Strip undefined attributes during StudyFile creation (SCP-5996)

[bistline]

BACKGROUND & CHANGES

This addresses a rare corner case where a user attempted to upload a classic plain text expression matrix file and encountered the following error:

(Mongoid::Errors::UnknownAttribute)
message:
  Attempted to set a value for 'raw_location' which is not allowed on the model ExpressionFileInfo.

This should not be possible, as raw_location is only present in the AnnData UX. The associated error report also shows that no upload is being provided by the user, so it is unclear how they got into this state.

Now, when a StudyFile is being processed by the API, a final sanitization step will run that strips out all key/value pairs that are not defined fields for either the StudyFile or any of the nested associations (ExpressionFileInfo, AnnDataFileInfo, etc). This will remove the need to manually prune any extra fields that are added to forms that don't map to model attributes, such as control-oriented fields like parse_on_upload.

MANUAL TESTING

Since it is unclear how the user got into this state, and all attempts to recreate it have failed, there is not currently a way to manually test as the Swagger API documentation does not allow adding additional fields. You could try directly via cURL, but this seems overly complicated as it requires reconstructing the exact form structure for the POST.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 71.03%. Comparing base (a42dab6) to head (6bd9cdf).
Report is 7 commits behind head on development.

Additional details and impacted files

@@               Coverage Diff               @@
##           development    #2265      +/-   ##
===============================================
+ Coverage        71.01%   71.03%   +0.01%     
===============================================
  Files              335      335              
  Lines            28820    28832      +12     
  Branches          2527     2527              
===============================================
+ Hits             20466    20480      +14     
+ Misses            8213     8211       -2     
  Partials           141      141              

Files with missing lines	Coverage Δ
app/controllers/api/v1/study_files_controller.rb	86.05% <100.00%> (+0.36%)	⬆️

... and 2 files with indirect coverage changes

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