Merge pull request #80 from yibeichan/fix-readonly

fix isVis based on Field annotation

Author: satra

pyproject.toml

@@ -14,7 +14,8 @@ dependencies = [
     "pyyaml",
     "beautifulsoup4",
     "lxml",
-    "pydantic >= 2.0"
+    "pydantic >= 2.0",
+    "pandas"
 ]
 description = "Reproschema Python library"
 # Version from setuptools_scm

reproschema/redcap2reproschema.py

@@ -1,8 +1,8 @@
-import csv
 import os
 import re
 from pathlib import Path
 
+import pandas as pd
 import yaml
 from bs4 import BeautifulSoup
 
@@ -17,7 +17,7 @@
     "Field Note": "description",
     # TODO: often "Field Annotation" has "@HIDDEN" and other markers
     # TODO: not sure if this can be every treated as description
-    # "Field Annotation": "description",  # column R
+    # "Field Annotation": "isVis",  # column R
     "Section Header": "preamble",  # column C (need double-check)
     "Field Label": "question",  # column E
     "Field Type": "inputType",  # column D
@@ -82,7 +82,9 @@ 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('"') if isinstance(k, str) else k
+        )
         cleaned_header[cleaned_key] = v
     return cleaned_header
 
@@ -99,6 +101,12 @@ def normalize_condition(condition_str, field_type=None):
         return False
     elif condition_str is None:
         return None
+    elif not isinstance(condition_str, str):
+        # Convert non-string types to string, or return as is if conversion doesn't make sense
+        try:
+            condition_str = str(condition_str)
+        except:
+            return condition_str
 
     re_parentheses = re.compile(r"\(([0-9]*)\)")
     re_non_gt_lt_equal = re.compile(r"([^>|<])=")
@@ -137,17 +145,42 @@ def process_field_properties(data):
     else:
         condition = True
 
+    # Check Field Annotation for special flags - safely handle non-string values
+    annotation = (
+        str(data.get("Field Annotation", "")).upper()
+        if data.get("Field Annotation") is not None
+        else ""
+    )
+    if (
+        condition
+        and isinstance(annotation, str)
+        and (
+            "@READONLY" in annotation
+            or "@HIDDEN" in annotation
+            or "@CALCTEXT" in annotation
+        )
+    ):
+        condition = False
+
     prop_obj = {
         "variableName": data["Variable / Field Name"],
         "isAbout": f"items/{data['Variable / Field Name']}",
         "isVis": condition,
     }
-    if data["Required Field?"]:
-        if data["Required Field?"] in "y":
+
+    # Handle Required Field check, accounting for NaN values and empty strings
+    required_field = data.get("Required Field?")
+    if (
+        pd.notna(required_field) and str(required_field).strip()
+    ):  # Check if value is not NaN and not empty
+        if str(required_field).lower() == "y":
             prop_obj["valueRequired"] = True
-        else:
-            raise (
-                f"value {data['Required Field?']} not supported yet for redcap:Required Field?"
+        elif str(required_field).lower() not in [
+            "",
+            "n",
+        ]:  # Only raise error for unexpected values
+            raise ValueError(
+                f"value {required_field} not supported yet for redcap:Required Field?"
             )
     return prop_obj
 
@@ -246,6 +279,16 @@ def process_choices(choices_str, field_name):
 
 def parse_html(input_string, default_language="en"):
     result = {}
+
+    # Handle non-string input
+    if not isinstance(input_string, str):
+        if pd.isna(input_string):  # Handle NaN values
+            return {default_language: ""}
+        try:
+            input_string = str(input_string)
+        except:
+            return {default_language: str(input_string)}
+
     soup = BeautifulSoup(input_string, "html.parser")
 
     lang_elements = soup.find_all(True, {"lang": True})
@@ -284,19 +327,30 @@ def process_row(
 
     field_type = field.get("Field Type", "")
     input_type, value_type = parse_field_type_and_value(field)
-    rowData["ui"] = {"inputType": input_type}
+
+    # Initialize ui object with common properties
+    ui_obj = {"inputType": input_type}
+
+    # Handle readonly status first - this affects UI behavior
+    annotation = str(field.get("Field Annotation", "")).upper()
+    if (
+        field_type in COMPUTE_LIST
+        or "@READONLY" in annotation
+        or "@CALCTEXT" in annotation
+    ):
+        ui_obj["readonlyValue"] = True
+
+    rowData["ui"] = ui_obj
     rowData["responseOptions"] = {"valueType": [value_type]}
 
-    # setting additional fields for some field types
+    # Handle specific field type configurations
     if field_type == "yesno":
         rowData["responseOptions"]["choices"] = [
             {"name": {"en": "Yes"}, "value": 1},
             {"name": {"en": "No"}, "value": 0},
         ]
     elif field_type == "checkbox":
         rowData["responseOptions"]["multipleChoice"] = True
-    elif field_type in COMPUTE_LIST:
-        rowData["ui"]["readonlyValue"] = True
 
     for key, value in field.items():
         if SCHEMA_MAP.get(key) in ["question", "description"] and value:
@@ -498,52 +552,79 @@ def parse_language_iso_codes(input_string):
     ]
 
 
-def process_csv(
-    csv_file,
-    abs_folder_path,
-    schema_context_url,
-    protocol_name,
-):
+def process_csv(csv_file, abs_folder_path, schema_context_url, protocol_name):
     datas = {}
     order = {}
     compute = {}
     languages = []
 
-    with open(csv_file, mode="r", encoding="utf-8") as csvfile:
-        reader = csv.DictReader(csvfile)
-        for row in reader:
-            row = clean_header(row)
-            form_name = row["Form Name"]
-            if form_name not in datas:
-                datas[form_name] = []
-                order[form_name] = []
-                compute[form_name] = []
-                os.makedirs(
-                    f"{abs_folder_path}/activities/{form_name}/items",
-                    exist_ok=True,
-                )
+    # Read CSV with explicit BOM handling, and maintain original order
+    df = pd.read_csv(
+        csv_file, encoding="utf-8-sig"
+    )  # utf-8-sig handles BOM automatically
 
-            datas[form_name].append(row)
+    # Clean column names (headers)
+    df.columns = df.columns.map(
+        lambda x: x.strip().strip('"').lstrip("\ufeff")
+    )
 
-            # TODO: should we bring back the language
-            # if not languages:
-            #    languages = parse_language_iso_codes(row["Field Label"])
+    # Clean string values in the dataframe
+    object_columns = df.select_dtypes(include=["object"]).columns
+    for col in object_columns:
+        df[col] = df[col].astype(str).replace("nan", "")
+
+    # Initialize structures for each unique form
+    unique_forms = df["Form Name"].unique()
+    for form_name in unique_forms:
+        datas[form_name] = []
+        order[form_name] = []
+        compute[form_name] = []
+        os.makedirs(
+            f"{abs_folder_path}/activities/{form_name}/items", exist_ok=True
+        )
 
-            field_name = row["Variable / Field Name"]
-            if row.get("Field Type", "") in COMPUTE_LIST:
-                # TODO: this right now doesn't give jsExpression
-                condition = normalize_condition(
-                    row["Choices, Calculations, OR Slider Labels"],
-                    field_type=row["Field Type"],
-                )
+    # TODO: should we bring back the language
+    # if not languages:
+    #    languages = parse_language_iso_codes(row["Field Label"])
+
+    # Process rows in original order
+    for _, row in df.iterrows():
+        form_name = row["Form Name"]
+        field_name = row["Variable / Field Name"]
+        field_type = row.get("Field Type", "")
+        field_annotation = row.get("Field Annotation")
+
+        # Add row data to datas dictionary
+        datas[form_name].append(row.to_dict())
+
+        if field_type in COMPUTE_LIST:
+            condition = normalize_condition(
+                row["Choices, Calculations, OR Slider Labels"],
+                field_type=field_type,
+            )
+            compute[form_name].append(
+                {
+                    "variableName": field_name,
+                    "jsExpression": condition,
+                }
+            )
+        elif (
+            isinstance(field_annotation, str)
+            and "@CALCTEXT" in field_annotation.upper()
+        ):
+            calc_text = field_annotation
+            match = re.search(r"@CALCTEXT\((.*)\)", calc_text)
+            if match:
+                js_expression = match.group(1)
+                js_expression = normalize_condition(js_expression)
                 compute[form_name].append(
                     {
                         "variableName": field_name,
-                        "jsExpression": condition,
+                        "jsExpression": js_expression,
                     }
                 )
-            else:
-                order[form_name].append(f"items/{field_name}")
+        else:
+            order[form_name].append(f"items/{field_name}")
 
     os.makedirs(f"{abs_folder_path}/{protocol_name}", exist_ok=True)
     return datas, order, compute, languages

reproschema/tests/test_field_property.py

@@ -0,0 +1,117 @@
+import csv
+
+import pytest
+
+from ..redcap2reproschema import process_field_properties
+
+
+def test_process_field_properties_calctext():
+    """Test different CALCTEXT annotations with realistic examples"""
+    test_cases = [
+        # Simple CALCTEXT
+        {
+            "input": {
+                "Variable / Field Name": "test_var",
+                "Required Field?": "",
+                "Field Annotation": "@CALCTEXT",
+                "Branching Logic (Show field only if...)": "",
+            },
+            "expected": {
+                "variableName": "test_var",
+                "isAbout": "items/test_var",
+                "isVis": False,
+            },
+        },
+        # Complex CALCTEXT with conditional logic
+        {
+            "input": {
+                "Variable / Field Name": "parkinsons_diagnosis",
+                "Required Field?": "",
+                "Field Annotation": "@CALCTEXT(if(([diagnosis_parkinsons_gsd_category_1(bradykinesia)] && ([diagnosis_parkinsons_gsd_category_1(tremor)] || [diagnosis_parkinsons_gsd_category_1(rigidity)])), 'Yes', 'No'))",
+                "Branching Logic (Show field only if...)": "[some_other_condition] = 1",
+            },
+            "expected": {
+                "variableName": "parkinsons_diagnosis",
+                "isAbout": "items/parkinsons_diagnosis",
+                "isVis": False,
+            },
+        },
+        # CALCTEXT with numerical operations
+        {
+            "input": {
+                "Variable / Field Name": "bmi",
+                "Required Field?": "",
+                "Field Annotation": "@CALCTEXT([weight]/([height]*[height]))",
+                "Branching Logic (Show field only if...)": "[weight] > 0 and [height] > 0",
+            },
+            "expected": {
+                "variableName": "bmi",
+                "isAbout": "items/bmi",
+                "isVis": False,
+            },
+        },
+        # CALCTEXT with multiple nested conditions
+        {
+            "input": {
+                "Variable / Field Name": "complex_score",
+                "Required Field?": "",
+                "Field Annotation": "@CALCTEXT(if([score1] > 10 && [score2] < 5, 'High', if([score1] > 5, 'Medium', 'Low')))",
+                "Branching Logic (Show field only if...)": "",
+            },
+            "expected": {
+                "variableName": "complex_score",
+                "isAbout": "items/complex_score",
+                "isVis": False,
+            },
+        },
+    ]
+
+    for test_case in test_cases:
+        result = process_field_properties(test_case["input"])
+        for key, expected_value in test_case["expected"].items():
+            assert (
+                result[key] == expected_value
+            ), f"Failed for {key} in test case with annotation: {test_case['input']['Field Annotation']}"
+
+
+def test_process_field_properties_mixed_annotations():
+    """Test fields with multiple annotations"""
+    test_cases = [
+        # CALCTEXT with READONLY
+        {
+            "input": {
+                "Variable / Field Name": "test_var",
+                "Required Field?": "",
+                "Field Annotation": "@CALCTEXT @READONLY",
+                "Branching Logic (Show field only if...)": "",
+            },
+            "expected": {"isVis": False},
+        },
+        # CALCTEXT with HIDDEN
+        {
+            "input": {
+                "Variable / Field Name": "test_var",
+                "Required Field?": "",
+                "Field Annotation": "@HIDDEN @CALCTEXT(if([var1] > 0, 1, 0))",
+                "Branching Logic (Show field only if...)": "",
+            },
+            "expected": {"isVis": False},
+        },
+        # Complex CALCTEXT with other annotations
+        {
+            "input": {
+                "Variable / Field Name": "test_var",
+                "Required Field?": "",
+                "Field Annotation": "@CALCTEXT(if(([var1] && [var2]), 'Yes', 'No')) @READONLY @HIDDEN-SURVEY",
+                "Branching Logic (Show field only if...)": "[condition] = 1",
+            },
+            "expected": {"isVis": False},
+        },
+    ]
+
+    for test_case in test_cases:
+        result = process_field_properties(test_case["input"])
+        for key, expected_value in test_case["expected"].items():
+            assert (
+                result[key] == expected_value
+            ), f"Failed for {key} in test case with annotation: {test_case['input']['Field Annotation']}"