Step 6:受试者(Subject)+ 访视(Visit)+ 随访进度

This commit is contained in:
Cheng Zhou
2025-12-16 17:43:11 +08:00
parent a9e15faedc
commit c77b20f932
69 changed files with 468 additions and 1 deletions
+3 -1
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@@ -1,6 +1,6 @@
from fastapi import APIRouter
from app.api.v1 import auth, users, studies, sites, members, comments, attachments, audit_logs, milestones, tasks, dashboard
from app.api.v1 import auth, users, studies, sites, members, comments, attachments, audit_logs, milestones, tasks, dashboard, subjects, visits
api_router = APIRouter()
api_router.include_router(auth.router, prefix="/auth", tags=["auth"])
@@ -14,3 +14,5 @@ api_router.include_router(audit_logs.router, prefix="/studies/{study_id}/audit-l
api_router.include_router(milestones.router, prefix="/studies/{study_id}/milestones", tags=["milestones"])
api_router.include_router(tasks.router, prefix="/studies/{study_id}/tasks", tags=["tasks"])
api_router.include_router(dashboard.router, prefix="/studies/{study_id}/dashboard", tags=["dashboard"])
api_router.include_router(subjects.router, prefix="/studies/{study_id}/subjects", tags=["subjects"])
api_router.include_router(visits.router, prefix="/studies/{study_id}/subjects/{subject_id}/visits", tags=["visits"])
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@@ -0,0 +1,102 @@
import uuid
from fastapi import APIRouter, Depends, HTTPException, status
from sqlalchemy.ext.asyncio import AsyncSession
from app.core.deps import get_current_user, get_db_session, require_study_member, require_study_roles
from app.crud import audit as audit_crud
from app.crud import subject as subject_crud
from app.crud import study as study_crud
from app.schemas.subject import SubjectCreate, SubjectRead, SubjectUpdate
router = APIRouter()
async def _ensure_study_exists(db: AsyncSession, study_id: uuid.UUID):
study = await study_crud.get(db, study_id)
if not study:
raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Study not found")
return study
@router.post(
"/",
response_model=SubjectRead,
status_code=status.HTTP_201_CREATED,
dependencies=[Depends(require_study_roles(["PM", "CRA"]))],
)
async def create_subject(
study_id: uuid.UUID,
subject_in: SubjectCreate,
db: AsyncSession = Depends(get_db_session),
current_user=Depends(get_current_user),
) -> SubjectRead:
await _ensure_study_exists(db, study_id)
try:
subject = await subject_crud.create_subject(db, study_id, subject_in)
except ValueError as exc:
raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail=str(exc)) from exc
await audit_crud.log_action(
db,
study_id=study_id,
entity_type="subject",
entity_id=subject.id,
action="CREATE_SUBJECT",
detail=f"Subject {subject.subject_no} created",
operator_id=current_user.id,
operator_role=current_user.role,
)
return subject
@router.get(
"/",
response_model=list[SubjectRead],
dependencies=[Depends(require_study_member())],
)
async def list_subjects(
study_id: uuid.UUID,
site_id: uuid.UUID | None = None,
status_filter: str | None = None,
db: AsyncSession = Depends(get_db_session),
) -> list[SubjectRead]:
await _ensure_study_exists(db, study_id)
subjects = await subject_crud.list_subjects(db, study_id, site_id=site_id, status=status_filter)
return list(subjects)
@router.patch(
"/{subject_id}",
response_model=SubjectRead,
dependencies=[Depends(require_study_roles(["PM", "CRA"]))],
)
async def update_subject(
study_id: uuid.UUID,
subject_id: uuid.UUID,
subject_in: SubjectUpdate,
db: AsyncSession = Depends(get_db_session),
current_user=Depends(get_current_user),
) -> SubjectRead:
await _ensure_study_exists(db, study_id)
subject = await subject_crud.get_subject(db, subject_id)
if not subject or subject.study_id != study_id:
raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Subject not found")
old_status = subject.status
updated = await subject_crud.update_subject(db, subject, subject_in)
# auto-generate visits when enrolled
if subject_in.status and subject_in.status == "ENROLLED" and (subject_in.enrollment_date or updated.enrollment_date):
await subject_crud.generate_default_visits(db, updated)
detail = None
if subject_in.status and subject_in.status != old_status:
detail = f"subject {updated.subject_no} status {old_status} -> {subject_in.status}"
await audit_crud.log_action(
db,
study_id=study_id,
entity_type="subject",
entity_id=subject_id,
action="SUBJECT_STATUS_CHANGE" if detail else "UPDATE_SUBJECT",
detail=detail or "Subject updated",
operator_id=current_user.id,
operator_role=current_user.role,
)
return updated
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@@ -0,0 +1,70 @@
import uuid
from fastapi import APIRouter, Depends, HTTPException, status
from sqlalchemy.ext.asyncio import AsyncSession
from app.core.deps import get_current_user, get_db_session, require_study_member, require_study_roles
from app.crud import audit as audit_crud
from app.crud import subject as subject_crud
from app.crud import visit as visit_crud
from app.schemas.visit import VisitRead, VisitUpdate
router = APIRouter()
async def _ensure_subject(db: AsyncSession, study_id: uuid.UUID, subject_id: uuid.UUID):
subject = await subject_crud.get_subject(db, subject_id)
if not subject or subject.study_id != study_id:
raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Subject not found")
return subject
@router.get(
"/",
response_model=list[VisitRead],
dependencies=[Depends(require_study_member())],
)
async def list_visits(
study_id: uuid.UUID,
subject_id: uuid.UUID,
db: AsyncSession = Depends(get_db_session),
) -> list[VisitRead]:
await _ensure_subject(db, study_id, subject_id)
visits = await visit_crud.list_visits(db, subject_id)
return list(visits)
@router.patch(
"/{visit_id}",
response_model=VisitRead,
dependencies=[Depends(require_study_roles(["PM", "CRA"]))],
)
async def update_visit(
study_id: uuid.UUID,
subject_id: uuid.UUID,
visit_id: uuid.UUID,
visit_in: VisitUpdate,
db: AsyncSession = Depends(get_db_session),
current_user=Depends(get_current_user),
) -> VisitRead:
await _ensure_subject(db, study_id, subject_id)
visit = await visit_crud.get_visit(db, visit_id)
if not visit or visit.subject_id != subject_id or visit.study_id != study_id:
raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Visit not found")
if visit_in.status == "DONE" and not visit_in.actual_date:
raise HTTPException(status_code=status.HTTP_400_BAD_REQUEST, detail="actual_date required when DONE")
updated = await visit_crud.update_visit(db, visit, visit_in)
detail = None
if visit_in.status:
detail = f"visit {visit.visit_code} {visit.status} -> {visit_in.status}"
await audit_crud.log_action(
db,
study_id=study_id,
entity_type="visit",
entity_id=visit_id,
action="VISIT_STATUS_CHANGE" if detail else "UPDATE_VISIT",
detail=detail or "Visit updated",
operator_id=current_user.id,
operator_role=current_user.role,
)
return updated
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import uuid
from datetime import date, timedelta
from typing import Sequence
from sqlalchemy import select, update as sa_update
from sqlalchemy.ext.asyncio import AsyncSession
from app.crud import visit as visit_crud
from app.models.site import Site
from app.models.subject import Subject
from app.schemas.subject import SubjectCreate, SubjectUpdate
async def _validate_site(db: AsyncSession, study_id: uuid.UUID, site_id: uuid.UUID) -> None:
result = await db.execute(select(Site).where(Site.id == site_id))
site = result.scalar_one_or_none()
if not site or site.study_id != study_id:
raise ValueError("Site not found in study")
async def create_subject(db: AsyncSession, study_id: uuid.UUID, subject_in: SubjectCreate) -> Subject:
await _validate_site(db, study_id, subject_in.site_id)
subject = Subject(
study_id=study_id,
site_id=subject_in.site_id,
subject_no=subject_in.subject_no,
status="SCREENING",
screening_date=subject_in.screening_date,
enrollment_date=None,
completion_date=None,
drop_reason=None,
)
db.add(subject)
await db.commit()
await db.refresh(subject)
# initial visit: Screening (V0)
await visit_crud.create_visit(
db,
study_id=study_id,
visit_in=None,
subject=subject,
visit_code="V0",
visit_name="Screening",
planned_date=subject.screening_date,
)
return subject
async def get_subject(db: AsyncSession, subject_id: uuid.UUID) -> Subject | None:
result = await db.execute(select(Subject).where(Subject.id == subject_id))
return result.scalar_one_or_none()
async def list_subjects(
db: AsyncSession,
study_id: uuid.UUID,
site_id: uuid.UUID | None = None,
status: str | None = None,
) -> Sequence[Subject]:
stmt = select(Subject).where(Subject.study_id == study_id)
if site_id:
stmt = stmt.where(Subject.site_id == site_id)
if status:
stmt = stmt.where(Subject.status == status)
result = await db.execute(stmt)
return result.scalars().all()
async def generate_default_visits(db: AsyncSession, subject: Subject) -> None:
# Baseline + Follow-up visits based on enrollment_date
if not subject.enrollment_date:
return
baseline_date = subject.enrollment_date
follow1 = baseline_date + timedelta(days=30)
follow2 = baseline_date + timedelta(days=60)
visits_data = [
("V1", "Baseline", baseline_date),
("FU1", "Follow-up 1", follow1),
("FU2", "Follow-up 2", follow2),
]
for code, name, plan_date in visits_data:
await visit_crud.create_visit(
db,
study_id=subject.study_id,
visit_in=None,
subject=subject,
visit_code=code,
visit_name=name,
planned_date=plan_date,
)
async def update_subject(db: AsyncSession, subject: Subject, subject_in: SubjectUpdate) -> Subject:
update_data = subject_in.model_dump(exclude_unset=True)
if update_data:
await db.execute(
sa_update(Subject)
.where(Subject.id == subject.id)
.values(**update_data)
)
await db.commit()
await db.refresh(subject)
return subject
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@@ -0,0 +1,60 @@
import uuid
from typing import Sequence
from sqlalchemy import select, update as sa_update
from sqlalchemy.ext.asyncio import AsyncSession
from app.models.subject import Subject
from app.models.visit import Visit
from app.schemas.visit import VisitCreate, VisitUpdate
async def create_visit(
db: AsyncSession,
*,
study_id: uuid.UUID,
visit_in: VisitCreate | None,
subject: Subject,
visit_code: str,
visit_name: str,
planned_date,
) -> Visit:
visit = Visit(
study_id=study_id,
subject_id=subject.id,
visit_code=visit_code,
visit_name=visit_name,
planned_date=planned_date,
actual_date=None,
status="PLANNED",
window_start=visit_in.window_start if visit_in else None,
window_end=visit_in.window_end if visit_in else None,
notes=None,
)
db.add(visit)
await db.commit()
await db.refresh(visit)
return visit
async def list_visits(db: AsyncSession, subject_id: uuid.UUID) -> Sequence[Visit]:
result = await db.execute(select(Visit).where(Visit.subject_id == subject_id).order_by(Visit.planned_date))
return result.scalars().all()
async def get_visit(db: AsyncSession, visit_id: uuid.UUID) -> Visit | None:
result = await db.execute(select(Visit).where(Visit.id == visit_id))
return result.scalar_one_or_none()
async def update_visit(db: AsyncSession, visit: Visit, visit_in: VisitUpdate) -> Visit:
update_data = visit_in.model_dump(exclude_unset=True)
if update_data:
await db.execute(
sa_update(Visit)
.where(Visit.id == visit.id)
.values(**update_data)
)
await db.commit()
await db.refresh(visit)
return visit
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@@ -10,3 +10,5 @@ from app.models.attachment import Attachment # noqa: F401
from app.models.audit_log import AuditLog # noqa: F401
from app.models.milestone import Milestone # noqa: F401
from app.models.task import Task # noqa: F401
from app.models.subject import Subject # noqa: F401
from app.models.visit import Visit # noqa: F401
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import uuid
from datetime import datetime, date
from sqlalchemy import Date, DateTime, ForeignKey, String, Text, UniqueConstraint, func
from sqlalchemy.dialects.postgresql import UUID
from sqlalchemy.orm import Mapped, mapped_column
from app.db.base_class import Base
class Subject(Base):
__tablename__ = "subjects"
__table_args__ = (UniqueConstraint("study_id", "subject_no", name="uq_subject_study_no"),)
id: Mapped[uuid.UUID] = mapped_column(UUID(as_uuid=True), primary_key=True, default=uuid.uuid4)
study_id: Mapped[uuid.UUID] = mapped_column(UUID(as_uuid=True), ForeignKey("studies.id"), index=True, nullable=False)
site_id: Mapped[uuid.UUID] = mapped_column(UUID(as_uuid=True), ForeignKey("sites.id"), index=True, nullable=False)
subject_no: Mapped[str] = mapped_column(String(50), nullable=False)
status: Mapped[str] = mapped_column(String(20), nullable=False, default="SCREENING")
screening_date: Mapped[date | None] = mapped_column(Date, nullable=True)
enrollment_date: Mapped[date | None] = mapped_column(Date, nullable=True)
completion_date: Mapped[date | None] = mapped_column(Date, nullable=True)
drop_reason: Mapped[str | None] = mapped_column(Text, nullable=True)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now(), onupdate=func.now()
)
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import uuid
from datetime import datetime, date
from sqlalchemy import Date, DateTime, ForeignKey, String, Text, func
from sqlalchemy.dialects.postgresql import UUID
from sqlalchemy.orm import Mapped, mapped_column
from app.db.base_class import Base
class Visit(Base):
__tablename__ = "visits"
id: Mapped[uuid.UUID] = mapped_column(UUID(as_uuid=True), primary_key=True, default=uuid.uuid4)
study_id: Mapped[uuid.UUID] = mapped_column(UUID(as_uuid=True), ForeignKey("studies.id"), nullable=False)
subject_id: Mapped[uuid.UUID] = mapped_column(UUID(as_uuid=True), ForeignKey("subjects.id"), index=True, nullable=False)
visit_code: Mapped[str] = mapped_column(String(50), nullable=False)
visit_name: Mapped[str] = mapped_column(String(200), nullable=False)
planned_date: Mapped[date | None] = mapped_column(Date, nullable=True)
actual_date: Mapped[date | None] = mapped_column(Date, nullable=True)
status: Mapped[str] = mapped_column(String(20), nullable=False, default="PLANNED")
window_start: Mapped[date | None] = mapped_column(Date, nullable=True)
window_end: Mapped[date | None] = mapped_column(Date, nullable=True)
notes: Mapped[str | None] = mapped_column(Text, nullable=True)
created_at: Mapped[datetime] = mapped_column(DateTime(timezone=True), nullable=False, server_default=func.now())
updated_at: Mapped[datetime] = mapped_column(
DateTime(timezone=True), nullable=False, server_default=func.now(), onupdate=func.now()
)
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import uuid
from datetime import date, datetime
from typing import Optional
from pydantic import BaseModel, ConfigDict
class SubjectCreate(BaseModel):
site_id: uuid.UUID
subject_no: str
screening_date: Optional[date] = None
class SubjectUpdate(BaseModel):
status: Optional[str] = None
enrollment_date: Optional[date] = None
completion_date: Optional[date] = None
drop_reason: Optional[str] = None
class SubjectRead(BaseModel):
id: uuid.UUID
study_id: uuid.UUID
site_id: uuid.UUID
subject_no: str
status: str
screening_date: Optional[date]
enrollment_date: Optional[date]
completion_date: Optional[date]
drop_reason: Optional[str]
created_at: datetime
updated_at: datetime
model_config = ConfigDict(from_attributes=True)
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import uuid
from datetime import date, datetime
from typing import Optional
from pydantic import BaseModel, ConfigDict
class VisitCreate(BaseModel):
subject_id: uuid.UUID
visit_code: str
visit_name: str
planned_date: Optional[date] = None
window_start: Optional[date] = None
window_end: Optional[date] = None
class VisitUpdate(BaseModel):
actual_date: Optional[date] = None
status: Optional[str] = None
notes: Optional[str] = None
class VisitRead(BaseModel):
id: uuid.UUID
study_id: uuid.UUID
subject_id: uuid.UUID
visit_code: str
visit_name: str
planned_date: Optional[date]
actual_date: Optional[date]
status: str
window_start: Optional[date]
window_end: Optional[date]
notes: Optional[str]
created_at: datetime
updated_at: datetime
model_config = ConfigDict(from_attributes=True)