Dom debug (#125)

* fixed #117 * fixed #119 * fixed #122 * Fixed #123 * fixed #120
precisiontox · Nov 27, 2023 · 2e42e8c · 2e42e8c
1 parent 1bdc60b
commit 2e42e8c
Show file tree

Hide file tree

Showing 6 changed files with 24 additions and 6 deletions.
diff --git a/ptmd/database/queries/chemicals.py b/ptmd/database/queries/chemicals.py
@@ -36,7 +36,7 @@ def create_chemicals(chemicals: list[dict]) -> dict[str, Chemical]:
     """
     LOGGER.info('Creating Chemicals')
     chemicals_in_database = {}
-    water: Chemical = Chemical(common_name='Water', ptx_code=997, cas='7732-18-5', formula='H2O')
+    water: Chemical = Chemical(common_name='Water', ptx_code=000, cas='7732-18-5', formula='H2O')
     dmso: Chemical = Chemical(common_name='DMSO', ptx_code=998, cas='67-68-5', formula='C2H6OS')
     session.add_all([water, dmso])
     session.commit()

diff --git a/ptmd/lib/creator/dataframes.py b/ptmd/lib/creator/dataframes.py
@@ -79,7 +79,7 @@ def build_sample_dataframe(harvester: Any, chemicals_mapping: dict[str, str], or
         timepoint_key = f'TP{tp}'
         timepoint = TIME_POINT_MAPPING[timepoint_key] if timepoint_key in TIME_POINT_MAPPING else 'X'
         timepoint_value = harvester.timepoints[tp - 1]
-        control_code = '999' if harvester.vehicle == 'DMSO' else '997'
+        control_code = '999' if harvester.vehicle == 'DMSO' else '000'
         for replicate in range(1, harvester.replicates4control + 1):
             hash_id = '%s%s%sZ%s%s' % (organism_code, harvester.exposure_batch, control_code, timepoint, replicate)
             series = Series([hash_id, BASE_IDENTIFIER + control_code, *EMPTY_FIELDS_VALUES,

diff --git a/ptmd/lib/validator/core.py b/ptmd/lib/validator/core.py
@@ -214,7 +214,7 @@ def add_node(self, node: dict) -> None:
             else:
                 self.collection_order.append(collection_order)
 
-            if replicate > self.replicates:
+            if compound_name not in self.controls_keys and replicate > self.replicates:
                 message = f"Replicate {replicate} is greater than the number of replicates {self.replicates}."
                 self.validator.add_error(label, message, 'replicate')
 
@@ -232,6 +232,9 @@ def add_node(self, node: dict) -> None:
                 if dose != 0:
                     message = "Controls must have a dose of 0."
                     self.validator.add_error(label, message, 'dose_code')
+                if replicate > self.controls:
+                    message = f"Control {replicate} is greater than the number of controls {self.controls}."
+                    self.validator.add_error(label, message, 'replicate')
 
             if compound_name not in self.compounds:
                 self.compounds[compound_name] = {

diff --git a/ptmd/lib/validator/validate_identifier.py b/ptmd/lib/validator/validate_identifier.py
@@ -164,9 +164,9 @@ def validate_controls_compound(validator: Any, compound_name: str, code: int) ->
         validator.add_error(validator.current_record['label'],
                             f"The identifier compound should be 999 but got {code}.",
                             PTX_ID_LABEL)
-    elif 'WATER' in compound_name and code != 997:
+    elif 'WATER' in compound_name and code != 000:
         validator.add_error(validator.current_record['label'],
-                            f"The identifier compound should be 997 but got {code}.",
+                            f"The identifier compound should be 000 but got {code}.",
                             PTX_ID_LABEL)
 
 

diff --git a/tests/test_lib/test_validator/test_core.py b/tests/test_lib/test_validator/test_core.py
@@ -230,6 +230,21 @@ def test_validate_replicate_too_many(self):
         self.assertEqual(validator.report['errors'][self.organism][0]['message'],
                          "Replicate 1 has too many timepoints.")
 
+    def test_validate_controls_too_many(self):
+        validator = MockValidator()
+        extra_node: dict = {**self.default_node}
+        self.general_information['control'] = 8
+        extra_node['data']['replicate'] = 12
+        extra_node['data']['compound_name'] = "CONTROL (DMSO)"
+        extra_node['data']['dose_code'] = 0
+        graph = VerticalValidator(self.general_information, validator)
+        graph.add_node(self.default_node)
+        graph.add_node(extra_node)
+        graph.validate()
+        self.assertFalse(validator.report['valid'])
+        self.assertEqual(validator.report['errors']['CP1'][0]['message'],
+                         "Control 12 is greater than the number of controls 8.")
+
     def test_validate_controls_dose_not_zero(self):
         validator = MockValidator()
         self.general_information['control'] = 1

diff --git a/tests/test_lib/test_validator/test_validate_identifier.py b/tests/test_lib/test_validator/test_validate_identifier.py
@@ -181,7 +181,7 @@ def test_validate_compound_controls(self, mock_chemical):
         validate_compound(validator)
         self.assertFalse(validator.report['valid'])
         self.assertEqual(validator.report['errors']['test'][0]['message'],
-                         "The identifier compound should be 997 but got 2.")
+                         "The identifier compound should be 000 but got 2.")
 
     def test_validate_compound_blanks(self):
         validator = ExcelValidatorMock()