Added unit test, corrected formatting

Author: bengtl

tests/test_filepattern.py

@@ -5,36 +5,30 @@
 import test_generate_filepattern_data
 import test_filepattern_data as fp_data
 
+
 class TestFilePatternFunctions():
-    
+
     def test_get_regex(self):
-        
+        # Test with a pattern that includes a single variable
         pattern = 'img_{row:c}{col:dd}f{f:dd}d{channel:d}.tif'
-
-        regex_pattern = fp.get_regex(pattern)
-        
+        regex_pattern = fp.get_regex(pattern)   
         assert regex_pattern == 'img_([a-zA-Z])([0-9][0-9])f([0-9][0-9])d([0-9]).tif'
-    
-    def test_get_variables(self):
 
+    def test_get_variables(self):
+        # Test with a pattern that includes a single variable
         pattern = 'img_r{r:ddd}_c{c:ddd}.tif'
-
         variables = fp.get_variables(pattern)
-
         assert (variables == ['r', 'c'] or variables == ['c', 'r'])
 
+
 class TestArrayPattern():
 
     test_generate_filepattern_data.generate_text_data()
-
     root_directory = os.path.dirname(os.path.realpath(__file__))
-
     filepath = root_directory + '/test_data/data100.txt'
-
     old_pattern = 'img_r{rrr}_c{ccc}.tif'
-
-    patterns = ['img_r{r:ddd}_c{c:ddd}.tif', 'img_r{r:d+}_c{c:d+}.tif', old_pattern]
-
+    patterns = ['img_r{r:ddd}_c{c:ddd}.tif', 'img_r{r:d+}_c{c:d+}.tif',
+                old_pattern]
     MAX_NUM = 9
 
     with open(filepath, 'r') as file:
@@ -273,18 +267,14 @@ def test_no_sorting(self):
         for i in range(len(data)):
             assert str(results[i][1][0]) == data[i]
 
+
 class TestFilePattern():
 
     root_directory = os.path.dirname(os.path.realpath(__file__))
-
     path = root_directory + '/test_data/data100'
-
     sorted_path = root_directory + '/test_data/sorted_data'
-
     old_pattern = 'img_r{rrr}_c{ccc}.tif'
-
     patterns = ['img_r00{r:d}_c{c:ddd}.tif', 'img_r{r:d+}_c{c:d+}.tif', old_pattern]
-
     MAX_NUM = 9
 
     test_generate_filepattern_data.generate_data()
@@ -293,6 +283,7 @@ class TestFilePattern():
     test_generate_filepattern_data.generate_bracket_data()
     test_generate_filepattern_data.generate_channel_data_sc()
     test_generate_filepattern_data.generate_channel_data_spaces()
+    test_generate_filepattern_data.generate_recursive_no_capture_data() # Added new generator call
 
     def test_file_pattern(self):
 
@@ -501,11 +492,11 @@ def test_group_by_all_pydantic(self):
                 assert fp_data.test_fp[i][0]["r"] == result[i].r
                 assert fp_data.test_fp[i][0]["c"] == result[i].c
                 assert os.path.basename(fp_data.test_fp[i][1][0]) == os.path.basename(result[i].path[0])
-                
+
     def test_named_group_direcotry(self):
-        
+
         path = self.root_directory + '/test_data/recursive_data'
-        
+
         path += '/(?P<dir>[a-zA-Z]+)/img_r{r:ddd}_c{c:ddd}.tif'
 
         for pattern in self.patterns:
@@ -532,13 +523,11 @@ def test_named_group_direcotry(self):
                 basename = os.path.basename(mapping[1][0])
                 for filepath in mapping[1]:
                     assert basename == os.path.basename(filepath)
-    
+
     def test_recursive_directory_fp(self):
-        
+
         path = self.root_directory + '/test_data/recursive_data'
-   
         filepattern = '/{directory:c+}/img_r{r:ddd}_c{c:ddd}.tif'
-        
         files = fp.FilePattern(path, filepattern, recursive=True)
 
         result = []
@@ -556,13 +545,11 @@ def test_recursive_directory_fp(self):
             assert fp_data.test_recursive_directory_fp[i][0]["c"] == result[i][0]["c"]
             assert fp_data.test_recursive_directory_fp[i][0]["directory"] == result[i][0]["directory"]
             assert str(os.path.basename(fp_data.test_recursive_directory_fp[i][1][0])) == os.path.basename(result[i][1][0])
-            
+
     def test_recursive_directory_regex_fp(self):
-        
+        # Test that recursive matching with a regex pattern
         path = self.root_directory + '/test_data/recursive_data'
-        
         filepattern = '/(?P<directory>[a-zA-Z]+)/img_r{r:ddd}_c{c:ddd}.tif'
-        
         files = fp.FilePattern(path, filepattern, recursive=True)
 
         result = []
@@ -580,13 +567,11 @@ def test_recursive_directory_regex_fp(self):
             assert fp_data.test_recursive_directory_fp[i][0]["c"] == result[i][0]["c"]
             assert fp_data.test_recursive_directory_fp[i][0]["directory"] == result[i][0]["directory"]
             assert str(os.path.basename(fp_data.test_recursive_directory_fp[i][1][0])) == os.path.basename(result[i][1][0])
-            
+
     def test_recursive_directory_regex_special_character_fp(self):
-        
+        # Test that recursive matching with a regex pattern
         path = self.root_directory + '/test_data/recursive_data_sc'
-        
         filepattern = '/(?P<directory>.*)/img_r{r:ddd}_c{c:ddd}.tif'
-        
         files = fp.FilePattern(path, filepattern, recursive=True)
 
         result = []
@@ -606,11 +591,9 @@ def test_recursive_directory_regex_special_character_fp(self):
             assert str(os.path.basename(fp_data.test_recursive_directory_fp[i][1][0])) == os.path.basename(result[i][1][0])
 
     def test_recursive_directory_spaces_fp(self):
-        
+
         path = self.root_directory + '/test_data/recursive_data_spaces/'
-        
         filepattern = 'img_r{r:ddd}_c{c:ddd}.tif'
-        
         files = fp.FilePattern(path, filepattern, recursive=True)
 
         result = []
@@ -631,11 +614,10 @@ def test_recursive_directory_spaces_fp(self):
             assert str(os.path.basename(fp_data.test_recursive_space[i][1][0])) == os.path.basename(result[i][1][0])
 
     def test_recursive_multi_directory_regex_fp(self):
-        
+        # Test that recursive matching with a regex pattern
+
         path = self.root_directory + '/test_data'
-        
         filepattern = '/.*/{directory:c+}/img_r{r:ddd}_c{c:ddd}.tif'
-        
         files = fp.FilePattern(path, filepattern, recursive=True)
 
         result = []
@@ -654,6 +636,22 @@ def test_recursive_multi_directory_regex_fp(self):
             assert fp_data.test_recursive_directory_fp[i][0]["directory"] == result[i][0]["directory"]
             assert str(os.path.basename(fp_data.test_recursive_directory_fp[i][1][0])) == os.path.basename(result[i][1][0])
 
+    def test_recursive_no_capture_group_returns_all_files(self):
+        # Test that recursive matching with a non-capturing pattern
+        # returns all matching files across subdirectories.
+        path_to_test_dir = os.path.join(self.root_directory, 'test_data', 'recursive_no_capture_data')
+        pattern_no_capture = '.*.tmp'  # Match all .tmp files
+        expected_file_count = 12  # 5 in subdir1 + 7 in subdir2
+
+        files_fp = fp.FilePattern(path_to_test_dir, pattern_no_capture, recursive=True)
+
+        # Using len() as it seems to be the standard way to get count in existing tests
+        actual_file_count = len(files_fp)
+
+        assert actual_file_count == expected_file_count, \
+            f"Expected {expected_file_count} '.tmp' files, but found {actual_file_count} " \
+            f"using recursive non-capturing pattern in {path_to_test_dir}."
+
     def test_file_pattern_iter(self):
 
         for pattern in self.patterns:
@@ -674,9 +672,8 @@ def test_file_pattern_iter(self):
                 assert fp_data.test_fp[i][0]["c"] == result[i][0]["c"]
                 assert os.path.basename(fp_data.test_fp[i][1][0]) == os.path.basename(result[i][1][0])
 
-    # test that numeric only, double digit numbers are sorted properly
     def test_file_pattern_sorting(self):
-        
+        # test that numeric only, double digit numbers are sorted properly   
         sorted_pattern = '{index:d+}.tif'
         files = fp.FilePattern(self.sorted_path, sorted_pattern)
 
@@ -687,6 +684,7 @@ def test_file_pattern_sorting(self):
         assert sorted(indices) == indices
 
     def test_file_pattern_brackets(self):
+        # test that numeric only, double digit numbers are sorted properly
 
         bracket_path = self.root_directory + '/test_data/bracket_data/'
 
@@ -703,7 +701,8 @@ def test_file_pattern_brackets(self):
 
         for i in range(len(result)):
             result[i][0]['c'] == i
-            os.path.basename(result[i][1][0]) == f'x(0-31)_y(01-48)_c{i}.ome.tif'
+            os.path.basename(
+                result[i][1][0]) == f'x(0-31)_y(01-48)_c{i}.ome.tif'
 
 
 # Todo: These tests need new data to be added after replacing the old version of filepattern.

tests/test_generate_filepattern_data.py

@@ -2,10 +2,12 @@
 import math
 import os
 
+
 directory = 'test_data'
 root_directory = os.path.dirname(os.path.realpath(__file__))
 path = os.path.join(root_directory, directory)
 
+
 def generate_data():
     MAX = 100
     length = 0
@@ -100,6 +102,7 @@ def generate_channel_data():
 
     print("Files generated.")
 
+
 def generate_channel_data_sc():
 
     MAX = 3
@@ -153,6 +156,7 @@ def generate_channel_data_sc():
 
     print("Files generated.")
 
+
 def generate_channel_data_spaces():
 
     MAX = 3
@@ -206,6 +210,7 @@ def generate_channel_data_spaces():
 
     print("Files generated.")
 
+
 def generate_sorted_data():
     MAX = 30
     length = 0
@@ -235,6 +240,7 @@ def generate_sorted_data():
 
     print(str(length) + " files generated.")
 
+
 def generate_text_data():
     output_file = path + '/data100.txt'
     print(output_file)
@@ -244,6 +250,7 @@ def generate_text_data():
                 filename = f"img_r{r:03}_c{c:03}.tif"
                 file.write(filename + "\n")
 
+
 def generate_bracket_data():
     directory = 'test_data'
     root_directory = os.path.dirname(os.path.realpath(__file__))
@@ -271,14 +278,58 @@ def generate_bracket_data():
         f2.close()
 
 
+def generate_recursive_no_capture_data():
+    base_data_dir_name = 'recursive_no_capture_data'
+    subdir1_name = 'subdir1'
+    subdir2_name = 'subdir2'
+    num_files_subdir1 = 5
+    num_files_subdir2 = 7
+    file_extension = '.tmp'
+
+    recursive_base_path = os.path.join(path, base_data_dir_name)
+    subdir1_path = os.path.join(recursive_base_path, subdir1_name)
+    subdir2_path = os.path.join(recursive_base_path, subdir2_name)
+
+    try:
+        os.makedirs(recursive_base_path, exist_ok=True)
+        os.makedirs(subdir1_path, exist_ok=True)
+        os.makedirs(subdir2_path, exist_ok=True)
+        print(f"Created directory structure at {recursive_base_path}")
+    except OSError as e:
+        print(f"Error creating directories: {e}")
+        return  # Stop if directories can't be created
+
+    # Create files in subdir1
+    for i in range(num_files_subdir1):
+        file_name = f"file{i+1}{file_extension}"
+        try:
+            with open(os.path.join(subdir1_path, file_name), 'w'):
+                pass  # Create empty file
+        except IOError as e:
+            print(f"Error creating file {os.path.join(subdir1_path, file_name)}: {e}")
+
+    # Create files in subdir2
+    for i in range(num_files_subdir2):
+        file_name = f"item{chr(ord('A')+i)}{file_extension}"  # e.g., itemA.tmp, itemB.tmp
+        try:
+            with open(os.path.join(subdir2_path, file_name), 'w'):
+                pass  # Create empty file
+        except IOError as e:
+            print(f"Error creating file {os.path.join(subdir2_path, file_name)}: {e}")
+
+    total_files = num_files_subdir1 + num_files_subdir2
+    print(f"{total_files} files generated in {recursive_base_path}")
+
+
 if __name__ == '__main__':
     generate_data()
     generate_channel_data()
     generate_sorted_data()
     generate_text_data()
     generate_bracket_data()
-    generate_channel_data_sc
-    generate_channel_data_spaces
+    generate_channel_data_sc()  # Corrected call
+    generate_channel_data_spaces()  # Corrected call
+    generate_recursive_no_capture_data()  # Added new generator call
 
 
 MAX = 3