gurudesh/pytracebugs huggingface dataset:
# Buggy code
def process(self):
    report = self.receive_message()

    columns = [
        "source.ip",
        "source.geolocation.cc",
        "event_description.text",
        "source.asn",
    ]

    headers = True
    raw_report = utils.base64_decode(report.get("raw"))
    for row in csv.reader(io.StringIO(raw_report)):
        # ignore headers
        if headers:
            headers = False
            continue

        event = self.new_event(report)

        for key, value in zip(columns, row):
            if key == "__IGNORE__":
                continue

            event.add(key, value)

        event.add("classification.type", "scanner")
        event.add("raw", ",".join(row))

        self.send_message(event)
    self.acknowledge_message()


# Traceback (_csv.Error)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib64/python3.4/csv.py", line 110, in __next__
row = next(self.reader)
_csv.Error: line contains NULL byte

# Fixed code
def process(self):
    report = self.receive_message()

    columns = [
        "source.ip",
        "source.geolocation.cc",
        "event_description.text",
        "source.asn",
    ]

    headers = True
    raw_report = utils.base64_decode(report.get("raw"))
    raw_report = raw_report.translate({0: None})
    for row in csv.reader(io.StringIO(raw_report)):
        # ignore headers
        if headers:
            headers = False
            continue

        event = self.new_event(report)

        for key, value in zip(columns, row):
            if key == "__IGNORE__":
                continue

            event.add(key, value)

        event.add("classification.type", "scanner")
        event.add("raw", ",".join(row))

        self.send_message(event)
    self.acknowledge_message()
# Buggy code
def parse_csv(self, report: dict):
    """
    A basic CSV parser.
    """
    raw_report = utils.base64_decode(report.get("raw")).strip()
    if self.ignore_lines_starting:
        raw_report = "\n".join(
            [
                line
                for line in raw_report.splitlines()
                if not any(
                    [line.startswith(prefix) for prefix in self.ignore_lines_starting]
                )
            ]
        )

    for line in csv.reader(io.StringIO(raw_report)):
        yield line


# Traceback (_csv.Error)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib64/python3.4/csv.py", line 110, in __next__
row = next(self.reader)
_csv.Error: line contains NULL byte

# Fixed code
def parse_csv(self, report: dict):
    """
    A basic CSV parser.
    """
    raw_report = utils.base64_decode(report.get("raw")).strip()
    raw_report = raw_report.translate({0: None})
    if self.ignore_lines_starting:
        raw_report = "\n".join(
            [
                line
                for line in raw_report.splitlines()
                if not any(
                    [line.startswith(prefix) for prefix in self.ignore_lines_starting]
                )
            ]
        )

    for line in csv.reader(io.StringIO(raw_report)):
        yield line
# Buggy code
def parse_csv_dict(self, report: dict):
    """
    A basic CSV Dictionary parser.
    """
    raw_report = utils.base64_decode(report.get("raw")).strip()
    if self.ignore_lines_starting:
        raw_report = "\n".join(
            [
                line
                for line in raw_report.splitlines()
                if not any(
                    [line.startswith(prefix) for prefix in self.ignore_lines_starting]
                )
            ]
        )

    for line in csv.DictReader(io.StringIO(raw_report)):
        yield line


# Traceback (_csv.Error)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib64/python3.4/csv.py", line 110, in __next__
row = next(self.reader)
_csv.Error: line contains NULL byte

# Fixed code
def parse_csv_dict(self, report: dict):
    """
    A basic CSV Dictionary parser.
    """
    raw_report = utils.base64_decode(report.get("raw")).strip()
    raw_report = raw_report.translate({0: None})
    if self.ignore_lines_starting:
        raw_report = "\n".join(
            [
                line
                for line in raw_report.splitlines()
                if not any(
                    [line.startswith(prefix) for prefix in self.ignore_lines_starting]
                )
            ]
        )

    for line in csv.DictReader(io.StringIO(raw_report)):
        yield line
# Buggy code
def parse(self, report):
    raw_report = utils.base64_decode(report.get("raw"))
    # ignore lines starting with #
    raw_report = re.sub(r"(?m)^#.*\n?", "", raw_report)
    # ignore null bytes
    raw_report = re.sub(r"(?m)\0", "", raw_report)
    # skip header
    if getattr(self.parameters, "skip_header", False):
        raw_report = raw_report[raw_report.find("\n") + 1 :]
    for row in csv.reader(
        io.StringIO(raw_report), delimiter=str(self.parameters.delimiter)
    ):
        if self.filter_text and self.filter_type:
            text_in_row = self.filter_text in self.parameters.delimiter.join(row)
            if text_in_row and self.filter_type == "whitelist":
                yield row
            elif not text_in_row and self.filter_type == "blacklist":
                yield row
            else:
                continue
        else:
            yield row


# Traceback (_csv.Error)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib64/python3.4/csv.py", line 110, in __next__
row = next(self.reader)
_csv.Error: line contains NULL byte

# Fixed code
def parse(self, report):
    raw_report = utils.base64_decode(report.get("raw"))
    raw_report = raw_report.translate({0: None})
    # ignore lines starting with #
    raw_report = re.sub(r"(?m)^#.*\n?", "", raw_report)
    # ignore null bytes
    raw_report = re.sub(r"(?m)\0", "", raw_report)
    # skip header
    if getattr(self.parameters, "skip_header", False):
        raw_report = raw_report[raw_report.find("\n") + 1 :]
    for row in csv.reader(
        io.StringIO(raw_report), delimiter=str(self.parameters.delimiter)
    ):
        if self.filter_text and self.filter_type:
            text_in_row = self.filter_text in self.parameters.delimiter.join(row)
            if text_in_row and self.filter_type == "whitelist":
                yield row
            elif not text_in_row and self.filter_type == "blacklist":
                yield row
            else:
                continue
        else:
            yield row
# Buggy code
def parse(self, report):
    raw_report = utils.base64_decode(report["raw"])
    csvr = csv.DictReader(io.StringIO(raw_report))

    # create an array of fieldnames,
    # those were automagically created by the dictreader
    self.fieldnames = csvr.fieldnames

    for row in csvr:
        yield row


# Traceback (_csv.Error)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib64/python3.4/csv.py", line 110, in __next__
row = next(self.reader)
_csv.Error: line contains NULL byte

# Fixed code
def parse(self, report):
    raw_report = utils.base64_decode(report["raw"])
    # Temporary fix for https://github.com/certtools/intelmq/issues/967
    raw_report = raw_report.translate({0: None})
    csvr = csv.DictReader(io.StringIO(raw_report))

    # create an array of fieldnames,
    # those were automagically created by the dictreader
    self.fieldnames = csvr.fieldnames

    for row in csvr:
        yield row
# Buggy code
def is_valid(value, sanitize=False):
    if sanitize:
        value = GenericType().sanitize(value)
        value = FQDN().sanitize(value)

    if not GenericType().is_valid(value):
        return False

    if value.rstrip(".") != value or value != value.lower():
        return False

    if IPAddress().is_valid(value):
        return False

    url = parse.urlsplit(value)
    if (
        url.scheme != ""
        or url.netloc != ""
        or url.query != ""
        or url.fragment != ""
        or url.path.find("/") >= 0
    ):
        return False

    if value.encode("idna").decode() != value:
        return False

    return True


# Traceback (UnicodeError)
'source_queue': 'shadowserver-parser-dns-open-resolvers-queue',
'traceback': ['Traceback (most recent call last):',
'  File "/usr/lib/python3.4/encodings/idna.py", line 165, in '
'encode',
'    raise UnicodeError("label empty or too long")',
'UnicodeError: label empty or too long',
'',
'The above exception was the direct cause of the following '
'exception:',
'',
'Traceback (most recent call last):',
'  File "/usr/lib/python3/dist-packages/intelmq/lib/bot.py", '
'line 606, in process',
'    events = list(filter(bool, self.parse_line(line,
report)))',
'  File '
'"/usr/lib/python3/dist-packages/intelmq/bots/parsers/shadowserver/parser.py", '
'line 150, in parse_line',
'    event.add(intelmqkey, value)',
'  File '
'"/usr/lib/python3/dist-packages/intelmq/lib/message.py",
line '
'202, in add',
'    value = self.__sanitize_value(key, value)',
'  File '
'"/usr/lib/python3/dist-packages/intelmq/lib/message.py",
line '
'298, in __sanitize_value',
'    return class_reference().sanitize(value)',
'  File '
'"/usr/lib/python3/dist-packages/intelmq/lib/harmonization.py", '
'line 374, in sanitize',
"    return value.encode('idna').decode().lower()",
"UnicodeError: encoding with 'idna' codec failed
(UnicodeError: "
'label empty or too long)']}

# Fixed code
def is_valid(value, sanitize=False):
    if sanitize:
        value = GenericType().sanitize(value)
        value = FQDN().sanitize(value)

    if not GenericType().is_valid(value):
        return False

    if value.strip(".") != value or value != value.lower():
        return False

    if IPAddress().is_valid(value):
        return False

    url = parse.urlsplit(value)
    if (
        url.scheme != ""
        or url.netloc != ""
        or url.query != ""
        or url.fragment != ""
        or url.path.find("/") >= 0
    ):
        return False

    if value.encode("idna").decode() != value:
        return False

    return True
# Buggy code
def sanitize(value):
    value = value.rstrip(".")
    if value:
        return value.encode("idna").decode().lower()


# Traceback (UnicodeError)
'source_queue': 'shadowserver-parser-dns-open-resolvers-queue',
'traceback': ['Traceback (most recent call last):',
'  File "/usr/lib/python3.4/encodings/idna.py", line 165, in '
'encode',
'    raise UnicodeError("label empty or too long")',
'UnicodeError: label empty or too long',
'',
'The above exception was the direct cause of the following '
'exception:',
'',
'Traceback (most recent call last):',
'  File "/usr/lib/python3/dist-packages/intelmq/lib/bot.py", '
'line 606, in process',
'    events = list(filter(bool, self.parse_line(line,
report)))',
'  File '
'"/usr/lib/python3/dist-packages/intelmq/bots/parsers/shadowserver/parser.py", '
'line 150, in parse_line',
'    event.add(intelmqkey, value)',
'  File '
'"/usr/lib/python3/dist-packages/intelmq/lib/message.py",
line '
'202, in add',
'    value = self.__sanitize_value(key, value)',
'  File '
'"/usr/lib/python3/dist-packages/intelmq/lib/message.py",
line '
'298, in __sanitize_value',
'    return class_reference().sanitize(value)',
'  File '
'"/usr/lib/python3/dist-packages/intelmq/lib/harmonization.py", '
'line 374, in sanitize',
"    return value.encode('idna').decode().lower()",
"UnicodeError: encoding with 'idna' codec failed
(UnicodeError: "
'label empty or too long)']}

# Fixed code
def sanitize(value):
    value = value.strip(".")
    if value:
        return value.encode("idna").decode().lower()
# Buggy code
def parse(self, report):
    report_split = utils.base64_decode(report["raw"]).strip().splitlines()
    self.tempdata = report_split[:2]
    for line in report_split[3:]:
        yield line.strip()


# Traceback (intelmq.lib.exceptions.InvalidValue)
2017-07-05 15:01:17,325 - vxvault-parser - ERROR - Failed to parse line.
Traceback (most recent call last):
File "/usr/lib/python3.4/site-packages/intelmq/lib/bot.py", line 643, in process
events = list(filter(bool, self.parse_line(line, report)))
File "/usr/lib/python3.4/site-packages/intelmq/bots/parsers/vxvault/parser.py", line 39, in parse_line
event.add("time.source", self.tempdata[1])
File "/usr/lib/python3.4/site-packages/intelmq/lib/message.py", line 205, in add
raise exceptions.InvalidValue(key, old_value)
intelmq.lib.exceptions.InvalidValue: invalid value 'VX Vault last 100 Links' (<class 'str'>) for key 'time.source'

# Fixed code
def parse(self, report):
    report_split = utils.base64_decode(report["raw"]).strip().splitlines()
    self.tempdata = report_split[:3]
    for line in report_split[4:]:
        yield line.strip()
# Buggy code
def parse_line(self, row, report):
    if not row.startswith("http"):
        return []

    url_object = urlparse(row)

    if not url_object:
        return []

    url = url_object.geturl()
    hostname = url_object.hostname
    port = url_object.port

    event = self.new_event(report)

    if not event.add("source.ip", hostname, raise_failure=False):
        event.add("source.fqdn", hostname)

    event.add("classification.type", "malware")
    event.add("source.url", url)
    if port:
        event.add("source.port", port)
    event.add("raw", row)
    event.add("time.source", self.tempdata[1])

    yield event


# Traceback (intelmq.lib.exceptions.InvalidValue)
2017-07-05 15:01:17,325 - vxvault-parser - ERROR - Failed to parse line.
Traceback (most recent call last):
File "/usr/lib/python3.4/site-packages/intelmq/lib/bot.py", line 643, in process
events = list(filter(bool, self.parse_line(line, report)))
File "/usr/lib/python3.4/site-packages/intelmq/bots/parsers/vxvault/parser.py", line 39, in parse_line
event.add("time.source", self.tempdata[1])
File "/usr/lib/python3.4/site-packages/intelmq/lib/message.py", line 205, in add
raise exceptions.InvalidValue(key, old_value)
intelmq.lib.exceptions.InvalidValue: invalid value 'VX Vault last 100 Links' (<class 'str'>) for key 'time.source'

# Fixed code
def parse_line(self, row, report):
    if not row.startswith("http"):
        return []

    url_object = urlparse(row)

    if not url_object:
        return []

    url = url_object.geturl()
    hostname = url_object.hostname
    port = url_object.port

    event = self.new_event(report)

    if not event.add("source.ip", hostname, raise_failure=False):
        event.add("source.fqdn", hostname)

    event.add("classification.type", "malware")
    event.add("source.url", url)
    if port:
        event.add("source.port", port)
    event.add("raw", row)
    event.add("time.source", self.tempdata[2])

    yield event
# Buggy code
def connect(self):
    self.logger.debug("Connecting to mongodb server.")
    try:
        self.client = pymongo.MongoClient(
            self.parameters.host, int(self.parameters.port)
        )
    except pymongo.errors.ConnectionFailure:
        raise ValueError("Connection to mongodb server failed.")
    else:
        db = self.client[self.parameters.database]
        if self.parameters.db_user and self.parameters.db_pass:
            self.logger.debug(
                "Trying to authenticate to database {}.".format(
                    self.parameters.database
                )
            )
            try:
                db.authenticate(
                    name=self.parameters.db_user, password=self.parameters.db_pass
                )
            except pymongo.errors.OperationFailure:
                raise ValueError(
                    "Authentication to database {} failed".format(
                        self.parameters.database
                    )
                )
        self.collection = db[self.parameters.collection]
        self.logger.info("Successfully connected to mongodb server.")


# Traceback (AttributeError)
# tail -f /opt/intelmq/var/log/mongodb-output.log
2017-04-08 03:30:41,021 - mongodb-output - ERROR - Bot initialization failed.
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/intelmq/lib/bot.py", line 78, in __init__
self.init()
File "/usr/local/lib/python3.5/dist-packages/intelmq/bots/outputs/mongodb/output.py", line 31, in init
self.connect()
File "/usr/local/lib/python3.5/dist-packages/intelmq/bots/outputs/mongodb/output.py", line 55, in connect
if self.parameters.db_user and self.parameters.db_pass:
AttributeError: 'Parameters' object has no attribute 'db_user'
2017-04-08 03:30:41,022 - mongodb-output - INFO - Bot stopped.

# Fixed code
def connect(self):
    self.logger.debug("Connecting to mongodb server.")
    try:
        self.client = pymongo.MongoClient(
            self.parameters.host, int(self.parameters.port)
        )
    except pymongo.errors.ConnectionFailure:
        raise ValueError("Connection to mongodb server failed.")
    else:
        db = self.client[self.parameters.database]
        if hasattr(self.parameters, "db_user") and hasattr(self.parameters, "db_pass"):
            self.logger.debug(
                "Trying to authenticate to database {}.".format(
                    self.parameters.database
                )
            )
            try:
                db.authenticate(
                    name=self.parameters.db_user, password=self.parameters.db_pass
                )
            except pymongo.errors.OperationFailure:
                raise ValueError(
                    "Authentication to database {} failed".format(
                        self.parameters.database
                    )
                )
        self.collection = db[self.parameters.collection]
        self.logger.info("Successfully connected to mongodb server.")
# Buggy code
def __asn_query(asn):
    query = ASN_QUERY % (asn)
    return list(Cymru.__query(query))[0]  # TODO: we assume there is only one result


# Traceback (IndexError)
{'bot_id': 'cymru-whois-expert',
'message': {'__type': 'Event',
'classification.identifier': 'scanner',
'classification.taxonomy': 'Information Gathering',
'classification.type': 'scanner',
'event_description.text': 'http_scan,low_ports,telnet',
'feed.accuracy': 100.0,
'feed.code': 'https://www.turris.cz/en/',
'feed.name': 'Turris Greylist',
'feed.url': 'https://www.turris.cz/greylist-data/greylist-latest.csv',
'raw': 'MjEyLjkyLjEyNy4xMjYsUlUsaHR0cF9zY2FuLGxvd19wb3J0cyx0ZWxuZXQsMTI3OTA=',
'source.asn': 12790,
'source.geolocation.cc': 'RU',
'source.geolocation.latitude': 55.75,
'source.geolocation.longitude': 37.6166,
'source.ip': '1.2.3.4',
'source.network': '1.2.3.0/20',
'time.observation': '2016-07-25T17:29:48+00:00',
'time.source': '2016-07-25T17:29:48+00:00'},
'source_queue': 'cymru-whois-expert-queue',
'traceback': ['Traceback (most recent call last):',
'  File "/home/aaron/intelmq/intelmq/lib/bot.py", line 125, '
'in start',
'    self.process()',
'  File '
'"/home/aaron/intelmq/intelmq/bots/experts/cymru_whois/expert.py", '
'line 54, in process',
'    result = Cymru.query(ip)',
'  File '
'"/home/aaron/intelmq/intelmq/bots/experts/cymru_whois/lib.py", '
'line 44, in query',
"    raw_result = Cymru.__asn_query(result['asn'])",
'  File '
'"/home/aaron/intelmq/intelmq/bots/experts/cymru_whois/lib.py", '
'line 81, in __asn_query',
'    return list(Cymru.__query(query))[0]  # TODO: we assume '
'there is only one result',
'IndexError: list index out of range']}

# Fixed code
def __asn_query(asn):
    """
    Querys ASN to get CC, registry, AS-name.

    Returns string object of first result in case of success
    or None if there's no result.

    TODO: Handle multiple results
    See https://github.com/certtools/intelmq/issues/543
    """
    query_string = ASN_QUERY % (asn)
    query = list(Cymru.__query(query_string))
    if query:
        return query[0]
# Buggy code
def process(self):
    self.tempdata = []  # temporary data for parse, parse_line and recover_line
    self.__failed = []
    report = self.receive_message()

    for line in self.parse(report):
        if not line:
            continue
        try:
            # filter out None
            events = list(filter(bool, self.parse_line(line, report)))
        except Exception as exc:
            self.logger.exception("Failed to parse line.")
            self.__failed.append((exc, line))
        else:
            self.send_message(*events)

    for exc, line in self.__failed:
        self._dump_message(exc, self.recover_line(line))

    self.acknowledge_message()


# Traceback (TypeError)
openmemcached-parser: Dumping message from pipeline to dump file.
openmemcached-parser: Bot has found a problem.
Traceback (most recent call last):
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 125, in start
self.process()
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 469, in process
self._dump_message(exc, self.recover_line(line))
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 337, in _dump_message
json.dump(dump_data, fp, indent=4, sort_keys=True)
File "/usr/lib/python3.4/json/__init__.py", line 178, in dump
for chunk in iterable:
File "/usr/lib/python3.4/json/encoder.py", line 422, in _iterencode
yield from _iterencode_dict(o, _current_indent_level)
File "/usr/lib/python3.4/json/encoder.py", line 396, in _iterencode_dict
yield from chunks
File "/usr/lib/python3.4/json/encoder.py", line 396, in _iterencode_dict
yield from chunks
File "/usr/lib/python3.4/json/encoder.py", line 429, in _iterencode
o = _default(o)
File "/usr/lib/python3.4/json/encoder.py", line 173, in default
raise TypeError(repr(o) + " is not JSON serializable")
TypeError: NotImplementedError() is not JSON serializable

# Fixed code
def process(self):
    self.tempdata = []  # temporary data for parse, parse_line and recover_line
    self.__failed = []
    report = self.receive_message()

    for line in self.parse(report):
        if not line:
            continue
        try:
            # filter out None
            events = list(filter(bool, self.parse_line(line, report)))
        except Exception:
            self.logger.exception("Failed to parse line.")
            self.__failed.append((traceback.format_exc(), line))
        else:
            self.send_message(*events)

    for exc, line in self.__failed:
        report_dump = report.copy()
        report_dump.update("raw", self.recover_line(line))
        self._dump_message(exc, report_dump)

    self.acknowledge_message()
# Buggy code
def bot_run(self, bot_id):
    try:
        bot_module = self.startup[bot_id]["module"]
    except KeyError:
        log_bot_error("notfound", bot_id)
        return "error"
    else:
        module = importlib.import_module(bot_module)
        botname = [
            name
            for name in dir(module)
            if hasattr(getattr(module, name), "process") and name.endswith("Bot")
        ][0]
        bot = getattr(module, botname)
        instance = bot(bot_id)
        instance.start()


# Traceback (TypeError)
openmongodb-parser: Failed to parse line: '"2015-08-09 11:11:53","1.2.3.4","tcp",27017,"046206184112.atmpu0022.XXXXXXX.net","mongodb","2.4.6",16305,"AT","WIEN","VIENNA",0,0,"nogitversion","Linux allspice 3.2.0-37-generic #58-Ubuntu SMP Thu Jan 24 15:28:10 UTC 2013 x86_64 BOOST_LIB_VERSION=1_53",,"tcmalloc","V8",64,16777216,1,"session | client | ssv | local | presentation"'
Traceback (most recent call last):
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 461, in process
events = list(filter(bool, self.parse_line(line, report)))
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 449, in parse_line
raise NotImplementedError
NotImplementedError
openmongodb-parser: Dumping message from pipeline to dump file.
openmongodb-parser: Bot has found a problem.
Traceback (most recent call last):
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 125, in start
self.process()
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 469, in process
self._dump_message(exc, self.recover_line(line))
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 337, in _dump_message
json.dump(dump_data, fp, indent=4, sort_keys=True)
File "/usr/lib/python3.4/json/__init__.py", line 178, in dump
for chunk in iterable:
File "/usr/lib/python3.4/json/encoder.py", line 422, in _iterencode
yield from _iterencode_dict(o, _current_indent_level)
File "/usr/lib/python3.4/json/encoder.py", line 396, in _iterencode_dict
yield from chunks
File "/usr/lib/python3.4/json/encoder.py", line 396, in _iterencode_dict
yield from chunks
File "/usr/lib/python3.4/json/encoder.py", line 429, in _iterencode
o = _default(o)
File "/usr/lib/python3.4/json/encoder.py", line 173, in default
raise TypeError(repr(o) + " is not JSON serializable")
TypeError: NotImplementedError() is not JSON serializable

# Fixed code
def bot_run(self, bot_id):
    try:
        bot_module = self.startup[bot_id]["module"]
    except KeyError:
        log_bot_error("notfound", bot_id)
        return "error"
    else:
        module = importlib.import_module(bot_module)
        # TODO: Search for bot class is dirty (but works)
        botname = [
            name
            for name in dir(module)
            if hasattr(getattr(module, name), "process")
            and name.endswith("Bot")
            and name != "ParserBot"
        ][0]
        bot = getattr(module, botname)
        instance = bot(bot_id)
        instance.start()
# Buggy code
def _dump_message(self, error_traceback, message):
    if message is None:
        return

    self.logger.info("Dumping message from pipeline to dump file.")
    timestamp = datetime.datetime.utcnow()
    timestamp = timestamp.isoformat()

    dump_file = "%s%s.dump" % (self.parameters.logging_path, self.__bot_id)

    new_dump_data = dict()
    new_dump_data[timestamp] = dict()
    new_dump_data[timestamp]["bot_id"] = self.__bot_id
    new_dump_data[timestamp]["source_queue"] = self.__source_queues
    new_dump_data[timestamp]["traceback"] = error_traceback

    new_dump_data[timestamp]["message"] = message.serialize()

    try:
        with open(dump_file, "r") as fp:
            dump_data = json.load(fp)
            dump_data.update(new_dump_data)
    except:
        dump_data = new_dump_data

    with open(dump_file, "w") as fp:
        json.dump(dump_data, fp, indent=4, sort_keys=True)

    self.logger.warn("Message dumped.")


# Traceback (AttributeError)
"source_queue": "openchargen-parser-queue",
"traceback": """Traceback (most recent call last):
File \"/home/aaron/intelmq/intelmq/lib/bot.py\", line 125, in start
self.process()
File \"/home/aaron/intelmq/intelmq/lib/bot.py\", line 466, in process
self._dump_message(exc, self.recover_line(line))
File \"/home/aaron/intelmq/intelmq/lib/bot.py\", line 324, in _dump_message
new_dump_data[timestamp][\"message\"] = message.serialize()
AttributeError: 'str' object has no attribute 'serialize'
"""
}
}

# Fixed code
def _dump_message(self, error_traceback, message):
    if message is None:
        return

    self.logger.info("Dumping message from pipeline to dump file.")
    timestamp = datetime.datetime.utcnow()
    timestamp = timestamp.isoformat()

    dump_file = "%s%s.dump" % (self.parameters.logging_path, self.__bot_id)

    new_dump_data = dict()
    new_dump_data[timestamp] = dict()
    new_dump_data[timestamp]["bot_id"] = self.__bot_id
    new_dump_data[timestamp]["source_queue"] = self.__source_queues
    new_dump_data[timestamp]["traceback"] = error_traceback

    if type(message) == str:
        new_dump_data[timestamp]["message"] = message
    else:
        new_dump_data[timestamp]["message"] = message.serialize()

    try:
        with open(dump_file, "r") as fp:
            dump_data = json.load(fp)
            dump_data.update(new_dump_data)
    except:
        dump_data = new_dump_data

    with open(dump_file, "w") as fp:
        json.dump(dump_data, fp, indent=4, sort_keys=True)

    self.logger.warn("Message dumped.")
# Buggy code
def _dump_message(self, error_traceback, message):
    if message is None:
        return

    self.logger.info("Dumping message from pipeline to dump file.")
    timestamp = datetime.datetime.utcnow()
    timestamp = timestamp.isoformat()

    dump_file = "%s%s.dump" % (self.parameters.logging_path, self.__bot_id)

    new_dump_data = dict()
    new_dump_data[timestamp] = dict()
    new_dump_data[timestamp]["bot_id"] = self.__bot_id
    new_dump_data[timestamp]["source_queue"] = self.__source_queues
    new_dump_data[timestamp]["traceback"] = error_traceback

    if type(message) == str:
        new_dump_data[timestamp]["message"] = message
    else:
        new_dump_data[timestamp]["message"] = message.serialize()

    try:
        with open(dump_file, "r") as fp:
            dump_data = json.load(fp)
            dump_data.update(new_dump_data)
    except:
        dump_data = new_dump_data

    with open(dump_file, "w") as fp:
        json.dump(dump_data, fp, indent=4, sort_keys=True)

    self.logger.warn("Message dumped.")


# Traceback (AttributeError)
"source_queue": "openchargen-parser-queue",
"traceback": """Traceback (most recent call last):
File \"/home/aaron/intelmq/intelmq/lib/bot.py\", line 125, in start
self.process()
File \"/home/aaron/intelmq/intelmq/lib/bot.py\", line 466, in process
self._dump_message(exc, self.recover_line(line))
File \"/home/aaron/intelmq/intelmq/lib/bot.py\", line 324, in _dump_message
new_dump_data[timestamp][\"message\"] = message.serialize()
AttributeError: 'str' object has no attribute 'serialize'
"""
}
}

# Fixed code
def _dump_message(self, error_traceback, message):
    if message is None:
        return

    self.logger.info("Dumping message from pipeline to dump file.")
    timestamp = datetime.datetime.utcnow()
    timestamp = timestamp.isoformat()

    dump_file = "%s%s.dump" % (self.parameters.logging_path, self.__bot_id)

    new_dump_data = dict()
    new_dump_data[timestamp] = dict()
    new_dump_data[timestamp]["bot_id"] = self.__bot_id
    new_dump_data[timestamp]["source_queue"] = self.__source_queues
    new_dump_data[timestamp]["traceback"] = error_traceback

    new_dump_data[timestamp]["message"] = message.serialize()

    try:
        with open(dump_file, "r") as fp:
            dump_data = json.load(fp)
            dump_data.update(new_dump_data)
    except:
        dump_data = new_dump_data

    with open(dump_file, "w") as fp:
        json.dump(dump_data, fp, indent=4, sort_keys=True)

    self.logger.warn("Message dumped.")
# Buggy code
def process(self):
    event = self.receive_message()

    keys = ["source.%s", "destination.%s"]

    for key in keys:
        ip_key = key % "ip"

        if not event.contains(ip_key):
            continue

        ip = event.get(ip_key)
        ip_version = IPAddress.version(ip)
        ip_integer = IPAddress.to_int(ip)

        if ip_version == 4:
            minimum = MINIMUM_BGP_PREFIX_IPV4

        elif ip_version == 6:
            minimum = MINIMUM_BGP_PREFIX_IPV6

        else:
            raise ValueError("Unexpected IP version {!r}.".format(ip_version))

        cache_key = bin(ip_integer)[2 : minimum + 2]
        result_json = self.cache.get(cache_key)

        if result_json:
            result = json.loads(result_json)
        else:
            result = Cymru.query(ip)
            result_json = json.dumps(result)
            self.cache.set(cache_key, result_json)

        for result_key, result_value in result.items():
            event.add(key % result_key, result_value, force=True)

    self.send_message(event)
    self.acknowledge_message()


# Traceback (TypeError)
Bot has found a problem.
Traceback (most recent call last):
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 125, in start
self.process()
File "/home/aaron/intelmq/intelmq/bots/experts/cymru_whois/expert.py", line 54, in process
result = Cymru.query(ip)
File "/home/aaron/intelmq/intelmq/bots/experts/cymru_whois/lib.py", line 40, in query
if "asn" in result:
TypeError: argument of type 'NoneType' is not iterable

# Fixed code
def process(self):
    event = self.receive_message()

    keys = ["source.%s", "destination.%s"]

    for key in keys:
        ip_key = key % "ip"

        if not event.contains(ip_key):
            continue

        ip = event.get(ip_key)
        ip_version = IPAddress.version(ip)
        ip_integer = IPAddress.to_int(ip)

        if ip_version == 4:
            minimum = MINIMUM_BGP_PREFIX_IPV4

        elif ip_version == 6:
            minimum = MINIMUM_BGP_PREFIX_IPV6

        else:
            raise ValueError("Unexpected IP version {!r}.".format(ip_version))

        cache_key = bin(ip_integer)[2 : minimum + 2]
        result_json = self.cache.get(cache_key)

        if result_json:
            result = json.loads(result_json)
        else:
            result = Cymru.query(ip)
            if not result:
                continue
            result_json = json.dumps(result)
            self.cache.set(cache_key, result_json)

        for result_key, result_value in result.items():
            event.add(key % result_key, result_value, force=True)

    self.send_message(event)
    self.acknowledge_message()
# Buggy code
def query(ip):
    raw_result = Cymru.__ip_query(ip)
    results = map(Cymru.__ip_query_parse, raw_result)
    result = None
    for res in results:
        if result is None:
            result = res
        elif "network" not in res:
            continue
        elif "network" not in result:
            result = res
        else:
            ips_a = ipaddress.ip_network(res["network"]).num_addresses
            ips_b = ipaddress.ip_network(result["network"]).num_addresses
            if ips_a < ips_b:
                result = res

    if "asn" in result:
        raw_result = Cymru.__asn_query(result["asn"])
        extra_info = Cymru.__asn_query_parse(raw_result)
        result.update(extra_info)

    return result


# Traceback (TypeError)
Bot has found a problem.
Traceback (most recent call last):
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 125, in start
self.process()
File "/home/aaron/intelmq/intelmq/bots/experts/cymru_whois/expert.py", line 54, in process
result = Cymru.query(ip)
File "/home/aaron/intelmq/intelmq/bots/experts/cymru_whois/lib.py", line 40, in query
if "asn" in result:
TypeError: argument of type 'NoneType' is not iterable

# Fixed code
def query(ip):
    raw_result = Cymru.__ip_query(ip)
    results = map(Cymru.__ip_query_parse, raw_result)
    result = None
    for res in results:
        if result is None:
            result = res
        elif "network" not in res:
            continue
        elif "network" not in result:
            result = res
        else:
            ips_a = ipaddress.ip_network(res["network"]).num_addresses
            ips_b = ipaddress.ip_network(result["network"]).num_addresses
            if ips_a < ips_b:
                result = res

    if not result:
        return

    if "asn" in result:
        raw_result = Cymru.__asn_query(result["asn"])
        extra_info = Cymru.__asn_query_parse(raw_result)
        result.update(extra_info)

    return result
# Buggy code
def recover_line(self, line):
    out = self.header + "\n"
    ordered_line = [line[v] for v in self.fieldnames]
    out += ",".join(ordered_line) + "\n"
    return out


# Traceback (TypeError)
2016-07-22 18:00:38,243 - openredis-parser - ERROR - Failed to parse line.
Traceback (most recent call last):
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 461, in process
events = list(filter(bool, self.parse_line(line, report)))
File "/home/aaron/intelmq/intelmq/bots/parsers/shadowserver/parser.py", line 182, in parse_line
event.add('raw', self.recover_line(raw_line))
File "/home/aaron/intelmq/intelmq/bots/parsers/shadowserver/parser.py", line 198, in recover_line
out += ','.join(ordered_line) + '\n'
TypeError: sequence item 13: expected str instance, NoneType found
2016-07-22 18:00:38,243 - openredis-parser - INFO - Dumping message from pipeline to dump file.

# Fixed code
def recover_line(self, line):
    out = self.header + "\n"
    ordered_line = [self.conv_csv_shadowserver(line[v]) for v in self.fieldnames]
    out += ",".join(ordered_line) + "\n"
    return out
# Buggy code
def conv_csv_shadowserver(self, value):
    """
    Converts a dict to shadowservers csv quoting format.

    Numeric: no quoting
    Empty string: no quoting
    Else: " quoting
    """
    try:
        if str(int(value)) == value:
            return str(value)
    except ValueError:
        if hasattr(value, "__len__") and not len(value):
            return ""
        else:
            return '"' + value + '"'


# Traceback (TypeError)
2016-07-22 18:00:38,243 - openredis-parser - ERROR - Failed to parse line.
Traceback (most recent call last):
File "/home/aaron/intelmq/intelmq/lib/bot.py", line 461, in process
events = list(filter(bool, self.parse_line(line, report)))
File "/home/aaron/intelmq/intelmq/bots/parsers/shadowserver/parser.py", line 182, in parse_line
event.add('raw', self.recover_line(raw_line))
File "/home/aaron/intelmq/intelmq/bots/parsers/shadowserver/parser.py", line 198, in recover_line
out += ','.join(ordered_line) + '\n'
TypeError: sequence item 13: expected str instance, NoneType found
2016-07-22 18:00:38,243 - openredis-parser - INFO - Dumping message from pipeline to dump file.

# Fixed code
def conv_csv_shadowserver(self, value):
    """
    Converts a dict to shadowservers csv quoting format.

    Numeric: no quoting
    Empty string: no quoting
    Else: " quoting
    """
    try:
        int(value)
        return value
    except ValueError:
        if hasattr(value, "__len__") and not len(value):
            return ""
        else:
            return '"' + value + '"'
# Buggy code
def list_bots(self):
    if self.args.type == "text":
        for bot_id in sorted(self.startup.keys()):
            print(
                "Bot ID: {}\nDescription: {}".format(
                    bot_id, self.startup[bot_id]["description"]
                )
            )
    return [
        {"id": bot_id, "description": self.startup[bot_id]["description"]}
        for bot_id in sorted(self.startup.keys())
    ]


# Traceback (KeyError)
$ intelmqctl list bots
(...)
Description: Turris Greylist Parser is the bot responsible to parse the report and sanitize the information.
Traceback (most recent call last):
File "/usr/local/bin/intelmqctl", line 9, in <module>
load_entry_point('intelmq==1.0.0.dev4', 'console_scripts', 'intelmqctl')()
File "/usr/local/lib/python3.4/dist-packages/intelmq/bin/intelmqctl.py", line 526, in main
x.run()
File "/usr/local/lib/python3.4/dist-packages/intelmq/bin/intelmqctl.py", line 269, in run
results = call_method()
File "/usr/local/lib/python3.4/dist-packages/intelmq/bin/intelmqctl.py", line 399, in list_bots
"".format(bot_id, self.startup[bot_id]['description']))
KeyError: 'description'

# Fixed code
def list_bots(self):
    """
    Lists all configured bots from startup.conf with bot id and
    description.

    If description is not set, None is used instead.
    """
    if self.args.type == "text":
        for bot_id in sorted(self.startup.keys()):
            print(
                "Bot ID: {}\nDescription: {}".format(
                    bot_id, self.startup[bot_id].get("description")
                )
            )
    return [
        {"id": bot_id, "description": self.startup[bot_id].get("description")}
        for bot_id in sorted(self.startup.keys())
    ]
# Buggy code
def receive(self):
    try:
        if self.pipe.llen(self.internal_queue) > 0:
            return utils.decode(self.pipe.lindex(self.internal_queue, -1))
        return utils.decode(
            self.pipe.brpoplpush(self.source_queue, self.internal_queue, 0)
        )
    except redis.exceptions.ConnectionError:
        pass  # raised e.g. on SIGHUP
    except Exception as exc:
        raise exceptions.PipelineError(exc)


# Traceback (AttributeError)
Pipeline failed.
Traceback (most recent call last):
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/lib/pipeline.py", line 113, in receive
return utils.decode(self.pipe.lindex(self.internal_queue, -1))
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/lib/utils.py", line 70, in decode
return str(text.decode(encoding))
AttributeError: 'NoneType' object has no attribute 'decode'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/lib/bot.py", line 102, in start
self.process()
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/bots/outputs/file/output.py", line 16, in process
event = self.receive_message()
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/lib/bot.py", line 258, in receive_message
message = self.source_pipeline.receive()
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/lib/pipeline.py", line 117, in receive
raise exceptions.PipelineError(exc)
intelmq.lib.exceptions.PipelineError: pipeline failed - AttributeError("'NoneType' object has no attribute 'decode'",)

# Fixed code
def receive(self):
    try:
        retval = self.pipe.lindex(self.internal_queue, -1)  # returns None if no value
        if not retval:
            retval = self.pipe.brpoplpush(self.source_queue, self.internal_queue, 0)
        return utils.decode(retval)
    except redis.exceptions.ConnectionError:
        pass  # raised e.g. on SIGHUP
    except Exception as exc:
        raise exceptions.PipelineError(exc)
# Buggy code
def matches(event, *rules):
    condition = {}
    for rule in rules:
        condition.update(rule)

    for name, rule in condition.items():
        # empty string means non-existant field
        if rule == "":
            if name in event:
                return False
            else:
                continue
        if name not in event:
            return False
        if not re.search(rule, event[name]):
            return False

    return True


# Traceback (TypeError)
Traceback (most recent call last):
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/lib/bot.py", line 102, in start
self.process()
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/bots/experts/modify/expert.py", line 55, in process
if matches(event, default_cond, rule_cond):
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/bots/experts/modify/expert.py", line 26, in matches
if not re.search(rule, event[name]):
File "/usr/lib64/python3.4/re.py", line 170, in search
return _compile(pattern, flags).search(string)
TypeError: expected string or buffer

# Fixed code
def matches(event, *rules):
    condition = {}
    for rule in rules:
        condition.update(rule)

    for name, rule in condition.items():
        # empty string means non-existant field
        if rule == "":
            if name in event:
                return False
            else:
                continue
        if name not in event:
            return False
        if not isinstance(event[name], str):  # int, float, etc
            return event[name] == rule
        else:
            if not re.search(rule, event[name]):
                return False

    return True
# Buggy code
def matches(self, identifiers, event, *rules):
    condition = {}
    for rule in rules:
        condition.update(rule)

    for name, rule in condition.items():
        # empty string means non-existant field
        if rule == "":
            if name in event:
                return False
            else:
                continue
        if name not in event:
            return False
        if not isinstance(rule, type(event[name])):
            self.logger.warn(
                "Type of rule ({!r}) and data ({!r}) do not match in {!s}, {}!".format(
                    type(rule), type(event[name]), identifiers, name
                )
            )
        if not isinstance(event[name], str):  # int, float, etc
            return event[name] == rule
        else:
            if not re.search(rule, event[name]):
                return False

    return True


# Traceback (TypeError)
Traceback (most recent call last):
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/lib/bot.py", line 102, in start
self.process()
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/bots/experts/modify/expert.py", line 55, in process
if matches(event, default_cond, rule_cond):
File "/usr/lib/python3.4/site-packages/intelmq-1.0.0.dev4-py3.4.egg/intelmq/bots/experts/modify/expert.py", line 26, in matches
if not re.search(rule, event[name]):
File "/usr/lib64/python3.4/re.py", line 170, in search
return _compile(pattern, flags).search(string)
TypeError: expected string or buffer

# Fixed code
def matches(self, identifiers, event, *rules):
    condition = {}
    for rule in rules:
        condition.update(rule)

    for name, rule in condition.items():
        # empty string means non-existant field
        if rule == "":
            if name in event:
                return False
            else:
                continue
        if name not in event:
            return False
        if not isinstance(rule, type(event[name])):
            if isinstance(rule, str) and isinstance(event[name], (int, float)):
                return bool(re.search(rule, str(event[name])))
            else:
                self.logger.warn(
                    "Type of rule ({!r}) and data ({!r}) do not "
                    "match in {!s}, {}!".format(
                        type(rule), type(event[name]), identifiers, name
                    )
                )
        elif not isinstance(event[name], str):  # int, float, etc
            return event[name] == rule
        else:
            return bool(re.search(rule, event[name]))

    return True
# Buggy code
def clear(self):
    """Clears the current session's history from both memory and disk."""
    # Wipe memory
    self.inps = []
    self.rtns = []
    self.outs = []
    self.tss = []

    # Wipe the current session's entries from the database.
    sql = "DELETE FROM xonsh_history WHERE sessionid = ?"
    with _xh_sqlite_get_conn(filename=self.filename) as conn:
        c = conn.cursor()
        _xh_sqlite_create_history_table(c)
        c.execute(sql, (str(self.sessionid),))


# Traceback (sqlite3.OperationalError)
Traceback (most recent call last):
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/main.py", line 421, in main
sys.exit(main_xonsh(args))
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/main.py", line 459, in main_xonsh
shell.shell.cmdloop()
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/ptk_shell/shell.py", line 344, in cmdloop
self.default(line, raw_line)
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/base_shell.py", line 389, in default
self._append_history(
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/base_shell.py", line 429, in _append_history
hist.append(info)
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/history/sqlite.py", line 275, in append
xh_sqlite_append_history(
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/history/sqlite.py", line 172, in xh_sqlite_append_history
_xh_sqlite_insert_command(c, cmd, sessionid, store_stdout, remove_duplicates)
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/history/sqlite.py", line 123, in _xh_sqlite_insert_command
values["frequency"] = _xh_sqlite_erase_dups(cursor, values["inp"]) + 1
File "/opt/miniconda/lib/python3.8/site-packages/xonsh/history/sqlite.py", line 91, in _xh_sqlite_erase_dups
cursor.execute(sql, (input,))
sqlite3.OperationalError: database or disk is full
Xonsh encountered an issue during launch
Failback to /bin/bash
(base) pc@pc:~$

# Fixed code
def clear(self):
    """Clears the current session's history from both memory and disk."""
    # Wipe memory
    self.inps = []
    self.rtns = []
    self.outs = []
    self.tss = []

    xh_sqlite_wipe_session(sessionid=self.sessionid, filename=self.filename)