Merge pull request #1746 from AllenNeuralDynamics/develop

[production merge] 2026-05-29

Author: micahwoodard

pyproject.toml

@@ -26,7 +26,6 @@ dependencies = [
     "pyOSC3@git+https://github.com/glopesdev/pyosc3.git@master",
     "newscale@git+https://github.com/AllenNeuralDynamics/python-newscale@axes-on-target",
     "aind-auto-train@git+https://github.com/AllenNeuralDynamics/aind-foraging-behavior-bonsai-automatic-training.git@main",
-    "aind-slims-api@git+https://github.com/AllenNeuralDynamics/aind-slims-api@main",
     "aind-dynamic-foraging-models >= 0.12.2",
     "aind-dynamic-foraging-basic-analysis >= 0.3.34",
     "aind-behavior-services >=0.8, <0.9",
@@ -48,6 +47,7 @@ dependencies = [
     "winkerberos; sys_platform == 'win32'",
     "ldap3; sys_platform == 'win32'",
     "msal; sys_platform == 'win32'",
+    "log-schema==0.2.10.dev1"
 ]
 
 [project.optional-dependencies]

src/foraging_gui/Foraging.py

@@ -28,10 +28,11 @@
 import requests
 import serial
 import yaml
+
+import log_schema
 from aind_auto_train.schema.task import TrainingStage
 from aind_behavior_services.session import AindBehaviorSessionModel
 from aind_data_schema.core.session import Session
-from aind_slims_api import SlimsClient, models
 from matplotlib.backends.backend_qt5agg import (
     NavigationToolbar2QT as NavigationToolbar,
 )
@@ -238,9 +239,6 @@ def __init__(self, parent=None, box_number=1, start_bonsai_ide=True):
         # Connect to Bonsai
         self._InitializeBonsai()
 
-        # connect to Slims
-        self._ConnectSlims()
-
         # Set up threads
         self.threadpool = QThreadPool()  # get animal response
         self.threadpool2 = QThreadPool()  # get animal lick
@@ -351,6 +349,9 @@ def __init__(self, parent=None, box_number=1, start_bonsai_ide=True):
 
         # load the rig metadata
         self._load_rig_metadata()
+        
+        # setup life-cycle logger
+        self.lifecycle_logger = self.setup_lifecycle_logger()
 
         # Initializes session log handler as None
         self.session_log_handler = None
@@ -365,6 +366,27 @@ def __init__(self, parent=None, box_number=1, start_bonsai_ide=True):
             self._ReconnectBonsai()
         logging.info("Start up complete")
 
+    def setup_lifecycle_logger(self) -> logging.Logger:
+        
+        """
+        Creates logger for start, stop, and failure events with formatter adhering to aind log standards.
+        """
+
+        # Ensure the directory exists
+        os.makedirs(Path(self.Settings["lifecycle_log_dir"]), exist_ok=True)
+
+        lifecycle_logger = logging.getLogger("lifecycle")
+        lifecycle_logger.setLevel(logging.INFO)
+
+        timestamp = datetime.now().strftime("%Y%m%dT%H%M%SZ")
+        filename = f"lifecycle_log_{timestamp}.jsonl"
+        file_handler = logging.FileHandler(os.path.join(self.Settings["lifecycle_log_dir"], filename), encoding="utf-8")
+        file_handler.setLevel(logging.INFO)
+        file_handler.setFormatter(log_schema.DefaultFormatter())
+        lifecycle_logger.addHandler(file_handler)
+
+        return lifecycle_logger
+
     def _load_rig_metadata(self):
         """Load the latest rig metadata"""
 
@@ -1594,6 +1616,7 @@ def _restartlogging(self, log_folder=None,start_from_camera=False):
             self.Save.setStyleSheet(
                 "color: white;background-color : mediumorchid"
             )
+
         else:
             # temporary logging
             loggingtype = 1
@@ -1961,11 +1984,17 @@ def _GetSettings(self):
                 "aind_watchdog_service",
                 "manifest",
             ),
+            "lifecycle_log_dir": os.path.join(
+                os.path.expanduser("~"),
+                "Documents",
+                "lifecycle_logs",
+            ),
             "transfer_service_job_type": "dynamic_foraging_compression",
             "auto_engage": True,
             "clear_figure_after_save": True,
             "add_default_project_name": True,
             "check_schedule": False,
+            "waterlog_exe_path": "C://Program Files/AIBS_MPE/waterlog/waterlog.exe",
         }
 
         # Try to load the ForagingSettings.json file
@@ -2097,71 +2126,8 @@ def _GetSettings(self):
         ]
         self.rig_name = "{}".format(self.current_box)
 
-    def _ConnectSlims(self):
-        """
-        Connect to Slims
-        """
-        try:
-            logging.info("Attempting to connect to Slims")
-            self.slims_client = SlimsClient(
-                username=os.environ["SLIMS_USERNAME"],
-                password=os.environ["SLIMS_PASSWORD"],
-            )
-        except KeyError as e:
-            raise KeyError(
-                "SLIMS_USERNAME and SLIMS_PASSWORD do not exist as "
-                f"environment variables on machine. Please add. {e}"
-            )
-
-        try:
-            self.slims_client.fetch_model(
-                models.SlimsMouseContent, barcode="00000000"
-            )
-        except Exception as e:
-            if "Status 401 – Unauthorized" in str(
-                e
-            ):  # catch error if username and password are incorrect
-                raise Exception(
-                    f"Exception trying to read from Slims: {e}.\n"
-                    f" Please check credentials:\n"
-                    f"Username: {os.environ['SLIMS_USERNAME']}\n"
-                    f"Password: {os.environ['SLIMS_PASSWORD']}"
-                )
-            elif "No record found" not in str(
-                e
-            ):  # bypass if mouse doesn't exist
-                raise Exception(f"Exception trying to read from Slims: {e}.\n")
-        logging.info("Successfully connected to Slims")
-
-    def _AddWaterLogResult(self, session: Session):
-        """
-        Add WaterLogResult to slims based on current state of gui
-
-        :param session: Session object to pull water information from
-
-        """
-
-        try:  # try and find mouse
-            logging.info(
-                f"Attempting to fetch mouse {session.subject_id} from Slims"
-            )
-            mouse = self.slims_client.fetch_model(
-                models.SlimsMouseContent, barcode=session.subject_id
-            )
-        except Exception as e:
-            if "No record found" in str(
-                e
-            ):  # if no mouse found or validation errors on mouse
-                logging.warning(
-                    f'"No record found" error while trying to fetch mouse {session.subject_id}. '
-                    f"Will not log water."
-                )
-                return
-            else:
-                logging.error(
-                    f"While fetching mouse {session.subject_id} model, unexpected error occurred: {e}"
-                )
-                raise e
+    def _AddWaterlogResult(self, session: Session):
+        """Send weight/water information to databases via waterlog app cli"""
 
         # extract water information
         logging.info("Extracting water information from first stimulus epoch")
@@ -2171,53 +2137,41 @@ def _AddWaterLogResult(self, session: Session):
             for k, v in water_json
         }
 
-        # extract software information
+        # extract software information to send to waterlog once it can accept it
         logging.info("Extracting software information from first data stream")
         software = session.stimulus_epochs[0].software[0]
+        # Access sw name/version with (software.url, software.version)
+
+        waterlog_args = [
+            self.Settings['waterlog_exe_path'],
+            '--username',
+            self.behavior_session_model.experimenter[0],
+            '--mouse-id',
+            session.subject_id,
+            '--mouse-weight',
+            session.animal_weight_post,
+            '--comment',
+            session.notes,
+            '--earned-water',
+            water["water_in_session_total"],
+            '--water-supplement-ml',
+            water["water_after_session"],
+            '--water-supplement-delivered',
+        ]
 
-        # create model
-        logging.info(
-            "Creating SlimsWaterlogResult based on session information."
-        )
-        print(water)
-        model = models.SlimsWaterlogResult(
-            mouse_pk=mouse.pk,
-            date=datetime.now(),
-            weight_g=session.animal_weight_post,
-            operator=self.behavior_session_model.experimenter[0],
-            water_earned_ml=water["water_in_session_total"],
-            water_supplement_delivered_ml=water["water_after_session"],
-            water_supplement_recommended_ml=None,
-            total_water_ml=water["water_in_session_total"]+water["water_after_session"],
-            comments=session.notes,
-            workstation=session.rig_id,
-            sw_source=software.url,
-            sw_version=software.version,
-            test_pk=self.slims_client.fetch_pk(
-                "Test", test_name="test_waterlog"
-            ),
-        )
+        logging.info("Sending water info to waterlog")
+        process = subprocess.run([str(arg) for arg in waterlog_args])
 
-        # check if mouse already has waterlog for at session time and if, so update model
-        logging.info(
-            f"Fetching previous waterlog for mouse {session.subject_id}"
-        )
-        waterlog = self.slims_client.fetch_models(
-            models.SlimsWaterlogResult, mouse_pk=mouse.pk, start=0, end=1
-        )
-        if waterlog != [] and waterlog[0].date.strftime(
-            "%Y-%m-%d %H:%M:%S"
-        ) == session.session_start_time.astimezone(timezone.utc).strftime(
-            "%Y-%m-%d %H:%M:%S"
-        ):
-            logging.info(
-                "Waterlog information already exists for this session. Updating waterlog in Slims."
-            )
-            model.pk = waterlog[0].pk
-            self.slims_client.update_model(model=model)
-        else:
-            logging.info("Adding waterlog to Slims.")
-            self.slims_client.add_model(model)
+        QMessageBox.information(self, "Waterlog", "Go to waterlog app to submit water information.")
+
+        try:
+            process.check_returncode()
+        except Exception:
+            logging.warning(
+                f"Waterlog data for mouse {self.behavior_session_model.subject} cannot be sent to waterlog exe"
+                f", message: {process.stdout}, {process.stderr}",
+                exc_info=True,
+                )
 
     def _InitializeBonsai(self):
         """
@@ -3937,7 +3891,7 @@ def _Save(self, ForceSave=0, SaveAs=0, SaveContinue=0, BackupSave=0):
         if self.CreateNewFolder == 1:
             self._GetSaveFolder()
             self.CreateNewFolder = 0
-
+            
         if not os.path.exists(os.path.dirname(self.SaveFileJson)):
             os.makedirs(os.path.dirname(self.SaveFileJson))
             logging.info(
@@ -4171,7 +4125,7 @@ def _Save(self, ForceSave=0, SaveAs=0, SaveContinue=0, BackupSave=0):
         # save random reward parameters
         Obj['random_reward_par']=self.RandomReward_dialog.random_reward_par
 
-        # generate the metadata file and update slims
+        # generate the metadata file and update waterlog
         try:
             # save the metadata collected in the metadata dialogue
             self.Metadata_dialog._save_metadata_dialog_parameters()
@@ -4218,13 +4172,19 @@ def _Save(self, ForceSave=0, SaveAs=0, SaveContinue=0, BackupSave=0):
                     ]
                     and session is not None
                 ):
-                    self._AddWaterLogResult(session)
+                    self._AddWaterlogResult(session)
                 elif self.BaseWeight.text() == "" or self.WeightAfter.text() == "":
-                    logging.warning(f"Waterlog for mouse {self.behavior_session_model.subject} cannot be added to slims"
+                    logging.warning(f"Waterlog for mouse {self.behavior_session_model.subject} cannot be added to database"
                                    f" due do unrecorded weight information.")
                 elif session is None:
-                    logging.warning(f"Waterlog for mouse {self.behavior_session_model.subject} cannot be added to slims"
+                    logging.warning(f"Waterlog for mouse {self.behavior_session_model.subject} cannot be added to database"
                                   f" due do metadata generation failure.")
+                    
+                # add complete log to lifecycle 
+                self.lifecycle_logger.info("Session ended.", extra={"subject_id": self.behavior_session_model.subject, 
+                                                                      "acquisition_name": self.behavior_session_model.session_name,
+                                                                      "event_type": "stage_complete"})
+                
         except Exception as e:
             logging.warning(
                 "Meta data is not saved!",
@@ -6186,6 +6146,10 @@ def _Start(self):
                 # Start logging if the formal logging is not started
                 if self.logging_type != 0:
                     self.Ot_log_folder = self._restartlogging()
+                # Need to log start event after session_name has been set in_restartlogging
+                self.lifecycle_logger.info("Session started.", extra={"subject_id": self.behavior_session_model.subject, 
+                                                                "acquisition_name": self.behavior_session_model.session_name,
+                                                                "event_type": "stage_start"})
             except Exception as e:
                 if "ConnectionAbortedError" in str(e):
                     logging.info("lost bonsai connection: restartlogging()")
@@ -6641,6 +6605,9 @@ def _StartTrialLoop(self, GeneratedTrials, worker1, worker_save):
                         self.ANewTrial = 1
                         self.Start.setChecked(False)
                         self.Start.setStyleSheet("background-color : none")
+                        self.lifecycle_logger.info("Session failed.", extra={"subject_id": self.behavior_session_model.subject, 
+                                                                      "acquisition_name": self.behavior_session_model.session_name,
+                                                                      "event_type": "stage_failure"})
                         break
                 # receive licks and update figures
                 if self.actionDrawing_after_stopping.isChecked() == False:
@@ -7432,7 +7399,6 @@ def setup_loki_logging(box_number):
     handler.setLevel(logging.INFO)
     logger.root.addHandler(handler)
 
-
 def start_gui_log_file(box_number):
     """
     Starts a log file for the gui.

src/foraging_gui/settings_model.py

@@ -1,7 +1,7 @@
 from typing import Literal, Optional
 
 from pydantic import BaseModel, Field
-
+from pathlib import Path
 
 class BonsaiSettingsModel(BaseModel):
     """
@@ -182,6 +182,7 @@ class DFTSettingsModel(BaseModel):
     save_each_trial: bool
     AutomaticUpload: bool
     manifest_flag_dir: str
+    lifecycle_log_dir: Path
     transfer_service_job_type: str
     auto_engage: bool
     clear_figure_after_save: bool