Add Image models and clean up test code structure
Introduced `ImageCreate` and `Image` models to handle image-related data in the backend. Improved the organization and readability of the testing notebook by consolidating and formatting code into distinct sections with markdown cells.
This commit is contained in:
GotthardG
parent
f588bc0cda
commit
1606e80f81
@ -249,6 +249,17 @@ class Beamtime(Base):
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dewars = relationship("Dewar", back_populates="beamtime")
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class Image(Base):
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__tablename__ = "images"
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id = Column(Integer, primary_key=True, index=True, autoincrement=True)
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pgroup = Column(String(255), nullable=False)
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comment = Column(String(200), nullable=True)
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filepath = Column(String(255), nullable=False)
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status = Column(String(255), nullable=True)
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sample_id = Column(Integer, ForeignKey("samples.id"), nullable=False)
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# class Results(Base):
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# __tablename__ = "results"
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#
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@ -1,4 +1,4 @@
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from fastapi import APIRouter, HTTPException, Depends, UploadFile, File
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from fastapi import APIRouter, HTTPException, Depends, UploadFile, File, Form
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from sqlalchemy.orm import Session
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from pathlib import Path
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from typing import List
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@ -9,11 +9,14 @@ from app.schemas import (
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Sample as SampleSchema,
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SampleEventCreate,
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Sample,
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Image,
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ImageCreate,
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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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SampleEvent as SampleEventModel,
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Image as ImageModel,
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)
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from app.dependencies import get_db
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import logging
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@ -89,29 +92,22 @@ async def create_sample_event(
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return sample # Return the sample, now including `mount_count`
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@router.post("/{sample_id}/upload-images")
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@router.post("/{sample_id}/upload-images", response_model=Image)
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async def upload_sample_image(
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sample_id: int,
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uploaded_file: UploadFile = File(...),
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comment: str = Form(None),
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db: Session = Depends(get_db),
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):
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logging.info(f"Received file: {uploaded_file.filename}")
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"""
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Uploads an image for a given sample and saves it to a directory structure.
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Args:
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sample_id (int): ID of the sample.
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uploaded_file (UploadFile): The file uploaded with the request.
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db (Session): Database session.
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"""
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# 1. Validate Sample
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# Validate Sample
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sample = db.query(SampleModel).filter(SampleModel.id == sample_id).first()
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if not sample:
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raise HTTPException(status_code=404, detail="Sample not found")
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# 2. Define Directory Structure
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pgroup = sample.puck.dewar.pgroups
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# Define Directory Structure
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pgroup = sample.puck.dewar.pgroups # adjust to sample or puck pgroups as needed
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today = datetime.now().strftime("%Y-%m-%d")
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dewar_name = (
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sample.puck.dewar.dewar_name
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@ -123,7 +119,7 @@ async def upload_sample_image(
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base_dir = Path(f"images/{pgroup}/{today}/{dewar_name}/{puck_name}/{position}")
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base_dir.mkdir(parents=True, exist_ok=True)
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# 3. Validate MIME type and Save the File
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# Validate MIME type and Save the File
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if not uploaded_file.content_type.startswith("image/"):
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raise HTTPException(
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status_code=400,
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@ -146,9 +142,26 @@ async def upload_sample_image(
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f" Ensure the server has correct permissions.",
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)
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# 4. Return Saved File Information
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logging.info(f"Uploaded 1 file for sample {sample_id}.")
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return {
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"message": "1 image uploaded successfully.",
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"file": str(file_path),
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}
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# Create the payload from the Pydantic schema
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image_payload = ImageCreate(
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pgroup=pgroup,
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comment=comment,
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filepath=str(file_path),
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status="active",
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sample_id=sample_id,
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).dict()
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# Convert the payload to your mapped SQLAlchemy model instance.
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# Make sure that ImageModel is your mapped model for images.
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new_image = ImageModel(**image_payload)
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db.add(new_image)
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db.commit()
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db.refresh(new_image)
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logging.info(
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f"Uploaded 1 file for sample {sample_id} and"
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f" added record {new_image.id} to the database."
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)
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# Returning the mapped SQLAlchemy object, which will be converted to the
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# Pydantic response model.
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return new_image
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@ -783,3 +783,24 @@ class Beamtime(BaseModel):
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proposal: Optional[Proposal]
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local_contact_id: Optional[int]
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local_contact: Optional[LocalContact]
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class Config:
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from_attributes = True
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class ImageCreate(BaseModel):
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pgroup: str
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sample_id: int
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filepath: str
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status: str = "active"
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comment: Optional[str] = None
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class Config:
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from_attributes = True
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class Image(ImageCreate):
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id: int
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class Config:
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from_attributes = True
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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 = "0.1.0a22"
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version = "0.1.0a23"
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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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@ -1,10 +1,13 @@
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{
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"cells": [
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{
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"metadata": {},
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-02-26T12:02:38.993926Z",
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"start_time": "2025-02-26T12:02:38.991283Z"
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}
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},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"import json\n",
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"\n",
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@ -32,7 +35,18 @@
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"configuration.verify_ssl = False # Disable SSL verification\n",
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"#print(dir(SamplesApi))"
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],
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"id": "3b7c27697a4d5c83"
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"id": "3b7c27697a4d5c83",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"0.1.0a21\n",
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"https://127.0.0.1:8000\n"
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]
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}
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],
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"execution_count": 74
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},
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{
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"metadata": {},
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@ -160,10 +174,13 @@
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"execution_count": 43
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},
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{
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"metadata": {},
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-02-26T12:04:05.046079Z",
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"start_time": "2025-02-26T12:04:04.954761Z"
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}
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},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"# Get a list of pucks that are \"at the beamline\"\n",
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"\n",
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@ -181,13 +198,42 @@
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" except ApiException as e:\n",
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" print(\"Exception when calling PucksApi->get_pucks_by_slot_pucks_slot_slot_identifier_get: %s\\n\" % e)"
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],
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"id": "9cf3457093751b61"
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"id": "9cf3457093751b61",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"The response of PucksApi->get_pucks_by_slot_pucks_slot_slot_identifier_get:\n",
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"\n",
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"[PuckWithTellPosition(id=1, puck_name='PUCK-001', puck_type='Unipuck', puck_location_in_dewar=1, dewar_id=1, dewar_name='Dewar One', pgroup='p20001, p20002', samples=None, tell_position=None),\n",
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" PuckWithTellPosition(id=2, puck_name='PUCK002', puck_type='Unipuck', puck_location_in_dewar=2, dewar_id=1, dewar_name='Dewar One', pgroup='p20001, p20002', samples=None, tell_position=None),\n",
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" PuckWithTellPosition(id=3, puck_name='PUCK003', puck_type='Unipuck', puck_location_in_dewar=3, dewar_id=1, dewar_name='Dewar One', pgroup='p20001, p20002', samples=None, tell_position=None),\n",
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" PuckWithTellPosition(id=4, puck_name='PUCK004', puck_type='Unipuck', puck_location_in_dewar=4, dewar_id=1, dewar_name='Dewar One', pgroup='p20001, p20002', samples=None, tell_position=None),\n",
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" PuckWithTellPosition(id=5, puck_name='PUCK005', puck_type='Unipuck', puck_location_in_dewar=5, dewar_id=1, dewar_name='Dewar One', pgroup='p20001, p20002', samples=None, tell_position=None),\n",
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" PuckWithTellPosition(id=6, puck_name='PUCK006', puck_type='Unipuck', puck_location_in_dewar=6, dewar_id=1, dewar_name='Dewar One', pgroup='p20001, p20002', samples=None, tell_position=None),\n",
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" PuckWithTellPosition(id=7, puck_name='PUCK007', puck_type='Unipuck', puck_location_in_dewar=7, dewar_id=1, dewar_name='Dewar One', pgroup='p20001, p20002', samples=None, tell_position=None)]\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1097: InsecureRequestWarning: Unverified HTTPS request is being made to host '127.0.0.1'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
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" warnings.warn(\n"
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]
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}
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],
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"execution_count": 77
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},
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{
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"metadata": {},
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-02-26T12:04:33.644201Z",
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"start_time": "2025-02-26T12:04:33.625894Z"
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}
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},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"from aareDBclient import SetTellPosition, SetTellPositionRequest\n",
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"\n",
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@ -214,10 +260,10 @@
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" # SetTellPosition(puck_name='PSIMX117', segment='A', puck_in_segment=2),\n",
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" #]\n",
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" pucks=[\n",
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" SetTellPosition(puck_name='PK006', segment='F', puck_in_segment=1),\n",
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" SetTellPosition(puck_name='PK003', segment='F', puck_in_segment=2),\n",
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" SetTellPosition(puck_name='PK002', segment='A', puck_in_segment=1),\n",
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" SetTellPosition(puck_name='PK001', segment='A', puck_in_segment=2),\n",
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" SetTellPosition(puck_name='PUCK006', segment='F', puck_in_segment=1),\n",
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" SetTellPosition(puck_name='PUCK003', segment='F', puck_in_segment=2),\n",
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" SetTellPosition(puck_name='PUCK002', segment='A', puck_in_segment=1),\n",
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" SetTellPosition(puck_name='PUCK001', segment='A', puck_in_segment=2),\n",
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" ]\n",
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" #pucks = []\n",
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" )\n",
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@ -234,13 +280,59 @@
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" except Exception as e:\n",
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" print(f\"Exception when calling PucksApi: {e}\")\n"
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],
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"id": "37e3eac6760150ee"
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"id": "37e3eac6760150ee",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"The response of PucksApi->pucks_puck_id_tell_position_put:\n",
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"\n",
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"[{'message': 'Tell position updated successfully.',\n",
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" 'new_position': 'F1',\n",
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" 'previous_position': None,\n",
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" 'puck_name': 'PUCK006',\n",
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" 'status': 'updated',\n",
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" 'tell': 'X06DA'},\n",
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" {'message': 'Tell position updated successfully.',\n",
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" 'new_position': 'F2',\n",
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" 'previous_position': None,\n",
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" 'puck_name': 'PUCK003',\n",
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" 'status': 'updated',\n",
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" 'tell': 'X06DA'},\n",
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" {'message': 'Tell position updated successfully.',\n",
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" 'new_position': 'A1',\n",
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" 'previous_position': None,\n",
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" 'puck_name': 'PUCK002',\n",
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" 'status': 'updated',\n",
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" 'tell': 'X06DA'},\n",
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" {'message': 'Tell position updated successfully.',\n",
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" 'new_position': 'A2',\n",
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" 'previous_position': None,\n",
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" 'puck_name': 'PUCK001',\n",
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" 'status': 'updated',\n",
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" 'tell': 'X06DA'}]\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1097: InsecureRequestWarning: Unverified HTTPS request is being made to host '127.0.0.1'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
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" warnings.warn(\n"
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]
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}
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],
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"execution_count": 78
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},
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{
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"metadata": {},
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-02-26T12:04:41.352140Z",
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"start_time": "2025-02-26T12:04:41.331320Z"
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}
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},
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"cell_type": "code",
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"outputs": [],
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"execution_count": null,
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"source": [
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"# Get puck_id puck_name sample_id sample_name of pucks in the tell\n",
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"\n",
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@ -275,13 +367,69 @@
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" except ApiException as e:\n",
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" print(\"Exception when calling PucksApi->get_all_pucks_in_tell: %s\\n\" % e)"
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],
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"id": "51578d944878db6a"
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"id": "51578d944878db6a",
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Puck ID: 6, Puck Name: PUCK006\n",
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" Sample ID: 44, Sample Name: Sample044, Position: 2, Mount count: 1\n",
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" Sample ID: 45, Sample Name: Sample045, Position: 3, Mount count: 0\n",
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" Sample ID: 46, Sample Name: Sample046, Position: 4, Mount count: 0\n",
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" Sample ID: 47, Sample Name: Sample047, Position: 5, Mount count: 1\n",
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"Puck ID: 3, Puck Name: PUCK003\n",
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" Sample ID: 24, Sample Name: Sample024, Position: 1, Mount count: 0\n",
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" Sample ID: 25, Sample Name: Sample025, Position: 5, Mount count: 1\n",
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" Sample ID: 26, Sample Name: Sample026, Position: 8, Mount count: 1\n",
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" Sample ID: 27, Sample Name: Sample027, Position: 11, Mount count: 1\n",
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" Sample ID: 28, Sample Name: Sample028, Position: 12, Mount count: 1\n",
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"Puck ID: 2, Puck Name: PUCK002\n",
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" Sample ID: 17, Sample Name: Sample017, Position: 4, Mount count: 1\n",
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" Sample ID: 18, Sample Name: Sample018, Position: 5, Mount count: 0\n",
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" Sample ID: 19, Sample Name: Sample019, Position: 7, Mount count: 1\n",
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" Sample ID: 20, Sample Name: Sample020, Position: 10, Mount count: 0\n",
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" Sample ID: 21, Sample Name: Sample021, Position: 11, Mount count: 1\n",
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" Sample ID: 22, Sample Name: Sample022, Position: 13, Mount count: 0\n",
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" Sample ID: 23, Sample Name: Sample023, Position: 16, Mount count: 1\n",
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"Puck ID: 1, Puck Name: PUCK-001\n",
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" Sample ID: 1, Sample Name: Sample001, Position: 1, Mount count: 1\n",
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" Sample ID: 2, Sample Name: Sample002, Position: 2, Mount count: 1\n",
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" Sample ID: 3, Sample Name: Sample003, Position: 3, Mount count: 0\n",
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" Sample ID: 4, Sample Name: Sample004, Position: 4, Mount count: 0\n",
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" Sample ID: 5, Sample Name: Sample005, Position: 5, Mount count: 0\n",
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" Sample ID: 6, Sample Name: Sample006, Position: 6, Mount count: 1\n",
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" Sample ID: 7, Sample Name: Sample007, Position: 7, Mount count: 0\n",
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" Sample ID: 8, Sample Name: Sample008, Position: 8, Mount count: 1\n",
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" Sample ID: 9, Sample Name: Sample009, Position: 9, Mount count: 1\n",
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" Sample ID: 10, Sample Name: Sample010, Position: 10, Mount count: 1\n",
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" Sample ID: 11, Sample Name: Sample011, Position: 11, Mount count: 1\n",
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" Sample ID: 12, Sample Name: Sample012, Position: 12, Mount count: 1\n",
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" Sample ID: 13, Sample Name: Sample013, Position: 13, Mount count: 0\n",
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" Sample ID: 14, Sample Name: Sample014, Position: 14, Mount count: 1\n",
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" Sample ID: 15, Sample Name: Sample015, Position: 15, Mount count: 0\n",
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" Sample ID: 16, Sample Name: Sample016, Position: 16, Mount count: 0\n"
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]
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},
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1097: InsecureRequestWarning: Unverified HTTPS request is being made to host '127.0.0.1'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
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" warnings.warn(\n"
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]
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}
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],
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"execution_count": 79
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},
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{
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"metadata": {},
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"metadata": {
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"ExecuteTime": {
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"end_time": "2025-02-26T12:05:03.257159Z",
|
||||
"start_time": "2025-02-26T12:05:03.232846Z"
|
||||
}
|
||||
},
|
||||
"cell_type": "code",
|
||||
"outputs": [],
|
||||
"execution_count": null,
|
||||
"source": [
|
||||
"from aareDBclient import SampleEventCreate\n",
|
||||
"\n",
|
||||
@ -294,7 +442,7 @@
|
||||
" try:\n",
|
||||
" # Define the payload with only `event_type`\n",
|
||||
" sample_event_create = SampleEventCreate(\n",
|
||||
" sample_id=58,\n",
|
||||
" sample_id=16,\n",
|
||||
" event_type=\"Mounted\" # Valid event type\n",
|
||||
" )\n",
|
||||
"\n",
|
||||
@ -304,7 +452,7 @@
|
||||
"\n",
|
||||
" # Call the API\n",
|
||||
" api_response = api_instance.create_sample_event_samples_samples_sample_id_events_post(\n",
|
||||
" sample_id=58, # Ensure this matches a valid sample ID in the database\n",
|
||||
" sample_id=16, # Ensure this matches a valid sample ID in the database\n",
|
||||
" sample_event_create=sample_event_create\n",
|
||||
" )\n",
|
||||
"\n",
|
||||
@ -320,7 +468,40 @@
|
||||
" if e.body:\n",
|
||||
" print(f\"Error Details: {e.body}\")\n"
|
||||
],
|
||||
"id": "4a0665f92756b486"
|
||||
"id": "4a0665f92756b486",
|
||||
"outputs": [
|
||||
{
|
||||
"name": "stdout",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"Payload being sent to API:\n",
|
||||
"{\"event_type\":\"Mounted\"}\n",
|
||||
"API response:\n",
|
||||
"('id', 16)\n",
|
||||
"('sample_name', 'Sample016')\n",
|
||||
"('position', 16)\n",
|
||||
"('puck_id', 1)\n",
|
||||
"('crystalname', None)\n",
|
||||
"('proteinname', None)\n",
|
||||
"('positioninpuck', None)\n",
|
||||
"('priority', None)\n",
|
||||
"('comments', None)\n",
|
||||
"('data_collection_parameters', None)\n",
|
||||
"('events', [SampleEventResponse(id=399, sample_id=16, event_type='Mounted', timestamp=datetime.datetime(2025, 2, 26, 13, 5, 3))])\n",
|
||||
"('mount_count', 1)\n",
|
||||
"('unmount_count', 0)\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
"name": "stderr",
|
||||
"output_type": "stream",
|
||||
"text": [
|
||||
"/Library/Frameworks/Python.framework/Versions/3.12/lib/python3.12/site-packages/urllib3/connectionpool.py:1097: InsecureRequestWarning: Unverified HTTPS request is being made to host '127.0.0.1'. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#tls-warnings\n",
|
||||
" warnings.warn(\n"
|
||||
]
|
||||
}
|
||||
],
|
||||
"execution_count": 80
|
||||
},
|
||||
{
|
||||
"metadata": {},
|
||||
@ -347,8 +528,8 @@
|
||||
{
|
||||
"metadata": {
|
||||
"ExecuteTime": {
|
||||
"end_time": "2025-02-26T08:45:41.872357Z",
|
||||
"start_time": "2025-02-26T08:45:41.847822Z"
|
||||
"end_time": "2025-02-26T12:29:51.615501Z",
|
||||
"start_time": "2025-02-26T12:29:51.592886Z"
|
||||
}
|
||||
},
|
||||
"cell_type": "code",
|
||||
@ -399,7 +580,7 @@
|
||||
"text": [
|
||||
"API Response:\n",
|
||||
"200\n",
|
||||
"{'message': '1 image uploaded successfully.', 'file': 'images/p20001, p20002/2025-02-26/Dewar Two/PK001/14/IMG_1942.jpg'}\n"
|
||||
"{'pgroup': 'p20001, p20002', 'sample_id': 58, 'filepath': 'images/p20001, p20002/2025-02-26/Dewar One/PUCK007/12/IMG_1942.jpg', 'status': 'active', 'comment': None, 'id': 1}\n"
|
||||
]
|
||||
},
|
||||
{
|
||||
@ -411,7 +592,7 @@
|
||||
]
|
||||
}
|
||||
],
|
||||
"execution_count": 70
|
||||
"execution_count": 85
|
||||
},
|
||||
{
|
||||
"metadata": {},
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user