Merge pull request #63 from VariantEffect/mappedVariant

Mapped variants

Author: jstone-dev

alembic/versions/33e99d4b90cc_add_mapped_variants_table.py

@@ -0,0 +1,37 @@
+"""Add mapped_variants table
+
+Revision ID: 33e99d4b90cc
+Revises: 988ca84c701b
+Create Date: 2023-05-15 17:24:07.847206
+
+"""
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = '33e99d4b90cc'
+down_revision = 'da9ba478647d'
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('mapped_variants',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('pre_mapped', postgresql.JSONB(astext_type=sa.Text()), nullable=False),
+    sa.Column('post_mapped', postgresql.JSONB(astext_type=sa.Text()), nullable=False),
+    sa.Column('variant_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['variant_id'], ['variants.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_mapped_variants_id'), 'mapped_variants', ['id'], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f('ix_mapped_variants_id'), table_name='mapped_variants')
+    op.drop_table('mapped_variants')
+    # ### end Alembic commands ###

src/mavedb/models/__init__.py

@@ -8,6 +8,7 @@
     "genome_identifier",
     "keyword",
     "license",
+    "mapped_variant",
     "publication_identifier",
     "raw_read_identifier",
     "reference_genome",

src/mavedb/models/mapped_variant.py

@@ -0,0 +1,16 @@
+from sqlalchemy import Column, ForeignKey, Integer
+from sqlalchemy.orm import relationship, backref
+
+from mavedb.db.base import Base
+from mavedb.deps import JSONB
+
+class MappedVariant(Base):
+    __tablename__ = "mapped_variants"
+
+    id = Column(Integer, primary_key=True, index=True)
+
+    pre_mapped = Column(JSONB, nullable=False)
+    post_mapped = Column(JSONB, nullable=False)
+
+    variant_id = Column(Integer, ForeignKey("variants.id"), nullable=False)
+    variant = relationship("Variant", backref=backref("mapped_variants", cascade="all,delete-orphan"))

src/mavedb/routers/mapped_variant.py

@@ -0,0 +1,42 @@
+from typing import Any, List, Optional
+
+from fastapi import APIRouter, Depends
+from fastapi.exceptions import HTTPException
+from sqlalchemy.orm import Session
+from sqlalchemy.exc import MultipleResultsFound
+
+from mavedb import deps
+
+from mavedb.models.mapped_variant import MappedVariant
+from mavedb.models.variant import Variant
+from mavedb.view_models import mapped_variant
+
+async def fetch_mapped_variant_by_variant_urn(db, urn: str) -> Optional[MappedVariant]:
+    """
+    We may combine this function back to show_mapped_variant if none of any new function call it.
+    Fetch one mapped variant by variant URN.
+
+    :param db: An active database session.
+    :param urn: The variant URN.
+    :return: The mapped variant, or None if the URL was not found or refers to a private score set not owned by the specified
+        user.
+    """
+    try:
+        item = db.query(MappedVariant).filter(Variant.urn == urn).filter(MappedVariant.variant_id == Variant.id).one_or_none()
+    except MultipleResultsFound:
+        raise HTTPException(status_code=500, detail=f"Multiple variants with URN {urn} were found.")
+    if not item:
+        raise HTTPException(status_code=404, detail=f"Mapped variant with URN {urn} not found")
+    return item
+
+router = APIRouter(prefix="/api/v1/mapped-variants", tags=["mapped variants"], responses={404: {"description": "Not found"}})
+
+@router.get("/{urn}", status_code=200, response_model=mapped_variant.MappedVariant, responses={404: {}, 500: {}})
+async def show_mapped_variant(
+    *, urn: str, db: Session = Depends(deps.get_db)
+) -> Any:
+    """
+    Fetch a mapped variant by URN.
+    """
+
+    return await fetch_mapped_variant_by_variant_urn(db, urn)

src/mavedb/routers/score_sets.py

@@ -35,12 +35,14 @@
 from mavedb.models.enums.processing_state import ProcessingState
 from mavedb.models.experiment import Experiment
 from mavedb.models.license import License
+from mavedb.models.mapped_variant import MappedVariant
 from mavedb.models.reference_map import ReferenceMap
 from mavedb.models.score_set import ScoreSet
 from mavedb.models.target_gene import TargetGene
 from mavedb.models.user import User
 from mavedb.models.variant import Variant
 from mavedb.models.wild_type_sequence import WildTypeSequence
+from mavedb.view_models import mapped_variant
 from mavedb.view_models import score_set
 from mavedb.view_models.search import ScoreSetsSearch
 
@@ -179,6 +181,25 @@ async def get_score_set_counts_csv(
     return StreamingResponse(iter([stream.getvalue()]), media_type="text/csv")
 
 
+@router.get(
+    "/score-sets/{urn}/mapped-variants", status_code=200, response_model=list[mapped_variant.MappedVariant])
+def get_score_set_mapped_variants(
+    *,
+    urn: str,
+    db: Session = Depends(deps.get_db),
+) -> Any:
+    """
+    Return mapped variants from a score set, identified by URN.
+    """
+    mapped_variants = (
+        db.query(MappedVariant).filter(ScoreSet.urn == urn).filter(ScoreSet.id == Variant.score_set_id).filter(Variant.id == MappedVariant.variant_id).all()
+    )
+
+    if not mapped_variants:
+        raise HTTPException(status_code=404, detail=f"No mapped variant associated with score set URN {urn} was found")
+
+    return mapped_variants
+
 class HGVSColumns:
     NUCLEOTIDE: str = "hgvs_nt"  # dataset.constants.hgvs_nt_column
     TRANSCRIPT: str = "hgvs_splice"  # dataset.constants.hgvs_splice_column

src/mavedb/server_main.py

@@ -24,6 +24,7 @@
     experiment_sets,
     experiments,
     licenses,
+    mapped_variant,
     publication_identifiers,
     target_gene_identifiers,
     raw_read_identifiers,
@@ -57,6 +58,7 @@
 app.include_router(experiment_sets.router)
 app.include_router(experiments.router)
 app.include_router(licenses.router)
+app.include_router(mapped_variant.router)
 app.include_router(publication_identifiers.router)
 app.include_router(raw_read_identifiers.router)
 app.include_router(reference_genomes.router)

src/mavedb/view_models/mapped_variant.py

@@ -0,0 +1,29 @@
+from typing import Any
+
+from .base.base import BaseModel
+
+
+class MappedVariantBase(BaseModel):
+    pre_mapped: Any
+    post_mapped: Any
+    variant_id: int
+
+
+class MappedVariantCreate(MappedVariantBase):
+    pass
+
+
+class MappedVariantUpdate(MappedVariantBase):
+    pass
+
+# Properties shared by models stored in DB
+class SavedMappedVariant(MappedVariantBase):
+    id: int
+
+    class Config:
+        orm_mode = True
+
+
+# Properties to return to non-admin clients
+class MappedVariant(SavedMappedVariant):
+    pass