Add function to check for existing column name in list of column names #1619
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Keys for the name of stimulus are different between eceephys and behavior ophys. This adds in a small function to get the key represented in each data type and raise an exception if one key is not found. This was added to allow ophys behavior experiments to write to nwb files.
I updated the function to be more generic and removed specific case verbaige. I also fixed the failing tests on Linux and Mac. The regex for the tests was returning an error on Linux and Mac.
Codecov Report
@@ Coverage Diff @@
## address-behavior-ophys-NWB-failures #1619 +/- ##
=======================================================================
+ Coverage 35.58% 35.60% +0.01%
=======================================================================
Files 344 345 +1
Lines 33568 33577 +9
=======================================================================
+ Hits 11946 11955 +9
Misses 21622 21622
Continue to review full report at Codecov.
|
Merged
pickles-bread-and-butter
changed the title
pickles-bread-and-butter
changed the base branch from
rc/2.1.0
to
address-behavior-ophys-NWB-failures
njmei
reviewed
Jun 18, 2020
| def get_column_name(table_cols: list, | ||
| possible_names: set) -> str: | ||
| """ | ||
| This function acts a identifier for which column name is present in the |
Contributor
There was a problem hiding this comment.
I would reword this bit:
This function returns a column name, given a table with unknown
column names and a set of possible column names which are expected.
The table column name returned should be the only name contained in
the "expected" possible names.
Because stimulus presentation table column names (and contents)
differ between ecephys and visual behavior, this function determines
the proper column name to use in order to select the 'name' of a
presented stimulus (e.g. "gabors", "dot_motion", "natural_movie_1", etc.).
Contributor
Author
There was a problem hiding this comment.
Good idea, changed the doc string to what you have provided.
Updated the Docstring to better capture the puprose of the function. This better aligns with the expectation of functional performance.
njmei
approved these changes
Jun 18, 2020
pickles-bread-and-butter
merged commit 61845d8
into
address-behavior-ophys-NWB-failures
pickles-bread-and-butter
deleted the
address-unpin-failures-behavior-ophys
branch
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Overview:
This pull request addresses a failure in NWB writing where Behavior Ophys experiments do not have the hard coded
stimulus_namekey available. This has now been rectified by adding in a small function that checks for the existance of equivalent keys in the stimulus table dataframe.Validation:
I've included test cases to test for the existance of the keys in the provided keys, ie: checking for a column name within a set of column names. These cases cover the cases where it finds the eccephys key or the behavior ophys key. It also covers the case where it finds no keys and the case where it finds more than one key.
I have also run the BehaviorOphysNWBAPI.save() function that calls this function and it proceeds past this point, correctly grabbing the names of the stimuli in the stimuli table.