Haim Ashkenazy

Year	Rank	Type	Title / Venue / Authors
2021	J	`jnl`	PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Res. Michael Bernhofer, Christian Dallago, Timothy Karl, Venkata P. Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, László Kaján, Seán I. O'Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost
2017	J	`jnl`	SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm. Nucleic Acids Res. Haim Ashkenazy, Eli Levy Karin, Zach Mertens, Reed A. Cartwright, Tal Pupko
2017	J	`jnl`	TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites. Nucleic Acids Res. Eli Levy Karin, Haim Ashkenazy, Susann Wicke, Tal Pupko, Itay Mayrose
2016	J	`jnl`	ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res. Haim Ashkenazy, Shiran Abadi, Eric Martz, Ofer Chay, Itay Mayrose, Tal Pupko, Nir Ben-Tal
2015	J	`jnl`	GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res. Itamar Sela, Haim Ashkenazy, Kazutaka Katoh, Tal Pupko
2015	J	`jnl`	Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations. BMC Bioinform. Aya Narunsky, Haim Ashkenazy, Rachel Kolodny, Nir Ben-Tal
2014	J	`jnl`	PredictProtein - an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. Guy Yachdav, Edda Kloppmann, László Kaján, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer, Lothar Richter, Haim Ashkenazy, Marco Punta, Avner Schlessinger, Yana Bromberg, Reinhard Schneider, Gerrit Vriend, Chris Sander, Nir Ben-Tal, Burkhard Rost
2013	J	`jnl`	CoPAP: Coevolution of Presence-Absence Patterns. Nucleic Acids Res. Ofir Cohen, Haim Ashkenazy, Eli Levy Karin, David Burstein, Tal Pupko
2012	J	`jnl`	FastML: a web server for probabilistic reconstruction of ancestral sequences. Nucleic Acids Res. Haim Ashkenazy, Osnat Penn, Adi Doron-Faigenboim, Ofir Cohen, Gina Cannarozzi, Oren Zomer, Tal Pupko
2012	J	`jnl`	Uncovering the co-evolutionary network among prokaryotic genes. Bioinform. Ofir Cohen, Haim Ashkenazy, David Burstein, Tal Pupko
2011	J	`jnl`	Hidden conformations in protein structures. Bioinform. Haim Ashkenazy, Ron Unger, Yossef Kliger
2011	J	`jnl`	Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site. Bioinform. Gilad Wainreb, Lior Wolf, Haim Ashkenazy, Yves Dehouck, Nir Ben-Tal
2010	J	`jnl`	ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. Haim Ashkenazy, Elana Erez, Eric Martz, Tal Pupko, Nir Ben-Tal
2010	J	`jnl`	GLOOME: gain loss mapping engine. Bioinform. Ofir Cohen, Haim Ashkenazy, Frida Belinky, Dorothée Huchon, Tal Pupko
2010	J	`jnl`	GUIDANCE: a web server for assessing alignment confidence scores. Nucleic Acids Res. Osnat Penn, Eyal Privman, Haim Ashkenazy, Giddy Landan, Dan Graur, Tal Pupko
2010	J	`jnl`	MuD: an interactive web server for the prediction of non-neutral substitutions using protein structural data. Nucleic Acids Res. Gilad Wainreb, Haim Ashkenazy, Yana Bromberg, Alina Starovolsky-Shitrit, Turkan Haliloglu, Eytan Ruppin, Karen B. Avraham, Burkhard Rost, Nir Ben-Tal

"""
Unit tests for database exporters.
"""
import pytest
import json
from dataclasses import dataclass, asdict
from datetime import datetime, timezone
from unittest.mock import Mock, patch, MagicMock

pytestmark = [pytest.mark.unit, pytest.mark.exporters]


# ============================================================================
# Sample Dataclass for Testing
# ============================================================================

@dataclass
class SampleData:
    """Sample dataclass for export testing."""
    sha256: str = "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855"
    name: str = "test_sample"
    value: int = 42
    _id: str = "test_id"


# ============================================================================
# PrintExporter Tests
# ============================================================================

class TestPrintExporter:
    """Tests for PrintExporter class."""

    def test_initialization(self, mock_logger):
        """Test PrintExporter initialization."""
        from redb.extractors.database_exporters import PrintExporter

        exporter = PrintExporter(mock_logger, "test_index")

        assert exporter.index_prefix == "test_index"
        assert exporter.log is mock_logger

    def test_export_dataclass(self, mock_logger, capsys):
        """Test exporting a dataclass."""
        from redb.extractors.database_exporters import PrintExporter

        exporter = PrintExporter(mock_logger, "test_index")
        sample = SampleData()

        result = exporter.export(sample)

        assert result is True
        captured = capsys.readouterr()
        assert "test_sample" in captured.out

    def test_export_list_of_dataclasses(self, mock_logger, capsys):
        """Test exporting a list of dataclasses."""
        from redb.extractors.database_exporters import PrintExporter

        exporter = PrintExporter(mock_logger, "test_index")
        samples = [SampleData(name="sample1"), SampleData(name="sample2")]

        result = exporter.export(samples)

        assert result is True
        captured = capsys.readouterr()
        assert "sample1" in captured.out
        assert "sample2" in captured.out

    def test_export_dict(self, mock_logger, capsys):
        """Test exporting a dictionary."""
        from redb.extractors.database_exporters import PrintExporter

        exporter = PrintExporter(mock_logger, "test_index")
        data = {"key": "value", "number": 42}

        result = exporter.export(data)

        assert result is True
        captured = capsys.readouterr()
        assert "key" in captured.out
        assert "value" in captured.out

    def test_export_none(self, mock_logger):
        """Test exporting None."""
        from redb.extractors.database_exporters import PrintExporter

        exporter = PrintExporter(mock_logger, "test_index")

        result = exporter.export(None)

        assert result is True

    def test_export_empty_list(self, mock_logger):
        """Test exporting empty list."""
        from redb.extractors.database_exporters import PrintExporter

        exporter = PrintExporter(mock_logger, "test_index")

        result = exporter.export([])

        assert result is True


# ============================================================================
# ElasticsearchExporter Tests
# ============================================================================

class TestElasticsearchExporter:
    """Tests for ElasticsearchExporter class."""

    def test_initialization(self, mock_logger):
        """Test ElasticsearchExporter initialization."""
        with patch('redb.settings.get_elasticsearch_client') as mock_client:
            mock_client.return_value = Mock()
            from redb.extractors.database_exporters import ElasticsearchExporter

            exporter = ElasticsearchExporter(mock_logger, "test_index")

            assert exporter.index_prefix == "test_index"
            assert exporter.log is mock_logger
            assert exporter.client is not None

    def test_export_dataclass(self, mock_logger):
        """Test exporting a dataclass to Elasticsearch."""
        with patch('redb.settings.get_elasticsearch_client') as mock_get_client:
            mock_client = Mock()
            mock_get_client.return_value = mock_client

            from redb.extractors.database_exporters import ElasticsearchExporter

            exporter = ElasticsearchExporter(mock_logger, "test_index")
            sample = SampleData()

            result = exporter.export(
                sample,
                index="test_index",
                tag="test_tag",
                hashes={"sha256": sample.sha256}
            )

            assert result is True
            mock_client.index.assert_called()

    def test_export_list(self, mock_logger):
        """Test exporting a list to Elasticsearch."""
        with patch('redb.settings.get_elasticsearch_client') as mock_get_client:
            mock_client = Mock()
            mock_get_client.return_value = mock_client

            from redb.extractors.database_exporters import ElasticsearchExporter

            exporter = ElasticsearchExporter(mock_logger, "test_index")
            samples = [SampleData(name="sample1"), SampleData(name="sample2")]

            result = exporter.export(
                samples,
                index="test_index",
                tag="test_tag",
                hashes={"sha256": "test_hash"}
            )

            assert result is True
            # Should be called twice (once per sample)
            assert mock_client.index.call_count == 2

    def test_export_failure(self, mock_logger):
        """Test handling export failure."""
        with patch('redb.settings.get_elasticsearch_client') as mock_get_client:
            mock_client = Mock()
            mock_client.index.side_effect = Exception("Connection failed")
            mock_get_client.return_value = mock_client

            from redb.extractors.database_exporters import ElasticsearchExporter

            exporter = ElasticsearchExporter(mock_logger, "test_index")
            sample = SampleData()

            result = exporter.export(
                sample,
                index="test_index",
                tag="test_tag",
                hashes={"sha256": sample.sha256}
            )

            assert result is False
            mock_logger.error.assert_called()

    def test_export_with_custom_id(self, mock_logger):
        """Test exporting with custom _id field."""
        with patch('redb.settings.get_elasticsearch_client') as mock_get_client:
            mock_client = Mock()
            mock_get_client.return_value = mock_client

            from redb.extractors.database_exporters import ElasticsearchExporter

            exporter = ElasticsearchExporter(mock_logger, "test_index")
            sample = SampleData(_id="custom_id")

            result = exporter.export(
                sample,
                index="test_index",
                tag="test_tag",
                hashes={"sha256": sample.sha256}
            )

            assert result is True


# ============================================================================
# ClickHouseExporter Tests
# ============================================================================

class TestClickHouseExporter:
    """Tests for ClickHouseExporter class."""

    def test_initialization(self, mock_logger):
        """Test ClickHouseExporter initialization."""
        from redb.extractors.database_exporters import ClickHouseExporter

        mock_client = Mock()
        exporter = ClickHouseExporter(mock_logger, "test_index", client=mock_client)

        assert exporter.index_prefix == "test_index"
        assert exporter.log is mock_logger
        assert exporter.client is mock_client

    def test_export_tuple_data(self, mock_logger):
        """Test exporting tuple data to ClickHouse."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_client.insert.return_value = True
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            data = [["hash123", "sample.exe", 1024]]
            column_names = ["sha256", "name", "size"]
            column_type_names = ["String", "String", "UInt64"]

            result = exporter.export(
                (data, column_names, column_type_names),
                table="test_table"
            )

            assert result is True

    def test_export_multi_table(self, mock_logger):
        """Test exporting multi-table data to ClickHouse."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_client.insert.return_value = True
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            data = {
                'multi_table': True,
                'table1': {
                    'table': 'test_table1',
                    'data': [["hash123", "sample.exe"]],
                    'column_names': ["sha256", "name"],
                    'column_type_names': ["String", "String"]
                }
            }

            result = exporter.export(data)

            assert result is True

    def test_export_failure(self, mock_logger):
        """Test handling export failure."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_client.insert.side_effect = Exception("Connection failed")
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            data = [["hash123", "sample.exe", 1024]]
            column_names = ["sha256", "name", "size"]
            column_type_names = ["String", "String", "UInt64"]

            result = exporter.export(
                (data, column_names, column_type_names),
                table="test_table"
            )

            assert result is False

    def test_export_missing_table(self, mock_logger):
        """Test export without table name raises error."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            data = [["hash123", "sample.exe", 1024]]
            column_names = ["sha256", "name", "size"]
            column_type_names = ["String", "String", "UInt64"]

            result = exporter.export(
                (data, column_names, column_type_names)
                # Missing table parameter
            )

            assert result is False

    def test_get_client(self, mock_logger):
        """Test get_client method."""
        from redb.extractors.database_exporters import ClickHouseExporter

        mock_client = Mock()
        exporter = ClickHouseExporter(mock_logger, "test_index", client=mock_client)

        result = exporter.get_client()

        assert result is mock_client

    def test_get_client_creates_new(self, mock_logger):
        """Test get_client creates new client if none exists."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_new_client = Mock()
            mock_create.return_value = mock_new_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            result = exporter.get_client()

            assert result is mock_new_client


# ============================================================================
# DatabaseExporter Abstract Base Class Tests
# ============================================================================

class TestDatabaseExporter:
    """Tests for DatabaseExporter abstract base class."""

    def test_cannot_instantiate_abstract(self):
        """Test that DatabaseExporter cannot be instantiated directly."""
        from redb.extractors.database_exporters import DatabaseExporter

        with pytest.raises(TypeError):
            DatabaseExporter()

    def test_subclass_must_implement_export(self):
        """Test that subclasses must implement export method."""
        from redb.extractors.database_exporters import DatabaseExporter

        # Define incomplete subclass
        class IncompleteExporter(DatabaseExporter):
            pass

        with pytest.raises(TypeError):
            IncompleteExporter()


# ============================================================================
# Null/Edge Case Tests
# ============================================================================

class TestExporterEdgeCases:
    """Tests for edge cases in exporters."""

    def test_print_exporter_with_complex_nested_data(self, mock_logger, capsys):
        """Test PrintExporter with complex nested data."""
        from redb.extractors.database_exporters import PrintExporter

        exporter = PrintExporter(mock_logger, "test_index")
        data = {
            "level1": {
                "level2": {
                    "level3": [1, 2, 3]
                }
            },
            "array": [{"a": 1}, {"b": 2}]
        }

        result = exporter.export(data)

        assert result is True
        captured = capsys.readouterr()
        assert "level1" in captured.out

    def test_clickhouse_null_handling(self, mock_logger):
        """Test ClickHouse exporter handles null values."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_client.insert.return_value = True
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            # Multi-table data with null values
            data = {
                'multi_table': True,
                'table1': {
                    'table': 'test_table',
                    'data': [[None, "sample.exe", None]],
                    'column_names': ["sha256", "name", "size"],
                    'column_type_names': ["Nullable(String)", "String", "Nullable(UInt64)"]
                }
            }

            result = exporter.export(data)

            # Should handle nulls appropriately
            assert result is True

    def test_clickhouse_array_handling(self, mock_logger):
        """Test ClickHouse exporter handles array types."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_client.insert.return_value = True
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            data = {
                'multi_table': True,
                'table1': {
                    'table': 'test_table',
                    'data': [["hash", ["tag1", "tag2"]]],
                    'column_names': ["sha256", "tags"],
                    'column_type_names': ["String", "Array(String)"]
                }
            }

            result = exporter.export(data)

            assert result is True


# ============================================================================
# Type Conversion Tests
# ============================================================================

class TestExporterTypeConversions:
    """Tests for type conversions in exporters."""

    def test_clickhouse_datetime_handling(self, mock_logger):
        """Test ClickHouse exporter handles datetime values."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_client.insert.return_value = True
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            now = datetime.now(timezone.utc)
            data = {
                'multi_table': True,
                'table1': {
                    'table': 'test_table',
                    'data': [["hash", now]],
                    'column_names': ["sha256", "timestamp"],
                    'column_type_names': ["String", "DateTime64(3, 'UTC')"]
                }
            }

            result = exporter.export(data)

            assert result is True

    def test_print_exporter_datetime_serialization(self, mock_logger, capsys):
        """Test PrintExporter handles datetime serialization."""
        from redb.extractors.database_exporters import PrintExporter

        exporter = PrintExporter(mock_logger, "test_index")
        now = datetime.now(timezone.utc)
        data = {"timestamp": now, "name": "test"}

        result = exporter.export(data)

        assert result is True
        captured = capsys.readouterr()
        assert "timestamp" in captured.out


# ============================================================================
# Connection Context Manager Tests
# ============================================================================

class TestClickHouseConnectionManager:
    """Tests for ClickHouse connection context manager."""

    def test_clickhouse_connection_context(self, mock_logger):
        """Test clickhouse_connection context manager."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            with exporter.clickhouse_connection() as client:
                assert client is mock_client

            # Client should be closed after context exits
            mock_client.close.assert_called()

    def test_clickhouse_connection_close_on_error(self, mock_logger):
        """Test client is closed even if operation fails."""
        with patch('redb.settings.create_clickhouse_client') as mock_create:
            mock_client = Mock()
            mock_create.return_value = mock_client

            from redb.extractors.database_exporters import ClickHouseExporter

            exporter = ClickHouseExporter(mock_logger, "test_index")

            try:
                with exporter.clickhouse_connection() as client:
                    raise ValueError("Test error")
            except ValueError:
                pass

            # Client should still be closed
            mock_client.close.assert_called()