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Replace SLIMS calls with subprocess call to waterlog app #1742

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Replace SLIMS calls with subprocess call to waterlog app #1742

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0bd225b
Replace SLIMS calls with subprocess call to waterlog app
patricklatimer May 7, 2026
2823f44
Clean up waterlog adapter communication
patricklatimer May 11, 2026
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1 change: 0 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down
152 changes: 37 additions & 115 deletions src/foraging_gui/Foraging.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,6 @@
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,
)
Expand Down Expand Up @@ -238,9 +237,6 @@ 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
Expand Down Expand Up @@ -1966,6 +1962,7 @@ def _GetSettings(self):
"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
Expand Down Expand Up @@ -2097,71 +2094,8 @@ 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")
Expand All @@ -2171,53 +2105,41 @@ 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.")

Comment thread
patricklatimer marked this conversation as resolved.
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):
"""
Expand Down Expand Up @@ -4171,7 +4093,7 @@ 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()
Expand Down Expand Up @@ -4220,10 +4142,10 @@ def _Save(self, ForceSave=0, SaveAs=0, SaveContinue=0, BackupSave=0):
):
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.")
except Exception as e:
logging.warning(
Expand Down