Allow ranges to contain a standalone baseline score

Previously, a score range with a baseline score had validation that required a normal score range. This has been temporarily (or perhaps not temporarily) relaxed. Because of this validation change, an associated change was also needed in annotation library code that checked the validity of incoming ranges for annotation.

Author: bencap

src/mavedb/lib/annotation/classification.py

@@ -33,7 +33,7 @@ def functional_classification_of_variant(
     # This view model object is much simpler to work with.
     score_ranges = ScoreSetRanges(**mapped_variant.variant.score_set.score_ranges).investigator_provided
 
-    if not score_ranges:
+    if not score_ranges or not score_ranges.ranges:
         raise ValueError(
             f"Variant {mapped_variant.variant.urn} does not have investigator-provided score ranges."
             " Unable to classify functional impact."
@@ -71,7 +71,7 @@ def zeiberg_calibration_clinical_classification_of_variant(
 
     score_ranges = ScoreSetRanges(**mapped_variant.variant.score_set.score_ranges).zeiberg_calibration
 
-    if not score_ranges:
+    if not score_ranges or not score_ranges.ranges:
         raise ValueError(
             f"Variant {mapped_variant.variant.urn} does not have pillar project score ranges."
             " Unable to classify clinical impact."

src/mavedb/lib/annotation/util.py

@@ -162,7 +162,7 @@ def _can_annotate_variant_base_assumptions(mapped_variant: MappedVariant) -> boo
     return True
 
 
-def _variant_score_ranges_have_required_keys_for_annotation(
+def _variant_score_ranges_have_required_keys_and_ranges_for_annotation(
     mapped_variant: MappedVariant, key_options: list[str]
 ) -> bool:
     """
@@ -173,7 +173,8 @@ def _variant_score_ranges_have_required_keys_for_annotation(
         key_options (list[str]): List of possible score range keys to check for in the score set.
 
     Returns:
-        bool: False if none of the required keys are found or if all found keys have None values.
+        bool: False if none of the required keys are found or if all found keys have None values or if all found keys
+              do not have range data.
               Returns True (implicitly) if at least one required key exists with a non-None value.
     """
     if mapped_variant.variant.score_set.score_ranges is None:
@@ -182,6 +183,7 @@ def _variant_score_ranges_have_required_keys_for_annotation(
     if not any(
         range_key in mapped_variant.variant.score_set.score_ranges
         and mapped_variant.variant.score_set.score_ranges[range_key] is not None
+        and mapped_variant.variant.score_set.score_ranges[range_key]["ranges"]
         for range_key in key_options
     ):
         return False
@@ -209,14 +211,14 @@ def can_annotate_variant_for_pathogenicity_evidence(mapped_variant: MappedVarian
     Notes:
         The function performs two main validation checks:
         1. Basic annotation assumptions via _can_annotate_variant_base_assumptions
-        2. Required clinical range keys via _variant_score_ranges_have_required_keys_for_annotation
+        2. Required clinical range keys via _variant_score_ranges_have_required_keys_and_ranges_for_annotation
 
         Both checks must pass for the variant to be considered eligible for
         pathogenicity evidence annotation.
     """
     if not _can_annotate_variant_base_assumptions(mapped_variant):
         return False
-    if not _variant_score_ranges_have_required_keys_for_annotation(mapped_variant, CLINICAL_RANGES):
+    if not _variant_score_ranges_have_required_keys_and_ranges_for_annotation(mapped_variant, CLINICAL_RANGES):
         return False
 
     return True
@@ -245,7 +247,7 @@ def can_annotate_variant_for_functional_statement(mapped_variant: MappedVariant)
     """
     if not _can_annotate_variant_base_assumptions(mapped_variant):
         return False
-    if not _variant_score_ranges_have_required_keys_for_annotation(mapped_variant, FUNCTIONAL_RANGES):
+    if not _variant_score_ranges_have_required_keys_and_ranges_for_annotation(mapped_variant, FUNCTIONAL_RANGES):
         return False
 
     return True

src/mavedb/view_models/score_range.py

@@ -205,7 +205,9 @@ def validate_baseline_score(self: "BrnichScoreRangesBase") -> "BrnichScoreRanges
 
         if baseline_score is not None:
             if not any(range_model.classification == "normal" for range_model in ranges):
-                raise ValidationError("A baseline score has been provided, but no normal classification range exists.")
+                # For now, we do not raise an error if a baseline score is provided but no normal range exists.
+                # raise ValidationError("A baseline score has been provided, but no normal classification range exists.")
+                return self
 
         normal_ranges = [range_model.range for range_model in ranges if range_model.classification == "normal"]
 

tests/lib/annotation/test_annotate.py

@@ -19,6 +19,13 @@ def test_variant_functional_impact_statement_no_score_ranges(mock_mapped_variant
     assert result is None
 
 
+def test_variant_functional_impact_statement_no_score_range_data(mock_mapped_variant):
+    mock_mapped_variant.variant.score_set.score_ranges["investigator_provided"]["ranges"] = []
+    result = variant_functional_impact_statement(mock_mapped_variant)
+
+    assert result is None
+
+
 def test_variant_functional_impact_statement_no_score(mock_mapped_variant):
     mock_mapped_variant.variant.data = {"score_data": {"score": None}}
     result = variant_functional_impact_statement(mock_mapped_variant)
@@ -73,6 +80,13 @@ def test_variant_pathogenicity_evidence_with_score_ranges_no_thresholds(mock_map
     assert result is None
 
 
+def test_variant_pathogenicity_evidence_with_score_ranges_no_threshold_data(mock_mapped_variant):
+    mock_mapped_variant.variant.score_set.score_ranges["zeiberg_calibration"]["ranges"] = []
+    result = variant_pathogenicity_evidence(mock_mapped_variant)
+
+    assert result is None
+
+
 def test_variant_pathogenicity_evidence_with_score_ranges_with_thresholds(mock_mapped_variant):
     result = variant_pathogenicity_evidence(mock_mapped_variant)
 

tests/lib/annotation/test_util.py

@@ -4,12 +4,16 @@
 from mavedb.lib.annotation.util import (
     variation_from_mapped_variant,
     _can_annotate_variant_base_assumptions,
-    _variant_score_ranges_have_required_keys_for_annotation,
+    _variant_score_ranges_have_required_keys_and_ranges_for_annotation,
     can_annotate_variant_for_functional_statement,
     can_annotate_variant_for_pathogenicity_evidence,
 )
 
-from tests.helpers.constants import TEST_VALID_POST_MAPPED_VRS_ALLELE, TEST_SEQUENCE_LOCATION_ACCESSION
+from tests.helpers.constants import (
+    TEST_VALID_POST_MAPPED_VRS_ALLELE,
+    TEST_SEQUENCE_LOCATION_ACCESSION,
+    TEST_BRNICH_SCORE_SET_RANGE_WITH_SOURCE,
+)
 from unittest.mock import patch
 
 
@@ -53,28 +57,35 @@ def test_score_range_check_returns_false_when_keys_are_none(mock_mapped_variant)
     mock_mapped_variant.variant.score_set.score_ranges = None
     key_options = ["required_key1", "required_key2"]
 
-    assert _variant_score_ranges_have_required_keys_for_annotation(mock_mapped_variant, key_options) is False
+    assert _variant_score_ranges_have_required_keys_and_ranges_for_annotation(mock_mapped_variant, key_options) is False
 
 
 def test_score_range_check_returns_false_when_no_keys_present(mock_mapped_variant):
-    mock_mapped_variant.variant.score_set.score_ranges = {"other_key": "value"}
+    mock_mapped_variant.variant.score_set.score_ranges = {"other_key": TEST_BRNICH_SCORE_SET_RANGE_WITH_SOURCE}
     key_options = ["required_key1", "required_key2"]
 
-    assert _variant_score_ranges_have_required_keys_for_annotation(mock_mapped_variant, key_options) is False
+    assert _variant_score_ranges_have_required_keys_and_ranges_for_annotation(mock_mapped_variant, key_options) is False
 
 
 def test_score_range_check_returns_false_when_key_present_but_value_is_none(mock_mapped_variant):
     mock_mapped_variant.variant.score_set.score_ranges = {"required_key1": None}
     key_options = ["required_key1", "required_key2"]
 
-    assert _variant_score_ranges_have_required_keys_for_annotation(mock_mapped_variant, key_options) is False
+    assert _variant_score_ranges_have_required_keys_and_ranges_for_annotation(mock_mapped_variant, key_options) is False
+
+
+def test_score_range_check_returns_false_when_key_present_but_range_value_is_empty(mock_mapped_variant):
+    mock_mapped_variant.variant.score_set.score_ranges = {"required_key1": {"ranges": []}}
+    key_options = ["required_key1", "required_key2"]
+
+    assert _variant_score_ranges_have_required_keys_and_ranges_for_annotation(mock_mapped_variant, key_options) is False
 
 
 def test_score_range_check_returns_none_when_at_least_one_key_has_value(mock_mapped_variant):
-    mock_mapped_variant.variant.score_set.score_ranges = {"required_key1": "value"}
+    mock_mapped_variant.variant.score_set.score_ranges = {"required_key1": TEST_BRNICH_SCORE_SET_RANGE_WITH_SOURCE}
     key_options = ["required_key1", "required_key2"]
 
-    assert _variant_score_ranges_have_required_keys_for_annotation(mock_mapped_variant, key_options) is True
+    assert _variant_score_ranges_have_required_keys_and_ranges_for_annotation(mock_mapped_variant, key_options) is True
 
 
 ## Test clinical range check
@@ -89,7 +100,7 @@ def test_clinical_range_check_returns_false_when_base_assumptions_fail(mock_mapp
 
 @pytest.mark.parametrize("clinical_ranges", [["clinical_range"], ["other_clinical_range"]])
 def test_clinical_range_check_returns_false_when_clinical_ranges_check_fails(mock_mapped_variant, clinical_ranges):
-    mock_mapped_variant.variant.score_set.score_ranges = {"unrelated_key": "value"}
+    mock_mapped_variant.variant.score_set.score_ranges = {"unrelated_key": TEST_BRNICH_SCORE_SET_RANGE_WITH_SOURCE}
 
     with patch("mavedb.lib.annotation.util.CLINICAL_RANGES", clinical_ranges):
         result = can_annotate_variant_for_pathogenicity_evidence(mock_mapped_variant)
@@ -116,7 +127,7 @@ def test_functional_range_check_returns_false_when_base_assumptions_fail(mock_ma
 def test_functional_range_check_returns_false_when_functional_ranges_check_fails(
     mock_mapped_variant, functional_ranges
 ):
-    mock_mapped_variant.variant.score_set.score_ranges = {"unrelated_key": "value"}
+    mock_mapped_variant.variant.score_set.score_ranges = {"unrelated_key": TEST_BRNICH_SCORE_SET_RANGE_WITH_SOURCE}
 
     with patch("mavedb.lib.annotation.util.FUNCTIONAL_RANGES", functional_ranges):
         result = can_annotate_variant_for_functional_statement(mock_mapped_variant)

tests/view_models/test_score_range.py

@@ -646,6 +646,7 @@ def test_score_ranges_zeiberg_calibration_ranges_boundaries_may_be_adjacent(
     ScoreRangesModel(**valid_data)
 
 
+@pytest.mark.skip("Not applicable currently. Baseline score may be provided on its own.")
 @pytest.mark.parametrize(
     "ScoreRangesModel",
     [