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[SCHEMA] Define YAML tables for PET common metadata fields and radiopharmaceutical data v2 #1027

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[SCHEMA] Define YAML tables for PET common metadata fields and radiopharmaceutical data v2 #1027

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bendhouseart
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References #1014 and #1002

Aped from tsalo's #1017, but just PET fields.

Changes proposed:

Add YAML definitions for PET page's common metadata sections.

Fixes ugly history view from previous (cancelled) PR #1026

bendhouseart and others added 2 commits March 14, 2022 15:49
@bendhouseart @tsalo
Update src/schema/rules/sidecars.yml
6e40318 
change addendum -> level_addendum per commit suggestion.

Co-authored-by: Taylor Salo <[email protected]>
@bendhouseart
fixed n - 1 yaml errors, 1 remaining
4a177c0
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bendhouseart commented Mar 14, 2022 •
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Hmm, yamllint is giving me fits:

Running: yamllint -f standard src/schema/ -c .yamllint.yml yields:

250:13 error syntax error: expected <block end>, but found '<scalar>' (syntax)

With respect to - "PET" in dataset.modalities:

PETMRISequenceSpecifics:
    selectors:
    - modality == "MRI"
    - "PET" in dataset.modalities
    fields:
        NonLinearGradientCorrection: REQUIRED

Thoughts?

@bendhouseart bendhouseart requested a review from tsalo March 17, 2022 19:14
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tsalo commented Mar 17, 2022

I saw that here as well: https://github.com/bids-standard/bids-specification/pull/1017/files#r814328092

I ended up dropping the quotes but @effigies proposed (https://github.com/bids-standard/bids-specification/pull/1017/files#r824140193) dataset.modalities contains "PET"

@bendhouseart
Add backticks
928eea2 
Added backticks
@tsalo tsalo mentioned this pull request Mar 17, 2022
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Switched PET in to -> dataset.modalities contains "PET" per your suggestion. Went right over my head if you mentioned this yesterday.

@tsalo tsalo added the schema Issues related to the YAML schema representation of the specification. Patch version release. label Mar 30, 2022
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tsalo commented Apr 7, 2022

@bendhouseart can you move your proposed changes into a new src/schema/rules/sidecars/pet.yaml file to deal with the conflict?

@bendhouseart bendhouseart self-assigned this Apr 7, 2022
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@tsalo done per your request.

effigies added a commit to effigies/bids-specification that referenced this pull request Apr 7, 2022
@effigies
Merge bids-standardgh-1027
6e0c348 
Squashed commit of the following:

commit ee5ff05
Author: anthony galassi <[email protected]>
Date:   Thu Apr 7 15:48:02 2022 -0400

    moved pet stuff to src/schema/rules/sidecars/pet.yaml

commit d00e683
Author: Anthony Galassi <[email protected]>
Date:   Fri Mar 18 09:40:55 2022 -0400

    Update src/schema/rules/sidecars.yml

commit 928eea2
Author: Anthony Galassi <[email protected]>
Date:   Thu Mar 17 15:42:10 2022 -0400

    Add backticks

    Added backticks

commit 50b0ae0
Author: anthony galassi <[email protected]>
Date:   Tue Mar 15 12:34:42 2022 -0400

    fixed level addendum's, removed quotes for selector in PETMRISequenceSpecifics to make linter happy

commit 4a177c0
Author: anthony galassi <[email protected]>
Date:   Mon Mar 14 15:59:54 2022 -0400

    fixed n - 1 yaml errors, 1 remaining

commit 6e40318
Author: Anthony Galassi <[email protected]>
Date:   Mon Mar 14 15:49:29 2022 -0400

    Update src/schema/rules/sidecars.yml

    change addendum -> level_addendum per commit suggestion.

    Co-authored-by: Taylor Salo <[email protected]>

commit 41bc816
Author: anthony galassi <[email protected]>
Date:   Thu Mar 10 15:49:58 2022 -0500

    fixed yaml formatting
effigies added a commit that referenced this pull request Apr 7, 2022
@effigies
Merge gh-1027
6aa9855 
Squashed commit of the following:

commit ee5ff05
Author: anthony galassi <[email protected]>
Date:   Thu Apr 7 15:48:02 2022 -0400

    moved pet stuff to src/schema/rules/sidecars/pet.yaml

commit d00e683
Author: Anthony Galassi <[email protected]>
Date:   Fri Mar 18 09:40:55 2022 -0400

    Update src/schema/rules/sidecars.yml

commit 928eea2
Author: Anthony Galassi <[email protected]>
Date:   Thu Mar 17 15:42:10 2022 -0400

    Add backticks

    Added backticks

commit 50b0ae0
Author: anthony galassi <[email protected]>
Date:   Tue Mar 15 12:34:42 2022 -0400

    fixed level addendum's, removed quotes for selector in PETMRISequenceSpecifics to make linter happy

commit 4a177c0
Author: anthony galassi <[email protected]>
Date:   Mon Mar 14 15:59:54 2022 -0400

    fixed n - 1 yaml errors, 1 remaining

commit 6e40318
Author: Anthony Galassi <[email protected]>
Date:   Mon Mar 14 15:49:29 2022 -0400

    Update src/schema/rules/sidecars.yml

    change addendum -> level_addendum per commit suggestion.

    Co-authored-by: Taylor Salo <[email protected]>

commit a4fb377
Merge: 41bc816 c5f89c6
Author: Anthony Galassi <[email protected]>
Date:   Mon Mar 14 15:17:00 2022 -0400

    Merge branch 'schema/sidecar_validation' into bendhouseart-tables

commit 41bc816
Author: anthony galassi <[email protected]>
Date:   Thu Mar 10 15:49:58 2022 -0500

    fixed yaml formatting
effigies pushed a commit that referenced this pull request Apr 7, 2022
@bendhouseart @effigies
Merge gh-1027
e332798 
Squashed commit of the following:

commit ee5ff05
Author: anthony galassi <[email protected]>
Date:   Thu Apr 7 15:48:02 2022 -0400

    moved pet stuff to src/schema/rules/sidecars/pet.yaml

commit d00e683
Author: Anthony Galassi <[email protected]>
Date:   Fri Mar 18 09:40:55 2022 -0400

    Update src/schema/rules/sidecars.yml

commit 928eea2
Author: Anthony Galassi <[email protected]>
Date:   Thu Mar 17 15:42:10 2022 -0400

    Add backticks

    Added backticks

commit 50b0ae0
Author: anthony galassi <[email protected]>
Date:   Tue Mar 15 12:34:42 2022 -0400

    fixed level addendum's, removed quotes for selector in PETMRISequenceSpecifics to make linter happy

commit 4a177c0
Author: anthony galassi <[email protected]>
Date:   Mon Mar 14 15:59:54 2022 -0400

    fixed n - 1 yaml errors, 1 remaining

commit 6e40318
Author: Anthony Galassi <[email protected]>
Date:   Mon Mar 14 15:49:29 2022 -0400

    Update src/schema/rules/sidecars.yml

    change addendum -> level_addendum per commit suggestion.

    Co-authored-by: Taylor Salo <[email protected]>

commit a4fb377
Merge: 41bc816 c5f89c6
Author: Anthony Galassi <[email protected]>
Date:   Mon Mar 14 15:17:00 2022 -0400

    Merge branch 'schema/sidecar_validation' into bendhouseart-tables

commit 41bc816
Author: anthony galassi <[email protected]>
Date:   Thu Mar 10 15:49:58 2022 -0500

    fixed yaml formatting
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effigies commented Apr 7, 2022

Squashed and merged manually to ensure minimal destruction.

Compare e332798 to validate.

@effigies effigies closed this Apr 7, 2022
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