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FATAL:json.decoder.JSONDecodeError: Expecting ',' delimiter: line 38728 column 13 (char 583263) #1104

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alexpiet opened this issue Dec 2, 2024 · 1 comment
Open

FATAL:json.decoder.JSONDecodeError: Expecting ',' delimiter: line 38728 column 13 (char 583263) #1104

alexpiet opened this issue Dec 2, 2024 · 1 comment
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@micahwoodard
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low priority - auto-generated autogenerated issues that have only occurred once

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@alexpiet
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alexpiet commented Dec 2, 2024

This issue was automatically generated from GUI logs.

file: Foraging.py
function: exception_hook
line 4769
logfile: W10DT714688/W10DT714688-D_gui_log_2024-11-27_16-06-17.txt
boxes: 8D
count: 3
text: FATAL:json.decoder.JSONDecodeError: Expecting ',' delimiter: line 38728 column 13 (char 583263)

GUI Log snippet (click for full log)

04:30:18 PM:INFO:Foraging:Foraging.py:_StopPhotometry:line 3428:Checking that photometry is not running
04:30:18 PM:INFO:Foraging:Foraging.py:_StopPhotometry:line 3438:Photometry excitation stopped
04:30:18 PM:INFO:Foraging:Foraging.py:_NewSession:line 3561:New Session complete
04:30:18 PM:ERROR:Foraging:Foraging.py:exception_hook:line 4769:FATAL ERROR: 
Traceback (most recent call last):
  File "C:\Users\svc_aind_behavior\Documents\GitHub\dynamic-foraging-task\src\foraging_gui\Foraging.py", line 2819, in _OpenLast
    self._Open(open_last=True)
  File "C:\Users\svc_aind_behavior\Documents\GitHub\dynamic-foraging-task\src\foraging_gui\Foraging.py", line 2973, in _Open
    Obj = json.loads(f.read())
          ^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\svc_aind_behavior\AppData\Local\miniconda3\envs\Foraging\Lib\json\__init__.py", line 346, in loads
    return _default_decoder.decode(s)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\svc_aind_behavior\AppData\Local\miniconda3\envs\Foraging\Lib\json\decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\svc_aind_behavior\AppData\Local\miniconda3\envs\Foraging\Lib\json\decoder.py", line 353, in raw_decode
    obj, end = self.scan_once(s, idx)
               ^^^^^^^^^^^^^^^^^^^^^^
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 38728 column 13 (char 583263)
Full GUI log 
04:06:17 PM:INFO:Foraging:Foraging.py:start_gui_log_file:line 4661:Starting logfile!
04:06:17 PM:INFO:Foraging:Foraging.py:log_git_hash:line 4672:Python version: 3.11.9 | packaged by Anaconda, Inc. | (main, Apr 19 2024, 16:40:41) [MSC v.1916 64 bit (AMD64)]
04:06:17 PM:INFO:Foraging:Foraging.py:log_git_hash:line 4689:Current git commit branch, hash: main, 1a7c9d3d1aa10284caed44ba9b223c6bfbb8ff5f
04:06:17 PM:INFO:Foraging:Foraging.py:log_git_hash:line 4693:Current foraging_gui version: 1.6.10
04:06:17 PM:WARNING:Foraging:Foraging.py:log_git_hash:line 4703:local repository is clean
04:06:17 PM:INFO:Foraging:Foraging.py:<module>:line 4804:Setting QApplication attributes
04:06:17 PM:INFO:Foraging:Foraging.py:<module>:line 4812:Starting QApplication and Window
04:06:17 PM:INFO:Foraging:Foraging.py:__init__:line 69:Creating Window
04:06:17 PM:INFO:Foraging:Foraging.py:_GetSettings:line 1174:Loaded settings_box file
04:06:17 PM:INFO:Foraging:Foraging.py:_GetSettings:line 1202:Loaded settings file
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (FIP_settings), using default: C:\Users\svc_aind_behavior\Documents\FIPSettings
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (bonsai_config_path), using default: C:\Users\svc_aind_behavior\Documents\GitHub\dynamic-foraging-task\bonsai\Bonsai.config
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (metadata_dialog_folder), using default: C:\Users\svc_aind_behavior\Documents\ForagingSettings\metadata_dialog\
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (rig_metadata_folder), using default: C:\Users\svc_aind_behavior\Documents\ForagingSettings\rig_metadata\
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (project_info_file), using default: C:\Users\svc_aind_behavior\Documents\ForagingSettings\Project Name and Funding Source v2.csv
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (schedule_path), using default: Z:\dynamic_foraging\DynamicForagingSchedule.csv
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (go_cue_decibel_box1), using default: 60
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (go_cue_decibel_box2), using default: 60
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (go_cue_decibel_box3), using default: 60
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (lick_spout_distance_box1), using default: 5000
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (lick_spout_distance_box2), using default: 5000
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (lick_spout_distance_box3), using default: 5000
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (lick_spout_distance_box4), using default: 5000
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (name_mapper_file), using default: C:\Users\svc_aind_behavior\Documents\ForagingSettings\name_mapper.json
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (create_rig_metadata), using default: True
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (save_each_trial), using default: True
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (AutomaticUpload), using default: True
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (manifest_flag_dir), using default: C:\Users\svc_aind_behavior\Documents\aind_watchdog_service\manifest
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (auto_engage), using default: True
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (clear_figure_after_save), using default: True
04:06:17 PM:WARNING:Foraging:Foraging.py:_GetSettings:line 1212:Missing setting (add_default_project_name), using default: True
04:06:17 PM:INFO:Foraging:Foraging.py:_LoadSchedule:line 1100:Loaded behavior schedule
04:06:17 PM:INFO:Foraging:Foraging.py:_GetWaterCalibration:line 1064:Loaded Water Calibration
04:06:17 PM:INFO:Foraging:Foraging.py:_load_most_recent_rig_json:line 1534:Found existing rig.json: rig_446-8-D_2024-11-26_11_16_28.json
04:06:17 PM:INFO:RigJsonBuilder:RigJsonBuilder.py:build_rig_json_core:line 60:building rig json
04:06:17 PM:INFO:RigJsonBuilder:RigJsonBuilder.py:build_rig_json_core:line 624:finished building rig json
04:06:17 PM:INFO:RigJsonBuilder:RigJsonBuilder.py:build_rig_json:line 53:Using existing rig json
04:06:17 PM:INFO:Foraging:Foraging.py:_LoadUI:line 275:Using ForagingGUI.ui interface
04:06:17 PM:INFO:Foraging:Foraging.py:__init__:line 119:Setting Window title: 446-8-D
04:06:17 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1371:Trying to connect to already running Bonsai
04:06:17 PM:INFO:Foraging:Foraging.py:_ConnectOSC:line 1418:connecting to GUI and Bonsai through OSC
04:06:18 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1375:Could not connect: timed out
04:06:18 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1384:Starting Bonsai
04:06:18 PM:INFO:Foraging:Foraging.py:log_subprocess_output:line 4776:BONSAI logging starting
04:06:19 PM:INFO:Foraging:Foraging.py:_ConnectOSC:line 1418:connecting to GUI and Bonsai through OSC
04:06:20 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1398:Could not connect, total waiting time 0.5 seconds: timed out
04:06:20 PM:INFO:Foraging:Foraging.py:_ConnectOSC:line 1418:connecting to GUI and Bonsai through OSC
04:06:21 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1398:Could not connect, total waiting time 1.0 seconds: timed out
04:06:22 PM:INFO:Foraging:Foraging.py:_ConnectOSC:line 1418:connecting to GUI and Bonsai through OSC
04:06:22 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1401:Connected to Bonsai after 1.5 seconds
04:06:22 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1402:Bonsai started successfully
04:06:22 PM:INFO:Foraging:Foraging.py:_ConnectSlims:line 1281:Attempting to connect to Slims
04:06:22 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 52:['/PhotometryFalling', 12342682.405536, '127.0.0.1', 4033], displaying at 0.5 Hz
04:06:22 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/RightRewardDeliveryTimeHarp', 12342682.413504, '127.0.0.1', 4033]
04:06:23 PM:INFO:Foraging:Foraging.py:_ConnectSlims:line 1298:Successfully connected to Slims
04:06:23 PM:WARNING:Dialogs:Dialogs.py:_LoadCalibrationParameters:line 480:could not find water calibration parameters: C:\Users\svc_aind_behavior\Documents\ForagingSettings\WaterCalibrationPar_4.json
04:06:23 PM:INFO:Foraging:Foraging.py:keyPressEvent:line 1863:processing parameter changes
04:06:23 PM:INFO:Foraging:Foraging.py:_InitializeMotorStage:line 875:Scanning for newscale stages
04:06:23 PM:INFO:Foraging:Foraging.py:_InitializeMotorStage:line 885:Could not find any instances of NewScale Stage
04:06:23 PM:INFO:Foraging:Foraging.py:_insert_stage_widget:line 255:Inserting Stage Widget
04:06:23 PM:INFO:connection:connection.py:_connect:line 688:Connecting to aibspi(10.128.108.106):2181, use_ssl: False
04:06:23 PM:INFO:client:client.py:_session_callback:line 561:Zookeeper connection established, state: CONNECTED
04:06:23 PM:INFO:connection:connection.py:_connect_attempt:line 655:Closing connection to aibspi:2181
04:06:23 PM:INFO:client:client.py:_session_callback:line 567:Zookeeper session closed, state: CLOSED
04:06:23 PM:INFO:stepper_motor_device:stepper_motor_device.py:__init__:line 68:Connected to COM4, device id: 1130
04:06:23 PM:INFO:stepper_motor_device:stepper_motor_device.py:load_registers:line 149:Getting available registers on device
04:06:23 PM:INFO:stage_model:stage_model.py:configure_device:line 81:Configuring registers with default values (can be modified in config file)
04:06:23 PM:INFO:move_worker:move_worker.py:goto_origin:line 194:(move to origin): Moving stage to origin
04:06:23 PM:INFO:move_worker:move_worker.py:move_relative:line 336:(move relative): Moved motors by steps specified in [0, -27200, -27200, 0]
04:06:23 PM:INFO:move_worker:move_worker.py:move_relative:line 336:(move relative): Moved motors by steps specified in [-27200, 0, 0, 0]
04:06:23 PM:INFO:move_worker:move_worker.py:move_relative:line 336:(move relative): Moved motors by steps specified in [0, 0, 0, -27200]
04:06:23 PM:INFO:stage_model:stage_model.py:configure_device:line 87:Zeroed all motor positions
04:06:23 PM:INFO:stage_model:stage_model.py:configure_device:line 88:Finished configuring stepper motor device
#############################################################
04:06:23 PM:INFO:Foraging:Foraging.py:_StopPhotometry:line 3428:Checking that photometry is not running
04:06:23 PM:INFO:Foraging:Foraging.py:_StopPhotometry:line 3438:Photometry excitation stopped
04:06:23 PM:INFO:Foraging:Foraging.py:_load_most_recent_rig_json:line 1534:Found existing rig.json: rig_446-8-D_2024-11-26_11_16_28.json
04:06:23 PM:INFO:Foraging:Foraging.py:_ReconnectBonsai:line 971:attempting to close bonsai connection
04:06:26 PM:INFO:Foraging:Foraging.py:_ReconnectBonsai:line 979:bonsai connection closed
04:06:26 PM:INFO:Foraging:Foraging.py:_ReconnectBonsai:line 981:attempting to restart bonsai
04:06:26 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1371:Trying to connect to already running Bonsai
04:06:26 PM:INFO:Foraging:Foraging.py:_ConnectOSC:line 1418:connecting to GUI and Bonsai through OSC
04:06:26 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1378:Connected to already running Bonsai
04:06:26 PM:INFO:Foraging:Foraging.py:_InitializeBonsai:line 1379:Bonsai started successfully
04:06:26 PM:INFO:Foraging:Foraging.py:__init__:line 219:Start up complete
04:06:27 PM:INFO:aws_util:aws_util.py:import_df_from_s3:line 115:Dataframe imported from s3://aind-behavior-data/foraging_nwb_bonsai_processed/df_sessions.pkl, len(df) = 5730
04:06:27 PM:INFO:aws_util:aws_util.py:import_df_from_s3:line 115:Dataframe imported from s3://aind-behavior-data/foraging_auto_training/df_manager_447_demo.pkl, len(df) = 4265
04:06:28 PM:INFO:aws_util:aws_util.py:download_dir_from_s3:line 140:134 objects downloaded from s3://aind-behavior-data/foraging_auto_training/saved_curriculums/ to C:\Users\svc_aind_behavior/capsule/scratch/saved_curriculums/
04:06:28 PM:INFO:curriculum_manager:curriculum_manager.py:download_curriculums:line 162:Found 26 curriculums in C:\Users\svc_aind_behavior/capsule/scratch/saved_curriculums/
04:06:28 PM:INFO:aws_util:aws_util.py:download_dir_from_s3:line 140:134 objects downloaded from s3://aind-behavior-data/foraging_auto_training/saved_curriculums/ to C:\Users\svc_aind_behavior/.aind_auto_train/curriculum_manager/
04:06:28 PM:INFO:curriculum_manager:curriculum_manager.py:download_curriculums:line 162:Found 26 curriculums in C:\Users\svc_aind_behavior/.aind_auto_train/curriculum_manager/
04:06:28 PM:INFO:Dialogs:Dialogs.py:update_auto_train_fields:line 2273:No entry found in df_training_manager for subject_id: 0
04:06:28 PM:INFO:Dialogs:Dialogs.py:_override_curriculum_clicked:line 2621:Override stage clicked: state=2
04:06:28 PM:INFO:Dialogs:Dialogs.py:_update_stage_to_apply:line 2647:Current stage to apply: unknown training stage @unknown curriculum
04:12:03 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/ManualLeftWaterStartTime', 12343023.090976, '127.0.0.1', 4033]
04:12:03 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/LeftRewardDeliveryTimeHarp', 12343023.094496, '127.0.0.1', 4033]
04:12:08 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/ManualLeftWaterStartTime', 12343028.780992, '127.0.0.1', 4033]
04:12:08 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/LeftRewardDeliveryTimeHarp', 12343028.782496, '127.0.0.1', 4033]
04:12:09 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/ManualRightWaterStartTime', 12343029.576992, '127.0.0.1', 4033]
04:12:09 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/RightRewardDeliveryTimeHarp', 12343029.579488, '127.0.0.1', 4033]
04:12:14 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/ManualRightWaterStartTime', 12343034.638976, '127.0.0.1', 4033]
04:12:14 PM:INFO:rigcontrol:rigcontrol.py:msg_handler:line 56:['/RightRewardDeliveryTimeHarp', 12343034.64048, '127.0.0.1', 4033]
04:29:58 PM:INFO:Foraging:Foraging.py:_StopCurrentSession:line 3581:Stopping current trials
04:30:18 PM:INFO:Foraging:Foraging.py:_Open:line 2948:Quick load success: C:\behavior_data\446-8-D\756567\behavior_756567_2024-11-26_16-38-38\behavior\756567_2024-11-26_16-38-38.json
04:30:18 PM:INFO:Foraging:Foraging.py:_NewSession:line 3491:New Session pressed
04:30:18 PM:INFO:Foraging:Foraging.py:_NewSession:line 3523:Resetting session run flag
04:30:18 PM:INFO:Foraging:Foraging.py:_StopPhotometry:line 3428:Checking that photometry is not running
04:30:18 PM:INFO:Foraging:Foraging.py:_StopPhotometry:line 3438:Photometry excitation stopped
04:30:18 PM:INFO:Foraging:Foraging.py:_NewSession:line 3561:New Session complete
04:30:18 PM:ERROR:Foraging:Foraging.py:exception_hook:line 4769:FATAL ERROR: 
Traceback (most recent call last):
  File "C:\Users\svc_aind_behavior\Documents\GitHub\dynamic-foraging-task\src\foraging_gui\Foraging.py", line 2819, in _OpenLast
    self._Open(open_last=True)
  File "C:\Users\svc_aind_behavior\Documents\GitHub\dynamic-foraging-task\src\foraging_gui\Foraging.py", line 2973, in _Open
    Obj = json.loads(f.read())
          ^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\svc_aind_behavior\AppData\Local\miniconda3\envs\Foraging\Lib\json\__init__.py", line 346, in loads
    return _default_decoder.decode(s)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\svc_aind_behavior\AppData\Local\miniconda3\envs\Foraging\Lib\json\decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\svc_aind_behavior\AppData\Local\miniconda3\envs\Foraging\Lib\json\decoder.py", line 353, in raw_decode
    obj, end = self.scan_once(s, idx)
               ^^^^^^^^^^^^^^^^^^^^^^
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 38728 column 13 (char 583263)
@alexpiet alexpiet added the low priority - auto-generated autogenerated issues that have only occurred once label Dec 2, 2024
@alexpiet
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alexpiet commented Dec 3, 2024

Hey @micahwoodard this appears to be happening every few weeks. (https://github.com/AllenNeuralDynamics/dynamic-foraging-task/issues?q=is%3Aissue+FATAL%3Ajson.decoder.JSONDecodeError)
Do you have any idea what is happening? Maybe the saving process is getting interrupted?

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