feat: Allow users to save acmg criteria on the server (#98)

backend/alembic/versions/d10fec1c88fc_init_acmgseqvar.py

@@ -0,0 +1,39 @@
+"""init acmgseqvar
+Revision ID: d10fec1c88fc
+Revises: 4f3b20f156c1
+Create Date: 2023-11-29 11:16:25.636296+01:00
+
+"""
+import fastapi_users_db_sqlalchemy.generics  # noqa
+import sqlalchemy as sa
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "d10fec1c88fc"
+down_revision = "4f3b20f156c1"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "acmgseqvar",
+        sa.Column("id", fastapi_users_db_sqlalchemy.generics.GUID(), nullable=False),
+        sa.Column("user", sa.Uuid(), nullable=False),
+        sa.Column("seqvar_name", sa.String(length=255), nullable=False),
+        sa.Column("acmg_rank", sa.JSON(), nullable=True),
+        sa.ForeignKeyConstraint(["user"], ["user.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("user", "seqvar_name", name="uq_acmgseqvar"),
+    )
+    op.create_index(op.f("ix_acmgseqvar_id"), "acmgseqvar", ["id"], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f("ix_acmgseqvar_id"), table_name="acmgseqvar")
+    op.drop_table("acmgseqvar")
+    # ### end Alembic commands ###

backend/app/api/api_v1/api.py

@@ -4,12 +4,13 @@
 from httpx_oauth.clients.openid import OpenID
 from httpx_oauth.errors import GetIdEmailError
 
-from app.api.api_v1.endpoints import adminmsgs, auth, bookmarks, caseinfo, utils
+from app.api.api_v1.endpoints import acmgseqvar, adminmsgs, auth, bookmarks, caseinfo, utils
 from app.core.auth import auth_backend_bearer, auth_backend_cookie, fastapi_users
 from app.core.config import settings
 from app.schemas.user import UserRead, UserUpdate
 
 api_router = APIRouter()
+api_router.include_router(acmgseqvar.router, prefix="/acmgseqvar", tags=["acmgseqvar"])
 api_router.include_router(adminmsgs.router, prefix="/adminmsgs", tags=["adminmsgs"])
 api_router.include_router(bookmarks.router, prefix="/bookmarks", tags=["bookmarks"])
 api_router.include_router(utils.router, prefix="/utils", tags=["utils"])

backend/app/api/api_v1/endpoints/acmgseqvar.py

@@ -0,0 +1,173 @@
+from fastapi import APIRouter, Depends, HTTPException
+from sqlalchemy.ext.asyncio import AsyncSession
+
+from app import crud, schemas
+from app.api import deps
+from app.api.deps import current_active_superuser, current_active_user
+from app.models.user import User
+
+router = APIRouter()
+
+
+@router.post("/create", response_model=schemas.AcmgSeqVarCreate)
+async def create_acmgseqvar(
+    acmgseqvar: schemas.AcmgSeqVarCreate,
+    db: AsyncSession = Depends(deps.get_db),
+    user: User = Depends(current_active_user),
+):
+    """
+    Create a new ACMG Sequence Variant.
+
+    :param acmgseqvar: ACMG Sequence Variant to create
+    :type acmgseqvar: dict or :class:`.schemas.AcmgSeqVarCreate`
+    :return: ACMG Sequence Variant
+    :rtype: dict
+    """
+    acmgseqvar.user = user.id
+    return await crud.acmgseqvar.create(db, obj_in=acmgseqvar)
+
+
+@router.get(
+    "/list-all",
+    dependencies=[Depends(current_active_superuser)],
+    response_model=list[schemas.AcmgSeqVarRead],
+)
+async def list_acmgseqvars(
+    skip: int = 0, limit: int = 100, db: AsyncSession = Depends(deps.get_db)
+):
+    """
+    List all ACMG Sequence Variants. Available only for superusers.
+
+    :param skip: number of ACMG Sequence Variants to skip
+    :type skip: int
+    :param limit: maximum number of ACMG Sequence Variants to return
+    :type limit: int
+    :return: list of ACMG Sequence Variants
+    :rtype: list
+    """
+    return await crud.acmgseqvar.get_multi(db, skip=skip, limit=limit)
+
+
+@router.get(
+    "/get-by-id",
+    dependencies=[Depends(current_active_superuser)],
+    response_model=schemas.AcmgSeqVarRead,
+)
+async def get_acmgseqvar(id: str, db: AsyncSession = Depends(deps.get_db)):
+    """
+    Get a ACMG Sequence Variant by id. Available only for superusers.
+
+    :param id: ACMG Sequence Variant id
+    :type id: uuid
+    :return: ACMG Sequence Variant
+    :rtype: dict
+    """
+    response = await crud.acmgseqvar.get(db, id)
+    if not response:
+        raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
+    else:
+        return response
+
+
+@router.get("/list", response_model=list[schemas.AcmgSeqVarRead])
+async def list_acmgseqvars_by_user(
+    skip: int = 0,
+    limit: int = 100,
+    db: AsyncSession = Depends(deps.get_db),
+    user: User = Depends(current_active_user),
+):
+    """
+    List ACMG Sequence Variants by user.
+
+    :return: list of ACMG Sequence Variants
+    :rtype: list
+    """
+    return await crud.acmgseqvar.get_multi_by_user(db, user_id=user.id, skip=skip, limit=limit)
+
+
+@router.get("/get", response_model=schemas.AcmgSeqVarRead)
+async def get_acmgseqvar_by_user(
+    seqvar: str,
+    db: AsyncSession = Depends(deps.get_db),
+    user: User = Depends(current_active_user),
+):
+    """
+    Get a ACMG Sequence Variant by id.
+
+    :param id: ACMG Sequence Variant id
+    :type id: uuid
+    :return: ACMG Sequence Variant
+    :rtype: dict
+    """
+    response = await crud.acmgseqvar.get_by_user(db, user_id=user.id, seqvar_name=seqvar)
+    if not response:
+        raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
+    else:
+        return response
+
+
+@router.put("/update", response_model=schemas.AcmgSeqVarRead)
+@router.patch("/update", response_model=schemas.AcmgSeqVarRead)
+async def update_acmgseqvar(
+    acmgseqvar: schemas.AcmgSeqVarUpdate,
+    db: AsyncSession = Depends(deps.get_db),
+    user: User = Depends(current_active_user),
+):
+    """
+    Update a ACMG Sequence Variant.
+
+    :param acmgseqvar: ACMG Sequence Variant to update
+    :type acmgseqvar: dict or :class:`.schemas.AcmgSeqVarUpdate`
+    :return: ACMG Sequence Variant
+    :rtype: dict
+    """
+    acmgseqvar.user = user.id
+    response = await crud.acmgseqvar.get_by_user(
+        db, user_id=user.id, seqvar_name=acmgseqvar.seqvar_name
+    )
+    if not response:
+        raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
+    else:
+        return await crud.acmgseqvar.update(db, db_obj=response, obj_in=acmgseqvar)
+
+
+@router.delete(
+    "/delete-by-id",
+    dependencies=[Depends(current_active_superuser)],
+    response_model=schemas.AcmgSeqVarRead,
+)
+async def delete_acmgseqvar(id: str, db: AsyncSession = Depends(deps.get_db)):
+    """
+    Delete a ACMG Sequence Variant by id. Available only for superusers.
+
+    :param id: ACMG Sequence Variant id
+    :type id: uuid
+    :return: ACMG Sequence Variant
+    :rtype: dict
+    """
+    response = await crud.acmgseqvar.get(db, id)
+    if not response:
+        raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
+    else:
+        return await crud.acmgseqvar.remove(db, id=id)
+
+
+@router.delete("/delete", response_model=schemas.AcmgSeqVarRead)
+async def delete_acmgseqvar_by_user(
+    seqvar: str,
+    db: AsyncSession = Depends(deps.get_db),
+    user: User = Depends(current_active_user),
+):
+    """
+    Delete a ACMG Sequence Variant by id.
+
+    :param id: ACMG Sequence Variant id
+    :type id: uuid
+    :return: ACMG Sequence Variant
+    :rtype: dict
+    """
+    response = await crud.acmgseqvar.get_by_user(db, user_id=user.id, seqvar_name=seqvar)
+    if not response:
+        raise HTTPException(status_code=404, detail="ACMG Sequence Variant not found")
+    else:
+        return await crud.acmgseqvar.remove(db, id=response.id)

backend/app/api/api_v1/endpoints/caseinfo.py

@@ -67,27 +67,6 @@ async def get_caseinfo(id: str, db: AsyncSession = Depends(deps.get_db)):
         return response
 
 
-@router.delete(
-    "/delete-by-id",
-    dependencies=[Depends(current_active_superuser)],
-    response_model=schemas.CaseInfoRead,
-)
-async def delete_caseinfo(id: str, db: AsyncSession = Depends(deps.get_db)):
-    """
-    Delete a Case Information by id. Available only for superusers.
-
-    :param id: Case Information id
-    :type id: uuid
-    :return: Case Information
-    :rtype: dict
-    """
-    response = await crud.caseinfo.remove(db, id=id)
-    if not response:
-        raise HTTPException(status_code=404, detail="Case Information not found")
-    else:
-        return response
-
-
 @router.get("/list", response_model=list[schemas.CaseInfoRead])
 async def list_caseinfos_for_user(
     db: AsyncSession = Depends(deps.get_db),
@@ -140,6 +119,27 @@ async def update_caseinfo_for_user(
     return await crud.caseinfo.update(db, db_obj=caseinfo, obj_in=caseinfoupdate)
 
 
+@router.delete(
+    "/delete-by-id",
+    dependencies=[Depends(current_active_superuser)],
+    response_model=schemas.CaseInfoRead,
+)
+async def delete_caseinfo(id: str, db: AsyncSession = Depends(deps.get_db)):
+    """
+    Delete a Case Information by id. Available only for superusers.
+
+    :param id: Case Information id
+    :type id: uuid
+    :return: Case Information
+    :rtype: dict
+    """
+    response = await crud.caseinfo.remove(db, id=id)
+    if not response:
+        raise HTTPException(status_code=404, detail="Case Information not found")
+    else:
+        return response
+
+
 @router.delete("/delete", response_model=schemas.CaseInfoRead)
 async def delete_caseinfo_for_user(
     db: AsyncSession = Depends(deps.get_db), user: User = Depends(current_active_user)

backend/app/crud/__init__.py

@@ -1,6 +1,8 @@
+from app.crud.acmgseqvar import CrudAcmgSeqVar
 from app.crud.base import CrudBase
 from app.crud.bookmarks import CrudBookmark
 from app.crud.caseinfo import CrudCaseInfo
+from app.models.acmgseqvar import AcmgSeqVar
 from app.models.adminmsg import AdminMessage
 from app.models.bookmark import Bookmark
 from app.models.caseinfo import CaseInfo
@@ -9,3 +11,4 @@
 adminmessage = CrudBase[AdminMessage, AdminMessageCreate, AdminMessageUpdate](AdminMessage)
 bookmark = CrudBookmark(Bookmark)
 caseinfo = CrudCaseInfo(CaseInfo)
+acmgseqvar = CrudAcmgSeqVar(AcmgSeqVar)

backend/app/crud/acmgseqvar.py

@@ -0,0 +1,27 @@
+from typing import Any, Sequence
+
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlalchemy.future import select
+
+from app.crud.base import CrudBase
+from app.models.acmgseqvar import AcmgSeqVar
+from app.schemas.acmgseqvar import AcmgSeqVarCreate, AcmgSeqVarUpdate
+
+
+class CrudAcmgSeqVar(CrudBase[AcmgSeqVar, AcmgSeqVarCreate, AcmgSeqVarUpdate]):
+    async def get_multi_by_user(
+        self, session: AsyncSession, *, skip: int = 0, limit: int = 100, user_id: Any
+    ) -> Sequence[AcmgSeqVar]:
+        query = select(self.model).filter(self.model.user == user_id).offset(skip).limit(limit)
+        result = await session.execute(query)
+        all_scalars: Sequence[AcmgSeqVar] = result.scalars().all()  # type: ignore[assignment]
+        return all_scalars
+
+    async def get_by_user(
+        self, session: AsyncSession, *, user_id: Any, seqvar_name: Any
+    ) -> AcmgSeqVar | None:
+        query = select(self.model).filter(
+            self.model.user == user_id, self.model.seqvar_name == seqvar_name
+        )
+        result = await session.execute(query)
+        return result.scalars().first()

backend/app/models/__init__.py

@@ -1,3 +1,4 @@
+from app.models.acmgseqvar import AcmgSeqVar  # noqa
 from app.models.adminmsg import AdminMessage  # noqa
 from app.models.bookmark import Bookmark  # noqa
 from app.models.caseinfo import CaseInfo  # noqa

backend/app/models/acmgseqvar.py

@@ -0,0 +1,38 @@
+"""Models for ACMG sequence variant."""
+
+import uuid as uuid_module
+from typing import TYPE_CHECKING
+
+from fastapi_users_db_sqlalchemy.generics import GUID  # noqa
+from sqlalchemy import JSON, Column, ForeignKey, String, UniqueConstraint, Uuid
+from sqlalchemy.orm import Mapped, mapped_column
+
+from app.db.session import Base
+from app.schemas.acmgseqvar import AcmgRank
+
+UUID_ID = uuid_module.UUID
+
+
+class AcmgSeqVar(Base):
+    """ACMG sequence variant."""
+
+    __tablename__ = "acmgseqvar"
+
+    __table_args__ = (UniqueConstraint("user", "seqvar_name", name="uq_acmgseqvar"),)
+
+    if TYPE_CHECKING:  # pragma: no cover
+        id: UUID_ID
+        user: UUID_ID
+        seqvar_name: str
+        acmg_rank: AcmgRank
+    else:
+        #: UUID of the ACMG sequence variant.
+        id: Mapped[UUID_ID] = mapped_column(
+            GUID, primary_key=True, index=True, default=uuid_module.uuid4
+        )
+        #: User who created the ACMG sequence variant.
+        user = Column(Uuid, ForeignKey("user.id", ondelete="CASCADE"), nullable=False)
+        #: Sequence variant ID.
+        seqvar_name = Column(String(255), nullable=False)
+        #: ACMG criteria.
+        acmg_rank = Column(JSON, nullable=True)

backend/app/schemas/__init__.py

@@ -1,3 +1,4 @@
+from app.schemas.acmgseqvar import AcmgSeqVarCreate, AcmgSeqVarRead, AcmgSeqVarUpdate  # noqa
 from app.schemas.adminmsg import AdminMessageCreate, AdminMessageRead, AdminMessageUpdate  # noqa
 from app.schemas.auth import OAuth2ProviderConfig, OAuth2ProviderPublic  # noqa
 from app.schemas.bookmark import BookmarkCreate, BookmarkRead, BookmarkUpdate  # noqa