[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

reproschema/redcap2reproschema.py

@@ -8,11 +8,12 @@
 
 matrix_group_count = {}
 
+
 def clean_header(header):
     cleaned_header = {}
     for k, v in header.items():
         # Strip BOM, whitespace, and enclosing quotation marks if present
-        cleaned_key = k.lstrip('\ufeff').strip().strip('"')
+        cleaned_key = k.lstrip("\ufeff").strip().strip('"')
         cleaned_header[cleaned_key] = v
     return cleaned_header
 
@@ -24,24 +25,28 @@ def normalize_condition(condition_str):
     re_brackets = re.compile(r"\[([^\]]*)\]")
     re_extra_spaces = re.compile(r"\s+")
     re_double_quotes = re.compile(r'"')
-    re_or = re.compile(r'\bor\b')  # Match 'or' as whole word
+    re_or = re.compile(r"\bor\b")  # Match 'or' as whole word
 
     # Apply regex replacements
     condition_str = re_parentheses.sub(r"___\1", condition_str)
     condition_str = re_non_gt_lt_equal.sub(r"\1 ==", condition_str)
     condition_str = re_brackets.sub(r" \1 ", condition_str)
 
     # Replace 'or' with '||', ensuring not to replace '||'
-    condition_str = re_or.sub('||', condition_str)
+    condition_str = re_or.sub("||", condition_str)
 
     # Replace 'and' with '&&'
     condition_str = condition_str.replace(" and ", " && ")
 
     # Trim extra spaces and replace double quotes with single quotes
-    condition_str = re_extra_spaces.sub(' ', condition_str).strip()  # Reduce multiple spaces to a single space
-    condition_str = re_double_quotes.sub("'", condition_str)  # Replace double quotes with single quotes
+    condition_str = re_extra_spaces.sub(
+        " ", condition_str
+    ).strip()  # Reduce multiple spaces to a single space
+    condition_str = re_double_quotes.sub(
+        "'", condition_str
+    )  # Replace double quotes with single quotes
 
-    return condition_str.strip() 
+    return condition_str.strip()
 
 
 def process_visibility(data):
@@ -116,7 +121,7 @@ def process_choices(field_type, choices_str):
             value = parts[0]
 
         choice_obj = {"name": " ".join(parts[1:]), "value": value}
-        # remove image for now 
+        # remove image for now
         # if len(parts) == 3:
         #     # Handle image url
         #     choice_obj["image"] = f"{parts[2]}.png"
@@ -204,10 +209,7 @@ def process_row(
         }
 
     for key, value in field.items():
-        if (
-            schema_map.get(key) in ["question", "description", "preamble"]
-            and value
-        ):
+        if schema_map.get(key) in ["question", "description", "preamble"] and value:
             rowData.update({schema_map[key]: parse_html(value)})
 
         elif schema_map.get(key) == "allow" and value:
@@ -349,7 +351,9 @@ def create_protocol_schema(
             "variableName": f"{activity}_schema",
             # Assuming activity name as prefLabel, update as needed
             "prefLabel": activity.replace("_", " ").title(),
-            "isVis": protocol_visibility_obj.get(activity, True),  # Default to True if not specified
+            "isVis": protocol_visibility_obj.get(
+                activity, True
+            ),  # Default to True if not specified
         }
         protocol_schema["ui"]["addProperties"].append(add_property)
         # Add the full path to the order list

reproschema/reproschema2redcap.py

@@ -150,10 +150,17 @@ def get_csv_data(dir_path):
                 activity_order = parsed_protocol_json.get("ui", {}).get("order", [])
                 for relative_activity_path in activity_order:
                     # Normalize the relative path and construct the absolute path
-                    normalized_relative_path = Path(relative_activity_path.lstrip("../"))
+                    normalized_relative_path = Path(
+                        relative_activity_path.lstrip("../")
+                    )
+
+                    activity_path = (
+                        dir_path
+                        / "activities"
+                        / normalized_relative_path
+                        / (normalized_relative_path.name + "_schema")
+                    )
 
-                    activity_path = dir_path / "activities" / normalized_relative_path / (normalized_relative_path.name + "_schema")
-
                     parsed_activity_json = read_json_file(activity_path)
 
                     if parsed_activity_json:
@@ -239,4 +246,4 @@ def main(input_dir_path, output_csv_filename):
         sys.exit(1)
     input_dir_path = Path(sys.argv[1])
     output_csv_filename = sys.argv[2]
-    main(input_dir_path, output_csv_filename)
+    main(input_dir_path, output_csv_filename)

reproschema/tests/test_redcap2reproschema.py

@@ -3,7 +3,7 @@
 import pytest
 import yaml
 from click.testing import CliRunner
-from ..cli import main 
+from ..cli import main
 
 CSV_FILE_NAME = "redcap_dict.csv"
 YAML_FILE_NAME = "redcap2rs.yaml"
@@ -14,6 +14,7 @@
     os.path.dirname(__file__), "test_redcap2rs_data", YAML_FILE_NAME
 )
 
+
 def test_redcap2reproschema(tmpdir):
     runner = CliRunner()
 
@@ -26,13 +27,22 @@ def test_redcap2reproschema(tmpdir):
     # Change the current working directory to tmpdir
     with tmpdir.as_cwd():
         # Read YAML to find the expected output directory name
-        with open(str(temp_yaml_file), 'r') as file:  # Convert to string
+        with open(str(temp_yaml_file), "r") as file:  # Convert to string
             protocol = yaml.safe_load(file)
         protocol_name = protocol.get("protocol_name", "").replace(" ", "_")
 
         result = runner.invoke(
-            main, ["redcap2reproschema", str(temp_csv_file), str(temp_yaml_file)]  # Convert to string
+            main,
+            [
+                "redcap2reproschema",
+                str(temp_csv_file),
+                str(temp_yaml_file),
+            ],  # Convert to string
         )
 
-        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"
+        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"

reproschema/tests/test_redcap2rs_data/redcap2rs.yaml

@@ -13,4 +13,4 @@ protocol_display_name: "redcap protocols"
 # Provide a brief description of your protocol.
 protocol_description: "testing"  # Example: "This protocol is for ..."
 
-redcap_version: "3.0.0"
+redcap_version: "3.0.0"

reproschema/tests/test_reproschema2redcap.py

@@ -6,6 +6,7 @@
 from pathlib import Path
 import csv
 
+
 def test_reproschema2redcap(tmpdir):
     runner = CliRunner()
 
@@ -16,7 +17,7 @@ def test_reproschema2redcap(tmpdir):
         )
         copytree(original_data_dir, "input_data")
 
-        input_path = Path("input_data") 
+        input_path = Path("input_data")
         output_csv_path = os.path.join(tmpdir, "output.csv")
 
         result = runner.invoke(
@@ -33,7 +34,9 @@ def test_reproschema2redcap(tmpdir):
             reader = csv.reader(csv_file)
             csv_contents = list(reader)
 
-        assert len(csv_contents) > 1  # More than one row indicates content beyond headers
+        assert (
+            len(csv_contents) > 1
+        )  # More than one row indicates content beyond headers
 
         # Clean up temporary directory after use (optional)
-        # rmtree(tmpdir)
+        # rmtree(tmpdir)

templates/redcap2rs.yaml

@@ -13,4 +13,4 @@ protocol_display_name: "Your protocol display name"
 # Provide a brief description of your protocol.
 protocol_description: "Description for your protocol"  # Example: "This protocol is for ..."
 
-redcap_version: "x.y.z" # Example: "3.0.0"
+redcap_version: "x.y.z" # Example: "3.0.0"