feat!: rename VRS 1.3 class

src/dcd_mapping/annotate.py

@@ -29,7 +29,7 @@
     ScoresetMetadata,
     TargetSequenceType,
     TxSelectResult,
-    VrsObject1_x,
+    VrsMapping1_3,
 )
 
 _logger = logging.getLogger(__name__)
@@ -247,7 +247,7 @@ def get_mapped_reference_sequence(
     )
 
 
-def _set_layer(ss: str, mappings: list[VrsObject1_x]) -> AnnotationLayer:
+def _set_layer(ss: str, mappings: list[VrsMapping1_3]) -> AnnotationLayer:
     if ss.startswith("urn:mavedb:00000097"):
         return AnnotationLayer.PROTEIN
     for var in mappings:
@@ -256,7 +256,7 @@ def _set_layer(ss: str, mappings: list[VrsObject1_x]) -> AnnotationLayer:
     return AnnotationLayer.PROTEIN
 
 
-def _format_score_mapping(var: VrsObject1_x, layer: AnnotationLayer) -> dict | None:
+def _format_score_mapping(var: VrsMapping1_3, layer: AnnotationLayer) -> dict | None:
     if var and var.layer == layer:
         if "members" in var.pre_mapped_variants:
             pre_mapped_members = []
@@ -282,7 +282,7 @@ def _format_score_mapping(var: VrsObject1_x, layer: AnnotationLayer) -> dict | N
 
 def save_mapped_output_json(
     ss: str,
-    mappings: list[VrsObject1_x],
+    mappings: list[VrsMapping1_3],
     align_result: AlignmentResult,
     tx_output: TxSelectResult | None = None,
     output_path: Path | None = None,
@@ -346,9 +346,9 @@ def _format_start_end(ss: str, start: int, end: int) -> list[int]:
 
 def annotate(
     tx_select_results: TxSelectResult | None,
-    vrs_results: list[VrsObject1_x],
+    vrs_results: list[VrsMapping1_3],
     metadata: ScoresetMetadata,
-) -> list[VrsObject1_x]:
+) -> list[VrsMapping1_3]:
     """TODO"""
     sr = get_seqrepo()
     for var in vrs_results:

src/dcd_mapping/schemas.py

@@ -168,7 +168,7 @@ class TxSelectResult(BaseModel):
 ###################### WORKING: ################################
 
 
-class VrsObject1_x(BaseModel):  # noqa: N801
+class VrsMapping1_3(BaseModel):  # noqa: N801
     """Define response object for VRS 1.x object"""
 
     mavedb_id: StrictStr
@@ -261,7 +261,7 @@ def generate_allele_structure(self, var: Allele) -> dict:
             },
         }
 
-    def output_vrs_variations(self, layer: AnnotationLayer) -> VrsObject1_x:
+    def output_vrs_variations(self, layer: AnnotationLayer) -> VrsMapping1_3:
         """Construct VRS 1.3 compatible objects from 2.0a models.
 
         :param layer: The Annotation Layer (genomic or protein)
@@ -319,7 +319,7 @@ def output_vrs_variations(self, layer: AnnotationLayer) -> VrsObject1_x:
         else:
             post_mapped_variants = post_mapped_variants[0]
 
-        return VrsObject1_x(
+        return VrsMapping1_3(
             mavedb_id=self.mavedb_id,
             pre_mapped_variants=pre_mapped_variants,
             post_mapped_variants=post_mapped_variants,

src/dcd_mapping/vrs_map.py

@@ -21,7 +21,7 @@
     TargetType,
     TxSelectResult,
     VrsMapping,
-    VrsObject1_x,
+    VrsMapping1_3,
 )
 
 __all__ = ["vrs_map"]
@@ -69,7 +69,7 @@ def _map_protein_coding_pro(
     align_result: AlignmentResult,
     sequence_id: str,
     transcript: TxSelectResult,
-) -> VrsObject1_x | None:
+) -> VrsMapping1_3 | None:
     """Construct VRS object mapping for ``hgvs_pro`` variant column entry
 
     These arguments are a little lazy and could be pruned down later
@@ -159,7 +159,7 @@ def _map_protein_coding(
     records: list[ScoreRow],
     transcript: TxSelectResult,
     align_result: AlignmentResult,
-) -> list[VrsObject1_x]:
+) -> list[VrsMapping1_3]:
     """Perform mapping on protein coding experiment results
 
     :param metadata: The metadata for a score set
@@ -168,7 +168,7 @@ def _map_protein_coding(
     :param align_results: The alignment data for a score set
     :return: A list of mappings
     """
-    variations: list[VrsObject1_x] = []
+    variations: list[VrsMapping1_3] = []
     if metadata.target_sequence_type == TargetSequenceType.DNA:
         sequence = str(
             Seq(metadata.target_sequence).translate(table="1", stop_symbol="")
@@ -223,15 +223,15 @@ def _map_regulatory_noncoding(
     metadata: ScoresetMetadata,
     records: list[ScoreRow],
     align_result: AlignmentResult,
-) -> list[VrsObject1_x]:
+) -> list[VrsMapping1_3]:
     """Perform mapping on noncoding/regulatory experiment results
 
     :param metadata: metadata for URN
     :param records: list of MAVE experiment result rows
     :param align_result: An AlignmentResult object for a score set
     :return: A list of VRS mappings
     """
-    variations: list[VrsObject1_x] = []
+    variations: list[VrsMapping1_3] = []
     sequence_id = store_sequence(metadata.target_sequence)
 
     for row in records:
@@ -380,7 +380,7 @@ def vrs_map(
     records: list[ScoreRow],
     transcript: TxSelectResult | None = None,
     silent: bool = True,
-) -> list[VrsObject1_x] | None:
+) -> list[VrsMapping1_3] | None:
     """Given a description of a MAVE scoreset and an aligned transcript, generate
     the corresponding VRS objects.
 

tests/test_vrs_map.py

@@ -9,13 +9,13 @@
     AlignmentResult,
     ScoresetMetadata,
     TxSelectResult,
-    VrsObject1_x,
+    VrsMapping1_3,
 )
 from dcd_mapping.vrs_map import vrs_map
 
 
 def _assert_correct_vrs_map(
-    mapping: VrsObject1_x, expected_mappings_data: dict[str, dict]
+    mapping: VrsMapping1_3, expected_mappings_data: dict[str, dict]
 ):
     assert (
         mapping.mavedb_id in expected_mappings_data