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Workaround/bids validator #37
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…ds-validation, and some flake8 conform
Is this happening with most recent version of the validator? Have you tried updating node and/or using this branch https://github.com/INCF/bids-validator/pull/346? |
sorry, I should have included versions, it's happening with the versions installed in the docker container, and with version bids-validator: EDIT: realized from the comments in INCF/bids-validator#346, that I didn't exclude dot files and dot directories, which may be the problem since I'm using datalad with this dataset. |
Might be also worth updating node.js |
I repeated the process with node:
bids-validator still appears to be traversing the sourcedata directory despite me trying to tell it not to.
or this:
So then my next step should be using the new branch? or am I not specifying the config file correctly? Should we move this conversation to the bids-validator github? |
That branch should help with avoiding traversing unwanted files. Please
give it a try.
Best,
Chris
…On Wed, Nov 1, 2017 at 10:15 PM, James Kent ***@***.***> wrote:
I repeated the process with node: v6.11.5, but got a similar result:
bids-validator --config bids-validator.config ~/mnt/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS
<--- Last few GCs --->
384744 ms: Mark-sweep 1377.8 (1437.8) -> 1377.8 (1437.8) MB, 1287.2 / 0.0 ms [allocation failure] [GC in old space requested].
385984 ms: Mark-sweep 1377.8 (1437.8) -> 1377.8 (1437.8) MB, 1240.0 / 0.0 ms [allocation failure] [GC in old space requested].
387265 ms: Mark-sweep 1377.8 (1437.8) -> 1377.8 (1417.8) MB, 1280.3 / 0.0 ms [last resort gc].
388510 ms: Mark-sweep 1377.8 (1417.8) -> 1377.8 (1417.8) MB, 1245.1 / 0.0 ms [last resort gc].
<--- JS stacktrace --->
==== JS stack trace =========================================
Security context: 0x2623298cf781 <JS Object>
2: getFiles [/usr/local/lib/node_modules/bids-validator/utils/files.js:102] [pc=0x2673977873f] (this=0x8a8b9d8db29 <JS Global Object>,dir=0x35537f496249 <String[168]: /home/jdkent/mnt/vosslabhpc/Projects/Bike_ATrain/Imaging/BIDS/sourcedata/RAW_BIDS/sub-GEP385/ses-activepost/func/sub-GEP385_ses-activepost_task-spatialnback_run-01_bold>,files_=0x1b7c942e5369 <JS Array[4861460]>)
3: getFil...
FATAL ERROR: CALL_AND_RETRY_LAST Allocation failed - JavaScript heap out of memory
1: node::Abort() [bids-validator]
2: 0x109f13c [bids-validator]
3: v8::Utils::ReportApiFailure(char const*, char const*) [bids-validator]
4: v8::internal::V8::FatalProcessOutOfMemory(char const*, bool) [bids-validator]
5: v8::internal::Factory::NewFixedArray(int, v8::internal::PretenureFlag) [bids-validator]
6: v8::internal::Factory::NewScopeInfo(int) [bids-validator]
7: v8::internal::ScopeInfo::Create(v8::internal::Isolate*, v8::internal::Zone*, v8::internal::Scope*) [bids-validator]
8: 0xb4f7b3 [bids-validator]
9: 0xb56e46 [bids-validator]
10: v8::internal::Compiler::Compile(v8::internal::Handle<v8::internal::JSFunction>, v8::internal::Compiler::ClearExceptionFlag) [bids-validator]
11: v8::internal::Runtime_CompileLazy(int, v8::internal::Object**, v8::internal::Isolate*) [bids-validator]
12: 0x267394092a7
Aborted (core dumped)
bids-validator still appears to be traversing the sourcedata directory
despite me trying to tell it not to.
I've tried this with the config file either containing this:
{
"ignoredFiles": ["derivatives/**", "sourcedata/**"]
}
or this:
{
"ignoredFiles": ["/derivatives/**", "/sourcedata/**"]
}
So then my next step should be using the new branch? or am I not
specifying the config file correctly?
Should we move this conversation to the bids-validator github?
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installed the branch like so: |
Thanks! |
Hi,
Another member of my lab was interested in using this utility, but we kept on getting stuck with the bids-validator getting an error like this
I played with the
--config
option for bids-validator with no avail, and for the interest of time, I provided this workaround to make the container run. I think the error is related tobids-validator
trying to read into sourcedata and derivatives, but I couldn't get the--config
option to work for me.P.S.
I also did some flake8 conforming with the code so that is more in line with PEP 8 standards.
best,
James