pr suggestions

Author: korikuzma

src/anyvlm/anyvar/base_client.py

@@ -4,7 +4,6 @@
 from collections.abc import Iterable, Sequence
 
 from anyvar.utils.liftover_utils import ReferenceAssembly
-from anyvar.utils.types import VrsVariation
 from ga4gh.vrs.models import Allele
 
 
@@ -23,7 +22,7 @@ class BaseAnyVarClient(abc.ABC):
     """Interface elements for an AnyVar client"""
 
     @abc.abstractmethod
-    def get_registered_allele_expression(
+    def get_registered_allele(
         self, expression: str, assembly: ReferenceAssembly = ReferenceAssembly.GRCH38
     ) -> Allele | None:
         """Retrieve registered VRS Allele for given allele expression
@@ -55,19 +54,6 @@ def put_allele_expressions(
             else `None`, for the i'th expression
         """
 
-    @abc.abstractmethod
-    def search_by_interval(
-        self, accession: str, start: int, end: int
-    ) -> list[VrsVariation]:
-        """Get all variation IDs located within the specified range
-
-        :param accession: sequence accession
-        :param start: start position for genomic region
-        :param end: end position for genomic region
-        :return: list of matching variant objects
-        :raise AnyVarClientConnectionError: if connection is unsuccessful during search query
-        """
-
     @abc.abstractmethod
     def close(self) -> None:
         """Clean up AnyVar connection."""

src/anyvlm/anyvar/http_client.py

@@ -6,7 +6,6 @@
 
 import requests
 from anyvar.utils.liftover_utils import ReferenceAssembly
-from anyvar.utils.types import VrsVariation
 from ga4gh.vrs import VrsType, models
 
 from anyvlm.anyvar.base_client import (
@@ -97,7 +96,7 @@ def _make_allele_expression_request(
             raise AnyVarClientError from e
         return response
 
-    def get_registered_allele_expression(
+    def get_registered_allele(
         self, expression: str, assembly: ReferenceAssembly = ReferenceAssembly.GRCH38
     ) -> models.Allele | None:
         """Retrieve registered VRS Allele for given allele expression
@@ -146,31 +145,6 @@ def put_allele_expressions(
                 results.append(response.json()["object_id"])
         return results
 
-    def search_by_interval(
-        self, accession: str, start: int, end: int
-    ) -> list[VrsVariation]:
-        """Get all variation IDs located within the specified range
-
-        :param accession: sequence accession
-        :param start: start position for genomic region
-        :param end: end position for genomic region
-        :return: list of matching variant objects
-        :raise AnyVarClientError: if connection is unsuccessful during search query
-        """
-        response = requests.get(
-            f"{self.hostname}/search?accession={accession}&start={start}&end={end}",
-            timeout=self.request_timeout,
-        )
-        try:
-            response.raise_for_status()
-        except requests.HTTPError as e:
-            if response.json() == {
-                "detail": "Unable to dereference provided accession ID"
-            }:
-                return []
-            raise AnyVarClientError from e
-        return [models.Allele(**v) for v in response.json()["variations"]]
-
     def close(self) -> None:
         """Clean up AnyVar connection.
 

src/anyvlm/anyvar/python_client.py

@@ -7,7 +7,7 @@
 from anyvar.storage.base_storage import Storage
 from anyvar.translate.translate import TranslationError, Translator
 from anyvar.utils.liftover_utils import ReferenceAssembly
-from anyvar.utils.types import SupportedVariationType, VrsVariation
+from anyvar.utils.types import SupportedVariationType
 from ga4gh.vrs.dataproxy import DataProxyValidationError
 from ga4gh.vrs.models import Allele
 
@@ -53,7 +53,7 @@ def _translate_allele_expression(
             _logger.exception("Failed to translate expression: %s", expression)
         return translated_variation  # type: ignore
 
-    def get_registered_allele_expression(
+    def get_registered_allele(
         self, expression: str, assembly: ReferenceAssembly = ReferenceAssembly.GRCH38
     ) -> Allele | None:
         """Retrieve registered VRS Allele for given allele expression
@@ -105,31 +105,6 @@ def put_allele_expressions(
                 results.append(None)
         return results
 
-    def search_by_interval(
-        self, accession: str, start: int, end: int
-    ) -> list[VrsVariation]:
-        """Get all variation IDs located within the specified range
-
-        :param accession: sequence accession
-        :param start: start position for genomic region
-        :param end: end position for genomic region
-        :return: list of matching variant objects
-        """
-        try:
-            if accession.startswith("ga4gh:"):
-                ga4gh_id = accession
-            else:
-                ga4gh_id = self.av.translator.get_sequence_id(accession)
-        except KeyError:
-            return []
-
-        alleles = []
-        if ga4gh_id:
-            refget_accession = ga4gh_id.split("ga4gh:")[-1]
-            alleles = self.av.object_store.search_alleles(refget_accession, start, end)
-
-        return alleles  # type: ignore[reportReturnType]
-
     def close(self) -> None:
         """Clean up AnyVar instance."""
         _logger.info("Closing AnyVar client.")

src/anyvlm/functions/get_caf.py

@@ -50,7 +50,7 @@ def get_caf(
         msg = "Unsupported assembly ID: {assembly_id}"
         raise ValueError(msg) from e
 
-    vrs_variation = anyvar_client.get_registered_allele_expression(gnomad_vcf, assembly)
+    vrs_variation = anyvar_client.get_registered_allele(gnomad_vcf, assembly)
     if not vrs_variation:
         msg = f"Variant {assembly.value} {gnomad_vcf} is not registered in AnyVar"
         raise VariantNotRegisteredError(msg)

tests/unit/anyvar/test_clients.py

@@ -82,9 +82,7 @@ def test_get_registered_allele_expressions_unpopulated(
         if "vcf_expression" not in allele_fixture:
             continue
         assert (
-            anyvar_client.get_registered_allele_expression(
-                allele_fixture["vcf_expression"]
-            )
+            anyvar_client.get_registered_allele(allele_fixture["vcf_expression"])
             is None
         )
 
@@ -98,7 +96,7 @@ def test_get_registered_allele_expressions_populated(
     for allele_fixture in alleles.values():
         if "vcf_expression" not in allele_fixture:
             continue
-        assert anyvar_client.get_registered_allele_expression(
+        assert anyvar_client.get_registered_allele(
             allele_fixture["vcf_expression"]
         ) == models.Allele(**allele_fixture["variation"])
 
@@ -129,76 +127,3 @@ def test_put_allele_expressions_handle_invalid(
         ["Y-2781761-A-C", allele_fixture["vcf_expression"]]
     )
     assert results == [None, allele_fixture["variation"]["id"]]
-
-
-@pytest.mark.vcr
-@pytest.mark.parametrize("anyvar_client", POPULATED_CLIENTS, indirect=True)
-def test_search_by_interval(anyvar_client: BaseAnyVarClient, alleles: dict):
-    """Test `search_by_interval` for a couple of basic cases"""
-    results = anyvar_client.search_by_interval(
-        "ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5", 2781760, 2781760
-    )
-    assert sorted(results, key=lambda r: r.id) == [
-        models.Allele(
-            **alleles["ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD"]["variation"]
-        ),
-        models.Allele(
-            **alleles["ga4gh:VA.R4kbmdsn5VldGrBiAaByO5N9zM3qCSFw"]["variation"]
-        ),
-    ]
-    results = anyvar_client.search_by_interval(
-        "ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5", 2781760, 2781768
-    )
-    assert sorted(results, key=lambda r: r.id) == [
-        models.Allele(
-            **alleles["ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD"]["variation"]
-        ),
-        models.Allele(
-            **alleles["ga4gh:VA.R4kbmdsn5VldGrBiAaByO5N9zM3qCSFw"]["variation"]
-        ),
-        models.Allele(
-            **alleles["ga4gh:VA.yi7A2l0uIUMaInQaJnHU_B2Cf_OuZRJg"]["variation"]
-        ),
-    ]
-
-
-@pytest.mark.vcr
-@pytest.mark.parametrize("anyvar_client", POPULATED_CLIENTS, indirect=True)
-def test_search_by_interval_with_alias(anyvar_client: BaseAnyVarClient, alleles: dict):
-    """Test use of sequence alias"""
-    results = anyvar_client.search_by_interval("GRCh38.p1:Y", 2781760, 2781760)
-    assert sorted(results, key=lambda r: r.id) == [
-        models.Allele(
-            **alleles["ga4gh:VA.9VDxL0stMBOZwcTKw3yb3UoWQkpaI9OD"]["variation"]
-        ),
-        models.Allele(
-            **alleles["ga4gh:VA.R4kbmdsn5VldGrBiAaByO5N9zM3qCSFw"]["variation"]
-        ),
-    ]
-
-
-@pytest.mark.vcr
-@pytest.mark.parametrize("anyvar_client", POPULATED_CLIENTS, indirect=True)
-def test_search_by_interval_unknown_alias(anyvar_client: BaseAnyVarClient):
-    """Test handling response when sequence alias isn't recognized."""
-    assert anyvar_client.search_by_interval("GRCh45.p1:Y", 2781760, 2781760) == []
-
-
-@pytest.mark.vcr
-@pytest.mark.parametrize("anyvar_client", POPULATED_CLIENTS, indirect=True)
-def test_search_by_interval_unknown_accession(anyvar_client: BaseAnyVarClient):
-    """Test handling response when accession ID isn't recognized"""
-    results = anyvar_client.search_by_interval(
-        "ga4gh:SQ.ZZZZZu1aycC0tPQPFmUaGXJLDs5SbPZ5", 2781760, 2781768
-    )
-    assert results == []
-
-
-@pytest.mark.vcr
-@pytest.mark.parametrize("anyvar_client", POPULATED_CLIENTS, indirect=True)
-def test_search_by_interval_not_found(anyvar_client: BaseAnyVarClient):
-    """Test handling response when no matching variants are found"""
-    results = anyvar_client.search_by_interval(
-        "ga4gh:SQ.8_liLu1aycC0tPQPFmUaGXJLDs5SbPZ5", 1, 100
-    )
-    assert results == []

tests/unit/functions/test_ingest_vcf.py

@@ -3,7 +3,6 @@
 
 import pytest
 from anyvar.utils.liftover_utils import ReferenceAssembly
-from anyvar.utils.types import VrsVariation
 
 from anyvlm.anyvar.base_client import BaseAnyVarClient
 from anyvlm.functions.ingest_vcf import VcfAfColumnsError, ingest_vcf
@@ -44,7 +43,7 @@ def stub_anyvar_client():
     }
 
     class TestAnyVarClient(BaseAnyVarClient):
-        def get_registered_allele_expression(
+        def get_registered_allele(
             self,
             expression: str,
             assembly: ReferenceAssembly = ReferenceAssembly.GRCH38,
@@ -61,11 +60,6 @@ def put_allele_expressions(
                 for expr in expressions
             ]
 
-        def search_by_interval(
-            self, accession: str, start: int, end: int
-        ) -> list[VrsVariation]:
-            raise NotImplementedError
-
         def close(self) -> None:
             """Clean up AnyVar connection."""