[Bug]: convertTrials Tutorial uses Out of Date Syntax

[jc192015]

What happened?

When running matnwb(2.6.0), I got an error message. I am wondering that is due to a bug with matnwb. Or Could you please let me know how to fix it?
Thank you in advance for your time and help.

Steps to Reproduce

nwb = NwbFile();
nwb.units = types.core.Units('colnames',...
    {'spike_times', 'trials', 'waveforms'},...
    'description', 'Analysed Spike Events');

Error Message

Error using assert
Value of type `types.core.ElementIdentifiers` cannot be converted to type `types.hdmf_common.ElementIdentifiers`.

Error in types.util.correctType (line 60)
        assert(isa(val, type), ...

Error in types.util.checkDtype (line 96)
correctedValue = types.util.correctType(val, type);

Error in types.hdmf_common.DynamicTable/validate_id (line 90)
        val = types.util.checkDtype('id', 'types.hdmf_common.ElementIdentifiers', val);

Error in types.hdmf_common.DynamicTable/set.id (line 46)
        obj.id = obj.validate_id(val);

Error in types.util.dynamictable.checkConfig (line 58)
            DynamicTable.id = types.core.ElementIdentifiers('data', idData);

Error in types.core.Units (line 60)
            types.util.dynamictable.checkConfig(obj);

Operating System

Windows

Matlab Version

Matlab R2023a

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you ensured this bug was not already reported?

[bendichter]

I cannot reproduce. Can you please make sure you MatNWB is up-to-date? If you used git clone you might be able to simply call !git pull inside MATLAB while in the matnwb repo

[bendichter]

If that doesn't work, you can delete MatNWB and download it again from here.

[jc192015]

Hi there, After deleting Matnwb and downloading it again, the mentioned problem has been resolved. Thank you. But I got another error message when I tried to run the script "MatNWB\tutorials\convertTrials.m." code at line 351: trials_epoch = types.core.TimeIntervals(... 'start_time', types.hdmf_common.VectorData('data', data.trialStartTimes,... 'description', 'Start time of epoch, in seconds.'),... 'colnames', [data.trialTypeStr; data.trialPropertiesHash.keyNames .';... {'start_time'; 'stop_time'; 'acquisition'; 'timeseries'}],... 'description', 'trial data and properties', ... 'id', types.hdmf_common.ElementIdentifiers('data', data.trialIds),... 'timeseries', types.hdmf_common.VectorData('description', 'Index into timeseries Data'),... 'timeseries_index', types.hdmf_common.VectorIndex(... 'description', 'Index into Timeseries VectorData',... 'target', types.untyped.ObjectView('/intervals/trials/timeseries'))); Error Message: Error using assert Value of type `types.hdmf_common.VectorData` cannot be converted to type `types.core.TimeSeriesReferenceVectorData`. Error in types.util.correctType (line 60) assert(isa(val, type), ... Error in types.util.checkDtype (line 96) correctedValue = types.util.correctType(val, type); Error in types.core.TimeIntervals/validate_timeseries (line 82) val = types.util.checkDtype('timeseries', 'types.core.TimeSeriesReferenceVectorData', val); Error in types.core.TimeIntervals/set.timeseries (line 62) obj.timeseries = obj.validate_timeseries(val); Error in types.core.TimeIntervals (line 39) obj.timeseries = p.Results.timeseries; Error in convertTrials4jia (line 407) trials_epoch = types.core.TimeIntervals(...

…

________________________________ From: Ben Dichter ***@***.***> Sent: Wednesday, July 19, 2023 2:54 PM To: NeurodataWithoutBorders/matnwb ***@***.***> Cc: Chen, Jian ***@***.***>; Author ***@***.***> Subject: Re: [NeurodataWithoutBorders/matnwb] [Bug]: types.core.Units (Issue #515) ***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.

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[bendichter]

yeah, this looks like outdated code

[jc192015]

So do you have an updated convertTrials.m?

[lawrence-mbf]

The code was probably added before validation changes to DynamicTable objects like TimeIntervals. There's no stop_time data for instance so the code needs to be reworked to include that.