Including a .json sidecar for events.tsv files causes a SQLAlchemy Tag conflict

We have an fMRIPrep user experiencing the following issue (more details here https://neurostars.org/t/naming-of-bids-events-tsv-files-seems-to-disrupt-fmriprep-1-5-0rc1/4771):

  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/cli/run.py", line 524, in build_workflow
    layout = BIDSLayout(str(bids_dir), validate=False)
  File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py", line 212, in __init__
    indexer.index_metadata()
  File "/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/index.py", line 338, in index_metadata
    self.session.commit()
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 1027, in commit
    self.transaction.commit()
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 494, in commit
    self._prepare_impl()
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 473, in _prepare_impl
    self.session.flush()
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2459, in flush
    self._flush(objects)
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2597, in _flush
    transaction.rollback(_capture_exception=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/langhelpers.py", line 68, in __exit__
    compat.reraise(exc_type, exc_value, exc_tb)
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 153, in reraise
    raise value
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/session.py", line 2557, in _flush
    flush_context.execute()
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 422, in execute
    rec.execute(self)
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/unitofwork.py", line 589, in execute
    uow,
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 213, in save_obj
    ) in _organize_states_for_save(base_mapper, states, uowtransaction):
  File "/usr/local/miniconda/lib/python3.7/site-packages/sqlalchemy/orm/persistence.py", line 408, in _organize_states_for_save
    % (state_str(state), instance_key, state_str(existing))
sqlalchemy.orm.exc.FlushError: New instance <Tag at 0x2b66784f7ba8> with identity key (<class 'bids.layout.models.Tag'>, ('/inp/sub-02/func/sub-02_task-Emotion_run-1_events.tsv', 'run'), None) conflicts with persistent instance <Tag at 0x2b66784c6630>

[tyarkoni]

@oesteban I fixed this in #468; we’ll cut a new release as soon as it’s merged so you can update fmriprep. Thanks for reporting!

[tyarkoni]

Per discussion in the linked NeuroStars thread, this seems like a bug induced by the inclusion of a .json file with the same filename (except for extension) as an events.tsv file.