[Loris-dev] BIDS Error

[Morales Pinzon, Alfredo]

Dear LorisDev team.

I am running the BIDS uploading functionality of LORIS (from this PR suggested by Cecile: https://github.com/aces/Loris-MRI/pull/558/files ) but I’m getting the following error (see all the output below):

===
ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n
===

After some debugging I saw that the array subjects in the following line is empty:
https://github.com/laemtl/Loris-MRI/blob/3742522fa46b0ee2b9e384e30650a0c1f425c7af/python/lib/bidsreader.py#L134

I thought the issue was that we have symbolic links in our folder structure but after setting a testing example I am getting the same exact error.

Any ideas why this is happening? The error does not help much. I’m happy to share the testing case, with all the BIDS structure to a LORIS developer, if this is helpful.

Looking forward to hearing from you.

Best.
Alfredo.

===
/PROJECT/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.6/site-packages/bids/layout/validation.py:46: UserWarning: The ability to pass arguments to BIDSLayout that control indexing is likely to be removed in future; possibly as early as PyBIDS 0.14. This includes the `config_filename`, `ignore`, `force_index`, and `index_metadata` arguments. The recommended usage pattern is to initialize a new BIDSLayoutIndexer with these arguments, and pass it to the BIDSLayout via the `indexer` argument.
  warnings.warn("The ability to pass arguments to BIDSLayout that control "

Connecting to:
        database: DATABASE
        username: USERDATABASE
        hostname: 111.222.333.444
        port    : 3306


Executing query:
        SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);

With arguments:
        ('default_bids_vl',)


Executing query:
        SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);

With arguments:
        ('dataDirBasepath',)

Loading the BIDS dataset with BIDS layout library...

        => BIDS dataset loaded with BIDS layout

Grepping candidates from the BIDS layout...
Validating the list of participants...

ERROR: Participant ID mismatch between participants.tsv and raw data found in the BIDS directory/n
===

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