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ChrisChilders-USDAChrisChilders-USDA
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test: expand low-risk coverage
1 parent 2f12729 commit 18bc4d3

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Lines changed: 1048 additions & 1 deletion

‎.github/workflows/build.yml‎

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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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run: |
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coverage report -m
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coverage report --fail-under=22 -m
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coveralls --service=github
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codecov
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‎tests/unit/test_gff3_QC_cli.py‎

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import io
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import unittest
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from argparse import Namespace
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from unittest import mock
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from gff3tool.bin import gff3_QC
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class TestGff3QcCli(unittest.TestCase):
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def test_script_main_exits_when_gff_missing_and_no_stdin(self):
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args = Namespace(
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gff=None,
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fasta='ref.fa',
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noncanonical_gene=False,
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initial_phase=False,
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allowed_num_of_n=0,
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check_n_feature_types=['CDS'],
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output=None,
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statistic=None,
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)
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stdin = mock.Mock()
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stdin.isatty.return_value = True
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch('sys.stdin', stdin), \
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mock.patch('argparse.ArgumentParser.print_help') as print_help, \
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self.assertRaises(SystemExit) as exc:
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gff3_QC.script_main()
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print_help.assert_called_once()
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self.assertEqual(exc.exception.code, 1)
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def test_script_main_exits_when_fasta_missing_and_no_stdin(self):
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args = Namespace(
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gff='input.gff3',
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fasta=None,
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noncanonical_gene=False,
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initial_phase=False,
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allowed_num_of_n=0,
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check_n_feature_types=['CDS'],
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output=None,
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statistic=None,
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)
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stdin = mock.Mock()
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stdin.isatty.return_value = True
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch('sys.stdin', stdin), \
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mock.patch('argparse.ArgumentParser.print_help') as print_help, \
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self.assertRaises(SystemExit) as exc:
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gff3_QC.script_main()
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print_help.assert_called_once()
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self.assertEqual(exc.exception.code, 1)
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def test_script_main_noncanonical_skips_phase_and_writes_default_reports(self):
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args = Namespace(
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gff='input.gff3',
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fasta='ref.fa',
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noncanonical_gene=True,
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initial_phase=False,
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allowed_num_of_n=0,
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check_n_feature_types=['CDS'],
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output=None,
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statistic=None,
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)
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gff3 = mock.Mock()
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gff3.check_parent_boundary.return_value = True
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extract_errors = [{'line_num': ['Line 2'], 'eCode': 'Emr0001', 'error_level': 'Error', 'eTag': 'internal'}]
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intra_errors = [{'line_num': ['Line 3'], 'eCode': 'Ema0006', 'error_level': 'Warning', 'eTag': 'intra'}]
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inter_errors = [{'line_num': ['Line 4'], 'eCode': 'Emr0002', 'error_level': 'Error', 'eTag': 'inter'}]
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single_errors = [{'line_num': ['Line 5'], 'eCode': 'Esf0003', 'error_level': 'Error', 'eTag': 'single'}]
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report_handle = io.StringIO()
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stat_handle = io.StringIO()
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def open_side_effect(path, mode='r', *args, **kwargs):
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if path == 'report.txt':
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return report_handle
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if path == 'statistic.txt':
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return stat_handle
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raise AssertionError(path)
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch.object(gff3_QC, 'Gff3', autospec=True, return_value=gff3), \
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mock.patch.object(gff3_QC.function4gff, 'FIX_MISSING_ATTR', autospec=True) as fix_missing, \
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mock.patch.object(gff3_QC.function4gff, 'extract_internal_detected_errors', autospec=True, return_value=extract_errors), \
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mock.patch.object(gff3_QC.intra_model, 'main', autospec=True, return_value=intra_errors), \
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mock.patch.object(gff3_QC.inter_model, 'main', autospec=True, return_value=inter_errors), \
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mock.patch.object(gff3_QC.single_feature, 'main', autospec=True, return_value=single_errors), \
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mock.patch('builtins.open', side_effect=open_side_effect):
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gff3_QC.script_main()
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gff3.check_phase.assert_not_called()
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gff3.check_reference.assert_called_once_with(
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fasta_external='ref.fa',
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check_n=True,
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allowed_num_of_n=0,
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feature_types=['CDS'],
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)
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fix_missing.assert_called_once_with(gff3, logger=mock.ANY)
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self.assertIn('Line_num\tError_code\tError_level\tError_tag', report_handle.getvalue())
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self.assertIn('Emr0001', report_handle.getvalue())
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self.assertIn('Esf0003', report_handle.getvalue())
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self.assertIn('Error_code\tNumber_of_problematic_models\tError_level\tError_tag', stat_handle.getvalue())
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self.assertIn('Esf0003', stat_handle.getvalue())
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def test_script_main_runs_phase_check_for_canonical_models(self):
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args = Namespace(
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gff='input.gff3',
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fasta='ref.fa',
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noncanonical_gene=False,
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initial_phase=True,
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allowed_num_of_n=0,
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check_n_feature_types=['CDS'],
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output='qc.txt',
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statistic='stats.txt',
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)
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gff3 = mock.Mock()
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gff3.check_parent_boundary.return_value = True
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch.object(gff3_QC, 'Gff3', autospec=True, return_value=gff3), \
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mock.patch.object(gff3_QC.function4gff, 'FIX_MISSING_ATTR', autospec=True), \
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mock.patch.object(gff3_QC.function4gff, 'extract_internal_detected_errors', autospec=True, return_value=[]), \
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mock.patch.object(gff3_QC.intra_model, 'main', autospec=True, return_value=[]), \
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mock.patch.object(gff3_QC.inter_model, 'main', autospec=True, return_value=[]), \
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mock.patch.object(gff3_QC.single_feature, 'main', autospec=True, return_value=[]), \
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mock.patch('builtins.open', side_effect=[io.StringIO(), io.StringIO()]):
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gff3_QC.script_main()
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gff3.check_phase.assert_called_once_with(True)
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def test_script_main_exits_early_when_parent_boundary_fails(self):
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args = Namespace(
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gff='input.gff3',
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fasta='ref.fa',
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noncanonical_gene=False,
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initial_phase=False,
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allowed_num_of_n=0,
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check_n_feature_types=['CDS'],
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output=None,
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statistic=None,
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)
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gff3 = mock.Mock()
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gff3.check_parent_boundary.return_value = False
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch.object(gff3_QC, 'Gff3', autospec=True, return_value=gff3), \
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self.assertRaises(SystemExit):
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gff3_QC.script_main()
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gff3.check_unresolved_parents.assert_not_called()
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if __name__ == '__main__':
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unittest.main()

‎tests/unit/test_gff3_fix_cli.py‎

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import io
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import unittest
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from argparse import Namespace
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from unittest import mock
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from gff3tool.bin import gff3_fix
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class TestGff3FixCli(unittest.TestCase):
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def test_script_main_exits_when_qc_report_missing(self):
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args = Namespace(qc_report=None, gff='input.gff3', output_gff='out.gff3')
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch('argparse.ArgumentParser.print_help') as print_help, \
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self.assertRaises(SystemExit):
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gff3_fix.script_main()
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print_help.assert_called_once()
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def test_script_main_exits_when_gff_missing(self):
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args = Namespace(qc_report='report.txt', gff=None, output_gff='out.gff3')
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch('argparse.ArgumentParser.print_help') as print_help, \
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self.assertRaises(SystemExit):
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gff3_fix.script_main()
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print_help.assert_called_once()
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def test_script_main_parses_qc_report_and_calls_fix_main(self):
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args = Namespace(qc_report='report.txt', gff='input.gff3', output_gff='out.gff3')
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report_content = (
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'Line_num\tError_code\tError_level\tError_tag\n'
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"['Line 2', 'Line 4']\tEmr0001\tError\ttag1\n"
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"['Line 3']\tEsf0003\tWarning\ttag2\n"
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'malformed line\n'
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)
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gff3 = object()
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def open_side_effect(path, mode='r', *args, **kwargs):
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if path == 'report.txt':
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return io.StringIO(report_content)
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raise AssertionError(path)
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch('builtins.open', side_effect=open_side_effect), \
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mock.patch.object(gff3_fix, 'Gff3', autospec=True, return_value=gff3), \
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mock.patch.object(gff3_fix.gff3_fix.fix, 'main', autospec=True) as fix_main:
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gff3_fix.script_main()
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fix_main.assert_called_once_with(
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gff3=gff3,
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output_gff='out.gff3',
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error_dict={'Emr0001': [[2, 4]], 'Esf0003': [[3]]},
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line_num_dict={2: {'Emr0001': 'Error'}, 4: {'Emr0001': 'Error'}, 3: {'Esf0003': 'Warning'}},
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logger=mock.ANY,
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)
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def test_script_main_exits_when_gff_cannot_be_read(self):
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args = Namespace(qc_report='report.txt', gff='input.gff3', output_gff='out.gff3')
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with mock.patch('argparse.ArgumentParser.parse_args', return_value=args), \
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mock.patch('builtins.open', return_value=io.StringIO('header\n')), \
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mock.patch.object(gff3_fix, 'Gff3', autospec=True, side_effect=OSError), \
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self.assertRaises(SystemExit) as exc:
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gff3_fix.script_main()
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self.assertEqual(exc.exception.code, 1)
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if __name__ == '__main__':
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unittest.main()

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