def test_rdflib_to_networkx():
try:
import networkx
except ImportError:
raise SkipTest("couldn't find networkx")
from rdflib.extras.external_graph_libs import rdflib_to_networkx_multidigraph
from rdflib.extras.external_graph_libs import rdflib_to_networkx_digraph
from rdflib.extras.external_graph_libs import rdflib_to_networkx_graph
g = Graph()
a, b, l = URIRef('a'), URIRef('b'), Literal('l')
p, q = URIRef('p'), URIRef('q')
edges = [(a, p, b), (a, q, b), (b, p, a), (b, p, l)]
for t in edges:
g.add(t)
mdg = rdflib_to_networkx_multidigraph(g)
assert len(mdg.edges()) == 4
assert mdg.has_edge(a, b)
assert mdg.has_edge(a, b, key=p)
assert mdg.has_edge(a, b, key=q)
mdg = rdflib_to_networkx_multidigraph(g, edge_attrs=lambda s, p, o: {})
assert mdg.has_edge(a, b, key=0)
assert mdg.has_edge(a, b, key=1)
dg = rdflib_to_networkx_digraph(g)
assert dg[a][b]['weight'] == 2
assert sorted(dg[a][b]['triples']) == [(a, p, b), (a, q, b)]
assert len(dg.edges()) == 3
assert dg.size() == 3
assert dg.size(weight='weight') == 4.0
dg = rdflib_to_networkx_graph(g, False, edge_attrs=lambda s, p, o:{})
assert 'weight' not in dg[a][b]
assert 'triples' not in dg[a][b]
ug = rdflib_to_networkx_graph(g)
assert ug[a][b]['weight'] == 3
assert sorted(ug[a][b]['triples']) == [(a, p, b), (a, q, b), (b, p, a)]
assert len(ug.edges()) == 2
assert ug.size() == 2
assert ug.size(weight='weight') == 4.0
ug = rdflib_to_networkx_graph(g, False, edge_attrs=lambda s, p, o:{})
assert 'weight' not in ug[a][b]
assert 'triples' not in ug[a][b]
def test_rdflib_to_networkx():
try:
import networkx
except ImportError:
raise SkipTest("couldn't find networkx")
from rdflib.extras.external_graph_libs import rdflib_to_networkx_multidigraph
from rdflib.extras.external_graph_libs import rdflib_to_networkx_digraph
from rdflib.extras.external_graph_libs import rdflib_to_networkx_graph
g = Graph()
a, b, l = URIRef("a"), URIRef("b"), Literal("l")
p, q = URIRef("p"), URIRef("q")
edges = [(a, p, b), (a, q, b), (b, p, a), (b, p, l)]
for t in edges:
g.add(t)
mdg = rdflib_to_networkx_multidigraph(g)
assert len(mdg.edges()) == 4
assert mdg.has_edge(a, b)
assert mdg.has_edge(a, b, key=p)
assert mdg.has_edge(a, b, key=q)
mdg = rdflib_to_networkx_multidigraph(g, edge_attrs=lambda s, p, o: {})
assert mdg.has_edge(a, b, key=0)
assert mdg.has_edge(a, b, key=1)
dg = rdflib_to_networkx_digraph(g)
assert dg[a][b]["weight"] == 2
assert sorted(dg[a][b]["triples"]) == [(a, p, b), (a, q, b)]
assert len(dg.edges()) == 3
assert dg.size() == 3
assert dg.size(weight="weight") == 4.0
dg = rdflib_to_networkx_graph(g, False, edge_attrs=lambda s, p, o: {})
assert "weight" not in dg[a][b]
assert "triples" not in dg[a][b]
ug = rdflib_to_networkx_graph(g)
assert ug[a][b]["weight"] == 3
assert sorted(ug[a][b]["triples"]) == [(a, p, b), (a, q, b), (b, p, a)]
assert len(ug.edges()) == 2
assert ug.size() == 2
assert ug.size(weight="weight") == 4.0
ug = rdflib_to_networkx_graph(g, False, edge_attrs=lambda s, p, o: {})
assert "weight" not in ug[a][b]
assert "triples" not in ug[a][b]
def rdflib_to_networkx(rdflib_obj):
"""Given an RDFlib graph object, convert it to a networkx
graph.
Some of the utilities and features of networkx graphs are
replicated by ComptoxAI's custom graph object, so internal methods
should be considered first.
"""
G = rdflib_to_networkx_graph(rdflib_obj)
return G
def to_sparse_matrix(file):
in_file = Path(file)
in_dir = in_file.parent
filename = in_file.name.replace(in_file.suffix, '')
print("Reading RDF graph ...")
g = Graph()
g.parse(str(in_file), format="nt")
print("Converting RDF graph to NetworkX graph ...")
netx_graph = rdflib_to_networkx_graph(g)
del g # free up some memory
print("Converting NetworkX graph to Scipy sparse matrix format ...")
graph_matrix = nx.to_scipy_sparse_matrix(netx_graph)
del netx_graph # free up some memory
outfile = f'{str(in_dir)}/{filename}.npz'
scipy.sparse.save_npz(outfile, graph_matrix)
def strip_and_produce_rdf_graph(self, rdf_graph: Graph):
"""
A function that takes in an rdflib.graph.Graph object
and transforms it into a datashader holoviews graph.
Also performs the sparql query on the graph that can be set
via the 'sparql' parameter
"""
sparql = self.sparql
qres = rdf_graph.query(sparql)
uri_graph = Graph()
for row in qres:
uri_graph.add(row)
new_netx = rdflib_to_networkx_graph(uri_graph)
original = hv.Graph.from_networkx(new_netx, self._nx_layout,
**self.graph_layout_params)
output_graph = bundle_graph(original)
return output_graph