feat(#639): add overwrites for implication severity check

pharme.code-workspace

@@ -122,6 +122,7 @@
       "screendocs",
       "sertraline",
       "simvastatin",
+      "siponimod",
       "SLCO",
       "statin",
       "Statins",

scripts/README.md

@@ -109,7 +109,7 @@ and which bricks are not used in guidelines.
 | Check | Description | `--correct`ed | Only for single-gene results* |
 | ----- | ----------- | ------------- | ----------------------------- |
 | `has_consult` | Is "consult your pharmacist..." included in recommendation? | ✅ | ❌ |
-| `check_metabolization_severity` | "Much" keyword, should only be used if reflected by guideline implication. | ❌ | ✅ |
+| `check_metabolization_severity` | "Much" keyword, should only be used if reflected by guideline implication (or guideline lookup in `METABOLIZATION_SEVERITY_OVERWRITES`). | ❌ | ✅ |
 | `red_warning` | Red warning level should be present with recommendation containing "may not be the right medication". | ❌ | ❌ |
 | `yellow_warning` | Yellow warning level should be present when the red warning level does not apply but the implication contains "may not work" or "side effects" or the recommendation contains non-standard dose. | ❌ | ❌ |
 | `green_warning` | Green warning level should be applied in all non-red and non-yellow cases and when the recommendation states "at standard dose" or similar formulations. | ❌ | ❌ |

scripts/analyze_functions/checks/fully_annotated_staged.py

@@ -1,12 +1,4 @@
-IGNORE_STAGED_CHECK = [#
-    'amikacin',
-    'gentamicin',
-    'kanamycin',
-    'paromomycin',
-    'tobramycin',
-    'streptomycin',
-    'plazomicin',
-]
+from analyze_functions.constants import IGNORE_STAGED_CHECK
 
 def check_if_fully_annotated_staged(args):
     if args['drug_name'] in IGNORE_STAGED_CHECK: return None

scripts/analyze_functions/checks/metabolization_severity.py

@@ -1,8 +1,26 @@
 import analyze_functions.constants as constants
 
+def _get_severity_overwrite(drug_name, guideline):
+    severity_overwrite = None
+    guideline_lookup = guideline['lookupkey']
+    present_overwrites = list(filter(
+        lambda overwrite: overwrite['drug'] == drug_name and \
+            overwrite['lookup'] == guideline_lookup,
+        constants.METABOLIZATION_SEVERITY_OVERWRITES,
+    ))
+    if len(present_overwrites) > 1:
+        print(
+            'WARNING: found multiple applying lookup overwrites for '
+            f'{drug_name}, {guideline_lookup}; only using first one'
+        )
+    if len(present_overwrites) > 0:
+        severity_overwrite = present_overwrites[0]['overwrite']
+    return severity_overwrite
+
 def check_metabolization_severity(args):
     guideline = args['item']
     annotations = args['annotations']
+    drug_name = args['drug_name']
     multiple_relevant_phenotypes = False
     relevant_gene = None
     for current_gene, current_phenotypes in guideline['phenotypes'].items():
@@ -22,10 +40,14 @@ def check_metabolization_severity(args):
             constants.MUCH_IMPLYING_METABOLIZATION_FORMULATIONS,
         )
     )
+    severity_overwrite = _get_severity_overwrite(drug_name, guideline)
+    should_have_much = severity_overwrite \
+        if severity_overwrite != None \
+        else much_is_implied
     implication_has_much = any(
         map(
             lambda much_formulation: much_formulation in annotations['implication'],
             constants.MUCH_METABOLIZATION_FORMULATIONS,
         )
     )
-    return much_is_implied == implication_has_much
+    return should_have_much == implication_has_much

scripts/analyze_functions/constants.py

@@ -1,3 +1,26 @@
+METABOLIZATION_SEVERITY_OVERWRITES = [
+    {
+        'drug': 'voriconazole',
+        'lookup': {'CYP2C19': ['Ultrarapid Metabolizer']},
+        'overwrite': True,
+    },
+    {
+        'drug': 'siponimod',
+        'lookup': {'CYP2C9': ['0.0']},
+        'overwrite': True,
+    },
+]
+
+IGNORE_STAGED_CHECK = [
+    'amikacin',
+    'gentamicin',
+    'kanamycin',
+    'paromomycin',
+    'tobramycin',
+    'streptomycin',
+    'plazomicin',
+]
+
 CONSULT_TEXT = 'consult your pharmacist or doctor'
 WHOLE_CONSULT_TEXT = '{} for more information.'.format(CONSULT_TEXT)
 NORMAL_RISK_TEXTS = [