VA-Spec tests for variant annotations

tests/lib/annotation/test_variant.py

@@ -0,0 +1,167 @@
+from unittest.mock import patch
+from ga4gh.va_spec.profiles import (
+    AssayVariantEffectMeasurementStudyResult,
+    AssayVariantEffectFunctionalClassificationStatement,
+    AssayVariantEffectClinicalClassificationStatement,
+)
+from ga4gh.vrs.models import MolecularVariation
+from ga4gh.va_spec.profiles.assay_var_effect import AveFunctionalClassification, AveClinicalClassification
+
+from mavedb.lib.annotation.dataset import score_set_to_data_set
+from mavedb.lib.annotation.document import variant_to_document, experiment_as_iri, score_set_to_document
+from mavedb.lib.annotation.contribution import (
+    mavedb_api_contribution,
+    mavedb_vrs_contribution,
+    mavedb_creator_contribution,
+    mavedb_modifier_contribution,
+)
+from mavedb.lib.annotation.variant import (
+    mapped_variant_to_variant_effect_measurement_study_result,
+    mapped_variant_to_functional_classification_statement,
+    mapped_variant_to_clinical_classification_statement,
+    annotation_for_variant,
+)
+
+from tests.helpers.constants import TEST_VALID_POST_MAPPED_VRS_ALLELE
+
+
+def test_mapped_variant_to_variant_effect_measurement_study_result(mock_mapped_variant):
+    result = mapped_variant_to_variant_effect_measurement_study_result(mock_mapped_variant)
+
+    assert isinstance(result, AssayVariantEffectMeasurementStudyResult)
+    assert result.score == 1.0
+    assert result.focusVariant == MolecularVariation(**TEST_VALID_POST_MAPPED_VRS_ALLELE)
+    assert len(result.sourceDataSet) > 0
+    assert score_set_to_data_set(mock_mapped_variant.variant.score_set) in result.sourceDataSet
+    assert len(result.reportedIn) > 0
+    assert variant_to_document(mock_mapped_variant.variant) in result.reportedIn
+    assert len(result.contributions) > 0
+    assert mavedb_api_contribution() in result.contributions
+    assert mavedb_vrs_contribution(mock_mapped_variant) in result.contributions
+
+
+def test_mapped_variant_to_functional_classification_statement(mock_mapped_variant):
+    classification = AveFunctionalClassification.NORMAL
+    with patch("mavedb.lib.annotation.variant.functional_classification_of_variant", return_value=classification):
+        result = mapped_variant_to_functional_classification_statement(mock_mapped_variant)
+
+    assert isinstance(result, AssayVariantEffectFunctionalClassificationStatement)
+    assert result.classification == classification
+    assert result.subjectVariant == MolecularVariation(**TEST_VALID_POST_MAPPED_VRS_ALLELE)
+    assert experiment_as_iri(mock_mapped_variant.variant.score_set.experiment) == result.objectAssay.root
+    assert len(result.reportedIn) > 0
+    assert variant_to_document(mock_mapped_variant.variant) in result.reportedIn
+    assert score_set_to_document(mock_mapped_variant.variant.score_set) in result.reportedIn
+    assert len(result.contributions) > 0
+    assert mavedb_api_contribution() in result.contributions
+    assert mavedb_vrs_contribution(mock_mapped_variant) in result.contributions
+    assert (
+        mavedb_creator_contribution(mock_mapped_variant.variant, mock_mapped_variant.variant.score_set.created_by)
+        in result.contributions
+    )
+    assert (
+        mavedb_creator_contribution(
+            mock_mapped_variant.variant.score_set, mock_mapped_variant.variant.score_set.created_by
+        )
+        in result.contributions
+    )
+    assert (
+        mavedb_modifier_contribution(
+            mock_mapped_variant.variant.score_set, mock_mapped_variant.variant.score_set.modified_by
+        )
+        in result.contributions
+    )
+
+
+def test_mapped_variant_to_functional_classification_statement_classification_is_none(mock_mapped_variant):
+    with patch("mavedb.lib.annotation.variant.functional_classification_of_variant", return_value=None):
+        result = mapped_variant_to_functional_classification_statement(mock_mapped_variant)
+        assert result is None
+
+
+def test_mapped_variant_to_clinical_classification_statement(mock_mapped_variant):
+    classification = AveClinicalClassification.BS3_MODERATE
+    with patch(
+        "mavedb.lib.annotation.variant.pillar_project_clinical_classification_of_variant",
+        return_value=classification,
+    ):
+        result = mapped_variant_to_clinical_classification_statement(mock_mapped_variant)
+
+    assert isinstance(result, AssayVariantEffectClinicalClassificationStatement)
+    assert result.classification == classification
+    assert result.subjectVariant == MolecularVariation(**TEST_VALID_POST_MAPPED_VRS_ALLELE)
+    assert experiment_as_iri(mock_mapped_variant.variant.score_set.experiment) == result.objectAssay.root
+    assert len(result.reportedIn) > 0
+    assert variant_to_document(mock_mapped_variant.variant) in result.reportedIn
+    assert score_set_to_document(mock_mapped_variant.variant.score_set) in result.reportedIn
+    assert len(result.contributions) > 0
+    assert mavedb_api_contribution() in result.contributions
+    assert mavedb_vrs_contribution(mock_mapped_variant) in result.contributions
+    assert (
+        mavedb_creator_contribution(mock_mapped_variant.variant, mock_mapped_variant.variant.score_set.created_by)
+        in result.contributions
+    )
+    assert (
+        mavedb_creator_contribution(
+            mock_mapped_variant.variant.score_set, mock_mapped_variant.variant.score_set.created_by
+        )
+        in result.contributions
+    )
+    assert (
+        mavedb_modifier_contribution(
+            mock_mapped_variant.variant.score_set, mock_mapped_variant.variant.score_set.modified_by
+        )
+        in result.contributions
+    )
+
+
+def test_mapped_variant_to_clinical_classification_statement_classification_is_none(mock_mapped_variant):
+    with patch("mavedb.lib.annotation.variant.pillar_project_clinical_classification_of_variant", return_value=None):
+        result = mapped_variant_to_clinical_classification_statement(mock_mapped_variant)
+        assert result is None
+
+
+def test_annotation_for_variant(mock_mapped_variant):
+    functional_classification = AveFunctionalClassification.ABNORMAL
+    clinical_classification = AveClinicalClassification.PS3_MODERATE
+    with (
+        patch(
+            "mavedb.lib.annotation.variant.functional_classification_of_variant",
+            return_value=functional_classification,
+        ),
+        patch(
+            "mavedb.lib.annotation.variant.pillar_project_clinical_classification_of_variant",
+            return_value=clinical_classification,
+        ),
+    ):
+        result = annotation_for_variant(mock_mapped_variant)
+        assert isinstance(result, dict)
+        assert result[mock_mapped_variant.variant.urn]["AssayVariantEffectMeasurementStudyResult"].score == 1.0
+        assert (
+            result[mock_mapped_variant.variant.urn][
+                "AssayVariantEffectFunctionalClassificationStatement"
+            ].classification
+            == functional_classification
+        )
+        assert (
+            result[mock_mapped_variant.variant.urn]["AssayVariantEffectClinicalClassificationStatement"].classification
+            == clinical_classification
+        )
+
+
+def test_annotation_for_variant_with_no_classifications(mock_mapped_variant):
+    with (
+        patch(
+            "mavedb.lib.annotation.variant.functional_classification_of_variant",
+            return_value=None,
+        ),
+        patch(
+            "mavedb.lib.annotation.variant.pillar_project_clinical_classification_of_variant",
+            return_value=None,
+        ),
+    ):
+        result = annotation_for_variant(mock_mapped_variant)
+        assert isinstance(result, dict)
+        assert result[mock_mapped_variant.variant.urn]["AssayVariantEffectMeasurementStudyResult"].score == 1.0
+        assert result[mock_mapped_variant.variant.urn]["AssayVariantEffectFunctionalClassificationStatement"] is None
+        assert result[mock_mapped_variant.variant.urn]["AssayVariantEffectClinicalClassificationStatement"] is None

tests/lib/conftest.py

@@ -9,6 +9,7 @@
 from mavedb.models.experiment import Experiment
 from mavedb.models.license import License
 from mavedb.models.publication_identifier import PublicationIdentifier
+from mavedb.models.score_set_publication_identifier import ScoreSetPublicationIdentifierAssociation
 from mavedb.models.role import Role
 from mavedb.models.taxonomy import Taxonomy
 from mavedb.models.score_set import ScoreSet
@@ -26,6 +27,9 @@
     VALID_EXPERIMENT_URN,
     VALID_EXPERIMENT_SET_URN,
     TEST_PUBMED_IDENTIFIER,
+    TEST_VALID_POST_MAPPED_VRS_ALLELE,
+    TEST_SCORE_SET_RANGE,
+    TEST_SCORE_CALIBRATION,
 )
 
 
@@ -67,19 +71,11 @@ def mock_publication():
 
 
 @pytest.fixture
-def mock_mapped_variant():
-    mv = mock.Mock(spec=MappedVariant)
-    mv.mapping_api_version = "1.0"
-    mv.mapped_date = datetime(2023, 1, 1)
-    return mv
-
-
-@pytest.fixture
-def mock_variant():
-    variant = mock.Mock(spec=Variant)
-    variant.urn = f"{VALID_SCORE_SET_URN}#1"
-    variant.score_set.urn = VALID_SCORE_SET_URN
-    return variant
+def mock_publication_associations(mock_publication):
+    mv = mock.Mock(spec=ScoreSetPublicationIdentifierAssociation)
+    mv.publication = mock_publication
+    mv.primary = True
+    return [mv]
 
 
 @pytest.fixture
@@ -102,14 +98,41 @@ def mock_experiment():
 
 
 @pytest.fixture
-def mock_score_set(mock_user):
+def mock_score_set(mock_user, mock_experiment, mock_publication_associations):
     score_set = mock.Mock(spec=ScoreSet)
     score_set.urn = VALID_SCORE_SET_URN
+    score_set.score_ranges = TEST_SCORE_SET_RANGE
+    score_set.score_calibrations = {"pillar_project": TEST_SCORE_CALIBRATION}
     score_set.license.short_name = "MIT"
     score_set.created_by = mock_user
     score_set.modified_by = mock_user
     score_set.published_date = datetime(2023, 1, 1)
     score_set.title = "Mock score set"
     score_set.creation_date = datetime(2023, 1, 2)
     score_set.modification_date = datetime(2023, 1, 3)
+    score_set.experiment = mock_experiment
+    score_set.publication_identifier_associations = mock_publication_associations
     return score_set
+
+
+@pytest.fixture
+def mock_variant(mock_score_set):
+    variant = mock.Mock(spec=Variant)
+    variant.urn = f"{VALID_SCORE_SET_URN}#1"
+    variant.score_set = mock_score_set
+    variant.data = {"score_data": {"score": 1.0}}
+    variant.creation_date = datetime(2023, 1, 2)
+    variant.modification_date = datetime(2023, 1, 3)
+    return variant
+
+
+@pytest.fixture
+def mock_mapped_variant(mock_variant):
+    mv = mock.Mock(spec=MappedVariant)
+    mv.mapping_api_version = "1.0"
+    mv.mapped_date = datetime(2023, 1, 1)
+    mv.variant = mock_variant
+    mv.post_mapped = TEST_VALID_POST_MAPPED_VRS_ALLELE
+    mv.mapped_date = datetime(2023, 1, 2)
+    mv.modification_date = datetime(2023, 1, 3)
+    return mv