Merge pull request #6 from yibeichan/local-test-branch

Local test branch

Author: djarecka

reproschema/redcap2reproschema.py

@@ -20,9 +20,9 @@
     REDCAP_COLUMN_REQUIRED,
     RESPONSE_COND,
     VALUE_TYPE_MAP,
+    get_value_type,
 )
 
-
 def process_input_value_types(input_type_rc, value_type_rc) -> (str, str):
     """
     Process input type and value type to determine the final input type and value type,
@@ -47,40 +47,36 @@ def process_input_value_types(input_type_rc, value_type_rc) -> (str, str):
         input_type = INPUT_TYPE_MAP.get(input_type_rc)
 
     if value_type_rc:
-        if value_type_rc not in VALUE_TYPE_MAP:
-            raise ValueError(
-                f"Validation type '{value_type_rc}' is not supported, "
-                f"supported types are: {', '.join(VALUE_TYPE_MAP.keys())}"
-            )
-
-        value_type = VALUE_TYPE_MAP[value_type_rc]
+        # Get value type using the new function
+        value_type = get_value_type(value_type_rc)
 
         # Adjust input type based on validation
-        if value_type_rc == "integer" and input_type_rc == "text":
+        if value_type_rc.startswith("date") or value_type_rc.startswith("datetime"):
+            if input_type_rc == "text":
+                input_type = "date"
+        elif value_type_rc.startswith("time"):
+            if input_type_rc == "text":
+                input_type = "time"
+        elif value_type_rc == "integer" and input_type_rc == "text":
             input_type = "number"
         elif value_type_rc in ["float", "number"] and input_type_rc == "text":
             input_type = "float"
-        elif (
-            value_type_rc == "email" and input_type_rc == "text"
-        ):  # todo: what if input type is not text
+        elif value_type_rc == "email" and input_type_rc == "text":
             input_type = "email"
         elif value_type_rc == "signature" and input_type_rc == "text":
             input_type = "sign"
-        elif (
-            value_type == "xsd:date" and input_type_rc == "text"
-        ):  # anything that maps to date in RS #todo: what about time?
-            input_type = "date"
 
     elif input_type_rc == "yesno":
         value_type = "xsd:boolean"
+    elif input_type_rc == "truefalse":
+        value_type = "xsd:boolean"
     elif input_type_rc in COMPUTE_LIST:
         value_type = "xsd:integer"
     else:  # if no validation type is set, default to string
         value_type = "xsd:string"
 
     return input_type, value_type
 
-
 def process_response_options(row, input_type_rc, value_type) -> Dict[str, Any]:
     """
     Process response options from the row and return a dictionary of response options
@@ -102,6 +98,11 @@ def process_response_options(row, input_type_rc, value_type) -> Dict[str, Any]:
             {"name": {"en": "Yes"}, "value": 1},
             {"name": {"en": "No"}, "value": 0},
         ]
+    elif input_type_rc == "truefalse": 
+        response_options["choices"] = [
+            {"name": {"en": "True"}, "value": 1},
+            {"name": {"en": "False"}, "value": 0},
+        ]
     elif input_type_rc == "checkbox":
         response_options["multipleChoice"] = True
 
@@ -418,7 +419,7 @@ def process_row(
 def process_csv(csv_file) -> (Dict[str, Any], list):
 
     df = pd.read_csv(
-        csv_file, encoding="utf-8-sig"
+        csv_file, encoding="utf-8-sig", low_memory=False
     )  # utf-8-sig handles BOM automatically
 
     df.columns = df.columns.map(

reproschema/redcap_mappings.py

@@ -34,6 +34,7 @@
     "sql": "number",
     "yesno": "radio",
     "radio": "radio",
+    "truefalse": "radio",
     "checkbox": "radio",
     "descriptive": "static",
     "dropdown": "select",
@@ -45,23 +46,23 @@
 
 # Map certain field types directly to xsd types
 VALUE_TYPE_MAP = {
+    # Basic types
     "text": "xsd:string",
-    "date_": "xsd:date",
-    "date_mdy": "xsd:date",  # it's not exactly xsd:date
-    "datetime_seconds_mdy": "xsd:date",  # it's not exactly xsd:date
-    "date_ymd": "xsd:date",
-    "date_dmy": "xsd:date",
-    "datetime_": "xsd:dateTime",
-    "datetime_ymd": "xsd:dateTime",
-    "time_": "xsd:time",
     "email": "xsd:string",
     "phone": "xsd:string",
-    "number": "xsd:decimal",  # could be an integer, but have no idea of knowing)
+    "signature": "xsd:string",
+    "zipcode": "xsd:string",
+    "autocomplete": "xsd:string",
+    
+    # Numeric types
+    "number": "xsd:decimal",
     "float": "xsd:decimal",
     "integer": "xsd:integer",
-    "signature": "xsd: string",
-    "zipcode": "xsd: string",
-    "autocomplete": "xsd: string",
+    
+    # Date and time types will be handled by pattern matching in process_input_value_types
+    # These entries are kept for backward compatibility
+    "date_": "xsd:date",
+    "time_": "xsd:time",
 }
 
 # field types that should be used as compute
@@ -80,3 +81,27 @@
     "Question Number (surveys only)",
     "Field Annotation",
 ]
+
+def get_value_type(validation_type):
+    """
+    Determine the XSD value type based on REDCap validation type
+    
+    Args:
+        validation_type (str): Validation type from REDCap
+        
+    Returns:
+        str: XSD value type for ReproSchema
+    """
+    if validation_type is None:
+        return "xsd:string"
+        
+    # Handle date and time formats with pattern matching
+    if validation_type.startswith("date_"):
+        return "xsd:date"
+    elif validation_type.startswith("datetime_"):
+        return "xsd:dateTime"
+    elif validation_type.startswith("time"):
+        return "xsd:time"
+    
+    # For other types, use the mapping
+    return VALUE_TYPE_MAP.get(validation_type, "xsd:string")