feat(#639): add slow titration check

scripts/README.md

@@ -113,6 +113,7 @@ and optionally correct what can be corrected easily in
 | `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 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`. | ❌ | ❌ |
+| `slow_titration` | If otherwise standard dose, "slow titration" and "cautiously and slowly" should be used together. | ❌ | ❌ |
 
 \* Skips guidelines with multiple genes unless all results but one are missing
 or indeterminate.

scripts/analyze.py

@@ -6,6 +6,7 @@
 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.slow_titration import check_slow_titration
 from analyze_functions.checks.warning_levels import check_green_warning_level, \
     check_none_warning_level, check_red_warning_level, \
         check_yellow_warning_level
@@ -43,6 +44,7 @@
     'annotated_but_not_staged': check_if_fully_annotated_staged,
     'should_not_have_normal_risk': check_normal_side_effect_risk,
     'non_metabolizer': check_non_metabolizer,
+    'slow_titration': check_slow_titration,
 }
 
 GUIDELINE_CORRECTIONS = {

scripts/analyze_functions/checks/normal_side_effect_risk.py

@@ -1,11 +1,12 @@
 from analyze_functions.constants import IGNORED_PHENOTYPES, NORMAL_RISK_TEXTS
+from analyze_functions.data_helpers import joint_annotation_text
 
 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(),
+            joint_annotation_text(guideline),
         NORMAL_RISK_TEXTS,
     )) or all(map(
         lambda gene:

scripts/analyze_functions/checks/slow_titration.py

@@ -0,0 +1,11 @@
+import analyze_functions.constants as constants
+from analyze_functions.data_helpers import get_guideline_content
+
+def check_slow_titration(args):
+    guideline = args['item']
+    annotations = args['annotations']
+    guideline_recommendation = get_guideline_content(guideline, 'recommendation')
+    should_have_slow_titration = 'slower titration' in guideline_recommendation \
+        and not 'lower dose' in annotations['recommendation']
+    has_slow_titration = 'cautiously and slowly' in annotations['recommendation']
+    return not should_have_slow_titration or has_slow_titration

scripts/analyze_functions/data_helpers.py

@@ -1,5 +1,11 @@
 from common.constants import BRICK_COLLECTION_NAME
 
+def get_guideline_content(guideline, key):
+    return guideline['externalData'][0][key]
+
+def joint_annotation_text(guideline):
+    return '–'.join(get_guideline_content(guideline, 'implications').values()).lower()
+
 def ensure_unique_item(item_filter, field_name, value):
     item = list(item_filter)
     if len(item) != 1: