def __init__(self, database, keys):
self.database = database
self.filepath = os.path.join(projects.output_dir, database + ".selection.gexf")
unfiltered_data = Database(self.database).load()
self.data = {
key: value for key, value in unfiltered_data.items() if key in keys
}
self.id_mapping = dict([(key, str(i)) for i, key in enumerate(self.data)])
class DatabaseToGEXF(object):
"""Export a Gephi graph for a database.
Call ``.export()`` to export the file after class instantiation.
Args:
* *database* (str): Database name.
* *include_descendants* (bool): Include databases which are linked from ``database``.
.. warning:: ``include_descendants`` is not yet implemented.
"""
def __init__(self, database, include_descendants=False):
self.database = database
self.descendants = include_descendants
if self.descendants:
raise NotImplemented
filename = database + ("_plus" if include_descendants else "")
self.filepath = os.path.join(projects.output_dir, filename + ".gexf")
self.data = Database(self.database).load()
self.id_mapping = dict([(key, str(i))
for i, key in enumerate(self.data)])
def export(self):
"""Export the Gephi XML file. Returns the filepath of the created file."""
E = ElementMaker(
namespace="http://www.gexf.net/1.2draft",
nsmap={None: "http://www.gexf.net/1.2draft"},
)
meta = E.meta(
E.creator("Brightway2"),
E.description(self.database),
lastmodified=datetime.date.today().strftime("%Y-%m-%d"),
)
attributes = E.attributes(
E.attribute(id="0", title="category", type="string"),
**{"class": "node"})
nodes, edges = self.get_data(E)
graph = E.graph(attributes,
nodes,
edges,
mode="static",
defaultedgetype="directed")
with open(self.filepath, "w", encoding="utf-8") as f:
# Need XML declaration, but then ``tostring`` returns bytes
# so need to decode.
# See https://bugs.python.org/issue10942
# and http://makble.com/python-why-lxml-etree-tostring-method-returns-bytes
f.write(
tostring(
E.gexf(meta, graph, version="1.2"),
xml_declaration=True,
encoding="utf-8",
pretty_print=True,
).decode("utf-8"))
return self.filepath
def get_data(self, E):
"""Get Gephi nodes and edges."""
count = itertools.count()
nodes = []
edges = []
pbar = pyprind.ProgBar(len(self.data),
title="Get nodes and edges:",
monitor=True)
for key, value in self.data.items():
nodes.append(
E.node(
E.attvalues(
E.attvalue(value="-".join(value.get("categories", [])),
**{"for": "0"})),
id=self.id_mapping[key],
label=value.get("name", "Unknown"),
))
for exc in value.get("exchanges", []):
if exc["input"] not in self.id_mapping:
continue
elif exc["input"] == key:
# Don't need production process in graph
continue
else:
edges.append(
E.edge(
id=str(next(count)),
source=self.id_mapping[exc["input"]],
target=self.id_mapping[key],
label="%.3g" % exc["amount"],
))
pbar.update()
print(pbar)
return E.nodes(*nodes), E.edges(*edges)