feat(#639): add normal risk check

pharme.code-workspace

@@ -94,6 +94,7 @@
       "Neoprofen",
       "noto",
       "NSAID",
+      "NUDT",
       "omeprazole",
       "oxcarbazepine",
       "Oxtellar",

scripts/README.md

@@ -110,6 +110,7 @@ and optionally correct what can be corrected easily in
 | `none_warning` | None warning level should be applied in all not handled warning level cases. | ❌ | ❌ |
 | `metabolization_before_consequence` | Metabolization implications should come before consequences. | ❌ | ❌ |
 | `annotated_but_not_staged` | Warns if a guideline is annotated but not staged (ignored drugs in `IGNORE_STAGED_CHECK`) | ❌ | ❌ |
+| `should_not_have_normal_risk` | Warns if a guideline uses "normal risk" if not mentioned in external data. | ❌ | ❌ |
 
 \* Skips guidelines with multiple genes unless all results but one are missing
 or indeterminate.

scripts/analyze.py

@@ -4,6 +4,7 @@
 from analyze_functions.checks.brand_name_whitespace import check_brand_name_whitespace
 from analyze_functions.checks.metabolization_before_consequence import check_metabolization_before_consequence
 from analyze_functions.checks.fallback_guidelines import check_single_any_fallback_guideline, check_single_lookup_fallback_guideline
+from analyze_functions.checks.normal_side_effect_risk import check_normal_side_effect_risk
 from analyze_functions.checks.warning_levels import check_green_warning_level, \
     check_none_warning_level, check_red_warning_level, \
         check_yellow_warning_level
@@ -38,6 +39,7 @@
     'none_warning_level': check_none_warning_level,
     'metabolization_before_consequence': check_metabolization_before_consequence,
     'annotated_but_not_staged': check_if_fully_annotated_staged,
+    'should_not_have_normal_risk': check_normal_side_effect_risk,
 }
 
 GUIDELINE_CORRECTIONS = {

scripts/analyze_functions/checks/metabolization_severity.py

@@ -3,11 +3,10 @@
 def check_metabolization_severity(args):
     guideline = args['item']
     annotations = args['annotations']
-    ignored_phenotypes = ['no result', 'indeterminate', 'normal metabolizer']
     multiple_relevant_phenotypes = False
     relevant_gene = None
     for current_gene, current_phenotypes in guideline['phenotypes'].items():
-        if not current_phenotypes[0].lower() in ignored_phenotypes:
+        if not current_phenotypes[0].lower() in constants.IGNORED_PHENOTYPES:
             if relevant_gene != None:
                 multiple_relevant_phenotypes = True
                 break

scripts/analyze_functions/checks/normal_side_effect_risk.py

@@ -0,0 +1,20 @@
+from analyze_functions.constants import IGNORED_PHENOTYPES, NORMAL_RISK_TEXTS
+
+def check_normal_side_effect_risk(args):
+    guideline = args['item']
+    annotations = args['annotations']
+    can_have_normal_risk = any(map(
+        lambda normal_risk_text: normal_risk_text in \
+            '–'.join(guideline['externalData'][0]['implications'].values()).lower(),
+        NORMAL_RISK_TEXTS,
+    )) or all(map(
+        lambda gene:
+            (gene == 'HLA-B' and 'negative' in guideline['phenotypes'][gene][0]) \
+                or guideline['phenotypes'][gene][0].lower() in IGNORED_PHENOTYPES,
+        guideline['phenotypes'].keys(),
+    ))
+    has_normal_risk_text = any(map(
+        lambda normal_risk_text: normal_risk_text in annotations['implication'],
+        NORMAL_RISK_TEXTS,
+    ))
+    return can_have_normal_risk or not has_normal_risk_text

scripts/analyze_functions/constants.py

@@ -1,5 +1,13 @@
 CONSULT_TEXT = 'consult your pharmacist or doctor'
 WHOLE_CONSULT_TEXT = '{} for more information.'.format(CONSULT_TEXT)
+NORMAL_RISK_TEXTS = [
+    'normal risk',
+    'low or reduced risk',
+    'typical myopathy risk',
+    'weak or no evidence for an increased risk',
+    '"normal" risk',
+]
+IGNORED_PHENOTYPES = ['no result', 'indeterminate', 'normal metabolizer']
 RED_TEXT = 'not be the right medication'
 NOT_RED_TEXTS = [
     'if more than this dose is needed',