def test_parse_graphml(self):
G=networkx.parse_graphml(self.simple_data)
assert_equals(sorted(G.nodes()),\
[u'n0', u'n1', u'n10', u'n2', u'n3', u'n4', u'n5', u'n6', u'n7', u'n8', u'n9'])
assert_equals( [sorted(e) for e in sorted(G.edges(keys=True))],\
[[u'foo', u'n0', u'n2'], [0, u'n1', u'n2'], [0, u'n10', u'n8'], \
[0, u'n2', u'n3'], [0, u'n3', u'n4'], [0, u'n3', u'n5'], \
[0, u'n4', u'n6'], [0, u'n5', u'n7'], [0, u'n5', u'n6'], \
[0, u'n6', u'n8'], [0, u'n10', u'n8'], [0, u'n7', u'n8'], \
[0, u'n8', u'n9']] )
G=networkx.parse_graphml(self.attribute_data.split('\n'))
assert_equals(sorted(G.nodes()),[u'n0', u'n1', u'n2', u'n3', u'n4', u'n5'])
assert_equals( sorted(G.edges(keys=True)),\
[(u'n0', u'n1', u'e1'), (u'n0', u'n2', u'e0'), (u'n1', u'n3', u'e2'), \
(u'n2', u'n4', u'e4'), (u'n3', u'n2', u'e3'), (u'n3', u'n5', u'e5'), \
(u'n5', u'n3', u'e5'), (u'n5', u'n4', u'e6')] )
assert_equals(sorted(G.nodes(data=True)),\
[(u'n0', {u'color': u'green', u'id': u'n0'}),\
(u'n1', {u'color': u'yellow', u'id': u'n1'}),\
(u'n2', {u'color': u'blue', u'id': u'n2'}),\
(u'n3', {u'color': u'yellow', u'id': u'n3', u'd3': u'red'}),\
(u'n4', {u'color': u'yellow', u'id': u'n4'}),\
(u'n5', {u'color': u'turquoise', u'id': u'n5'})] )
assert_equals( sorted(G.edges(keys=True,data=True)),\
[(u'n0', u'n1', u'e1', {u'source': u'n0', u'id': u'e1', u'weight': 1.0, u'target': u'n1'}),\
(u'n0', u'n2', u'e0', {u'source': u'n0', u'id': u'e0', u'weight': 1.0, u'target': u'n2'}),\
(u'n1', u'n3', u'e2', {u'source': u'n1', u'id': u'e2', u'weight': 2.0, u'target': u'n3'}),\
(u'n2', u'n4', u'e4', {u'source': u'n2', u'id': u'e4', u'target': u'n4'}),\
(u'n3', u'n2', u'e3', {u'source': u'n3', u'id': u'e3', u'target': u'n2'}),\
(u'n3', u'n5', u'e5', {u'directed': u'false', u'source': u'n3', u'target': u'n5', u'id': u'e5'}),\
(u'n5', u'n3', u'e5', {u'directed': u'false', u'source': u'n3', u'target': u'n5', u'id': u'e5'}),\
(u'n5', u'n4', u'e6', {u'source': u'n5', u'id': u'e6', u'weight': 1.1, u'target': u'n4'})] )
def test_parse_graphml(self):
G = networkx.parse_graphml(self.simple_data)
assert_equals(sorted(G.nodes()),\
[u'n0', u'n1', u'n10', u'n2', u'n3', u'n4', u'n5', u'n6', u'n7', u'n8', u'n9'])
assert_equals( [sorted(e) for e in sorted(G.edges(keys=True))],\
[[u'foo', u'n0', u'n2'], [0, u'n1', u'n2'], [0, u'n10', u'n8'], \
[0, u'n2', u'n3'], [0, u'n3', u'n4'], [0, u'n3', u'n5'], \
[0, u'n4', u'n6'], [0, u'n5', u'n7'], [0, u'n5', u'n6'], \
[0, u'n6', u'n8'], [0, u'n10', u'n8'], [0, u'n7', u'n8'], \
[0, u'n8', u'n9']] )
G = networkx.parse_graphml(self.attribute_data.split('\n'))
assert_equals(sorted(G.nodes()),
[u'n0', u'n1', u'n2', u'n3', u'n4', u'n5'])
assert_equals( sorted(G.edges(keys=True)),\
[(u'n0', u'n1', u'e1'), (u'n0', u'n2', u'e0'), (u'n1', u'n3', u'e2'), \
(u'n2', u'n4', u'e4'), (u'n3', u'n2', u'e3'), (u'n3', u'n5', u'e5'), \
(u'n5', u'n3', u'e5'), (u'n5', u'n4', u'e6')] )
assert_equals(sorted(G.nodes(data=True)),\
[(u'n0', {u'color': u'green', u'id': u'n0'}),\
(u'n1', {u'color': u'yellow', u'id': u'n1'}),\
(u'n2', {u'color': u'blue', u'id': u'n2'}),\
(u'n3', {u'color': u'yellow', u'id': u'n3', u'd3': u'red'}),\
(u'n4', {u'color': u'yellow', u'id': u'n4'}),\
(u'n5', {u'color': u'turquoise', u'id': u'n5'})] )
assert_equals( sorted(G.edges(keys=True,data=True)),\
[(u'n0', u'n1', u'e1', {u'source': u'n0', u'id': u'e1', u'weight': 1.0, u'target': u'n1'}),\
(u'n0', u'n2', u'e0', {u'source': u'n0', u'id': u'e0', u'weight': 1.0, u'target': u'n2'}),\
(u'n1', u'n3', u'e2', {u'source': u'n1', u'id': u'e2', u'weight': 2.0, u'target': u'n3'}),\
(u'n2', u'n4', u'e4', {u'source': u'n2', u'id': u'e4', u'target': u'n4'}),\
(u'n3', u'n2', u'e3', {u'source': u'n3', u'id': u'e3', u'target': u'n2'}),\
(u'n3', u'n5', u'e5', {u'directed': u'false', u'source': u'n3', u'target': u'n5', u'id': u'e5'}),\
(u'n5', u'n3', u'e5', {u'directed': u'false', u'source': u'n3', u'target': u'n5', u'id': u'e5'}),\
(u'n5', u'n4', u'e6', {u'source': u'n5', u'id': u'e6', u'weight': 1.1, u'target': u'n4'})] )
def convert_traitgraph_to_dot(record_id, rec_num, format_string, directory):
query = dict()
query['_id'] = ObjectId(record_id)
res = data.AxelrodStatsTreestructured.m.find(query)
log.debug("converting traitgraphs from %s to dot", record_id)
for result in res:
graph_list = result['culture_graphml_repr']
graphs = []
#log.debug("num graphs in graphml list: %s", len(graph_list))
for g in graph_list:
g_c = g['content']
graph = nx.parse_graphml(g_c)
graphs.append(graph)
for i in range(0, len(graphs)):
#log.debug("writing file for graph: %s", i)
name = str(record_id)
name += "-"
name += str(i)
fname = directory
fname += "/sample-"
fname += format_string % rec_num
fname += "-"
fname += str(i)
fname += "-"
fname += str(record_id)
fname += ".dot"
write_ordered_dot(graphs[i], fname, name)
def convert_traitgraph_to_dot(record_id, rec_num, format_string, directory):
query = dict()
query['_id'] = ObjectId(record_id)
res = data.AxelrodStatsTreestructured.m.find(query)
log.debug("converting traitgraphs from %s to dot", record_id)
for result in res:
graph_list = result['culture_graphml_repr']
graphs = []
#log.debug("num graphs in graphml list: %s", len(graph_list))
for g in graph_list:
g_c = g['content']
graph = nx.parse_graphml(g_c)
graphs.append(graph)
for i in range(0, len(graphs)):
#log.debug("writing file for graph: %s", i)
name = str(record_id)
name += "-"
name += str(i)
fname = directory
fname += "/sample-"
fname += format_string % rec_num
fname += "-"
fname += str(i)
fname += "-"
fname += str(record_id)
fname += ".dot"
write_ordered_dot(graphs[i], fname, name)
def main():
parser = argparse.ArgumentParser(description='Process some integers.')
parser.add_argument('task', help='GNPS FBMN Task ID')
parser.add_argument('metadata_column', help='GNPS FBMN metadata_column')
parser.add_argument('time_series',
help='GNPS FBMN time_series, comma separated')
parser.add_argument('output_folder', help='output folder')
parser.add_argument('--filter_metadata',
default="None",
help='filter_metadata_column')
parser.add_argument('--filter_metadata_term',
default="None",
help='filter_metadata_term')
parser.add_argument('--min_area_threshold',
type=int,
default=0,
help='min_area_threshold')
args = parser.parse_args()
# Acquiring Data
task = args.task
metadata_column = args.metadata_column
time_series = args.time_series.split(",")
filter_metadata_column = args.filter_metadata
filter_metadata_term = args.filter_metadata_term
MIN_AREA_THRESHOLD = args.min_area_threshold
long_data_df = pd.read_csv(
"http://gnps.ucsd.edu/ProteoSAFe/DownloadResultFile?task={}&block=main&file=feature_statistics/data_long.csv"
.format(task))
pairs_df = pd.DataFrame(
requests.get(
"https://gnps.ucsd.edu/ProteoSAFe/result_json.jsp?task={}&view=network_pairs_specnets_allcomponents"
.format(task)).json()["blockData"])
pairs_chemdir_df = calculate_chemdir(
long_data_df,
pairs_df,
metadata_column,
time_series,
filter_metadata=filter_metadata_column,
filter_metadata_term=filter_metadata_term,
min_area_threshold=MIN_AREA_THRESHOLD)
output_pairs_filename = os.path.join(args.output_folder,
"chemdir_pairs.tsv")
pairs_chemdir_df.to_csv(output_pairs_filename, sep="\t", index=False)
# Formatting for GraphML
r = requests.get(
"http://gnps.ucsd.edu/ProteoSAFe/DownloadResultFile?task={}&block=main&file=gnps_molecular_network_graphml/"
.format(task))
G = nx.parse_graphml(r.text)
merged_G = add_edges_network(G, pairs_chemdir_df)
nx.write_graphml(merged_G,
os.path.join(args.output_folder,
"chemdir_network.graphml"),
prettyprint=True)
def test_read_simple_undirected_graphml(self):
G = self.simple_undirected_graph
H = nx.read_graphml(self.simple_undirected_fh)
assert_equal(sorted(G.nodes()), sorted(H.nodes()))
assert_equal(sorted(sorted(e) for e in G.edges()), sorted(sorted(e) for e in H.edges()))
self.simple_undirected_fh.seek(0)
I = nx.parse_graphml(self.simple_undirected_data)
assert_equal(sorted(G.nodes()), sorted(I.nodes()))
assert_equal(sorted(sorted(e) for e in G.edges()), sorted(sorted(e) for e in I.edges()))
def test_read_simple_undirected_graphml(self):
G = self.simple_undirected_graph
H = nx.read_graphml(self.simple_undirected_fh)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
self.simple_undirected_fh.seek(0)
I = nx.parse_graphml(self.simple_undirected_data)
assert_nodes_equal(G.nodes(), I.nodes())
assert_edges_equal(G.edges(), I.edges())
def test_read_simple_undirected_graphml(self):
G = self.simple_undirected_graph
H = nx.read_graphml(self.simple_undirected_fh)
assert_nodes_equal(G.nodes(), H.nodes())
assert_edges_equal(G.edges(), H.edges())
self.simple_undirected_fh.seek(0)
I = nx.parse_graphml(self.simple_undirected_data)
assert_nodes_equal(G.nodes(), I.nodes())
assert_edges_equal(G.edges(), I.edges())
def test_read_simple_directed_graphml(self):
G = self.simple_directed_graph
H = nx.read_graphml(self.simple_directed_fh)
assert_equal(sorted(G.nodes()), sorted(H.nodes()))
assert_equal(sorted(G.edges()), sorted(H.edges()))
assert_equal(sorted(G.edges(data=True)), sorted(H.edges(data=True)))
self.simple_directed_fh.seek(0)
I = nx.parse_graphml(self.simple_directed_data)
assert_equal(sorted(G.nodes()), sorted(I.nodes()))
assert_equal(sorted(G.edges()), sorted(I.edges()))
assert_equal(sorted(G.edges(data=True)), sorted(I.edges(data=True)))
def test_read_graphml(self):
import os,tempfile
(fd,fname)=tempfile.mkstemp()
fh=open(fname,'w')
fh.write(self.simple_data)
fh.close()
Gin=networkx.read_graphml(fname)
G=networkx.parse_graphml(self.simple_data)
assert_equals( sorted(G.nodes(data=True)), sorted(Gin.nodes(data=True)))
assert_equals( sorted(G.edges(data=True)), sorted(Gin.edges(data=True)))
os.close(fd)
os.unlink(fname)
def test_read_graphml(self):
import os, tempfile
(fd, fname) = tempfile.mkstemp()
fh = open(fname, 'w')
fh.write(self.simple_data)
fh.close()
Gin = networkx.read_graphml(fname)
G = networkx.parse_graphml(self.simple_data)
assert_equals(sorted(G.nodes(data=True)), sorted(Gin.nodes(data=True)))
assert_equals(sorted(G.edges(data=True)), sorted(Gin.edges(data=True)))
os.close(fd)
os.unlink(fname)
def test_graphml_header_line(self):
good = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
bad = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml>
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
ugly = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="https://ghghgh">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
for s in (good, bad):
fh = io.BytesIO(s.encode('UTF-8'))
G = nx.read_graphml(fh)
H = nx.parse_graphml(s)
for graph in [G, H]:
assert_equal(graph.nodes['n0']['test'], True)
fh = io.BytesIO(ugly.encode('UTF-8'))
assert_raises(nx.NetworkXError, nx.read_graphml, fh)
assert_raises(nx.NetworkXError, nx.parse_graphml, ugly)
def test_graphml_header_line(self):
good = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
bad = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml>
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
ugly = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="https://ghghgh">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G">
<node id="n0">
<data key="d0">true</data>
</node>
</graph>
</graphml>
"""
for s in (good, bad):
fh = io.BytesIO(s.encode('UTF-8'))
G = nx.read_graphml(fh)
H = nx.parse_graphml(s)
for graph in [G, H]:
assert_equal(graph.nodes['n0']['test'], True)
fh = io.BytesIO(ugly.encode('UTF-8'))
assert_raises(nx.NetworkXError, nx.read_graphml, fh)
assert_raises(nx.NetworkXError, nx.parse_graphml, ugly)
def test_command_graph(self):
matches = [
((0, 0), (3, 3)),
((1, 11), (4, 14)),
((8, 12), (11, 15)),
]
regions = utils.serialize_json(matches)
result = self.runner.invoke(
cli.graph,
[regions, self.image_grid]
)
out = nx.parse_graphml(result.output.strip())
graph = nx.read_gml(fixtures_path('graph.gml'))
assert nodeset(out) == nodeset(graph)
assert edgeset(out) == edgeset(graph)
def test_read_attribute_graphml(self):
G = self.attribute_graph
H = nx.read_graphml(self.attribute_fh)
assert_nodes_equal(G.nodes(True), sorted(H.nodes(data=True)))
ge = sorted(G.edges(data=True))
he = sorted(H.edges(data=True))
for a, b in zip(ge, he):
assert_equal(a, b)
self.attribute_fh.seek(0)
I = nx.parse_graphml(self.attribute_data)
assert_equal(sorted(G.nodes(True)), sorted(I.nodes(data=True)))
ge = sorted(G.edges(data=True))
he = sorted(I.edges(data=True))
for a, b in zip(ge, he):
assert_equal(a, b)
def test_read_attribute_graphml(self):
G = self.attribute_graph
H = nx.read_graphml(self.attribute_fh)
assert_equal(sorted(G.nodes(True)), sorted(H.nodes(data=True)))
ge = sorted(G.edges(data=True))
he = sorted(H.edges(data=True))
for a, b in zip(ge, he):
assert_equal(a, b)
self.attribute_fh.seek(0)
I = nx.parse_graphml(self.attribute_data)
assert_equal(sorted(G.nodes(True)), sorted(I.nodes(data=True)))
ge = sorted(G.edges(data=True))
he = sorted(I.edges(data=True))
for a, b in zip(ge, he):
assert_equal(a, b)
def test_bool(self):
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G" edgedefault="directed">
<node id="n0">
<data key="d0">true</data>
</node>
<node id="n1"/>
<node id="n2">
<data key="d0">false</data>
</node>
<node id="n3">
<data key="d0">FaLsE</data>
</node>
<node id="n4">
<data key="d0">True</data>
</node>
<node id="n5">
<data key="d0">0</data>
</node>
<node id="n6">
<data key="d0">1</data>
</node>
</graph>
</graphml>
"""
fh = io.BytesIO(s.encode('UTF-8'))
G = nx.read_graphml(fh)
H = nx.parse_graphml(s)
for graph in [G, H]:
assert_equal(graph.nodes['n0']['test'], True)
assert_equal(graph.nodes['n2']['test'], False)
assert_equal(graph.nodes['n3']['test'], False)
assert_equal(graph.nodes['n4']['test'], True)
assert_equal(graph.nodes['n5']['test'], False)
assert_equal(graph.nodes['n6']['test'], True)
def test_bool(self):
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<key id="d0" for="node" attr.name="test" attr.type="boolean">
<default>false</default>
</key>
<graph id="G" edgedefault="directed">
<node id="n0">
<data key="d0">true</data>
</node>
<node id="n1"/>
<node id="n2">
<data key="d0">false</data>
</node>
<node id="n3">
<data key="d0">FaLsE</data>
</node>
<node id="n4">
<data key="d0">True</data>
</node>
<node id="n5">
<data key="d0">0</data>
</node>
<node id="n6">
<data key="d0">1</data>
</node>
</graph>
</graphml>
"""
fh = io.BytesIO(s.encode('UTF-8'))
G = nx.read_graphml(fh)
H = nx.parse_graphml(s)
for graph in [G, H]:
assert_equal(graph.node['n0']['test'], True)
assert_equal(graph.node['n2']['test'], False)
assert_equal(graph.node['n3']['test'], False)
assert_equal(graph.node['n4']['test'], True)
assert_equal(graph.node['n5']['test'], False)
assert_equal(graph.node['n6']['test'], True)
def test_multigraph_keys(self):
# Test that reading multigraphs uses edge id attributes as keys
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G" edgedefault="directed">
<node id="n0"/>
<node id="n1"/>
<edge id="e0" source="n0" target="n1"/>
<edge id="e1" source="n0" target="n1"/>
</graph>
</graphml>
"""
fh = io.BytesIO(s.encode('UTF-8'))
G = nx.read_graphml(fh)
expected = [("n0", "n1", "e0"), ("n0", "n1", "e1")]
assert_equal(sorted(G.edges(keys=True)), expected)
fh.seek(0)
H = nx.parse_graphml(s)
assert_equal(sorted(H.edges(keys=True)), expected)
def test_multigraph_keys(self):
# Test that reading multigraphs uses edge id attributes as keys
s = """<?xml version="1.0" encoding="UTF-8"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<graph id="G" edgedefault="directed">
<node id="n0"/>
<node id="n1"/>
<edge id="e0" source="n0" target="n1"/>
<edge id="e1" source="n0" target="n1"/>
</graph>
</graphml>
"""
fh = io.BytesIO(s.encode('UTF-8'))
G = nx.read_graphml(fh)
expected = [("n0", "n1", "e0"), ("n0", "n1", "e1")]
assert_equal(sorted(G.edges(keys=True)), expected)
fh.seek(0)
H = nx.parse_graphml(s)
assert_equal(sorted(H.edges(keys=True)), expected)
continue
url = query_result['url']
try:
if query_result['name'][-3:].lower() == 'zip':
base_dir_graphml_tagged = base_dir_harvard + 'graph_ml_tagged/'
zipped_fp = utils.get_zip_fp(query_result['url'])
for contents in zipped_fp.infolist():
if not contents.is_dir():
name = contents.filename
base_name = contents.filename.split('.')[-2].replace(
'/', '-')
edge_path = base_dir_graphml_tagged + 'edge_lists/' + base_name + '.csv'
if exists(edge_path):
continue
G = nx.parse_graphml(
zipped_fp.read(contents.filename).decode('utf-8'))
else:
base_dir_graphml_tagged = base_dir_harvard + 'graph_ml_tagged_non_zipped/'
base_name = query_result['name'].split('.')[-2].replace(
'/', '-')
edge_path = base_dir_graphml_tagged + 'edge_lists/' + base_name + '.csv'
if exists(edge_path):
continue
name = base_name
with urllib.request.urlopen(url) as graph_ml_fp:
graph_ml_lines = graph_ml_fp.read().decode('utf-8')
G = nx.parse_graphml(graph_ml_lines)
except:
print("Couldn't parse: " + name)
continue
edge_path = base_dir_graphml_tagged + 'edge_lists/' + base_name + '.csv'
def test_yfiles_extension(self):
data = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:y="http://www.yworks.com/xml/graphml"
xmlns:yed="http://www.yworks.com/xml/yed/3"
xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns
http://graphml.graphdrawing.org/xmlns/1.0/graphml.xsd">
<!--Created by yFiles for Java 2.7-->
<key for="graphml" id="d0" yfiles.type="resources"/>
<key attr.name="url" attr.type="string" for="node" id="d1"/>
<key attr.name="description" attr.type="string" for="node" id="d2"/>
<key for="node" id="d3" yfiles.type="nodegraphics"/>
<key attr.name="Description" attr.type="string" for="graph" id="d4">
<default/>
</key>
<key attr.name="url" attr.type="string" for="edge" id="d5"/>
<key attr.name="description" attr.type="string" for="edge" id="d6"/>
<key for="edge" id="d7" yfiles.type="edgegraphics"/>
<graph edgedefault="directed" id="G">
<node id="n0">
<data key="d3">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="125.0" y="100.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content"
borderDistance="0.0" fontFamily="Dialog" fontSize="13"
fontStyle="plain" hasBackgroundColor="false" hasLineColor="false"
height="19.1328125" modelName="internal" modelPosition="c"
textColor="#000000" visible="true" width="12.27099609375"
x="8.864501953125" y="5.43359375">1</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<node id="n1">
<data key="d3">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="183.0" y="205.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content"
borderDistance="0.0" fontFamily="Dialog" fontSize="13"
fontStyle="plain" hasBackgroundColor="false" hasLineColor="false"
height="19.1328125" modelName="internal" modelPosition="c"
textColor="#000000" visible="true" width="12.27099609375"
x="8.864501953125" y="5.43359375">2</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<edge id="e0" source="n0" target="n1">
<data key="d7">
<y:PolyLineEdge>
<y:Path sx="0.0" sy="0.0" tx="0.0" ty="0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="standard"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
</edge>
</graph>
<data key="d0">
<y:Resources/>
</data>
</graphml>
"""
fh = io.BytesIO(data.encode('UTF-8'))
G = nx.read_graphml(fh)
assert_equal(list(G.edges()), [('n0', 'n1')])
assert_equal(G['n0']['n1']['id'], 'e0')
assert_equal(G.nodes['n0']['label'], '1')
assert_equal(G.nodes['n1']['label'], '2')
H = nx.parse_graphml(data)
assert_equal(list(H.edges()), [('n0', 'n1')])
assert_equal(H['n0']['n1']['id'], 'e0')
assert_equal(H.nodes['n0']['label'], '1')
assert_equal(H.nodes['n1']['label'], '2')
def show_graph(graph_str: str):
G = nx.parse_graphml(graph_str)
nx.draw(G, pos=(nx.planar_layout(G)), with_labels=True)
plt.show()
def convert_topology(xml_root, out_file, set_labels):
graphml_ns = 'http://graphml.graphdrawing.org/xmlns'
graphml_ns_prefix = '{' + graphml_ns + '}'
ET.register_namespace('', graphml_ns)
# map of functions to apply to text/values for elements with a given id
id_type_conversions = {}
# remap any of the attribute names and types, and build `id_type_conversions`
for x in xml_root.findall('{}key'.format(graphml_ns_prefix)):
if x.attrib['attr.name'] in ATTR_CONVERSIONS:
(attr_name, attr_type,
attr_map_fn) = ATTR_CONVERSIONS[x.attrib['attr.name']]
x.attrib['attr.name'] = attr_name
if attr_type != None:
x.attrib['attr.type'] = attr_type
if attr_map_fn != None:
id_type_conversions[x.attrib['id']] = attr_map_fn
# transform the text/values
for x in xml_root.findall('{}graph'.format(graphml_ns_prefix)):
for y in x.findall('{}data'.format(graphml_ns_prefix)):
if y.attrib['key'] in id_type_conversions:
y.text = id_type_conversions[y.attrib['key']](y.text)
nodes = x.findall('{}node'.format(graphml_ns_prefix))
edges = x.findall('{}edge'.format(graphml_ns_prefix))
for y in nodes + edges:
for z in y.findall('{}data'.format(graphml_ns_prefix)):
if z.attrib['key'] in id_type_conversions:
z.text = id_type_conversions[z.attrib['key']](z.text)
removed_graph_keys = {}
removed_graph_data = {}
# collect and remove the keys for any unsupported graph attributes
for x in xml_root.findall('{}key'.format(graphml_ns_prefix)):
# if x.attrib['attr.name'] in UNSUPPORTED_ATTRS:
if x.attrib['for'] == 'graph':
removed_graph_keys[x.attrib['id']] = x.attrib['attr.name']
xml_root.remove(x)
# store and remove the text/values for any unsupported graph attributes
for x in xml_root.findall('{}graph'.format(graphml_ns_prefix)):
for y in x.findall('{}data'.format(graphml_ns_prefix)):
if y.attrib['key'] in removed_graph_keys:
removed_graph_data[removed_graph_keys[
y.attrib['key']]] = y.text
x.remove(y)
# build the graph from the xml
xml = ET.tostring(xml_root, encoding='utf-8', method='xml').decode('utf-8')
graph = nx.parse_graphml(xml)
# shadow doesn't use any attributes that would go in 'node_default' or
# 'edge_default', so we don't expect there to be any
if 'node_default' in graph.graph:
assert len(graph.graph['node_default']) == 0
del graph.graph['node_default']
if 'edge_default' in graph.graph:
assert len(graph.graph['edge_default']) == 0
del graph.graph['edge_default']
# Only change node and edge labels if the label option was given.
# Our custom labels help avoid cross-ref from an edge to a node via the node's
# numeric id, which can be a pain especially on large graphs.
if set_labels:
graph = nx.relabel_nodes(
graph, lambda x: f"node at {graph.nodes[x]['ip_address']}")
for (source, target) in graph.edges:
src_ip = graph.nodes[source]['ip_address']
tgt_ip = graph.nodes[target]['ip_address']
graph[source][target]['label'] = f"path from {src_ip} to {tgt_ip}"
# generate gml from the graph
try:
nx.write_gml(graph, out_file)
except nx.exception.NetworkXError:
# we require keys with underscores which isn't technically allowed by the
# spec, but both igraph and recent versions of networkx allow them
print("Unable to write GML. Do you have networkx version >= 2.5?",
file=sys.stderr)
raise
return removed_graph_data
def test_yfiles_extension(self):
data = """<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:y="http://www.yworks.com/xml/graphml" xmlns:yed="http://www.yworks.com/xml/yed/3" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://www.yworks.com/xml/schema/graphml/1.1/ygraphml.xsd">
<!--Created by yFiles for Java 2.7-->
<key for="graphml" id="d0" yfiles.type="resources"/>
<key attr.name="url" attr.type="string" for="node" id="d1"/>
<key attr.name="description" attr.type="string" for="node" id="d2"/>
<key for="node" id="d3" yfiles.type="nodegraphics"/>
<key attr.name="Description" attr.type="string" for="graph" id="d4">
<default/>
</key>
<key attr.name="url" attr.type="string" for="edge" id="d5"/>
<key attr.name="description" attr.type="string" for="edge" id="d6"/>
<key for="edge" id="d7" yfiles.type="edgegraphics"/>
<graph edgedefault="directed" id="G">
<node id="n0">
<data key="d3">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="125.0" y="100.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" borderDistance="0.0" fontFamily="Dialog" fontSize="13" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="19.1328125" modelName="internal" modelPosition="c" textColor="#000000" visible="true" width="12.27099609375" x="8.864501953125" y="5.43359375">1</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<node id="n1">
<data key="d3">
<y:ShapeNode>
<y:Geometry height="30.0" width="30.0" x="183.0" y="205.0"/>
<y:Fill color="#FFCC00" transparent="false"/>
<y:BorderStyle color="#000000" type="line" width="1.0"/>
<y:NodeLabel alignment="center" autoSizePolicy="content" borderDistance="0.0" fontFamily="Dialog" fontSize="13" fontStyle="plain" hasBackgroundColor="false" hasLineColor="false" height="19.1328125" modelName="internal" modelPosition="c" textColor="#000000" visible="true" width="12.27099609375" x="8.864501953125" y="5.43359375">2</y:NodeLabel>
<y:Shape type="rectangle"/>
</y:ShapeNode>
</data>
</node>
<edge id="e0" source="n0" target="n1">
<data key="d7">
<y:PolyLineEdge>
<y:Path sx="0.0" sy="0.0" tx="0.0" ty="0.0"/>
<y:LineStyle color="#000000" type="line" width="1.0"/>
<y:Arrows source="none" target="standard"/>
<y:BendStyle smoothed="false"/>
</y:PolyLineEdge>
</data>
</edge>
</graph>
<data key="d0">
<y:Resources/>
</data>
</graphml>
"""
fh = io.BytesIO(data.encode("UTF-8"))
G = nx.read_graphml(fh)
assert_equal(G.edges(), [("n0", "n1")])
assert_equal(G["n0"]["n1"]["id"], "e0")
assert_equal(G.node["n0"]["label"], "1")
assert_equal(G.node["n1"]["label"], "2")
H = nx.parse_graphml(data)
assert_equal(H.edges(), [("n0", "n1")])
assert_equal(H["n0"]["n1"]["id"], "e0")
assert_equal(H.node["n0"]["label"], "1")
assert_equal(H.node["n1"]["label"], "2")