rm consequence, ac, and af from table

Author: korikuzma

src/anyvlm/storage/mappers.py

@@ -36,17 +36,22 @@ def from_db_entity(
         :return: VA-Spec Cohort Allele Frequency Study Result instance. Will use
             iriReference for focusAllele
         """
+        homozygotes = db_entity.ac_hom
+        heterozygotes = db_entity.ac_het
+        hemizygotes = db_entity.ac_hemi
+        ac = sum((homozygotes, heterozygotes, hemizygotes))
+        an = db_entity.an
+
         return CohortAlleleFrequencyStudyResult(
             focusAllele=iriReference(db_entity.vrs_id),
-            focusAlleleCount=db_entity.ac,
-            locusAlleleCount=db_entity.an,
-            focusAlleleFrequency=db_entity.af,
+            focusAlleleCount=ac,
+            locusAlleleCount=an,
+            focusAlleleFrequency=ac / an,
             qualityMeasures={"qcFilters": db_entity.filter},
             ancillaryResults={
-                "homozygotes": db_entity.ac_hom,
-                "heterozygotes": db_entity.ac_het,
-                "hemizygotes": db_entity.ac_hemi,
-                "consequence": db_entity.consequence,
+                "homozygotes": homozygotes,
+                "heterozygotes": heterozygotes,
+                "hemizygotes": hemizygotes,
             },
             cohort=StudyGroup(name="rare disease"),
         )
@@ -69,12 +74,9 @@ def to_db_entity(
 
         return orm.AlleleFrequencyData(
             vrs_id=vrs_id,
-            af=va_model.focusAlleleFrequency,
-            ac=va_model.focusAlleleCount,
             an=va_model.locusAlleleCount,
             ac_het=ancillary_results["heterozygotes"],
             ac_hom=ancillary_results["homozygotes"],
             ac_hemi=ancillary_results["hemizygotes"],
-            consequence=ancillary_results["consequence"],
             filter=va_model.qualityMeasures["qcFilters"],
         )

src/anyvlm/storage/orm.py

@@ -2,7 +2,6 @@
 
 from anyvar.utils.funcs import camel_case_to_snake_case
 from sqlalchemy import (
-    Float,
     Integer,
     String,
     create_engine,
@@ -42,13 +41,10 @@ def __tablename__(self) -> str:
         return "allele_frequency_data"
 
     vrs_id: Mapped[str] = mapped_column(String, primary_key=True)
-    af: Mapped[float] = mapped_column(Float)
-    ac: Mapped[int] = mapped_column(Integer)
     an: Mapped[int] = mapped_column(Integer)
     ac_het: Mapped[int] = mapped_column(Integer)
     ac_hom: Mapped[int] = mapped_column(Integer)
     ac_hemi: Mapped[int] = mapped_column(Integer)
-    consequence: Mapped[str] = mapped_column(String)
     filter: Mapped[list[str]] = mapped_column(ARRAY(String))
 
 

tests/conftest.py

@@ -99,7 +99,6 @@ def caf_iri():
             "homozygotes": 0,
             "heterozygotes": 1,
             "hemizygotes": 0,
-            "consequence": "intron_variant",
         },
         cohort=StudyGroup(name="rare disease"),
     )

tests/unit/storage/test_postgres_unit.py

@@ -40,12 +40,9 @@ def insert_and_verify_one_row():
         db_record = rows[0]
 
         assert db_record.vrs_id == "ga4gh:VA.J3Hi64dkKFKdnKIwB2419Qz3STDB2sJq"
-        assert db_record.af == 0.000162232
-        assert db_record.ac == 1
         assert db_record.an == 6164
         assert db_record.ac_het == 1
         assert db_record.ac_hom == 0
-        assert db_record.consequence == "intron_variant"
         assert db_record.filter == ["LowQual", "NO_HQ_GENOTYPES"]
 
     # first insert