feat(scripts): adapt warning level checks

scripts/README.md

@@ -93,9 +93,10 @@ optionally correct what can be corrected easily in
 | ----- | ----------- | ------------- | ----------------------------- |
 | `has_consult` | Is "consult your pharmacist..." included in recommendation? | ✅ | ❌ |
 | `implication_severity` | "Much" keyword, should only be used if reflected by guideline implication. | ❌ | ✅ |
-| `red_warning` | Red warning level should always have recommendation "may not be the right medication" and vice versa. | ❌ | ❌ |
-| `yellow_warning` | Recommendation containing "adjusted" or "higher" or "lower" but not "may not be the right" should have yellow warning level. | ❌ | ❌ |
-| `green_warning` | Green warning level should have recommendation "at standard dose" but not "adjusted" and vise versa. | ❌ | ❌ |
+| `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. | ❌ | ❌ |
+| `none_warning` | None warning level should be applied in all not handled warning level cases. | ❌ | ❌ |
 | `brand_whitespace` | Drug brand names should not have leading or trailing white space. | ✅ | ❌ |
 
 \* Skips guidelines with multiple genes unless all results but one are missing

scripts/analyze.py

@@ -5,10 +5,27 @@
 from common.write_data import write_data, write_log
 
 CONSULT_TEXT = 'consult your pharmacist or doctor'
-RED_TEXT = 'may not be the right medication'
+RED_TEXT = 'not be the right medication'
+NOT_RED_TEXTS = [
+    'if more than this dose is needed',
+    "if #drug-name isn't working for you",
+]
 ADJUST_TEXT = 'adjusted'
-YELLOW_TEXTS = [ADJUST_TEXT, 'higher', 'lower']
-GREEN_TEXT = 'at standard dose'
+YELLOW_RECOMMENDATION_TEXTS = NOT_RED_TEXTS + [
+    ADJUST_TEXT,
+    'increased',
+    'decreased',
+    'lower dose',
+    'higher dose',
+    'up to a certain dose',
+    'dose increases should be done cautiously and slowly',
+    'further testing is recommended',
+]
+YELLOW_IMPLICATION_TEXTS = [
+    'increased risk',
+    'may not work',
+]
+GREEN_TEXTS = ['at standard dose', 'there is no reason to avoid']
 
 def ensure_unique_item(item_filter, field_name, value):
     item = list(item_filter)
@@ -109,22 +126,54 @@ def check_implication_severity(guideline, annotations):
     )
     return much_is_implied == implication_has_much
 
+def should_be_red(annotations):
+    return RED_TEXT in annotations['recommendation'] and all(map(
+        lambda not_red_text: not_red_text not in annotations['recommendation'],
+        NOT_RED_TEXTS,
+    ))
+
+def should_be_yellow(annotations):
+    return any(map(
+        lambda yellow_text: yellow_text in annotations['recommendation'],
+        YELLOW_RECOMMENDATION_TEXTS,
+    )) or any(map(
+        lambda yellow_text: yellow_text in annotations['implication'],
+        YELLOW_IMPLICATION_TEXTS,
+    )) or (
+        # Special case: no other recommendation given
+        annotations['recommendation'] == \
+            'consult your pharmacist or doctor for more information.'
+    )
+
+def should_be_green(annotations):
+    return any(map(
+        lambda green_text: green_text in annotations['recommendation'],
+        GREEN_TEXTS,
+    ))
+
 def check_red_warning_level(_, annotations):
     has_warning_level = annotations['warning_level'] == 'red'
-    should_have_warning_level = RED_TEXT in annotations['recommendation']
+    should_have_warning_level = should_be_red(annotations)
     return has_warning_level == should_have_warning_level
 
 def check_yellow_warning_level(_, annotations):
     has_warning_level = annotations['warning_level'] == 'yellow'
-    should_have_warning_level = any(map(
-        lambda yellow_text: yellow_text in annotations['recommendation'],
-        YELLOW_TEXTS)) and not RED_TEXT in annotations['recommendation']
+    should_have_warning_level = not should_be_red(annotations) and \
+        should_be_yellow(annotations)
     return has_warning_level if should_have_warning_level else True
 
 def check_green_warning_level(_, annotations):
     has_warning_level = annotations['warning_level'] == 'green'
-    should_have_warning_level = GREEN_TEXT in annotations['recommendation'] \
-        and not ADJUST_TEXT in annotations['recommendation']
+    should_have_warning_level = not should_be_red(annotations) and \
+        not should_be_yellow(annotations) and \
+        should_be_green(annotations)
+    return has_warning_level == should_have_warning_level
+
+def check_none_warning_level(_, annotations):
+    has_warning_level = annotations['warning_level'] == 'none'
+    should_have_warning_level = not should_be_red(annotations) and \
+        not should_be_yellow(annotations) and \
+        not should_be_green(annotations)
     return has_warning_level == should_have_warning_level
 
 def analyze_annotations(item, annotations, checks):
@@ -212,6 +261,7 @@ def handle_failed_checks(
     'red_warning_level': check_red_warning_level,
     'yellow_warning_level': check_yellow_warning_level,
     'green_warning_level': check_green_warning_level,
+    'none_warning_level': check_none_warning_level,
 }
 
 GUIDELINE_CORRECTIONS = {