Merge branch 'fixes' into eb-extensions

src/variation/gnomad_vcf_to_protein_variation.py

@@ -10,6 +10,7 @@
 from gene.query import QueryHandler as GeneQueryHandler
 from gene.schemas import MatchType as GeneMatchType
 
+from variation import __version__
 from variation.classify import Classify
 from variation.schemas.classification_response_schema import Nomenclature
 from variation.schemas.gnomad_vcf_to_protein_schema import GnomadVcfToProteinService
@@ -19,7 +20,6 @@
 from variation.tokenize import Tokenize
 from variation.translate import Translate
 from variation.validate import Validate
-from variation import __version__
 
 
 class GnomadVcfToProteinError(Exception):

src/variation/hgvs_dup_del_mode.py

@@ -11,6 +11,25 @@
 # Define deletion alt types
 DELS = {AltType.DELETION_AMBIGUOUS, AltType.DELETION}
 
+# Define supported alt types for HGVS Dup Del Mode
+DELS_DUPS = {
+    AltType.DELETION,
+    AltType.DELETION_AMBIGUOUS,
+    AltType.DUPLICATION,
+    AltType.DUPLICATION_AMBIGUOUS,
+}
+
+
+def _check_supported_alt_type(alt_type: AltType) -> None:
+    """Check that ``alt_type`` is one of ``DUP_DELS``
+
+    :param alt_type: Alteration type
+    :raises ValueError: If ``alt_type`` not one of ``DELS_DUPS``.
+    """
+    if alt_type not in DELS_DUPS:
+        err_msg = f"`alt_type` must be one of: {DELS_DUPS}"
+        raise ValueError(err_msg)
+
 
 class HGVSDupDelMode:
     """Class for handling how to interpret HGVS duplications and deletions."""
@@ -24,10 +43,7 @@ def __init__(self, seqrepo_access: SeqRepoAccess) -> None:
 
     def default_mode(
         self,
-        alt_type: AltType.DELETION
-        | AltType.DELETION_AMBIGUOUS
-        | AltType.DUPLICATION
-        | AltType.DUPLICATION_AMBIGUOUS,
+        alt_type: AltType,
         location: dict,
         vrs_seq_loc_ac: str,
         baseline_copies: int | None = None,
@@ -43,14 +59,17 @@ def default_mode(
         else
             allele
 
-        :param alt_type: The type of alteration
+        :param alt_type: The type of alteration. Must be one of ``DELS_DUPS``.
         :param location: Sequence Location object
         :param vrs_seq_loc_ac: Accession used in VRS Sequence Location
         :param baseline_copies: Baseline copies for Copy Number Count variation
         :param copy_change: copy change for Copy Number Change Variation
         :param alt: Alteration
+        :raises ValueError: If ``alt_type`` not one of ``DELS_DUPS``.
         :return: VRS Variation object represented as a dict
         """
+        _check_supported_alt_type(alt_type)
+
         variation = None
         if not baseline_copies and alt_type in AMBIGUOUS_REGIONS:
             variation = self.copy_number_change_mode(alt_type, location, copy_change)
@@ -62,20 +81,20 @@ def default_mode(
 
     def copy_number_count_mode(
         self,
-        alt_type: AltType.DELETION
-        | AltType.DELETION_AMBIGUOUS
-        | AltType.DUPLICATION
-        | AltType.DUPLICATION_AMBIGUOUS,
+        alt_type: AltType,
         location: dict,
         baseline_copies: int,
     ) -> dict:
         """Return a VRS Copy Number Variation.
 
-        :param alt_type: The type of alteration
+        :param alt_type: The type of alteration. Must be one of ``DELS_DUPS``.
         :param location: VRS SequenceLocation
         :param baseline_copies: Baseline copies number
+        :raises ValueError: If ``alt_type`` not one of ``DELS_DUPS``.
         :return: VRS Copy Number object represented as a dict
         """
+        _check_supported_alt_type(alt_type)
+
         copies = baseline_copies - 1 if alt_type in DELS else baseline_copies + 1
         seq_loc = models.SequenceLocation(**location)
         seq_loc.id = ga4gh_identify(seq_loc)
@@ -85,20 +104,20 @@ def copy_number_count_mode(
 
     def copy_number_change_mode(
         self,
-        alt_type: AltType.DELETION
-        | AltType.DELETION_AMBIGUOUS
-        | AltType.DUPLICATION
-        | AltType.DUPLICATION_AMBIGUOUS,
+        alt_type: AltType,
         location: dict,
         copy_change: models.CopyChange | None = None,
     ) -> dict:
         """Return copy number change variation
 
-        :param alt_type: The type of alteration
+        :param alt_type: The type of alteration. Must be one of ``DELS_DUPS``.
         :param location: VRS SequenceLocation
         :param copy_change: The copy change
+        :raises ValueError: If ``alt_type`` not one of ``DELS_DUPS``.
         :return: Copy Number Change variation as a dict
         """
+        _check_supported_alt_type(alt_type)
+
         if not copy_change:
             copy_change = (
                 models.CopyChange.EFO_0030067

src/variation/normalize.py

@@ -7,6 +7,7 @@
 from cool_seq_tool.sources import UtaDatabase
 from ga4gh.vrs import models
 
+from variation import __version__
 from variation.classify import Classify
 from variation.schemas.app_schemas import Endpoint
 from variation.schemas.normalize_response_schema import (
@@ -25,7 +26,6 @@
 from variation.translate import Translate
 from variation.utils import update_warnings_for_no_resp
 from variation.validate import Validate
-from variation import __version__
 
 
 class Normalize(ToVRS):

src/variation/schemas/copy_number_schema.py

@@ -14,8 +14,8 @@
     model_validator,
 )
 
-from variation.schemas.normalize_response_schema import ServiceResponse
 from variation import __version__
+from variation.schemas.normalize_response_schema import ServiceResponse
 
 
 class ParsedPosType(str, Enum):

src/variation/schemas/hgvs_to_copy_number_schema.py

@@ -3,8 +3,8 @@
 from ga4gh.vrs import models
 from pydantic import ConfigDict, StrictStr
 
-from variation.schemas.normalize_response_schema import ServiceResponse
 from variation import __version__
+from variation.schemas.normalize_response_schema import ServiceResponse
 
 
 class HgvsToCopyNumberCountService(ServiceResponse):

src/variation/schemas/service_schema.py

@@ -6,8 +6,8 @@
 from cool_seq_tool.schemas import ToGenomicService as ToGenomic
 from pydantic import ConfigDict
 
-from variation.schemas.normalize_response_schema import ServiceMeta
 from variation import __version__
+from variation.schemas.normalize_response_schema import ServiceMeta
 
 
 class ClinVarAssembly(str, Enum):

src/variation/to_copy_number_variation.py

@@ -14,6 +14,7 @@
 from gene.schemas import MatchType as GeneMatchType
 from pydantic import ValidationError
 
+from variation import __version__
 from variation.classify import Classify
 from variation.schemas.app_schemas import Endpoint
 from variation.schemas.classification_response_schema import ClassificationType
@@ -43,7 +44,6 @@
 from variation.translate import Translate
 from variation.utils import get_priority_sequence_location
 from variation.validate import Validate
-from variation import __version__
 
 VALID_CLASSIFICATION_TYPES = [
     ClassificationType.GENOMIC_DUPLICATION,

src/variation/to_vrs.py

@@ -6,6 +6,7 @@
 from cool_seq_tool.handlers import SeqRepoAccess
 from ga4gh.vrs import models
 
+from variation import __version__
 from variation.classify import Classify
 from variation.schemas.app_schemas import Endpoint
 from variation.schemas.normalize_response_schema import (
@@ -18,7 +19,6 @@
 from variation.tokenize import Tokenize
 from variation.translate import Translate
 from variation.validate import Validate
-from variation import __version__
 from variation.vrs_representation import VRSRepresentation
 
 

src/variation/translators/translator.py

@@ -164,7 +164,7 @@ async def get_p_or_cdna_translation_result(
         start_pos: int,
         end_pos: int,
         alt_type: AltType,
-        coordinate_type: AnnotationLayer.PROTEIN | AnnotationLayer.CDNA,
+        coordinate_type: AnnotationLayer,
         errors: list[str],
         cds_start: int | None = None,
         ref: str | None = None,
@@ -184,8 +184,15 @@ async def get_p_or_cdna_translation_result(
             `coordinate_type == AnnotationLayer.CDNA`.
         :param ref: Expected reference sequence
         :param alt: Expected change
+        :raises ValueError: If ``coordinate`` type not one of
+            ``AnnotationLayer.PROTEIN`` or ``AnnotationLayer.CDNA``
         :return: Translation result if successful. Else, `None`
         """
+        supported_coordinate_types = {AnnotationLayer.PROTEIN, AnnotationLayer.CDNA}
+        if coordinate_type not in supported_coordinate_types:
+            err_msg = f"`coordinate_type` must be one of {supported_coordinate_types}"
+            raise ValueError(err_msg)
+
         vrs_allele = None
         vrs_seq_loc_ac = None
         vrs_seq_loc_ac_status = VrsSeqLocAcStatus.NA