GotthardG 9739b8cfe9 Make shipment fields optional and refactor test scripts.
Updated the `number_of_pucks` and `number_of_samples` fields in the `schemas.py` to be optional for greater flexibility. Simplified the test Jupyter Notebook by restructuring imports and consolidating function calls for better readability and maintainability.
2025-01-17 09:36:16 +01:00

668 lines
22 KiB
Python

import os
import tempfile
import time
import random
import hashlib
from fastapi import APIRouter, HTTPException, status, Depends, Response
from sqlalchemy.orm import Session, joinedload
from typing import List
import logging
from sqlalchemy.exc import SQLAlchemyError
from app.schemas import (
Dewar as DewarSchema,
DewarCreate,
DewarUpdate,
DewarType as DewarTypeSchema,
DewarTypeCreate,
DewarSerialNumber as DewarSerialNumberSchema,
DewarSerialNumberCreate,
Shipment as ShipmentSchema,
Dewar,
SampleUpdate,
Sample,
Puck,
SampleEventResponse, # Clearer name for schema
)
from app.models import (
Dewar as DewarModel,
Puck as PuckModel,
Sample as SampleModel,
DewarType as DewarTypeModel,
DewarSerialNumber as DewarSerialNumberModel,
LogisticsEvent,
PuckEvent,
SampleEvent,
)
from app.dependencies import get_db
import qrcode
import io
from io import BytesIO
from PIL import Image
from reportlab.lib.pagesizes import A5, landscape
from reportlab.lib.units import cm
from reportlab.pdfgen import canvas
from app.crud import (
get_shipments,
get_shipment_by_id,
) # Import CRUD functions for shipment
router = APIRouter()
def generate_unique_id(db: Session, length: int = 16) -> str:
while True:
base_string = f"{time.time()}{random.randint(0, 10 ** 6)}"
hash_object = hashlib.sha256(base_string.encode())
hash_digest = hash_object.hexdigest()
unique_id = "".join(random.choices(hash_digest, k=length))
existing_dewar = (
db.query(DewarModel).filter(DewarModel.unique_id == unique_id).first()
)
if not existing_dewar:
break
return unique_id
@router.post("/", response_model=DewarSchema, status_code=status.HTTP_201_CREATED)
async def create_or_update_dewar(
shipment_id: int,
dewar: DewarCreate,
db: Session = Depends(get_db),
) -> DewarSchema:
try:
# Query existing dewar by name within the shipment
existing_dewar = (
db.query(DewarModel)
.filter(
DewarModel.dewar_name == dewar.dewar_name,
DewarModel.shipment_id == shipment_id,
)
.first()
)
if existing_dewar:
logging.debug(
f"Updating existing dewar with name "
f"{dewar.dewar_name} in shipment {shipment_id}"
)
# Check for associated puck events
for puck in existing_dewar.pucks:
puck_event_exists = (
db.query(PuckEvent).filter(PuckEvent.puck_id == puck.id).first()
)
if puck_event_exists:
raise HTTPException(
status_code=400,
detail=f"Puck {puck.id} "
f"associated with Dewar {existing_dewar.id}"
f" has events. "
f"Update not allowed.",
)
# Check for associated sample events within each puck
for sample in puck.samples:
sample_event_exists = (
db.query(SampleEvent)
.filter(SampleEvent.sample_id == sample.id)
.first()
)
if sample_event_exists:
raise HTTPException(
status_code=400,
detail=f"Sample {sample.id} "
f"associated with Puck "
f"{puck.id} in Dewar "
f"{existing_dewar.id} "
f"has events. Update not allowed.",
)
# Delete associated pucks and samples if no events are found
for puck in existing_dewar.pucks:
for sample in puck.samples:
db.delete(sample)
db.delete(puck)
db.commit()
# Update dewar metadata
for key, value in dewar.dict(
exclude={"pucks", "number_of_pucks", "number_of_samples"}
).items():
if (
hasattr(existing_dewar, key)
and hasattr(type(existing_dewar), key)
and isinstance(getattr(type(existing_dewar), key), property)
and getattr(type(existing_dewar), key).fset
):
setattr(existing_dewar, key, value)
# Commit updates to existing dewar
db.commit()
# Add new pucks and samples
for puck_data in dewar.pucks:
puck = PuckModel(
dewar_id=existing_dewar.id,
puck_name=puck_data.puck_name,
puck_type=puck_data.puck_type,
puck_location_in_dewar=puck_data.puck_location_in_dewar,
)
db.add(puck)
db.commit()
db.refresh(puck)
for sample_data in puck_data.samples:
sample = SampleModel(
puck_id=puck.id,
sample_name=sample_data.sample_name,
proteinname=sample_data.proteinname,
position=sample_data.position,
priority=sample_data.priority,
comments=sample_data.comments,
data_collection_parameters=dict(
sample_data.data_collection_parameters or {}
),
)
db.add(sample)
db.commit()
db.refresh(sample)
db.refresh(existing_dewar)
return existing_dewar
# Create a completely new dewar if none exists
dewar_obj = DewarModel(
dewar_name=dewar.dewar_name,
tracking_number=dewar.tracking_number,
status=dewar.status,
ready_date=dewar.ready_date,
shipping_date=dewar.shipping_date,
arrival_date=dewar.arrival_date,
returning_date=dewar.returning_date,
contact_person_id=dewar.contact_person_id,
return_address_id=dewar.return_address_id,
shipment_id=shipment_id, # Associate with the shipment
)
db.add(dewar_obj)
db.commit()
db.refresh(dewar_obj)
# Add pucks and samples for the new dewar
for puck_data in dewar.pucks:
puck = PuckModel(
dewar_id=dewar_obj.id,
puck_name=puck_data.puck_name,
puck_type=puck_data.puck_type,
puck_location_in_dewar=puck_data.puck_location_in_dewar,
)
db.add(puck)
db.commit()
db.refresh(puck)
for sample_data in puck_data.samples:
sample = SampleModel(
puck_id=puck.id,
sample_name=sample_data.sample_name,
proteinname=sample_data.proteinname,
position=sample_data.position,
priority=sample_data.priority,
comments=sample_data.comments,
data_collection_parameters=dict(
sample_data.data_collection_parameters or {}
),
)
db.add(sample)
db.commit()
db.refresh(sample)
return dewar_obj
except SQLAlchemyError as e:
logging.error(f"Database error occurred: {e}")
raise HTTPException(status_code=500, detail="Internal server error")
@router.post("/{dewar_id}/generate-qrcode")
async def generate_dewar_qrcode(dewar_id: int, db: Session = Depends(get_db)):
dewar = db.query(DewarModel).filter(DewarModel.id == dewar_id).first()
if not dewar:
raise HTTPException(status_code=404, detail="Dewar not found")
if not dewar.unique_id:
dewar.unique_id = generate_unique_id(db)
db.commit()
qr = qrcode.QRCode(version=1, box_size=10, border=5)
qr.add_data(dewar.unique_id)
qr.make(fit=True)
img = qr.make_image(fill="black", back_color="white")
buf = io.BytesIO()
img.save(buf)
buf.seek(0)
dewar.qrcode = dewar.unique_id
dewar.qrcode_image = buf.getvalue()
db.commit()
return {"message": "QR Code generated", "qrcode": dewar.unique_id}
def generate_label(dewar):
buffer = BytesIO()
# Set page orientation to landscape
c = canvas.Canvas(buffer, pagesize=landscape(A5))
# Dimensions for the A5 landscape
page_width, page_height = landscape(A5)
# Path to the PNG logo
file_dir = os.path.dirname(os.path.abspath(__file__))
png_logo_path = os.path.join(file_dir, "Heidi-logo.png")
# Open the logo with PIL to get its size
logo_image = Image.open(png_logo_path)
logo_aspect_ratio = logo_image.width / logo_image.height # original aspect ratio
# Desired logo width in the PDF (you can adjust this size)
desired_logo_width = 4 * cm
desired_logo_height = (
desired_logo_width / logo_aspect_ratio
) # maintain aspect ratio
# Draw header text
c.setFont("Helvetica-Bold", 16)
c.drawString(2 * cm, page_height - 2 * cm, "Paul Scherrer Institut")
# Draw the Heidi logo with preserved aspect ratio
c.drawImage(
png_logo_path,
page_width - desired_logo_width - 2 * cm,
page_height - desired_logo_height - 2 * cm,
width=desired_logo_width,
height=desired_logo_height,
mask="auto",
)
# Draw details section
c.setFont("Helvetica", 12)
y_position = (
page_height - 4 * cm
) # Adjusted to ensure text doesn't overlap with the logo
line_height = 0.8 * cm
if dewar.shipment:
c.drawString(
2 * cm, y_position, f"Shipment Name: {dewar.shipment.shipment_name}"
)
y_position -= line_height
c.drawString(2 * cm, y_position, f"Dewar Name: {dewar.dewar_name}")
y_position -= line_height
c.drawString(2 * cm, y_position, f"Unique ID: {dewar.unique_id}")
y_position -= line_height
if dewar.contact_person:
contact_person = dewar.contact_person
c.drawString(
2 * cm,
y_position,
f"Contact: {contact_person.firstname} {contact_person.lastname}",
)
y_position -= line_height
c.drawString(2 * cm, y_position, f"Email: {contact_person.email}")
y_position -= line_height
c.drawString(2 * cm, y_position, f"Phone: {contact_person.phone_number}")
y_position -= line_height
if dewar.return_address:
return_address = dewar.return_address
c.drawString(2 * cm, y_position, f"Return Address: {return_address.street}")
y_position -= line_height
c.drawString(2 * cm, y_position, f"City: {return_address.city}")
y_position -= line_height
c.drawString(2 * cm, y_position, f"Postal Code: {return_address.zipcode}")
y_position -= line_height
c.drawString(2 * cm, y_position, f"Country: {return_address.country}")
y_position -= line_height
c.drawString(2 * cm, y_position, "Beamtime Information: Placeholder")
# Generate QR code
qr = qrcode.QRCode(version=1, box_size=10, border=4)
qr.add_data(dewar.unique_id)
qr.make(fit=True)
qr_img = qr.make_image(fill="black", back_color="white").convert("RGBA")
# Save this QR code to a temporary file
with tempfile.NamedTemporaryFile(delete=False, suffix=".png") as temp_file:
qr_img.save(temp_file, format="PNG")
temp_file_path = temp_file.name
# Add QR code to PDF
c.drawImage(
temp_file_path, page_width - 6 * cm, 5 * cm, width=4 * cm, height=4 * cm
)
# Add footer text
c.setFont("Helvetica", 10)
c.drawCentredString(page_width / 2, 2 * cm, "Scan for more information")
# Draw border
c.setLineWidth(1)
c.rect(
1 * cm, 1 * cm, page_width - 2 * cm, page_height - 2 * cm
) # Adjusted dimensions
# Finalize the canvas
c.showPage()
c.save()
buffer.seek(0)
# Cleanup temporary file
os.remove(temp_file_path)
return buffer
@router.get("/{dewar_id}/download-label", response_class=Response)
async def download_dewar_label(dewar_id: int, db: Session = Depends(get_db)):
dewar = (
db.query(DewarModel)
.options(
joinedload(DewarModel.pucks).joinedload(PuckModel.samples),
joinedload(DewarModel.contact_person),
joinedload(DewarModel.return_address),
joinedload(DewarModel.shipment),
)
.filter(DewarModel.id == dewar_id)
.first()
)
if not dewar:
raise HTTPException(status_code=404, detail="Dewar not found")
if not dewar.unique_id:
raise HTTPException(
status_code=404, detail="QR Code not generated for this dewar"
)
buffer = generate_label(dewar)
return Response(
buffer.getvalue(),
media_type="application/pdf",
headers={
"Content-Disposition": f"attachment; filename=dewar_label_{dewar.id}.pdf"
},
)
@router.put("/samples/{sample_id}", response_model=Sample)
async def update_sample(
sample_id: int,
sample_update: SampleUpdate,
db: Session = Depends(get_db),
):
# Log the payload received from the frontend
logging.info(
f"Payload received for sample ID {sample_id}: "
f"{sample_update.dict(exclude_unset=True)}"
)
# Query the sample from the database
sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
if not sample:
logging.error(f"Sample with ID {sample_id} not found")
raise HTTPException(status_code=404, detail="Sample not found")
# Apply updates
for key, value in sample_update.dict(exclude_unset=True).items():
if hasattr(sample, key):
setattr(sample, key, value)
# Commit changes to the database
db.commit()
db.refresh(sample) # Reload the updated sample object
# Log the updated sample before returning it
logging.info(f"Updated sample with ID {sample_id}: {Sample.from_orm(sample)}")
return Sample.from_orm(sample)
@router.get("/dewars/{dewar_id}/samples", response_model=Dewar)
async def get_dewar_samples(dewar_id: int, db: Session = Depends(get_db)):
# Fetch the Dewar with nested relationships
dewar = db.query(DewarModel).filter(DewarModel.id == dewar_id).first()
if not dewar:
raise HTTPException(status_code=404, detail="Dewar not found")
# Explicitly map nested relationships
dewar_data = {
"id": dewar.id,
"dewar_name": dewar.dewar_name,
"tracking_number": dewar.tracking_number,
"status": dewar.status,
"number_of_pucks": len(dewar.pucks), # Calculate number of pucks
"number_of_samples": sum(
len(puck.samples) for puck in dewar.pucks
), # Calculate total samples
"ready_date": dewar.ready_date,
"shipping_date": dewar.shipping_date,
"arrival_date": dewar.arrival_date,
"returning_date": dewar.returning_date,
"contact_person_id": dewar.contact_person.id if dewar.contact_person else None,
"return_address_id": dewar.return_address.id if dewar.return_address else None,
"shipment_id": dewar.shipment_id,
"contact_person": dewar.contact_person,
"return_address": dewar.return_address,
"pucks": [
Puck(
id=puck.id,
puck_name=puck.puck_name,
puck_type=puck.puck_type,
puck_location_in_dewar=puck.puck_location_in_dewar,
dewar_id=dewar.id,
samples=[
Sample(
id=sample.id,
sample_name=sample.sample_name,
position=sample.position,
puck_id=sample.puck_id,
crystalname=getattr(sample, "crystalname", None),
proteinname=getattr(sample, "proteinname", None),
positioninpuck=getattr(sample, "positioninpuck", None),
priority=sample.priority,
comments=sample.comments,
data_collection_parameters=sample.data_collection_parameters,
events=[
SampleEventResponse.from_orm(event)
for event in sample.events
],
)
for sample in puck.samples
],
)
for puck in dewar.pucks
],
}
# Return the Pydantic Dewar model
return Dewar(**dewar_data)
@router.get("/", response_model=List[DewarSchema])
async def get_dewars(db: Session = Depends(get_db)):
try:
dewars = db.query(DewarModel).options(joinedload(DewarModel.pucks)).all()
return dewars
except SQLAlchemyError as e:
logging.error(f"Database error occurred: {e}")
raise HTTPException(status_code=500, detail="Internal server error")
@router.get("/dewar-types", response_model=List[DewarTypeSchema])
def get_dewar_types(db: Session = Depends(get_db)):
return db.query(DewarTypeModel).all()
@router.get(
"/dewar-types/{type_id}/serial-numbers",
response_model=List[DewarSerialNumberSchema],
)
def get_serial_numbers(type_id: int, db: Session = Depends(get_db)):
return (
db.query(DewarSerialNumberModel)
.filter(DewarSerialNumberModel.dewar_type_id == type_id)
.all()
)
@router.post("/dewar-types", response_model=DewarTypeSchema)
def create_dewar_type(dewar_type: DewarTypeCreate, db: Session = Depends(get_db)):
db_type = DewarTypeModel(**dewar_type.dict())
db.add(db_type)
db.commit()
db.refresh(db_type)
return db_type
@router.post("/dewar-serial-numbers", response_model=DewarSerialNumberSchema)
def create_dewar_serial_number(
serial_number: DewarSerialNumberCreate, db: Session = Depends(get_db)
):
db_serial = DewarSerialNumberModel(**serial_number.dict())
db.add(db_serial)
db.commit()
db.refresh(db_serial)
return db_serial
@router.get("/dewar-serial-numbers", response_model=List[DewarSerialNumberSchema])
def get_all_serial_numbers(db: Session = Depends(get_db)):
try:
serial_numbers = db.query(DewarSerialNumberModel).all()
return serial_numbers
except SQLAlchemyError as e:
logging.error(f"Database error occurred: {e}")
raise HTTPException(status_code=500, detail="Internal server error")
@router.get("/{dewar_id}", response_model=DewarSchema)
async def get_dewar(dewar_id: int, db: Session = Depends(get_db)):
dewar = (
db.query(DewarModel)
.options(
joinedload(DewarModel.pucks).joinedload(PuckModel.samples),
joinedload(DewarModel.contact_person),
joinedload(DewarModel.return_address),
joinedload(DewarModel.shipment),
)
.filter(DewarModel.id == dewar_id)
.first()
)
if not dewar:
raise HTTPException(status_code=404, detail="Dewar not found")
return DewarSchema.from_orm(dewar)
@router.put("/{dewar_id}", response_model=DewarSchema)
async def update_dewar(
dewar_id: int, dewar_update: DewarUpdate, db: Session = Depends(get_db)
) -> DewarSchema:
dewar = db.query(DewarModel).filter(DewarModel.id == dewar_id).first()
if not dewar:
raise HTTPException(status_code=404, detail="Dewar not found")
for key, value in dewar_update.dict(exclude_unset=True).items():
if hasattr(dewar, key):
setattr(dewar, key, value)
db.commit()
db.refresh(dewar)
return dewar
@router.delete("/{dewar_id}", status_code=status.HTTP_204_NO_CONTENT)
async def delete_dewar(dewar_id: int, db: Session = Depends(get_db)):
# Fetch the Dewar from the database
dewar = db.query(DewarModel).filter(DewarModel.id == dewar_id).first()
if not dewar:
raise HTTPException(status_code=404, detail="Dewar not found")
# Check for associated logistics events
logistics_event_exists = (
db.query(LogisticsEvent).filter(LogisticsEvent.dewar_id == dewar_id).first()
)
if logistics_event_exists:
raise HTTPException(
status_code=400,
detail=f"Dewar {dewar_id} has associated logistics events."
f"Deletion not allowed.",
)
# Check associated pucks and their events
for puck in dewar.pucks:
puck_event_exists = (
db.query(PuckEvent).filter(PuckEvent.puck_id == puck.id).first()
)
if puck_event_exists:
raise HTTPException(
status_code=400,
detail=f"Puck {puck.id} "
f"associated with this Dewar has events."
f"Deletion not allowed.",
)
# Check associated samples and their events
for sample in puck.samples:
sample_event_exists = (
db.query(SampleEvent).filter(SampleEvent.sample_id == sample.id).first()
)
if sample_event_exists:
raise HTTPException(
status_code=400,
detail=f"Sample {sample.id} "
f"associated with Puck {puck.id} has events."
f" Deletion not allowed.",
)
# Perform cascade deletion: Delete samples, pucks, and the dewar
for puck in dewar.pucks:
for sample in puck.samples:
db.delete(sample) # Delete associated samples
db.delete(puck) # Delete associated puck
db.delete(dewar) # Finally, delete the dewar itself
db.commit()
return
# New routes for shipments
@router.get("/shipments", response_model=List[ShipmentSchema])
async def get_all_shipments(db: Session = Depends(get_db)):
try:
shipments = get_shipments(db)
return shipments
except SQLAlchemyError as e:
logging.error(f"Database error occurred: {e}")
raise HTTPException(status_code=500, detail="Internal server error")
@router.get("/shipments/{id}", response_model=ShipmentSchema)
async def get_single_shipment(id: int, db: Session = Depends(get_db)):
try:
shipment = get_shipment_by_id(db, id)
if shipment is None:
raise HTTPException(status_code=404, detail="Shipment not found")
return shipment
except SQLAlchemyError as e:
logging.error(f"Database error occurred: {e}")
raise HTTPException(status_code=500, detail="Internal server error")