[Bug]: convertTrials Tutorial uses Out of Date Syntax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

• [X] I agree to follow this project's Code of Conduct
• [X] 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.

---

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

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_NeurodataWithoutBorders_matnwb_issues_515-23issuecomment-2D1642669789&d=DwMCaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=9Gl8TqypehHm7acAeymJOA&m=uZYmThSPMyqB_VkqqTDcYyajN0KuMwuSIJAcQ3W7anfCFRXOzNpAL7U-ZjHlUydb&s=-8pEDRIWM8tXwrdrSeKpnsqXGqsMNTsSX2k27Udy5Hw&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ACQUAUTWVEIV5SMNJKNW3CTXRA3NRANCNFSM6AAAAAA2QJULUE&d=DwMCaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=9Gl8TqypehHm7acAeymJOA&m=uZYmThSPMyqB_VkqqTDcYyajN0KuMwuSIJAcQ3W7anfCFRXOzNpAL7U-ZjHlUydb&s=6OAtznhWx-qTpNBbwOiH1phuPAAMBjteOE9w4w5SL-U&e=. You are receiving this because you authored the thread.Message ID: @.***>

[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.