wip: remove canonical variation work

variation/main.py

@@ -20,9 +20,9 @@
 from variation.schemas.hgvs_to_copy_number_schema import \
     HgvsToCopyNumberCountService, HgvsToCopyNumberChangeService
 from variation.query import QueryHandler
-from variation.schemas.normalize_response_schema \
-    import HGVSDupDelMode as HGVSDupDelModeEnum, ToCanonicalVariationFmt, \
-    ToCanonicalVariationService, TranslateIdentifierService
+from variation.schemas.normalize_response_schema import (
+    HGVSDupDelMode as HGVSDupDelModeEnum, TranslateIdentifierService
+)
 from variation.schemas.service_schema import AmplificationToCxVarService, \
     ClinVarAssembly, ParsedToCnVarService, ToGenomicService, ToCdnaService
 from .version import __version__
@@ -36,7 +36,6 @@ class Tags(Enum):
 
     SEQREPO = "SeqRepo"
     TO_PROTEIN_VARIATION = "To Protein Variation"
-    TO_CANONICAL = "To Canonical Variation"
     VRS_PYTHON = "VRS-Python"
     TO_COPY_NUMBER_VARIATION = "To Copy Number Variation"
     ALIGNMENT_MAPPER = "Alignment Mapper"
@@ -313,58 +312,6 @@ async def gnomad_vcf_to_protein(
                         "`fmt`=`hgvs` and Copy Number Count Variation.`"
 
 
-@app.get("/variation/to_canonical_variation",
-         summary="Given SPDI or HGVS, return VRSATILE Canonical Variation",
-         response_description="A response to a validly-formed query.",
-         description="Return VRSATILE Canonical Variation",
-         response_model=ToCanonicalVariationService,
-         tags=[Tags.TO_CANONICAL])
-async def to_canonical_variation(
-        q: str = Query(..., description="HGVS or SPDI query"),
-        fmt: ToCanonicalVariationFmt = Query(...,
-                                             description="Format of the input variation. Must be `spdi` or `hgvs`"),  # noqa: E501
-        complement: bool = Query(False, description=complement_descr),
-        do_liftover: bool = Query(False, description="Whether or not to liftover to "
-                                  "GRCh38 assembly."),
-        hgvs_dup_del_mode: Optional[HGVSDupDelModeEnum] = Query(
-            HGVSDupDelModeEnum.DEFAULT, description=hgvs_dup_del_mode_decsr),
-        copy_change: Optional[CopyChange] = Query(
-            None, description=copy_change_descr),
-        baseline_copies: Optional[int] = Query(
-            None, description=baseline_copies_descr),
-        untranslatable_returns_text: bool = Query(
-            False, description=untranslatable_descr)
-) -> ToCanonicalVariationService:
-    """Return categorical variation for canonical SPDI
-
-    :param str q: HGVS or SPDI query
-    :param ToCanonicalVariationFmt fmt: Format of the input variation. Must be
-        `spdi` or `hgvs`.
-    :param bool complement: This field indicates that a categorical variation
-        is defined to include (false) or exclude (true) variation concepts matching the
-        categorical variation. This is equivalent to a logical NOT operation on the
-        categorical variation properties.
-    :param Optional[HGVSDupDelModeEnum] hgvs_dup_del_mode: Determines how to interpret
-        HGVS dup/del expressions in VRS. Must be one of: `default`, `copy_number_count`,
-        `copy_number_change`, `repeated_seq_expr`, `literal_seq_expr`
-    :param Optional[CopyChange] copy_change: copy change.
-        Only used when `fmt`=`hgvs` and Copy Number Change Variation.
-    :param Optional[int] baseline_copies: Baseline copies number
-        Only used when `fmt`=`hgvs` and Copy Number Count Variation
-    :param bool untranslatable_returns_text: `True` return VRS Text Object when
-        unable to translate or normalize query. `False` return `None` when
-        unable to translate or normalize query.
-    :return: ToCanonicalVariationService for variation query
-    """
-    q = unquote(q)
-    resp = await query_handler.to_canonical_handler.to_canonical_variation(
-        q, fmt, complement, do_liftover=do_liftover,
-        hgvs_dup_del_mode=hgvs_dup_del_mode, baseline_copies=baseline_copies,
-        copy_change=copy_change,
-        untranslatable_returns_text=untranslatable_returns_text)
-    return resp
-
-
 def _get_allele(request_body: Union[TranslateToQuery, TranslateToHGVSQuery],
                 warnings: List) -> Optional[models.Allele]:
     """Return VRS allele object from request body. `warnings` will get updated if

variation/query.py

@@ -19,7 +19,6 @@
 from variation.to_vrsatile import ToVRSATILE
 from variation.gnomad_vcf_to_protein_variation import GnomadVcfToProteinVariation
 from variation.normalize import Normalize
-from variation.to_canonical_variation import ToCanonicalVariation
 from variation.to_copy_number_variation import ToCopyNumberVariation
 
 
@@ -100,6 +99,4 @@ def __init__(
                                              mane_transcript_mappings, codon_table]
         self.gnomad_vcf_to_protein_handler = GnomadVcfToProteinVariation(
             *to_protein_params)
-        self.to_canonical_handler = ToCanonicalVariation(
-            *to_vrs_params + [self._tlr, uta_db])
         self.to_copy_number_handler = ToCopyNumberVariation(*to_vrs_params)

variation/schemas/app_schemas.py

@@ -12,4 +12,3 @@ class Endpoint(str, Enum):
     TRANSLATE_FROM = "translate_from"
     HGVS_TO_COPY_NUMBER_COUNT = "hgvs_to_copy_number_count"
     HGVS_TO_COPY_NUMBER_CHANGE = "hgvs_to_copy_number_change"
-    TO_CANONICAL = "to_canonical"

variation/schemas/normalize_response_schema.py

@@ -5,8 +5,7 @@
 
 from pydantic import BaseModel
 from pydantic.types import StrictStr
-from ga4gh.vrsatile.pydantic.vrsatile_models import VariationDescriptor, \
-    CanonicalVariation
+from ga4gh.vrsatile.pydantic.vrsatile_models import VariationDescriptor
 
 
 class HGVSDupDelMode(str, Enum):
@@ -275,69 +274,3 @@ def schema_extra(schema: Dict[str, Any],
                     "url": "https://github.com/cancervariants/variation-normalization"  # noqa: E501
                 }
             }
-
-
-class ToCanonicalVariationFmt(str, Enum):
-    """Define formats for to_canonical endpoint"""
-
-    HGVS = "hgvs"
-    SPDI = "spdi"
-
-
-class ToCanonicalVariationService(ServiceResponse):
-    """A response model for the to canonical variation service"""
-
-    query: str
-    canonical_variation: Optional[CanonicalVariation]
-
-    class Config:
-        """Configure model."""
-
-        @staticmethod
-        def schema_extra(
-                schema: Dict[str, Any],
-                model: Type["ToCanonicalVariationService"]) -> None:
-            """Configure OpenAPI schema."""
-            if "title" in schema.keys():
-                schema.pop("title", None)
-            for prop in schema.get("properties", {}).values():
-                prop.pop("title", None)
-            schema["example"] = {
-                "query": "NC_000007.14:140753335:A:T",
-                "warnings": [],
-                "canonical_variation": {
-                    "_id": "ga4gh:VCC.W0r_NF_ecKXjgvTwcMNkyVS1pB_CXMj9",
-                    "type": "CanonicalVariation",
-                    "complement": False,
-                    "variation": {
-                        "_id": "ga4gh:VA.fZiBjQEolbkL0AxjoTZf4SOkFy9J0ebU",
-                        "type": "Allele",
-                        "location": {
-                            "_id": "ga4gh:VSL.zga82-TpYiNmBESCfvDvAz9DyvJF98I-",
-                            "type": "SequenceLocation",
-                            "sequence_id": "ga4gh:SQ.F-LrLMe1SRpfUZHkQmvkVKFEGaoDeHul",
-                            "interval": {
-                                "type": "SequenceInterval",
-                                "start": {
-                                    "type": "Number",
-                                    "value": 140753335
-                                },
-                                "end": {
-                                    "type": "Number",
-                                    "value": 140753336
-                                }
-                            }
-                        },
-                        "state": {
-                            "type": "LiteralSequenceExpression",
-                            "sequence": "T"
-                        }
-                    }
-                },
-                "service_meta_": {
-                    "version": "0.2.20",
-                    "response_datetime": "2022-02-20T17:16:19.415675",
-                    "name": "variation-normalizer",
-                    "url": "https://github.com/cancervariants/variation-normalization"
-                }
-            }