error in foraging.data_to_change_detection_core

[farznaj]

@jeromelecoq

session_id: 855711263
experiment: 856123117
(mesoscope session ; The workflow for the experiment is QC).

I get the error below when running the convert code. Any thoughts?

File "", line 2, in
ophys_data = convert_level_1_to_level_2(experiment_id, cache_dir) #, plot_roi_validation=False);

File "/home/farzaneh/Documents/analysis_codes/visual_behavior_analysis/visual_behavior/ophys/io/convert_level_1_to_level_2.py", line 976, in convert_level_1_to_level_2
core_data = get_core_data(pkl, timestamps_stimulus)

File "/home/farzaneh/Documents/analysis_codes/visual_behavior_analysis/visual_behavior/ophys/io/convert_level_1_to_level_2.py", line 415, in get_core_data
core_data = foraging.data_to_change_detection_core(pkl, time=timestamps_stimulus)

File "/home/farzaneh/Documents/analysis_codes/visual_behavior_analysis/visual_behavior/translator/foraging/init.py", line 40, in data_to_change_detection_core
handler = ListHandler(log_messages)

File "/home/farzaneh/Documents/analysis_codes/visual_behavior_analysis/visual_behavior/utilities.py", line 174, in init
super(ListHandler, self).init()

TypeError: super(type, obj): obj must be an instance or subtype of type

[nickponvert]

@farznaj this looks like the same error you were getting after you switched to the fix/issue533 branch to try and debug #562, is this still on that same branch?

[farznaj]

@nickponvert I know... no I am not ... I'm on feature/ production

[nickponvert]

Ok I'm going to try and reproduce it.

[farznaj]

I am getting this error for more sessions now:
session_id: 850894918
One point that might be helpful is that this session is just fixed by LIMS folks in service now .....
what's going on? is it about pkl files?

[farznaj]

@nickponvert Same error with two experiments (from session_id: 851428829) that had issues with motion correction, and just got fixed by LIMS people....

[farznaj]

@jeromelecoq @nickponvert I am in a python environment, after I check out a new git branch, for the codes to take effect, do I need to restart my python session? I am just surprised that why I used to get a platform_info error on feature/production ... and a type error on fix/issue533 .... but I am not back to feature branch , however I am getting the same error as in fix branch ....

there is something, I am up to date with new git changes (did git pull very recently) ... I cant remember if the platform error was before I did git pull or after .... is there a chance that feature codes are updated to what was in fix branch, and hence I am getting a similar type of error now on feature branch?

or is it that somehow I am not running feature branch code, even though I am in it (based on git branch start indication)....

[jeromelecoq]

Yes, I usually restart my kernel when I update a package.
You can also use the reload function
https://www.geeksforgeeks.org/reloading-modules-python/

[nickponvert]

@farznaj that fix branch hasn't yet been merged into production analysis, so that shouldn't be the issue. Would you copy/paste the code you are running to get the error? It would be helpful for me to debug the other issue in the fix branch too

[farznaj]

I found this that might be helpful:
https://thomas-cokelaer.info/blog/2011/09/382/
The error happens on super function below: (I've already sent the exact files).

class ListHandler(logging.Handler):
"""docstring for ListHandler."""
def init(self, log_list):
super(ListHandler, self).init()
self.log_list = log_list

def emit(self, record):
    entry = self.format(record)
    self.log_list.append(entry)

[farznaj]

thanks @jeromelecoq
@nickponvert after restarting the kernel, now the error changes back to platform_info .... the interesting thing is that all these sessions that just got fixed by lims folks (which initially had segmentation problems), are now failing due to this platform error....

[farznaj]

@nickponvert update: after restarting the kernel, the newly fixed sessions (by lims folks) are working... the only failed sessions are the ones that I originally sent you about the platform error:
session_id:

845444695

846652517

[nickponvert]

@farznaj since the feature/production_analysis branch got merged into master (master should now be the default branch for all analysis) could we re-check this issue to see if it is still a problem?