Cangzhi Jia

26 papers Journal 26
YearRankTypeTitle / Venue / Authors
2026 J jnl
Comput. Biol. Chem.
Kunbo Wu, Jia Zheng, Ying Zhang, Cangzhi Jia
2024 J jnl
Briefings Bioinform.
Yetong Zhou, Shengming Zhou, Yue Bi, Quan Zou, Cangzhi Jia
2024 J jnl
J. Chem. Inf. Model.
Changjiang Li, Quan Zou, Cangzhi Jia, Jia Zheng
2024 J jnl
IEEE J. Biomed. Health Informatics
Yuanyi Tian, Quan Zou, Chunyu Wang, Cangzhi Jia
2024 J jnl
Briefings Bioinform.
Tianxiang Liu, Cangzhi Jia, Yue Bi, Xudong Guo, Quan Zou, Fuyi Li
2023 J jnl
Briefings Bioinform.
Shengming Zhou, Yetong Zhou, Tian Liu, Jia Zheng, Cangzhi Jia
2023 J jnl
Briefings Bioinform.
Yan Zhu, Fuyi Li, Xudong Guo, Xiaoyu Wang, Lachlan J. M. Coin, Geoffrey I. Webb, Jiangning Song, Cangzhi Jia
2022 J jnl
Briefings Bioinform.
Yue Bi, Fuyi Li, Xudong Guo, Zhikang Wang, Tong Pan, Yuming Guo, Geoffrey I. Webb, Jianhua Yao, Cangzhi Jia, Jiangning Song
2022 J jnl
Briefings Bioinform.
Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li, Yan Zhu, Tatsuya Akutsu, Geoffrey I. Webb, Quan Zou, Lachlan J. M. Coin, Jiangning Song
2022 J jnl
J. Bioinform. Comput. Biol.
Yan Zhu, Shuwan Yin, Jia Zheng, Yixia Shi, Cangzhi Jia
2022 J jnl
Briefings Bioinform.
Fuyi Li, Shuangyu Dong, André Leier, Meiya Han, Xudong Guo, Jing Xu, Xiaoyu Wang, Shirui Pan, Cangzhi Jia, Yang Zhang, Geoffrey I. Webb, Lachlan J. M. Coin, Chen Li, Jiangning Song
2021 J jnl
Briefings Bioinform.
Yan Zhu, Fuyi Li, Dongxu Xiang, Tatsuya Akutsu, Jiangning Song, Cangzhi Jia
2021 J jnl
Briefings Bioinform.
Yu Zhang, Cangzhi Jia, Melissa Jane Fullwood, Chee Keong Kwoh
2021 J jnl
Briefings Bioinform.
Quanzhong Liu, Jinxiang Chen, Yanze Wang, Shuqin Li, Cangzhi Jia, Jiangning Song, Fuyi Li
2021 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Cangzhi Jia, Meng Zhang, Cunshuo Fan, Fuyi Li, Jiangning Song
2021 J jnl
Briefings Bioinform.
Yu Zhang, Cangzhi Jia, Chee Keong Kwoh
2020 J jnl
IEEE Access
Yue Bi, Dong Jin, Cangzhi Jia
2020 J jnl
Bioinform.
Cangzhi Jia, Yue Bi, Jinxiang Chen, André Leier, Fuyi Li, Jiangning Song
2020 J jnl
Briefings Bioinform.
Fuyi Li, Cunshuo Fan, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Cangzhi Jia, Yan Zhu, Alexander Ian Smith, Geoffrey I. Webb, Quanzhong Liu, Leyi Wei, Jian Li, Jiangning Song
2020 J jnl
J. Bioinform. Comput. Biol.
Pengyu Li, He Zhang, Xuyang Zhao, Cangzhi Jia, Fuyi Li, Jiangning Song
2019 J jnl
Bioinform.
Wenying He, Cangzhi Jia, Quan Zou
2019 J jnl
Bioinform.
Meng Zhang, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Cunshuo Fan, Chee Keong Kwoh, Kuo-Chen Chou, Jiangning Song, Cangzhi Jia
2018 J jnl
BMC Syst. Biol.
Wenying He, Cangzhi Jia, Yucong Duan, Quan Zou
2018 J jnl
Bioinform.
Cangzhi Jia, Yun Zuo, Quan Zou
2008 J jnl
J. Comb. Theory A
Wenchang Chu, Cangzhi Jia
2008 J jnl
Comput. Math. Appl.
Weiping Wang, Cangzhi Jia, Tian-ming Wang
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
    #         )