final improvments on tests

Author: yibeichan

reproschema/redcap2reproschema.py

@@ -16,6 +16,7 @@ def clean_header(header):
         cleaned_header[cleaned_key] = v
     return cleaned_header
 
+
 def normalize_condition(condition_str):
     # Regular expressions for various pattern replacements
     re_parentheses = re.compile(r"\(([0-9]*)\)")
@@ -42,6 +43,7 @@ def normalize_condition(condition_str):
 
     return condition_str.strip() 
 
+
 def process_visibility(data):
     condition = data.get("Branching Logic (Show field only if...)")
     if condition:
@@ -94,7 +96,6 @@ def parse_field_type_and_value(field, input_type_map):
     return input_type, value_type
 
 
-
 def process_choices(field_type, choices_str):
     if field_type not in ["radio", "dropdown"]:  # Handle only radio and dropdown types
         return None

reproschema/reproschema2redcap.py

@@ -164,7 +164,6 @@ def get_csv_data(dir_path):
                             if item_json:
                                 row_data = process_item(item_json, activity_path.stem)
                                 csv_data.append(row_data)
-                                print(f"Processed item {item_path}")
 
                 # Break after finding the first _schema file
                 break

reproschema/tests/test_redcap2reproschema.py

@@ -14,14 +14,12 @@
     os.path.dirname(__file__), "test_redcap2rs_data", YAML_FILE_NAME
 )
 
-def test_redcap2reproschema_success(tmpdir):
+def test_redcap2reproschema(tmpdir):
     runner = CliRunner()
 
-    # Define the paths to the CSV and YAML files in the temporary directory
     temp_csv_file = tmpdir.join(CSV_FILE_NAME)
     temp_yaml_file = tmpdir.join(YAML_FILE_NAME)
 
-    # Copy the test files to the temporary directory
     shutil.copy(CSV_TEST_FILE, str(temp_csv_file))  # Convert to string
     shutil.copy(YAML_TEST_FILE, str(temp_yaml_file))  # Convert to string
 
@@ -32,12 +30,9 @@ def test_redcap2reproschema_success(tmpdir):
             protocol = yaml.safe_load(file)
         protocol_name = protocol.get("protocol_name", "").replace(" ", "_")
 
-        # Run the command with the path arguments pointing to the temp directory files
         result = runner.invoke(
             main, ["redcap2reproschema", str(temp_csv_file), str(temp_yaml_file)]  # Convert to string
         )
 
-        # Assertions
         assert result.exit_code == 0, f"The command failed to execute successfully: {result.output}"
         assert os.path.isdir(protocol_name), f"Expected output directory '{protocol_name}' does not exist"
-        print("Command output:", result.output)

reproschema/tests/test_reproschema2redcap.py

@@ -5,49 +5,35 @@
 from shutil import copytree, rmtree
 from pathlib import Path
 import csv
-import tempfile
 
-def test_reproschema2redcap_success():
+def test_reproschema2redcap(tmpdir):
     runner = CliRunner()
 
     with runner.isolated_filesystem():
-        # Create a temporary directory for output
-        temp_dir = tempfile.mkdtemp(dir='.')
-        print(f"Temporary directory: {temp_dir}")
         # Copy necessary test data into the isolated filesystem
         original_data_dir = os.path.join(
             os.path.dirname(__file__), "test_rs2redcap_data", "test_redcap2rs"
         )
         copytree(original_data_dir, "input_data")
 
-        input_path = Path("input_data")  # Using Path object
-        output_csv_path = os.path.join(temp_dir, "output.csv")
+        input_path = Path("input_data") 
+        output_csv_path = os.path.join(tmpdir, "output.csv")
 
-        # Invoke the reproschema2redcap command
         result = runner.invoke(
             main, ["reproschema2redcap", str(input_path), output_csv_path]
         )
 
-        # Print the output for debugging
         print(result.output)
 
-        # Assert the expected outcomes
         assert result.exit_code == 0
 
-        # Check if the output CSV file has been created
         assert os.path.exists(output_csv_path)
 
-        # Read and print the contents of the CSV file
         with open(output_csv_path, "r", encoding="utf-8") as csv_file:
             reader = csv.reader(csv_file)
             csv_contents = list(reader)
-            print("CSV File Contents:")
-            for row in csv_contents:
-                print(row)
 
-        # Optionally, assert conditions about the CSV contents
-        # For example, assert that the file has more than just headers
         assert len(csv_contents) > 1  # More than one row indicates content beyond headers
 
         # Clean up temporary directory after use (optional)
-        # rmtree(temp_dir)
+        # rmtree(tmpdir)