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[REF] Consistently reference object keys in rules #1203

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[REF] Consistently reference object keys in rules #1203

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e2f0b24
Move test_rules.
tsalo Aug 16, 2022
b4055e8
Replace extension values with extension keys.
tsalo Aug 16, 2022
9958fec
Replace suffix values with suffix keys.
tsalo Aug 16, 2022
b3c55dc
Move rules/sidecars/entities.yaml.
tsalo Aug 16, 2022
6d06174
Fix column names in rules.
tsalo Aug 16, 2022
25a8e2e
Finish replacing extensions.
tsalo Aug 16, 2022
9765900
Merge branch 'master' into fix-test
tsalo Aug 16, 2022
586bf94
Still need to skip derivatives folder.
tsalo Aug 16, 2022
4288f24
Skip the derivatives folder.
tsalo Aug 16, 2022
c8c9c0c
Keep fixing.
tsalo Aug 16, 2022
0b99c32
Merge remote-tracking branch 'upstream/master' into fix-test
tsalo Aug 16, 2022
1e03f4a
Update tools/schemacode/bidsschematools/tests/test_rules.py
tsalo Aug 16, 2022
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54 changes: 27 additions & 27 deletions src/schema/rules/datatypes/anat.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,9 @@ nonparametric:
- FLASH # deprecated
- PD # deprecated
extensions:
- .nii.gz
- .nii
- .json
- niigz
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can we maybe not do this? =^.^=

see #1203 (comment)

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I mean, I still think we should, but it's up to the maintainers/steering group now.

- nii
- json
datatypes:
- anat
entities:
Expand Down Expand Up @@ -48,9 +48,9 @@ parametric:
- S0map
- M0map
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- anat
entities:
Expand All @@ -65,9 +65,9 @@ defacemask:
suffixes:
- defacemask
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- anat
entities:
Expand All @@ -84,9 +84,9 @@ multiecho:
- MESE
- MEGRE
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- anat
entities:
Expand All @@ -103,9 +103,9 @@ multiflip:
suffixes:
- VFA
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- anat
entities:
Expand All @@ -123,9 +123,9 @@ multiinversion:
suffixes:
- IRT1
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- anat
entities:
Expand All @@ -142,9 +142,9 @@ mp2rage:
suffixes:
- MP2RAGE
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- anat
entities:
Expand All @@ -164,9 +164,9 @@ vfamt:
- MPM
- MTS
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- anat
entities:
Expand All @@ -185,9 +185,9 @@ mtr:
suffixes:
- MTR
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- anat
entities:
Expand Down
8 changes: 4 additions & 4 deletions src/schema/rules/datatypes/beh.yaml
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Expand Up @@ -4,8 +4,8 @@ timeseries:
- stim
- physio
extensions:
- .tsv.gz
- .json
- tsvgz
- json
datatypes:
- beh
entities:
Expand All @@ -22,8 +22,8 @@ noncontinuous:
- events
- beh
extensions:
- .tsv
- .json
- tsv
- json
datatypes:
- beh
entities:
Expand Down
32 changes: 16 additions & 16 deletions src/schema/rules/datatypes/derivatives/common_imaging_derivatives.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ anat_parametric_mask:
suffixes:
- mask
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.anat.parametric.entities
space: OPTIONAL
Expand All @@ -54,7 +54,7 @@ anat_nonparametric_mask:
suffixes:
- mask
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.anat.nonparametric.entities
space: OPTIONAL
Expand All @@ -68,7 +68,7 @@ dwi_mask:
suffixes:
- mask
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.dwi.dwi.entities
space: OPTIONAL
Expand All @@ -82,7 +82,7 @@ func_mask:
suffixes:
- mask
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.func.func.entities
space: OPTIONAL
Expand All @@ -96,7 +96,7 @@ anat_parametric_discrete_segmentation:
suffixes:
- dseg
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.anat.parametric.entities
space: OPTIONAL
Expand All @@ -108,7 +108,7 @@ anat_nonparametric_discrete_segmentation:
suffixes:
- dseg
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.anat.nonparametric.entities
space: OPTIONAL
Expand All @@ -120,7 +120,7 @@ func_discrete_segmentation:
suffixes:
- dseg
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.func.func.entities
space: OPTIONAL
Expand All @@ -132,7 +132,7 @@ dwi_discrete_segmentation:
suffixes:
- dseg
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.dwi.dwi.entities
space: OPTIONAL
Expand All @@ -144,7 +144,7 @@ anat_parametric_probabilistic_segmentation:
suffixes:
- probseg
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.anat.parametric.entities
space: OPTIONAL
Expand All @@ -157,7 +157,7 @@ anat_nonparametric_probabilistic_segmentation:
suffixes:
- probseg
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.anat.nonparametric.entities
space: OPTIONAL
Expand All @@ -170,7 +170,7 @@ func_probabilistic_segmentation:
suffixes:
- probseg
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.func.func.entities
space: OPTIONAL
Expand All @@ -183,7 +183,7 @@ dwi_probabilistic_segmentation:
suffixes:
- probseg
extensions:
- .nii.gz
- niigz
entities:
$ref: rules.datatypes.dwi.dwi.entities
space: OPTIONAL
Expand All @@ -196,8 +196,8 @@ anat_parametic_discrete_surface:
suffixes:
- dseg
extensions:
- .label.gii
- .dlabel.nii
- labelgii
- dlabelnii
entities:
$ref: rules.datatypes.anat.parametric.entities
hemisphere: OPTIONAL
Expand All @@ -210,8 +210,8 @@ anat_nonparametic_discrete_surface:
suffixes:
- dseg
extensions:
- .label.gii
- .dlabel.nii
- labelgii
- dlabelnii
entities:
$ref: rules.datatypes.anat.nonparametric.entities
hemisphere: OPTIONAL
Expand Down
20 changes: 10 additions & 10 deletions src/schema/rules/datatypes/dwi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@ dwi:
suffixes:
- dwi
extensions:
- .nii.gz
- .nii
- .json
- .bvec
- .bval
- niigz
- nii
- json
- bvec
- bval
datatypes:
- dwi
entities:
Expand All @@ -23,9 +23,9 @@ sbref:
suffixes:
- sbref
extensions:
- .nii.gz
- .nii
- .json
- niigz
- nii
- json
datatypes:
- dwi
entities:
Expand All @@ -42,8 +42,8 @@ timeseries:
- physio
- stim
extensions:
- .tsv.gz
- .json
- tsvgz
- json
datatypes:
- dwi
entities:
Expand Down
40 changes: 20 additions & 20 deletions src/schema/rules/datatypes/eeg.yaml
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Expand Up @@ -3,14 +3,14 @@ eeg:
suffixes:
- eeg
extensions:
- .json
- .edf
- .vhdr
- .vmrk
- .eeg
- .set
- .fdt
- .bdf
- json
- edf
- vhdr
- vmrk
- eeg
- set
- fdt
- bdf
datatypes:
- eeg
entities:
Expand All @@ -24,8 +24,8 @@ channels:
suffixes:
- channels
extensions:
- .json
- .tsv
- json
- tsv
datatypes:
- eeg
entities:
Expand All @@ -39,7 +39,7 @@ coordsystem:
suffixes:
- coordsystem
extensions:
- .json
- json
datatypes:
- eeg
entities:
Expand All @@ -52,8 +52,8 @@ electrodes:
suffixes:
- electrodes
extensions:
- .json
- .tsv
- json
- tsv
datatypes:
- eeg
entities:
Expand All @@ -66,8 +66,8 @@ events:
suffixes:
- events
extensions:
- .json
- .tsv
- json
- tsv
datatypes:
- eeg
entities:
Expand All @@ -81,9 +81,9 @@ photo:
suffixes:
- photo
extensions:
- .jpg
- .png
- .tif
- jpg
- png
- tif
datatypes:
- eeg
entities:
Expand All @@ -96,8 +96,8 @@ timeseries:
- physio
- stim
extensions:
- .tsv.gz
- .json
- tsvgz
- json
datatypes:
- eeg
entities:
Expand Down
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