add cli for rs2redcap (need test data)

reproschema/cli.py

@@ -1,5 +1,6 @@
 import os
 import click
+from pathlib import Path
 
 from . import get_logger, set_logger_level
 from . import __version__
@@ -104,11 +105,8 @@ def serve(port):
 def reproschema2redcap(input_path, output_csv_path):
     """
     Convert reproschema JSON to Redcap CSV format.
-
-    INPUT_PATH: Directory containing reproschema JSON files.
-    OUTPUT_CSV_PATH: Path to the output CSV file.
     """
-    rs2redcap(input_path, output_csv_path)
-    click.echo(
-        f"Converted reproschema JSON from {input_path} to Redcap CSV at {output_csv_path}"
-    )
+    # Convert input_path to a Path object
+    input_path_obj = Path(input_path)
+    rs2redcap(input_path_obj, output_csv_path)
+    click.echo(f"Converted reproschema JSON from {input_path} to Redcap CSV at {output_csv_path}")

reproschema/reproschema2redcap.py

@@ -121,6 +121,7 @@ def get_csv_data(dir_path):
                         relative_activity_path.lstrip("../")
                     )
                     activity_path = dir_path / normalized_relative_path
+                    print(f"Processing activity {activity_path}")
                     parsed_activity_json = read_json_file(activity_path)
 
                     if parsed_activity_json:

reproschema/tests/test_reproschema2redcap.py

@@ -0,0 +1,43 @@
+import os
+import pytest
+from click.testing import CliRunner
+from ..cli import main  
+from shutil import copytree
+from pathlib import Path
+import csv
+
+def test_reproschema2redcap_success():
+    runner = CliRunner()
+
+    with runner.isolated_filesystem():
+        # Copy necessary test data into the isolated filesystem
+        original_data_dir = os.path.join(os.path.dirname(__file__), "test_rs2redcap_data")
+        copytree(original_data_dir, "input_data")
+
+        input_path = Path("input_data")  # Using Path object
+        output_csv_path = "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
+        assert f"Converted reproschema JSON from {input_path} to Redcap CSV at {output_csv_path}" in result.output
+
+        # 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 is not empty
+        assert len(csv_contents) > 0