M. James C. Crabbe

29 papers Journal 27Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Database J. Biol. Databases Curation
Honglian Huang, Danqi Huang, Ziyi Wei, Yanling Qi, M. James C. Crabbe, Xiaoyan Zhang, Ying Wang
2024 J jnl
Remote. Sens.
Tao Hao, Zhihua Zhang, M. James C. Crabbe
2024 J jnl
Remote. Sens.
Xudong Xu, Zhihua Zhang, M. James C. Crabbe
2023 J jnl
IEEE Access
Batyr B. Orazbayev, Ainur Zhumadillayeva, Madyar Kabibullin, M. James C. Crabbe, Kulman Orazbayeva, Xiaoguang Yue
2023 conf
ICIIP
Lulu Hao, M. James C. Crabbe, Gabriel Xiao-Guang Yue
2023 J jnl
Bioinform.
Yuantao Tong, Fanglin Tan, Honglian Huang, Zeyu Zhang, Hui Zong, Yujia Xie, Danqi Huang, Shiyang Cheng, Ziyi Wei, Meng Fang, M. James C. Crabbe, Ying Wang, Xiaoyan Zhang
2021 J jnl
Int. J. Emerg. Technol. Learn.
Quan Liu, Haiyan Chen, M. James C. Crabbe
2021 J jnl
Int. J. Emerg. Technol. Learn.
Jing Gao, Xiao-Guang Yue, Lulu Hao, M. James C. Crabbe, Otilia Manta, Nelson Duarte
2020 J jnl
IEEE Access
Sai Zhang, Caiwu Lu, Song Jiang, Lu Shan, M. James C. Crabbe, Neal Naixue Xiong
2020 ed.
ISBDAI
M. James C. Crabbe, Rita Yi Man Li, Rebecca Kechen Dong, Otilia Manta, Ubaldo Comite
2020 J jnl
Inf.
Ainur Zhumadillayeva, Batyr B. Orazbayev, Saya Santeyeva, Kanagat Dyussekeyev, Rita Yi Man Li, M. James C. Crabbe, Xiao-Guang Yue
2018 J jnl
Comput. Biol. Chem.
QingBiao Wang, Yiqin Xu, Zhuoya Gu, Nian Liu, Ke Jin, Yao Li, M. James C. Crabbe, Yang Zhong
2009 J jnl
Comput. Biol. Chem.
M. James C. Crabbe
2008 J jnl
Comput. Biol. Chem.
M. James C. Crabbe
2008 J jnl
Comput. Biol. Chem.
Andrzej K. Konopka, M. James C. Crabbe
2007 J jnl
Comput. Biol. Chem.
M. James C. Crabbe
2006 J jnl
Comput. Biol. Chem.
M. James C. Crabbe, David J. Smith
2005 J jnl
Comput. Biol. Chem.
B. Samuel Lattimore, Stijn van Dongen, M. James C. Crabbe
2003 J jnl
Comput. Biol. Chem.
M. James C. Crabbe, David J. Smith
2003 J jnl
Comput. Biol. Chem.
M. James C. Crabbe, Andrzej K. Konopka
2003 J jnl
Comput. Biol. Chem.
M. James C. Crabbe
2003 J jnl
Comput. Biol. Chem.
M. James C. Crabbe, David J. Smith
2003 J jnl
Comput. Biol. Chem.
B. Samuel Lattimore, M. James C. Crabbe
2003 J jnl
Comput. Biol. Chem.
Lee R. Cooper, David W. Corne, M. James C. Crabbe
2003 J jnl
Comput. Biol. Chem.
M. James C. Crabbe, Lee R. Cooper, David W. Corne
2002 J jnl
Comput. Chem.
M. James C. Crabbe
2001 J jnl
Comput. Chem.
M. James C. Crabbe
1995 J jnl
Comput. Chem.
Derek Goode, M. James C. Crabbe
1995 J jnl
Comput. Chem.
M. James C. Crabbe, Derek Goode
redb/extractors/extractor.py
← Index redb/extractors/extractor.py python
import hashlib
import inspect
from abc import ABCMeta, abstractmethod
from dataclasses import asdict
from functools import cached_property
from datetime import datetime, timezone
import math
from typing import Counter, List, Optional, Dict, Any, Tuple
from redb import settings
from redb.models.dataclasses import Hash
from .database_exporters import DatabaseExporter, ElasticsearchExporter, ClickHouseExporter, PrintExporter

class Extractor(metaclass=ABCMeta):
    def __init__(
        self,
        filepath: str,
        log: Any,
        exporters: Optional[List[DatabaseExporter]] = None,
        index_prefix: Optional[str] = None,
        source: Optional[str] = None,
        elastic_index: Optional[str] = None,
        known_benign: bool = False,
        known_malicious: bool = False,
        precomputed_hashes: Optional[Dict[str, str]] = None,
    ):
        self.log = log
        self.log.debug(f"Creating {self.__class__.__name__}")
        self.filepath = filepath
        self.source = source
        self.exporters = exporters or []
        self.index_prefix = index_prefix if index_prefix else settings.ELASTIC_BINARIES_COLLECTION
        self.elastic_index = self.index_prefix + (elastic_index if elastic_index else "")
        self.known_benign = known_benign
        self.known_malicious = known_malicious

        # Use precomputed hashes if provided (e.g., from machofile, pefile)
        # Otherwise compute them from binary
        if precomputed_hashes:
            self.md5 = precomputed_hashes.get('md5') or precomputed_hashes.get('MD5')
            self.sha1 = precomputed_hashes.get('sha1') or precomputed_hashes.get('SHA1')
            self.sha256 = precomputed_hashes.get('sha256') or precomputed_hashes.get('SHA256')
        else:
            self.md5 = hashlib.md5(self.binary).hexdigest()
            self.sha1 = hashlib.sha1(self.binary).hexdigest()
            self.sha256 = hashlib.sha256(self.binary).hexdigest()
        self.hash = Hash(self.md5, self.sha1, self.sha256)

    @cached_property
    def binary(self):
        with open(self.filepath, "rb") as f:
            data = f.read()
        return data

    @property
    @abstractmethod
    def tag(self):
        pass

    @abstractmethod
    def extract(self):
        """
        this method defines the extracted data
        """

    @staticmethod
    def process_binary_string(s):
        # Remove \x00 padding
        s = s.rstrip(b"\x00")

        # Check if there are any non-printable characters
        has_non_printable = any(byte < 32 or byte > 126 for byte in s)

        if not has_non_printable:
            # If all characters are printable, decode the string
            return s.decode()
        else:
            # If there are non-printable characters, represent them as \xDD
            return "".join(
                [
                    f"\\x{byte:02x}" if byte < 32 or byte > 126 else chr(byte)
                    for byte in s
                ]
            )

    @staticmethod
    def remove_non_utf8(binary_string):
        decoded = b""
        for i in range(len(binary_string)):
            try:
                # Try to decode each byte
                char = binary_string[i : i + 1].decode("utf-8")
                decoded += char.encode("utf-8")
            except UnicodeDecodeError:
                # Skip this byte if it can't be decoded
                continue
        return decoded

    def calculate_entropy(self, data):
        """Calculate the entropy of a chunk of data.
        Based on pefile.SectionStructure.entropy_H.
        """
        # self.log.debug(inspect.currentframe().f_code.co_name)
        if not data:
            return 0.0

        if type(data) == str:
            counts = Counter(data)
            frequencies = ((i / len(data)) for i in counts.values())
            return - sum(f * math.log(f, 2) for f in frequencies)
        else:
            occurences = Counter(bytearray(data))
            entropy = 0
            for x in occurences.values():
                p_x = float(x) / len(data)
                entropy -= p_x * math.log(p_x, 2)
            return entropy

    @abstractmethod
    def prepare_export_data(self, exporter_type: str) -> Tuple[List[Any], List[str], List[str]]:
        """
        Prepare data for specific export type
        Returns:
            Tuple containing:
            - data: List of values to insert
            - column_names: List of column names
            - column_type_names: List of column types
        """
        pass

    def export_data(self):
        """Export data to all configured exporters

        Returns:
            True: Export succeeded
            False: Export failed (actual error)
            None: No data to export (not an error, e.g., no overlay, no signature)
        """
        self.log.debug(inspect.currentframe().f_code.co_name)
        success = True
        extracted_data = self.extract()

        if extracted_data is None:
            self.log.debug("extract() returned None, skipping export")
            return None  # No data to export, not a failure
            
        for exporter in self.exporters:
            if isinstance(exporter, PrintExporter):
                # For PrintExporter, we pass the extracted data directly
                success &= exporter.export(extracted_data)
            else:
                # Get the data prepared for this specific exporter type
                export_data = self.prepare_export_data(exporter.__class__.__name__)
                
                if export_data is None:
                    self.log.debug(f"prepare_export_data returned None for {exporter.__class__.__name__}")
                    return False
                
                if isinstance(exporter, ElasticsearchExporter):
                    success &= exporter.export(
                        export_data,
                        index=self.elastic_index,
                        tag=self.tag(),
                        hashes=asdict(self.hash),
                        known_benign=self.known_benign,
                        known_malicious=self.known_malicious
                    )
                elif isinstance(exporter, ClickHouseExporter):
                    # For ClickHouse, we need to pass the table name and the prepared data
                    success &= exporter.export(
                        export_data,
                        table=self.get_clickhouse_table(),
                        # Add these parameters explicitly
                        column_names=export_data[1] if isinstance(export_data, tuple) else None,
                        column_type_names=export_data[2] if isinstance(export_data, tuple) else None
                    )
                
        return success

    @abstractmethod
    def get_clickhouse_table(self) -> str:
        """Return the appropriate ClickHouse table name"""
        pass
    # def export_to_elastic(self, list_of_dataclasses, tag=None):
    #     self.log.debug(inspect.currentframe().f_code.co_name)

    #     if not isinstance(list_of_dataclasses, list):
    #         self.log.error("Called export_to_elastic wrongly")

    #     now_t = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S")
    #     for dataclass_ in list_of_dataclasses:
    #         if not settings.ELASTIC_CLIENT.ping():
    #             self.log.error("[CONNECTION ERROR] ping to elastic failed")
            
    #         # Convert dataclass to dict and filter out None values
    #         document = {k: v for k, v in asdict(dataclass_).items() if v is not None}
            
    #         if tag:
    #             document["tag"] = [tag, self.tag()]
    #         else:
    #             document["tag"] = self.tag()
    #         hashes = asdict(self.hash)
    #         document |= hashes
    #         document["timestamp_utc"] = now_t
    #         # document["source"] = self.source
    #         document["known_benign"] = self.known_benign
    #         document["known_malicious"] = self.known_malicious

    #         if "_id" in document:
    #             tmp_id = document.pop("_id") + document["sha256"]
    #             _id = hashlib.sha256(tmp_id.encode()).hexdigest()
    #         else:
    #             _id = document["sha256"]

    #         # self.log.debug(f"[DEBUG] about to export {type(document)} {document}")
    #         try:
    #             doc_dump = json.dumps(document)
    #         except TypeError as e:
    #             self.log.error(
    #                 f"Failed export of document. " f"full document: {document}"
    #             )
    #             raise e

    #         # body={"doc": doc_dump,
    #         #       "doc_as_upsert": True  # Create the document if it doesn't exist
    #         # }

    #         # Check if the index exists, and create it if it doesn't
    #         # if not settings.ELASTIC_CLIENT.indices.exists(index=self.elastic_index):
    #         #     settings.ELASTIC_CLIENT.indices.create(index=self.elastic_index)
    #         # pprint(doc_dump) #DEBUG
    #         # print("[DEBUG] _id: " + _id)
    #         # print("[DEBUG] index: " + self.elastic_index)
    #         settings.ELASTIC_CLIENT.index(
    #             index=self.elastic_index, id=_id, document=doc_dump
    #         )