Database redesign to add upstream recording schema

[Alvalunasan]

First draft of recording schema (schema for automatic process of acquisitions. Also serve as "Parent" for ephys/imaging)

[kabilar]

Suggested change

	['ephys', '', '/braininit/Data/eletrophysiology'],
	['imaging', '', '/braininit/Data/eletrophysiology'],
	['video_acquisition', '', '/braininit/Data/video_acquisition']
	['ephys', 'Neuropixels', '/mnt/cup/braininit/Data/electrophysiology'],
	['imaging', 'Two-photon calcium imaging', '/mnt/cup/braininit/Data/imaging'],
	['video_acquisition', '', '/mnt/cup/braininit/Data/video_acquisition']

[kabilar]

I prepended /mnt/cup. Is this required?

[Alvalunasan]

well I was thinking just /braininit is ok to be a reference for the actual path.
/braininit is /mnt/cup/braininit in spock, scotty
/braininit is /Volumes/braininit on Mac
/braininit is \cup.pni.princeton.edu\braininit\ on Windows

[kabilar]

Thanks for clarifying. Sounds great.

[kabilar]

Suggested change

	root_direcory: varchar(255) # root directory where that modality is stored (e.g. ephys = /braininit/Data/eletrophysiology)
	root_directory: varchar(255) # root directory where that modality is stored

Since we have the contents property, perhaps we don't need the example.

[Alvalunasan]

Agreed !

[kabilar]

This would not effect the functionality of this module, but perhaps the Recording table should be placed directly after the RecordingModality table?

[Alvalunasan]

All right,
My "logic" was to put all lookup tables first.
But your proposal makes a lot of sense

[kabilar]

Thanks! Either way works. I am just used to ordering the tables in approximately the same order as how the data flows.

[kabilar]

This is a difficult task to implement. Perhaps we could use Part tables.

class Recording(dj.Manual):
    definition = """
        recording_id: INT(11) AUTO_INCREMENT
        ---
        -> RecordingModality                         
        recording_directory: varchar(255)
        """
    class BehaviorSession(dj.Part):
        definition = """
        -> master
        ---
        -> acquisition.Session.proj(recording_datetime='session_start_time')
        """
    class RecordingSession(dj.Part):
        definition = """
        -> master
        ---
        -> subject.Subject
        recording_datetime: datetime
        """

[Alvalunasan]

I think this design is indeed cleaner

[kabilar]

Great!

[kabilar]

Perhaps we do not need to define a separate function (get_content_list_from_status_dict)?

[Alvalunasan]

I will do it without a separate function

[kabilar]

Should we set Session to EphysRecording or EphysSorting? Not sure what the correct answer is.

[kabilar]

Hi @Alvalunasan, within the TestAutomaticPipeline.ipynb notebook there is a reference to the acquisition.AcquisitionSessionsTestAutoPipeline table but I am not sure where this is declared. Thanks.

[kabilar]

Great work @Alvalunasan! Very thorough design. Looking forward to seeing it in action.