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updating filepattern and vaex package
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,92 +1,91 @@ | ||
| # """Test Command line Tool.""" | ||
| # from typer.testing import CliRunner | ||
| # from polus.plugins.clustering.feature_subsetting.__main__ import app | ||
| # import shutil | ||
| # from pathlib import Path | ||
| """Test Command line Tool.""" | ||
| from typer.testing import CliRunner | ||
| from polus.plugins.clustering.feature_subsetting.__main__ import app | ||
| import shutil | ||
| from pathlib import Path | ||
|
|
||
|
|
||
| # def test_cli(generate_synthetic_data: tuple[Path, Path, Path, str]) -> None: | ||
| # """Test the command line.""" | ||
| # inp_dir, tabular_dir, out_dir, _ = generate_synthetic_data | ||
| # file_pattern='x{x+}_y{y+}_p{p+}_c{c+}.ome.tif' | ||
| # image_feature="intensity_image" | ||
| # tabular_feature = "MEAN" | ||
| # padding=0 | ||
| # group_var="p,c" | ||
| def test_cli(generate_synthetic_data: tuple[Path, Path, Path, str]) -> None: | ||
| """Test the command line.""" | ||
| inp_dir, tabular_dir, out_dir, _ = generate_synthetic_data | ||
| file_pattern = "x{x+}_y{y+}_p{p+}_c{c+}.ome.tif" | ||
| image_feature = "intensity_image" | ||
| tabular_feature = "MEAN" | ||
| padding = 0 | ||
| group_var = "p,c" | ||
|
|
||
| runner = CliRunner() | ||
| result = runner.invoke( | ||
| app, | ||
| [ | ||
| "--inpDir", | ||
| inp_dir, | ||
| "--tabularDir", | ||
| tabular_dir, | ||
| "--filePattern", | ||
| file_pattern, | ||
| "--imageFeature", | ||
| image_feature, | ||
| "--tabularFeature", | ||
| tabular_feature, | ||
| "--padding", | ||
| padding, | ||
| "--groupVar", | ||
| group_var, | ||
| "--percentile", | ||
| 0.8, | ||
| "--removeDirection", | ||
| "Below", | ||
| "--writeOutput", | ||
| "--outDir", | ||
| out_dir, | ||
| ], | ||
| ) | ||
|
|
||
| # runner = CliRunner() | ||
| # result = runner.invoke( | ||
| # app, | ||
| # [ | ||
| # "--inpDir", | ||
| # inp_dir, | ||
| # "--tabularDir", | ||
| # tabular_dir, | ||
| # "--filePattern", | ||
| # file_pattern, | ||
| # "--imageFeature", | ||
| # image_feature, | ||
| # "--tabularFeature", | ||
| # tabular_feature, | ||
| # "--padding", | ||
| # padding, | ||
| # "--groupVar", | ||
| # group_var, | ||
| # "--percentile", | ||
| # 0.8, | ||
| # "--removeDirection", | ||
| # "Below", | ||
| # "--writeOutput", | ||
| # "--outDir", | ||
| # out_dir, | ||
| # ], | ||
| # ) | ||
| assert result.exit_code == 0 | ||
| shutil.rmtree(inp_dir) | ||
| shutil.rmtree(out_dir) | ||
| shutil.rmtree(tabular_dir) | ||
|
|
||
| # assert result.exit_code == 0 | ||
| # shutil.rmtree(inp_dir) | ||
| # shutil.rmtree(out_dir) | ||
| # shutil.rmtree(tabular_dir) | ||
|
|
||
| def test_short_cli(generate_synthetic_data: tuple[Path, Path, Path, str]) -> None: | ||
| """Test short cli command line.""" | ||
| inp_dir, tabular_dir, out_dir, _ = generate_synthetic_data | ||
| file_pattern = "x{x+}_y{y+}_p{p+}_c{c+}.ome.tif" | ||
| image_feature = "intensity_image" | ||
| tabular_feature = "MEAN" | ||
| padding = 0 | ||
| group_var = "p,c" | ||
|
|
||
| # def test_short_cli(generate_synthetic_data: tuple[Path, Path, Path, str]) -> None: | ||
| # """Test short cli command line.""" | ||
| # inp_dir, tabular_dir, out_dir, _ = generate_synthetic_data | ||
| # file_pattern='x{x+}_y{y+}_p{p+}_c{c+}.ome.tif' | ||
| # image_feature="intensity_image" | ||
| # tabular_feature = "MEAN" | ||
| # padding=0 | ||
| # group_var="p,c" | ||
| runner = CliRunner() | ||
| result = runner.invoke( | ||
| app, | ||
| [ | ||
| "-i", | ||
| inp_dir, | ||
| "-t", | ||
| tabular_dir, | ||
| "-f", | ||
| file_pattern, | ||
| "-if", | ||
| image_feature, | ||
| "-tf", | ||
| tabular_feature, | ||
| "-p", | ||
| padding, | ||
| "-g", | ||
| group_var, | ||
| "-pc", | ||
| 0.8, | ||
| "-r", | ||
| "Below", | ||
| "-w", | ||
| "-o", | ||
| out_dir, | ||
| ], | ||
| ) | ||
|
|
||
| # runner = CliRunner() | ||
| # result = runner.invoke( | ||
| # app, | ||
| # [ | ||
| # "-i", | ||
| # inp_dir, | ||
| # "-t", | ||
| # tabular_dir, | ||
| # "-f", | ||
| # file_pattern, | ||
| # "-if", | ||
| # image_feature, | ||
| # "-tf", | ||
| # tabular_feature, | ||
| # "-p", | ||
| # padding, | ||
| # "-g", | ||
| # group_var, | ||
| # "-pc", | ||
| # 0.8, | ||
| # "-r", | ||
| # "Below", | ||
| # "-w", | ||
| # "-o", | ||
| # out_dir, | ||
| # ], | ||
| # ) | ||
|
|
||
| # assert result.exit_code == 0 | ||
| # shutil.rmtree(inp_dir) | ||
| # shutil.rmtree(out_dir) | ||
| # shutil.rmtree(tabular_dir) | ||
| assert result.exit_code == 0 | ||
| shutil.rmtree(inp_dir) | ||
| shutil.rmtree(out_dir) | ||
| shutil.rmtree(tabular_dir) |