Dom fix controls (#160)

* fixed #158 and #159

Author: terazus

ptmd/lib/validator/core.py

@@ -170,7 +170,7 @@ class VerticalValidator:
 
     def __init__(self, definitions: dict, validator: ExcelValidator) -> None:
         """ The validator constructor. """
-        self.controls_keys: list[str] = ['CONTROL (DMSO)', 'CONTROL (WATER)']
+        self.controls_keys: list[str] = ['CONTROL (DMSO)', 'CONTROL (Water)']
         self.validator: ExcelValidator = validator
         self.timepoints: list = definitions['timepoints']
         self.replicates: int = definitions['replicates']
@@ -263,6 +263,10 @@ def validate(self) -> None:
             if compound_name == 'EXTRACTION BLANK':
                 break
 
+            if compound_name in self.controls_keys:
+                self.validate_controls(compound_val)
+                break
+
             for timepoint in compound_val['replicates']:
                 if timepoint in self.timepoints:
                     replicate: int = compound_val['replicates'][timepoint]
@@ -283,3 +287,27 @@ def validate(self) -> None:
                 elif timepoint < len(self.timepoints):
                     message = f"Timepoint {replicate} is missing {len(self.timepoints) - timepoint} replicate(s)."
                     self.validator.add_error(compound_name, message, 'replicates')
+
+    def validate_controls(self, compound_values: dict) -> None:
+        """ Validates the controls points against the general information. Verify the number of replicates and
+        timepoints.
+
+        :param compound_values: The compound values to validate.
+        """
+        message: str
+        for timepoint, replicate in compound_values['replicates'].items():
+            if replicate < self.controls:
+                message = f"Control at timepoint {timepoint} is missing {self.controls - replicate} replicate(s)."
+                self.validator.add_error('Control', message, 'replicates')
+            elif replicate > self.controls:
+                message = f"Control at timepoint {timepoint} has too many replicates ({replicate})."
+                self.validator.add_error('Control', message, 'replicates')
+
+        for replicate, timepoint in compound_values['timepoints'].items():
+            if timepoint > len(self.timepoints):
+                message = f"Timepoint {replicate} has greater number of controls {timepoint} " \
+                          f"than expected ({self.controls})."
+                self.validator.add_error('Control', message, 'timepoints')
+            elif timepoint < len(self.timepoints):
+                message = f"Timepoint {replicate} is missing {len(self.timepoints) - timepoint} control(s)."
+                self.validator.add_error('Control', message, 'timepoints')

tests/test_lib/test_validator/test_core.py

@@ -287,3 +287,61 @@ def test_validate_failed_box_id(self):
         }
         self.assertFalse(validator.report['valid'])
         self.assertEqual(validator.report['errors'], expected_error)
+
+    def test_validate_failed_too_many_controls(self):
+        validator = MockValidator()
+        self.general_information['controls'] = 1
+        self.general_information['timepoints'] = [4]
+        vertical_validator = VerticalValidator(self.general_information, validator)
+        vertical_validator.add_node({
+            'data': {
+                'compound_name': 'CONTROL (Water)',
+                'replicate': 1,
+                'timepoint_(hours)': 4,
+                'dose_code': 0,
+                'box_id': 'Box1',
+                'box_column': 1,
+                'box_row': 'A',
+                'collection_order': 1
+            },
+            'label': 'CP1'
+        })
+        vertical_validator.add_node({
+            'data': {
+                'compound_name': 'CONTROL (Water)',
+                'replicate': 2,
+                'timepoint_(hours)': 4,
+                'dose_code': 0,
+                'box_id': 'Box1',
+                'box_column': 1,
+                'box_row': 'B',
+                'collection_order': 2
+            },
+            'label': 'CP2'
+        })
+        vertical_validator.validate()
+        errors = validator.report['errors']
+        self.assertEqual(errors['CP2'][0]['message'], 'Control 2 is greater than the number of controls 1.')
+        self.assertEqual(errors['Control'][0]['message'], 'Control at timepoint 4 has too many replicates (2).')
+
+    def test_validate_failed_not_enough_controls(self):
+        validator = MockValidator()
+        self.general_information['controls'] = 1
+        self.general_information['timepoints'] = [4, 12]
+        vertical_validator = VerticalValidator(self.general_information, validator)
+        vertical_validator.add_node({
+            'data': {
+                'compound_name': 'CONTROL (Water)',
+                'replicate': 1,
+                'timepoint_(hours)': 4,
+                'dose_code': 0,
+                'box_id': 'Box1',
+                'box_column': 1,
+                'box_row': 'A',
+                'collection_order': 1
+            },
+            'label': 'CP1'
+        })
+        vertical_validator.validate()
+        errors = validator.report['errors']
+        self.assertEqual(errors['Control'][0]['message'], 'Timepoint 1 is missing 1 control(s).')