Closed matchings closed 2 years ago
Can you make
passed_only
be an input argument forget_filtered_ophys_experiment_table()
? I'm ok with it defaulting to True, it just would be nice to have the ability to control the behavior
That would be the equivalent of setting the existing argument include_failed_data
to False. Do you want me to change the name of the argument?
Also, I'll point out that setting include_failed_data
to False gives back all passed experiments in lims. To get only published experiments you would also set release_data_only
to True.
Oh duh. Nevermind
This PR adds
passed_only
=False to the SDK call to get the experiments table inget_filtered_ophys_experiment_table()
to make sure that failed experiments are also returned whenrelease_data_only
=False andinclude_failed_data
=True.This
passed_only
flag was recently added to the SDK with the default being True, which has caused much confusion (see https://github.com/AllenInstitute/AllenSDK/issues/2243). I have requested that instead they make a published_only flag and set it to False by default so that users can do their own filtering, which is typically what you want to do when loading from lims. Otherwise we can just use the S3 cache to get published data.The PR also sets
add_extra_columns
to False by default because it is slow and most of the extra columns that we had been adding in the past are now part of the SDK experiments table itself. The remaining extra columns are primarily for detailed QC evaluations and dont need to be there by default.