[BUG]: `PatternDataGrabber` does not respect the `"format"` parameter required for `BOLD_confounds` data type #158

Merged

synchon merged 8 commits from fix/confounds-format-pattern-dg into main

2022-12-22 13:47:19 +00:00

synchon commented

2022-12-21 18:02:10 +00:00

(Migrated from github.com)

Is there an existing issue for this?

I have searched the existing issues

Current Behavior

As of c6508a76, when loading the data for BOLD_confounds data type, the PatternDataGrabber (hence other dependent datagrabbers) does not add the "format" key to the Junifer Data object's BOLD_confounds data type. This causes the fMRIPrepConfoundRemover to raise error later on when removing the confounds.

Expected Behavior

The "format" key should be available to the BOLD_confounds data type so that fMRIPrepConfoundRemover can pre-process normally.

Steps To Reproduce

As of c6508a76, DataladAOMICPIOP1 > DefaultDataReader > fMRIPrepConfoundRemover > FunctionalConnectivityParcels.

Environment

junifer:
  version: 0.0.1
python:
  version: 3.11.0
  implementation: CPython
dependencies:
  click: 8.1.3
  numpy: 1.23.4
  datalad: 0.17.8
  pandas: 1.4.4
  nibabel: 4.0.2
  nilearn: 0.9.2
  sqlalchemy: 1.4.42
  yaml: '6.0'
system:
  platform: macOS-13.1-arm64-arm-64bit
environment:
  LC_CTYPE: UTF-8
  LC_TERMINAL: iTerm2
  LC_TERMINAL_VERSION: 3.4.18
  PATH: /Users/synchon/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/opt/homebrew/sbin:/opt/homebrew/bin:/Users/synchon/.local/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/synchon/opt/miniconda3/envs/junifer-dev/bin:/Users/synchon/opt/miniconda3/condabin:/Users/synchon/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/opt/homebrew/sbin:/opt/homebrew/bin

Relevant log output

No response

Anything else?

No response

### Is there an existing issue for this? - [X] I have searched the existing issues ### Current Behavior As of c6508a76, when loading the data for `BOLD_confounds` data type, the `PatternDataGrabber` (hence other dependent datagrabbers) does not add the `"format"` key to the `Junifer Data object`'s `BOLD_confounds` data type. This causes the `fMRIPrepConfoundRemover` to raise error later on when removing the confounds. ### Expected Behavior The `"format"` key should be available to the `BOLD_confounds` data type so that `fMRIPrepConfoundRemover` can pre-process normally. ### Steps To Reproduce As of c6508a76, `DataladAOMICPIOP1 > DefaultDataReader > fMRIPrepConfoundRemover > FunctionalConnectivityParcels`. ### Environment ```markdown junifer: version: 0.0.1 python: version: 3.11.0 implementation: CPython dependencies: click: 8.1.3 numpy: 1.23.4 datalad: 0.17.8 pandas: 1.4.4 nibabel: 4.0.2 nilearn: 0.9.2 sqlalchemy: 1.4.42 yaml: '6.0' system: platform: macOS-13.1-arm64-arm-64bit environment: LC_CTYPE: UTF-8 LC_TERMINAL: iTerm2 LC_TERMINAL_VERSION: 3.4.18 PATH: /Users/synchon/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/opt/homebrew/sbin:/opt/homebrew/bin:/Users/synchon/.local/bin:/usr/local/bin:/System/Cryptexes/App/usr/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Users/synchon/opt/miniconda3/envs/junifer-dev/bin:/Users/synchon/opt/miniconda3/condabin:/Users/synchon/.nix-profile/bin:/nix/var/nix/profiles/default/bin:/opt/homebrew/sbin:/opt/homebrew/bin ``` ### Relevant log output _No response_ ### Anything else? _No response_

github-actions[bot] commented

2022-12-21 18:06:53 +00:00

(Migrated from github.com)

PR Preview Action v1.2.0
Preview removed because the pull request was closed.
2022-12-22 13:51 UTC

[PR Preview Action](https://github.com/rossjrw/pr-preview-action) v1.2.0 :---: Preview removed because the pull request was closed. 2022-12-22 13:51 UTC

codecov[bot] commented

2022-12-22 12:57:07 +00:00

(Migrated from github.com)

Codecov Report

Merging #158 (905b2f9) into main (5ef5ca4) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main     #158      +/-   ##
==========================================
+ Coverage   93.45%   93.47%   +0.01%     
==========================================
  Files          71       71              
  Lines        2796     2804       +8     
  Branches      500      503       +3     
==========================================
+ Hits         2613     2621       +8     
  Misses        124      124              
  Partials       59       59

Flag	Coverage Δ
docs	`100.00% <ø> (ø)`
junifer	`93.46% <100.00%> (+0.01%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
junifer/datagrabber/aomic/id1000.py	`100.00% <ø> (ø)`
junifer/datagrabber/aomic/piop1.py	`100.00% <ø> (ø)`
junifer/datagrabber/aomic/piop2.py	`100.00% <ø> (ø)`
junifer/datagrabber/pattern.py	`97.93% <100.00%> (+0.18%)`	⬆️

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