Add example scripts and enhance puck event queries

Introduced a new Jupyter Notebook with API usage examples for managing pucks and samples. Refactored puck retrieval logic to include the latest event type and `tell_position`, improving data accuracy. Updated backend version to 0.1.0a16 accordingly.

backend/app/routers/puck.py

@@ -271,7 +271,8 @@ async def get_last_tell_position(puck_id: str, db: Session = Depends(get_db)):
 @router.get("/slot/{slot_identifier}", response_model=List[PuckWithTellPosition])
 async def get_pucks_by_slot(slot_identifier: str, db: Session = Depends(get_db)):
     """
-    Retrieve all pucks in a slot with their latest `tell_position`.
+    Retrieve all pucks in a slot, reporting their latest event and
+     `tell_position` value.
     """
     # Map keywords to slot IDs
     slot_aliases = {
@@ -328,50 +329,64 @@ async def get_pucks_by_slot(slot_identifier: str, db: Session = Depends(get_db))
     dewar_ids = [dewar.id for dewar in dewars]
     dewar_map = {dewar.id: dewar.dewar_name for dewar in dewars}
 
-    # Subquery to fetch the latest tell_position for each puck
+    # Subquery to fetch the latest event for each puck (any type of event)
-    subquery = (
+    latest_event_subquery = (
         db.query(
-            PuckEventModel.puck_id,
+            PuckEventModel.puck_id.label("puck_id"),
             func.max(PuckEventModel.timestamp).label("latest_event_time"),
         )
-        .filter(PuckEventModel.event_type == "tell_position_set")
         .group_by(PuckEventModel.puck_id)
-        .subquery()
+        .subquery(name="latest_event_subquery")  # Explicitly name the subquery
     )
 
-    # Fetch pucks with their latest tell_position
+    # Main query to fetch pucks and their latest events
-    pucks_with_positions = (
+    pucks_with_latest_events = (
-        db.query(PuckModel, PuckEventModel.tell_position)
+        db.query(
-        .outerjoin(subquery, subquery.c.puck_id == PuckModel.id)
+            PuckModel,
-        .outerjoin(
+            PuckEventModel.event_type,
-            PuckEventModel,
+            PuckEventModel.tell_position,
-            (PuckEventModel.puck_id == PuckModel.id)
-            & (PuckEventModel.timestamp == subquery.c.latest_event_time),
         )
-        .filter(PuckModel.dewar_id.in_(dewar_ids))
+        .join(  # Join pucks with the latest event
+            # (outer join to include pucks without events)
+            latest_event_subquery,
+            PuckModel.id == latest_event_subquery.c.puck_id,
+            isouter=True,
+        )
+        .join(  # Fetch event details from the latest event timestamp
+            PuckEventModel,
+            (PuckEventModel.puck_id == latest_event_subquery.c.puck_id)
+            & (PuckEventModel.timestamp == latest_event_subquery.c.latest_event_time),
+            isouter=True,
+        )
+        .filter(PuckModel.dewar_id.in_(dewar_ids))  # Restrict pucks to relevant dewars
         .all()
     )
 
-    # Log the results of the subquery and pucks fetched:
+    # Log the results of the query
-    logger.debug(f"Results from subquery (tell_position): {pucks_with_positions}")
+    logger.debug(f"Results from query (latest events): {pucks_with_latest_events}")
 
-    if not pucks_with_positions:
+    if not pucks_with_latest_events:
         logger.warning(f"No pucks found for slot: {slot_identifier}")
         raise HTTPException(
-            status_code=404, detail=f"No pucks found for slot '{slot_identifier}'"
+            status_code=404, detail=f"No pucks found for slot {slot_identifier}"
         )
 
-    # Prepare results:
+    # Prepare the final response
     results = []
-    for puck, tell_position in pucks_with_positions:
+    for puck, event_type, tell_position in pucks_with_latest_events:
         logger.debug(
-            f"Puck ID: {puck.id}, Name: {puck.puck_name},"
+            f"Puck ID: {puck.id}, Name: {puck.puck_name}, Event Type: {event_type}, "
-            f" Tell Position: {tell_position}"
+            f"Tell Position: {tell_position}"
         )
 
         dewar_name = dewar_map.get(puck.dewar_id, "Unknown")
 
-        # Prepare the PuckWithTellPosition instance
+        # For pucks with no events or whose latest event is `puck_removed`, set
+        # `tell_position` to None
+        if event_type is None or event_type == "puck_removed":
+            tell_position = None
+
+        # Construct the response model
         results.append(
             PuckWithTellPosition(
                 id=puck.id,
@@ -382,11 +397,11 @@ async def get_pucks_by_slot(slot_identifier: str, db: Session = Depends(get_db))
                 else None,
                 dewar_id=puck.dewar_id,
                 dewar_name=dewar_name,
-                tell_position=tell_position,  # Latest tell_position from subquery
+                tell_position=tell_position,
             )
         )
 
-    logger.info(f"Final response prepared for slot {slot_identifier}: {results}")
+    logger.info(f"Final response for slot {slot_identifier}: {results}")
     return results
 
 
@@ -396,8 +411,7 @@ async def get_pucks_with_tell_position(db: Session = Depends(get_db)):
     Retrieve all pucks with a `tell_position` set (not null),
     their associated samples, and the latest `tell_position` value (if any).
     """
-    # Query pucks with their latest `tell_position_set` event where
+
-    # `tell_position` is not null
     pucks_with_events = (
         db.query(PuckModel, PuckEventModel)
         .join(PuckEventModel, PuckModel.id == PuckEventModel.puck_id)

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "aareDB"
-version = "0.1.0a15"
+version = "0.1.0a16"
 description = "Backend for next gen sample management system"
 authors = [{name = "Guillaume Gotthard", email = "guillaume.gotthard@psi.ch"}]
 license = {text = "MIT"}

testfunctions.ipynb

@@ -0,0 +1,233 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "id": "initial_id",
+   "metadata": {
+    "collapsed": true,
+    "ExecuteTime": {
+     "end_time": "2025-01-09T15:53:14.008758Z",
+     "start_time": "2025-01-09T15:53:14.005084Z"
+    }
+   },
+   "source": [
+    "import aareDBclient\n",
+    "from aareDBclient.rest import ApiException\n",
+    "from pprint import pprint\n",
+    "from aareDBclient import SamplesApi\n",
+    "from aareDBclient.models import SampleEventCreate, SetTellPosition\n",
+    "\n",
+    "print(aareDBclient.__version__)\n",
+    "\n",
+    "configuration = aareDBclient.Configuration(\n",
+    "    host = \"https://127.0.0.1:8000\"\n",
+    ")\n",
+    "\n",
+    "configuration.verify_ssl = False  # Disable SSL verification\n",
+    "print(dir(SamplesApi))"
+   ],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "0.1.0a15\n",
+      "['__class__', '__delattr__', '__dict__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__getstate__', '__gt__', '__hash__', '__init__', '__init_subclass__', '__le__', '__lt__', '__module__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_create_sample_event_samples_samples_sample_id_events_post_serialize', '_get_all_pucks_with_samples_and_events_samples_pucks_samples_get_serialize', '_get_last_sample_event_samples_samples_sample_id_events_last_get_serialize', '_get_samples_with_events_samples_puck_id_samples_get_serialize', 'create_sample_event_samples_samples_sample_id_events_post', 'create_sample_event_samples_samples_sample_id_events_post_with_http_info', 'create_sample_event_samples_samples_sample_id_events_post_without_preload_content', 'get_all_pucks_with_samples_and_events_samples_pucks_samples_get', 'get_all_pucks_with_samples_and_events_samples_pucks_samples_get_with_http_info', 'get_all_pucks_with_samples_and_events_samples_pucks_samples_get_without_preload_content', 'get_last_sample_event_samples_samples_sample_id_events_last_get', 'get_last_sample_event_samples_samples_sample_id_events_last_get_with_http_info', 'get_last_sample_event_samples_samples_sample_id_events_last_get_without_preload_content', 'get_samples_with_events_samples_puck_id_samples_get', 'get_samples_with_events_samples_puck_id_samples_get_with_http_info', 'get_samples_with_events_samples_puck_id_samples_get_without_preload_content']\n"
+     ]
+    }
+   ],
+   "execution_count": 6
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-01-09T15:55:27.795447Z",
+     "start_time": "2025-01-09T15:55:27.775421Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "with aareDBclient.ApiClient(configuration) as api_client:\n",
+    "    # Create an instance of the API class\n",
+    "    api_instance = aareDBclient.PucksApi(api_client)\n",
+    "    get_pucks_at_beamline = aareDBclient.PucksApi(api_client)\n",
+    "\n",
+    "    try:\n",
+    "        # Create Return Address\n",
+    "        api_response = api_instance.get_pucks_by_slot_pucks_slot_slot_identifier_get(slot_identifier='X06DA')\n",
+    "        print(\"The response of PucksApi->get_pucks_by_slot_pucks_slot_slot_identifier_get:\\n\")\n",
+    "        pprint(api_response)\n",
+    "\n",
+    "    except ApiException as e:\n",
+    "        print(\"Exception when calling PucksApi->get_pucks_by_slot_pucks_slot_slot_identifier_get: %s\\n\" % e)"
+   ],
+   "id": "bbee7c94bf14000c",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The response of PucksApi->get_pucks_by_slot_pucks_slot_slot_identifier_get:\n",
+      "\n",
+      "[PuckWithTellPosition(id=31, puck_name='CPS-4093', puck_type='unipuck', puck_location_in_dewar='1', dewar_id=6, dewar_name='Dewar_test', user='e16371', samples=None, tell_position='B1'),\n",
+      " PuckWithTellPosition(id=32, puck_name='CPS-4178', puck_type='unipuck', puck_location_in_dewar='2', dewar_id=6, dewar_name='Dewar_test', user='e16371', samples=None, tell_position='B2'),\n",
+      " PuckWithTellPosition(id=33, puck_name='PSIMX-122', puck_type='unipuck', puck_location_in_dewar='3', dewar_id=6, dewar_name='Dewar_test', user='e16371', samples=None, tell_position=None),\n",
+      " PuckWithTellPosition(id=34, puck_name='E-07', puck_type='unipuck', puck_location_in_dewar='4', dewar_id=6, dewar_name='Dewar_test', user='e16371', samples=None, tell_position=None),\n",
+      " PuckWithTellPosition(id=35, puck_name='CPS-6597', puck_type='unipuck', puck_location_in_dewar='5', dewar_id=6, dewar_name='Dewar_test', user='e16371', samples=None, tell_position=None),\n",
+      " PuckWithTellPosition(id=36, puck_name='PSIMX-078', puck_type='unipuck', puck_location_in_dewar='6', dewar_id=6, dewar_name='Dewar_test', user='e16371', samples=None, tell_position=None),\n",
+      " PuckWithTellPosition(id=37, puck_name='1002', puck_type='unipuck', puck_location_in_dewar='7', dewar_id=6, dewar_name='Dewar_test', user='e16371', samples=None, tell_position=None)]\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": 14
+  },
+  {
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2025-01-09T15:55:22.123038Z",
+     "start_time": "2025-01-09T15:55:22.091256Z"
+    }
+   },
+   "cell_type": "code",
+   "source": [
+    "with aareDBclient.ApiClient(configuration) as api_client:\n",
+    "    # Create an instance of the API class\n",
+    "    api_instance = aareDBclient.PucksApi(api_client)\n",
+    "    get_pucks_at_beamline = aareDBclient.PucksApi(api_client)\n",
+    "\n",
+    "    # This part is commented but will be used to attribute a puck to a position of the TELL\n",
+    "    # Define the puck ID and payload\n",
+    "\n",
+    "    payload = [SetTellPosition(puck_name='CPS-4093', segment='B', puck_in_segment=1),SetTellPosition(puck_name='CPS-4178', segment='B', puck_in_segment=2)]\n",
+    "    #payload = []\n",
+    "\n",
+    "    try:\n",
+    "        # Call the PUT method to update the tell_position\n",
+    "        api_response = api_instance.set_tell_positions_pucks_set_tell_positions_put(payload)\n",
+    "        print(\"The response of PucksApi->pucks_puck_id_tell_position_put:\\n\")\n",
+    "        pprint(api_response)\n",
+    "\n",
+    "    except ApiException as e:\n",
+    "        print(\"Exception when calling PucksApi->pucks_puck_id_tell_position_put: %s\\n\" % e)"
+   ],
+   "id": "d52d12287dd63299",
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "The response of PucksApi->pucks_puck_id_tell_position_put:\n",
+      "\n",
+      "[{'message': 'The tell_position was updated successfully.',\n",
+      "  'new_position': 'B1',\n",
+      "  'previous_position': None,\n",
+      "  'puck_name': 'CPS-4093',\n",
+      "  'status': 'updated'},\n",
+      " {'message': 'The tell_position was updated successfully.',\n",
+      "  'new_position': 'B2',\n",
+      "  'previous_position': None,\n",
+      "  'puck_name': 'CPS-4178',\n",
+      "  'status': 'updated'}]\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": 13
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "\n",
+    "\n",
+    "    # GET request: Fetch all pucks in the tell\n",
+    "    try:\n",
+    "        all_pucks_response = api_instance.get_pucks_with_tell_position_pucks_with_tell_position_get()  # Replace with appropriate method\n",
+    "        print(\"The response of PucksApi->get_all_pucks_in_tell:\\n\")\n",
+    "        pprint(all_pucks_response)\n",
+    "\n",
+    "    except ApiException as e:\n",
+    "        print(\"Exception when calling PucksApi->get_all_pucks_in_tell: %s\\n\" % e)"
+   ],
+   "id": "95f8c133359945d5",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "\n",
+    "with aareDBclient.ApiClient(configuration) as api_client:\n",
+    "    # Create an instance of the Samples API class\n",
+    "    api_instance = aareDBclient.SamplesApi(api_client)\n",
+    "\n",
+    "    # Define the sample ID and event payload using the expected model\n",
+    "    sample_id = 1\n",
+    "    event_payload = SampleEventCreate(\n",
+    "        event_type=\"Unmounted\"  # Replace with actual event type if different\n",
+    "    )\n",
+    "\n",
+    "    try:\n",
+    "        # Post the sample event\n",
+    "        api_response = api_instance.create_sample_event_samples_samples_sample_id_events_post(\n",
+    "            sample_id=sample_id,\n",
+    "            sample_event_create=event_payload  # Pass the model instance here\n",
+    "        )\n",
+    "        print(\"The response of post_sample_event:\\n\")\n",
+    "        pprint(api_response)\n",
+    "\n",
+    "    except ApiException as e:\n",
+    "        print(\"Exception when calling post_sample_event: %s\\n\" % e)\n",
+    "\n",
+    "    try:\n",
+    "        # Get the last sample event\n",
+    "        last_event_response = api_instance.get_last_sample_event_samples_samples_sample_id_events_last_get(1)\n",
+    "        print(\"The response of get_last_sample_event:\\n\")\n",
+    "        pprint(last_event_response)\n",
+    "\n",
+    "    except ApiException as e:\n",
+    "        print(\"Exception when calling get_last_sample_event: %s\\n\" % e)\n"
+   ],
+   "id": "ee8abb293096334a",
+   "outputs": [],
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}