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bids-standard / bids-validator

Validator for the Brain Imaging Data Structure
https://bids-standard.github.io/bids-validator/
MIT License
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range error on validation #1083

Open riddlet opened 4 years ago

riddlet commented 4 years ago

Here's the error message I receive when trying to upload to openneuro:

Internal error. SOME VALIDATION STEPS MAY NOT HAVE OCCURRED
REASON:
Maximum call stack size exceeded; please help the BIDS team and community by opening an issue at (https://github.com/bids-standard/bids-validator/issues) with the evidence here.

EVIDENCE:
RangeError: Maximum call stack size exceeded at Zt (https://openneuro.org/0-c51dd9db.bundle.worker.js:69:122016) at https://openneuro.org/0-c51dd9db.bundle.worker.js:69:132485
riddlet commented 4 years ago

Maybe related to #1063

hjmjohnson commented 4 years ago

I too have a similar error: Maximum call stack size exceeded; please help the BIDS team and community by opening an issue at (https://github.com/bids-standard/bids-validator/issues) with the evidence here.

This is for a bids dirctory with 1500+ subjects, and 4000+ scan session. The scan sessions have globally unique identifiers (to align with historical practices). We do NOT want to verify that all subjects have the same session names.

rwblair commented 4 years ago

@hjmjohnson If its convenient for you to test it here's a branch of the validator with a flag --ignoreSessionConsistency that should skip the code that verifies all subjects have the same session names: https://github.com/bids-standard/bids-validator/tree/skip_session_checks

Also If possible could you re-run the validator passing --heap-prof to node. Depending on how you have the validator installed might be something like node --heap-prof $(which bids-validator) /path/to/dataset for a global npm install, or

node --heap-prof /path/to/bids-validator/bids-validator/bin/bids-validator /path/to/dataset for an install from source code.

--heap-prof fill generate a file in the directory where the command was called from, file name will start with "Heap" and end with ".heapprofile". I can load that in chrome and take a look at whats used memory up until the crash. Not guaranteed to identify the max call stack problem because its concerned with frame size, but it may point to where the problem is. I haven't found an easy way to just profile the stack count.

@riddlet How many subjects and sessions is your dataset?

hjmjohnson commented 4 years ago

@rwblair I will test this out later tonight, or tomorrow morning. Thank you for your assistance.

hjmjohnson commented 4 years ago

THIS WORKED!!! Thanks you.  I am making progress towards validation again. Hans