[WIP] add enhanced subject

[bendichter]

No description provided.

[bendichter]

@ln-vidrio

I'm playing with including more information in the Subject object, and I am running into an issue that I think may be a bug in matnwb. On this branch, when I run types.core.Subject I get:

Error using types.util.checkDtype (line 107)
Property `surgeries` must be a types.core.Surgeries.

Error in types.core.Subject/validate_surgeries (line 134)
        val = types.util.checkDtype('surgeries', 'types.core.Surgeries',
        val);

Error in types.core.Subject/set.surgeries (line 99)
        obj.surgeries = obj.validate_surgeries(val);

Error in types.core.Subject (line 64)
        obj.surgeries = p.Results.surgeries;

Surgeries is optional (quantity=: '?'), so I don't think I should be getting this error.

[bendichter]

fyi @oruebel

NeurodataWithoutBorders/nwb-schema#148

[lawrence-mbf]

119c4e1
This seems to fix it. Requires generating again.

[bendichter]

@ln-vidrio thanks! That works but now I think I found another quantity bug.

The following code:

subject = types.core.Subject('surgeries',types.core.Surgeries());

file = nwbfile('session_description', 'a test NWB File', ...
'identifier', 'blockname', ...
'session_start_time', datestr(now, 'yyyy-mm-dd HH:MM:SS'), ...
'file_create_date', datestr(now, 'yyyy-mm-dd HH:MM:SS'),...
'general_subject',subject);

nwbExport(file, 'test.nwb')

runs but should throw an error.

types.core.Surgery is defined as a group of types.core.Surgeries with quantity: +, which means Surgeries must contain "one or more" Surgery objects. This code creates Subject.surgeries.surgery with an empty set, which is a violation of the schema. I would prefer if this was caught in the constructor, but it could also be caught during nwbExport (it currently is not).

[lawrence-mbf]

8a91480 should be correct. I opted against checking on construction since these are also called when reading nwbfiles.

[bendichter]

Yeah that's reasonable

[yarikoptic]

is it really still WiP @bendichter or might want to be closed (or converted to draft at least)?