fix age tests

smartvadhis2/core/helpers.py

@@ -77,4 +77,4 @@ def days_to_years(days):
 
 def years_to_days(years):
     """Convert years to days"""
-    return int(round((years * DAYS_IN_YEAR)))
+    return years * DAYS_IN_YEAR

smartvadhis2/core/verbalautopsy.py

@@ -30,7 +30,7 @@
     InterviewDateMissingWarning,
     InterviewDateParseWarning
 )
-from .helpers import sanitize, is_uid, days_to_years, years_to_days, DAYS_IN_YEAR
+from .helpers import sanitize, is_uid, years_to_days
 from .mapping import Mapping, Sex, AgeCategory, Icd10, cause_of_death_option_code
 from ..__version__ import __version__
 
@@ -103,6 +103,9 @@ def __getattr__(self, _):
         """Return None if instance attribute does not exist"""
         return None
 
+    def keys(self):
+        return [k for k in dir(self) if not k.startswith('_') and not callable(self[k])]
+
     def __str__(self):
         """Print VerbalAutopsy instance as JSON"""
         return json.dumps(dict(self))
@@ -116,40 +119,21 @@ def age(self, value):
         lower_limit = 0
         upper_limit = 131
         if value:
-            if 'days' in value:
-                try:
-                    days = int(value.replace('days', '').strip())
-                except ValueError:
-                    raise AgeParseError()
-                else:
-                    if days < 0 or days > years_to_days(upper_limit):
-                        raise AgeParseError()
-                    self._age_days = days
-                    self._age_years = days_to_years(days)
-                    self._age = None
-
-            elif 'years' in value:
-                try:
-                    years = int(value.replace('years', '').strip())
-                except ValueError:
-                    raise AgeParseError()
-                else:
-                    if years not in range(lower_limit, upper_limit):
-                        raise AgeOutOfBoundsError()
-                    else:
-                        self._age_years = years
-                        self._age_days = years_to_days(years)
-                        self._age = None
-            else:
+            try:
+                f = float(value)
+            except ValueError:
                 raise AgeParseError()
-
-            if self._age_days <= 28:
-                self._age_category = AgeCategory.options['Neonate']
-            elif self._age_years <= 12:
-                self._age_category = AgeCategory.options['Child']
             else:
-                self._age_category = AgeCategory.options['Adult']
-
+                if int(f) not in range(lower_limit, upper_limit):
+                    raise AgeOutOfBoundsError()
+                else:
+                    self._age = round(f, 2)
+                    if years_to_days(f) <= 28:
+                        self._age_category = AgeCategory.options['Neonate']
+                    elif int(f) < 12:
+                        self._age_category = AgeCategory.options['Child']
+                    else:
+                        self._age_category = AgeCategory.options['Adult']
         else:
             raise AgeMissingWarning()
 

tests/test_helpers.py

@@ -96,23 +96,14 @@ def test_csv_with_content_headers_only():
 
 
 @pytest.mark.parametrize("years, expected", [
-    (1, 365),
-    (10, 3652),
-    (15, 5479)
+    (0.01, 3.652425),
+    (1, 365.2425),
+    (10, 3652.425)
 ])
 def test_years_to_days(years, expected):
     assert years_to_days(years) == expected
 
 
-@pytest.mark.parametrize("days, expected", [
-    (365, 1),
-    (3652, 10),
-    (5479, 15)
-])
-def test_years_to_days(days, expected):
-    assert days_to_years(days) == expected
-
-
 def test_read_csv():
     data = file_testdata('smartva_test.csv')
     assert os.path.exists(data)

tests/test_verbalautopsy.py

@@ -8,7 +8,7 @@
 from smartvadhis2.core.exceptions.warnings import *
 from smartvadhis2.core.mapping import *
 from smartvadhis2.core.config import ODKConfig, SmartVAConfig
-from smartvadhis2.core.verbalautopsy import VerbalAutopsy, Event, process_row_data, verbal_autopsy_factory, DAYS_IN_YEAR
+from smartvadhis2.core.verbalautopsy import VerbalAutopsy, Event, process_row_data, verbal_autopsy_factory
 
 
 class VaAbstractClass(object):
@@ -19,76 +19,54 @@ def va(self):
 
 class TestAge(VaAbstractClass):
 
-    def test_va_age_years(self, va):
-        va.age = '22 years'
-        assert va.age_years == 22
-        assert va.age_days == 8035
-        assert va.age is None
+    def test_va_age(self, va):
+        va.age = '0.0273972602739726'
+        assert va.age == 0.03
 
-    def test_va_age_number_without_indicator(self, va):
-        with pytest.raises(AgeParseError):
-            va.age = '22'
+    def test_va_age_inaccurate(self, va):
+        va.age = '0.3'
+        assert va.age == 0.3
 
-    def test_va_age_days(self, va):
-        va.age = '12 days'
-        assert va.age_years == 0
-        assert va.age_days == 12
-        assert va.age is None
+    def test_va_age_int(self, va):
+        va.age = '12'
+        assert va.age == 12
 
     def test_va_age_days_parse_error(self, va):
         with pytest.raises(AgeParseError):
-            va.age = '12 days butrestiswrong'
+            va.age = '0.0273972602739726 butrestiswrong'
 
-    def test_va_age_years_out_of_bounds(self, va):
+    def test_va_age_out_of_bounds(self, va):
         with pytest.raises(AgeOutOfBoundsError):
-            va.age = '140 years'
+            va.age = '140.021'
         with pytest.raises(AgeOutOfBoundsError):
-            va.age = '-10 years'
-
-    def test_va_age_days_out_of_bounds(self, va):
-        with pytest.raises(AgeParseError):
-            va.age = '50000 days'
-        with pytest.raises(AgeParseError):
-            va.age = '-2 days'
-
-    def test_va_age_days_to_years(self, va):
-        va.age = '400 days'
-        assert va.age_years == 1
-        assert va.age_days == 400
-        assert va.age is None
+            va.age = '-10'
 
     def test_va_age_invalid(self, va):
         with pytest.raises(AgeParseError):
             va.age = 'not an age'
 
-        with pytest.raises(AgeParseError):
-            va.age = 'not an age days'
-
-        with pytest.raises(AgeParseError):
-            va.age = 'not an age years'
-
-        with pytest.raises(AgeOutOfBoundsError):
-            va.age = '135 years'
-
+    def test_va_age_missing(self, va):
         with pytest.raises(AgeMissingWarning):
             va.age = ''
 
-    def test_va_age_category_adult(self, va):
-        va.age = '13 years'
-        assert va.age_years == 13
-        assert va.age_days == int(round(13 * DAYS_IN_YEAR))
+    def test_va_age_category_adult_lower(self, va):
+        va.age = '12.0'
+        assert va.age == 12.0
         assert va.age_category == AgeCategory.options['Adult']
 
-    def test_va_age_category_child(self, va):
-        va.age = '10 years'
-        assert va.age_years == 10
-        assert va.age_days == int(round(10 * DAYS_IN_YEAR))
+    def test_va_age_category_child_upper(self, va):
+        va.age = '0.07939930320266672'
+        assert va.age == 0.08
+        assert va.age_category == AgeCategory.options['Child']
+
+    def test_va_age_category_child_lower(self, va):
+        va.age = '11.0111'
+        assert va.age == 11.01
         assert va.age_category == AgeCategory.options['Child']
 
     def test_va_age_category_neonate(self, va):
-        va.age = '12 days'
-        assert va.age_years == 0
-        assert va.age_days == 12
+        va.age = '0.07666139619567822'
+        assert va.age == 0.08
         assert va.age_category == AgeCategory.options['Neonate']
 
 
@@ -107,7 +85,7 @@ class TestCauseOfDeath(VaAbstractClass):
 
     def test_va_cause_of_death(self, va):
         va.icd10 = 'B24'
-        va.age_in_years = 90
+        va.age = 90.34
         va.age_category = 1
         assert va.icd10 == 12
         assert va.age_category == 1
@@ -267,30 +245,34 @@ def test_questionnaire_version(self, va):
 class TestVAClassMethods(VaAbstractClass):
 
     def test_getitem(self, va):
-        va.age = '22 years'
-        assert va['age_years'] == 22
+        va.age = '22.0'
+        assert va['age'] == 22.0
 
     def test_setitem(self, va):
-        va['age'] = '22 years'
-        assert va.age_years == 22
+        va['age'] = '22.0'
+        assert va.age == 22.0
 
     def test_getattr(self, va):
         assert va.notexistent is None
 
-    """
-    TODO
     def test_str(self, capsys, va):
         va.age = '22.0'
-        expected = {'age': 22.0}
+        va.icd10 = 'C16'
+        expected = {
+            'age': 22.0,
+            'age_category': 1,
+            'icd10': 15,
+            'cause_of_death': 131
+        }
         print(va)
         captured = capsys.readouterr()
-        assert captured.out == expected
-    """
+        removed_nulls = {k: v for k, v in json.loads(captured.out).items() if v is not None}
+        assert removed_nulls == expected
 
 
 def test_process_row_data():
     data = {
-        'age': '22 years',
+        'age': '22.999',
         'death_date': '2018-01-01',
         'interview_date': '2018-02-01'
     }
@@ -299,7 +281,7 @@ def test_process_row_data():
 
     from collections import OrderedDict
     exp = OrderedDict(sorted({
-        Age.code_name: '22 years',
+        Age.code_name: '22.999',
         BirthDate.code_name: None,
         FirstName.code_name: None,
         FirstName2nd.code_name: None,
@@ -321,7 +303,7 @@ def test_process_row_data():
 
 def test_verbal_autopsy_factory_full():
     data = {
-        Age.csv_name: '22 years',
+        Age.csv_name: '22.01231',
         BirthDate.csv_name: '1990-01-01',
         CauseCode.csv_name: '23',
         CauseOfDeath.csv_name: '1',
@@ -338,10 +320,8 @@ def test_verbal_autopsy_factory_full():
     }
     va, exc, w = verbal_autopsy_factory(data)
     assert isinstance(va, VerbalAutopsy)
-    assert va.age_years == 22
-    assert va.age_days == 8035
+    assert va.age == 22.01
     assert va.age_category == 1
-    assert va.age is None
     assert va.birth_date == '1990-01-01'
     assert va.cause_of_death == 101
     assert va.first_name == 'Toni'
@@ -386,7 +366,7 @@ class TestEvent(object):
     @pytest.fixture
     def va(self):
         va_instance = VerbalAutopsy()
-        va_instance.age_years = 22
+        va_instance.age = 22.03
         va_instance.age_category = 1
         va_instance.birth_date = '1990-01-01'
         va_instance.icd10 = 'B24'
@@ -415,8 +395,7 @@ def test_event_datavalues(self, va):
         ev = Event(va)
 
         expected = [
-            {"dataElement": AgeInYears.dhis_uid, "value": 22},
-            {"dataElement": AgeInDays.dhis_uid, "value": 8035},
+            {"dataElement": Age.dhis_uid, "value": 22.03},
             {"dataElement": AgeCategory.dhis_uid, "value": AgeCategory.options["Adult"]},
             {"dataElement": CauseOfDeath.dhis_uid, "value": 101},
             {"dataElement": BirthDate.dhis_uid, "value": "1990-01-01"},