merge: migrate main into v3

pyproject.toml

@@ -51,7 +51,7 @@ extras = [
     "hgvs>=2.0.0a0,<3.0",
     "dill~=0.3.7",
     "click",
-    "pysam==0.23.0",  # pinned pending https://github.com/ga4gh/vrs-python/issues/560
+    "pysam>=0.24.0",
 ]
 tests = [
     "pytest",

src/ga4gh/vrs/extras/translator.py

@@ -156,16 +156,15 @@ def hgvs_tools(self) -> HgvsTools:
         return HgvsTools(self.data_proxy)
 
     def _from_vrs(self, var: dict, **kwargs) -> models._VariationBase | None:  # noqa: ARG002
-        """Convert from dict representation of VRS JSON to VRS object"""
+        """Convert from dict representation of VRS JSON to VRS object
+
+        :raise pydantic.ValidationError: If `var` is not a valid VRS variation
+        """
         if not isinstance(var, Mapping):
             return None
         if "type" not in var:
             return None
-        try:
-            model = models[var["type"]]
-        except KeyError:
-            return None
-        return model(**var)
+        return models.Variation.model_validate(var).root
 
 
 class AlleleTranslator(_Translator):
@@ -254,7 +253,7 @@ def _from_gnomad(self, gnomad_expr: str, **kwargs) -> models.Allele | None:
         """
         if not isinstance(gnomad_expr, str):
             return None
-        m = self.gnomad_re.match(gnomad_expr)
+        m = self.gnomad_re.fullmatch(gnomad_expr)
         if not m:
             return None
 
@@ -341,7 +340,7 @@ def _from_spdi(self, spdi_expr: str, **kwargs) -> models.Allele | None:
         if not isinstance(spdi_expr, str):
             return None
 
-        m = self.spdi_re.match(spdi_expr)
+        m = self.spdi_re.fullmatch(spdi_expr)
         if not m:
             return None
 

tests/extras/test_allele_translator.py

@@ -1,4 +1,5 @@
 import pytest
+from pydantic import ValidationError
 
 from ga4gh.vrs import models
 from ga4gh.vrs.dataproxy import DataProxyValidationError
@@ -335,6 +336,21 @@ def test_from_invalid(tlr):
         tlr.translate_from("BRAF amplication", assembly_name="GRCh37")
 
 
+@pytest.mark.parametrize(
+    ("expr", "fmt"),
+    [
+        # multi-allelic gnomAD-style input must not be truncated to its first ALT
+        ("1-55516888-G-GA,GT", "gnomad"),
+        ("19-44908822-C-T;foo", "gnomad"),
+        ("NC_000019.10:44908821:1:T:extra", "spdi"),
+    ],
+)
+def test_from_trailing_input_rejected(tlr, expr, fmt):
+    """Expressions with trailing content must be rejected, not partially parsed"""
+    with pytest.raises(ValueError, match=f"Unable to parse data as {fmt}"):
+        tlr.translate_from(expr, fmt=fmt)
+
+
 @pytest.mark.vcr
 def test_from_gnomad(tlr):
     do_normalize = False
@@ -962,6 +978,48 @@ def test_translate_to_invalid_fmt(tlr):
         tlr.translate_to(models.Allele.model_validate(snv_output), fmt="gnomad")
 
 
+def test_from_vrs_dict():
+    """Regression test for ga4gh/vrs-python#489.
+
+    Translating a VRS dict must resolve the model class from its `type`
+    instead of crashing with TypeError (the `models` module was subscripted).
+    """
+    tlr = AlleleTranslator(data_proxy=None, identify=False)
+
+    # valid VRS dict translates to a VRS object (previously raised TypeError)
+    allele = tlr.translate_from(snv_output, fmt="vrs")
+    assert isinstance(allele, models.Allele)
+    assert allele.type == "Allele"
+    assert allele.location.start == snv_output["location"]["start"]
+    assert allele.location.end == snv_output["location"]["end"]
+
+    # non-dict and missing-type inputs still return None
+    assert tlr._from_vrs("NC_000019.10:g.44908822C>T") is None
+    assert tlr._from_vrs({"location": {}}) is None
+
+
+from_vrs_non_variation_type_cases = [
+    {"id": "unknown-name", "type": "NotARealModel"},
+    {"id": "non-variation-vrs-class", "type": "SequenceLocation"},
+    {"id": "non-model-module-attribute", "type": "Field"},
+    {"id": "variation-base-class", "type": "_VariationBase"},
+    {"id": "non-string", "type": 5},
+]
+
+
+@pytest.mark.parametrize(
+    "case", from_vrs_non_variation_type_cases, ids=lambda c: c["id"]
+)
+def test_from_vrs_non_variation_type(case):
+    """A VRS dict whose `type` is not a VRS variation class is rejected, rather than
+    resolved to whatever `ga4gh.vrs.models` attribute has that name
+    """
+    tlr = AlleleTranslator(data_proxy=None, identify=False)
+    with pytest.raises(ValidationError) as e:
+        tlr.translate_from({"type": case["type"]}, fmt="vrs")
+    assert e.value.errors()[0]["type"] == "union_tag_invalid"
+
+
 def test_from_hgvs_uncertain_range_raises(tlr):
     """Uncertain-range HGVS cannot be represented as an Allele with a literal
     sequence state; use CnvTranslator instead. See issue #609.

tests/extras/test_annotate_vcf.py

@@ -233,7 +233,7 @@ def test_get_vrs_object_invalid_input(vcf_annotator: VcfAnnotator, caplog):
 
 
 @pytest.mark.vcr
-def test_annotate_vcf_rle(vcf_annotator: VcfAnnotator, vcr_cassette):
+def test_annotate_vcf_rle(vcf_annotator: VcfAnnotator, vcr_cassette, tmp_path: Path):
     """Test VCF annotation with ReferenceLengthExpression states.
 
     Tests two variants that should produce ReferenceLengthExpression states:
@@ -242,8 +242,8 @@ def test_annotate_vcf_rle(vcf_annotator: VcfAnnotator, vcr_cassette):
     """
     vcr_cassette.allow_playback_repeats = False
     input_vcf = TEST_DATA_DIR / "test_rle.vcf"
-    output_vcf = TEST_DATA_DIR / "test_rle_output.vcf"
-    output_vrs_pkl = TEST_DATA_DIR / "test_rle_output.pkl"
+    output_vcf = tmp_path / "test_rle_output.vcf"
+    output_vrs_pkl = tmp_path / "test_rle_output.pkl"
 
     # Annotate the VCF with VRS attributes enabled
     vcf_annotator.annotate(