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Refactor tests to be more independent (#165)
* converting tests to use pathlib.Path instead of os converting stream tests to use CliRunner with input=fh * removed slow fixtures, added intermediate files for filter tweaked some test code to look more consistent * use isolated_filesystem to not keep test output files * created a new fixture for test_correct and made the piped version of the test work
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,54 +1,34 @@ | ||
| import pytest | ||
| import os | ||
| import sys | ||
| import subprocess | ||
| import tempfile | ||
| import pathlib | ||
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| from click.testing import CliRunner | ||
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| from longbow.__main__ import main_entry as longbow | ||
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| from ..utils import cat_file_to_pipe | ||
| TEST_DATA_FOLDER = pathlib.Path(__file__).parent.parent / "test_data" | ||
| TEST_PARAMS = [ | ||
| TEST_DATA_FOLDER / "annotate" / "mas15v2_expected.bam", | ||
| TEST_DATA_FOLDER / "annotate" / "mas10v2_expected.bam", | ||
| ] | ||
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| TEST_DATA_FOLDER = path = os.path.abspath( | ||
| __file__ + os.path.sep + "../../" + os.path.sep + "test_data" | ||
| ) + os.path.sep | ||
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| @pytest.fixture(scope="module", params=[ | ||
| (TEST_DATA_FOLDER + "mas15_test_input.bam", "mas_15_sc_10x5p_single_none"), | ||
| (TEST_DATA_FOLDER + "mas10_test_input.bam", "mas_10_sc_10x5p_single_none"), | ||
| ]) | ||
| def annotated_bam_file_from_pipeline(request): | ||
| input_bam, model_name = request.param | ||
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| with tempfile.NamedTemporaryFile(delete=True) as annotate_bam: | ||
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| runner = CliRunner() | ||
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| result_annotate = runner.invoke(longbow, ["annotate", "-m", model_name, "-f", "-o", annotate_bam.name, input_bam]) | ||
| assert result_annotate.exit_code == 0 | ||
|
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| # Yield file here so that when we return, we get to clean up automatically | ||
| yield annotate_bam.name | ||
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| def test_demultiplex_from_file(tmpdir, annotated_bam_file_from_pipeline): | ||
| args = ["demultiplex", "-d", "YN", "-o", "demux", annotated_bam_file_from_pipeline] | ||
| @pytest.mark.parametrize("input_bam", TEST_PARAMS) | ||
| def test_demultiplex_from_file(tmpdir, input_bam): | ||
| args = ["demultiplex", "-d", "YN", "-o", "demux", str(input_bam)] | ||
|
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| runner = CliRunner() | ||
| result = runner.invoke(longbow, args) | ||
| with runner.isolated_filesystem(): | ||
| result = runner.invoke(longbow, args) | ||
|
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| assert result.exit_code == 0 | ||
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| @pytest.mark.skip(reason="this test is broken and I don't know why") | ||
| def test_demultiplex_from_pipe(tmpdir, annotated_bam_file_from_pipeline): | ||
| proc = subprocess.Popen( | ||
| [ sys.executable, "-m", "longbow", "demultiplex", "-d", "YN", "-o", "demux", annotated_bam_file_from_pipeline ], | ||
| stdin=subprocess.PIPE | ||
| ) | ||
| @pytest.mark.parametrize("input_bam", TEST_PARAMS) | ||
| def test_demultiplex_from_pipe(tmpdir, input_bam): | ||
| args = ["demultiplex", "-d", "YN", "-o" "demux"] | ||
|
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| cat_file_to_pipe(annotated_bam_file_from_pipeline, proc) | ||
| runner = CliRunner() | ||
| with runner.isolated_filesystem(), open(input_bam, "rb") as fh: | ||
| result = runner.invoke(longbow, args, input=fh) | ||
|
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| assert proc.returncode == 0 | ||
| assert result.exit_code == 0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,63 +1,37 @@ | ||
| import pytest | ||
| import os | ||
| import sys | ||
| import subprocess | ||
| import tempfile | ||
| import pathlib | ||
|
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| from click.testing import CliRunner | ||
|
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| from longbow.__main__ import main_entry as longbow | ||
|
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| from ..utils import cat_file_to_pipe | ||
|
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| TEST_DATA_FOLDER = path = os.path.abspath( | ||
| __file__ + os.path.sep + "../../" + os.path.sep + "test_data" | ||
| ) + os.path.sep | ||
| TEST_DATA_FOLDER = pathlib.Path(__file__).parent.parent / "test_data" | ||
| TEST_PARAMS = [ | ||
| TEST_DATA_FOLDER / "segment" / "mas_15_sc_10x5p_single_none.expected.bam", | ||
| TEST_DATA_FOLDER / "segment" / "mas_10_sc_10x5p_single_none.expected.bam", | ||
| ] | ||
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| @pytest.fixture(scope="module", params=[ | ||
| (TEST_DATA_FOLDER + "mas15_test_input.bam", "mas_15_sc_10x5p_single_none"), | ||
| (TEST_DATA_FOLDER + "mas10_test_input.bam", "mas_10_sc_10x5p_single_none"), | ||
| ]) | ||
| def segmented_bam_file_from_pipeline(request): | ||
| input_bam, model_name = request.param | ||
|
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| with tempfile.NamedTemporaryFile(delete=True) as annotate_bam, \ | ||
| tempfile.NamedTemporaryFile(delete=True) as filter_bam, \ | ||
| tempfile.NamedTemporaryFile(delete=True) as segment_bam: | ||
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| runner = CliRunner() | ||
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| result_annotate = runner.invoke(longbow, ["annotate", "-t", 1, "-m", model_name, "-f", "-o", annotate_bam.name, input_bam]) | ||
| assert result_annotate.exit_code == 0 | ||
|
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| result_filter = runner.invoke(longbow, ["filter", "-m", model_name, "-f", "-o", filter_bam.name, annotate_bam.name]) | ||
| assert result_filter.exit_code == 0 | ||
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| result_segment = runner.invoke(longbow, ["segment", "-t", 1, "-m", model_name, "-f", "-o", segment_bam.name, filter_bam.name]) | ||
| assert result_segment.exit_code == 0 | ||
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| # Yield file here so that when we return, we get to clean up automatically | ||
| yield segment_bam.name | ||
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| def test_extract_from_file(tmpdir, segmented_bam_file_from_pipeline): | ||
| @pytest.mark.parametrize("input_bam", TEST_PARAMS) | ||
| def test_extract_from_file(tmpdir, input_bam): | ||
| actual_file = tmpdir.join("extract_actual_out.bam") | ||
| args = ["extract", "-f", "-o", actual_file, segmented_bam_file_from_pipeline] | ||
| args = ["extract", "-f", "-o", actual_file, str(input_bam)] | ||
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| runner = CliRunner() | ||
| result = runner.invoke(longbow, args) | ||
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| assert result.exit_code == 0 | ||
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| def test_extract_from_pipe(tmpdir, segmented_bam_file_from_pipeline): | ||
| @pytest.mark.parametrize("input_bam", TEST_PARAMS) | ||
| def test_extract_from_pipe(tmpdir, input_bam): | ||
| actual_file = tmpdir.join("extract_actual_out.pipe.bam") | ||
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| args = ["extract", "-f", "-o", actual_file] | ||
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| runner = CliRunner() | ||
| with open(segmented_bam_file_from_pipeline, "rb") as fh: | ||
| with open(input_bam, "rb") as fh: | ||
| result = runner.invoke(longbow, args, input=fh) | ||
|
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| assert result.exit_code == 0 |
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