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Merge pull request #24 from xabiugarte/dev
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Scripts for database migration (MongoDB -> MySQL)
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@xabiugarte
xabiugarte authored Feb 28, 2019
2 parents 7d1f021 + 8ad31bc commit a70385b
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245 changes: 245 additions & 0 deletions server/utilities/migrate_data.py
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#!/usr/bin/python
import json
import os
import base64
import binascii
import argparse

def main(prefix):

# Declarations for ID counters
function_ids = {}
function_id_counter = 1

apis_ids = {}
apis_id_counter = 1

user_ids = {}
user_id_counter = 1

sample_ids = {}
sample_id_counter = 1

engine_ids = {}
engine_id_counter = 1

metadata_details_ids = {}
metadata_details_id_counter = 1

metadata_id_counter = 1

# Collections used to keep temporary data
applied_metadata_temp = []

# User
with open(os.path.join(prefix, "user.json"), "r") as f:
with open(os.path.join(prefix, "User"), "w") as f_out:
for l in f:
d = json.loads(l.strip())
f_out.write(("0|%s|%s|%s|%d|%s|%s|%d|%d|%s|%s\n" % (d['name'],
d['email'],
d['handle'],
d['number'],
binascii.hexlify(base64.b64decode(d['api_key']["$binary"])).lower(),
str(d['created']['$date'])[:-5] + "Z",
int(d['rank']['$numberLong']),
1 if d['active'] else 0,
d['service'],
d['auth_data'])).encode('UTF-8'))
user_ids[d["_id"]["$oid"]] = user_id_counter
user_id_counter += 1

# Functions, Function APIs, Metadata
with open(os.path.join(prefix, "function.json"), "r") as f:
f_FunctionApis = open(os.path.join(prefix, "FunctionApis"), "w")
f_Function = open(os.path.join(prefix, "Function"), "w")
f_Function_apis = open(os.path.join(prefix, "Function_apis"), "w")
f_Metadata = open(os.path.join(prefix, "Metadata"), "w")
f_Function_metadata = open(os.path.join(prefix, "Function_metadata"), "w")
f_MetadataDetails = open(os.path.join(prefix, "MetadataDetails"), "w")
f_Metadata_details = open(os.path.join(prefix, "Metadata_details"), "w")

# We need to keep track of unique functions, otherwise we might
# insert repeated records in the CSV.
unique_functions = {}

# Keep track of unique metadata details, to avoid repetitions
unique_metadata_details = {}

for l in f:
d = json.loads(l.strip())

opcodes_text = binascii.hexlify(base64.b64decode(d["opcodes"]["$binary"])).upper()

if (d['sha256'], d['architecture']) not in unique_functions:
# Add new function
unique_functions[(d['sha256'], d['architecture'])] = function_id_counter
f_Function.write(("0|%s|%s|%s\n") % (d["sha256"], opcodes_text, d["architecture"]))
# Map of function_ids
function_ids[d["_id"]["$oid"]] = function_id_counter
function_id_counter += 1
else:
# Duplicate function, reuse previous function id, but consider its linked data
function_ids[d["_id"]["$oid"]] = unique_functions[(d['sha256'], d['architecture'])]
#print("Discarding duplicate function... Reusing id %d" % function_ids[d["_id"]["$oid"]])

if "apis" in d:
for a in d["apis"]:
if a not in apis_ids:
apis_ids[a] = apis_id_counter
apis_id_counter += 1
f_FunctionApis.write("0|%s\n" % (a))
f_Function_apis.write("0|%d|%d\n" % (function_ids[d["_id"]["$oid"]], apis_ids[a]))

if "metadata" in d:
# 0 - N Metadata records, each record is associated to a User and Function,
# and each Metadata record can be associated to several MetadataDetails.
for m in d["metadata"]:
# Get user id
if "user" in m and "$oid" in m["user"] and m["user"]["$oid"] in user_ids:
user_id = user_ids[m["user"]["$oid"]]
else:
user_id = 0

# This is an 1-N relationship between Metadata and User
f_Metadata.write("0|%d\n" % (user_id))
# This an N-M relationship between Function and Metadata
f_Function_metadata.write("0|%d|%d\n" % (function_ids[d["_id"]["$oid"]], metadata_id_counter))

# Store temporarly the Applied relationship (N-M) between User, Metadata, and Sample
# We temporarily store the oid because we don't have the mapped ids yet.
if "applied" in m:
for application in m["applied"]:
applied_metadata_temp.append((metadata_id_counter, application[0], application[1]))

if metadata_id_counter not in unique_metadata_details:
unique_metadata_details[metadata_id_counter] = []

# Metadata details (name, comment, committed, prototype)
nb_details = max(len(m.get("name", [])), len(m.get("comment", [])),len(m.get("committed", [])),len(m.get("prototype", [])))
for i in range(0, nb_details):
name = m["name"][i] if "name" in m and (len(m["name"]) > i) else ""
comment = m["comment"][i] if "comment" in m and (len(m["comment"]) > i) else ""
committed = m["committed"][i]["$date"][:-5] + "Z" if "committed" in m and (len(m["committed"]) > i) else ""
prototype = m["prototype"][i] if "prototype" in m and (len(m["prototype"]) > i) else ""

# We consider only unique entries. Unique by: name, comment, prototype and metadata_id
# where metadata_id represents each unique (User,Function) tuple.
if (name, comment, prototype) not in unique_metadata_details[metadata_id_counter]:
unique_metadata_details[metadata_id_counter].append((name, comment, prototype))
f_MetadataDetails.write("0|%s|%s|%s|%s\t\n" % (name, prototype, comment, committed))
f_Metadata_details.write(("0|%d|%d\n" % (metadata_id_counter, metadata_details_id_counter)))
metadata_details_id_counter += 1

metadata_id_counter += 1

f_FunctionApis.close()
f_Function.close()
f_Function_apis.close()
f_Metadata.close()
f_Function_metadata.close()
f_MetadataDetails.close()
f_Metadata_details.close()

# Sample

sample_seen_by = []
sample_functions = {}

with open(os.path.join(prefix, "sample.json"), "r") as f:
f_Sample = open(os.path.join(prefix, "Sample"), "w")
f_Sample_seen_by = open(os.path.join(prefix, "Sample_seen_by"), "w")

for l in f:
d = json.loads(l.strip())

if isinstance(d['crc32'], dict) and "$numberLong" in d['crc32']:
d['crc32'] = int(d['crc32']['$numberLong'])
if not 'sha1' in d:
d['sha1'] = ""
if not 'sha256' in d:
d['sha256'] = ""

f_Sample.write("0|%s|%d|%s|%s|%s\n" % (d['md5'], d['crc32'], d['sha1'], d['sha256'], str(d['last_seen']['$date'])[:-5] + "Z"))

# Seen by
for l in d['seen_by']:
if l['$oid'] in user_ids:
f_Sample_seen_by.write("0|%d|%d\n" % (sample_id_counter, user_ids[l['$oid']]))

if sample_id_counter not in sample_functions:
sample_functions[sample_id_counter] = []

# Functions
for l in d['functions']:
if l['$oid'] in function_ids:
if function_ids[l['$oid']] not in sample_functions[sample_id_counter]:
sample_functions[sample_id_counter].append(function_ids[l['$oid']])

sample_ids[d["_id"]["$oid"]] = sample_id_counter
sample_id_counter += 1

f_Sample.close()
f_Sample_seen_by.close()

f_Sample_functions = open(os.path.join(prefix, "Sample_functions"), "w")
for sid in sample_functions:
for fid in sample_functions[sid]:
f_Sample_functions.write("0|%d|%d\n" % (sid, fid))
f_Sample_functions.close()

# Engine
with open(os.path.join(prefix, "engine.json"), "r") as f:
f_Engine = open(os.path.join(prefix, "Engine"), "w")
for l in f:
d = json.loads(l.strip())

if 'developer' in d and '$oid' in d['developer'] and d['developer']['$oid'] in user_ids:
developer_id = user_ids[d['developer']['$oid']]
else:
developer_id = 0

f_Engine.write("0|%s|%s|%s|%s|%d|%d\n" % (d['name'], d['description'], d['path'], d['obj_name'], 1 if d['active'] else 0, developer_id))
engine_ids[d["_id"]["$oid"]] = engine_id_counter
engine_id_counter += 1

# Applied metadata

f = open(os.path.join(prefix, "AppliedMetadata"), "w")
for metadata_id, sample_oid, user_oid in applied_metadata_temp:
f.write("0|%d|%d|%d\n" % (metadata_id, sample_ids[sample_oid], user_ids[user_oid]))
f.close()

if __name__ == "__main__":
description = """Convert mongoexport generated JSON Files into MySQL import CSV files.
Expected input files:
function.json
sample.json
engine.json
user.json
These files should be generated by running the following commands over the
mongo database:
mongoexport -d [database name] -c function -o function.json
mongoexport -d [database name] -c sample -o sample.json
mongoexport -d [database name] -c engine -o function.json
mongoexport -d [database name] -c user -o user.json
Finally, the generated files can be imported into MySQL by running the mysql queries
in mysql_import.sql, from the directory where the output files were generated.
mysql --user [user] --password --host [host] < /path/to/mysql_import.sql
WARNING: These MySQL script requires the database tables to be created before-hand:
See FIRST-server documentation to understand how to generate and apply
the corresponding Django migrations.
WARNING: This script handles function duplications, so the number of functions
in the mongo export and the resulting MySQL database might vary.
"""
parser = argparse.ArgumentParser(description=description, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('path', type=str, help='The path where the input json files (see --help) are located, and where the output files will be generated.')
args = parser.parse_args()
main(args.path)
66 changes: 66 additions & 0 deletions server/utilities/mysql_import.sql
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USE first_db;

DELETE FROM AppliedMetadata;
ALTER TABLE AppliedMetadata AUTO_INCREMENT = 1;

DELETE FROM Metadata_details;
ALTER TABLE Metadata_details AUTO_INCREMENT = 1;

DELETE FROM Function_metadata;
ALTER TABLE Function_metadata AUTO_INCREMENT = 1;

DELETE FROM MetadataDetails;
ALTER TABLE MetadataDetails AUTO_INCREMENT = 1;

DELETE FROM Metadata;
ALTER TABLE Metadata AUTO_INCREMENT = 1;

DELETE FROM Engine;
ALTER TABLE Engine AUTO_INCREMENT = 1;

DELETE FROM Sample_seen_by;
ALTER TABLE Sample_seen_by AUTO_INCREMENT = 1;

DELETE FROM Sample_functions;
ALTER TABLE Sample_functions AUTO_INCREMENT = 1;

DELETE FROM Function_apis;
ALTER TABLE Function_apis AUTO_INCREMENT = 1;

DELETE FROM FunctionApis;
ALTER TABLE FunctionApis AUTO_INCREMENT = 1;

DELETE FROM Sample;
ALTER TABLE Sample AUTO_INCREMENT = 1;

DELETE FROM Function;
ALTER TABLE Function AUTO_INCREMENT = 1;

DELETE FROM User;
ALTER TABLE User AUTO_INCREMENT = 1;

LOAD DATA LOCAL INFILE "FunctionApis" INTO TABLE FunctionApis COLUMNS TERMINATED BY "|";

LOAD DATA LOCAL INFILE "Function" INTO TABLE Function FIELDS TERMINATED BY "|" (id, sha256, @var1, architecture) SET opcodes = UNHEX(@var1);

LOAD DATA LOCAL INFILE"Function_apis" INTO TABLE Function_apis FIELDS TERMINATED BY "|";

LOAD DATA LOCAL INFILE "User" INTO TABLE User FIELDS TERMINATED BY "|" (id, name, email, handle, number, api_key, @var1, rank, active, service, auth_data) SET created = STR_TO_DATE(@var1, '%Y-%m-%dT%H:%i:%SZ');

LOAD DATA LOCAL INFILE"Sample" INTO TABLE Sample FIELDS TERMINATED BY "|" (id, md5, crc32, sha1, sha256, @var1) SET last_seen = STR_TO_DATE(@var1, '%Y-%m-%dT%H:%i:%SZ');

LOAD DATA LOCAL INFILE"Sample_functions" INTO TABLE Sample_functions FIELDS TERMINATED BY "|";

LOAD DATA LOCAL INFILE"MetadataDetails" INTO TABLE MetadataDetails FIELDS TERMINATED BY "|" LINES TERMINATED BY "\t\n" (id, name, prototype, comment, @var1) SET committed = STR_TO_DATE(@var1, '%Y-%m-%dT%H:%i:%SZ');

LOAD DATA LOCAL INFILE"Sample_seen_by" INTO TABLE Sample_seen_by FIELDS TERMINATED BY "|";

LOAD DATA LOCAL INFILE"Engine" INTO TABLE Engine FIELDS TERMINATED BY "|";

LOAD DATA LOCAL INFILE"Metadata" INTO TABLE Metadata FIELDS TERMINATED BY "|";

LOAD DATA LOCAL INFILE"Metadata_details" INTO TABLE Metadata_details FIELDS TERMINATED BY "|";

LOAD DATA LOCAL INFILE"AppliedMetadata" INTO TABLE AppliedMetadata FIELDS TERMINATED BY "|";

LOAD DATA LOCAL INFILE"Function_metadata" INTO TABLE Function_metadata FIELDS TERMINATED BY "|";

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