Merge pull request #78 from yibeichan/fix-strip

fix strip() issue for choices

reproschema/redcap2reproschema.py

@@ -201,7 +201,10 @@ def process_choices(choices_str, field_name):
     choices = []
     choices_value_type = []
     for ii, choice in enumerate(choices_str.split("|")):
-        parts = choice.split(", ")
+        choice = (
+            choice.strip()
+        )  # Strip leading/trailing whitespace for each choice
+        parts = [p.strip() for p in choice.split(",")]
 
         # Handle the case where the choice is something like "1,"
         if len(parts) == 1:
@@ -213,14 +216,22 @@ def process_choices(choices_str, field_name):
                 )
                 parts = [ii, parts[0]]
 
-        # Try to convert the first part to an integer, if it fails, keep it as a string
-        try:
-            value = int(parts[0])
+        # Determine if value should be treated as an integer or string
+        if parts[0] == "0":
+            # Special case for "0", treat it as an integer
+            value = 0
             choices_value_type.append("xsd:integer")
-        except ValueError:
+        elif parts[0].isdigit() and parts[0][0] == "0":
+            # If it has leading zeros, treat it as a string
             value = parts[0]
             choices_value_type.append("xsd:string")
-
+        else:
+            try:
+                value = int(parts[0])
+                choices_value_type.append("xsd:integer")
+            except ValueError:
+                value = parts[0]
+                choices_value_type.append("xsd:string")
         choice_obj = {
             "name": {"en": " ".join(parts[1:]).strip()},
             "value": value,

reproschema/tests/test_process_choices.py

@@ -0,0 +1,121 @@
+import os
+import shutil
+
+import pytest
+import yaml
+from click.testing import CliRunner
+
+from ..cli import main
+from ..redcap2reproschema import process_choices
+
+
+def test_process_choices_numeric_codes():
+    # Test standard numeric codes with descriptions
+    choices_str = "1, Male    | 2, Female | 3, Other"
+    choices, value_types = process_choices(choices_str, "gender")
+    assert choices == [
+        {"name": {"en": "Male"}, "value": 1},
+        {"name": {"en": "Female"}, "value": 2},
+        {"name": {"en": "Other"}, "value": 3},
+    ]
+    assert value_types == ["xsd:integer"]
+
+
+def test_process_choices_boolean():
+    # Test boolean choices (Yes/No)
+    choices_str = "1, Yes | 0, No"
+    choices, value_types = process_choices(choices_str, "boolean_field")
+    assert choices == [
+        {"name": {"en": "Yes"}, "value": 1},
+        {"name": {"en": "No"}, "value": 0},
+    ]
+    assert value_types == ["xsd:integer"]
+
+
+def test_process_choices_special_characters():
+    # Test choices with special characters
+    choices_str = "1, Option A | 2, \"Option B\" | 3, Option C with 'quotes'"
+    choices, value_types = process_choices(choices_str, "special_chars")
+    assert choices == [
+        {"name": {"en": "Option A"}, "value": 1},
+        {"name": {"en": '"Option B"'}, "value": 2},
+        {"name": {"en": "Option C with 'quotes'"}, "value": 3},
+    ]
+    assert value_types == ["xsd:integer"]
+
+
+def test_process_choices_with_missing_values():
+    # Test choices with a missing value (commonly used for "Not applicable" or "Prefer not to say")
+    choices_str = "1, Yes | 2, No | 99, Not applicable"
+    choices, value_types = process_choices(choices_str, "missing_values")
+    assert choices == [
+        {"name": {"en": "Yes"}, "value": 1},
+        {"name": {"en": "No"}, "value": 2},
+        {"name": {"en": "Not applicable"}, "value": 99},
+    ]
+    assert value_types == ["xsd:integer"]
+
+
+def test_process_choices_with_unicode():
+    # Test choices with Unicode characters (e.g., accents, symbols)
+    choices_str = "1, Café | 2, Niño | 3, Résumé | 4, ☺"
+    choices, value_types = process_choices(choices_str, "unicode_field")
+    assert choices == [
+        {"name": {"en": "Café"}, "value": 1},
+        {"name": {"en": "Niño"}, "value": 2},
+        {"name": {"en": "Résumé"}, "value": 3},
+        {"name": {"en": "☺"}, "value": 4},
+    ]
+    assert value_types == ["xsd:integer"]
+
+
+def test_process_choices_alpha_codes():
+    # Test alpha codes (e.g., categorical text codes)
+    choices_str = "A, Apple | B, Banana | C, Cherry"
+    choices, value_types = process_choices(choices_str, "alpha_codes")
+    assert choices == [
+        {"name": {"en": "Apple"}, "value": "A"},
+        {"name": {"en": "Banana"}, "value": "B"},
+        {"name": {"en": "Cherry"}, "value": "C"},
+    ]
+    assert sorted(value_types) == ["xsd:string"]
+
+
+def test_process_choices_incomplete_values():
+    # Test choices with missing descriptions
+    choices_str = "1, Yes | 2, | 3, No"
+    choices, value_types = process_choices(choices_str, "incomplete_values")
+    assert choices == [
+        {"name": {"en": "Yes"}, "value": 1},
+        {"name": {"en": ""}, "value": 2},
+        {"name": {"en": "No"}, "value": 3},
+    ]
+    assert value_types == ["xsd:integer"]
+
+
+def test_process_choices_numeric_strings():
+    # Test numeric strings as values (e.g., not converted to integers)
+    choices_str = "001, Option 001 | 002, Option 002 | 003, Option 003"
+    choices, value_types = process_choices(choices_str, "numeric_strings")
+    assert choices == [
+        {"name": {"en": "Option 001"}, "value": "001"},
+        {"name": {"en": "Option 002"}, "value": "002"},
+        {"name": {"en": "Option 003"}, "value": "003"},
+    ]
+    assert sorted(value_types) == ["xsd:string"]
+
+
+def test_process_choices_spaces_in_values():
+    # Test choices with spaces in values and names
+    choices_str = "A B, Choice AB | C D, Choice CD"
+    choices, value_types = process_choices(choices_str, "spaces_in_values")
+    assert choices == [
+        {"name": {"en": "Choice AB"}, "value": "A B"},
+        {"name": {"en": "Choice CD"}, "value": "C D"},
+    ]
+    assert sorted(value_types) == ["xsd:string"]
+
+
+# Run pytest if script is called directly
+if __name__ == "__main__":
+    pytest.main()