Kalpana Karra

13 papers Journal 11Unranked 2
YearRankTypeTitle / Venue / Authors
2020 J jnl
Nucleic Acids Res.
Julie Agapite, Laurent-Philippe Albou, Suzi A. Aleksander, Joanna Argasinska, Valerio Arnaboldi, Helen Attrill, Susan M. Bello, Judith A. Blake, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jae-Hyoung Cho, Karen R. Christie, Madeline A. Crosby, Jeff de Pons, Mary E. Dolan, Gilberto dos Santos, Barbara Dunn, Nathan A. Dunn, Anne E. Eagle, Dustin Ebert, Stacia R. Engel, David Fashena, Ken Frazer, Sibyl Gao, Felix Gondwe, Joshua L. Goodman, L. Sian Gramates, Christian A. Grove, Todd W. Harris, Marie-Claire Harrison, Douglas G. Howe, Kevin L. Howe, Sagar Jha, James A. Kadin, Thomas C. Kaufman, Patrick Kalita, Kalpana Karra, Ranjana Kishore, Stanley J. F. Laulederkind, Raymond Y. N. Lee, Kevin A. MacPherson, Steven J. Marygold, Beverley Matthews, Gillian H. Millburn, Stuart R. Miyasato, Sierra A. T. Moxon, Hans-Michael Müller, Christopher J. Mungall, Anushya Muruganujan, Tremayne Mushayahama, Robert S. Nash, Patrick Ng, Michael Paulini, Norbert Perrimon, Christian Pich, Daniela Raciti, Joel E. Richardson, Matthew Russell, Susan Russo Gelbart, Leyla Ruzicka, Kevin Schaper, Mary Shimoyama, Matt Simison, Cynthia L. Smith, David R. Shaw, Ajay Shrivatsav, Marek S. Skrzypek, Jennifer R. Smith, Paul W. Sternberg, Christopher J. Tabone, Paul D. Thomas, Jyothi Thota, Sabrina Toro, Monika Tomczuk, Marek Tutaj, Monika Tutaj, Jose-Maria Urbano, Kimberly Van Auken, Ceri E. Van Slyke, Shur-Jen Wang, Shuai Weng, Monte Westerfield, Gary Williams, Edith D. Wong, Adam Wright, Karen Yook
2020 J jnl
Database J. Biol. Databases Curation
Robert S. Nash, Shuai Weng, Kalpana Karra, Edith D. Wong, Stacia R. Engel, J. Michael Cherry, SGD Project
2020 J jnl
Nucleic Acids Res.
Patrick C. Ng, Edith D. Wong, Kevin A. MacPherson, Suzi A. Aleksander, Joanna Argasinska, Barbara Dunn, Robert S. Nash, Marek S. Skrzypek, Felix Gondwe, Sagar Jha, Kalpana Karra, Shuai Weng, Stuart R. Miyasato, Matt Simison, Stacia R. Engel, J. Michael Cherry
2018 J jnl
Nucleic Acids Res.
Marek S. Skrzypek, Robert S. Nash, Edith D. Wong, Kevin A. MacPherson, Sage T. Hellerstedt, Stacia R. Engel, Kalpana Karra, Shuai Weng, Travis K. Sheppard, Gail Binkley, Matt Simison, Stuart R. Miyasato, J. Michael Cherry
2018 J jnl
Database J. Biol. Databases Curation
Stacia R. Engel, Marek S. Skrzypek, Sage T. Hellerstedt, Edith D. Wong, Robert S. Nash, Shuai Weng, Gail Binkley, Travis K. Sheppard, Kalpana Karra, J. Michael Cherry
2017 J jnl
Database J. Biol. Databases Curation
Sage T. Hellerstedt, Robert S. Nash, Shuai Weng, Kelley M. Paskov, Edith D. Wong, Kalpana Karra, Stacia R. Engel, J. Michael Cherry
2016 J jnl
Database J. Biol. Databases Curation
Giltae Song, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla S. Dalusag, Janos Demeter, Stacia R. Engel, Sage T. Hellerstedt, Kalpana Karra, Benjamin C. Hitz, Robert S. Nash, Kelley M. Paskov, Travis K. Sheppard, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, J. Michael Cherry
2016 conf
SWAT4LS
Maxime Déraspe, Gail Binkley, Daniela Butano, Matthew Chadwick, J. Michael Cherry, Justin Clark-Casey, Sergio Contrino, Jacques Corbeil, Joshua Heimbach, Kalpana Karra, Rachel Lyne, Julie M. Sullivan, Yo Yehudi, Gos Micklem, Michel Dumontier
2016 conf
BMDID@ISWC
Maxime Déraspe, Kalpana Karra, Gail Binkley, Julie M. Sullivan, Gos Micklem, Jacques Corbeil, J. Michael Cherry, Michel Dumontier
2016 J jnl
Nucleic Acids Res.
Travis K. Sheppard, Benjamin C. Hitz, Stacia R. Engel, Giltae Song, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla S. Dalusag, Janos Demeter, Sage T. Hellerstedt, Kalpana Karra, Robert S. Nash, Kelley M. Paskov, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, J. Michael Cherry
2013 J jnl
Database J. Biol. Databases Curation
Edith D. Wong, Kalpana Karra, Benjamin C. Hitz, Eurie L. Hong, J. Michael Cherry
2012 J jnl
Nucleic Acids Res.
J. Michael Cherry, Eurie L. Hong, Craig Amundsen, Rama Balakrishnan, Gail Binkley, Esther T. Chan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Kalpana Karra, Cynthia J. Krieger, Stuart R. Miyasato, Robert S. Nash, Julie Park, Marek S. Skrzypek, Matt Simison, Shuai Weng, Edith D. Wong
2012 J jnl
Database J. Biol. Databases Curation
Rama Balakrishnan, Julie Park, Kalpana Karra, Benjamin C. Hitz, Gail Binkley, Eurie L. Hong, Julie M. Sullivan, Gos Micklem, J. Michael Cherry
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
    #         )