HED Validator integration into bids schema based validator.

[rwblair]

For #1639.

bids-validator/src/deps/hed-validator dependency was generated by running npm run build on latest commit for hed-javascript:
hed-standard/hed-javascript@bba927b

Two main functions located in bids-validator/src/validators/hed.ts are hedAccumulator and hedValidate

hedAccumulator is called once per context like other checks (filename validation, schema checks) in bids-validator/src/validators/bids.ts. It catches any events.tsv files and json files and builds up an object to be passed to the actual validator call.

Instead of recreating the old data structures that were passed into bids-validator/validators/events/hed.js I tried to get everything in shape a bit closer to where the outgoing calls were made, not sure if I got it quite right. The contexts have the proper sidecar data in them already so no need to mess with potentialSidecars.

hedValidate is called once, after the context walk is complete.

• copy over the hed-validator issue to bids-validator issue functions, modify to work with new issue objects.
• Add new issues to bids-validator/src/issues/list.ts as needed.
• Copy over detectHed function to skip calls when no HED data present.
• Pin dependency to actual release of hed-validator.
• Add tests

Currently am getting "ERROR: [HED_SCHEMA_LOAD_FAILED] The supplied schema specification is invalid. Specification: no sche..." when run on bids-examples/eeg_ds003645s_hed

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 85.80%. Comparing base (cfc4664) to head (a89d682).
Report is 63 commits behind head on master.

❗ Current head a89d682 differs from pull request most recent head d927cab. Consider uploading reports for the commit d927cab to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1648      +/-   ##
==========================================
- Coverage   88.57%   85.80%   -2.77%     
==========================================
  Files          39      134      +95     
  Lines        2372     6405    +4033     
  Branches      273     1529    +1256     
==========================================
+ Hits         2101     5496    +3395     
- Misses        265      802     +537     
- Partials        6      107     +101     

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[VisLab]

@rwblair --- should we be nervous that this is PR is still a draft? Is there anything that we need to prepare for? Thx! VisLab

[VisLab]

I know you have been swamped, but could you give us an update on this @nellh? Thx.

[nellh]

I think this is ready to merge. I ran through some test cases and was able to match the failures to the legacy validator. ds004395 runs out of memory with the default heap size but does pass increasing the size to 8GB. There could be some memory optimization to be done because this doesn't happen without the HED patches but that dataset is an exception, every other test case passed with the default heap size.

[VisLab]

@nellh ... thx for update. I am not sure what is going on with ds004395 -- I looked at it on openNeuro and it doesn't have any HED in it. The new HED validator works directly from the list of .tsv files and their associated sidecars as produced from the BIDS side. I wonder if we are somehow copying the data inadvertently before determining whether to even look at the files. @alexander Jones ***@***.***> let's look at this more closely. Version 3.13.3 should be released in the next day or so. It has some minor bug fixes.

…

On Thu, Jan 11, 2024 at 11:58 AM Nell Hardcastle ***@***.***> wrote: ***@***.**** approved this pull request. I think this is ready to merge. I ran through some test cases and was able to match the failures to the legacy validator. ds004395 runs out of memory with the default heap size but does pass increasing the size to 8GB. There could be some memory optimization to be done because this doesn't happen without the HED patches but that dataset is an exception, every other test case passed with the default heap size. — Reply to this email directly, view it on GitHub <#1648 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJCJOWF6OFLORSN5CB55JTYOAR4BAVCNFSM6AAAAAAWJW4A2SVHI2DSMVQWIX3LMV43YUDVNRWFEZLROVSXG5CSMV3GSZLXHMYTQMJWGE3TEMJVHE> . You are receiving this because you commented.Message ID: ***@***.***>

[rwblair]

Looks like the memory issue is coming from code I wrote, via the hedAccumulator in the bids-validator. Commenting out the call to the hed-validator and to the file accumulator allows ds004395 to finish validation. Commenting out just the call to the hed-validator but leaving the accumulator active causes it to run out of memory on default heap size.

I should finish profiling before running my mouth.

[happy5214]

I'm not sure what's going on with the Deno build. The lines in the errors do not appear in the version of that file in our code base, and we don't use Buffer objects directly (though some dependencies might).

[happy5214]

@rwblair Has there been any further progress on this?