NWB file lacks required metadata for upload #169
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Hi @nsdesai, thanks for the report. Is the error being returned from the website or the CLI? Yes, please send us a file. Google drive, dropbox, etc. would be fine. Hi @h-mayorquin, could you please look into this issue once we receive the file? Thanks. |
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Thanks for the prompt reply!
I was trying to use NWB Guide to upload, even though I didn't use it to
convert.
An example NWB file can be found here:
https://drive.google.com/file/d/1LQuCNM9lQ4rtnIBGKsuDdiKI5NMF-Vjs/view?usp=drive_link
Thanks for your help.
Niraj
…On Wed, Dec 11, 2024 at 1:11 PM Kabilar Gunalan ***@***.***> wrote:
Hi @nsdesai <https://github.com/nsdesai>, thanks for the report. Is the
error being returned from the website or the CLI? Yes, please send us a
file. Google drive, dropbox, etc. would be fine.
Hi @h-mayorquin <https://github.com/h-mayorquin>, could you please look
into this issue once we receive the file? Thanks.
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Hi, @nsdesai You need to give me access to the file or make it public (I requested it already). Also, if you can copy-paste the error that you are getting that would be useful for future users and for us to solve this quickly. |
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Sorry about that. You should have access now.
This is screenshot of the NWB Guide window containing the error message.
Niraj
[image: image.png]
…On Wed, Dec 11, 2024 at 1:47 PM Heberto Mayorquin ***@***.***> wrote:
Hi, @nsdesai <https://github.com/nsdesai>
You need to give me access to the file or make it public (I requested it
already).
Also, if you can copy-paste the error that you are getting that would be
useful for future users and for us to solve this quickly.
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You need to enter the github plataform to attach images I think. Right now, it is not correctly displayed. |
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Does this display correctly? |
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Interesting, so I try to open your file and the problem is that your This is marked as an optional argument in the schema: https://nwb-schema.readthedocs.io/en/latest/format.html#sec-currentclampseries-src So in theory, your file is correct but is not opening. This seems like a PyNWB but maybe they were changes recently. I will check with the pynwb team. Error. |
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The original data were acquired using a custom MATLAB script and so I used
matNWB to convert (not pyNWB).
I thought I included everything from their example, but maybe I missed
"gain".
Let me try converting again and seeing what happens.
Niraj
…On Wed, Dec 11, 2024 at 2:05 PM Heberto Mayorquin ***@***.***> wrote:
Interesting, so I try to open your file and the problem is that your
CurrentClampSeries does not have a gain (Error at the bottom)
This is marked as an optional argument in the schema:
https://nwb-schema.readthedocs.io/en/latest/format.html#sec-currentclampseries-src
So in theory, your file is correct but is not opening. This seems like a
PyNWB but maybe they were changes recently. I will check with the pynwb
team.
Error.
ConstructError: (root/acquisition/constant_response_001 GroupBuilder {'attributes': {'comments': 'no comments', 'description': 'no description', 'namespace': 'core', 'neurodata_type': 'CurrentClampSeries', 'object_id': 'a7bf8a22-ef0f-4b22-ae45-d5b1f03f3832', 'stimulus_description': 'constant_injection_001', 'sweep_number': 1}, 'groups': {}, 'datasets': {'bias_current': root/acquisition/constant_response_001/bias_current DatasetBuilder {'attributes': {}, 'data': 1e-11}, 'bridge_balance': root/acquisition/constant_response_001/bridge_balance DatasetBuilder {'attributes': {}, 'data': 20000000.0}, 'capacitance_compensation': root/acquisition/constant_response_001/capacitance_compensation DatasetBuilder {'attributes': {}, 'data': 1e-12}, 'data': root/acquisition/constant_response_001/data DatasetBuilder {'attributes': {'conversion': 1.0, 'offset': 0.0, 'resolution': -1.0, 'unit': 'volts'}, 'data': <HDF5 dataset \"data\": shape (50000,), type \"<f8\">}, 'timestamps': root/acquisition/constant_response_001/timestamps DatasetBuilder {'attributes': {'interval': 1, 'unit': 'seconds'}, 'data': <HDF5 dataset \"timestamps\": shape (15,), type \"<f8\">}}, 'links': {'electrode': root/acquisition/constant_response_001/electrode LinkBuilder {'builder': root/general/intracellular_ephys/elec0 GroupBuilder {'attributes': {'namespace': 'core', 'neurodata_type': 'IntracellularElectrode', 'object_id': 'c05e8a6f-ee55-4eed-81cf-ebd1abe9b090'}, 'groups': {}, 'datasets': {'cell_id': root/general/intracellular_ephys/elec0/cell_id DatasetBuilder {'attributes': {}, 'data': 'NBM/SI neuron'}, 'description': root/general/intracellular_ephys/elec0/description DatasetBuilder {'attributes': {}, 'data': 'patch clamp electrode (~5 MOhms)'}}, 'links': {'device': root/general/intracellular_ephys/elec0/device LinkBuilder {'builder': root/general/devices/National Instruments PCIe-6353 GroupBuilder {'attributes': {'namespace': 'core', 'neurodata_type': 'Device', 'object_id': '6eb5a13a-dc5d-4a48-ad16-fc252a98188a'}, 'groups': {}, 'datasets': {}, 'links': {}}}}}}}}, \"Could not construct CurrentClampSeries object due to: CurrentClampSeries.__init__: missing argument 'gain'\")"
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OK, so this was fixed recently: NeurodataWithoutBorders/pynwb#1975 But then I get another error that your timestamps do not have a time zone. Can you add that as well? This is the error that I get with the latest version of the inspector: |
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I added a time zone. Here is a link: https://drive.google.com/file/d/1xz5h8b_jJ1RNN4vpTlL3koFnl-eOFOZT/view?usp=sharing |
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I should add that I've been using this as a template: https://matnwb.readthedocs.io/en/latest/pages/tutorials/icephys.html So to add a time zone, I simply added a "Time Zone" argument to session_start_time and specified "local." |
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Hi, so this file can be opened with pynwb (which is progress) but you still have many issues to solve with the nwbinspector: The issues marked as critical should be solved before the file can be uploaded. Have you tried putting this file in the guide, I think ti should show you some similar output right? |
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It might take me a while to address these errors. I will let you know as soon as I do. thanks for your help |
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Inching ever closer ... I fixed the errors except for some of the ones that are marked "Can safely be ignored." I can deal with those later. Now I can see the data using the Explore option in Guide. Everything seems to be there. But using the Upload option, I now get a new error:
This is a link to a revised file: https://drive.google.com/file/d/1lQCXaalvLX2SuXZetn6vRc8Hy09nUGlD/view?usp=sharing |
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This is a guide problem. I am not very familiar with it, any ideas @bendichter ? |
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The |
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In the meantime, a quick workaround @nsdesai is to remove the "/" from your session IDs. |
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Thanks, I will try that. |
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Thank you! That worked. Thanks also, @h-mayorquin , for your help this afternoon. I should be able to upload all our data now (fingers crossed). -- Niraj |
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We should create a check for this in the inspector |
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I am trying to upload NWB files to the DANDI (development) server. I keep getting an error saying that all required metadata are not included, but there is no indication of what is missing.
The original data were acquired in MATLAB and I converted them to NWB using this: https://neurodatawithoutborders.github.io/matnwb/
I can send an example NWB file if that would be helpful. (This interface won't let me attach NWB files.)
thanks,
Niraj
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