Natalia Ivanova

27 papers A* 1B 1C 2Journal 22Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
CoRR
Xingzhi Sun, João F. Rocha, Brett Phelan, Dhananjay Bhaskar, Guillaume Huguet, Yanlei Zhang, Daniel Sumner Magruder, Alexander Tong, Ke Xu, Oluwadamilola Fasina, Mark Gerstein, Guy Wolf, Natalia Ivanova, Christine L. Chaffer, Smita Krishnaswamy
2025 J jnl
Comput. Electron. Agric.
Natalia Ivanova, Denis Klyuev
2024 B conf
RECOMB
Holly R. Steach, Siddharth Viswanath, Yixuan He, Xitong Zhang, Natalia Ivanova, Matthew J. Hirn, Michael Perlmutter, Smita Krishnaswamy
2023 J jnl
Nucleic Acids Res.
I-Min A. Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan Ritter, Cody Webb, Dongying Wu, Neha Varghese, T. B. K. Reddy, Supratim Mukherjee, Galina Ovchinnikova, Matt Nolan, Rekha Seshadri, Simon Roux, Axel Visel, Tanja Woyke, Emiley A. Eloe-Fadrosh, Nikos Kyrpides, Natalia Ivanova
2021 J jnl
Bioinform.
Joan Carles Pons, David Páez-Espino, Gabriel Riera, Natalia Ivanova, Nikos Kyrpides, Mercè Llabrés
2020 J jnl
SoftwareX
Dmitry Drozin, Sergey Sozykin, Natalia Ivanova, Tatiana Olenchikova, Tatyana G. Krupnova, Natalia Krupina, Viacheslav Avdin
2020 J jnl
Int. J. Manuf. Technol. Manag.
Sergey Egorov, Alexey Kapitanov, Vladimir Mitrofanov, Leonid Shvartsburg, Natalia Ivanova, Sergey Ryabov
2017 J jnl
Nucleic Acids Res.
Michalis Hadjithomas, I-Min A. Chen, Ken Chu, Jinghua Huang, Anna Ratner, Krishna Palaniappan, Evan Andersen, Victor M. Markowitz, Nikos Kyrpides, Natalia Ivanova
2017 J jnl
Nucleic Acids Res.
I-Min A. Chen, Victor M. Markowitz, Ken Chu, Krishna Palaniappan, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Evan Andersen, Marcel Huntemann, Neha Varghese, Michalis Hadjithomas, Kristin Tennessen, Torben Nielsen, Natalia Ivanova, Nikos Kyrpides
2017 J jnl
Nucleic Acids Res.
David Páez-Espino, I-Min A. Chen, Krishna Palaniappan, Anna Ratner, Ken Chu, Ernest Szeto, Manoj Pillay, Jinghua Huang, Victor M. Markowitz, Torben Nielsen, Marcel Huntemann, T. B. K. Reddy, Georgios A. Pavlopoulos, Matthew B. Sullivan, Barbara J. Campbell, Feng Chen, Katherine D. McMahon, Steven J. Hallam, Vincent J. Denef, Ricardo Cavicchioli, Sean M. Caffrey, Wolfgang R. Streit, John Webster, Kim M. Handley, Ghasem H. Salekdeh, Nicolas Tsesmetzis, João C. Setubal, Phillip B. Pope, Wen-Tso Liu, Adam R. Rivers, Natalia Ivanova, Nikos Kyrpides
2014 J jnl
Nucleic Acids Res.
Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Manoj Pillay, Anna Ratner, Jinghua Huang, Tanja Woyke, Marcel Huntemann, Iain Anderson, Konstantinos Billis, Neha Varghese, Konstantinos Mavrommatis, Amrita Pati, Natalia Ivanova, Nikos Kyrpides
2014 J jnl
Nucleic Acids Res.
Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Manoj Pillay, Anna Ratner, Jinghua Huang, Ioanna Pagani, Susannah Tringe, Marcel Huntemann, Konstantinos Billis, Neha Varghese, Kristin Tennessen, Konstantinos Mavrommatis, Amrita Pati, Natalia Ivanova, Nikos Kyrpides
2014 C conf
IGARSS
Georg C. Heygster, Marcus Huntemann, Natalia Ivanova, Roberto Saldo, Leif Toudal Pedersen
2014 J jnl
IEEE Trans. Geosci. Remote. Sens.
Natalia Ivanova, Ola M. Johannessen, Leif Toudal Pedersen, Rasmus T. Tonboe
2012 J jnl
Nucleic Acids Res.
Victor M. Markowitz, I-Min A. Chen, Ken Chu, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Anna Ratner, Biju Jacob, Amrita Pati, Marcel Huntemann, Konstantinos Liolios, Ioanna Pagani, Iain Anderson, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides
2012 J jnl
Nucleic Acids Res.
Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Biju Jacob, Jinghua Huang, Peter Williams, Marcel Huntemann, Iain Anderson, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides
2010 J jnl
Bioinform.
Sean D. Hooper, Daniel Dalevi, Amrita Pati, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides
2010 J jnl
Nucleic Acids Res.
Victor M. Markowitz, I-Min A. Chen, Krishna Palaniappan, Ken Chu, Ernest Szeto, Yuri Grechkin, Anna Ratner, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides
2009 J jnl
Bioinform.
Victor M. Markowitz, Konstantinos Mavrommatis, Natalia Ivanova, I-Min A. Chen, Ken Chu, Nikos Kyrpides
2008 C conf
ECCB
Daniel Dalevi, Natalia Ivanova, Konstantinos Mavrommatis, Sean D. Hooper, Ernest Szeto, Philip Hugenholtz, Nikos Kyrpides, Victor M. Markowitz
2008 J jnl
Nucleic Acids Res.
Victor M. Markowitz, Natalia Ivanova, Ernest Szeto, Krishna Palaniappan, Ken Chu, Daniel Dalevi, I-Min A. Chen, Yuri Grechkin, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Philip Hugenholtz, Nikos Kyrpides
2008 J jnl
Nucleic Acids Res.
Victor M. Markowitz, Ernest Szeto, Krishna Palaniappan, Yuri Grechkin, Ken Chu, I-Min A. Chen, Inna Dubchak, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides
2006 conf
ISMB (Supplement of Bioinformatics)
Victor M. Markowitz, Natalia Ivanova, Krishna Palaniappan, Ernest Szeto, Frank Korzeniewski, Athanasios Lykidis, Iain Anderson, Konstantinos Mavrommatis, Victor Kunin, Héctor García Martín, Inna Dubchak, Philip Hugenholtz, Nikos Kyrpides
2006 J jnl
Nucleic Acids Res.
Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Greg Werner, Anu Padki, Xueling Zhao, Inna Dubchak, Philip Hugenholtz, Iain Anderson, Athanasios Lykidis, Konstantinos Mavrommatis, Natalia Ivanova, Nikos Kyrpides
2005 A* conf
VLDB
Victor M. Markowitz, Frank Korzeniewski, Krishna Palaniappan, Ernest Szeto, Natalia Ivanova, Nikos Kyrpides
2003 J jnl
Nucleic Acids Res.
Ross A. Overbeek, Niels Larsen, Theresa Walunas, Mark D'Souza, Gordon D. Pusch, Evgeni Selkov Jr., Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vassieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, Nikos Kyrpides
1997 J jnl
Nucleic Acids Res.
Evgeni Selkov, Miliusha Galimova, Igor Goryanin, Yuri Grechkin, Natalia Ivanova, Yuri Komarov, Natalia Maltsev, Natalia Mikhailova, Valeri Nenashev, Ross A. Overbeek, Elena Panyushkina, Lyudmila Pronevitch, Evgeni Selkov Jr.
redb/extractors/database_exporters.py
← Index redb/extractors/database_exporters.py python
from abc import ABC, abstractmethod
from datetime import datetime, timezone
from dataclasses import asdict
import hashlib
import json
import inspect
from typing import Any, Dict, List, Union
from redb import settings
import traceback
from contextlib import contextmanager

class DatabaseExporter(ABC):
    @abstractmethod
    def export(self, data: Any, **kwargs) -> bool:
        """Export data to the database"""
        pass

class ElasticsearchExporter(DatabaseExporter):
    def __init__(self, logger: Any, index_prefix: str):
        self.client = settings.get_elasticsearch_client()
        self.index_prefix = index_prefix
        self.log = logger

    def export(self, data: Any, **kwargs) -> bool:
        self.log.debug(inspect.currentframe().f_code.co_name)
        if not isinstance(data, list):
            data = [data]
            
        now_t = datetime.now(timezone.utc).strftime("%Y-%m-%d %H:%M:%S")
        index = kwargs.get('index')
        tag = kwargs.get('tag')
        hashes = kwargs.get('hashes')
        
        for dataclass_ in data:
            try:
                # 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
                document |= hashes
                document["timestamp_utc"] = now_t
                document["known_benign"] = kwargs.get('known_benign', False)
                document["known_malicious"] = kwargs.get('known_malicious', False)

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

                doc_dump = json.dumps(document)
                self.client.index(index=index, id=_id, document=doc_dump)
                
            except Exception as e:
                self.log.error(f"Failed to export to Elasticsearch: {e}")
                return False
                
        return True

class PrintExporter(DatabaseExporter):
    """Exporter that prints results instead of uploading to database (for dry-run mode)"""
    def __init__(self, logger: Any, index_prefix: str):
        self.index_prefix = index_prefix
        self.log = logger
        self.log.debug(f"PrintExporter initialized with index_prefix: {index_prefix}")

    def export(self, data: Any, **kwargs) -> bool:
        try:
            import json
            from dataclasses import asdict, is_dataclass

            self.log.debug(f"PrintExporter.export called with data type: {type(data)}")

            if data is None:
                self.log.debug("PrintExporter.export: data is None, returning True")
                return True

            if not isinstance(data, list):
                data = [data]

            for i, item in enumerate(data):
                if is_dataclass(item) and not isinstance(item, type):
                    # Convert dataclass instance to dict
                    try:
                        item_dict = asdict(item)
                        print(json.dumps(item_dict, indent=2, default=str))
                    except Exception as e:
                        self.log.error(f"PrintExporter.export: Error converting dataclass: {e}")
                        print(str(item))
                elif isinstance(item, dict):
                    # Already a dict, print as JSON
                    print(json.dumps(item, indent=2, default=str))
                else:
                    # Fallback for other types
                    print(json.dumps(item, indent=2, default=str) if not isinstance(item, str) else item)

            self.log.debug("PrintExporter.export: completed successfully")
            return True
        except Exception as e:
            self.log.error(f"PrintExporter.export: Failed to print data: {e}")
            return False


class ClickHouseExporter(DatabaseExporter):
    def __init__(self, logger: Any, index_prefix: str, client=None):
        self.index_prefix = index_prefix
        self.log = logger
        self.client = client

    @contextmanager
    def clickhouse_connection(self):
        client = settings.create_clickhouse_client()
        try:
            yield client
        finally:
            try:
                client.close()
            except:
                pass
    # def export(self, data: Any, **kwargs) -> bool:
    #     try:
    #         # Handle multi-table export case
    #         # if isinstance(data, dict) and 'multi_table' in data:
    #         #     for table_name, table_data in data.items():
    #         #         if table_name != 'multi_table' and isinstance(table_data, dict) and 'table' in table_data:
    #         #             self.log.debug(f"Exporting to table: {table_data['table']}")
    #         #             self.log.debug(f"Column names: {table_data['column_names']}")
    #         #             self.log.debug(f"Column types: {table_data['column_type_names']}")
    #         #             self.log.debug(f"Data sample: {table_data['data'][0] if table_data['data'] else 'No data'}")
                        
    #         #             try:
    #         #                 result = self.client.insert(
    #         #                     table_data['table'],
    #         #                     table_data['data'],
    #         #                     column_names=table_data['column_names'],
    #         #                     column_type_names=table_data['column_type_names']
    #         #                 )
    #         #                 if not result:
    #         #                     self.log.error(f"Failed to insert into table {table_data['table']}")
    #         #                     return False
    #         #             except Exception as e:
    #         #                 self.log.error(f"Error inserting into table {table_data['table']}: {e}")
    #         #                 self.log.error(f"Data that caused error: {table_data['data']}")
    #         #                 return False
    #         #     return True

    #         if isinstance(data, dict) and 'multi_table' in data:
    #             for table_name, table_data in data.items():
    #                 if table_name != 'multi_table' and isinstance(table_data, dict) and 'table' in table_data:
    #                     self.log.debug(f"Exporting to table: {table_data['table']}")
                        
    #                     # Validate each row before insert
    #                     for row in table_data['data']:
    #                         for val, col_name, col_type in zip(row, table_data['column_names'], 
    #                                                         table_data['column_type_names']):
    #                             # Check for empty strings
    #                             if isinstance(val, str) and not val:
    #                                 self.log.error(f"Empty string found for column {col_name}")
    #                                 raise ValueError(f"Empty string not allowed for column {col_name}")
                                
    #                             # Log all string values for certificate_serial_number
    #                             if col_name == 'certificate_serial_number':
    #                                 self.log.debug(f"Serial number value: '{val}', type: {type(val)}, "
    #                                             f"repr: {repr(val)}")
                        
    #                     try:
    #                         result = self.client.insert(
    #                             table_data['table'],
    #                             table_data['data'],
    #                             column_names=table_data['column_names'],
    #                             column_type_names=table_data['column_type_names']
    #                         )
    #                         if not result:
    #                             self.log.error(f"Failed to insert into table {table_data['table']}")
    #                             return False
    #                     except Exception as e:
    #                         self.log.error(f"Error inserting into table {table_data['table']}: {e}")
    #                         self.log.error(f"Data that caused error: {table_data['data']}")
    #                         return False
    #             return True

    #         # Handle single table case
    #         table = kwargs.get('table')
    #         if not table:
    #             raise ValueError("Table name must be provided for ClickHouse export")
            
    #         # Unpack the tuple returned by prepare_export_data
    #         if isinstance(data, tuple):
    #             if len(data) != 3:
    #                 raise ValueError("Data tuple must contain exactly 3 elements: (data, column_names, column_type_names)")
    #             insert_data, column_names, column_type_names = data
    #         else:
    #             # Use provided column names and types from kwargs
    #             insert_data = data
    #             column_names = kwargs.get('column_names')
    #             column_type_names = kwargs.get('column_type_names')
                
    #         if not (column_names and column_type_names):
    #             raise ValueError("column_names and column_type_names must be provided")

    #         # Ensure data is in list format for batch insert
    #         if not isinstance(insert_data, list):
    #             insert_data = [insert_data]
                
    #         self.client.insert(
    #             table,
    #             insert_data,
    #             column_names=column_names,
    #             column_type_names=column_type_names
    #         )
    #         return True
            
    #     except Exception as e:
    #         self.log.error(f"Failed to export to ClickHouse: {e}")
    #         return False

    def get_client(self):
        """Get existing client or create new one if needed"""
        if self.client:
            return self.client
        try:
            return settings.create_clickhouse_client() 
        except Exception as e:
            self.log.error(f"Failed to create ClickHouse client: {e}")
            return None
            
    # WORKING SIMPLE VERSION
    def export(self, data: Any, **kwargs) -> bool:
        try:
            # # Handle multi-table export case
            # # if isinstance(data, dict) and 'multi_table' in data:
            # #     for table_data in data.values():
            # #         if isinstance(table_data, dict) and 'table' in table_data:
            # #             result = self.client.insert(
            # #                 table_data['table'],
            # #                 table_data['data'],
            # #                 column_names=table_data['column_names'],
            # #                 column_type_names=table_data['column_type_names']
            # #             )
            # #             if not result:  # If any insert fails, return False
            # #                 return False
            # #     return True
            # if isinstance(data, dict) and 'multi_table' in data:
            #     for key, table_data in data.items():
            #         if key != 'multi_table' and isinstance(table_data, dict) and 'table' in table_data:
            #             # Add type hints
            #             typed_data = []
            #             for row in table_data['data']:
            #                 typed_row = []
            #                 for val, type_name in zip(row, table_data['column_type_names']):
            #                     if isinstance(val, str) and not val:
            #                         val = 'UNKNOWN'
            #                     if type_name == 'String' or 'LowCardinality(String)' in type_name:
            #                         val = str(val) if val is not None else 'UNKNOWN'
            #                     typed_row.append(val)
            #                 typed_data.append(typed_row)
                        
            #             table_data['data'] = typed_data
                        
            #             result = self.client.insert(
            #                 table_data['table'],
            #                 table_data['data'],
            #                 column_names=table_data['column_names'],
            #                 column_type_names=table_data['column_type_names'],
            #                 settings={'input_format_values_interpret_expressions': 0}  # Disable type inference
            #             )
            #             if not result:
            #                 return False
            #         return True

            # Get a new client connection for this export operation
            with self.clickhouse_connection() as client:
                if not client:
                    return False

                # LAST WORKING VERSION
                if isinstance(data, dict) and 'multi_table' in data:
                    for key, table_data in data.items():
                        if key != 'multi_table' and isinstance(table_data, dict) and 'table' in table_data:
                            # Debug logging
                            self.log.debug(f"Processing table: {table_data['table']}")
                            self.log.debug(f"Column names: {table_data['column_names']}")
                            self.log.debug(f"Column types: {table_data['column_type_names']}")
                            
                            typed_data = []
                            for row_idx, row in enumerate(table_data['data']):
                                typed_row = []
                                for val_idx, (val, type_name, col_name) in enumerate(
                                    zip(row, table_data['column_type_names'], table_data['column_names'])
                                ):
                                    try:
                                        # Handle different types
                                        if val is None:
                                            if 'Nullable' in type_name:
                                                val = None  # Keep None for Nullable columns
                                            elif 'Array' in type_name:
                                                val = []
                                            elif 'Int' in type_name or 'UInt' in type_name:
                                                val = 0
                                            elif 'FixedString(16)' in type_name:
                                                val = b'\x00' * 16  # Binary FixedString
                                            elif 'String' in type_name or 'LowCardinality' in type_name:
                                                val = 'UNKNOWN'
                                            elif 'DateTime' in type_name:
                                                val = datetime.now(timezone.utc)
                                            elif 'Boolean' in type_name:
                                                val = False
                                            else:
                                                self.log.error(f"Unhandled type {type_name} for null value")
                                                val = 'UNKNOWN'
                                        
                                        # Log problematic values
                                        if isinstance(val, str) and not val.strip():
                                            self.log.warning(f"Empty string found in table {table_data['table']}, "
                                                        f"column {col_name}, row {row_idx}")
                                        
                                        # Ensure array types are always lists
                                        if 'Array' in type_name and not isinstance(val, list):
                                            val = [val]
                                        
                                        typed_row.append(val)
                                    except Exception as e:
                                        self.log.error(f"Error processing value in table {table_data['table']}, "
                                                    f"column {col_name} ({type_name}), "
                                                    f"row {row_idx}, value: {repr(val)}")
                                        raise
                                        
                                typed_data.append(typed_row)
                            
                            table_data['data'] = typed_data

                            # Skip insert if there is nothing to insert
                            if not typed_data:
                                self.log.debug(f"No data to insert for table {table_data['table']}, skipping.")
                                continue

                            # Debug log the first row of data
                            self.log.debug(f"Sample row for {table_data['table']}: {typed_data[0]}")

                            result = client.insert(
                                table_data['table'],
                                table_data['data'],
                                column_names=table_data['column_names'],
                                column_type_names=table_data['column_type_names'],
                                settings={'input_format_values_interpret_expressions': 0}
                            )
                            if not result:
                                self.log.error(f"Insert failed for table {table_data['table']}")
                                return False
                    return True

                # Handle single table case
                table = kwargs.get('table')
                if not table:
                    raise ValueError("Table name must be provided for ClickHouse export")
                
                # Unpack the tuple returned by prepare_export_data
                if isinstance(data, tuple):
                    if len(data) != 3:
                        raise ValueError("Data tuple must contain exactly 3 elements: (data, column_names, column_type_names)")
                    insert_data, column_names, column_type_names = data
                else:
                    # Use provided column names and types from kwargs
                    insert_data = data
                    column_names = kwargs.get('column_names')
                    column_type_names = kwargs.get('column_type_names')
                    
                if not (column_names and column_type_names):
                    raise ValueError("column_names and column_type_names must be provided")

                # Ensure data is in list format for batch insert
                if not isinstance(insert_data, list):
                    insert_data = [insert_data]

                # Skip insert if there is nothing to insert
                if not insert_data:
                    self.log.debug(f"No data to insert for table {table}, skipping.")
                    return True

                client.insert(
                    table,
                    insert_data,
                    column_names=column_names,
                    column_type_names=column_type_names,
                    settings={'input_format_values_interpret_expressions': 0}  # Disable type inference
                )
                return True

        except TypeError as e:
            # Get the actual value causing the error from the exception traceback
            import sys
            exc_type, exc_value, exc_traceback = sys.exc_info()
            
            # Walk through the traceback to find the frame with the problematic value
            current = exc_traceback
            while current:
                if 'string.py' in current.tb_frame.f_code.co_filename and '_data_size' in current.tb_frame.f_code.co_name:
                    locals_dict = current.tb_frame.f_locals
                    problematic_value = locals_dict.get('x')
                    self.log.error(f"TypeError with value: {problematic_value} (type: {type(problematic_value)})")
                    self.log.error(f"Full locals at error: {locals_dict}")
                    break
                current = current.tb_next
            
            self.log.error(f"Failed to export to ClickHouse: {e}")
            self.log.error("Full traceback:")
            self.log.error(traceback.format_exc())
            return False
        except Exception as e:
            self.log.error(f"Failed to export to ClickHouse: {e}")
            self.log.error(traceback.format_exc())
            return False
        finally:
            # Only close if we created a new client
            if client and client != self.client:
                # Close the client connection
                try:
                    client.close()
                except:
                    pass