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(TESTS)[Multi File]: Add unit tests for multi-format spectrum parsing
Browse files- Created comprehensive tests for spectrum parsing from TXT, CSV, and JSON file formats.
- Validates correct extraction of wavenumber and intensity values from various data layouts.
- Covers error handling for malformed files, verifies format detection logic, and ensures compatibility with new multi-format upload pipeline.
- Protects against regression and parsing failures as input support expands.
- tests/test_multi_format.py +218 -0
tests/test_multi_format.py
ADDED
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"""Tests for multi-format file parsing functionality."""
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import pytest
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import numpy as np
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from utils.multifile import (
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parse_spectrum_data,
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detect_file_format,
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parse_json_spectrum,
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parse_csv_spectrum,
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parse_txt_spectrum,
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)
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def test_detect_file_format():
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"""Test automatic file format detection."""
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# JSON detection
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json_content = '{"wavenumbers": [1, 2, 3], "intensities": [0.1, 0.2, 0.3]}'
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assert detect_file_format("test.json", json_content) == "json"
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# CSV detection
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csv_content = "wavenumber,intensity\n1000,0.5\n1001,0.6"
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assert detect_file_format("test.csv", csv_content) == "csv"
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# TXT detection (default)
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txt_content = "1000 0.5\n1001 0.6"
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assert detect_file_format("test.txt", txt_content) == "txt"
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def test_parse_json_spectrum():
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"""Test JSON spectrum parsing."""
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# Test object format
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json_content = '{"wavenumbers": [1000, 1001, 1002], "intensities": [0.1, 0.2, 0.3]}'
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x, y = parse_json_spectrum(json_content)
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expected_x = np.array([1000, 1001, 1002])
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expected_y = np.array([0.1, 0.2, 0.3])
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np.testing.assert_array_equal(x, expected_x)
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np.testing.assert_array_equal(y, expected_y)
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# Test alternative key names
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json_content_alt = '{"x": [1000, 1001, 1002], "y": [0.1, 0.2, 0.3]}'
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x_alt, y_alt = parse_json_spectrum(json_content_alt)
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np.testing.assert_array_equal(x_alt, expected_x)
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np.testing.assert_array_equal(y_alt, expected_y)
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# Test array of objects format
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json_array = """[
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{"wavenumber": 1000, "intensity": 0.1},
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{"wavenumber": 1001, "intensity": 0.2},
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{"wavenumber": 1002, "intensity": 0.3}
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]"""
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x_arr, y_arr = parse_json_spectrum(json_array)
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np.testing.assert_array_equal(x_arr, expected_x)
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np.testing.assert_array_equal(y_arr, expected_y)
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def test_parse_csv_spectrum():
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"""Test CSV spectrum parsing."""
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# Test with headers
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csv_with_headers = """wavenumber,intensity
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1000,0.1
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1001,0.2
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1002,0.3
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1003,0.4
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1004,0.5
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1005,0.6
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1006,0.7
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1007,0.8
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1008,0.9
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1009,1.0
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1010,1.1
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1011,1.2"""
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x, y = parse_csv_spectrum(csv_with_headers)
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expected_x = np.array(
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[1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011]
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)
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expected_y = np.array([0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2])
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np.testing.assert_array_equal(x, expected_x)
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np.testing.assert_array_equal(y, expected_y)
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# Test without headers
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csv_no_headers = """1000,0.1
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1001,0.2
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1002,0.3
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1003,0.4
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1004,0.5
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1005,0.6
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1006,0.7
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1007,0.8
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1008,0.9
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1009,1.0
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1010,1.1
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1011,1.2"""
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x_no_h, y_no_h = parse_csv_spectrum(csv_no_headers)
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np.testing.assert_array_equal(x_no_h, expected_x)
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np.testing.assert_array_equal(y_no_h, expected_y)
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# Test semicolon delimiter
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csv_semicolon = """1000;0.1
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1001;0.2
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1002;0.3
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1003;0.4
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1004;0.5
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1005;0.6
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1006;0.7
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1007;0.8
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1008;0.9
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1009;1.0
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1010;1.1
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1011;1.2"""
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x_semi, y_semi = parse_csv_spectrum(csv_semicolon)
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np.testing.assert_array_equal(x_semi, expected_x)
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np.testing.assert_array_equal(y_semi, expected_y)
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def test_parse_txt_spectrum():
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"""Test TXT spectrum parsing."""
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txt_content = """# Comment line
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1000 0.1
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1001 0.2
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1002 0.3
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1003 0.4
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1004 0.5
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1005 0.6
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1006 0.7
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1007 0.8
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1008 0.9
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1009 1.0
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1010 1.1
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1011 1.2"""
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x, y = parse_txt_spectrum(txt_content)
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expected_x = np.array(
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[1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011]
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)
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expected_y = np.array([0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2])
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np.testing.assert_array_equal(x, expected_x)
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np.testing.assert_array_equal(y, expected_y)
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# Test comma-separated
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txt_comma = """1000,0.1
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1001,0.2
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1002,0.3
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1003,0.4
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1004,0.5
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1005,0.6
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1006,0.7
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1007,0.8
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1008,0.9
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1009,1.0
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1010,1.1
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1011,1.2"""
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x_comma, y_comma = parse_txt_spectrum(txt_comma)
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np.testing.assert_array_equal(x_comma, expected_x)
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np.testing.assert_array_equal(y_comma, expected_y)
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def test_parse_spectrum_data_integration():
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"""Test integrated spectrum data parsing with format detection."""
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# Test automatic format detection and parsing
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test_cases = [
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(
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'{"wavenumbers": [1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011], "intensities": [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2]}',
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"test.json",
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),
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(
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"wavenumber,intensity\n1000,0.1\n1001,0.2\n1002,0.3\n1003,0.4\n1004,0.5\n1005,0.6\n1006,0.7\n1007,0.8\n1008,0.9\n1009,1.0\n1010,1.1\n1011,1.2",
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"test.csv",
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),
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(
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"1000 0.1\n1001 0.2\n1002 0.3\n1003 0.4\n1004 0.5\n1005 0.6\n1006 0.7\n1007 0.8\n1008 0.9\n1009 1.0\n1010 1.1\n1011 1.2",
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"test.txt",
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),
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]
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for content, filename in test_cases:
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x, y = parse_spectrum_data(content, filename)
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assert len(x) >= 10
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assert len(y) >= 10
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assert len(x) == len(y)
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def test_insufficient_data_points():
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"""Test handling of insufficient data points."""
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# Test with too few points
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insufficient_data = "1000 0.1\n1001 0.2" # Only 2 points, need at least 10
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with pytest.raises(ValueError, match="Insufficient data points"):
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parse_txt_spectrum(insufficient_data, "test.txt")
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def test_invalid_json():
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"""Test handling of invalid JSON."""
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invalid_json = (
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'{"wavenumbers": [1000, 1001], "intensities": [0.1}' # Missing closing bracket
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)
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with pytest.raises(ValueError, match="Invalid JSON format"):
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parse_json_spectrum(invalid_json)
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def test_empty_file():
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"""Test handling of empty files."""
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empty_content = ""
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with pytest.raises(ValueError, match="No data lines found"):
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parse_txt_spectrum(empty_content, "empty.txt")
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if __name__ == "__main__":
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pytest.main([__file__])
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