Raja Mazumder

40 papers Misc 1Journal 36Unranked 3
YearRankTypeTitle / Venue / Authors
2025 J jnl
PLoS Comput. Biol.
Daniel J. B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino, Anna I. Byrd, Mano Ram Maurya, Sumana Srinivasan, Keyang Yu, Varduhi Petrosyan, Matthew E. Roth, Miroslav Milinkov, Charles Hadley King, Jeet Kiran Vora, Jonathon Keeney, Christopher Nemarich, William Khan, Alexander Lachmann, Nasheath Ahmed, Alexandra Agris, Juncheng Pan, Srinivasan Ramachandran, Eoin Fahy, Emmanuel Esquivel, Aleksandar Mihajlovic, Bosko Jevtic, Vuk Milinovic, Sean Kim, Patrick McNeely, Tianyi Wang, Eric Wenger, Miguel A. Brown, Alexander Sickler, Yuankun Zhu, Sherry L. Jenkins, Philip D. Blood, Deanne M. Taylor, Adam C. Resnick, Raja Mazumder, Aleksandar Milosavljevic, Shankar Subramaniam, Avi Ma'ayan
2024 J jnl
CoRR
Sean Kim, Raja Mazumder
2024 J jnl
Database J. Biol. Databases Curation
Karina Martinez, Jon Agirre, Yukie Akune, Kiyoko F. Aoki-Kinoshita, Cecilia N. Arighi, Kristian B. Axelsen, Evan Bolton, Emily Bordeleau, Nathan J. Edwards, Elisa Fadda, Ten Feizi, Catherine A. Hayes, Callum M. Ives, Hiren J. Joshi, Khakurel Krishna Prasad, Sofia Kossida, Frédérique Lisacek, Yan Liu, Thomas Lütteke, Junfeng Ma, Adnan Malik, Maria Jesus Martin, Akul Y. Mehta, Sriram Neelamegham, Kalpana Panneerselvam, René Ranzinger, Sylvie Ricard-Blum, Gaoussou Sanou, Vijay Shanker, Paul D. Thomas, Michael Tiemeyer, James Urban, Randi Vita, Jeet Vora, Yasunori Yamamoto, Raja Mazumder
2022 conf
ICBO
Michelle G. Giglio, Suvarna Nadendla, Arthur Brady, Amanda Charbonneau, Karl Czajkowski, Jeremy Yang, Tom Gillespie, Philippe Rocca-Serra, Jeffrey S. Grethe, Raja Mazumder, Bernard de Bono, Jonathan C. Silverstein, Daniel Clark, Mark A. Musen, Owen White
2021 conf
ICBO
Daniel Lyman, Darren A. Natale, Lynn M. Schriml, Kriston Anton, Daniel C. Crichton, Raja Mazumder
2021 J jnl
Database J. Biol. Databases Curation
Janisha A. Patel, Dennis A. Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Y. Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney
2021 J jnl
Briefings Bioinform.
Nikhita Gogate, Daniel Lyman, Amanda Bell, Edmund Cauley, Keith A. Crandall, Ashia Joseph, Robel Y. Kahsay, Darren A. Natale, Lynn M. Schriml, Sabyasach Sen, Raja Mazumder
2021 J jnl
Briefings Bioinform.
John Torcivia-Rodriguez, Raja Mazumder
2020 J jnl
Bioinform.
Robel Y. Kahsay, Jeet Vora, Rahi Navelkar, Reza Mousavi, Brian C. Fochtman, Xavier Holmes, Nagarajan Pattabiraman, René Ranzinger, Rupali Mahadik, Tatiana Williamson, Sujeet Kulkarni, Gaurav Agarwal, Maria Jesus Martin, Preethi Vasudev, Leyla J. García, Nathan Edwards, Wenjin Zhang, Darren A. Natale, Karen Ross, Kiyoko F. Aoki-Kinoshita, Matthew P. Campbell, William S. York, Raja Mazumder
2019 Misc conf
AMIA
Amanda Bell, Raja Mazumder, Daniel J. Crichton, Vijay K. Shanker, Frédéric B. Bastian, Hayley Dingerdissen, Samir Gupta, Evan Holmes, Robel Y. Kahsay, Heather L. Kincaid, A. S. M. Ashique Mahmood, Marc Robinson-Rechavi, Stephanie S. Singleton
2018 J jnl
Nucleic Acids Res.
Hayley Dingerdissen, John Torcivia-Rodriguez, Yu Hu, Ting-Chia Chang, Raja Mazumder, Robel Y. Kahsay
2018 J jnl
Database J. Biol. Databases Curation
Samir Gupta, Hayley Dingerdissen, Karen E. Ross, Yu Hu, Cathy H. Wu, Raja Mazumder, K. Vijay-Shanker
2018 J jnl
Comput. Biol. Medicine
Yu Hu, Hayley Dingerdissen, Samir Gupta, Robel Y. Kahsay, K. Vijay-Shanker, Quan Wan, Cheng Yan, Raja Mazumder
2017 J jnl
IEEE ACM Trans. Comput. Biol. Bioinform.
Scott Goldweber, Jamal Theodore, John Torcivia-Rodriguez, Vahan Simonyan, Raja Mazumder
2016 J jnl
Bioinform.
Chuming Chen, Hongzhan Huang, Raja Mazumder, Darren A. Natale, Peter B. McGarvey, Jian Zhang, Shawn W. Polson, Yuqi Wang, Cathy H. Wu
2016 J jnl
Database J. Biol. Databases Curation
Vahan Simonyan, Konstantin Chumakov, Hayley Dingerdissen, William J. Faison, Scott Goldweber, Anton Golikov, Naila Gulzar, Konstantinos Karagiannis, Phuc Vinh Nguyen Lam, Thomas Maudru, Olesja Muravitskaja, Ekaterina Osipova, Yang Pan, Alexey Pschenichnov, Alexandre Rostovtsev, Luis V. Santana-Quintero, Krista Smith, Elaine E. Thompson, Valery Tkachenko, John Torcivia-Rodriguez, Alin Voskanian, Quan Wan, Jing Wang, Tsung-Jung Wu, Carolyn Wilson, Raja Mazumder
2015 J jnl
F1000Research
Priti Kumari, Raja Mazumder, Vahan Simonyan, Konstantinos Krampis
2015 J jnl
Database J. Biol. Databases Curation
Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang, Raja Mazumder
2015 J jnl
Database J. Biol. Databases Curation
Tsung-Jung Wu, Lynn M. Schriml, Qingrong Chen, Maureen Colbert, Daniel J. Crichton, Richard P. Finney, Ying Hu, Warren A. Kibbe, Heather Kincaid, Daoud M. Meerzaman, Elvira Mitraka, Yang Pan, Krista Smith, Sudhir Srivastava, Sari Ward, Cheng Yan, Raja Mazumder
2014 J jnl
Database J. Biol. Databases Curation
Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, Raja Mazumder
2014 J jnl
BMC Bioinform.
Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas S. Almeida, William J. Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, Raja Mazumder
2013 J jnl
Genom. Proteom. Bioinform.
Konstantinos Karagiannis, Vahan Simonyan, Raja Mazumder
2013 J jnl
Genom. Proteom. Bioinform.
Phuc Vinh Nguyen Lam, Radoslav Goldman, Konstantinos Karagiannis, Tejas Narsule, Vahan Simonyan, Valerii Soika, Raja Mazumder
2012 J jnl
Database J. Biol. Databases Curation
Pascale Gaudet, Raja Mazumder
2012 J jnl
Database J. Biol. Databases Curation
Pascale Gaudet, Cecilia N. Arighi, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, Raja Mazumder
2011 J jnl
Bioinform.
Hongzhan Huang, Peter B. McGarvey, Baris E. Suzek, Raja Mazumder, Jian Zhang, Yongxing Chen, Cathy H. Wu
2008 J jnl
Nucleic Acids Res.
C. Zhang, Oswald Crasta, Stephen A. Cammer, Rebecca Will, Ron Kenyon, Daniel E. Sullivan, Q. Yu, W. Sun, R. Jha, D. Liu, Tian Xue, Y. Zhang, M. Moore, Peter B. McGarvey, Hongzhan Huang, Yongxing Chen, J. Zhang, Raja Mazumder, Cathy H. Wu, Bruno W. S. Sobral
2008 J jnl
PLoS Comput. Biol.
Raja Mazumder, Sona Vasudevan
2007 J jnl
Bioinform.
Baris E. Suzek, Hongzhan Huang, Peter B. McGarvey, Raja Mazumder, Cathy H. Wu
2006 J jnl
Nucleic Acids Res.
Cathy H. Wu, Rolf Apweiler, Amos Bairoch, Darren A. Natale, Winona C. Barker, Brigitte Boeckmann, Serenella Ferro, Elisabeth Gasteiger, Hongzhan Huang, Rodrigo Lopez, Michele Magrane, Maria Jesus Martin, Raja Mazumder, Claire O'Donovan, Nicole Redaschi, Baris E. Suzek
2005 J jnl
BMC Bioinform.
Raja Mazumder, Darren A. Natale, Sudhir Murthy, Rathi Thiagarajan, Cathy H. Wu
2004 J jnl
BMC Bioinform.
Srikanth Celamkoti, Sashidhara Kundeti, Anjan Purkayastha, Raja Mazumder, Charles Buck, Donald Seto
2004 J jnl
Nucleic Acids Res.
Cathy H. Wu, Anastasia N. Nikolskaya, Hongzhan Huang, Lai-Su L. Yeh, Darren A. Natale, Cholanayakanahalli R. Vinayaka, Zhang-Zhi Hu, Raja Mazumder, Sandeep Kumar, Panagiotis Kourtesis, Robert S. Ledley, Baris E. Suzek, Leslie Arminski, Yongxing Chen, Jian Zhang, Jorge Louie Cardenas, Sehee Chung, Jorge Castro-Alvear, Georgi Dinkov, Winona C. Barker
2003 J jnl
Nucleic Acids Res.
Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant
2003 J jnl
Nucleic Acids Res.
Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant
2003 J jnl
BMC Bioinform.
Roman L. Tatusov, Natalie D. Fedorova, John D. Jackson, Aviva R. Jacobs, Boris Kiryutin, Eugene V. Koonin, Dmitri M. Krylov, Raja Mazumder, Sergei L. Mekhedov, Anastasia N. Nikolskaya, B. Sridhar Rao, Sergei Smirnov, Alexander V. Sverdlov, Sona Vasudevan, Yuri I. Wolf, Jodie J. Yin, Darren A. Natale
2002 conf
JCIS
Nikhat Zafar, Raja Mazumder, Donald Seto
2002 J jnl
Inf. Sci.
Nikhat Zafar, Raja Mazumder, Donald Seto
2002 J jnl
BMC Bioinform.
Nikhat Zafar, Raja Mazumder, Donald Seto
2001 J jnl
Bioinform.
Raja Mazumder, Ashok S. Kolaskar, Donald Seto
tests/integration/test_pe_extractor.py
← Index tests/integration/test_pe_extractor.py python
"""
Integration tests for the PEExtractor base class.
"""
import pytest
from unittest.mock import Mock, patch, MagicMock

pytestmark = [pytest.mark.integration, pytest.mark.pe]


class TestPEExtractorInitialization:
    """Tests for PEExtractor initialization."""

    def test_pe_extractor_with_valid_pe(self, pe_binary_path, mock_logger):
        """Test PEExtractor initialization with valid PE file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)

            assert extractor.pe is not None
            assert extractor.filepath == pe_binary_path

    def test_pe_extractor_with_provided_pe_object(self, pe_binary_path, mock_logger, pe_object):
        """Test PEExtractor initialization with pre-existing PE object."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger, pe=pe_object)

            # Should use the provided PE object, not create a new one
            assert extractor.pe is pe_object

    def test_pe_extractor_with_invalid_file(self, elf_binary_path, mock_logger):
        """Test PEExtractor initialization with non-PE file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(elf_binary_path, mock_logger)

            # Should return None for pe when file is not a valid PE
            assert extractor.pe is None
            # Logger should have recorded an error
            assert mock_logger.error.called


class TestPEExtractorMethods:
    """Tests for PEExtractor helper methods."""

    def test_check_dotnet_true(self, pe_binary_path, mock_logger):
        """Test _check_dotnet returns True for .NET PE."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)

            # The test PE file is a .NET binary
            if extractor.pe is not None:
                result = extractor._check_dotnet()
                # d8637bdbcfc9112fcb1f0167b398e771 is a .NET binary
                assert result is True

    def test_check_dotnet_false(self, elf_binary_path, mock_logger):
        """Test _check_dotnet returns False for non-PE file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(elf_binary_path, mock_logger)

            # Should return False when PE is None
            result = extractor._check_dotnet()
            assert result is False

    def test_is_signed_false(self, pe_binary_path, mock_logger):
        """Test _is_signed method."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)

            if extractor.pe is not None:
                result = extractor._is_signed()
                # Result depends on the actual binary
                assert isinstance(result, bool)

    def test_has_overlay(self, pe_binary_path, mock_logger):
        """Test _has_overlay method."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)

            if extractor.pe is not None:
                result = extractor._has_overlay()
                assert isinstance(result, bool)


class TestGeneratePEFileObject:
    """Tests for _generate_pefile_object method."""

    def test_generate_pefile_object_valid(self, pe_binary_path, mock_logger):
        """Test _generate_pefile_object with valid PE file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)

            # The PE object should be created successfully
            assert extractor.pe is not None

    def test_generate_pefile_object_invalid(self, temp_text_file, mock_logger):
        """Test _generate_pefile_object with invalid file."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(temp_text_file, mock_logger)

            # Should return None for invalid PE
            assert extractor.pe is None


class TestGenerateDotNetFileObject:
    """Tests for _generate_dotnetfile_object method."""

    def test_generate_dotnetfile_object_valid(self, pe_binary_path, mock_logger):
        """Test _generate_dotnetfile_object with .NET PE file."""
        from redb.extractors.pe_extractors.pe_dotnet import PEDotNetExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEDotNetExtractor(pe_binary_path, mock_logger)

            if extractor.pe is not None and extractor._check_dotnet():
                dotnet, error = extractor._generate_dotnetfile_object()
                # Should create dotnet object for .NET PE
                assert dotnet is not None
                assert error is None

    def test_generate_dotnetfile_object_invalid(self, elf_binary_path, mock_logger):
        """Test _generate_dotnetfile_object with non-.NET file."""
        from redb.extractors.pe_extractors.pe_dotnet import PEDotNetExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEDotNetExtractor(elf_binary_path, mock_logger)

            dotnet, error = extractor._generate_dotnetfile_object()
            # Should return error for non-.NET file
            assert dotnet is None
            assert error is not None


class TestPEExtractorTag:
    """Tests for tag method in PE extractors."""

    def test_pe_features_tag(self, pe_binary_path, mock_logger):
        """Test that PEFeaturesExtractor returns correct tag."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor
        from redb.extractors.enum import Tag

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)
            assert extractor.tag() == Tag.PE_FEATURES.value

    def test_pe_import_tag(self, pe_binary_path, mock_logger):
        """Test that PEImportExtractor returns correct tag."""
        from redb.extractors.pe_extractors.pe_imports import PEImportExtractor
        from redb.extractors.enum import Tag

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEImportExtractor(pe_binary_path, mock_logger)
            assert extractor.tag() == Tag.PE_IMPORT.value

    def test_pe_section_tag(self, pe_binary_path, mock_logger):
        """Test that PESectionExtractor returns correct tag."""
        from redb.extractors.pe_extractors.pe_sections import PESectionExtractor
        from redb.extractors.enum import Tag

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PESectionExtractor(pe_binary_path, mock_logger)
            assert extractor.tag() == Tag.PE_SECTION.value


class TestPEExtractorClickHouseTable:
    """Tests for get_clickhouse_table method in PE extractors."""

    def test_pe_features_clickhouse_table(self, pe_binary_path, mock_logger):
        """Test that PEFeaturesExtractor returns correct ClickHouse table name."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)
            assert extractor.get_clickhouse_table() == "redb_pe_features"

    def test_pe_import_clickhouse_table(self, pe_binary_path, mock_logger):
        """Test that PEImportExtractor returns correct ClickHouse table name."""
        from redb.extractors.pe_extractors.pe_imports import PEImportExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEImportExtractor(pe_binary_path, mock_logger)
            assert extractor.get_clickhouse_table() == "redb_pe_imports"

    def test_pe_section_clickhouse_table(self, pe_binary_path, mock_logger):
        """Test that PESectionExtractor returns correct ClickHouse table name."""
        from redb.extractors.pe_extractors.pe_sections import PESectionExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PESectionExtractor(pe_binary_path, mock_logger)
            assert extractor.get_clickhouse_table() == "redb_pe_sections"


class TestPEExtractorPrepareExportData:
    """Tests for prepare_export_data method in PE extractors."""

    def test_pe_features_prepare_export_elasticsearch(self, pe_binary_path, mock_logger):
        """Test prepare_export_data for Elasticsearch."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)

            if extractor.pe is not None:
                # First extract
                extractor.extract()
                result = extractor.prepare_export_data("ElasticsearchExporter")
                # Should return the pe_features dataclass
                assert result is extractor.pe_features

    def test_pe_features_prepare_export_clickhouse(self, pe_binary_path, mock_logger):
        """Test prepare_export_data for ClickHouse."""
        from redb.extractors.pe_extractors.pe_features import PEFeaturesExtractor

        with patch('redb.settings.ELASTIC_BINARIES_COLLECTION', 'test'):
            extractor = PEFeaturesExtractor(pe_binary_path, mock_logger)

            if extractor.pe is not None:
                # First extract
                extractor.extract()
                result = extractor.prepare_export_data("ClickHouseExporter")

                # Should return tuple of (data, column_names, column_type_names)
                assert isinstance(result, tuple)
                assert len(result) == 3
                data, column_names, column_type_names = result
                assert isinstance(data, list)
                assert isinstance(column_names, list)
                assert isinstance(column_type_names, list)
                # Column names and types should match in length
                assert len(column_names) == len(column_type_names)