feat(#639): add same metabolization check

scripts/analyze.py

@@ -4,6 +4,7 @@
 from analyze_functions.checks.brand_name import check_brand_name_comma, 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.metabolization_type import check_same_metabolization_type
 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.slow_titration import check_slow_titration
@@ -27,6 +28,7 @@
     'single_any_fallback': check_single_any_fallback_guideline,
     'fallback_single_lookup': check_single_lookup_fallback_guideline,
     'annotated_but_not_staged': check_if_fully_annotated_staged,
+    'same_metabolization': check_same_metabolization_type,
 }
 
 DRUG_CORRECTIONS = {
@@ -115,6 +117,11 @@ def run_analyses():
         log_content.append(f'* {drug_name}')
         used_bricks += get_used_bricks(drug)
         drug_annotations = get_drug_annotations(data, drug)
+        guideline_ids = drug['guidelines']
+        guidelines = list(map(
+            lambda guideline_id: get_guideline_by_id(data, guideline_id),
+            guideline_ids,
+        ))
         if not has_annotations(drug_annotations):
             missing_drug_annotation_count += 1
             log_not_annotated(log_content)
@@ -126,6 +133,7 @@ def run_analyses():
                     'annotations': drug_annotations,
                     'data': data,
                     'drug_name': drug_name,
+                    'drug_guidelines': guidelines,
                 },
             )
             if not all(drug_result.values()):
@@ -136,8 +144,7 @@ def run_analyses():
                 failed_drug_annotation_count += failed
             else:
                 log_all_passed(log_content)
-        for guideline_id in drug['guidelines']:
-            guideline = get_guideline_by_id(data, guideline_id)
+        for guideline in guidelines:
             used_bricks += get_used_bricks(guideline)
             phenotype = get_phenotype_key(guideline)
             log_content.append(f'  * {phenotype}')
@@ -167,7 +174,7 @@ def run_analyses():
     log_header = [
         '# Analyze annotation data\n\n',
         f'Correct if possible: {correct_inconsistencies}\n\n',
-        'Failed annotation checks (search for `_some checks failed_`):\n\n',
+        '**Failed annotation checks** (search for `_some checks failed_`):\n\n',
         f'* Drugs: {failed_drug_annotation_count}\n',
         f'* Guidelines: {failed_guideline_annotation_count}\n\n',
         'Missing annotations (search for `_not annotated_`):\n\n',

scripts/analyze_functions/checks/metabolization_type.py

@@ -0,0 +1,16 @@
+from analyze_functions.constants import ACTIVATE_TEXT, BREAK_DOWN_TEXT
+from analyze_functions.data_helpers import get_guideline_annotations
+
+def check_same_metabolization_type(args):
+    data = args['data']
+    guidelines = args['drug_guidelines']
+    has_activate = False
+    has_break_down = False
+    for guideline in guidelines:
+        if has_activate and has_break_down: break
+        annotations = get_guideline_annotations(data, guideline)
+        implication = annotations['implication']
+        if implication == None: continue
+        if ACTIVATE_TEXT in implication: has_activate = True
+        if BREAK_DOWN_TEXT in implication: has_break_down = True
+    return not (has_activate and has_break_down)

scripts/analyze_functions/constants.py

@@ -14,7 +14,9 @@
     'HLA-B',
     'HLA-A',
 ]
-METABOLIZER_TEXTS = ['break down', 'activate']
+BREAK_DOWN_TEXT = 'break down'
+ACTIVATE_TEXT = 'activate'
+METABOLIZER_TEXTS = [BREAK_DOWN_TEXT, ACTIVATE_TEXT]
 MISSING_PHENOTYPES = ['no result', 'indeterminate']
 IGNORED_PHENOTYPES = [*MISSING_PHENOTYPES, 'normal metabolizer']
 RED_TEXT = 'not be the right medication'