bids-validator config file example with ignoredFiles?

[d.jon.p...@gmail.com]

Hi Everyone,

   I'm trying to get bids-validator to ignore two main-level directories in my project called "download" and "documentation". I've tried all kinds of iterations of :

"ignoredFiles": [ "/download*" , "/documentation*" ]

"ignoredFiles": [ "*download*" , "*documentation*" ]

"ignoredFiles": [ "download*" , "documentation*" ]

"ignoredFiles": [ "download/*" ,  "documentation/*" ]

  in the config file, and the bids validator still tries to validate files in these directories. Is there some example of a config file that I can take a look at that has a non-empty ignoredFiles value that I can use as a template? I'm sure that there's something simple and dumb that I'm missing. I know that the validator is parsing my config file because it gives an error on a mis-formed config.

Thanks,

-Dan

[Chris Gorgolewski]

Hi,

I'm really happy people are using the config file! I'm looking into the default config and it seems to be using double asterix:

https://github.com/INCF/bids-validator/blob/7b31778c7e9398e51f883ee9de772bfe16560f30/tests/utils/config.spec.js#L17

Could you try this syntax?

Best,

Chris

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[d.jon.p...@gmail.com]

This syntax exactly gives me json parsing errors because of the lack of double-quotes. 

I tried downloading one of the example BIDS datasets and running the validator on that - that works as expected. 

Then I added a directory called "invalid_directory", with an "invalid_file" under that.

I can't get the validator to ignore the invalid directory with any combination of single/double quotes or single/double asterisks in the config file. I also tried double AND single quotes.

On Friday, April 7, 2017 at 1:32:49 PM UTC-7, Chris Gorgolewski wrote:

Hi,

I'm really happy people are using the config file! I'm looking into the default config and it seems to be using double asterix:

https://github.com/INCF/bids-validator/blob/7b31778c7e9398e51f883ee9de772bfe16560f30/tests/utils/config.spec.js#L17

Could you try this syntax?

Best,

Chris

On Fri, Apr 7, 2017 at 12:57 PM, <d.jon.p...@gmail.com> wrote:

Hi Everyone,

   I'm trying to get bids-validator to ignore two main-level directories in my project called "download" and "documentation". I've tried all kinds of iterations of :

"ignoredFiles": [ "/download*" , "/documentation*" ]

"ignoredFiles": [ "*download*" , "*documentation*" ]

"ignoredFiles": [ "download*" , "documentation*" ]

"ignoredFiles": [ "download/*" ,  "documentation/*" ]

  in the config file, and the bids validator still tries to validate files in these directories. Is there some example of a config file that I can take a look at that has a non-empty ignoredFiles value that I can use as a template? I'm sure that there's something simple and dumb that I'm missing. I know that the validator is parsing my config file because it gives an error on a mis-formed config.

Thanks,

-Dan

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[Chris Gorgolewski]

I do not seem to be able to replicate this bug. This is the simple example I used:

filo@MSI MINGW64 ~

$ bids-validator /d/data/ds000114_R2.0.1

        1: This file is not part of the BIDS specification, make sure it isn't included in the dataset by accident. Data derivatives (processed data) should be placed in /derivatives folder. (code: 1 - NOT_INCLUDED)

                /test

                        Evidence: test

                /test2

                        Evidence: test2

        2: Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)

                /sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz

        Summary:                 Available Tasks:        Available Modalities:

        212 Files, 3.66GB        finger_foot_lips        T1w

        10 - Subjects                                    bold

        1 - Session

filo@MSI MINGW64 ~

$ cat config.json

{

"ignoredFiles": ["/test*", "/another"]

}

filo@MSI MINGW64 ~

$ bids-validator /d/data/ds000114_R2.0.1 -c config.json

        1: Not all subjects/sessions/runs have the same scanning parameters. (code: 39 - INCONSISTENT_PARAMETERS)

                /sub-02/ses-test/anat/sub-02_ses-test_T1w.nii.gz

        Summary:                 Available Tasks:        Available Modalities:

        212 Files, 3.66GB        finger_foot_lips        T1w

        10 - Subjects                                    bold

        1 - Session

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[d.jon.p...@gmail.com]

Great, I was able to get it to work on the test data set, then apply it.

The trick was getting it to recognize all the files and sub-directories below it as well, so this pattern works:

"ignoredFiles": [ "/download/**" , "/documentation/**" ]

Thanks!!

-Dan