feat(#639): add non metabolizer check

scripts/README.md

@@ -110,7 +110,8 @@ 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. | ❌ | ❌ |
+| `should_not_have_normal_risk` | Warns if an annotation uses "normal risk" if not mentioned in external data. | ❌ | ❌ |
+| `non_metabolizer` | Warns if an annotation uses "break down" or "activate" but is for `NON_METABOLIZERS`. | ❌ | ❌ |
 
 \* 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.non_metabolizer import check_non_metabolizer
 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, \
@@ -40,6 +41,7 @@
     '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,
+    'non_metabolizer': check_non_metabolizer,
 }
 
 GUIDELINE_CORRECTIONS = {

scripts/analyze_functions/checks/non_metabolizer.py

@@ -0,0 +1,18 @@
+import analyze_functions.constants as constants
+
+def check_non_metabolizer(args):
+    guideline = args['item']
+    annotations = args['annotations']
+    is_non_metabolizer_guideline = any(map(
+        lambda gene: gene in constants.NON_METABOLIZERS,
+        guideline['phenotypes'].keys(),
+    )) and all(map(
+        lambda gene: gene in constants.NON_METABOLIZERS or \
+            guideline['phenotypes'][gene][0].lower() in constants.MISSING_PHENOTYPES,
+        guideline['phenotypes'].keys(),
+    ))
+    has_metabolizer_text = any(map(
+        lambda metabolizer_text: metabolizer_text in annotations['implication'],
+        constants.METABOLIZER_TEXTS,
+    ))
+    return not is_non_metabolizer_guideline or not has_metabolizer_text

scripts/analyze_functions/constants.py

@@ -7,7 +7,16 @@
     'weak or no evidence for an increased risk',
     '"normal" risk',
 ]
-IGNORED_PHENOTYPES = ['no result', 'indeterminate', 'normal metabolizer']
+NON_METABOLIZERS = [
+    'G6PD',
+    'SLCO1B1',
+    'MT-RNR1',
+    'HLA-B',
+    'HLA-A',
+]
+METABOLIZER_TEXTS = ['break down', 'activate']
+MISSING_PHENOTYPES = ['no result', 'indeterminate']
+IGNORED_PHENOTYPES = [*MISSING_PHENOTYPES, 'normal metabolizer']
 RED_TEXT = 'not be the right medication'
 NOT_RED_TEXTS = [
     'if more than this dose is needed',