Cheng Zhou
113 lines
3.5 KiB
Python
113 lines
3.5 KiB
Python
import uuid
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from datetime import date, timedelta
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from typing import Sequence
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from sqlalchemy import select, update as sa_update
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from sqlalchemy.ext.asyncio import AsyncSession
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from app.crud import visit as visit_crud
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from app.models.site import Site
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from app.models.subject import Subject
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from app.schemas.subject import SubjectCreate, SubjectUpdate
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async def _validate_site(db: AsyncSession, study_id: uuid.UUID, site_id: uuid.UUID) -> None:
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result = await db.execute(select(Site).where(Site.id == site_id))
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site = result.scalar_one_or_none()
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if not site or site.study_id != study_id:
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raise ValueError("Site not found in study")
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async def create_subject(db: AsyncSession, study_id: uuid.UUID, subject_in: SubjectCreate) -> Subject:
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await _validate_site(db, study_id, subject_in.site_id)
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subject = Subject(
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study_id=study_id,
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site_id=subject_in.site_id,
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subject_no=subject_in.subject_no,
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status="SCREENING",
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screening_date=subject_in.screening_date,
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enrollment_date=None,
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completion_date=None,
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drop_reason=None,
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)
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db.add(subject)
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await db.commit()
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await db.refresh(subject)
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# initial visit: Screening (V0)
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await visit_crud.create_visit(
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db,
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study_id=study_id,
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visit_in=None,
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subject=subject,
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visit_code="V0",
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visit_name="Screening",
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planned_date=subject.screening_date,
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)
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return subject
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async def get_subject(db: AsyncSession, subject_id: uuid.UUID) -> Subject | None:
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result = await db.execute(select(Subject).where(Subject.id == subject_id))
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return result.scalar_one_or_none()
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async def list_subjects(
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db: AsyncSession,
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study_id: uuid.UUID,
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site_id: uuid.UUID | None = None,
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status: str | None = None,
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subject_no: str | None = None,
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) -> Sequence[Subject]:
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stmt = select(Subject).where(Subject.study_id == study_id)
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if site_id:
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stmt = stmt.where(Subject.site_id == site_id)
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if status:
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stmt = stmt.where(Subject.status == status)
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if subject_no:
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stmt = stmt.where(Subject.subject_no.ilike(f"%{subject_no}%"))
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result = await db.execute(stmt)
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return result.scalars().all()
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async def generate_default_visits(db: AsyncSession, subject: Subject) -> None:
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# Baseline + Follow-up visits based on enrollment_date
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if not subject.enrollment_date:
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return
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baseline_date = subject.enrollment_date
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follow1 = baseline_date + timedelta(days=30)
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follow2 = baseline_date + timedelta(days=60)
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visits_data = [
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("V1", "Baseline", baseline_date),
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("FU1", "Follow-up 1", follow1),
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("FU2", "Follow-up 2", follow2),
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]
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for code, name, plan_date in visits_data:
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await visit_crud.create_visit(
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db,
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study_id=subject.study_id,
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visit_in=None,
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subject=subject,
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visit_code=code,
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visit_name=name,
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planned_date=plan_date,
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)
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async def update_subject(db: AsyncSession, subject: Subject, subject_in: SubjectUpdate) -> Subject:
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update_data = subject_in.model_dump(exclude_unset=True)
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if update_data:
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await db.execute(
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sa_update(Subject)
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.where(Subject.id == subject.id)
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.values(**update_data)
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)
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await db.commit()
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await db.refresh(subject)
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return subject
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async def delete_subject(db: AsyncSession, subject: Subject) -> None:
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await db.delete(subject)
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await db.commit()
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