def test_write_with_node_attributes(self):
# Addresses #673.
G = nx.path_graph(4)
for i in range(4):
G.node[i]['id'] = i
G.node[i]['label'] = i
G.node[i]['pid'] = i
expected = """<gexf version="1.1" xmlns="http://www.gexf.net/1.1draft" xmlns:viz="http://www.gexf.net/1.1draft/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="static">
<nodes>
<node id="0" label="0" pid="0" />
<node id="1" label="1" pid="1" />
<node id="2" label="2" pid="2" />
<node id="3" label="3" pid="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="1" source="1" target="2" />
<edge id="2" source="2" target="3" />
</edges>
</graph>
</gexf>"""
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def test_edge_id_construct(self):
G = nx.Graph()
G.add_edges_from([(0, 1, {"id": 0}), (1, 2, {"id": 2}), (2, 3)])
expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\
="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.\
gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2">
<meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
<creator>NetworkX {nx.__version__}</creator>
</meta>
<graph defaultedgetype="undirected" mode="static" name="">
<nodes>
<node id="0" label="0" />
<node id="1" label="1" />
<node id="2" label="2" />
<node id="3" label="3" />
</nodes>
<edges>
<edge source="0" target="1" id="0" />
<edge source="1" target="2" id="2" />
<edge source="2" target="3" id="1" />
</edges>
</graph>
</gexf>"""
obtained = "\n".join(nx.generate_gexf(G))
assert expected == obtained
def test_write_with_node_attributes(self):
# Addresses #673.
G = nx.path_graph(4)
for i in range(4):
G.node[i]['id'] = i
G.node[i]['label'] = i
G.node[i]['pid'] = i
expected = """<gexf version="1.1" xmlns="http://www.gexf.net/1.1draft" xmlns:viz="http://www.gexf.net/1.1draft/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="static" name="path_graph(4)">
<meta>
<creator>NetworkX {}</creator>
<lastmodified>{}</lastmodified>
</meta>
<nodes>
<node id="0" label="0" pid="0" />
<node id="1" label="1" pid="1" />
<node id="2" label="2" pid="2" />
<node id="3" label="3" pid="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="1" source="1" target="2" />
<edge id="2" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(nx.__version__, time.strftime('%d/%m/%Y'))
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def test_write_with_node_attributes(self):
# Addresses #673.
G = nx.path_graph(4)
for i in range(4):
G.node[i]['id'] = i
G.node[i]['label'] = i
G.node[i]['pid'] = i
expected = """<gexf version="1.1" xmlns="http://www.gexf.net/1.1draft" xmlns:viz="http://www.gexf.net/1.1draft/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="static" name="path_graph(4)">
<meta>
<creator>NetworkX {}</creator>
<lastmodified>{}</lastmodified>
</meta>
<nodes>
<node id="0" label="0" pid="0" />
<node id="1" label="1" pid="1" />
<node id="2" label="2" pid="2" />
<node id="3" label="3" pid="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="1" source="1" target="2" />
<edge id="2" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(nx.__version__, time.strftime('%d/%m/%Y'))
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def test_write_with_node_attributes(self):
# Addresses #673.
G = nx.OrderedGraph()
G.add_edges_from([(0, 1), (1, 2), (2, 3)])
for i in range(4):
G.nodes[i]["id"] = i
G.nodes[i]["label"] = i
G.nodes[i]["pid"] = i
G.nodes[i]["start"] = i
G.nodes[i]["end"] = i + 1
expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\
="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation=\
"http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\
gexf.xsd" version="1.2">
<meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
<creator>NetworkX {nx.__version__}</creator>
</meta>
<graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long">
<nodes>
<node id="0" label="0" pid="0" start="0" end="1" />
<node id="1" label="1" pid="1" start="1" end="2" />
<node id="2" label="2" pid="2" start="2" end="3" />
<node id="3" label="3" pid="3" start="3" end="4" />
</nodes>
<edges>
<edge source="0" target="1" id="0" />
<edge source="1" target="2" id="1" />
<edge source="2" target="3" id="2" />
</edges>
</graph>
</gexf>"""
obtained = "\n".join(nx.generate_gexf(G))
assert expected == obtained
def test_write_with_node_attributes(self):
# Addresses #673.
G = nx.OrderedGraph()
G.add_edges_from([(0, 1), (1, 2), (2, 3)])
for i in range(4):
G.nodes[i]['id'] = i
G.nodes[i]['label'] = i
G.nodes[i]['pid'] = i
G.nodes[i]['start'] = i
G.nodes[i]['end'] = i + 1
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long">
<meta>
<creator>NetworkX {}</creator>
<lastmodified>{}</lastmodified>
</meta>
<nodes>
<node end="1" id="0" label="0" pid="0" start="0" />
<node end="2" id="1" label="1" pid="1" start="1" />
<node end="3" id="2" label="2" pid="2" start="2" />
<node end="4" id="3" label="3" pid="3" start="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="1" source="1" target="2" />
<edge id="2" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(nx.__version__, time.strftime('%d/%m/%Y'))
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def generate_gexf(df_annotation, fileLocationStr):
if len(df_annotation) > 0:
df_annotation_dup = df_annotation.copy()
df_annotation_dup['workflowName'] = df_annotation_dup[
'workflowName'].str.replace(fileLocationStr, "")
df_annotation_dup['invokedBy'] = df_annotation_dup[
'invokedBy'].str.replace(fileLocationStr, "")
df_invokeWf = df_annotation_dup.loc[:, ['workflowName', 'invokedBy'
]].drop_duplicates()
#combine source and target with no dupes
df_node_list = list(
pd.concat([
df_invokeWf.loc[:, 'invokedBy'],
df_invokeWf.loc[:, 'workflowName']
],
ignore_index=True).drop_duplicates())
df_node_list_wl = [(node, {
'label': node.split("/")[-1].replace(".xaml", "")
}) for node in df_node_list]
# translate workflow calls to a path graph
G = nx.DiGraph()
G.add_nodes_from(df_node_list_wl)
for index, row in df_invokeWf.iterrows():
G.add_edge(row['invokedBy'], row['workflowName'])
#ajax request
str_gexf = '<?xml version="1.0" encoding="UTF-8"?>\n' + "".join(
nx.generate_gexf(
G, encoding='utf-8', prettyprint=True, version='1.2draft'))
return str_gexf
else:
return None
def test_write_with_node_attributes(self):
# Addresses #673.
G = nx.OrderedGraph()
G.add_edges_from([(0, 1), (1, 2), (2, 3)])
for i in range(4):
G.nodes[i]['id'] = i
G.nodes[i]['label'] = i
G.nodes[i]['pid'] = i
G.nodes[i]['start'] = i
G.nodes[i]['end'] = i + 1
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="dynamic" name="" timeformat="long">
<meta>
<creator>NetworkX {}</creator>
<lastmodified>{}</lastmodified>
</meta>
<nodes>
<node end="1" id="0" label="0" pid="0" start="0" />
<node end="2" id="1" label="1" pid="1" start="1" />
<node end="3" id="2" label="2" pid="2" start="2" />
<node end="4" id="3" label="3" pid="3" start="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="1" source="1" target="2" />
<edge id="2" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(nx.__version__, time.strftime('%d/%m/%Y'))
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def test_write_with_node_attributes(self):
# Addresses #673.
G = nx.path_graph(4)
for i in range(4):
G.node[i]['id'] = i
G.node[i]['label'] = i
G.node[i]['pid'] = i
expected = """<gexf version="1.1" xmlns="http://www.gexf.net/1.1draft" xmlns:viz="http://www.gexf.net/1.1draft/viz" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="static">
<nodes>
<node id="0" label="0" pid="0" />
<node id="1" label="1" pid="1" />
<node id="2" label="2" pid="2" />
<node id="3" label="3" pid="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="1" source="1" target="2" />
<edge id="2" source="2" target="3" />
</edges>
</graph>
</gexf>"""
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal( expected, obtained )
def graph(nodes):
"""
Dessine un graphe et l'enregistre dans un fichier.
Enregistre aussi un fichier gexf pour un usage dans Gephi.
"""
G = nx.DiGraph()
G.add_weighted_edges_from(nodes)
options = {
'node_color': 'red',
'node_size': 7,
'edge_color': 'tab:gray',
'with_labels': False
}
plt.figure(figsize=(50, 50))
pos = nx.spring_layout(G, k=0.2, iterations=50) #50 : défaut
nx.draw(G, pos, **options)
plt.savefig("graphe.png")
linefeed = chr(10)
s = linefeed.join(nx.generate_gexf(G))
with open("graphe.gexf", "w") as f:
f.write(s)
def exportGEXF(self, filename):
"""
Método exportar la red a formato GEXF
Args:
filename: ruta del nuevo fichero
"""
self.writeFile(filename, nx.generate_gexf(self.__G))
def test_numpy_type(self):
G = nx.path_graph(4)
try:
import numpy
except ImportError:
return
nx.set_node_attributes(G, {n: n for n in numpy.arange(4)}, 'number')
G[0][1]['edge-number'] = numpy.float64(1.1)
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft"\
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\
="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd">
<meta lastmodifieddate="{}">
<creator>NetworkX {}</creator>
</meta>
<graph defaultedgetype="undirected" mode="static" name="">
<attributes class="edge" mode="static">
<attribute id="1" title="edge-number" type="float" />
</attributes>
<attributes class="node" mode="static">
<attribute id="0" title="number" type="int" />
</attributes>
<nodes>
<node id="0" label="0">
<attvalues>
<attvalue for="0" value="0" />
</attvalues>
</node>
<node id="1" label="1">
<attvalues>
<attvalue for="0" value="1" />
</attvalues>
</node>
<node id="2" label="2">
<attvalues>
<attvalue for="0" value="2" />
</attvalues>
</node>
<node id="3" label="3">
<attvalues>
<attvalue for="0" value="3" />
</attvalues>
</node>
</nodes>
<edges>
<edge id="0" source="0" target="1">
<attvalues>
<attvalue for="1" value="1.1" />
</attvalues>
</edge>
<edge id="1" source="1" target="2" />
<edge id="2" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
obtained = '\n'.join(nx.generate_gexf(G))
assert expected == obtained
def test_numpy_type(self):
G = nx.path_graph(4)
try:
import numpy
except ImportError:
return
nx.set_node_attributes(G, {n:n for n in numpy.arange(4)}, 'number')
G[0][1]['edge-number'] = numpy.float64(1.1)
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="static" name="">
<attributes class="edge" mode="static">
<attribute id="1" title="edge-number" type="float" />
</attributes>
<attributes class="node" mode="static">
<attribute id="0" title="number" type="int" />
</attributes>
<meta>
<creator>NetworkX {}</creator>
<lastmodified>{}</lastmodified>
</meta>
<nodes>
<node id="0" label="0">
<attvalues>
<attvalue for="0" value="0" />
</attvalues>
</node>
<node id="1" label="1">
<attvalues>
<attvalue for="0" value="1" />
</attvalues>
</node>
<node id="2" label="2">
<attvalues>
<attvalue for="0" value="2" />
</attvalues>
</node>
<node id="3" label="3">
<attvalues>
<attvalue for="0" value="3" />
</attvalues>
</node>
</nodes>
<edges>
<edge id="0" source="0" target="1">
<attvalues>
<attvalue for="1" value="1.1" />
</attvalues>
</edge>
<edge id="1" source="1" target="2" />
<edge id="2" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(nx.__version__, time.strftime('%d/%m/%Y'))
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def test_numpy_type(self):
np = pytest.importorskip("numpy")
G = nx.path_graph(4)
nx.set_node_attributes(G, {n: n for n in np.arange(4)}, "number")
G[0][1]["edge-number"] = np.float64(1.1)
expected = f"""<gexf xmlns="http://www.gexf.net/1.2draft"\
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation\
="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd"\
version="1.2">
<meta lastmodifieddate="{time.strftime('%Y-%m-%d')}">
<creator>NetworkX {nx.__version__}</creator>
</meta>
<graph defaultedgetype="undirected" mode="static" name="">
<attributes mode="static" class="edge">
<attribute id="1" title="edge-number" type="float" />
</attributes>
<attributes mode="static" class="node">
<attribute id="0" title="number" type="int" />
</attributes>
<nodes>
<node id="0" label="0">
<attvalues>
<attvalue for="0" value="0" />
</attvalues>
</node>
<node id="1" label="1">
<attvalues>
<attvalue for="0" value="1" />
</attvalues>
</node>
<node id="2" label="2">
<attvalues>
<attvalue for="0" value="2" />
</attvalues>
</node>
<node id="3" label="3">
<attvalues>
<attvalue for="0" value="3" />
</attvalues>
</node>
</nodes>
<edges>
<edge source="0" target="1" id="0">
<attvalues>
<attvalue for="1" value="1.1" />
</attvalues>
</edge>
<edge source="1" target="2" id="1" />
<edge source="2" target="3" id="2" />
</edges>
</graph>
</gexf>"""
obtained = "\n".join(nx.generate_gexf(G))
assert expected == obtained
def _generate_network_of_frames(topics_id, timespans_id, num_of_sources, out_name, top_media_sort,
remove_media_list=None, remove_word_list=[], generate_word_lists=False,
include_media_list=None, media_attribs=None, num_words=None):
if remove_media_list is None:
remove_media_list = []
# use this specify attributes on the media source that should be added to the node as attributes
# if(media_attribs == None):
# media_attribs = {}
if include_media_list is None:
media_sources_md = topic_media_list(user_mediacloud_key(), topics_id, timespans_id=timespans_id,
limit=num_of_sources + len(remove_media_list), sort=top_media_sort)['media']
else:
media_sources_md = include_media_list
if remove_media_list is not None:
for r in remove_media_list:
media_sources_md = _remove_media_source(r, media_sources_md)
top_words = _build_top_words(media_sources_md, topics_id, timespans_id, remove_word_list, num_words)
if remove_word_list is not None:
top_words = _clean_top_words(top_words, remove_word_list)
frame_network = _build_network(top_words, media_sources_md, media_attribs)
_export_gexf_network(frame_network, '%s.gexf' % out_name)
_export_d3_network(frame_network, '%s' % out_name)
if generate_word_lists:
with open('%s.txt' % out_name, 'w', encoding="utf-8") as wl:
all_words = []
media_sources = {ms['media_id']: ms['name'] for ms in media_sources_md}
# counts = {}
for ms in top_words:
# wl.write("\n\n%s (media id: %d):\n" % (media_sources[ms].encode('ascii', 'ignore'), ms))
wl.write("\n\n{} (media id: {}):\n".format(media_sources[ms], ms))
for w in top_words[ms]:
all_words.append(w['term'])
# increment count to see how many media source include each word
# counts[ms]
# wl.write("- %s (%d)\n" % (w['term'].encode('ascii', 'ignore'), w['count']))
wl.write("- {} ({})\n".format(w['term'], w['count']))
wl.write("\n")
linefeed = chr(10) # linefeed=\n
s = linefeed.join(nx.generate_gexf(frame_network)) # doctest: +SKIP
# for line in nx.generate_gexf(frame_network): # doctest: +SKIP
# logger.debug line
return s
def test_edge_id_construct(self):
G = nx.Graph()
G.add_edges_from([(0, 1, {'id': 0}), (1, 2, {'id': 2}), (2, 3)])
if sys.version_info < (3, 8):
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/\
1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:\
schemaLocation="http://www.gexf.net/1.2draft http://www.gexf.net/1.2draft/\
gexf.xsd">
<meta lastmodifieddate="{}">
<creator>NetworkX {}</creator>
</meta>
<graph defaultedgetype="undirected" mode="static" name="">
<nodes>
<node id="0" label="0" />
<node id="1" label="1" />
<node id="2" label="2" />
<node id="3" label="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="2" source="1" target="2" />
<edge id="1" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
else:
expected = """<gexf xmlns="http://www.gexf.net/1.2draft" xmlns:xsi\
="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.\
gexf.net/1.2draft http://www.gexf.net/1.2draft/gexf.xsd" version="1.2">
<meta lastmodifieddate="{}">
<creator>NetworkX {}</creator>
</meta>
<graph defaultedgetype="undirected" mode="static" name="">
<nodes>
<node id="0" label="0" />
<node id="1" label="1" />
<node id="2" label="2" />
<node id="3" label="3" />
</nodes>
<edges>
<edge source="0" target="1" id="0" />
<edge source="1" target="2" id="2" />
<edge source="2" target="3" id="1" />
</edges>
</graph>
</gexf>""".format(time.strftime('%Y-%m-%d'), nx.__version__)
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def generate_network_of_frames(controversy_id, dump_id, timeslice_id, num_of_sources, out_name=None, remove_media_list=None, remove_word_list=[], generate_word_lists=False, include_media_list=None, media_attribs=None):
if(out_name == None):
out_name = 'network_of_frames-%s' % datetime.datetime.now().isoformat()
if(remove_media_list == None):
remove_media_list = []
# if(media_attribs == None):
# media_attribs = {}
if(include_media_list == None):
media_sources_md = get_top_x_sources(controversy_id, num_of_sources+len(remove_media_list), dump_id, timeslice_id)
else:
media_sources_md = include_media_list
if(remove_media_list != None):
for r in remove_media_list:
media_sources_md = remove_media_source(r, media_sources_md)
top_words = build_top_words(media_sources_md, timeslice_id, remove_word_list)
if(remove_word_list != None):
top_words = clean_top_words(top_words, remove_word_list)
frame_network = build_network(top_words, media_sources_md, media_attribs)
export_gexf_network(frame_network, '%s.gexf' % out_name)
export_d3_network(frame_network, '%s' % out_name)
if(generate_word_lists == True):
with open('%s-word-usage.txt' % out_name, 'wb') as wl:
all_words = []
media_sources = {ms['media_id']: ms['name'] for ms in media_sources_md}
counts = {}
for ms in top_words:
wl.write("\n\n%s (media id: %d):\n" % (media_sources[ms].encode('ascii', 'ignore'), ms))
for w in top_words[ms]:
all_words.append(w['term'])
# increment count to see how many media source include each word
# counts[ms]
wl.write("- %s (%d)\n" % (w['term'].encode('ascii', 'ignore'), w['count']))
wl.write("\n")
linefeed=chr(10) # linefeed=\n
s=linefeed.join(nx.generate_gexf(frame_network)) # doctest: +SKIP
# for line in nx.generate_gexf(frame_network): # doctest: +SKIP
# print line
return s
def graph(slug):
""" Get a JSON representation of the network. """
network = _get_network(slug)
graph = nx.DiGraph()
for entity in network.entities:
entity.as_nx(graph)
for relation in network.relations:
relation.as_nx(graph)
out = ""
for line in nx.generate_gexf(graph):
# print [line]
out += line
return Response(out, status=200, content_type="text/xml")
def graph(slug):
""" Get a JSON representation of the network. """
network = _get_network(slug)
graph = nx.DiGraph()
for entity in network.entities:
entity.as_nx(graph)
for relation in network.relations:
relation.as_nx(graph)
out = ''
for line in nx.generate_gexf(graph):
#print [line]
out += line
return Response(out, status=200, content_type='text/xml')
def exportgefx(final_devices_list,neighborship_dict):
G = nx.Graph()
G.add_edges_from(neighborship_dict.keys())
#loop through and add label for edges
for edge in neighborship_dict.keys():
G.edges[edge]['label'] = neighborship_dict[edge]
nodes =id_to_name(final_devices_list)
#loop through and add label attribute for nodes
for node in nodes.keys():
G.add_node(node)
G.node[node]['label'] = nodes[node]
s = '\n'.join([line for line in nx.generate_gexf(G)])
return s
def graph(slug, id):
""" Get a JSON representation of the network. """
network, entity = _get_entity(slug, id)
entity_types = request.args.getlist('entity_type')
rel_types = request.args.getlist('relation_type')
exports = set()
graph = nx.DiGraph()
def export(entity, depth):
if entity.id in exports or \
(len(entity_types) and entity.type not in entity_types):
return False
entity.as_nx(graph)
exports.add(entity.id)
if depth > 0:
for rel in entity.incoming:
if len(rel_types) and not rel.type in rel_types:
continue
if rel.id not in exports and export(rel.source, depth - 1):
rel.as_nx(graph)
exports.add(rel.id)
for rel in entity.outgoing:
if len(rel_types) and not rel.type in rel_types:
continue
if rel.id not in exports and export(rel.target, depth - 1):
rel.as_nx(graph)
exports.add(rel.id)
return True
export(entity, 2)
out = ''
for line in nx.generate_gexf(graph):
#print [line]
out += line
# JSONP for XML. Will now go vomit quietly somewhere.
if request.args.get('wrap') == 'json':
return jsonify({'xml': out})
return Response(out, status=200,
content_type='text/xml')
def graph(slug, id):
""" Get a JSON representation of the network. """
network, entity = _get_entity(slug, id)
entity_types = request.args.getlist('entity_type')
rel_types = request.args.getlist('relation_type')
exports = set()
graph = nx.DiGraph()
def export(entity, depth):
if entity.id in exports or \
(len(entity_types) and entity.type not in entity_types):
return False
entity.as_nx(graph)
exports.add(entity.id)
if depth > 0:
for rel in entity.incoming:
if len(rel_types) and not rel.type in rel_types:
continue
if rel.id not in exports and export(rel.source, depth - 1):
rel.as_nx(graph)
exports.add(rel.id)
for rel in entity.outgoing:
if len(rel_types) and not rel.type in rel_types:
continue
if rel.id not in exports and export(rel.target, depth - 1):
rel.as_nx(graph)
exports.add(rel.id)
return True
export(entity, 2)
out = ''
for line in nx.generate_gexf(graph):
#print [line]
out += line
# JSONP for XML. Will now go vomit quietly somewhere.
if request.args.get('wrap') == 'json':
return jsonify({'xml': out})
return Response(out, status=200, content_type='text/xml')
def download_cmtys(request, ds, did, cd, cdname, layer, format):
fname_requested = format
format = format.rsplit('.')[-1]
fname = '%s-%s%s.%s'%(os.path.basename(ds.netfile.name), cdname, layer, format)
if fname_requested != fname:
return redirect(download_cmtys, did=did, cdname=cdname, layer=layer,
format=fname)
cmtys = cd.get_results()[layer]
data = [ ]
content_type = 'text/plain'
force_download = False
if format == 'txt':
for cname, cnodes in cmtys.iteritems():
data.append(' '.join(str(x) for x in cnodes))
data = '\n'.join(data)
elif format == 'nc':
for cname, cnodes in cmtys.iteritems():
for node in cnodes:
data.append('%s %s'%(node, cname))
data = '\n'.join(data)
elif format == 'gexf':
g = ds.get_networkx()
for node, cs in cmtys.nodecmtys().iteritems():
g.node[node]['cmty'] = ' '.join(str(x) for x in cs)
data = nx.generate_gexf(g)
data = '\n'.join(data)
elif format == 'gml':
g = ds.get_networkx()
for node, cs in cmtys.nodecmtys().iteritems():
g.node[node]['cmty'] = ','.join(str(x) for x in cs)
data = nx.generate_gml(g)
data = '\n'.join(data)
response = HttpResponse(content=data, content_type=content_type, )
# If the data size is too big, force a download instead of viewing as text.
if force_download or len(data) > 50 * 2**10:
response['Content-Disposition'] = 'attachment; filename=%s'%fname
return response
def test_edge_id_construct(self):
G = nx.Graph()
G.add_edges_from([(0, 1, {'id': 0}), (1, 2, {'id': 2}), (2, 3)])
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="static" name="">
<meta>
<creator>NetworkX {}</creator>
<lastmodified>{}</lastmodified>
</meta>
<nodes>
<node id="0" label="0" />
<node id="1" label="1" />
<node id="2" label="2" />
<node id="3" label="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="2" source="1" target="2" />
<edge id="1" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(nx.__version__, time.strftime('%d/%m/%Y'))
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def test_edge_id_construct(self):
G = nx.Graph()
G.add_edges_from([(0, 1, {'id': 0}), (1, 2, {'id': 2}), (2, 3)])
expected = """<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
<graph defaultedgetype="undirected" mode="static" name="">
<meta>
<creator>NetworkX {}</creator>
<lastmodified>{}</lastmodified>
</meta>
<nodes>
<node id="0" label="0" />
<node id="1" label="1" />
<node id="2" label="2" />
<node id="3" label="3" />
</nodes>
<edges>
<edge id="0" source="0" target="1" />
<edge id="2" source="1" target="2" />
<edge id="1" source="2" target="3" />
</edges>
</graph>
</gexf>""".format(nx.__version__, time.strftime('%d/%m/%Y'))
obtained = '\n'.join(nx.generate_gexf(G))
assert_equal(expected, obtained)
def generate_network_of_frames(topics_id,
timespans_id,
num_of_sources,
out_name,
remove_media_list=None,
remove_word_list=[],
generate_word_lists=False,
include_media_list=None,
media_attribs=None,
num_words=None):
if (remove_media_list == None):
remove_media_list = []
# use this specify attributes on the media source that should be added to the node as attributes
# if(media_attribs == None):
# media_attribs = {}
if (include_media_list == None):
media_sources_md = get_top_x_sources(
topics_id, num_of_sources + len(remove_media_list), timespans_id)
else:
media_sources_md = include_media_list
if (remove_media_list != None):
for r in remove_media_list:
media_sources_md = remove_media_source(r, media_sources_md)
top_words = build_top_words(media_sources_md, topics_id, timespans_id,
remove_word_list, num_words)
if (remove_word_list != None):
top_words = clean_top_words(top_words, remove_word_list)
frame_network = build_network(top_words, media_sources_md, media_attribs)
export_gexf_network(frame_network, '%s.gexf' % out_name)
export_d3_network(frame_network, '%s' % out_name)
if (generate_word_lists == True):
with open('%s.txt' % out_name, 'wb') as wl:
all_words = []
media_sources = {
ms['media_id']: ms['name']
for ms in media_sources_md
}
counts = {}
for ms in top_words:
wl.write("\n\n%s (media id: %d):\n" %
(media_sources[ms].encode('ascii', 'ignore'), ms))
for w in top_words[ms]:
all_words.append(w['term'])
# increment count to see how many media source include each word
# counts[ms]
wl.write("- %s (%d)\n" %
(w['term'].encode('ascii', 'ignore'), w['count']))
wl.write("\n")
linefeed = chr(10) # linefeed=\n
s = linefeed.join(nx.generate_gexf(frame_network)) # doctest: +SKIP
# for line in nx.generate_gexf(frame_network): # doctest: +SKIP
# logger.debug line
return s
def generator_gexf_from_query(
self,
query: Query,
with_relation: str = "reply_to") -> Generator[str]:
graph = self.graph_from_query(query, with_relation=with_relation)
return generate_gexf(graph)
def graph_to_gexf(G: nx.DiGraph):
return nx.generate_gexf(G)
def _generate_network_of_frames(topics_id,
timespans_id,
num_of_sources,
out_name,
top_media_sort,
remove_media_list=None,
remove_word_list=[],
generate_word_lists=False,
include_media_list=None,
media_attribs=None,
num_words=None):
if remove_media_list is None:
remove_media_list = []
# use this specify attributes on the media source that should be added to the node as attributes
# if(media_attribs == None):
# media_attribs = {}
if include_media_list is None:
media_sources_md = topic_media_list(user_mediacloud_key(),
topics_id,
timespans_id=timespans_id,
limit=num_of_sources +
len(remove_media_list),
sort=top_media_sort)['media']
else:
media_sources_md = include_media_list
if remove_media_list is not None:
for r in remove_media_list:
media_sources_md = _remove_media_source(r, media_sources_md)
top_words = _build_top_words(media_sources_md, topics_id, timespans_id,
remove_word_list, num_words)
if remove_word_list is not None:
top_words = _clean_top_words(top_words, remove_word_list)
frame_network = _build_network(top_words, media_sources_md, media_attribs)
_export_gexf_network(frame_network, '%s.gexf' % out_name)
_export_d3_network(frame_network, '%s' % out_name)
if generate_word_lists:
with open('%s.txt' % out_name, 'w', encoding="utf-8") as wl:
all_words = []
media_sources = {
ms['media_id']: ms['name']
for ms in media_sources_md
}
# counts = {}
for ms in top_words:
# wl.write("\n\n%s (media id: %d):\n" % (media_sources[ms].encode('ascii', 'ignore'), ms))
wl.write("\n\n{} (media id: {}):\n".format(
media_sources[ms], ms))
for w in top_words[ms]:
all_words.append(w['term'])
# increment count to see how many media source include each word
# counts[ms]
# wl.write("- %s (%d)\n" % (w['term'].encode('ascii', 'ignore'), w['count']))
wl.write("- {} ({})\n".format(w['term'], w['count']))
wl.write("\n")
linefeed = chr(10) # linefeed=\n
s = linefeed.join(nx.generate_gexf(frame_network)) # doctest: +SKIP
# for line in nx.generate_gexf(frame_network): # doctest: +SKIP
# logger.debug line
return s
