Merge pull request LREN-CHUV#52 from LREN-CHUV/fix-anova

raise error in anova when data is empty

Author: ludovicc

python-anova/anova.py

@@ -69,7 +69,12 @@ def format_output(statsmodels_dict):
 def compute_anova(dep_var, indep_vars, data, design='factorial'):
     formula = generate_formula(dep_var, indep_vars, design)
     logging.info("Formula: %s" % formula)
-    lm = ols(data=DataFrame(data), formula=formula).fit()
+    data = DataFrame(data)
+
+    if data.empty:
+        raise errors.UserError('SQL returned no data, check your dataset and null values.')
+
+    lm = ols(data=data, formula=formula).fit()
     logging.info(lm.summary())
     return anova_lm(lm)
 

python-anova/tests/unit/test_anova.py

@@ -1,6 +1,9 @@
 import pytest
-from anova import generate_formula
+import mock
+import json
+from anova import generate_formula, main
 from mip_helper import errors
+from mip_helper import testing as t
 
 
 def test_generate_formula():
@@ -9,3 +12,52 @@ def test_generate_formula():
     indep_vars = [{'name': str(i)} for i in range(10)]
     with pytest.raises(errors.UserError):
         generate_formula(dep_var, indep_vars, 'factorial')
+
+
+@mock.patch('anova.io_helper.fetch_data')
+@mock.patch('anova.io_helper.save_results')
+def test_main(mock_save_results, mock_fetch_data):
+    mock_fetch_data.return_value = t.inputs_regression(include_nominal=False)
+    main()
+    result = json.loads(mock_save_results.call_args[0][0])
+    assert t.round_dict(result) == {
+        'Residual': {
+            'F': 'NaN',
+            'PR(>F)': 'NaN',
+            'df': 1.0,
+            'mean_sq': 0.019,
+            'sum_sq': 0.019
+        },
+        'minimentalstate': {
+            'F': 12.831,
+            'PR(>F)': 0.173,
+            'df': 1.0,
+            'mean_sq': 0.248,
+            'sum_sq': 0.248
+        },
+        'subjectage': {
+            'F': 0.958,
+            'PR(>F)': 0.507,
+            'df': 1.0,
+            'mean_sq': 0.019,
+            'sum_sq': 0.019
+        },
+        'subjectage:minimentalstate': {
+            'F': 0.096,
+            'PR(>F)': 0.808,
+            'df': 1.0,
+            'mean_sq': 0.002,
+            'sum_sq': 0.002
+        }
+    }
+
+
+@mock.patch('anova.io_helper.fetch_data')
+@mock.patch('anova.io_helper.save_error')
+@mock.patch('sys.exit')
+def test_main_empty_input(mock_exit, mock_save_error, mock_fetch_data):
+    mock_fetch_data.return_value = t.inputs_regression(limit_to=0)
+    main()
+
+    mock_exit.assert_called_once_with(1)
+    mock_save_error.assert_called_once()