From d8c6e4ef88871cbd72c7d5c8006b6791b38e8f8d Mon Sep 17 00:00:00 2001
From: hamshkhawar <hamdahshafqat@hotmail.com>
Date: Thu, 25 Jan 2024 11:22:24 -0600
Subject: [PATCH] updating filepattern and vaex package

---
 .../tests/test_cli.py                         | 167 +++++++++---------
 1 file changed, 83 insertions(+), 84 deletions(-)

diff --git a/clustering/feature-subsetting-plugin/tests/test_cli.py b/clustering/feature-subsetting-plugin/tests/test_cli.py
index 4ea128cd0..b41d795c8 100644
--- a/clustering/feature-subsetting-plugin/tests/test_cli.py
+++ b/clustering/feature-subsetting-plugin/tests/test_cli.py
@@ -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)