Refactor puck handling and update tell position setting
Simplify and standardize puck name normalization and validation. Refactor `set_tell_positions` to handle batch operations, improve error handling, and provide detailed responses for each puck. Removed unnecessary `with-tell-position` endpoint for better clarity and maintainability.
This commit is contained in:
GotthardG
parent
d1bc70665f
commit
da5dbb9e31
@ -291,7 +291,7 @@ shipments = [
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pucks = [
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Puck(
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id=1,
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puck_name="PUCK001",
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puck_name="PUCK-001",
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puck_type="Unipuck",
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puck_location_in_dewar=1,
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dewar_id=1,
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@ -1,7 +1,10 @@
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from datetime import datetime
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from fastapi import APIRouter, HTTPException, status, Depends
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from sqlalchemy.orm import Session
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from sqlalchemy.sql import func
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from typing import List
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import uuid
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import re
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from app.schemas import (
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Puck as PuckSchema,
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PuckCreate,
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@ -9,7 +12,6 @@ from app.schemas import (
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)
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from app.models import (
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Puck as PuckModel,
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Sample as SampleModel,
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PuckEvent as PuckEventModel,
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Slot as SlotModel,
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LogisticsEvent as LogisticsEventModel,
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@ -24,174 +26,146 @@ logging.basicConfig(level=logging.INFO)
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logger = logging.getLogger(__name__)
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def normalize_puck_name(name: str) -> str:
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"""
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Normalize a puck_name to remove special characters and ensure consistent formatting.
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"""
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name = str(name).strip().replace(" ", "_").upper()
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name = re.sub(r"[^A-Z0-9]", "", name) # Remove special characters
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return name
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@router.get("/", response_model=List[PuckSchema])
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async def get_pucks(db: Session = Depends(get_db)):
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return db.query(PuckModel).all()
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@router.get("/with-tell-position", response_model=List[dict])
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async def get_pucks_with_tell_position(db: Session = Depends(get_db)):
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"""
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Retrieve all pucks with a `tell_position`
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set (not null) and their associated samples.
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"""
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# Query all pucks that have an event with a non-null tell_position
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pucks = (
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db.query(PuckModel)
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.join(PuckEventModel, PuckModel.id == PuckEventModel.puck_id)
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.filter(PuckEventModel.tell_position.isnot(None))
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.all()
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)
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logger.info(f"Pucks with tell position: {pucks}")
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if not pucks:
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logger.info("No pucks with tell_position found.") # Log for debugging
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raise HTTPException(
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status_code=404, detail="No pucks with a `tell_position` found."
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)
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result = []
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for puck in pucks:
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# Get associated samples for the puck
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samples = db.query(SampleModel).filter(SampleModel.puck_id == puck.id).all()
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sample_data = [
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{
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"id": sample.id,
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"sample_name": sample.sample_name,
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"position": sample.position, # Updated field based on schema
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}
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for sample in samples
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]
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# Add puck and sample info to the result
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result.append(
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{
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"id": puck.id,
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"puck_name": puck.puck_name,
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"puck_type": puck.puck_type,
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"puck_location_in_dewar": puck.puck_location_in_dewar,
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"dewar_id": puck.dewar_id,
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"samples": sample_data, # Add associated samples
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}
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)
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return result
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@router.put("/set-tell-positions", status_code=status.HTTP_200_OK)
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async def set_tell_positions(
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puck_name: str,
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segment: str,
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puck_in_segment: int,
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pucks: List[dict], # Accept a list of puck definitions from the client
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db: Session = Depends(get_db),
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):
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"""
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Set the tell position for a puck based on the last beamline event.
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- Validates `puck_name`, `segment`, and `puck_in_segment`.
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- Finds the most recent logistics event of type "beamline" for the associated dewar.
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- Ensures the logistics event is associated with a valid slot.
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- Creates a new puck event with the specified `tell_position`.
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Set the tell positions for multiple pucks.
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Args:
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puck_name (str): Name of the puck to set the tell position for.
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segment (str): Segment label (A-F).
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puck_in_segment (int): Position in the segment (1-5).
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pucks (List[dict]): A list of puck definitions, where each puck contains:
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- `puck_name` (str): The cleaned name of the puck.
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- `segment` (str): The segment in the dewar (e.g., "A-F").
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- `puck_in_segment` (int): The position within the segment (1-5).
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Returns:
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JSON response containing puck and associated information.
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List[dict]: A list of responses, one for each successfully processed puck.
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"""
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results = []
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from datetime import datetime
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for puck_data in pucks:
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try:
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# Extract data from input
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puck_name = puck_data.get("puckname")
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segment = puck_data.get("segment")
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puck_in_segment = puck_data.get("puck_in_segment")
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# 1. Validate `segment` and `puck_in_segment`
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if not segment or segment not in "ABCDEF":
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raise HTTPException(
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status_code=status.HTTP_400_BAD_REQUEST,
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detail="Invalid segment. Valid segments are A, B, C, D, E, F.",
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)
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if not (1 <= puck_in_segment <= 5):
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raise HTTPException(
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status_code=status.HTTP_400_BAD_REQUEST,
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detail="Invalid puck_in_segment. Valid positions are 1 to 5.",
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)
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# 1. Validate `segment` and `puck_in_segment`
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if not segment or segment not in "ABCDEF":
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raise ValueError(
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f"Invalid segment '{segment}'. Must be A, B, C, D, E, or F."
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)
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if not (1 <= puck_in_segment <= 5):
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raise ValueError(
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f"Invalid puck_in_segment "
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f"'{puck_in_segment}'. Must be in range 1-5."
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)
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# Generate tell_position
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tell_position = f"{segment}{puck_in_segment}"
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# Generate tell_position
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tell_position = f"{segment}{puck_in_segment}"
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# 2. Find the puck by its name and ensure it exists
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puck = db.query(PuckModel).filter(PuckModel.puck_name == puck_name).first()
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if not puck:
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print(f"DEBUG: Puck '{puck_name}' not found in the database.")
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raise HTTPException(
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status_code=status.HTTP_404_NOT_FOUND,
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# This should match the error returned
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detail=f"Puck with name '{puck_name}' not found.",
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)
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print(f"DEBUG: Found puck: {puck}")
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# 2. Find the puck by its cleaned name
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normalized_name = normalize_puck_name(puck_name)
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# 3. Find the dewar associated with the puck
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dewar = db.query(DewarModel).filter(DewarModel.id == puck.dewar_id).first()
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if not dewar:
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raise HTTPException(
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status_code=status.HTTP_404_NOT_FOUND,
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detail=f"Dewar associated with puck '{puck_name}' not found.",
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)
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# Use SQLAlchemy to match normalized names
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puck = (
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db.query(PuckModel)
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.filter(
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func.replace(func.upper(PuckModel.puck_name), "-", "")
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== normalized_name
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)
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.first()
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)
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# 4. Find the most recent logistics event for the dewar (type 'beamline')
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# and ensure not null
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logistics_event = (
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db.query(LogisticsEventModel)
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.filter(
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LogisticsEventModel.dewar_id == dewar.id,
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LogisticsEventModel.event_type == "beamline",
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)
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.order_by(LogisticsEventModel.timestamp.desc())
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.first()
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)
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if not logistics_event:
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raise HTTPException(
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status_code=status.HTTP_404_NOT_FOUND,
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detail=(
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f"No recent 'beamline' logistics event found for dewar '"
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f"{dewar.dewar_name}' "
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f"(puck '{puck_name}')."
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),
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)
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if not puck:
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raise ValueError(
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f"Puck with cleaned name '{puck_name}' not found in the database."
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)
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# 5. Retrieve the slot from the logistics event
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slot = db.query(SlotModel).filter(SlotModel.id == logistics_event.slot_id).first()
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if not slot:
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raise HTTPException(
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status_code=status.HTTP_404_NOT_FOUND,
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detail=(
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f"No slot associated with the most recent 'beamline' logistics event "
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f"for dewar '{dewar.dewar_name}'."
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),
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)
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# 3. Find the dewar associated with the puck
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dewar = db.query(DewarModel).filter(DewarModel.id == puck.dewar_id).first()
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if not dewar:
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raise ValueError(f"Dewar associated with puck '{puck_name}' not found.")
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# 6. Set the tell position for the puck by creating a PuckEvent
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new_puck_event = PuckEventModel(
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puck_id=puck.id,
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tell_position=tell_position,
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event_type="tell_position_set",
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timestamp=datetime.utcnow(),
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)
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db.add(new_puck_event)
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db.commit()
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db.refresh(new_puck_event)
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# 4. Find the most recent logistics event for the dewar (type 'beamline')
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logistics_event = (
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db.query(LogisticsEventModel)
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.filter(
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LogisticsEventModel.dewar_id == dewar.id,
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LogisticsEventModel.event_type == "beamline",
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)
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.order_by(LogisticsEventModel.timestamp.desc())
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.first()
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)
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if not logistics_event:
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raise ValueError(
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f"No recent 'beamline' logistics event found for dewar "
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f"'{dewar.dewar_name}'."
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)
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# 7. Return the result
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return {
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"puck_id": puck.id,
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"puck_name": puck_name,
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"dewar_id": dewar.id,
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"dewar_name": dewar.dewar_name,
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"slot_id": slot.id,
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"slot_label": slot.label,
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"tell_position": tell_position,
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"event_timestamp": new_puck_event.timestamp,
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}
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# 5. Retrieve the slot from the logistics event
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slot = (
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db.query(SlotModel)
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.filter(SlotModel.id == logistics_event.slot_id)
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.first()
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)
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if not slot:
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raise ValueError(
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f"No slot associated with the most recent 'beamline' "
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f"logistics event "
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f"for dewar '{dewar.dewar_name}'."
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)
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# 6. Create a PuckEvent to set the 'tell_position'
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new_puck_event = PuckEventModel(
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puck_id=puck.id,
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tell_position=tell_position,
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event_type="tell_position_set",
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timestamp=datetime.utcnow(),
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)
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db.add(new_puck_event)
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db.commit()
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db.refresh(new_puck_event)
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# Add success result to the results list
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results.append(
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{
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"puck_id": puck.id,
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"puck_name": puck.puck_name,
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"dewar_id": dewar.id,
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"dewar_name": dewar.dewar_name,
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"slot_id": slot.id,
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"slot_label": slot.label,
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"tell_position": tell_position,
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"event_timestamp": new_puck_event.timestamp,
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}
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)
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except Exception as e:
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# Handle errors for individual pucks and continue processing others
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results.append(
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{
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"puck_name": puck_name,
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"error": str(e),
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}
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)
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return results
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@router.get("/{puck_id}", response_model=PuckSchema)
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@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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[project]
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name = "aareDB"
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version = "0.1.0a8"
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version = "0.1.0a9"
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description = "Backend for next gen sample management system"
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authors = [{name = "Guillaume Gotthard", email = "guillaume.gotthard@psi.ch"}]
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license = {text = "MIT"}
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