False
flagged_regular = False
for path in paths:
assert path[0].value == "ABC"
assert path[-1].value == "CDE"
if len(path) == 2 and not flagged_shortcut:
# This is the shortcut
flagged_shortcut = True
assert True
elif len(path) == 3 and not flagged_regular:
flagged_regular = True
assert path[1].value == "BCD"
else:
log.fatal("Reached the end of path iteration unexpectedly.")
assert False
def test_graph_connected_repeats_full_path(g: Graph):
n1 = Node(value="ABC")
n2 = Node(value="BCD")
n3 = Node(value="CDE")
g.upsert_node(n1)
g.upsert_node(n2)
g.upsert_node(n3)
e1 = Edge(src="ABC", tgt="BCD", edge_value=0)
g.add_edge(e1)
e2 = Edge(src="BCD", tgt="CDE", edge_value=1)
g.add_edge(e2)
e3 = Edge(src="CDE", tgt="ABC", edge_value=2)
g.add_edge(e3)
e4 = Edge(src="ABC", tgt="BCD", edge_value=3)
g.add_edge(e4)
e5 = Edge(src="BCD", tgt="CDE", edge_value=4)
g.add_edge(e5)
g.save()
try:
paths, _ = g.path('ABC', 'CDE')
except:
raise GraphException(g)
assert len(paths) == 3
c = 0
for path in paths:
assert path[0].value == "ABC"
assert path[-1].value == "CDE"
if len(path) == 3:
assert path[1].value == "BCD"
# There are 2 copies of this
c += 1
elif len(path) == 6:
assert path[1].value == "BCD"
assert path[2].value == "CDE"
assert path[3].value == "ABC"
assert path[4].value == "BCD"
assert path[5].value == "CDE"
assert c == 2
def _setup_connected_shortcut(g: Graph):
n1 = Node(value="ABC")
n2 = Node(value="BCD")
n3 = Node(value="CDE")
g.upsert_node(n1)
g.upsert_node(n2)
g.upsert_node(n3)
e1 = Edge(src="ABC", tgt="BCD", edge_type="path1", edge_value=0)
g.add_edge(e1)
e2 = Edge(src="BCD", tgt="CDE", edge_type="path1", edge_value=1)
g.add_edge(e2)
e1_short = Edge(src="ABC", tgt="CDE", edge_type="path2", edge_value=0)
g.add_edge(e1_short)
g.save()
def test_graph_connected_no_node_path(g: Graph):
_setup_connected_no_node(g)
paths, _ = g.path('ABC', 'BCD')
assert len(paths) == 0
def test_lemongraph_not_connected_path(prebuilt_graph: Graph):
paths, _ = prebuilt_graph.path('GCTGGATACGT', 'CGTCCGGACGT')
assert len(paths) == 0
def _setup_connected_no_node(g: Graph):
n1 = Node(value="ABC")
g.upsert_node(n1)
g.save()
def _setup_not_connected(g: Graph):
n1 = Node(value="ABC")
n2 = Node(value="BCD")
g.upsert_node(n1)
g.upsert_node(n2)
g.save()
def _setup_connected_multiple(g: Graph):
n1 = Node(value="ABC")
n2 = Node(value="BCD")
n2_alt = Node(value="XYZ")
n3 = Node(value="CDE")
g.upsert_node(n1)
g.upsert_node(n2)
g.upsert_node(n3)
g.upsert_node(n2_alt)
e1 = Edge(src="ABC", tgt="BCD", edge_type="path1", edge_value=0)
g.add_edge(e1)
e2 = Edge(src="BCD", tgt="CDE", edge_type="path1", edge_value=1)
g.add_edge(e2)
e1_alt = Edge(src="ABC", tgt="XYZ", edge_type="path2", edge_value=0)
g.add_edge(e1_alt)
e2_alt = Edge(src="XYZ", tgt="CDE", edge_type="path2", edge_value=1)
g.add_edge(e2_alt)
g.save()
def test_graph_connected_repeats_one_long_path(g: Graph):
n1 = Node(value="ABC")
n2 = Node(value="BCD")
n3 = Node(value="CDE")
n4 = Node(value="DEF")
g.upsert_node(n1)
g.upsert_node(n2)
g.upsert_node(n3)
g.upsert_node(n4)
e1 = Edge(src="ABC", tgt="BCD", edge_value=0)
g.add_edge(e1)
e2 = Edge(src="BCD", tgt="CDE", edge_value=1)
g.add_edge(e2)
e3 = Edge(src="CDE", tgt="BCD", edge_value=2)
g.add_edge(e3)
e4 = Edge(src="BCD", tgt="CDE", edge_value=3)
g.add_edge(e4)
e4 = Edge(src="CDE", tgt="DEF", edge_value=4)
g.add_edge(e4)
g.save()
paths, _ = g.path('ABC', 'DEF')
assert len(paths) == 1