Converting MySQL Table Data to a Graphml File

I recently found myself in the situation where I was given access to a huge MySQL database that contained network traffic flows and IDS signature match data. As I work a lot with graph-based approaches, I needed to convert the table’s flow data into a graphml file for later visualization and analysis with scripts I have already written. Now without further ado here’s the code:

import pymysql.cursors
import pymysql
import networkx as nx
import sys

# Connect to the database
conn = pymysql.connect(

graph = nx.DiGraph()

cursor = conn.cursor()
cursor.execute('SELECT src_ip, dst_ip FROM flows')
for i, row in enumerate(cursor):
    sys.stdout.write("\rReading line %s" % i)
    graph.add_edge(row[0], row[1])

nx.write_graphml(graph, "trente-flowgraph.graphml")

It’s obvious to see that I only need the data from the first two columns as they contain source and destination IP. The trick here is to use pymysql.cursors.SSCursor. This will prevent pymysql from loading the whole result set from the SELECT * ... query into RAM. Another catch is that pymysql apparently is not available for Python 3 yet. SQLAlchemy is a good workaround for bigger projects (such as my Pastebin Scraper) but in this case it’s complete overkill. Just run the script with python2.7 and you’re good.