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ENH: Allow passing a database_path to create a BIDSLayout #788

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merged 1 commit into from
Mar 11, 2023
Merged

ENH: Allow passing a database_path to create a BIDSLayout #788

merged 1 commit into from
Mar 11, 2023

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oesteban
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Resolves: #786.

@oesteban
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Works locally:

230311-00:34:47,353 nipype.workflow INFO:
         [Node] Executing "metadata" <niworkflows.interfaces.bids.ReadSidecarJSON>
230311-00:34:47,359 nipype.workflow INFO:
         [Node] Finished "metadata", elapsed time 0.005727s.

This node used to take ~50s on the main thread and ~80s on workers.

@oesteban oesteban requested a review from effigies March 10, 2023 23:44
@oesteban oesteban marked this pull request as ready for review March 10, 2023 23:44
@effigies
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Don't you need to hook it up to something?

@oesteban
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What do you mean?

From pybids, this doesn't require anything specific other than a release supporting database_path. From MRIQC/xPreps just to set the config.execution.bids_database_dir (or wherever name that config has) at workflow definition

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It'd be prudent to deprecate the layout member of the interface though - it can only be used with the linear plugging of nipype

oesteban added a commit to nipreps/mriqc that referenced this pull request Mar 11, 2023
@oesteban
ENH: Optimize metadata gathering reusing BIDSLayout db
a656f25 
There's no need to index the BIDS folder repeatedly with each of these
interfaces.

Requires: nipreps/niworkflows#788.
oesteban added a commit to nipreps/mriqc that referenced this pull request Mar 11, 2023
@oesteban
ENH: Optimize metadata gathering reusing BIDSLayout db
fe6eb69 
There's no need to index the BIDS folder repeatedly with each of these
interfaces.

Requires: nipreps/niworkflows#788.
@oesteban oesteban mentioned this pull request Mar 11, 2023
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Sorry, I thought this was on mriqc.

@effigies effigies merged commit c2b8e0f into master Mar 11, 2023
@effigies effigies deleted the fix/786-read-bids-meta branch March 11, 2023 17:30
oesteban added a commit to nipreps/mriqc that referenced this pull request Mar 12, 2023
@oesteban
ENH: Optimize metadata gathering reusing BIDSLayout db
2a5988e 
There's no need to index the BIDS folder repeatedly with each of these
interfaces.

Requires: nipreps/niworkflows#788.
effigies added a commit that referenced this pull request Mar 24, 2023
@effigies
Merge tag '1.7.7' into maint/1.7.x
c0279e0 
1.7.7 (March 24, 2023)

Patch release that optimizes BIDS metadata handling by reusing cached index databases.

* ENH: Allow passing a ``database_path`` to create a ``BIDSLayout`` (#788)
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Successfully merging this pull request may close these issues.

ReadSidecarJSON always indexes the layout (or breaks)
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@oesteban @effigies