Add remaining VRS draft

src/dcd_mapping/lookup.py

@@ -12,7 +12,7 @@
 from cool_seq_tool.schemas import TranscriptPriority
 from ga4gh.core._internal.models import Extension, Gene
 from ga4gh.vrs._internal.models import Allele, SequenceLocation
-from ga4gh.vrs.extras.translator import Translator
+from ga4gh.vrs.extras.translator import AlleleTranslator
 from gene.database import create_db
 from gene.query import QueryHandler
 from gene.schemas import SourceName
@@ -79,15 +79,14 @@ def __new__(cls) -> QueryHandler:
 class VrsTranslatorBuilder:
     """Singleton constructor for VRS-Python translator instance."""
 
-    # TODO this looks.... very wrong?
-    def __new__(cls) -> Translator:
+    def __new__(cls) -> AlleleTranslator:
         """Provide VRS-Python translator. Construct if unavailable.
 
         :return: singleton instances of Translator
         """
         if not hasattr(cls, "instance"):
             cst = CoolSeqToolBuilder()
-            cls.instance = Translator(cst.seqrepo_access, normalize=False)
+            cls.instance = AlleleTranslator(cst.seqrepo_access, normalize=False)
         return cls.instance
 
 

src/dcd_mapping/resources.py

@@ -28,6 +28,7 @@
     "get_scoreset_urns",
     "get_human_urns",
     "get_raw_scoreset_metadata",
+    "get_scoreset_records",
     "get_scoreset_metadata",
     "get_human_urns",
     "get_ref_genome_file",

src/dcd_mapping/schemas.py

@@ -125,13 +125,19 @@ class TxSelectResult(BaseModel):
 
 
 class VrsMapping(BaseModel):
-    """Define pre-post mapping pair structure for VRS-structured variations."""
+    """Define pre-post mapping pair structure for VRS-structured variations.
+
+    Probably need to add score and accession to make json writing easier
+    """
 
     pre_mapping: Union[Allele, Haplotype]
     mapped: Union[Allele, Haplotype]
 
 
 class VrsMappingResult(BaseModel):
-    """Define response object from VRS mappings method."""
+    """Define response object from VRS mappings method.
+
+    Might not be necessary (should just be list of VrsMappings?)
+    """
 
     variations: List[VrsMapping]